Hi Fs Experts, I am working on FA ROI analysis for my subjects, I did the following:
1. Mri_vol2vol -mov fa.nii -reg register.dat -fstarg -interp nearest -o fa.anat.mgh
2. Mri_segstat wmparc.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt -I fa.anat.mgh -sum fa.stats Then I used less fa.stats in order to view the statistics results... my question here is: can I use aparc+aseg.mgz instead of wmparc.mgz in my command line in step 2 in order to exclude the unsegmentedwhite matter in the output stats.
Thanks, Mohamad
yes On 06/26/2014 04:49 PM, Alshikho, Mohamad J. wrote:
Hi Fs Experts,
I am working on FA ROI analysis for my subjects, I did the following:
1.Mri_vol2vol –mov fa.nii –reg register.dat –fstarg –interp nearest –o fa.anat.mgh
2.Mri_segstat wmparc.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt –I fa.anat.mgh –sum fa.stats
Then I used less fa.stats in order to view the statistics results… my question here is:
can I use aparc+aseg.mgz instead of wmparc.mgz in my command line in step 2 in order to exclude the unsegmentedwhite matter in the output stats.
Thanks,
Mohamad
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thank you Doug, Kindly I have one more question.. What is the best way to deal with unsegmented white matter in wmparc.mgz and is there any other atlases that can give me better results regarding this huge structure of unsegmented white matter?
Mohamad
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Thursday, June 26, 2014 5:03 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] aparc+aseg OR wmparc
yes On 06/26/2014 04:49 PM, Alshikho, Mohamad J. wrote:
Hi Fs Experts,
I am working on FA ROI analysis for my subjects, I did the following:
1.Mri_vol2vol -mov fa.nii -reg register.dat -fstarg -interp nearest -o fa.anat.mgh
2.Mri_segstat wmparc.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt -I fa.anat.mgh -sum fa.stats
Then I used less fa.stats in order to view the statistics results... my question here is:
can I use aparc+aseg.mgz instead of wmparc.mgz in my command line in step 2 in order to exclude the unsegmentedwhite matter in the output stats.
Thanks,
Mohamad
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
Sorry, I think I misunderstood your first question. What do you mean you want to exclude the unsegmented WM? doug
On 06/26/2014 05:27 PM, Alshikho, Mohamad J. wrote:
Thank you Doug, Kindly I have one more question.. What is the best way to deal with unsegmented white matter in wmparc.mgz and is there any other atlases that can give me better results regarding this huge structure of unsegmented white matter?
Mohamad
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Thursday, June 26, 2014 5:03 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] aparc+aseg OR wmparc
yes On 06/26/2014 04:49 PM, Alshikho, Mohamad J. wrote:
Hi Fs Experts,
I am working on FA ROI analysis for my subjects, I did the following:
1.Mri_vol2vol -mov fa.nii -reg register.dat -fstarg -interp nearest -o fa.anat.mgh
2.Mri_segstat wmparc.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt -I fa.anat.mgh -sum fa.stats
Then I used less fa.stats in order to view the statistics results... my question here is:
can I use aparc+aseg.mgz instead of wmparc.mgz in my command line in step 2 in order to exclude the unsegmentedwhite matter in the output stats.
Thanks,
Mohamad
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I thought that I will find more details about this unsegmented white matter in aparc+aseg; Actually my problem here is how can I deal with this huge unsegmented white matter?
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Thursday, June 26, 2014 5:43 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] aparc+aseg OR wmparc
Sorry, I think I misunderstood your first question. What do you mean you want to exclude the unsegmented WM? doug
On 06/26/2014 05:27 PM, Alshikho, Mohamad J. wrote:
Thank you Doug, Kindly I have one more question.. What is the best way to deal with unsegmented white matter in wmparc.mgz and is there any other atlases that can give me better results regarding this huge structure of unsegmented white matter?
Mohamad
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Thursday, June 26, 2014 5:03 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] aparc+aseg OR wmparc
yes On 06/26/2014 04:49 PM, Alshikho, Mohamad J. wrote:
Hi Fs Experts,
I am working on FA ROI analysis for my subjects, I did the following:
1.Mri_vol2vol -mov fa.nii -reg register.dat -fstarg -interp nearest -o fa.anat.mgh
2.Mri_segstat wmparc.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt -I fa.anat.mgh -sum fa.stats
Then I used less fa.stats in order to view the statistics results... my question here is:
can I use aparc+aseg.mgz instead of wmparc.mgz in my command line in step 2 in order to exclude the unsegmentedwhite matter in the output stats.
Thanks,
Mohamad
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
what do you mean? Do you want to have it labelled as something instead of being "unsegmented"? wmparc is a gyral segmentation of WM, so away from a gyrus it does not have much meaning. We semi-arbitrarily set the threshold to be 5mm. But you can set the number to be something very large, and all WM will be assigned to a gyrus
On 06/26/2014 06:00 PM, Alshikho, Mohamad J. wrote:
I thought that I will find more details about this unsegmented white matter in aparc+aseg; Actually my problem here is how can I deal with this huge unsegmented white matter?
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Thursday, June 26, 2014 5:43 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] aparc+aseg OR wmparc
Sorry, I think I misunderstood your first question. What do you mean you want to exclude the unsegmented WM? doug
On 06/26/2014 05:27 PM, Alshikho, Mohamad J. wrote:
Thank you Doug, Kindly I have one more question.. What is the best way to deal with unsegmented white matter in wmparc.mgz and is there any other atlases that can give me better results regarding this huge structure of unsegmented white matter?
Mohamad
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Thursday, June 26, 2014 5:03 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] aparc+aseg OR wmparc
yes On 06/26/2014 04:49 PM, Alshikho, Mohamad J. wrote:
Hi Fs Experts,
I am working on FA ROI analysis for my subjects, I did the following:
1.Mri_vol2vol -mov fa.nii -reg register.dat -fstarg -interp nearest -o fa.anat.mgh
2.Mri_segstat wmparc.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt -I fa.anat.mgh -sum fa.stats
Then I used less fa.stats in order to view the statistics results... my question here is:
can I use aparc+aseg.mgz instead of wmparc.mgz in my command line in step 2 in order to exclude the unsegmentedwhite matter in the output stats.
Thanks,
Mohamad
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Can I classify this unsegmented white matter into lobes?!
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Friday, June 27, 2014 2:25 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] aparc+aseg OR wmparc
what do you mean? Do you want to have it labelled as something instead of being "unsegmented"? wmparc is a gyral segmentation of WM, so away from a gyrus it does not have much meaning. We semi-arbitrarily set the threshold to be 5mm. But you can set the number to be something very large, and all WM will be assigned to a gyrus
On 06/26/2014 06:00 PM, Alshikho, Mohamad J. wrote:
I thought that I will find more details about this unsegmented white matter in aparc+aseg; Actually my problem here is how can I deal with this huge unsegmented white matter?
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Thursday, June 26, 2014 5:43 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] aparc+aseg OR wmparc
Sorry, I think I misunderstood your first question. What do you mean you want to exclude the unsegmented WM? doug
On 06/26/2014 05:27 PM, Alshikho, Mohamad J. wrote:
Thank you Doug, Kindly I have one more question.. What is the best way to deal with unsegmented white matter in wmparc.mgz and is there any other atlases that can give me better results regarding this huge structure of unsegmented white matter?
Mohamad
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Thursday, June 26, 2014 5:03 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] aparc+aseg OR wmparc
yes On 06/26/2014 04:49 PM, Alshikho, Mohamad J. wrote:
Hi Fs Experts,
I am working on FA ROI analysis for my subjects, I did the following:
1.Mri_vol2vol -mov fa.nii -reg register.dat -fstarg -interp nearest -o fa.anat.mgh
2.Mri_segstat wmparc.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt -I fa.anat.mgh -sum fa.stats
Then I used less fa.stats in order to view the statistics results... my question here is:
can I use aparc+aseg.mgz instead of wmparc.mgz in my command line in step 2 in order to exclude the unsegmentedwhite matter in the output stats.
Thanks,
Mohamad
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
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
You could create a 2nd wmparc allowing it to fill in the unsegmented with the closest gyral parcellation, then merge the parcellations into lobes, then only look at the lobes in the unsegmented region from the 1st wmparc.
or you could also run
mri_annotation2label --subject $subject --hemi $hemi --lobesStrict lobes
to create a lobes surface annotation (or customize it to make your own), then you could run mri_aparc2aseg to create a new wmpar with the lobes annotation.
On 06/27/2014 02:35 PM, Alshikho, Mohamad J. wrote:
Can I classify this unsegmented white matter into lobes?!
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Friday, June 27, 2014 2:25 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] aparc+aseg OR wmparc
what do you mean? Do you want to have it labelled as something instead of being "unsegmented"? wmparc is a gyral segmentation of WM, so away from a gyrus it does not have much meaning. We semi-arbitrarily set the threshold to be 5mm. But you can set the number to be something very large, and all WM will be assigned to a gyrus
On 06/26/2014 06:00 PM, Alshikho, Mohamad J. wrote:
I thought that I will find more details about this unsegmented white matter in aparc+aseg; Actually my problem here is how can I deal with this huge unsegmented white matter?
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Thursday, June 26, 2014 5:43 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] aparc+aseg OR wmparc
Sorry, I think I misunderstood your first question. What do you mean you want to exclude the unsegmented WM? doug
On 06/26/2014 05:27 PM, Alshikho, Mohamad J. wrote:
Thank you Doug, Kindly I have one more question.. What is the best way to deal with unsegmented white matter in wmparc.mgz and is there any other atlases that can give me better results regarding this huge structure of unsegmented white matter?
Mohamad
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Thursday, June 26, 2014 5:03 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] aparc+aseg OR wmparc
yes On 06/26/2014 04:49 PM, Alshikho, Mohamad J. wrote:
Hi Fs Experts,
I am working on FA ROI analysis for my subjects, I did the following:
1.Mri_vol2vol -mov fa.nii -reg register.dat -fstarg -interp nearest -o fa.anat.mgh
2.Mri_segstat wmparc.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt -I fa.anat.mgh -sum fa.stats
Then I used less fa.stats in order to view the statistics results... my question here is:
can I use aparc+aseg.mgz instead of wmparc.mgz in my command line in step 2 in order to exclude the unsegmentedwhite matter in the output stats.
Thanks,
Mohamad
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
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thank you Doug, This is ammazing!
Mohamad
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Friday, June 27, 2014 3:19 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] aparc+aseg OR wmparc
You could create a 2nd wmparc allowing it to fill in the unsegmented with the closest gyral parcellation, then merge the parcellations into lobes, then only look at the lobes in the unsegmented region from the 1st wmparc.
or you could also run
mri_annotation2label --subject $subject --hemi $hemi --lobesStrict lobes
to create a lobes surface annotation (or customize it to make your own), then you could run mri_aparc2aseg to create a new wmpar with the lobes annotation.
On 06/27/2014 02:35 PM, Alshikho, Mohamad J. wrote:
Can I classify this unsegmented white matter into lobes?!
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Friday, June 27, 2014 2:25 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] aparc+aseg OR wmparc
what do you mean? Do you want to have it labelled as something instead of being "unsegmented"? wmparc is a gyral segmentation of WM, so away from a gyrus it does not have much meaning. We semi-arbitrarily set the threshold to be 5mm. But you can set the number to be something very large, and all WM will be assigned to a gyrus
On 06/26/2014 06:00 PM, Alshikho, Mohamad J. wrote:
I thought that I will find more details about this unsegmented white matter in aparc+aseg; Actually my problem here is how can I deal with this huge unsegmented white matter?
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Thursday, June 26, 2014 5:43 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] aparc+aseg OR wmparc
Sorry, I think I misunderstood your first question. What do you mean you want to exclude the unsegmented WM? doug
On 06/26/2014 05:27 PM, Alshikho, Mohamad J. wrote:
Thank you Doug, Kindly I have one more question.. What is the best way to deal with unsegmented white matter in wmparc.mgz and is there any other atlases that can give me better results regarding this huge structure of unsegmented white matter?
Mohamad
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Thursday, June 26, 2014 5:03 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] aparc+aseg OR wmparc
yes On 06/26/2014 04:49 PM, Alshikho, Mohamad J. wrote:
Hi Fs Experts,
I am working on FA ROI analysis for my subjects, I did the following:
1.Mri_vol2vol -mov fa.nii -reg register.dat -fstarg -interp nearest -o fa.anat.mgh
2.Mri_segstat wmparc.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt -I fa.anat.mgh -sum fa.stats
Then I used less fa.stats in order to view the statistics results... my question here is:
can I use aparc+aseg.mgz instead of wmparc.mgz in my command line in step 2 in order to exclude the unsegmentedwhite matter in the output stats.
Thanks,
Mohamad
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
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
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
freesurfer@nmr.mgh.harvard.edu
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Alshikho, Mohamad J. -
Douglas N Greve