Freesurfer June 2013

freesurfer@nmr.mgh.harvard.edu

170 participants
298 discussions

v 5.3 pial- FLAIR vs T2
by octavian lie 04 Jun '13

04 Jun '13

Dear All, Among T2 FLAIR, eT2W FLAIR sense, T2, which sequence should be preferably used as auxiliary for pial definition? Does Freesurfer take care of coregistration between these and the MPRAGE? What would be the command line (Linux Ubuntu) if I want to use SPM generated nifti DICOM concatenations for the T2 or FLAIR, instead of native DICOMs? Thank you, Octavian

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<no>motioncor
by Gabriel Obregon 04 Jun '13

04 Jun '13

Hi, Could someone please help me with the following concerns: A. If I have multiple source volumes in mri/orig/ and run recon-all using the -nomotioncor option, how are these inputs processed compared to the case in which motion correction is employed, and what should I expect as my output? B. If I want to process only one of the multiple source volumes, i.e., the "best", how should I proceed? C. I've been encountering displaying issues of the raw volumes using tkmedit. What other interfaces are readily available for browsing through the source volumes in order to assess their quality? D. Finally, if in one of my studies I could afford running only two MPRAGE sessions per subject, is motion correction advisable for segmenting the surfaces? Thanks! Gabriel

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Recon-all difficulties off-site
by Nitenson, Adam 04 Jun '13

04 Jun '13

Hello users, I am trying to get Freesurfer (5.2) working properly off-site and am encountering errors I did not have while working at the Martinos center. We use the same Siemens 3T Tim Trio scanner at Brown, so I would hope the data is similar to work with. I have been using dcmunpack since unpacksdcmdir is not identifying the DICOM files properly. I have successfully unpacked the structural and bold scans using the command (entered from the raw scan data folder: dcmunpack -src DICOM -targ (path)/FreesurferPractice/unpack3 -run 2 MPRAGE nii struct (I also tried using mgz instead of nii, and also changed struct to other things as it appears to be a naming argument) dcmunpack -src DICOM -targ (path)/FreesurferPractice/unpack3 -fsfast -run 3 bold nii f.nii -run 4 bold nii f.nii -run 5 bold nii f.nii -run 6 bold nii f.nii -run 7 bold nii f.nii -run 8 bold nii f.nii -run 9 bold nii f.nii (path) just being an abbreviate piece of the relevant pathway These generate the MPRAGE and bold folders in the subject folder as expected. I have difficulties with the next commands (environment has been set). I try: recon-all -i <path to structural data> -s <subject name> -force recon-all -i (path)/FreesurferPractice/unpack/MPRAGE/002 -s unpack3 (I got an error about using -force so I omitted that from my command) and get the following Error ERROR: You are trying to re-run an existing subject with (possibly) new input data (-i). If this is truly new input data, you should delete the subject folder and re-run, or specify a different subject name. If you are just continuing an analysis of an existing subject, then omit all -i flags. Yet when I omit -i and just use "recon-all -s unpack3", I get "ERROR: nothing to do" I tried a different tactic and used "recon-all -s unpack3 -autorecon1" as well as "recon-all -autorecon-all -s unpack3" which both created the various folders (bem, label, mri, surf, etc) but failed with "ERROR: no run data found in (path)/FreesurferPractice/unpack3/mri. Make sure to have a volume called 001.mgz in (path)/FreesurferPractice/unpack3/mri/orig. If you have a second run of data call it 002.mgz, etc." I have tried these commands in both bash and tcsh shells with the same effect. So the problem, it seems, is that my "mri" file is blank, and this was not a problem I had running these commands at Martinos. Any idea what the issue might be? Best, Adam Nitenson Neuroscience Graduate Program Laboratory of Affective Neuroscience Brown University

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mri_convert mgz to nifti
by Ray, Siddharth 04 Jun '13

04 Jun '13

Hi all, I just want to convert .mgz files to .nifti using mri_convert, do I have to flip my image when I do that using RAS ? or I should simply use: Mri_convert input_file_name.mgz output_file_name.nii Thanks in advance, Siddharth

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Fwd: [All] freesurfer and centos6 updates!
by Emily Boeke 04 Jun '13

04 Jun '13

Hi all, I would like to save copy of the CentOS5 release of Freesurfer in my group's work space as described in the email below. The link in the email that is supposed to explain this doesn't work; could someone please let me know how to do this or point me to another webpage that explains it? Thanks! Emily Begin forwarded message: > From: Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> > Subject: [All] freesurfer and centos6 updates! > Date: December 10, 2012 4:08:30 PM EST > To: all(a)nmr.mgh.harvard.edu > Cc: Martinos-tech <martinos-tech(a)yahoogroups.com>, Help <help(a)nmr.mgh.harvard.edu> > > > WARNING! The default Freesurfer version that runs on CentOS6 machines is > going to change next Monday the 17th to a new CentOS6 specific version. > > Right now at the Martinos Center we have a mix of CentOS4, CentOS5 and > CentOS6 machines at the center. All these currently use a version of > freesurfer built on CentOS4 for maximum compatibility. However, this > means those users with CentOS6 systems are using a version that is > slower than they could be using if properly optimized. > > It is time for users of CentOS6 system to no longer be held back by the > older systems. So on next Monday the 17th, the default Freesufer on all > CentOS6 systems (which includes launchpad, tensor, and the icepuffs) > will be updated to a new CentOS6-specific build. > > The mixed environment this results in can result in confusion for groups > with a mix of CentOS versions among their workstations. To avoid this > your group should do one of the following: > > (1) contact the Martinos IT Help Desk to upgrade your old CentOS4 > and CentOS5 systems to CentOS6. Sometime in the near > future we will drop support all together for the old systems. > > (2) make a copy of the current CentOS4 release for your study into > your group's work area and point your users' environments to > use that copy. This is what is recommended for study > consistancy anyway and instructions can be found on the wiki at > > http://surfer.nmr.mgh.harvard.edu/fswiki/MakingPrivateCopiesOfDistributions > > NOTES: > > (1) to tell what CentOS version your workstation is running, run > on it: > > cat /etc/redhat-release > > (2) you are using the default freesurfer release if your PATH has > in it directories that start with /usr/local/freesurfer. > This is a symlink that currently points to the CentOS4 release > on all Linux machines at the center but will change to point at > the CentOS6 release on all CentOS6 machines next Monday, the > 17th. > > Feel free to email me with questions. > > Nick Schmansky > > > > > > > _______________________________________________ > All mailing list > All(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/all > >

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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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Freesurfer June 2013