Hi Nick, Thank you very much for your help in the previous email. Recently, I read and thought your manual very carefully and tried some other ways.
The first one: I tried to transfer ROI5.nii directly to subject's surface (not via fsaverage). i.e., 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? I got the same error information to that after strictly following your manual (see details in the last email I sent to you).Do you the reason for this error informaton? Another way is transfering all data into volume. 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 Is it OK? This followship works without any error information. However, I do not know what is the value in each voxel in "lh-talairach.ribbon.nii". Do you know it? 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
