RE: [Freesurfer] ANOVA and co-variable

al Message- From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: Thursday, July 16, 2009 11:30 AM To: Zhang, Xiaochu (NIH/NIDA) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] ANOVA and co-variable Hi Zhang, when reporting a bug or problem, please refer to the following s

RE: [Freesurfer] ANOVA and co-variable

- IRP Biomedical Research Center 251 Bayview Blvd. Suite 200 (NIDA) Baltimore MD 21224 Tel: 443-740-2619 -Original Message- From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: Wednesday, July 15, 2009 12:31 PM To: Zhang, Xiaochu (NIH/NIDA) [F] Cc: freesurfer

[Freesurfer] ANOVA and co-variable

Hi Freesurfer experts, I want to do a group ANOVA analysis with one co-variable. I have read the corresponding wiki but still have some problems. I need your help. I have 4 group subjects (A1B1, A1B2, A2B1, A2B2) and one co-vaiable (C). I want to get the interaction between A and B. However, bec

[Freesurfer] Where can I read the manual for old freesurfer version (some new information)

The freesurfer I am using now is this version, "freesurfer-Linux-centos4_x86_64-stable-pub-v3.0.4". I knew there is much improved in the current version.However, I have about 80 participants done in this old version. I only want to add several new participants and do some group anlaysis. Today

[Freesurfer] Where can I read the old manual

Hi Freesurfer experts, I want to use the old freesurfer version. However, I read the wiki today and found the manual has been changed. I need read the "GroupAnalysis" in the old version. Who can help me? Thanks a lot! Xiaochu Zhang PhD Visiting Research Fellow Neuroimaging Research Branch Nation

[Freesurfer] Hi and for clustering and tksurfer showing

Hi Freesurfer Experts, Thank you very much for your previous help! Thank you Nick so much for your really nice help! Everything is going on, now. The old problem has been resolved. However, the new problem was coming. I did a group analysis following the instruction in https://surfer.nmr.mgh.harvar

RE: [Freesurfer] RE: for cortical thickness

008 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 cre

RE: [Freesurfer] a display problem, again!

Thank you very much! However, I just checked it and I used ATI graphic card but not NVIDIA card. What information do you think is benefit to clear the problem? I will send to you. Thanks a lot! Xiaochu Zhang PhD Visiting Research Fellow Neuroimaging Research Branch National Institute on Drug

RE: [Freesurfer] RE: for cortical thickness

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

RE: [Freesurfer] RE: for cortical thickness

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 def

[Freesurfer] a display problem, again!

Biomedical Research Center 251 Bayview Blvd. Suite 200 (NIDA) Baltimore MD 21224 Tel: 443-740-2619 From: Zhang, Xiaochu (NIH/NIDA) [F] Sent: Thursday, December 04, 2008 6:44 PM To: Freesurfer Mailing List Subject: [Freesurfer] a display problem Hi

[Freesurfer] a display problem

Hi Freesurfer expert, I just started to use freesurfer. I tried to follow the instruction to learn how to use "tksurfer". However, when I type "tksurfer bert lh inflated". Only a very small part of brain was showed (see the attachement). I do not know the reason. Could you please do me a favor and

RE: [Freesurfer] RE: for cortical thickness

l: 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 s

RE: [Freesurfer] RE: for cortical thickness

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

RE: [Freesurfer] RE: for cortical thickness

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: [Free

[Freesurfer] RE: for cortical thickness

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 ${su

RE: [Freesurfer] for cortical thickness

ranch 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 14, 2008 2:38 PM To: Zhang, Xiaochu (NIH/NIDA) [

[Freesurfer] for cortical thickness

Hi FreeSurfer Expert, Can I transfer the thickness data into other form, for example, Nifti, AFNI or SPM? 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 (NID

[Freesurfer] Hi and for transfer AFNI data to Free Surfer

Hi FreeSurfer experts, I am a beginner of free surfer. Now I am working on my previous dataset with new hypothesis. In this dataset, I found a ROI (located almost in gray matter) showed significant functional difference between groups. I want to test whether the cortical thickness is changed or not