On 07/03/2013 02:09 PM, Garikoitz Lerma-Usabiaga wrote:

Thanks Doug and Bruce! this is the process I followed (just in case is of help for somebody else). Questions below.

One subject to fsaverage

mri_vol2vol --mov $SUBJECTS_DIR/fsaverage/label/myROI.nii --o $SUBJECTS_DIR/fsaverage/label/myROI.mgh --reg from_mySubject_to_fsaverage.dat --targ fsaverage/mri/T1.mgz

.mgh to .label

mri_cor2label --i $SUBJECTS_DIR/fsaverage/label/myROI.mgh --id 1 --l $SUBJECTS_DIR/fsaverage/label/myROI.label

.label in fsaverage to rest of subjects

mri_label2label --srcsubject fsaverage --srclabel $SUBJECTS_DIR/fsaverage/label/myROI.label --trgsubject S_01 --trglabel $SUBJECTS_DIR/S_01/label/myROI.label --regmethod volume

.label to .mgh

mri_label2vol --label $SUBJECTS_DIR/S_01/label/myROI.label --o $SUBJECTS_DIR/S_01/label/myROI.mgh --identity --temp $SUBJECTS_DIR/S_01/mri/T1.mgz

statistics with mri_segstats and myROI.mgh

My question is: how can I save couple of steps? 1.- Can I use mri_vol2vol as mri_label2label, just specifying the source and target subjects without knowing the reg matrix? I couldn't make it work...

No, you have to have a registration.

or at least:

2.- Is it possible to use .label with mri_segstats? I am not interested in the .label in any case but...

only if it is a surface-based label

many thanks again for your help! Gari

On Wednesday, July 3, 2013, Douglas Greve wrote:

Hi Gari, use --targ for a target volume (not a subject) to use as
the template for the output. The target subject is actually stored
in the register.dat file, so you can just spec --fstarg (no arguments)
doug




On 7/1/13 2:45 PM, Garikoitz Lerma-Usabiaga wrote:

...

Hi,
I want to obtain volume statistics from a ROI in fsaverage.
I have register.dat and a .nii file (the ROI), but I don't now
how to get to the .label.

The last try has been:
mri_vol2vol --mov $SUBJECTS_DIR/fsaverage/label/ROI.nii
--o $SUBJECTS_DIR/fsaverage/label/ROI.mgh
--reg
$SUBJECTS_DIR/fsaverage/mri/transforms/my_own_register_created_with_bbregister.dat
--targ fsaverage

(but it is failing, error:
corRead(): can't open file $SUBJECTS_DIR/fsaverage/COR-.info)

My next steps were:
cor2label (in fsaverage)
mri_label2label (per every subject)
mri_segstats (per every subject)


Is there any simpler method to accomplish the same? Or at least
that it works?
many thanks,
Gari


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