This mask is from functional group analysis. Before I did do group analysis, I have to transfer all individual data into standard space. Therefore, there is no special reference for this mask. The only reference whole brain data is the standard talarich dataset in AFNI. I know if I want to get a perfect anatomical ROI mask, I should draw it based on the subject's own T1 data. However, because I want to run a functional and anatomical combined study, I prefer to use one exactly standard ROI from funcitonal result although it has high variability. Usually, in this case when I do a ROI analysis, I will transfer the ROI from the standard space back to the individual space.

Please feel free to contact me if you still have some questions about the ROI mask. Thanks a lot!

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 2:37 PM To: Zhang, Xiaochu (NIH/NIDA) [F] Subject: RE: [Freesurfer] RE: for cortical thickness

can you send the file from which ROI5.nii was created? we would need something, even if it is a functional scan, that shows the whole brain, so that we have a reference of just where the mask voxels are located in the brain. our surface tools do not work directly with talairach coords because those coords have such high variability (that can off by as much as 2cm, or more).

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?

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