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