Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30070 discussions

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/

1 0

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

2 4

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

2 2

Brainhack Donostia 2018
by Sanjeev Nara 19 Apr '18

19 Apr '18

External Email - Use Caution Hello Everyone The Basque Center on Cognition Brain and Language (BCBL) will host the first edition of the BrainhackDonostia2018. The event aims at bringing together students and scientists at all levels of their careers to enjoy science and a couple of Cider glasses together. This year's edition will focus on Neuroimaging techniques, in particular fMRI (functional magnetic resonance) MEG (magnetoencephalography, EEG (electroencephalogaphy) and fNIRS (functional near infrared spectroscopy). Through a combination of lectures and tutorials, participants will be introduced on these techniques, and how they can be used to study the mind and brain. For those that have more experience, and have an interest in three days of project development, there is also the possibility to propose and develop a project related to neuroimaging and/or electrophysiology recruiting participants on site. The event is open to people from different disciplines and backgrounds, with a genuine interest in neuroimaging methods, psychology, neuroscience, and more generally interdisciplinary research. Feel free to explore our website for further information. http://www.bcbl.eu/events/BrainhackDonostia2018/en/ The event will be hosted on May 2nd-4th 2018 in the Basque Center on Cognition Brain and Language in San Sebastian, Spain. The cost is 10€ for Master Students, 15€ for PhD and PostDocs, 40€ for Seniors and "Industrials" + optional 13€ for the T-shirt. Registration to the event is needed and can be done on the website, until the 25th of April. A certificate of attendance will be provided to participants. If you have more questions, we remain at your disposal at the address info.bhg-donostia(a)bcbl.eu We look forward to see you in May!

1 0

QDEC Interaction of Two Covariates
by David S Lee 19 Apr '18

19 Apr '18

External Email - Use Caution Hi FreeSurfer Experts, I want to test the relationship between cortical thickness and two continuous covariates (interaction) while controlling for one categorical variable. In QDEC, I can only choose one covariate, so I created a new variable that is a dot product (covariate1*covariate2) of the two to represent interaction. After analyzing, when I look at the data points at a single voxel, there is no visual indication of interaction. There also is no fitted line. Am I utilizing QDEC correctly? Thank you for your help! -- David S. Lee Associate Research Specialist Center for Healthy Minds University of Wisconsin - Madison (608) 890-1115

2 1

Recon-all with custom atlas
by Ting Li 19 Apr '18

19 Apr '18

External Email - Use Caution Hi Freesurfer Experts, We want to run recon-all with a custom atlas which is generated from ANTs multivariate template construction. What is the right procedure to run recon-all? Run recon-all to my atlas itself first and them use this output as a template or I use the custom template directly. I looked up your email database to search related topic and got lost. I have sent another email to your group and no response received. Please help me. Thanks for you time. I look forward to hearing from you. Best, Ting

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