Freesurfer

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30132 discussions

Tracula preprocessing step error
by Allison Gruber 08 Jan '13

08 Jan '13

Dear Freesurfer experts, I have encountered the following error while running the tracula pre-processing command and was hoping you could help me understand how to correct this. Selection from log: mri_convert /Users/Desktop/Tracula/diffusion_DTI/ /Users/Desktop/Tracula/diffusion_DTI/SubjectX/dmri/b0mag.nii.gz mri_convert /Users/Desktop/Tracula/diffusion_DTI/ /Users/Desktop/Tracula/diffusion_DTI/SubjectX/dmri/b0mag.nii.gz corRead(): can't open file /Users/Desktop/Tracula/diffusion_DTI/COR-.info $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /Users/Desktop/Tracula/diffusion_DTI/... Darwin MacBook-Pro.local 11.4.0 Darwin Kernel Version 11.4.0: Mon Apr 9 19:32:15 PDT 2012; root:xnu-1699.26.8~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Tue Jan 8 14:34:39 EST 2013 Please let me know if this is not enough information. Thank you for your help. Allison

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Longitudinal stream with special options
by Jürgen Hänggi 08 Jan '13

08 Jan '13

Dear FS experts I run the cross sectional step (step 1) for a longitudinal analysis with the following options: recon-all -s $s -all -talairach -use-mritotal -nuintensitycor-3T I would like to know whether I have also use these options in the creation of the base template (step 2) and in the longitudinal runs (step 3). What is the recommendation when using these special options? Thanks in advance Regards Jürgen Hänggi ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

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Re: [Freesurfer] trac-all bval bvecs bedpostx not running
by Anastasia Yendiki 07 Jan '13

07 Jan '13

Great. Just keep in mind that if you use the newer version of FSL, which has a new syntax for bedpostx, you might have to run bedpostx outside of tracula to get it to work. (This is a recurrent topic in the email list archives.) On Mon, 7 Jan 2013, Gerit Pfuhl wrote: > I redid everything from scratch, now it seems to work > having processed 1 slice ... > I cross my finger that this (new) subject and new calling of Terminal > did the "trick" > > thanks > gerit > > On 7 January 2013 08:35, Gerit Pfuhl <gerit.pfuhl(a)gmail.com> wrote: >> unfortunately changing Language of the system did not help, same error message >> attached the log file. >> >> Regards >> Gerit >> >> On 4 January 2013 16:49, Gerit Pfuhl <gerit.pfuhl(a)gmail.com> wrote: >>> thanks, rerunning now, should know the result in a few hours (plus >>> when bedpostx runs, so more like one day) >>> >>> -g >>> >>> On 4 January 2013 16:33, Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> wrote: >>>> setenv LANG en_US.UTF-8 >> >> >> >> -- >> http://gerit-orientation.blogspot.com >> http://team-arzgebirg.blogspot.com > > > >

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Re: [Freesurfer] Differences between avg33 and avg32 in dpath folders
by Anastasia Yendiki 07 Jan '13

07 Jan '13

You need to rerun the -prior and -path steps, without the trainfile set to anything, so that it uses the default trainfile with the 33 subjects. Do not set the reinit option, that has nothing to do with this. The reinit option is used when initialization fails but his hasn't happened here. On Mon, 7 Jan 2013, Alessia Sarica wrote: > Dear Anastasia,I checked the scripts of those patients with folders named > avg32 and I noticed that there is setted the trainfile ...difftutorial32.txt > I suppose that is the problem. > > Now, can I relauch TRACULA with reinit parameter equals to 1, or is it > better to delete all folders? > > Thanks for you help, > Alessia. > > 2013/1/6 Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> > > That shows you how many subjects were included in the atlas. > There's a total of 33 subjects in the atlas, and for a general > purpose study there's no reason not to use all of them. Did you > change the trainlist parameter in the configuration file at any > point? > > On Sun, 6 Jan 2013, Alessia Sarica wrote: > > Dear Freesurfer Experts,i'm here again, maybe for a > trivial question, but > I didn't find any information about my doubt. > > I'm doing tractography on 36 patients and I noticed > that some of them have > dpath folders named "_avg33_mni_flt" and in other > patients, they are named > "_avg32_mni_flt". > Which is the reason for this? Something has gone > wrong? > > Thanks a lot, > Alessia. > > > -- > Alessia Sarica > Ph.D. Student Biomedical and Informatics > Engineering, > Bioinformatics Laboratory, Department of Surgical > and Medical Sciences, > University "Magna Græcia" of Catanzaro, > Viale Europa (Località Germaneto), 88100 CATANZARO, > ITALY. > Phone: +3909613694193 > > > > 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. > > > > > -- > Alessia Sarica > Ph.D. Student Biomedical and Informatics Engineering, > Bioinformatics Laboratory, Department of Surgical and Medical Sciences, > University "Magna Græcia" of Catanzaro, > Viale Europa (Località Germaneto), 88100 CATANZARO, ITALY. > Phone: +3909613694193 > >

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Recon-all 5.2 crashes after 30s
by Jonathan Holt 07 Jan '13

07 Jan '13

Hello all, Having a slight issue with recon-all 5.2. For reference, we're using Freesurfer 5.0.0 and trying to use recon-all 5.2 to alleviate some issues with disappearing white matter. I'm wondering if it is necessary to have Freesurfer 5.2 in order for recon-all 5.2 to work properly? When I say "crash" I mean it runs to completion after 30 seconds. Log files are not revelatory. best, jon

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Crash with full install of 5.2
by Carl Anderson 07 Jan '13

07 Jan '13

Hi Everyone, I did the full install for 5.2 but got the following crash during Talairach: #@# Talairach Failure Detection Mon Jan 7 13:43:33 EST 2013 /Applications/freesurfer/subjects/all_SP_mprage/SP037/mri \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.8143, pval=0.8469 >= threshold=0.0050) \n awk -f /Applications/freesurfer/bin/extract_talairach_avi_QA.awk /Applications/freesurfer/subjects/all_SP_mprage/SP037/mri/transforms/talairach_avi.log \n \n tal_QC_AZS /Applications/freesurfer/subjects/all_SP_mprage/SP037/mri/transforms/talairach_avi.log \n TalAviQA: 0.97598 z-score: 0 TalAviQA2: (standard_in) 1: parse error (standard_in) 1: parse error if: Expression Syntax. Thanks for all your hard work, Carl -- <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>> Carl M. Anderson, Ph.D. (mail stop 204) Assistant Professor of Psychiatry, Harvard Medical School & The Neuroimaging Center, McLean Hospital 115 Mill St. Belmont, MA 02478 Ph: 617-855-2972; Fax: 617-855-2770 e-mail: remfract(a)gmail.com; carl_anderson(a)hms.harvard.edu <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>

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Trouble performing Monte Carlo simulation constrained to label
by Susan Alice McLaughlin 07 Jan '13

07 Jan '13

Hi, I am trying to run a Monte Carlo simulation on functional data constrained to a label using Freesurfer 4.0.1. I did not use Qdec for data analysis. Looking at a previous post - https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-November/016290… - I see that I should: 1) constrain when running mri_glmfit, then 2) use mri_glmfit-sim (as opposed to running mri_glmfit with the simulation options). I have done step 1, however when I try to mri_glmfit-sim, I receive a "command not found" message. Is mri_glmfit-sim not available in 4.0.1? Can I copy a workable version of mri_glmfit-sim into 4.0.1? Thanks, Susan McLaughlin Doctoral Candidate SPACE Lab (Stimulus-Parametric Imaging of Auditory Cortex) Dept. of Speech and Hearing Sciences University of Washington

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Rejoindre mon réseau sur LinkedIn
by didac vidal via LinkedIn 07 Jan '13

07 Jan '13

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Re: [Freesurfer] aparc stats file; missing 'mean cortical thickness' value
by Douglas N Greve 07 Jan '13

07 Jan '13

Oh, I see now, you are including -noaseg and that is causing the problem. Why are you including that? You can rerun like recon-all -parcstats -parcstats2 -s subject and it should regenerate the stats with the mean cortical thickness doug On 01/07/2013 02:32 PM, Deirdre O Shea wrote: > sure, here it is > > On Mon, Jan 7, 2013 at 2:24 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > hmmm, that is bizarre. Can you send me the recon-all.log file for > this subject? > > > On 01/07/2013 02:23 PM, Deirdre O Shea wrote: > > I just ran ran recon-all myself. I have attached the script i > have been using for all my subjects. > > thanks, > deirdre > > On Mon, Jan 7, 2013 at 1:45 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > > I can see that the command line is not set up to create > the mean > cortical thickness, but I don't know why the arguments for the > command are not being set up properly. Did you run > mris_anatomical_stats yourself or did you just run recon-all > again? If you ran recon-all, can you send me your > recon-all script? > > doug > > > > On 01/07/2013 01:25 PM, Deirdre O Shea wrote: > > Thanks Doug, > > I have attached two files. You will see in > 'aparc.stats' that > there is no mean for cortical thickness and in the > aparc.stats2 file there is. > > thanks > Deirdre > > On Mon, Jan 7, 2013 at 12:48 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: > > Can you send the aparc.stats file in question? > doug > On 01/07/2013 11:44 AM, Deirdre O Shea wrote: > > Dear FreeSurfers, > > > > My query relates to the aparc stats file in > FreeSurfer. > Upon the > > editing and reconstruction of my subjects I have > noticed > that > the Mean > > Thickness for the cortex was missing, i.e., no > value was > provided > > despite it being there before I ran another > reconstruction. > While this > > has only occurred in a couple of my subjects (out of > many) I'm > > wondering what may be the cause and how I may I > now go > about getting > > this value? > > > > > > Best, > > Deirdre > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 > <tel:617-724-2358>>> > Fax: 617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 > <tel:617-726-7422> > > <tel:617-726-7422 <tel:617-726-7422>>> > > Bugs: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@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. > > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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expected directory structure
by Satrajit Ghosh 07 Jan '13

07 Jan '13

hi folks, happy new year. we are trying to create an object model for the freesurfer directory. is there a function/script in freesurfer that would return me effectively something `ls -lR` but only the items that are mandatory for a subjects' directory? if not, is there a document that lists the relevant outputs along the lines of something like this: http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FEAT/UserGuide#FEAT_Output and if anybody is interested, here is our work in progress in cataloging freesurfer directory structure and stats (coming soon) in the w3c-prov model format. http://nbviewer.ipython.org/urls/dl.dropbox.com/s/1ssv4i1dyraa46h/freesurfe… (the link doesn't have versioning yet - but will keep changing as we work on it) cheers, satra

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