oh, sorry, I had not seen that the LECN...nii file was already in subject space. In that case use --regheader subjectname instead of --srcreg
doug On 03/13/2014 05:53 PM, Barbara Weiland wrote: > Hi Doug - > > Using the overlay threshold flags, I see that the .mgh (yes, the .mg > was a cut/paste typo) is in the occipital region and should be > frontal, temporal and parietal regions. So, I must be doing something > wrong in the mri_vol2surf command: > > >/ mri_vol2surf --src $SUBJECTS_DIR/[subj]/label/LECN_subjXXX.nii//--out > >$SUBJECTS_DIR/[subj]/label/LECN_subjXXX_lh_surf.mgh//--srcreg > >$SUBJECTS_DIR/[subj]/mri/transforms/reg.mni152.2.dat --hemi lh/ > Plus - as the original ROI encompasses regions in both hemispheres > (i.e., the left executive network has a region in the right > cerebellum), I thought I would need to repeat this command with --hemi > rh? > > I assumed I would have to run /mris_aatomical_stats /on each > hemisphere -- after I have labels for the ROI for each hemisphere? > > Thanks, > Barbara > > > > >> The vol2surf command output >> should be .mgh or .mgz, not .mg (or maybe that is just a typo in the >> email). If it is, then you should load the mgh file as an overlay, not >> as a surface, eg >> >> tksurfer [subj] lh inflated -overlay file.mgh -fminmax .5 1000 >> >> setting the min threshold to .5 assures that you can see the ROI >> >> doug > > > On 03/13/2014 05:10 PM, Barbara Weiland wrote: >> Hi - >> >> Sorry to not have been clearer. >> >> I have /functional ROIs defined by the Greicius >> lab// (http://findlab.stanford.edu/functional_ROIs.html) just as in >> this post to the Freesurfer list from //Mon Dec 2 15:22:08 EST 2013:/ >> / >> / >>> Doug, Thank you for your very helpful suggestion. Indeed, doing so >>> made it so I could quickly take any parts (or all) of each Greicius >>> network and put them in individual subject space. In case this may >>> help anyone else, the final series of commands were (in this case, >>> for the whole anterior salience network): *mni152reg --s [subj]* >>> mri_label2vol *--seg anterior_Salience.nii.gz \* --reg >>> $SUBJECTS_DIR/[subj]/mri/transforms/reg.mni152.2mm.dat \ --invertmtx >>> --o anterior_Salience_[subj].nii.gz \ --temp >>> $SUBJECTS_DIR/[subj]/mri/orig.mgz Cheers, Paul >> >> These ROIs were originally in MNI space and I used the commands listed >> above from Paul to move them to subject space first creating the >> reg.mni152.2mm.dat for each subject. LECN….nii is one of these >> network ROIs. I can see this ROI using free view and it looks >> correct. What I want is to extract volume and thickness for this ROI. >> As outlined below,I thought I needed to first convert this to a >> surface and tried: >> >>>> mri_vol2surf --src $SUBJECTS_DIR/[subj]/label/LECN_subjXXX.nii --out >>>> $SUBJECTS_DIR/[subj]/label/LECN_subjXXX_lh_surf.mg --srcreg >>>> $SUBJECTS_DIR/[subj]/mri/transforms/reg.mni152.2.dat --hemi lh >>> >> >> I tried to look at the output (LECN_subjXXX_lh_surf.mg) by using >> tksurfer [subj] lh inflated and then load the it from the GUI onto the >> inflated surface -- this says that the >> file (LECN_subjXXX_lh_surf.mg) "has 0 vertices! >> Probably trying to use a scalar data file as a surface!" >> >> Do I need to move the LECN….nii to be a surface or should I just be >> able to make a label from it? I assumed I need the ROI information to >> be a label to use mris_anatomical_stats? >> Thank you, > BarbaraBarbara Weiland, Ph.D. > Research Asst. Professor > CU Change Lab > Dept. of Psychology & Neuroscience > University of Colorado Boulder > barbara.weil...@colorado.edu <mailto:barbara.weil...@colorado.edu> > > > > > > _______________________________________________ > 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.
