Freesurfer

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Re: [Freesurfer] Java / Matlab Runtime error
by Snedden, Ali 27 Jan '21

27 Jan '21

External Email - Use Caution Thank you. That seemed to work. Best, ====================================== Ali Snedden, Ph.D. HPC Scientific Programmer The High Performance Computing Facility Abigail Wexner Research Institute at Nationwide Children’s Hospital From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Hoopes, Andrew" <AHOOPES(a)mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Wednesday, January 27, 2021 at 12:30 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Java / Matlab Runtime error Hi Ali, Can you please remove the MCR directory and install it using the instructions found at https://secure-web.cisco.com/1q7ncSDiVmdcDnctxyRxdS9kfvzlqFQOUr2mbgA1_jcZ_p…<https://secure-web.cisco.com/1aQ1JL_davGdsj7PjO6BlRnaxg04WJ-LS2csZQb4UUpwC4…>? I think this will fix the issue. Best, Andrew From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Snedden, Ali <Ali.Snedden(a)nationwidechildrens.org> Date: Wednesday, January 27, 2021 at 11:46 AM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Java / Matlab Runtime error External Email - Use Caution Hello, I’m helping a user run freesurfer/7.1.0 on CentOS 8.1. They initially encountered an error due to the missing Matlab Compiler Runtime (MCR). I downloaded the package and installed it in the location suggested by the error message : LINUX: cd /gpfs0/export/apps/opt/freesurfer/7.1.0/binary_download curl "https://secure-web.cisco.com/13fqwuJ0h6N_rVfDgy4zeeSfP8PW_Zucrne8PLs-s210IB…"<https://secure-web.cisco.com/12fg_q2Z2ANsbb7Ptww7Z4aEcjmFodLwyk84-oiY-5QwyP…> -o "runtime2014b.tar.gz" tar xvf runtime2014b.tar.gz After installing the MCR, I had to change all the subdirectories’ in MCRv84 to 755 permissions so our user could access it. When trying to run `segmentHA_T1.sh`, she gets the error : [user@computer-name Subjects]$ export FS_LICENSE=/gpfs0/home1/group/lab/Software/FreeSurfer/license.txt [user@computer-name Subjects]$ export SUBJECTS_DIR=/gpfs0/home1/group/lab/DATA/ANALYSES/Test/FreeSurfer7/Subjects [user@computer-name Subjects]$ cd /gpfs0/home1/group/lab/DATA/ANALYSES/Test/FreeSurfer7/Subjects [user@computer-name Subjects]$ segmentHA_T1.sh subject1 #-------------------------------------------- #@# Hippocampal Subfields processing (T1) left Wed Jan 27 10:53:02 EST 2021 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/lib64:/gpfs0/export/apps/opt/freesurfer/7.1.0/binary_download/MCRv84//runtime/glnxa64:/gpfs0/export/apps/opt/freesurfer/7.1.0/binary_download/MCRv84//bin/glnxa64:/gpfs0/export/apps/opt/freesurfer/7.1.0/binary_download/MCRv84//sys/os/glnxa64:/gpfs0/export/apps/opt/freesurfer/7.1.0/binary_download/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/gpfs0/export/apps/opt/freesurfer/7.1.0/binary_download/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/gpfs0/export/apps/opt/freesurfer/7.1.0/binary_download/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/gpfs0/export/apps/opt/freesurfer/7.1.0/binary_download/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:/gpfs0/export/apps/opt/freesurfer/7.1.0/binary_download/lib:/gpfs0/export/apps/easybuild/software/binutils/2.34-GCCcore-9.3.0/lib:/gpfs0/export/apps/easybuild/software/zlib/1.2.11-GCCcore-9.3.0/lib:/gpfs0/export/apps/easybuild/software/GCCcore/9.3.0/lib64:/gpfs0/export/apps/easybuild/software/GCCcore/9.3.0/lib 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 2021:01:27:10:53:02 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 e 35.91 S 0.42 U 2.80 P 8% M 184232 F 0 R 52021 W 0 c 11 w 7851 I 0 O 84128 L 0.02 0.06 0.08 @#@FSLOADPOST 2021:01:27:10:53:38 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 0.35 0.15 0.11 Linux computer-name 4.18.0-147.el8.x86_64 #1 SMP Wed Dec 4 21:51:45 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux T1 hippocampal subfields exited with ERRORS at Wed Jan 27 10:53:38 EST 2021 For more details, see the log file /gpfs0/home1/group/lab/DATA/ANALYSES/Test/FreeSurfer7/Subjects/subject1/scripts/hippocampal-subfields-T1.log In the archive, it seems that this has been encountered before (here<https://secure-web.cisco.com/13Rrk4VKAg12XFtc5SdBaCyFLuQnrsUWASWx4vhQPLsBPH…> and there<https://secure-web.cisco.com/1Wvet5W4lNlADueS5IfQSLWQ1iZZgHk4dYGyuj_e4cd6w5…>). Unfortunately the only solution is to ‘fix the permissions’ without specifying which files and to what permissions. Question: 1. Is there any resolution to this issue? 2. Is the Matlab 2014b compatible with CentOS 8.1? Best regards, ====================================== Ali Snedden, Ph.D. HPC Scientific Programmer The High Performance Computing Facility Abigail Wexner Research Institute at Nationwide Children’s Hospital

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Java / Matlab Runtime error
by Snedden, Ali 27 Jan '21

27 Jan '21

External Email - Use Caution Hello, I’m helping a user run freesurfer/7.1.0 on CentOS 8.1. They initially encountered an error due to the missing Matlab Compiler Runtime (MCR). I downloaded the package and installed it in the location suggested by the error message : LINUX: cd /gpfs0/export/apps/opt/freesurfer/7.1.0/binary_download curl "https://secure-web.cisco.com/1kndLvKpZL1UBdLUASJnez7XZI1ViFdFpXT5jhFPzHZej0…" -o "runtime2014b.tar.gz" tar xvf runtime2014b.tar.gz After installing the MCR, I had to change all the subdirectories’ in MCRv84 to 755 permissions so our user could access it. When trying to run `segmentHA_T1.sh`, she gets the error : [user@computer-name Subjects]$ export FS_LICENSE=/gpfs0/home1/group/lab/Software/FreeSurfer/license.txt [user@computer-name Subjects]$ export SUBJECTS_DIR=/gpfs0/home1/group/lab/DATA/ANALYSES/Test/FreeSurfer7/Subjects [user@computer-name Subjects]$ cd /gpfs0/home1/group/lab/DATA/ANALYSES/Test/FreeSurfer7/Subjects [user@computer-name Subjects]$ segmentHA_T1.sh subject1 #-------------------------------------------- #@# Hippocampal Subfields processing (T1) left Wed Jan 27 10:53:02 EST 2021 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/lib64:/gpfs0/export/apps/opt/freesurfer/7.1.0/binary_download/MCRv84//runtime/glnxa64:/gpfs0/export/apps/opt/freesurfer/7.1.0/binary_download/MCRv84//bin/glnxa64:/gpfs0/export/apps/opt/freesurfer/7.1.0/binary_download/MCRv84//sys/os/glnxa64:/gpfs0/export/apps/opt/freesurfer/7.1.0/binary_download/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/gpfs0/export/apps/opt/freesurfer/7.1.0/binary_download/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/gpfs0/export/apps/opt/freesurfer/7.1.0/binary_download/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/gpfs0/export/apps/opt/freesurfer/7.1.0/binary_download/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:/gpfs0/export/apps/opt/freesurfer/7.1.0/binary_download/lib:/gpfs0/export/apps/easybuild/software/binutils/2.34-GCCcore-9.3.0/lib:/gpfs0/export/apps/easybuild/software/zlib/1.2.11-GCCcore-9.3.0/lib:/gpfs0/export/apps/easybuild/software/GCCcore/9.3.0/lib64:/gpfs0/export/apps/easybuild/software/GCCcore/9.3.0/lib 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 2021:01:27:10:53:02 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 e 35.91 S 0.42 U 2.80 P 8% M 184232 F 0 R 52021 W 0 c 11 w 7851 I 0 O 84128 L 0.02 0.06 0.08 @#@FSLOADPOST 2021:01:27:10:53:38 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 0.35 0.15 0.11 Linux computer-name 4.18.0-147.el8.x86_64 #1 SMP Wed Dec 4 21:51:45 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux T1 hippocampal subfields exited with ERRORS at Wed Jan 27 10:53:38 EST 2021 For more details, see the log file /gpfs0/home1/group/lab/DATA/ANALYSES/Test/FreeSurfer7/Subjects/subject1/scripts/hippocampal-subfields-T1.log In the archive, it seems that this has been encountered before (here<https://secure-web.cisco.com/19si_oaGGE_Rf_ZxUuvB_adcHrxJiJjhP5iL5nhhr9Xa79…> and there<https://secure-web.cisco.com/13EvbbtOVHHlv-B8zjJFgKM0MEuIpwNHOsMVGI6vp_BOjF…>). Unfortunately the only solution is to ‘fix the permissions’ without specifying which files and to what permissions. Question: 1. Is there any resolution to this issue? 2. Is the Matlab 2014b compatible with CentOS 8.1? Best regards, ====================================== Ali Snedden, Ph.D. HPC Scientific Programmer The High Performance Computing Facility Abigail Wexner Research Institute at Nationwide Children’s Hospital

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Saving more than one figure using freeview
by Peled, Noam 27 Jan '21

27 Jan '21

Hello all, Can I use the -ss flag in freeview to save more than one figure? Currently, I'm calling freeiew 3 times, each time with a different viewport (sagittal, coronal, and axial) Thanks, Noam

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Help with mergecontrasts-sess function
by Paula Maldonado 27 Jan '21

27 Jan '21

External Email - Use Caution Dear experts, I am running an fMRI experiment in which I have four conditions: two main conditions (condition A and condition B) and two respective control conditions (condition Acontrol and condition Bcontrol). I would like to create a map showing significantly greater activity for condition A relative to condition B, after subtracting out the activity for the respective control conditions. In other words, I would like to perform the following contrast: (condition A - condition A control) - (condition B - condition B control) Then I would like to have a map that shows the reverse contrast too:(condition B - condition B control) - (condition A - condition A control). How do I do that?To obtain the first map: (condition A - condition A control) - (condition B - condition B control) I have tried with the mergecontrasts-sess function with the -conjunction flag and the OR option as detailed below: mergecontrasts-sess -mergedcontrast conjres -conjunction or -analysis analysisname -map sig -space sph -isxavg fixed -contrast Contrast1 2 pos 0 -contrast Contrast 2 pos 0 -s sessionsfMRI/Sub01/bold -hemi lh where Contrast1= (condition A - condition A control) and Contrast2= (condition B - condition B control) however the map I get is exactly the same as (condition A - condition A control), as if subtracting out Contrast 2 had no impact on the map. Thanks, Paula

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mri_convert error: GetSDCMFileInfo(): dcmGetDWIParams() 7
by Hannah Eichhorn 27 Jan '21

27 Jan '21

External Email - Use Caution Dear all, I am trying to convert Dicom volumes from a DWI Siemens sequence into nifty format, but I get the following error when I run the mri_convert Test.IMA Test.nii command: ERROR: GetSDCMFileInfo(): dcmGetDWIParams() 7 DICOM File: Test.IMA break /autofs/space/topaz_001/topaz_nightly_build/trunk/ah221-7.1.1/utils/DICOMRead.cpp:2639 ERROR: reading Test.IMA INFO: sorting. Segmentation fault (core dumped) I have searched the mail archive and didn't find similar errors. Does anyone have any thoughts on how to solve this error? I am using FreeSurfer version: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 Thank you, Hannah Eichhorn

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Re: [Freesurfer] Cerebellar Segmentation Definitions
by Horn, Mitchell Jacob 26 Jan '21

26 Jan '21

Hi Doug, Thanks for your reply. Would it be safe to say that these deep grey nuclei are included in the cerebellar white matter? Thanks, Mitch

2 1

question on data quality - examples in appendix
by Nils B. 26 Jan '21

26 Jan '21

External Email - Use Caution Hello everyone, I'm analyzing 1,5T scans and I've two problems with the data quality of my participants, where I hope you can help me. 1. In two of my scans the participants have blurry areas near the cerebellum, which makes it nearly impossible for Freesurfer (Version 7.1) to set the pials correctly (see Appendix: Scan 1). Is this problem caused by movement while scanning or is there something i can do? 2. Sometimes when I'm using the manual tool "recon-edit" for manual skullstrips the pials look weird after another recon (see Appendix: Scan 2, green box). I hope you can help me with this. Best regards, Nils -- Nils Böer Research Assistant with Bachelor Degree (WHB) *Psychology and Movement* University of Paderborn Department of Sports and Health Warburger Str. 100 33098 Paderborn Room: Sp 1.401 Email: nils.tobias94(a)gmail.com / nboeer(a)mail.uni-paderborn.de <nils.tobias94(a)gmail.com> Web: https://secure-web.cisco.com/1sdaOuw1w6xyPqwqvnfOnG1YnnOoL0wPJv31_m4I1ILytx… https://secure-web.cisco.com/1NHLN6uk84Fg2OJdTXds9YwLtGRW66xYxts-UQXUDXfvlp… <https://secure-web.cisco.com/1sdaOuw1w6xyPqwqvnfOnG1YnnOoL0wPJv31_m4I1ILytx…>

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HCP T1w scans on FreeSurfer 7.1
by Trisanna Sprung-Much 26 Jan '21

26 Jan '21

External Email - Use Caution Hi there If I want to run some HCP subjects that are 0.5mm iso T1w scans (MPRAGE) in FreeSurfer 7.1, would I simply use the following flags, or am I missing something? -3T -MPRAGE -hires Do we need an expert file with version 7.1 to specify the number of iterations for surface inflation or is this now done automatically? Thank you Trisanna

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monkey atlas resampling
by Francesca Strappini 26 Jan '21

26 Jan '21

External Email - Use Caution Dear FreeSurfer experts, I'm trying to resample an anatomical monkey atlas D99 to the functional space. I run this command line: mri_vol2vol --reg registerNMT2toCassis.dat --mov D99_atlas_in_NMT_v2.0_asym_fh.nii.gz --targ /usr/local/freesurfer/fsfast/ Monkeys/MonkeyCassis-FF-event-sm03-AVGmonkey/bold/template.nii.gz --o D99_registered2func.nii.gz However, the registration was completely lost and I had to register it again manually. Maybe I did something wrong? Thanks. Francesca -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strappini(a)weizmann.ac.il

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ROI Correlations
by Swanson,Clayton 26 Jan '21

26 Jan '21

External Email - Use Caution Hi Freesurfer Folks, I am wondering if it is possible to perform an ROI correlation which can then be viewed on the brain similar to whole brain GLM analysis in Freeview. If so, how would I go about performing this type of operation as to specify that particular region. I have two groups (HC and MS) and would like to see if there is an association between paracentral gyrus thickness and performance of a lower limb motor task. Thanks for any help you can provide, Clayton ________________________________ Clayton Swanson MS Graduate Research Assistant & PhD Candidate Sensorimotor Neuroimaging Laboratory Colorado State University Office: (970) 491-6160 Clayton.Swanson(a)colostate.edu<mailto:Clayton.Swanson@colostate.edu> (He/Him)

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