Freesurfer April 2018

freesurfer@nmr.mgh.harvard.edu

118 participants
177 discussions

SLURM - speed processing
by Alexandre Obert 19 Apr '18

19 Apr '18

External Email - Use Caution Hi all, I'm definitively a noob with both freesurfer and SLURM processes and I wonder if anyone could give me some advice. I tried processing a subject (including hippocampal segmentation) using the following command (freesurfer 6.0.0): recon-all -all -s s03 -hippocampal-subfields-T1 It took nearly 12h to process. I then submit this job to a supercomputer (using slurm) and I asked for nearly 30Go RAM It took nearly 7h to process. That seems good but I wonder if it's possible to speed it up a little more? Regards, Alex

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Re: [Freesurfer] Freesurfer dev version : recon all error mpr2mni305
by Hoopes, Andrew 19 Apr '18

19 Apr '18

Hi Richard, thanks for pointing this out – I’ll take a look into it. best Andrew From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Jones, Richard" <richard.jones(a)choa.org> Reply-To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Date: Thursday, April 19, 2018 at 9:49 AM To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Freesurfer dev version : recon all error mpr2mni305 I ran the command shown below to do recon-all on DICOM images from a Philips Ingenia scanner using the development version of freesurfer on a Mac running high Sierra. recon-all -i /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat/IM-0001-0001.dcm -subject HOPE_SS020 –all The program crashed with the error “ERROR: mpr2mni305 failed, see transforms/talairach_avi.log” The talairach_avi.log file is shown below, followed by the log file. As a test I ran the same command, on the same data, using Freesurfer 6 and that ran without problems (except that it didn’t handle the diffusion tags in the Philips DICOM header correctly so I had to set FS_LOAD_DWI=0, this was not a problem in the development version). Any suggestions as to what may be causing the problems with the library in the development version? Thanks, Richard /Applications/freesurfer_dev/subjects/HOPE_SS020/mri /Applications/freesurfer_dev/bin/talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ Darwin meshuga.choa.org 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar 5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64 Thu Apr 19 08:45:01 EDT 2018 mri_convert.bin orig_nu.mgz talsrcimg.img $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ reading from orig_nu.mgz... TR=6.98, TE=3.14, TI=0.00, flip angle=8.00 i_ras = (-1, 7.45058e-09, 0) j_ras = (3.72529e-09, -4.88944e-09, -1) k_ras = (0, 1, 4.88944e-09) writing to talsrcimg.img... Analyze Output Matrix -1.00000 0.00000 0.00000 128.15305; 0.00000 -0.00000 1.00000 -116.15433; 0.00000 -1.00000 0.00000 128.60870; 0.00000 0.00000 0.00000 1.00000; -------------------- INFO: set hdr.hist.orient to -1 mpr2mni305 talsrcimg Thu Apr 19 08:45:02 EDT 2018 /Applications/freesurfer_dev/bin/mpr2mni305 talsrcimg $Id: mpr2mni305,v 1.5 2015/12/18 23:56:21 zkaufman Exp $ target=711-2C_as_mni_average_305 --------------------------------------------------------------------- analyzeto4dfp talsrcimg -O0 -y --------------------------------------------------------------------- $Id: ifh2hdr.c,v 1.3 2007/05/05 10:45:03 nicks Exp $ Thu Apr 19 08:45:02 2018 Writing: talsrcimg.4dfp.hdr $Id: analyzeto4dfp.c,v 1.2 2007/05/05 00:00:06 nicks Exp $ Reading: talsrcimg.hdr header size 348 bytes hdr.dime.datatype offset=70 value=2 hdr.dime.bitpix offset=72 value=8 hdr.hist.orient offset=252 value=-1 dimensionality 4 dimensions 256 256 256 1 Reading: talsrcimg.img Writing: talsrcimg.4dfp.img Writing: talsrcimg.4dfp.ifh ifh2hdr talsrcimg -r0to255 ori=2 --------------------------------------------------------------------- gauss_4dfp talsrcimg 1.1 --------------------------------------------------------------------- dyld: Library not loaded: /usr/local/opt/gcc/lib/gcc/7/libgfortran.4.dylib Referenced from: /Applications/freesurfer_dev/bin/gauss_4dfp Reason: image not found Abort ERROR: 'gauss_4dfp talsrcimg 1.1' failed! status=134 ERROR: mpr2mni305 execution aborted Subject Stamp: freesurfer-darwin-OSX-ElCapitan-dev-20180415-0d56499 Current Stamp: freesurfer-darwin-OSX-ElCapitan-dev-20180415-0d56499 INFO: SUBJECTS_DIR is /Applications/freesurfer_dev/subjects Actual FREESURFER_HOME /Applications/freesurfer_dev Darwin meshuga.choa.org 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar 5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64 /Applications/freesurfer_dev/subjects/HOPE_SS020 \n mri_convert /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat/IM-0001-0001.dcm /Applications/freesurfer_dev/subjects/HOPE_SS020/mri/orig/001.mgz \n mri_convert.bin /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat/IM-0001-0001.dcm /Applications/freesurfer_dev/subjects/HOPE_SS020/mri/orig/001.mgz $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ reading from /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat/IM-0001-0001.dcm... Starting DICOMRead2() dcmfile = /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat/IM-0001-0001.dcm dcmdir = /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat Ref Series No = 301 Found 202 files, checking for dicoms Found 200 dicom files in series. First Sorting Computing Slice Direction Vs: -0.897217 -0.0611658 0.0354633 Vs: -0.996909 -0.0679621 0.0394038 Second Sorting IsDWI = 0, IsPhilipsDWI = 0 Counting frames nframes = 1 nslices = 200 ndcmfiles = 200 PE Dir = ROW (dicom read) Loading pixel data TR=6.98, TE=3.14, TI=0.00, flip angle=8.00 i_ras = (0.0644896, -0.994415, 0.0835493) j_ras = (0.0448617, -0.08075, -0.995724) k_ras = (0.996909, 0.0679621, 0.0394038) writing to /Applications/freesurfer_dev/subjects/HOPE_SS020/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Thu Apr 19 08:44:06 EDT 2018 Found 1 runs /Applications/freesurfer_dev/subjects/HOPE_SS020/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... Only one run found so motion correction will not be performed. I'll copy the run to rawavg and continue. \n cp /Applications/freesurfer_dev/subjects/HOPE_SS020/mri/orig/001.mgz /Applications/freesurfer_dev/subjects/HOPE_SS020/mri/rawavg.mgz \n /Applications/freesurfer_dev/subjects/HOPE_SS020 \n mri_convert /Applications/freesurfer_dev/subjects/HOPE_SS020/mri/rawavg.mgz /Applications/freesurfer_dev/subjects/HOPE_SS020/mri/orig.mgz --conform \n mri_convert.bin /Applications/freesurfer_dev/subjects/HOPE_SS020/mri/rawavg.mgz /Applications/freesurfer_dev/subjects/HOPE_SS020/mri/orig.mgz --conform $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ reading from /Applications/freesurfer_dev/subjects/HOPE_SS020/mri/rawavg.mgz... TR=6.98, TE=3.14, TI=0.00, flip angle=8.00 i_ras = (0.0644896, -0.994415, 0.0835493) j_ras = (0.0448617, -0.08075, -0.995724) k_ras = (0.996909, 0.0679621, 0.0394038) changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /Applications/freesurfer_dev/subjects/HOPE_SS020/mri/orig.mgz... \n mri_add_xform_to_header -c /Applications/freesurfer_dev/subjects/HOPE_SS020/mri/transforms/talairach.xfm /Applications/freesurfer_dev/subjects/HOPE_SS020/mri/orig.mgz /Applications/freesurfer_dev/subjects/HOPE_SS020/mri/orig.mgz \n INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu Apr 19 08:44:12 EDT 2018 /Applications/freesurfer_dev/subjects/HOPE_SS020/mri \n mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 \n /Applications/freesurfer_dev/subjects/HOPE_SS020/mri /Applications/freesurfer_dev/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 nIters 1 $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ Darwin meshuga.choa.org 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar 5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64 Thu Apr 19 08:44:12 EDT 2018 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks(a)gust.nmr.mgh.harvard.edu (x86_64-apple-darwin11.4.2) on 2015-06-19 at 15:37:08 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.9696 /Applications/freesurfer_dev/subjects/HOPE_SS020/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.9696/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.9696/nu0.mnc -odt float $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ reading from orig.mgz... TR=6.98, TE=3.14, TI=0.00, flip angle=8.00 i_ras = (-1, 7.45058e-09, 0) j_ras = (3.72529e-09, -4.88944e-09, -1) k_ras = (0, 1, 4.88944e-09) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.9696/nu0.mnc... -------------------------------------------------------- Iteration 1 Thu Apr 19 08:44:14 EDT 2018 nu_correct -clobber ./tmp.mri_nu_correct.mni.9696/nu0.mnc ./tmp.mri_nu_correct.mni.9696/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.9696/0/ -iterations 1000 -distance 50 [fsdev@meshuga.choa.org:/Applications/freesurfer_dev/subjects/HOPE_SS020/mri/] [2018-04-19 08:44:14] running: /Applications/freesurfer_dev/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.9696/0/ ./tmp.mri_nu_correct.mni.9696/nu0.mnc ./tmp.mri_nu_correct.mni.9696/nu1.imp 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Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 55 CV of field change: 0.000965325 mri_convert ./tmp.mri_nu_correct.mni.9696/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.9696/nu1.mnc orig_nu.mgz --like orig.mgz --conform $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ reading from ./tmp.mri_nu_correct.mni.9696/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 7.45058e-09, 0) j_ras = (3.72529e-09, -4.88944e-09, -1) k_ras = (0, 1, 4.88944e-09) INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to orig_nu.mgz... Thu Apr 19 08:45:01 EDT 2018 mri_nu_correct.mni done \n talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm \n talairach_avi log file is transforms/talairach_avi.log... ERROR: mpr2mni305 failed, see transforms/talairach_avi.log

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hippocampal segmentation development version question
by Maureen McHugo 19 Apr '18

19 Apr '18

Hi, I am interested in using the head/body/tail output from the hippocampal subfield segmentation module. Is there a reference or description of what landmarks were used to separate head/body and body/tail? Thanks! Maureen

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Lateral Geniculate Nucleus (LGN) roi or volume measures?
by Yash Patel 18 Apr '18

18 Apr '18

Hi all, Is there any way to obtain (automatically, n~1000 subjects), LGN volumes from the Freesurfer set of tools? Or somehow transform the ROI from an atlas into subject space, then extract volume data? Thanks, Yash

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HCP Course 2018 at Oxford: Final Course Schedule posted -- Register Now!
by Jennifer Elam 18 Apr '18

18 Apr '18

Faculty listings and the full schedule of covered topics <https://store.humanconnectome.org/courses/2018/exploring-the-human-connecto…> are now available for the *2018 HCP Course: "Exploring the Human Connectome" <http://store.humanconnectome.org/courses/2018/exploring-the-human-connectom…>*, to be held *June 25 – 29, 2018* at the Blavatnik School of Government <https://www.bsg.ox.ac.uk/partner/contact-us>, at the University of Oxford <http://www.ox.ac.uk/>, in Oxford, UK! FreeSurfer is a major part of the HCP structural processing pipeline, has been critical to the processing of the HCP Young Adult project's over 1100 released high quality imaging datasets, and continues to be used in the processing of forthcoming Lifespan HCP data. The 5-day intensive HCP course is a great opportunity to learn directly from HCP investigators and gain practical experience with the Human Connectome Project's approach to multimodal whole brain imaging acquisition, processing, analysis, visualization, and sharing of data and results. For more info and to register visit the HCP Course 2018 website <http://store.humanconnectome.org/courses/2018/exploring-the-human-connectom…> . Don't delay, registration is limited, and the course is filling up fast! Nearby affordable accommodations are available at Worcester College at Oxford by selecting registration with accommodations on the site. If you have any questions, please contact us at: hcpcourse@humanconnectome. org We look forward to seeing you in Oxford! Best, 2018 HCP Course Staff -- Jennifer Elam, Ph.D. Scientific Outreach, Human Connectome Project Washington University School of Medicine Department of Neuroscience, Box 8108 660 South Euclid Avenue St. Louis, MO 63110 314-362-9387 elam(a)wustl.edu www.humanconnectome.org

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problem with mri_label2vol for aseg
by Michelle VanTieghem 17 Apr '18

17 Apr '18

Hi Freesurfer experts, I am trying to convert the aseg back into native space of the anatomical T1 image. I followed the instructions as in the webpage: https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat specifically this line of code: cd $SUBJECTS_DIR/<subjid>/mri mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz --regheader aseg.mgz However, the result is very odd. The aseg boundaries appear correct in the subcortical regions. however, at the gray mater boundaries, there are single voxels incorrectly labeled as different subcortical-regions. As a result, in the viewer, the gray matter boundaries look multicolored. This is problematic, as I would like to extract a mask of specific ROIs (e.g. right amygdala) but there are many other voxels labeled '54' in addition to the right amygdala. See attached images. I would greatly appreciate your assistance!! Thank you, Michelle -- Michelle VanTieghem PhD student in Psychology Developmental Affective Neuroscience Lab Columbia University mrv2115(a)columbia.edu

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Map the vertices that show a relationship between the FC (obtained by FS-FAST)
by Piero Chiacchiaretta 17 Apr '18

17 Apr '18

Hi there, I wonder if the fsgd file and the command lines listed below are corrected. My sample included 4 groups with different diagnosis (g1, g2, g3, g4). I'm interested to map the vertices that show a relationship between the FC (obtained by FS-FAST) and cortical thickeness, regressing out the diagnosis. To this aim I used the --pvr option: mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --surface fsaverage rh --glmdir Thickness.wls --nii.gz --fsgd g4v1_thickness.fsgd --C intercept.mtx --C slope.mtx --pvr $SUBJECTS_DIR/rh.thickness.10B.mgh The fsgd file lists: ------------------------------------------------------------- GroupDescriptorFile 1 Title Relationship FC-thick reg out dignosis Class g1 Class g2 Class g3 Class g4 Input XX1 g1 Input XX2 g1 ... Input YY1 g2 Input XX2 g2 ... Input XY1 g3 Input XY2 g3 ... Input YX1 g4 Input YX2 g4 ... -------------------------------------------------------------- intercept.mtx 0.25 0.25 0.25 0.25 0 slope.mtx 0 0 0 0 1 thanks piero Piero Chiacchiaretta, PhD Institute for Advanced Biomedical Technologies - ITAB - University “G. d’Annunzio” of Chieti - Pescara Department of Neuroscience, Imaging and Clinical Sciences Via dei Vestini, 31 66013 Chieti, Italy tel: 39-0871-3556919 fax: 39-0871-3556930 e-mail: p.chiacchiaretta(a)unich.it

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FSFAST, Beta values and Percent Signal Change questions
by Sarah Cole 17 Apr '18

17 Apr '18

Hi Doug, I need your recommendations on two topics. I really appreciate your help. 1.) I have two runs of the same experiment, each for about 12 minutes. These 2 runs are different only in the presentation order of the stimuli. I also have one localizer session which first, I calculated my contrasts in it, found the active voxels with positive values, and made a mask of those voxels. Then, mapped the masks on those 2 runs and got the raw data within those voxels. So far, so good. Now, I am looking at the Beta values in these 2 runs for those active voxels, they are very different from each other. For example, in the first run, they are mostly positive but in the second run, they are mostly negative. My intuition was that they should be in the same ballpark. I cannot make sense of this. Do you have any suggestions on why this is happening? 2.) To calculate the % signal change, is it ok to pick the baseline whatever is suitable to my research question. For example, if I need to know the % signal change relative to* the average signal in the first TR of a specific block*, can I use that as a baseline? Or does it always need to be the rest or the mean? Thank you so much and looking forward to hearing from you. Sarah

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mri_anatomical_stats with lobeStrict annot for multiple subjects
by Fernanda Hansen P. de Moraes 17 Apr '18

17 Apr '18

Good night, I would like some help to extract mri_anatomical_stats with lobeStrict annot for multiple subjects in a table format, with the results for all subjects there. I've already tried aparcstats2table and I don't got how to insert the lobeStrict annot there. Thank you very much, Fernanda Moraes -- Fernanda Hansen P. de Moraes Física Médica | Instituto D'Or de Pesquisa e Ensino | Rede D'Or São Luiz

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how to use annotation file in FSFAST for seed based analysis
by Sims, Sara A 17 Apr '18

17 Apr '18

Hello, I am trying to use Glasser’s parcellation to create a correlation matrix that compares all parcels to all parcels. I am new to FSFAST, but so far I have gotten the data preprocessed and ready to go. But I am unsure how to proceed. I have rh and lh annotation files of the parcellation in fsaverage space and I am not sure what to do to them to get to the point that I can use “fcseed-sess”? Should I convert them to labels and then put them on each subject? But what do I do after that? Help please, Sara Sims

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Freesurfer April 2018