Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30090 discussions

error in 5.3
by Welsh, Robert 04 Jun '13

04 Jun '13

Hi, We were re-processing a subject to test the fix for 5.2 to 5.3. The initial recon-all and subsequent autrecon2 and autorecon3 were run a few days ago under 5.2. Yesterday I installed 5.3 and we ran the following: export SUBJECTS_DIR=/net/data4/FreeSurferDaze/FreeSurfer recon-all -s s_ALS51 -white -smooth2 -inflate2 –autorecon3 It ran for about 4.5 hours and then gave this error: ------------------------------------------------------------------------------------------------------- [rcwelsh@schizo s_ALS51]$ tail scripts/recon-all.log SUBJECTS_DIR /net/data4/ALSSCI/FreeSurferDaze/FreeSurfer FREESURFER_HOME /net/misc/freesurfer_5.3.0_centos4 Loading source label. Invalid argument ERROR reading /net/data4/ALSSCI/FreeSurferDaze/FreeSurfer/fsaverage/label/lh.BA1.thresh.label Linux schizo.psych.med.umich.edu 2.6.18-92.1.13.el5 #1 SMP Wed Sep 24 19:32:05 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux recon-all -s s_ALS51 exited with ERRORS at Mon Jun 3 18:32:01 EDT 2013 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ------------------------------------------------------------------------------------------------------- Some help would be appreciated. There is a file lh.BA1.label but not lh.BA1.thresh.label, indeed there are no files with "thresh" in their name under that subject. Thanks! -Robert ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

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error with trying 5.3 on 5.2 data for autorecon2 and autorecon3, balabel throwing error.
by Welsh, Robert 04 Jun '13

04 Jun '13

Hi all, In our efforts to take our 5.2 edits to 5.3 we tried the command below (in the attached thread), but we also tried the command recon-all –s [subject-d] -autorecon2 –autorecon3 and those jobs are also running for some time but then crashing with the same error complaining that lh.BA1.thresh.label does not exist. We are on RedHat 5.2, running the 2.6.18-19.1.13.e15 kernel and using the BASH environment. We are using the release 5.3.0-centos04. The log and other relevant files can be found at: http://www-personal.umich.edu/~rcwelsh/bug/recon-all.cmd http://www-personal.umich.edu/~rcwelsh/bug/recon-all.log http://www-personal.umich.edu/~rcwelsh/bug/recon-all.env http://www-personal.umich.edu/~rcwelsh/bug/recon-all.error I've dug into the code and see that the block of code in recon-all was introduced going from 5.2 to 5.3. # generate .thresh labels foreach balabel (BA1 BA2 BA3a BA3b BA4a BA4p BA6 BA44 BA45 V1 V2 MT) set cmd=(mri_label2label \ --srcsubject fsaverage \ --srclabel $SUBJECTS_DIR/fsaverage/label/${hemi}.${balabel}.thresh.label \ --trgsubject $subjid \ --trglabel ./${hemi}.${balabel}.thresh.label \ --hemi ${hemi} \ --regmethod surface) echo "\n $cmd \n"|& tee -a $LF |& tee -a $CF if($RunIt) $fs_time $cmd |& tee -a $LF if($status) goto error_exit; end # balabel This is what is throwing the error. Hopefully, we can get this resolved soon. (Also as a side note in the version 5.2 we had to comment out the reference to perirhinal in the first "foreach balabel" loop as perirhinal was giving a bug) Thanks, -Robert ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

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recon-all error
by Rafa X 04 Jun '13

04 Jun '13

Dear freesurfer experts, I was running an autorecon2 in the recon-all but always gives me this memory allocation error, only on this subject. Im using FS v5.1 #@# ASeg Stats Mon Jun 3 20:13:11 CEST 2013 /root/trabajo/freesurfer/subjects/qsm1_17_stats2_g mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /root/trabajo/freesurfer/ASegStatsLUT.txt --subject qsm1_17_stats2_g $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /root/trabajo/freesurfer/ASegStatsLUT.txt --subject qsm1_17_stats2_g sysname Linux hostname localhost.localdomain machine x86_64 user root atlas_icv (eTIV) = 1196346 mm^3 (det: 1.628380 ) Loading mri/aseg.mgz Getting Cerebral WM volumes from surface lh white matter volume 206011 rh white matter volume 198149 Getting Cerebral GM and WM volumes from surfaces lh surface-based volumes (mm3): wTot = 235659.045132, pTot = 416409.266434 c = 180750.221302 rh surface-based volumes (mm3): wTot = 223785.748405, pTot = 402494.420361 c = 178708.671956 MRIalloc: could not allocate 540094766 frames Computing SupraTentVolCor Cannot allocate memory Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all -s qsm1_17_stats2_g exited with ERRORS at Mon Jun 3 20:18:36 CEST 2013 For more details, see the log file /root/trabajo/freesurfer/subjects/qsm1_17_stats2_g/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Any help will be appreaciated, Many thanks in advance Rafa

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Postdoctoral Fellow - University of Oslo
by Lars Tjelta Westlye 04 Jun '13

04 Jun '13

A three-year term position as Postdoctoral Fellow (governmental position code 1352) is available at the Norwegian Centre for Mental Disorders Research (NORMENT) and the KG Jebsen Centre for Psychosis Research – TOP Study Group, Institute of Clinical Medicine, University of Oslo and Oslo University Hospital, Norway. http://uio.easycruit.com/vacancy/983405/70331?iso=no ** Job Description NORMENT coordinates a translational multicenter study involving all psychiatric hospital departments in Oslo and several research groups at the University of Oslo. The main purpose of the research is to disentangle and characterize the neurobiological, genetic, psychological and environmental factors contributing to the development of severe mental disorders. Through our extensive infrastructure for clinical evaluations, neuropsychological testing, MRI brain imaging and biobanking we are assembling a comprehensive database comprising genetic and brain imaging data from a large number of healthy controls and patients suffering from psychotic disorders including schizophrenia and bipolar disorders. The postdoctoral fellow will play a central role in the analysis and dissemination of data from this large imaging genetics database. The research will be carried out as part of a cross-disciplinary team of researchers in the Multimodal Imaging and Biostatistics groups at NORMENT in close collaboration with researchers at the University of California San Diego and deCODE Genetics. ** We offer An ambitious and exciting research environment with a strong multidisciplinary profile and excellent opportunities for academic development at NORMENT, which was recently granted Centre of Excellence Status by the Research Council of Norway. A postdoctoral position in Norway is equivalent to the US position of assistant professor and is intended to prepare and qualify talented candidates for a research career. Salary is in the range between ltr 57 and ltr 65, i.e. from NOK 473 400 to NOK 548 700, depending on qualifications. Pension and national health insurance is included in addition to several attractive welfare arrangements (http://www.uio.no/english/for-employees/employment/welfare) ** Qualifications The ideal candidate is ambitious and highly motivated for pursuing a career in science, hold a PhD in neuroimaging, computational neuroscience, biomedical engineering, cognitive neuroscience, or equivalent, have a strong background and interest in neuroscience, MRI analysis and statistics, and an excellent publication record. Candidates with a strong interest in and experience with methods for integrating multimodal imaging measures, including structural MRI, diffusion tensor imaging (DTI), and functional MRI, are in particular encouraged to apply. Experience with imaging genetics is an advantage. ** The application Applications are submitted through the University online recruitment system and must include application letter including motivation for applying for the position, CV summarizing education, relevant work experience, grants etc, a complete list of publications and academic work, and contact details of 2-3 references. Application deadline: June 30 2013. After the initial screening process, short-listed candidates may be asked to submit selected publications, educational certificates and transcripts of records. Interviews may be included as part of the selection process. For any informal enquiries regarding the position, please contact professor Ole A. Andreassen (o.a.andreassen(a)medisin.uio.no) and associate professor Lars T. Westlye (l.t.westlye(a)psykologi.uio.no) http://uio.easycruit.com/vacancy/983405/70331?iso=no

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SORRY POSTED THE WRONG ERROR..This is the the right one
by Manish Dalwani 03 Jun '13

03 Jun '13

I need help with this error...I do see the a LICENSE file in the freesurfer directory. -------------------------------------------------------------------------- ERROR: FreeSurfer license file /Applications/freesurfer/license.txt not found. If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -------------------------------------------------------------------------- $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Applications/freesurfer/subjects/anat_5214/MR1000200001.dcm... Darwin server.imaging.private 12.1.0 Darwin Kernel Version 12.1.0: Tue Aug 14 13:29:55 PDT 2012; root:xnu-2050.9.2~1/RELEASE_X86_64 x86_64 recon-all -s 5214 exited with ERRORS at Mon Jun 3 16:24:01 MDT 2013 For more details, see the log file /Applications/freesurfer/subjects/5214/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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help with this error
by Manish Dalwani 03 Jun '13

03 Jun '13

Dear Freesurfer's I have been using (a slightly older version) Freesurfer on linux and it works fine. I just recently installed freesurfer on the mac workstation OS X 10.8.1. I get the following error: server:subjects manishdalwani$ cd anat_5214 server:anat_5214 manishdalwani$ recon-all -i MR1000200001.dcm -s 5214 ERROR: MR1000200001.dcm exists but is not readable Darwin server.imaging.private 12.1.0 Darwin Kernel Version 12.1.0: Tue Aug 14 13:29:55 PDT 2012; root:xnu-2050.9.2~1/RELEASE_X86_64 x86_64 recon-all -s exited with ERRORS at Mon Jun 3 15:57:24 MDT 2013 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Kindly help! Regards, Manish

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BrainSegNotVent
by Derek James Dean 03 Jun '13

03 Jun '13

2 1

image with Cerebellum
by Ray, Siddharth 03 Jun '13

03 Jun '13

Hi, I am new to freesurfer and just want to know can I just have skull-stripped image (with cerebellum) anywhere between stages in Freesurfer 5.3?? Please let me know. Thanks, Siddharth

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possible to display data obtained through mri_segment as heatmap?
by Salil Soman 03 Jun '13

03 Jun '13

Dear Doug, Thank you for your recent advise with using freesurfer to extract mean values from non structural image data. Is there a way to generate an image (e.g. heat map) displaying those values in free view? Best wishes, Sal

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freeview v5.3 reposition surface
by Adam Martersteck 03 Jun '13

03 Jun '13

Hi Freesurfer experts, I noticed that Freeview has gotten an upgrade from v5.1 to v5.3 and the reposition tool now has a GUI and it works! Dr. Fischl said in response to Dr. Pietro De Rossi on October 24th, 2012 that the pipeline for the reposition surface tool was not yet implemented and you still needed to rerun “mris_make_surface (including mris_thickness to regenerate the thickness map)”. [ https://mail.nmr.mgh.harvard.edu/pipermail///freesurfer/2012-October/026209… I noticed that the freeview virtual representation of the surfaces are immediately regenerated. Should I be running the mris_make_surface command after saving the new surface(s)? Thanks, Adam Martersteck Cognitive Neurology and Alzheimer's Disease Center Northwestern University Feinberg School of Medicine 320 E. Superior Street, Searle 11 Chicago, IL 60611

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