Freesurfer September 2010

freesurfer@nmr.mgh.harvard.edu

93 participants
127 discussions

Question about 'mri_surf2surf' and vertex index sorting
by orangekic 23 Sep '10

23 Sep '10

Hi, Could someone tell me the way how 'mri_surf2surf' resample one subject onto fsaverage? How can I know the specific point comes from in the native space? for example: [subject A] vertex index 1, (x, y, z) ---------<mri_surf2surf>--------> [subject A in subject B coordinate] vertex index ??, (x', y', z') I'm using 'mris_convert' to convert the thickness file to ascii format, include vertex index, (x, y, z), and thickness information. I'm wondering that what's the rule to sort the vertex index? And, how can I know the relationship between vertex index and the label other than in tksurfer or tkmedit? Best

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Re: [Freesurfer] iPhone and IPad FreeSurfer based atlas
by Pedro Paulo de Magalhães Oliveira Junior 22 Sep '10

22 Sep '10

http://itunes.apple.com/us/app/isurf-brainview/id381072423?mt=8 The download link for United States -- via iPhone iOS4 Em 22/09/2010, às 20:50, Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> escreveu: > > On Wed, 2010-09-22 at 19:17 -0300, Pedro Paulo de Magalhães Oliveira > Junior wrote: >> More news on the free brain atlas app for IPhone using FreeSurfer >> aseg. >> >> Today we have another major upgrade: >> >> >> - Pinch and Zoom >> - Many papers for Reading >> - Improved documentation of FreeSurfer >> >> http://itunes.apple.com/br/app/isurf-brainview/id381072423?mt=8 >> >> Suggestions for the upcoming version are welcome. >> >> Cheers >> >> Pedro Paulo Jr. >> >> -- via iPhone iOS4 >> --------------------------------------------------------------------- >> Pedro Paulo de Magalhães Oliveira Junior >> Diretor de Operações >> Netfilter & SpeedComm Telecom >> -- www.netfilter.com.br >> -- For mobile: http://www.netfilter.com.br/mobile >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail.

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iPhone and IPad FreeSurfer based atlas
by Pedro Paulo de Magalhães Oliveira Junior 22 Sep '10

22 Sep '10

More news on the free brain atlas app for IPhone using FreeSurfer aseg. Today we have another major upgrade: - Pinch and Zoom - Many papers for Reading - Improved documentation of FreeSurfer http://itunes.apple.com/br/app/isurf-brainview/id381072423?mt=8 Suggestions for the upcoming version are welcome. Cheers Pedro Paulo Jr. -- via iPhone iOS4 --------------------------------------------------------------------- Pedro Paulo de Magalhães Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://www.netfilter.com.br/mobile

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RAM question
by O'Shea, Colin (NIH/NIMH) [V] 22 Sep '10

22 Sep '10

I realize that FreeSurfer requires at least 4 GB RAM, and I'm in the process of getting extra ram for my computer. If I install FreeSurfer now, will the program simply not work or just run slow (or something in between)? Thanks, Colin

7 8

GLM question
by Gabriel Go.Es. 22 Sep '10

22 Sep '10

Hello everybody I'm wondering about how to perform an FDR correction using the glmfit on FS?, I mean using command line if there is one; And Could it be applied the same sentence to correct at cortex level and clusters label, or need some special arguments on the command line for any of them? Thanks in advance Gabriel

2 1

nframes file parameter...
by Gonzalo Rojas Costa 22 Sep '10

22 Sep '10

Hi: What it means the "nframes" parameter ?... Which is the difference between a 001 mgz file that has "dimensions: 256 x 256 x 176" and another that has "dimensions: 256 x 256 x 176 x 2" ?... Sincerely, Gonzalo Rojas Costa

3 3

changing f.nii nframes
by raij＠nmr.mgh.harvard.edu 22 Sep '10

22 Sep '10

Dear Free Surfers, I am analyzing fMRI time series that were reconstructed offline (GRAPPA data that needed some artifact corrections, long story). Unfortunately, the offline reconstructed f.nii do not include proper header info. I think I was able to set the orientations correctly using mri_convert, but now FSFAST preprocessing (specifically, mc-sess) fails because the headers say that the number of TRs (number of full volume acquisitions) in the measurement is 1, whereas in fact the correct value is 316. I could not find a tool that could change the "nframes" value (mri_convert can adjust many other things but not this one it seems). Any suggestions? Bests, Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.

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CSF volume
by Ed Gronenschild 22 Sep '10

22 Sep '10

Hi, One of the volumes listed in the aseg.stats is called "CSF". Its volume is too small to indicate the total CSF volume of the brain. What is its meaning? If I would like to get the total CSF volume how should I proceed? Ed

2 1

preproc-sess failing
by Adam Nitenson 22 Sep '10

22 Sep '10

Hello freesurfers, I am trying to unpack a couple of recent subjects in Stable 4. I ran all steps through recon-all without error. However, when I try to run the next step, preproc-sess, it keeps failing. This is the command I enter: preproc-sess -s FB0011060AA -fwhm 5 It works for about 30 seconds, and then I get the following in return niiRead(): bad number of dimensions (0) in 013/tmp.mc-afni2.15211/outvol.nii.gz reading info from 013/f.nii... $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from 013/tmp.mc-afni2.15211/outvol.nii.gz... ERROR: converting output Invalid null command. ERROR: mc-sess failed the error for the other subject was slightly different: niiRead(): error reading from 013/tmp.mc-afni2.15452/outvol.nii.gz reading info from 012/f.nii... $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from 013/tmp.mc-afni2.15452/outvol.nii.gz... ERROR: Read 14, expected 64 ERROR: converting output Invalid null command. ERROR: mc-sess failed Any idea what might be going on? I've done these same steps many times for processing data and have not before received this error. Thanks! Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital

1 0

PPC or Intel
by O'Shea, Colin (NIH/NIMH) [V] 21 Sep '10

21 Sep '10

Will FreeSurfer work with a PPC processor? Thanks, Colin

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Freesurfer September 2010