Freesurfer

freesurfer@nmr.mgh.harvard.edu

3 participants
30135 discussions

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

2 1

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

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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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Brining Freesurfer colomaps and/or lookup table to MRIcron
by Dorian P. 17 Jun '14

17 Jun '14

Dear Freesurfers, Is there a way to bring the colormaps of Freesurfer to MRIcron. Right now when I bring parcellations in MRIcron there is no good way to distinguish parcels, because the parcels are numerated 1000+ for left hemisphere, 2000+ for right, 3000+ for white matter left, etc. This makes MRIcron to color all 1000 with the same color, all 2000 with another, etc. Any suggestion would be welcome. Dorian TJU

1 0

Number of Slices
by Caroline Lewis 17 Jun '14

17 Jun '14

Hi, I want to perform recon-all on four different structural sequences for the same participant. Three of the sequences have the same number of slices, whereas the T1 has fewer slices, so when I input the different sequences with the recon-all command, I get the following error: ERROR: inputs have mismatched dimensions! Is there a way to bypass this or make each sequence have the same number of slices? And if so, will this affect data quality? Many thanks, Caroline

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problem of Label file
by 王康程 17 Jun '14

17 Jun '14

Hi all, I create a label file according to my result using QDEC, does it correct? why some number is so large? #!ascii label , from subject vox2ras=TkReg 260 963 -9.181 41.343 -47.222 0.0000000000 1515 -9.022 44.425 -43.083 0.0000000000 1516 -7.070 45.386 -46.312 0.0000000000 3485 -8.162 46.694 -42.879 0.0000000000 3486 -8.111 44.955 -44.755 199456282314100703232.0000000000 3487 -7.235 47.186 -44.476 0.0000000000 6341 -10.194 40.795 -45.508 0.0000000000 6342 -11.386 38.884 -45.964 0.0000000000 6343 -10.382 39.516 -47.765 0.0000000000 7376 -9.101 42.821 -45.101 0.0000000000 7377 -8.073 43.300 -46.733 0.0000000000 7378 -6.918 43.647 -48.225 0.0000000000 9843 -6.168 47.599 -45.963 72719596043655881627927828234240.0000000000 9844 -5.895 45.704 -47.732 0.0000000000 9845 -5.637 43.852 -49.553 0.0000000000 11163 -7.843 48.753 -41.943 0.0000000000 11165 -7.775 47.849 -42.800 0.0000000000 11166 -7.714 46.949 -43.690 0.0000000000 11167 -7.323 48.099 -43.592 0.0000000000 14408 -9.705 41.086 -46.381 0.0000000000 14409 -10.290 40.137 -46.625 53662309296634309728540819456.0000000000 14410 -9.770 40.413 -47.487 0.0000000000 16216 -9.565 42.537 -44.238 0.0000000000 16218 -7.607 45.184 -45.549 0.0000000000 16219 -8.091 44.116 -45.733 0.0000000000 16220 -7.558 44.327 -46.514 0.0000000000 16221 -7.511 43.491 -47.498 0.0000000000 16222 -6.993 44.507 -47.260 0.0000000000 18751 -11.537 38.329 -47.146 0.0000000000 18752 -12.021 37.968 -46.208 0.0000000000 22043 -6.312 48.554 -45.102 0.0000000000 22048 -5.765 44.771 -48.637 0.0000000000 23621 -8.623 41.563 -48.026 0.0000000000 23622 -9.215 40.651 -48.313 0.0000000000 24705 -8.577 45.552 -42.973 0.0000000000 24706 -8.583 44.702 -43.932 0.0000000000 24707 -8.134 45.816 -43.803 0.0000006824 24708 -7.659 46.059 -44.607 0.0000000000 24709 -7.151 46.280 -45.383 0.0000000000 30157 -10.777 39.826 -45.730 0.0000000000 30158 -10.900 39.219 -46.881 0.0000000000 30159 -11.019 38.650 -48.053 0.0000000000 30160 -9.829 39.773 -48.612 0.0000000000 30161 -10.467 38.928 -48.923 0.0000000000 32636 -10.096 41.492 -44.414 0.0000000006 32637 -9.636 41.794 -45.297 0.0000000000 32638 -9.142 42.066 -46.150 0.0000000000 32639 -8.592 43.875 -44.920 0.0000000000 32640 -8.603 43.076 -45.933 0.0000000000 32641 -8.615 42.306 -46.970 0.0000000000 32642 -8.055 42.510 -47.754 0.0000000000 32643 -7.464 42.677 -48.499 0.0000000000 32644 -6.842 42.806 -49.203 70680060550261023833231196160.0000000000 39765 -6.836 48.334 -44.361 0.0000000000 39766 -6.720 47.403 -45.234 0.0000000000 39767 -6.608 46.477 -46.128 0.0000000000 39769 -6.030 46.648 -46.840 0.0000000000 39770 -6.500 45.560 -47.041 0.0000000000 39771 -6.395 44.656 -47.968 0.0000000000 39772 -6.292 43.768 -48.910 0.0000000000 39773 -6.191 42.896 -49.864 1198670724329189084508911654928384.0000000000 41883 -7.634 48.885 -42.342 0.0000000000 41884 -7.808 48.301 -42.368 0.0000000000 41885 -7.593 48.430 -42.767 0.0000000000 41886 -7.553 47.976 -43.199 0.0000000000 41887 -7.369 48.557 -43.161 0.0000000000 45128 -9.447 41.219 -46.806 0.0000000000 45129 -9.738 40.745 -46.932 0.0000000000 45130 -9.472 40.874 -47.353 16928685348014293778432.0000000000 46935 -9.255 43.868 -43.144 0.0000000000 46937 -9.041 44.013 -43.576 0.0000000000 46938 -7.343 45.288 -45.935 0.0000000000 46939 -7.582 44.753 -46.029 0.0000000000 46940 -7.311 44.852 -46.411 0.0000000000 46941 -7.280 44.421 -46.892 0.0000000000 46942 -7.031 44.945 -46.784 0.0000000000 54728 -8.332 41.659 -48.414 0.0000000000 54729 -8.626 41.203 -48.560 0.0000000000 56535 -8.366 46.121 -42.923 0.0000000000 56536 -8.360 45.686 -43.391 0.0000000000 56537 -8.147 46.253 -43.337 0.0000000000 56538 -7.479 47.070 -44.086 0.0000000000 56539 -7.686 46.502 -44.145 0.0000000000 56540 -7.443 46.620 -44.539 0.0000000000 56541 -7.409 46.172 -44.999 4742407148412851825182397956096.0000000000 56542 -7.192 46.732 -44.927 0.0000000000 66263 -10.427 40.638 -45.059 0.0000000000 66264 -10.714 40.144 -45.164 0.0000000000 66265 -10.483 40.307 -45.618 0.0000000000 66266 -10.337 39.822 -47.192 0.0000000000 66267 -10.592 39.675 -46.752 0.0000000000 66268 -10.645 39.373 -47.327 0.0000000000 66269 -10.960 38.930 -47.464 273757759681993900032.0000000000 66270 -10.697 39.079 -47.907 0.0000000000 Wang Kangcheng

2 1

Tracula preprocessing error ( set dob0 = 1 )
by Elia S. 17 Jun '14

17 Jun '14

Dear Freesurfer community, Whenever i try to launch the tracula preprocessing, using "set dob0 = 1 " and the following command line: trac-all -prep -no-isrunning -c '/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/tracula.config It stops, giving me errors like these: niiRead(): error opening file /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi.nii.gz ERROR: reading /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_frame0.nii.gz While setting "dob0 = 0" everything runs smoothly. Can you help me please? I'll attach the log + dmrirc (tracula.config) Best,Elia. -------------------------------------------------------------------------------------------------------------- Freesurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 Linux Distribution: Ubuntu 12.04 precise - Ubuntu 12.04.4 LTS Environment/Version: Linux king-ubuntu 3.2.0-56-generic #86-Ubuntu SMP Wed Oct 23 09:20:45 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux

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