Thanks for your prompt reply. I tried the way you suggested and made success. However, the problem is that when I use mri_vol2surf,only --id 1 and --id 0 can make the command successful, prducing lh.aal_1.label and lh.aal_0.label. I use the two labels above to extract the thickness. To my surprise,the thickness are the same. I am so confused about the --id number in  mri_vol2surf. Could you please give me some help? How can I get every ROI's thickness of aal.nii. Thanks a lot.
I am looking forward for your prompt reply.

2017-04-27 0:16 GMT+08:00 Douglas N Greve <greve@nmr.mgh.harvard.edu>:
In the mri_label2label command you have lh.aal.label as the input and
output. Are you overwriting the input and so now it does not match the
original subject?


On 04/25/2017 09:23 PM, haidong wang wrote:
> 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
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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