Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30128 discussions

Processing woes
by Kai Schreiber 08 Oct '04

08 Oct '04

Hi there, I just installed freesurfer, and I apologize if I'm missing something simple. We read in structural data in AFNI's BRIK and HEAD format. Everything works fine, until we run the white matter fill. This will write about 20K/second of error messages to error.log and run for several hours, only to complete without creating usable output. We then of course get an error message for Tesselation complaining about the previous step's lack of output. The error.log file contains just a gazillion copies of this single line (recently it ran up to almost 1GB of it) MRIvoxelToTalairachVoxel: unsupported slice direction -1 What gives? Cheers, Kai -- Kai Schreiber PhD, School of Optometry, UC Berkeley 360 Minor Hall, Berkeley, CA 94720-2020, USA Phone ++1 510 642 7710 http://genista.de/kai/kschreiber.html

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displaying annotation
by Keyma Prince 08 Oct '04

08 Oct '04

Hello, I would like to import the annotation file into the csurf but with only certain labels produced by parcellate subject. I would like to use this to display some of the labels produced by the parcellate subject onto the inflated brain. Do I have to extract the labels from the annotation file first? -Keyma Keyma Prince Massachusetts Institute of Technology Department of Brain and Cognitive Sciences NE20-392 Cambridge, MA 02139

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Hi, question
by Wan Park 08 Oct '04

08 Oct '04

After processing the volume, creating the surface, making the final surface and registering the surface, I would like to measure the cortical thickness with freesurfer. Could you please give me hints about how and where to start? thanks Wan Park

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mcflirt syntax
by Keith Schneider 06 Oct '04

06 Oct '04

Hi, I have a simple question for which I can find no answer. What is the command line input for mcflirt in order to register all of the volumes within a directory? mcflirt -in * doesn't seem to work. Thanks for any info. keith

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Problem Running 'csurf'
by Kushal Koolwal 06 Oct '04

06 Oct '04

Hi, I have installed the XDarwin package on my Mac System as instructed in the installation guide. The manual says after installing refer to FREESURFER_HOME/docs/FreeSurferManual.pdf (ftp://surfer.nmr.mgh.harvard.edu/pub/docs/FreeSurferGuide.pdf) to get started. In this manual it says to edit the FreeSurferDefs.csh file and change the following line where specified: setenv CSURF_DIR XXXXXXXX # CHANGE_THIS_DEFINITION and then type 'csurf' on the prompt to run the software. My problem is: 1) I can't find FreeSurferDefs.csh file in my installation directory. 2) As soon as give the command 'csurf' at the prompt it gives me an error message: "Application initialization failed: no display name and no $DISPLAY environment variable tix not found--setenv problem?" is the Problem because of the missing file or there is some problem with my configuration display? Kindly tell me where I went wrong? Thanks Kushal __________________________________ Do you Yahoo!? Yahoo! Mail Address AutoComplete - You start. We finish. http://promotions.yahoo.com/new_mail

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Re: mris_glm-sess (fwd)
by Trinity Urban 04 Oct '04

04 Oct '04

Hi Doug - Any luck with my mris_glm-sess problem? Thank you!! -- On Fri, 1 Oct 2004, Trinity Urban wrote: > i've attached the .fsgd, .sessid, and .log file. the data is in > /space/curmudgeon/4/users/trinity/ALCFAST/ > > thank you!!

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flattening problems
by Jack Grinband 01 Oct '04

01 Oct '04

Hi All, I'm new to FS and I'm having trouble with the flattening step. After making the cuts, the instructions in the FreeSurferGuide (p44) are to fill the non-midbrain regions and save the patch. 1. It's not clear to me what the difference is between the blue and the white fill. 2. I filled the non-midbrain areas (white fill) and did "save patch as". But when I load the patch, I get back all the brain regions including the midbrain. In other words I can't seem to make a midbrain-free image that looks like the last figure on page 44. 3. When I try to flatten the brain, it processes the data for a while, but doesn't seem to produce a flattened image (I suspect because I can't get rid of the midbrain). Any ideas how I might solve these problems would be much appreciated. thanks, jack grinband

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license key
by Margaret Duff 01 Oct '04

01 Oct '04

Hello, I received a license key by email, but cannot find where in the license it should go. Thanks, Margaret

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mris_glm-sess
by Trinity Urban 01 Oct '04

01 Oct '04

I'm trying to use mris_glm-ses for the first time but something is going > wrong. It seems to run ok but there is no output file. What am I doing > wrong? > > mris_glm-sess -hemi rh -projfrac 0.5 -fsgd test.fsgd -sf test.sessid -a > individual_anal_FE -contrast allvfix_de --trgsubj average7 --gcv 1 -1 0 0 > --sigt sigt-average7-rh.w paint >

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problem to source FreeSurfer.cshrc
by Sepideh Sadaghiani 29 Sep '04

29 Sep '04

Hello, I'm trying to install FreeSurfer0.8 on linux. Since the linux computer doesn't have an internet connection, I write off what from the shell: [sepirat@localhost sepirat]$ ls etc/ FreeSurfer.cshrc [sepirat@localhost sepirat]$tcsh : Command not found. : Command not found. : label not found. [sepirat@localhost ~]$ source etc/FreeSurfer.cshrc : Command not found. : Command not found. : label not found. [sepirat@localhost ~]$ newdefs newdefs: Command not found. I don't have a solid unix background. Is this a problem with tcsh? Sep -- +++ GMX DSL Premiumtarife 3 Monate gratis* + WLAN-Router 0,- EUR* +++ Clevere DSL-Nutzer wechseln jetzt zu GMX: http://www.gmx.net/de/go/dsl

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