Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

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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curvature of flattening
by Gabriel Go.Es. 31 May '11

31 May '11

Dear FS experts, I'm making some flattenings of one subject on FS and I'm wondering if it is possible to see the ?h.curv or the ?h.sulc on grayscale and not in red-green nor in the binary gray representations of tksurfer. Regards, Gabriel.

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Full-time Research Assistant position in Clinically-Oriented Cogn itive Neuroscience at Virginia Tech
by John Richey 31 May '11

31 May '11

Dear freesurfer users, The following advertisement is for a full-time research assistantship in cognitive neuroscience in the Department of Psychology at Virginia Tech. Please feel free to distribute to interested parties. **Full-Time Lab/Research Assistant Position: Social-Clinical-Affective Neuroscience Lab Description of Position & Duties: A full-time R.A. position is available in the lab of Dr. John Richey in the Department of Psychology at Virginia Tech. The Assistant will be involved in implementing and organizing studies that investigate brain function and structure in the context of autism and affective disorders. The central research program seeks to investigate and quantify in vivo the the relation between particular cortical regions and social-cognitive dysfunction across a range of pathological states. Ultimately, we aim to assess the impact of neurocognitive intervention on cortical function and behavioral/cognitive outcomes in patients. To investigate this, the laboratory utilizes several neuroimaging modalities, including functional magnetic resonance imaging (fMRI), high-resolution structural MRI and diffusion tensor imaging (DTI). The position involves data acquisition in human research subjects, data analysis and administrative tasks. It is expected that the candidate will be able to work collaboratively with an interdisciplinary group of clinicians, psychologists and cognitive neuroscientists to accomplish our research objectives.This is an excellent position for someone wishing to enter graduate or medical school. The start date is negotiable, but would be no earlier than August 1st 2011, and ideally no later than October 1st 2011. A one-year commitment is expected. Requirements: 1) Bachelor's degree in psychology, neuroscience, biomedical engineering, computer science or related field. 2) Strong organizational skills, including ability to prioritize tasks and make decisions independently. 3) Strong interpersonal skills and ability to work with patients. Although not required, experience in the technical aspects of fMRI, including Unix/Linux shell scripting and basic knowledge of common statistical software platforms (MATLAB, freesurfer, FSL) is desirable. The ideal candidate will also have a strong background in statistics, biology and/or neuroscience and a demonstrated interest in research Any interested candidates should provide a cover letter, a resume and the names and contact information of 2-3 references to Dr. John Richey (richey(a)vt.edu) Candidates are also welcome to contact with any questions about the position.

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Appropriate positive control to for overall quality?
by Joakim Vinberg 31 May '11

31 May '11

Hi everybody, I have been analyzing a dataset that has produced some unusual results. Does anybody have any suggestions for a general positive control to ensure data and segmentation quality? I am thinking along the lines of comparing the results of measurements with age to Salat, 2004: Thinning of the Cerebral Cortex in Aging, or perhaps sex differences (both of these measurements would be relatively independent of my investigations). Thanks in advance! Joakim

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poor wm segmentation
by kwa1＠rice.edu 31 May '11

31 May '11

Hello all, I have a subject for whom I have been trying to edit the wm segmentation. This last time was the fifth time I have run the subject through autorecon2 and I am still achieving quite poor wm segmentation and pial tracings. To try and solve the problem I keep drawing in more of where the wm should be and removing it where it should not (on the aux surface). I have also tried adding control points but to no avail. Does anyone have a solution for how to proceed? This subject has no abnormalities that would otherwise limit the accuracy of the segmentation and I see no reason for it not to work. The scan also has decent contrast (same as all the other subjects who had great segmentation in FS). Thank you in advance, Kareem

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