[Freesurfer] Hippocampal/Amygdala subfield segmentation error - Freesurfer devel-20180612
External Email - Use Caution Dear experts, I am running the hippocampal/amygdala segmentation on T1's preprocessed in -reconall in FS 5.3 using FS devel-20180612 using the command segmentHA_T1.sh bert [SUBJECTS_DIR] This has worked successfully for roughly 1000 participants but for one participant I keep getting the error below, despite several troubleshooting attempts. The error appears to be "Fitting mesh to synthetic image resulted in no deformation" - I have had a look at the hippocampus masks and they appear to be registered incorrectly, despite the grey matter volume output from -reconall having no errors. Do you have any idea what I can do to troubleshoot or fix this? Thanks in advance, Sally. Error Log: -- USER valentil HOST m3a007 PROCESSID 29440 PROCESSOR x86_64 OS Linux Linux m3a007 3.10.0-514.26.1.el7.x86_64 #1 SMP Thu Jun 29 16:05:25 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux -- # #@# Hippocampal Subfields processing (T1) left Tue Sep 25 10:18:56 AEST 2018 -- Setting up environment variables --- LD_LIBRARY_PATH is .:/usr/local/freesurfer/devel-20180612/MCRv84//runtime/glnxa64:/usr/local/freesurfer/devel-20180612/MCRv84//bin/glnxa64:/usr/local/freesurfer/devel-20180612/MCRv84//sys/os/glnxa64:/usr/local/freesurfer/devel-20180612/lib/tcltktixblt:/usr/local/freesurfer/devel-20180612/lib/qt/lib:/usr/local/freesurfer/devel-20180612/lib/petsc/lib:/usr/local/freesurfer/devel-20180612/lib/KWWidgets/lib/KWWidgets:/usr/local/freesurfer/devel-20180612/lib/cuda/lib64:/usr/local/freesurfer/devel-20180612/lib/cuda/lib:/usr/local/freesurfer/devel-20180612/lib/bem:/usr/local/freesurfer/devel-20180612/lib:/usr/local/freesurfer/devel-20180612/lib/vtk/lib/vtk-5.6:/usr/local/fsl/5.0.11/fsl/lib:/usr/local/libjpeg-turbo/1.4.2/lib64:/usr/local/cuda/7.5/extras/CUPTI/lib64:/usr/local/cuda/7.5/lib64:/usr/local/cuda/7.5/lib:/usr/local/cuda/7.5/lib64/stubs:/opt/munge-0.5.11/lib:/opt/slurm-17.11.4/lib:/opt/slurm-17.11.4/lib/slurm:/usr/local/tigervnc/1.8.0/lib64:/usr/local/tigervnc/1.8.0/lib:/opt/munge-0.5.11/lib:/opt/slurm-17.11.4/lib:/opt/slurm-17.11.4/lib/slurm::/usr/local/freesurfer/devel-20180612/MCRv84//sys/opengl/lib/glnxa64:/usr/local/freesurfer/devel-20180612/lib/tcltktixblt:/usr/local/freesurfer/devel-20180612/lib/qt/lib:/usr/local/freesurfer/devel-20180612/lib/petsc/lib:/usr/local/freesurfer/devel-20180612/lib/KWWidgets/lib/KWWidgets:/usr/local/freesurfer/devel-20180612/lib/cuda/lib64:/usr/local/freesurfer/devel-20180612/lib/cuda/lib:/usr/local/freesurfer/devel-20180612/lib/bem:/usr/local/freesurfer/devel-20180612/lib:/usr/local/freesurfer/devel-20180612/lib/vtk/lib/vtk-5.6:/usr/local/fsl/5.0.11/fsl/lib:/usr/local/libjpeg-turbo/1.4.2/lib64:/usr/local/cuda/7.5/extras/CUPTI/lib64:/usr/local/cuda/7.5/lib64:/usr/local/cuda/7.5/lib:/usr/local/cuda/7.5/lib64/stubs:/opt/munge-0.5.11/lib:/opt/slurm-17.11.4/lib:/opt/slurm-17.11.4/lib/slurm:/usr/local/tigervnc/1.8.0/lib64:/usr/local/tigervnc/1.8.0/lib:/opt/munge-0.5.11/lib:/opt/slurm-17.11.4/lib:/opt/slurm-17.11.4/lib/slurm: Registering imageDump.mgz to hippocampal mask from ASEG $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ --mov: Using imageDump.mgz as movable/source volume. --dst: Using /home/valentil/kg98/Valentina/ENIGMA_sex_differences/Scripts/rerun_reconall/NIAAA_MRI00032_1-out/tmp/hippoSF_T1_v21_left//hippoAmygBinaryMask_autoCropped.mgz as target volume. --lta: Output transform as trash.lta . --mapmovhdr: Will save header adjusted movable as imageDump_coregistered.mgz ! --sat: Using saturation 50 in M-estimator! reading source 'imageDump.mgz'... reading target '/home/valentil/kg98/Valentina/ENIGMA_sex_differences/Scripts/rerun_reconall/NIAAA_MRI00032_1-out/tmp/hippoSF_T1_v21_left//hippoAmygBinaryMask_autoCropped.mgz'... Registration::setSourceAndTarget(MRI s, MRI t, keeptype = TRUE ) Type Source : 0 Type Target : 3 ensure both FLOAT (3) Reordering axes in mov to better fit dst... ( -1 3 -2 ) MRIreorder() --- xdim=-1 ydim=3 zdim=-2 src 131 241 99, 0.25 0.25 0.25 dst 131 99 241, 0.25 0.25 0.25 Determinant after swap : 0.015625 Mov: (0.25, 0.25, 0.25)mm and dim (131, 99, 241) Dst: (1, 1, 1)mm and dim (36, 31, 52) Asserting both images: 1mm isotropic - reslicing Mov ... -- changing data type from 0 to 3 (noscale = 0)... -- Original : (0.25, 0.25, 0.25)mm and (131, 99, 241) voxels. -- Resampled: (1, 1, 1)mm and (36, 31, 61) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3 - reslicing Dst ... -- Original : (1, 1, 1)mm and (36, 31, 52) voxels. -- Resampled: (1, 1, 1)mm and (36, 31, 61) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3 Registration::computeMultiresRegistration - computing centroids - computing initial transform
Re: [Freesurfer] recon-all -make all error
Hi Vasudev you don't need the whole path for the -s switch, just the subject ID (in this case it looks like HC13) cheers Bruce On Mon, 8 Oct 2018, Dev vasu wrote: External Email - Use Caution Dear all, I am encountering following error whenever i re-rerun my recon-all on cluster,,although i have downloaded new development version of recon-all.makefile, this error persists,kindly let me know what i am doing wrong recon-all -make all -s /home/hpc/u7x32/ru37veh2/emilie_struc/HC13 -sd /home/hpc/u7x32/ru37veh2/emilie_struc/new_recon -- recon-all -make all -s /home/hpc/u7x32/ru37veh2/emilie_struc/HC13 -sd /home/hpc/u7x32/ru37veh2/emilie_struc/new_recon /home/hpc/u7x32/ru37veh2/freesurfer_dev/bin/recon-all.makefile:195: recipe for target '/home/hpc/u7x32/ru37veh2/emilie_struc/new_recon/HC13/surf/lh.white.preaparc' failed recon-all -make all -s /home/hpc/u7x32/ru37veh2/emilie_struc/HC13 -sd /home/hpc/u7x32/ru37veh2/emilie_struc/new_recon make: *** [/home/hpc/u7x32/ru37veh2/emilie_struc/new_recon/HC13/surf/lh.white.preaparc] Error 1 Thanks Vasudev ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] recon-all -make all error
External Email - Use Caution Dear all, I am encountering following error whenever i re-rerun my recon-all on cluster,,although i have downloaded new development version of recon-all.makefile, this error persists,kindly let me know what i am doing wrong recon-all -make all -s /home/hpc/u7x32/ru37veh2/emilie_struc/HC13 -sd /home/hpc/u7x32/ru37veh2/emilie_struc/new_recon -- recon-all -make all -s /home/hpc/u7x32/ru37veh2/emilie_struc/HC13 -sd /home/hpc/u7x32/ru37veh2/emilie_struc/new_recon /home/hpc/u7x32/ru37veh2/freesurfer_dev/bin/recon-all.makefile:195: recipe for target '/home/hpc/u7x32/ru37veh2/emilie_struc/new_recon/HC13/surf/lh.white.preaparc' failed recon-all -make all -s /home/hpc/u7x32/ru37veh2/emilie_struc/HC13 -sd /home/hpc/u7x32/ru37veh2/emilie_struc/new_reconmake: *** [/home/hpc/u7x32/ru37veh2/emilie_struc/new_recon/HC13/surf/lh.white.preaparc] Error 1 Thanks Vasudev ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] recon-all terminated in middle : continuing an analysis of an existing subject
Hi Vasudev there is a patch to recon-all that fixes the -make all functionality, that should start wherever you left off. Andrew: can you post the location of the makefile patches? thanks Bruce On Sun, 7 Oct 2018, Dev vasu wrote: External Email - Use Caution Dear all, I was trying to run recon-all, the pipeline terminated in middle now i would like to know if there is any way i can restart it from the point where it was terminated?. Thanks Vasudev ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] masking cortical thickness
External Email - Use Caution Dear Douglos, I did not understand how to use mri_label2label with the mask option(there is srcmask options not mask alone !). I extract my labels and as you explained I wanted to create i.e. binary mask of rh.fusiform.label with mri_label2label : mri_label2label --srcsubject case1 --srclabel rh.fusiform.label --trgsubject case1 --trglabel outputlabel.mgh --regmethod surface --hemi rh but it creats another label file not binary with mgh format I did not get how can I create mybinary.mgh mask in order to use in third command "mri_binarize --i lh.thickness --mask youmask.mgh --o lh.thickness.masked.mgh" would you please help me with this, it would be a great favor. Best regards, Nazanin On Mon, Jul 30, 2018 at 10:59 PM Douglas N. Greve wrote: > Yes, that should work. You can create a mask by breaking the annotation > into labels (mri_annotation2label), then converting the label into a > binary mask (mri_label2label with --mask option), then mri_binarize --i > lh.thickness --mask youmask.mgh --o lh.thickness.masked.mgh > > > On 07/30/2018 01:47 AM, N Saf wrote: > > > > External Email - Use Caution > > > > Dear Freesurfer Experts, > > > > I wonder how can I show the cortical thickness surface on just one > > region of my interest in Freeview. assume that I want to see the > > thickness surface of one of the regions in DKTatlas. does it work if I > > make a binary mask of that specific region on aparcDKTatlas.annot and > > then multiply it to the ?h.thickness surface ?? any help will be > > appreciated. > > > > Best Regards, > > Nazanin > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] nu_correct disk i/o issues
External Email - Use Caution
Michael, I can't thank you enough.
Knowing that it writes to /tmp made all the difference.
In my case I mounted an external directory on /tmp instead of the
sessiondir approach, but it now runs fine.
Jasper
On Fri, 5 Oct 2018 at 23:47, Michael Krause
wrote:
> Dear *,
>
> we also run Freesurfer on a cluster and are starting to use singularity, so
> naturally I'm curious about this issue.
>
> I was able to reproduce the error with a clean singularity run (-c -e).
> Then, I rebuilt a container to start nu_correct with "strace -f -e
> open,write" and I believe I found the problem:
>
> [pid 35994] open("/subs/testsub/mri/tmp.mri_nu_correct.mni.35410/nu1.imp",
> O_RDONLY) = 3
> [pid 35994] open("/tmp/minc-qKdMD4", O_RDWR|O_CREAT|O_EXCL, 0600) = 5
> [pid 35994] open("/tmp/minc-qKdMD4", O_RDWR|O_CREAT|O_TRUNC, 0666) = 5
> [pid 35994] write(5, "\0\0\0\0\0\0\0\0", 8) = 8
> [pid 35994] write(5,
> "CDF\1\0\0\0\0\0\0\0\n\0\0\0\3\0\0\0\6xspace\0\0\0\0\1\0"..., 8192) = 8192
> [pid 35994] write(5,
>
> "|\360\0\0|\360\0\0|\360\0\0|\360\0\0|\360\0\0|\360\0\0|\360\0\0|\360\0\0"...,
> 8192) = 8192
> [...]
> [pid 35994] write(5,
>
> "|\360\0\0|\360\0\0|\360\0\0|\360\0\0|\360\0\0|\360\0\0|\360\0\0|\360\0\0"...,
> 8192) = -1 ENOSPC (No space left on device)
> [pid 35994] write(2, "ncendef: ", 9ncendef: )= 9
> [pid 35994] write(2, "ncid 5", 6ncid 5) = 6
> [pid 35994] write(2, ": No space left on device", 25: No space left on
> device) = 25
>
>
> So there are two issues here I think:
>
> 1) nu_correct is saving things to /tmp when it could just use ./tmp
> 2) the singularity default for "sessiondir max size" is 16MB, which
> includes
> /tmp, is too small for the minc-tmp files
>
> I changed the value from 16 to 1024 and it passed the nu_correct step.
>
> cheers,
> Michael
>
> On 10/5/18 5:57 PM, Greve, Douglas N.,Ph.D. wrote:
> > Not that I know of, but this is not a native FS script, it comes from the
> > MNI, so it could be doing something we don't understand. Can you do an
> > experiment for us? Can you run it outside of the container using reprozip
> > (or something equivalent) to see all the files it touches?
> >
> > On 10/5/18 5:31 AM, Jasper van den Bosch wrote:
> >>
> >> External Email - Use Caution
> >>
> >> We are trying to run recon_all inside an fmriprep singularity container,
> >> but are running into an issue with nu_correct. It says it cannot write
> to
> >> disk, however there is plenty of space on the tmpdir and output dir.
> Does
> >> this script try to write to any other locations? Because this would fail
> >> inside the container, where each writable location has to be 'mounted'.
> >>
> >> Error message:
> >>
> >> ncendef: ncid 5: No space left on device
> >> Error outputting volume: possibly disk full?
> >> nu_evaluate: crashed while running evaluate_field (termination
> status=139)
> >> nu_correct: crashed while running nu_evaluate (termination status=65280)
> >> ERROR: nu_correct
> >>
> >> Command ran:
> >>
> >> nu_correct -clobber ./tmp.mri_nu_correct.mni.1121/nu0.mnc
> >> ./tmp.mri_nu_correct.mni.1121/nu1.mnc -tmpdir
> >> ./tmp.mri_nu_correct.mni.1121/0/ -iterations 1000 -distance 50
> >> [xxx@.cluster:/data/BIDS/derivatives/freesurfer/sub-1/mri/]
> >> [2018-10-04 14:59:29] running:
> >> /opt/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.1121/0/ ./tmp.mri_nu_correct.mni.1121/nu0.mnc
> >> ./tmp.mri_nu_correct.mni.1121/nu1.imp
> >>
> >>
> >> this issue at the fmriprep
> >> repo: https://github.com/poldracklab/fmriprep/issues/1308
> >> possibly related: https://github.com/freesurfer/freesurfer/issues/462
> >>
> >> Many thanks for any advice,
> >> Jasper van den Bosch
> >>
> >>
> >>
> >> ___
> >> Freesurfer mailing list
> >> Freesurfer@nmr.mgh.harvard.edu
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
>
> External Email - Use Caution
>
> ___
> Freesurfer mailing list
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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[Freesurfer] recon-all terminated in middle : continuing an analysis of an existing subject
External Email - Use Caution Dear all, I was trying to run recon-all, the pipeline terminated in middle now i would like to know if there is any way i can restart it from the point where it was terminated?. Thanks Vasudev ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
