Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30070 discussions

Slackware 10.0.0
by Chacko Cherian 07 Aug '06

07 Aug '06

Hello all, I have a small query.Just wanted to know which stable Freesurfer version I should install for Linux Slackware 10.0.0 version. Has anybody experienced any issues usig this platform. Thanks in advance. Chacko Cherian. Arizona State University. __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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Recon all finished with errors, How do I see what errors?
by Jake Freimer 07 Aug '06

07 Aug '06

I was running autorecon2-cp and it said it finished with errors, below are the recon-all.log and recon-all-status.log, I couldn't figure out what the error is. Mon Aug 7 10:37:16 PDT 2006 #@# Intensity Normalization2 Mon Aug 7 10:37:16 PDT 2006 #@# Mask BFS Mon Aug 7 11:01:39 PDT 2006 #@# WM Segmentation Mon Aug 7 11:01:59 PDT 2006 Darwin lion.bmap.ucla.edu 8.7.0 Darwin Kernel Version 8.7.0: Fri May 26 15:20:53 PDT 2006; root:xnu-792.6.76.obj~1/RELEASE_PPC Power Macintosh powerpc recon-all exited with ERRORS at Mon Aug 7 11:12:31 PDT 2006 ...... #@# Mask BFS Mon Aug 7 11:01:39 PDT 2006 /private/Network/Servers/dns2.bmap.ucla.edu/Volumes/BMC3/BMCUsers3/ascott/Documents/freesurfer/subjects/td21new/mri \n mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz \n threshold mask volume at 5 Talairach transform /usr/local/freesurfer/subjects/td21new/mri/transforms/talairach.xfm does not exist ... Loading tal xfm file /private/Network/Servers/dns2.bmap.ucla.edu/Volumes/BMC3/BMCUsers3/ascott/Documents/freesurfer/subjects/td21new/mri/transforms/talairach.xfm writing masked volume to brain.finalsurfs.mgz... #-------------------------------------------- #@# WM Segmentation Mon Aug 7 11:01:59 PDT 2006 \n cp wm.mgz wm.seg.mgz \n \n mri_segment -keep brain.mgz wm.seg.mgz \n preserving editing changes in output volume... doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM: 105.9 +- 5.5 [80.0 --> 125.0] GM: 70.1 +- 9.7 [30.0 --> 96.0] setting bottom of white matter range to 79.7 setting top of gray matter range to 89.4 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 4126 sparsely connected voxels removed... thickening thin strands.... 20 segments, 2519 filled 2784 bright non-wm voxels segmented. 2121 diagonally connected voxels added... white matter segmentation took 10.4 minutes writing output to wm.seg.mgz... Darwin lion.bmap.ucla.edu 8.7.0 Darwin Kernel Version 8.7.0: Fri May 26 15:20:53 PDT 2006; root:xnu-792.6.76.obj~1/RELEASE_PPC Power Macintosh powerpc recon-all exited with ERRORS at Mon Aug 7 11:12:31 PDT 2006 Thanks -Jake

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Skull Stripping
by Derin Cobia 07 Aug '06

07 Aug '06

Hello, After having run -autorecon1 on all of my subjects I've noticed skullstripping has edited out the cerebellum/brainstem on some, but not on others. Because I'm not interested in these structures, can I just leave the files as is (i.e.-not bother adjusting the wsthreshold level, re-running, etc)? Or will I run into problems with the -autorecon2 & 3 processing streams down the line? Thanks again! -Derin

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surface format
by Anqi Qiu 07 Aug '06

07 Aug '06

Hi, Could you let me know the format of the surface generated by freesurfer? Is that easy to convert it to *.vtk? And also is the surface in the original subject space or in Talairach space? Thanks Anqi Qiu Center for Imaging Science The Johns Hopkins University

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having problem in running recon-all...
by Shahabuddin Ansari 07 Aug '06

07 Aug '06

Hello, I am having problem in running the following command: recon-all -i 2996926_02.img -s 2996926_02 I used to run the command before without any problem. Recently my linux has been updated to suse version, would that be a source of problem. The console display the following error: INFO: SUBJECTS_DIR is /ensc/IMAGE/opt/FREESURFER/subjects Actual FREESURFER_HOME /ensc/IMAGE/opt/FREESURFER Linux ilpc5 2.6.13-15.10-bigsmp #1 SMP Fri May 12 16:36:41 UTC 2006 i686 i686 i386 GNU/Linux mri_convert: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mri_convert: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mri_normalize: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mri_watershed: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mri_segment: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mri_fill: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mri_tessellate: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mris_smooth: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mris_inflate: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mris_sphere: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mris_fix_topology: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mris_euler_number: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mris_make_surfaces: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mris_register: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mrisp_paint: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mri_label2label: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mri_em_register: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mri_ca_normalize: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mri_ca_register: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mri_ca_label: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory /ensc/IMAGE/opt/FREESURFER/subjects/2996926_02 mri_convert /ensc/IMAGE4/PROJECTS/HD_AYLWARD/DATA/PATIENTDATA/SHAHAB/2996926_02/2996926_02.img /ensc/IMAGE/opt/FREESURFER/subjects/2996926_02/mri/orig/001.mgz mri_convert: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory Linux ilpc5 2.6.13-15.10-bigsmp #1 SMP Fri May 12 16:36:41 UTC 2006 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Sun Aug 6 19:08:34 PDT 2006 Shahab --------------------------------- Do you Yahoo!? Everyone is raving about the all-new Yahoo! Mail Beta.

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Problem copying subject directories
by Henry Lütcke 05 Aug '06

05 Aug '06

Hi, I ran autorecon-all on a Suse10.0 computer and it finished fine. when I copy the respective subject directory to another computer (Suse10.1) I can no longer view the surfaces with tksurfer (only a very tiny part is displayed; see attachment). I can view the volume in tkmedit fine and the surface is displayed on the computer where the analysis has been run. any ideas what might be causing this problem? thanks a lot, Henry

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Labels from segmentation
by Johannes Haushofer 03 Aug '06

03 Aug '06

Dear all, I'd like to create labels for certain structures based on their segmentation labels (e.g. a label containing all voxels in orbitofrontal cortex). Is there a way to automatize this? At the moment I'm using tkmedit to mark all voxels with the same segmentation label, then saving them as a label; that's a bit cumbersome... any hints? Many thanks! johannes

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DICOM conversion
by Valentin Piech 03 Aug '06

03 Aug '06

Hello everyone, I ran into the same problem converting GE multi-volume data from DICOM to nifti 4D with mri_convert as Adam Thomas in the [Freesurfer] mri_convert: dicom to nifti 4D <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2006-July/003324.html> thread did: I got one volume containing several thousand slices instead of the 4D volume. I also downloaded the improved version that Doug posted in the thread, and it solved my problems until recently. I have a new data set that won't convert anymore, and "mri_convert -it dicom -ot nii -dicomread2 ./mydicomfile.DCM ./myniftifile.nii" exists with the following error: *** glibc detected *** malloc(): memory corruption 0x083ba568 *** The data set is taken with the exact same protocol, except that it contains more volumes (227 instead of 176 volumes with 29 slices each). According to Doug in this thread [Freesurfer] generic dicom converting <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2006-July/003477.html>, there is a new version out that may solve my problem, but as it is part of the DEV version, I cannot download it as far as I know since I am not at MGH. Is there any way to download it that I don't know of? Also, I am normally using the x86_64 version, while the one posted in the previous thread is only the x86 one, so I have to have the 32 bit version of freesurfer installed and use its path when I run this version of mri_convert. Thank you very much for your help, Valentin -- Valentin Piech, Graduate Fellow Gilbert Lab for Neurobiology & Reeke Lab for Biological Modelling Rockefeller University 1230 York Ave Box 193 New York, NY 10021 PH: (212) 327-7646

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query regarding T2/T1
by Chacko Cherian 03 Aug '06

03 Aug '06

Hello all, Can we use tkmedit for T2-weighted images or is it restricted to T1 -weighted? Thanks Chacko.

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importing high-res scans
by Marie Schaer 03 Aug '06

03 Aug '06

Hi everybody, I am trying to process high res monkey scans in FreeSurfer (voxel size 0.31 x 1 x 0.31 mm). For converting them I use: mri_convert rawdata.img orig.mgz -iis 0.31 -ijs 1 -iks 0.31 -cm But I actually get a very small image in tkmedit. Further, moving each slice in any of the three directions give a volume index change of 1 and voxel RAS change of 3 (i.e. on the coronal slice number 128, the volume index 128 128 128 is equivalent to the volume RAS 0 0 0; going to the coronal slice 129 without moving the cursor will give the volume index 128 128 131, and RAS 0 1 0). Since RAS are the coordinates in millimeter, I actually expected that any change of slice would be accompanied by a 0.31 change on RAS and variation of 1 on volume index... Is there any basic step that I missed? Thank you very much, Marie Schaer

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