Freesurfer May 2006

freesurfer@nmr.mgh.harvard.edu

50 participants
74 discussions

TIV and TBV
by Lee HL 09 May '06

09 May '06

Hi, I was wondering if anyone knows where to extract the values for TIV and TBV after autorecon1? I was planning to compare with and without talairach transformation and how the TIV and TBV, manual and automated methods, would be affected. Thanks. Best regards, HweeLing

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aseg step bypass
by Joao Pereira 09 May '06

09 May '06

I am using freesurfer for an inter-subject cortical thickness analysis. In order to speed things up, I was considering removing the sub-cortical segmentation step with -noaseg in the recon-all command line. I believe this will not affect my results, but I am not sure if some of the subsequent procedures are affected. Is it OK to do this then? Thank you! Joao Pereira

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autorecon2 on rh only
by anthony gallo 08 May '06

08 May '06

Can you please tell me the command line for running recon-all autorecon2 on only the right hemisphere? It isn't entirely clear to me from the wiki. I appreciate it, Anthony

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Noncompletion of autorecon2
by anthony gallo 08 May '06

08 May '06

Hello, I am having some trouble. I have all of the left hemisphere data that autorecon2 makes but not all from the right hemisphere. I have 2 questions: 1. If freesurfer encountered a problem and ended with an "error" would that error appear at the end of the recon-all log? 2. If the computer shut down and that was the problem (some form of auto shutdown) would an error appear in the freesurfer log? Thanks in advance, Anthony

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Re: [Freesurfer] fill stats
by Kevin Teich 08 May '06

08 May '06

Unless Doug has a tool for this, then no; it can't be done within tksurfer. Sorry. On Thu, May 04, 2006 at 06:16:31PM -0400, Chris Baker wrote: > > Yes- we're trying to select labels based on negative regions. If > there's no way to do this, is there a way to change which is the > positive and which the negative contrast in sfa-sess or does it > always take the first condition as being the positive contrast. -- Kevin Teich

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edit surfaces combined with MRI
by Michael Rullmann 08 May '06

08 May '06

hey, i used mri_watershed to produce different surfaces of the brain such as inner/outer skull, outer skin and brain. often the produced surfaces aren't totally correct. tkmedit shows me the surfaces and the MRI at the same time. now i want to edit the shown surfaces with tkmedit. is it possible? for editing i need to see the MRI and the surfaces at the same time. i didn't found an "edit surface tool" there. thanks, michael.

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mri_convert - 256^3 voxels at 1mm^3
by Darren Weber 05 May '06

05 May '06

Hi Bruce etal, It appears that the new 3.0.2 version of freesurfer does no longer require volumes to be 256^3 voxels at 1mm^3 each. Is there a wiki page on revised coordinate systems for the MRI and surface data? I would prefer to continue working with 256^3 @ 1mm^3 voxels (some other software we are using benefits from this reslicing). Can I specify this at the stage of mri_convert? Will it carry through to recon-all? Thanks, Darren -- Darren L. Weber, Ph.D. Postdoctoral Scholar Dynamic Neuroimaging Laboratory, UCSF Department of Radiology, 185 Berry Street, Suite 350, Box 0946, San Francisco, CA 94107, USA. Tel: +1 415 353-9444 Fax: +1 415 353-9421 www: http://dnl.ucsf.edu/users/dweber "To explicate the uses of the brain seems as difficult a task as to paint the soul, of which it is commonly said, that it understands all things but itself." Thomas Willis (The Anatomy of the Brain and Nerves, 1664)

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medial pial rh and lh surfaces crossing
by Josh Snyder 05 May '06

05 May '06

I see this on a ton of datasets. Is it a known issue? Is there an easy correction? Thanks, Josh

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segmentation
by Durastanti, Valentina (NIH/NINDS) [F] 05 May '06

05 May '06

Hi, I have a question: at the end of the segmentation (before the manual editing) I found that there are some voxel exceeding the yellow line and I can't figure out if they will be included in the WM count or if they will be included in the GM count. Have I to remove them even if they go over the line? Thanks Valentina

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mri_ms_fitparms
by adam walczak 05 May '06

05 May '06

At what point in the processing pipeline is mri_ms_fitparms? I am trying to convert data without header information (TE, TR, Flip angle) to data that freesurfer can use using mri_ms_fitparms and entering that info. This creates a T1 and PD image but I want to run it through the entire reconstruction. So I was wondering two things: 1) when should the mri_ms_fitparms be done on the data and 2) what point in the pipeline does it "spit out" the data? Thanks Adam --------------------------------- Yahoo! Messenger with Voice. Make PC-to-Phone Calls to the US (and 30+ countries) for 2¢/min or less.

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Freesurfer May 2006