Freesurfer

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30084 discussions

segmentHA_T1.sh outputs "Error using myMRIread (line 16)"
by Soichi Hayashi 11 May '20

11 May '20

External Email - Use Caution Hello. I am testing freesurfer 7.0.0 with segmentHA processing. I've run recon-all successfully, and now I am trying to run "segmentHA_T1.sh". When I do, it generates the following error message. $ segmentHA_T1.sh output . > ------------------------------ > USER user > HOST slurm3-compute2 > PROCESSID 14892 > PROCESSOR x86_64 > OS Linux > ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS 1 > Linux slurm3-compute2 4.15.0-99-generic #100-Ubuntu SMP Wed Apr 22 > 20:32:56 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux > ------------------------------ > > freesurfer-linux-centos7_x86_64-7.0.0-20200429-3a03ebd > > setenv SUBJECTS_DIR . > cd /export/prod/5eb5c3986d02b3164bd1ad8b/5eb5c8506d02b3677ed1add8 > /usr/local/freesurfer/bin/segmentHA_T1.sh output . > #-------------------------------------------- > #@# Hippocampal Subfields processing (T1) left Sat May 9 00:23:06 UTC 2020 > ------------------------------------------ > Setting up environment variables > --- > LD_LIBRARY_PATH is > .:/lib64:/usr/local/freesurfer/MCRv84//runtime/glnxa64:/usr/local/freesurfer/MCRv84//bin/glnxa64:/usr/local/freesurfer/MCRv84//sys/os/glnxa64:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:/.singularity.d/libs > Registering imageDump.mgz to hippocampal mask from ASEG > Error using myMRIread (line 16) > Error in myMRIread: temporary directory does not exist > Error in segmentSubjectT1_autoEstimateAlveusML (line 157) > Linux slurm3-compute2 4.15.0-99-generic #100-Ubuntu SMP Wed Apr 22 > 20:32:56 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux > T1 hippocampal subfields exited with ERRORS at Sat May 9 00:23:16 UTC 2020 I am not sure what it means by "temporary directory does not exist", but I see that it's written some files under my freesurfer subject output directory. [image: image.png] Could you help me troubleshoot this problem? Thank you! Soichi Hayashi

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Regarding OS
by Rahul Sharma 11 May '20

11 May '20

External Email - Use Caution Can anyone please help me out which OS will be suitable for using freesurfer from now onwards. Regards: Rahul Sharma Research Scholar NIT Silchar (Assam) 9827834360

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Re: [Freesurfer] unable to set everything to version 7
by fsbuild 11 May '20

11 May '20

External Email - Use Caution Hello Safi, I would make a directory named /usr/local/freesurfer/7.0.0-1 and put the freesurfer 7 release under that directory. Then set FREESURFER_HOME to one of /usr/local/freesurfer/6.0.0-1/usr/local/freesurfer/7.0.0-0.1b1/usr/local/freesurfer/7.0.0-1 If your $HOME/.bashrc file sets FREESURFER_HOME such that when you start a new terminal, you see the output from the SetUpFreeSurfer script listing a FREESURFER_HOME=/usr/local/freesurfer/<something> that is not what you want, then change how FREESURFER_HOME is set in that startup file. - R. On May 10, 2020, at 22:48, Safi Ullah . <safi.ullah(a)uog.edu.pk> wrote:        External Email - Use Caution        Dear List, I installed version 7 into a directory named 'freesurfer' where there are already Verion 6 and Version 7(beta) is installed. My OS is 'Ubuntu_FS_600_700b1_TutorialData'"/usr/local/freesurfer/6.0.0-1""/usr/local/freesurfer/7.0.0-0.1b1"So I installed Version 7 (stable) in the same directory  "/usr/local/freesurfer/"but when I export my necessities$export FREESURFER_HOME=/usr/local/freesurfer$export SUBJECTS_DIR=/usr/local/freesurfer/subjects    $source $FREESURFER_HOME/SetUpFreeSurfer.sh-------- freesurfer-linux-centos7_x86_64-7.0.0-20200429-3a03ebd --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   /usr/local/freesurferFSFAST_HOME       /usr/local/freesurfer/6.0.0-1/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      /usr/local/freesurfer/subjectsTUTORIAL_DATA     /home/developer/tutorial_dataMNI_DIR           /usr/local/freesurfer/6.0.0-1/mniFSL_DIR           /usr/local/freesurfer/6.0.0-1/fsl_507Although, I checked the creation dates of files from the mismatching directories in both versions, there is no update in the latest version, so it should not be a problem, however I wonder, why are some variables still pointing toward the old version? any solution,please? Regards, Safi_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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unable to start freevie from within matlab
by Knut J Bjuland 11 May '20

11 May '20

External Email - Use Caution Dear FreeSurfer experts I have used this script to start Freeview from within Matlab fs=getenv('FREESURFER_HOME'); setenv('FS_QT_HOME',fullfile(fs,'lib','qt')); setenv('QTLIBPATH',fullfile(fs,'lib','qt','lib')) setenv('qtplugin',fullfile(fs,'lib','qt','plugins')) setenv('vtk',fullfile(fs,'lib','vtk')) lib=getenv('LD_LIBRARY_PATH'); qtlib=getenv('QTLIBPATH'); plugins=getenv('qtplugin'); setenv('LD_LIBRARY_PATH',strcat(lib,':',qtlib,':',plugins,fullfile(fs,'lib','vtk'))) if upper < fdrtreshold upper = fdrtreshold + 1; fdrtreshold=num2str(fdrtreshold);upper=num2str(upper); fdrtreshold=sprintf('%s,%s',fdrtreshold,upper); leftcommand=sprintf('%s/%s/surf/lh.%s:annot=aparc.annot:annot_outline=1:overlay=%s:overlay_threshold=%s',SUBJECTS_DIR,template,surface,leftmgh,fdrtreshold); rightcommand=sprintf('%s/%s/surf/rh.%s:annot=aparc.annot:annot_outline=1:overlay=%s:overlay_threshold=%s ',SUBJECTS_DIR,template,surface,rightmgh,fdrtreshold); freeview='freeview'; commandline=sprintf('%s -f %s -f %s -viewport 3d &',freeview,leftcommand,rightcommand); system(commandline) but with Freesurfer 7 I have been unable to start Freeview. Are there any option that I am missing. I get this error message This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem. Available platform plugins are: linuxfb, minimal, offscreen, vnc, xcb. /usr/local/freesurfer/7.0.0-1/bin/freeview_matlab: line 13: 330961 Aborted (core dumped) freeview $argv:q /usr/local/freesurfer/7.0.0-1/bin/freeview_matlab: Aborted Knut Jørgen Bjuland

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unable to set everything to version 7
by Safi Ullah . 10 May '20

10 May '20

External Email - Use Caution Dear List, I installed version 7 into a directory named 'freesurfer' where there are already Verion 6 and Version 7(beta) is installed. My OS is 'Ubuntu_FS_600_700b1_TutorialData' "/usr/local/freesurfer/6.0.0-1" "/usr/local/freesurfer/7.0.0-0.1b1" So I installed Version 7 (stable) in the same directory "/usr/local/freesurfer/" but when I export my necessities *$export FREESURFER_HOME=/usr/local/freesurfer* *$export SUBJECTS_DIR=/usr/local/freesurfer/subjects* *$source $FREESURFER_HOME/SetUpFreeSurfer.sh* -------- freesurfer-linux-centos7_x86_64-7.0.0-20200429-3a03ebd -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/6.0.0-1/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects TUTORIAL_DATA /home/developer/tutorial_data MNI_DIR /usr/local/freesurfer/6.0.0-1/mni FSL_DIR /usr/local/freesurfer/6.0.0-1/fsl_507 Although, I checked the creation dates of files from the mismatching directories in both versions, there is no update in the latest version, so it should not be a problem, however I wonder, why are some variables still pointing toward the old version? any solution,please? Regards, Safi

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mris_fix_topology command does not finish
by Billah, Tashrif 10 May '20

10 May '20

Hi there, The following commands part of `recon-alll -i some_T1w.nii.gz -autorecon2` does not finish for some of our data: #@# Fix Topology lh Sat May 9 14:17:52 EDT 2020 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 sub-7049_ses-01_desc-XcMaN4_T1w lh #@# Fix Topology rh Sat May 9 14:17:52 EDT 2020 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 sub-7049_ses-01_desc-XcMaN4_T1w rh Waiting for PID 57296 of (57296 57299) to complete... Waiting for PID 57299 of (57296 57299) to complete... We kept them running for about 48 hours in multiple attempts, yet no luck. Moreover, mris_fix_topology is a binary file so I am unable to debug through. Any suggestion on where to look at? Best, Tashrif

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[CFP] The 3rd International workshop on Machine Learning in Clinical Neuroimaging (MLCN 2020)
by MLCN Workshop 09 May '20

09 May '20

External Email - Use Caution *Please find below the call for papers for the International Workshop of Machine Learning in Clinical Neuroimaging (MLCN) on 4 October 2020 at MICCAI 2020 in Lima, Peru. We welcome contributions on novel machine learning methods and their applications to clinical neuroimaging data.* The submission deadline is *30 June 2020*, and all MLCN accepted papers will be eligible for the best paper award of 500 USD. For more information, please visit https://mlcnws.com/. Best wishes, The MLCN 2020 committee Christos Davatzikos Andre Marquand Jonas Richiardi Emma Robinson Ahmed Abdulkadir Cher Bass Mohamad Habes Seyed Mostafa Kia Jane Maryam Rondina Chantal Tax Hongzhi Wang Thomas Wolfers International Workshop on Machine Learning in Clinical Neuroimaging 4 October 2020 in Lima, Peru The International Workshop of Machine Learning in Clinical Neuroimaging ( https://mlcnws.com/) a satellite event of MICCAI (https://miccai2020.org) calls for original papers in the field of clinical neuroimaging data analysis with machine learning. The two tracks of the workshop include methodological innovations as well as clinical applications. This highly interdisciplinary topic provides an excellent platform to connect researchers of varying disciplines and to collectively advance the field in multiple directions. For the machine learning track, we seek contributions with substantial methodological novelty in analyzing high-dimensional, longitudinal, and heterogeneous neuroimaging data using stable, scalable, and interpretable machine learning models. Topics of interest include but are not limited to: - Spatio-temporal brain data analysis - Structural data analysis - Graph theory and complex network analysis - Longitudinal data analysis - Model stability and interpretability - Model scalability in large neuroimaging datasets - Multi-source data integration and multi-view learning - Multi-site data analysis, from preprocessing to modeling - Domain adaptation, data harmonization, and transfer learning in neuroimaging - Unsupervised methods for stratifying brain disorders - Deep learning in clinical neuroimaging - Model uncertainty in clinical predictions - ... In the clinical neuroimaging track, we seek contributions that explore how the application of advanced machine learning methods help us to move towards precision medicine for complex brain disorders. Topics of interest include but are not limited to: - Biomarker discovery - Refinement of nosology and diagnostics - Biological validation of clinical syndromes - Treatment outcome prediction - Course prediction - Analysis of wearable sensors - Neurogenetics and brain imaging genetics - Mechanistic modeling - Brain aging - ... Submission Process: The workshop seeks high quality, original, and unpublished work that addresses one or more challenges described above. Papers should be submitted electronically in Springer Lecture Notes in Computer Science (LCNS) style (see https://www.miccai2020.org/en/PAPER-SUBMISSION-GUIDELINE.html#manuscript-fo… for detailed author guidelines) using the CMT system at https://cmt3.research.microsoft.com/MLCN2020. The page limit is 8-pages (text, figures, and tables) plus up to 2-pages of references. We review the submissions in a double-blind process. Please make sure that your submission is anonymous. Accepted papers will be published in a joint proceeding with the MICCAI 2020 conference. Best Paper Award: This year, all MLCN accepted papers will be eligible for the best paper award. The recipient of the award will be chosen by the MLCN scientific committee based on the scientific quality and novelty of contributions. The winner will be announced at the end of the workshop and will receive 500 USD honorarium. Important Dates: - Paper submission deadline: June 30th, 2020 - Notification of Acceptance: July 24th, 2020 - Camera-ready Submission: July 31st, 2020 - Workshop Date: 4 October 2020

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Parcellation of files containing within subject summary measures
by Martin Gell 08 May '20

08 May '20

External Email - Use Caution Dear experts, I calculated vertex-wise standard deviation across multiple thickness (lh.thickness.fwhm10.fsaverage.mgh) and volume files (lh.volume.fwhm10.fsaverage.mgh) of one individual, calculated from scans at different time points. I used the freesurfer library for R to calculate the sd in thickness and volume between scans and saved the sd in each vertex as a new mgh file (one for thickness and one for volume). I now need to parcellate (calculate the mean value in each parcel) my new mgh files containing the vertex-wise sd using the Desikan-Killiany Atlas and Destrieux Atlas as definitions for the parcels. What is the best way to approach this? Thank you! Martin <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> Virus-free. www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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tracula stats summary
by Zeng, Qi 08 May '20

08 May '20

External Email - Use Caution Hi, Is it possible to collect all 18 tracts stats into a single file? Has tried: "tractstats2table --load-pathstats-from-file paths.txt --overall --tablefile tractAll.txt" Path.txt contains all the subjects' 18 paths' full path directory Error message: "all stats files need to have the same pathwayname. try verbose option These are the pathwaynames found: ['fmajor', 'fminor', 'lh.atr', 'lh.cab', 'lh.ccg', 'lh.cst', 'lh.ilf', 'lh.slfp', 'lh.slft', 'lh.unc', 'rh.atr', 'rh.cab', 'rh.ccg', 'rh.cst', 'rh.ilf', 'rh.slfp', 'rh.slft', 'rh.unc']" Best, Qi -- Ph.D. candidate Icahn School of Medicine at Mount Sinai

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Hippocampal subfield tool for 6.0.0 data
by O'Shea,Andrew 08 May '20

08 May '20

External Email - Use Caution Hello, Would you be able to point me to the right version of the hippocampal subfield tool as described here: https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAm… The data have been processed in 6.0.0, but the stable pub version we have doesn't seem to have the segmentHA_T1.sh within it. I see 7.0.0 is out with these hippocampal tools but I know mixing versions is cautioned against. Where would I find the appropriate hippocampal tools for 6.0.0 data? Thanks! Andrew O'Shea, MSc. Research Coordinator III Woods Lab Center for Cognitive Aging and Memory McKnight Brain Institute Department of Clinical and Health Psychology College of Public Health and Health Professions University of Florida Phone (Office): (352) 294-5827 Phone (Cell): (586) 899-2771 Email: aoshea(a)phhp.ufl.edu

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