Hi Barbara, please post to the list. Thanks! 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, Barbara
Barbara Weiland, Ph.D. Research Asst. Professor CU Change Lab Dept. of Psychology & Neuroscience University of Colorado Boulder barbara.weiland@colorado.edu mailto:barbara.weiland@colorado.edu
On Mar 13, 2014, at 1:14 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Can you give more details? What is LECN_...nii? Where did it come from? What space is it in? MNI152 I assume? What does it mean you can't load it? Load it with what? What is your command line? doug
On 03/13/2014 01:36 PM, Barbara Weiland wrote:
Hi -
I am trying to extract volumes & thickness stats of networks and followed the commands from the post in the subject line to create network .nii files in each subject's space. Based on some other postings, I thought I needed to first move the volumes to surf for each hemisphere, i.e.:
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
But this does not seem to create the surf correctly - I am unable to load it. I have also tried to use mri_cor2labels to create labels directly front the .nii files but found that the first column in the label files were all -1 (which I found in a previous posting meant the volumes needed to be moved to surface first as I tried above)?? I ultimately want to use mris_aatomical_stats with these labels to output stats. Any help would be appreciated, thanks, Barbara
Barbara Weiland, Ph.D. Research Asst. Professor CU Change Lab Dept. of Psychology & Neuroscience University of Colorado Boulder barbara.weiland@colorado.edu mailto:barbara.weiland@colorado.edu mailto:barbara.weiland@colorado.edu
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