from:"Anastasia Yendiki"


Hi Alan - Glad to hear that you have an interesting finding! Can you 
describe what type of thing you want to visualize a bit more? If it's not 
on the surface, freeview will more likely do the trick rather than qdec.

a.y

On Fri, 13 Sep 2013, Alan Francis wrote:

 Hi Anastasia and FreeSurfers:
 
 Is it possible to model Tracula data on Qdec? I have some interesting
 findings in FA and AD between two groups that I am hoping to visually
 represent on a single brain.
 
 Any advice would be deeply appreciated.
 
 thank you,
 
 Alan
 

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Tracula and Qdec


Hi Alan - Are you looking at average AD over the whole tract, or AD along 
the tract?

a.y

On Fri, 13 Sep 2013, Alan Francis wrote:

 Hi Anastasia:
 
 Thanks for your quick reply. We would like to look at the left and right
 Cortico-spinal tract AD between the groups. Also left and right ATR AD if
 possible.
 
 thanks again,
 
 Alan
 
 
 On Fri, Sep 13, 2013 at 10:53 AM, Anastasia Yendiki
 ayend...@nmr.mgh.harvard.edu wrote:

   Hi Alan - Glad to hear that you have an interesting finding! Can
   you describe what type of thing you want to visualize a bit
   more? If it's not on the surface, freeview will more likely do
   the trick rather than qdec.

   a.y

   On Fri, 13 Sep 2013, Alan Francis wrote:

 Hi Anastasia and FreeSurfers:

 Is it possible to model Tracula data on Qdec? I have
 some interesting
 findings in FA and AD between two groups that I am
 hoping to visually
 represent on a single brain.

 Any advice would be deeply appreciated.

 thank you,

 Alan
 
 
 
 
 The information in this e-mail is intended only for the person to whom
 it is
 addressed. If you believe this e-mail was sent to you in error and the
 e-mail
 contains patient information, please contact the Partners Compliance
 HelpLine at
 http://www.partners.org/complianceline . If the e-mail was sent to you
 in error
 but does not contain patient information, please contact the sender
 and properly
 dispose of the e-mail.
 
 
 

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Tracula and Qdec



I see, then it's an ROI analysis, where the tract is the ROI. Isn't it 
sufficient for you to visualize the tracts in an example subject with the 
-tv option in freeview? What would you like to do beyond that?


On Fri, 13 Sep 2013, Alan Francis wrote:


Hi Anastasia:

I am looking at Average AD in these tracts.

thanks,

Alan


On Fri, Sep 13, 2013 at 11:37 AM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:

  Hi Alan - Are you looking at average AD over the whole tract, or
  AD along the tract?

  a.y

  On Fri, 13 Sep 2013, Alan Francis wrote:

Hi Anastasia:

Thanks for your quick reply. We would like to look
at the left and right
Cortico-spinal tract AD between the groups. Also
left and right ATR AD if
possible.

thanks again,

Alan


On Fri, Sep 13, 2013 at 10:53 AM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:

      Hi Alan - Glad to hear that you have an
interesting finding! Can
      you describe what type of thing you want to
visualize a bit
      more? If it's not on the surface, freeview
will more likely do
      the trick rather than qdec.

      a.y

      On Fri, 13 Sep 2013, Alan Francis wrote:

            Hi Anastasia and FreeSurfers:

            Is it possible to model Tracula data on
Qdec? I have
            some interesting
            findings in FA and AD between two groups
that I am
            hoping to visually
            represent on a single brain.

            Any advice would be deeply appreciated.

            thank you,

            Alan




The information in this e-mail is intended only for
the person to whom
it is
addressed. If you believe this e-mail was sent to
you in error and the
e-mail
contains patient information, please contact the
Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If the
e-mail was sent to you
in error
but does not contain patient information, please
contact the sender
and properly
dispose of the e-mail.






___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Tracula and Qdec



Hi Alan - Sorry, tracula doesn't do voxel-based analyses, only 
tract-based.


a.y

On Fri, 13 Sep 2013, Alan Francis wrote:


Hi Anastasia:

Yes I generated the left CST on a single subject using the Freeview -tv
option. But my boss wanted to know if it was possible to do a voxelwise
group analysis and show mean differences on a single inflated brain.

thanks,

Alan


On Fri, Sep 13, 2013 at 11:43 AM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:

  I see, then it's an ROI analysis, where the tract is the ROI.
  Isn't it sufficient for you to visualize the tracts in an
  example subject with the -tv option in freeview? What would you
  like to do beyond that?

  On Fri, 13 Sep 2013, Alan Francis wrote:

Hi Anastasia:

I am looking at Average AD in these tracts.

thanks,

Alan


On Fri, Sep 13, 2013 at 11:37 AM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:

      Hi Alan - Are you looking at average AD over
the whole tract, or
      AD along the tract?

      a.y

      On Fri, 13 Sep 2013, Alan Francis wrote:

            Hi Anastasia:

            Thanks for your quick reply. We would
like to look
            at the left and right
            Cortico-spinal tract AD between the
groups. Also
            left and right ATR AD if
            possible.

            thanks again,

            Alan


            On Fri, Sep 13, 2013 at 10:53 AM,
Anastasia Yendiki
            ayend...@nmr.mgh.harvard.edu wrote:

                  Hi Alan - Glad to hear that you
have an
            interesting finding! Can
                  you describe what type of thing
you want to
            visualize a bit
                  more? If it's not on the surface,
freeview
            will more likely do
                  the trick rather than qdec.

                  a.y

                  On Fri, 13 Sep 2013, Alan Francis
wrote:

                        Hi Anastasia and
FreeSurfers:

                        Is it possible to model
Tracula data on
            Qdec? I have
                        some interesting
                        findings in FA and AD
between two groups
            that I am
                        hoping to visually
                        represent on a single brain.

                        Any advice would be deeply
appreciated.

                        thank you,

                        Alan




            The information in this e-mail is
intended only for
            the person to whom
            it is
            addressed. If you believe this e-mail
was sent to
            you in error and the
            e-mail
            contains patient information, please
contact the
            Partners Compliance
            HelpLine at
            http://www.partners.org/complianceline .
If the
            e-mail was sent to you
            in error
            but does not contain patient
information, please
            contact the sender
            and properly
            dispose of the e-mail.








___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Cortical labels for WM seeding

2013-09-09 Thread Anastasia Yendiki



Hi Sean - Do you mean that the streamlines go through non-brain voxels? 
You could you a slightly dilated version of the aparc+aseg as a mask. You 
can use bbregister to map it to the subject's DWI space.


a.y

On Mon, 9 Sep 2013, Sean Hatton wrote:


Hello FS Gurus,

I would like to export FS labels as seed regions for deterministic 
tractography in TrackVis (probabilistic is not appropriate in this 
investigation). I run mri_label2vol with “--proj abs -4 0 .1” to try and 
grow the label into the WM and exclude GM. While I get a biologically 
plausible ROIs and plenty of good streamlines, I do get some stray 
streamlines that jump across the sulci into adjacent gyri which (I have 
read) is an artefact of seeding from GM. Have I got the right approach? 
Should I create an inverse intracranial volume mask as an exclusion 
mask? Something else?


Kind regards,

Sean Hatton
Brain  Mind Research Institute
University of Sydney, Australia.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Cortical labels for WM seeding

2013-09-09 Thread Anastasia Yendiki



I'd probably try GM plus a (DWI-sized) voxel or so into the WM.

On Mon, 9 Sep 2013, Sean Hatton wrote:


Great, I will give that a shot. In the seeding ROI should I combine the gm and 
wm labels or is the GM sufficient to encapsulate, say, the superior temporal 
gurus GM and WM?

Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote:


Hi Sean - Do you mean that the streamlines go through non-brain voxels?
You could you a slightly dilated version of the aparc+aseg as a mask. You
can use bbregister to map it to the subject's DWI space.

a.y

On Mon, 9 Sep 2013, Sean Hatton wrote:


Hello FS Gurus,

I would like to export FS labels as seed regions for deterministic
tractography in TrackVis (probabilistic is not appropriate in this
investigation). I run mri_label2vol with “--proj abs -4 0 .1” to try and
grow the label into the WM and exclude GM. While I get a biologically
plausible ROIs and plenty of good streamlines, I do get some stray
streamlines that jump across the sulci into adjacent gyri which (I have
read) is an artefact of seeding from GM. Have I got the right approach?
Should I create an inverse intracranial volume mask as an exclusion
mask? Something else?

Kind regards,

Sean Hatton
Brain  Mind Research Institute
University of Sydney, Australia.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer






The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Tracula error - unknown queue long.q, short.q

2013-09-05 Thread Anastasia Yendiki

Hm, this looks uniformly bad. Have you checked that the gradient
directions are correct? You can check that by looking at the eigenvectors
from the tensor fit that's done as part of the preprocessing. Although
tracula doesn't use tensors for tractography, it's a quick way to check
that your inputs are correct.

In fslview, overlay dmri/dtifit_V1.nii.gz on dmri/dtifit_FA.nii.gz, and
display dtifit_V1 as lines. Then make sure that the lines follow the basic
anatomy e.g. in the corpus callosum (L-R), cingulum (A-P), corticospinal
tract (I-S).

On Thu, 5 Sep 2013, Joana Braga Pereira wrote:

Hi,
Thanks for all the replies, I solved the problem I had before.

However, after finishing the Tracula pre-processing steps I tried to visualize
the tracts by typing:

freeview -tv CTR01/dpath/merged_avg33_mni_bbr.mgz

And, as you can see in the picture I'm attaching to this email, it seems the
tracts were not properly
reconstructed.

Does anyone know why?

Should I make some changes and for example set the control points differently
from the ones proposed on
Tracula website?

Any help will be greatly appreciated!

Thanks,

joana

2013/9/2 Watson, Christopher christopher.wat...@childrens.harvard.edu
Indeed. It's actually really easy to set up, too.

From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu]
Sent: Monday, September 02, 2013 3:46 PM
To: Watson, Christopher
Cc: Joana Braga Pereira; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Tracula error - unknown queue long.q,
short.q

Thanks for the pointers, Chris. I'd call it an opportunity for FSL
customization rather than an FSL problem per se :o)

On Mon, 2 Sep 2013, Watson, Christopher wrote:

This is an FSL problem. You can try the FSL list, and check out some
links:
https://www2.fmrib.ox.ac.uk/phpwiki/index/FslSge

http://neuro.debian.net/blog/2012/2012-03-09_parallelize_fsl_with_condor.html

http://chrisfilo.tumblr.com/post/579493955/how-to-configure-sun-grid-engine-for-fsl-under-ubuntu

From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on
behalf of Joana Braga Pereira [jbragapere...@gmail.com]
Sent: Monday, September 02, 2013 9:53 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Tracula error - unknown queue long.q, short.q

Dear Anastasia and FreeSurfers,

I was preprocessing some data using tracula and found this error after
running trac-all
-bedp -c dmrirc:

INFO: SUBJECTS_DIR is /data-02/joana/Last
INFO: Diffusion root is /data-02/joana/tracula/
Actual FREESURFER_HOME /usr/local/freesurfer-5.3
WARN: Running FSL's bedbost locally - this might take a while
WARN: It is recommended to run this step on a cluster
bedpostx_mgh -n 2 /data-02/joana/tracula//XXX/dmri
subjectdir is /data-02/joana/tracula/XXX/dmri
Making bedpostx directory structure
Queuing preprocessing stages
Unable to run job: Job was rejected because job requests unknown queue
short.q.
Exiting.
Queuing parallel processing stage
Unable to run job: Job was rejected because job requests unknown queue
long.q.
Exiting.
Queuing post processing stage
Unable to run job: denied: 60 is not a valid object name (cannot
start with a digit)
Job was rejected because job requests unknown queue long.q.
Exiting.

Type /data-02/joana/tracula/3119/dmri.bedpostX/monitor to show progress.
Type /data-02/joana/tracula/3119/dmri.bedpostX/cancel to terminate all
the queued tasks.

You will get an email at the end of the post-processing stage.

So far no slices have been processed. Does anyone know how to solve it?

Thanks!

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it
is
addressed. If you believe this e-mail was sent to you in error and the
e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in
error
but does not contain patient information, please contact the sender and
properly
dispose of the e-mail.

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error

Re: [Freesurfer] Tracula error - unknown queue long.q, short.q

2013-09-05 Thread Anastasia Yendiki

Yes, it does look from the images like the L-R and A-P directions are
swapped. So you can switch around the x and y columns of you gradient
table and rerun the preprocessing and check the eigenvectors again. It may
be some other combination of swaps that needs to be done, but the x and y
looks like the most likely to me. For sure the gradient table is wrong.

On Thu, 5 Sep 2013, Joana Braga Pereira wrote:

Thanks!
I've uploaded those files as well as dmrirc and bvecs and bvals.

Let me know what you think.

2013/9/5 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu

Indeed, they look like they're oriented A-P in the corpus callosum and
L-R in the cinglulum,
when it should be the opposite obviously. This'd mean you'd have to swap
things in the gradient
table. It's hard to tell for sure from the screenshot though. If you
upload the dtifit_FA and
dtifit_V1 volumes for me here, I'll look at them:
https://gate.nmr.mgh.harvard.edu/filedrop2/

On Thu, 5 Sep 2013, Joana Braga Pereira wrote:

Hi Anastasia,
Thanks! I checked dtifit_FA and did the overlay with V1.

They don't look ok to me (see attached picture). Any suggestions on
how to solve
this? Perhaps by modifying
any of the previous steps?

Thanks!

2013/9/5 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu

Hm, this looks uniformly bad. Have you checked that the
gradient directions
are correct? You
can check that by looking at the eigenvectors from the tensor
fit that's done
as part of the
preprocessing. Although tracula doesn't use tensors for
tractography, it's a
quick way to check
that your inputs are correct.

In fslview, overlay dmri/dtifit_V1.nii.gz on
dmri/dtifit_FA.nii.gz, and
display dtifit_V1 as
lines. Then make sure that the lines follow the basic anatomy
e.g. in the
corpus callosum
(L-R), cingulum (A-P), corticospinal tract (I-S).

On Thu, 5 Sep 2013, Joana Braga Pereira wrote:

Hi,
Thanks for all the replies, I solved the problem I had
before.

However, after finishing the Tracula pre-processing
steps I tried to
visualize the
tracts by typing:

freeview -tv CTR01/dpath/merged_avg33_mni_bbr.mgz

And, as you can see in the picture I'm attaching to
this email, it
seems the tracts
were not properly
reconstructed.

Does anyone know why?

Should I make some changes and for example set the
control points
differently from
the ones proposed on
Tracula website?

Any help will be greatly appreciated!

Thanks,

joana

2013/9/2 Watson, Christopher
christopher.wat...@childrens.harvard.edu
Indeed. It's actually really easy to set up, too.
From: Anastasia Yendiki
[ayend...@nmr.mgh.harvard.edu]
Sent: Monday, September 02, 2013 3:46 PM
To: Watson, Christopher
Cc: Joana Braga Pereira;
freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Tracula error - unknown queue
long.q,
short.q

Thanks for the pointers, Chris. I'd call it an
opportunity for
FSL
customization rather than an FSL problem per
se :o)

On Mon, 2 Sep 2013, Watson, Christopher wrote:

This is an FSL problem. You can try the FSL
list, and check out
some links:
https://www2.fmrib.ox.ac.uk/phpwiki/index/FslSge

http://neuro.debian.net/blog/2012/2012-03-09_parallelize_fsl_with_condor.html

Re: [Freesurfer] Tracula error - unknown queue long.q, short.q

2013-09-05 Thread Anastasia Yendiki

Indeed, they look like they're oriented A-P in the corpus callosum and L-R
in the cinglulum, when it should be the opposite obviously. This'd mean
you'd have to swap things in the gradient table. It's hard to tell for
sure from the screenshot though. If you upload the dtifit_FA and dtifit_V1
volumes for me here, I'll look at them:

https://gate.nmr.mgh.harvard.edu/filedrop2/

On Thu, 5 Sep 2013, Joana Braga Pereira wrote:

Hi Anastasia,
Thanks! I checked dtifit_FA and did the overlay with V1.

They don't look ok to me (see attached picture). Any suggestions on how to
solve this? Perhaps by modifying
any of the previous steps?

Thanks!

2013/9/5 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu

Hm, this looks uniformly bad. Have you checked that the gradient
directions are correct? You
can check that by looking at the eigenvectors from the tensor fit that's
done as part of the
preprocessing. Although tracula doesn't use tensors for tractography,
it's a quick way to check
that your inputs are correct.

In fslview, overlay dmri/dtifit_V1.nii.gz on dmri/dtifit_FA.nii.gz, and
display dtifit_V1 as
lines. Then make sure that the lines follow the basic anatomy e.g. in the
corpus callosum
(L-R), cingulum (A-P), corticospinal tract (I-S).

On Thu, 5 Sep 2013, Joana Braga Pereira wrote:

Hi,
Thanks for all the replies, I solved the problem I had before.

However, after finishing the Tracula pre-processing steps I tried
to visualize the
tracts by typing:

freeview -tv CTR01/dpath/merged_avg33_mni_bbr.mgz

And, as you can see in the picture I'm attaching to this email, it
seems the tracts
were not properly
reconstructed.

Does anyone know why?

Should I make some changes and for example set the control points
differently from
the ones proposed on
Tracula website?

Any help will be greatly appreciated!

Thanks,

joana

2013/9/2 Watson, Christopher
christopher.wat...@childrens.harvard.edu
Indeed. It's actually really easy to set up, too.
From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu]
Sent: Monday, September 02, 2013 3:46 PM
To: Watson, Christopher
Cc: Joana Braga Pereira; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Tracula error - unknown queue long.q,
short.q

Thanks for the pointers, Chris. I'd call it an opportunity
for FSL
customization rather than an FSL problem per se :o)

On Mon, 2 Sep 2013, Watson, Christopher wrote:

This is an FSL problem. You can try the FSL list, and check
out some links:
https://www2.fmrib.ox.ac.uk/phpwiki/index/FslSge

http://neuro.debian.net/blog/2012/2012-03-09_parallelize_fsl_with_condor.html

http://chrisfilo.tumblr.com/post/579493955/how-to-configure-sun-grid-engine-for-fsl-under-ubuntu
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on
behalf of Joana Braga Pereira [jbragapere...@gmail.com]
Sent: Monday, September 02, 2013 9:53 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Tracula error - unknown queue long.q,
short.q
Dear Anastasia and FreeSurfers,
I was preprocessing some data using tracula and found this
error after
running trac-all
-bedp -c dmrirc:
INFO: SUBJECTS_DIR is /data-02/joana/Last
INFO: Diffusion root is /data-02/joana/tracula/
Actual FREESURFER_HOME /usr/local/freesurfer-5.3
WARN: Running FSL's bedbost locally - this might take a
while
WARN: It is recommended to run this step on a cluster
bedpostx_mgh -n 2 /data-02/joana/tracula//XXX/dmri
subjectdir is /data-02/joana/tracula/XXX/dmri
Making bedpostx directory structure
Queuing preprocessing stages
Unable to run job: Job was rejected because job requests
unknown queue
short.q.
Exiting.
Queuing parallel processing stage
Unable to run job: Job was rejected because job requests
unknown queue
long.q.
Exiting.
Queuing post processing stage

Re: [Freesurfer] Tracula threshold path

2013-09-04 Thread Anastasia Yendiki


Hi Celine - The path.pd.nii.gz file contains the full probability 
distribution without any thresholding. This distribution, as with any 
probabilistic tractography method, expresses the amount of uncertainty in 
which is the path of most coherent diffusion between the two end regions. 
(In tracula's case, it's actually both most coherent diffusion and most 
consistent with the anatomy of the CST, or whichever pathway, based on the 
atlas.) If in a patient there's widespread degeneration over the entire 
path, this could manifest itself as more uncertainty and hence a more 
spread out distribution. So depending on the variability among your 
subjects you could get wider or narrower pathway ROIs. If you find that a 
threshold based on path.pd.nii.gz alone is not consistent for your 
purposes, you could try combining it with an FA threshold.

Hope this helps,
a.y

On Wed, 4 Sep 2013, cel...@nmr.mgh.harvard.edu wrote:

 Dear experts,
 I read some previous answers about the thresholding of the paths obtained
 after tracula process, but I am not completely sure I had the right
 answer.
 I will need to get an roi from a path for example the cortico-spinal tract
 that will be consistent amongst patients. I will further use this roi to
 calculate the lesion volume (my subjects are patients with MS) within a
 specific path.
 My question is: is the path.pd.nii.gz file already threshold or should I
 threshold it to a specific value? If I use the same threshold for each
 subject for example at 10% of the maximum value, will I obtain an ROI that
 is consistent among subjects or is is possible that I would get a very
 thin CST in some subjects, or a very wide cst for example?
 Thanks for your help
 Celine


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Tracula error - unknown queue long.q, short.q

2013-09-02 Thread Anastasia Yendiki



Hi Joana - What system are you running this on?

a.y

On Mon, 2 Sep 2013, Joana Braga Pereira wrote:


Dear Anastasia and FreeSurfers,
I was preprocessing some data using tracula and found this error after
running  trac-all -bedp -c dmrirc:

INFO: SUBJECTS_DIR is /data-02/joana/Last
INFO: Diffusion root is /data-02/joana/tracula/
Actual FREESURFER_HOME /usr/local/freesurfer-5.3
WARN: Running FSL's bedbost locally - this might take a while
WARN: It is recommended to run this step on a cluster
bedpostx_mgh -n 2 /data-02/joana/tracula//XXX/dmri
subjectdir is /data-02/joana/tracula/XXX/dmri
Making bedpostx directory structure
Queuing preprocessing stages
Unable to run job: Job was rejected because job requests unknown queue
short.q.
Exiting.
Queuing parallel processing stage
Unable to run job: Job was rejected because job requests unknown queue
long.q.
Exiting.
Queuing post processing stage
Unable to run job: denied: 60 is not a valid object name (cannot start
with a digit)
Job was rejected because job requests unknown queue long.q.
Exiting.

Type /data-02/joana/tracula/3119/dmri.bedpostX/monitor to show progress.
Type /data-02/joana/tracula/3119/dmri.bedpostX/cancel to terminate all the
queued tasks.

You will get an email at the end of the post-processing stage.


So far no slices have been processed. Does anyone know how to solve it?

Thanks!


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Tracula error - unknown queue long.q, short.q

2013-09-02 Thread Anastasia Yendiki

Thanks for the pointers, Chris. I'd call it an opportunity for FSL
customization rather than an FSL problem per se :o)

On Mon, 2 Sep 2013, Watson, Christopher wrote:

This is an FSL problem. You can try the FSL list, and check out some links:
https://www2.fmrib.ox.ac.uk/phpwiki/index/FslSge
http://neuro.debian.net/blog/2012/2012-03-09_parallelize_fsl_with_condor.html
http://chrisfilo.tumblr.com/post/579493955/how-to-configure-sun-grid-engine-for-fsl-under-ubuntu

From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Joana Braga Pereira
[jbragapere...@gmail.com]
Sent: Monday, September 02, 2013 9:53 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Tracula error - unknown queue long.q, short.q

Dear Anastasia and FreeSurfers,

I was preprocessing some data using tracula and found this error after
running trac-all -bedp -c dmrirc:

INFO: SUBJECTS_DIR is /data-02/joana/Last
INFO: Diffusion root is /data-02/joana/tracula/
Actual FREESURFER_HOME /usr/local/freesurfer-5.3
WARN: Running FSL's bedbost locally - this might take a while
WARN: It is recommended to run this step on a cluster
bedpostx_mgh -n 2 /data-02/joana/tracula//XXX/dmri
subjectdir is /data-02/joana/tracula/XXX/dmri
Making bedpostx directory structure
Queuing preprocessing stages
Unable to run job: Job was rejected because job requests unknown queue
short.q.
Exiting.
Queuing parallel processing stage
Unable to run job: Job was rejected because job requests unknown queue
long.q.
Exiting.
Queuing post processing stage
Unable to run job: denied: 60 is not a valid object name (cannot start with
a digit)
Job was rejected because job requests unknown queue long.q.
Exiting.

Type /data-02/joana/tracula/3119/dmri.bedpostX/monitor to show progress.
Type /data-02/joana/tracula/3119/dmri.bedpostX/cancel to terminate all the
queued tasks.

You will get an email at the end of the post-processing stage.

So far no slices have been processed. Does anyone know how to solve it?

Thanks!

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Clarification regarding bvec processing in TRACULA

2013-08-27 Thread Anastasia Yendiki



Nope, there's no flipping in tracula. But, *both* the gradient vectors and 
the DWIs are converted to LAS orientation as the first step in the 
preprocessing. This makes the FSL tools that are run later in the 
preprocessing (dtifit and bedpostx) run smoothly without any flipping.


On Mon, 26 Aug 2013, Salil Soman wrote:


Hi,
After much searching, it appears to be pretty uniform that the product DTI
sequence performed on GE requires the y gradient to be flipped. For the
datasets with which I am working diffusion toolkit, vistalab and  exploredti
all require the y gradient to be flipped. However, Tracula makes appropriate
outputs when I give it the default gradient table without flipping Y.  When
I flip Y and run it through Tracula, the forceps major is inverted (noted by
checking the overlay of dtifit_fa and dtifit_V1 using fslview and by using
TVglyphView using DTI-TK.

I suspect that somehow Tracula  is flipping the Y sign for the gradient
(while the other programs I mentioned do not) - can anyone confirm this?

Thanks!

-Sal


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] [tracula] error running trac-all -prep

2013-08-22 Thread Anastasia Yendiki



Hi Florian - My guess is that everything ran fine and you don't need to 
change anything else. Check that all the output files were created in the 
dmri.bedpostX directory:

http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/fdt/fdt_bedpostx.html

a.y

On Thu, 22 Aug 2013, Borsodi Florian wrote:


Hi Anastasia,

This Ubuntu-related error is a tricky one.
I changed the first line in those files you told me and reran trac-all. All
three steps of trac-all ran without any errrors. I checked the FA maps and
the MNI registration and everything looks fine. 

After running trac-all -bedp, the step stopped with the following line:
Queuing post processing stage
/usr/local/freesurfer/bin/bedpostx_mgh: line 439:  9381 Terminated    
${subjdir}.bedpostX/monitor.
I think it's fine, because line 439 is the last line of the script, so it
worked well.
Maybe I have to change all .sh in the files to .bash to get all
messages.

Thank you so much for your big help.
I hope I didn't cause you much trouble with my problems and questions.

Sincerely,
Florian

 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu 20.08.13 17.56 Uhr 

This is an Ubuntu-related error that has surfaced recently because in
Ubuntu /bin/sh is not a bash shell any more. To get around this, you can
edit the first line of the scripts $FREESURFER_HOME/bin/bedpostx_mgh and
$FREESURFER_HOME/bin/fsl_sub_mgh. You'll have to replace /bin/sh with
/bin/bash on the first line of those two scripts.

On Tue, 20 Aug 2013, Borsodi Florian wrote:

 Hi Anastasia,

 Yes, i am running this on ubuntu 12.04.

 Sincerely,
 Florian

  Anastasia Yendiki ayend...@nmr.mgh.harvard.edu 20.08.13 17.38 Uhr


 Hi Florian - Are you running this on an ubuntu system by any chance?

 a.y

 On Tue, 20 Aug 2013, Borsodi Florian wrote:

  Hi Anastasia,
 
  Thank you for your help.
  I changed the commas in /dmri/bvecs to dots and reran trac-all. But
the command xfmrot changed the dots back to
  commas. So, I changed our system language from de_AUT.UTF-8 to
en_US.UTF-8 and reran trac-all. After changing the
  system language everything was genereted correctly and trac-all -prep
ran without any errors.
  I'm so glad.
 
  Then, I started the next step trac-all -bedp and got a syntax error
/usr/local/freesurfer/bin/bedpostx_mgh: 131:
  /usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: ( unexpected. 
I also attached the the logfile. I was
 reading
  about this error in the mail archive. Would I have to run bedpostx
outside of tracula ?
 
  Sincerely,
  Florian
 
   Anastasia Yendiki ayend...@nmr.mgh.harvard.edu 19.08.13 17.54 Uhr

 
  Hi Florian - Can you please change the decimal commas to points and try
  again?
 
  a.y
 
  On Mon, 19 Aug 2013, Borsodi Florian wrote:
 
   Hi Anastasia,
  
   Here are the bvec and bval files you asked me about.
  
   Sincerely,
   Florian
  
Anastasia Yendiki ayend...@nmr.mgh.harvard.edu 18.08.13 22.52
Uhr 
  
   Hi Florian - Can you please also attach the bvecs/bvals files from the
   dmri directory?
  
   Thanks,
   a.y
  
   On Sun, 18 Aug 2013, Borsodi Florian wrote:
  
Hi Anastasia,
   
Thanks for your help. I renamed the directories and reran trac-all.
It
worked for the moment.
However, then I got another error: bvecs and bvals don't have the
same
number of entries.
I don't know why, because they actually have the same number of
entries.
   
I attached the logfile so that you may see what is going on. The
error
occours at line 1463.
   
Thank you in advance for your help.
   
Sincerely,
Florian
   
   
 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu 15.08.13 18.01
Uhr 
   
Hi Florian - I see what's going on. Can you please rename the
directory
/data/physics/florian/nii into something that doesn't include nii,
and
rerun? Because nii is a file extension, this confuses some of the
scripts.
   
Thanks,
a.y
   
On Thu, 15 Aug 2013, Borsodi Florian wrote:
   
 Hi Anastasia

 I ran the command you sent me and it runs without any errors.
 I also attached the command line for you.

 Furthermore i ran data with 12 diffusion directions and i keep
getting the
 same kind of problems.

 sincerely
 Florian

  Anastasia Yendiki ayend...@nmr.mgh.harvard.edu 02.08.13
19.59 Uhr


 Hi Florian - Can you please run this command directly on the
command line
 and see if there are any errors?

 flip4fsl

/data/physics/florian/nii/102485074_20080319/dmri/dwi_orig.nii.gz

/data/physics/florian/nii/102485074_20080319/dmri/dwi_orig_flip.nii.gz

 Thanks,
 a.y

 On Fri, 2 Aug 2013, Borsodi Florian wrote:

  Hi Anastasia
 
  Thank you for your answer.
 
  Yes, those files exist.
  I also extracted the bvec an bval files with anotther software
then
 dcm2nii
  and i keep getting the same kind of error.
  Also, about the 6 diffusion direction, those data i sent you

Re: [Freesurfer] gradient table question for Tracula

2013-08-22 Thread Anastasia Yendiki



Hi Sal - Sorry but I don't know what the interaction of dcm2nii and GE 
dicom headers is. If anyone else on the list uses dcm2nii on GE dicoms, 
they can chime in.


To make sure the gradient table is right, I'd always check the primary 
eigenvector directions (overlaying dmri/dtifit_V1.nii.gz on 
dmri/dtifit_FA.nii.gz and viewing the former as lines). You just need to 
do this on one of the data sets from your sequence just to make sure 
they're oriented correctly. Also, if the gradient vectors need flipping, 
the tracts from tracula will come out looking visibly wrong. So you'll 
know that something went wrong.


Hope this helps,
a.y

On Thu, 22 Aug 2013, Salil Soman wrote:


Hi Anastasia,
A question I had about the gradient tables for Tracula - I recently came
across this passage from Hui Zhang:

To correct for any errors that you identify, you need to first modify the
gradient table, then repeat the tensor reconstruction. The modification of
the gradient table typically involves flipping the signs of the x or y
component of all gradient vectors. To determine the correct flipping of the
signs in a systematic way, it is necessary to understand why this happens.
The reason is that the gradient directions are always defined with respect
to some right-handed frame of reference, while the frame of reference of the
acquired image data is typically NOT right-handed. This mismatch is the
cause of the problem. The sign flipping intends to fix this mismatch and the
key is to identify the difference between the two frames of reference in
question. In our experience, if the data is acquired on SIEMENS scanners,
the signs of x gradient components need to be flipped; for GE scanners, it
is usually the y components.(from 
http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Documentation.Visua
lizationTool). 

Does this mean that the gradient tables i get from dcm2nii need to have the
Y component flipped for my GE acquisitions or is this adjusted in the
tracula processing?

Thank you.

--
Salil Soman, MD, MS
Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory
Fellow - Palo Alto War Related Illness and Injury Study Center
WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Track stats and covariates

2013-08-20 Thread Anastasia Yendiki


Definitely age. You don't need to adjust for volume since these are not 
volume/area/length measures that you're comparing. You should also check 
for any group differences in motion before you proceed and make sure your 
groups are matched in terms of motion. If you do separate t-tests for each 
tract, you'll need to adjust for multiple comparisons (by the number of 
tracts).

On Tue, 20 Aug 2013, Alan Francis wrote:

 Hi Anastasia:
 Just a quick question. When comparing FA, AD, RD etc between 2 groups, do we 
 need to use covariates like Intra Cranial
 volume or AGE?
 
 If the answer is no, should I do an ANOVA or will T tests be sufficient?
 
 thank you,
 
 Alan
 

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] [tracula] error running trac-all -prep

2013-08-20 Thread Anastasia Yendiki



Hi Florian - Are you running this on an ubuntu system by any chance?

a.y

On Tue, 20 Aug 2013, Borsodi Florian wrote:


Hi Anastasia,

Thank you for your help.
I changed the commas in /dmri/bvecs to dots and reran trac-all. But the command 
xfmrot changed the dots back to
commas. So, I changed our system language from de_AUT.UTF-8 to en_US.UTF-8 and 
reran trac-all. After changing the
system language everything was genereted correctly and trac-all -prep ran 
without any errors.
I'm so glad. 

Then, I started the next step trac-all -bedp and got a syntax error 
/usr/local/freesurfer/bin/bedpostx_mgh: 131:
/usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: ( unexpected.  I also 
attached the the logfile. I was reading
about this error in the mail archive. Would I have to run bedpostx outside of 
tracula ?

Sincerely,
Florian

 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu 19.08.13 17.54 Uhr 

Hi Florian - Can you please change the decimal commas to points and try
again?

a.y

On Mon, 19 Aug 2013, Borsodi Florian wrote:

 Hi Anastasia,

 Here are the bvec and bval files you asked me about.

 Sincerely,
 Florian

  Anastasia Yendiki ayend...@nmr.mgh.harvard.edu 18.08.13 22.52 Uhr 

 Hi Florian - Can you please also attach the bvecs/bvals files from the
 dmri directory?

 Thanks,
 a.y

 On Sun, 18 Aug 2013, Borsodi Florian wrote:

  Hi Anastasia,
 
  Thanks for your help. I renamed the directories and reran trac-all. It
  worked for the moment.
  However, then I got another error: bvecs and bvals don't have the same
  number of entries.
  I don't know why, because they actually have the same number of entries.
 
  I attached the logfile so that you may see what is going on. The error
  occours at line 1463.
 
  Thank you in advance for your help.
 
  Sincerely,
  Florian
 
 
   Anastasia Yendiki ayend...@nmr.mgh.harvard.edu 15.08.13 18.01 Uhr 
 
  Hi Florian - I see what's going on. Can you please rename the directory
  /data/physics/florian/nii into something that doesn't include nii, and
  rerun? Because nii is a file extension, this confuses some of the
  scripts.
 
  Thanks,
  a.y
 
  On Thu, 15 Aug 2013, Borsodi Florian wrote:
 
   Hi Anastasia
  
   I ran the command you sent me and it runs without any errors.
   I also attached the command line for you.
  
   Furthermore i ran data with 12 diffusion directions and i keep getting the
   same kind of problems.
  
   sincerely
   Florian
  
Anastasia Yendiki ayend...@nmr.mgh.harvard.edu 02.08.13 19.59 Uhr
  
  
   Hi Florian - Can you please run this command directly on the command line
   and see if there are any errors?
  
   flip4fsl
   /data/physics/florian/nii/102485074_20080319/dmri/dwi_orig.nii.gz
   /data/physics/florian/nii/102485074_20080319/dmri/dwi_orig_flip.nii.gz
  
   Thanks,
   a.y
  
   On Fri, 2 Aug 2013, Borsodi Florian wrote:
  
Hi Anastasia
   
Thank you for your answer.
   
Yes, those files exist.
I also extracted the bvec an bval files with anotther software then
   dcm2nii
and i keep getting the same kind of error.
Also, about the 6 diffusion direction, those data i sent you, are just
testdata for running tracula.
   
sincerely
Florian
   
 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu 02.08.13 0.41 Uhr
  
   
Hi Florian - Do these files exist?
  /data/physics/florian/nii/102485074_20080319/dmri/dwi_orig.mghdti.bvec
  s
  
   
  /data/physics/florian/nii/102485074_20080319/dmri/dwi_orig.mghdti.bval
  s
  
   
   
The format of the bvecs and bvals that you sent seems fine, but (and
  this
has nothing to do with the error you're getting) I have to warn you that
you may not be able to get good results running probabilistic
  tractography
on this data. It looks like you're acquiring the same 6 diffusion
directions, repeated 8 times. Six directions is the absolute minimum for
reconstructing the tensor model, but will probably not be sufficient for
the crossing fiber model that bedpostx reconstructs (and is used by
tracula). Your scan time is better spent acquiring 48 different
directions, rather than the same 6 directions 8 times.
   
a.y
   
On Mon, 29 Jul 2013, Borsodi Florian wrote:
   
 Hello,

 I have been trying to run tracula on my data and i keep getting the
  same
 kind of error repeatedly.
 For my imput I am using dicoms from a Siemens scanner with a stadard
 diffusion protocol. However, tracula cannot read the bvec and bval
  data
out
 of the dicom header. Therefore, I implemented bvec and bval files into
   the
 config file.
 After doing so, I got the error which says that tracula cannot find
  the
 dwi_orig_flip.mghdti.bvecs and dwi_orig_flip.mghdti.bvals files.
 I have tried many options, but still cannot find a solution.
 I am hoping to get some troubleshooting help.

 I have atteched my log- and config- files, as well as my bvec and bval
 files

Re: [Freesurfer] [tracula] error running trac-all -prep

2013-08-20 Thread Anastasia Yendiki


This is an Ubuntu-related error that has surfaced recently because in 
Ubuntu /bin/sh is not a bash shell any more. To get around this, you can 
edit the first line of the scripts $FREESURFER_HOME/bin/bedpostx_mgh and 
$FREESURFER_HOME/bin/fsl_sub_mgh. You'll have to replace /bin/sh with 
/bin/bash on the first line of those two scripts.

On Tue, 20 Aug 2013, Borsodi Florian wrote:

 Hi Anastasia,
 
 Yes, i am running this on ubuntu 12.04.
 
 Sincerely,
 Florian
 
  Anastasia Yendiki ayend...@nmr.mgh.harvard.edu 20.08.13 17.38 Uhr 
 
 Hi Florian - Are you running this on an ubuntu system by any chance?
 
 a.y
 
 On Tue, 20 Aug 2013, Borsodi Florian wrote:
 
  Hi Anastasia,
 
  Thank you for your help.
  I changed the commas in /dmri/bvecs to dots and reran trac-all. But the 
  command xfmrot changed the dots back to
  commas. So, I changed our system language from de_AUT.UTF-8 to en_US.UTF-8 
  and reran trac-all. After changing the
  system language everything was genereted correctly and trac-all -prep ran 
  without any errors.
  I'm so glad.
 
  Then, I started the next step trac-all -bedp and got a syntax error 
  /usr/local/freesurfer/bin/bedpostx_mgh: 131:
  /usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: ( unexpected.  I 
  also attached the the logfile. I was
 reading
  about this error in the mail archive. Would I have to run bedpostx 
  outside of tracula ?
 
  Sincerely,
  Florian
 
   Anastasia Yendiki ayend...@nmr.mgh.harvard.edu 19.08.13 17.54 Uhr 
 
  Hi Florian - Can you please change the decimal commas to points and try
  again?
 
  a.y
 
  On Mon, 19 Aug 2013, Borsodi Florian wrote:
 
   Hi Anastasia,
  
   Here are the bvec and bval files you asked me about.
  
   Sincerely,
   Florian
  
Anastasia Yendiki ayend...@nmr.mgh.harvard.edu 18.08.13 22.52 Uhr 

  
   Hi Florian - Can you please also attach the bvecs/bvals files from the
   dmri directory?
  
   Thanks,
   a.y
  
   On Sun, 18 Aug 2013, Borsodi Florian wrote:
  
Hi Anastasia,
   
Thanks for your help. I renamed the directories and reran trac-all. It
worked for the moment.
However, then I got another error: bvecs and bvals don't have the same
number of entries.
I don't know why, because they actually have the same number of entries.
   
I attached the logfile so that you may see what is going on. The error
occours at line 1463.
   
Thank you in advance for your help.
   
Sincerely,
Florian
   
   
 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu 15.08.13 18.01 Uhr 
 
   
Hi Florian - I see what's going on. Can you please rename the directory
/data/physics/florian/nii into something that doesn't include nii, and
rerun? Because nii is a file extension, this confuses some of the
scripts.
   
Thanks,
a.y
   
On Thu, 15 Aug 2013, Borsodi Florian wrote:
   
 Hi Anastasia

 I ran the command you sent me and it runs without any errors.
 I also attached the command line for you.

 Furthermore i ran data with 12 diffusion directions and i keep 
 getting the
 same kind of problems.

 sincerely
 Florian

  Anastasia Yendiki ayend...@nmr.mgh.harvard.edu 02.08.13 19.59 
  Uhr


 Hi Florian - Can you please run this command directly on the command 
 line
 and see if there are any errors?

 flip4fsl
 /data/physics/florian/nii/102485074_20080319/dmri/dwi_orig.nii.gz
 /data/physics/florian/nii/102485074_20080319/dmri/dwi_orig_flip.nii.gz

 Thanks,
 a.y

 On Fri, 2 Aug 2013, Borsodi Florian wrote:

  Hi Anastasia
 
  Thank you for your answer.
 
  Yes, those files exist.
  I also extracted the bvec an bval files with anotther software then
 dcm2nii
  and i keep getting the same kind of error.
  Also, about the 6 diffusion direction, those data i sent you, are 
  just
  testdata for running tracula.
 
  sincerely
  Florian
 
   Anastasia Yendiki ayend...@nmr.mgh.harvard.edu 02.08.13 0.41 
   Uhr

 
  Hi Florian - Do these files exist?
/data/physics/florian/nii/102485074_20080319/dmri/dwi_orig.mghdti.bvec
s

 
/data/physics/florian/nii/102485074_20080319/dmri/dwi_orig.mghdti.bval
s

 
 
  The format of the bvecs and bvals that you sent seems fine, but (and
this
  has nothing to do with the error you're getting) I have to warn you 
  that
  you may not be able to get good results running probabilistic
tractography
  on this data. It looks like you're acquiring the same 6 diffusion
  directions, repeated 8 times. Six directions is the absolute 
  minimum for
  reconstructing the tensor model, but will probably not be 
  sufficient for
  the crossing fiber model that bedpostx reconstructs (and is used by
  tracula). Your scan time is better spent acquiring 48

Re: [Freesurfer] [Tracula] error running trac-all –path –c Configuration_file.txt

2013-08-19 Thread Anastasia Yendiki



Hi Francesco - There's a list of bedpostx output files here:
http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/fdt/fdt_bedpostx.html

The best way to determine if bedpostx finished running properly is to 
check if those files were created in the dmri.bedpostX directory.


a.y

On Mon, 19 Aug 2013, Francesco Siciliano wrote:


Hello,
I received an error on several terminals running trac-all –path –c 
Configuration_file.txt

55 slices processed
56 slices processed
56 slices processed
57 slices processed
57 slices processed
58 slices processed
59 slices processed
60 slices processed
61 slices processed
Queuing post processing stage
70 slices processed
For some reason the bedpostX process DOES NOT appear
to have successfully completed. Please examine your
results carefully.
/Users/jonathanposner/Desktop/MRI_Software/FSL_installer/fsl/bin/bedpostx: line 
262: kill: (15849) - No such process

Is this an indication that the processing did not finish? Could this have 
anything to do with limited computer
memory? 

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] [Tracula] error running trac-all –path –c Configuration_file.txt

2013-08-19 Thread Anastasia Yendiki



Hi Francesco - The bedpostx files are created when you run trac-all -bedp. 
Then you need to run trac-all -path to reconstruct the paths under 
dpath/... as the final step. Did you run this?


a.y

On Mon, 19 Aug 2013, Francesco Siciliano wrote:


Thank you!

Is it normal, however, not to have a dpath folder with summary statistics? I 
have all of the bedpostx output files, however, I seem to be missing the dpath 
folder as well as a script confirming that -path was completed.

Thanks,
Francesco

From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu]
Sent: Monday, August 19, 2013 1:56 PM
To: Francesco Siciliano
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] [Tracula] error running trac-all –path –c 
Configuration_file.txt

Hi Francesco - There's a list of bedpostx output files here:
   http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/fdt/fdt_bedpostx.html

The best way to determine if bedpostx finished running properly is to
check if those files were created in the dmri.bedpostX directory.

a.y

On Mon, 19 Aug 2013, Francesco Siciliano wrote:


Hello,
I received an error on several terminals running trac-all –path –c 
Configuration_file.txt

55 slices processed
56 slices processed
56 slices processed
57 slices processed
57 slices processed
58 slices processed
59 slices processed
60 slices processed
61 slices processed
Queuing post processing stage
70 slices processed
For some reason the bedpostX process DOES NOT appear
to have successfully completed. Please examine your
results carefully.
/Users/jonathanposner/Desktop/MRI_Software/FSL_installer/fsl/bin/bedpostx: line 
262: kill: (15849) - No such process

Is this an indication that the processing did not finish? Could this have 
anything to do with limited computer
memory?





The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] trac-all inquiry

2013-08-16 Thread Anastasia Yendiki


Ok, actually the error about the data and bvals/bvecs not having the same 
size occured the first time you ran trac-all, but it seems to have been 
fixed the second time you ran it, based on the log file.

I suspect the current problem is caused by poor registration. Have you 
checked the aparc+aseg and/or the registration from diffusion to 
anatomical and from anatomical to MNI?

On Fri, 16 Aug 2013, David Soto wrote:

 hi - yes it as 65 -output pasted below, cheers

 dsoto@wmen-dsoto3:~/Documents/fmri/rsdtianawmgui/14AB/dmri$ mri_info 
 dwi.nii.gz Volume information for dwi.nii.gz
  type: nii
dimensions: 96 x 96 x 46 x 65
   voxel sizes: 2., 2., 2.2999
  type: FLOAT (3)
   fov: 224.000
   dof: 0
xstart: -112.0, xend: 112.0
ystart: -112.0, yend: 112.0
zstart: -52.9, zend: 52.9
TR: 1000.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 
 degrees
   nframes: 65
   PhEncDir: UNKNOWN
 ras xform present
xform info: x_r =  -1., y_r =   0., z_r =   0., c_r = 
 0.
  : x_a =   0., y_a =   0.9774, z_a =  -0.2112, c_a = 
 2.1015
  : x_s =   0., y_s =   0.2112, z_s =   0.9774, c_s = 
 19.9194
 Orientation   : LAS
 Primary Slice Direction: axial

 voxel to ras transform:
   -2.   0.   0.   112.
0.   2.2807  -0.4858   -96.1994
0.   0.4928   2.2480   -55.4405
0.   0.   0. 1.

 voxel-to-ras determinant -12.5217

 ras to voxel transform:
   -0.4286   0.   0.48.
   -0.   0.4189   0.090545.3166
   -0.  -0.0918   0.425014.7274
0.   0.   0. 1.

 http://www1.imperial.ac.uk/medicine/people/d.soto/
 On 16/08/13 16:13, Anastasia Yendiki wrote:
 mri_info dmri/dwi.nii.gz



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Trac Stats

2013-08-15 Thread Anastasia Yendiki


Is it really autofs without the '/' in front?

On Thu, 15 Aug 2013, Alan Francis wrote:

 Hi Anastasia:
 
 Sorry to bother you again. I am trying to extract trac stats from the FS
 data. When I run the following script, it gives me an error message:
 
 csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
 recons] : tractstats2table 
 --load-pathstats-from-file/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
 econs/Forceps_Major_CC.list.txt --overall 
 --tablefile/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
 econs/Forceps_Major_CC.All.table
 
 Parsing the .stats files
 
 ERROR: The stats 
 fileautofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_re
 cons/BW_101/dpath/fmajor_PP_avg33_mni_bbr/pathstats.overall.txt is not found
 or is too small to be a valid statsfile
 
 However, when I manually checked the pathstats.overall.txt, the data is
 physically there. Am I doing something wrong?
 
 thanks so much,
 
 Alan
 

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Trac Stats

2013-08-15 Thread Anastasia Yendiki



Can you please attach the file Forceps_Major_CC.list.txt?

On Thu, 15 Aug 2013, Alan Francis wrote:


Hi Anastasia:

Yes the '/' is really there before the autofs. It is puzzling.

thanks,

Alan


On Thu, Aug 15, 2013 at 3:15 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:

  I didn't suggest taking it off, I meant make sure that the '/'
  is there, because the error message suggested to me that a '/'
  was missing from a filename listed IN that text file. Check your
  original error message.

  On Thu, 15 Aug 2013, Alan Francis wrote:

  Hi Anastasia:

  I took off the '/' before the autofs, but then it gave me
  a different
  problem.

csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5
  .3_Data/diffusion_
  recons] : 
tractstats2table--load-pathstats-from-fileautofs/space/dali_003/users/BW_project_DTI/FreeSu
  rfer_5.3_Data/diffusion_re
  cons/Forceps_Major_CC.list.txt 
--overall--tablefileautofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/d
  iffusion_re
cons/Forceps_Major_CC.All.table

ERROR: 
thefileautofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusio
n_re
cons/Forceps_Major_CC.list.txt doesnt exist

Actually it does exist.

thanks,

Alan


On Thu, Aug 15, 2013 at 2:40 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:

      Is it really autofs without the '/' in front?

      On Thu, 15 Aug 2013, Alan Francis wrote:

      Hi Anastasia:

      Sorry to bother you again. I am trying to extract trac
      stats from the FS
      data. When I run the following script, it gives me an
      error message:

csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5

      .3_Data/diffusion_
      recons] 
:tractstats2table--load-pathstats-from-file/autofs/space/dali_003/users/BW_p
roject_DTI/FreeS
      urfer_5.3_Data/diffusion_r
      
econs/Forceps_Major_CC.list.txt--overall--tablefile/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_
5.3_Data/
      diffusion_r
econs/Forceps_Major_CC.All.table

Parsing the .stats files

ERROR: 
Thestatsfileautofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/dif
fusio
n_re
cons/BW_101/dpath/fmajor_PP_avg33_mni_bbr/pathstats.overall.txt
is not found
or is too small to be a valid statsfile

However, when I manually checked the pathstats.overall.txt, the
data is
physically there. Am I doing something wrong?

thanks so much,

Alan




The information in this e-mail is intended only for the person
to whom
it is
addressed. If you believe this e-mail was sent to you in error
and the
e-mail
contains patient information, please contact the Partners
Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent
to you
in error
but does not contain patient information, please contact the
sender
and properly
dispose of the e-mail.






___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Tracula failed


Hi Alan - I'm not sure where the output from the one subject ends the the 
other starts. For future reference, it's best to attach the entire 
trac-all.log files instead of copying and pasting parts of them into your 
message.

I see two error messages here:
1.  ERROR: must specify as many DWI dicoms as subjects
This is as it says. Check your configuration file and see if the numbers 
of entries in subjlist and dcmlist are the same.

2.  ERROR: reading 
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_frame.nii.gz
I'm guessing the problem is in the b-value table. How many entries are 
there that correspond to low-b images?

a.y

On Tue, 13 Aug 2013, Alan Francis wrote:

 Hi Anastasia:
 
 Thanks to your advice most of the data have been processed using Tracula. Two 
 brains gave me error messages that are
 as follows:
 
 
 csh::alanf@cerebro 
 [/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons]
  : trac-all -prep
 -c 
 /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc-124
 ERROR: must specify as many DWI dicoms as subjects
 csh::alanf@cerebro 
 [/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons]
  : trac-all -prep
 -c 
 /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc-118
 INFO: SUBJECTS_DIR is 
 /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons
 INFO: Diffusion root is 
 /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/
 Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable5_3_0
 trac-preproc -c
 /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/scripts/dmrirc.local
  -log
 /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/scripts/trac-all.log
  -cmd
 /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/scripts/trac-all.cmd
 #-
 /usr/local/freesurfer/stable5_3_0//bin/trac-preproc
 #-
 #@# Image corrections Mon Aug 12 17:11:05 EDT 2013
 mri_convert/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/Diffusion_Recons/20090224_14110
 2DIFFUSIONHighRess016a001.nii
 /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.nii.gz
 mri_convert/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/Diffusion_Recons/20090224_14110
 2DIFFUSIONHighRess016a001.nii
 /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.nii.gz
 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
 reading 
 from/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/Diffusion_Recons/20090224_14110
 2DIFFUSIONHighRess016a001.nii...
 TR=7640.00, TE=0.00, TI=0.00, flip angle=0.00
 i_ras = (-0.997762, -0.0667414, -0.00403802)
 j_ras = (-0.0662713, 0.979101, 0.192276)
 k_ras = (0.00887916, -0.192114, 0.981333)
 writing to
 /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.nii.gz...
 cp 
 /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/118/Diffusion_Recons/118.bvecs
 /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.mghdti.bvecs
 cp 
 /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/118/Diffusion_Recons/118.bvals
 /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.mghdti.bvals
 flip4fsl 
 /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.nii.gz
 /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig_flip.nii.gz
 INFO: input image orientation is LAS
 INFO: input image determinant is -6.8719
 fslswapdim 
 /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.nii.gz
 x y z 
 /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig_flip.nii.gz
 fslorient -forceradiological
 /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig_flip.nii.gz
 INFO: found
 /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.mghdti.bvals,
 converting to FSL format
 INFO: found
 /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.mghdti.bvecs,
 converting to FSL format
 mv 
 -f/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig_flip.mghdti.bvecs
 /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/bvecs
 mv

Re: [Freesurfer] trac-all download


Hi Ana - If you notice the release notes, this was relevant to an old 
version of tracula. You should now be using the latest version of tracula 
that's included in freesurfer 5.3, in which case you don't need any extra 
downloads.

a.y

On Wed, 14 Aug 2013, ana ;osp wrote:

 hi'm trying to download the trac-all file from the site in the tracula 
 release notes, it is the download from
 2012/1/09 recommended for all, but hen i click it open a page and gives me an 
 errorshould i do something different
 than just click?
 thanks
 
 

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Tracula failed



Where did you get this command line? You should set the SUBJECTS_DIR to 
the location on disk where your freesurfer recons are.



On Wed, 14 Aug 2013, Alan Francis wrote:


Hi Anastasia:

I fixed that problem - thank you. However, I have another question. i am trying 
extract trac data but when I set
environment, I get an error message:

csh::alanf@cerebro 
[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons]
 : setenv
SUBJECTS_DIR $FreeSurfer_Data/diffusion_recons

FreeSurfer_Data: Undefined variable.

How do I solve this?

Thanks again,

Alan



On Wed, Aug 14, 2013 at 11:06 AM, Anastasia Yendiki 
ayend...@nmr.mgh.harvard.edu wrote:

  Hi Alan - I'm not sure where the output from the one subject ends the the 
other starts. For future
  reference, it's best to attach the entire trac-all.log files instead of 
copying and pasting parts of them
  into your message.

  I see two error messages here:
  1.      ERROR: must specify as many DWI dicoms as subjects
  This is as it says. Check your configuration file and see if the numbers 
of entries in subjlist and
  dcmlist are the same.

  2.      ERROR: reading
  
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_frame.nii.gz
  I'm guessing the problem is in the b-value table. How many entries are 
there that correspond to low-b
  images?

  a.y

  On Tue, 13 Aug 2013, Alan Francis wrote:

  Hi Anastasia:

  Thanks to your advice most of the data have been processed using Tracula. 
Two brains gave me error
  messages that are
  as follows:


  csh::alanf@cerebro
  
[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons]
 : trac-all -prep
  -c 
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc-124
  ERROR: must specify as many DWI dicoms as subjects
  csh::alanf@cerebro
  
[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons]
 : trac-all -prep
  -c 
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc-118
  INFO: SUBJECTS_DIR is
  
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons
  INFO: Diffusion root is
  
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/
  Actual FREESURFER_HOME 
/autofs/cluster/freesurfer/centos6_x86_64/stable5_3_0
  trac-preproc -c
  
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/scripts/dmrirc.local
  -log
  
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/scripts/trac-all.log
  -cmd
  
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/scripts/trac-all.cmd
  #-
  /usr/local/freesurfer/stable5_3_0//bin/trac-preproc
  #-
  #@# Image corrections Mon Aug 12 17:11:05 EDT 2013
mri_convert/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/Diffusion_Recons/200
  90224_14110
  2DIFFUSIONHighRess016a001.nii
  
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.nii.gz
mri_convert/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/Diffusion_Recons/200
  90224_14110
2DIFFUSIONHighRess016a001.nii
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.nii.gz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
readingfrom/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/Diffusion_Recons/20090224_1
4110
2DIFFUSIONHighRess016a001.nii...
TR=7640.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.997762, -0.0667414, -0.00403802)
j_ras = (-0.0662713, 0.979101, 0.192276)
k_ras = (0.00887916, -0.192114, 0.981333)
writing to
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.nii.gz...
cp
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/118/Diffusion_Recons/118.bvecs
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.mghdti.bvecs
cp
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/118/Diffusion_Recons/118.bvals
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.mghdti.bvals
flip4fsl
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.nii.gz
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig_flip.nii.gz
INFO: input image orientation is LAS
INFO: input image determinant is -6.8719
fslswapdim
/autofs/space/dali_003/users/BW_project_DTI

Re: [Freesurfer] Tracula failed



Alan - Where is the location that has plenty of space? You should set your 
SUBJECTS_DIR to that location, e.g.,


setenv SUBJECTS_DIR 
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons


On Wed, 14 Aug 2013, Alan Francis wrote:


Hi Anastasia/ FreeSurfers

I did not use the conventional path usr/local/freesurfer. since there is very 
little disc space in this location.
Alternately I set the environment at a location where is plenty of disc space 
and then sourced it.

For the SUBJECTS_DIR I set the environment without using the dollar sign $.

The Freesurfer recons and Tracula ran without problem and saved the processed 
data to this location.  So the
FReeSurfer recons and tracula data are in the same location.

Now I am trying to use the dollar sign, so that I can extract the trac data, 
but I keep getting the error message.

csh::alanf@cerebro 
[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons]
 : setenv
SUBJECTS_DIR $FreeSurfer_Data/diffusion_recons

FreeSurfer_Data: Undefined variable.


thanks,

Alan


On Wed, Aug 14, 2013 at 1:08 PM, Anastasia Yendiki 
ayend...@nmr.mgh.harvard.edu wrote:

  Where did you get this command line? You should set the SUBJECTS_DIR to 
the location on disk where your
  freesurfer recons are.


  On Wed, 14 Aug 2013, Alan Francis wrote:

  Hi Anastasia:

  I fixed that problem - thank you. However, I have another question. i am 
trying extract trac data
  but when I set
  environment, I get an error message:

  csh::alanf@cerebro
  
[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons]
 : setenv
  SUBJECTS_DIR $FreeSurfer_Data/diffusion_recons

  FreeSurfer_Data: Undefined variable.

  How do I solve this?

  Thanks again,

  Alan



  On Wed, Aug 14, 2013 at 11:06 AM, Anastasia Yendiki 
ayend...@nmr.mgh.harvard.edu wrote:

        Hi Alan - I'm not sure where the output from the one subject ends 
the the other starts. For
  future
        reference, it's best to attach the entire trac-all.log files 
instead of copying and pasting
  parts of them
        into your message.

        I see two error messages here:
        1.      ERROR: must specify as many DWI dicoms as subjects
        This is as it says. Check your configuration file and see if the 
numbers of entries in
  subjlist and
        dcmlist are the same.

        2.      ERROR: reading
       
  
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_frame.nii.gz
        I'm guessing the problem is in the b-value table. How many entries 
are there that correspond
  to low-b
        images?

        a.y

        On Tue, 13 Aug 2013, Alan Francis wrote:

        Hi Anastasia:

        Thanks to your advice most of the data have been processed using 
Tracula. Two brains gave me
  error
        messages that are
        as follows:


        csh::alanf@cerebro
        
[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons]
 : trac-all
  -prep
        -c 
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc-124
        ERROR: must specify as many DWI dicoms as subjects
        csh::alanf@cerebro
        
[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons]
 : trac-all
  -prep
        -c 
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc-118
        INFO: SUBJECTS_DIR is
        
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons
        INFO: Diffusion root is
        
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/
        Actual FREESURFER_HOME 
/autofs/cluster/freesurfer/centos6_x86_64/stable5_3_0
        trac-preproc -c
       
  
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/scripts/dmrirc.local
        -log
       
  
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/scripts/trac-all.log
        -cmd
       
  
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/scripts/trac-all.cmd
        #-
        /usr/local/freesurfer/stable5_3_0//bin/trac-preproc
        #-
        #@# Image corrections Mon Aug 12 17:11:05 EDT 2013
mri_convert/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/Diffusion_Recons/200

        90224_14110
        2DIFFUSIONHighRess016a001.nii
       
  
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.nii.gz
mri_convert/autofs/space

Re: [Freesurfer] Tracula failed



Why do you want to use a '$'?

On Wed, 14 Aug 2013, Alan Francis wrote:


Hi Anastasia:

Yes the path that you pointed out is the one I presently use. Is there no way 
to use the '$' as a substitute?

thanks,

Alan


On Wed, Aug 14, 2013 at 1:46 PM, Anastasia Yendiki 
ayend...@nmr.mgh.harvard.edu wrote:

  Alan - Where is the location that has plenty of space? You should set 
your SUBJECTS_DIR to that location,
  e.g.,

  setenv SUBJECTS_DIR 
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons


  On Wed, 14 Aug 2013, Alan Francis wrote:

  Hi Anastasia/ FreeSurfers

  I did not use the conventional path usr/local/freesurfer. since there is 
very little disc space in
  this location.
  Alternately I set the environment at a location where is plenty of disc 
space and then sourced it.

  For the SUBJECTS_DIR I set the environment without using the dollar sign 
$.

  The Freesurfer recons and Tracula ran without problem and saved the 
processed data to this
  location.  So the
  FReeSurfer recons and tracula data are in the same location.

  Now I am trying to use the dollar sign, so that I can extract the trac 
data, but I keep getting the
  error message.

csh::alanf@cerebro 
[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons]
 :
setenv
SUBJECTS_DIR $FreeSurfer_Data/diffusion_recons

FreeSurfer_Data: Undefined variable.


thanks,

Alan


On Wed, Aug 14, 2013 at 1:08 PM, Anastasia Yendiki 
ayend...@nmr.mgh.harvard.edu wrote:

      Where did you get this command line? You should set the SUBJECTS_DIR to 
the location on disk where
your
      freesurfer recons are.


      On Wed, 14 Aug 2013, Alan Francis wrote:

      Hi Anastasia:

      I fixed that problem - thank you. However, I have another question. i am 
trying extract trac data
      but when I set
      environment, I get an error message:

      csh::alanf@cerebro
      
[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons]
 : setenv
      SUBJECTS_DIR $FreeSurfer_Data/diffusion_recons

      FreeSurfer_Data: Undefined variable.

      How do I solve this?

      Thanks again,

      Alan



      On Wed, Aug 14, 2013 at 11:06 AM, Anastasia Yendiki 
ayend...@nmr.mgh.harvard.edu wrote:

            Hi Alan - I'm not sure where the output from the one subject ends 
the the other starts. For
      future
            reference, it's best to attach the entire trac-all.log files 
instead of copying and pasting
      parts of them
            into your message.

            I see two error messages here:
            1.      ERROR: must specify as many DWI dicoms as subjects
            This is as it says. Check your configuration file and see if the 
numbers of entries in
      subjlist and
            dcmlist are the same.

            2.      ERROR: reading
           
     
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_frame.nii.gz
            I'm guessing the problem is in the b-value table. How many entries 
are there that correspond
      to low-b
            images?

            a.y

            On Tue, 13 Aug 2013, Alan Francis wrote:

            Hi Anastasia:

            Thanks to your advice most of the data have been processed using 
Tracula. Two brains gave me
      error
            messages that are
            as follows:


            csh::alanf@cerebro
            
[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons]
 : trac-all
      -prep
            -c 
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc-124
            ERROR: must specify as many DWI dicoms as subjects
            csh::alanf@cerebro
            
[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons]
 : trac-all
      -prep
            -c 
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc-118
            INFO: SUBJECTS_DIR is
            
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons
            INFO: Diffusion root is
            
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/
            Actual FREESURFER_HOME 
/autofs/cluster/freesurfer/centos6_x86_64/stable5_3_0
            trac-preproc -c
           
     
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/scripts/dmrirc.local
            -log
           
     
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/scripts/trac-all.log
            -cmd
           
     
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/scripts/trac-all.cmd
            #-
            /usr/local/freesurfer/stable5_3_0//bin/trac-preproc

Re: [Freesurfer] trac-all download



If you already have the 5.1 version and have used it on some subjects, you 
can of course use the same version on the other subjects. But if you're 
going to download something new, that should be the 5.3 version, not an 
intermediate update to 5.1. It's highly recommended to use the 5.3 version 
of tracula b/c there are several improvements to it.


On Wed, 14 Aug 2013, ana ;osp wrote:


thanksbut i'have all the data processed with 5.1 and i still have a few 
subjects to process so i didn't want to
download the 5.3 and mix versions...  is there anyway to have it without 
download the 5.3?
thanks



On Wed, Aug 14, 2013 at 11:11 AM, Anastasia Yendiki 
ayend...@nmr.mgh.harvard.edu wrote:

  Hi Ana - If you notice the release notes, this was relevant to an old 
version of tracula. You should now
  be using the latest version of tracula that's included in freesurfer 5.3, 
in which case you don't need any
  extra downloads.

  a.y

  On Wed, 14 Aug 2013, ana ;osp wrote:

  hi'm trying to download the trac-all file from the site in the tracula 
release notes, it is the
  download from
2012/1/09 recommended for all, but hen i click it open a page and gives me an 
errorshould i do something
different
than just click?
thanks





The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Preproc


Hi Alan - This appears to be the same error message as the one for subject 
118 that you sent yesterday. So I'd try here whatever you did to fix that 
one.

a.y

On Wed, 14 Aug 2013, Alan Francis wrote:

 Hi Anastasia:
 
 Sorry to bother you again. Another of my brains gave an error message. I
 have enclosed the trac-all log as an attachment.
 
 Thanks ever so much for your help,
 
 Alan
 

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] trac-all inquiry

2013-08-09 Thread Anastasia Yendiki



When you apply a rotation to the DWIs (as eddy_correct does), you need to 
apply the same rotation to the corresponding gradient vectors. See for 
example: Leemans, A., Jones, D. K., Jun 2009. The B-matrix must be rotated 
when correcting for subject motion in DTI data. Magn Reson Med 61 (6), 
1336–49.


If you don't want to pass the dicoms to trac-all directly, you can use 
mri_convert to convert from dicom to nifti.


On Fri, 9 Aug 2013, Soto, David wrote:


hi - am afraid not because I am feeding to trac-all
already eddycorrected images then in the config file
I have

# Perform registration-based eddy-current compensation?
# Default: 1 (yes)
set doeddy = 0
# Rotate diffusion gradient vectors to match eddy-current compensation?
# Only used if doeddy = 1
# Default: 1 (yes)

is this critical??

unfortunately, this is the only way I manage to get it to work
as said my diffusion outputs from mriconverter
are not read by FS, only through mediation
of some FSL operation on the files, then FS
likes those.

I could start from scratch using dicoms but would prefer
not to  as the data is already well organised 

cheers
ds
http://www1.imperial.ac.uk/medicine/people/d.soto/


From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu]
Sent: 09 August 2013 22:44
To: Soto, David
Subject: Re: [Freesurfer]  trac-all inquiry

Are you rotating the gradient vectors accordingly? This is done in
trac-all after running eddy_correct.

On Fri, 9 Aug 2013, Soto, David wrote:


Hi Anastasia, stuff is running smoothly at last one quick question, is there
any 'disadvantage' in
using FSL to do the eddy correct and then feed
those images to trace-all ?
cheers
ds
http://www1.imperial.ac.uk/medicine/people/d.soto/

On 9 Aug 2013, at 15:33, David Soto ds...@imperial.ac.uk
 wrote:

  hi, for some reason FS does not like the
  nii file from Mriconverter, ( I saw
  a post about this
  http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg19526.html
  ) but does like
  the nii.gz outputs from FSL...

  I'll try to debug the bepostx error

  thanks!

  ds

  http://www1.imperial.ac.uk/medicine/people/d.soto/
On 09/08/13 14:26, Anastasia Yendiki wrote:

  There is no reason to conevrt to .mnc. You should use your
  original .nii, if that shows up correctly in freeview.

  As for the bedpostx error, this is an Ubuntu issue that
  has come to my attention very recently. In Ubuntu /bin/sh
  is not a bash shell any more. To get around this, you'll
  have to edit the first line of the scripts
  $FREESURFER_HOME/bin/bedpostx_mgh and
  $FREESURFER_HOME/bin/fsl_sub_mgh. You'll have to replace
  /bin/sh with /bin/bash on the first line of those two
  scripts.

  On Fri, 9 Aug 2013, David Soto wrote:

hi- I tried to convert from nii to mnc becos
that is what i did when
I did recon-all

but I also tried with nii at the beggining and
got the same issues.
In fact in my last post (pasted below
again)the input was a nii file
could you please check the stuff below?
thanks! ds


Hi, further to my prior email
I made some progress. I noted that nii2mnc
does not seem to work on the diffusion
output.nii that I got from Mriconverter as the
output.mnc brain has parts chopped in
Freeview.

(I think there may be something funny about
this, as the recon-all does like the T1 output
form Mriconverter)

HENCE I tried use the output of eddycorrect
from FSL (which I already run for other thing)
Then I created a new folder where i placed the
output of FSL eddycorrect and in the
configuration file I did
(i)  set dcmlist =
(fsleddycorrectoutput.nii.gz)
(ii) turned 'set doeddy = 0'

then run it
trac-all -c traculatest.txt -prep -log
trac_from_fsleddy


it seemed to complete without errors (log
attached)n and I checked the preprocessing
outputs in Freeview (FA, masks and
aparc+asegs) and all seemed
fine.

However when I attempt the next stage in
trac-all
i.e. trac-all -c traculatest.txt -bedp -log
trac_from_fsleddy_bedp
it fails saying the following
/usr/local/freesurfer/bin/bedpostx_mgh: 131:
/usr/local/freesurfer/bin/bedpostx_mgh: Syntax
error: ( unexpected


the log is also attached.

any advise appreciated!

cheers
ds
http://www1.imperial.ac.uk/medicine/people/d.soto/
http://www1.imperial.ac.uk/medicine/people/d.soto/
On 09/08/13 14:02, Anastasia Yendiki wrote

Re: [Freesurfer] trac-all inquiry

2013-08-09 Thread Anastasia Yendiki



I didn't mean run mri_convert on the nifti output of another program. I 
meant run mri_convert directly on the original dicom to convert it to 
nifti:

mri_convert yourimage.dcm yourimage.nii.gz

On Fri, 9 Aug 2013, Soto, David wrote:


I see - as said the diffusion output.nii from MRIConverter
http://lcni.uoregon.edu/~jolinda/MRIConvert/ [to not confound it with 
mri_converter)
is not read by Freeview and mri_converter does not like it either
---
MD00071523-2:RSDTI_WMGUI/ACH_AMO/diff] dsoto% mri_convert output.nii data.mgz
mri_convert output.nii data.mgz 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from output.nii...
nifti1Read(): unsupported slice timing pattern 5 in 
/Users/dsoto/Documents/fMRI/RSDTI_WMGUI/ACH_AMO/diff/output.nii
No such file or directory
---

NOW, I find that if I use FSL and run bet with a fractional intensity threshold 
of 0,
I get an output file which is read by Freeview- which should allow me to proceed
with all the necessary preprocessing steps in trac-all

would this be fine? I dont think the bet I run will affect the image

cheers
ds
http://www1.imperial.ac.uk/medicine/people/d.soto/


From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu]
Sent: 09 August 2013 23:15
To: Soto, David
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer]  trac-all inquiry

When you apply a rotation to the DWIs (as eddy_correct does), you need to
apply the same rotation to the corresponding gradient vectors. See for
example: Leemans, A., Jones, D. K., Jun 2009. The B-matrix must be rotated
when correcting for subject motion in DTI data. Magn Reson Med 61 (6),
1336–49.

If you don't want to pass the dicoms to trac-all directly, you can use
mri_convert to convert from dicom to nifti.

On Fri, 9 Aug 2013, Soto, David wrote:


hi - am afraid not because I am feeding to trac-all
already eddycorrected images then in the config file
I have

# Perform registration-based eddy-current compensation?
# Default: 1 (yes)
set doeddy = 0
# Rotate diffusion gradient vectors to match eddy-current compensation?
# Only used if doeddy = 1
# Default: 1 (yes)

is this critical??

unfortunately, this is the only way I manage to get it to work
as said my diffusion outputs from mriconverter
are not read by FS, only through mediation
of some FSL operation on the files, then FS
likes those.

I could start from scratch using dicoms but would prefer
not to  as the data is already well organised

cheers
ds
http://www1.imperial.ac.uk/medicine/people/d.soto/


From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu]
Sent: 09 August 2013 22:44
To: Soto, David
Subject: Re: [Freesurfer]  trac-all inquiry

Are you rotating the gradient vectors accordingly? This is done in
trac-all after running eddy_correct.

On Fri, 9 Aug 2013, Soto, David wrote:


Hi Anastasia, stuff is running smoothly at last one quick question, is there
any 'disadvantage' in
using FSL to do the eddy correct and then feed
those images to trace-all ?
cheers
ds
http://www1.imperial.ac.uk/medicine/people/d.soto/

On 9 Aug 2013, at 15:33, David Soto ds...@imperial.ac.uk
 wrote:

  hi, for some reason FS does not like the
  nii file from Mriconverter, ( I saw
  a post about this
  http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg19526.html
  ) but does like
  the nii.gz outputs from FSL...

  I'll try to debug the bepostx error

  thanks!

  ds

  http://www1.imperial.ac.uk/medicine/people/d.soto/
On 09/08/13 14:26, Anastasia Yendiki wrote:

  There is no reason to conevrt to .mnc. You should use your
  original .nii, if that shows up correctly in freeview.

  As for the bedpostx error, this is an Ubuntu issue that
  has come to my attention very recently. In Ubuntu /bin/sh
  is not a bash shell any more. To get around this, you'll
  have to edit the first line of the scripts
  $FREESURFER_HOME/bin/bedpostx_mgh and
  $FREESURFER_HOME/bin/fsl_sub_mgh. You'll have to replace
  /bin/sh with /bin/bash on the first line of those two
  scripts.

  On Fri, 9 Aug 2013, David Soto wrote:

hi- I tried to convert from nii to mnc becos
that is what i did when
I did recon-all

but I also tried with nii at the beggining and
got the same issues.
In fact in my last post (pasted below
again)the input was a nii file
could you please check the stuff below?
thanks! ds


Hi, further to my prior email
I made some progress. I noted that nii2mnc
does not seem to work on the diffusion
output.nii that I got from Mriconverter as the
output.mnc brain

Re: [Freesurfer] trac-all inquiry

2013-08-08 Thread Anastasia Yendiki



Hi David - The fact that it's taking so many tries to initialize the left 
ILF tells me that something has gone wrong with the data, either with the 
T1 to DWI registration, or with the mask, or something like that. Have you 
looked at any of the output files of the pre-processing? The FA map, the 
aparc+aseg, etc?


a.y

On Wed, 7 Aug 2013, Soto, David wrote:


Hi Anastasia, I checked the becs and bvals files,
there was a bug in the transposition of the columns into
3 rows in the bvecs. But i still have problems..
I rerun trac-all -prep and seemed fine but ended
with a Segmentation fault (core dumped) 
which however is not present in the last line of the 
trac-all.log (Attached).

Writing output files to 
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_*
Writing spline volume to 
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_cpts_5.nii.gz
Segmentation fault (core dumped) 


Just in case I tried trac-all -bedp complains like these below, any advise 
appreciated, cheers - ds 
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/diffree/tracula02ST.txt -bedp
INFO: SUBJECTS_DIR is /home/dsoto/Documents/fmri/rsdtianawmgui
INFO: Diffusion root is /home/dsoto/Documents/fmri/rsdtianawmgui
Actual FREESURFER_HOME /usr/local/freesurfer
WARN: Running FSL's bedbost locally - this might take a while
WARN: It is recommended to run this step on a cluster
bedpostx_mgh -n 2 /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri
/usr/local/freesurfer/bin/bedpostx_mgh: 131: /usr/local/freesurfer/bin/bedpostx_mgh: 
Syntax error: ( unexpected
http://www1.imperial.ac.uk/medicine/people/d.soto/


From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu]
Sent: 07 August 2013 17:22
To: Soto, David
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer]  trac-all inquiry

Hi David - Every time you run trac-all, the results get appended to this
file, so you need to look for error messages only in the more recent
invocation of trac-all. The first error there seems to be:

   Error: bvecs and bvals don't have the same number of entries

Do you have the same number of b-values and gradient vectors and volumes
in your DWI series?

a.y

On Tue, 6 Aug 2013, Soto, David wrote:


hi

I upgraded to FS 5.3 but still encountering issues with
trac-all prep.

The log is attached, things I noted after inspecting it

1)  INFO: FreeSurfer build stamps do not match
Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0

2) Error: input image /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb 
not valid
3) Image Exception : #22 :: ERROR: Could not open image 
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb_brain
4) Image Exception : #22 :: ERROR: Could not open image
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/diff/White-Matter++.
5) ERROR: Could not read 
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/dtifit_FA.nii.gz
but despite all this it says:
trac-preproc finished without error at Tue Aug  6 21:27:30 BST 2013

thanks for your help

cheers
ds

http://www1.imperial.ac.uk/medicine/people/d.soto/





From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu]
Sent: 06 August 2013 19:30
To: Soto, David
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer]  trac-all inquiry

I see, you're using the old version of tracula (from freesurfer 5.1). In
that version, you had to define the number of low-b images in the
configuration file. I strongly recommend updating to freesurfer 5.3. A lot
of things have improved in tracula since then.

Also, in the future please attach any log files as separate attachments
instead of pasting them into the body of your email - this causes the body
of the email to exceed the limit allowable on the list.

Thanks,
a.y


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] trac-all inquiry



Hi David - Every time you run trac-all, the results get appended to this 
file, so you need to look for error messages only in the more recent 
invocation of trac-all. The first error there seems to be:


Error: bvecs and bvals don't have the same number of entries

Do you have the same number of b-values and gradient vectors and volumes 
in your DWI series?


a.y

On Tue, 6 Aug 2013, Soto, David wrote:


hi

I upgraded to FS 5.3 but still encountering issues with
trac-all prep.

The log is attached, things I noted after inspecting it

1)  INFO: FreeSurfer build stamps do not match
Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0

2) Error: input image /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb 
not valid
3) Image Exception : #22 :: ERROR: Could not open image 
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb_brain
4) Image Exception : #22 :: ERROR: Could not open image
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/diff/White-Matter++.
5) ERROR: Could not read 
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/dtifit_FA.nii.gz
but despite all this it says:
trac-preproc finished without error at Tue Aug  6 21:27:30 BST 2013

thanks for your help

cheers
ds

http://www1.imperial.ac.uk/medicine/people/d.soto/





From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu]
Sent: 06 August 2013 19:30
To: Soto, David
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer]  trac-all inquiry

I see, you're using the old version of tracula (from freesurfer 5.1). In
that version, you had to define the number of low-b images in the
configuration file. I strongly recommend updating to freesurfer 5.3. A lot
of things have improved in tracula since then.

Also, in the future please attach any log files as separate attachments
instead of pasting them into the body of your email - this causes the body
of the email to exceed the limit allowable on the list.

Thanks,
a.y


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Tracula question


Yes, please attach the dmrirc and trac-all.log. Thanks!

a.y

On Wed, 7 Aug 2013, Alan Francis wrote:

 Hi Anastasia:
 
 For one brain I got this error message :
 
 csh::alanf@cerebro 
 [/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons]
  : trac-all -prep
 -c 
 /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc-107
 
 Too many ('s.
 ERROR: must specify as many DWI dicoms as subjects
 
 I tried specifying the exact number of DWI dicoms but it is not working. 
 Should I send you my dmrirc for this brain?
 
 thanks,
 
 Alan
 

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Tracula question

Please attach the file trac-all.log. I can't tell what's going on just by
looking at the end of it.

On Wed, 7 Aug 2013, Alan Francis wrote:

Thank you Anastasia. Another brain had a different problem: Here is the
trac-all log:

mri_concat --i
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_frame.nii.gz
--mean --o
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/lowb.nii.gz
niiRead(): error opening file
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_frame.nii.gz
ninputs = 1
Checking inputs
ERROR: reading
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_frame.nii.gz
Linux cerebro 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013
x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Wed Aug 7 13:01:21 EDT 2013

thanks so much,

Alan

On Wed, Aug 7, 2013 at 1:11 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:

Hi Alan - Try removing the \ character from the end of the dcmlist
definition. That's a change of line
character.

a.y

On Wed, 7 Aug 2013, Alan Francis wrote:

Hi Anastasia:

Here is the trac-all log. Please find attached the dmrirc file.

csh::alanf@cerebro

[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons]
: trac-all
-prep
-c
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc-107

Too many ('s.
ERROR: must specify as many DWI dicoms as subjects

Thank you so much.

Alan

On Wed, Aug 7, 2013 at 12:32 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:

Yes, please attach the dmrirc and trac-all.log. Thanks!

a.y

On Wed, 7 Aug 2013, Alan Francis wrote:

Hi Anastasia:

For one brain I got this error message :

csh::alanf@cerebro
[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons]
: trac-all
-prep
-c

/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc-107

Too many ('s.
ERROR: must specify as many DWI dicoms as subjects

I tried specifying the exact number of DWI dicoms but
it is not working. Should I
send you my
dmrirc for this brain?

thanks,

Alan

The information in this e-mail is intended only for the person to
whom it is
addressed. If you believe this e-mail was sent to you in error and
the e-mail
contains patient information, please contact the Partners
Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to
you in error
but does not contain patient information, please contact the sender
and properly
dispose of the e-mail.

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Tracula question

/diffusion_recons//106/dmri/dwi_frame.nii.gz
ninputs = 1
Checking inputs
ERROR: reading
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_frame.nii.gz
Linux cerebro 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 
x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Wed Aug  7 13:34:45 EDT 2013



On Wed, Aug 7, 2013 at 1:20 PM, Anastasia Yendiki 
ayend...@nmr.mgh.harvard.edu wrote:

  Please attach the file trac-all.log. I can't tell what's going on just by 
looking at the end of it.

  On Wed, 7 Aug 2013, Alan Francis wrote:

Thank you Anastasia. Another brain had a different problem: Here is 
the trac-all log:

mri_concat --i

/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_frame.nii.gz
--mean --o

/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/lowb.nii.gz
niiRead(): error opening file

/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_frame.nii.gz
ninputs = 1
Checking inputs
ERROR: reading

/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_frame.nii.gz
Linux cerebro 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 
UTC 2013 x86_64 x86_64
x86_64 GNU/Linux

trac-preproc exited with ERRORS at Wed Aug  7 13:01:21 EDT 2013

thanks so much,

Alan


On Wed, Aug 7, 2013 at 1:11 PM, Anastasia Yendiki 
ayend...@nmr.mgh.harvard.edu wrote:

      Hi Alan - Try removing the \ character from the end of the 
dcmlist definition. That's
a change of line
      character.

      a.y

      On Wed, 7 Aug 2013, Alan Francis wrote:

            Hi Anastasia:

            Here is the trac-all log. Please find attached the 
dmrirc file.

            csh::alanf@cerebro
            
[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons]
: trac-all
            -prep
            -c

/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc-107

            Too many ('s.
            ERROR: must specify as many DWI dicoms as subjects

            Thank you so much.

            Alan


            On Wed, Aug 7, 2013 at 12:32 PM, Anastasia Yendiki 
ayend...@nmr.mgh.harvard.edu
wrote:

                  Yes, please attach the dmrirc and trac-all.log. 
Thanks!

                  a.y

                  On Wed, 7 Aug 2013, Alan Francis wrote:

                        Hi Anastasia:

                        For one brain I got this error message :

                        csh::alanf@cerebro
                       

[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons]
            : trac-all
                        -prep
                        -c
           

/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc-107

                        Too many ('s.
                        ERROR: must specify as many DWI dicoms as 
subjects

                        I tried specifying the exact number of DWI 
dicoms but it is not
working. Should I
            send you my
                        dmrirc for this brain?

                        thanks,

                        Alan




            The information in this e-mail is intended only for the 
person to whom it is
            addressed. If you believe this e-mail was sent to you 
in error and the e-mail
            contains patient information, please contact the 
Partners Compliance HelpLine at
            http://www.partners.org/complianceline . If the e-mail 
was sent to you in error
            but does not contain patient information, please 
contact the sender and properly
            dispose of the e-mail.








___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you

Re: [Freesurfer] preferred method for generating appropriate bvecs for tracula


set x = `cat bvecs | awk '{if (NR==1) print}'`
set y = `cat bvecs | awk '{if (NR==2) print}'`
set z = `cat bvecs | awk '{if (NR==3) print}'`

@ k = 1
while ( $k = `head -1 bvecs|wc -w` )
   echo $x[$k] $y[$k] $z[$k]
   @ k = $k + 1
end

I'd make sure though dcm2nii doesn't L-R flip the gradient vectors, I 
think there was a thread recently that suggested it might.

On Wed, 7 Aug 2013, Salil Soman wrote:

 Hi,
 I have dicoms that I turn to nifti using dcm2nii (with the default settings 
 plus anonymization option turned on [-a
 y]). The bvec files it generates by default are 3 rows by n columns (where n 
 is b0 number + directions). I am under
 the impression tracula requires this to be converted to a n row by 3 column 
 file. 1) is this correct, 2) is there a
 preferred way to perform this transformation on linux systems?
 
 Thanks you,
 
 -Sal
 

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] preferred method for generating appropriate bvecs for tracula



Hi Sal - Right now you'd just have to try it on one data set and look at 
the eigenvectors of the tensor (display dmri/dtifit_V1.nii.gz as lines) to 
make sure they're pointing in the right way.


I'm hoping for the next freesurfer release to finally get mri_convert to 
read gradient vectors off the dicom header in a way that ends this 
gradient flipping madness once and for all. But for now you just have to 
check before you proceed, sorry!


a.y

On Wed, 7 Aug 2013, Salil Soman wrote:


Thank you for the email.
I saw a warning to check for flipping L-R from the dcm2nii site:
http://www.mccauslandcenter.sc.edu/mricro/mricron/dcm2nii.html

Is the problem you mentioned vendor specific (I have all GE data). Is there a 
different tool you would recommend for
generating the bvec files? I would prefer to run tracula right off the original 
dicom images but transferring them to
the cluster and anonymizing them would be prohibitively difficult.

I could not find the freesurfer archive message you referred to. Any pointers 
would be greatly appreciated.

Best wishes,

Sal


On Wed, Aug 7, 2013 at 1:12 PM, Anastasia Yendiki 
ayend...@nmr.mgh.harvard.edu wrote:

  set x = `cat bvecs | awk '{if (NR==1) print}'`
  set y = `cat bvecs | awk '{if (NR==2) print}'`
  set z = `cat bvecs | awk '{if (NR==3) print}'`

  @ k = 1
  while ( $k = `head -1 bvecs|wc -w` )
    echo $x[$k] $y[$k] $z[$k]
    @ k = $k + 1
  end

  I'd make sure though dcm2nii doesn't L-R flip the gradient vectors, I 
think there was a thread recently
  that suggested it might.

  On Wed, 7 Aug 2013, Salil Soman wrote:

Hi,
I have dicoms that I turn to nifti using dcm2nii (with the default 
settings plus anonymization
option turned on [-a
y]). The bvec files it generates by default are 3 rows by n columns 
(where n is b0 number +
directions). I am under
the impression tracula requires this to be converted to a n row by 
3 column file. 1) is this
correct, 2) is there a
preferred way to perform this transformation on linux systems?

Thanks you,

-Sal




The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.




--
Salil Soman, MD, MS
Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory
Fellow - Palo Alto War Related Illness and Injury Study Center
WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] preferred method for generating appropriate bvecs for tracula



Freeview can do this in principle, but the current version of freeview has 
a known bug with displaying eigenvectors as lines (see known issues in 
http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes), so for now you can 
use fslview.


On Wed, 7 Aug 2013, Salil Soman wrote:


Thank you for your response. Is there a best way to review the eigenvectors 
(tkmedit, freeview, other program?). 
Thank you.


-S

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] trac-preproc

2013-08-06 Thread Anastasia Yendiki



You're welcome. It seems like it can't find this file:
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data//bin/dmri_train

I can't tell exactly what's going on without looking at your trac-all.log 
in its entirety. Can you please send it?


On Tue, 6 Aug 2013, Alan Francis wrote:


Thank you. It worked. I have been running a few brains and they have been 
preprocessed successfully. One brain gave me
an error message. Can you please help me address this:

/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dmri/xfms/mni2diff.bbr.mat
--ncpts 6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5 --trunc

/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data//bin/dmri_train:
 Command not found.

Linux cerebro 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 
x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Tue Aug  6 10:22:18 EDT 2013

Thanks so much,

Alan




On Mon, Aug 5, 2013 at 3:55 PM, Anastasia Yendiki 
ayend...@nmr.mgh.harvard.edu wrote:

  Hi Alan - The file doesn't need to have an extension, .txt or other. But 
you do need to set bvecfile to
  the full name of the file, including the extension, if it has one.

  a.y

  On Mon, 5 Aug 2013, Alan Francis wrote:

  Hi Anastasia:

  Yes this file does exist but it did not have the *.txt suffix. Maybe I 
will
  change the suffix and run this again.

  thanks,

  Alan


  On Mon, Aug 5, 2013 at 1:57 PM, Anastasia Yendiki
  ayend...@nmr.mgh.harvard.edu wrote:

        The error says:
  
`/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
        recons/bvecs.txt': No such file or directory

  Does this file exist?

  On Mon, 5 Aug 2013, Alan Francis wrote:

        Hi All:

        When I ran trac-preproc I got an error that read s as
        follows:

        trac-preproc exited with ERRORS at Mon Aug  5 13:12:53 EDT
        2013. I do have a bvec.txt and bval file in each
        directory.

        thanks for your help,

        Alan


        The following are the messages:

        csh::alanf@cerebro
        [/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data]
        : trac-all -prep -c
  
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
        econs/dmrirc
        INFO: SUBJECTS_DIR
  
is/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
        econs
        INFO: Diffusion root
  
is/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
        econs/
        Actual FREESURFER_HOME
        /autofs/cluster/freesurfer/centos6_x86_64/stable5_3_0
        trac-preproc 
-c/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
        econs//BW_101/scripts/dmrirc.local -log
  
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
        econs//BW_101/scripts/trac-all.log -cmd
  
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
        econs//BW_101/scripts/trac-all.cmd
        #-
        /usr/local/freesurfer/stable5_3_0//bin/trac-preproc
        #-
        #@# Image corrections Mon Aug  5 13:12:10 EDT 2013
        
mri_convert/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
  
econs//BW_101/Diffusion_Recons/20080424_182054563000-12-01DTIValera
        s012a001.nii
  
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
        econs//BW_101/dmri/dwi_orig.nii.gz
        
mri_convert/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
  
econs//BW_101/Diffusion_Recons/20080424_182054563000-12-01DTIValera
        s012a001.nii
  
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
        econs//BW_101/dmri/dwi_orig.nii.gz
        $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter
        Exp $
        reading from
  
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
  
econs//BW_101/Diffusion_Recons/20080424_182054563000-12-01DTIValera
        s012a001.nii...
        TR=7570.00, TE=0.00, TI=0.00, flip angle=0.00
        i_ras = (-0.989696, 0.0161603, 0.142271)
        j_ras = (0.0163, 0.999867, -0.000183368)
        k_ras = (0.142255, -0.00213754, 0.989828)
        writing 
to/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
        econs//BW_101/dmri/dwi_orig.nii.gz...
        
cp/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
        econs/bvecs.txt
  
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r

Re: [Freesurfer] trac-all inquiry

2013-08-06 Thread Anastasia Yendiki


I see, you're using the old version of tracula (from freesurfer 5.1). In 
that version, you had to define the number of low-b images in the 
configuration file. I strongly recommend updating to freesurfer 5.3. A lot 
of things have improved in tracula since then.

Also, in the future please attach any log files as separate attachments 
instead of pasting them into the body of your email - this causes the body 
of the email to exceed the limit allowable on the list.

Thanks,
a.y
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Trac-all question

2013-08-05 Thread Anastasia Yendiki



Hi Alan - On the tutorial page you need to follow the directions under If 
you are not at an organized course, and $TUTORIAL_DATA is whatever 
directory you have downloaded the tutorial data in.


Please address questions to the list and not to me personally, as other 
people may have the same issue and this way the answers get archived.


Thanks,
a.y

On Mon, 5 Aug 2013, Alan Francis wrote:


Hi Anastasia:

Sorry about being a pest. One more question. I am running the Tutorial data
to get a better understanding of Tracula. When I type $TUTORIAL_DATA,  it
keeps saying Undefined variable. Could you please help me.

Thanks,

Alan

csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/TUTORIAL_D
ATA/diffusion_recons] : setenv FREESURFER_HOME
/usr/local/freesurfer/stable5_3_0/
csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/TUTORIAL_D
ATA/diffusion_recons] : source $FREESURFER_HOME/Set
SetUpFreeSurfer.csh* SetUpFreeSurfer.sh* 
csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/TUTORIAL_D
ATA/diffusion_recons] : source $FREESURFER_HOME/SetUpFreeSurfer.csh
 freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer/stable5_3_0/
FSFAST_HOME   /usr/local/freesurfer/stable5_3_0//fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /usr/local/freesurfer/stable5_3_0//subjects
MNI_DIR   /usr/local/freesurfer/stable5_3_0//mni
FSL_DIR   /usr/pubsw/packages/fsl/current
csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/TUTORIAL_D
ATA/diffusion_recons] : setenv SUBJECTS_DIR $TUTORIAL_DATA/d
$TUTORIAL_DATA/ not found

csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/TUTORIAL_D
ATA/diffusion_recons] : setenv SUBJECTS_DIR /autofs/space/d
dali_001/ dali_002/ dali_003/
csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/TUTORIAL_D
ATA/diffusion_recons] : setenv 
SUBJECTS_DIR/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/TUTORIAL_DA
TA/diffusion_recons/
csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/TUTORIAL_D
ATA/diffusion_recons] : gedit
$TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial 
TUTORIAL_DATA: Undefined variable.
csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/TUTORIAL_D
ATA/diffusion_recons] : gedit
/TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial 
[1] 32742
csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/TUTORIAL_D
ATA/diffusion_recons] : trac-all -prep -c
$TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial
TUTORIAL_DATA: Undefined variable.



On Fri, Aug 2, 2013 at 7:16 PM, Alan Francis alandarkene...@gmail.com
wrote:
  thanks again.


On Fri, Aug 2, 2013 at 3:51 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:

  It can have any name you want. You just have to type the
  right name next to the -c ...

  On Fri, 2 Aug 2013, Alan Francis wrote:

Sorry. I have another question. Should I name
the config file dmrirc.txt or
is there any other name?
thank you so much,

Alan


On Fri, Aug 2, 2013 at 2:45 PM, Alan Francis
alandarkene...@gmail.com
wrote:
      Thanks Anastasia.


On Fri, Aug 2, 2013 at 2:26 PM, Anastasia
Yendiki
ayend...@nmr.mgh.harvard.edu wrote:

      Hi Alan - All the set ... commands for
tracula need to
      be in a configuration file. You then
pass that
      configuration file as an argument to the
-c option of
      trac-all. See tutorial:
             
     
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula

      Hope this helps,
      a.y

      On Fri, 2 Aug 2013, Alan Francis wrote:

      Hi Anastasia and others:
      I have been trying to run Trac all on
five brains.
      It keeps giving me the
      error message:

      ERROR: run list is longer than subject
list

      My run list is equal to the subject
list: Here is
      the environment:

      Thanks for your help,

      Alan
      Martinos Center for Biomedical Imaging

     
__

      
     
freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514
      

      Setting up environment for
FreeSurfer/FS-FAST (and
      FSL

Re: [Freesurfer] trac-preproc

2013-08-05 Thread Anastasia Yendiki



The error says:
`/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/bvecs.txt': 
No such file or directory


Does this file exist?

On Mon, 5 Aug 2013, Alan Francis wrote:


Hi All:

When I ran trac-preproc I got an error that read s as follows:

trac-preproc exited with ERRORS at Mon Aug  5 13:12:53 EDT 2013. I do have a 
bvec.txt and bval file in each directory.

thanks for your help,

Alan


The following are the messages:

csh::alanf@cerebro 
[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data] : trac-all 
-prep -c
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc
INFO: SUBJECTS_DIR is 
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons
INFO: Diffusion root is 
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/
Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable5_3_0
trac-preproc -c 
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_101/scripts/dmrirc.local
 -log
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_101/scripts/trac-all.log
 -cmd
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_101/scripts/trac-all.cmd
#-
/usr/local/freesurfer/stable5_3_0//bin/trac-preproc
#-
#@# Image corrections Mon Aug  5 13:12:10 EDT 2013
mri_convert 
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_101/Diffusion_Recons/20080424_182054563000-12-01DTIValeras012a001.nii
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_101/dmri/dwi_orig.nii.gz
mri_convert 
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_101/Diffusion_Recons/20080424_182054563000-12-01DTIValeras012a001.nii
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_101/dmri/dwi_orig.nii.gz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_101/Diffusion_Recons/20080424_182054563000-12-01DTIValeras012a001.nii...
TR=7570.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.989696, 0.0161603, 0.142271)
j_ras = (0.0163, 0.999867, -0.000183368)
k_ras = (0.142255, -0.00213754, 0.989828)
writing to 
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_101/dmri/dwi_orig.nii.gz...
cp 
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/bvecs.txt
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_101/dmri/dwi_orig.mghdti.bvecs
cp: cannot stat 
`/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/bvecs.txt':
 No such file or directory
Linux cerebro 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 
x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Mon Aug  5 13:12:53 EDT 2013




___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] trac-preproc

2013-08-05 Thread Anastasia Yendiki



Hi Alan - The file doesn't need to have an extension, .txt or other. But 
you do need to set bvecfile to the full name of the file, including the 
extension, if it has one.


a.y

On Mon, 5 Aug 2013, Alan Francis wrote:


Hi Anastasia:

Yes this file does exist but it did not have the *.txt suffix. Maybe I will
change the suffix and run this again.

thanks,

Alan


On Mon, Aug 5, 2013 at 1:57 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:

  The error says:
`/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
  recons/bvecs.txt': No such file or directory

Does this file exist?

On Mon, 5 Aug 2013, Alan Francis wrote:

  Hi All:

  When I ran trac-preproc I got an error that read s as
  follows:

  trac-preproc exited with ERRORS at Mon Aug  5 13:12:53 EDT
  2013. I do have a bvec.txt and bval file in each
  directory.

  thanks for your help,

  Alan


  The following are the messages:

  csh::alanf@cerebro
  [/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data]
  : trac-all -prep -c
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
  econs/dmrirc
  INFO: SUBJECTS_DIR 
is/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
  econs
  INFO: Diffusion root 
is/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
  econs/
  Actual FREESURFER_HOME
  /autofs/cluster/freesurfer/centos6_x86_64/stable5_3_0
  trac-preproc 
-c/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
  econs//BW_101/scripts/dmrirc.local -log
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
  econs//BW_101/scripts/trac-all.log -cmd
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
  econs//BW_101/scripts/trac-all.cmd
  #-
  /usr/local/freesurfer/stable5_3_0//bin/trac-preproc
  #-
  #@# Image corrections Mon Aug  5 13:12:10 EDT 2013
  
mri_convert/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
econs//BW_101/Diffusion_Recons/20080424_182054563000-12-01DTIValera
  s012a001.nii
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
  econs//BW_101/dmri/dwi_orig.nii.gz
  
mri_convert/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
econs//BW_101/Diffusion_Recons/20080424_182054563000-12-01DTIValera
  s012a001.nii
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
  econs//BW_101/dmri/dwi_orig.nii.gz
  $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter
  Exp $
  reading from
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
econs//BW_101/Diffusion_Recons/20080424_182054563000-12-01DTIValera
  s012a001.nii...
  TR=7570.00, TE=0.00, TI=0.00, flip angle=0.00
  i_ras = (-0.989696, 0.0161603, 0.142271)
  j_ras = (0.0163, 0.999867, -0.000183368)
  k_ras = (0.142255, -0.00213754, 0.989828)
  writing 
to/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
  econs//BW_101/dmri/dwi_orig.nii.gz...
  
cp/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
  econs/bvecs.txt
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
  econs//BW_101/dmri/dwi_orig.mghdti.bvecs
  cp: cannot 
stat`/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
  recons/bvecs.txt': No such file or directory
  Linux cerebro 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13
  00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux

  trac-preproc exited with ERRORS at Mon Aug  5 13:12:53 EDT
  2013







The information in this e-mail is intended only for the person to whom
it is
addressed. If you believe this e-mail was sent to you in error and the
e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you
in error
but does not contain patient information, please contact the sender
and properly
dispose of the e-mail.



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] trac-all inquiry

2013-08-02 Thread Anastasia Yendiki


Hi David - You need to run each of the steps (-prep, -bedp, -path) 
separately. You can't run them all at the same time. See tutorial:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/RunningTracula

Hope this helps,
a.y

On Fri, 2 Aug 2013, David Soto wrote:

 Hi,

 I have successfully run recon-all in my dataset
 and now am attempting to use trac-all on my diffusion data
 obtained on a Siemens scanner.

 Diffusion dicoms were transformed to .nii using MRIConverter
 and then to .mnc using

 nii2mnc output.nii output_t.mnc.

 I am trying to run trac-all on a single subject and for this I
 have created the configuration file attached (tracula02ST)

 As you can see the SUBJECTS_DIR is /home/dsoto/Documents/fmri/rsdtianawmgui
 and within each subject the T1 serving as input for recon-all are in
 mri/orig

 while the diffusion images are in a folder call diffdata (named output_t.mnc)
 which also contains the bvecs and bvals files, which were transposed and 
 organised
 according to the tutorial (named as bvecs_t.txt and bvals_t.txt)

 When I run:
 trac-all -c tracula02ST.txt

 I get:
 ERROR: no analysis step (-{prep,bedp,path}) has been selected

 THEN I run:
 trac-all -prep -bedp -path -c tracula02ST.txt which runs for 5 seconds or so
 and then gives the long output text below with an error message.

 Segmentation fault (core dumped)
 foreach: No match.

 The trac-all.log is attached also.

 Could you please help?

 Cheers

 David



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Trac-all question

2013-08-02 Thread Anastasia Yendiki



Hi Alan - All the set ... commands for tracula need to be in a 
configuration file. You then pass that configuration file as an argument 
to the -c option of trac-all. See tutorial:

http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula

Hope this helps,
a.y

On Fri, 2 Aug 2013, Alan Francis wrote:


Hi Anastasia and others:
I have been trying to run Trac all on five brains. It keeps giving me the
error message:

ERROR: run list is longer than subject list

My run list is equal to the subject list: Here is the environment:

Thanks for your help,

Alan
Martinos Center for Biomedical Imaging

__

 freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 

Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer/stable5_3_0/
FSFAST_HOME       /usr/local/freesurfer/stable5_3_0//fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR      /usr/local/freesurfer/stable5_3_0//subjects
MNI_DIR           /usr/local/freesurfer/stable5_3_0//mni
FSL_DIR           /usr/pubsw/packages/fsl/current
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
recons] : setenv SUBJECTS_DIR /autofs/space/d
dali_001/ dali_002/ dali_003/ 
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
recons] : setenv 
SUBJECTS_DIR/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
econs/
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
recons] : set dtroot = /autofs/space/d
dali_001/ dali_002/ dali_003/ 
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
recons] : set dtroot 
=/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
econs/
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
recons] : set subjlist = (101/ 102/ 103/ 104/ 105/)
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
recons] : set dcmroot = /autofs/space/d
dali_001/ dali_002/ dali_003/ 
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
recons] : set dcmroot 
=/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
econs/
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
recons] : set dcmlist 
=(101/Diffusion_Recons/20080424_182054563000-12-01DTIValeras012a001.
nii \
?102/Diffusion_Recons/20080911_101015358000-10-01DIFFUSIONHighResval
erabi1002s010a001.nii \
?103/Diffusion_Recons/20080911_140753578000-10-01DIFFUSIONHighResval
eraBI1003s010a001.nii \
?104/Diffusion_Recons/20080915_160812745000-10-01DIFFUSIONHighResVal
eraBI104s010a001.nii \
?105/Diffusion_Recons/20080917_190940899000-16-01DIFFUSIONHighResVal
eraBI105s016a001.nii \
? )
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
recons] : set runlist = (101/ 102/ 103/ 104/
bem/              mri/              stats/            touch/
Diffusion_Recons/ scripts/          surf/             trash/
label/            src/              tmp/              
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
recons] : set runlist = (101/ 102/ 103/ 104/ 105/)
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
recons] : set bvecfile = /autofs/space/dbvecs.txt
dali_001/ dali_002/ dali_003/ 
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
recons] : set bvecfile 
=/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
econs/bvecs.txt
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
recons] : set bvalfile 
=/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
econs/bvals.txt
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
recons] : set doeddy = 1
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
recons] : set dorotbvecs = 1
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
recons] : set usemaskanat = 1
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
recons] : set thrbet = 0.3
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
recons] : set doregflt = 0
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
recons] : set doregbbr = 1
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
recons] : set doregmni = 1
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
recons] : set doregcvs = 0

Re: [Freesurfer] Trac-all question

2013-08-02 Thread Anastasia Yendiki



It can have any name you want. You just have to type the right name next 
to the -c ...


On Fri, 2 Aug 2013, Alan Francis wrote:


Sorry. I have another question. Should I name the config file dmrirc.txt or
is there any other name?
thank you so much,

Alan


On Fri, Aug 2, 2013 at 2:45 PM, Alan Francis alandarkene...@gmail.com
wrote:
  Thanks Anastasia.


On Fri, Aug 2, 2013 at 2:26 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:

  Hi Alan - All the set ... commands for tracula need to
  be in a configuration file. You then pass that
  configuration file as an argument to the -c option of
  trac-all. See tutorial:
         
  http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula

  Hope this helps,
  a.y

  On Fri, 2 Aug 2013, Alan Francis wrote:

  Hi Anastasia and others:
  I have been trying to run Trac all on five brains.
  It keeps giving me the
  error message:

  ERROR: run list is longer than subject list

  My run list is equal to the subject list: Here is
  the environment:

  Thanks for your help,

  Alan
  Martinos Center for Biomedical Imaging

  __

  
  freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514
  

  Setting up environment for FreeSurfer/FS-FAST (and
  FSL)
  FREESURFER_HOME   /usr/local/freesurfer/stable5_3_0/
  FSFAST_HOME      
  /usr/local/freesurfer/stable5_3_0//fsfast
  FSF_OUTPUT_FORMAT nii.gz
  SUBJECTS_DIR    
   /usr/local/freesurfer/stable5_3_0//subjects
  MNI_DIR          
  /usr/local/freesurfer/stable5_3_0//mni
  FSL_DIR           /usr/pubsw/packages/fsl/current
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_
  Data/diffusion_
  recons] : setenv SUBJECTS_DIR /autofs/space/d
  dali_001/ dali_002/ dali_003/ 
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_
  Data/diffusion_
  recons] : 
setenvSUBJECTS_DIR/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data
  /diffusion_r
  econs/
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_
  Data/diffusion_
  recons] : set dtroot = /autofs/space/d
  dali_001/ dali_002/ dali_003/ 
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_
  Data/diffusion_
  recons] : set 
dtroot=/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
  r
  econs/
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_
  Data/diffusion_
  recons] : set subjlist = (101/ 102/ 103/ 104/ 105/)
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_
  Data/diffusion_
  recons] : set dcmroot = /autofs/space/d
  dali_001/ dali_002/ dali_003/ 
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_
  Data/diffusion_
  recons] : set 
dcmroot=/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
  r
  econs/
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_
  Data/diffusion_
  recons] : set 
dcmlist=(101/Diffusion_Recons/20080424_182054563000-12-01DTIValeras012a001
  .
  nii \
?102/Diffusion_Recons/20080911_101015358000-10-01DIFFUSIONHighResva
  l
erabi1002s010a001.nii \
?103/Diffusion_Recons/20080911_140753578000-10-01DIFFUSIONHighResva
l
eraBI1003s010a001.nii \
?104/Diffusion_Recons/20080915_160812745000-10-01DIFFUSIONHighResVa
l
eraBI104s010a001.nii \
?105/Diffusion_Recons/20080917_190940899000-16-01DIFFUSIONHighResVa
l
eraBI105s016a001.nii \
? )
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_
Data/diffusion_
recons] : set runlist = (101/ 102/ 103/ 104/
bem/              mri/              stats/          
 touch/
Diffusion_Recons/ scripts/          surf/            
trash/
label/            src/              tmp/              
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_
Data/diffusion_
recons] : set runlist = (101/ 102/ 103/ 104/ 105/)
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_
Data/diffusion_
recons] : set bvecfile = /autofs/space/dbvecs.txt
dali_001/ dali_002/ dali_003/ 
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_
Data/diffusion_
recons] : set 
bvecfile=/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
r
econs/bvecs.txt
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_
Data/diffusion_
recons] : set 
bvalfile=/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
r
econs/bvals.txt
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_
Data/diffusion_
recons] : set doeddy = 1
csh::alanf@dali[/autofs/space/dali_003/users

Re: [Freesurfer] bvecs error from Tracula

2013-08-01 Thread Anastasia Yendiki



Hi Amirhossein - The memory error doesn't occur when bbregister is 
running, but when dmri_train is running and loading the atlas data. You 
seem to have the snow leopard version of freesurfer installed, based on 
your build stamp (freesurfer-Darwin-snowleopard-__i686-stable-pub-v5.3.0). 
What version of the operating system do you have on your computer and how 
much memory?


Thanks,
a.y

On Mon, 29 Jul 2013, amirhossein manzouri wrote:


Hi, 
Kindly find attched the trac-all.log !


On Thu, Jul 25, 2013 at 6:25 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:

  Hi Amirhossein - If your error happens when bbregister is run,
  then it's not the error that the dmri_5.1_snow_leopard.tar.gz
  fix was meant to address. In any case that fix is not relevant
  to you b/c you're using 5.3 and not 5.1. Can you please send
  your trac-all.log to establish where exactly the error is
  happening?

  Thanks,
  a.y

  On Thu, 25 Jul 2013, amirhossein manzouri wrote:


Hi ZeKe,
I am getting this error during Tracula procedure
somewhere between
bbregister!
BR

On Jul 24, 2013 5:42 PM, Z K
zkauf...@nmr.mgh.harvard.edu wrote:
      Hello Amir,

      According to the log file you've attached,
recon-all finished to
      completion without any errors. Are you sure
you are encountering
      a memory error? If so, why?

      -Zeke

      On 07/24/2013 11:28 AM, amirhossein manzouri
wrote:
            Kindly find attached the recon-all.log


            On Wed, Jul 24, 2013 at 4:50 PM, Z K
            zkauf...@nmr.mgh.harvard.edu
            mailto:zkauf...@nmr.mgh.harvard.edu
wrote:

                Hello Amir,

                Thanks for that... could you also
please provide
            the recon-all.log
                file? It will be located in
               
           
$SUBJECT_DIR/subject_name/__scripts/recon-all.log

                -Zeke


                On 07/24/2013 03:01 AM, amirhossein
manzouri
            wrote:

                    Hi,
                    The content is :
                   
           
freesurfer-Darwin-snowleopard-__i686-stable-pub-v5.3.0
                    Can it help?


                    On Mon, Jul 22, 2013 at 10:31
PM, Z K
                    zkauf...@nmr.mgh.harvard.edu
            mailto:zkauf...@nmr.mgh.harvard.edu
                   
mailto:zkauf...@nmr.mgh.__harvard.edu
                   
mailto:zkauf...@nmr.mgh.harvard.edu
            wrote:

                         Hello Amirhossein,

                         Can you please provide me
with the
            contents of
                    build-stamp.txt in
                         the
/Applications/freesurfer directory?

                         -Zeke


                         On 07/22/2013 04:23 PM,
amirhossein
            manzouri wrote:

                             Hi,
                             Yes I am getting the
memory error
            with version 5.3,
                    exactly the
                             one that
                             is reported in this
link:
                  
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-July/0
1
            9392.html


                  
https://mail.nmr.mgh.harvard.__edu/pipermail//freesurfer/__2011-July/0193
9
            2.html
                  
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-July/019392.h
t
            ml
                             Thanks,


                             On Mon, Jul 22, 2013 at
8:15 PM,
            Anastasia Yendiki
                           
 ayend...@nmr.mgh.harvard.edu
                   
mailto:ayend...@nmr.mgh.harvard.edu
                           
             mailto:ayend...@nmr.mgh.__harvard.edu
                   
mailto:ayend...@nmr.mgh.harvard.edu
                           
 mailto:ayend...@nmr.mgh.
                   
mailto:ayend...@nmr.mgh

Re: [Freesurfer] [tracula] error running trac-all -prep

2013-08-01 Thread Anastasia Yendiki



Hi Florian - Do these files exist?
/data/physics/florian/nii/102485074_20080319/dmri/dwi_orig.mghdti.bvecs
/data/physics/florian/nii/102485074_20080319/dmri/dwi_orig.mghdti.bvals

The format of the bvecs and bvals that you sent seems fine, but (and this 
has nothing to do with the error you're getting) I have to warn you that 
you may not be able to get good results running probabilistic tractography 
on this data. It looks like you're acquiring the same 6 diffusion 
directions, repeated 8 times. Six directions is the absolute minimum for 
reconstructing the tensor model, but will probably not be sufficient for 
the crossing fiber model that bedpostx reconstructs (and is used by 
tracula). Your scan time is better spent acquiring 48 different 
directions, rather than the same 6 directions 8 times.


a.y

On Mon, 29 Jul 2013, Borsodi Florian wrote:


Hello,

I have been trying to run tracula on my data and i keep getting the same
kind of error repeatedly.
For my imput I am using dicoms from a Siemens scanner with a stadard
diffusion protocol. However, tracula cannot read the bvec and bval data out
of the dicom header. Therefore, I implemented bvec and bval files into the
config file.
After doing so, I got the error which says that tracula cannot find the
dwi_orig_flip.mghdti.bvecs and dwi_orig_flip.mghdti.bvals files.
I have tried many options, but still cannot find a solution.
I am hoping to get some troubleshooting help.

I have atteched my log- and config- files, as well as my bvec and bval
files.
To uphold patient confidentiality, I have encode the name patient's data as
AA.

I believe the problems are the bvec and bval files or their structures. The
log-file lete me assume this, especially the lines 202 - 205, 264 - 268 and
1480 - 1484.

Thank you in advance for your help, and your speedy response.

With kind regards,

Florian Borsodi
Department of Neurology
Medical University of Graz
   
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] correspondance between broadmann areas and freesurfer labels

2013-07-26 Thread Anastasia Yendiki



There is a *.thresh.label version of all the BA labels in 5.3, but I don't 
think it's used by default. You can try using those labels instead.


On Fri, 26 Jul 2013, Satrajit Ghosh wrote:


hi bruce,
currently 5.3, but the data i was looking at was processed with 5.1 and in
that right ba44/45 was always larger.

cheers,

satra


On Fri, Jul 26, 2013 at 9:47 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:
  Hi Satra,

  what version are you using? I think Anastasia implemented a
  thresholded version in 5.3, but perhaps she can comment.
  Bruce
  On Fri, 26 Jul 2013, Satrajit Ghosh wrote:

hi bruce,
related to this question, how are the stats/volumes
of the BAs computed?

cheers,

satra

On Fri, Jul 26, 2013 at 9:33 AM, Bruce Fischl
fis...@nmr.mgh.harvard.edu
wrote:
      Hi Laouchedi

      that is a big research question! The answer is
a qualified yes,
      but it depends strongly on what labels you
mean. In general we
      find that the closer you are to primary areas
like V1/M1, the
      stronger the correspondence is. We do supply
some explicit
      estimates of Brodmann areas, have you looked
at them?

      Bruce


      On Fri, 26 Jul 2013, LAOUCHEDI MAKHLOUF wrote:

            Hi
                i used freesurfer labels in a study
and i want
            to identify the broadmann
            areas corresponding to some labels, is
there any
            correspondence between the
            two ?

            Thanks


     
___
      Freesurfer mailing list
      Freesurfer@nmr.mgh.harvard.edu
     
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


      The information in this e-mail is intended
only for the person
      to whom it is
      addressed. If you believe this e-mail was sent
to you in error
      and the e-mail
      contains patient information, please contact
the Partners
      Compliance HelpLine at
      http://www.partners.org/complianceline . If
the e-mail was sent
      to you in error
      but does not contain patient information,
please contact the
      sender and properly
      dispose of the e-mail.





___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] correspondance between broadmann areas and freesurfer labels

2013-07-26 Thread Anastasia Yendiki



You can search recon-all.log for the command that generates those stats 
and appply it to the ?h.BA.thresh.annot instead of ?h.BA.annot.


On Fri, 26 Jul 2013, Satrajit Ghosh wrote:


thanks guys. any thoughts on when the ba*.stats files will use these? right
now i agree with bruce that they are biased by the predictability of the
region. less accurate prediction - greater volume.
cheers,

satra


On Fri, Jul 26, 2013 at 10:28 AM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:

  There is a *.thresh.label version of all the BA labels in 5.3,
  but I don't think it's used by default. You can try using those
  labels instead.

  On Fri, 26 Jul 2013, Satrajit Ghosh wrote:

hi bruce,
currently 5.3, but the data i was looking at was
processed with 5.1 and in
that right ba44/45 was always larger.

cheers,

satra


On Fri, Jul 26, 2013 at 9:47 AM, Bruce Fischl
fis...@nmr.mgh.harvard.edu
wrote:
      Hi Satra,

      what version are you using? I think Anastasia
implemented a
      thresholded version in 5.3, but perhaps she
can comment.
      Bruce
      On Fri, 26 Jul 2013, Satrajit Ghosh wrote:

            hi bruce,
            related to this question, how are the
stats/volumes
            of the BAs computed?

            cheers,

            satra

            On Fri, Jul 26, 2013 at 9:33 AM, Bruce
Fischl
            fis...@nmr.mgh.harvard.edu
            wrote:
                  Hi Laouchedi

                  that is a big research question!
The answer is
            a qualified yes,
                  but it depends strongly on what
labels you
            mean. In general we
                  find that the closer you are to
primary areas
            like V1/M1, the
                  stronger the correspondence is. We
do supply
            some explicit
                  estimates of Brodmann areas, have
you looked
            at them?

                  Bruce


                  On Fri, 26 Jul 2013, LAOUCHEDI
MAKHLOUF wrote:

                        Hi
                            i used freesurfer labels
in a study
            and i want
                        to identify the broadmann
                        areas corresponding to some
labels, is
            there any
                        correspondence between the
                        two ?

                        Thanks


                 
           
___
                  Freesurfer mailing list
                  Freesurfer@nmr.mgh.harvard.edu
                 
           
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


                  The information in this e-mail is
intended
            only for the person
                  to whom it is
                  addressed. If you believe this
e-mail was sent
            to you in error
                  and the e-mail
                  contains patient information,
please contact
            the Partners
                  Compliance HelpLine at
                 
http://www.partners.org/complianceline . If
            the e-mail was sent
                  to you in error
                  but does not contain patient
information,
            please contact the
                  sender and properly
                  dispose of the e-mail.







___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] bvecs error from Tracula

2013-07-25 Thread Anastasia Yendiki



Hi Amirhossein - If your error happens when bbregister is run, then it's 
not the error that the dmri_5.1_snow_leopard.tar.gz fix was meant to 
address. In any case that fix is not relevant to you b/c you're using 5.3 
and not 5.1. Can you please send your trac-all.log to establish where 
exactly the error is happening?


Thanks,
a.y

On Thu, 25 Jul 2013, amirhossein manzouri wrote:



Hi ZeKe,
I am getting this error during Tracula procedure somewhere between
bbregister!
BR

On Jul 24, 2013 5:42 PM, Z K zkauf...@nmr.mgh.harvard.edu wrote:
  Hello Amir,

  According to the log file you've attached, recon-all finished to
  completion without any errors. Are you sure you are encountering
  a memory error? If so, why?

  -Zeke

  On 07/24/2013 11:28 AM, amirhossein manzouri wrote:
Kindly find attached the recon-all.log


On Wed, Jul 24, 2013 at 4:50 PM, Z K
zkauf...@nmr.mgh.harvard.edu
mailto:zkauf...@nmr.mgh.harvard.edu wrote:

    Hello Amir,

    Thanks for that... could you also please provide
the recon-all.log
    file? It will be located in
   
$SUBJECT_DIR/subject_name/__scripts/recon-all.log

    -Zeke


    On 07/24/2013 03:01 AM, amirhossein manzouri
wrote:

        Hi,
        The content is :
       
freesurfer-Darwin-snowleopard-__i686-stable-pub-v5.3.0
        Can it help?


        On Mon, Jul 22, 2013 at 10:31 PM, Z K
        zkauf...@nmr.mgh.harvard.edu
mailto:zkauf...@nmr.mgh.harvard.edu
        mailto:zkauf...@nmr.mgh.__harvard.edu
        mailto:zkauf...@nmr.mgh.harvard.edu
wrote:

             Hello Amirhossein,

             Can you please provide me with the
contents of
        build-stamp.txt in
             the /Applications/freesurfer directory?

             -Zeke


             On 07/22/2013 04:23 PM, amirhossein
manzouri wrote:

                 Hi,
                 Yes I am getting the memory error
with version 5.3,
        exactly the
                 one that
                 is reported in this link:
       
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-July/01
9392.html


       
https://mail.nmr.mgh.harvard.__edu/pipermail//freesurfer/__2011-July/01939
2.html
       
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-July/019392.ht
ml
                 Thanks,


                 On Mon, Jul 22, 2013 at 8:15 PM,
Anastasia Yendiki
                 ayend...@nmr.mgh.harvard.edu
        mailto:ayend...@nmr.mgh.harvard.edu
               
 mailto:ayend...@nmr.mgh.__harvard.edu
        mailto:ayend...@nmr.mgh.harvard.edu
                 mailto:ayend...@nmr.mgh.
        mailto:ayend...@nmr.mgh.__har__vard.edu
http://harvard.edu

               
 mailto:ayend...@nmr.mgh.__harvard.edu
        mailto:ayend...@nmr.mgh.harvard.edu
wrote:


                      Hi Amirhossein - That fix
applied only to the 5.1
        version. I'd
                      recommend using the 5.3
version for tracula. Are
        you getting a
                      memory error, and if so with
which version?

                      Thanks,
                      a.y


                      On Mon, 22 Jul 2013,
amirhossein manzouri wrote:

                          Dear Anastasia,
                          I am trying to download
the
                 dmri_5.1_snow_leopard.tar.__gz from

                          FreeSurfer
                          website to solve memory
problem but it is not
                 available. Would
                          you please
                          check the source to the
link?


                          On Wed, Jul 17, 2013 at
5:51 PM, amirhossein
        manzouri
                          a.h.manzo...@gmail.com
        mailto:a.h.manzo...@gmail.com
mailto:a.h.manzo...@gmail.com
        mailto:a.h.manzo...@gmail.com__
                 mailto:a.h.manzo...@gmail.com
        mailto:a.h.manzo...@gmail.com

Re: [Freesurfer] bvecs error from Tracula

2013-07-22 Thread Anastasia Yendiki



Hi Amirhossein - That fix applied only to the 5.1 version. I'd recommend 
using the 5.3 version for tracula. Are you getting a memory error, and if 
so with which version?


Thanks,
a.y

On Mon, 22 Jul 2013, amirhossein manzouri wrote:


Dear Anastasia, 
I am trying to download the dmri_5.1_snow_leopard.tar.gz from FreeSurfer
website to solve memory problem but it is not available. Would you please
check the source to the link? 


On Wed, Jul 17, 2013 at 5:51 PM, amirhossein manzouri
a.h.manzo...@gmail.com wrote:
  The format of my bval file was wrong so I edited your file and
  tried and it worked, also bvec should be in three columns as you
  have mentioned before.


On Wed, Jul 17, 2013 at 5:11 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:

  Good to hear! Can you please share with all of us what was
  wrong with your original files? It may help others who
  have the same problem in the future. Thanks!

  On Wed, 17 Jul 2013, amirhossein manzouri wrote:

Thanks Anastasia, 
IT HELPED!


On Tue, Jul 16, 2013 at 5:25 PM, Anastasia
Yendiki ayend...@nmr.mgh.harvard.edu
wrote:

      Hi Amirhossein - I'm attaching sample
files.

      a.y

      On Tue, 16 Jul 2013, amirhossein
manzouri wrote:

            Hi Anastasia, 
            I have tried both , 3-row and
3-column format and still
            wrong bvecc and bval
            from flip4fsl. Could you please
send me a sample of your
            original files so I
            can compare?


            On Mon, Jul 15, 2013 at 7:44 PM,
Anastasia Yendiki
            ayend...@nmr.mgh.harvard.edu
wrote:

                  Hi Amirhossein - Are your
original bvecs/bvals in
            3-row format
                  instead of 3-column format?
                 
           
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula

                  Thanks,
                  a.y

                  On Mon, 15 Jul 2013,
amirhossein manzouri wrote:

                        Dear Experts, 
                        I am running trac-all
-prep -c dmrirc on my
            DWI
                        data. After flip4fsl
step I get the attached
            bval
                        and bvec file which
the bvec one is wrong so
            the
                        process exits
                        with error in dtifit.
I have also attached
             original
                        bvec and bval.

                        --
                        Best regards,
                        Amirhossein Manzouri 

                         





            The information in this e-mail is
intended only for the
            person to whom
            it is
            addressed. If you believe this
e-mail was sent to you in
            error and the
            e-mail
            contains patient information,
please contact the Partners
            Compliance
            HelpLine at
           
http://www.partners.org/complianceline . If
the e-mail was
            sent to you
            in error
            but does not contain patient
information, please contact
            the sender
            and properly
            dispose of the e-mail.




            --
            Best regards,
            Amirhossein Manzouri 

             





--
Best regards,
Amirhossein Manzouri 

 





--
Best regards,
Amirhossein Manzouri 

 




--
Best regards,
Amirhossein Manzouri 

 


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] possible to use multiple B value DTI in Tracula?

2013-07-22 Thread Anastasia Yendiki


Hi Sal - Are these different scans that you want to merge? If they're all 
in one file, then you just define the b-value for each frame as usual in 
the bvalfile. There's no rule that all the b-values have to be the same.

Hope this helps,
a.y

On Sun, 21 Jul 2013, Salil Soman wrote:

 Hi,
 I was wondering - is it possible to use DTI data of multiple B values in
 Tracula (acquired during the same session and same TE)?
 
 Best wishes,
 
 Sal
 
 Salil Soman, MD, MS
 

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] [Tracula] Run trac-all with 2 time points for DTI scan but 1 time point for T1 scan. How to?

2013-07-22 Thread Anastasia Yendiki


Hi Riccardo - The way this is designed is that you have to have 
longitudinal T1 data and run the longitudinal stream of recon-all on it, 
before you run the longitudinal version of tracula on your DWI.

You could fake this by simply creating a copy of the recon-all directory 
of your first T1 time point and name it as the 2nd time point, then run 
longitudinal recon-all on them to generate all the files that tracula 
expects to find. This of course may bias your study towards the first time 
point, and the whole point of the longitudinal stream is to make sure 
there is no bias.

Hope this helps,
a.y

On Mon, 22 Jul 2013, r.nava...@itab.unich.it wrote:

 Hi,
 I need to run trac-all on subjects scanned first time in T1 and DTI, second 
 time DTI only. How to configure dmrirc?
 I've seen long.example but it seems that it require T1 second run too.
 Tnx,

 Riccardo


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] bvecs error from Tracula

2013-07-17 Thread Anastasia Yendiki



Good to hear! Can you please share with all of us what was wrong with your 
original files? It may help others who have the same problem in the 
future. Thanks!


On Wed, 17 Jul 2013, amirhossein manzouri wrote:


Thanks Anastasia, 
IT HELPED!


On Tue, Jul 16, 2013 at 5:25 PM, Anastasia Yendiki 
ayend...@nmr.mgh.harvard.edu
wrote:

  Hi Amirhossein - I'm attaching sample files.

  a.y

  On Tue, 16 Jul 2013, amirhossein manzouri wrote:

Hi Anastasia, 
I have tried both , 3-row and 3-column format and still
wrong bvecc and bval
from flip4fsl. Could you please send me a sample of your
original files so I
can compare?


On Mon, Jul 15, 2013 at 7:44 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:

      Hi Amirhossein - Are your original bvecs/bvals in
3-row format
      instead of 3-column format?
     
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula

      Thanks,
      a.y

      On Mon, 15 Jul 2013, amirhossein manzouri wrote:

            Dear Experts, 
            I am running trac-all -prep -c dmrirc on my
DWI
            data. After flip4fsl step I get the attached
bval
            and bvec file which the bvec one is wrong so
the
            process exits
            with error in dtifit. I have also attached
 original
            bvec and bval.

            --
            Best regards,
            Amirhossein Manzouri 

             





The information in this e-mail is intended only for the
person to whom
it is
addressed. If you believe this e-mail was sent to you in
error and the
e-mail
contains patient information, please contact the Partners
Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail was
sent to you
in error
but does not contain patient information, please contact
the sender
and properly
dispose of the e-mail.




--
Best regards,
Amirhossein Manzouri 

 





--
Best regards,
Amirhossein Manzouri 

 


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] bvecs error from Tracula

2013-07-16 Thread Anastasia Yendiki



Hi Amirhossein - I'm attaching sample files.

a.y

On Tue, 16 Jul 2013, amirhossein manzouri wrote:


Hi Anastasia, 
I have tried both , 3-row and 3-column format and still wrong bvecc and bval
from flip4fsl. Could you please send me a sample of your original files so I
can compare?


On Mon, Jul 15, 2013 at 7:44 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:

  Hi Amirhossein - Are your original bvecs/bvals in 3-row format
  instead of 3-column format?
  http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula

  Thanks,
  a.y

  On Mon, 15 Jul 2013, amirhossein manzouri wrote:

Dear Experts, 
I am running trac-all -prep -c dmrirc on my DWI
data. After flip4fsl step I get the attached bval
and bvec file which the bvec one is wrong so the
process exits
with error in dtifit. I have also attached  original
bvec and bval.

--
Best regards,
Amirhossein Manzouri 

 





The information in this e-mail is intended only for the person to whom
it is
addressed. If you believe this e-mail was sent to you in error and the
e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you
in error
but does not contain patient information, please contact the sender
and properly
dispose of the e-mail.




--
Best regards,
Amirhossein Manzouri 

 


0.00 0.00 0.00
0.00 0.00 0.00
0.00 0.00 0.00
0.00 0.00 0.00
0.00 0.00 0.00
0.00 0.00 0.00
0.00 0.00 0.00
0.00 0.00 0.00
0.00 0.00 0.00
0.00 0.00 0.00
1.00 0.00 0.00
0.586792 -0.376583 -0.716841
0.894195 0.022917 0.447091
0.729281 -0.410970 0.547041
-0.154251 0.964369 -0.214941
0.117136 0.773539 -0.622830
-0.407575 -0.414994 -0.813427
0.211330 0.753738 0.622269
0.095375 -0.969517 0.225700
-0.135450 -0.033490 -0.990218
-0.142125 -0.750521 -0.645383
-0.637009 0.746109 -0.193757
0.080563 0.971669 0.222192
0.106871 -0.021213 0.994047
0.298747 0.387214 0.872247
-0.207492 -0.803432 0.558072
0.331125 -0.040337 -0.942724
-0.805294 -0.589494 -0.063231
0.337278 -0.749774 -0.569282
0.592396 -0.761390 0.263348
-0.088979 -0.465650 0.880485
-0.527982 -0.430927 0.731803
-0.369111 -0.927082 0.065397
0.311914 0.926381 -0.211018
-0.684511 0.439336 -0.581746
-0.030114 -0.966623 -0.254425
-0.337568 0.744654 -0.575794
-0.574804 0.024806 -0.817915
0.271135 -0.747834 0.605996
-0.935185 0.185421 0.301743
0.889083 0.309665 -0.337104
-0.884343 0.033574 -0.465629
0.545045 0.586317 -0.599298
-0.350774 -0.016274 0.936319
0.416158 -0.900528 -0.125943
-0.732654 0.003250 0.680593
-0.739209 0.611423 0.282368
-0.256353 0.406875 -0.876776
-0.919023 0.372522 -0.128933
-0.257293 0.765486 0.589773
-0.589833 0.433953 0.681016
0.891136 -0.185957 -0.413881
0.679067 0.142105 -0.720190
-0.879811 -0.309554 0.360705
-0.621609 -0.697195 0.357102
0.897050 -0.430209 0.101102
-0.163347 0.417893 0.893691
-0.507183 -0.778309 -0.370136
0.107015 -0.446398 -0.888412
0.883485 0.435264 0.173205
0.598171 0.029843 0.800812
0.696192 0.698104 -0.167236
-0.393556 0.900808 0.183464
-0.761088 -0.402897 -0.508350
0.210324 0.396164 -0.893766
0.376032 -0.378955 0.845572
0.735763 -0.611461 -0.291148
-0.987214 -0.145866 -0.064273
0.529212 0.807365 0.260953
0.662918 0.472672 0.580621
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] tracula -path option 0 unknown

Hi Gerit - Can you please send the entire trac-all.log for this subject?
There could be some clues in the info that's printed out from the earlier
steps, even if there's no outright error in those steps.

Thanks,
a.y

On Fri, 5 Jul 2013, Gerit Pfuhl wrote:

Dear Freesurfer experts,

for one subject (out of over 80 already processed) I get i nthe last step an
error I am unable to locate. The output from the tracula -path command says
at the
end: option 0 unknown.
There are no reported problems in -prep, and -bedp. The script uses default
values (I run this subject 3 times, always gets stuck on -path, not before).
The subject was processed fine in tracule 5.1.0 with flt. Now in 5.2.0 we use
bbr

Excerpt of the output
...
/igis/MRI_fs_rec_dti/64-10-094-1/dlabel/diff/rh.cab_PP_avg33_mni_bbr_cpts_5_std.txt
/fastfs/igis/MRI_fs_rec_dti/64-10-094-1/dlabel/diff/lh.ccg_PP_avg33_mni_bbr_cpts_4_std.txt
/fastfs/igis/MRI_fs_rec_dti/64-10-094-1/dlabel/diff/rh.ccg_PP_avg33_mni_bbr_cpts_4_std.txt
/fastfs/igis/MRI_fs_rec_dti/64-10-094-1/dlabel/diff/lh.slfp_PP_avg33_mni_bbr_cpts_5_std.txt
/fastfs/igis/MRI_fs_rec_dti/64-10-094-1/dlabel/diff/rh.slfp_PP_avg33_mni_bbr_cpts_5_std.txt
/fastfs/igis/MRI_fs_rec_dti/64-10-094-1/dlabel/diff/lh.slft_PP_avg33_mni_bbr_cpts_5_std.txt
/fastfs/igis/MRI_fs_rec_dti/64-10-094-1/dlabel/diff/rh.slft_PP_avg33_mni_bbr_cpts_5_std.txt
ERROR: Option 0 unknown

Thanks for all help to understand this

Gerit

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] application of mri_cvs_register question



Hi Matt - For how to tell tracula to use CVS registration, see Specify 
the inter-subject registration method here:

http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula

Does this answer your question?

a.y

On Mon, 8 Jul 2013, Hoptman, Matthew wrote:



Hi all,

I see how to apply mri_vol2vol to DTI data from dt_recon, but I’m not clear on 
how to do so to DTI data processed in Tracula.  The command in the “Multimodal
integration and inter-subject registration” tutorial is:

mri_vol2vol   --targ templateid --m3z morph.m3z --noDefM3zPath --reg 
2anat.register.dat --mov diffvol --o diffvol2CVS --no-save-reg

 

But in Tracula, there are no “register.dat” files, or indeed no *.dat files.  
Is there a way to convert one of the *.mat files in the dmri/xfms directory to a
*.dat file?  Also, given that I think Tracula and dt_recon use different 
transformation algorithms, which Tracula transform should I choose?

 

Thanks,

Matt

 

Matthew J. Hoptman, PhD
Research Scientist V
Nathan S. Kline Institute for Psychiatric Research

Research Associate Professor in Psychiatry
NYU School of Medicine

 

IMPORTANT NOTICE: This e-mail is meant only for the use of the intended 
recipient. It may contain confidential information which is legally privileged 
or
otherwise protected by law. If you received this
e-mail in error or from someone who was not authorized to send it to you, you 
are strictly prohibited from reviewing, using, disseminating, distributing or
copying the e-mail.

PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS 
MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation.

 

_
Conserve Resources. Print only when necessary.

IMPORTANT NOTICE: This e-mail is meant only for the use of the intended 
recipient. It may contain confidential information which is legally privilegedor
otherwise protected by law. If you received this e-mail in error or from 
someone who is not authorized to send it to you, you are strictly prohibited 
from
reviewing, using, disseminating, distributing or copying the e-mail. PLEASE 
NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE 
FROM YOUR
SYSTEM. Thank you for your cooperation.

IMPORTANT NOTICE: This e-mail is meant only for the use of the intended 
recipient. It may contain confidential information which is legally privileged 
or
otherwise protected by law. If you received this e-mail in error or from 
someone who is not authorized to send it to you, you are strictly prohibited 
from
reviewing, using, disseminating, distributing or copying the e-mail. PLEASE 
NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE 
FROM YOUR
SYSTEM. Thank you for your cooperation.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Tracula problem in pre-processing


Hi Andrew - My guess is that it's something about the file 
dmri/dwi_orig.mghdti.bvals that's causing the error. Could you please send 
along that file?

Also, how did you fix your previous configuration file problem? Letting 
the list know about the resolution of the issue would help other users, 
who may have the same issue in the future and search the list archives. 
It'll also help me figure out if there are any checks I could add to 
trac-all to preclude this.

Thanks!
a.y

On Tue, 9 Jul 2013, Gundran, Andrew wrote:

 Helo all,

 I was finally able to figure out my configuration file problem. But when I 
 run the first step of pre-processing I receive an error about freesurfer 
 being unable to read a certain dwi_frame file.

 ln -sf /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi.nii.gz 
 /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/data.nii.gz
 awk: can't open file 1000
 source line number 1
 mri_concat --i 
 /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_frame.nii.gz 
 --mean --o 
 /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/lowb.nii.gz
 niiRead(): error opening file 
 /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_frame.nii.gz
 ninputs = 1
 Checking inputs
 ERROR: reading 
 /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_frame.nii.gz
 Darwin Wayne-Feng-s-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: 
 Tue Jun  7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64


 I have also attached the trac-all log.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Editing the endpoint ROIs, and re-running trac-all -path



Hi Susie - The initial placement of the control points plays a much bigger 
role than the end ROIs. The path being initialized in a bad location would 
be more of a problem than the end ROIs being too generous. So I'd check 
rh.unc_AS_avg32_mni_bbr_cpts_5.nii.gz before editing the end ROIs. Does 
that look like it's better placed on right than the left? I'd also check 
if the brain mask (aparc+aseg_mask) is any different in that area on one 
side.


Hope this helps,
a.y

On Tue, 9 Jul 2013, Susan Kuo wrote:


Hi Anastasia, 
  For one of my subjects, I am noticing that the right uncinate fasciculus is 
very diffuse and more importantly, erroneously crosses from the frontal to the
temporal lobe. I looked at the original endpoint ROI generated by trac-all 
-prior (rh.unc_AS_avg33_mni_bbr_end1.nii.gz) and the dilated endpoint ROI in the
temporal lobe (rh.unc_AS_avg33_mni_bbr_end1_dil.nii.gz) and noticed that the 
endpoints appeared to cross over into the frontal lobe.

  Attached is a snapshot for your perusal. On the left side is a display of the 
subject/dmri/dtifit_FA.nii with the
subject/dpath/rh.unc_AS_avg33_mni_bbr/path.pd.nii.gz tract superimposed over. 
As you can see, the right unc tract crosses from the frontal to the temporal
lobe. On the right side is a display of the subject/dmri/brain_anat_mni.nii.gz with 
the endpoints subject/dlabel/mni/rh.unc_AS_avg33_mni_bbr_end2.nii.gz in
green and subject/dlabel/mni/rh.unc_AS_avg33_mni_bbr_end1.nii.gz in blue (the 
red dots are control points). As you can see, the blue endpoints bleed over from
the temporal to the frontal lobe. 

  I tried to eliminate these blue points with fslview and then writing over 
rh.unc_AS_avg33_mni_bbr_end1.nii.gz. I performed a similar function manually 
editing
rh.unc_AS_avg33_mni_bbr_end1_dil.nii.gz to better reflect the boundaries . I 
subsequently tried to re-run trac-all -path, and  unfortunately, all my tracts
looked much worse. 


   Do you know if incorrectly placed endpoints impair the path reconstruction? 
Do you think you can help me? Any advice you can give would be much 
appreciated. 


--
Susie Kuo
NIH

Mediocrity knows nothing higher than itself, but talent instantly recognizes 
genius. - Sir Arthur Conan Doyle, Sherlock Holmes- Valley of Fear

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] bvecs error from Tracula



Hi Amirhossein - Are your original bvecs/bvals in 3-row format instead of 
3-column format? 
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula


Thanks,
a.y

On Mon, 15 Jul 2013, amirhossein manzouri wrote:


Dear Experts, 
I am running trac-all -prep -c dmrirc on my DWI data. After flip4fsl step I get 
the attached bval and bvec file which the bvec one is wrong so the process exits
with error in dtifit. I have also attached  original bvec and bval.

--
Best regards,
Amirhossein Manzouri 

 


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] application of mri_cvs_register question



Hi Matt - The CVS morph under xfms/cvs/ maps the individual anatomical to 
the CVS template. To map from individual diffusion to the CVS template, 
you'd have to first use diffusion-to-anatomical affine transform file 
under xfms/.


Hope this helps,
a.y

On Mon, 15 Jul 2013, Hoptman, Matthew wrote:


Hi Anastasia,
Not really, what I now have is:
subject/dmri/xfms/cvs
Within cvs, there are anatomical files that are registered to the CVS template, 
as below, but what I DON'T have is the application of these transforms to the 
DTI data.  That's what I'm trying to puzzle out.

The files in subject/dmri/xfms/cvs are:
c159001_to_cvs_avg35_inMNI152.mri_cvs_register.1307051306.log
c159001_to_cvs_avg35_inMNI152.mri_cvs_register.1307051310.log
final_CVSmorphed_tocvs_avg35_inMNI152_aseg.mgz
final_CVSmorphed_tocvs_avg35_inMNI152_norm.mgz
final_CVSmorph_tocvs_avg35_inMNI152.m3z
lh.dbg_surf.pial
lh.dbg_surf.white
lh.resample.aparc.annot
lh.resample.pial
lh.resample.white
nlalign-afteraseg-norm.mgz
nlalign-aseg.mgz
rh.dbg_surf.pial
rh.dbg_surf.white
rh.resample.aparc.annot
rh.resample.pial
rh.resample.white
summary.c159001_to_cvs_avg35_inMNI152.mri_cvs_register.1307051306.log
summary.c159001_to_cvs_avg35_inMNI152.mri_cvs_register.1307051310.log
transform.txt


-Original Message-
From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
Sent: Monday, July 15, 2013 12:19 PM
To: Hoptman, Matthew
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] application of mri_cvs_register question


Hi Matt - For how to tell tracula to use CVS registration, see Specify
the inter-subject registration method here:
   http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula

Does this answer your question?

a.y

On Mon, 8 Jul 2013, Hoptman, Matthew wrote:



Hi all,

I see how to apply mri_vol2vol to DTI data from dt_recon, but I’m not clear on 
how to do so to DTI data processed in Tracula.  The command in the “Multimodal
integration and inter-subject registration” tutorial is:

mri_vol2vol   --targ templateid --m3z morph.m3z --noDefM3zPath --reg 
2anat.register.dat --mov diffvol --o diffvol2CVS --no-save-reg



But in Tracula, there are no “register.dat” files, or indeed no *.dat files.  
Is there a way to convert one of the *.mat files in the dmri/xfms directory to a
*.dat file?  Also, given that I think Tracula and dt_recon use different 
transformation algorithms, which Tracula transform should I choose?



Thanks,

Matt



Matthew J. Hoptman, PhD
Research Scientist V
Nathan S. Kline Institute for Psychiatric Research

Research Associate Professor in Psychiatry
NYU School of Medicine



IMPORTANT NOTICE: This e-mail is meant only for the use of the intended 
recipient. It may contain confidential information which is legally privileged 
or
otherwise protected by law. If you received this
e-mail in error or from someone who was not authorized to send it to you, you 
are strictly prohibited from reviewing, using, disseminating, distributing or
copying the e-mail.

PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS 
MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation.



_
Conserve Resources. Print only when necessary.

IMPORTANT NOTICE: This e-mail is meant only for the use of the intended 
recipient. It may contain confidential information which is legally privilegedor
otherwise protected by law. If you received this e-mail in error or from 
someone who is not authorized to send it to you, you are strictly prohibited 
from
reviewing, using, disseminating, distributing or copying the e-mail. PLEASE 
NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE 
FROM YOUR
SYSTEM. Thank you for your cooperation.

IMPORTANT NOTICE: This e-mail is meant only for the use of the intended 
recipient. It may contain confidential information which is legally privileged 
or
otherwise protected by law. If you received this e-mail in error or from 
someone who is not authorized to send it to you, you are strictly prohibited 
from
reviewing, using, disseminating, distributing or copying the e-mail. PLEASE 
NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE 
FROM YOUR
SYSTEM. Thank you for your cooperation.




The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
IMPORTANT NOTICE: This e-mail is meant only for the use of the intended 
recipient. It may contain confidential information which is legally privileged 
or otherwise

Re: [Freesurfer] pathstats.byvoxel.txt



That is exactly right! Those were added after 5.1.

On Mon, 15 Jul 2013, Susan Kuo wrote:


Hi Anastasia,   I believe the issue I had with the pathstats.byvoxel.txt not 
displaying the last four values (AD_Avg RD_Avg MD_Avg FA_Avg ) is owing to the 
fact
that trac-all was run with FREESURFER 5.1. I believe that FREESURFER 5.2 may be 
needed to generate path.pd.trk, and from that, the above values are derived. Is
this correct? Thank you again, and have a good day!
--
Susie Kuo

Mediocrity knows nothing higher than itself, but talent instantly recognizes 
genius. - Sir Arthur Conan Doyle, Sherlock Holmes- Valley of Fear

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] pathstats.byvoxel.txt



I should add that there several other reasons to be using the newer 
version of tracula (from 5.2 or 5.3), including speed and other 
improvements listed here:

http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates

Also note that using 5.2 or 5.3 won't make a difference in terms of the 
tracula code, but for recon-all purposes you should not be using 5.2.


On Mon, 15 Jul 2013, Susan Kuo wrote:


Hi Anastasia,   I believe the issue I had with the pathstats.byvoxel.txt not 
displaying the last four values (AD_Avg RD_Avg MD_Avg FA_Avg ) is owing to the 
fact
that trac-all was run with FREESURFER 5.1. I believe that FREESURFER 5.2 may be 
needed to generate path.pd.trk, and from that, the above values are derived. Is
this correct? Thank you again, and have a good day!
--
Susie Kuo

Mediocrity knows nothing higher than itself, but talent instantly recognizes 
genius. - Sir Arthur Conan Doyle, Sherlock Holmes- Valley of Fear

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] application of mri_cvs_register question



Hi Matt - The --reg option expects a .dat file. There should be one 
produced by bbregister in the xfms/ directory?


a.y

On Mon, 15 Jul 2013, Hoptman, Matthew wrote:


Hi Anastasia,
Yes, that was my problem. I think I need to use
mri_vol2vol --targ ../../../cvs_avg35_inMNI152/mri/norm.mgz --m3z
../../cvs/cvs_avg35_inMNI152/final_CVSmorph_tocvs_avg35_inMNI152.m3z
--noDefM3zPath --reg diff2anat.bbr.mat --mov ../dtifit_FA.nii.gz --o
diffvol2CVS.nii.gz --no-save-reg


I now get:
Using the m3z file as it is; no assumed location.
regio_read_register(): Success
Error reading R[3][0] from diff2anat.bbr.mat

Matrix from regfile:
-0.001   0.972  -0.234  -3.311;
-0.001   0.234   0.972   69.949;
0.000   0.000   0.000   1.000;
0.000   0.000   0.000   0.000;

I was stuck at that point.  Lilla Zollei told me she'd look into it, but maybe 
you've communicated with her?
Thanks
Matt

-Original Message-
From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
Sent: Monday, July 15, 2013 2:30 PM
To: Hoptman, Matthew
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] application of mri_cvs_register question


Hi Matt - The CVS morph under xfms/cvs/ maps the individual anatomical to
the CVS template. To map from individual diffusion to the CVS template,
you'd have to first use diffusion-to-anatomical affine transform file
under xfms/.

Hope this helps,
a.y

On Mon, 15 Jul 2013, Hoptman, Matthew wrote:


Hi Anastasia,
Not really, what I now have is:
subject/dmri/xfms/cvs
Within cvs, there are anatomical files that are registered to the CVS template, 
as below, but what I DON'T have is the application of these transforms to the 
DTI data.  That's what I'm trying to puzzle out.

The files in subject/dmri/xfms/cvs are:
c159001_to_cvs_avg35_inMNI152.mri_cvs_register.1307051306.log
c159001_to_cvs_avg35_inMNI152.mri_cvs_register.1307051310.log
final_CVSmorphed_tocvs_avg35_inMNI152_aseg.mgz
final_CVSmorphed_tocvs_avg35_inMNI152_norm.mgz
final_CVSmorph_tocvs_avg35_inMNI152.m3z
lh.dbg_surf.pial
lh.dbg_surf.white
lh.resample.aparc.annot
lh.resample.pial
lh.resample.white
nlalign-afteraseg-norm.mgz
nlalign-aseg.mgz
rh.dbg_surf.pial
rh.dbg_surf.white
rh.resample.aparc.annot
rh.resample.pial
rh.resample.white
summary.c159001_to_cvs_avg35_inMNI152.mri_cvs_register.1307051306.log
summary.c159001_to_cvs_avg35_inMNI152.mri_cvs_register.1307051310.log
transform.txt


-Original Message-
From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
Sent: Monday, July 15, 2013 12:19 PM
To: Hoptman, Matthew
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] application of mri_cvs_register question


Hi Matt - For how to tell tracula to use CVS registration, see Specify
the inter-subject registration method here:
   http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula

Does this answer your question?

a.y

On Mon, 8 Jul 2013, Hoptman, Matthew wrote:



Hi all,

I see how to apply mri_vol2vol to DTI data from dt_recon, but I’m not clear on 
how to do so to DTI data processed in Tracula.  The command in the “Multimodal
integration and inter-subject registration” tutorial is:

mri_vol2vol   --targ templateid --m3z morph.m3z --noDefM3zPath --reg 
2anat.register.dat --mov diffvol --o diffvol2CVS --no-save-reg



But in Tracula, there are no “register.dat” files, or indeed no *.dat files.  
Is there a way to convert one of the *.mat files in the dmri/xfms directory to a
*.dat file?  Also, given that I think Tracula and dt_recon use different 
transformation algorithms, which Tracula transform should I choose?



Thanks,

Matt



Matthew J. Hoptman, PhD
Research Scientist V
Nathan S. Kline Institute for Psychiatric Research

Research Associate Professor in Psychiatry
NYU School of Medicine



IMPORTANT NOTICE: This e-mail is meant only for the use of the intended 
recipient. It may contain confidential information which is legally privileged 
or
otherwise protected by law. If you received this
e-mail in error or from someone who was not authorized to send it to you, you 
are strictly prohibited from reviewing, using, disseminating, distributing or
copying the e-mail.

PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS 
MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation.



_
Conserve Resources. Print only when necessary.

IMPORTANT NOTICE: This e-mail is meant only for the use of the intended 
recipient. It may contain confidential information which is legally privilegedor
otherwise protected by law. If you received this e-mail in error or from 
someone who is not authorized to send it to you, you are strictly prohibited 
from
reviewing, using, disseminating, distributing or copying the e-mail. PLEASE 
NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE 
FROM YOUR
SYSTEM. Thank you

Re: [Freesurfer] application of mri_cvs_register question



Got it. Can you send me a listing of the contents of the xfms/ directory? 
Conversions b/w formats can be done with tkregister2, but the .dat file 
should normally be there since it's the default format for bbregister.


On Mon, 15 Jul 2013, Hoptman, Matthew wrote:


Right, that's been my problem :(  Maybe something went wrong, but I didn't see 
any problem in the log files.  Actually, the command I showed below had a typo 
(I used --mat rather than --reg to get that error).  Is there a way to  convert 
*.mat to *.dat?

-Original Message-
From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
Sent: Monday, July 15, 2013 2:44 PM
To: Hoptman, Matthew
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] application of mri_cvs_register question


Hi Matt - The --reg option expects a .dat file. There should be one
produced by bbregister in the xfms/ directory?

a.y

On Mon, 15 Jul 2013, Hoptman, Matthew wrote:


Hi Anastasia,
Yes, that was my problem. I think I need to use
mri_vol2vol --targ ../../../cvs_avg35_inMNI152/mri/norm.mgz --m3z
../../cvs/cvs_avg35_inMNI152/final_CVSmorph_tocvs_avg35_inMNI152.m3z
--noDefM3zPath --reg diff2anat.bbr.mat --mov ../dtifit_FA.nii.gz --o
diffvol2CVS.nii.gz --no-save-reg


I now get:
Using the m3z file as it is; no assumed location.
regio_read_register(): Success
Error reading R[3][0] from diff2anat.bbr.mat

Matrix from regfile:
-0.001   0.972  -0.234  -3.311;
-0.001   0.234   0.972   69.949;
0.000   0.000   0.000   1.000;
0.000   0.000   0.000   0.000;

I was stuck at that point.  Lilla Zollei told me she'd look into it, but maybe 
you've communicated with her?
Thanks
Matt

-Original Message-
From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
Sent: Monday, July 15, 2013 2:30 PM
To: Hoptman, Matthew
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] application of mri_cvs_register question


Hi Matt - The CVS morph under xfms/cvs/ maps the individual anatomical to
the CVS template. To map from individual diffusion to the CVS template,
you'd have to first use diffusion-to-anatomical affine transform file
under xfms/.

Hope this helps,
a.y

On Mon, 15 Jul 2013, Hoptman, Matthew wrote:


Hi Anastasia,
Not really, what I now have is:
subject/dmri/xfms/cvs
Within cvs, there are anatomical files that are registered to the CVS template, 
as below, but what I DON'T have is the application of these transforms to the 
DTI data.  That's what I'm trying to puzzle out.

The files in subject/dmri/xfms/cvs are:
c159001_to_cvs_avg35_inMNI152.mri_cvs_register.1307051306.log
c159001_to_cvs_avg35_inMNI152.mri_cvs_register.1307051310.log
final_CVSmorphed_tocvs_avg35_inMNI152_aseg.mgz
final_CVSmorphed_tocvs_avg35_inMNI152_norm.mgz
final_CVSmorph_tocvs_avg35_inMNI152.m3z
lh.dbg_surf.pial
lh.dbg_surf.white
lh.resample.aparc.annot
lh.resample.pial
lh.resample.white
nlalign-afteraseg-norm.mgz
nlalign-aseg.mgz
rh.dbg_surf.pial
rh.dbg_surf.white
rh.resample.aparc.annot
rh.resample.pial
rh.resample.white
summary.c159001_to_cvs_avg35_inMNI152.mri_cvs_register.1307051306.log
summary.c159001_to_cvs_avg35_inMNI152.mri_cvs_register.1307051310.log
transform.txt


-Original Message-
From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
Sent: Monday, July 15, 2013 12:19 PM
To: Hoptman, Matthew
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] application of mri_cvs_register question


Hi Matt - For how to tell tracula to use CVS registration, see Specify
the inter-subject registration method here:
   http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula

Does this answer your question?

a.y

On Mon, 8 Jul 2013, Hoptman, Matthew wrote:



Hi all,

I see how to apply mri_vol2vol to DTI data from dt_recon, but I’m not clear on 
how to do so to DTI data processed in Tracula.  The command in the “Multimodal
integration and inter-subject registration” tutorial is:

mri_vol2vol   --targ templateid --m3z morph.m3z --noDefM3zPath --reg 
2anat.register.dat --mov diffvol --o diffvol2CVS --no-save-reg



But in Tracula, there are no “register.dat” files, or indeed no *.dat files.  
Is there a way to convert one of the *.mat files in the dmri/xfms directory to a
*.dat file?  Also, given that I think Tracula and dt_recon use different 
transformation algorithms, which Tracula transform should I choose?



Thanks,

Matt



Matthew J. Hoptman, PhD
Research Scientist V
Nathan S. Kline Institute for Psychiatric Research

Research Associate Professor in Psychiatry
NYU School of Medicine



IMPORTANT NOTICE: This e-mail is meant only for the use of the intended 
recipient. It may contain confidential information which is legally privileged 
or
otherwise protected by law. If you received this
e-mail in error or from someone who was not authorized to send it to you, you 
are strictly prohibited from reviewing, using, disseminating, distributing or
copying the e-mail.

PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE

Re: [Freesurfer] application of mri_cvs_register question



Hi Matt - Try anatorig2diff.bbr.dat.

a.y

On Mon, 15 Jul 2013, Hoptman, Matthew wrote:


Hi Anastasia,
Here it is:
anat2anatorig.dat   anatorig2diff.bbr.dat  anatorig2diff.bbr.dat.sum  
diff2mni.bbr.mat
anat2anatorig.dat~  anatorig2diff.bbr.dat~ anatorig2diff.bbr.mat  
mni2anat.mat
anat2anatorig.mat   anatorig2diff.bbr.dat.log  anatorig2mni.mat   
mni2anatorig.mat
anat2diff.bbr.mat   anatorig2diff.bbr.dat.log.old  cvs
mni2diff.bbr.mat
anat2mni.matanatorig2diff.bbr.dat.mincost  diff2anat.bbr.mat
anatorig2anat.mat   anatorig2diff.bbr.dat.paramdiff2anatorig.bbr.mat

-Original Message-
From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
Sent: Monday, July 15, 2013 2:56 PM
To: Hoptman, Matthew
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] application of mri_cvs_register question


Got it. Can you send me a listing of the contents of the xfms/ directory?
Conversions b/w formats can be done with tkregister2, but the .dat file
should normally be there since it's the default format for bbregister.

On Mon, 15 Jul 2013, Hoptman, Matthew wrote:


Right, that's been my problem :(  Maybe something went wrong, but I didn't see 
any problem in the log files.  Actually, the command I showed below had a typo 
(I used --mat rather than --reg to get that error).  Is there a way to  convert 
*.mat to *.dat?

-Original Message-
From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
Sent: Monday, July 15, 2013 2:44 PM
To: Hoptman, Matthew
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] application of mri_cvs_register question


Hi Matt - The --reg option expects a .dat file. There should be one
produced by bbregister in the xfms/ directory?

a.y

On Mon, 15 Jul 2013, Hoptman, Matthew wrote:


Hi Anastasia,
Yes, that was my problem. I think I need to use
mri_vol2vol --targ ../../../cvs_avg35_inMNI152/mri/norm.mgz --m3z
../../cvs/cvs_avg35_inMNI152/final_CVSmorph_tocvs_avg35_inMNI152.m3z
--noDefM3zPath --reg diff2anat.bbr.mat --mov ../dtifit_FA.nii.gz --o
diffvol2CVS.nii.gz --no-save-reg


I now get:
Using the m3z file as it is; no assumed location.
regio_read_register(): Success
Error reading R[3][0] from diff2anat.bbr.mat

Matrix from regfile:
-0.001   0.972  -0.234  -3.311;
-0.001   0.234   0.972   69.949;
0.000   0.000   0.000   1.000;
0.000   0.000   0.000   0.000;

I was stuck at that point.  Lilla Zollei told me she'd look into it, but maybe 
you've communicated with her?
Thanks
Matt

-Original Message-
From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
Sent: Monday, July 15, 2013 2:30 PM
To: Hoptman, Matthew
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] application of mri_cvs_register question


Hi Matt - The CVS morph under xfms/cvs/ maps the individual anatomical to
the CVS template. To map from individual diffusion to the CVS template,
you'd have to first use diffusion-to-anatomical affine transform file
under xfms/.

Hope this helps,
a.y

On Mon, 15 Jul 2013, Hoptman, Matthew wrote:


Hi Anastasia,
Not really, what I now have is:
subject/dmri/xfms/cvs
Within cvs, there are anatomical files that are registered to the CVS template, 
as below, but what I DON'T have is the application of these transforms to the 
DTI data.  That's what I'm trying to puzzle out.

The files in subject/dmri/xfms/cvs are:
c159001_to_cvs_avg35_inMNI152.mri_cvs_register.1307051306.log
c159001_to_cvs_avg35_inMNI152.mri_cvs_register.1307051310.log
final_CVSmorphed_tocvs_avg35_inMNI152_aseg.mgz
final_CVSmorphed_tocvs_avg35_inMNI152_norm.mgz
final_CVSmorph_tocvs_avg35_inMNI152.m3z
lh.dbg_surf.pial
lh.dbg_surf.white
lh.resample.aparc.annot
lh.resample.pial
lh.resample.white
nlalign-afteraseg-norm.mgz
nlalign-aseg.mgz
rh.dbg_surf.pial
rh.dbg_surf.white
rh.resample.aparc.annot
rh.resample.pial
rh.resample.white
summary.c159001_to_cvs_avg35_inMNI152.mri_cvs_register.1307051306.log
summary.c159001_to_cvs_avg35_inMNI152.mri_cvs_register.1307051310.log
transform.txt


-Original Message-
From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
Sent: Monday, July 15, 2013 12:19 PM
To: Hoptman, Matthew
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] application of mri_cvs_register question


Hi Matt - For how to tell tracula to use CVS registration, see Specify
the inter-subject registration method here:
   http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula

Does this answer your question?

a.y

On Mon, 8 Jul 2013, Hoptman, Matthew wrote:



Hi all,

I see how to apply mri_vol2vol to DTI data from dt_recon, but I’m not clear on 
how to do so to DTI data processed in Tracula.  The command in the “Multimodal
integration and inter-subject registration” tutorial is:

mri_vol2vol   --targ templateid --m3z morph.m3z --noDefM3zPath --reg 
2anat.register.dat --mov diffvol --o diffvol2CVS --no-save-reg



But in Tracula, there are no “register.dat” files

Re: [Freesurfer] [tracula] running into trouble with nifti data

2013-07-03 Thread Anastasia Yendiki



Hi Satra - There are 2 ways to put things in proper orientation for fsl 
tools:


1. L-R flip the gradient vectors: This is a hack, in the sense that it 
anticipates that FSL will treat your volume as L-R flipped when it has a 
certain type of orientation, but now you've broken your bvecs for the 
purposes of any software that doesn't do that (like freesurfer).


2. Convert both the volume and the gradient vectors to LAS orientation: 
This is not a hack, in the sense that now you have volumes and vectors 
that work both for FSL and otherwise, and work regardless of the original 
orientation.


Obviously, you want to do 1 OR 2, not both. What's breaking things for 
you is that your preprocessing is doing 1 and then trac-all preprocessing 
does 2.


I've opted for 2 in trac-all b/c I need the files to work for both FSL i/o 
routines (in bedpostx, most critically) and for freesurfer i/o routines 
(in my own code for tracula). Alternatively, I could keep two sets of 
everything and feed one set into the FSL routines and the other into the 
freesurfer routines, but this would be inelegant, a pain to implement, a 
recipe for introducing bugs, and, unltimately, a sure way to wipe out 
whatever little is left of my sanity.


Any other aspect of default preprocessing in trac-all (eddy currents, 
susceptibility) can be turned off if you want to use another method to do 
it. But it's not possible to turn off this way of making things compatible 
with FSL to use that way of making things compatible with FSL. If you want 
to try it, you can replace every instance of flip4fsl with cp and let me 
know what happens, I'd be really curious.


Hope this helps,
a.y

On Tue, 2 Jul 2013, Satrajit Ghosh wrote:


hi ay,
so this is what i did. i flipped the gradient LR intentionally, ran flip4fsl
and then dtifit and now the eigenvec 1 looks good, but not if i run dtifit
prior to flip4fsl.

but this brings me back to my original point which is that my image and the
gradients are (i think) already in proper orientation for fsl tools (since
the preflip output in the previous email looks correct) and flip4fsl is
making it inappropriate for fsl. 

also as some additional info:
- yes this is the siemens 60 dir scan but that predefined gradient table
doesn't take into account the slice orientation 
- if you use dcm2nii to extract these dicoms, the first two gradients are:

0.996362388134 0.0389195755124 -0.07581084221601
-0.65292024612426  0.00993375014513 -0.75736147165298

this is because dcm2nii, much like DTIPrep takes the image orientation
matrix into account when doing the conversion, which mri_convert doesn't.

so i think tracula should have an option of not flipping 4 fsl in the
scenario where other processes (e.g., my script, dcm2nii) automatically take
care of generating an fsl compatible file + gradient info.

please let me know if i'm misinterpreting something here. 

cheers,

satra

On Tue, Jul 2, 2013 at 8:21 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:

  Hi Satra - What you're showing in the screenshots would be
  consistent with a L-R flip of the gradient directions, which is
  what my comparison of your gradients to the original Siemens
  gradients indicated. (Assuming the data was acquired with the
  standard Siemens 60 gradient directions.)

  a.y

  On Tue, 2 Jul 2013, Satrajit Ghosh wrote:

hi ay,
i'll look into the orientations a little later
tonight, but here is V1
overlaid on FA for preflip and postflip execution of
dtifit. 

cheers,

satra


On Tue, Jul 2, 2013 at 7:48 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:

      Hi Satra - The orientation of your
dwi_orig.nii.gz is LPS. What
      flip4fsl will do is convert it to LAS, and
perform the same
      conversion on the gradient table that you
provide. This of
      course assumes that dwi_orig.nii.gz and your
gradient table are
      consistent as they come out of your custom
preprocessing. Is
      there any chance that they're not?

      Looking at the sample data set that you sent
me, I can only see
      what came out of your preprocessing and not
what went in. I'm
      assuming that this is from the standard
Siemens 60 direction
      sequence, and it has 57 directions b/c 3 of
them were thrown out
      by your preprocessing. I don't know which
directions were thrown
      out obviously, but the first 2 directions in
your gradient table
      are:
      -0.99699027939850948 -0.057720153020443053
0.051758263409041924
      0.63287878858184599 0.066164234845749903

Re: [Freesurfer] [tracula] running into trouble with nifti data

2013-07-02 Thread Anastasia Yendiki



Hi Satra - The orientation of your dwi_orig.nii.gz is LPS. What flip4fsl 
will do is convert it to LAS, and perform the same conversion on the 
gradient table that you provide. This of course assumes that 
dwi_orig.nii.gz and your gradient table are consistent as they come out of 
your custom preprocessing. Is there any chance that they're not?


Looking at the sample data set that you sent me, I can only see what 
came out of your preprocessing and not what went in. I'm assuming that 
this is from the standard Siemens 60 direction sequence, and it has 57 
directions b/c 3 of them were thrown out by your preprocessing. I don't 
know which directions were thrown out obviously, but the first 2 
directions in your gradient table are:

-0.99699027939850948 -0.057720153020443053 0.051758263409041924
0.63287878858184599 0.066164234845749903 0.77141869630019422

The first two directions in the Siemens 60 direction gradient table are:
1.00  0.00  0.00
0.5867917880 -0.3765825401 -0.7168409782

There's not only a small adjustment of the direction but also a sign 
change there. So I'd look into that.


Let me know if any of my assumptions about your original data is wrong.

a.y

On Tue, 2 Jul 2013, Satrajit Ghosh wrote:


hi anastasia,
i'm trying to debug a seg fault that some folks are seeing deep into a
tracula run.

process:

1. feed dicoms to a script that runs DTIPrep and outputs a nifti file, bvec,
bval 

(among checking for many artifacts, this reduces the b=0 volumes to a single
registered mean volume, runs eddy correction, discards bad directions,
reorients the gradients appropriately and generates a report of the quality)

2. run tracula on this nifti file

observation:

when i run fsl/dtifit on the same nifti file + bvec + bval, i get the proper
orientation for eigvec1 lines. however, when i feed this into tracula, the
output of the dtifit step looks terrible - i.e. the lines are not oriented
as how one might expect water to diffuse.

suspicion:

although i have not reached the crash yet, i believe it might be related to
this fact that the gradients are not oriented properly relative to the
volume.

i also suspect that this has something to do with the flip4fsl step inside
tracula, which is possibly unnecessary because fsl already likes the input
files. but it seems this step is encoded quite heavily within the trac-all
scripts. 

questions: 

a. is there a quick way to turn the flip4fsl step off?
b. alternatively do you have any suggestions for what to do here? 

the whole point of running through DTIPrep is to clean up the data before
giving it to tracula or other programs, so i would really like to keep that
step.

cheers,

satra


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] [tracula] running into trouble with nifti data

2013-07-02 Thread Anastasia Yendiki



Hi Satra - What you're showing in the screenshots would be consistent with 
a L-R flip of the gradient directions, which is what my comparison of your 
gradients to the original Siemens gradients indicated. (Assuming the data 
was acquired with the standard Siemens 60 gradient directions.)


a.y

On Tue, 2 Jul 2013, Satrajit Ghosh wrote:


hi ay,
i'll look into the orientations a little later tonight, but here is V1
overlaid on FA for preflip and postflip execution of dtifit. 

cheers,

satra


On Tue, Jul 2, 2013 at 7:48 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:

  Hi Satra - The orientation of your dwi_orig.nii.gz is LPS. What
  flip4fsl will do is convert it to LAS, and perform the same
  conversion on the gradient table that you provide. This of
  course assumes that dwi_orig.nii.gz and your gradient table are
  consistent as they come out of your custom preprocessing. Is
  there any chance that they're not?

  Looking at the sample data set that you sent me, I can only see
  what came out of your preprocessing and not what went in. I'm
  assuming that this is from the standard Siemens 60 direction
  sequence, and it has 57 directions b/c 3 of them were thrown out
  by your preprocessing. I don't know which directions were thrown
  out obviously, but the first 2 directions in your gradient table
  are:
  -0.99699027939850948 -0.057720153020443053 0.051758263409041924
  0.63287878858184599 0.066164234845749903 0.77141869630019422

  The first two directions in the Siemens 60 direction gradient
  table are:
  1.00  0.00  0.00
  0.5867917880 -0.3765825401 -0.7168409782

  There's not only a small adjustment of the direction but also a
  sign change there. So I'd look into that.

  Let me know if any of my assumptions about your original data is
  wrong.

  a.y

  On Tue, 2 Jul 2013, Satrajit Ghosh wrote:

hi anastasia,
i'm trying to debug a seg fault that some folks are
seeing deep into a
tracula run.

process:

1. feed dicoms to a script that runs DTIPrep and
outputs a nifti file, bvec,
bval 

(among checking for many artifacts, this reduces the
b=0 volumes to a single
registered mean volume, runs eddy correction,
discards bad directions,
reorients the gradients appropriately and generates
a report of the quality)

2. run tracula on this nifti file

observation:

when i run fsl/dtifit on the same nifti file + bvec
+ bval, i get the proper
orientation for eigvec1 lines. however, when i feed
this into tracula, the
output of the dtifit step looks terrible - i.e. the
lines are not oriented
as how one might expect water to diffuse.

suspicion:

although i have not reached the crash yet, i believe
it might be related to
this fact that the gradients are not oriented
properly relative to the
volume.

i also suspect that this has something to do with
the flip4fsl step inside
tracula, which is possibly unnecessary because fsl
already likes the input
files. but it seems this step is encoded quite
heavily within the trac-all
scripts. 

questions: 

a. is there a quick way to turn the flip4fsl step
off?
b. alternatively do you have any suggestions for
what to do here? 

the whole point of running through DTIPrep is to
clean up the data before
giving it to tracula or other programs, so i would
really like to keep that
step.

cheers,

satra





The information in this e-mail is intended only for the person to whom
it is
addressed. If you believe this e-mail was sent to you in error and the
e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you
in error
but does not contain patient information, please contact the sender
and properly
dispose of the e-mail.



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly

Re: [Freesurfer] Tracula/ config file error



Hi Andrew - I'm sorry that you're annoyed. I can feel your pain. Take a 
deep breath and let it all go.


More to the point, when I view the text file that you sent, I see that 
several of the lines are joined together, so both the dcmroot and dcmlist 
variables appear commented out. Is this intentional? Was this text file 
saved on a unix system?


a.y

On Mon, 1 Jul 2013, Gundran, Andrew wrote:



I have been trying to run tracula with a config file but keep getting the
same error message when I use the trac-all command for pre-processing

    set: Variable name must begin with a letter

 

It has become very, very annoying. PLEASE SOMEONE HELP!!!

 

Andrew

 

--

# FreeSurfer SUBJECTS_DIR

# /home/baileype/Desktop/JG005/freesurfer/mri

#

setenv SUBJECTS_DIR /home/baileype/Desktop/JG005

 

# Output directory where trac-all results will be saved # Default: Same as
SUBJECTS_DIR # set dtroot = /home/baileype/Desktop/JG005

 

# Subject IDs

#

set subjlist = (freesurfer)

 

# In case you want to analyze only Huey and Louie # Default: Run analysis on
all subjects # set runlist = (1)

 

# Input diffusion DICOMs (file names relative to dcmroot) # If original
DICOMs don't exist, these can be in other image format # but then bvecfile
and bvalfile must be specified (see below) # set dcmroot =
/home/baileype/Desktop/JG005 set dcmlist = (DKI.nii.gz)

 

# Diffusion gradient table

# Must be specified if inputs are not MGH DICOMs # Three-column format, one
row for each volume in the diffusion data set # Default: Read from DICOM
header # set bvecfile = /home/baileype/Desktop/JG005/bvecs

 

# Diffusion b-value table

# Must be specified if inputs are not MGH DICOMs # Single-column format, one
value for each volume in the diffusion data set # Default: Read from DICOM
header # set bvalfile = /home/baileype/Desktop/JG005/bvals

 

# Perform registration-based B0-inhomogeneity compensation?

# Default: 0 (no)

#

# set dob0 = 1

 

# Input B0 field map magnitude DICOMs (file names relative to dcmroot) #
Only used if dob0 = 1 # Default: None # # set b0mlist = (huey/fmag/XXX-1.dcm
dewey/fmag/XXX-1.dcm louie/fmag/XXX-1.dcm)

 

# Input B0 field map phase DICOMs (file names relative to dcmroot) # Only
used if dob0 = 1 # Default: None # # set b0plist = (huey/fphas/XXX-1.dcm
dewey/fphas/XXX-1.dcm louie/fphas/XXX-1

 

# Echo spacing for field mapping sequence (from sequence printout) # Only
used if dob0 = 1 # Default: None # # set echospacing = 0.7

 

# Perform registration-based eddy-current compensation?

# Default: 1 (yes)

#

set doeddy = 1

 

# Rotate diffusion gradient vectors to match eddy-current compensation?

# Only used if doeddy = 1

# Default: 1 (yes)

#

set dorotbvecs = 1

 

# Fractional intensity threshold for BET mask extraction from low-b images #
This mask is used only if usemaskanat = 0 # Default: 0.3 # set thrbet = 0.2

 

# Perform diffusion-to-T1 registration by flirt?

# Default: 0 (no)

#

set doregflt = 0

 

# Perform diffusion-to-T1 registration by bbregister?

# Default: 1 (yes)

#

set doregbbr = 1

 

# Perform registration of T1 to MNI template?

# Default: 1 (yes)

#

set doregmni = 1

 

# MNI template

# Only used if doregmni = 1

# Default: $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz

#

# set mnitemp = /path/to/mni_template.nii.gz

 

# Perform registration of T1 to CVS template?

# Default: 0 (no)

#

# set doregcvs = 0

 

# CVS template subject ID

# Only used if doregcvs = 1

# Default: cvs_avg35

#

# set cvstemp = donald

 

# Parent directory of the CVS template subject # Only used if doregcvs = 1 #
Default: $FREESURFER_HOME/subjects # # set cvstempdir =
/path/to/cvs/atlases/of/ducks

 

# Use brain mask extracted from T1 image instead of low-b diffusion image?

# Has no effect if there is no T1 data

# Default: 1 (yes)

#

set usemaskanat = 1

 

# Paths to reconstruct

# Default: All paths in the atlas

#

set pathlist = (lh.cst_AS rh.cst_AS \

    lh.unc_AS rh.unc_AS \

    lh.ilf_AS rh.ilf_AS \

    fmajor_PP fminor_PP \

    lh.atr_PP rh.atr_PP \

    lh.ccg_PP rh.ccg_PP \

    lh.cab_PP rh.cab_PP \

    lh.slfp_PP rh.slfp_PP \

    lh.slft_PP rh.slft_PP)

 

# Number of path control points

# It can be a single number for all paths or a different number for each of
the # paths specified in pathlist # Default: 7 for the forceps major, 6 for
the corticospinal tract,

#  4 for the angular bundle, and 5 for all other paths

#

set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5)

 

# List of training subjects

# This text file lists the locations of training subject directories #
Default: $FREESURFER_HOME/trctrain/trainlist.txt

#

set trainfile = $FREESURFER_HOME/trctrain/trainlist.txt

 

# Number of sticks (anisotropic diffusion compartments) in the bedpostx #
ball-and-stick model # Default: 2 # set nstick = 2

 

# Number of MCMC burn-in iterations

# (Path

Re: [Freesurfer] Tracula/ config file error



Can you see that this is all one line?

# Input diffusion DICOMs (file names relative to dcmroot) # If original 
DICOMs don't exist, these can be in other image format # but then bvecfile 
and bvalfile must be specified (see below) # set dcmroot = 
/home/baileype/Desktop/JG005 set dcmlist = (DKI.nii.gz)



On Mon, 1 Jul 2013, Gundran, Andrew wrote:


Yes, the text was saved on a unix system

-Original Message-
From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
Sent: Monday, July 01, 2013 2:34 PM
To: Gundran, Andrew
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Tracula/ config file error


Hi Andrew - I'm sorry that you're annoyed. I can feel your pain. Take a deep 
breath and let it all go.

More to the point, when I view the text file that you sent, I see that several 
of the lines are joined together, so both the dcmroot and dcmlist variables 
appear commented out. Is this intentional? Was this text file saved on a unix 
system?

a.y

On Mon, 1 Jul 2013, Gundran, Andrew wrote:



I have been trying to run tracula with a config file but keep getting
the same error message when I use the trac-all command for
pre-processing

    set: Variable name must begin with a letter

 

It has become very, very annoying. PLEASE SOMEONE HELP!!!

 

Andrew

 

--

# FreeSurfer SUBJECTS_DIR

# /home/baileype/Desktop/JG005/freesurfer/mri

#

setenv SUBJECTS_DIR /home/baileype/Desktop/JG005

 

# Output directory where trac-all results will be saved # Default:
Same as SUBJECTS_DIR # set dtroot = /home/baileype/Desktop/JG005

 

# Subject IDs

#

set subjlist = (freesurfer)

 

# In case you want to analyze only Huey and Louie # Default: Run
analysis on all subjects # set runlist = (1)

 

# Input diffusion DICOMs (file names relative to dcmroot) # If
original DICOMs don't exist, these can be in other image format # but
then bvecfile and bvalfile must be specified (see below) # set dcmroot
=
/home/baileype/Desktop/JG005 set dcmlist = (DKI.nii.gz)

 

# Diffusion gradient table

# Must be specified if inputs are not MGH DICOMs # Three-column
format, one row for each volume in the diffusion data set # Default:
Read from DICOM header # set bvecfile =
/home/baileype/Desktop/JG005/bvecs

 

# Diffusion b-value table

# Must be specified if inputs are not MGH DICOMs # Single-column
format, one value for each volume in the diffusion data set # Default:
Read from DICOM header # set bvalfile =
/home/baileype/Desktop/JG005/bvals

 

# Perform registration-based B0-inhomogeneity compensation?

# Default: 0 (no)

#

# set dob0 = 1

 

# Input B0 field map magnitude DICOMs (file names relative to dcmroot)
# Only used if dob0 = 1 # Default: None # # set b0mlist =
(huey/fmag/XXX-1.dcm dewey/fmag/XXX-1.dcm louie/fmag/XXX-1.dcm)

 

# Input B0 field map phase DICOMs (file names relative to dcmroot) #
Only used if dob0 = 1 # Default: None # # set b0plist =
(huey/fphas/XXX-1.dcm dewey/fphas/XXX-1.dcm louie/fphas/XXX-1

 

# Echo spacing for field mapping sequence (from sequence printout) #
Only used if dob0 = 1 # Default: None # # set echospacing = 0.7

 

# Perform registration-based eddy-current compensation?

# Default: 1 (yes)

#

set doeddy = 1

 

# Rotate diffusion gradient vectors to match eddy-current compensation?

# Only used if doeddy = 1

# Default: 1 (yes)

#

set dorotbvecs = 1

 

# Fractional intensity threshold for BET mask extraction from low-b
images # This mask is used only if usemaskanat = 0 # Default: 0.3 #
set thrbet = 0.2

 

# Perform diffusion-to-T1 registration by flirt?

# Default: 0 (no)

#

set doregflt = 0

 

# Perform diffusion-to-T1 registration by bbregister?

# Default: 1 (yes)

#

set doregbbr = 1

 

# Perform registration of T1 to MNI template?

# Default: 1 (yes)

#

set doregmni = 1

 

# MNI template

# Only used if doregmni = 1

# Default: $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz

#

# set mnitemp = /path/to/mni_template.nii.gz

 

# Perform registration of T1 to CVS template?

# Default: 0 (no)

#

# set doregcvs = 0

 

# CVS template subject ID

# Only used if doregcvs = 1

# Default: cvs_avg35

#

# set cvstemp = donald

 

# Parent directory of the CVS template subject # Only used if doregcvs
= 1 #
Default: $FREESURFER_HOME/subjects # # set cvstempdir =
/path/to/cvs/atlases/of/ducks

 

# Use brain mask extracted from T1 image instead of low-b diffusion image?

# Has no effect if there is no T1 data

# Default: 1 (yes)

#

set usemaskanat = 1

 

# Paths to reconstruct

# Default: All paths in the atlas

#

set pathlist = (lh.cst_AS rh.cst_AS \

    lh.unc_AS rh.unc_AS \

    lh.ilf_AS rh.ilf_AS \

    fmajor_PP fminor_PP \

    lh.atr_PP rh.atr_PP \

    lh.ccg_PP rh.ccg_PP \

    lh.cab_PP rh.cab_PP \

    lh.slfp_PP rh.slfp_PP \

    lh.slft_PP rh.slft_PP)

 

# Number of path control points

# It can be a single number for all paths or a different

Re: [Freesurfer] Tracula/ config file error



What program are you viewing it in? If you add a line at the end of 
config.txt that says echo $dcmlist (without the quotation marks) and 
then run source config.txt on the command line, does it print out 
DKI.nii.gz?


On Mon, 1 Jul 2013, Gundran, Andrew wrote:


It reads like

# Input diffusion DICOMs (file names relative to dcmroot)
# If original DICOMs don't exist, these can be in other image format
# but then bvecfile and bvalfile must be specified (see below)
#
set dcmroot = /home/baileype/Desktop/JG005
set dcmlist = (DKI.nii.gz)

-Original Message-
From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
Sent: Monday, July 01, 2013 2:48 PM
To: Gundran, Andrew
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] Tracula/ config file error


Can you see that this is all one line?

# Input diffusion DICOMs (file names relative to dcmroot) # If original DICOMs 
don't exist, these can be in other image format # but then bvecfile and 
bvalfile must be specified (see below) # set dcmroot =
/home/baileype/Desktop/JG005 set dcmlist = (DKI.nii.gz)


On Mon, 1 Jul 2013, Gundran, Andrew wrote:


Yes, the text was saved on a unix system

-Original Message-
From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
Sent: Monday, July 01, 2013 2:34 PM
To: Gundran, Andrew
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Tracula/ config file error


Hi Andrew - I'm sorry that you're annoyed. I can feel your pain. Take a deep 
breath and let it all go.

More to the point, when I view the text file that you sent, I see that several 
of the lines are joined together, so both the dcmroot and dcmlist variables 
appear commented out. Is this intentional? Was this text file saved on a unix 
system?

a.y

On Mon, 1 Jul 2013, Gundran, Andrew wrote:



I have been trying to run tracula with a config file but keep getting
the same error message when I use the trac-all command for
pre-processing

    set: Variable name must begin with a letter

 

It has become very, very annoying. PLEASE SOMEONE HELP!!!

 

Andrew

 

--

# FreeSurfer SUBJECTS_DIR

# /home/baileype/Desktop/JG005/freesurfer/mri

#

setenv SUBJECTS_DIR /home/baileype/Desktop/JG005

 

# Output directory where trac-all results will be saved # Default:
Same as SUBJECTS_DIR # set dtroot = /home/baileype/Desktop/JG005

 

# Subject IDs

#

set subjlist = (freesurfer)

 

# In case you want to analyze only Huey and Louie # Default: Run
analysis on all subjects # set runlist = (1)

 

# Input diffusion DICOMs (file names relative to dcmroot) # If
original DICOMs don't exist, these can be in other image format # but
then bvecfile and bvalfile must be specified (see below) # set
dcmroot =
/home/baileype/Desktop/JG005 set dcmlist = (DKI.nii.gz)

 

# Diffusion gradient table

# Must be specified if inputs are not MGH DICOMs # Three-column
format, one row for each volume in the diffusion data set # Default:
Read from DICOM header # set bvecfile =
/home/baileype/Desktop/JG005/bvecs

 

# Diffusion b-value table

# Must be specified if inputs are not MGH DICOMs # Single-column
format, one value for each volume in the diffusion data set # Default:
Read from DICOM header # set bvalfile =
/home/baileype/Desktop/JG005/bvals

 

# Perform registration-based B0-inhomogeneity compensation?

# Default: 0 (no)

#

# set dob0 = 1

 

# Input B0 field map magnitude DICOMs (file names relative to
dcmroot) # Only used if dob0 = 1 # Default: None # # set b0mlist =
(huey/fmag/XXX-1.dcm dewey/fmag/XXX-1.dcm louie/fmag/XXX-1.dcm)

 

# Input B0 field map phase DICOMs (file names relative to dcmroot) #
Only used if dob0 = 1 # Default: None # # set b0plist =
(huey/fphas/XXX-1.dcm dewey/fphas/XXX-1.dcm louie/fphas/XXX-1

 

# Echo spacing for field mapping sequence (from sequence printout) #
Only used if dob0 = 1 # Default: None # # set echospacing = 0.7

 

# Perform registration-based eddy-current compensation?

# Default: 1 (yes)

#

set doeddy = 1

 

# Rotate diffusion gradient vectors to match eddy-current compensation?

# Only used if doeddy = 1

# Default: 1 (yes)

#

set dorotbvecs = 1

 

# Fractional intensity threshold for BET mask extraction from low-b
images # This mask is used only if usemaskanat = 0 # Default: 0.3 #
set thrbet = 0.2

 

# Perform diffusion-to-T1 registration by flirt?

# Default: 0 (no)

#

set doregflt = 0

 

# Perform diffusion-to-T1 registration by bbregister?

# Default: 1 (yes)

#

set doregbbr = 1

 

# Perform registration of T1 to MNI template?

# Default: 1 (yes)

#

set doregmni = 1

 

# MNI template

# Only used if doregmni = 1

# Default: $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz

#

# set mnitemp = /path/to/mni_template.nii.gz

 

# Perform registration of T1 to CVS template?

# Default: 0 (no)

#

# set doregcvs = 0

 

# CVS template subject ID

# Only used if doregcvs = 1

# Default: cvs_avg35

#

# set cvstemp = donald

 

# Parent directory of the CVS template subject # Only used

Re: [Freesurfer] Tracula/ config file error



That probably means you're not running a C shell. That's fine, can you 
instead try running trac-all and see if it prints out the value of 
dcmlist now that you've added that line?


I'll repeat my other question: What program are you using to view the text 
file?


On Mon, 1 Jul 2013, Gundran, Andrew wrote:


Whoops. It doesn't read like that every # is a new line along with each set

I did that and the error was

Line13: syntax error near unexpected token `('
Line 13: `set subjlist = (freesurfer)


-Original Message-
From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
Sent: Monday, July 01, 2013 3:09 PM
To: Gundran, Andrew
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] Tracula/ config file error


What program are you viewing it in? If you add a line at the end of config.txt that says echo 
$dcmlist (without the quotation marks) and then run source config.txt on the command line, 
does it print out DKI.nii.gz?

On Mon, 1 Jul 2013, Gundran, Andrew wrote:


It reads like

# Input diffusion DICOMs (file names relative to dcmroot) # If
original DICOMs don't exist, these can be in other image format # but
then bvecfile and bvalfile must be specified (see below) # set dcmroot
= /home/baileype/Desktop/JG005 set dcmlist = (DKI.nii.gz)

-Original Message-
From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
Sent: Monday, July 01, 2013 2:48 PM
To: Gundran, Andrew
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] Tracula/ config file error


Can you see that this is all one line?

# Input diffusion DICOMs (file names relative to dcmroot) # If
original DICOMs don't exist, these can be in other image format # but
then bvecfile and bvalfile must be specified (see below) # set dcmroot
=
/home/baileype/Desktop/JG005 set dcmlist = (DKI.nii.gz)


On Mon, 1 Jul 2013, Gundran, Andrew wrote:


Yes, the text was saved on a unix system

-Original Message-
From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
Sent: Monday, July 01, 2013 2:34 PM
To: Gundran, Andrew
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Tracula/ config file error


Hi Andrew - I'm sorry that you're annoyed. I can feel your pain. Take a deep 
breath and let it all go.

More to the point, when I view the text file that you sent, I see that several 
of the lines are joined together, so both the dcmroot and dcmlist variables 
appear commented out. Is this intentional? Was this text file saved on a unix 
system?

a.y

On Mon, 1 Jul 2013, Gundran, Andrew wrote:



I have been trying to run tracula with a config file but keep
getting the same error message when I use the trac-all command for
pre-processing

    set: Variable name must begin with a letter

 

It has become very, very annoying. PLEASE SOMEONE HELP!!!

 

Andrew

 

--

# FreeSurfer SUBJECTS_DIR

# /home/baileype/Desktop/JG005/freesurfer/mri

#

setenv SUBJECTS_DIR /home/baileype/Desktop/JG005

 

# Output directory where trac-all results will be saved # Default:
Same as SUBJECTS_DIR # set dtroot = /home/baileype/Desktop/JG005

 

# Subject IDs

#

set subjlist = (freesurfer)

 

# In case you want to analyze only Huey and Louie # Default: Run
analysis on all subjects # set runlist = (1)

 

# Input diffusion DICOMs (file names relative to dcmroot) # If
original DICOMs don't exist, these can be in other image format #
but then bvecfile and bvalfile must be specified (see below) # set
dcmroot =
/home/baileype/Desktop/JG005 set dcmlist = (DKI.nii.gz)

 

# Diffusion gradient table

# Must be specified if inputs are not MGH DICOMs # Three-column
format, one row for each volume in the diffusion data set # Default:
Read from DICOM header # set bvecfile =
/home/baileype/Desktop/JG005/bvecs

 

# Diffusion b-value table

# Must be specified if inputs are not MGH DICOMs # Single-column
format, one value for each volume in the diffusion data set # Default:
Read from DICOM header # set bvalfile =
/home/baileype/Desktop/JG005/bvals

 

# Perform registration-based B0-inhomogeneity compensation?

# Default: 0 (no)

#

# set dob0 = 1

 

# Input B0 field map magnitude DICOMs (file names relative to
dcmroot) # Only used if dob0 = 1 # Default: None # # set b0mlist =
(huey/fmag/XXX-1.dcm dewey/fmag/XXX-1.dcm louie/fmag/XXX-1.dcm)

 

# Input B0 field map phase DICOMs (file names relative to dcmroot) #
Only used if dob0 = 1 # Default: None # # set b0plist =
(huey/fphas/XXX-1.dcm dewey/fphas/XXX-1.dcm louie/fphas/XXX-1

 

# Echo spacing for field mapping sequence (from sequence printout) #
Only used if dob0 = 1 # Default: None # # set echospacing = 0.7

 

# Perform registration-based eddy-current compensation?

# Default: 1 (yes)

#

set doeddy = 1

 

# Rotate diffusion gradient vectors to match eddy-current compensation?

# Only used if doeddy = 1

# Default: 1 (yes)

#

set dorotbvecs = 1

 

# Fractional intensity threshold for BET mask extraction from low-b
images # This mask is used only if usemaskanat = 0

Re: [Freesurfer] [FreeSurfer] Corpus Callosum tracts

2013-06-26 Thread Anastasia Yendiki


Hi Roxana - How tracula works is decribed in detail here:
http://www.frontiersin.org/Journal/DownloadFile.ashx?pdf=1FileId=8155articleId=10815Version=1ContentTypeId=21FileName=fninf-05-00023.pdf

To add a new tract to the tracula atlas that is not currently part of it, 
the tract would first have to be labeled manually in the 33 subjects that 
make up our atlas.

Hope this helps,
a.y

On Wed, 26 Jun 2013, Teodorescu, Roxana wrote:

 Dear FreeSurfers,

 I would like to get the tracts in Corpus Callosum body, not just the forceps 
 major and forceps minor given by tracula. Is there a way to get that with 
 Tracula?

 Thank you.

 Roxana.


 ---
 Roxana O. Teodorescu, PhD
 Postdoctoral Fellow

 Department of Neurology
 Mount Sinai School of Medicine


 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Fwd: DTI questions

2013-06-24 Thread Anastasia Yendiki



Sorry, can't open the image.

On Sun, 23 Jun 2013, Rotem Saar wrote:


Hi there,

Long time:). Well I wrote to the list several times regarding high FA values
I got when performing DTI analysis.
Today we know that the problem was an additional direction (we had 17
directions instead of 16 - we used a Philips scanner,1.5T). So we deleted
the additional slices and the high values indeed disappeared, but then
another problem came up (tried several subjects so the problem is not
specific to a subject) -

I noticed an artifact that I can't explain - please see the attached
pictures.

This artifact existed even before I deleted the additional slices, also - I
see the artifact also when loading the masked volume...It is cyclic - run
over all slices...

any ideas ?
 
I'm using version 5.2 and I know the command lines are correct (send it to u
in the past).

Thanks for your help

Rotem

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Fwd: DTI questions

2013-06-24 Thread Anastasia Yendiki



Hi Rotem - No problem. Were these scans by any chance acquired with a 
coronal slice prescription? In the axial views that you sent, the artifact 
that you're pointing to looks like misalignment between consecutive 
coronal slices, which could be due to head motion.


a.y

On Tue, 25 Jun 2013, Rotem Saar wrote:


Dear Anastasia,
 
I tried several times to upload these images in a non-compressed way, but
they were too big and my posts were rejected, with no opportunity for any
other upload way.
Is there any other way for me to upload it so that everyone can see it ?
 
Attached are the images in a non-compressed fashion. I will be very happy if
u will have a look, and post your answer to me and the list to save some
time, until I will be able to consider another way to upload them.
 
I know that we should write to all the list, but at the moment if the images
are not visible this won't help - so I will really appreciate if u will have
a look but also tell me what is the best way to upload them so that all list
members will be able to see them.
 
Thank u very much for your help.
 
Rotem

2013/6/25 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu

  Sorry, can't open the image.

  On Sun, 23 Jun 2013, Rotem Saar wrote:

Hi there,

Long time:). Well I wrote to the list several times
regarding high FA values
I got when performing DTI analysis.
Today we know that the problem was an additional
direction (we had 17
directions instead of 16 - we used a Philips
scanner,1.5T). So we deleted
the additional slices and the high values indeed
disappeared, but then
another problem came up (tried several subjects so
the problem is not
specific to a subject) -

I noticed an artifact that I can't explain - please
see the attached
pictures.

This artifact existed even before I deleted the
additional slices, also - I
see the artifact also when loading the masked
volume...It is cyclic - run
over all slices...

any ideas ?
 
I'm using version 5.2 and I know the command lines
are correct (send it to u
in the past).

Thanks for your help

Rotem




The information in this e-mail is intended only for the person to whom
it is
addressed. If you believe this e-mail was sent to you in error and the
e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you
in error
but does not contain patient information, please contact the sender
and properly
dispose of the e-mail.



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Possible to generate connectivity map using FS and Tracula

2013-06-22 Thread Anastasia Yendiki


Hi Sal - Not sure what you mean by connectivity maps, can you be more 
specific? Tracula is not a method for exploratory analyses of the type 
what is my seed region connected to? It's a method for reconstructing a 
set of 18 major white-matter pathways, which are listed here:

http://www.frontiersin.org/Journal/DownloadFile.ashx?pdf=1FileId=8155articleId=10815Version=1ContentTypeId=21FileName=fninf-05-00023.pdf

Hope this helps,
a.y

On Thu, 20 Jun 2013, Salil Soman wrote:

 
 Dear Doug,
 
 Is there a way to use the Freesurfer and Tracula output to compute 
 connectivity
 maps?
 
 Thanks!
 
 Sal
 
 

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] TRACULA - tract volume and length

2013-06-22 Thread Anastasia Yendiki



Hi Fred - As with any probabilistic method, volume here is a measure of 
the spread of the probability distribution of the pathway (i.e. of 
path.pd.nii.gz), so it can be interpreted as the amount of uncertainty in 
the data. A more spread out distribution means more uncertainty, a tighter 
distribution means less uncertainty.


Please note that TRACULA performs tractography in each subject's native 
DWI space, so volume/length are not calculated in a common/normalized 
space for all subjects. So beware when comparing volume/length across 
subjects.


If you use the weighted FA/MD/etc measures, these are weighted by the 
value of the probability distribution at every voxel, so they are the mean 
values in a probabilistic sense.


Hope this helps,
a.y

On Wed, 19 Jun 2013, Fred Sanders wrote:


Dear DTI experts,

I am trying to understand how to interpret tract length  volume
measurements that TRACULA provides.  For example, let’s say a clinical
population differs from a control group in mean FA of a particular
tract, and tract length  volume are comparable across the 2 groups.
I think this would support the notion that the tract’s diffusion
properties are indeed different across the two groups and that the FA
finding are unlikely to be an artifact of probabilistic tractography.
Is this a correct interpretation?  Conversely, if group differences in
tract volumes were detected, would you recommend comparing mean FA
across the two group while covarying for tract volume?

Thanks!

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] generate pathstats.overall.txt file from tract volume

2013-06-16 Thread Anastasia Yendiki



Sorry, there's no command that will generate that file for anything other 
than the output generated by tracula, but if you want to average FA etc 
over a volume it's pretty easy to do with fslstats.


On Fri, 14 Jun 2013, Jayachandra Raghava wrote:


Hello All,
Is it possible to generate pathstats.overall.txt file from tract volume?
I would like to do some tract statistics on the tract volumes generated by
FSL.

Best
Jay

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Coupling cortical and TRACULA results

2013-06-10 Thread Anastasia Yendiki



You can find the aparc+aseg mapped from T1 space to DWI space in the 
dlabel/diff directory. You can overlay it on the paths reconstructed from 
tracula to see which aparc+aseg labels the paths overlap with. The 
identities of the labels in the aparc+aseg are in 
$FREESURFER_HOME/FreeSurferColorLUT.txt.


On Mon, 10 Jun 2013, std...@virgilio.it wrote:


Hi list,
Thiebaut de Schotten et al., in an article on cortex (Monkey to human
comparative anatomy of the frontal lobe association tracts reported that 

The superior longitudinal fasciculus has three distinct branches (Petrides
and Pandya, 1984). 
In humans, the first branch of the superior longitudinal fasciculus (SLF I)
connects to the superior parietal lobule and precuneus (BA 5 and 7), to the
superior frontal (BA 8, 9, 32) and perhaps to some anterior cingulate areas
(BA 24). The second branch (SLF II) originatesin the anterior intraparietal
sulcus and the angular gyrus (BA 39 and 40) and terminates in the posterior
regions of the superior and middle frontal gyrus (BA 6, 8, 9). The third
branch (SLF III) connects the intraparietal sulcus and inferior parietal
lobule to the inferior frontal gyrus (BA 44, 45, 47)

By TRACULA output we have 2 output SLFp and SLFt.

Having also cortical results, I wonder if possible to know which are the
seed and target areas of SLF p and SLFt or al least to know which is that
branch that is described by SLFp output.

Thanks,


Stefano

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] averaging tracts?

2013-06-06 Thread Anastasia Yendiki



Hi Matt - Thanks for your kind words!

The merged_*.mgz file is just a 4D mgz file where each frame corresponds 
to one of the 18 tracts. The only special thing about this mgz file is 
that it has some special fields in its header that tell freeview how to 
display each tract (color, name, and threshold). I haven't tried this, but 
I would guess that if you performed any operation on that mgz file, those 
header fields would be preserved. And if they're not they should be, so we 
should know about it.


You can try to map each mgz file from individual DWI space to a common 
space with mri_vol2vol and then average them with mri_concat. Let us know 
if this ends up working or if you have any questions about these steps.


Thanks!
a.y

On Thu, 6 Jun 2013, Hoptman, Matthew wrote:



Hi all,

Thanks for tracula , which I think is a terrific tool.  Is there any way to
average tracts across subjects for viewing purposes?  I have in mind
somehting along the line of a group average merged_avg33_mni_bbi.mgz.

Thanks,

Matt

 

Matthew J. Hoptman, PhD
Research Scientist V
Nathan S. Kline Institute for Psychiatric Research

Research Associate Professor in Psychiatry
NYU School of Medicine

 

IMPORTANT NOTICE: This e-mail is meant only for the use of the intended
recipient. It may contain confidential information which is legally
privileged or otherwise protected by law. If you received this
e-mail in error or from someone who was not authorized to send it to you,
you are strictly prohibited from reviewing, using, disseminating,
distributing or copying the e-mail.

PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS
MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation.

 


Conserve Resources. Print only when necessary.

IMPORTANT NOTICE: This e-mail is meant only for the use of the intended
recipient. It may contain confidential information which is legally
privilegedor otherwise protected by law. If you received this e-mail in
error or from someone who is not authorized to send it to you, you are
strictly prohibited from reviewing, using, disseminating, distributing or
copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN
E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your
cooperation.

IMPORTANT NOTICE: This e-mail is meant only for the use of the intended
recipient. It may contain confidential information which is legally
privileged or otherwise protected by law. If you received this e-mail in
error or from someone who is not authorized to send it to you, you are
strictly prohibited from reviewing, using, disseminating, distributing or
copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN
E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your
cooperation.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] R: R: Re: R: Re: Tracula

2013-06-06 Thread Anastasia Yendiki



This issue has come up on the list a few times recently. Please search for 
your error in the email archives before posting to the list. Thanks.


On Thu, 6 Jun 2013, std...@virgilio.it wrote:


Hi Anastasia,

I have resolved the previous problem by writing configuration file with sudo
nano in command line.

Now I'm running trac-all -prep but I have this error:


writing registered surface 
to/Applications/freesurfer/subjects/subject_prova/Diff03/surf/rh.cvs.tocvs_av
g35.sphere.reg...
expanding nbhd size to 1
mris_resample: Command not found.

What's happened?

Thanks,


Stefano



Messaggio originale
Da: std...@virgilio.it
Data: 6-giu-2013 0.51
A: ayend...@nmr.mgh.harvard.edu
Cc: freesurfer@nmr.mgh.harvard.edu
Ogg: [Freesurfer] R: Re: R: Re: Tracula

I obtain /Applications/freesurfer/subjects/subject_prova
my DWI file is in Diff01, Diff02 ... that are in subject_prova folder.

Thanks,


Stefano


Messaggio originale
Da: ayend...@nmr.mgh.harvard.edu
Data: 6-giu-2013 0.42
A: std...@virgilio.it
Cc: freesurfer@nmr.mgh.harvard.edu
Ogg: Re: [Freesurfer] R: Re: Tracula


What do you get when you run echo $SUBJECTS_DIR?

On Thu, 6 Jun 2013, std...@virgilio.it wrote:

 Hi Anastasia,

 yes, I have check the SUBJECTS_DIR. I do not understand why all previous
 configuration file start normally and this no.
 Do you note some line that might be wrong additionally to setenv
 SUBJECTS_DIR line.


 Stefano



 Messaggio originale
 Da: ayend...@nmr.mgh.harvard.edu
 Data: 5-giu-2013 16.09
 A: std...@virgilio.it
 Cc: freesurfer@nmr.mgh.harvard.edu
 Ogg: Re: Tracula


 Is the setenv SUBJECTS_DIR line really commented out? You must set
 SUBJECTS_DIR, see the example configuration file on the wiki and under
 $FREESURFER_HOME/bin/dmrirc.example.

 On Wed, 5 Jun 2013, std...@virgilio.it wrote:

  Hi list and Anastasia,
  I'm performing a set of data with tracula version 3.0. I have change my
  dmrirc file respect to previous analyses and now I have one problem 
 
  set: Variable name must begin with a letter.
  ERROR: must specify as many DWI dicoms as subjects.
 
  I do not find the line that is wrong. I think to have approximately used
 the
  same lines of previous and correct analysis.
 
  I have attached the configuration file. Note that I'm using nii.gz.
 
  Thanks and best regards.
 
 
  Stefano
 
 


 The information in this e-mail is intended only for the person to whom it
is
 addressed. If you believe this e-mail was sent to you in error and the
 e-mail
 contains patient information, please contact the Partners Compliance
 HelpLine at
 http://www.partners.org/complianceline . If the e-mail was sent to you in
 error
 but does not contain patient information, please contact the sender and
 properly
 dispose of the e-mail.



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the
e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in
error
but does not contain patient information, please contact the sender and
properly
dispose of the e-mail.





___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Tracula

2013-06-05 Thread Anastasia Yendiki



Is the setenv SUBJECTS_DIR line really commented out? You must set 
SUBJECTS_DIR, see the example configuration file on the wiki and under 
$FREESURFER_HOME/bin/dmrirc.example.


On Wed, 5 Jun 2013, std...@virgilio.it wrote:


Hi list and Anastasia,
I'm performing a set of data with tracula version 3.0. I have change my
dmrirc file respect to previous analyses and now I have one problem 

set: Variable name must begin with a letter.
ERROR: must specify as many DWI dicoms as subjects.

I do not find the line that is wrong. I think to have approximately used the
same lines of previous and correct analysis.

I have attached the configuration file. Note that I'm using nii.gz.

Thanks and best regards.


Stefano

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] R: Re: Tracula

2013-06-05 Thread Anastasia Yendiki



What do you get when you run echo $SUBJECTS_DIR?

On Thu, 6 Jun 2013, std...@virgilio.it wrote:


Hi Anastasia,

yes, I have check the SUBJECTS_DIR. I do not understand why all previous
configuration file start normally and this no.
Do you note some line that might be wrong additionally to setenv
SUBJECTS_DIR line.


Stefano



Messaggio originale
Da: ayend...@nmr.mgh.harvard.edu
Data: 5-giu-2013 16.09
A: std...@virgilio.it
Cc: freesurfer@nmr.mgh.harvard.edu
Ogg: Re: Tracula


Is the setenv SUBJECTS_DIR line really commented out? You must set
SUBJECTS_DIR, see the example configuration file on the wiki and under
$FREESURFER_HOME/bin/dmrirc.example.

On Wed, 5 Jun 2013, std...@virgilio.it wrote:

 Hi list and Anastasia,
 I'm performing a set of data with tracula version 3.0. I have change my
 dmrirc file respect to previous analyses and now I have one problem 

 set: Variable name must begin with a letter.
 ERROR: must specify as many DWI dicoms as subjects.

 I do not find the line that is wrong. I think to have approximately used
the
 same lines of previous and correct analysis.

 I have attached the configuration file. Note that I'm using nii.gz.

 Thanks and best regards.


 Stefano




The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the
e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in
error
but does not contain patient information, please contact the sender and
properly
dispose of the e-mail.



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] tracula error

2013-05-21 Thread Anastasia Yendiki


Hi Skyler - When you say it's been working fine, have you checked that the 
orientations are correct by viewing dtifit_V1.nii.gz and dtifit_FA.nii.gz, 
like in the snapshot that I sent you? If those orientations aren't 
correct, the gradient table isn't correct either.

a.y

On Tue, 21 May 2013, Skyler Gabriel Shollenbarger wrote:

 Hi Anastasia,

 Thank you for all of your help! 'trac-all' has been working fine with 
 the other subjects, so it doesn't appear to be the gradient vector file. 
 Yes, unfortunately the resolution is not the best.

 Would you consider this subject a loss or are there other fixes you suggest?

 Thanks again!
 Skyler


 - Original Message -
 From: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu
 To: sholl...@uwm.edu
 Cc: freesurfer@nmr.mgh.harvard.edu
 Sent: Tuesday, May 21, 2013 10:40:59 AM
 Subject: Re: [Freesurfer] tracula error


 Hi Skyler - A couple of things. I'm attaching a screenshot of the FA map
 and primary tensor eigenvectors of your subject. First, it looks like your
 gradient directions are incorrect, given how the eigenvectors are oriented
 in the corpus callosum (yellow arrows in the coronal and axial slice). The
 eigenvectors follow the shape of the corpus callosum in the axial view but
 not in the coronal view. My guess is your gradient vectors need to be
 flipped in the z-direction.

 Second, your resolution is 4mm. There's going to be a lot of partial
 voluming. You'll have to give up on the thinner tracts, like ccg/cab (see
 purple arrow in sagittal view pointing to cingulum, you can barely resolve
 it from the corpus callosum).

 Third, you have 14 gradient directions, so fitting the ball-and-stick
 model to this data, which is done by bedpostx and which you need for the
 tract reconstruction step, is going to be challening.

 I don't want to discourage you, but tractography may be a bit more than
 this data can support.

 Please let me know if you have more questions,
 a.y

 On Mon, 20 May 2013, sholl...@uwm.edu wrote:

 Hi Anastasia,

 They were uploaded. Thanks for your help!

 Skyler

 Sent from my iPhone

 On May 20, 2013, at 10:20 AM, Anastasia Yendiki 
 ayend...@nmr.mgh.harvard.edu wrote:


 Hi Skyler - If you upload the dmri/dmri.bedpostX/dlabel/scripts directories 
 of your subject for me, I'll take a look.

 http://gate.nmr.mgh.harvard.edu/filedrop2/

 a.y

 On Fri, 17 May 2013, sholl...@uwm.edu wrote:

 Hi Anastasia,

 The brain mask looks fine. Any other suggestions?

 Thanks for your help,
 Skyler
 Sent from my iPhone

 On May 17, 2013, at 12:24 PM, Anastasia Yendiki 
 ayend...@nmr.mgh.harvard.edu wrote:


 Hi Skyler - How does the brain mask look like? Any major chunks of brain 
 missing in the area of the left uncinate? That's the tract where the 
 error occurs, and based on this info in the log file, I'm guessing it's a 
 masking issue:

 [...]
 INFO: Rejected 4221 streamlines for straying off mask
 INFO: Rejected 2 streamlines for reversing direction
 INFO: Rejected 9 streamlines as length outliers
 INFO: Have 56 total streamlines (min/mean/max length: 1/13/33)
 [...]

 Hope this helps,
 a.y

 On Wed, 15 May 2013, Skyler Gabriel Shollenbarger wrote:

 Hi all,

 We ran tracula prep stage and it exited with errors: 'Selected 
 streamline has fewer than 5 points'. We have attached the log and error 
 files if needed.

 Thank you in advance!
 Skyler


 The information in this e-mail is intended only for the person to whom it 
 is
 addressed. If you believe this e-mail was sent to you in error and the 
 e-mail
 contains patient information, please contact the Partners Compliance 
 HelpLine at
 http://www.partners.org/complianceline . If the e-mail was sent to you in 
 error
 but does not contain patient information, please contact the sender and 
 properly
 dispose of the e-mail.








___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Tracula problem



Hi Matt - Yes, the dcmroot variable can be used if you have the same root 
directory for *all* input files. If not, don't define dcmroot and instead 
give the full path to each input file. Then you shouldn't have to modify 
any scrips.


a.y

On Fri, 17 May 2013, Hoptman, Matthew wrote:


Hi Anastasia,
I solved this particular problem in a new dmrirc, but it seemed that I had to 
modify trac-all to remove the ${dcmroot} in front of:
infile, b0mfile and b0pfile:

diff bin/trac-preproc bin/trac-preproc.orig

   if ($#dcmroot  0) set infile = $infile
---

  if ($#dcmroot  0) set infile = $dcmroot/$infile

259c259
endif
---

endif

296c296
 set dcmfile = $b0mfile
---

set dcmfile = $dcmroot/$b0mfile

311c311
 set dcmfile = $b0pfile
---

set dcmfile = $dcmroot/$b0pfile


But now it doesn't seem to loop through the subjects, so I'm doing them one at 
a time (painful).

Also, if, as in my other question, I try to run this as a cluster job, I don't 
know how I can substitute a new subject into  subjlist.  I have 64 subjects and 
would like to do trac-all -prep -c dmri on all of them simultaneously.  I have 
used bedpostx in SGE, but there you can just write loop to get it to go through 
your subjects.

If I could make the subject variable external to dmrirc, I could do easily 
script the trac-all job to run in SGE, but I can't fiugre out how to pass it to 
the trac-all command.  Is there any way to pass the subject number directly to 
the command?
Does this make sense?
Matt

-Original Message-
From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
Sent: Friday, May 17, 2013 12:31 PM
To: Hoptman, Matthew
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Tracula problem


Hi Matt - Can you source try this on the command line:
   source dmrirc_53beta
   echo $b0mlist
   echo $b0plist

Are these filenames correct, do these files exist? This is how you define
them in your configuration file:
set b0mlist = (`ls ${subjlist}/fmag/MR.* | sort -n | head -1`)
set b0plist = (`ls ${SUBJECTS_DIR}/${subjlist}/fphas/ | sort -n | head -1`)

Thanks,
a.y

On Wed, 15 May 2013, Hoptman, Matthew wrote:



Hi all,



I’m having a problem with tracula.  I’m trying to run in version 5.3 beta (is 
that
version very different from the newer 5.3?).  If I run

trac-preproc   -c dmrirc –prep,


I get:

mri_convert /home/hoptman/freesurfer/subjects/c159032/
/home/hoptman/freesurfer/subjects/c159032/dmri/b0mag.nii.gz

mri_convert /home/hoptman/freesurfer/subjects/c159032/
/home/hoptman/freesurfer/subjects/c159032/dmri/b0mag.nii.gz

corRead(): can't open file /home/hoptman/freesurfer/subjects/c159032/COR-.info



I don’t know why it would look for COR-.info in the subjects’ root directory.  
I’m
attaching my dmrirc file in case that helps.



Thanks,
Matt

Matthew J. Hoptman, PhD
Research Scientist V
Nathan S. Kline Institute for Psychiatric Research

Research Associate Professor in Psychiatry
NYU School of Medicine



IMPORTANT NOTICE: This e-mail is meant only for the use of the intended 
recipient.
It may contain confidential information which is legally privileged or otherwise
protected by law. If you received this
e-mail in error or from someone who was not authorized to send it to you, you 
are
strictly prohibited from reviewing, using, disseminating, distributing or 
copying
the e-mail.

PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS 
MESSAGE
FROM YOUR SYSTEM. Thank you for your cooperation.



__
Conserve Resources. Print only when necessary.

IMPORTANT NOTICE: This e-mail is meant only for the use of the intended 
recipient.
It may contain confidential information which is legally privilegedor otherwise
protected by law. If you received this e-mail in error or from someone who is 
not
authorized to send it to you, you are strictly prohibited from reviewing, using,
disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY 
OF
THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you 
for
your cooperation.

IMPORTANT NOTICE: This e-mail is meant only for the use of the intended 
recipient.
It may contain confidential information which is legally privileged or otherwise
protected by law. If you received this e-mail in error or from someone who is 
not
authorized to send it to you, you are strictly prohibited from reviewing, using,
disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY 
OF
THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you 
for
your cooperation.




The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error

Re: [Freesurfer] DTI metrics along the whole tract?


Hi Celine - The way this average is computed for pathstats.byvoxel.txt is 
by averaging the values for each one of the sample paths that are drawn by 
the MCM algorithm. This essentially weighted sinced voxels that more 
sample paths go through will be counted more than voxels that fewer sample 
paths go through.

a.y

On Fri, 17 May 2013, cel...@nmr.mgh.harvard.edu wrote:

 Hi Anastasia
 I am very sorry I didn't see this email so it may be a doubloon with my
 question I just post.
 Indeed I am interested in a profile of the DTI metrics along the tract. So
 if I take the average value of each section it can give me a kind of
 profile, and so I was just wondering if taking a weighted metrics would be
 possible in order to remove values that are a bit far from the highest
 probability of the tract.
 Thanks a lot!
 Celine


 Hi Celine - Since 5.2, there are 2 types of measures in the
 pathstats.byvoxel.txt file: The value at every point along the trajectory
 sampled at roughly the center of the bundle, or the value at every point
 along the trajectory averaged over the width of the bundle. Sorry, there
 are no other measures available at this point. If I understand correctly,
 you would like to see something like a profile of the measure of interest
 at every point along the trajectory?

 a.y

 On Mon, 6 May 2013, cel...@nmr.mgh.harvard.edu wrote:

 Hi Tracula team
 I am using tracula to study the corticospinal tract in a patient
 population. I am wondering if there would be a way to have the different
 DTI metrics from the whole tract at different depth/portion of the
 tracts.
 Something like the information given by the pathstats.byvoxel.txt file,
 but for the whole width of the tract?
 If not, do you see a way to sample the value of the diffusion metrics on
 a
 certain tract starting from the cortex (like with projfrac or projdist
 with the WM surface)?
 Thanks very much for your help
 Celine










___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Tracula longitudinal nan values for highest probability path


Hi Vincent - Thanks for bringing this to my attention. I can see what 
might cause this glitch (only in the longitudinal case) and I'll fix it in 
the next version.

In the meantime, if you delete one of the two identical lines from 
cpts.map.txt, and then rerun the dmri_pathstats command line that you'll 
find in the trac-all.log of your subject, it should regenerate the stats 
files correctly. Sorry for the inconvenience.

a.y

On Fri, 17 May 2013, vbrun...@nmr.mgh.harvard.edu wrote:

 Dear Anastasia,

 When running the longitudinal tracula version on our 39 subjects I found
 for some of them nan-values for the center_avg variables of some tracts.
 When I have a look at the tract distribution and the highest probability
 path, everything seems to be ok. However, when checking the control points
 of this path, two of them are the same. Do you know how this could have
 happened / what to do?

 E.g. control points of forceps major from a subject (cpts.map.txt), see
 4th and 5th control point:

 63 20 39
 67 31 39
 59 43 38
 52 42 38
 52 42 38
 43 32 38
 50 19 33

 And the respective pathstats.overall.txt:
 Count 1500
 Volume 370
 Len_Min 62
 Len_Max 99
 Len_Avg 78.9307
 Len_Center 0
 AD_Avg 0.00155598
 AD_Avg_Weight 0.00158424
 AD_Avg_Center -nan
 RD_Avg 0.000438439
 RD_Avg_Weight 0.000401328
 RD_Avg_Center -nan
 MD_Avg 0.000810952
 MD_Avg_Weight 0.000795633
 MD_Avg_Center -nan
 FA_Avg 0.662419
 FA_Avg_Weight 0.696257
 FA_Avg_Center -nan

 Thanks for your help!! :)
 Best,
 Vincent

 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Tracula longitudinal nan values for highest probability path


Hi Vincent - If you upload the tracula dirs for this particular time 
point, I'll take a look.

a.y

On Mon, 20 May 2013, Vincent Brunsch wrote:

 Hi Anastasia,
 Thanks for your help! I had this issue with 4 tracts in total. I just want to 
 add that before rerunning dmri_pathstats not only pathstats.overall but also 
 pathstats.byvoxel was affected (in the latter there were no matrix entries at 
 all).
 I found some information in the trac-all.log but not explicitly the command 
 line - this was found in pathstats.overall.txt, though.

 After rerunning dmri_pathstats everything looks great now for 3 out of the 4 
 tracts, YEAH! I am not sure what to do with the last one, though: Here, the 
 same error occurs but in cpts.map.txt no two lines are identical:

 For lh.cst:
 58 48 10
 62 51 21
 65 55 26
 70 58 35
 72 57 39
 64 55 56

 Would you suggest deleting randomly one time point for this tract of this 
 subject? Thanks!
 Vincent


 Am 5/20/2013 10:31 AM, schrieb Anastasia Yendiki:
 
 Hi Vincent - Thanks for bringing this to my attention. I can see what might 
 cause this glitch (only in the longitudinal case) and I'll fix it in the 
 next version.
 
 In the meantime, if you delete one of the two identical lines from 
 cpts.map.txt, and then rerun the dmri_pathstats command line that you'll 
 find in the trac-all.log of your subject, it should regenerate the stats 
 files correctly. Sorry for the inconvenience.
 
 a.y
 
 On Fri, 17 May 2013, vbrun...@nmr.mgh.harvard.edu wrote:
 
 Dear Anastasia,
 
 When running the longitudinal tracula version on our 39 subjects I found
 for some of them nan-values for the center_avg variables of some tracts.
 When I have a look at the tract distribution and the highest probability
 path, everything seems to be ok. However, when checking the control points
 of this path, two of them are the same. Do you know how this could have
 happened / what to do?
 
 E.g. control points of forceps major from a subject (cpts.map.txt), see
 4th and 5th control point:
 
 63 20 39
 67 31 39
 59 43 38
 52 42 38
 52 42 38
 43 32 38
 50 19 33
 
 And the respective pathstats.overall.txt:
 Count 1500
 Volume 370
 Len_Min 62
 Len_Max 99
 Len_Avg 78.9307
 Len_Center 0
 AD_Avg 0.00155598
 AD_Avg_Weight 0.00158424
 AD_Avg_Center -nan
 RD_Avg 0.000438439
 RD_Avg_Weight 0.000401328
 RD_Avg_Center -nan
 MD_Avg 0.000810952
 MD_Avg_Weight 0.000795633
 MD_Avg_Center -nan
 FA_Avg 0.662419
 FA_Avg_Weight 0.696257
 FA_Avg_Center -nan
 
 Thanks for your help!! :)
 Best,
 Vincent
 
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 
 
 
 
 



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] TRACULA outputs out of expected range


Hi Ali - The last row of your gradient table is 0 0 0. And yet, based on 
the b-value table, it is supposed to correspond to a diffusion-weighted 
volume with b=800. So there must have been a diffusion-encoding gradient 
vector that was applied to acquire that volume, and you need to find out 
what that gradient vector was and put it in that line.

Also, some of the lines in the gradient table follow the Xe-Y notation and 
some don't. I don't know if this will cause a problem, it's possible that 
it might depending on the platform. In any case, it's good to be 
consistent to be safe.

Hope this helps,
a.y

On Mon, 6 May 2013, Ali Ezzati wrote:

 Hi Anastasia,

 I think I still have the previous problem of out of range outputs. For 
 example: based on literature ( your previous TRACULA-bases articles) the 
 expected range of mean FA value is around 0.4-0.5, but the average FA for my 
 data is 0.7-0.8. The same is true with MD, RD, AD values. Comparative 
 analysis between groups is not promising too. This makes me think something 
 is going wrong with my analysis/settings, although I get no error during 
 processing.

 I can only think of settings in .dmricr or bvec file to be a source of error, 
 so I have attached a sample of them for one of the subjects to this email. I 
 would be grateful if you could take a look at them and let me know if they 
 are as expected. 

 There are 3 .bvec files inside the dmri folder: 
 1- dwi_orig.mghdti.bvecs
 2- bvecs.norot
 3- bvecs
 The first 2 files are the same as my input .bvec file (bvecs.norot is 
 rotated to 3 rows instead of 3 columns).
 File 3 -bevecs- is different from the other 2 files.


 Thank you again for your help,
 Ali
 
 From: Ali Ezzati
 Sent: Friday, May 03, 2013 11:54 AM
 To: Anastasia Yendiki
 Cc: freesurfer@nmr.mgh.harvard.edu
 Subject: RE: [Freesurfer] TRACULA outputs out of expected range

 Hi Anastasia,

 Thank you for your response. I think I figured out what was the problem:  The 
 delimiter for the 3 column .bvec file MUST be SPACE/TAB, otherwise the 
 program fails to reshape it correctly. In my case the delimiter was , and 
 the program was reading only the 1st column of it.

 I have one more question:   I know that FA values might differ from study to 
 study and from MRI to MRI, but what is a reasonable range for that after 
 analysis with Tracula?  In your study (20011) the range was ~ 0.3-0.6. But 
 for in elderly population the average is around 0.2 higher. Does it sound 
 normal to you? I was not able to find any study using your method in elderly 
 population for comparison.

 Thank you,
 Ali
 
 From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu]
 Sent: Tuesday, April 30, 2013 3:11 PM
 To: Ali Ezzati
 Cc: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] TRACULA outputs out of expected range

 Hi Ali - This is unusual. It may have something to do with system
 settings. Can you send an example of the two versions of the bvecs files
 that have the different values?

 Thanks,
 a.y

 On Mon, 29 Apr 2013, Ali Ezzati wrote:

 Hello Experts,
 I would be grateful if you could help me with this problem:

 I was able to run all steps of TRACULA on several subjects without any error 
 message, but all the final
 outcomes (FA,MD,RD,AD values) are out of the expected range (i.e average FA 
 values for all tracts are 1).

 I tried to identify the source of this problem... clearly FA values in 
 dmri/dtifit_FA, which is an output
 of  prep step are all out of range. The only source of error that I can 
 think of is .bvecs file. My input
 .bvecs files are in 3 columns, exactly as described in the manual.

 There are two .bvecs file in the dmri folder. one is 
 dwi_orig.mghdti.bvecs which is exactly the same as
 my input .bvecs file and the other one's name is just bvecs, which has 
 completely different values. Could
 this be the source of my problem? or something else is causing this.

 Thank you,
 Ali






 The information in this e-mail is intended only for the person to whom it is
 addressed. If you believe this e-mail was sent to you in error and the e-mail
 contains patient information, please contact the Partners Compliance HelpLine 
 at
 http://www.partners.org/complianceline . If the e-mail was sent to you in 
 error
 but does not contain patient information, please contact the sender and 
 properly
 dispose of the e-mail.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] incomplete forceps



Hi Benjamin - This means that the initial guess for the path based on the 
atlas average is way off, due to poor alignment between your subject and 
the atlas subejcts. Ways to get around this is to look into the options 
for registration, whether diffusion-to-anatomical or anatomical-to-atlas, 
and to increase the number of control points used for fminor.


Hope this helps,
a.y

On Mon, 6 May 2013, Roschinski, Benjamin wrote:


Dear Freesurfer experts,

we have a problem with the forceps.
After the first trac-all we had a forcpes minor with a really unusually 
structure so we tried to fix it with an rerun of the trac-all.
The result was a forceps minor with a third thigh in the sagittal axis.
We did a second rerun and now the forceps minor normalized.
Our problem is that we don´t know if we should do more trac-all reruns by other 
patients with difficult tracula or how we should interpret this result.
Do you have any ideas to solve this?
The second problem is that we have many many  tracula results with incomplete 
forcepes minor or major.
We know that the forcepes are the most difficult tracts because of the 
curvature but do you have some ideas to fix that problem?

Kind regards
Benjamin


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] DTI metrics along the whole tract?


Hi Celine - Since 5.2, there are 2 types of measures in the 
pathstats.byvoxel.txt file: The value at every point along the trajectory 
sampled at roughly the center of the bundle, or the value at every point 
along the trajectory averaged over the width of the bundle. Sorry, there 
are no other measures available at this point. If I understand correctly, 
you would like to see something like a profile of the measure of interest 
at every point along the trajectory?

a.y

On Mon, 6 May 2013, cel...@nmr.mgh.harvard.edu wrote:

 Hi Tracula team
 I am using tracula to study the corticospinal tract in a patient
 population. I am wondering if there would be a way to have the different
 DTI metrics from the whole tract at different depth/portion of the tracts.
 Something like the information given by the pathstats.byvoxel.txt file,
 but for the whole width of the tract?
 If not, do you see a way to sample the value of the diffusion metrics on a
 certain tract starting from the cortex (like with projfrac or projdist
 with the WM surface)?
 Thanks very much for your help
 Celine




___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] tracula error


Hi Skyler - How does the brain mask look like? Any major chunks of brain 
missing in the area of the left uncinate? That's the tract where the error 
occurs, and based on this info in the log file, I'm guessing it's a 
masking issue:

[...]
INFO: Rejected 4221 streamlines for straying off mask
INFO: Rejected 2 streamlines for reversing direction
INFO: Rejected 9 streamlines as length outliers
INFO: Have 56 total streamlines (min/mean/max length: 1/13/33)
[...]

Hope this helps,
a.y

On Wed, 15 May 2013, Skyler Gabriel Shollenbarger wrote:

 Hi all,

 We ran tracula prep stage and it exited with errors: 'Selected streamline has 
 fewer than 5 points'. We have attached the log and error files if needed.

 Thank you in advance!
 Skyler


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Tracula problem