Freesurfer

freesurfer@nmr.mgh.harvard.edu

6 participants
30054 discussions

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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tkmedit question
by George Papadimitriou 29 Sep '04

29 Sep '04

Hi all, How can I compute the volume of a label created using tkmedit? Is there a program to do this, or is it sufficient to count the number of points listed in the label file and multiply by the volume per voxel? (And if so, is the volume per voxel the voxel size for my original 40 slice axial volume, or the voxel size for the 256 slice resampled volume that tkmedit displays?) Thanks, George P.

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MacOSX mri_convert probelm fixed
by Yasunari Tosa 20 Sep '04

20 Sep '04

Hi, MacOSX people: We discovered a major problem in mri_convert for MacOSX. The problem ========= mri_convert COR file into mnc format produces the wrong byte order and thus "mincinfo" on that file does not work. The new binary =========== The file was compiled under Panther 10.3.5 (Darwin 7.5.0) and optimized for G4 (new trend). (Note that otool reveals the dependency in two fink libraries /sw/lib/libjpeg.62.dylib, /sw/lib/libtiff.3.dylib, and two system libraries: /usr/lib/libz.1.dylib, /usr/lib/libSystem.B.dylib). The check with minc compatibility ========================= I downloaded the latest MNI MacOSX binaries from http://www.bic.mni.mcgill.ca/software/distribution/#osx installed in /usr/local/mni. The comments =========== 1. If you need Jaguar version 10.2.x, please let me know. 2. If it won't run on your powerful G5, I will try to find G5 to compile. How-to-get-it ========== ftp surfer.nmr.mgh.harvard.edu use anonymous and passwd as your email address > cd pub/dist > get mri_convert-040920-Darwin.gz Thank you. Tosa Yasunari Tosa, Ph.D. Email: tosa(a)nmr.mgh.harvard.edu NMR Ctr, Mass. General Hospital TEL: 617-726-4050 Building 149, 13th Street Charlestown, MA 02129 USA

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questions on mkbrainmask-sess
by Jia Liu 20 Sep '04

20 Sep '04

Dear all- Today I tried mkbrainmask-sess (first time), and got the error message shown below: +++++++++++++++++++++++++++++++++ zion:/nfs/home/jliu/VM/myProc> mkbrainmask-sess -sf sessid_S001 -df sesspar -funcstem fmcss ------------------------------------------------ ------------------------------------------------ /nfs/home/jliu/VM/S001 Mon Sep 20 21:20:40 CST 2004 -------------------------------------------------- /nfs/home/jliu/VM/S001/bold mkbrainmask -i 004/fmcss -o masks/brain -thresh 0.1 -umask 2 -------------------------------------------------- Scratch Dir is /tmp/mkbrainmask_23685 # ---------- Converting bvolume to .img ------------------ # mri_convert 004/fmcss_000.bshort /tmp/mkbrainmask_23685/fmcss.img reading from 004/fmcss_000.bshort... INFO: bvolumeRead: min = 25, max = 1325 TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, -0.995227, 0.0975827) k_ras = (-0, 0.097583, 0.995227) writing to /tmp/mkbrainmask_23685/fmcss.img... Analyze Output Matrix -1.406 0.000 -0.000 94.016; 0.000 -1.400 0.195 101.727; 0.000 0.137 1.990 -42.636; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to 3 # ---------- Using FSL's BET to Extract Brain------------------ # This program has not been compiled for this data type /nfs/home/jliu/VM/S001/bold bet /tmp/mkbrainmask_23685/fmcss /tmp/mkbrainmask_23685/brain -m -f 0.1 ERROR: bet failed ERROR: mkbrainmask failed Exit 1 +++++++++++++++++++++++++++++end+++++++++++++++++++++++++ The input data (fmcss) were motion-corrected, spatial-smoothed, and intensity-normalized using fsfast (the newest version released). Could anyone tell me how to fix this problem? Thanks for your help! jia

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mincinfo error opening "orig.mnc"
by Mithun Mukherjee 17 Sep '04

17 Sep '04

Hi everybody, I am trying to run segment_subject on one run of data which was originally in BRIK format and then converted to COR using mri_convert. In the initial registration to talairach process, mincinfo can't seem to read the .mnc file that mri_convert gave it. As a result the talairach.xfm transformation matrix is not created by mritotal. The remaining procedures continue but I'm not sure if the registration to talairach space worked. I checked the file permissions on orig.mnc and that doesn't seem to be the problem. Is the COR to .mnc conversion the source of the error ? I tried reading the image information from "orig.mnc" independently with mincinfo but that didn't work either. Below are the error logs for both mincinfo and segment_subject. Thanks for your help. Mithun -- Rochester Center for Brain Imaging University of Rochester Medical Center 575 Elmwood Avenue, Annex Room 1B-101 Rochester, NY 14642 Ph: 585-275-4585 [pyramidal:aparna/mri/orig] madmin% mincinfo -image_info orig.mnc ncopen: filename "orig.mnc": Invalid dimension id or name miopen: MINC package entry point [pyramidal:aparna/mri/orig] madmin% [pyramidal:/usr/local/freesurfer] root# segment_subject aparna cp: /usr/local/freesurfer/subjects/scripts/brain.dat: No such file or directory /usr/local/freesurfer/subjects/aparna/scripts /usr/local/freesurfer registering aparna mri_convert orig orig/orig.mnc reading from orig... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to orig/orig.mnc... mincinfo: Error opening file "orig/orig.mnc" Error executing mincinfo on orig/orig.mnc Error: could not open file "/usr/local/freesurfer/subjects/aparna/mri/transforms/talairach.xfm". System message: No such file or directory mri_add_xform_to_header: could not read xform file '/usr/local/freesurfer/subjects/aparna/mri/transforms/talairach.xfm' No such file or directory reading from ../mri/orig... normalizing image... MRInormInit: Talairach origin at (128, 147, 114) wsize 10, windows 14 above, 9 below max gradient 1.000 0: 82 --> 82 1: 87 --> 113 2: 92 --> 119 3: 97 --> 121 ........ ........ .........

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