Xiaochu, The dimensions for lh.thickness.fsaverage.mgh are correct, the ones for lh.fsaverage.ROI5.mgh are not. They should be the same (163842x1x1). Did you create lh.fsaverage.ROI5.mgh like this:
cd $SUBJECTS_DIR/fsaverage/surf mri_vol2surf \ --mov /path/to/ROI5.nii \ --reg TT_avg152T1_to_fsaverage.dat \ --projdist-max 0 1 0.1 \ --interp nearest \ --hemi lh \ --out lh.fsaverage.ROI5.mgh Nick On Fri, 2008-12-05 at 16:56 -0500, Zhang, Xiaochu (NIH/NIDA) [F] wrote: > I just checked the demension information and found they are not same. > Do you think which one is wrong? > Thanks a lot! > > Volume information for lh.thickness.fsaverage.mgh > type: MGH > dimensions: 163842 x 1 x 1 > voxel sizes: 1.0000, 1.0000, 1.0000 > type: FLOAT (3) > fov: 163842.000 > dof: 0 > xstart: -81921.0, xend: 81921.0 > ystart: -0.5, yend: 0.5 > zstart: -0.5, zend: 0.5 > > Volume information for lh.fsaverage.ROI5.mgh > type: MGH > dimensions: 23406 x 1 x 7 > voxel sizes: 1.0000, 1.0000, 1.0000 > type: FLOAT (3) > fov: 23406.000 > dof: 0 > xstart: -11703.0, xend: 11703.0 > ystart: -0.5, yend: 0.5 > zstart: -3.5, zend: 3.5 > > > Xiaochu Zhang PhD > > Visiting Research Fellow > > Neuroimaging Research Branch > > National Institute on Drug Abuse - IRP > > Biomedical Research Center > > 251 Bayview Blvd. > > Suite 200 (NIDA) > > Baltimore MD > > 21224 > > Tel: 443-740-2619 > > > -----Original Message----- > From: Nick Schmansky [mailto:[EMAIL PROTECTED] > Sent: Friday, December 05, 2008 3:51 PM > To: Zhang, Xiaochu (NIH/NIDA) [F] > Cc: Freesurfer Mailing List > Subject: RE: [Freesurfer] RE: for cortical thickness > > Zhang, > > You could perform the steps you show in 1., where you sample your ROI > directly to the subjects surface, rather than going through the > fsaverage subject. Ultimately, you would (or should) end-up with the > same result as that from following the steps in the wiki page (going > through fsaverage). The difference is that you only need to do the > sampling of the ROI to fsaverage only once, whereas with what you want > to do, you do it for every subject. Not a big deal if you dont have > that many subjects. btw, fsaverage is in talairach space, so its not > distorting things much by performing that registration (the .dat file > from fslregister has very small values). > > I'm not sure about the useful of performing 2., where you sample the > thickness data to the volume. This is not usually done (I dont think). > You will have a volume with voxel values equal to the thickness of the > cortex around that voxel, but there is no hard meaning of that value for > that voxel. Typically mri_surf2vol is used to sample parcellation > labels into volume space. > > I'm not sure why you are getting dimension mismatch errors. Use mri_info > on the files in question to get the dimensions. Note this part of the > wiki instructions in the last two steps: > > cd $SUBJECTS_DIR/subjid/surf > > noting that 'subjid' is the name of your subject. If you remain in the > $SUBJECTS_DIR/fsaverage/surf directory from the previous steps, you will > get the mismatch error (which i just discovered myself). > > Nick > > > > On Fri, 2008-12-05 at 15:06 -0500, Zhang, Xiaochu (NIH/NIDA) [F] wrote: > > Hi Nick, > > Thank you so much for your help! > > Recently, I tested it strictly following your instruction. However, I > > met a problem in the last step "mri_segstats ". They gave me the error > > information: "ERROR: dimension mismatch between input volume and seg". > > I checked the old mails in the list. Some one talked about dimension > > mismatch but not related to my issue. Could you please do me a favor > > and give some suggestion for the reason? > > > > There are another two issues: > > 1. I noted you transfer ROI5.nii to fsaverage space. Because my > > ROI5.nii have been in the Talairach space, can I transfer it to > > subjects's space directly? > > For example: > > cd $SUBJECTS_DIR/subjid/surf > > Fslregister --s subjid --mov /path/to/TT_avg152T1.nii --reg > > TT_avg152T1_to_subjid.dat Mri_vol2surf --mov /path/to/ROI5.nii --reg > > TT_avg152T1_to_subjid.dat --projdist 0 1 0.1 --interp nearest --hemi > > lh --out lh.ROI5.mgh Mri_segstats --seg lh.ROI5.mgh --in lh.thickness > > --sum segstats-ROI5.txt > > > > Is it OK? What is the benefit for using fsaverage data? > > BTW, I got the same dimension mismatch error information in the last > > step. > > > > 2. Can we transfer all data into the volume space. i.e., Mri_surf2vol > > --surfval lh.thickness --hemi lh --fillribbon --template orig.mgz > > --volregidentity subjid --outvol lh.ribbon.nii Mri_convert > > lh.ribbon.nii --apply_transform transforms/talairach.auto.xfm -o > > lh-talairach.ribbon.nii > > > > I tried it and no error information appear. However, I don't know it > > is correct or not. > > > > Thanks, again! > > > > Xiaochu Zhang PhD > > > > Visiting Research Fellow > > > > Neuroimaging Research Branch > > > > National Institute on Drug Abuse - IRP > > > > Biomedical Research Center > > > > 251 Bayview Blvd. > > > > Suite 200 (NIDA) > > > > Baltimore MD > > > > 21224 > > > > Tel: 443-740-2619 > > > > > > -----Original Message----- > > From: Nick Schmansky [mailto:[EMAIL PROTECTED] > > Sent: Friday, November 21, 2008 5:15 PM > > To: Zhang, Xiaochu (NIH/NIDA) [F] > > Cc: Freesurfer Mailing List; Allison Stevens > > Subject: RE: [Freesurfer] RE: for cortical thickness > > > > Zhang, > > > > The web page describing the steps to extract cortical thickness data > > for your volume-space defined ROI is found here: > > > > https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness > > > > Nick > > > > > > On Mon, 2008-11-17 at 14:02 -0500, Zhang, Xiaochu (NIH/NIDA) [F] > wrote: > > > Thank you so much for your response, Nick! > > > I uploaded "ROI5.nii" (i.e., abc.nii) just now. This ROI has been in > > > > Talarich space. > > > Actually, it is from my group functional data. So I did not have > > > corresponding T1-data. > > > > > > BTW: when can I read the web page describing the steps taken to get > > > cortical thickness from an ROI defined by a volume mask? I hope I > > > can read it ASAP. If it is possible, could you please do me a favor > > > and send the draft to me? > > > Thanks, again! > > > > > > > > > Xiaochu Zhang PhD > > > > > > Visiting Research Fellow > > > > > > Neuroimaging Research Branch > > > > > > National Institute on Drug Abuse - IRP > > > > > > Biomedical Research Center > > > > > > 251 Bayview Blvd. > > > > > > Suite 200 (NIDA) > > > > > > Baltimore MD > > > > > > 21224 > > > > > > Tel: 443-740-2619 > > > > > > > > > -----Original Message----- > > > From: Nick Schmansky [mailto:[EMAIL PROTECTED] > > > Sent: Monday, November 17, 2008 12:59 PM > > > To: Zhang, Xiaochu (NIH/NIDA) [F] > > > Cc: Freesurfer Mailing List > > > Subject: Re: [Freesurfer] RE: for cortical thickness > > > > > > Xiaochu, > > > > > > I'm putting together a web page describing the steps taken to get > > > cortical thickness from an ROI defined by a volume mask. Can you > > > send > > > > > me these two files so that I can make sure the steps work correctly? > > > > > > 1) the ROI mask file (what you are calling 'abc.nii') > > > 2) the T1-weighted anatomical volume of the subject from which > > > abc.nii > > > > > was created. i need this file to register to a template volume. > > > > > > You can post those files (available only to me) by uploading to our > > > file > > > drop: > > > > > > https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > > > Nick > > > > > > > > > On Sat, 2008-11-15 at 00:48 -0500, Zhang, Xiaochu (NIH/NIDA) [F] > > wrote: > > > > Hi, FreeSurfer export, > > > > > > > > Thank you very much for response! > > > > Now, under some export's help, I used to the mri_surf2vol to > > > > transfer > > > cortex thickness into nifti. > > > > The below line is what I used. > > > > mri_surf2vol --surfval ../surf/lh.thickness --hemi lh --fillribbon > > > > > --template orig.mgz --volregidentity ${subid} --outvol > > > > lh.ribbon.nii > > > > > > > > I checked the result and found the voxel outside the gray matter > > > > is > > > always zero and in the gray matter is about 0-3. Could you please do > > > > me a favor and tell me whether these data is cortex thickness or > not? > > > > If they are cortex thickness, why are they always different. In my > > > mind, it should be same in one direction because we calculate the > > > distance between the white matter line and the gray matter line. > > > > > > > > Thanks a lot! > > > > All the best, > > > > Xiaochu > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer@nmr.mgh.harvard.edu > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
