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
suvr.wmparc.stats
Description: suvr.wmparc.stats
_______________________________________________ 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.
