Hello FS experts,

I want to get the thickness of 90 ROIs of AAL using freesurfer. I use the following commands to transform aal.nii to lh.aal.label.

1.bbregister --s sub_con_sub01 --mov ch2.nii --t1 --init-fsl --reg register_vol2surf.dat

2.mri_vol2surf --mov aal.nii --reg register_vol2surf.dat --hemi lh --out_type mgh --o lh.aal.mgh --interp nearest

3.mri_cor2label --i lh.aal.mgh --id 1 --l ./lh.aal.label --surf sub_con_sub01

4.mri_label2label --srclabel lh.aal.label --srcsubject fsaverage --trgsubject sub_con_sub01 --trglabel lh.aal.label --regmethod surface --hemi lh

5.mris_anatomical_stats -l lh.aal.label -t lh.thickness -b -f sub_con_sub01/stats/lh.aal.stats sub_con_sub01 lh

6.aparcstats2table --hemi lh --subjects sub_con_sub01 --parc aal --meas thickness -t ./aal_thickness.txt

The result is that there is no measurement in the produced document named lh.aal.stats.

I am also confused about how to set id in mri_cor2label.Could you please give me some suggestions?

I am looking forwad for your prompt reply.

Yours,

Haidong

The attachment is the screenshot of my working directory.

Here is the error:

mri_cor2label --i lh.aal.mgh --id 1 --l ./lh.aal.label --surf sub_con_sub01

$Id: mri_cor2label.c,v 1.12 2011/03/02 00:04:14 nicks Exp $

Loading mri lh.aal.mgh

------- Vox2RAS of input volume -----------

-1.000 0.000 0.000 75659.000;

0.000 0.000 1.000 -0.500;

0.000 -1.000 0.000 0.500;

0.000 0.000 0.000 1.000;

Scanning the volume

Found 6451 label voxels

Writing label file ./lh.aal.label

LabelWrite: saving to ./lh.aal.label

Centroid: -9707.33 -0.50 0.50

mri_cor2label completed SUCCESSFULLY

admi@admi:~/Desktop/freesurfer_thickness$ mri_label2label --srclabel lh.aal.label --srcsubject fsaverage --trgsubject sub_con_sub01 --trglabel lh.aal.label --regmethod surface --hemi lh

srclabel = lh.aal.label

srcsubject = fsaverage

trgsubject = sub_con_sub01

trglabel = lh.aal.label

regmethod = surface

srchemi = lh

trghemi = lh

trgsurface = white

srcsurfreg = sphere.reg

trgsurfreg = sphere.reg

usehash = 1

Use ProjAbs = 0, 0

Use ProjFrac = 0, 0

DoPaint 0

SUBJECTS_DIR /home/admi/Desktop/freesurfer_thickness

FREESURFER_HOME /usr/local/freesurfer

Loading source label.

Found 6451 points in source label.

Starting surface-based mapping

Reading source registration

/home/admi/Desktop/freesurfer_thickness/fsaverage/surf/lh.sphere.reg

Rescaling ... original radius = 100

Reading target surface

/home/admi/Desktop/freesurfer_thickness/sub_con_sub01/surf/lh.white

Reading target registration

/home/admi/Desktop/freesurfer_thickness/sub_con_sub01/surf/lh.sphere.reg

Rescaling ... original radius = 100

Building target registration hash (res=16).

Building source registration hash (res=16).

ERROR: there is a vertex in the label that cannot be

matched to the surface. This usually occurs when

the label and surface are from different subjects or

hemispheres or the surface has been changed since

the label was created.

Label point 0: vno = -1, max = 163842