Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30099 discussions

Re: [Freesurfer] problem of Label file
by kangchengwang0808＠gmail.com 18 Jun '14

18 Jun '14

Dear Bruce, Thank you very much for your response. The area which I made label could be seen in the figure (below). Is the reason for large number that the line was outside the blue area? Wang Kangcheng

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label from volume on decimated surface
by Kai Schlamp 18 Jun '14

18 Jun '14

Hello Freesurfer experts, I want to project a label from a volume on a decimated surface. Normally I do something like this to generate a label from the volume: mri_vol2surf --src subjects/foobar/mri/aparc+aseg.mgz --regheader foobar --hemi lh --surf pial --out test.mgh mri_cor2label --i test.mgh --id 1024 --surf foobar lh pial --l test.label Unfortunately this does not work if I decimated the lh.pial surface before (for example using mris_decimate). Do you have a suggestion how to accomplish this? Kai

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Researcher/Postdoctoral position: Multimodal Neuroimaging, Twins, Autism and ADHD, Karolinska Institutet
by Elodie Cauvet 18 Jun '14

18 Jun '14

Dear list, One Researcher/postdoc position is available in our group at Karolinska Institutet in Stockholm. Application Deadline is June the 30th 2014. --- Group and Project --- Karolinska Institutet Center of Neurodevelopmental Disorders (KIND) http://ki.se/kind KIND is an excellence center for research, development, education and clinical practice in the area of developmental psychopathology. The Roots of Autism and ADHD Twin Study Sweden (RATSS) is a frontline research project within KIND, focusing on monozygotic twins discordant for autism spectrum disorder and other neurodevelopmental disorders. For the first time ever, twins are examined on multiple levels: behavior, cognition, neurobiology, environment, and genetics to elucidate the etiology of neuropsychiatric disorders. Functional and structural neuroimaging using MRI are an integral part of RATSS. Scanning is performed at the Karolinska Institutet MR Research Center, using a 3 Tesla MR scanner (GE MR750). To date, 80 pairs have been examined. --- Position --- As a neuroimaging researcher (typically, but not necessarily post-doc) in RATSS, while working in a team of scientists, you are mainly responsible for the acquisition and analyses of the multimodal brain imaging data. Diffusion Tensor Imaging (DTI), resting state functional MRI and structural T1 analyses will be integrated into hierarchical network models such as brain connectome. We expect motivation, routine and professionalism in administrative tasks, grant application and article writing. This work will be done in close collaboration with other partners (e.g. Dr. Peter Fransson, the Dept. of Clinical Neuroscience (KI); Institute Pasteur (Paris), EUAIMS project, Mt Sinai (New York)). All details about the position can be found here: https://ki.mynetworkglobal.com/se/what:job/jobID:37590/where:4/ Applications should be submitted here: https://ki.mynetworkglobal.com/en/what:login/jobID:37590/where:4/ Please note that we DO NOT ACCEPT applications being submitted by email. To be considered, your application must be submitted through the application system. Best regards, Elodie Cauvet for KIND Élodie CAUVET | PhD Karolinska Institutet Center of Neurodevelopmental Disorders (KIND) Gävlegatan 22B, floor 8 | 113 30 Stockholm +46 (0)8 51452706 | +46 (0)728 774 058 elodie<mailto:elodie.cauvet@ki.se>.cauvet(a)ki.se<mailto:elodie.cauvet@ki.se> | ki.se/kind<http://ki.se/ki/jsp/polopoly.jsp;jsessionid=aMdk8ad4iRL6OYOdFn?l=en&d=130> ___________________________________________________________________________________ Karolinska Institutet – a medical university

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smoothing functional data on smoothwm surface
by Milde, Christopher 18 Jun '14

18 Jun '14

Dear Freesurfers, I'm interested in smoothing preprocessed (but unsmoothed) functional FEAT data, which was coregistered and resampled to the anatomical surface (using: reg-feat2anat/feat2surf). I want to apply smoothing on the functional data preferentially on a surface which doesn't suffer from metric distortions (like the inflated OR sphere). I thought about using the smoothwm surface. Questions: Which command can I use for smoothing the feat functional data on the smoothwm AND furthermore, how can I extract the cluster maxima afterwards??? I'm thankful for any helpful comment, Greetz, Christopher

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question about recon-all autorecon2 "Automatic Topology Fixer"
by Cheng Peng 17 Jun '14

17 Jun '14

Hi! I am a relative beginner with freesurfer and was going through the steps listed on freesurfer wiki about detailed description of each steps autorecon2 covers. During "Automatic Topology Fixer (-<no>fix)", the description stated that "user should check the orig surface in the volume to make sure that it looks appropriate". I am wondering how should i check and compare the orig surface and result since i can't find a way to open surf/?h.orig.nofix or surf/?h.orig. Any help or insight is appreciated! Thanks! Cheng Peng

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Fwd: Job opportunity at Pfizer
by dgw 17 Jun '14

17 Jun '14

Attention Statisticians, Pfizer is looking for a statistician, who has some neuroimaging experience. If you are interested in applying, please see the email below. Thanks, D Begin forwarded message: > From: Brandon Whitcher <bwhitcher(a)gmail.com> > Date: June 11, 2014 8:30:23 AM EDT > To: Dan Wakeman <dgwakeman(a)gmail.com> > Subject: Job opportunity at Pfizer > > Dear Dan, > > I have attached a job description from the Statistics group at Pfizer with particular emphasis on supporting the Neuroscience research unit in Boston/Cambridge. The colored text has been added to emphasize additional skills around neuroimaging experience. Essentially, my colleague in Statistics is looking for someone who has worked with functional neuroimaging data (MRI and/or PET) and is interested in being a project statistician on early-phase clinical and some pre-clinical studies. The job would not be 100% neuroimaging, but those skills are needed in the group. She's looking for a recent postdoc or graduate student, though the role could support more experienced candidates (5+ years of experience) too. If you know of anyone who is interested please feel free to forward the attachment. Also, there is a Pfizer job ID (990274) in order to apply or I'm happy to be a point of contact. > > cheers... > > Brandon > >

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Version 5.3 recon-all run time
by Linden Parkes 17 Jun '14

17 Jun '14

Hi FSers, I have an Ubuntu machine (14.04 LTS) with a quad-core i7 4770k/32gb RAM and recon-all is taking me approximately 6 hours per subject without using openmp (haven't tried this yet). According to the terminal, it finishes without errors. I've read (e.g., https://surfer.nmr.mgh.harvard.edu/fswiki/FsQuizAnswers) and heard that recon-all should take 20-24 hours per participant to complete. So, should I be celebrating my 6 hour run time or should I be very suspicious of it? Also, how does freesurfer go with hyper threaded CPUs? (as is the case with the 4770k; 4 cores, 8 threads). I've read that you should restrict parallel processing to one subject per core. Can I take advantage of the hyper threading and run 8 subjects simultaneously or should I be more conservative and only run 4? Cheers, Linden

5 5

subcortical segment NIFTI files
by Yang, Daniel 17 Jun '14

17 Jun '14

Dear all, While it is possible to obtain NIfTI files for cortical parcellation using mri_annotation2label, I am running if it is possible to obtain NIfTI files associated with aseg parts? Thanks! Daniel

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mni/bin/nu_correct: Exec format error. Binary file not executable.
by Bill Taylor 17 Jun '14

17 Jun '14

I have cruised the mailing list for 5.3 specific causes. Some runs work and some hit this error.recon-all -autorecon1 -skullstrip -gcut -subjid 1217_1 We are crunching a set of over 300 and I have checked the obvious. This is what I downloaded: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz We are running scientific linux 6.3 in our cluster and the one machine I checked did indeed have perl in /usr/bin and we are all x86_64. I recently upgraded our pipeline from 5.1 to 5.3 but this is the first time running with these exact options. I am not the one doing the research, I only automated it to run in our HTCondor cluster. If it helps stdout for that one job is: Linux glow-c112.cs.wisc.edu 2.6.32-358.2.1.el6.x86_64 #1 SMP Tue Mar 12 14:18:09 CDT 2013 x86_64 x86_64 x86_64 GNU/Linux #-------------------------------------------- #@# MotionCor Fri Jun 13 19:00:45 CDT 2014 Found 1 runs /var/lib/condor/execute/slot1/dir_4596/1217_1/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /var/lib/condor/execute/slot1/dir_4596/1217_1/mri/orig/001.mgz /var/lib/condor/execute/slot1/dir_4596/1217_1/mri/rawavg.mgz /var/lib/condor/execute/slot1/dir_4596/1217_1 mri_convert /var/lib/condor/execute/slot1/dir_4596/1217_1/mri/rawavg.mgz /var/lib/condor/execute/slot1/dir_4596/1217_1/mri/orig.mgz --conform mri_convert /var/lib/condor/execute/slot1/dir_4596/1217_1/mri/rawavg.mgz /var/lib/condor/execute/slot1/dir_4596/1217_1/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /var/lib/condor/execute/slot1/dir_4596/1217_1/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (-1, -0, 0) Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /var/lib/condor/execute/slot1/dir_4596/1217_1/mri/orig.mgz... mri_add_xform_to_header -c /var/lib/condor/execute/slot1/dir_4596/1217_1/mri/transforms/talairach.xfm /var/lib/condor/execute/slot1/dir_4596/1217_1/mri/orig.mgz /var/lib/condor/execute/slot1/dir_4596/1217_1/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Fri Jun 13 19:01:08 CDT 2014 /var/lib/condor/execute/slot1/dir_4596/1217_1/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Linux glow-c112.cs.wisc.edu 2.6.32-358.2.1.el6.x86_64 #1 SMP Tue Mar 12 14:18:09 CDT 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 1217_1 exited with ERRORS at Fri Jun 13 19:01:11 CDT 2014 For more details, see the log file /var/lib/condor/execute/slot1/dir_4596/1217_1/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Command requested is <recon-all -autorecon1 -skullstrip -gcut -subjid 1217_1 > finished with result<256> Non-zero recon-all -autorecon1 -skullstrip -gcut -subjid 1217_1 Changing to 1217_1 to read scripts/recon-all.log ................................................................................................................................... Finished WITH freesurfer errors<<<<To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>>> Tar up subject directory before leaving 1217_1/ 1217_1/mri/ 1217_1/mri/orig/ 1217_1/mri/orig/001.mgz 1217_1/mri/transforms/ 1217_1/mri/transforms/bak/ 1217_1/mri/rawavg.mgz 1217_1/mri/orig.mgz 1217_1/mri/orig_nu.log 1217_1/mri/mri_nu_correct.mni.log 1217_1/mri/tmp.mri_nu_correct.mni.5252/ 1217_1/mri/tmp.mri_nu_correct.mni.5252/nu0.mnc 1217_1/scripts/ 1217_1/scripts/build-stamp.txt 1217_1/scripts/recon-all.env 1217_1/scripts/recon-all.log 1217_1/scripts/csurfdir 1217_1/scripts/recon-all-status.log 1217_1/scripts/recon-all.local-copy 1217_1/scripts/recon-all.cmd 1217_1/scripts/recon-all.error 1217_1/surf/ 1217_1/tmp/ 1217_1/label/ 1217_1/touch/ 1217_1/touch/conform.touch 1217_1/stats/ 1217_1/src/ 1217_1/trash/ 1217_1/bem/ total 152 -- Bill Taylor 608-263-2656 (608-219-4430) Center for High Throughput Computing(CHTC) HTCondor project Computer Sciences University of Wisconsin, Madison

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fsfast preproc question
by dgw 17 Jun '14

17 Jun '14

The volume produced from the -mni305 option in preproc-sess, does not look like a brain (it seems to be mostly cerebellum. I have attached an image). Is this the expected behavior? I have included the relevant path and information below: source /cluster/neuromind/dwakeman/wmh/software/nmr-stable53-env #<note this just points to the Martinos stable53 env> setenv SUBJECTS_DIR /cluster/neuromind/dwakeman/wmh/analysis_1 preproc-sess -surface fsaverage5 lhrh -s $SUBJECT -fwhm 6 -fsd e_o -mni305 -per-run -stc odd Any of the subjects in that subjects directory have the same effect. including nmr00809 (if you want a specific example). The only guess I have is that maybe fsaverage5 is somehow interacting with the mni305 option? Thanks, D

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