Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30085 discussions

Trouble installing freesurfer to a cluster
by Tamara Knutsen 09 Feb '10

09 Feb '10

Hi, I am trying to install the freesurfer-Linux-suse-ia64-stable-pub-v4.5.0.tar to my user home directory (/home/knutsen) on the following Caltech cluster: Neuroecon Cluster 12 Dell Poweredge 1950 nodes 16 GB RAM per node Gigabit ethernet interconnect Matlab Distributed compute engine Rocks 5.1 Provisioning Maui/Torque scheduling and resource management 60 TB Lustre File System DDN 9700 The files seem to have unpacked correctly. ls -a /home/knutsen/freesurfer . build-stamp.txt FreeSurferEnv.sh mni subjects .. DefectLUT.txt fsafd SegmentNoLUT.txt tkmeditParcColorsCMA ASegStatsLUT.txt diffusion fsfast sessions AUTHORS docs lib SetUpFreeSurfer.csh average FreeSurferColorLUT.txt .license SetUpFreeSurfer.sh bin FreeSurferEnv.csh matlab Simple_surface_labels2009.txt I ran the SetUpFreesurfer.sh and it properly recognizes $FREESURFER_HOME I then tried to import some Siemens dicom files to the subjects dir using the following command from /home/knutsen: recon-all -s ATM -i Subjects/100/Anatomy/2/1.3.12.2.1107.5.2.13.20524.30000010011116574178100000018.dcm -i Subjects/100/Anatomy/3/1.3.12.2.1107.5.2.13.20524.30000010011116574178100000196.dcm -i Subjects/100/Anatomy/4/1.3.12.2.1107.5.2.13.20524.30000010011116574178100000374.dcm -i Subjects/100/Anatomy/5/1.3.12.2.1107.5.2.13.20524.30000010011116574178100000552.dcm And get the following errors: Subject Stamp: freesurfer-ia64-suse-linux-stable4-20090905 Current Stamp: freesurfer-ia64-suse-linux-stable4-20090905 INFO: SUBJECTS_DIR is /home/knutsen/freesurfer/subjects Actual FREESURFER_HOME /home/knutsen/freesurfer Linux neuroecon.caltech.edu 2.6.18-128.1.14.el5 #1 SMP Mon Jun 1 15:52:58 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux /home/knutsen/freesurfer/bin/mri_convert: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/flirt: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mri_convert: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/tkregister2_cmdl: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mri_normalize: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mri_watershed: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mri_segment: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mri_label2label: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mri_em_register: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mri_ca_normalize: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mri_ca_register: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mri_ca_label: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mri_pretess: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mri_fill: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mri_tessellate: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mri_concatenate_lta: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mri_normalize_tp2: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mris_smooth: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mris_inflate: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mris_curvature: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mris_sphere: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mris_fix_topology: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mris_topo_fixer: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mris_ca_label: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mris_euler_number: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mris_make_surfaces: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mris_register: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mris_anatomical_stats: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mrisp_paint: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mris_curvature_stats: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mri_robust_register: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mri_robust_template: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mri_and: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mri_or: Exec format error. Binary file not executable. /home/knutsen/freesurfer/bin/mri_fuse_segmentations: Exec format error. Binary file not executable. /home/knutsen/freesurfer/subjects/ATM mri_convert /home/knutsen/Subjects/100/Anatomy/2/1.3.12.2.1107.5.2.13.20524.30000010011116574178100000018.dcm /home/knutsen/freesurfer/subjects/ATM/mri/orig/001.mgz /home/knutsen/freesurfer/bin/mri_convert: Exec format error. Binary file not executable. Linux neuroecon.caltech.edu 2.6.18-128.1.14.el5 #1 SMP Mon Jun 1 15:52:58 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Tue Feb 9 17:24:49 PST 2010 Wondering what I did wrong in the install that all the binaries are not executable. It's probably something obvious. Thanks for any help/advice, Tamara

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Pallidum Volume Assymetry in hemispheres and fs versions
by Jeff Sadino 09 Feb '10

09 Feb '10

Hello Everyone, I ran 106 subjects through fs 3.0.5 and also through fs 4.3.1 and then compared the volumes of the subcortical structures. Most of them correlated well between versions, but for the pallidum, there was a strong bias both hemispherically and between versions. In fs3, the left pallidum was 1995 and the right was 1756 for a difference of 239. In fs4, the left pallidum was 1882 and the right was 1593 for a difference of 289. Between fs versions, this gives a 6% difference [ (1995-1882) / ((1995+1882)/2) ] for the left pallidum and a 9.7% difference [ (1756-1593) / ((1756+1593)/2) ] for the right pallidum. Between hemispheres, the difference is 19% [ (289-239) / ((289+239)/2) ]. I was wondering particularly as to the 19% variability of the pallidum measurements between fs versions. Is this much of a difference common between these two freesurfer versions, or is it unique to our study? Also, is 6% and 9.7% difference for the pallidum between hemispheres typical in freesurfer? Attachment is plotting automated results between fs3 and fs4. Thank you very much for your feedback! Jeff Sadino

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diagnostic level
by Guang Zeng 09 Feb '10

09 Feb '10

Hi, there, Both mris_ca_label and mris_ca_train have a -v option which is called: diagnostic level. What is the meaning of this diagnostic level? Thanks! Guang _________________________________________________________________ Hotmail: Trusted email with powerful SPAM protection. http://clk.atdmt.com/GBL/go/201469227/direct/01/

2 1

Editing Parcellations
by Jennifer Bramen 09 Feb '10

09 Feb '10

Dear Freesurfer List I am trying to edit the parcellations using tkmedit, but I am unable to effect the Segmentation Brush label using the Configure Segmentation Brush window. Regardless of my selection, my drawing is labeled "out of bounds". I don;t see an apply button or anything like that, so I assumed simply highlighting the tissue class in the Configuration window would change the brush to my selected label. Is there some step I may be moissing when trying to make a selection? I am using the most up to date version of Freesurfer, and have also tried reverting to older versions, all with no success. Thanks for you your assistance. Best regards, Jennifer Bramen, Ph.D. Assistant Research Neuroscientist David Geffen School of Medicine at UCLA Developmental Cognitive Neuroimaging 635 Charles Young Drive South Los Angeles, CA 90095-7332 Phone: (310)525-0865 Fax: (310)206-5518 Email: jbramen(a)mednet.ucla.edu Campus Mail Code 176919

2 1

Skull Stripping extra dura & vasculature
by Sherri Novis 09 Feb '10

09 Feb '10

Hello, I have a series of datasets with skull stripping issues - namely left over dura/vasculature in the occipital cortex, and some in frontal areas.(Attached is a jpeg of the type of issue. It's pervasive throughout the slices, across a handful of subject data.) I have rerun skull stripping changing the watershed value, however it's not making the distinction between dura and gray matter. (recon-all -skullstrip -wsthresh [tried 0..35] -clean-bm -no-wsgcaatlas -subjid [subject_id] - FS version: freesurfer-Linux-centos4-stable-pub-v4.3.0) I also attempted to edit 50% of the slices by erasing voxels to make a clear boundary between the dura and cortex and then re-ran autorecon2 to see if it would at least adjust the pial surfaces - however that did not work (pial surfaces still crossed the one pixel boundary I made into the dura). Can you recommend any other flags or things to try before I edit/erase the excess by hand? Thanks for your time - Sherri

2 1

smooth pial surface in occipital pole region
by yzhangd＠artsci.wustl.edu 09 Feb '10

09 Feb '10

Hi experts, I found that the pial surface in the occipital pole region tends to be smooth, after running recon-all. Shallow sulci and fused sulci render a smooth surface (attached surface images). i tried to delete some voxels (arrows on the "flatpialsurf_volume.tiff") to force freesurfer to recognize these sulci. Are deleting voxels from the brainmask.mgz image an appropriate approach to correct the surface in this region ?? Thanks a lot Yuning

2 1

ITI/ISI in optseq2
by Asaf Kaftory 09 Feb '10

09 Feb '10

hello list, 1. Is there a way to make sure Optseq2 inserts a "null" after each event (and thus creating an ISI/ITI between every conditions)? If not - how is it possible to make sure there's a minimal ITI/ISI between each stimuli? 2. If defining an ITI is possible in optseq2, Is there a way to determine its average and SD? thanks, asaf.

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dt-recon output file format
by Ed Gronenschild 09 Feb '10

09 Feb '10

Hi, Question for the developers. Is it possible to adjust the dt-recon tool such that the output files are in zipped NIFTI format (.nii.gz) in view of the enormous amount of data that is generated. It can accept .nii.gz files as input. Thank you in advance, Ed

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FS Deformable Xform
by Suresh Joshi 09 Feb '10

09 Feb '10

Hello all, short time reader, first time poster... I have a question regarding the current FreeSurfer volumetric pipeline. This page: http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferAnalysisPipelineOverview states that FreeSurfer has 5 stages and they are described in Fischl 2002,2004 (which I have read). As well, there is a "a high dimensional nonlinear volumetric alignment" (which I take to be deformable registration). So, now my question is: Can anyone give me any specifics about this non-linear transform? In the Fischl paper, the second transform gets reduced to a 12 parameter affine transform. As well, here is the new pipeline: http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllBlockDiagram And it doesn't clearly answer my question. As well, there are talks of intensity normalization (ie. elimination of bias fields), but it there ever an intensity normalization step performed between the atlas and the target??? Thanks for the help, -SJ

2 1

Invitation to connect on LinkedIn
by John Drozd 09 Feb '10

09 Feb '10

LinkedIn ------------ Freesurfer, I'd like to add you to my professional network on LinkedIn. - John Confirm that you know John Drozd https://www.linkedin.com/e/isd/1058664165/nSlXVFJx/ ------ (c) 2010, LinkedIn Corporation

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