[Freesurfer] FastSurfer with FreeSurfer version 7.1.0?

[Barbara Kreilkamp]

External Email - Use Caution

Dear all,

I noticed FastSurfer also seems to run with a 7.1.0 FS version.

Or is there any reason not to do this?

Thank you,

Kind wishes,
Barbara


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

Re: [Freesurfer] Freeview Scrolling through slices on a Mac

[Barbara Kreilkamp]

External Email - Use Caution

Dear Chris,

We're actually working on control points in our group as well - on Mac 
you have to press the 'fn' (very left bottom key) along with the up-down 
arrow keys.

Hope that helps,

Cheers,
Barbara


On 11/12/2018 18:36, Ruopeng Wang wrote:
> What version of freesurfer are you running? I think in 6.0, up/down
> arrow keys will scroll through slices. If not, the latest dev build
> should have it. You can get the latest freeview build here:
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview
>
> Best,
> Ruopeng
>
>
> On 12/11/2018 01:23 PM, Chris Petty wrote:
>>   External Email - Use Caution
>>
>>
>> Maybe I am missing something, but how can I scroll through slices with 
>> keyboard or mouse in Freeview on a Mac?
>>
>> Nothing I’ve tried works thus far.
>>
>> Any typical key ( cmd, ctrl, shift ) with scroll just zooms.  Up/down moves 
>> the image up and down … shift / option / cmd with up / down either zooms or 
>> moves up / down.
>>
>> I’m just trying to add control points and definitely need to scroll through 
>> slices without clicking on the image.
>>
>> Thanks,
>> -Chris
>>
>> ___
>> 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


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

Re: [Freesurfer] TRACULA tract reconstruction

[Barbara Kreilkamp]

Hi Joëlle,

Which scanner was used to acquire the images? I have used Osirix light 
in the past to anonymize my dicom images, maybe you'd like to try that?


Best wishes,

Barbara


On 29/03/2017 13:30, Joëlle Ismay Rosanne Van Der Molen wrote:


​Hi Anastasia,


Yes, I use dicom images as input for Tracula. I also specify the bvecs 
files, as Tracula returns an error if I try to run it with a 
configuration file that does not contain them.


Unfortunately, our dicom images are not anonymised, so I cannot 
provide them.



Best,


Joëlle



*De :* freesurfer-boun...@nmr.mgh.harvard.edu 
 de la part de Yendiki, 
Anastasia 

*Envoyé :* mercredi 22 mars 2017 15:40
*À :* Freesurfer support list
*Objet :* Re: [Freesurfer] TRACULA tract reconstruction
Hi Joëlle – What images do you pass as input to TRACULA? Do you pass 
the dicom itself, or a converted file? Happy to look at your dicom, if 
it’s anonymized.


a.y

From: > on behalf of Joëlle 
Ismay Rosanne Van Der Molen >
Reply-To: Freesurfer support list >

Date: Wednesday, March 22, 2017 at 3:55 AM
To: Freesurfer support list >

Subject: Re: [Freesurfer] TRACULA tract reconstruction

Hi Anastasia and Antonin,

I apologize for the late response.
Thank you very much for the explanations!

Regarding the gradient tables, I realized that I was indeed using the 
old version of mrtrix3, and was getting tables with a flipped x 
component (sign inversion), which corresponds to the bug that 
is highlighted in the blog link you sent me. After having updated 
mrtrix3, the tables now look correct.


What seems odd, however, is that in fact mri_convert outputs the 
same gradient tables as the /old/ version of mrtrix3, that is, with a 
flipped x component.
I tried running tracula on one of our subjects using gradient 
tables obtained with the updated mrtrix3, versus those obtained 
with mri_convert, and the results are quite different. I 
attached several files, so that you could maybe take a look and tell 
me how to best interpret this:


- the bvecs from the updated mrtrix3 (mrtrix3up_bvecs)
- a screenshot from the gradient directions (FA map overlaid with V1 
map) resulting from usage of the bvecs tables from the updated mrtrix3 
(mrtrix3up_graddirs)
- a screenshot from the path reconstruction resulting from usage of 
the bvecs tables from the updated mrtrix3 (mrtrix3up_tracts)


- the bvecs from mri_convert (mriconvert_bvecs)
- a screenshot from the gradient directions resulting from usage of 
the bvecs tables from mri_convert (mriconvert_graddirs)
- a screenshot from the path reconstruction resulting from usage of 
the bvecs tables from mri_convert (mriconvert_tracts)


Note that the TRACULA steps were done using version 6.0.

Based on these outputs, my guess is that the correct bvec table is the 
one obtained with the updated version of mrtrix and not the one 
obtained with mri_convert. But I would appreciate your opinion on that.


Thanks again for your help!

Best,

Joëlle van der Molen



*De :* freesurfer-boun...@nmr.mgh.harvard.edu 
 
> de la part de 
Yendiki, Anastasia >

*Envoyé :* jeudi 16 mars 2017 22:27
*À :* Freesurfer support list
*Objet :* Re: [Freesurfer] TRACULA tract reconstruction
One potential difference is that TRACULA does not need the gradient 
vectors to be flipped. It needs to get them the way they are stored in 
the DICOM header, and that's what mri_convert outputs.


Best,
a.y


*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 
[freesurfer-boun...@nmr.mgh.harvard.edu 
] on behalf of Antonin 
Skoch [a...@ikem.cz ]

*Sent:* Wednesday, March 08, 2017 10:03 AM
*To:* freesurfer@nmr.mgh.harvard.edu 


*Subject:* Re: [Freesurfer] TRACULA tract reconstruction

Dear Joelle,

regarding the conversion to .bvecs, could you please show the example 
of difference between bvecs converted by mri_convert of FreeSurfer and 
mrconvert of mrtrix3?


Do you have most recent version of mrtrix3? There have been a quite 
extensive discussion on implementation of FSL .bvec convention in 
mrtrix3 in spring 2016:

Re: [Freesurfer] Unpacking DWI Data

[Barbara Kreilkamp]

Hi Emily,


Yes, Osirix Lite should be sufficient, I think it works by picking 
File-import and then File-export-export DICOMs (decompression is 
sometimes helpful). It should be straightforward, just have a go at it.


Hope it helps.


Best wishes,
Barbara


On 19/09/2016 00:36, Emily Louise Belleau wrote:


Hi Barbara,


Thank you so much! I have downloaded Osirix Lite, since regular Osirix 
costs a pretty penny!



So, once I have imported the dicoms, is it simply a matter of 
exporting them onto my hardrive where I would like them to be?



Thanks so much!


Emily


*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Barbara 
Kreilkamp <bakk@googlemail.com>

*Sent:* Sunday, September 18, 2016 3:21:00 PM
*To:* Freesurfer support list
*Subject:* Re: [Freesurfer] Unpacking DWI Data

Hi Emily,


I've never tried to use unpacksdcmdir but you may try the Osirix tool, 
it allows you to read in a dicom folder and save a new folder with 
subfolders according to the sequences that were run. At the same time 
you can also anonymize your data.



Does this help?

Best wishes,

Barbara


On 17/09/2016 22:17, Emily Louise Belleau wrote:


Hello Freesurfer Experts,


Our research team has recently collected data from Martinos Center. 
The entire scanning protocol (including anatomical, functional runs, 
DWI) is in one directory.



Therefore I have been using unpacksdcmdir to tell me what runs go 
with each scanning sequence. I have had no trouble unpacking the 
functional and anatomical runs. I have had difficulties unpacking the 
DWI data.  I have been recently warned that unpackdcmdir does not 
correctly unpack DWI data. Is there a work around or another tool I 
could use? It seems that most tools are for unpacking per run 
(dcmtonii), and would not work in my situation where all scans are in 
one folder?



The runs that say "err" which typically indicated something is 
missing in the scan appear to be unpacking. However, it does say on 
the terminal that there is an error but attempting to unpack anyway.


Some of the runs that say "ok" in the scan log are not unpacking 
properly.  Additionally, we are finding that  when we unpack on of 
the DWI sequences we used, we get bvec and bval files. However, we do 
not when we unpack a different DWI sequence we also ran we do not 
get  the corresponding bvec and bval files.


The command I am using, where I put related runs into related folders:
unpacksdcmdir -src dicomdir -targ  targetdir -fsfast \
  -run 2 bold nii f.nii  \
  -run 3 bold nii f.nii  \
  -run 4 bold nii f.nii  \
  -run 5 bold nii f.nii  \
  -run 6 bold nii f.nii  \
  -run 8 3danat mgz  001.mgz \
  -run 9 3danat mgz  001.mgz
Any help would be great appreciated! Thanks!
Rmily


___
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.


___
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] Unpacking DWI Data

[Barbara Kreilkamp]

Hi Emily,


I've never tried to use unpacksdcmdir but you may try the Osirix tool, 
it allows you to read in a dicom folder and save a new folder with 
subfolders according to the sequences that were run. At the same time 
you can also anonymize your data.



Does this help?

Best wishes,

Barbara


On 17/09/2016 22:17, Emily Louise Belleau wrote:


Hello Freesurfer Experts,


Our research team has recently collected data from Martinos Center. 
The entire scanning protocol (including anatomical, functional runs, 
DWI) is in one directory.



Therefore I have been using unpacksdcmdir to tell me what runs go with 
each scanning sequence. I have had no trouble unpacking the functional 
and anatomical runs. I have had difficulties unpacking the DWI data. 
 I have been recently warned that unpackdcmdir does not correctly 
unpack DWI data. Is there a work around or another tool I could use? 
It seems that most tools are for unpacking per run (dcmtonii), and 
would not work in my situation where all scans are in one folder?



The runs that say "err" which typically indicated something is missing 
in the scan appear to be unpacking. However, it does say on the 
terminal that there is an error but attempting to unpack anyway.


Some of the runs that say "ok" in the scan log are not unpacking 
properly.  Additionally, we are finding that  when we unpack on of the 
DWI sequences we used, we get bvec and bval files. However, we do not 
when we unpack a different DWI sequence we also ran we do not get  the 
corresponding bvec and bval files.


The command I am using, where I put related runs into related folders:
unpacksdcmdir -src dicomdir -targ  targetdir -fsfast \
  -run 2 bold nii f.nii  \
  -run 3 bold nii f.nii  \
  -run 4 bold nii f.nii  \
  -run 5 bold nii f.nii  \
  -run 6 bold nii f.nii  \
  -run 8 3danat mgz  001.mgz \
  -run 9 3danat mgz  001.mgz
Any help would be great appreciated! Thanks!
Rmily


___
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 tract endpoints on cortical surface

[Barbara Kreilkamp]

Thank you Anastasia, I'll try this.

Best wishes,
Barbara


On 12/08/2016 23:19, Anastasia Yendiki wrote:
> Hi Barbara - This can be done with mri_vol2surf. The projection that's
> described in that passage can be done with --projdist-max -6 6 1, and the
> surface smoothing with --surf-fwhm 6. There are other options in
> mri_vol2surf, I'd recommend playing with the settings to see what works
> better for your data.
>
> Best,
>
> a.y
>
>
> On Fri, 5 Aug 2016, Barbara Kreilkamp wrote:
>
>> Dear Freesurfers and TRACULA experts,
>>
>> Thank you for your help so far. I am trying to map the endpoints of the
>> tract probability distributions onto the cortical surface (as mentioned
>> in Solsnes et al. 2016 NI and Storsve et al. 2016 PLos).
>>
>> I've somehow gathered that I need to do this (example one endpoint):
>>
>> flirt -ref /mri/orig/T1.nii.gz -in
>> dpath/rh.ilf_AS_avg33_mni_bbr/endpt2.pd.nii.gz -applyxfm -init
>> /dmri/xfms/diff2anat.bbr.mat
>>
>> I then loaded the images in Freeview and they look reasonable together
>> with the lh.white and lh.pial surfaces: freeview -v /mri/brain -tv
>> dapth/rh.ilf_AS_agv33_mni_bbr/endpt2_anat.pd.nii.gz
>>
>> What I don't get is how to do this:
>>
>> "we projected the tract endpoints onto the gray/white matter surface by
>> sampling along the surface normal vector, anywhere within 6 mm (3
>> DWI-space voxels) of the gray/white junction and then smoothing along
>> the surface with a 2D Gaussian kernel of 6mm full width at half max."
>> (Solsnes et al. 2016)
>>
>> Any help would be greatly appreciated.
>>
>> Best wishes,
>> Barbara
>>
>> ___
>> 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.
>

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

[Freesurfer] Fwd: TRACULA tract endpoints on cortical surface

[Barbara Kreilkamp]

Dear all,

If you have some suggestions I'd greatly appreciate them.

Thank you very much,

Best wishes,

Barbara



 Forwarded Message 
Subject:TRACULA tract endpoints on cortical surface
Date:   Fri, 5 Aug 2016 12:03:02 +0200
From:   Barbara Kreilkamp <bakk@googlemail.com>
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>



Dear Freesurfers and TRACULA experts,

Thank you for your help so far. I am trying to map the endpoints of the
tract probability distributions onto the cortical surface (as mentioned
in Solsnes et al. 2016 NI and Storsve et al. 2016 PLos).

I've somehow gathered that I need to do this (example one endpoint):

flirt -ref /mri/orig/T1.nii.gz -in
dpath/rh.ilf_AS_avg33_mni_bbr/endpt2.pd.nii.gz -applyxfm -init
/dmri/xfms/diff2anat.bbr.mat

I then loaded the images in Freeview and they look reasonable together
with the lh.white and lh.pial surfaces: freeview -v /mri/brain -tv
dapth/rh.ilf_AS_agv33_mni_bbr/endpt2_anat.pd.nii.gz

What I don't get is how to do this:

"we projected the tract endpoints onto the gray/white matter surface by
sampling along the surface normal vector, anywhere within 6 mm (3
DWI-space voxels) of the gray/white junction and then smoothing along
the surface with a 2D Gaussian kernel of 6mm full width at half max."
(Solsnes et al. 2016)

Any help would be greatly appreciated.

Best wishes,
Barbara

___
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] TRACULA tract endpoints on cortical surface

[Barbara Kreilkamp]

Dear Freesurfers and TRACULA experts,

Thank you for your help so far. I am trying to map the endpoints of the
tract probability distributions onto the cortical surface (as mentioned
in Solsnes et al. 2016 NI and Storsve et al. 2016 PLos).

I've somehow gathered that I need to do this (example one endpoint):

flirt -ref /mri/orig/T1.nii.gz -in
dpath/rh.ilf_AS_avg33_mni_bbr/endpt2.pd.nii.gz -applyxfm -init
/dmri/xfms/diff2anat.bbr.mat

I then loaded the images in Freeview and they look reasonable together
with the lh.white and lh.pial surfaces: freeview -v /mri/brain -tv
dapth/rh.ilf_AS_agv33_mni_bbr/endpt2_anat.pd.nii.gz

What I don't get is how to do this:

"we projected the tract endpoints onto the gray/white matter surface by
sampling along the surface normal vector, anywhere within 6 mm (3
DWI-space voxels) of the gray/white junction and then smoothing along
the surface with a 2D Gaussian kernel of 6mm full width at half max."
(Solsnes et al. 2016)

Any help would be greatly appreciated.

Best wishes,
Barbara

___
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] flipping TRACULA tracts

[Barbara Kreilkamp]

Dear Freesurfers,

I've got data pertaining to patients with left and right-sided temporal 
lobe epilepsy (TLE).
My aim is to group those tracts according to side of epilepsy for 
waypoint comparisons.

Basically for patients with right TLE I'd like to look at right tracts 
and at the same time for patients with left TLE I'd like to look at left 
tracts (ipsilateral tracts), I need to do the same for the contralateral 
tracts.
Is there a straightforward way of doing this?

I've already copied the tracts to respective ipsi and contralateral 
byvoxel.txt files. Like so: for i in R*/dpath/rh*/pathstats.byvoxel.txt; 
do cp $i ${i/byvoxel./byvoxel_ipsiRTLE.}; done ; for i in 
R*/dpath/lh*/pathstats.byvoxel.txt; do cp $i 
${i/byvoxel./byvoxel_contraRTLE.}; done
Now I have to flip the x-coordinates in the patients with right TLE (to 
make them more comparable to the tracts of the patients with left TLE). 
That will not be a problem, but I wonder if I am missing something?
Can I then just go ahead and run trac-all -stats -c dmrircfile to 
generate the mean waypoint tracts etc.?

Thank you very much,
Best wishes,

Barbara

___
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] TRACULA fornix tractography

[Barbara Kreilkamp]

Dear Anastasia,

As we are analyzing DTI data acquired in patients with epilepsy we are 
especially interested in the fornix.
I've come across the mri_cc -f option for fornix segmentation (native 
space) but I've also read that manual tracing/labeling of the tracts 
would be needed in the 33 controls for TRACULA (training set - trctrain).
In Wakana et al. 2011 I see that the fornix was not included due to low 
reproducibility and it further states:


"the reason for the poor reproducibility is most likely due to not 
enough spatial resolution with respect to the diameter"


I wonder if you could please guide us in how to best add this tract to 
TRACULA so that it would be consistent in the methods compared with the 
other tract ROI definitions or perhaps state what were the difficulties 
in adding this particular tract to TRACULA.


Thank you very much,
Best wishes,
Barbara
___
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 group comparison p-values

[Barbara Kreilkamp]

That's great, thank you Anastasia!

Best wishes,

Barbara


On 12/07/2016 22:52, Anastasia Yendiki wrote:
> Hi Barbara - Unfortunately we are very limited right now in our options
> for point set overlay display. I guess there's nothing that would be more
> suitable for displaying values that go all the way from negative to
> positive (which is what I suspect you have).
>
> I'll submit this request to freeview headquarters :) Hopefully we can get
> it in there quickly. Thanks for your patience!
>
> a.y
>
> On Sun, 10 Jul 2016, Barbara Kreilkamp wrote:
>
>> Dear Anastasia,
>>
>> Thank you, yes that was exactly what I was attempting to do. Would you
>> be able to assist me with this following question as well please?
>>
>> How would I be able to use a different colormap under point sets please?
>> I can only find "solid color" and "heatmap" but for example a
>> blue-yellow-to-red colormap would suit my needs more.
>>
>> Thank you,
>>
>> Best wishes,
>>
>> Barbara
>>
>>
>> On 07/07/2016 13:52, Anastasia Yendiki wrote:
>>> Hi Barbara - I don't believe that freeview has an option to show colorbars
>>> for heat maps that are loaded onto waypoints (if that's what you're
>>> trying to display). We should definitely add it in the future.
>>>
>>> Best,
>>> a.y
>>>
>>> On Wed, 6 Jul 2016, Barbara Kreilkamp wrote:
>>>
>>>> Dear Freesurfers,
>>>>
>>>> I am looking for a way to add a colorbar to my p-value tract cores
>>>> generated through TRACULA.
>>>>
>>>> When I load up the images as described in the tutorial here
>>>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics
>>>>
>>>> I only get a colorbar from 0 to 28.5 which cannot reflect pvalues, and
>>>> there is no option to select my textfile with the p-values unfortunately.
>>>>
>>>> Would you please help?
>>>>
>>>> Thanks ever so,
>>>>
>>>> Barbara
>>>>
>>>> ___
>>>> 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.
>>>
>> ___
>> 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

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

Re: [Freesurfer] TRACULA tract group comparison p-values

[Barbara Kreilkamp]

Dear Anastasia,

Thank you, yes that was exactly what I was attempting to do. Would you 
be able to assist me with this following question as well please?

How would I be able to use a different colormap under point sets please? 
I can only find "solid color" and "heatmap" but for example a 
blue-yellow-to-red colormap would suit my needs more.

Thank you,

Best wishes,

Barbara


On 07/07/2016 13:52, Anastasia Yendiki wrote:
> Hi Barbara - I don't believe that freeview has an option to show colorbars
> for heat maps that are loaded onto waypoints (if that's what you're
> trying to display). We should definitely add it in the future.
>
> Best,
> a.y
>
> On Wed, 6 Jul 2016, Barbara Kreilkamp wrote:
>
>> Dear Freesurfers,
>>
>> I am looking for a way to add a colorbar to my p-value tract cores
>> generated through TRACULA.
>>
>> When I load up the images as described in the tutorial here
>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics
>>
>> I only get a colorbar from 0 to 28.5 which cannot reflect pvalues, and
>> there is no option to select my textfile with the p-values unfortunately.
>>
>> Would you please help?
>>
>> Thanks ever so,
>>
>> Barbara
>>
>> ___
>> 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.
>

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

[Freesurfer] Freeview: how to change spline color bar

[Barbara Kreilkamp]

Dear Freesurfers,

How would I be able to use a different colormap under point sets please?

I can only find "solid color" and "heatmap" but a blue to red colorbar 
would suit my needs more.

Any assistance is greatly appreciated.

Thank you,

Best wishes,

Barbara

___
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] question about white matter edits

[Barbara Kreilkamp]

Hi Rito,

I just read this today myself "Select a few control points around your 
trouble areas, space them out throughout the brain and on different 
slices. You want to pick points in a region where the wm intensity is 
lower than it should be (that is, having a voxel value less than 110)." 
from 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints_freeview


Could it be that those control points grasp voxels that already have an 
intensity of at least 110?


Best wishes,

Barbara




On 06/07/2016 17:25, Ritobrato Datta wrote:

Hi All,

We have run recon-all on T1 FLASH images have identified regions where the 
sulci were included inside the white matter boundary. We added controls points 
around the sulci (please see attached pic) and reran recon-all as follows

recon-all -autorecon2-cp -autorecon3 -subjid 

but on a lot of instances, the specified control points were not incorporated 
(please see attached image). How do we fix this, now that we have already run 
the recon-all with -autorecon2-cp and the error persists ?

Can someone please suggest ?

Thank you,

Rito and Jack



___
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.

[Freesurfer] TRACULA tract group comparison p-values

[Barbara Kreilkamp]

Dear Freesurfers,

I am looking for a way to add a colorbar to my p-value tract cores 
generated through TRACULA.

When I load up the images as described in the tutorial here 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics

I only get a colorbar from 0 to 28.5 which cannot reflect pvalues, and 
there is no option to select my textfile with the p-values unfortunately.

Would you please help?

Thanks ever so,

Barbara

___
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] segmentation issues in Temporal Lobes

[Barbara Kreilkamp]

Dear Bruce,

Thanks a lot for clarifying.

Best wishes,

Barbara


On 06/07/2016 15:57, Bruce Fischl wrote:
> Hi Barbara
>
> yes, this is intentional and shouldn't be a problem. The hippocampus has
> lots of internal structure that we don't model with the surfaces (but we do
> with the subfield stuff), but we exclude it from our analyses so you should
> be fine
>
> cheers
> Bruce
>
> On Wed, 6 Jul 2016, Barbara Kreilkamp
> wrote:
>
>> Dear Freesurfers,
>>
>> Unfortunately I am having a problem with recon-all segmentation in some of my
>> participants.
>>
>> It seems that part of the brain is cut off in the medial part of the Temporal
>> lobes (please see attachment), around the region where the hippocampus is.
>>
>> I am unable to place WM region control points, as the algorithm does not have
>> seemed to miss white matter, rather only gray matter of the hippocampus.
>>
>> I've seen on your website that also there the cortical surface does not
>> include the hippocampus, so I wonder if this is intentional? Problem is that
>> the surface here grasps some of the hippocampus but not all of it.
>>
>> What is the best way of solving this?
>>
>> Thanks very much.
>>
>> Best wishes,
>>
>> Barbara
>>
>>
> ___
> 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

[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 <bakk@googlemail.com>
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>



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

___
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] ERROR: mpr2mni305 failed

[Barbara Kreilkamp]

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.datatype offset=70 value=2

hdr.dime.bitpix offset=72 value=8

hdr.hist.orient offset=252 value=-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
___
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] hippo subfield segmentation new beta version (version 6)

[Barbara Kreilkamp]

Dear all,

Would you please help me on this one?
Thank you,
best wishes,
Barbara


 Forwarded Message 
Subject:hippo subfield segmentation new beta version (version 6)
Date:   Wed, 20 Apr 2016 11:45:02 +0100
From:   Barbara Kreilkamp <bakk@gmail.com>
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>



Dear all,

I've been reading the manuscript on version 6 freesurfer hippocampal
subfield segmentation "A computational atlas of the hippocampal
formation using ex vivo, ultra-high resolution MRI: application to
adaptive segmentation of in vivo MRI"

Can you please tell me if the type of sequence (e.g. coronal T2FLAIR vs
T2STIR) and voxel sizes of .4x.4x2mm^3 vs .4x.4x4mm^3 really make a
difference for this multi-modal algorithm?
I previously ran recon-all on 1mm isotropic T1-w scans all with similar
contrast.

It seems that the mesh fitting in version 6 is driven by the relation of
the subfields to each other rather than by contrast or signal
intensities; and also I notice the algorithm brings everything to
isotropic space anyway.

Is this correct?
Do you see a major methodological issue when using T2FLAIR (.4x.4x4mm^3)
and T2STIR (.4x.4x2mm^3) subfield volumes together?

Thank you very much,
Best wishes,
Barbara

P.s. as a side-note, I've not noticed any major differences in subfield
segmentations visually, when comparing segmentations via these two
different T2 scans.



___
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] hippo subfield segmentation new beta version (version 6)

[Barbara Kreilkamp]

Dear all,

I've been reading the manuscript on version 6 freesurfer hippocampal 
subfield segmentation "A computational atlas of the hippocampal 
formation using ex vivo, ultra-high resolution MRI: application to 
adaptive segmentation of in vivo MRI"

Can you please tell me if the type of sequence (e.g. coronal T2FLAIR vs 
T2STIR) and voxel sizes of .4x.4x2mm^3 vs .4x.4x4mm^3 really make a 
difference for this multi-modal algorithm?
I previously ran recon-all on 1mm isotropic T1-w scans all with similar 
contrast.

It seems that the mesh fitting in version 6 is driven by the relation of 
the subfields to each other rather than by contrast or signal 
intensities; and also I notice the algorithm brings everything to 
isotropic space anyway.

Is this correct?
Do you see a major methodological issue when using T2FLAIR (.4x.4x4mm^3) 
and T2STIR (.4x.4x2mm^3) subfield volumes together?

Thank you very much,
Best wishes,
Barbara

P.s. as a side-note, I've not noticed any major differences in subfield 
segmentations visually, when comparing segmentations via these two 
different T2 scans.
___
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] Freesurfer version 6.0

[Barbara Kreilkamp]

Dear Zeke,

Great, thanks for the clarification!
All the best,
Barbara

On 17/02/2016 16:53, Z K wrote:
> hello Barbara,
>
> A freesurfer v6.0-beta was released some months ago. But after various
> rounds of QA testing it was decided that additional significant
> development was required. So the beta version was withdrawn and active
> development remains ongoing in the dev version. You can download the
> latest dev version using the following link:
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/Download
>
> Anyone claiming to use "version 6.0" is using the 6.0-beta version
> released several months ago, which has been significantly modified since
> its beta release.
>
> -Zeke
>
> On 02/17/2016 11:45 AM, Barbara Kreilkamp wrote:
>> Dear all,
>>
>> Sorry to bother you again. I am a bit confused as others seem to use a
>> 'version 6.0' but I cannot find reference inthe nightly development (
>> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev ) of it being
>> called a version 6.0.
>>
>> Am I missing something?
>> I don't know where I got this link from
>> https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-beta/
>> but it does not seem to point anywhere anymore.
>>
>> Thank you very much,
>> Barbara
>>
>>
>>
>>
>> On 17/02/2016 14:30, Barbara Kreilkamp wrote:
>>> Dear Douglas,
>>>
>>> Thanks a lot, I found the version.
>>> Best wishes,
>>> Barbara
>>>
>>> On 16/02/2016 20:44, Douglas N Greve wrote:
>>>> We don't have a v6 ready. You can get a development version, you just
>>>> have to keep in mind that it is a snapshot and that the software will
>>>> change without notice.
>>>>
>>>> On 02/16/2016 02:12 PM, Barbara Kreilkamp wrote:
>>>>> Dear Freesurfer experts,
>>>>>
>>>>> How may I get Freesurfer v 6 ?
>>>>>
>>>>> Thank you very much,
>>>>> Best wishes,
>>>>> Barbara
>>>>> ___
>>>>> 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
>>
>>
> ___
> 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

Re: [Freesurfer] Freesurfer version 6.0

[Barbara Kreilkamp]

Dear all,

Sorry to bother you again. I am a bit confused as others seem to use a 
'version 6.0' but I cannot find reference inthe nightly development ( 
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev ) of it being 
called a version 6.0.

Am I missing something?
I don't know where I got this link from 
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-beta/
but it does not seem to point anywhere anymore.

Thank you very much,
Barbara




On 17/02/2016 14:30, Barbara Kreilkamp wrote:
> Dear Douglas,
>
> Thanks a lot, I found the version.
> Best wishes,
> Barbara
>
> On 16/02/2016 20:44, Douglas N Greve wrote:
>> We don't have a v6 ready. You can get a development version, you just
>> have to keep in mind that it is a snapshot and that the software will
>> change without notice.
>>
>> On 02/16/2016 02:12 PM, Barbara Kreilkamp wrote:
>>> Dear Freesurfer experts,
>>>
>>> How may I get Freesurfer v 6 ?
>>>
>>> Thank you very much,
>>> Best wishes,
>>> Barbara
>>> ___
>>> 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] Freesurfer version 6.0

[Barbara Kreilkamp]

Dear Douglas,

Thanks a lot, I found the version.
Best wishes,
Barbara

On 16/02/2016 20:44, Douglas N Greve wrote:
> We don't have a v6 ready. You can get a development version, you just
> have to keep in mind that it is a snapshot and that the software will
> change without notice.
>
> On 02/16/2016 02:12 PM, Barbara Kreilkamp wrote:
>> Dear Freesurfer experts,
>>
>> How may I get Freesurfer v 6 ?
>>
>> Thank you very much,
>> Best wishes,
>> Barbara
>> ___
>> 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.

[Freesurfer] Freesurfer version 6.0

[Barbara Kreilkamp]

Dear Freesurfer experts,

How may I get Freesurfer v 6 ?

Thank you very much,
Best wishes,
Barbara
___
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] PhD position: MRI markers of neuroinflammation in treatment pharmacoresistant epilepsy

[Barbara Kreilkamp]

Dear Freesurfers,

A PhD studentship „Identifying non-invasive imaging markers of
neuroinflammation in treatment pharmacoresistant epilepsy“ is available in
the Epilepsy Research Group (ERG) at the University of Liverpool, UK and is
supervised by Dr Simon Keller and Prof Tony Marson.

Please find all details about this position via this link:

http://www.findaphd.com/search/ProjectDetails.aspx?PJID=70289=3417

*Deadline:* Friday, January 22, 2016 - apply ASAP!

Best wishes and a Happy New Year!
Barbara Kreilkamp

PhD researcher
University of Liverpool
___
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] SNR Tracula

[Barbara Kreilkamp]

Hi Scott,

This previous post might help you.
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg41439.html

Best wishes,
Barbara

On Sun, Nov 8, 2015 at 10:43 PM, Scott Quadrelli  wrote:

> Hi,
>
> Tracula outputs the SNR for each volume in a txt file. I was wondering if
> anyone can point me to some literature on how the SNR is being calculated?
>
> Cheers,
>
> Scott Quadrelli
>
> ___
> 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 and eddy (FSL)

[Barbara Kreilkamp]

Dear Anastasia,

Thank you very much for the quick help.

Best wishes,
Barbara Anne

On 25/08/2015 22:10, Anastasia Yendiki wrote:
 Hi Barbara - Yes, just correct with the method of your choice, apply the
 rotation to the gradient vectors, pass the corrected images and gradient
 vectors to tracula, and turn off the default eddy correction (then it
 won't rotate anything, either). I'll probably make it an option in the
 upcoming version to use eddy.

 Best,
 a.y

 On Tue, 25 Aug 2015, Barbara Kreilkamp wrote:

 Dear TRACULA experts and developers,

 I am wondering whether TRACULA will allow usage of eddy, the newer
 eddy-correction tool from FSL in a newer version?

 Alternatively, it seems it would be possible to use the eddy corrected
 nifti plus bvec and bval as the original input to TRACULA and turn off
 eddy-correct and the b-vector rotation.

 Please let me know if this would be a valid approach.

 Thank you very much,
 Best wishes,
 Barbara Anne
 ___
 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.


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

[Freesurfer] TRACULA and eddy (FSL)

[Barbara Kreilkamp]

Dear TRACULA experts and developers,

I am wondering whether TRACULA will allow usage of eddy, the newer 
eddy-correction tool from FSL in a newer version?

Alternatively, it seems it would be possible to use the eddy corrected 
nifti plus bvec and bval as the original input to TRACULA and turn off 
eddy-correct and the b-vector rotation.

Please let me know if this would be a valid approach.

Thank you very much,
Best wishes,
Barbara Anne
___
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] Using TRACULA ROI for image in diffusionspace

[Barbara Kreilkamp]

Thank you very much Anastasia,
May I please check with you if what I am thinking of doing sounds correct?
I would use fslstats in FSL with the flag -R which gives me the maximum
value. For Forceps major I get a value of 200, 20% of this value would be
40, so then in the path.pd.nii.gz image I threshold every value below 40
away.
Is it fine to use the -R flag in fslstats (I do not believe I should use
the -r flag)?

Best wishes,
Barbara Anne

Usage: fslstats [-t] input [options]

-t will give a separate output line for each 3D volume of a 4D timeseries
Note - options are applied in order, e.g. -M -l 10 -M will report the
non-zero mean, apply a threshold and then report the new nonzero mean

-l lthresh : set lower threshold
-u uthresh : set upper threshold
-r   : output robust min intensity robust max intensity
-R   : output min intensity max intensity





 On 17/02/2015 14:47, Anastasia Yendiki wrote:


 Hi Barbara Anne - In each tract's directory, you'll find the tract as a
 volumetric probability distribution in the file path.pd.nii.gz. You can use
 that as an ROI to extract statistics from any other volume that's in the
 same space as the tracts (native DWI space). To be consistent with the FA,
 MD, etc stats that are produced by default by trac-all, you'd threshold
 path.pd.nii.gz to 20% of its max value before using it as an ROI.

 Hope this helps,
 a.y

 On Mon, 16 Feb 2015, Barbara Kreilkamp wrote:

 Dear TRACULA experts,

 I wonder if you could please assist me in extracting tract values from an
 image I
 transferred to diffusion space.

 I ran TRACULA on my DTI dataset, however from other structural images I
 aim to extract
 values for tracts as well.

 I also extracted DTI derived measures from these tracts of my DTI data
 (FA,MD,RD,AD),
 using this command: trac-all -stat -c dmrirc
 And now I wonder whether I could add another line to the source code of
 the stats
 command so that it would output values from that other image I have in
 diffusion
 space.

 Best wishes and thank you,
 Barbara Anne




 ___
 Freesurfer mailing 
 listfreesur...@nmr.mgh.harvard.eduhttps://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 
 athttp://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] Using TRACULA ROI for image in diffusionspace

[Barbara Kreilkamp]

Merci bien :).

On Wed, Feb 18, 2015 at 2:54 PM, Anastasia Yendiki 
ayend...@nmr.mgh.harvard.edu wrote:


 Hi Barbara Anne - Actually it's fine if you use the -r flag in fslstats,
 because that will give you a robust maximum (i.e., if there are a couple of
 voxels that are outliers with a very high value it won't take them into
 account, which is probably a good idea here). Then use 20% of that robust
 maximum as your lower threshold and voila, you have your ROI.

 Best,
 a.y


 On Wed, 18 Feb 2015, Barbara Kreilkamp wrote:

  Thank you very much Anastasia,
 May I please check with you if what I am thinking of doing sounds correct?
 I would use fslstats in FSL with the flag -R which gives me the maximum
 value. For Forceps major I get a value of 200, 20% of this value would be
 40, so then in the path.pd.nii.gz image I threshold every value below 40
 away.
 Is it fine to use the -R flag in fslstats (I do not believe I should use
 the
 -r flag)?

 Best wishes,
 Barbara Anne

 Usage: fslstats [-t] input [options]

 -t will give a separate output line for each 3D volume of a 4D timeseries
 Note - options are applied in order, e.g. -M -l 10 -M will report the
 non-zero mean, apply a threshold and then report the new nonzero mean

 -l lthresh : set lower threshold
 -u uthresh : set upper threshold
 -r   : output robust min intensity robust max intensity
 -R   : output min intensity max intensity





   On 17/02/2015 14:47, Anastasia Yendiki wrote:

   Hi Barbara Anne - In each tract's directory, you'll find
   the tract as a volumetric probability distribution in the
   file path.pd.nii.gz. You can use that as an ROI to extract
   statistics from any other volume that's in the same space
   as the tracts (native DWI space). To be consistent with
   the FA, MD, etc stats that are produced by default by
   trac-all, you'd threshold path.pd.nii.gz to 20% of its max
   value before using it as an ROI.

   Hope this helps,
   a.y

   On Mon, 16 Feb 2015, Barbara Kreilkamp wrote:

 Dear TRACULA experts,

 I wonder if you could please assist me in
 extracting tract values from an image I
 transferred to diffusion space.

 I ran TRACULA on my DTI dataset, however from
 other structural images I aim to extract
 values for tracts as well.

 I also extracted DTI derived measures from
 these tracts of my DTI data (FA,MD,RD,AD),
 using this command: trac-all -stat -c dmrirc
 And now I wonder whether I could add another
 line to the source code of the stats
 command so that it would output values from
 that other image I have in diffusion
 space.

 Best wishes and thank you,
 Barbara Anne




 ___
 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-mai
 l
 contains patient information, please contact the Partners Compliance
 HelpLin
 e at
 http://www.partners.org/complianceline . If the e-mail was sent to you
 in er
 ror
 but does not contain patient information, please contact the sender and
 prop
 erly
 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.

[Freesurfer] Using TRACULA ROI for image in diffusionspace

[Barbara Kreilkamp]

Dear TRACULA experts,

I wonder if you could please assist me in extracting tract values from an
image I transferred to diffusion space.

I ran TRACULA on my DTI dataset, however from other structural images I aim
to extract values for tracts as well.

I also extracted DTI derived measures from these tracts of my DTI data
(FA,MD,RD,AD), using this command: trac-all -stat -c dmrirc
And now I wonder whether I could add another line to the source code of the
stats command so that it would output values from that other image I have
in diffusion space.

Best wishes and thank you,
Barbara Anne
___
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 dwi flipping

[Barbara Kreilkamp]

Thank you Anastasia.
Best wishes,
Barbara


On 21/11/2014 21:45, Anastasia Yendiki wrote:
 Hi Barbara - It's converting to LAS orientation. If it the images are
 already in LAS orientation, that command will have no effect, as you say.

 a.y

 On Fri, 17 Oct 2014, Barbara Kreilkamp wrote:

 Dear all,

 Would you please explain why TRACULA is flipping the data so often? And
 what does the flip4fsl command do? The data I have is already in the
 right (radiological) orientation. fslswapdim does not seem to have an
 effect either, as the parameters are just set to 'x y z'.
 Are these commands only effective if the data is not in radiological
 convention?

 Thank you,
 Barbara

 flip4fsl
 /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/bsplineT2bet_all_controls_patients/c3826/dmri/dwi_orig.nii.gz/Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/bsplineT2bet_all_controls_patients/c3826/dmri/dwi_orig_flip.nii.gz
 INFO: input image orientation is LAS
 INFO: input image determinant is -5.02198
 fslswapdim
 /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/bsplineT2bet_all_controls_patients/c3826/dmri/dwi_orig.nii.gz
 x y z
 /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/bsplineT2bet_all_controls_patients/c3826/dmri/dwi_orig_flip.nii.gz
 fslorient -forceradiological
 /Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/bsplineT2bet_all_controls_patients/c3826/dmri/dwi_orig_flip.nii.gz

 ___
 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.


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

[Freesurfer] TRACULA dwi flipping

[Barbara Kreilkamp]

Dear all,

Would you please explain why TRACULA is flipping the data so often? And 
what does the flip4fsl command do? The data I have is already in the 
right (radiological) orientation. fslswapdim does not seem to have an 
effect either, as the parameters are just set to 'x y z'.
Are these commands only effective if the data is not in radiological 
convention?

Thank you,
Barbara

flip4fsl 
/Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/bsplineT2bet_all_controls_patients/c3826/dmri/dwi_orig.nii.gz/Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/bsplineT2bet_all_controls_patients/c3826/dmri/dwi_orig_flip.nii.gz
INFO: input image orientation is LAS
INFO: input image determinant is -5.02198
fslswapdim 
/Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/bsplineT2bet_all_controls_patients/c3826/dmri/dwi_orig.nii.gz
 
x y z 
/Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/bsplineT2bet_all_controls_patients/c3826/dmri/dwi_orig_flip.nii.gz
fslorient -forceradiological 
/Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/bsplineT2bet_all_controls_patients/c3826/dmri/dwi_orig_flip.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.

[Freesurfer] TRACULA preprocessing: bvector rotation, negative eigenvalues

[Barbara Kreilkamp]

Dear all,
Do you have suggestions/ideas for me please?
Thank you,
Barbara


 Original Message 
Subject:TRACULA preprocessing: bvector rotation, negative eigenvalues
Date:   Tue, 07 Oct 2014 19:09:00 +0100
From:   Barbara Kreilkamp bakk@gmail.com
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu



Dear Freesurfers,

I am looking for information on how exactly the b-table gets rotated.

1. It seems that eddy_correct runs once with 12 doF, and then the
bmatrix gets updated based on this registration. Would you please confirm?

2. I know that my data has negative eigenvalues (most of them seem to
appear in the 'halo' around the images), and I would like to save L2, L3
voxel values within tracts in the pathstats.byvoxel.txt file. How may I
edit dmri_pathstats to accommodate this? My aim is to identify MD, RD,
FA, AD (L1) voxel values that were biased by a lot of noise.

Thank you very much,
Best,
Barbara




___
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] TRACULA preprocessing: bvector rotation, negative eigenvalues

[Barbara Kreilkamp]

Dear Freesurfers,

I am looking for information on how exactly the b-table gets rotated.

1. It seems that eddy_correct runs once with 12 doF, and then the 
bmatrix gets updated based on this registration. Would you please confirm?

2. I know that my data has negative eigenvalues (most of them seem to 
appear in the 'halo' around the images), and I would like to save L2, L3 
voxel values within tracts in the pathstats.byvoxel.txt file. How may I 
edit dmri_pathstats to accommodate this? My aim is to identify MD, RD, 
FA, AD (L1) voxel values that were biased by a lot of noise.

Thank you very much,
Best,
Barbara


___
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] problems with tracula pre-processing (bvecs)

[Barbara Kreilkamp]

Dear all,

What does this mean? That tracula is more robust when running it seperately
for the tracts I am interested in?
Thanks,
Barbara

On Mon, Sep 15, 2014 at 4:44 PM, Michele Cavallari 
cavallari.mich...@gmail.com wrote:

 errata corrige: it did work! I had to re-run the whole thing including
 only that specific tract...and eventually it worked.

 On Fri, Sep 12, 2014 at 11:19 AM, Michele Cavallari 
 cavallari.mich...@gmail.com wrote:

 Tried...unfortunately it didn't improve

 On Thu, Sep 11, 2014 at 4:56 PM, Chris Watson 
 christopher.wat...@childrens.harvard.edu wrote:

  You can try just re-running trac-prep -prior and trac-paths for
 the L uncinate and no other tracts

  On 09/11/2014 02:58 PM, Michele Cavallari wrote:

 So, I re-ran the case with the set reinit option. It half
 worked!...in the sense that the new results show the left uncinate right,
 but the right-side one is still a dot (see screenshot of the brain view
 from the bottom).
 Any further suggestion?
 Thanks.

  [image: Inline image 2]





 On Thu, Sep 11, 2014 at 1:36 PM, Michele Cavallari 
 cavallari.mich...@gmail.com wrote:

 Thanks! it's running...

 On Thu, Sep 11, 2014 at 1:31 PM, Barbara Kreilkamp 
 bakk@googlemail.com wrote:

  Hi Michele,

 Don't think there is anything wrong with the attached dmrirc.tutorial
 file.
 You definitely need to add the '-c' flag infront of the path to your
 configuration file.
 Right now it reads the path to your file as a flag, which is of course
 not what you want.

 Best,
 Barbara




 On 11/09/2014 17:49, Michele Cavallari wrote:

 Hi Anastasia,
 I am probably doing something wrong with the syntax of the dmrirc
 file.
 I get this error message

   trac-all -prior
 /Users/michele/Desktop/tracula/sages_diff_test_tracula/sages_uncinate_dmrirc.tutorial

 ERROR: flag
 /Users/michele/Desktop/tracula/sages_diff_test_tracula/sages_uncinate_dmrirc.tutorial
 unrecognized

 -prior
 /Users/michele/Desktop/tracula/sages_diff_test_tracula/sages_uncinate_dmrirc.tutorial

  Could you please check the attached file?


 On Wed, Sep 10, 2014 at 1:51 PM, Anastasia Yendiki 
 ayend...@nmr.mgh.harvard.edu wrote:


 Thanks, Michele. Hard to tell what's causing this, perhaps a bit of
 distortion orbitofrontally. You may be able to fix this type of thing by
 reinitializing the tract reconstruction: Add set reinit = 1 to your
 configuration file, set the pathlist to include only the left and right
 uncinate, and then rerun the -prior and -path steps of trac-all on this
 subject.

 On Wed, 10 Sep 2014, Michele Cavallari wrote:

  uploaded (and activated).Thanks!



 On Wed, Sep 10, 2014 at 1:14 PM, Anastasia Yendiki 
 ayend...@nmr.mgh.harvard.edu wrote:

   Hi Michele - The anatomical segmentation does look good, but
 from the
   screenshot the DWI data seems to be noisy in the orbitofrontal
 area, which
   may be affecting the uncinate. It's hard to tell just from one
 slice.

   If you upload all the tracula output directories of this
 subject (dmri,
   dmri.bedpostX, dlabel, dpath) for me here, I'll take a look:
   https://gate.nmr.mgh.harvard.edu/filedrop2/

   Thanks!
   a.y

   On Wed, 10 Sep 2014, Michele Cavallari wrote:

 Hi Anastasia,I completed the tracula processing.
 By looking at the tractography results in the viewer I
 noticed
 that the uncinate
 fasciculus is pretty small (see attached screenshot). It
 actually appears as a small
 blue dot. And the problem is both on the left and right
 side.
 The other tracts look
 fine. I played with threshold, but the size didn't
 increase. So,
 I guess that something
 wrong happened with the tractography of that particular
 bundle.
 I checked the aparc+aseg
 output (attached): it seems right to me, but could you
 please
 double-check?
 Let me also know if you have any suggestions, and if you
 need
 more information or output
 files.
 Best,
 Michele

 Inline image 1



 On Thu, Sep 4, 2014 at 11:55 PM, Anastasia Yendiki
 ayend...@nmr.mgh.harvard.edu wrote:

   Hi Ludy - If your gradient table is formatted in 3
 rows
 you need to
   either:

   1. Convert it to 3 columns so you can use it with
 the 5.3
 version of
   tracula, which requires the gradient table to be
 formatted
 in columns

   OR

   2. Download the tracula update that can use
 gradient
 tables formatted in
   rows

   Hope this helps,
   a.y

   On Thu, 4 Sep 2014, ls...@bidmc.harvard.edu wrote:

Hi,
   
I was having similar errors as Michele

[Freesurfer] bbregister with T2 in trac-preproc

[Barbara Kreilkamp]

Dear Freesurfers,

I would like to alter the trac-preproc to include an EPI to T2 registration
(diffeomorphic) as I do not have a field map, is there a way of doing this?
I saw that bbregister actually only uses 6 doF.

Thank you very much,
Barbara
___
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] trac-all: saving tensor in dtifit

[Barbara Kreilkamp]

Dear all,

I would like to make amendments to the FSL dtifit call during trac-preproc.
In which way can I edit the call in trac-preproc?
  # LS tensor estimation
  set cmd = dtifit
  set cmd = ($cmd -k $dwidir/dwi.nii.gz)
  set cmd = ($cmd -m $brainmask)
  set cmd = ($cmd -r $dwidir/bvecs)
  set cmd = ($cmd -b $dwidir/bvals)
  set cmd = ($cmd -o $dwidir/dtifit)
  echo $cmd | tee -a $LF | tee -a $CF
  if ($RunIt) then
$fs_time $cmd | tee -a $LF
if ($status) goto error_exit
  endif

The background is that I would like to save the tensor file for being able
to correct the tensor to be positive-definite (not possible within FSL).
Then I would have to map the scalar outputs of the tensor fit (originating
from the new corrected, positive-definite tensor) to the MNI template after
that (would it be sufficient then to re-run step 1.7 in trac-all)?

Thanks a lot
Barbara
___
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] problems with tracula pre-processing (bvecs)

[Barbara Kreilkamp]

Hi Michele,

Don't think there is anything wrong with the attached dmrirc.tutorial file.
You definitely need to add the '-c' flag infront of the path to your 
configuration file.
Right now it reads the path to your file as a flag, which is of course 
not what you want.


Best,
Barbara



On 11/09/2014 17:49, Michele Cavallari wrote:

Hi Anastasia,
I am probably doing something wrong with the syntax of the dmrirc file.
I get this error message

trac-all -prior 
/Users/michele/Desktop/tracula/sages_diff_test_tracula/sages_uncinate_dmrirc.tutorial


ERROR: flag 
/Users/michele/Desktop/tracula/sages_diff_test_tracula/sages_uncinate_dmrirc.tutorial 
unrecognized


-prior 
/Users/michele/Desktop/tracula/sages_diff_test_tracula/sages_uncinate_dmrirc.tutorial



Could you please check the attached file?


On Wed, Sep 10, 2014 at 1:51 PM, Anastasia Yendiki 
ayend...@nmr.mgh.harvard.edu mailto:ayend...@nmr.mgh.harvard.edu 
wrote:



Thanks, Michele. Hard to tell what's causing this, perhaps a bit
of distortion orbitofrontally. You may be able to fix this type of
thing by reinitializing the tract reconstruction: Add set reinit
= 1 to your configuration file, set the pathlist to include only
the left and right uncinate, and then rerun the -prior and -path
steps of trac-all on this subject.

On Wed, 10 Sep 2014, Michele Cavallari wrote:

uploaded (and activated).Thanks!



On Wed, Sep 10, 2014 at 1:14 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu
mailto:ayend...@nmr.mgh.harvard.edu wrote:

  Hi Michele - The anatomical segmentation does look good,
but from the
  screenshot the DWI data seems to be noisy in the
orbitofrontal area, which
  may be affecting the uncinate. It's hard to tell just
from one slice.

  If you upload all the tracula output directories of this
subject (dmri,
  dmri.bedpostX, dlabel, dpath) for me here, I'll take a look:
https://gate.nmr.mgh.harvard.edu/filedrop2/

  Thanks!
  a.y

  On Wed, 10 Sep 2014, Michele Cavallari wrote:

Hi Anastasia,I completed the tracula processing.
By looking at the tractography results in the
viewer I noticed
that the uncinate
fasciculus is pretty small (see attached
screenshot). It
actually appears as a small
blue dot. And the problem is both on the left and
right side.
The other tracts look
fine. I played with threshold, but the size didn't
increase. So,
I guess that something
wrong happened with the tractography of that
particular bundle.
I checked the aparc+aseg
output (attached): it seems right to me, but could
you please
double-check?
Let me also know if you have any suggestions, and
if you need
more information or output
files.
Best,
Michele

Inline image 1



On Thu, Sep 4, 2014 at 11:55 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu
mailto:ayend...@nmr.mgh.harvard.edu wrote:

  Hi Ludy - If your gradient table is
formatted in 3 rows
you need to
  either:

  1. Convert it to 3 columns so you can use it
with the 5.3
version of
  tracula, which requires the gradient table
to be formatted
in columns

  OR

  2. Download the tracula update that can use
gradient
tables formatted in
  rows

  Hope this helps,
  a.y

  On Thu, 4 Sep 2014, ls...@bidmc.harvard.edu
mailto:ls...@bidmc.harvard.edu wrote:

   Hi,
  
   I was having similar errors as Michele
Cavallari
regarding error reading
  /path/to/subject/dmri/dwi_frame, but I'm
not sure it's
related to my bvecs
  file. I did try reconfiguring my bvecs file
into columns
instead of row just
  in case, but that didn't solve the problem.
It really just
looks like it
  can't find the dwi_frame file after the
mri_concat
command.
  
   I am 

[Freesurfer] freesurfer commands from MATLAB

[Barbara Kreilkamp]

Dear Freesurfers,

Is there a way of calling freesurfer-scripts from within MATLAB?
I know there are some setups needed to make MATLAB understand where it can
find the commands (I have done this before with FSL).
I am using bash, and when I type the Freesurfer commands in a terminal by
hand, they work. So I am guessing it must have to do with setting up the
environment:

freesurf_path ='Applications/freesurfer';
setenv('FREESURFDIR',freesurf_path)

setenv('FREESURFOUTPUTTYPE','NIFTI_GZ')
curpath = getenv('PATH');
setenv('PATH',sprintf('%s:%s',fullfile(freesurf_path,'bin'),curpath));

Thanks a lot for any help,
Barbara
___
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] freesurfer commands from MATLAB

[Barbara Kreilkamp]

Hi Markus,

Thank you for this, yes I am running Mac OS 10.9.2, and the freesurfer
command freeview loads the data fine when I start up matlab from the bash
terminal (even without using XQuartz, my equivalent of X11) and call this
command.
Thanks for the quick help!
Barbara



On Tue, Sep 9, 2014 at 12:59 PM, Markus Gschwind markus.gschw...@gmail.com
wrote:

 Hi Barbara,

 You haven't told us which OS you use.
 For example in Mac OS it is necessary to start up MATLAB by typing matlab
 into the X11 terminal, otherwise the system OS will not recognize the
 commands given via matlab (e.g. system('mycommand') .)

 Best,
 Markus

 2014-09-09 13:45 GMT+02:00 Barbara Kreilkamp bakk@googlemail.com:

 Dear Freesurfers,

 Is there a way of calling freesurfer-scripts from within MATLAB?
 I know there are some setups needed to make MATLAB understand where it
 can find the commands (I have done this before with FSL).
 I am using bash, and when I type the Freesurfer commands in a terminal by
 hand, they work. So I am guessing it must have to do with setting up the
 environment:

 freesurf_path ='Applications/freesurfer';
 setenv('FREESURFDIR',freesurf_path)

 setenv('FREESURFOUTPUTTYPE','NIFTI_GZ')
 curpath = getenv('PATH');
 setenv('PATH',sprintf('%s:%s',fullfile(freesurf_path,'bin'),curpath));

 Thanks a lot for any help,
 Barbara

 ___
 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.


___
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: bvec-error

[Barbara Kreilkamp]

Hi Robby,

Thanks for sharing this and making me aware of the update (great that 
this one will give you the motion parameters as well!).

So also for me it works now!
Have fun with your tracts of many subjects then :)!
Barbara


On 05/09/2014 09:22, Robby De Pauw wrote:

Hi Anastasia and Barbara

I updated Tracula and now everything is running fine.

Thx,

Robby

Robby De Pauw, drs.
*Ghent University*
Department of Physiotherapy and Rehabilitation Sciences
3B3
De Pintelaan 185
B-9000 Ghent

robby.dep...@ugent.be mailto:robby.dep...@ugent.be






On 04 Sep 2014, at 22:01, Anastasia Yendiki 
ayend...@nmr.mgh.harvard.edu mailto:ayend...@nmr.mgh.harvard.edu 
wrote:




Hi Robby - The option to specify a different gradient table for each 
scan (with bveclist) was introduced more recently. See:

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

The version that you're using doesn't recognize bveclist.

Hope this helps,
a.y

On Tue, 26 Aug 2014, Robby De Pauw wrote:


Hi Anastasia,

I'm using this version of tracula.

trac-all,v 1.22.2.12 2013/02/23 02:01:02 ayendiki Exp

I've attached the log-file you requested.

Robby De Pauw, dra.
Ghent University
Department of Physiotherapy and Rehabilitation Sciences
3B3
De Pintelaan 185
B-9000 Ghent

robby.dep...@ugent.be






___
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.


___
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] problems with tracula pre-processing (bvecs)

[Barbara Kreilkamp]

Hi Michele,

You would have to make sure that the files are written to the same 
folder for both commands (recon-all and trac-all)

Right now it seems you wrote the output of recon-all to
/PHShome/my738/FSout/FSout_P0401_e20130813_s002_Cor7minMDEFT_T1_b/

and trac-all output to
 /Users/michele/Desktop/tracula/sages_diff_test_tracula/SD40_1/

This is what the code was looking for but did not find:
Location of aparc+aseg's relative to base: dlabel/mni/aparc+aseg.nii.gz

What path did you specify for the T1 segmentations (by recon-all) in 
your configuration file?


Hope it helps,
All the best,
Barbara

On 03.09.14 17:31, Michele Cavallari wrote:

Hi Barbara,
thanks again for your help.
I checked the bvecs file using the 'more' command, and (as you pointed 
out) there was some extra text. This was likely due to MS-excel 
formatting, which I have used to reshape the bvecs file from row to 
column configuration. Such extra text was not part of the original 
bvecs file organized in rows though, but tracula was not giving errors 
as well.

So, take home message#1
It is not true that FreeSurfer 5.3 allows both rows and columns 
configuration of the bvecs (as stated in the wiki page). Or at least 
that's not true for all the scanners. I'd recommend a column 
configuration of the bvecs, even with FreeSurfer 5.3.

Also - take home message#2
verify that there's no extra text due to excel formatting in the 
reshaped bvecs file.


That said, now this lead me to the next error!
It seems that there's a problem with the recon-all output that I'm 
using (?). However, both the log file and the output of the recon-all 
processing seem fine to me.

Here is the detail of the error message I am getting
ERROR: fio_pushd: path/to/dlabel/mni
And attached are the log files of both tracula pre-processing (with 
errors) and recon-all (apparently without errors).


Any help/suggestions?
Thanks.



On Mon, Sep 1, 2014 at 5:51 AM, Barbara Kreilkamp 
bakk@googlemail.com mailto:bakk@googlemail.com wrote:


Hi Michele,

This might be the solution - try the command 'more' in unix on
your column bvec and bval, they should each have one (bval) and
three (bvec) columns and no strange symbols. But you have these
symbols in the bvec-file (probably because you have extra
formatting information, that is not needed and an obstacle to
Tracula).

more original_columns.bval

0

0

0

0

0

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

NEURO-222:tracula_help NEURO-222$ more original_columns.bvec

0 0 0

0 0 0 ^M0 0 0 ^M0 0 0 ^M0 0 0 ^M-1 0 0 ^M-0.166 0.986 0 ^M0.11
0.664 0.74 ^M-0.901 -0.419 -0.11 ^M0.169 -0.601 0.781 ^M0.815
-0.386 0.433 ^M-0.656 0.366 0.66 ^M^M-0.582 0.8 0.143 ^M-0.9 0.259
0.35 ^M-0.693 -0.698 0.178 ^M-0.357 -0.924 -0.14 ^M-0.543 -0.488
-0.683 ^M0.525 -0.396 0.753 ^M0.639 0.689 0.341 ^M0.33 -0.013
-0.944 ^M0.524 -0.783 0.335 ^M-0.609 -0.065 -0.791 ^M-0.22 -0.233
-0.947 ^M0.004 -0.91 -0.415 ^M0.511 0.627 -0.589 ^M-0.414 0.737
0.535 ^M0.679 0.139 -0.721 ^M-0.884 -0.296 0.362 ^M-0.262 0.432
0.863 ^M-0.088 0.185 -0.979 ^M-0.294 -0.907 0.302 ^M-0.887 -0.089
-0.453 ^M-0.257 -0.443 0.859 ^M-0.086 0.867 -0.491 ^M-0.863 0.504
-0.025


You are ending up with multiple columns in the second row, please
make sure they are 3 columns.


Good luck,

Barbara



On Mon, Sep 1, 2014 at 10:36 AM, Barbara Kreilkamp
bakk@googlemail.com mailto:bakk@googlemail.com wrote:

Hi Michele,

Do you use the dicoms or the nifti files as input to TRACULA?
Also, I think the complete trac-all.log could be even more
helpful.
I am a newbie myself but I am having a similar problem, so I
am trying to find a solution as well :).

Best,
Barbara


On Fri, Aug 29, 2014 at 4:48 PM, Michele Cavallari
mic...@bwh.harvard.edu mailto:mic...@bwh.harvard.edu wrote:

Hi Barbara,
thanks for your reply. I checked the dwi series on a
viewer and it looks
fine: I have 1960 dicoms, corresponding to 56 slices x 35
directions
specified in the bval/bvec. Also, I was able to obtain the
FA and MD maps
through fsl using the very same dicoms and bval/bvec.
Any suggestion?
Thanks


On Thu, Aug 28, 2014 at 7:30 PM, Barbara Kreilkamp
bakk@googlemail.com mailto:bakk@googlemail.com
wrote:
Dear Michele,

I cannot find anything wrong with your bvec and bval files.
Seeing as you had an errormessage related to the dwi

Re: [Freesurfer] problems with tracula pre-processing (bvecs)

[Barbara Kreilkamp]

Hi Michele,

Yes, tracula would have complained at the very first call, if the dwi 
data was not there.


So here is the problem, you write:
setenv 
/Users/michele/Desktop/tracula/sages_diff_test_tracula/SD40_1/FSout_P0401_e20130813_s002_Cor7minMDEFT_T1_b


in the very first line in your config file, it should read

setenv SUBJECTS_DIR 
/Users/michele/Desktop/tracula/sages_diff_test_tracula/SD40_1/FSout_P0401_e20130813_s002_Cor7minMDEFT_T1_b


The problem was that recon-all files were not found (because the path 
was never set to the right environment variable SUBJECTS_DIR.

Try now.

Best,
Barbara


On 03/09/2014 18:04, Michele Cavallari wrote:

Hi Barbara,
I checked the path. The folder with the trac-all output is is the very 
same folder of the dwi dicoms.

Attached is the dmrirc file I am using, with all the specs.
Thanks


On Wed, Sep 3, 2014 at 12:59 PM, Barbara Kreilkamp 
bakk@googlemail.com mailto:bakk@googlemail.com wrote:


Hi Michele,

You would have to make sure that the files are written to the same
folder for both commands (recon-all and trac-all)
Right now it seems you wrote the output of recon-all to
/PHShome/my738/FSout/FSout_P0401_e20130813_s002_Cor7minMDEFT_T1_b/

and trac-all output to
 /Users/michele/Desktop/tracula/sages_diff_test_tracula/SD40_1/

This is what the code was looking for but did not find:
Location of aparc+aseg's relative to base:
dlabel/mni/aparc+aseg.nii.gz

What path did you specify for the T1 segmentations (by recon-all)
in your configuration file?

Hope it helps,
All the best,
Barbara


On 03.09.14 17:31, Michele Cavallari wrote:

Hi Barbara,
thanks again for your help.
I checked the bvecs file using the 'more' command, and (as you
pointed out) there was some extra text. This was likely due to
MS-excel formatting, which I have used to reshape the bvecs file
from row to column configuration. Such extra text was not part of
the original bvecs file organized in rows though, but tracula was
not giving errors as well.
So, take home message#1
It is not true that FreeSurfer 5.3 allows both rows and columns
configuration of the bvecs (as stated in the wiki page). Or at
least that's not true for all the scanners. I'd recommend a
column configuration of the bvecs, even with FreeSurfer 5.3.
Also - take home message#2
verify that there's no extra text due to excel formatting in the
reshaped bvecs file.

That said, now this lead me to the next error!
It seems that there's a problem with the recon-all output that
I'm using (?). However, both the log file and the output of the
recon-all processing seem fine to me.
Here is the detail of the error message I am getting
ERROR: fio_pushd: path/to/dlabel/mni
And attached are the log files of both tracula pre-processing
(with errors) and recon-all (apparently without errors).

Any help/suggestions?
Thanks.



On Mon, Sep 1, 2014 at 5:51 AM, Barbara Kreilkamp
bakk@googlemail.com mailto:bakk@googlemail.com wrote:

Hi Michele,

This might be the solution - try the command 'more' in unix
on your column bvec and bval, they should each have one
(bval) and three (bvec) columns and no strange symbols. But
you have these symbols in the bvec-file (probably because you
have extra formatting information, that is not needed and an
obstacle to Tracula).

more original_columns.bval

0

0

0

0

0

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

NEURO-222:tracula_help NEURO-222$ more original_columns.bvec

0 0 0

0 0 0 ^M0 0 0 ^M0 0 0 ^M0 0 0 ^M-1 0 0 ^M-0.166 0.986 0
^M0.11 0.664 0.74 ^M-0.901 -0.419 -0.11 ^M0.169 -0.601 0.781
^M0.815 -0.386 0.433 ^M-0.656 0.366 0.66 ^M^M-0.582 0.8 0.143
^M-0.9 0.259 0.35 ^M-0.693 -0.698 0.178 ^M-0.357 -0.924 -0.14
^M-0.543 -0.488 -0.683 ^M0.525 -0.396 0.753 ^M0.639 0.689
0.341 ^M0.33 -0.013 -0.944 ^M0.524 -0.783 0.335 ^M-0.609
-0.065 -0.791 ^M-0.22 -0.233 -0.947 ^M0.004 -0.91 -0.415
^M0.511 0.627 -0.589 ^M-0.414 0.737 0.535 ^M0.679 0.139
-0.721 ^M-0.884 -0.296 0.362 ^M-0.262 0.432 0.863 ^M-0.088
0.185 -0.979 ^M-0.294 -0.907 0.302 ^M-0.887 -0.089 -0.453
^M-0.257 -0.443 0.859 ^M-0.086 0.867 -0.491 ^M-0.863 0.504
-0.025


You are ending up with multiple columns in the second row,
please make sure they are 3 columns

Re: [Freesurfer] problems with tracula pre-processing (bvecs)

[Barbara Kreilkamp]

Hi Michele,

Do you use the dicoms or the nifti files as input to TRACULA?
Also, I think the complete trac-all.log could be even more helpful.
I am a newbie myself but I am having a similar problem, so I am trying to
find a solution as well :).

Best,
Barbara


On Fri, Aug 29, 2014 at 4:48 PM, Michele Cavallari mic...@bwh.harvard.edu
wrote:

 Hi Barbara,
 thanks for your reply. I checked the dwi series on a viewer and it looks
 fine: I have 1960 dicoms, corresponding to 56 slices x 35 directions
 specified in the bval/bvec. Also, I was able to obtain the FA and MD maps
 through fsl using the very same dicoms and bval/bvec.
 Any suggestion?
 Thanks


 On Thu, Aug 28, 2014 at 7:30 PM, Barbara Kreilkamp
 bakk@googlemail.com wrote:
 Dear Michele,

 I cannot find anything wrong with your bvec and bval files.
 Seeing as you had an errormessage related to the dwi (the one about the
 dwi_frame.nii.gz): Did you check that your dwi data have the same amount of
 volumes as entries in bvec and bval?

 Good luck,
 Barbara



 On 28/08/2014 22:47, Michele Cavallari wrote:
 Hi,
 I'm having some problems with the first command of the tracula pipeline.
 I am using FreeSurfer 5.3 on a mac (OS 10.9).
 The problem seems to be related to the bvecs file. I received the following
 error message:
 niiRead(): error opening file /path/to/dmri/dwi_frame.nii.gz

 I read some threads available on your website, but couldn't figured out a
 solution yet. I tried to organize the bvecs in columns, as opposed to the
 original configuration in rows. By doing that and re-launching the
 pre-processing command I obtained a differente error message:
 Error: bvecs and bvals don't have the same number of entries

 The original bvals and bvecs files seem to have the same numbers of entries
 to me. But the bvecs file produced by the processing - both the bvecs.norot
 and the bvecs files in the dmri folder - don't have all the information of
 the vectors.

 I am enclosing a zip folder with attachments:
 1) original bvecs and bvals files organized in rows and columns
 2) bvecs and bvals files generated by tracula
 3) error logs

 Let me know if you need any other information.
 Thanks in advance for your help.


 ___
 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.

 ___
 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] problems with tracula pre-processing (bvecs)

[Barbara Kreilkamp]

Hi Michele,

This might be the solution - try the command 'more' in unix on your column
bvec and bval, they should each have one (bval) and three (bvec) columns
and no strange symbols. But you have these symbols in the bvec-file
(probably because you have extra formatting information, that is not needed
and an obstacle to Tracula).

more original_columns.bval

0

0

0

0

0

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

1000

NEURO-222:tracula_help NEURO-222$ more original_columns.bvec

0 0 0

0 0 0 ^M0 0 0 ^M0 0 0 ^M0 0 0 ^M-1 0 0 ^M-0.166 0.986 0 ^M0.11 0.664
0.74 ^M-0.901
-0.419 -0.11 ^M0.169 -0.601 0.781 ^M0.815 -0.386 0.433 ^M-0.656 0.366 0.66
^M^M-0.582 0.8 0.143 ^M-0.9 0.259 0.35 ^M-0.693 -0.698 0.178 ^M-0.357
-0.924 -0.14 ^M-0.543 -0.488 -0.683 ^M0.525 -0.396 0.753 ^M0.639 0.689
0.341 ^M0.33 -0.013 -0.944 ^M0.524 -0.783 0.335 ^M-0.609 -0.065 -0.791 ^M-0.22
-0.233 -0.947 ^M0.004 -0.91 -0.415 ^M0.511 0.627 -0.589 ^M-0.414 0.737
0.535 ^M0.679 0.139 -0.721 ^M-0.884 -0.296 0.362 ^M-0.262 0.432 0.863 ^M-0.088
0.185 -0.979 ^M-0.294 -0.907 0.302 ^M-0.887 -0.089 -0.453 ^M-0.257 -0.443
0.859 ^M-0.086 0.867 -0.491 ^M-0.863 0.504 -0.025


You are ending up with multiple columns in the second row, please make sure
they are 3 columns.


Good luck,

Barbara


On Mon, Sep 1, 2014 at 10:36 AM, Barbara Kreilkamp bakk@googlemail.com
wrote:

 Hi Michele,

 Do you use the dicoms or the nifti files as input to TRACULA?
 Also, I think the complete trac-all.log could be even more helpful.
 I am a newbie myself but I am having a similar problem, so I am trying to
 find a solution as well :).

 Best,
 Barbara


 On Fri, Aug 29, 2014 at 4:48 PM, Michele Cavallari mic...@bwh.harvard.edu
  wrote:

 Hi Barbara,
 thanks for your reply. I checked the dwi series on a viewer and it looks
 fine: I have 1960 dicoms, corresponding to 56 slices x 35 directions
 specified in the bval/bvec. Also, I was able to obtain the FA and MD maps
 through fsl using the very same dicoms and bval/bvec.
 Any suggestion?
 Thanks


 On Thu, Aug 28, 2014 at 7:30 PM, Barbara Kreilkamp
 bakk@googlemail.com wrote:
 Dear Michele,

 I cannot find anything wrong with your bvec and bval files.
 Seeing as you had an errormessage related to the dwi (the one about the
 dwi_frame.nii.gz): Did you check that your dwi data have the same amount
 of
 volumes as entries in bvec and bval?

 Good luck,
 Barbara



 On 28/08/2014 22:47, Michele Cavallari wrote:
 Hi,
 I'm having some problems with the first command of the tracula pipeline.
 I am using FreeSurfer 5.3 on a mac (OS 10.9).
 The problem seems to be related to the bvecs file. I received the
 following
 error message:
 niiRead(): error opening file /path/to/dmri/dwi_frame.nii.gz

 I read some threads available on your website, but couldn't figured out a
 solution yet. I tried to organize the bvecs in columns, as opposed to the
 original configuration in rows. By doing that and re-launching the
 pre-processing command I obtained a differente error message:
 Error: bvecs and bvals don't have the same number of entries

 The original bvals and bvecs files seem to have the same numbers of
 entries
 to me. But the bvecs file produced by the processing - both the
 bvecs.norot
 and the bvecs files in the dmri folder - don't have all the information of
 the vectors.

 I am enclosing a zip folder with attachments:
 1) original bvecs and bvals files organized in rows and columns
 2) bvecs and bvals files generated by tracula
 3) error logs

 Let me know if you need any other information.
 Thanks in advance for your help.


 ___
 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.

 ___
 Freesurfer mailing list
 Freesurfer

Re: [Freesurfer] tracula: bvec-error

[Barbara Kreilkamp]

Dear all,

Robby, are you still having the problem? Did you solve it?
I am really having the same problem, just that I am using nifti files
instead of dicoms. I am using the same version as Robby. Please find my
command+output, trac-all.log and configuration file in the attachment.
I would also appreciate any help.
Thank you,
Barbara


On Tue, Aug 26, 2014 at 8:21 AM, Robby De Pauw robby.dep...@ugent.be
 wrote:

 Hi Anastasia,

 I’m using this version of tracula.

 trac-all,v 1.22.2.12 2013/02/23 02:01:02 ayendiki Exp

 I’ve attached the log-file you requested.

  Robby De Pauw, dra.
 *Ghent University*
 Department of Physiotherapy and Rehabilitation Sciences
 3B3
 De Pintelaan 185
 B-9000 Ghent

 robby.dep...@ugent.be









 ___
 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.



Command + Output

trac-all -prep -c dmrirc_bonn_running2only.txt -no-isrunning
INFO: SUBJECTS_DIR is 
/Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients
INFO: Diffusion root is 
/Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients
Actual FREESURFER_HOME /Applications/freesurfer
trac-preproc -c 
/Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/scripts/dmrirc.local
 -log 
/Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/scripts/trac-all.log
 -cmd 
/Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/scripts/trac-all.cmd
 -no-isrunning
#-
/Applications/freesurfer/bin/trac-preproc 
#-
#@# Image corrections Tue 26 Aug 2014 10:34:54 BST
mri_convert 
/Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/data.nii.gz
 
/Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/dwi_orig.nii.gz
mri_convert 
/Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/data.nii.gz
 
/Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/dwi_orig.nii.gz
 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from 
/Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/data.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999333, -0.0350092, 0.0104045)
j_ras = (-0.0349891, 0.999385, 0.00210945)
k_ras = (0.010472, -0.001744, 0.44)
writing to 
/Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/dwi_orig.nii.gz...
flip4fsl 
/Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/dwi_orig.nii.gz
 
/Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/dwi_orig_flip.nii.gz
INFO: input image orientation is LAS
INFO: input image determinant is -5.02198
fslswapdim 
/Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/dwi_orig.nii.gz
 x y z 
/Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/dwi_orig_flip.nii.gz
fslorient -forceradiological 
/Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/dwi_orig_flip.nii.gz
mv -f 
/Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/dwi_orig_flip.mghdti.bvecs
 
/Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/bvecs
mv: rename 
/Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/dwi_orig_flip.mghdti.bvecs
 to 
/Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/bvecs:
 No such file or directory
Darwin NEURO-220.local 13.1.0 Darwin Kernel Version 13.1.0: Wed Apr  2 23:52:02 
PDT 2014; root:xnu-2422.92.1~2/RELEASE_X86_64 x86_64



My configuration file looks like this:
#
# This file contains commands that will be run by 

Re: [Freesurfer] tracula: bvec-error

[Barbara Kreilkamp]

Hi Robby,

Try this (with the backslashes), applied only to bveclist, if that does 
not work, also to subjlist and dcmlist at the same time, and let me know 
please.
I have started to process my data with a separate configuration file for 
every subject :( - as no combination of alterations to the multiple 
subject configuration file helped me.
Maybe you are luckier though. And I am still not sure if there is 
another way to solve the issue...


Thanks,
Barbara

set bveclist = ( INP_080_LISA_V_1/bvec.txt \ INP_091_KIVA_V_1/bvec.txt \ 
INP_092_LACH_V_1/bvec.txt \ INP_097_LADH_V_1/bvec.txt \ 
WAD_090_MASU_V_1/bvec.txt \ WAD_IWT047_KIMO/bvec.txt \ 
WAD_IWT043_NAME/bvec.txt \ WAD_IWT021_ALAS/bvec.txt \ 
WAD_057_PACA/bvec.txt \ WAD_047_JESE/bvec.txt \ WAD_019_NADE/bvec.txt \ 
WAD_017_CACO/bvec.txt \ INP_IWT046_KATU/bvec.txt \ 
INP_IWT045_INDE/bvec.txt \ INP_IWT007_CIHA/bvec.txt \ 
INP_IWT001_MOTA/bvec.txt \ INP_082_JAPA/bvec.txt \ INP_081_ELBA/bvec.txt 
\ INP_079_STEVA/bvec.txt \ INP_063_STCO/bvec.txt \ INP_059_CABR/bvec.txt 
\ INP_058_NEVA/bvec.txt \ INP_054_LUSO/bvec.txt \ INP_045_ELDA/bvec.txt 
\ INP_028_JEVE/bvec.txt \ INP_024_LUDE/bvec.txt \ INP_012_JAGU/bvec.txt 
\ GEZ_078_HEVA/bvec.txt \ GEZ_075_ISKL/bvec.txt \ GEZ_074_FIOR/bvec.txt 
\ GEZ_049_ELWE/bvec.txt \ GEZ_042_MADE/bvec.txt \ GEZ_038_LIDA/bvec.txt 
\ GEZ_033_LOVE/bvec.txt \ GEZ_014_GRBU/bvec.txt \ GEZ_006_ELDE/bvec.txt 
\ GEZ_004_HACO/bvec.txt )




On 01/09/2014 15:04, Robby De Pauw wrote:

Dear Barbara,

Unfortunately I haven't found a solution yet. I'll keep you up to date.

Greetings,

Robby

Robby De Pauw, dra.
*Ghent University*
Department of Physiotherapy and Rehabilitation Sciences
3B3
De Pintelaan 185
B-9000 Ghent

robby.dep...@ugent.be mailto:robby.dep...@ugent.be





On 01 Sep 2014, at 12:22, Barbara Kreilkamp bakk@googlemail.com 
mailto:bakk@googlemail.com wrote:



Dear all,

Robby, are you still having the problem? Did you solve it?
I am really having the same problem, just that I am using nifti files 
instead of dicoms. I am using the same version as Robby. Please find 
my command+output, trac-all.log and configuration file in the attachment.

I would also appreciate any help.
Thank you,
Barbara


On Tue, Aug 26, 2014 at 8:21 AM, Robby De Pauw
robby.dep...@ugent.be mailto:robby.dep...@ugent.be wrote:

Hi Anastasia,

I'm using this version of tracula.

trac-all,v 1.22.2.12 2013/02/23 02:01:02 ayendiki Exp

I've attached the log-file you requested.

Robby De Pauw, dra.
*Ghent University*
Department of Physiotherapy and Rehabilitation Sciences
3B3
De Pintelaan 185
B-9000 Ghent

robby.dep...@ugent.be mailto:robby.dep...@ugent.be









___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
mailto: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.



trac-all_error_dwi_orig_flip.mghdti.bvecs_notfound.txt 
\___

Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu mailto: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.


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


The information in this e-mail

Re: [Freesurfer] recon-all normalization: bias field output

[Barbara Kreilkamp]

Dear Freesurfers,

The recon-all.log does not give info about the intermediate outputs (like
nu2_est and nu2_field mnc-files),
could you please confirm that the nu2_field.mnc is the bias field volume?
It is the biggest file of all and is one of the last files generated by the
script, but I would like to be sure.

Thank you very much,
Barbara


On Thu, Aug 28, 2014 at 3:27 PM, Barbara Kreilkamp bakk@googlemail.com
wrote:

 Dear Bruce and Christian,

 I found the easy way of simply writing 'set cleanup = 0' at the beginning
 of mri_nu_correct.mni and then I run this command
 mri_nu_correct.mni --i T2-scic/mri/orig/001.mgz --o nu.mgz --n 2

 This way I get all the masks and iterations that were computed.

 Now I also see that it generates as many folders as there are iterations,
 ending with nu2_field and nu2_est if there are two iterations. I see more
 files now and now I am thinking that the last output is nu2_field, which
 would be the bias field.
 So this is why I did not divide anything by hand (also because my 001.mgz
 and the nu.mgz do not have the same image dimensions) and the info about
 masked-out voxel would be missing in that case.

 All the best and thanks.
 Barbara



 On 28/08/2014 14:46, Bruce Fischl wrote:

 Hi Barbara
 what exactly did you divide? If you look at the recon-all.log it will
 show the exact inputs and outputs of nu_correct.

 cheers
 Bruce


 On Thu, 28 Aug 2014, Barbara Kreilkamp wrote:

  Dear Christian,

 Thanks a bunch for this answer. I ran all the steps you mentioned
 (except for the one where I simply do uncorrected/corrected, as these
 images have different dimensions, it seems nu3 does more than just
 normalization of intensities, but also image cropping). Do you know
 anything about the image cropping?

 I ended up with the output nu1_mask and nu1_est and I think the last one
 is the bias field, at least it looks very much like one :). Am I right?

 Thanks for your help,
 Barbara


 On 27/08/2014 22:53, Christian Thode Larsen wrote:

 Hi Barbara,

 I'm not aware of any way that you can do it directly by passing
 arguments to recon-all (some might correct me on that), but it is
 possible:

 1) As N3 models the bias as a multiplicative effect uncorrected =
 corrected * bias, the simplest way is to divide each voxel of the volume
 before and after correction, in order to obtain a volume containing the
 bias. Note that N3 (by default) works within a mask where low-intensity
 voxels have been thresholded away. These voxels will contain garbage if
 you divide all voxels in the volume.

 2) Somewhat more complicated: you can specify the -keeptmp flag combined
 with -tmp SOMEDIR/ (remember the trailing slash) to N3, in order to
 preserve its working files. This requires you to modify the N3 binary
 call in the mri_nu_correct.mni script. You also need to convert the mnc
 files from the tmp dir, so that you can work with the volumes.

 3) if you do 2), you also get hold of the low-intensity voxel mask that
 N3 operates within. You can use this to constrain the division mentioned
 in 1).

 Best,
 Christian

 On 8/27/2014 11:18 PM, Barbara Kreilkamp wrote:

 Dear all,

 Is there a way to output the N3's (non-parametric normalization step)
 output?
 I am interested in the bias field that was computed to correct the
 image
 intensities.

 Thank you for your help,
 Barbara
 ___
 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

 ___
 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



___
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

Re: [Freesurfer] recon-all normalization: bias field output

[Barbara Kreilkamp]

Dear Christian,

Thanks a bunch for this answer. I ran all the steps you mentioned 
(except for the one where I simply do uncorrected/corrected, as these 
images have different dimensions, it seems nu3 does more than just 
normalization of intensities, but also image cropping). Do you know 
anything about the image cropping?

I ended up with the output nu1_mask and nu1_est and I think the last one 
is the bias field, at least it looks very much like one :). Am I right?

Thanks for your help,
Barbara


On 27/08/2014 22:53, Christian Thode Larsen wrote:
 Hi Barbara,

 I'm not aware of any way that you can do it directly by passing
 arguments to recon-all (some might correct me on that), but it is possible:

 1) As N3 models the bias as a multiplicative effect uncorrected =
 corrected * bias, the simplest way is to divide each voxel of the volume
 before and after correction, in order to obtain a volume containing the
 bias. Note that N3 (by default) works within a mask where low-intensity
 voxels have been thresholded away. These voxels will contain garbage if
 you divide all voxels in the volume.

 2) Somewhat more complicated: you can specify the -keeptmp flag combined
 with -tmp SOMEDIR/ (remember the trailing slash) to N3, in order to
 preserve its working files. This requires you to modify the N3 binary
 call in the mri_nu_correct.mni script. You also need to convert the mnc
 files from the tmp dir, so that you can work with the volumes.

 3) if you do 2), you also get hold of the low-intensity voxel mask that
 N3 operates within. You can use this to constrain the division mentioned
 in 1).

 Best,
 Christian

 On 8/27/2014 11:18 PM, Barbara Kreilkamp wrote:
 Dear all,

 Is there a way to output the N3's (non-parametric normalization step)
 output?
 I am interested in the bias field that was computed to correct the image
 intensities.

 Thank you for your help,
 Barbara
 ___
 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

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

Re: [Freesurfer] recon-all normalization: bias field output

[Barbara Kreilkamp]

Dear Bruce and Christian,

I found the easy way of simply writing 'set cleanup = 0' at the 
beginning of mri_nu_correct.mni and then I run this command
mri_nu_correct.mni --i T2-scic/mri/orig/001.mgz --o nu.mgz --n 2

This way I get all the masks and iterations that were computed.

Now I also see that it generates as many folders as there are 
iterations, ending with nu2_field and nu2_est if there are two 
iterations. I see more files now and now I am thinking that the last 
output is nu2_field, which would be the bias field.
So this is why I did not divide anything by hand (also because my 
001.mgz and the nu.mgz do not have the same image dimensions) and the 
info about masked-out voxel would be missing in that case.

All the best and thanks.
Barbara


On 28/08/2014 14:46, Bruce Fischl wrote:
 Hi Barbara
 what exactly did you divide? If you look at the recon-all.log it will
 show the exact inputs and outputs of nu_correct.

 cheers
 Bruce


 On Thu, 28 Aug 2014, Barbara Kreilkamp wrote:

 Dear Christian,

 Thanks a bunch for this answer. I ran all the steps you mentioned
 (except for the one where I simply do uncorrected/corrected, as these
 images have different dimensions, it seems nu3 does more than just
 normalization of intensities, but also image cropping). Do you know
 anything about the image cropping?

 I ended up with the output nu1_mask and nu1_est and I think the last one
 is the bias field, at least it looks very much like one :). Am I right?

 Thanks for your help,
 Barbara


 On 27/08/2014 22:53, Christian Thode Larsen wrote:
 Hi Barbara,

 I'm not aware of any way that you can do it directly by passing
 arguments to recon-all (some might correct me on that), but it is possible:

 1) As N3 models the bias as a multiplicative effect uncorrected =
 corrected * bias, the simplest way is to divide each voxel of the volume
 before and after correction, in order to obtain a volume containing the
 bias. Note that N3 (by default) works within a mask where low-intensity
 voxels have been thresholded away. These voxels will contain garbage if
 you divide all voxels in the volume.

 2) Somewhat more complicated: you can specify the -keeptmp flag combined
 with -tmp SOMEDIR/ (remember the trailing slash) to N3, in order to
 preserve its working files. This requires you to modify the N3 binary
 call in the mri_nu_correct.mni script. You also need to convert the mnc
 files from the tmp dir, so that you can work with the volumes.

 3) if you do 2), you also get hold of the low-intensity voxel mask that
 N3 operates within. You can use this to constrain the division mentioned
 in 1).

 Best,
 Christian

 On 8/27/2014 11:18 PM, Barbara Kreilkamp wrote:
 Dear all,

 Is there a way to output the N3's (non-parametric normalization step)
 output?
 I am interested in the bias field that was computed to correct the image
 intensities.

 Thank you for your help,
 Barbara
 ___
 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
 ___
 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

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

Re: [Freesurfer] problems with tracula pre-processing (bvecs)

[Barbara Kreilkamp]

Dear Michele,

I cannot find anything wrong with your bvec and bval files.
Seeing as you had an errormessage related to the dwi (the one about the 
dwi_frame.nii.gz): Did you check that your dwi data have the same amount 
of volumes as entries in bvec and bval?


Good luck,
Barbara


On 28/08/2014 22:47, Michele Cavallari wrote:

Hi,
I'm having some problems with the first command of the tracula pipeline.
I am using FreeSurfer 5.3 on a mac (OS 10.9).
The problem seems to be related to the bvecs file. I received the following
error message:
niiRead(): error opening file /path/to/dmri/dwi_frame.nii.gz

I read some threads available on your website, but couldn't figured out a
solution yet. I tried to organize the bvecs in columns, as opposed to the
original configuration in rows. By doing that and re-launching the
pre-processing command I obtained a differente error message:
Error: bvecs and bvals don't have the same number of entries

The original bvals and bvecs files seem to have the same numbers of entries
to me. But the bvecs file produced by the processing - both the bvecs.norot
and the bvecs files in the dmri folder - don't have all the information of
the vectors.

I am enclosing a zip folder with attachments:
1) original bvecs and bvals files organized in rows and columns
2) bvecs and bvals files generated by tracula
3) error logs

Let me know if you need any other information.
Thanks in advance for your help.


___
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.

[Freesurfer] recon-all normalization: bias field output

[Barbara Kreilkamp]

Dear all,

Is there a way to output the N3's (non-parametric normalization step) 
output?
I am interested in the bias field that was computed to correct the image 
intensities.

Thank you for your help,
Barbara
___
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] trac-all bvec (nifti many subjects)

[Barbara Kreilkamp]

Dear Freesurfers,

I am trying to run trac-all with many subjects through a configuration file.
The first subject gets processed without error, but after that I keep
getting errors, that the dwi_orig_flip.mghdti.bvecs file cannot be found.

This is my command with the output (below configuration file and the log
file)

trac-all -prep -c dmrirc_bonn_running2only.txt -no-isrunning
INFO: SUBJECTS_DIR is
/Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients
INFO: Diffusion root is
/Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients
Actual FREESURFER_HOME /Applications/freesurfer
trac-preproc -c
/Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/scripts/dmrirc.local
-log
/Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/scripts/trac-all.log
-cmd
/Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/scripts/trac-all.cmd
-no-isrunning
#-
/Applications/freesurfer/bin/trac-preproc
#-
#@# Image corrections Tue 26 Aug 2014 10:34:54 BST
mri_convert
/Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/data.nii.gz
/Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/dwi_orig.nii.gz
mri_convert
/Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/data.nii.gz
/Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/dwi_orig.nii.gz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from
/Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/data.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999333, -0.0350092, 0.0104045)
j_ras = (-0.0349891, 0.999385, 0.00210945)
k_ras = (0.010472, -0.001744, 0.44)
writing to
/Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/dwi_orig.nii.gz...
flip4fsl
/Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/dwi_orig.nii.gz
/Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/dwi_orig_flip.nii.gz
INFO: input image orientation is LAS
INFO: input image determinant is -5.02198
fslswapdim
/Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/dwi_orig.nii.gz
x y z
/Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/dwi_orig_flip.nii.gz
fslorient -forceradiological
/Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/dwi_orig_flip.nii.gz
mv -f
/Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/dwi_orig_flip.mghdti.bvecs
/Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/bvecs
mv: rename
/Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/dwi_orig_flip.mghdti.bvecs
to
/Users/NEURO-220/Desktop/Neuroimaging/KREILKAMP/Freesurfer_test_data_results/Bonn/all_controls_patients/4099/dmri/bvecs:
No such file or directory
Darwin NEURO-220.local 13.1.0 Darwin Kernel Version 13.1.0: Wed Apr  2
23:52:02 PDT 2014; root:xnu-2422.92.1~2/RELEASE_X86_64 x86_64


Thanks in advance for all your help!
All the best,
Barbara



My configuration file looks like this:
#
# 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: 2013/02/16 22:49:06 $
#$Revision: 1.3.2.4 $
#
# 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