Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30085 discussions

problem on freesurfer
by Xiaoying Tang 08 Mar '10

08 Mar '10

Hi Nick, Sorry, I am not sure whether I can successfully post my problem on the mailing list. So I send you the email and cc it to the mailing list. I now have a problem on freesurfer. After run auto-recon2, I am supposed to get grey matter and white matter. The white matter is in the form of wm.mgz, but I can't find something like gm.mgz. Can you tell me where is the grey matter? Is it aseg.mgz? Looking forward to your early reply. Sincerely, Xiaoying

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Cluster-wise correction error
by lordowen 08 Mar '10

08 Mar '10

Dear Freesurfer experts: We used QDEC to generate the script for cluster-wise correction. After 2 days running, we get error message : ERROR: opening /usr/local/freesurfer/subjects/qdec/group_thickness_age_rh/csd/mc-z.abs.2.69.j001-rh-Avg-Intercept-thickness.csd We checked /csd and find the .csd file already there. But in /contrast, there is no results files (i.e., sig.cluster.summary) exist. And a /tmp.mri_glmfit-sim-8708 exist in the main folder. We need your advise to point out what's the problem and how to solve it. Thank you very much. -- Best regards -- 杜政昊 Cheng-Hao Tu, PhD Student Laboratory of Integrated Brain Research Department of Medical Research and Education Taipei Veterans General Hospital No.201, Sect.2, Shih-Pai Rd. Taipei Taiwan Email: lordowen(a)ms10.hinet.net or lordowentu(a)gmail.com Tel: +886-2-28712121 ext 3474 Fax: +886-2-28745182

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Cortical thickness measurement
by Janani Dhinakaran 08 Mar '10

08 Mar '10

Hello all, Can anyone tell me the commands I'll need to use to extract and measure the cortical thickness and volume of certain regions of the brain? thanks -- I am the Sun, I know no darkness.

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Error with Talairach Transform during recon-all
by Janani Dhinakaran 08 Mar '10

08 Mar '10

Any idea what this means and what I can do about it? Mon Mar 8 12:46:58 GMT 2010 talairach_avi done #-------------------------------------------- #@# Talairach Failure Detection Mon Mar 8 12:46:58 GMT 2010 /home/s0964091/Desktop/Newdata/JS/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Linux CRIC-0012 2.6.31-20-generic #57-Ubuntu SMP Mon Feb 8 09:02:26 UTC 2010 x86_64 GNU/Linux recon-all exited with ERRORS at Mon Mar 8 12:46:58 GMT 2010 Thank you Jan -- I am the Sun, I know no darkness.

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problem on the grey matter
by Xiaoying Tang 06 Mar '10

06 Mar '10

Hi all, Is there someone who can teach me how to get the separate grey matter like the white matter(wm.seg.mgz)? I have run the commands autorecon1 autorecon2 and autorecon3, but I still can't find the separate grey matter. I would be most grateful if someone who can help me. Best, Xiaoying

2 1

Viewing AFNI data on FreeSurfer surface: The Basics
by Dickinson, Annelise (NIH/NIMH) [F] 05 Mar '10

05 Mar '10

Hi all, Sorry if this is a REALLY dumb question, I'm a total newbie. I'm trying to view some fMRI data (preprocessed and analyzed in AFNI) on a surface in FreeSurfer. I have the subject's completed surface and analyzed fMRI files all ready to go, but I have no idea how to register them together, nor view them in the FreeSurfer GUI. Any FreeSurfer gurus out there who might be able to explain the process? I've tried to work through the FS-FAST tutorial, but I'm getting stuck on what I need to do, since I already have the data preprocessed and analyzed. Please let me know! Thank you so much! Sorry to ask a silly question! ***************************************************** Annelise Dickinson Post-Bac IRTA Laboratory of Brain and Cognition, NIMH/NIH/DHHS Building 10, Room 4C212 10 CENTER DR MSC 1366 BETHESDA MD 20892-1366 ***************************************************** Phone: (301) 435-4941 FAX: (301) 402-0921 E-Mail : dickinsona(a)mail.nih.gov

3 2

surface label values
by Gregory Dierksen 05 Mar '10

05 Mar '10

Hi, I'm trying to use a surface label (generated by V1 predict) to extract values that have been painted onto a surface using mri_vol2surf. Is there a FreeSurfer tool that will do this? I've been looking but nothing is popping out at me. Thanks, Greg --

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Standard Desikan map and/or QDEC blurb?
by Dankner, Nathan (NIH/NIMH) [F] 05 Mar '10

05 Mar '10

Hi all, I'm about to start writing up a paper, and was curious as to whether there is a standard figure displaying the Desikan parcellations that is floating around out there, and also whether or not there is a standard blurb describing QDEC's GLM analyses. Thanks! Nathan

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Recon-all times
by Gregory Cogan 05 Mar '10

05 Mar '10

Good morning, I imagine that this problem gets posted about once a week, but I'm having some issues with the recon -all step. Initially, I ran data off of a PC (Duo E8400 3.00 GHz, 4 Gigs of ram) and the reconstruction took overnight (so about 12-15 hours). We've recently purchased a new mac (quadcore 2.66 GHz, 8 gigs of ram) for our lab that is going to be dedicated for freesurfer and MNE and so far I've run 2 reconstructions on 2 subjects and the first one took about 96 hours and the second took about 50 hours. My feeling is that this is far too long. Are there any issues with freesurfer and snow leopard? Can anyone else think of a reason why this would be so slow given that it's running on a new (and relatively powerful) computer? I'm happy to send the log files if that helps, but it is worth noting that the stages that diverged from the guideline times listed on the wiki were different for each subject. Thank you all in advance -Greg Cogan

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Generating contrast images within a ROI
by Lena Palaniyappan 05 Mar '10

05 Mar '10

I want to generate some pretty pictures to help my dopamine levels this weekend!! Hoep someone can help.. I want to display statistical thickness difference in 5 ROIs (based on Destrieux atlas) only across two diagnostic groups. When I run Qdec I get whole brain thickness maps but I am interested in only few of the Destrieux parcellations: is there any way I can do this? Cheers Lena _______________________________________________________ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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