External Email - Use Caution Hi Doug,
I apologise for the time I left this question unanswered… I have done some work on the issue, and discovered that the orientation was wrong (eg left ROI was on the right side), but this did not appear on step 2. Anyway, this is now fixed. I have checked with Freeview how were the ROIs on ?h.white, and it looks pretty decent. The whole pipeline seems to be working fine all the way, but for some subjects and for some ROIs, mris_anatomical_stats cannot extract anything! I thought because I registered my ROIs on fsaverage, mris_anatomical_stats would be able to capture and extract teh average value within the ROI mask for all subjects? Is there anything I am missing here? Any idea on what I could do to capture what is in my ROIs for all my subjects? Thanks again for your time. Yann > On 16 Feb 2018, at 6:18 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > > At what step is the failure happening? Do the masks look ok on the surface? > > > On 02/12/2018 08:06 PM, Yann Quidé wrote: >> Dear FS experts, >> >> I am trying to extract values for cortical thickness, surface area and >> volumes, from different functional ROIs. These cortical ROIs have been >> defined using SPM tools, and are in .nii format. My scans have been >> processed using FS v5.3. >> >> Although the conversion seems to go well, the “end product” does not really >> look good, some of the extracted ROI for some subjects are empty. Does >> anyone have a clue of why? >> >> Here is what I have done: >> >> 1) transform .nii file to .mgz file >> >> $FREESURFER_HOME/bin/mri_convert $MASKS_DIR/ROI.nii $MASKS_DIR/L_ROI.mgz >> $FREESURFER_HOME/bin/mri_convert $MASKS_DIR/ROI.nii $MASKS_DIR/R_ROI.mgz >> >> >> 2) to make sure our masks from SPM will match fsaverage templates, I did >> >> tkmedit -f $MASKS_DIR/avg152T1.mgz -overlay $MASKS_DIR/L_ROI.mgz -fthresh 0.5 >> tkmedit -f $MASKS_DIR/avg152T1.mgz -overlay $MASKS_DIR/R_ROI.mgz -fthresh 0.5 >> >> It was fine. >> >> >> 3) I created a .dat file containing the registration matrix from avg152T1 >> onto fsaverage >> >> cd $SUBJECTS_DIR/fsaverage/surf >> spmregister --s fsaverage --mov $MASKS_DIR/avg152T1.nii --reg >> $REG_DIR/avg152T1_to_fsaverage.dat >> >> >> 4) Visualisation of the registration >> >> tkregister2 --mov $MASKS_DIR/avg152T1.nii --targ >> $SUBJECTS_DIR/fsaverage/mri/brainmask.mgz --reg >> $REG_DIR/avg152T1_to_fsaverage.dat --surf orig >> >> The registration was bad, so… I manually relocate the TAL template onto the >> fsaverage template and saved a new avg152T1_to_fsaverage.dat file called >> avg152T1_to_fsaverage_edited.dat. This file is used for the next steps. >> >> >> 5) Visualisation of the registration of our mask onto fsaverage T1 >> >> cd $SUBJECTS_DIR/fsaverage/surf >> tkmedit fsaverage T1.mgz \ >> -overlay $MASKS_DIR/L_ROI.mgz \ >> -overlay-reg $REG_DIR/avg152T1_to_fsaverage_edited.dat \ >> -fthresh 0.5 \ >> -surface lh.white -aux-surface rh.white >> >> tkmedit fsaverage T1.mgz \ >> -overlay $MASKS_DIR/R_ROI.mgz \ >> -overlay-reg $REG_DIR/avg152T1_to_fsaverage_edited.dat \ >> -fthresh 0.5 \ >> -surface lh.white -aux-surface rh.white >> >> Up to this sep, everything looks good. >> >> >> 6) Transformation of the ROI mask to surface and thickness >> >> mri_vol2surf --src $MASKS_DIR/L_ROI.mgz --reg >> $REG_DIR/avg152T1_to_fsaverage_edited.dat --hemi lh --o $MASKS_DIR/L_ROI.mgh >> mri_vol2surf --src $MASKS_DIR/R_ROI.mgz --reg >> $REG_DIR/avg152T1_to_fsaverage_edited.dat --hemi rh --o $MASKS_DIR/R_ROI.mgh >> >> mri_cor2label --i $MASKS_DIR/L_ROI.mgh --surf fsaverage lh --id 1 --l >> $MASKS_DIR/L_ROI.label >> mri_cor2label --i $MASKS_DIR/R_ROI.mgh --surf fsaverage rh --id 1 --l >> $MASKS_DIR/R_ROI.label >> >> >> 7) Extraction of the ROI surface and thickness for analyses >> >> mris_anatomical_stats -l $MASKS_DIR/L_ROI.label -f >> $OUT_DIR/results_L_ROI_SubjID SubjID lh >> mris_anatomical_stats -l $MASKS_DIR/R_ROI.label -f >> $OUT_DIR/results_R_ROI_SubjID SubjID rh >> >> Thanks to anyone who will be able to help me with that! >> >> Yann >> _______________________________________________ >> 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 . 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