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:nicks@nmr.mgh.harvard.edu] 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:nicks@nmr.mgh.harvard.edu] 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?
- the ROI mask file (what you are calling 'abc.nii')
- 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
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