[Freesurfer] correct thinking?

[Marja Caverlé]

Hi guys,

I just wanted to make sure I am understanding everything correct.
I have done recon -all -all on all my subjects. Can I now just use the
numbers in the .stats files to compare these with my other measures?

It seems to be very (almost too) simple, so I that's why I am checking to
see whether I am correct.

Thanks,

Marja
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Re: [Freesurfer] Tracula skip steps

[Jacobs H (NP)]

Aha, Ok, I will try to get my hands on that data and give it a go.
Thanks for the help!
Heidi

On 6/1/16, 4:01 AM, "Anastasia Yendiki" 
wrote:

>
>The input needs to be the diffusion-weighted images, not the FA, MD, etc.
>There should be as many volumes in this input nifti as there are b-values
>in bval file and gradient vectors in the bvec file. The image
>registration, tractography, etc etc is performed on the
>diffusion-weighted
>images, not on the FA, MD, etc. The FA, MD, etc are used only in the very
>end, to extract FA, MD, etc for each tract. But to get the tracts in the
>first place, you need the images.
>
>On Tue, 31 May 2016, Jacobs H (NP) wrote:
>
>> Yes, each nifti contains one volume. I have different nifti’s for the
>> different metrics (FA, MD,..)
>> Is there a way I can use the trac-all on these files?
>>
>> On 5/31/16, 9:26 PM, "Anastasia Yendiki" 
>> wrote:
>>
>>>
>>> Some of the errors make me suspect that your input DWI files contain
>>>only
>>> one volume. Could this be the case?
>>>
>>> On Tue, 31 May 2016, Jacobs H (NP) wrote:
>>>
 Hmm, weird, as I put a #  in front of it. Putting the eddy current to
0
 gives the same error. Enclosed is the config file.
 Thank you so much
 Heidi

 On 5/31/16, 8:13 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf
 of
 Anastasia Yendiki" >>>of
 ayend...@nmr.mgh.harvard.edu> wrote:

>
> Hi Heidi - It knows where to find the freesurfer recons of the T1's
> from
> SUBJECTS_DIR (see example config file). Based on your log file, it
> looks
> like you haven't turned off the eddy current compensation, because
>it's
> trying to run it. If you attach your config file, I'll take a look.
>
> Best,
> a.y
>
> On Tue, 31 May 2016, Jacobs H (NP) wrote:
>
>> Thanks! I tried to adapt the configuration file and it got a bit
>> further,
>> but then crashes again. Not sure why? I have added the log file, so
>> that
>> maybe you could have a look at what is happening?
>> Also, how does the trac-all command knows where to find the T1 data?
>> Thanks
>> Heidi
>>
>> On 5/31/16, 5:07 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on
>>behalf
>> of
>> Anastasia Yendiki" > of
>> ayend...@nmr.mgh.harvard.edu> wrote:
>>
>>>
>>> No, it should be pointed to the DWI data, which can be corrected
>>> niftis
>>> instead of the original dicoms. I would recommend turning off all
>>>the
>>> corrections in the configuration file, and then running everything
>>> without
>>> skipping steps. This will create all the files that are expected to
>>> be
>>> there for the registration.
>>>
>>> On Tue, 31 May 2016, Jacobs H (NP) wrote:
>>>
 Dear Anastasia,

 Thanks for the feedback. So, does this mean that the dcm root
should
 be
 pointed towards the T1¹s? I have the FreeSurfer recon-all output
in
 a
 different folder.
 Enclosed is the log file (of one subject) and the configuration
 file.
 You
 will see that I tried the inter and intra option, because I
thought
 that
 for the inter it would not need anything else than the MNI
template
 and
 the DTI images.

 Thanks

 Best
 Heidi

 On 5/31/16, 4:01 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on
 behalf
 of
 Anastasia Yendiki" >>>behalf
 of
 ayend...@nmr.mgh.harvard.edu> wrote:

>
> Hi Heidi - The intra-subject registration step that you're trying
> to
> run
> registers your subject's DWI and T1 images. It expects to find
> those
> images. It doesn't use the FA, MD, etc in any way.
>
> Did the log file get created in scripts/trac-all.log? If so, can
> you
> please send that file and your configuration file? Thanks!
>
> a.y
>
> On Tue, 31 May 2016, Jacobs H (NP) wrote:
>
>> Dear FreeSurfers,
>>
>> The data I have is preprocessed, so I have the all the metrics
>> (FA,
>> MD,
>> L1, L2, L3,..) in nifti format.
>> On this data I would like to start tracula starting from step
>>1.3.
>>
>> I have organized the data as mentioned on the wiki:
>> For example:
>> / dtifit_FA.nii.gz
>>
>> I have also filled in the configuration file, canceling out the
>> things
>> I don¹t need and then I tried to run:
>> Trac-all ­intra ­c 
>>
>> Unfortunately, it does not work, it says: dcmlist: subscript out
>> of
>> range
>>
>> I do not have the original filesŠ is there a way that I can get
>

Re: [Freesurfer] Tracula skip steps

[Anastasia Yendiki]

The input needs to be the diffusion-weighted images, not the FA, MD, etc. 
There should be as many volumes in this input nifti as there are b-values 
in bval file and gradient vectors in the bvec file. The image 
registration, tractography, etc etc is performed on the diffusion-weighted 
images, not on the FA, MD, etc. The FA, MD, etc are used only in the very 
end, to extract FA, MD, etc for each tract. But to get the tracts in the 
first place, you need the images.


On Tue, 31 May 2016, Jacobs H (NP) wrote:


Yes, each nifti contains one volume. I have different nifti’s for the
different metrics (FA, MD,..)
Is there a way I can use the trac-all on these files?

On 5/31/16, 9:26 PM, "Anastasia Yendiki" 
wrote:



Some of the errors make me suspect that your input DWI files contain only
one volume. Could this be the case?

On Tue, 31 May 2016, Jacobs H (NP) wrote:


Hmm, weird, as I put a #  in front of it. Putting the eddy current to 0
gives the same error. Enclosed is the config file.
Thank you so much
Heidi

On 5/31/16, 8:13 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf
of
Anastasia Yendiki"  wrote:



Hi Heidi - It knows where to find the freesurfer recons of the T1's
from
SUBJECTS_DIR (see example config file). Based on your log file, it
looks
like you haven't turned off the eddy current compensation, because it's
trying to run it. If you attach your config file, I'll take a look.

Best,
a.y

On Tue, 31 May 2016, Jacobs H (NP) wrote:


Thanks! I tried to adapt the configuration file and it got a bit
further,
but then crashes again. Not sure why? I have added the log file, so
that
maybe you could have a look at what is happening?
Also, how does the trac-all command knows where to find the T1 data?
Thanks
Heidi

On 5/31/16, 5:07 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf
of
Anastasia Yendiki"  wrote:



No, it should be pointed to the DWI data, which can be corrected
niftis
instead of the original dicoms. I would recommend turning off all the
corrections in the configuration file, and then running everything
without
skipping steps. This will create all the files that are expected to
be
there for the registration.

On Tue, 31 May 2016, Jacobs H (NP) wrote:


Dear Anastasia,

Thanks for the feedback. So, does this mean that the dcm root should
be
pointed towards the T1¹s? I have the FreeSurfer recon-all output in
a
different folder.
Enclosed is the log file (of one subject) and the configuration
file.
You
will see that I tried the inter and intra option, because I thought
that
for the inter it would not need anything else than the MNI template
and
the DTI images.

Thanks

Best
Heidi

On 5/31/16, 4:01 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on
behalf
of
Anastasia Yendiki"  wrote:



Hi Heidi - The intra-subject registration step that you're trying
to
run
registers your subject's DWI and T1 images. It expects to find
those
images. It doesn't use the FA, MD, etc in any way.

Did the log file get created in scripts/trac-all.log? If so, can
you
please send that file and your configuration file? Thanks!

a.y

On Tue, 31 May 2016, Jacobs H (NP) wrote:


Dear FreeSurfers,

The data I have is preprocessed, so I have the all the metrics
(FA,
MD,
L1, L2, L3,..) in nifti format.
On this data I would like to start tracula starting from step 1.3.

I have organized the data as mentioned on the wiki:
For example:
/ dtifit_FA.nii.gz

I have also filled in the configuration file, canceling out the
things
I don¹t need and then I tried to run:
Trac-all ­intra ­c 

Unfortunately, it does not work, it says: dcmlist: subscript out
of
range

I do not have the original filesŠ is there a way that I can get
the
script working?

Many thanks.
Heidi










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[Freesurfer] mri_cc

[Arash Nazeri]

Dear Freesurfer experts,

Sorry for resending this post.

mri_cc does not seem to be working properly to parcellate corpus callosum.
As per one of the previous posts, there is a bug in the current release of
mri_cc. However, the link provided in the same thread for an updated
version of mri_cc is no longer existent. Our cluster runs on 64bit Ubuntu
14.04 systems. I'd be grateful if someone can post a new link for the
corrected mri_cc.

Thanks in advance.

Cheers,

Arash
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Re: [Freesurfer] Extracting White Matter Structures without using Tracula

[Syeda Wajiha Maryam]

Hi Bruce,

Our main concern is that we will be incorporating additional sources of
error by doing so! But it seems there is no way to get around it.

Thanks for the prompt response!
Maryam


On Tue, May 31, 2016 at 7:07 PM, Bruce Fischl 
wrote:

> Hi Maryam
>
> why don't you want to use tracula? That is what it is designed for
>
> cheers
> Bruce
> On Tue,
> 31 May 2016, Syeda Wajiha Maryam wrote:
>
> > Hello Freesurfer experts,
> >
> > I am looking to extract certain white matter pathways (for instance, the
> > superior longitudinal fasciculus, uncinate fasciculus) with freesurfer
> which
> > I believe are affected by Alzheimer's Disease. But it seems that these
> can
> > only be obtained by performing tractography using Tracula. I was
> wondering
> > if there was some other way to obtain the labels for these structures
> > without having to do so?
> >
> > Thanks in advance.
> >
> > Regards,
> > Maryam
> >
> >
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>
>
> The information in this e-mail is intended only for the person to whom it
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> addressed. If you believe this e-mail was sent to you in error and the
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> contains patient information, please contact the Partners Compliance
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> properly
> dispose of the e-mail.
>
>
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Re: [Freesurfer] Extracting White Matter Structures without using Tracula

[Bruce Fischl]

Hi Maryam

why don't you want to use tracula? That is what it is designed for

cheers
Bruce
On Tue, 
31 May 2016, Syeda Wajiha Maryam wrote:

> Hello Freesurfer experts,
> 
> I am looking to extract certain white matter pathways (for instance, the
> superior longitudinal fasciculus, uncinate fasciculus) with freesurfer which
> I believe are affected by Alzheimer's Disease. But it seems that these can
> only be obtained by performing tractography using Tracula. I was wondering
> if there was some other way to obtain the labels for these structures
> without having to do so?
> 
> Thanks in advance.
> 
> Regards,
> Maryam
> 
>
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[Freesurfer] Extracting White Matter Structures without using Tracula

[Syeda Wajiha Maryam]

Hello Freesurfer experts,

I am looking to extract certain white matter pathways (for instance, the
superior longitudinal fasciculus, uncinate fasciculus) with freesurfer
which I believe are affected by Alzheimer's Disease. But it seems that
these can only be obtained by performing tractography using Tracula. I was
wondering if there was some other way to obtain the labels for these
structures without having to do so?

Thanks in advance.

Regards,
Maryam
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Re: [Freesurfer] WM & GM Parcellation Edit

[Bruce Fischl]

I see. Can you tell us a bit about the input data? It looks pretty blurry. 
I suspect that you have topological defects that are incorrectly fixed in 
those regions, probably because a bunch of the white matter was missed. Is 
the white matter significantly darker than 110 there? You could try some 
control points in those region (in the interior of the wm, but where it is 
<<110, say in the 90s or so)


Alternatively, if you upload the subject we will take a look.

On Tue, 31 May 2016, Limachia, Gaurang (NIH/NINDS) 
[F] wrote:



Hi Bruce,

I am attaching a zoomed in version which will hopefully will show what we
are trying to do.

Thanks,

Shyam

On 5/31/16, 4:20 PM, "Bruce Fischl"  wrote:


Hi Shyam

it's hard to give you an answer unless I understand what the source of
your inaccuracy is. Perhaps you can point an image that is zoomed in on a
region with arrows to indicate where you think things need improving? I
don't really understand your image. If the green circles are control
points, then they are definitely in the wrong place and will mess
everything up. Typically we place control points in the white matter
where
the intensity in the brain.mgz volume is <110, so typically near the
gray/white boundary (but not close enough to be voxels that have some
gray
matter in them).

cheers
Bruce



On
Tue, 31 May 2016, Limachia, Gaurang (NIH/NINDS) [F] wrote:


Yes the green circles are control points. The control points shown in
the
picture show surfaces we feel are not accurate.

Additionally, how are we supposed to use the control points, do we place
them on the inner most boundary of the WM?

Also, going back to the original questions: How do you recommend that we
proceed to obtain the most accurate results?
Should we continue making changes to the wm.mgz file as well as adding
control points, or is it sufficient just to add control points?


Thanks,

Shyam

On 5/31/16, 3:33 PM, "Bruce Fischl"  wrote:


Hi Shyam

can you add arrows to show where you don't think the surfaces are
accurate?

And are the green circles meant to be control points? If so, I'm
surprised that didn't break everything since they need to be added to
the
interior of the WM.

cheers
Bruce


On Tue, 31 May 2016, Limachia,
Gaurang (NIH/NINDS) [F] wrote:


Hi freesurfer community,

We are checking to see the accuracy of our subjects¹ white and gray
matter
parcellation. We have found that for some subjects the contour lines
for
white matter surface and pial surface are somewhat inaccurate, and
have
been
making modifications using the tutorials.

Specifically, we made changes to the white matter wm.mgz file; this
however
did not alter the contour lines. We also used control points, and were
able
to see changes to the white matter surface contour lines using this
approach.

How do you recommend that we proceed to obtain the most accurate
results?
Should we continue making changes to the wm.mgz file as well as adding
control points, or is it sufficient just to add control points?

I am attaching a screen shot which shows changes to the contour lines
after
we added control points.

Best Regards,

Shyam [IMAGE][IMAGE]




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Re: [Freesurfer] Tracula skip steps

[Jacobs H (NP)]

Yes, each nifti contains one volume. I have different nifti’s for the
different metrics (FA, MD,..)
Is there a way I can use the trac-all on these files?

On 5/31/16, 9:26 PM, "Anastasia Yendiki" 
wrote:

>
>Some of the errors make me suspect that your input DWI files contain only
>one volume. Could this be the case?
>
>On Tue, 31 May 2016, Jacobs H (NP) wrote:
>
>> Hmm, weird, as I put a #  in front of it. Putting the eddy current to 0
>> gives the same error. Enclosed is the config file.
>> Thank you so much
>> Heidi
>>
>> On 5/31/16, 8:13 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf
>>of
>> Anastasia Yendiki" > ayend...@nmr.mgh.harvard.edu> wrote:
>>
>>>
>>> Hi Heidi - It knows where to find the freesurfer recons of the T1's
>>>from
>>> SUBJECTS_DIR (see example config file). Based on your log file, it
>>>looks
>>> like you haven't turned off the eddy current compensation, because it's
>>> trying to run it. If you attach your config file, I'll take a look.
>>>
>>> Best,
>>> a.y
>>>
>>> On Tue, 31 May 2016, Jacobs H (NP) wrote:
>>>
 Thanks! I tried to adapt the configuration file and it got a bit
 further,
 but then crashes again. Not sure why? I have added the log file, so
that
 maybe you could have a look at what is happening?
 Also, how does the trac-all command knows where to find the T1 data?
 Thanks
 Heidi

 On 5/31/16, 5:07 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf
 of
 Anastasia Yendiki" >>>of
 ayend...@nmr.mgh.harvard.edu> wrote:

>
> No, it should be pointed to the DWI data, which can be corrected
>niftis
> instead of the original dicoms. I would recommend turning off all the
> corrections in the configuration file, and then running everything
> without
> skipping steps. This will create all the files that are expected to
>be
> there for the registration.
>
> On Tue, 31 May 2016, Jacobs H (NP) wrote:
>
>> Dear Anastasia,
>>
>> Thanks for the feedback. So, does this mean that the dcm root should
>> be
>> pointed towards the T1¹s? I have the FreeSurfer recon-all output in
>>a
>> different folder.
>> Enclosed is the log file (of one subject) and the configuration
>>file.
>> You
>> will see that I tried the inter and intra option, because I thought
>> that
>> for the inter it would not need anything else than the MNI template
>> and
>> the DTI images.
>>
>> Thanks
>>
>> Best
>> Heidi
>>
>> On 5/31/16, 4:01 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on
>>behalf
>> of
>> Anastasia Yendiki" > of
>> ayend...@nmr.mgh.harvard.edu> wrote:
>>
>>>
>>> Hi Heidi - The intra-subject registration step that you're trying
>>>to
>>> run
>>> registers your subject's DWI and T1 images. It expects to find
>>>those
>>> images. It doesn't use the FA, MD, etc in any way.
>>>
>>> Did the log file get created in scripts/trac-all.log? If so, can
>>>you
>>> please send that file and your configuration file? Thanks!
>>>
>>> a.y
>>>
>>> On Tue, 31 May 2016, Jacobs H (NP) wrote:
>>>
 Dear FreeSurfers,

 The data I have is preprocessed, so I have the all the metrics
(FA,
 MD,
 L1, L2, L3,..) in nifti format.
 On this data I would like to start tracula starting from step 1.3.

 I have organized the data as mentioned on the wiki:
 For example:
 / dtifit_FA.nii.gz

 I have also filled in the configuration file, canceling out the
 things
 I don¹t need and then I tried to run:
 Trac-all ­intra ­c 

 Unfortunately, it does not work, it says: dcmlist: subscript out
of
 range

 I do not have the original filesŠ is there a way that I can get
the
 script working?

 Many thanks.
 Heidi

>>

>>


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Re: [Freesurfer] working with cluster annotations in fs-fast

[Douglas N Greve]

We precluded the use of mris_anatomical_stats with fsaverage because by 
default it will not compute the area appropriately. You can use 
mri_segstats with --annot fsaverage lh yourparc --i 
$SUBJECTS_DIR/fsaverage/surf/lh.white.avg.area.mgh --accumulate --sum 
summary.stats



On 05/31/2016 04:31 PM, Abigail Noyce wrote:
> Hi folks,
>
> I'm trying to split a cluster from mri_glmfit-sim into two separate
> regions. (Ginormous blob of activation across multiple structures of
> interest...)
>
> I've gotten to the point of generating a new annotation with the
> separate labels for my separate regions, but am stuck getting a
> "cluster size" for the new labels. It looks like one can't use
> mris_anatomical_stats on fsaverage... but something like that must be
> happening inside of mri_glmfit-sim to get cluster sizes? What's the
> best way to get these values for my new annotation? (Or is this a
> terrible idea for some reason I haven't yet considered?)
>
> Thanks!
> Abby Noyce
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] recon-all with input T1s at different resolutions

[Bruce Fischl]

yes, typically it is a mistake that we want to catch

cheers
Bruce
On Tue, 31 May 2016, 
Satrajit Ghosh wrote:

> thank you doug, martin, and bruce.
> martin: i believe she was doing this for motion correction
> 
> i've attached the error this person observed below. so it does seem that
> mri_robust_template at present doesn't do any resampling.
> 
> bruce: we can definitely see ways in which this could be done outside
> recon-all and then sent to recon-all as a single image. but i just wanted to
> verify that the error we were observing was expected behavior at present.
> 
> cheers,
> 
> satra
> 
> 
> RuntimeError: Command:
> mri_robust_template --satit --average 1 --fixtp --mov /Volumes/LaCie/RaquelA
> lmeida/workflow_dir/workflow_dir/l1workflow/ReconAll/AutoRecon1/_subject_id_
> 006_S_4150/T1_prep/mapflow/_T1_prep0/001.mgz /Volumes/LaCie/RaquelAlmeida/wo
> rkflow_dir/workflow_dir/l1workflow/ReconAll/AutoRecon1/_subject_id_006_S_415
> 0/T1_prep/mapflow/_T1_prep1/002.mgz /Volumes/LaCie/RaquelAlmeida/workflow_di
> r/workflow_dir/l1workflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep
> /mapflow/_T1_prep2/003.mgz /Volumes/LaCie/RaquelAlmeida/workflow_dir/workflo
> w_dir/l1workflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/
> _T1_prep3/004.mgz /Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1w
> orkflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep4
> /005.mgz --inittp 1 --iscale --noit --template rawavg.mgz --iscaleout 001-is
> cale.txt 002-iscale.txt 003-iscale.txt 004-iscale.txt 005-iscale.txt --subsa
> mple 200 --lta 001.lta 002.lta 003.lta 004.lta 005.lta
> Standard output:
> $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $
> 
> --satit: Will estimate SAT iteratively!
> --average: Using method 1 for template computation.
> --fixtp: Will map everything to init TP!
> --mov: Using /Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1workfl
> ow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep0/001.
> mgz as movable/source volume.
> --mov: Using /Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1workfl
> ow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep1/002.
> mgz as movable/source volume.
> --mov: Using /Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1workfl
> ow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep2/003.
> mgz as movable/source volume.
> --mov: Using /Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1workfl
> ow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep3/004.
> mgz as movable/source volume.
> --mov: Using /Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1workfl
> ow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep4/005.
> mgz as movable/source volume.
> Total: 5 input volumes
> --inittp: Using TP 1 as target for initialization
> --iscale: Enableing intensity scaling!
> --noit: Will output only first template (no iterations)!
> --template: Using rawavg.mgz as template output volume.
> --iscaleout: Will perform intensity scaling and output results
> --subsample: Will subsample if size is larger than 200 on all axes!
> --lta: Will output LTA transforms
> reading source '/Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1wor
> kflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep0/0
> 01.mgz'...
> converting source '/Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1
> workflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep
> 0/001.mgz' to bspline ...
> MRItoBSpline degree 3
> reading source '/Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1wor
> kflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep1/0
> 02.mgz'...
> converting source '/Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1
> workflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep
> 1/002.mgz' to bspline ...
> MRItoBSpline degree 3
> reading source '/Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1wor
> kflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep2/0
> 03.mgz'...
> converting source '/Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1
> workflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep
> 2/003.mgz' to bspline ...
> MRItoBSpline degree 3
> reading source '/Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1wor
> kflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep3/0
> 04.mgz'...
> converting source '/Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1
> workflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep
> 3/004.mgz' to bspline ...
> MRItoBSpline degree 3
> reading source '/Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1wor
> kflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep4/0
> 05.mgz'...
> converting source '/Volumes/LaCie/RaquelAlmeida/workflow_dir/workfl

[Freesurfer] working with cluster annotations in fs-fast

[Abigail Noyce]

Hi folks,

I'm trying to split a cluster from mri_glmfit-sim into two separate
regions. (Ginormous blob of activation across multiple structures of
interest...)

I've gotten to the point of generating a new annotation with the
separate labels for my separate regions, but am stuck getting a
"cluster size" for the new labels. It looks like one can't use
mris_anatomical_stats on fsaverage... but something like that must be
happening inside of mri_glmfit-sim to get cluster sizes? What's the
best way to get these values for my new annotation? (Or is this a
terrible idea for some reason I haven't yet considered?)

Thanks!
Abby Noyce

-- 
Abigail Noyce, Ph.D.

Department of Psychological & Brain Sciences
Boston University

ano...@bu.edu
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Re: [Freesurfer] recon-all with input T1s at different resolutions

[Satrajit Ghosh]

thank you doug, martin, and bruce.

martin: i believe she was doing this for motion correction

i've attached the error this person observed below. so it does seem that
mri_robust_template at present doesn't do any resampling.

bruce: we can definitely see ways in which this could be done outside
recon-all and then sent to recon-all as a single image. but i just wanted
to verify that the error we were observing was expected behavior at present.

cheers,

satra


RuntimeError: Command:
mri_robust_template --satit --average 1 --fixtp --mov
/Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1workflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep0/001.mgz
/Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1workflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep1/002.mgz
/Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1workflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep2/003.mgz
/Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1workflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep3/004.mgz
/Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1workflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep4/005.mgz
--inittp 1 --iscale --noit --template rawavg.mgz --iscaleout
001-iscale.txt 002-iscale.txt 003-iscale.txt 004-iscale.txt
005-iscale.txt --subsample 200 --lta 001.lta 002.lta 003.lta 004.lta
005.lta
Standard output:
$Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $

--satit: Will estimate SAT iteratively!
--average: Using method 1 for template computation.
--fixtp: Will map everything to init TP!
--mov: Using 
/Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1workflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep0/001.mgz
as movable/source volume.
--mov: Using 
/Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1workflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep1/002.mgz
as movable/source volume.
--mov: Using 
/Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1workflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep2/003.mgz
as movable/source volume.
--mov: Using 
/Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1workflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep3/004.mgz
as movable/source volume.
--mov: Using 
/Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1workflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep4/005.mgz
as movable/source volume.
Total: 5 input volumes
--inittp: Using TP 1 as target for initialization
--iscale: Enableing intensity scaling!
--noit: Will output only first template (no iterations)!
--template: Using rawavg.mgz as template output volume.
--iscaleout: Will perform intensity scaling and output results
--subsample: Will subsample if size is larger than 200 on all axes!
--lta: Will output LTA transforms
reading source 
'/Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1workflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep0/001.mgz'...
converting source
'/Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1workflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep0/001.mgz'
to bspline ...
MRItoBSpline degree 3
reading source 
'/Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1workflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep1/002.mgz'...
converting source
'/Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1workflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep1/002.mgz'
to bspline ...
MRItoBSpline degree 3
reading source 
'/Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1workflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep2/003.mgz'...
converting source
'/Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1workflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep2/003.mgz'
to bspline ...
MRItoBSpline degree 3
reading source 
'/Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1workflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep3/004.mgz'...
converting source
'/Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1workflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep3/004.mgz'
to bspline ...
MRItoBSpline degree 3
reading source 
'/Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1workflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep4/005.mgz'...
converting source
'/Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1workflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep4/005.mgz'
to bspline ...
MRItoBSpline degree 3
Standard error:
ERROR: MultiRegistration::loadMovables: images have different voxel sizes.
  Currently not supported, maybe first make conform?
  Debug info: size(1) = 1, 1, 1.2   size(0) 

Re: [Freesurfer] WM & GM Parcellation Edit

[Bruce Fischl]

Hi Shyam

it's hard to give you an answer unless I understand what the source of 
your inaccuracy is. Perhaps you can point an image that is zoomed in on a 
region with arrows to indicate where you think things need improving? I 
don't really understand your image. If the green circles are control 
points, then they are definitely in the wrong place and will mess 
everything up. Typically we place control points in the white matter where 
the intensity in the brain.mgz volume is <110, so typically near the 
gray/white boundary (but not close enough to be voxels that have some gray 
matter in them).


cheers
Bruce



On 
Tue, 31 May 2016, Limachia, Gaurang (NIH/NINDS) [F] wrote:



Yes the green circles are control points. The control points shown in the
picture show surfaces we feel are not accurate.

Additionally, how are we supposed to use the control points, do we place
them on the inner most boundary of the WM?

Also, going back to the original questions: How do you recommend that we
proceed to obtain the most accurate results?
Should we continue making changes to the wm.mgz file as well as adding
control points, or is it sufficient just to add control points?


Thanks,

Shyam

On 5/31/16, 3:33 PM, "Bruce Fischl"  wrote:


Hi Shyam

can you add arrows to show where you don't think the surfaces are
accurate?

And are the green circles meant to be control points? If so, I'm
surprised that didn't break everything since they need to be added to the
interior of the WM.

cheers
Bruce


On Tue, 31 May 2016, Limachia,
Gaurang (NIH/NINDS) [F] wrote:


Hi freesurfer community,

We are checking to see the accuracy of our subjects¹ white and gray
matter
parcellation. We have found that for some subjects the contour lines for
white matter surface and pial surface are somewhat inaccurate, and have
been
making modifications using the tutorials.

Specifically, we made changes to the white matter wm.mgz file; this
however
did not alter the contour lines. We also used control points, and were
able
to see changes to the white matter surface contour lines using this
approach.

How do you recommend that we proceed to obtain the most accurate
results?
Should we continue making changes to the wm.mgz file as well as adding
control points, or is it sufficient just to add control points?

I am attaching a screen shot which shows changes to the contour lines
after
we added control points.

Best Regards,

Shyam [IMAGE][IMAGE]




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Re: [Freesurfer] WM & GM Parcellation Edit

[Limachia, Gaurang (NIH/NINDS) [F]]

Yes the green circles are control points. The control points shown in the
picture show surfaces we feel are not accurate.

Additionally, how are we supposed to use the control points, do we place
them on the inner most boundary of the WM?

Also, going back to the original questions: How do you recommend that we
proceed to obtain the most accurate results?
Should we continue making changes to the wm.mgz file as well as adding
control points, or is it sufficient just to add control points?


Thanks,

Shyam

On 5/31/16, 3:33 PM, "Bruce Fischl"  wrote:

>Hi Shyam
>
>can you add arrows to show where you don't think the surfaces are
>accurate?
>
>And are the green circles meant to be control points? If so, I'm
>surprised that didn't break everything since they need to be added to the
>interior of the WM.
>
>cheers
>Bruce
>
>
>On Tue, 31 May 2016, Limachia,
>Gaurang (NIH/NINDS) [F] wrote:
>
>> Hi freesurfer community,
>> 
>> We are checking to see the accuracy of our subjects¹ white and gray
>>matter
>> parcellation. We have found that for some subjects the contour lines for
>> white matter surface and pial surface are somewhat inaccurate, and have
>>been
>> making modifications using the tutorials.
>> 
>> Specifically, we made changes to the white matter wm.mgz file; this
>>however
>> did not alter the contour lines. We also used control points, and were
>>able
>> to see changes to the white matter surface contour lines using this
>> approach.
>> 
>> How do you recommend that we proceed to obtain the most accurate
>>results?
>> Should we continue making changes to the wm.mgz file as well as adding
>> control points, or is it sufficient just to add control points?
>> 
>> I am attaching a screen shot which shows changes to the contour lines
>>after
>> we added control points.
>> 
>> Best Regards,
>> 
>> Shyam [IMAGE][IMAGE]
>> 


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Re: [Freesurfer] WM & GM Parcellation Edit

[Bruce Fischl]

Hi Shyam

can you add arrows to show where you don't think the surfaces are 
accurate?


And are the green circles meant to be control points? If so, I'm 
surprised that didn't break everything since they need to be added to the 
interior of the WM.


cheers
Bruce


On Tue, 31 May 2016, Limachia, 
Gaurang (NIH/NINDS) [F] wrote:



Hi freesurfer community,

We are checking to see the accuracy of our subjects’ white and gray matter
parcellation. We have found that for some subjects the contour lines for
white matter surface and pial surface are somewhat inaccurate, and have been
making modifications using the tutorials.

Specifically, we made changes to the white matter wm.mgz file; this however
did not alter the contour lines. We also used control points, and were able
to see changes to the white matter surface contour lines using this
approach.

How do you recommend that we proceed to obtain the most accurate results?
Should we continue making changes to the wm.mgz file as well as adding
control points, or is it sufficient just to add control points? 

I am attaching a screen shot which shows changes to the contour lines after
we added control points.

Best Regards,

Shyam [IMAGE][IMAGE]

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Re: [Freesurfer] Tracula skip steps

[Anastasia Yendiki]

Some of the errors make me suspect that your input DWI files contain only 
one volume. Could this be the case?


On Tue, 31 May 2016, Jacobs H (NP) wrote:


Hmm, weird, as I put a #  in front of it. Putting the eddy current to 0
gives the same error. Enclosed is the config file.
Thank you so much
Heidi

On 5/31/16, 8:13 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Anastasia Yendiki"  wrote:



Hi Heidi - It knows where to find the freesurfer recons of the T1's from
SUBJECTS_DIR (see example config file). Based on your log file, it looks
like you haven't turned off the eddy current compensation, because it's
trying to run it. If you attach your config file, I'll take a look.

Best,
a.y

On Tue, 31 May 2016, Jacobs H (NP) wrote:


Thanks! I tried to adapt the configuration file and it got a bit
further,
but then crashes again. Not sure why? I have added the log file, so that
maybe you could have a look at what is happening?
Also, how does the trac-all command knows where to find the T1 data?
Thanks
Heidi

On 5/31/16, 5:07 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf
of
Anastasia Yendiki"  wrote:



No, it should be pointed to the DWI data, which can be corrected niftis
instead of the original dicoms. I would recommend turning off all the
corrections in the configuration file, and then running everything
without
skipping steps. This will create all the files that are expected to be
there for the registration.

On Tue, 31 May 2016, Jacobs H (NP) wrote:


Dear Anastasia,

Thanks for the feedback. So, does this mean that the dcm root should
be
pointed towards the T1¹s? I have the FreeSurfer recon-all output in a
different folder.
Enclosed is the log file (of one subject) and the configuration file.
You
will see that I tried the inter and intra option, because I thought
that
for the inter it would not need anything else than the MNI template
and
the DTI images.

Thanks

Best
Heidi

On 5/31/16, 4:01 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf
of
Anastasia Yendiki"  wrote:



Hi Heidi - The intra-subject registration step that you're trying to
run
registers your subject's DWI and T1 images. It expects to find those
images. It doesn't use the FA, MD, etc in any way.

Did the log file get created in scripts/trac-all.log? If so, can you
please send that file and your configuration file? Thanks!

a.y

On Tue, 31 May 2016, Jacobs H (NP) wrote:


Dear FreeSurfers,

The data I have is preprocessed, so I have the all the metrics (FA,
MD,
L1, L2, L3,..) in nifti format.
On this data I would like to start tracula starting from step 1.3.

I have organized the data as mentioned on the wiki:
For example:
/ dtifit_FA.nii.gz

I have also filled in the configuration file, canceling out the
things
I don¹t need and then I tried to run:
Trac-all ­intra ­c 

Unfortunately, it does not work, it says: dcmlist: subscript out of
range

I do not have the original filesŠ is there a way that I can get the
script working?

Many thanks.
Heidi







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Re: [Freesurfer] recon-all with input T1s at different resolutions

[Bruce Fischl]

Hi Satra

it will probably reject this by default, which you can get around be 
reslicing one of them to be like the other. Or "conforming" both of them.

cheers
Bruce
On 
Tue, 31 May 2016, Satrajit Ghosh wrote:

> hi folks,
> does recon-all work if the input T1s for the same participant have different
> resolutions? (i don't have a dataset to test, but trying to debug some
> issues another group has been having).
> 
> cheers,
> 
> satra
> 
> 
>
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Re: [Freesurfer] Algebraic operations with scalars

[Francesco Cardinale]

Thanks a lot!

Cico

Francesco Cardinale, MD

Neurosurgeon
"Claudio Munari" Centre for Epilepsy and Parkinson Surgery - Ospedale Niguarda 
"Ca' Granda"
Piazza dell'Ospedale Maggiore, 3 - 20162 - Milano - Italia
phone 0039 02 64442917
fax 0039 02 64442868
e-mail francesco.cardin...@ospedaleniguarda.it

> Il giorno 31 mag 2016, alle ore 19:39, Douglas N Greve 
>  ha scritto:
> 
> You can use mri_convert, like
> 
> mri_convert lh.thickness --ascii lh.thickness.txt
> 
> this will create a text file with a single column, one row for each 
> vertex. You can also use
> 
> 
> mri_convert lh.thickness --ascii+crsf lh.thickness.txt
> 
> This will create 5 columns, the first being the column number, then row 
> number, then slice number, then frame number, then thickness value. In 
> this case, the column number will be the vertex number, and the row, 
> slice, and frame will always be 0.
> 
> 
> 
>> On 05/29/2016 12:19 PM, Francesco Cardinale wrote:
>> Dear Freesurfer experts,
>> 
>> I would like to make some algebraic operations with scalars, such as 
>> ?h.thickness or sig.mgh. They are referred to the same surface, of course.
>> 
>> How can I export the thickness values to a spreadsheet? (?h.thickness 
>> 2 table)
>> 
>> How can I export the significance values to a spreadsheet? (sig.mgh 2 
>> table)
>> 
>> All my best
>> 
>> Cico
>> 
>> Francesco Cardinale, MD
>> 
>> Neurosurgeon
>> "Claudio Munari" Centre for Epilepsy and Parkinson Surgery - Ospedale 
>> Niguarda "Ca' Granda"
>> Piazza dell'Ospedale Maggiore, 3 - 20162 - Milano - Italia 
>> 
>> phone 0039 02 64442917 
>> fax 0039 02 64442868 
>> e-mail francesco.cardin...@ospedaleniguarda.it 
>> 
>> 
>> 
>> 
>> 
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
> 
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> 
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> 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.
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Re: [Freesurfer] Tracula skip steps

[Jacobs H (NP)]

Hmm, weird, as I put a #  in front of it. Putting the eddy current to 0
gives the same error. Enclosed is the config file.
Thank you so much
Heidi

On 5/31/16, 8:13 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Anastasia Yendiki"  wrote:

>
>Hi Heidi - It knows where to find the freesurfer recons of the T1's from
>SUBJECTS_DIR (see example config file). Based on your log file, it looks
>like you haven't turned off the eddy current compensation, because it's
>trying to run it. If you attach your config file, I'll take a look.
>
>Best,
>a.y
>
>On Tue, 31 May 2016, Jacobs H (NP) wrote:
>
>> Thanks! I tried to adapt the configuration file and it got a bit
>>further,
>> but then crashes again. Not sure why? I have added the log file, so that
>> maybe you could have a look at what is happening?
>> Also, how does the trac-all command knows where to find the T1 data?
>> Thanks
>> Heidi
>>
>> On 5/31/16, 5:07 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf
>>of
>> Anastasia Yendiki" > ayend...@nmr.mgh.harvard.edu> wrote:
>>
>>>
>>> No, it should be pointed to the DWI data, which can be corrected niftis
>>> instead of the original dicoms. I would recommend turning off all the
>>> corrections in the configuration file, and then running everything
>>> without
>>> skipping steps. This will create all the files that are expected to be
>>> there for the registration.
>>>
>>> On Tue, 31 May 2016, Jacobs H (NP) wrote:
>>>
 Dear Anastasia,

 Thanks for the feedback. So, does this mean that the dcm root should
be
 pointed towards the T1¹s? I have the FreeSurfer recon-all output in a
 different folder.
 Enclosed is the log file (of one subject) and the configuration file.
 You
 will see that I tried the inter and intra option, because I thought
that
 for the inter it would not need anything else than the MNI template
and
 the DTI images.

 Thanks

 Best
 Heidi

 On 5/31/16, 4:01 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf
 of
 Anastasia Yendiki" >>>of
 ayend...@nmr.mgh.harvard.edu> wrote:

>
> Hi Heidi - The intra-subject registration step that you're trying to
> run
> registers your subject's DWI and T1 images. It expects to find those
> images. It doesn't use the FA, MD, etc in any way.
>
> Did the log file get created in scripts/trac-all.log? If so, can you
> please send that file and your configuration file? Thanks!
>
> a.y
>
> On Tue, 31 May 2016, Jacobs H (NP) wrote:
>
>> Dear FreeSurfers,
>>
>> The data I have is preprocessed, so I have the all the metrics (FA,
>> MD,
>> L1, L2, L3,..) in nifti format.
>> On this data I would like to start tracula starting from step 1.3.
>>
>> I have organized the data as mentioned on the wiki:
>> For example:
>> / dtifit_FA.nii.gz
>>
>> I have also filled in the configuration file, canceling out the
>>things
>> I don¹t need and then I tried to run:
>> Trac-all ­intra ­c 
>>
>> Unfortunately, it does not work, it says: dcmlist: subscript out of
>> range
>>
>> I do not have the original filesŠ is there a way that I can get the
>> script working?
>>
>> Many thanks.
>> Heidi
>>

>>

#
# dmrirc.example
#
# This file contains commands that will be run by trac-all before an analysis.
# It is used to set all parameters needed for the analysis.
#
# Remove a parameter from your dmrirc file if you want use the default value.
# Parameters that don't have default values must be specified.
#
# Any other commands that you might want to run before an analysis can be added
# to this file.
#
# Original Author: Anastasia Yendiki
# CVS Revision Info:
#$Author: ayendiki $
#$Date: 2013/12/05 23:08:54 $
#$Revision: 1.12 $
#
# Copyright © 2011 The General Hospital Corporation (Boston, MA) "MGH"
#
# Terms and conditions for use, reproduction, distribution and contribution
# are found in the 'FreeSurfer Software License Agreement' contained
# in the file 'LICENSE' found in the FreeSurfer distribution, and here:
#
# https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLicense
#
# Reporting: freesurfer@nmr.mgh.harvard.edu
#
#

# FreeSurfer SUBJECTS_DIR
# T1 images and FreeSurfer segmentations are expected to be found here
# 
#setenv SUBJECTS_DIR /path/to/recons/of/ducks
#
# Output directory where trac-all results will be saved
# Default: Same as SUBJECTS_DIR
#
set dtroot = /Volumes/MACPRO1/EXPLORE_DTI_analyses/dtifit/

# Subject IDs

set subjlist = ` echo S_11XDXA S_1GQ9QV S_1OR6QC S_22ZHN3 S_2AL8RA S_2BB4H2 
S_2C71QF S_2N88VA S_38ZNK5 S_3RSPPP S_3VZEQN S_46JBNZ S_4MPQCY S_4WJ2CR 
S_556CFT S_591HTP S_5KA3RS S_65UK1S S_693X4P S_6D51EY S_6FWKZD S_6FZL4U 
S_6SB9KZ S_6YRT6A S_71GPF7 S_7HSOBN S_7KFHPW S_7NOX7M S_7WP6BG S_82FZ4L 
S_8BWFJ6 S_9737MM S_9EUNFD S_9K8SLX S_9N8KQW S_9P3JR7 S_9ZVDZV S_A1F2CM 
S_ALV5CB S_AUL7R4 S_BZ4

Re: [Freesurfer] Tracula skip steps

[Anastasia Yendiki]

Hi Heidi - It knows where to find the freesurfer recons of the T1's from
SUBJECTS_DIR (see example config file). Based on your log file, it looks 
like you haven't turned off the eddy current compensation, because it's 
trying to run it. If you attach your config file, I'll take a look.


Best,
a.y

On Tue, 31 May 2016, Jacobs H (NP) wrote:


Thanks! I tried to adapt the configuration file and it got a bit further,
but then crashes again. Not sure why? I have added the log file, so that
maybe you could have a look at what is happening?
Also, how does the trac-all command knows where to find the T1 data?
Thanks
Heidi

On 5/31/16, 5:07 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Anastasia Yendiki"  wrote:



No, it should be pointed to the DWI data, which can be corrected niftis
instead of the original dicoms. I would recommend turning off all the
corrections in the configuration file, and then running everything
without
skipping steps. This will create all the files that are expected to be
there for the registration.

On Tue, 31 May 2016, Jacobs H (NP) wrote:


Dear Anastasia,

Thanks for the feedback. So, does this mean that the dcm root should be
pointed towards the T1¹s? I have the FreeSurfer recon-all output in a
different folder.
Enclosed is the log file (of one subject) and the configuration file.
You
will see that I tried the inter and intra option, because I thought that
for the inter it would not need anything else than the MNI template and
the DTI images.

Thanks

Best
Heidi

On 5/31/16, 4:01 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf
of
Anastasia Yendiki"  wrote:



Hi Heidi - The intra-subject registration step that you're trying to
run
registers your subject's DWI and T1 images. It expects to find those
images. It doesn't use the FA, MD, etc in any way.

Did the log file get created in scripts/trac-all.log? If so, can you
please send that file and your configuration file? Thanks!

a.y

On Tue, 31 May 2016, Jacobs H (NP) wrote:


Dear FreeSurfers,

The data I have is preprocessed, so I have the all the metrics (FA,
MD,
L1, L2, L3,..) in nifti format.
On this data I would like to start tracula starting from step 1.3.

I have organized the data as mentioned on the wiki:
For example:
/ dtifit_FA.nii.gz

I have also filled in the configuration file, canceling out the things
I don¹t need and then I tried to run:
Trac-all ­intra ­c 

Unfortunately, it does not work, it says: dcmlist: subscript out of
range

I do not have the original filesŠ is there a way that I can get the
script working?

Many thanks.
Heidi





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Re: [Freesurfer] Tracula skip steps

[Jacobs H (NP)]

Thanks! I tried to adapt the configuration file and it got a bit further,
but then crashes again. Not sure why? I have added the log file, so that
maybe you could have a look at what is happening?
Also, how does the trac-all command knows where to find the T1 data?
Thanks
Heidi

On 5/31/16, 5:07 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Anastasia Yendiki"  wrote:

>
>No, it should be pointed to the DWI data, which can be corrected niftis
>instead of the original dicoms. I would recommend turning off all the
>corrections in the configuration file, and then running everything
>without 
>skipping steps. This will create all the files that are expected to be
>there for the registration.
>
>On Tue, 31 May 2016, Jacobs H (NP) wrote:
>
>> Dear Anastasia,
>>
>> Thanks for the feedback. So, does this mean that the dcm root should be
>> pointed towards the T1¹s? I have the FreeSurfer recon-all output in a
>> different folder.
>> Enclosed is the log file (of one subject) and the configuration file.
>>You
>> will see that I tried the inter and intra option, because I thought that
>> for the inter it would not need anything else than the MNI template and
>> the DTI images.
>>
>> Thanks
>>
>> Best
>> Heidi
>>
>> On 5/31/16, 4:01 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf
>>of
>> Anastasia Yendiki" > ayend...@nmr.mgh.harvard.edu> wrote:
>>
>>>
>>> Hi Heidi - The intra-subject registration step that you're trying to
>>>run
>>> registers your subject's DWI and T1 images. It expects to find those
>>> images. It doesn't use the FA, MD, etc in any way.
>>>
>>> Did the log file get created in scripts/trac-all.log? If so, can you
>>> please send that file and your configuration file? Thanks!
>>>
>>> a.y
>>>
>>> On Tue, 31 May 2016, Jacobs H (NP) wrote:
>>>
 Dear FreeSurfers,

 The data I have is preprocessed, so I have the all the metrics (FA,
MD,
 L1, L2, L3,..) in nifti format.
 On this data I would like to start tracula starting from step 1.3.

 I have organized the data as mentioned on the wiki:
 For example:
 / dtifit_FA.nii.gz

 I have also filled in the configuration file, canceling out the things
 I don¹t need and then I tried to run:
 Trac-all ­intra ­c 

 Unfortunately, it does not work, it says: dcmlist: subscript out of
 range

 I do not have the original filesŠ is there a way that I can get the
 script working?

 Many thanks.
 Heidi

>>



dwi.ecclog
Description: dwi.ecclog


trac-all.log
Description: trac-all.log
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Re: [Freesurfer] Algebraic operations with scalars

[Douglas N Greve]

You can use mri_convert, like

mri_convert lh.thickness --ascii lh.thickness.txt

this will create a text file with a single column, one row for each 
vertex. You can also use


mri_convert lh.thickness --ascii+crsf lh.thickness.txt

This will create 5 columns, the first being the column number, then row 
number, then slice number, then frame number, then thickness value. In 
this case, the column number will be the vertex number, and the row, 
slice, and frame will always be 0.



On 05/29/2016 12:19 PM, Francesco Cardinale wrote:
> Dear Freesurfer experts,
>
> I would like to make some algebraic operations with scalars, such as 
> ?h.thickness or sig.mgh. They are referred to the same surface, of course.
>
> How can I export the thickness values to a spreadsheet? (?h.thickness 
> 2 table)
>
> How can I export the significance values to a spreadsheet? (sig.mgh 2 
> table)
>
> All my best
>
> Cico
>
> Francesco Cardinale, MD
>
> Neurosurgeon
> "Claudio Munari" Centre for Epilepsy and Parkinson Surgery - Ospedale 
> Niguarda "Ca' Granda"
> Piazza dell'Ospedale Maggiore, 3 - 20162 - Milano - Italia 
> 
> phone 0039 02 64442917 
> fax 0039 02 64442868 
> e-mail francesco.cardin...@ospedaleniguarda.it 
> 
>
>
>
>
> ___
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] recon-all with input T1s at different resolutions

[Martin Reuter]

I see. Could be we specifically test for that and stop processing. It is 
a bad idea to average from different resolutions. Probably averaging is 
not even helpful at all, especially with newer images.

Anyway, if someone points me at some data, I can take a look.

Best, Martin


On 05/31/2016 01:34 PM, Douglas N Greve wrote:
> I tried this recently and it failed. I did not pursue it any further
>
> On 05/31/2016 01:32 PM, Martin Reuter wrote:
>> Do you mean several inputs for motion correction (averaging), or for a
>> longitudinal study?
>>
>> I haven't tested it, but for averaging, we use mri_robust_template and
>> I see no reason why it should not work. It probably reslices at the
>> resolution of the first input to create rawavg and then conforms that.
>>
>> Best, Martin
>>
>>
>> On 05/31/2016 10:13 AM, Satrajit Ghosh wrote:
>>> hi folks,
>>>
>>> does recon-all work if the input T1s for the same participant have
>>> different resolutions? (i don't have a dataset to test, but trying to
>>> debug some issues another group has been having).
>>>
>>> cheers,
>>>
>>> satra
>>>
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
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>> -- 
>> Martin Reuter, PhD
>> Assistant Professor of Radiology, Harvard Medical School
>> Assistant Professor of Neurology, Harvard Medical School
>> A.A.Martinos Center for Biomedical Imaging
>> Massachusetts General Hospital
>> Research Affiliate, CSAIL, MIT
>> Phone: +1-617-724-5652
>> Web  :http://reuter.mit.edu
>>
>>
>> ___
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>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web  : http://reuter.mit.edu

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Re: [Freesurfer] Retinotopy - Error in fast_selxavg3 (line 279)

[Douglas N Greve]

It expects both polar and eccen. You can "fake" an eccentricity run by 
just copying one of the polar runs and calling it eccen

On 05/31/2016 07:35 AM, Steinmann, Iris wrote:
>
> Dear freesurfers,
>
> I try to run a retinotopy analysis following the instruction on
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis
>
> (using Ubuntu 14.4 and freesurfer 5.3)
>
> My subject folder contains 4 runs (all 'positive polar'). After 
> preprocessing I performed the following steps:
>
> mkanalysis-sess -a retinotopy_polar_pos_rh -TR 2 -paradigm 
> polar_pos.par -retinotopy 30 -surface self rh -per-run -fsd bold -fwhm 
> 5 -nskip 4
>
> selxavg3-sess -s EP_polar -a retinotopy_polar_pos_rh
>
> The polar_pos.par file contains only the two following lines:
>
> stimtype polar
>
> direction pos
>
> selxavg3-sess stops with the following error:
>
> ...
>
> Saving X matrix to 
> ~/PROJECTS/Retinotopy/subjects/EP_polar/bold/retinotopy_polar_pos_rh/Xtmp.mat
>
> Error using svd
>
> Input to SVD must not contain NaN or Inf.
>
> Error in cond (line 35)
>
> s = svd(A);
>
> Error in fast_selxavg3 (line 279)
>
>   XCond = cond(XtX);
>
> >> --
>
> ERROR: fast_selxavg3() failed\n
>
> I found a lot of similar error reports in the mailing list, but 
> unfortunately no explanation that fix my problem.
>
> Is it maybe a problem when I only process 'polar positve' measurements?
>
> I also attached the Xtmp.mat file that contains a lot of NaN.
>
> Does someone has an idea what’s going wrong here?
>
> Thanks in advance!
>
> Iris
>
>
>
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] recon-all with input T1s at different resolutions

[Douglas N Greve]

I tried this recently and it failed. I did not pursue it any further

On 05/31/2016 01:32 PM, Martin Reuter wrote:
> Do you mean several inputs for motion correction (averaging), or for a 
> longitudinal study?
>
> I haven't tested it, but for averaging, we use mri_robust_template and 
> I see no reason why it should not work. It probably reslices at the 
> resolution of the first input to create rawavg and then conforms that.
>
> Best, Martin
>
>
> On 05/31/2016 10:13 AM, Satrajit Ghosh wrote:
>> hi folks,
>>
>> does recon-all work if the input T1s for the same participant have 
>> different resolutions? (i don't have a dataset to test, but trying to 
>> debug some issues another group has been having).
>>
>> cheers,
>>
>> satra
>>
>>
>>
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>
> -- 
> Martin Reuter, PhD
> Assistant Professor of Radiology, Harvard Medical School
> Assistant Professor of Neurology, Harvard Medical School
> A.A.Martinos Center for Biomedical Imaging
> Massachusetts General Hospital
> Research Affiliate, CSAIL, MIT
> Phone: +1-617-724-5652
> Web  :http://reuter.mit.edu  
>
>
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Re: [Freesurfer] Group_analysis_FSGD_contrast_matrix

[Douglas N Greve]

Sorry, not sure what you are asking. It sounds like you have exactly the 
situation in that web page except you have diagnosis as a factor instead 
of handedness.

On 05/30/2016 09:39 AM, Hao wen wrote:
>
> Hello, FS experts:
>
> I am now doing the group analysis with covariates(age, gender), I am 
> using command line, not QDEC, so my Null hypothesis is:
>
> there is no significant difference for the thickness between my two 
> groups( 'AD' and 'CN'),  my covariates are age and gender, so if I 
> define the classes like in the tutorial, is there an interaction 
> between the group laber and gender, no? My question is that:
>
> If I define the FSGD file like the example here(we have two factors, 1 
> variable):https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V
>
> 
>   
> Fsgdf4G1V - Free Surfer Wiki 
> 
> surfer.nmr.mgh.harvard.edu
> FSGD File (g4v1.fsgd) GroupDescriptorFile 1 Title OSGM Class MaleRight 
> Class MaleLeft Class FemaleRight Class FemaleLeft Variables Age Input 
> subject1 MaleRight 30 ...
>
> Follow the tutorial, I think my contrast matrix should be like this:
> 0.5 -0.5 0.5 -0.5 0 0 0 0
>
> So I know that if you have just one factor, for example, the gender,
> we should have four columns, like:
>
>  1. Intercept for Females
>  2. Intercept for Males
>  3. Slope for Females
>  4. Slope for Males
>
> But for my data, I also have the group lable(AD, CN), so anyone can 
> explain this to me a little?
>
> Thanks in advance!
>
>
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Re: [Freesurfer] recon-all with input T1s at different resolutions

[Martin Reuter]

Do you mean several inputs for motion correction (averaging), or for a 
longitudinal study?


I haven't tested it, but for averaging, we use mri_robust_template and I 
see no reason why it should not work. It probably reslices at the 
resolution of the first input to create rawavg and then conforms that.


Best, Martin


On 05/31/2016 10:13 AM, Satrajit Ghosh wrote:

hi folks,

does recon-all work if the input T1s for the same participant have 
different resolutions? (i don't have a dataset to test, but trying to 
debug some issues another group has been having).


cheers,

satra



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Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web  : http://reuter.mit.edu

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Re: [Freesurfer] recon-all with input T1s at different resolutions

[Douglas N Greve]

No, I don't think it does

On 05/31/2016 10:13 AM, Satrajit Ghosh wrote:
> hi folks,
>
> does recon-all work if the input T1s for the same participant have 
> different resolutions? (i don't have a dataset to test, but trying to 
> debug some issues another group has been having).
>
> cheers,
>
> satra
>
>
>
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Re: [Freesurfer] Question about selxavg3-sess -no-con-ok

[Douglas N Greve]

No, that just allows you to run selxavg3-sess without having specified 
any contrasts with mkcontrast-sess

On 05/31/2016 08:05 AM, Leila Reddy wrote:
> Sorry I meant to ask if the weight for the baseline/fixation is set to 
> -1 (not 0).
>
> Thanks,
> Leila
>
>
> On Tuesday, May 31, 2016 1:44 PM, Leila Reddy  wrote:
>
>
> Hi,
> I was just wondering what exactly the -no-con-ok option does in 
> selxavg3-sess. Is it the same as setting the weights for all 
> conditions to 1 and give the baseline/fixation (i.e., 0s in the para 
> files) a weight of 0?
>
> Thanks,
> Leila
>
>
>
>
>
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Re: [Freesurfer] correlation with glm

[Douglas N Greve]

have you seen our worked-out examples?

http://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples

On 05/31/2016 03:39 AM, Clara Kühn wrote:
> Dear FreeSurfer experts,
>
> I would like to correlate my thickness data with behavioral measures. Can I 
> do that with glmfit? If so, could you explain how to specify the contrast for 
> that?
> My fsgd file looks like this:
>
> GroupDescriptorFile 1
> Class 1male plus blue
> Class 1female plus red
> Class 2male circle blue
> Class 2female circle red
> Class 3male triangle blue
> Class 3female triangle red
> Variables age_sc1 Mottier
> Input subject1 1female 51.61 10
> Input subject2 1female 48.89 15
> ...
>
> Thank you!
> Clara
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>

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Re: [Freesurfer] Segmentation fault: Core dumped

[Douglas N Greve]

It did not find any voxels in the ROI. This can happen for several 
reasons. First, check your registratoin (tkregister-sess). Second, it 
can happen because the size of the ROI is too small and does not occupy 
enough space in a voxel. Try changing the -fillthresh to something 
smaller than the default 0.5 (bet 0 and 1).


On 05/27/2016 04:08 PM, Sahil Bajaj wrote:
> Hello FS experts,
>
> I am running a command "fcseed-sess -s S01 -cfg abc.config" to get 
> *.dat file for further analysis. I used the same steps to calculate FC 
> for 40 subjects, all steps run fine with 38 subjects but for 2 
> subjects I am getting an error: Segmentation fault: Core dumped.
>
> I checked the segmentation of anatomical data (generated using 
> recon-all), and it looks fine to me.
> Here I am also attaching the log file created when I run this command.
>
> Any help would be really appreciated.
>
> Thanks,
> Sahil
> -- 
> -
> Sahil Bajaj
> Post-doctoral Fellow
> Nantz National Alzheimer's Center, Department of Neurology
> The Houston Methodist Research Institute (THMRI)
> Houston, TX, USA.
> E-mail:sahil.br...@gmail.com 
>
>
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Re: [Freesurfer] mris_preproc - srcsubjreg

[Douglas N Greve]

Sorry for the delay. This is because sphere.reg only applies to 
fsaverage. Previously, the specification of a different target would 
only influence smoothing done as part of mris_preproc; the registration 
would still be done to fsaverage. This is probably not the intent of 
people who are specifying a target, so I changed mris_preproc to require 
a targets-specific registration. You can generate this with

surfreg --s subject --t target

then run mris_preproc specifying the given target
doug


On 05/24/2016 04:23 PM, Makaretz, Sara Johanna wrote:
> Hi Doug, I¹m curious why the newer mris_preproc does not use sphere.reg as
> the default srcsurfreg when the target is not fsaverage - see below
>
> Thanks for any info! (not urgent)
>
>
> On 2016-5-24, 11:30, "Z K"  wrote:
>
>> Good question, and I dont know the answer. mris_preproc is Dougs baby so
>> I suggest just posting this question to the list with "mris_preproc" in
>> the subject, and I bet he will give you the answer.
>>
>> -Zeke
>>
>> On 05/23/2016 10:31 PM, Makaretz, Sara Johanna wrote:
>>> Hi Zeke,
>>>
>>> I am running some surface glms where targ is a patient surface. The help
>>> says --target TargetSubject (requires ?h.TargetSubject.sphere.reg), and
>>> I was getting errors because dev-default mris_preproc wanted
>>> mri_surf2surf to have srcsurfreg =
>>> $SUBJECTS_DIR/$srcsubject/surf/$h.$TARGSUBJ.sphere.reg
>>>
>>> But mris_preproc in 5.3 let me do target = patient surface with no extra
>>> surf reg files or extra flags to get mri_surf2surf to use srcsurfreg =
>>> $SUBJECTS_DIR/$srcsubject/surf/$h.sphere.reg
>>>
>>> I had been running this with 5.3:
>>> mris_preproc\
>>>   --target $TARGSUBJ\
>>>   --hemi lh\
>>>   --meas thickness\
>>>   --fsgd file.fsgd\
>>>   --out lh.output.mgh
>>>
>>> And I was about to email freesurfer@nmr but "for fun" tried adding
>>> --surfreg sphere.reg which got mris_surf2surf to use the right reg
>>> files. So now I'm selfishly trying to figure this out - do you know what
>>> prompted the switch from sphere.reg "opt-out" to sphere.reg "opt-in"?
>>> Aka why sphere.reg is non-default when the target is non-fsaverage? Did
>>> that make sense? I know there must be some reason, so I really want to
>>> know a bit more so I can stay sane when old scripts break.
>>>
>>> Thanks for any info! Sorry to bother you!
>>> Sara
>>>
>>>
>>>
>>>
>>>
>>>
>>> Outputs from the FS-dev one:
>>>
>>> $Id: mris_preproc,v 1.76 2015/12/09 20:02:53 zkaufman Exp $
>>> 
>>> Src lh $TARGSUBJ.sphere.reg
>>> Trg lh sphere.reg
>>> 
>>> mri_surf2surf --srcsubject $SRCSUBJ --srchemi lh --srcsurfreg
>>> $TARGSUBJ.sphere.reg --trgsubject $TARGSUBJ --trghemi lh --trgsurfreg
>>> sphere.reg --etcetcetc
>>> 
>>> ERROR can't find $SUBJECTS_DIR/$SRCSUBJ/surf/$TARGSUBJ.sphere.reg
>>> because I never made it
>>>
>>>
>>>
>>> Outputs from the FS-dev one with fsaverage as the targ subj:
>>>
>>> $Id: mris_preproc,v 1.76 2015/12/09 20:02:53 zkaufman Exp $
>>> 
>>> Src lh sphere.reg
>>> Trg lh sphere.reg
>>> 
>>> mri_surf2surf --srcsubject $SRCSUBJ --srchemi lh --srcsurfreg sphere.reg
>>> --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --etcetcetc
>>> 
>>> mris_preproc finds everything, runs no problem
>>>
>>>
>>>
>>> Outputs from the FS-5.3 one:
>>>
>>> $Id: mris_preproc,v 1.59.2.4 2012/12/06 16:06:52 mreuter Exp $
>>> 
>>> Src lh sphere.reg
>>> Trg lh sphere.reg
>>> 
>>> mri_surf2surf --srcsubject $SRCSUBJ --srchemi lh --srcsurfreg sphere.reg
>>> --trgsubject $TARGSUBJ --trghemi lh --trgsurfreg sphere.reg --etcetcetc
>>> 
>>> mris_preproc exits with no errors because everything exists
>>>
>>>
>>>
>>>
>
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Re: [Freesurfer] Freesurfer V6 beta

[Francis Tyson Thomas]

Hi Bruce,

Is there any new timeline regarding the release of the v6 beta? Because I'm
currently waiting on that version for my project's work because of the new
hipppocampal module and knowing that will help me a lot.

Thanks,
Tyson

On Tue, May 3, 2016 at 5:51 AM, Bruce Fischl 
wrote:

> Hi Tyson
>
> we are moving through our testing and hoping to get it out soon. Hard to
> say more definitively than that
>
> sorry
> Bruce
>
>
> On Mon, 2 May 2016, Francis Tyson Thomas wrote:
>
> > Hello Fresurfer admin!
> > I was looking for the v6 beta and it looks like it still hasn't been
> > released after it was pulled down the last time. I would like to know
> what
> > is the expected ETA for the beta. Last I remember it was mentioned it was
> > on the verge of release about two weeks ago.I'm looking forward to get my
> > hands on the beta!
> >
> > Thanks,
> > Tyson
> >
> >
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[Freesurfer] Postdoctoral position available

[Olivier Coulon]

Dear list members,
please find below a link to a postdoc position annoucement that might be 
of interest, in the field of cortical morphometry for developmental 
studies and autism.


http://www.meca-brain.org/2016/05/31/we-are-looking-for-a-post-doc/

O. Coulon
--

Olivier Coulon,
Aix-Marseille University,
LSIS Laboratory
CNRS Director of Research,

olivier.cou...@univ-amu.fr 
http://olivier.meca-brain.org
MeCA Research Group
http://www.meca-brain.org
Institut des Neurosciences de La Timone
Faculté de Médecine,
27 Bd Jean Moulin,
13005 - Marseille, France
Tél: +33 (0)4 91 32 40 59


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Re: [Freesurfer] Tracula skip steps

[Anastasia Yendiki]

No, it should be pointed to the DWI data, which can be corrected niftis 
instead of the original dicoms. I would recommend turning off all the 
corrections in the configuration file, and then running everything without 
skipping steps. This will create all the files that are expected to be 
there for the registration.


On Tue, 31 May 2016, Jacobs H (NP) wrote:


Dear Anastasia,

Thanks for the feedback. So, does this mean that the dcm root should be
pointed towards the T1¹s? I have the FreeSurfer recon-all output in a
different folder.
Enclosed is the log file (of one subject) and the configuration file. You
will see that I tried the inter and intra option, because I thought that
for the inter it would not need anything else than the MNI template and
the DTI images.

Thanks

Best
Heidi

On 5/31/16, 4:01 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Anastasia Yendiki"  wrote:



Hi Heidi - The intra-subject registration step that you're trying to run
registers your subject's DWI and T1 images. It expects to find those
images. It doesn't use the FA, MD, etc in any way.

Did the log file get created in scripts/trac-all.log? If so, can you
please send that file and your configuration file? Thanks!

a.y

On Tue, 31 May 2016, Jacobs H (NP) wrote:


Dear FreeSurfers,

The data I have is preprocessed, so I have the all the metrics (FA, MD,
L1, L2, L3,..) in nifti format.
On this data I would like to start tracula starting from step 1.3.

I have organized the data as mentioned on the wiki:
For example:
/ dtifit_FA.nii.gz

I have also filled in the configuration file, canceling out the things
I don¹t need and then I tried to run:
Trac-all ­intra ­c 

Unfortunately, it does not work, it says: dcmlist: subscript out of
range

I do not have the original filesŠ is there a way that I can get the
script working?

Many thanks.
Heidi



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[Freesurfer] Fwd: ERROR: mpr2mni305 failed gauss_4dfp mpr2mni305

[Barbara Kreilkamp]

Dear Freesurfers,

I wonder if you could please help me with this issue, it may be similar 
to this post?


https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg40092.html

Ran it just fine a while back, but now it is failing with this error.

Thank you very much,
Best wishes,
Barbara


 Forwarded Message 
Subject:ERROR: mpr2mni305 failed
Date:   Sat, 28 May 2016 14:27:29 +0200
From:   Barbara Kreilkamp 
To: Freesurfer support list 



Dear FSL experts,

I am running freesurfer-Darwin-lion-stable-pub-v5.3.0 on MAC 10.10.5.
Could you please help me with this error message? I think it relates to 
the library, this is what it states in talairach_avi.log.


But I am unsure how to solve this issue.

Any help is greatly appreciated,
Thank you very much,
Barbara



#@# Talairach Sat May 28 14:18:53 CEST 2016

/Users/barbarakreilkamp/projects/Pipelines_ExampleData/REF088c/T1w/REF088c/mri

\n mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 
--no-rescale --i orig.mgz --o orig_nu.mgz \n


\n talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm \n

ERROR: mpr2mni305 failed, see transforms/talairach_avi.log

Darwin iMac.local 14.5.0 Darwin Kernel Version 14.5.0: Mon Jan 11 
18:48:35 PST 2016; root:xnu-2782.50.2~1/RELEASE_X86_64 x86_64



recon-all -s REF088c exited with ERRORS at Sat May 28 14:19:12 CEST 2016


For more details, see the log file 
/Users/barbarakreilkamp/projects/Pipelines_ExampleData/REF088c/T1w/REF088c/scripts/recon-all.log


To report a problem, see 
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting






talaraich_avi.log output


/Users/barbarakreilkamp/projects/Pipelines_ExampleData/REF088c/T1w/REF088c/mri

/Applications/freesurfer/bin/talairach_avi

--i orig_nu.mgz --xfm transforms/talairach.auto.xfm

$Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $

Darwin iMac.local 14.5.0 Darwin Kernel Version 14.5.0: Mon Jan 11 
18:48:35 PST 2016; root:xnu-2782.50.2~1/RELEASE_X86_64 x86_64


Sat May 28 13:27:28 CEST 2016

mri_convert orig_nu.mgz talsrcimg.img

$Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $

reading from orig_nu.mgz...

crypt_gkey = FSaWN44YqKOYA

TR=8.21, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-1, 0, 0)

j_ras = (0, 0, -1)

k_ras = (0, 1, 0)

writing to talsrcimg.img...

crypt_gkey = FSaWN44YqKOYA

Analyze Output Matrix

-1.0   0.0   0.0   128.0;

 0.0   0.0   1.0  -146.0;

 0.0  -1.0   0.0   148.0;

 0.0   0.0   0.0   1.0;



INFO: set hdr.hist.orient to -1

mpr2mni305 talsrcimg

Sat May 28 13:27:29 CEST 2016

/Applications/freesurfer/bin/mpr2mni305 talsrcimg

$Id: mpr2mni305,v 1.4 2009/06/03 16:01:38 nicks Exp $

target=711-2C_as_mni_average_305


-

analyzeto4dfp talsrcimg -O0 -y

-


$Id: ifh2hdr.c,v 1.3 2007/05/05 10:45:03 nicks Exp $

Sat May 28 13:27:30 2016

Writing: talsrcimg.4dfp.hdr

$Id: analyzeto4dfp.c,v 1.2 2007/05/05 00:00:06 nicks Exp $

Reading: talsrcimg.hdr

header size 348 bytes

hdr.dime.datatypeoffset=70value=2

hdr.dime.bitpixoffset=72value=8

hdr.hist.orientoffset=252value=-1

dimensionality 4

dimensions   256   256   256 1

Reading: talsrcimg.img

Writing: talsrcimg.4dfp.img

Writing: talsrcimg.4dfp.ifh

ifh2hdr talsrcimg -r0to255

ori=2


-

gauss_4dfp talsrcimg 1.1

-


dyld: Library not loaded: /usr/local/gfortran/lib/libgcc_s.1.dylib

Referenced from: /Applications/freesurfer/bin/gauss_4dfp

Reason: image not found

Trace/BPT trap

ERROR: 'gauss_4dfp talsrcimg 1.1' failed! status=133

ERROR: mpr2mni305 execution aborted

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Re: [Freesurfer] Tracula skip steps

[Jacobs H (NP)]

Dear Anastasia,

Thanks for the feedback. So, does this mean that the dcm root should be
pointed towards the T1¹s? I have the FreeSurfer recon-all output in a
different folder.
Enclosed is the log file (of one subject) and the configuration file. You
will see that I tried the inter and intra option, because I thought that
for the inter it would not need anything else than the MNI template and
the DTI images.

Thanks

Best
Heidi

On 5/31/16, 4:01 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Anastasia Yendiki"  wrote:

>
>Hi Heidi - The intra-subject registration step that you're trying to run
>registers your subject's DWI and T1 images. It expects to find those
>images. It doesn't use the FA, MD, etc in any way.
>
>Did the log file get created in scripts/trac-all.log? If so, can you
>please send that file and your configuration file? Thanks!
>
>a.y
>
>On Tue, 31 May 2016, Jacobs H (NP) wrote:
>
>> Dear FreeSurfers,
>> 
>> The data I have is preprocessed, so I have the all the metrics (FA, MD,
>>L1, L2, L3,..) in nifti format.
>> On this data I would like to start tracula starting from step 1.3.
>> 
>> I have organized the data as mentioned on the wiki:
>> For example:
>> / dtifit_FA.nii.gz
>> 
>> I have also filled in the configuration file, canceling out the things
>>I don¹t need and then I tried to run:
>> Trac-all ­intra ­c 
>> 
>> Unfortunately, it does not work, it says: dcmlist: subscript out of
>>range
>> 
>> I do not have the original filesŠ is there a way that I can get the
>>script working?
>> 
>> Many thanks.
>> Heidi
>> 

#
# dmrirc.example
#
# This file contains commands that will be run by trac-all before an analysis.
# It is used to set all parameters needed for the analysis.
#
# Remove a parameter from your dmrirc file if you want use the default value.
# Parameters that don't have default values must be specified.
#
# Any other commands that you might want to run before an analysis can be added
# to this file.
#
# Original Author: Anastasia Yendiki
# CVS Revision Info:
#$Author: ayendiki $
#$Date: 2013/12/05 23:08:54 $
#$Revision: 1.12 $
#
# Copyright © 2011 The General Hospital Corporation (Boston, MA) "MGH"
#
# Terms and conditions for use, reproduction, distribution and contribution
# are found in the 'FreeSurfer Software License Agreement' contained
# in the file 'LICENSE' found in the FreeSurfer distribution, and here:
#
# https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLicense
#
# Reporting: freesurfer@nmr.mgh.harvard.edu
#
#

# FreeSurfer SUBJECTS_DIR
# T1 images and FreeSurfer segmentations are expected to be found here
# 
#setenv SUBJECTS_DIR /path/to/recons/of/ducks
#
# Output directory where trac-all results will be saved
# Default: Same as SUBJECTS_DIR
#
set dtroot = /Volumes/MACPRO1/EXPLORE_DTI_analyses/dtifit/

# Subject IDs
#
set subjlist = ` echo S_11XDXA S_1GQ9QV S_1OR6QC S_22ZHN3 S_2AL8RA S_2BB4H2 
S_2C71QF S_2N88VA S_38ZNK5 S_3RSPPP S_3VZEQN S_46JBNZ S_4MPQCY S_4WJ2CR 
S_556CFT S_591HTP S_5KA3RS S_65UK1S S_693X4P S_6D51EY S_6FWKZD S_6FZL4U 
S_6SB9KZ S_6YRT6A S_71GPF7 S_7HSOBN S_7KFHPW S_7NOX7M S_7WP6BG S_82FZ4L 
S_8BWFJ6 S_9737MM S_9EUNFD S_9K8SLX S_9N8KQW S_9P3JR7 S_9ZVDZV S_A1F2CM 
S_ALV5CB S_AUL7R4 S_BZ4FBH S_CCCMW3 S_CMM2WL S_CTY2ER S_CU4FZA S_CURLLB 
S_DL4N2Q S_DNQ9KU S_DQ1ZSG S_DTW7J6 S_DWA2LP S_DXM9JK S_EHDWX1 S_ENG47C 
S_F4PH5M S_F8P42D S_FCBAMR S_FDJ6UU S_FMSJER S_FQHJWH S_FSK1HD S_FWFNC5 
S_G7KP27 S_H7YAA1 S_HCFNSF S_HW7R19 S_HWGXLJ S_J9HY8A S_JY5M58 S_K1K5LS 
S_K8ZC3B S_KBGJQU S_KCT9S6 S_KL5Q3P S_KMUW5L S_L33YSL S_LABYUQ S_LJ1GWN 
S_LLPPCW S_MEEDAH S_MFUFDS S_MX83QU S_NE58SM S_NIQUVD S_P4K6DM S_PE9J6U 
S_Q9A2UG S_QS6SFY S_R3BPAK S_RANV43 S_RFDRD6 S_RHXWND S_SO63PR S_SVAQUY 
S_T1LVDV S_T8CBM1 S_TJIU8X S_TMNXYB S_TNS7IM S_U2V5FD S_U98RJE S_U9U9QL 
S_UHC6WM S_V36DLL S_VTMXMZ S_WA1CLD S_WDVBAY S_X69RWA S_XFNM9K S_XRZQKV 
S_XTDEMR S_XXMGFN S_XY62WP S_Y97L76 S_YANQMX S_YEFGQ2 S_ZASXXZ S_ZNUP4E 
S_ZPBHLL TAU_001 TAU_024 TAU_029 TAU_064 TAU_074 TAU_122 TAU_151 TAU_154 
TAU_156 TAU_157 TAU_160 TAU_161 TAU_169 TAU_175 TAU_178 TAU_180`

# In case you want to analyze only Huey and Louie
# Default: Run analysis on all subjects
#
#set runlist = (1 3)
#
# Input diffusion DICOMs (file names relative to dcmroot)
# If original DICOMs don't exist, these can be in other image format
# but then the gradient table and b-value table must be specified (see below)
#
#set dcmroot = /Volumes/MACPRO1/EXPLORE_DTI_analyses/prep/
#set dcmlist = (huey/day1/XXX-1.dcm dewey/day1/XXX-1.dcm louie/day2/XXX-1.dcm)

# Diffusion gradient tables (if there is a different one for each scan)
# Must be specified if inputs are not MGH DICOMs
# The tables must have either three columns, where each row is a gradient vector
# or three rows, where each column is a gradient vector
# There must be as many gradient vectors as volumes in the diffusion data set
# Default: Read from DICOM header
#
#set bveclist = (/path/to/huey/bvecs.txt \
#/path/to/dewey/bvecs.tx

[Freesurfer] recon-all with input T1s at different resolutions

[Satrajit Ghosh]

hi folks,

does recon-all work if the input T1s for the same participant have
different resolutions? (i don't have a dataset to test, but trying to debug
some issues another group has been having).

cheers,

satra
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Re: [Freesurfer] Tracula skip steps

[Anastasia Yendiki]

Hi Heidi - The intra-subject registration step that you're trying to run 
registers your subject's DWI and T1 images. It expects to find those 
images. It doesn't use the FA, MD, etc in any way.


Did the log file get created in scripts/trac-all.log? If so, can you 
please send that file and your configuration file? Thanks!


a.y

On Tue, 31 May 2016, Jacobs H (NP) wrote:


Dear FreeSurfers,

The data I have is preprocessed, so I have the all the metrics (FA, MD, L1, L2, 
L3,..) in nifti format.
On this data I would like to start tracula starting from step 1.3. 

I have organized the data as mentioned on the wiki:
For example:
/ dtifit_FA.nii.gz

I have also filled in the configuration file, canceling out the things I don’t 
need and then I tried to run:
Trac-all –intra –c 

Unfortunately, it does not work, it says: dcmlist: subscript out of range

I do not have the original files… is there a way that I can get the script 
working?

Many thanks.
Heidi

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Re: [Freesurfer] Coordinates in TRACULA group analysis

[Anastasia Yendiki]

Hi Anri - Can you also send your log file (scripts/trac-all.log)? I'll 
need to see what exactly was running when the error occurred. Thanks!


a.y

On Sat, 28 May 2016, Anri WATANABE wrote:


Hello Anastasia,sorry for few information and let me tell you command and error 
log.
Command: trac-all –stat –c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.example

Error log: Loading output reference volume from 
/Applications/freesurfer/subjects/cvs_avg35

corRead(): can't open file /Applications/freesurfer/subjects/cvs_avg35/COR-.info

ERROR: Could not read /Applications/freesurfer/subjects/cvs_avg35


dmrirc.example (configuration file) is attached to this e-mail.

Thanks in advance,
Anri



**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里
**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
**

2016-05-27 22:57 GMT+09:00 Anastasia Yendiki :

  Hi Anri - I do not know what command line you ran and what your 
configuration file looks like, so it is very
  hard for me to suggest solutions.

  Best,
  a.y

  On Fri, 27 May 2016, Anri WATANABE wrote:

Hi Anastasia, 
Thank you for your answer.
There aren't stats/*.path.mean.txt files and terminal says 'Could 
not read
/Applications/freesurfer/subjects/cvs_avg35.' I
checked /Application/freesurfer/subjects/cvs_avg35 folder and 
couldn't find COR-.info file.
Could you tell me any resolutions, please?

Thanks, 
Anri


**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里

**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine

**

2016-05-21 6:48 GMT+09:00 Anastasia Yendiki 
:

      Hi Anri - The FA values are extracted in the native space of 
each subject, which is why
those are the only
      coordinates that you see. If you want to display the results 
of your analysis on an average
path, after
      running trac-all -stat, you can use the stats/*.path.mean.txt 
files (see also the last part
of the TRACULA
      tutorial).

      Best,
      a.y

      On Wed, 18 May 2016, Anri WATANABE wrote:

            Dear experts, 
            I use TRACULA to examine a measure (FA) at each voxel 
in one pathway.
            pathstats.byvoxel.txt files show coordinates in native 
space and after converting
those the new
            files don't show any coordinates which are in MNI space.
            Could you tell me how can I know MNI coordinate values?

            Thank you!


            Regards, 
            Anri



            
**
            京都府立医科大学附属病院
            精神科・心療内科
            渡辺 杏里
            
**
            Anri WATANABE, M.D.
            Department of Psychiatry,
            University Hospital, Kyoto Prefectural University of 
Medicine
            
**


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Re: [Freesurfer] Question about selxavg3-sess -no-con-ok

[Leila Reddy]

Sorry I meant to ask if the weight for the baseline/fixation is set to -1 (not 
0).
Thanks,Leila 

On Tuesday, May 31, 2016 1:44 PM, Leila Reddy  wrote:
 

 Hi,I was just wondering what exactly the -no-con-ok option does in 
selxavg3-sess. Is it the same as setting the weights for all conditions to 1 
and give the baseline/fixation (i.e., 0s in the para files) a weight of 0?
Thanks,
Leila


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[Freesurfer] Question about selxavg3-sess -no-con-ok

[Leila Reddy]

Hi,I was just wondering what exactly the -no-con-ok option does in 
selxavg3-sess. Is it the same as setting the weights for all conditions to 1 
and give the baseline/fixation (i.e., 0s in the para files) a weight of 0?
Thanks,
Leila
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[Freesurfer] correlation with glm

[Clara Kühn]

Dear FreeSurfer experts,

I would like to correlate my thickness data with behavioral measures. Can I do 
that with glmfit? If so, could you explain how to specify the contrast for that?
My fsgd file looks like this:

GroupDescriptorFile 1  
Class 1male plus blue
Class 1female plus red
Class 2male circle blue
Class 2female circle red
Class 3male triangle blue
Class 3female triangle red
Variables age_sc1 Mottier  
Input subject1 1female 51.61 10
Input subject2 1female 48.89 15
...

Thank you!
Clara
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