Freesurfer February 2010

freesurfer@nmr.mgh.harvard.edu

96 participants
153 discussions

projection depth using tksurfer or mri_vol2surf
by Sepideh Sadaghiani 10 Feb '10

10 Feb '10

Hi, I am rendering an analyze format img onto the fsaverage surface. I was wondering whether it is possible to specify the MAXIMAL depth of activation that is supposed to be projected onto the surface. Hereby I mean an ADDITIVE depth: The option --projdist (and also --projfrac) are not doing what I want. They lead to a translation of the projection surface into depth, but I seem to loose the more superficial activations. I know that my goal could be achieved in the older versions of FreeSurfer using --dmax for the paint command. So I wonder how I can do the same thing in the current FreeSurfer. Thanks, Sepideh -- NEU: Mit GMX DSL über 1000,- ¿ sparen! http://portal.gmx.net/de/go/dsl02

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SPM vol .nii to w file surface overlay
by Nela Cicmil 10 Feb '10

10 Feb '10

Dear Freesurfer users, I have tried to convert a volumetric SPM activity image from the form of a .nii file (created against the subjects T1.nii image) into a w file (paint file) to be overlaid on the inflated surface of the same subject's brain anatomy (created with Freesurfer recon-all), using the command below: mri_vol2surf --mov ~/<name>.nii --out ~/<name>-rh.w --hemi rh --surf inflated --out_type paint --regheader $SUBJECT However, the pattern on the surface does not *quite* match what I see from the volumetric image, and one of the reasons for this could be that I am not converting from volume image to surface overlay correctly - I would be very grateful, if there is a better way to do this, if someone could let me know. Thanks and best wishes, Nela ---- Nela Cicmil D.Phil Candidate, Neurophysiology Dept. Physiology, Anatomy & Genetics University of Oxford

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recon-all analyze 7.5 format
by SG KIM 10 Feb '10

10 Feb '10

Hi all, I've got .IMG and .HDR files in analyze 7.5 format, and ran recon-all -s subject -i file.img it doesn't seem to refer the .hdr file. What else should I do to use analyze format in Freesurfer? SG

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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/

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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

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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

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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

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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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Freesurfer February 2010