Freesurfer March 2019

freesurfer@nmr.mgh.harvard.edu

114 participants
172 discussions

mris_fix_topology stuck running
by Soichi Hayashi 24 Mar '19

24 Mar '19

External Email - Use Caution Hello. I am trying to troubleshoot an issue where recon_all is not finishing after >24 hours. It's getting stuck when it tries to run the following command. $ mris_fix_topology -rusage ./output/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 output rh INFO: assuming .mgz format reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading input surface /home/hayashis/Downloads/output/surf/rh.qsphere.nofix... before topology correction, eno=-696 (nv=191488, nf=384368, ne=576552, g=349) reading brain volume from brain... reading wm segmentation from wm... using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 9 iterations marking ambiguous vertices... 133741 ambiguous faces found in tessellation segmenting defects... 63 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 16 into 0 -merging segment 23 into 0 -merging segment 48 into 0 -merging segment 32 into 22 -merging segment 49 into 47 -merging segment 54 into 51 57 defects to be corrected 0 vertices coincident Computing Initial Surface Statistics -face loglikelihood: -9.3123 (-4.6561) -vertex loglikelihood: -6.5427 (-3.2713) -normal dot loglikelihood: -3.5794 (-3.5794) -quad curv loglikelihood: -6.0564 (-3.0282) Total Loglikelihood : -25.4907 CORRECTING DEFECT 0 (vertices=65141, convex hull=8287, v0=517) --------------- After displaying the last line, the process seems to be stuck running with 100% cpu (single core) for >24 hours until our batch scheduler kills it. I think the issue is with my input data, but it looks clean and well ACPC aligned, and I don't know what's wrong with it. The input image dimensions are 182 x 218 x 182. Does anyone have any suggestion on how to troubleshoot this problem? Thank you, Soichi Hayashi Indiana University

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segmentHA_T1_long.sh: Command not found.
by Daniel Callow 23 Mar '19

23 Mar '19

External Email - Use Caution Hello, I am trying to use the segmentHA_T1_long.sh command on my longitudinal data. I have already run all the previous steps and have even successfully run longHippoSubfieldsT1.sh. However I want to use the segmentHA version to get my hippocampal segmentations. I assume the issue has something to do with the script not being in the FS6.0 version I downloaded? When looking at the literature for installation all I could find was info on installing runtime which I already have. Any help debugging the issue would be greatly appreciated. Below is the code I ran. #!/bin/tcsh setenv FREESURFER_HOME /Applications/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh foreach subj (MCIP0031 MCIP0032 MCIP0033 MCIP0035 MCIP0036 MCIP0041 MCIP0048 MCIP0052 MCIP0053 MCIP0054 MCIP0055 MCIP0058 MCIP0061) setenv SUBJECTS_DIR /Volumes/DANIEL/freesurfer_MCIP segmentHA_T1_long.sh base_${subj} end I get the following error. [hlhp-105:/Volumes/DANIEL/freesurfer_MCIP] administrator% ./recon-all_longitudinal_hippo.sh segmentHA_T1_long.sh: Command not found. segmentHA_T1_long.sh: Command not found. segmentHA_T1_long.sh: Command not found. segmentHA_T1_long.sh: Command not found. segmentHA_T1_long.sh: Command not found. segmentHA_T1_long.sh: Command not found. segmentHA_T1_long.sh: Command not found. segmentHA_T1_long.sh: Command not found. segmentHA_T1_long.sh: Command not found. segmentHA_T1_long.sh: Command not found. segmentHA_T1_long.sh: Command not found. segmentHA_T1_long.sh: Command not found. segmentHA_T1_long.sh: Command not found. *Best,* *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442(a)gmail.com <ddcc2442(a)gmail.com>* 443-254-6298

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DK atlas using method
by 杨国元 23 Mar '19

23 Mar '19

External Email - Use Caution Hello FreeSurfer Developers,I'm attempting to using DK atlas as label to mask my global brain index. I found the lh/rh.DKTatlas40.gcs in /freesurfer/average folder. But I don't know how to read this gcs files. Can I convert this file from gcs to gifit or annot version. Then using MRIread or nilabel to read it label files? Guoyuan Yang Center for MRI Research School of Physics Peking University Beijing, China Tel：18800172884 Email：yangguoyuan(a)pku.edu.cn

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help
by Van Ombergen Angelique 22 Mar '19

22 Mar '19

External Email - Use Caution Please unsubscribe me from the mailing list. Best wishes, Angelique > On 22 Mar 2019, at 15:16, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Re: Build stamp missing in current dev release (Hoopes, Andrew) > 2. VT images from pmod to freesurfer (Donatienne Van Weehaeghe) > 3. Re: recon-all error (Daniel Callow) > 4. Gray matter normalized intensity (Dorothy Sincasto) > 5. Re: Gray matter normalized intensity (Glasser, Matthew) > 6. Re: Gray matter normalized intensity (Bruce Fischl) > 7. help ( Lance ) > 8. recon-all could not read surface file error (Daniel Callow) > 9. Re: help (Bruce Fischl) > 10. Re: recon-all could not read surface file error (Bruce Fischl) > 11. Cerebellum within the pial surface (Matthieu VANHOUTTE) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 21 Mar 2019 16:43:13 +0000 > From: "Hoopes, Andrew" <AHOOPES(a)mgh.harvard.edu> > Subject: Re: [Freesurfer] Build stamp missing in current dev release > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <5698A83B-BBA5-4EB7-A96F-CC515378666C(a)mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > Hi Baxter, this is a bug. Thanks for pointing it out, I'll fix it now. > Andrew > > ?On 3/20/19, 2:43 PM, "freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of Baxter P. Rogers" <freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of baxter.rogers(a)vanderbilt.edu> wrote: > > External Email - Use Caution > > This one: > https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-linux… > The build-stamp.txt file currently contains "freesurfer" with no version > info. It used to be something like > "freesurfer-linux-centos7_x86_64-dev-20181114-4f05c76" which is > considerably more helpful :) > > Thanks much, > Baxter > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > ------------------------------ > > Message: 2 > Date: Thu, 21 Mar 2019 12:49:54 -0400 > From: Donatienne Van Weehaeghe <donatiennevanweehaeghe(a)gmail.com> > Subject: [Freesurfer] VT images from pmod to freesurfer > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: > <CA+W1dKxXS5FjNhYxerphn6RJcc5Jf0Sf_KjoBT6o74iEk4akQw(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > Dear, > > > I encountered a problem when going from pmod to freesurfer. > > > I made Vt images in pmod using the logan plot, then I used the following > commands to convert them to freesurfer space: > > > > #flirt -noresample -in > /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.nii > -ref > /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/T1-2mm_skullstripped.nii.gz > -applyxfm -init > /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/SUVR/SUV.lrrev_lin_T1.mat > -out > /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.fsl.nii > > #3dresample -master > /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/occipital.nii.gz > -inset > /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.nii > -prefix > /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.fsl.nii > > > > Then I did partial volume correction using this command: > > #mri_gtmpvc --i > /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.fsl.nii > --reg Vt.reg.lta --psf 5 --seg > /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/gtmseg.mgz > --default-seg-merge --auto-mask 5 0.01 --rbv --o > /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg > --no-rescale --threads 8 > > > > > > Then I did surface projection: > > #mri_vol2surf --mov > /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/rbv.nii.gz > --reg > /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/aux/rbv2anat.lta > --hemi lh --projfrac 0.5 --o > /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/lh.mgx.ctxgm.fsaverage.pvc.VT.sm00.proj-0.5.nii.gz > --cortex --trgsubject fsaverage > > #mri_vol2surf --mov > /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/rbv.nii.gz > --reg > /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/aux/rbv2anat.lta > --hemi rh --projfrac 0.5 --o > /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/rh.mgx.ctxgm.fsaverage.pvc.VT.sm00.proj-0.5.nii.gz > --cortex --trgsubject fsaverage > > > > followed by smoothing, concatening and then a group comparison. However > then I obtained the following error: > > ERROR: cannot find > /usr/local/freesurfer/stable6_0_0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm37/pos/th13/mc-z.csd > > > Kind regards > > Donatienne >

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Cerebellum within the pial surface
by Matthieu VANHOUTTE 22 Mar '19

22 Mar '19

External Email - Use Caution Dear FreeSurfer's experts, I encountered one problem following a recon-all: small part of the gray matter cerebellum has been taken as cortical gray matter within the occipital pial surface (see image attached below on right hemisphere). How could I correct for this defect? Best, Matthieu

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recon-all could not read surface file error
by Daniel Callow 22 Mar '19

22 Mar '19

External Email - Use Caution Hello, During recon-all I keep running into the same error for one of my subjects. #@# Make White Surf rh Fri Mar 22 00:57:11 EDT 2019 /Volumes/DANIEL/freesurfer/Rest.AES118/scripts \n mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs Rest.AES118 rh \n using white.preaparc as white matter name... only generating white matter surface using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /Volumes/DANIEL/freesurfer/Rest.AES118/mri/filled.mgz... reading volume /Volumes/DANIEL/freesurfer/Rest.AES118/mri/brain.finalsurfs.mgz... reading volume /Volumes/DANIEL/freesurfer/Rest.AES118/mri/../mri/aseg.presurf.mgz... reading volume /Volumes/DANIEL/freesurfer/Rest.AES118/mri/wm.mgz... 25155 bright wm thresholded. 1843 bright non-wm voxels segmented. reading original surface position from /Volumes/DANIEL/freesurfer/Rest.AES118/surf/rh.orig... mris_make_surfaces: could not read surface file /Volumes/DANIEL/freesurfer/Rest.AES118/surf/rh.orig ERROR: reading /Volumes/DANIEL/freesurfer/Rest.AES118/surf/rh.orig Read 0 bytes, expected 1 Argument list too long Darwin hlhp-105.umd.edu 16.7.0 Darwin Kernel Version 16.7.0: Wed Oct 10 20:06:00 PDT 2018; root:xnu-3789.73.24~1/RELEASE_X86_64 x86_64 recon-all -s Rest.AES118 exited with ERRORS at Fri Mar 22 00:57:16 EDT 2019 For more details, see the log file /Volumes/DANIEL/freesurfer/Rest.AES118/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Thanks for any help you can provide with debugging! *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442(a)gmail.com <ddcc2442(a)gmail.com>* 443-254-6298

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help
by Lance 22 Mar '19

22 Mar '19

External Email - Use Caution Hi there, I want to calculate the significance of grayvol between two groups, but the data i noticed in the 'lh.aparc.stats' file shew some problem.The pic below shows the grayvol of entorhinal of some subjects,but one of them appears to be 136,far more lower than the others, what's the problem? is it a normal systematic error or is there something wrong with my operation while calculating? The same situation is also found in CurvInd and FoldInd. Thank you for your help!

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recon-all error
by Daniel Callow 21 Mar '19

21 Mar '19

External Email - Use Caution Hello, I am trying to run recon-all on a dataset and am running into errors with one of my subjects. I get an error at the following point -------------------------------------------------------- Iteration 1 Tue Mar 19 10:11:08 EDT 2019 nu_correct -clobber ./tmp.mri_nu_correct.mni.40972/nu0.mnc ./tmp.mri_nu_correct.mni.40972/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.40972/0/ -iterations 1000 -distance 50 [administrator@hlhp-105.umd.edu:/Volumes/DANIEL/freesurfer/Ex.AES118/mri/] [2019-03-19 10:11:09] running: /Applications/freesurfer//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.40972/0/ ./tmp.mri_nu_correct.mni.40972/nu0.mnc ./tmp.mri_nu_correct.mni.40972/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done ncvarget: ncid 4; varid 6: Argument list too long miicv_get: MINC package entry point nu_estimate_np_and_em: crashed while running mincmath (termination status=768) nu_correct: crashed while running nu_estimate_np_and_em (termination status=768) ERROR: nu_correct Darwin hlhp-105.umd.edu 16.7.0 Darwin Kernel Version 16.7.0: Wed Oct 10 20:06:00 PDT 2018; root:xnu-3789.73.24~1/RELEASE_X86_64 x86_64 recon-all -s Ex.AES118 exited with ERRORS at Tue Mar 19 10:11:18 EDT 2019 For more details, see the log file /Volumes/DANIEL/freesurfer/Ex.AES118/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Any help you can provide for troubleshooting would be greatly appreciated. *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442(a)gmail.com <ddcc2442(a)gmail.com>* 443-254-6298

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Build stamp missing in current dev release
by Baxter P. Rogers 21 Mar '19

21 Mar '19

External Email - Use Caution This one: https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-linux… The build-stamp.txt file currently contains "freesurfer" with no version info. It used to be something like "freesurfer-linux-centos7_x86_64-dev-20181114-4f05c76" which is considerably more helpful :) Thanks much, Baxter

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Strange annotations in Freeview?
by Funk, Quentin 21 Mar '19

21 Mar '19

External Email - Use Caution See the link here: https://imgur.com/a/ACsG73A [https://i.imgur.com/1zEaYUT.jpg?fb]<https://imgur.com/a/ACsG73A> Annotations?<https://imgur.com/a/ACsG73A> imgur.com Post with 0 views. Annotations? There's not actually any voxel values in those regions. The labels go away if I load in other images and shuffle the order in the window, so at least easy to eliminate. But any ideas what's causing this? Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & World Report as the No. 1 hospital in Texas for patient care. Houston Methodist is nationally ranked in 8 specialties and is designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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Freesurfer March 2019