Register the suvr to the anatomical (mri_coreg) then use mri_vol2vol
On 7/18/16 6:58 PM, Alshikho, Mohamad J. wrote: > Thank you Doug, > Kindly how can I make the suvr and the anatomical images in the same slice? > > -----Original Message----- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve > Sent: Monday, July 18, 2016 6:56 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] mri_segstats > > Your suvr is axially sliced whereas the anatomical is corronally sliced. > They must be in exact pixel-for-pixel alignment for mri_segstats to work. > > On 07/18/2016 06:27 PM, Alshikho, Mohamad J. wrote: >> Thank you Doug! >> >> Attached is a report for one of the subjects showing how the cerebellum >> structures have zeros for the mean, SD , ...etc ( red circles) Also if we >> scroll down ( not included), all the cerebellum parcellates ( white and >> cortex) are zeros. >> I have this issue with 70 % of the subjects. >> I applied the first command on all the subjects. >> I never tried the second command, but I was inquiring because I >> thought that maybe the first command is missing some flags so >> "mri-segstats" is unable to read the cerebellum parcellates >> >> For the subjects who have zeros for the cerebellum parcellates. I checked >> the functional images one by one ( the registration is perfect) and the >> images are fine. >> >> I can't explain why this is happening so thank you for any suggestion. >> >> -----Original Message----- >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N >> Greve >> Sent: Monday, July 18, 2016 5:45 PM >> To: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] mri_segstats >> >> What do you mean you got 0s only for the cblum segs? Did all other segs have >> non-zeros, but clbum have 0s? And did you get non-0s in the 2nd commandline? >> >> On 07/07/2016 05:16 PM, Alshikho, Mohamad J. wrote: >>> Thank you very much Doug for your answer. >>> Kindly I have one more question: >>> Although the registration between my functional data and "wmparc.mgz" is >>> perfect. When I run the first command bellow, I get zeros ( in the report >>> wmparc.stats) only for the cerebellum parcellates, and this was prominent >>> in many of my subjects. >>> Is this issue related to a missing flags in my "mri_segstats" command line? >>> >>> -----Original Message----- >>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas >>> N Greve >>> Sent: Thursday, July 7, 2016 12:17 PM >>> To: freesurfer@nmr.mgh.harvard.edu >>> Subject: Re: [Freesurfer] mri_segstats >>> >>> The first one >>> >>> On 07/06/2016 08:22 PM, Alshikho, Mohamad J. wrote: >>>> Dear FS experts, >>>> >>>> I have PET image "pet.anat.mgz" in subject space. I want to >>>> calculate the mean PET signal for every parcellate and segment in >>>> the atlas "wmparc.mgz". >>>> >>>> _Which one of the following commands is more accurate? _ >>>> >>>> __ >>>> >>>> 1.mri_segstats --seg $SUBJECTS_DIR/${subj}/mri/wmparc.mgz --ctab >>>> $FREESURFER_HOME/FREESURFERColorLUT.txt --i PET.anat.mgz --sum >>>> PET.wmparc.stats >>>> >>>> 2.mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv >>>> mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/ >>>> PET.anat.mgz--in-intensity-name norm --in-intensity-units MR >>>> --subject ${subj} --surf-wm-vol --ctab >>>> /usr/local/freesurfer/stable5_3_0/WMParcStatsLUT.txt --etiv >>>> >>>> Best, >>>> >>>> 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 >>> gr...@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 >> gr...@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 > gr...@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 > > _______________________________________________ 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. 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