That label2vol command maps the aseg into the epi space to create test1
so it will only have 1 frame. The epi never comes into play there
except as a geometry template. If you want to extract a time course from
the epi, then map it to the anatomical space with that vol2vol command
using the epi as the --mov, then run mri_segstats. That label2vol
command is not necessary.
doug
On 1/27/15 12:13 PM, sabin khadka wrote:
Hi doug. I now see the problem. When I run mri_info the test1.nii.gz
and test2.nii.gz both have only 1 frame. But when I run
# mri_label2vol --aparc+aseg --subject <sub id> --temp <EPI.nii.gz>
--fillthresh 0.5 --reg regsiter.dat --o test1.nii.gz
# mri_vol2vol --mov test1.nii.gz --targ <sub id/mri/aparc+aseg.mgz>
--reg register.dat --o test2.nii.gz
EPI.nii.gz is 4D image with 210 frames. How can I get test1.nii.gz and
test2.nii.gz in 4D format? Should be something basic but I could not
figure out how.
I appreciate your help!!
Cheers,
Sabin Khadka
------------------------------------------------------------------------
*From:* Douglas Greve <gr...@nmr.mgh.harvard.edu>
*To:* sabin khadka <sabink...@yahoo.com>; Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu>
*Sent:* Tuesday, January 27, 2015 10:31 AM
*Subject:* Re: [Freesurfer] Extract mean time series from parcellated
region
It all looks correct. How many frames does test2.nii.gz have? Try
running mri_info test2.nii.gz to see
On 1/27/15 9:05 AM, sabin khadka wrote:
Hi Doug- The command doesn't error out but it just give me one value.
I was assuming the following command would give me value in time
series x mean value in text file. Am I following correct
strategy/commands?
Cheers,
Sabin Khadka
------------------------------------------------------------------------
*From:* Douglas Greve <gr...@nmr.mgh.harvard.edu>
<mailto:gr...@nmr.mgh.harvard.edu>
*To:* sabin khadka <sabink...@yahoo.com>
<mailto:sabink...@yahoo.com>; Freesurfer Support List
<freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu>
*Sent:* Monday, January 26, 2015 5:33 PM
*Subject:* Re: [Freesurfer] Extract mean time series from parcellated
region
what do you mean you can't get them? The program fails? It produces 0s?
On 1/26/15 3:48 PM, sabin khadka wrote:
Hi FS user,
I am trying to extract time series of fmri rest data of certain
parcellated regions (both cortical and subcortical). for that I am
doing following
# bbregister --s <sub id> --mov <EPI.nii.gz> --init-fsl --reg
register.dat --bold
# mri_label2vol --aparc+aseg --subject <sub id> --temp <EPI.nii.gz>
--fillthresh 0.5 --reg regsiter.dat --o test1.nii.gz
# mri_vol2vol --mov test1.nii.gz --targ <sub id/mri/aparc+aseg.mgz>
--reg register.dat --o test2.nii.gz
# mri_segstats --seg <sub id/mri/aparc+aseg.mgz> --id <e.g. 11 for L
caudate> --in test2.nii.gz --avgwf <textfile.txt>
I am not able to get the mean time series values. Could anyone tell
me what I am missing?
Cheers,
Sabin Khadka
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