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
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
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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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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