Freesurfer

freesurfer@nmr.mgh.harvard.edu

6 participants
30091 discussions

mean cortical thickness of significant clusters in qdec
by Richter, Julia 29 Jan '13

29 Jan '13

Dear FreeSurfer experts, I did a group analysis in qdec, found several significant clusters and would now like to extract the mean cortical thickness of each significant cluster. I know that I have to run mri_glmfit-sim to do this, but I do not understand which commands I need to get the xxx.y.ocn.dat as output by running mri_glmfit-sim. Any ideas? Any help is appreciated. :) Best wishes, Julia

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VTK surface
by Alexander Hunold 29 Jan '13

29 Jan '13

Hi, Recently I ran into a problem regarding vtk surfaces created and saved with FreeView. My goal is to mark brain lesions and to save the surface in the FreeSurfer surface format. In the first step I generated the surface of the lesion in FreeView and saved it in vtk format. Secondly, I tried to convert the vtk surface with mris_convert in the surf format. Unfortunately, I received the following error: $ mris_convert Tubers.vtk Tubers.surf MRISreadVTK: error parsing POLYGONS in file Tubers.vtk mris_convert: could not read surface file Tubers.vtk Please find the vtk file attached. >From comparisons with older vtk files generated by FreeView, I understood that recently polygons instead of triangles are defined in the vtk file. Is there a way to extract the surface triangles again? Thanks, Alex

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Job offer: Neuroimaging scientist or clinician in Frankfurt
by Dr.med. Johannes C. Klein 29 Jan '13

29 Jan '13

Dear all, I'm attaching a job offer for a fully-funded neuroimaging position at Frankfurt University, available immediately. The position is based at the Brain Imaging Center of Goethe University, a facility that hosts two dedicated research MR scanners and an MEG facility. A full clinical salary is available for applicants with a medical degree. Best, Johannes ==== Dr Johannes C Klein Goethe-University of Frankfurt Department of Neurology, Brain Imaging Center Schleusenweg 2-16 D-60528 Frankfurt/Main Germany email: klein(a)med.uni-frankfurt.de http://www.bic.uni-frankfurt.de/ ============ The Department of Neurology and Brain Imaging Center (BIC) at the Goethe-University Frankfurt am Main invites applications for a full-time position as Clinician scientist (m/f) Or Doctoral/Postdoctoral researcher (m/f) We are seeking to recruit a highly motivated individual to develop a programme of research into imaging biomarkers of neurological diseases. Topics include the evolution of lesions in Multiple Sclerosis, the differentiation of neurodegenerative diseases, and the evaluation of target sites for deep brain stimulation (DBS) in movement disorders. Essential qualifications and interests include · a background in medicine, neuroscience, or a related field (e.g., a degree in psychology, engineering, physics, biology) · programming skills (Linux shell scripting, MATLAB) · an interest in biomedical questions and systems neuroscience · interpersonal skills when dealing with research subjects and colleagues Additionally, the ideal applicant · has experience with imaging software packages (e.g. FSL, SPM) · enjoys inter-disciplinary interactions with physicists and clinicians · has experience with conducting MRI scans · speaks (basic) German to interact with study subjects The successful candidate should have a demonstrated capacity for independent work and be capable of initiating research in a lively research environment. The post will involve collecting MRI data from patients with neurological conditions and normal volunteers. The post will also involve data analysis and writing of manuscripts for submission to peer-reviewed journals, as well as writing ethics applications for research projects. For Doctoral researchers, Goethe-University provides the opportunity to obtain a PhD degree. The Brain Imaging Center offers excellent imaging facilities, with two research-only 3T Siemens MRI scanners, MEG, various stimulus presentation methods, and an active physics group. The position is available immediately and can be split up. The appointment will be initially for 2 years, with the possibility of extension. Salary will be based on TV-Ä Hessen for Clinicians, and up to TVÖD-E13 for Postdoctoral Researchers. Goethe University is an equal opportunity employer. Applications from female candidates are encouraged. Where qualifications are equal, preference will be given to applicants with disabilities. Candidates should submit their applications (as a PDF including CV, names of at least two referees, and a brief letter of motivation outlining their interests and explaining how they meet the qualifications listed above) to Dr Johannes Klein (klein(a)med.uni-frankfurt.de) Dr Klein is also available for informal enquiries. Applications will be considered until the post is filled.

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R: Re: R: Re: R: Re: R: Re: R: R: Re: TRACULA
by stdp82＠virgilio.it 29 Jan '13

29 Jan '13

Hi Anastasia, I put my files in a folder /Application/freesurfer/subjects/subject_prova/Diff01/ File are these:data.nii.gz (DWI data, 16 directions)TI_CON_01.nii.gz (T1 structural images)bvals.txt and bvecs.txt (as you can see in the previously attacked files). Could error depends from the use of the . or , that was used to separate the decimal?Is corrects the name of the 4 files in the Diff01 folder (FSL.nii.gz and its directory)I have previously used this data in FSL for TBSS. I only inverted the matrix of bvals (FLS:1x16, fs:16x1) and (FSL:3x16; fs:16x3)Is the configuration file good? Thank you very much for you kindness and avaibility. Stefano ----Messaggio originale---- Da: ayendiki(a)nmr.mgh.harvard.edu Data: 29-gen-2013 15.42 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: R: Re: TRACULA Hi Stefano - Are the files that you're attaching the ones from the dmri directory or are they the original files that you specified in your configuration file? I'm guessing they're not the dmri/bv??s files because then they'd be formatted in rows and not columns. Without seeing the bvecs from your dmri directory my best guess for what could be causing the error is this: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg26026.html a.y On Tue, 29 Jan 2013, stdp82(a)virgilio.it wrote: > > Hi list, > > I'm trying to run trac-all on one subject and have a problem with the > bvecs file at the -prep stage. > After dtifit is started an error massage occurs: Error: bvecs and bvals don' > t have the same number of entries: > > [iMac-di-Stefano:/Applications/freesurfer/subjects] Stefano% trac-all -prep > -c /Users/Stefano/Desktop/dmrirc_single_subject > INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/subject_prova > INFO: Diffusion root is /Applications/freesurfer/subjects/subject_prova > Actual FREESURFER_HOME /Applications/freesurfer > trac-preproc -c /Applications/freesurfer/subjects/subject_prova/Diff01/scrip > ts/dmrirc.local -log /Applications/freesurfer/subjects/subject_prova/Diff01/ > scripts/trac-all.log -cmd /Applications/freesurfer/subjects/subject_prova/Di > ff01/scripts/trac-all.cmd > #------------------------------------- > /Applications/freesurfer/bin/trac-preproc > #------------------------------------- > #@# Image corrections Mar 29 Gen 2013 13:51:50 CET > mri_convert /Applications/freesurfer/subjects/subject_prova/Diff01/data.nii. > gz /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.nii. > gz > mri_convert /Applications/freesurfer/subjects/subject_prova/Diff01/data.nii. > gz /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.nii. > gz > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ > reading from /Applications/freesurfer/subjects/subject_prova/Diff01/data.nii > .gz... > TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-1, 0, 0) > j_ras = (0, 1, 0) > k_ras = (0, 0, 1) > writing to /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_o > rig.nii.gz... > cp /Applications/freesurfer/subjects/subject_prova/Diff01/bvecs.txt /Applica > tions/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.mghdti.bvecs > cp /Applications/freesurfer/subjects/subject_prova/Diff01/bvals.txt /Applica > tions/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.mghdti.bvals > flip4fsl /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_ori > g.nii.gz /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_ori > g_flip.nii.gz > INFO: input image orientation is LAS > INFO: input image determinant is -1 > fslswapdim /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_o > rig.nii.gz x y z /Applications/freesurfer/subjects/subject_prova/Diff01/dmri > /dwi_orig_flip.nii.gz > fslorient -forceradiological /Applications/freesurfer/subjects/subject_prova > /Diff01/dmri/dwi_orig_flip.nii.gz > INFO: found /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_ > orig.mghdti.bvals, converting to FSL format > INFO: found /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_ > orig.mghdti.bvecs, converting to FSL format > mv -f /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig_f > lip.mghdti.bvecs /Applications/freesurfer/subjects/subject_prova/Diff01/dmri > /bvecs > mv -f /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig_f > lip.mghdti.bvals /Applications/freesurfer/subjects/subject_prova/Diff01/dmri > /bvals > eddy_correct /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi > _orig_flip.nii.gz /Applications/freesurfer/subjects/subject_prova/Diff01/dmr > i/dwi.nii.gz 0 > processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t > mp0000 > processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t > mp0001 > processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t > mp0002 > processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t > mp0003 > processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t > mp0004 > processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t > mp0005 > processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t > mp0006 > processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t > mp0007 > processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t > mp0008 > processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t > mp0009 > processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t > mp0010 > processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t > mp0011 > processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t > mp0012 > processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t > mp0013 > processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t > mp0014 > processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t > mp0015 > mv -f /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvecs /App > lications/freesurfer/subjects/subject_prova/Diff01/dmri/bvecs.norot > xfmrot /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi.ecclo > g /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvecs.norot /A > pplications/freesurfer/subjects/subject_prova/Diff01/dmri/bvecs > fslroi /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi.nii.g > z /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb.nii.gz 0 > 1 > fslmaths /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb.ni > i.gz -Tmean /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb > .nii.gz > bet /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb.nii.gz > /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb_brain.nii.g > z -m -f 0.3 > mv -f /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb_brain > _mask.nii.gz /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/d > iff > #------------------------------------- > #@# Inter-subject registration Mar 29 Gen 2013 14:05:11 CET > flirt -in /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb_b > rain.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -ou > t /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb_brain_mni > .nii.gz -omat /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/xf > ms/diff2mni.mat -cost mutualinfo > convert_xfm -omat /Applications/freesurfer/subjects/subject_prova/Diff01/dmr > i/xfms/mni2diff.mat -inverse /Applications/freesurfer/subjects/subject_prova > /Diff01/dmri/xfms/diff2mni.mat > #------------------------------------- > #@# Masks Mar 29 Gen 2013 14:06:35 CET > #------------------------------------- > #@# Tensor fit Mar 29 Gen 2013 14:06:35 CET > dtifit -k /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi.ni > i.gz -m /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/diff/l > owb_brain_mask.nii.gz -r /Applications/freesurfer/subjects/subject_prova/Dif > f01/dmri/bvecs -b /Applications/freesurfer/subjects/subject_prova/Diff01/dmr > i/bvals -o /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dtifi > t > Error: bvecs and bvals don't have the same number of entries > Darwin iMac-di-Stefano.local 12.2.1 Darwin Kernel Version 12.2.1: Thu Oct 18 > 12:13:47 PDT 2012; root:xnu-2050.20.9~1/RELEASE_X86_64 x86_64 > > I checked the dmri/bvals and dmri/bvecs and attached them. > > Thank you very much. > > Stefano > > > ----Messaggio originale---- > Da: ayendiki(a)nmr.mgh.harvard.edu > Data: 29-gen-2013 0.44 > A: <stdp82(a)virgilio.it> > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] R: Re: R: Re: R: R: Re: TRACULA > > > Hi Stefano - The file that you defined as your gradient vector file (set > bvecfile = ...) doesn't exist. This file has to exist. > > Hope this helps, > a.y > > On Tue, 29 Jan 2013, stdp82(a)virgilio.it wrote: > > > Hi Anastasia, > > > > I have prepared this configuration file: > > > > > > # > > # Set locations of diffusion DICOMs, diffusion output, FreeSurfer recons > > # > > # This file contains commands that will be run by trac-all before an > > analysis. > > # It is used to set all parameters needed for the analysis. > > # > > # Remove a parameter from your dmrirc file if you want to use the default > > value. > > # Parameters that don't have default values must be specified. > > # > > # Any other commands that you might want to run before an analysis can be > > added > > # to this file. > > # > > # Original Author: Anastasia Yendiki > > # CVS Revision Info: > > # $Author: ayendiki $ > > # $Date: 2010/12/15 08:36:00 $ > > # $Revision: 1.1 $ > > # > > # Copyright (C) 2010 > > # The General Hospital Corporation (Boston, MA). > > # All rights reserved. > > # > > # Distribution, usage and copying of this software is covered under the > > # terms found in the License Agreement file named 'COPYING' found in the > > # FreeSurfer source code root directory, and duplicated here: > > # https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOpenSourceLicense > > # > > # General inquiries: freesurfer(a)nmr.mgh.harvard.edu > > # > > # FreeSurfer SUBJECTS_DIR > > # setenv SUBJECTS_DIR $FREESURFER_HOME/subjects/subject_prova > > # Output directory where trac-all results will be saved > > set dtroot = $SUBJECTS_DIR > > # Subject IDs > > set subjlist = (Diff01) > > set runlist = (1) > > # Input diffusion DICOMs (file names relative to dcmroot) > > set dcmroot = $SUBJECTS_DIR > > set dcmlist = (Diff01/data.nii.gz) > > set bvalfile = $SUBJECTS_DIR/bvals.txt > > set bvecfile = $SUBJECTS_DIR/bvecs.txt > > set nb0 = 1 > > set doeddy = 1 > > set dorotbvecs = 1 > > set thrbet = 0.3 > > set doregflt = 1 > > set doregbbr = 1 > > set doregmni = 1 > > set mnitemp = Users/Stefano/Desktop/MNI152_T1_1mm_brain.nii.gz > > set trainfile = > > $TUTORIAL_DATA/diffusion_tutorial/scripts/subj,train,difftutorial32.txt > > # Paths to reconstruct > > # Default: All paths > > set pathlist = (lh.cst_AS rh.cst_AS \ > > lh.ilf_AS rh.ilf_AS \ > > lh.unc_AS rh.unc_AS \ > > fmajor_PP fminor_PP \ > > lh.atr_PP rh.atr_PP \ > > lh.cab_PP rh.cab_PP \ > > lh.ccg_PP rh.ccg_PP \ > > lh.slfp_PP rh.slfp_PP \ > > lh.slft_PP rh.slft_PP) > > > > # Number of path control points > > # Default: 5 > > set ncpts = 5 > > > > When I run this, I have: > > > > [iMac-di-Stefano:/Applications/freesurfer/subjects] Stefano% trac-all > -prep > > -c /Users/Stefano/Desktop/dmrirc_single_subject > > INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/subject_prova > > INFO: Diffusion root is /Applications/freesurfer/subjects/subject_prova > > Actual FREESURFER_HOME /Applications/freesurfer > > trac-preproc-c/Applications/freesurfer/subjects/subject_prova/Diff01/scripts/dmrirc.loc > al > >-log/Applications/freesurfer/subjects/subject_prova/Diff01/scripts/trac-all > .log > >-cmd/Applications/freesurfer/subjects/subject_prova/Diff01/scripts/trac-all > .cmd > > #------------------------------------- > > /Applications/freesurfer/bin/trac-preproc > > #------------------------------------- > > #@# Image corrections Mar 29 Gen 2013 00:32:23 CET > > mri_convert > >/Applications/freesurfer/subjects/subject_prova/Diff01/data.nii.gz/Applicat > ions/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.nii.gz > > mri_convert > >/Applications/freesurfer/subjects/subject_prova/Diff01/data.nii.gz/Applicat > ions/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.nii.gz > > > > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ > > reading from > > /Applications/freesurfer/subjects/subject_prova/Diff01/data.nii.gz... > > TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 > > i_ras = (-1, 0, 0) > > j_ras = (0, 1, 0) > > k_ras = (0, 0, 1) > > writingto/Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.nii. > gz > > ... > > cp/Applications/freesurfer/subjects/subject_prova/bvecs.txt/Applications/free > surfer/subjects/subject_prova/Diff01/dmri/dwi_orig.mghdti > > .bvecs > > cp: /Applications/freesurfer/subjects/subject_prova/bvecs.txt: No such > file > > or directory > > Darwin iMac-di-Stefano.local 12.2.1 Darwin Kernel Version 12.2.1: Thu Oct > 18 > > 12:13:47 PDT 2012; root:xnu-2050.20.9~1/RELEASE_X86_64 x86_64 > > > > I apologize but I need to have your help. > > > > Thank you very much, > > > > > > Stefano > > > > > > > > ----Messaggio originale---- > > Da: ayendiki(a)nmr.mgh.harvard.edu > > Data: 28-gen-2013 20.03 > > A: <stdp82(a)virgilio.it> > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > Ogg: Re: [Freesurfer] R: Re: R: R: Re: TRACULA > > > > > > Hi Stefano - Type "which trac-all" to find out where trac-all lives on > > your computer, then copy the updated version over it. > > > > a.y > > > > On Mon, 28 Jan 2013, stdp82(a)virgilio.it wrote: > > > > > Thank you very much for you kindness Anastasia. > > > The folder that contains .nii.gz file is correct? > > > I'm looking the recommended trac-all update. Where can I put it? > > > > > > Stefano > > > > > > > > > ----Messaggio originale---- > > > Da: ayendiki(a)nmr.mgh.harvard.edu > > > Data: 28-gen-2013 16.45 > > > A: <stdp82(a)virgilio.it> > > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > > Ogg: Re: [Freesurfer] R: R: Re: TRACULA > > > > > > > > > Hi Stefano - The argument of the -c option is a configuration file, not > a > > > directory. For more info on trac-all and setting up the configuration > > > file, please see the trac-all wiki page: > > > http://www.freesurfer.net/fswiki/trac-all > > > and tracula tutorials: > > > http://www.freesurfer.net/fswiki/FsTutorial/Tracula > > > > > > a.y > > > > > > On Mon, 28 Jan 2013, stdp82(a)virgilio.it wrote: > > > > > > > Hi and thank you very much for your availability. > > > > Now, I'm running tracula as following: > > > > > > > > trac-all -prep -c > /Applications/freesurfer/subjects/subject_prova/CON_01 > > > > > > > > my CON_01 forder contains: data.nii.gz (DWI), bvals and bvecs (as used > > in > > > > > previous FSL analysis) and T1-images.nii.gz. File.niii.gz are the > same > > > > that I have previously used in FSL analysis. > > > > > > > > Please, my questions are: > > > > a- Are correct the command and the files (dyrectory positioning and > > their > > > > extensions)? > > > > b- Now my computer seem to running but after 1 h from the start, I > > > visualize > > > > on my desktop this message "Your Mac 0SX has no more space available > for > > > > application memory". > > > > My pc is a iMAC OS X Mountain Lion. 2.7 GHz Intel Core i5; 8GB 1600 > MHz > > > > DDR3; NVIDIA GeForce DT640M 512 MB; 762,42 GB are free on a total of > > > 999,35 > > > > I have download the package for (Snow)Leopard (10.5/6.x) Intel. > > > > > > > > Thanks, > > > > > > > > > > > > Stefano > > > > > > > > > > > > ----Messaggio originale---- > > > > Da: ayendiki(a)nmr.mgh.harvard.edu > > > > Data: 27-gen-2013 19.36 > > > > A: <stdp82(a)virgilio.it> > > > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > > > Ogg: Re: [Freesurfer] TRACULA > > > > > > > > Hi Stefano - The -prep option doesn't take an argument. Please run > > > > trac-all with no arguments to see usage info. > > > > > > > > a.y > > > > > > > > > Hi list, > > > > > I'm trying to run a test subject with TRACULA. > > > > > I placed a folder in /Applications/freesurfer/subject/subject_prova > > > which > > > > > contains these files: data.nii.gz (DWI), bvals and bvecs (as used in > > > > > previous FSL analysis) and T1-images.in > > > > > /Applications/freesurfer/subject/subject_prova > > > > > This is the command that I'm running:[iMac-di-Stefano:~] Stefano% > > > trac-all > > > > > -prep $FREESURFER_HOME/subjects/subject_prova/CON_01 --i > > > > > $FREESURFER_HOME/subjects/subject_prova > > > > > ERROR: flag > > > > > > > /Applications/freesurfer/subjects/subject_prova/CON_01unrecognized-prep > > > > > /Applications/freesurfer/subjects/subject_prova/CON_01 --i > > > > > /Applications/freesurfer/subjects/subject_prova > > > > > Please, give me an help. > > > > > > > > > > Thanks in advance, > > > > > > > > > > Stefano _______________________________________________ > > > > > Freesurfer mailing list > > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > The information in this e-mail is intended only for the person to whom > > it > > > is > > > > addressed. If you believe this e-mail was sent to you in error and the > > > > e-mail > > > > contains patient information, please contact the Partners Compliance > > > > HelpLine at > > > > http://www.partners.org/complianceline . If the e-mail was sent to you > > in > > > > error > > > > but does not contain patient information, please contact the sender > and > > > > properly > > > > dispose of the e-mail. > > > > > > > > > > > > > > > > > > > > > > > > > > > >_______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > The information in this e-mail is intended only for the person to whom > it > > is > > > addressed. If you believe this e-mail was sent to you in error and the > > > e-mail > > > contains patient information, please contact the Partners Compliance > > > HelpLine at > > > http://www.partners.org/complianceline . If the e-mail was sent to you > in > > > error > > > but does not contain patient information, please contact the sender and > > > properly > > > dispose of the e-mail. > > > > > > > > > > > >_______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > The information in this e-mail is intended only for the person to whom it > is > > addressed. If you believe this e-mail was sent to you in error and the > > e-mail > > contains patient information, please contact the Partners Compliance > > HelpLine at > > http://www.partners.org/complianceline . If the e-mail was sent to you in > > error > > but does not contain patient information, please contact the sender and > > properly > > dispose of the e-mail. > > > > > > > >_______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > > >_______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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R: Re: R: Re: R: Re: R: R: Re: TRACULA
by stdp82＠virgilio.it 29 Jan '13

29 Jan '13

Hi list, I'm trying to run trac-all on one subject and have a problem with the bvecs file at the -prep stage. After dtifit is started an error massage occurs: Error: bvecs and bvals don't have the same number of entries: [iMac-di-Stefano:/Applications/freesurfer/subjects] Stefano% trac-all -prep -c /Users/Stefano/Desktop/dmrirc_single_subject INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/subject_prova INFO: Diffusion root is /Applications/freesurfer/subjects/subject_prova Actual FREESURFER_HOME /Applications/freesurfer trac-preproc -c /Applications/freesurfer/subjects/subject_prova/Diff01/scripts/dmrirc.local -log /Applications/freesurfer/subjects/subject_prova/Diff01/scripts/trac-all.log -cmd /Applications/freesurfer/subjects/subject_prova/Diff01/scripts/trac-all.cmd #------------------------------------- /Applications/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Mar 29 Gen 2013 13:51:50 CET mri_convert /Applications/freesurfer/subjects/subject_prova/Diff01/data.nii.gz /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.nii.gz mri_convert /Applications/freesurfer/subjects/subject_prova/Diff01/data.nii.gz /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /Applications/freesurfer/subjects/subject_prova/Diff01/data.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.nii.gz... cp /Applications/freesurfer/subjects/subject_prova/Diff01/bvecs.txt /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.mghdti.bvecs cp /Applications/freesurfer/subjects/subject_prova/Diff01/bvals.txt /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.mghdti.bvals flip4fsl /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.nii.gz /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LAS INFO: input image determinant is -1 fslswapdim /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.nii.gz x y z /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig_flip.nii.gz fslorient -forceradiological /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig_flip.nii.gz INFO: found /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig_flip.mghdti.bvecs /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvecs mv -f /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig_flip.mghdti.bvals /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvals eddy_correct /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig_flip.nii.gz /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi.nii.gz 0 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0000 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0001 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0002 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0003 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0004 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0005 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0006 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0007 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0008 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0009 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0010 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0011 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0012 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0013 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0014 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0015 mv -f /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvecs /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvecs.norot xfmrot /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi.ecclog /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvecs.norot /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvecs fslroi /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi.nii.gz /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb.nii.gz 0 1 fslmaths /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb.nii.gz -Tmean /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb.nii.gz bet /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb.nii.gz /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb_brain.nii.gz -m -f 0.3 mv -f /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb_brain_mask.nii.gz /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/diff #------------------------------------- #@# Inter-subject registration Mar 29 Gen 2013 14:05:11 CET flirt -in /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb_brain.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb_brain_mni.nii.gz -omat /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/xfms/diff2mni.mat -cost mutualinfo convert_xfm -omat /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/xfms/mni2diff.mat -inverse /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/xfms/diff2mni.mat #------------------------------------- #@# Masks Mar 29 Gen 2013 14:06:35 CET #------------------------------------- #@# Tensor fit Mar 29 Gen 2013 14:06:35 CET dtifit -k /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi.nii.gz -m /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/diff/lowb_brain_mask.nii.gz -r /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvecs -b /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvals -o /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dtifit Error: bvecs and bvals don't have the same number of entries Darwin iMac-di-Stefano.local 12.2.1 Darwin Kernel Version 12.2.1: Thu Oct 18 12:13:47 PDT 2012; root:xnu-2050.20.9~1/RELEASE_X86_64 x86_64 I checked the dmri/bvals and dmri/bvecs and attached them. Thank you very much. Stefano ----Messaggio originale---- Da: ayendiki(a)nmr.mgh.harvard.edu Data: 29-gen-2013 0.44 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: R: Re: R: R: Re: TRACULA Hi Stefano - The file that you defined as your gradient vector file (set bvecfile = ...) doesn't exist. This file has to exist. Hope this helps, a.y On Tue, 29 Jan 2013, stdp82(a)virgilio.it wrote: > Hi Anastasia, > > I have prepared this configuration file: > > > # > # Set locations of diffusion DICOMs, diffusion output, FreeSurfer recons > # > # This file contains commands that will be run by trac-all before an > analysis. > # It is used to set all parameters needed for the analysis. > # > # Remove a parameter from your dmrirc file if you want to use the default > value. > # Parameters that don't have default values must be specified. > # > # Any other commands that you might want to run before an analysis can be > added > # to this file. > # > # Original Author: Anastasia Yendiki > # CVS Revision Info: > # $Author: ayendiki $ > # $Date: 2010/12/15 08:36:00 $ > # $Revision: 1.1 $ > # > # Copyright (C) 2010 > # The General Hospital Corporation (Boston, MA). > # All rights reserved. > # > # Distribution, usage and copying of this software is covered under the > # terms found in the License Agreement file named 'COPYING' found in the > # FreeSurfer source code root directory, and duplicated here: > # https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOpenSourceLicense > # > # General inquiries: freesurfer(a)nmr.mgh.harvard.edu > # > # FreeSurfer SUBJECTS_DIR > # setenv SUBJECTS_DIR $FREESURFER_HOME/subjects/subject_prova > # Output directory where trac-all results will be saved > set dtroot = $SUBJECTS_DIR > # Subject IDs > set subjlist = (Diff01) > set runlist = (1) > # Input diffusion DICOMs (file names relative to dcmroot) > set dcmroot = $SUBJECTS_DIR > set dcmlist = (Diff01/data.nii.gz) > set bvalfile = $SUBJECTS_DIR/bvals.txt > set bvecfile = $SUBJECTS_DIR/bvecs.txt > set nb0 = 1 > set doeddy = 1 > set dorotbvecs = 1 > set thrbet = 0.3 > set doregflt = 1 > set doregbbr = 1 > set doregmni = 1 > set mnitemp = Users/Stefano/Desktop/MNI152_T1_1mm_brain.nii.gz > set trainfile = > $TUTORIAL_DATA/diffusion_tutorial/scripts/subj,train,difftutorial32.txt > # Paths to reconstruct > # Default: All paths > set pathlist = (lh.cst_AS rh.cst_AS \ > lh.ilf_AS rh.ilf_AS \ > lh.unc_AS rh.unc_AS \ > fmajor_PP fminor_PP \ > lh.atr_PP rh.atr_PP \ > lh.cab_PP rh.cab_PP \ > lh.ccg_PP rh.ccg_PP \ > lh.slfp_PP rh.slfp_PP \ > lh.slft_PP rh.slft_PP) > > # Number of path control points > # Default: 5 > set ncpts = 5 > > When I run this, I have: > > [iMac-di-Stefano:/Applications/freesurfer/subjects] Stefano% trac-all -prep > -c /Users/Stefano/Desktop/dmrirc_single_subject > INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/subject_prova > INFO: Diffusion root is /Applications/freesurfer/subjects/subject_prova > Actual FREESURFER_HOME /Applications/freesurfer > trac-preproc -c/Applications/freesurfer/subjects/subject_prova/Diff01/scripts/dmrirc.local > -log/Applications/freesurfer/subjects/subject_prova/Diff01/scripts/trac-all.log > -cmd/Applications/freesurfer/subjects/subject_prova/Diff01/scripts/trac-all.cmd > #------------------------------------- > /Applications/freesurfer/bin/trac-preproc > #------------------------------------- > #@# Image corrections Mar 29 Gen 2013 00:32:23 CET > mri_convert > /Applications/freesurfer/subjects/subject_prova/Diff01/data.nii.gz/Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.nii.gz > mri_convert > /Applications/freesurfer/subjects/subject_prova/Diff01/data.nii.gz/Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.nii.gz > > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ > reading from > /Applications/freesurfer/subjects/subject_prova/Diff01/data.nii.gz... > TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-1, 0, 0) > j_ras = (0, 1, 0) > k_ras = (0, 0, 1) > writing to/Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.nii.gz > ... > cp /Applications/freesurfer/subjects/subject_prova/bvecs.txt/Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.mghdti > .bvecs > cp: /Applications/freesurfer/subjects/subject_prova/bvecs.txt: No such file > or directory > Darwin iMac-di-Stefano.local 12.2.1 Darwin Kernel Version 12.2.1: Thu Oct 18 > 12:13:47 PDT 2012; root:xnu-2050.20.9~1/RELEASE_X86_64 x86_64 > > I apologize but I need to have your help. > > Thank you very much, > > > Stefano > > > > ----Messaggio originale---- > Da: ayendiki(a)nmr.mgh.harvard.edu > Data: 28-gen-2013 20.03 > A: <stdp82(a)virgilio.it> > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] R: Re: R: R: Re: TRACULA > > > Hi Stefano - Type "which trac-all" to find out where trac-all lives on > your computer, then copy the updated version over it. > > a.y > > On Mon, 28 Jan 2013, stdp82(a)virgilio.it wrote: > > > Thank you very much for you kindness Anastasia. > > The folder that contains .nii.gz file is correct? > > I'm looking the recommended trac-all update. Where can I put it? > > > > Stefano > > > > > > ----Messaggio originale---- > > Da: ayendiki(a)nmr.mgh.harvard.edu > > Data: 28-gen-2013 16.45 > > A: <stdp82(a)virgilio.it> > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > Ogg: Re: [Freesurfer] R: R: Re: TRACULA > > > > > > Hi Stefano - The argument of the -c option is a configuration file, not a > > directory. For more info on trac-all and setting up the configuration > > file, please see the trac-all wiki page: > > http://www.freesurfer.net/fswiki/trac-all > > and tracula tutorials: > > http://www.freesurfer.net/fswiki/FsTutorial/Tracula > > > > a.y > > > > On Mon, 28 Jan 2013, stdp82(a)virgilio.it wrote: > > > > > Hi and thank you very much for your availability. > > > Now, I'm running tracula as following: > > > > > > trac-all -prep -c /Applications/freesurfer/subjects/subject_prova/CON_01 > > > > > > my CON_01 forder contains: data.nii.gz (DWI), bvals and bvecs (as used > in > > > > previous FSL analysis) and T1-images.nii.gz. File.niii.gz are the same > > > that I have previously used in FSL analysis. > > > > > > Please, my questions are: > > > a- Are correct the command and the files (dyrectory positioning and > their > > > extensions)? > > > b- Now my computer seem to running but after 1 h from the start, I > > visualize > > > on my desktop this message "Your Mac 0SX has no more space available for > > > application memory". > > > My pc is a iMAC OS X Mountain Lion. 2.7 GHz Intel Core i5; 8GB 1600 MHz > > > DDR3; NVIDIA GeForce DT640M 512 MB; 762,42 GB are free on a total of > > 999,35 > > > I have download the package for (Snow)Leopard (10.5/6.x) Intel. > > > > > > Thanks, > > > > > > > > > Stefano > > > > > > > > > ----Messaggio originale---- > > > Da: ayendiki(a)nmr.mgh.harvard.edu > > > Data: 27-gen-2013 19.36 > > > A: <stdp82(a)virgilio.it> > > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > > Ogg: Re: [Freesurfer] TRACULA > > > > > > Hi Stefano - The -prep option doesn't take an argument. Please run > > > trac-all with no arguments to see usage info. > > > > > > a.y > > > > > > > Hi list, > > > > I'm trying to run a test subject with TRACULA. > > > > I placed a folder in /Applications/freesurfer/subject/subject_prova > > which > > > > contains these files: data.nii.gz (DWI), bvals and bvecs (as used in > > > > previous FSL analysis) and T1-images.in > > > > /Applications/freesurfer/subject/subject_prova > > > > This is the command that I'm running:[iMac-di-Stefano:~] Stefano% > > trac-all > > > > -prep $FREESURFER_HOME/subjects/subject_prova/CON_01 --i > > > > $FREESURFER_HOME/subjects/subject_prova > > > > ERROR: flag > > > > > /Applications/freesurfer/subjects/subject_prova/CON_01unrecognized-prep > > > > /Applications/freesurfer/subjects/subject_prova/CON_01 --i > > > > /Applications/freesurfer/subjects/subject_prova > > > > Please, give me an help. > > > > > > > > Thanks in advance, > > > > > > > > Stefano _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > The information in this e-mail is intended only for the person to whom > it > > is > > > addressed. If you believe this e-mail was sent to you in error and the > > > e-mail > > > contains patient information, please contact the Partners Compliance > > > HelpLine at > > > http://www.partners.org/complianceline . If the e-mail was sent to you > in > > > error > > > but does not contain patient information, please contact the sender and > > > properly > > > dispose of the e-mail. > > > > > > > > > > > > > > > > > > > > >_______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > The information in this e-mail is intended only for the person to whom it > is > > addressed. If you believe this e-mail was sent to you in error and the > > e-mail > > contains patient information, please contact the Partners Compliance > > HelpLine at > > http://www.partners.org/complianceline . If the e-mail was sent to you in > > error > > but does not contain patient information, please contact the sender and > > properly > > dispose of the e-mail. > > > > > > > >_______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > > >_______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

2 1

Post-doc position within the Collaborative Research Centre 940 "Volition and Cognitive Control: Mechanisms, Modulators, and Dysfunctions"
by Geisler, Daniel 29 Jan '13

29 Jan '13

Post-doc position within the Collaborative Research Centre 940 "Volition and Cognitive Control: Mechanisms, Modulators, and Dysfunctions" at the Department of Child and Adolescent Psychiatry, University Hospital C. G. Carus, Dresden University of Technology, Germany Job Description: The Eating Disorder Section of the Department of Child and Adolescent Psychiatry, Dresden University of Technology, Germany (Prof. Stefan Ehrlich) invites applications for a postdoctoral research position in neuroimaging of eating disorders. The new project is part of the aforementioned Collaborative Research Centre (CRC, Steering Committee: Profs. T. Goschke, C. Kirschbaum, M. Smolka, A. Strobel, H.-U. Wittchen) and will focus on cognitive control, reward system and the processing of emotions in patients with anorexia nervosa. This is a full time position within the Translational Developmental Neuroscience Group. Responsibilities will include the coordination of our ongoing clinical research study and the acquisition and analysis of a range of behavioral and magnetic resonance imaging (MRI) data. Together with a doctoral student new functional MRI paradigms need to be implemented. Imaging sessions will take place on the Neuroimaging Center's 3T Siemens TIM-Trio scanner and data collected includes high-quality structural, diffusion, and functional MRI data. A variety of additional information will also be collected, including neuropsychological and psychiatric scales, physiological and endocrinological markers. Summarizing results and writing research articles will be another central aspect of the work. The successful applicant will work in a team of young investigators and also start to supervise doctoral students, interns and medical students working in the project. Thanks to the CRC the applicant will have ample opportunity to work with peers and senior scientists in similar project in the Medical School and the Psychology Department. Applicants for the position must hold (a) a PhD, MD or comparable degree in a relevant field (Psychology, Neurosciences or Medicine; if you have additional qualifications a degree in Biology, Biomedicine, Biophysics, Computer Science or Electrical Engineering may also be sufficient), (b) have had some exposure to cognitive and emotional neurosciences, (c) participated in research activities within the past years (d) published in peer-reviewed journals, e) possess strong organizational skills and (f) be able to communicate in basic German with non-scientific staff members. Some experience in computer programming (Linux/Unix shell scripting, Python and/or MATLAB), neuroimaging analysis methods (FSL, SPM, FreeSurfer or others), advanced statistical analyses and scientific publishing is necessary. The successful applicant will join a multidisciplinary team of researchers and clinicians, will receive further training and train doctoral students (informally). The position is available for a start date as soon as February 15th 2012 (to be confirmed). Review of applications will begin immediately and will continue until the position is filled. The position is guaranteed for two years with the possibility of renewal after positive evaluation. The CRC funding has been granted for 4 years. Salary will be consistent with levels in accordance with the German Research Foundation (100% TV-L: E 13). Compensation includes health insurance, and vacation time. To apply you can use our online portal (https://www.uniklinikum-dresden.de/Bewerbung/?id=5e0f53e16050a1fa4845830ba9…) The application should include a cover letter detailing professional objectives and interests, CV (with grades and language skills), and the names and email addresses of two references. The application can be written in German or English. The position is open to qualified international applicants but the knowledge of some German is necessary since the position includes the coordination of an ongoing clinical study. Applicants with a disability will be given preference in the selection process. Please refer to our homepage: http://www.kjp-dresden.de/en/Eating-disorders, http://www.kjp-dresden.de/en/Schizophrenia, http://tu-dresden.de/die_tu_dresden/fakultaeten/fakultaet_mathematik_und_na…, and http://kjp-dresden.de/de/Publikationsliste-Prof-Dr-S-Ehrlich for more detailed information. *** PLEASE REPOST FOR INTERESTED PARTIES *** :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: Für das Forschungsprogramm der Professur für Angewandte Entwicklungsneurowissenschaften (Prof. S. Ehrlich) wird für die Projekte zum Thema "Increased volitional control of rewarding stimuli in eating disorders: Neural mechanisms and real-world costs" im Rahmen des neuen Sonderforschungsbereichs (SFB) 940 "Volition und kognitive Kontrolle" ab frühestens dem 15. Februar 2012 ein Wissenschaftlicher Mitarbeiter / Post-Doktorand (m/w) gesucht. Die Stelle ist zunächst befristet für 2-3 Jahre (Entgeltgruppe 13 TV-L, 100 %). Bei Eignung streben wir eine längerfristige Zusammenarbeit mit Ihnen an. Der SFB 940 ist dementsprechend auf 4 Jahre angelegt. Der Schwerpunkt der Projekte liegt auf Neuroimaging-Verfahren. Die Durchführung dieser Projekte geschieht in Kooperation mit dem Neuroimaging Center Dresden (Prof. Smolka) und der Fachrichtung Psychologie der TU Dresden (Profs. Goschke, Wittchen, Kirschbaum, Strobel). Zu Ihren Aufgaben gehören die Koordination der Studie, die Etablierung neuer Paradigmen, die Akquise und Analyse von behavioralen, SCR und MRT-Daten sowie das Schreiben von wissenschaftlichen Publikationen. Die SCR- und MRT-Messungen erfolgen am Neuroimaging Center (3T Siemens TIM-Trio Scanner) und umfassen strukturelles MRT, Diffusion Tensor Imaging und funktionelles MRT. Es werden auch neuropsychologische, psychiatrische, physiologische, endokrinologische und genetische Daten erhoben. Die Arbeit erfolgt im Team und umfasst auch die Anleitung und Supervision von naturwissenschaftlichen Doktoranden, Praktikanten und Medizinstudenten innerhalb des Projektes. Sie werden in einem interdisziplinären Team von Wissenschaftlern und Klinikern arbeiten, Personalverantwortung übernehmen und die Möglichkeit haben, Ihre Kenntnisse in den o.g. Techniken zu vertiefen. Neben den neu geplanten Studien innerhalb des SFBs führen wir bereits seit über 2 Jahren verschiedene andere neurowissenschaftliche Projekte zu Essstörungen (Magersucht) durch. Durch den neu geschaffenen SFB 940 "Volition und kognitive Kontrolle" ergeben sich vielfältige weitere Lern- und Austauschmöglichkeiten. Ihr Profil: . Abgeschlossene Doktorarbeit oder ein entsprechendes Äquivalent . Master- oder Diplomabschluss in Psychologie oder Neurowissenschaften, bei geeignetem Profil auch in Biologie, Biomedizin, Biophysik, Informatik oder anderen Ingenieurwissenschaften . wissenschaftliche Erfahrungen in zumindest einigen der o.g. Bereichen . erste wissenschaftliche Publikationen . Erfahrungen in der Analyse von Bildgebungsdaten (FSL, SPM, FreeSurfer oder vergleichbare), in der statistischen Modellierung sowie Grundkenntnisse im Programmieren (z.B. Linux/Unix shell scripting, Python oder MATLAB) Wir bieten Ihnen die Möglichkeit zur: . Tätigkeit in der medizinisch führenden Forschung in einem hochspezialisierten Arbeitsumfeld . Vereinbarung von flexiblen Arbeitszeiten, um die Verbindung von Familie und Beruf in die Realität umzusetzen . Nutzung von betrieblichen Präventionsangebote, Kursen und Fitness in unserem Gesundheitszentrum Carus Vital . Vorsorge für die Zeit nach der aktiven Berufstätigkeit in Form einer betrieblichen Altersvorsorge Unsere Personalentscheidungen treffen wir nach Eignung, Befähigung und fachlicher Leistung. Schwerbehinderte Menschen werden bei gleicher Eignung bevorzugt berücksichtigt. Die Ausschreibung endet, wenn ein geeigneter Bewerber gefunden wurde. Wir bitten Sie, sich vorzugsweise online zu bewerben, um so den Personalauswahlprozess schneller und effektiver zu gestalten. Wir freuen uns über Ihre vollständigen Bewerbungsunterlagen bis zum 05.02.2013 unter der Kennziffer KJP0913308 (Anschreiben, Lebenslauf, Empfehlungsschreiben, Zeugnisse sowie Namen und Email/Telefon möglicher empfehlender Hochschullehrer für persönliche Rückfragen). Nähere Informationen erhalten Sie telefonisch unter 0351 - 458 2244 oder auf unserer Homepage unter http://www.kjp-dresden.de/en/Eating-disorders, http://tu-dresden.de/die_tu_dresden/fakultaeten/fakultaet_mathematik_und_na…, sowie unter http://www.kjp-dresden.de/en/Schizophrenia und http://kjp-dresden.de/de/Publikationsliste-Prof-Dr-S-Ehrlich. ::::::::::::::::::::::::::::::::::::::::: Dipl.-Inf. Daniel Geisler Wissenschaftlicher Mitarbeiter Bereich Angewandte Entwicklungsneurowissenschaften Klinik und Poliklinik für Kinder- und Jugendpsychiatrie und -psychotherapie Tel. +49 (0)351 458-7071 Fax +49 (0)351 458-7206 Universitätsklinikum Carl Gustav Carus an der Technischen Universität Dresden Anstalt des öffentlichen Rechts des Freistaates Sachsen Fetscherstraße 74 (Haus 25, Raum 233A), 01307 Dresden http://www.uniklinikum-dresden.de Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer Vorsitzender des Aufsichtsrates: Prof. Dr. med. Peter C. Scriba USt.-IDNr.: DE 140 135 217, St.-Nr.: 201 145 00020

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5.2 CENTOS x_64 > ERROR > tal_QC_AZS
by Garikoitz Lerma-Usabiaga 29 Jan '13

29 Jan '13

Hi FS experts, I just downloaded the latest version again today: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.2.0-BETA/freesurfer-… 4.2 GB 1/28/13 9:47:00 PM, fsaverage has been copied to /subjects/myproject location) When running this command: recon-all -i xxxx -s xxxxx -qcache -hippo-subfields -all The system is giving me the following error: tal_QC_AZS /home/glerma/fs/52/freesurfer/subjects/TNT/S_03/mri/transforms/talairach_avi.log ERROR: tal_QC_AZS /home/glerma/fs/52/freesurfer/subjects/TNT/S_03/mri/transforms/talairach_avi.log failed! See logfile /home/glerma/fs/52/freesurfer/subjects/TNT/S_03/mri/transforms/talairach_avi_QA2.log The logfile talairach_avi_QA2.log is empty. This is the end of /mri/transforms/talairach_avi.log: start time Tue Jan 29 11:45:59 CET 2013 1661 end time Tue Jan 29 11:46:32 CET 2013 1662 1663 mpr2mni305 success 1664 1665 avi2talxfm orig_nu.mgz /home/glerma/fs/52/freesurfer/average/mni305.cor.mgz talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt transforms/talairach.auto.xfm 1666 avi2talxfm done 1667 1668 1669 Tue Jan 29 11:46:34 CET 2013 1670 talairach_avi done Is there something else I should check to make it work? thanks! Gari

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R: Re: R: Re: R: R: Re: TRACULA
by stdp82＠virgilio.it 28 Jan '13

28 Jan '13

Hi Anastasia, I have prepared this configuration file: ## Set locations of diffusion DICOMs, diffusion output, FreeSurfer recons## This file contains commands that will be run by trac-all before an analysis.# It is used to set all parameters needed for the analysis.## Remove a parameter from your dmrirc file if you want to use the default value.# Parameters that don't have default values must be specified.## Any other commands that you might want to run before an analysis can be added# to this file.## Original Author: Anastasia Yendiki# CVS Revision Info:# $Author: ayendiki $# $Date: 2010/12/15 08:36:00 $# $Revision: 1.1 $## Copyright (C) 2010# The General Hospital Corporation (Boston, MA).# All rights reserved.## Distribution, usage and copying of this software is covered under the# terms found in the License Agreement file named 'COPYING' found in the# FreeSurfer source code root directory, and duplicated here:# https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOpenSourceLicense## General inquiries: freesurfer(a)nmr.mgh.harvard.edu## FreeSurfer SUBJECTS_DIR# setenv SUBJECTS_DIR $FREESURFER_HOME/subjects/subject_prova# Output directory where trac-all results will be savedset dtroot = $SUBJECTS_DIR# Subject IDsset subjlist = (Diff01)set runlist = (1)# Input diffusion DICOMs (file names relative to dcmroot)set dcmroot = $SUBJECTS_DIRset dcmlist = (Diff01/data.nii.gz)set bvalfile = $SUBJECTS_DIR/bvals.txtset bvecfile = $SUBJECTS_DIR/bvecs.txtset nb0 = 1set doeddy = 1set dorotbvecs = 1set thrbet = 0.3set doregflt = 1set doregbbr = 1set doregmni = 1set mnitemp = Users/Stefano/Desktop/MNI152_T1_1mm_brain.nii.gzset trainfile = $TUTORIAL_DATA/diffusion_tutorial/scripts/subj,train,difftutorial32.txt# Paths to reconstruct# Default: All pathsset pathlist = (lh.cst_AS rh.cst_AS \ lh.ilf_AS rh.ilf_AS \ lh.unc_AS rh.unc_AS \ fmajor_PP fminor_PP \ lh.atr_PP rh.atr_PP \ lh.cab_PP rh.cab_PP \ lh.ccg_PP rh.ccg_PP \ lh.slfp_PP rh.slfp_PP \ lh.slft_PP rh.slft_PP) # Number of path control points# Default: 5set ncpts = 5 When I run this, I have: [iMac-di-Stefano:/Applications/freesurfer/subjects] Stefano% trac-all -prep -c /Users/Stefano/Desktop/dmrirc_single_subjectINFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/subject_provaINFO: Diffusion root is /Applications/freesurfer/subjects/subject_provaActual FREESURFER_HOME /Applications/freesurfertrac-preproc -c /Applications/freesurfer/subjects/subject_prova/Diff01/scripts/dmrirc.local -log /Applications/freesurfer/subjects/subject_prova/Diff01/scripts/trac-all.log -cmd /Applications/freesurfer/subjects/subject_prova/Diff01/scripts/trac-all.cmd#-------------------------------------/Applications/freesurfer/bin/trac-preproc #-------------------------------------#@# Image corrections Mar 29 Gen 2013 00:32:23 CETmri_convert /Applications/freesurfer/subjects/subject_prova/Diff01/data.nii.gz /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.nii.gzmri_convert /Applications/freesurfer/subjects/subject_prova/Diff01/data.nii.gz /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $reading from /Applications/freesurfer/subjects/subject_prova/Diff01/data.nii.gz...TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00i_ras = (-1, 0, 0)j_ras = (0, 1, 0)k_ras = (0, 0, 1)writing to /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.nii.gz...cp /Applications/freesurfer/subjects/subject_prova/bvecs.txt /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.mghdti.bvecscp: /Applications/freesurfer/subjects/subject_prova/bvecs.txt: No such file or directoryDarwin iMac-di-Stefano.local 12.2.1 Darwin Kernel Version 12.2.1: Thu Oct 18 12:13:47 PDT 2012; root:xnu-2050.20.9~1/RELEASE_X86_64 x86_64 I apologize but I need to have your help. Thank you very much, Stefano ----Messaggio originale---- Da: ayendiki(a)nmr.mgh.harvard.edu Data: 28-gen-2013 20.03 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: R: R: Re: TRACULA Hi Stefano - Type "which trac-all" to find out where trac-all lives on your computer, then copy the updated version over it. a.y On Mon, 28 Jan 2013, stdp82(a)virgilio.it wrote: > Thank you very much for you kindness Anastasia. > The folder that contains .nii.gz file is correct? > I'm looking the recommended trac-all update. Where can I put it? > > Stefano > > > ----Messaggio originale---- > Da: ayendiki(a)nmr.mgh.harvard.edu > Data: 28-gen-2013 16.45 > A: <stdp82(a)virgilio.it> > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] R: R: Re: TRACULA > > > Hi Stefano - The argument of the -c option is a configuration file, not a > directory. For more info on trac-all and setting up the configuration > file, please see the trac-all wiki page: > http://www.freesurfer.net/fswiki/trac-all > and tracula tutorials: > http://www.freesurfer.net/fswiki/FsTutorial/Tracula > > a.y > > On Mon, 28 Jan 2013, stdp82(a)virgilio.it wrote: > > > Hi and thank you very much for your availability. > > Now, I'm running tracula as following: > > > > trac-all -prep -c /Applications/freesurfer/subjects/subject_prova/CON_01 > > > > my CON_01 forder contains: data.nii.gz (DWI), bvals and bvecs (as used in > > > previous FSL analysis) and T1-images.nii.gz. File.niii.gz are the same > > that I have previously used in FSL analysis. > > > > Please, my questions are: > > a- Are correct the command and the files (dyrectory positioning and their > > extensions)? > > b- Now my computer seem to running but after 1 h from the start, I > visualize > > on my desktop this message "Your Mac 0SX has no more space available for > > application memory". > > My pc is a iMAC OS X Mountain Lion. 2.7 GHz Intel Core i5; 8GB 1600 MHz > > DDR3; NVIDIA GeForce DT640M 512 MB; 762,42 GB are free on a total of > 999,35 > > I have download the package for (Snow)Leopard (10.5/6.x) Intel. > > > > Thanks, > > > > > > Stefano > > > > > > ----Messaggio originale---- > > Da: ayendiki(a)nmr.mgh.harvard.edu > > Data: 27-gen-2013 19.36 > > A: <stdp82(a)virgilio.it> > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > Ogg: Re: [Freesurfer] TRACULA > > > > Hi Stefano - The -prep option doesn't take an argument. Please run > > trac-all with no arguments to see usage info. > > > > a.y > > > > > Hi list, > > > I'm trying to run a test subject with TRACULA. > > > I placed a folder in /Applications/freesurfer/subject/subject_prova > which > > > contains these files: data.nii.gz (DWI), bvals and bvecs (as used in > > > previous FSL analysis) and T1-images.in > > > /Applications/freesurfer/subject/subject_prova > > > This is the command that I'm running:[iMac-di-Stefano:~] Stefano% > trac-all > > > -prep $FREESURFER_HOME/subjects/subject_prova/CON_01 --i > > > $FREESURFER_HOME/subjects/subject_prova > > > ERROR: flag > > > /Applications/freesurfer/subjects/subject_prova/CON_01unrecognized-prep > > > /Applications/freesurfer/subjects/subject_prova/CON_01 --i > > > /Applications/freesurfer/subjects/subject_prova > > > Please, give me an help. > > > > > > Thanks in advance, > > > > > > Stefano _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > The information in this e-mail is intended only for the person to whom it > is > > addressed. If you believe this e-mail was sent to you in error and the > > e-mail > > contains patient information, please contact the Partners Compliance > > HelpLine at > > http://www.partners.org/complianceline . If the e-mail was sent to you in > > error > > but does not contain patient information, please contact the sender and > > properly > > dispose of the e-mail. > > > > > > > > > > > > > >_______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > > >_______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

2 1

recon-all v5.2 slightly changed
by Jonathan Holt 28 Jan '13

28 Jan '13

hello all, Just for reference, we were having an issue with recon-all v 5.2 exiting with errors due to issues with the perirhinal cortex. We were able to simply commented out the parts of the script dealing with the perirhinal cortex. Just an FYI to those who may be having a similar problem. Jon

3 5

Skull Striping
by Pedro Rosa 28 Jan '13

28 Jan '13

Dear all, I am currently working on a 1.5T SPGR 1.5mm MRI longitudinal dataset, and I would like to know if one is expected to manually skull strip the images before de recon -all procedure. I am aware that the image quality may be a limiting factor for the freesurfer processing. Regards, Pedro Rosa.

2 1

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