Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

OpenGL link errors
by Melvin Robinson 02 Jan '18

02 Jan '18

I posted this to the Freesurfer github site, but didn't exactly know if that was the most appropriate place. The Freesurfer build fails at this command: libtool: link: g++ -fdata-sections -ffunction-sections -Wl,--gc-sections -Wl,-Map -Wl,ld_map.txt -Wl,--no-demangle -o mris_show mris_show.o /usr/lib64/libuuid.so -L/home/melrobin/packages/centos6-x86_64-packages/qt/current/lib -L/usr/lib64 -L/usr/X11R6/lib64 -L/home/melrobin/packages/centos6-x86_64-packages//mni/current/lib -L/home/melrobin/packages/centos6-x86_64-packages//vxl/current/lib -L/home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit ../utils/libutils.a ../minc_substitute/libminc_substitute.a ../fsgdf/libfsgdf.a ../rgb/librgb.a ../unix/libunix.a ../dicom/libdicom.a ../hipsstubs/libhipsstubs.a ../log/liblog.a ../xml2/libxml2.a ../jpeg/libjpeg.a ../tiff/libtiff.a ../expat/libexpat.a ../glut/libglut.a -L/lib64 -lX11 -lXmu /home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libITKIO.a /home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libITKAlgorithms.a /home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libITKCommon.a /home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libITKNumerics.a /home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libITKMetaIO.a /home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libITKniftiio.a /home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libITKNrrdIO.a /home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libitkpng.a /home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libitksys.a /home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libitktiff.a /home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libitkv3p_netlib.a /home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libitkzlib.a /home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libitkgdcm.a /home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libitkopenjpeg.a /home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libitkjpeg8.a /home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libitkjpeg12.a /home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libitkjpeg16.a /home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libITKDICOMParser.a -lz -lm -lcrypt -ldl -lpthread /home/melrobin/packages/centos6-x86_64-packages//mni/current/lib/libvolume_io.a /home/melrobin/packages/centos6-x86_64-packages//mni/current/lib/libminc.a /home/melrobin/packages/centos6-x86_64-packages//mni/current/lib/libnetcdf.a -lvnl_algo -lvnl -lvcl -lnetlib -lv3p_netlib and produces lots of these types of errors /home/melrobin/packages/freesurfer/mris_show/mris_show.c:878: undefined reference to glViewport' mris_show.o: In functionspecial_key_handler': /home/melrobin/packages/freesurfer/mris_show/mris_show.c:923: undefined reference to glMatrixMode' /home/melrobin/packages/freesurfer/mris_show/mris_show.c:937: undefined reference toglRotatef' /home/melrobin/packages/freesurfer/mris_show/mris_show.c:955: undefined reference to glRotatef' /home/melrobin/packages/freesurfer/mris_show/mris_show.c:945: undefined reference toglRotatef' /home/melrobin/packages/freesurfer/mris_show/mris_show.c:951: undefined reference to glRotatef' /home/melrobin/packages/freesurfer/mris_show/mris_show.c:933: undefined reference toglRotatef' The build seems not to include the OpenGL libraries when building mris_show as you can see from the link line. I'm trying to trace this up the Autotools chain, but need some help. I can work a little more on a fix with a little guidance telling me where to look.

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Re: [Freesurfer] mris_convert error in finding file: fread error
by Douglas Greve 02 Jan '18

02 Jan '18

Hi Joao, please remember to send to the list. We don't have anything to merge two hemis together. Manybe the other software has this functionality. On 1/2/18 11:11 AM, João V. Dornas wrote: > Hi Douglass, > > thank you for your response. > > I created two surfaces overlay files like this: > > lh.mgz > rh.mgz > > I can load and view the information using FreeView. > > I need to merge these files as a single surface file to load them > together at the same time in another software. > > This other software accepts Freesurfer ASC, Freesurfer BINARY, Text > files and Gifti. > > Do you mind to give me a hint in how I could accomplish this? > > thank you very much, > > best regards, > > João V. Dornas >

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mri_gtmpvc & mri_gtmseg errors - failed tissue type check
by Makaretz, Sara Johanna 02 Jan '18

02 Jan '18

Hi Doug, I ran mri_gtmseg on a subject & got no errors, and the gtmseg.mgz/apas+head.mgz outputs looked fine: $Id: mri_gtmseg.c,v 1.9.2.1 2016/08/02 21:07:49 greve Exp $ mri_gtmseg --s $s etc, exited fine Then I tried running mri_gtmpvc, and got a 'failed tissue type check' error: [weckl:FDG_2017-11-15] (nmr-stable6-env) cat MR_2017-11-07/pvc.psf06/mri_gtmpvc.log $Id: mri_gtmpvc.c,v 1.69.2.1 2016/07/08 19:50:25 zkaufman Exp $ setenv SUBJECTS_DIR $SUBJECTS_DIR mri_gtmpvc --auto-mask 11 .001 --rbv --mgx .25 --lgtm --threads 8 --seg gtmseg.mgz --no-rescale --save-input --i $PET_DIR/MeanPET.nii --reg $PET_DIR/reg.pet2t1.lta --psf 6 --o $PET_DIR/pvc.psf06 --default-seg-merge sysname Linux hostname weckl.nmr.mgh.harvard.edu machine x86_64 user makaretz vgthresh 0.001000 nReplace 18 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 Loading seg for gtm $SUBJECTS_DIR/$s/mri/gtmseg.mgz Loading ctab $SUBJECTS_DIR/$s/mri/gtmseg.ctab Reading $SUBJECTS_DIR/$s/mri/gtmseg.lta Failed tissue type check [weckl:FDG_2017-11-15] (nmr-stable6-env) I tried re-running mri_gtmseg and adding --keep-cc, as recommended in this thread (I left out --no-xcerseg since I think it's now the default): https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-January/043523.… But I got a different error, where it's trying to write to a file called (null): [weckl:FDG_2017-11-15] (nmr-stable6-env) mri_gtmseg --s $s --keep-cc $Id: mri_gtmseg.c,v 1.9.2.1 2016/08/02 21:07:49 greve Exp $ cwd $PET_DIR cmdline mri_gtmseg --s $s--keep-cc sysname Linux hostname weckl.nmr.mgh.harvard.edu machine x86_64 user makaretz subject $s USF 2 OutputUSF 2 apasfile apas+head.mgz wmannotfile NULL ctxannotfile aparc.annot ctxlhbase 1000 ctxrhbase 2000 SubSegWM 0 KeepHypo 0 KeepCC 1 dmax 5.000000 nlist 0 lhmin 1000 lhmax 1900 rhmin 2000 rhmax 2900 Starting MRIgtmSeg() Starting MRIgtmSeg() USF=2 Loading $SUBJECTS_DIR/$s/mri/apas+head.mgz Loading surfaces t = 2.1280 Loading annotations t = 6.2390 Not segmenting WM reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Relabeling any unlateralized hypointenities as lateralized hypointenities MRIrelabelHypoHemi(): looping over volume nthreads = 1 Relabeling any hypointensities as WM MRIunsegmentWM(): looping over volume nthreads = 1 Upsampling segmentation USF = 2 t = 32.3010 MRIhiresSeg(): filling unknowns with 257 Beginning cortical segmentation using aparc.annot t = 83.9890 MRIannot2CorticalSeg(): looping over volume nthreads = 1 MRIannot2CorticalSeg(): found 1517 unknown, filled with 257 Not subsegmenting WM Found 115 segs in the final list MRIgtmSeg() done, t = 358.8340 Computing colortable WARNING: segid 29 Left-undetermined tissue type is not set Writing output file to $SUBJECTS_DIR/$s/mri/(null) unknown file type for file ($SUBJECTS_DIR/$s/mri/(null)) [weckl:FDG_2017-11-15] (nmr-stable6-env) I think I ruled out the usual operator errors (typos/SUBJECTS_DIR/permissions). Do you have any advice? Thank you in advance for any help! Sara

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low quality reconstructions
by Seth Foster 02 Jan '18

02 Jan '18

Hi freesurfer members, I have a T1 (with contrast) sprg 1mm sequencing MRI for a few patients. Recon-all runs to completion, with no errors, but the pial surfaces look quite bad (see pial.jpg<https://drive.google.com/open?id=172UOGsrYDnMInQNEDcj6LQ8IUxXNMFiR>). Some notes: The tessellation steps take a long time – usually there are ~200 defects to correct, and 1 or 2 defects have 20000+ vertices. Because of the contrast agent, there is a layer of dura and blood vessels visible after the skull strip, perhaps this is causing issues with gray matter segmentation (see slice_with_pial.png<https://drive.google.com/open?id=1FExPxgPN4x-bvxp3wAYx9mR9RXQ7vJ1M>). The visible contrast between gray and white matter is very low for these MRIs. What I’ve tried so far, but did not help Define white matter control points as seeds into the auto-recon2 phase. Adjust (lower) watershed_preflood_heights for the skull stripping process. The dura still remain, and it appears that some of the throat is still present, but I’m not sure that is the main issue. Because the tessellation step takes 30+ hours to run, it’s too difficult to do trial-and-error parameter adjustments and see their effects on the outcome. So I am hoping to get some advice and direction. Are my MRI scans too poor quality for freesurfer to reconstruct a 3D model from? link to raw data <https://gate.nmr.mgh.harvard.edu/filedrop2/index.php?p=3xqqbhtsgsp> https://drive.google.com/open?id=1PWzrKZ37RN08rxy_Nv7mMn1sxTo2nyao Thanks, Seth Foster Research Assistant, Cogan Lab Department of Neurosurgery Duke University seth.foster(a)duke.edu<mailto:seth.foster@duke.edu>

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Re: [Freesurfer] Recon on resected brain
by Xiaosong He 02 Jan '18

02 Jan '18

Yes indeed you are :) Thanks anyway! Sincerely, Xiaosong -------------------------------------------------------------------------------- No, nothing specific. We're just that good (or lucky:). On 12/26/17 9:51 AM, Xiaosong He wrote: > Dear experts, > > ??? I recently accidentally found that the v6.0 version of freesurfer > did a nice job on brain with resection (i.e., clear resection for > brain tumor or epilepsy). I am wondering was there any specific > optimization done for this version? If there was, where can I found > corresponding citations? > > ??? Thanks all in advance and happy holidays! > > ??? With kind regards. > ??? Sincerely, > ??? Xiaosong > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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analysis research postdoc position at WIN/FMRIB Oxford (fwd)
by Bruce Fischl 02 Jan '18

02 Jan '18

FYI ---------- Forwarded message ---------- Date: Thu, 28 Dec 2017 11:25:14 +0000 From: Stephen Smith <steve(a)fmrib.ox.ac.uk> To: Stephen Smith <steve(a)fmrib.ox.ac.uk> Subject: analysis research postdoc position at WIN/FMRIB Oxford Hi friends - please could you forward this around your lab and to anyone you think might be interested in this postdoc position in Oxford? Many many thanks! Steve Smith https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec_version_4.disp… internal_external=E&p_display_in_irish=N&p_process_type=&p_applicant_no=&p_form_profile_detail=&p_d isplay_apply_ind=Y&p_refresh_search=Y&p_recruitment_id=132426 Postdoctoral Research Assistant - Modelling the Development of Functional Connectivity in the Perinatal Brain WIN/FMRIB Centre, University of Oxford, John Radcliffe Hospital, Oxford Grade 8: £39,992 - £52,132 p.a. The Centre for Functional Magnetic Resonance Imaging of the Brain (FMRIB) seeks a postdoctoral researcher to work with Professor Stephen Smith and collaborators in cutting edge research into analytic methods for using FMRI to understand developing connectivity of the perinatal brain. Employment would ideally start early in 2018 and is funded by the European Research Council for a period of 2 years, in the first instance, as part of the Developing Human Connectome Project (dHCP). The dHCP is a collaboration between King’s College, FMRIB and Imperial College and is charting the growth of connections in the human brain, before (in utero) and after birth in 1000 babies using diffusion and functional MRI. The postholder’s contribution to this project will be to develop models of functional connectivity for mapping brain networks. Candidates should have a doctorate in a relevant discipline, together with knowledge of engineering maths and/or statistics and preferably Bayesian learning, with the necessary mathematical and computational skills to put these into practice. Knowledge in methods for analysing neuroimaging data, in particular resting-state functional MRI, is desirable but not essential. Skills in computer programming (especially Matlab and C++) are essential. A Grade 7 (£31,604 - £38,833) appointment, with an appropriate adjustment in duties, would be considered should a suitable candidate not be sourced at Grade 8. For an outline of the lab's research interests and links to further information see Analysis Group and FMRIB www.fmrib.ox.ac.uk. For more dHCP information (including vacancies in the other dHCP groups) see developingconnectome.org. The closing date for applications is 12.00 noon on 15th January 2018. Interviews will be held as soon as possible thereafter. Please note that the University of Oxford's retirement policy is changing. With effect from October 1 2017, all employees at Grade 8 and above will have a retirement age of 68, and all employees at Grades 6 and 7 will no longer have a set retirement age. Further details are available at: www.ox.ac.uk/about/jobs/preemploymentscreening. Contact Person : HR Administrator Vacancy ID : 132426 Contact Phone : 01865 234388 Closing Date : 15-Jan-2018 Contact Email : hr(a)ndcn.ox.ac.uk --------------------------------------------------------------------------- Stephen M. Smith, Professor of Biomedical Engineering Head of Analysis, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) steve(a)fmrib.ox.ac.uk http://www.fmrib.ox.ac.uk/~steve --------------------------------------------------------------------------- Stop the cultural destruction of Tibet

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[freesurfer] version differences for pial matter / skull strip?
by Michelle VanTieghem 02 Jan '18

02 Jan '18

Hello, I have posted several times about problems with skull-stripping with our dataset. We have tried gcut and multiple other options in other packages (AFNI, FSL, ANTS) to remove skull from structural images in our dataset with little success. Recently, a colleague suggested this may be due to versions: that 6.0 deals with skull stripping much better than 5.3. I wanted to ask if indeed this could be the case before I go install 6.0 and re-run everything in my study. Thank you, Michelle -- Michelle VanTieghem PhD student in Psychology Developmental Affective Neuroscience Lab Columbia University mrv2115(a)columbia.edu

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About the contrast matrix in LME toolbox
by Gong, Liang 02 Jan '18

02 Jan '18

Dear LME developer and expert, I am using LME recently, based on longitudinal brain structural data, but I have two confusions in using it. 1) I followed the tutorial at: https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels However, I don't actually understand the Contrast matrix design in this tool. In the example the contrast C matrix is a 3*14, is there any explain about this matrix design? For my study, I want to explore 3 treatment (2 therapy methods and 1 waitlist) effects on the brain structural, If I want to explore the main effect of treatment, how could I write the Contrast matrix, and whether I can explore each treatment effect on the brain structural? And how can explore the time*treatment effect contrast matrix? 2) For the mass-univariate analysis, the example C matrix is 3*17, and it will explore the group differences in the rate of change over time among the four groups, and if I get the four group difference maps, How can I know the difference between each two groups? If I need to do the another qdec file and do the following steps as mris_preproc and mri_surf2surf? Thank you very much! Best, Gallen

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Question about an error during recon-all process
by 박경일 01 Jan '18

01 Jan '18

Dear experts, I am sorry for asking again. I have some problems in running recon-all. Recon-all process was shut down with this error message ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string." I guess this is because of low resolution or small size of images. is it right? Thank you so much for you help in advance. FYI, log file is attached. Kyung

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mris_convert error in finding file: fread error
by João V. Dornas 01 Jan '18

01 Jan '18

Dear Friend, I am trying to run this command using the last version of Freesurfer: mris_convert --combinesurfs my-left-surface.mgz my-right-surface.mgz lh.rh.asc But I receive this error: No such file or directory freadFloat: fread failed The input data file are inside the root directory. I tried to put these files in several other folders but still it does not work. Do you have any ideas in how can I combine my left and right surfaces? thank you very much, best regards, João V. Dornas

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