Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Error in recon-all on seychelles
by Chindhuri Selvadurai 02 Jun '11

02 Jun '11

Hello, I am not able to do a regular recon-all of my data on seychelles-- I am doing the same thing I used to do. We have started moving our data to a different location, however, since this is all new data, I don't see how this could be the problem. I am using freesurfer 4, so I set this var before sourcing the script: >setenv USE_STABLE_4_5_0 >source /usr/local/freesurfer/stable4 My subjects_dir is /space/ventzl/36/users/RespMon12C/subjects And my command is what it has always been: >/usr/bin/pbsubmit -q sergeant -l nodes=1:opteron -m chinsel -c 'recon-all -s RMOCD025 -all -i /cluster/archive/292/siemens/TrioTim-35006-20110504-155020-764000/764000-000004-000001.dcm -mail chinsel(a)nmr.mgh.harvard.edu -force' I would appreciate your help! Thank you, Chindhuri S ---------------------------- Original Message ---------------------------- Subject: PBS JOB 1380351.seychelles.nmr.mgh.harvard.edu From: "adm" <adm(a)nmr.mgh.harvard.edu> Date: Thu, June 2, 2011 2:03 pm To: chinsel(a)nmr.mgh.harvard.edu -------------------------------------------------------------------------- PBS Job Id: 1380351.seychelles.nmr.mgh.harvard.edu Job Name: pbsjob_14 Execution terminated Exit_status=1 resources_used.cput=00:00:00 resources_used.mem=0kb resources_used.vmem=0kb resources_used.walltime=00:00:01 Best, Chindhuri Selvadurai Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging, MGH Phone: (617)726-0307

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Error: talairach_avi: Command not found.
by ANN40＠pitt.edu 02 Jun '11

02 Jun '11

Hi all, I am running recon-all -autorecon1 -subjid subject and I have been getting an error saying: \n talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm \n talairach_avi: Command not found. And then the program exits with errors. I looked in the transforms directory within my subject directory and there is not talairach.auto.xfm there. However, the other preceding output files are there. I am new to freesurfer and was wondering if anyone could help me figure out what I am doing wrong. Thanks, Ashley

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Surface Normals in Freesurfer
by Michael Waskom 02 Jun '11

02 Jun '11

Hi Bruce et al. I have a quick question about the interpretation of surface normal files and the various ways you can create them with Freesurfer. As far as I know, there are two ways to get the normals information: mris_convert -n lh.inflated lh.inflated.normals2 and mri_surf2surf --s fsaverage --hemi lh --sval-nxyz inflated --tval lh.inflated.normals2.mgz The first writes an ascii file with 491522 rows and 4 columns (the last of which is all 0's), while the second writes a surface scalar "image" with dimensions 163842 x 1 x 1 x 3. Am I right to assume that the coordinates in the mgz image and the first n_vtx rows of coordinates in the ascii file correspond to the surface normals at the vertices of the mesh? And, furthermore, do the remaining coordinates in the ascii file correspond to the surface normals of the triangle faces on the mesh? Thanks! Michael

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mri_convert and timeseries data
by Jennifer Bramen 01 Jun '11

01 Jun '11

Dear Freesurfer Users I am trying to use mri_convert to reorient a nifti file. The file is a bold sequence, but for some reason, mri_convert is only outputting the first volume. I get this error as well: WARNING: niiRead(): unknown time units 0 in 2010_10_20_21_bold_gp2.nii Any idea regarding what I am doing wrong? Here is the command I used: mri_convert --in_orientation SLP --out_orientation LPI 2010_10_20_21_bold_gp2.nii 2010_10_20_21_bold_gp_RPI2.nii Any help would be greatly appreciated! Best regards Jen

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reshape command
by Jose Luis Cantero Lorente 01 Jun '11

01 Jun '11

Dear Freesurfers, I am trying to reduce the number of vertices to display with the wireframe overlay on the inflated cortical surface. To this aim, I am using the following command line: mri_surf2surf --s Estudio_EHM_average --sval-xyz inflated --tval /root/trabajo/freesurfer/subjects/Estudio_EHM_average/surf/lh.reshaped.inflated --tval-xyz --hemi lh --reshape --reshape-factor 7 But when I load the reshaped surface in Matlab it contains the same number of vertices as originally. Why the reshape command (factor 7) is not decreasing the number of vertices on cortical surfaces? Thanks in advance. Best regards, Jose --- Jose L. Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Seville - Spain - Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcanlor(a)upo.es http://www.upo.es/neuroaging/es/

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Extracting WMPARC stats
by Alan Francis 01 Jun '11

01 Jun '11

Hi All: I am trying to extract Volumes from the WMParc files into a txt file. Just as you have the *asegstats2table* command for segmentation stats and the * aparcstats2table* command for parcellation stats, is there a command you use to extract data from the wmparc.stats file? I tried manipulating the *aparcstats2table but it only generates volumes from the lh.aparc files.* thanks so much, Alan Francis Beth Israel Deaconess medical Center

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freeview and wm-segmentation errors
by von Polier, Georg Ferdinand Anto 01 Jun '11

01 Jun '11

Hi, using FS 5.1 now, I encountered two problems: 1. when I try to start freeview on my personal laptop, this errors appears: [georg@localhost ~]$ freeview freeview.bin: error while loading shared libraries: libXss.so.1: cannot open shared object file: No such file or directory However, libXss.so.1 is installed on my system running linux (Fedora 15). Do you habe any idea? 2. Running recon-all with -all flag on a cluster (Linux CentOs 5.6) the stream finishes with errors repeatedly showing this message: #@# WM Segmentation Tue May 31 12:36:00 CEST 2011 mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt znzTAGskip: tag=544043625, failed to calloc 1952413696 bytes! $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /rwthfs/rz/cluster/work/gg855262/subjects_AN/4550/mri cmdline mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt sysname Linux input wm.mgz frame 0 nErode3d 0 nErode2d 0 output wm255.mgz Binarizing based on threshold min 255 max 255 binval 1 binvalnot 0 Cannot allocate memory recon-all -s 4550 exited with ERRORS at Tue May 31 12:36:01 CEST 2011 ------------------------------------------------------------------------------ | Execution of Batch-Request stopped at Tue May 31 12:36:01 CEST 2011 | peak memory value: 2.386G | real time used: 04:58:38 I did allocate 4 GB of memory and did not face this error when using FS 5.0 or FS 5.1-beta-release with same settings. Any recommendations? Thanks, Georg

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display tessellation
by Jose Luis Cantero Lorente 01 Jun '11

01 Jun '11

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Job advertisement! - Germany
by Loose, Daniel 01 Jun '11

01 Jun '11

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color scales for retinotopy
by abdurahman elkhetali 31 May '11

31 May '11

I am having trouble getting the script "rtview" to work so that I can use the color scale to see phase of the polar and eccentric angles. After chmoding the script I run the following command ./rtview --reg LOAF_08/bold/002/register.dof6.dat --lh --ploar --real LOAF_08/bold/rtopy.self.lh/eccen/real.nii --imag LOAF_08/bold/rtopy.self.lh/eccen/imag.nii --fsig LOAF_08/bold/rtopy.self.lh/eccen/fsig.nii But wasn't able to get any overlay, Is there any guide on how get a color wheel or the rtview script? Thasnks Abdoul Any help much apprechitated

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