$FREESURFER_HOME/FreeSurferColorLUT.txt

On 11/05/2013 05:42 PM, Martin Luessi wrote:

Hi Doug,

Thanks for your reply. I will do it in Python then ;). Is there a table somewhere with a list of values used for each label (17 = left hippo etc.)?

Martin

On 11/05/13 17:32, Douglas N Greve wrote:

...

no, sorry, you'll have to do it with matlab. You can do something like

mri_vol2vol --mov func.nii --reg register.dat --fstarg --o func.anat.nii

aseg = MRIread('aseg.mgz'); indroi = find(aseg.vol == 17); % 17 = left hippo func = MRIread('func.anat.nii'); funcmat = fast_vol2mat(func); funcroi = funcmat(:,indroi);

funcroi will be the ntimepoints by nroivoxels matrix that you are looking for

doug

On 11/05/2013 05:30 PM, Martin Luessi wrote:

...

Hi,

I have fMRI data which has been co-registered with the FS reconstruction using "bbregister". I would like to extract the voxel time series for the voxels in the subcortical labels from the "aseg" subcortical segmentation. I know that "mri_segstats" can be used with the "--avgwf" option to extract an average time series for each label, but is there a way to extract a time series for each voxel inside each label without averaging?

Thanks,

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

Thanks Satra, very helpful.

On 11/05/13 17:34, Satrajit Ghosh wrote:

hi martin,

if you had one region you can use mri_segstats to extract for each voxel in that roi, but not for multiple rois.

here is a snippet i use for timecourses in each roi.

https://github.com/nipy/nipype/blob/master/examples/rsfmri_preprocessing.py#...

cheers,

satra

On Tue, Nov 5, 2013 at 5:30 PM, Martin Luessi <mluessi@nmr.mgh.harvard.edu mailto:mluessi@nmr.mgh.harvard.edu> wrote:

Hi,

I have fMRI data which has been co-registered with the FS reconstruction
using "bbregister". I would like to extract the voxel time series for
the voxels in the subcortical labels from the "aseg" subcortical
segmentation. I know that "mri_segstats" can be used with the "--avgwf"
option to extract an average time series for each label, but is there a
way to extract a time series for each voxel inside each label without
averaging?

Thanks,

Martin
_______________________________________________
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.