Thanks Doug! It works!

Best Wishes, Elijah  On 21 June 2017 at 16:09:29, Douglas N Greve (greve@nmr.mgh.harvard.edu) wrote:

use this script

https://gate.nmr.mgh.harvard.edu/safelinks/greve/gtmstats2table

On 06/21/2017 10:53 AM, Elijah Mak wrote:

Hi Freesurfer Team

Apologies for bumping this thread up again. I am wondering if is there is a way to extract the ROI stats in gtm.stats.dat after mri_gtmpvc (using a similar approach such as asegstats2table)?

Thanks for your help!

Best Wishes, Elijah

On 16 June 2017 at 16:53:33, Elijah Mak (fkm24@medschl.cam.ac.uk mailto:fkm24@medschl.cam.ac.uk) wrote:

...

Hi Unix experts,

I am trying to extract the PVC-ed values from gtm.stats.dat for every subject. Is there a fast way to do this using a similar workflow with asegstats2table? Thanks.

Best Wishes, Elijah

---

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

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

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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.

Hi Paul,

I did the following steps

1. Save the file into $FREESURFER/bin (you might need to modify permissions)

2. Create a list of GTM directories from the subjects

for i in `cat list_of_subjects`; do echo $i/gtmpvc.output  >> gtmdirlist

3. Run gtmstats2table with gtmdirlist as the input

gtmstats2table --f gtmdirlist --o data/gtmstats.csv

Hope that helps.

Best Wishes, Elijah

Elijah Mak, Research Associate Department of Psychiatry,  Old Age Psychiatry Group University of Cambridge Trinity College, CB21TQ, UK http://www.neuroscience.cam.ac.uk/directory/profile.php?fkm24

On 29 June 2017 at 18:27:13, miracle ozzoude (miracooloz@gmail.com) wrote:

Hello Elijah,

I want to extract this values like you did. How do I use the script doug recommended?

Thanks Paul

On Wed, Jun 21, 2017 at 11:47 AM, Elijah Mak fkm24@medschl.cam.ac.uk wrote: Thanks Doug! It works!

Best Wishes, Elijah  On 21 June 2017 at 16:09:29, Douglas N Greve (greve@nmr.mgh.harvard.edu) wrote:

use this script

https://gate.nmr.mgh.harvard.edu/safelinks/greve/gtmstats2table

On 06/21/2017 10:53 AM, Elijah Mak wrote:

Hi Freesurfer Team

Apologies for bumping this thread up again. I am wondering if is there is a way to extract the ROI stats in gtm.stats.dat after mri_gtmpvc (using a similar approach such as asegstats2table)?

Thanks for your help!

Best Wishes, Elijah

On 16 June 2017 at 16:53:33, Elijah Mak (fkm24@medschl.cam.ac.uk mailto:fkm24@medschl.cam.ac.uk) wrote:

...

Hi Unix experts,

I am trying to extract the PVC-ed values from gtm.stats.dat for every subject. Is there a fast way to do this using a similar workflow with asegstats2table? Thanks.

Best Wishes, Elijah

---

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

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

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

_______________________________________________ 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.