Freesurfer August 2021

freesurfer@nmr.mgh.harvard.edu

73 participants
101 discussions

FSFAST (mkcontrast-sess) with Octave
by Lauri Tuominen 17 Aug '21

17 Aug '21

External Email - Use Caution Dear Surfers, I am trying to run fsfast mkcontrast-sess with octave. I used the following command: "mkcontrast-sess -analysis ../mkanalysis/ftap.sm05.lh -contrast ftap -a 1 -octave" I get the output below. I wonder if you could help me out? Am I missing a file or a path? Thank you so much Lauri Tuominen INFO: Found 2 Non-Null Conditions INFO: Found 1 Delays Condition Weights: 1.00000000000000000000 0 mkcontrast2 -config ../mkanalysis/ftap.sm05.lh/ftap.config -anadir ../mkanalysis/ftap.sm05.lh -wcond 1.00000000000000000000 0 -sumconds -o ../mkanalysis/ftap.sm05.lh/ftap.mat -prestim 0 -wdelay 1 -octave mkcontrast2 7.1.1 cmtxfile ../mkanalysis/ftap.sm05.lh/ftap.mat nconds 2, wcond 1.00000000000000000000 0 ndelays 1, wdelay 1 ndelays 1, wpsa sumconds 1 sumdelays 0 nircorr 0 TER 0.050000 rdelta rtau cmtxfile ../mkanalysis/ftap.sm05.lh/ftap.mat monly 0 NCond 2 WCond 1.00000000000000000000 0 NDelay 1 WDelay 1 TER 0.050000 sumconds 1 sumdelays 0 nircorr 0 TPreStim 0 RmPreStim 0 rdelta 0 0 rtau 0 0 ndelays 1 CNorm 1 setwdelay 0 setwcond 0 Matlab file is /tmp/mkcontrast2.28236.m ------- octave output -------------------- error: 'mkcontrast2m' undefined near line 1, column 1 Tue 17 Aug 2021 15:04:43 EDT

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Setting up Freesurfer
by Haley Park 17 Aug '21

17 Aug '21

External Email - Use Caution Hello, I was able to run Freesurfer before but when I try to source it now with the code source $FREESURFER_HOME/7.1.1/SetUpFreesurfer.sh I get the message: /Applications/freesurfer/7.1.1/SetUpFreeSurfer.sh:source:42: no such file or directory: /Applications/freesurfer/FreeSurferEnv.sh But I do see that file in the directory in Finder. Any ideas? Thank you, Haley

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longitudinal LME stats
by Erik O'Hanlon 17 Aug '21

17 Aug '21

External Email - Use Caution Dear FS experts, I have run the longitudinal pipeline on a dataset with three timepoints. I am particularly interested in the longitudinal hippocampal and amygdala data and want to run LME on these. I've made the qdec table with the id age, sex and time between scans etc. and have exported all the hippocamapal and amygdala volumes to csv files to merge with demographic data. Should I smooth the hippocampal and amygdala measures before running the LME? Do I run Qcache and if so do I use recon-all -long SubID_tp1 subIDbase -qcache In the LME wiki instructions it gives an example for the mass-univariate approach on thickness. Is the study_average referring to the fsaverage ? Should I be using the ICV from the cross-sectional runs or the ICV measures in the "long" folders which refer? Thanks and any help is very much appreciated. Erik

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bbregister on DWI volumes using DOF 12 for epi distortions ?
by Shane Schofield 17 Aug '21

17 Aug '21

External Email - Use Caution Hi Freesurfer Experts, I am trying to obtain coregister diffusion data b0 with T1. One problem is that I do not have any means to correct for EPI distortions. Because of this, I am experimenting with DOF = 9 and DOF = 12. The mincost for 12 was consistently the lowest compared to 6 and 9 across my datasets [DOF 6 = 0.23, DOF 9 = 0.22, DOF 12 = 0.19]. However, it is hard to tell that DOF 12 is the best just by looking at the coregistered B0s overlaid on the brainmask. Would it be fine to proceed with the DOF 12 option? Thank you. Best Wishes,Shane

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Fwd: Base correction, longitudinal analysis
by Eszter Boros 17 Aug '21

17 Aug '21

External Email - Use Caution Dear FreeSurfer Team, I am working on a longitudinal pipeline and after correcting the Cross and generating the Base, I can still see some pial problems sometimes (on the Base). I read on the Freesurfer website that it is possible to correct and regenerate only the Base, but when I use this command: recon-all -base OAS2_0057 -autorecon-pial /where OAS2_0057 is the name of the Base/ I get the following error message: ERROR: must specify subjects for base subject using -base-tp Why is this not working? I am using Freesurefer 7.1.1. Thank you so much! All the best, Eszter Boros

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qcache option for post recon-all longitudinal data
by Zeng, Qi 17 Aug '21

17 Aug '21

External Email - Use Caution Hi Freesurfer experts, I've done running a longitudinal analysis pipeline for individuals in 3 groups. Now, I need to get prepared for QDEC group analysis. I cp all groups of individuals to the same directory and each subject contains one base and multiple long files. I want to run "-qcache" option for the prep. Got a couple of questions here? 1) I failed to run "recon-all -s 001 -qcache", said: "missing 001/surf/lh.thickness", so for a longitudinal run, should I run "recon-all -s 001_base -qcache" or 'recon-all -s 001_ses-1.long.001_base" instead? 2) Where will the output be stored for each individual? 3) To run multiple qcache in parallel, will the following code generate the same outputs as that I run each individually: " find . -type d -name '*_base" -exec bash -c 'for i in "$@"; do recon-all -s "$i" -qcache; done". Thank you so much! Best, Qi

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Re: [Freesurfer] Subfields error
by fsbuild 16 Aug '21

16 Aug '21

External Email - Use Caution Hello James, In this thread from January 2021, https://secure-web.cisco.com/1_ezGYyWFKiVAojF3gcdp8pGH5ZDmCAz1KucNZh4oW5ZYO…, someone who got the same deployrc error was advised to try the following:Can you please remove the MCR directory and install it using the instructions found at https://secure-web.cisco.com/1euGMRsVtt4HFP_v7Lx9opw-gd8TRT1kiHLB6hHaSoy0XG… I think this will fix the issue.So I would take a look at that thread, and maybe give that a try if you have not already done the matlab runtime installation that way. - R. On Aug 16, 2021, at 21:57, James Allebone <james.allebone(a)gmail.com> wrote:        External Email - Use Caution        Hello,I am trying to run the new hippocampal module. I successfully complete recon-all, but the receive the following error message when attempting to run the hippocampal module - any help would be greatly appreciated:USER developerHOST developer-VirtualBoxPROCESSID 14407 PROCESSOR x86_64OS LinuxITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS 1 Linux developer-VirtualBox 5.3.0-53-generic #47~18.04.1-Ubuntu SMP Thu May 7 13:10:50 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux------------------------------ freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b setenv SUBJECTS_DIR /usr/local/freesurfer/7.1.0-1/subjectscd /usr/local/freesurfer/7.1.0-1/subjects/usr/local/freesurfer/7.1.0-1/bin/segmentHA_T1.sh sub1#--------------------------------------------#@# Hippocampal Subfields processing (T1) left Mon Aug 16 21:52:59 EDT 2021------------------------------------------Setting up environment variables---LD_LIBRARY_PATH is .:/usr/lib/x86_64-linux-gnu:/usr/local/freesurfer/7.1.0-1/MCRv84//runtime/glnxa64:/usr/local/freesurfer/7.1.0-1/MCRv84//bin/glnxa64:/usr/local/freesurfer/7.1.0-1/MCRv84//sys/os/glnxa64:/usr/local/freesurfer/7.1.0-1/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/7.1.0-1/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/7.1.0-1/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/7.1.0-1/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64::/usr/lib/libreoffice/programError using checkRequiredMCRProducts (line 25)Java exception occurred: java.lang.NullPointerExceptionat com.mathworks.install.InstalledProductFactory$1.execute(InstalledProductFactory.java:56)at com.mathworks.install.InstalledProductFactory$1.execute(InstalledProductFactory.java:49)at com.mathworks.install.InstalledProductFactory$InstallerWorkSpace.executeTask(InstalledProductFactory.java:193)at com.mathworks.install.InstalledProductFactory$InstallerWorkSpace.access$200(InstalledProductFactory.java:108)at com.mathworks.install.InstalledProductFactory.getInstalledProducts(InstalledProductFactory.java:67)Error in deployrc (line 9)Error in matlabrc (line 238)Command exited with non-zero status 255@#@FSTIME  2021:08:16:21:52:59 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 e 27.66 S 0.35 U 4.99 P 19% M 230080 F 1257 R 31454 W 0 c 1432 w 5142 I 386408 O 84096 L 1.33 1.10 0.95@#@FSLOADPOST 2021:08:16:21:53:27 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 1.47 1.17 0.98Linux developer-VirtualBox 5.3.0-53-generic #47~18.04.1-Ubuntu SMP Thu May 7 13:10:50 UTC 2020 x86_64 x86_64 x86_64 GNU/LinuxT1 hippocampal subfields exited with ERRORS at Mon Aug 16 21:53:27 EDT 2021-- James Allebone | MPsych, Ph.D. (Clinical Neuropsychology)Melbourne School of Psychological SciencesThe University of MelbourneFlorey Institute of Neuroscience and Mental HealthMelbourne Brain Centre, Austin Campus245 Burgundy Street, Heidelberg VIC 3084 MailScanner has detected a possible fraud attempt from "secure-web..cisco.com" claiming to be http://secure-web.cisco.com/1AQK4e4G_gYVm-sqzpIO3xlVCN5-yUUR9qW0Eg_… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Subfields error
by James Allebone 16 Aug '21

16 Aug '21

External Email - Use Caution Hello, I am trying to run the new hippocampal module. I successfully complete recon-all, but the receive the following error message when attempting to run the hippocampal module - any help would be greatly appreciated: USER developer HOST developer-VirtualBox PROCESSID 14407 PROCESSOR x86_64 OS Linux ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS 1 Linux developer-VirtualBox 5.3.0-53-generic #47~18.04.1-Ubuntu SMP Thu May 7 13:10:50 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux ------------------------------ freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b setenv SUBJECTS_DIR /usr/local/freesurfer/7.1.0-1/subjects cd /usr/local/freesurfer/7.1.0-1/subjects /usr/local/freesurfer/7.1.0-1/bin/segmentHA_T1.sh sub1 #-------------------------------------------- #@# Hippocampal Subfields processing (T1) left Mon Aug 16 21:52:59 EDT 2021 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/usr/lib/x86_64-linux-gnu:/usr/local/freesurfer/7.1.0-1/MCRv84//runtime/glnxa64:/usr/local/freesurfer/7.1.0-1/MCRv84//bin/glnxa64:/usr/local/freesurfer/7.1.0-1/MCRv84//sys/os/glnxa64:/usr/local/freesurfer/7.1.0-1/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/7.1.0-1/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/7.1.0-1/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/7.1.0-1/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64::/usr/lib/libreoffice/program Error using checkRequiredMCRProducts (line 25) Java exception occurred: java.lang.NullPointerException at com.mathworks.install.InstalledProductFactory$1.execute(InstalledProductFactory.java:56) at com.mathworks.install.InstalledProductFactory$1.execute(InstalledProductFactory.java:49) at com.mathworks.install.InstalledProductFactory$InstallerWorkSpace.executeTask(InstalledProductFactory.java:193) at com.mathworks.install.InstalledProductFactory$InstallerWorkSpace.access$200(InstalledProductFactory.java:108) at com.mathworks.install.InstalledProductFactory.getInstalledProducts(InstalledProductFactory.java:67) Error in deployrc (line 9) Error in matlabrc (line 238) Command exited with non-zero status 255 @#@FSTIME 2021:08:16:21:52:59 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 e 27.66 S 0.35 U 4.99 P 19% M 230080 F 1257 R 31454 W 0 c 1432 w 5142 I 386408 O 84096 L 1.33 1.10 0.95 @#@FSLOADPOST 2021:08:16:21:53:27 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 1.47 1.17 0.98 Linux developer-VirtualBox 5.3.0-53-generic #47~18.04.1-Ubuntu SMP Thu May 7 13:10:50 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux T1 hippocampal subfields exited with ERRORS at Mon Aug 16 21:53:27 EDT 2021 -- *James Allebone | **MPsych, Ph.D. (Clinical Neuropsychology)* Melbourne School of Psychological Sciences The University of Melbourne Florey Institute of Neuroscience and Mental Health Melbourne Brain Centre, Austin Campus 245 Burgundy Street, Heidelberg VIC 3084 http://secure-web.cisco.com/1N3BscAG29fPIUx3Blytu4slH8u-syFNePbcB_kngqs92Oo…

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fsfast selxavg3 runtime and processing errors
by Eli Bulger 13 Aug '21

13 Aug '21

External Email - Use Caution Hello Freesurfer Users, I am running selxavg3 on functional MRI data from 2 runs, with a block design (paradigm files attached) and select external regressors originating from fMRIPrep (attached). There are 5 non-fixation conditions in the design. I am having errors come up during this analysis. _____ Without external regressors, there are no runtime errors and one contrast looks okay (corresponding to -a 3 -c 2), however: - 2 contrasts yield t-stats that are the exact opposites of each other, which was not expected (corresponding to -a 2 -c 4 and -a 3 -c 5) - Another contrast yields erroneous results, with t-stats on the order of 10^-11 ( corresponding to -a 3 -a 5 -c 2 -c 4). _____ With external regressors, only one contrast will run (again, -a 3 -c 2) - the rest give a "design is ill-conditioned error" (log attached). I have attached the corresponding Xtmp.mat file (zipped). _____ I am wondering if there are any strategies someone can recommend for figuring out why these runtime / processing errors occur. Could this be a problem with the task design itself? Any advice is appreciated! Thank you very much, _______________________ Eli Bulger Research Assistant Lab in Multisensory Neuroscience Carnegie Mellon University

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Open Postdoctoral fellowships - Martinos Center - MGH
by Price, Julie C. 13 Aug '21

13 Aug '21

T32 postdoctoral fellowship opportunities are available for innovative research in multimodal imaging and neurodegeneration at Massachusetts General Hospital – Martinos Center. The trainee will pursue a targeted research project under the mentorship of world-class researchers in the Harvard research community in one or more of three key areas: [1] data sciences, computational biology, statistics, math/engineering/physics, radiochemistry; [2] biology of aging and neurodegeneration; [3] drug discovery and development. A mission of this program is to promote the development of a diverse, translational research workforce for cross-disciplinary team science relevant for Alzheimer’s disease and AD-related dementias. Eligibility: PhD, MD, MD/PhD and U.S. citizen or permanent resident, with rolling admission for 4 training slots. See https://pricelab.martinos.org/t32-adrd/ for further information including application instructions. Please submit questions to: Krystal Whitfield (T32 Administrative Contact) at T32ADRD(a)mgh.harvard.edu<mailto:T32ADRD@mgh.harvard.edu>. Program Director: Julie Price, PhD, Professor of Radiology, Martinos Center for Biomedical Imaging - T32 AG066592

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Freesurfer August 2021