Freesurfer April 2018

freesurfer@nmr.mgh.harvard.edu

118 participants
177 discussions

mris_convert Segmentation fault.
by Xiuyi Wang 24 Apr '18

24 Apr '18

External Email - Use Caution Hi, I am planning to convert an ASCII file to a gifti file using mris_convert. I am using FreeSurfer 5.3 on Linux 9 stretch. The ASCII file includes the vertex id , its MNI305 coordinates and p value. Vertex id is 0-based, from 0 to 20483. I used fsaverage5 as the template and extracted the coordinates of each vertex on that surface using the following commands. SW = SurfStatReadSurf({[template_path 'fsaverage5/surf/lh.white'],[template_path 'fsaverage5/surf/rh.white']}); coordis = SurfStatInd2Coord(vertex_id, SW) Then I typed mris_convert unthreshold_file_SW.asc lh_unthreshold_SW.gii # because I learnt that generally surface files starts with a hemisphere specifier. or mris_convert unthreshold_file_SW.asc unthreshold_SW.gii The error message is ERROR: MRISalloc: nfaces=-36 < 0. I guess one possible reason is the first coordinate of the first index is negative (-36). So I generated a new file, replacing all the negative x coordinates with its absolute value - unthreshold_file_SW_abs.asc and then typed: mris_convert unthreshold_file_SW_abs.asc lh_unthreshold_SW_abs.gii This time the error message is Segmentation fault. I have attached the ascii file. Could you please give me any clue how to solve this problem? I also tried this command and it works well, suggesting I can use mris_convert smoothly. mris_convert -v lh.white lh.white.neighbors.asc # This command works well. I generated lh.white.neighbors.asc, suggesting my preparation work is good. Many thanks in advance, Xiuyi Wang

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Surface projection w/ FLIRT Coreg
by Lauren Beard 23 Apr '18

23 Apr '18

External Email - Use Caution Hi FreeSurfer Team, We would like to project functional volumes to an FS average surface in a number of large datasets (several thousand scans). We have already calculated and conducted detailed QA on co-registrations from the functional to structural image using BBR in FLIRT, and would like to use these transforms (in .mat format) rather than re-calculating them. We have already run FS on all images as well (using version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0). Is there a way to use the pre-computed co-registration in the .mat file to project the functional data to the surface without re-computing a new co-registration with bbregister? Thanks for your help! Lauren Beard Brain Behavior Lab

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curv to label
by Christiane Jockwitz 22 Apr '18

22 Apr '18

External Email - Use Caution Dear FreeSurfer experts, I would like to extract some surface values from the Cognitive Ontology maps from Yeo and collegues (2015). These maps are available in terms of curvature files. However, I would need them in terms of labels or annotations. Is there either the possibility to download these maps as label files, or otherwise is there a possibility to convert them into label files? Thank you very much in advance. Best Christiane -- Dr. rer. medic. Christiane Jockwitz Arbeitsgruppe Konnektivität Institut für Neurowissenschaften und Medizin INM-1 Forschungszentrum Jülich Tel: 02461-61-85040 Email: c.jockwitz(a)fz-juelich.de Arbeitsgruppe Konnektivität im menschlichen Gehirn C. und O. Vogt Institut für Hirnforschung Heinrich-Heine-Universität Düsseldorf Klinik für Psychiatrie, Psychotherapie und Psychosomatik RWTH Aachen ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

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ERROR: nu_correct
by Dusan Hirjak 22 Apr '18

22 Apr '18

External Email - Use Caution Dear Freesurfer Experts, I am having trouble with recon-all (Freesurfer 6.0). After running a shell script on my subjects I get the following error: Iteration 1 Fri Apr 20 13:22:37 CEST 2018 nu_correct -clobber ./tmp.mri_nu_correct.mni.14731/nu0.mnc ./tmp.mri_nu_correct.mni.14731/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.14731/0/ -iterations 1000 -distance 50 Cannot read input file: ./tmp.mri_nu_correct.mni.14731/nu0.mnc [XXX.XXX@XXX-pc26:/xxxx/projects/xxxx/main/user/xxxx/subject_c0_200/mri/] [2018-04-20 13:22:37] running: /ropt/freesurfer_6.0.0/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.14731/0/ ./tmp.mri_nu_correct.mni.14731/nu0.mnc ./tmp.mri_nu_correct.mni.14731/nu1.imp nu_correct: crashed while running nu_estimate_np_and_em (termination status=512) ERROR: nu_correct Linux xxx-pc26 4.9.0-4-amd64 #1 SMP Debian 4.9.65-3 (2017-12-03) x86_64 GNU/Linux recon-all -s subject_c0_200 exited with ERRORS at Fri Apr 20 13:22:37 CEST 2018 Any suggestions what I can do are welcome! Best regards Dusan

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Re: [Freesurfer] using T2 for hippo subfields
by Iglesias Gonzalez, Eugenio 20 Apr '18

20 Apr '18

Hi Jim, In the end it’s an empirical question, but my gut feeling is that the T1 with hi-res flag will be best. Cheers, /E -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Alexopoulos, Dimitrios" <dimitriosalexopoulos(a)wustl.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Friday, 23 March 2018 at 16:00 To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] using T2 for hippo subfields Hi. We are acquiring sequences on a pediatric cohort that include a T1-mprage (0.8mm isotropic) and a T2-space (1mm isotropic), and I’d like to run the hippocampal subfields module on the subjects using FS 6.0. Is it recommended/useful to run the multispectral segmentation mode with the additional lower resolution T2 sequence? I read that you really only benefit if the T2 is of similar or better resolution than the T1. If that’s the case, would it be best to just run with the single T1 but with the hi-res flag in the recon-all command? Thanks. Jim ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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SLURM - speed processing
by Alexandre Obert 20 Apr '18

20 Apr '18

External Email - Use Caution Hi Lea, Thanks for the tips! I think I did something similar for a previous test without hipo segmentation (took nearly 3 to 4h). I will check the way I've got to set the number of cpu per tasks, just in case. Thanks Alex > Message: 20 > Date: Fri, 20 Apr 2018 09:19:12 +0000 > From: "Backhausen, Lea" <Lea.Backhausen(a)uniklinikum-dresden.de> > Subject: Re: [Freesurfer] SLURM - speed processing (Alexandre Obert) > To: "'freesurfer(a)nmr.mgh.harvard.edu'" > <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <1D0E7A9ED60D3E4399550C3A60C0BADC394606B6(a)G06EDBN1.med.tu-dr > esden.de> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > Hi Alex, > > I am also running FreeSurfer 6.0.0 on SLURM and recently did some tests on > how to parallelize it, how much ressources to ask for? This is what I > learned: > > 1) FreeSurfer 6.0.0 is able to use OpenMP parallelization (I guess > for the commands mri_em_register, mri_ca_register and mri_ca label used in > the steps Skull Stripping, EM registration, CA reg and Subcortical > registration). > 2) From Version 6.0.0 FreeSurfer is also able to process the two > hemispheres in parallel instead of sequentially (steps 16 ? 30). > > Taking advantage of these changes reduces processing time dramatically. If > I use 4 CPU per task on SLURM instead of 1 the processing time drops form > around 8 hours to around 4 or 4 ? hours. Increasing the CPU per task did > not improve processing time much though, so to save a bit CPU time now use > 4 CPU regularly. > I don?t know if you have to submit your jobs exactly the same way but a > typical job file for me looks like this: > > ------------------------------------------------------------ > ------------------------ > #!/bin/bash > #SBATCH --time=10:00:00 > #SBATCH --output=/your_working_directory/job-%j.out > #SBATCH --error=/your_working_directory/job-%j.err > #SBATCH --nodes=1 > #SBATCH --ntasks=1 > #SBATCH --tasks-per-node=1 > #SBATCH --cpus-per-task=4 > #SBATCH --partition=haswell > #SBATCH --mem-per-cpu=2500 > #SBATCH -A your_project_name > > module load modenv/eb > module load FreeSurfer > source $FREESURFER_HOME/SetUpFreeSurfer.sh > > export SUBJECTS_DIR=/your_subjects_directory > > recon-all -s your_subject_ID -all -parallel -openmp 4 > ------------------------------------------------------------ > -------------------------- > > > Of course you can just add the ?hippocampal-subfields-T1 tag flag your > command. > I found that asking for 2500 MB works just fine for 4CPU per task (as the > 2500 is multiplied times 4 in this case). The maximum RAM was about 7000 KB > for my jobs. > Just make sure you add the? -parallel -openmp 4? flag to your command line > AND ?#SBATCH --cpus-per-task=4? to your job file, otherwise the > parallelization will not work. > > > Hope this helps! Get back to me if you have any more questions! > > Best, > Lea > > ------------------------------ > Lea Backhausen > Research Assistant > > Department of Child and Adolescent Psychiatry, Faculty of Medicine of the > TU Dresden, Germany > http://www.uniklinikum-dresden.de > > > ------------------------------ > > Message: 5 > Date: Thu, 19 Apr 2018 17:05:46 +0200 > From: Alexandre Obert <obert.alexandre(a)gmail.com> > Subject: [Freesurfer] SLURM - speed processing > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: > <CAGTEUh_XypWu4h+4ban62BfH8idf96HEquUL+OMMaWT_GEk4Cw@mail. > gmail.com> > Content-Type: text/plain; charset="utf-8" > > 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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8th Annual Brain-Art Competition @ OHBM open for submissions!
by Daniel Margulies 20 Apr '18

20 Apr '18

External Email - Use Caution In order to recognize the beauty and creativity of artistic renderings emerging from the neuroimaging community, we are launching the eighth annual Brain-Art Competition. Countless hours are devoted to the creation of informative visualizations for communicating neuroscientific findings. The Brain-Art Competition aims to recognize this often unappreciated aspect of the publication process, and highlight the artistic creativity of our community. We are inviting researchers to submit their favorite unpublished works for entry. Both team and single-person entries are welcomed. The competition will have six award categories: 1. Best Representation of the Human Connectome 2. Best Abstract Brain Illustration 3. Best Humorous Brain Illustration 4. Best Video Illustration of the Brain 5. Updating classics 6. Special Topic: Comparative neuroanatomy The last two categories are new additions for the 2018 competition: "Updating classics" invites submissions that bring fresh ideas, data, and visualization techniques to famous illustrations from the neuroscience canon. With the increasing availability of non-human brain data, the special topic in "comparative neuroanatomy" invites submissions that address the visualization challenge of translating findings across species. How can cross-species information be more effectively be presented? Submission Deadline: 11:59PM CDT, Wednesday, June 6th, 2018 Award Notification: Monday, June 18th, 2018 For more information, check out the competition details: http://www.neurobureau.org/brainart/

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Re: [Freesurfer] SLURM - speed processing (Alexandre Obert)
by Backhausen, Lea 20 Apr '18

20 Apr '18

External Email - Use Caution Hi Alex, I am also running FreeSurfer 6.0.0 on SLURM and recently did some tests on how to parallelize it, how much ressources to ask for… This is what I learned: 1) FreeSurfer 6.0.0 is able to use OpenMP parallelization (I guess for the commands mri_em_register, mri_ca_register and mri_ca label used in the steps Skull Stripping, EM registration, CA reg and Subcortical registration). 2) From Version 6.0.0 FreeSurfer is also able to process the two hemispheres in parallel instead of sequentially (steps 16 – 30). Taking advantage of these changes reduces processing time dramatically. If I use 4 CPU per task on SLURM instead of 1 the processing time drops form around 8 hours to around 4 or 4 ½ hours. Increasing the CPU per task did not improve processing time much though, so to save a bit CPU time now use 4 CPU regularly. I don’t know if you have to submit your jobs exactly the same way but a typical job file for me looks like this: ------------------------------------------------------------------------------------ #!/bin/bash #SBATCH --time=10:00:00 #SBATCH --output=/your_working_directory/job-%j.out #SBATCH --error=/your_working_directory/job-%j.err #SBATCH --nodes=1 #SBATCH --ntasks=1 #SBATCH --tasks-per-node=1 #SBATCH --cpus-per-task=4 #SBATCH --partition=haswell #SBATCH --mem-per-cpu=2500 #SBATCH -A your_project_name module load modenv/eb module load FreeSurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh export SUBJECTS_DIR=/your_subjects_directory recon-all -s your_subject_ID -all -parallel -openmp 4 -------------------------------------------------------------------------------------- Of course you can just add the –hippocampal-subfields-T1 tag flag your command. I found that asking for 2500 MB works just fine for 4CPU per task (as the 2500 is multiplied times 4 in this case). The maximum RAM was about 7000 KB for my jobs. Just make sure you add the” -parallel -openmp 4” flag to your command line AND “#SBATCH --cpus-per-task=4” to your job file, otherwise the parallelization will not work. Hope this helps! Get back to me if you have any more questions! Best, Lea ------------------------------ Lea Backhausen Research Assistant Department of Child and Adolescent Psychiatry, Faculty of Medicine of the TU Dresden, Germany http://www.uniklinikum-dresden.de ------------------------------ Message: 5 Date: Thu, 19 Apr 2018 17:05:46 +0200 From: Alexandre Obert <obert.alexandre(a)gmail.com> Subject: [Freesurfer] SLURM - speed processing To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <CAGTEUh_XypWu4h+4ban62BfH8idf96HEquUL+OMMaWT_GEk4Cw(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" 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

1 0

Freesurfer and crypt
by Bennet Fauber 19 Apr '18

19 Apr '18

I have a couple of users here who are reporting that on machines with FIPS enabled, which in turn disables certain cryptographic functions, FreeSurfer core dumps with a call to the crypt() function, which FIPS disables. Someone speculated based on output from strace that this is FreeSurfer possibly attempting to validate its license. Is this a known problem? Is there a solution? We have a university compliance office and possibly similar people from our local VA who are insisting that FIPS be enabled. If you need more information, please let me know and I will try to obtain it for you. Thanks, -- bennet

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mni152reg yields bad registration
by Zimmerman, Jared 19 Apr '18

19 Apr '18

Hi All, I’m trying to register the aparc+aseg volumes from subject T1 space to MNI152 space and running into problems. I’ve taken the following steps 1. mri152reg –s Subj241 2. mri_vol2vol --targ $FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz --mov $SUBJECTS_DIR/Subj241/mri/aparc+aseg.mgz --o Subj241_aparc+aseg_mni2mm.nii.gz --reg $SUBJECTS_DIR/Subj241/mri/transforms/reg.mni152.2mm.dat This yields an image that is rotated and shrunken relative to the MNI152_T1_2mm template as shown in the attached image. I’m wondering if this is the right way to do what I’d like to do. The reg.mni152.2mm.dat file is only a linear transform, but I’d like to apply a non-linear transformation to the subject aparc+aseg to get it well matched to the MNI152 template space. Some of my subjects have atypical head shapes and I really think a non-linear warp will be necessary to achieve a good fit. I’ve run the MNI152 1mm template through recon-all so I have that as a reference. Is there a way to map volumes from one subject space to another via fsaverage or sphere sort of like mri_label2label does for labels? Alternatively, I could just calculate the appropriate T1 to MNI warps with FNIRT or ANTs and apply those to the aparc+aseg, but I figured it would be possible to do with FreeSurfer without calculating any new transforms. Thanks, Jared

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Freesurfer April 2018