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 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.
