Freesurfer

freesurfer@nmr.mgh.harvard.edu

14 participants
30096 discussions

(no subject)
by Shani Ben Amitay 08 May '13

08 May '13

Hello Freesurfer I would like to extract the stream for surface-based analysis on the output of an in-house segmentation process. Is this possible?How? Thanks Shani

2 5

mri_convert Segmentation fault
by Oscar Esteban 08 May '13

08 May '13

Dear all, I am experiencing segfaults when trying to convert from nifti to mgz. Ubuntu 13.04 Freesurfer 5.1, 5.2 and 5.3-BETA. I tried to find the problem using ldd, gdb, etc. but there is no debug information. I tried to compile 5.3-BETA but it does not find libminc-dev (while it is installed)... I think this is the same problem (related to the new libc in ubuntu 13.04) that those posted in https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-May/029581.html , https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-January/027532.h… and https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-May/029679.html. I'm looking forward to helping, but since there is no debug information in the binaries and I'm stucked with compilation... I don't know what to do. Best, Oscar Esteban -- Oscar Esteban PhD Student / Researcher Biomedical Image Technologies (BIT), UPM ETSI Telecomunicación Lab. C203, Av. Complutense s/n - E-28040 Madrid (Spain) +34 915 495 700 ext.4234 Signal Processing Laboratory (LTS5), EPFL-STI-IEL-LTS5 ELD 224 (Bâtiment ELD), Station 11, CH-1015 Lausanne, Switzerland

2 1

Issues in version 5.2
by stdp82＠virgilio.it 08 May '13

08 May '13

I apologize for the trivial question, but for me is urgent to understand if the issues that affect the version 5.2 are referred also to TRACULA and hippo-subfield.Do you advice me to cancel my analysis performed by 5.2. and re-run it by new version 5.3? Are the results obtained with version 5.2 reliable? Thank you very much for reply and for your work. Stefano

2 1

Google Talk 使用邀请
by Google Talk 08 May '13

08 May '13

----------------------------------------------------------------------- yufeng huang邀请您使用 Google Talk。如果您已经拥有 Google 帐户，请登录 Gmail 并接受此聊天邀请： http://mail.google.com/mail/b-60fdfa524c-703f0dba08-8eKfT6qRXAGCd7RaLzjh4b7… 要注册 Google 帐户并开始使用 Google Talk，您可以访问： http://mail.google.com/mail/a-60fdfa524c-703f0dba08-8eKfT6qRXAGCd7RaLzjh4b7… 要了解详情，请访问： http://www.google.com/intl/zh-CN/landing/accounts/ 此致， Google 小组敬上

1 0

ICV
by Alejandra Infante 07 May '13

07 May '13

Hi, I understand that ICV is an estimated measure based on a standard talairach transformation; however, I want to know how freesurfer is defining intracranial volume (i.e., is this a representation of everything within the cranium as the name implies or is it an estimate of total brain volume, which would not include space between skull and dura)?. We are using fs vesion 5.1 -- M. Alejandra Infante Doctoral Student SDSU/UCSD Joint Doctoral Program in Clinical Psychology Phone: (858) 449-2950 E-Mail: infante.alejandra.m(a)gmail.com

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Freesurfer segmntation for ICBM or Colin27
by Priyanka 07 May '13

07 May '13

Hello FreeSurferusers, Has anyone processed ICBM or Colin27 template through Freesurfer V5.0.0 (or higher) or does anyone know if such data is available in public database? Thank you. Priyanka Bhatt

2 1

Qdec and GLM ROI analysis
by Jon Wieser 07 May '13

07 May '13

I am interested ing doing a group surfaces analysis like that specified in: ftp.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis, or http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis?highlight… but I want to limit the analysis to a specific ROI. how do i do this? -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219

1 0

segfault during rfx with mri_glmfit
by Alex Kell 07 May '13

07 May '13

hi freesurfers, i am running into a segfault whenever i try to use mri_glmfit to run a random effects analysis. (this is in the volume, not on the surface.) here's my call: mri_glmfit \ --y $ces_fpath \ --X $design_mat_fpath \ --C $c1_fpath \ --C $c2_fpath \ --C $c3_fpath \ --mask $mask_fpath \ --glmdir $glmdir_fpath \ --nii.gz i've tried a number of things to reduce the memory footprint of the call: -- originally i was using WLS, but i was worried about the memory demands of the cesvar, so i switched to OLS -- i introduced a GM mask -- i downsampled the ces and cesvar images (from 1 mm isotropic [cvs space] to 2 mm isotropic) any thoughts on what could be going wrong here? thanks, guys! alex ps. below are my build stamp, my info dump from mri_glmfit, and an example stderr & stdout. my fs build stamp: freesurfer-Linux-centos4_x86_64-dev-20120104 the "all info" dump from mri_glmfit: ProgramName: mri_glmfit ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2013/05/07-14:15:28-GMT BuildTimeStamp: Jan 4 2012 05:11:02 CVS: $Id: mri_glmfit.c,v 1.209 2011/12/16 19:02:28 greve Exp $ User: alexkell Machine: ba7 Platform: Linux PlatformVersion: 2.6.38-16-generic CompilerName: GCC CompilerVersion: 30400 an example stderr and stdout: $Id: mri_glmfit.c,v 1.209 2011/12/16 19:02:28 greve Exp $ cwd /mindhive/nklab2/ellison_on_nklab2/adultasd/vss/4_rfx/glm_output/F-O cmdline mri_glmfit --y /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_input//cvs.all.ces.F-O.runs_1234.2x2x2.nii.gz --wls /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_input//cvs.all.cesvar.F-O.runs_1234.2x2x2.nii.gz --X /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_input//design_matrix.dat --C /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_input//asd.mtx --C /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_input//tc.mtx --C /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_input//tc-asd.mtx --mask /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_input/cvs.gmMask.2x2x2.nii.gz --glmdir /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_output//F-O --yhat-save --eres-save --save-cond --nii.gz sysname Linux hostname ba7 machine x86_64 user alexkell FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /mindhive/nklab2/ellison_on_nklab2/adultasd/vss/4_rfx/glm_input/cvs.all.ces.F-O.runs_1234.2x2x2.nii.gz logyflag 0 X /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_input//design_matrix.dat usedti 0 mask /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_input/cvs.gmMask.2x2x2.nii.gz maskinv 0 glmdir /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_output//F-O IllCondOK 0 ReScaleX 1 DoFFx 0 wFile /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_input//cvs.all.cesvar.F-O.runs_1234.2x2x2.nii.gz weightinv 1 weightsqrt 1 Creating output directory /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_output//F-O Loading y from /mindhive/nklab2/ellison_on_nklab2/adultasd/vss/4_rfx/glm_input/cvs.all.ces.F-O.runs_1234.2x2x2.nii.gz Saving design matrix to /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_output//F-O/Xg.dat Normalized matrix condition is 1 Matrix condition is 2.21429 Pruning voxels by thr: 0.000000 Found 115353 voxels in mask Saving mask to /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_output//F-O/mask.nii.gz search space = 922824.000000 Segmentation fault

2 2

Using FSL matrix for Talairach transform
by Johannes Klein 07 May '13

07 May '13

Dear all, I have some tricky subjects that I cannot get to register properly with the standard Talairach process, or even the use-mritotal option. However, with some fiddling, I've produced a reasonable registration matrix with FSL's FLIRT. I'm now looking to convert my FSL registration matrix, and use it as Freesurfer's Talairach transform. From the documentation, I gathered that I need to get it into Freesurfer's xfm format, and I suppose this is a two step process. I converted the FLIRT-provided matrix cor2raw.xfm like so: tkregister2 --mov /usr/local/freesurfer/average/mni305.cor.mgz --fslreg cor2raw.xfm --s mysubject --noedit --reg register.dat I then converted register.dat to the xfm data format: regdat2xfm /usr/local/freesurfer/average/mni305.cor.mgz rawavg.mgz register.dat tal.xfm and finally replaced talairach.xfm in the transforms directory with the output of the last command. Unfortunately, this doesn't work, and the transform is very much off target when I view it in tkregister2. Obviously, I've made a mistake when converting between the different transforms - could anybody point me in the right direction? Thanks all, Johannes

2 1

Probably activation due to vessels
by Jörg Pfannmöller 07 May '13

07 May '13

Dear Freesurfers, I computed the functional activation in a sensory task using freesurfer's fsfast stream. In the cortex surface line like activated regions are present. Their extension is much larger than the extension of the expected regions. Therefore, I suppose that those regions are due to vessels. Is there a possibility in freesurfer to remove them. Ideally there would be something like a volume based mode which does not sxclude the cortex. In this mode the vessels couls be identified and removed. Any help is highly apprexiated. Respectfully yours pfannmoe

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