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.weiland@colorado.edu mailto:barbara.weiland@colorado.edu

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