[Freesurfer] optseq2 downloading pb
Dear all, I would like to download optseq2 from https://surfer.nmr.mgh.harvard.edu/optseq/ it remains unavailable for several days. Is there any other way to obtain it ? Regards, Alexandre Obert -- Alexandre OBERT Doctorant en Psychologie Cognitive Université de Reims Champagne-Ardenne Laboratoire C2S : Cognition, Santé, Socialisation (EA6291) 57, rue Pierre Taittinger - 51096 Reims Cedex - France http://www.univ-reims.fr/C2S ___ 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] optseq help
Dear all, I would like to optimize my design by inserting null-events between my trials (in order to better catch the HRF shape with reasonable duration of the experiment) using optseq. I'm not very familiar with this useful tool and I wonder if you could check my setup? Here my design : I've got 12 trials per run (2 runs per participants). Each of my trial is 34s long and is composed as follow : -An instruction reminder screen of 4s -A video stimulus of 12s to 20s. This screen will be my "stimulus of interest". It's followed by a fixation cross in such a way that their cumulated durations will not exceed 20s -A question about the video followed by a fixation cross in such a way that their cumulated durations will not exceed 20s. -A jitter (a fixation cross), determined by optseq It's a 2 (A1; A2) x2 (B1; B2) design and I'm interested in these following contrasts: A1 vs A2 B1 vs B2 (The interaction contrast will have an exploratory value in my analysis.) In order to determine the jitters and the order of the stimuli, I set the optseq as follow: --ntp 210\ --tr 2\ --psdwin 0 40 1\ --ev evA1B1 34 3\ --ev evA1B2 34 3\ --ev evA2B1 34 3\ --ev evA2B2 34 3\ --ecv 1 1 -1 -1\ --evc 1 -1 1 -1\ --nsearch 1\ --nkeep 3 I'm not very confident with my setup and if it's correct? I also wonder if I correctly set the ev durations and the psdwin. The stimulus of interest is the video but I set the ev using the trial duration in order to obtain ITI jitters and psdwin to the trial duration. This results in a poor efficiency and I wonder if it's possible to better optimized this design... Any help will be appreciated... Regards, Alexandre ___ 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] freesurfer errors-windows bash
Dear all, I'm would like to run a hippocampal segmentation on my data. However, I'm a beginner with freesurfer thus, I juste try to run the commands with subject training data. I first try to run commands following the recent development ( https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala). However, terminal says that the command segmentHA.sh doesn't exist. I guess that it could be linked to the fact that I used bash in Windows but I can't find a way to check this..; Any idea ? Regards, Alexandre ___ 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.
Re: [Freesurfer] freesurfer errors-windows bash
Dear Eugenio, The freesurfer version commands tells me that I run the freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c version. Before using segmentHA_T1.sh command, I run the recon-all -all -s bert one and it worked. Of course, recon-all also worked, telling be how to use it properly. Regards, Alexandre 2017-10-26 17:08 GMT+02:00 Alexandre Obert <obert.alexan...@gmail.com>: > Dear all, > > I'm would like to run a hippocampal segmentation on my data. > However, I'm a beginner with freesurfer thus, I juste try to run the > commands with subject training data. > I first try to run commands following the recent development ( > https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiO > fAmygdala). However, terminal says that the command segmentHA.sh doesn't > exist. > > I guess that it could be linked to the fact that I used bash in Windows > but I can't find a way to check this..; > > Any idea ? > > Regards, > > Alexandre > ___ 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] SLURM - speed processing
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 ___ 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] SLURM - speed processing
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 + > From: "Backhausen, Lea" <lea.backhau...@uniklinikum-dresden.de> > Subject: Re: [Freesurfer] SLURM - speed processing (Alexandre Obert) > To: "'freesurfer@nmr.mgh.harvard.edu'" > <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <1d0e7a9ed60d3e4399550c3a60c0badc39460...@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.alexan...@gmail.com> > Subject: [Freesurfer] SLURM - speed processing > To: freesurfer@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 > -- next part -- > An HTML attachment was scrubbed... > URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachm > ents/20180419/cbcc829a/attachment-0001.html > > -- > > Message: 6 > Date: Thu, 19 Apr 2018 11:57:45 -0400 > From: "Douglas N. Greve" <dgr...@mgh.harvard.edu> > Subject: Re: [Freesurfer] LGI for the loba
