Xiaochu, My bad, I see the problem now. I was using our 'dev' enviro, which doesnt 'reshape' the data (never mind that detail) whereas 'stable' (public) does.
So, just add --reshape to the end of the mri_surf2surf command, as the updated instruction here show: https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness and the dimensions of those two files should match (correct is 23406 x 1 x 7). Nick On Fri, 2008-12-05 at 17:21 -0500, Zhang, Xiaochu (NIH/NIDA) [F] wrote: > I RUN: > [EMAIL PROTECTED]:/data2/379/ASL/temp/fsaverage/surf> mri_vol2surf --mov > ../../ROI5.nii --reg TT_avg152T1_to_fsaverage.dat --projdist-max 0 1 0.1 > --interp nearest --hemi lh --out lh.fsaverage.ROI5.mgh > > THE OUTPUT: > srcvol = ../../ROI5.nii > srcreg = TT_avg152T1_to_fsaverage.dat > srcregold = 0 > srcwarp unspecified > surf = white > hemi = lh > ProjDist = 0.5 > interp = nearest > float2int = round > GetProjMax = 1 > INFO: float2int code = 0 > INFO: changing type to float > Done loading volume > Reading surface /data2/379/ASL/temp/fsaverage/surf/lh.white > reading group avg surface area 822 cm^2 from file > Reading in average area > /data2/379/ASL/temp/fsaverage/surf/lh.white.avg.area.mgh > Done reading source surface > Reading thickness /data2/379/ASL/temp/fsaverage/surf/lh.thickness > Done > Mapping Source Volume onto Source Subject Surface > 1 0 0 1 > vol2surf_linear: nhits = 163842/163842 > 2 0.1 0 1 > vol2surf_linear: nhits = 163842/163842 > 3 0.2 0 1 > vol2surf_linear: nhits = 163842/163842 > 4 0.3 0 1 > vol2surf_linear: nhits = 163842/163842 > 5 0.4 0 1 > vol2surf_linear: nhits = 163842/163842 > 6 0.5 0 1 > vol2surf_linear: nhits = 163842/163842 > 7 0.6 0 1 > vol2surf_linear: nhits = 163842/163842 > 8 0.7 0 1 > vol2surf_linear: nhits = 163842/163842 > 9 0.8 0 1 > vol2surf_linear: nhits = 163842/163842 > 10 0.9 0 1 > vol2surf_linear: nhits = 163842/163842 > Done mapping volume to surface > Number of source voxels hit = 75048 > Reshaping 7 (nvertices = 163842) > Writing to lh.fsaverage.ROI5.mgh > Dim: 23406 1 7 > > > 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 5:10 PM > To: Zhang, Xiaochu (NIH/NIDA) [F] > Cc: Freesurfer Mailing List > Subject: RE: [Freesurfer] RE: for cortical thickness > > 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
