Freesurfer

freesurfer@nmr.mgh.harvard.edu

5 participants
30076 discussions

How to do functional connectivity analysis in fs or fsfast?
by Zhen Zonglei 20 Sep '07

20 Sep '07

Hi, all: I am a naive user of fs and fsfast. Now, I am trying to do functional connectivity analysis with fsfast. But, I actually do not know how to do correlation analysis with a reference time course (a mean time course from a specific ROI) in fs and fsfast? Can someone give me some cues on this issue? Or, can someone tell me how to do regression analysis just with some external regressors rather than the regressors from experiment design? Sincerely Z.L Zhen

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Average surface of mris_register
by Jiefeng Jiang 20 Sep '07

20 Sep '07

Hi, I am using the ?h.sphere.reg files automatically generated by reconall. However, I found that the area distortion compromise the results of my following resample step. I wonder whether replacing the default average surface "$FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif" with the ?h.sphere in the /average/surf directory would reduce the distortion. If so, could anyone tell me how to get a .tif file using files in /average/surf directory? Thank you!

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Alternative Standard Brain
by Dick, Rachel 19 Sep '07

19 Sep '07

Hi there, Is there a "simple" way to plug in and use your own standard brain instead of the mni in the recon-all process? I am using the new 4.0 version. Thanks in advance! Rachel Rachel Marie Dick Research Assistant/Coordinator Brain Research and Imaging Neurosciences Dept. of Psychiatry & Behavioral Neuroscience WSU Medical School brain.wayne.edu <mailto:rcondon@med.wayne.edu> (313)577-6279 CONFIDENTIALITY NOTICE This message is confidential, intended only for the named recipient(s) and may contain information that is privileged, or exempt from disclosure under applicable law. If you are not the intended recipient(s), you are notified that the dissemination, distribution or copying of this message is strictly prohibited. If you receive this message in error, or are not the named recipient(s), please notify the sender at the e-mail address. Delete this e-mail from your computer, and destroy any copies in any form immediately. Thank you.

2 1

error: no gl window open
by Xiangchuan Chen 19 Sep '07

19 Sep '07

Hi all, I have got the following error message when running tksurfer to load inflated surface: surfer: ### redraw failed: no gl window open The result is that no surface appears. Any suggestions for solving this issue? My system: HP NC8430 laptop (ATI X1600 video card) Fedora 6 (X86_64) Freesurfer V4.0 Thanks in advance, Xiangchuan Chen

2 1

pictures from the freesurfer digest
by bell0368＠umn.edu 19 Sep '07

19 Sep '07

Hello all, I am subscribed to the freesurfer list in digest format. If someone sends pictures to the list I am not able to see/open them from the digest or from the archives. Is there an option I need to change? Or do I need to switch off digest mode completely? Thanks in advance, Chris Bell

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monkeys' surfaces registration
by Marie Schaer 19 Sep '07

19 Sep '07

Hello everybody, I am working with monkeys brain, and I had trouble in both creating an average surface and co-registering the monkeys' surfaces together. I was thus wondering if accessing the canonical spherical template and replacing it by a monkey template with less sulci would solve the problem? If yes, how can I specify to mris_sphere which template to use? If no, has someone a miracle solution to register monkeys' surfaces? Many thanks, Marie Schaer

2 1

question re: ventromedial and dorsolateral frontal lobe volumes
by Bird, Anne 18 Sep '07

18 Sep '07

Will Freesurfer allow me to measure ventromedial and dorsolateral frontal lobe volumes? Thanks, Anne C. Bird, M.S. Clinical Research Coordinator Memory and Aging Center 350 Parnassus Avenue Suite 706 University of California-San Francisco San Francisco, California 94143 Telephone: 415-476-8592 Email: abird(a)memory.ucsf.edu

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multi-channel lesion segmentation.
by Mehul Sampat 18 Sep '07

18 Sep '07

Hi all, I would like to segment lesions using both T1 and FLAIR images. I think this is not possible with the current version of freesurfer. Is that right ? Could I somehow combine the segmentation results from aseg with the FLAIR images ? Regards Mehul

2 1

freesurfer release v4.0.1
by Nick Schmansky 18 Sep '07

18 Sep '07

Freesurfer stable release v4.0.1 is now available. This is a bug-fix release, described on the Release Notes page: http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes

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re-run FreeSurfer with v4
by Xiangchuan Chen 17 Sep '07

17 Sep '07

Hi all, I am working on 80 subjects' data with the following work flow: 1. -autorecon1 2. edit talairach registration 3. -autorecon1 4. -autorecon2 5. edit brainmask.mgz 6. edit wm.mgz 7. -autorecon2-wm 8. -autorecon3 I have already finished this work flow for 30 subjects with FreeSurfer v3.05. I have spent a lot of time on steps 2, 5 and 6. I am not worrying about the other steps because they are my computer's tasks, but not mine. So, if I re-run the same work flow with v4, do I have to go through all these steps? Any suggestions are greatly appreciated. Thanks in advance, Xiangchuan Chen

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