Freesurfer May 2023

freesurfer@nmr.mgh.harvard.edu

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109 discussions

Re: [Freesurfer] Uncaught exceptions when processing some images with MiDeFace
by fsbuild 17 May '23

17 May '23

External Email - Use Caution While I do no know and have not looked at the source code in question, if you lookup that error online, one explanation is memory corruption is happening by writing beyond the end of allocated memory, e.g., by using free(g) incorrectly. However the code is written, an issue with memory allocation might be exacerbated depending upon how memory management is done on the platform.  Memory management on MacOS is extremely aggressive about swapping out to disk well before physical RAM is in danger of being underrun..   Or it is virtually impossible to run out of physical RAM on macOS though things may slow down to a crawl and/or thrash.   It might be informative to know if you are hitting memory limits in the cluster and in the container (where it crashes) - but for some reason not on MacOS.  Similarly, it would be interesting to know if the memory error occurs when run on a stand alone linux workstation. - R. On May 17, 2023, at 16:27, Douglas N. Greve <dgreve(a)mgh.harvard.edu> wrote:        External Email - Use Caution        So the same input volume will sometimes succeed and sometimes fail depending upon the platform? On 5/17/2023 12:05 PM, Patrick Sadil wrote:        External Email - Use Caution        Hello,     I am trying to process several images with MiDeFace but running into issues with memory and uncaught exceptions.Of 50 images, about half are processed successfully. On the other half MiDeFace fails consistently. However, whether the images fail seems to depend on the platform. Here's what I've triedFailsfreesurfer-linux-centos7_x86_64-7.4.0.tar.gz install on HPC, CentOS Linux release 7.9.2009 (Core)freesurfer-linux-centos7_x86_64-7.3.2.tar.gz install on HPC, CentOS Linux release 7.9.2009 (Core)Apptainer image from docker://freesurfer/freesurfer:7.3.2, (this is built on CentOS:7) run on HPCDocker image from docker://freesurfer/freesurfer:7.3.2, (this is built on CentOS:7) Apple M1 Pro; 13.3.1Custom docker image (below), built and run on Apple M1 Pro; 13.3.1Succeedsfreesurfer-darwin-macOS-7.4.0.pkg, installed and run on Apple M1 Pro; 13.3.1So, I'm not sure whether this is a bug or something that I need to configure differently.############Example apptainer command$ apptainer exec -e -B $(pwd):/data docker://freesurfer/freesurfer:7.3.2 mideface --i /data/volume.nii.gz --o /data/defaced.nii.gz --odir /data/qaExample docker command> docker run --rm -it -v $(pwd):/data freesurfer/freesurfer:7.3.2 mideface --i /data/volume.nii.gz --o /data/defaced.nii.gz --odir /data/qaExample "bare" command> mideface --i volume.nii.gz --o defaced.nii.gz --odir qa############On the CentOS runs, the error isMiDeface::SegFace()*** Error in `mri_defacer': double free or corruption (!prev): 0x000000000e4d64f0 ***======= Backtrace: =========/lib64/libc.so.6(+0x81329)[0x4001f6b329]mri_defacer[0x4b0ebe]mri_defacer[0x422c15]mri_defacer[0x415308]/lib64/libc.so.6(__libc_start_main+0xf5)[0x4001f0c555]mri_defacer[0x418367]======= Memory map: ========400000-700000 r-xp 00000000 fe:01 4223092                                /usr/local/freesurfer/bin/mri_defacer700000-900000 ---p 00000000 00:00 0                                      900000-908000 r--p 00300000 fe:01 4223092                                /usr/local/freesurfer/bin/mri_defacer908000-932000 rw-p 00308000 fe:01 4223092                                /usr/local/freesurfer/bin/mri_defacer932000-13ee1000 rw-p 00000000 00:00 0                                    4000000000-4000001000 ---p 00000000 00:00 0                              4000001000-4000801000 rw-p 00000000 00:00 0                              [stack]4000801000-4000823000 r-xp 00000000 fe:01 2527596                        /usr/lib64/ld-2.17.so4000823000-4000a22000 ---p 00000000 00:00 0                              4000a22000-4000a23000 r--p 00021000 fe:01 2527596                        /usr/lib64/ld-2.17.so4000a23000-4000a24000 rw-p 00022000 fe:01 2527596                        /usr/lib64/ld-2.17.so4000a24000-4000a27000 rw-p 00000000 00:00 0                              4000a2b000-4000a2c000 rw-p 00000000 00:00 0                              4000a2c000-4000a41000 r-xp 00000000 fe:01 2527648                        /usr/lib64/libz.so.1.2.74000a41000-4000c40000 ---p 00015000 fe:01 2527648                        /usr/lib64/libz.so.1.2.74000c40000-4000c41000 r--p 00014000 fe:01 2527648                        /usr/lib64/libz.so.1.2..74000c41000-4000c42000 rw-p 00015000 fe:01 2527648                        /usr/lib64/libz..so.1.2.74000c42000-4000c59000 r-xp 00000000 fe:01 2527629                        /usr/lib64/libpthread-2.17.so4000c59000-4000e58000 ---p 00017000 fe:01 2527629                        /usr/lib64/libpthread-2.17.so4000e58000-4000e59000 r--p 00016000 fe:01 2527629                        /usr/lib64/libpthread-2.17.so4000e59000-4000e5a000 rw-p 00017000 fe:01 2527629                        /usr/lib64/libpthread-2.17.so4000e5a000-4000e5e000 rw-p 00000000 00:00 0                              4000e5e000-4000e60000 r-xp 00000000 fe:01 2527609                        /usr/lib64/libdl-2.17.so4000e60000-4001060000 ---p 00002000 fe:01 2527609                        /usr/lib64/libdl-2.17.so4001060000-4001061000 r--p 00002000 fe:01 2527609                        /usr/lib64/libdl-2.17.so4001061000-4001062000 rw-p 00003000 fe:01 2527609                        /usr/lib64/libdl-2.17.so4001062000-4001063000 rw-p 00000000 00:00 0                              4001063000-4001164000 r-xp 00000000 fe:01 2527611                        /usr/lib64/libm-2.17.so4001164000-4001363000 ---p 00101000 fe:01 2527611                        /usr/lib64/libm-2.17.so4001363000-4001364000 r--p 00100000 fe:01 2527611                        /usr/lib64/libm-2.17.so4001364000-4001365000 rw-p 00101000 fe:01 2527611                        /usr/lib64/libm-2.17.so4001365000-400138a000 r-xp 00000000 fe:01 2527938                        /usr/lib64/libgomp.so.1.0.0400138a000-4001589000 ---p 00025000 fe:01 2527938                        /usr/lib64/libgomp.so.1.0.04001589000-400158a000 r--p 00024000 fe:01 2527938                        /usr/lib64/libgomp.so.1.0.0400158a000-400158b000 rw-p 00025000 fe:01 2527938                        /usr/lib64/libgomp.so.1.0.0400158b000-4001593000 r-xp 00000000 fe:01 2527607                        /usr/lib64/libcrypt-2.17.so4001593000-4001792000 ---p 00008000 fe:01 2527607                        /usr/lib64/libcrypt-2.17.so4001792000-4001793000 r--p 00007000 fe:01 2527607                        /usr/lib64/libcrypt-2.17.so4001793000-4001794000 rw-p 00008000 fe:01 2527607                        /usr/lib64/libcrypt-2.17.so4001794000-40017c3000 rw-p 00000000 00:00 0                              40017c3000-40017ca000 r-xp 00000000 fe:01 2527633                        /usr/lib64/librt-2.17.so40017ca000-40019c9000 ---p 00007000 fe:01 2527633                        /usr/lib64/librt-2.17.so40019c9000-40019ca000 r--p 00006000 fe:01 2527633                        /usr/lib64/librt-2.17.so40019ca000-40019cb000 rw-p 00007000 fe:01 2527633                        /usr/lib64/librt-2.17.so40019cb000-4001ab4000 r-xp 00000000 fe:01 2123191                        /usr/lib64/libstdc++.so.6.0.194001ab4000-4001cb4000 ---p 000e9000 fe:01 2123191                        /usr/lib64/libstdc++.so.6.0.194001cb4000-4001cbc000 r--p 000e9000 fe:01 2123191                        /usr/lib64/libstdc++.so.6.0.194001cbc000-4001cbe000 rw-p 000f1000 fe:01 2123191                        /usr/lib64/libstdc++.so.6.0.194001cbe000-4001cd3000 rw-p 00000000 00:00 0                              4001cd3000-4001ce8000 r-xp 00000000 fe:01 2123006                        /usr/lib64/libgcc_s-4.8.5-20150702.so.14001ce8000-4001ee7000 ---p 00015000 fe:01 2123006                        /usr/lib64/libgcc_s-4.8.5-20150702..so.14001ee7000-4001ee8000 r--p 00014000 fe:01 2123006                        /usr/lib64/libgcc_s-4.8.5-20150702.so.14001ee8000-4001ee9000 rw-p 00015000 fe:01 2123006                        /usr/lib64/libgcc_s-4.8.5-20150702.so.14001ee9000-4001eea000 rw-p 00000000 00:00 0                              4001eea000-40020ae000 r-xp 00000000 fe:01 2527603                        /usr/lib64/libc-2.17.so40020ae000-40022ad000 ---p 001c4000 fe:01 2527603                        /usr/lib64/libc-2.17.so40022ad000-40022b1000 r--p 001c3000 fe:01 2527603                        /usr/lib64/libc-2.17.so40022b1000-40022b3000 rw-p 001c7000 fe:01 2527603                        /usr/lib64/libc-2.17.so40022b3000-40022b8000 rw-p 00000000 00:00 0                              40022b8000-40022ba000 r-xp 00000000 fe:01 2527589                        /usr/lib64/libfreebl3.so40022ba000-40024b9000 ---p 00002000 fe:01 2527589                        /usr/lib64/libfreebl3.so40024b9000-40024ba000 r--p 00001000 fe:01 2527589                        /usr/lib64/libfreebl3.so40024ba000-40024bb000 rw-p 00002000 fe:01 2527589                        /usr/lib64/libfreebl3.so40024bb000-40024c0000 rw-p 00000000 00:00 0                              40024c1000-40024c2000 rw-p 00000000 00:00 0                              40024c7000-40024d3000 r-xp 00000000 fe:01 2527621                        /usr/lib64/libnss_files-2.17.so40024d3000-40026d2000 ---p 0000c000 fe:01 2527621                        /usr/lib64/libnss_files-2.17.so40026d2000-40026d3000 r--p 0000b000 fe:01 2527621                        /usr/lib64/libnss_files-2.17.so40026d3000-40026d4000 rw-p 0000c000 fe:01 2527621                        /usr/lib64/libnss_files-2.17.so40026d4000-40026da000 rw-p 00000000 00:00 0                              40026dc000-4004767000 rw-p 00000000 00:00 0                              400476a000-400c2f1000 rw-p 00000000 00:00 0                              400db9d000-400e3c0000 rw-p 00000000 00:00 0                              400e3c1000-401044c000 rw-p 00000000 00:00 0                              401044d000-40215ba000 rw-p 00000000 00:00 0                              40215bd000-4023648000 rw-p 00000000 00:00 0                              4023649000-4023ec1000 rw-p 00000000 00:00 0                              4023eca000-4023ecb000 rw-p 00000000 00:00 0                              4024000000-4024021000 rw-p 00000000 00:00 0                              4024021000-4028000000 ---p 00000000 00:00 0                              ffffffffff600000-ffffffffff601000 --xp 00000000 00:00 0                  [vsyscall]===============================================MiDeface::FaceIntensityStats()Mode2 12 12  4362qemu: uncaught target signal 6 (Aborted) - core dumpedAbortERROR:############With a docker image using Ubuntu base, the error is MiDeface::SegFace()qemu: uncaught target signal 11 (Segmentation fault) - core dumpedSegmentation faultERROR:############# model: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://github.com/freesurfer/freesurfer/blob/dev/Dockerfile# DockerfileFROM ubuntu:22.04COPY freesurfer_ubuntu22-7.4.0_amd64.deb /tmp/fs.deb# installRUN apt-get update \    && apt-get install -y /tmp/fs.deb \    && rm -rf /var/lib/apt/lists/* \    && rm /tmp/fs..debCOPY license /usr/local/freesurfer/7.4.0/.license# setup fs envENV OS LinuxENV FREESURFER_HOME /usr/local/freesurfer/7.4.0ENV PATH ${FREESURFER_HOME}/bin:${FREESURFER_HOME}/fsfast/bin:${FREESURFER_HOME}/tktools:{$FREESURFER_HOME}/mni/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/binENV FREESURFER ${FREESURFER_HOME}ENV SUBJECTS_DIR ${FREESURFER_HOME}/subjectsENV LOCAL_DIR ${FREESURFER_HOME}/localENV FSFAST_HOME ${FREESURFER_HOME}/fsfastENV FMRI_ANALYSIS_DIR ${FREESURFER_HOME}/fsfastENV FUNCTIONALS_DIR ${FREESURFER_HOME}/sessionsENV FS_LICENSE ${FREESURFER_HOME}/.license# set default fs optionsENV FS_OVERRIDE 0ENV FIX_VERTEX_AREA ""ENV FSF_OUTPUT_FORMAT nii.gz# mni env requirementsENV MINC_BIN_DIR ${FREESURFER_HOME}/mni/binENV MINC_LIB_DIR ${FREESURFER_HOME}/mni/libENV MNI_DIR ${FREESURFER_HOME}/mniENV MNI_DATAPATH ${FREESURFER_HOME}/mni/dataENV MNI_PERL5LIB ${FREESURFER_HOME}/mni/share/perl5ENV PERL5LIB ${FREESURFER_HOME}/mni/share/perl5Thanks!Patrick Sadil, PhD (he/him/his)Research Associatepsadil.github.io/psadil_______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1laBDOs68qgMCwS6DLNr5FqHfBCv5WY81hMckdEareZx45… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] recon-all
by fsbuild 17 May '23

17 May '23

External Email - Use Caution I think your SUBJECTS_DIR environment variable is still set to the default spath to ubject data that is set by default in the 7.2.0 release.  It is not intended that you add your own subjects in the freesurfer distribution as those are examples (and you don’t have write permission there on purpose). I would try manually setting (override) SUBJECTS_DIR in your environment to point to a path that is not under /usr/local, e.g., in your home drectory.  The akira subject data needs to live under a path set in SUBJECTS_DIR where you have both read/write permission. - R. On May 17, 2023, at 16:27, Douglas N. Greve <dgreve(a)mgh.harvard.edu> wrote:        External Email - Use Caution        can't read that. can you cut-and-paste into the email?On 5/17/2023 1:29 PM, mahmoodasdfzjy wrote:        External Email - Use Caution        SorryI have a problem when I want to recon-all my T1-MPRAGE data.I face with this probmlem that attached it.Can you help me?<storage_emulated_0_DCIM_Camera_%DB%B2%DB%B0%DB%B2%DB%B3%DB%B0%DB%B5%DB%B1%DB%B7_%DB%B2%DB%B1%DB%B5%DB%B9%DB%B2%DB%B5_jpg_1684344578234.jpeg>ارسال شده از دستگاه Galaxy من_______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/10Ij9n2Z5PYSrTFqoz6-gzphOQum4VEDByrvSWKsyQTPci… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

recon-all
by mahmoodasdfzjy 17 May '23

17 May '23

External Email - Use Caution SorryI have a problem when I want to recon-all my T1-MPRAGE data.I face with this probmlem that attached it.Can you help me?ارسال شده از دستگاه Galaxy من

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Uncaught exceptions when processing some images with MiDeFace
by Patrick Sadil 17 May '23

17 May '23

External Email - Use Caution Hello, I am trying to process several images with MiDeFace but running into issues with memory and uncaught exceptions. Of 50 images, about half are processed successfully. On the other half MiDeFace fails consistently. However, whether the images fail seems to depend on the platform. Here's what I've tried * Fails * freesurfer-linux-centos7_x86_64-7.4.0.tar.gz install on HPC, CentOS Linux release 7.9.2009 (Core) * freesurfer-linux-centos7_x86_64-7.3.2.tar.gz install on HPC, CentOS Linux release 7.9.2009 (Core) * Apptainer image from docker://freesurfer/freesurfer<https://secure-web.cisco.com/1DvhrFu1kaP9PaSAhS39FlCLj-NcldxBMN98KtNtuXGp8B…>:7.3.2, (this is built on CentOS:7) run on HPC * Docker image from docker://freesurfer/freesurfer<https://secure-web.cisco.com/1DvhrFu1kaP9PaSAhS39FlCLj-NcldxBMN98KtNtuXGp8B…>:7.3.2, (this is built on CentOS:7) Apple M1 Pro; 13.3.1 * Custom docker image (below), built and run on Apple M1 Pro; 13.3.1 * Succeeds * freesurfer-darwin-macOS-7.4.0.pkg, installed and run on Apple M1 Pro; 13.3.1 So, I'm not sure whether this is a bug or something that I need to configure differently. ############ Example apptainer command $ apptainer exec -e -B $(pwd):/data docker://freesurfer/freesurfer:7.3.2 mideface --i /data/volume.nii.gz --o /data/defaced.nii.gz --odir /data/qa Example docker command > docker run --rm -it -v $(pwd):/data freesurfer/freesurfer:7.3.2 mideface --i /data/volume.nii.gz --o /data/defaced.nii.gz --odir /data/qa Example "bare" command > mideface --i volume.nii.gz --o defaced.nii.gz --odir qa ############ On the CentOS runs, the error is MiDeface::SegFace() *** Error in `mri_defacer': double free or corruption (!prev): 0x000000000e4d64f0 *** ======= Backtrace: ========= /lib64/libc.so.6(+0x81329)[0x4001f6b329] mri_defacer[0x4b0ebe] mri_defacer[0x422c15] mri_defacer[0x415308] /lib64/libc.so.6(__libc_start_main+0xf5)[0x4001f0c555] mri_defacer[0x418367] ======= Memory map: ======== 400000-700000 r-xp 00000000 fe:01 4223092 /usr/local/freesurfer/bin/mri_defacer 700000-900000 ---p 00000000 00:00 0 900000-908000 r--p 00300000 fe:01 4223092 /usr/local/freesurfer/bin/mri_defacer 908000-932000 rw-p 00308000 fe:01 4223092 /usr/local/freesurfer/bin/mri_defacer 932000-13ee1000 rw-p 00000000 00:00 0 4000000000-4000001000 ---p 00000000 00:00 0 4000001000-4000801000 rw-p 00000000 00:00 0 [stack] 4000801000-4000823000 r-xp 00000000 fe:01 2527596 /usr/lib64/ld-2.17.so 4000823000-4000a22000 ---p 00000000 00:00 0 4000a22000-4000a23000 r--p 00021000 fe:01 2527596 /usr/lib64/ld-2.17.so 4000a23000-4000a24000 rw-p 00022000 fe:01 2527596 /usr/lib64/ld-2.17.so 4000a24000-4000a27000 rw-p 00000000 00:00 0 4000a2b000-4000a2c000 rw-p 00000000 00:00 0 4000a2c000-4000a41000 r-xp 00000000 fe:01 2527648 /usr/lib64/libz.so.1.2.7 4000a41000-4000c40000 ---p 00015000 fe:01 2527648 /usr/lib64/libz.so.1.2.7 4000c40000-4000c41000 r--p 00014000 fe:01 2527648 /usr/lib64/libz.so.1.2.7 4000c41000-4000c42000 rw-p 00015000 fe:01 2527648 /usr/lib64/libz.so.1.2.7 4000c42000-4000c59000 r-xp 00000000 fe:01 2527629 /usr/lib64/libpthread-2.17.so 4000c59000-4000e58000 ---p 00017000 fe:01 2527629 /usr/lib64/libpthread-2.17.so 4000e58000-4000e59000 r--p 00016000 fe:01 2527629 /usr/lib64/libpthread-2.17.so 4000e59000-4000e5a000 rw-p 00017000 fe:01 2527629 /usr/lib64/libpthread-2.17.so 4000e5a000-4000e5e000 rw-p 00000000 00:00 0 4000e5e000-4000e60000 r-xp 00000000 fe:01 2527609 /usr/lib64/libdl-2.17.so 4000e60000-4001060000 ---p 00002000 fe:01 2527609 /usr/lib64/libdl-2.17.so 4001060000-4001061000 r--p 00002000 fe:01 2527609 /usr/lib64/libdl-2.17.so 4001061000-4001062000 rw-p 00003000 fe:01 2527609 /usr/lib64/libdl-2.17.so 4001062000-4001063000 rw-p 00000000 00:00 0 4001063000-4001164000 r-xp 00000000 fe:01 2527611 /usr/lib64/libm-2.17.so 4001164000-4001363000 ---p 00101000 fe:01 2527611 /usr/lib64/libm-2.17.so 4001363000-4001364000 r--p 00100000 fe:01 2527611 /usr/lib64/libm-2.17.so 4001364000-4001365000 rw-p 00101000 fe:01 2527611 /usr/lib64/libm-2.17.so 4001365000-400138a000 r-xp 00000000 fe:01 2527938 /usr/lib64/libgomp.so.1.0.0 400138a000-4001589000 ---p 00025000 fe:01 2527938 /usr/lib64/libgomp.so.1.0.0 4001589000-400158a000 r--p 00024000 fe:01 2527938 /usr/lib64/libgomp.so.1.0.0 400158a000-400158b000 rw-p 00025000 fe:01 2527938 /usr/lib64/libgomp.so.1.0.0 400158b000-4001593000 r-xp 00000000 fe:01 2527607 /usr/lib64/libcrypt-2.17.so 4001593000-4001792000 ---p 00008000 fe:01 2527607 /usr/lib64/libcrypt-2.17.so 4001792000-4001793000 r--p 00007000 fe:01 2527607 /usr/lib64/libcrypt-2.17.so 4001793000-4001794000 rw-p 00008000 fe:01 2527607 /usr/lib64/libcrypt-2.17.so 4001794000-40017c3000 rw-p 00000000 00:00 0 40017c3000-40017ca000 r-xp 00000000 fe:01 2527633 /usr/lib64/librt-2.17.so 40017ca000-40019c9000 ---p 00007000 fe:01 2527633 /usr/lib64/librt-2.17.so 40019c9000-40019ca000 r--p 00006000 fe:01 2527633 /usr/lib64/librt-2.17.so 40019ca000-40019cb000 rw-p 00007000 fe:01 2527633 /usr/lib64/librt-2.17.so 40019cb000-4001ab4000 r-xp 00000000 fe:01 2123191 /usr/lib64/libstdc++.so.6.0.19 4001ab4000-4001cb4000 ---p 000e9000 fe:01 2123191 /usr/lib64/libstdc++.so.6.0.19 4001cb4000-4001cbc000 r--p 000e9000 fe:01 2123191 /usr/lib64/libstdc++.so.6.0.19 4001cbc000-4001cbe000 rw-p 000f1000 fe:01 2123191 /usr/lib64/libstdc++.so.6.0.19 4001cbe000-4001cd3000 rw-p 00000000 00:00 0 4001cd3000-4001ce8000 r-xp 00000000 fe:01 2123006 /usr/lib64/libgcc_s-4.8.5-20150702.so.1 4001ce8000-4001ee7000 ---p 00015000 fe:01 2123006 /usr/lib64/libgcc_s-4.8.5-20150702.so.1 4001ee7000-4001ee8000 r--p 00014000 fe:01 2123006 /usr/lib64/libgcc_s-4.8.5-20150702.so.1 4001ee8000-4001ee9000 rw-p 00015000 fe:01 2123006 /usr/lib64/libgcc_s-4.8.5-20150702.so.1 4001ee9000-4001eea000 rw-p 00000000 00:00 0 4001eea000-40020ae000 r-xp 00000000 fe:01 2527603 /usr/lib64/libc-2.17.so 40020ae000-40022ad000 ---p 001c4000 fe:01 2527603 /usr/lib64/libc-2.17.so 40022ad000-40022b1000 r--p 001c3000 fe:01 2527603 /usr/lib64/libc-2.17.so 40022b1000-40022b3000 rw-p 001c7000 fe:01 2527603 /usr/lib64/libc-2.17.so 40022b3000-40022b8000 rw-p 00000000 00:00 0 40022b8000-40022ba000 r-xp 00000000 fe:01 2527589 /usr/lib64/libfreebl3.so 40022ba000-40024b9000 ---p 00002000 fe:01 2527589 /usr/lib64/libfreebl3.so 40024b9000-40024ba000 r--p 00001000 fe:01 2527589 /usr/lib64/libfreebl3.so 40024ba000-40024bb000 rw-p 00002000 fe:01 2527589 /usr/lib64/libfreebl3.so 40024bb000-40024c0000 rw-p 00000000 00:00 0 40024c1000-40024c2000 rw-p 00000000 00:00 0 40024c7000-40024d3000 r-xp 00000000 fe:01 2527621 /usr/lib64/libnss_files-2.17.so 40024d3000-40026d2000 ---p 0000c000 fe:01 2527621 /usr/lib64/libnss_files-2.17.so 40026d2000-40026d3000 r--p 0000b000 fe:01 2527621 /usr/lib64/libnss_files-2.17.so 40026d3000-40026d4000 rw-p 0000c000 fe:01 2527621 /usr/lib64/libnss_files-2.17.so 40026d4000-40026da000 rw-p 00000000 00:00 0 40026dc000-4004767000 rw-p 00000000 00:00 0 400476a000-400c2f1000 rw-p 00000000 00:00 0 400db9d000-400e3c0000 rw-p 00000000 00:00 0 400e3c1000-401044c000 rw-p 00000000 00:00 0 401044d000-40215ba000 rw-p 00000000 00:00 0 40215bd000-4023648000 rw-p 00000000 00:00 0 4023649000-4023ec1000 rw-p 00000000 00:00 0 4023eca000-4023ecb000 rw-p 00000000 00:00 0 4024000000-4024021000 rw-p 00000000 00:00 0 4024021000-4028000000 ---p 00000000 00:00 0 ffffffffff600000-ffffffffff601000 --xp 00000000 00:00 0 [vsyscall] =============================================== MiDeface::FaceIntensityStats() Mode2 12 12 4362 qemu: uncaught target signal 6 (Aborted) - core dumped Abort ERROR: ############ With a docker image using Ubuntu base, the error is MiDeface::SegFace() qemu: uncaught target signal 11 (Segmentation fault) - core dumped Segmentation fault ERROR: ############ # model: https://secure-web.cisco.com/136_Zz066Z8cbbdchcsatHGiXtRECWueMMcLlf0uVeUENN… # Dockerfile FROM ubuntu:22.04 COPY freesurfer_ubuntu22-7.4.0_amd64.deb /tmp/fs.deb # install RUN apt-get update \ && apt-get install -y /tmp/fs.deb \ && rm -rf /var/lib/apt/lists/* \ && rm /tmp/fs.deb COPY license /usr/local/freesurfer/7.4.0/.license # setup fs env ENV OS Linux ENV FREESURFER_HOME /usr/local/freesurfer/7.4.0 ENV PATH ${FREESURFER_HOME}/bin:${FREESURFER_HOME}/fsfast/bin:${FREESURFER_HOME}/tktools:{$FREESURFER_HOME}/mni/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ENV FREESURFER ${FREESURFER_HOME} ENV SUBJECTS_DIR ${FREESURFER_HOME}/subjects ENV LOCAL_DIR ${FREESURFER_HOME}/local ENV FSFAST_HOME ${FREESURFER_HOME}/fsfast ENV FMRI_ANALYSIS_DIR ${FREESURFER_HOME}/fsfast ENV FUNCTIONALS_DIR ${FREESURFER_HOME}/sessions ENV FS_LICENSE ${FREESURFER_HOME}/.license # set default fs options ENV FS_OVERRIDE 0 ENV FIX_VERTEX_AREA "" ENV FSF_OUTPUT_FORMAT nii.gz # mni env requirements ENV MINC_BIN_DIR ${FREESURFER_HOME}/mni/bin ENV MINC_LIB_DIR ${FREESURFER_HOME}/mni/lib ENV MNI_DIR ${FREESURFER_HOME}/mni ENV MNI_DATAPATH ${FREESURFER_HOME}/mni/data ENV MNI_PERL5LIB ${FREESURFER_HOME}/mni/share/perl5 ENV PERL5LIB ${FREESURFER_HOME}/mni/share/perl5 Thanks! Patrick Sadil, PhD (he/him/his) Research Associate psadil.github.io/psadil

2 1

Virtual Machine Passcode
by Mert T 16 May '23

16 May '23

External Email - Use Caution Hi guys, I've just installed the VirtualBox and downloaded the virtual machine file. It seems I need a passcode to unzip this file. Can you kindly send the password to me? Kind regards.

1 0

Imaging Neuroscience
by Thomas Yeo 16 May '23

16 May '23

External Email - Use Caution Hi Everyone, As you might have heard, all NeuroImage and NeuroImage:Reports editors have resigned over Elsevier's very high publication fee, and have started a new non-profit Open Access journal with MIT Press: https://secure-web.cisco.com/1d8gc4yQK--K6_pnZ9cOod_o0laFRAu2-c0A6lgqNZKpRU… Our resignation came with great regret, and a huge amount of thought and discussion - please read our announcement (on the web page above) to get more details. We are now open for submission of new papers to Imaging Neuroscience. This allows for the review process to proceed without delay. The production & publication process for accepted papers will then wait until full journal opening (aiming for mid-July). Also, some authors with papers under review at NeuroImage have asked to transfer over, into review at Imaging Neuroscience. We are ready for this; please include all information about your review process to date in your cover letter. Thanks, Thomas

1 0

Password for ubuntu .7z file extraction
by Leonidas Georgiou 16 May '23

16 May '23

External Email - Use Caution Hello, I am in the process of installing the software in ubuntu and download the file suggested from tour website. It however asks for a password to open the .7z file. Can you please send it to me? Regards, Leonidas

1 0

Re: [Freesurfer] EasyReg Troubleshoot - Killed
by Nadia Kane 15 May '23

15 May '23

External Email - Use Caution Hi, Would you be able to provide any more insight to this? I'd like to see if I could get it working on my dataset. Thanks! Nadia Nadia Kane Junior Imaging Specialist University Imaging Centers | University of Minnesota https://secure-web.cisco.com/1Dp0KeyuQGxjGxxQG4cd3dICoCOK5g0SzcXsZbujsLbuHd… On Fri, May 12, 2023 at 7:54 PM Nadia Kane <kanex161(a)umn.edu> wrote: > Thank you for your response! I checked the segmentations and they don't > look right either. I've uploaded the original files as well as the > segmentation files. Would you be able to check it out closer? Again these > are synthetic ABA brain data. > > Here is information about the file names: > brain_00.nii.gz: floating image > atlas.nii.gz: reference image > flo_seg.nii.gz: floating segmentation image > ref_seg.nii.gz: reference segmentation image > > Thanks, > Nadia > > > Nadia Kane > > Junior Imaging Specialist > > University Imaging Centers | University of Minnesota > https://secure-web.cisco.com/1Dp0KeyuQGxjGxxQG4cd3dICoCOK5g0SzcXsZbujsLbuHd… > brain_00.nii.gz > <https://secure-web.cisco.com/1a8DaiQkMUIj_ISi7JKFGZKgog8TiVHLvYkH0-5Z8SW84o…> > > > > > On Fri, May 12, 2023 at 5:17 PM Iglesias Gonzalez, Juan E. < > JIGLESIASGONZALEZ(a)mgh.harvard.edu> wrote: > >> External Email - Use Caution >> >> Dear Nadia, >> >> It seems like many centroids are missing. Did you visually check the >> segmentations of the reference and floating image, e.g., with Freeview? Do >> they look good? >> >> Cheers, >> >> /Eugenio >> >> >> >> -- >> >> Juan Eugenio Iglesias >> >> http://secure-web.cisco.com/1gIMOiLDRYDqwQu7fG8TejC0-ir5JMzHUhFQTuFjxEk69xR… >> >> >> >> *From: *freesurfer-bounces(a)nmr.mgh.harvard.edu < >> freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Nadia Kane < >> kanex161(a)umn.edu> >> *Date: *Wednesday, May 10, 2023 at 6:57 PM >> *To: *freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> >> *Subject: *Re: [Freesurfer] EasyReg Troubleshoot - Killed >> >> * External Email - Use Caution * >> >> Hi, >> >> I increased the memory, and it ran partially to create the segmented >> input images, however I reached this error that I don't quite understand: >> >> >> >> 2023-05-10 17:16:15.526359: I tensorflow/tsl/cuda/cudart_stub.cc:28] >> Could not find cuda drivers on your machine, GPU will not be used. >> 2023-05-10 17:16:15.609260: I tensorflow/tsl/cuda/cudart_stub.cc:28] >> Could not find cuda drivers on your machine, GPU will not be used. >> 2023-05-10 17:16:18.907335: W >> tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could >> not find TensorRT >> using 1 thread >> Segmentation of reference image already exists; reading from disk >> Segmentation of floating image already exists; reading from disk >> Linear registration >> Computing centroids and estimating affine transform >> Traceback (most recent call last): >> File "/scratch.global/tpengo/freesurfer/python/scripts/mri_easyreg", >> line 1809, in <module> >> main() >> File "/scratch.global/tpengo/freesurfer/python/scripts/mri_easyreg", >> line 194, in main >> Mflo = getM(atlasCOG[:, ok > 0], floCOG[:, ok > 0]) >> File "/scratch.global/tpengo/freesurfer/python/scripts/mri_easyreg", >> line 1198, in getM >> x = np.matmul(np.linalg.inv(np.matmul(np.transpose(A), A)), >> np.matmul(np.transpose(A), b)) >> File "<__array_function__ internals>", line 180, in inv >> File >> "/scratch.global/tpengo/freesurfer/python/lib/python3.8/site-packages/numpy/linalg/linalg.py", >> line 552, in inv >> ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj) >> File >> "/scratch.global/tpengo/freesurfer/python/lib/python3.8/site-packages/numpy/linalg/linalg.py", >> line 89, in _raise_linalgerror_singular >> raise LinAlgError("Singular matrix") >> numpy.linalg.LinAlgError: Singular matrix >> >> >> >> >> Nadia Kane >> >> Junior Imaging Specialist >> >> University Imaging Centers | University of Minnesota >> >> *MailScanner has detected a possible fraud attempt from >> "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1Dp0KeyuQGxjGxxQG4cd3dICoCOK5g0SzcXsZbujsLbuHd… >> <https://secure-web.cisco.com/1CgfJ293M5EIHLM0zgv8CWqjm5qLHzRSUoMULMp0eirEbB…> >> >> >> >> >> >> >> >> On Tue, May 9, 2023 at 12:38 PM Nadia Kane <kanex161(a)umn.edu> wrote: >> >> Hi, >> >> I'm working on applying deep learning in image registration for a >> master's project. The overarching goal was to use real tissue clearing >> lightsheet data to perform the image registration, but first created some >> synthetically deformed brains based on the Allen Brain Atlas and Lab2im >> algorithm >> <https://secure-web.cisco.com/1LleH4XmcSc3vbFU8r_dMj1epTIr9qgP95cyHn0T9IwgC_…>. >> However, I'm having some issues implementing the command in an Centos Linux >> 7 (Core) HPC environment. The command gets Killed, I'm wondering if you >> could provide some more insight? Thank you! >> >> >> >> I've set up my environment as follows: >> >> >> >> module load mamba >> mamba create -n freesurf # I named the environment freesurf >> conda activate freesurf >> mamba install tensorflow-gpu cuda-version=11.8 >> >> >> >> >> I've attached the easyreg.sh shell script that I run. Here's the output: >> >> >> >> (freesurfer) kanex161@agc02 [~/Documents/Thesis/code] % bash easyreg.sh >> 2023-05-09 11:19:32.374206: I tensorflow/tsl/cuda/cudart_stub.cc:28] >> Could not find cuda drivers on your machine, GPU will not be used. >> 2023-05-09 11:19:32.405672: I tensorflow/tsl/cuda/cudart_stub.cc:28] >> Could not find cuda drivers on your machine, GPU will not be used. >> 2023-05-09 11:19:32.405981: I >> tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary >> is optimized to use available CPU instructions in performance-critical >> operations. >> To enable the following instructions: AVX2 FMA, in other operations, >> rebuild TensorFlow with the appropriate compiler flags. >> 2023-05-09 11:19:33.258226: W >> tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could >> not find TensorRT >> [W interface.cpp:47] Warning: Loading nvfuser library failed with: Error >> in dlopen: libnvfuser_codegen.so: cannot open shared object file: No such >> file or directory (function LoadingNvfuserLibrary) >> using 1 thread >> Segmenting reference image >> Reading reference image >> Setting up segmentation net >> 2023-05-09 11:19:38.489093: E >> tensorflow/compiler/xla/stream_executor/cuda/cuda_driver.cc:266] failed >> call to cuInit: CUDA_ERROR_NO_DEVICE: no CUDA-capable device is detected >> 2023-05-09 11:19:38.489166: I >> tensorflow/compiler/xla/stream_executor/cuda/cuda_diagnostics.cc:168] >> retrieving CUDA diagnostic information for host: agc02 >> 2023-05-09 11:19:38.489202: I >> tensorflow/compiler/xla/stream_executor/cuda/cuda_diagnostics.cc:175] >> hostname: agc02 >> 2023-05-09 11:19:38.489460: I >> tensorflow/compiler/xla/stream_executor/cuda/cuda_diagnostics.cc:199] >> libcuda reported version is: 470.103.1 >> 2023-05-09 11:19:38.489502: I >> tensorflow/compiler/xla/stream_executor/cuda/cuda_diagnostics.cc:203] >> kernel reported version is: 470.103.1 >> 2023-05-09 11:19:38.489530: I >> tensorflow/compiler/xla/stream_executor/cuda/cuda_diagnostics.cc:309] >> kernel version seems to match DSO: 470.103.1 >> Inference / segmentation >> easyreg.sh: line 8: 1108392 Killed ./mri_easyreg --ref >> /home/umii/kanex161/Documents/Thesis/data/outputs/atlas/atlas.nii.gz --flo >> /home/umii/kanex161/Documents/Thesis/data/outputs/lab2im/brains/brain_00.nii.gz >> --ref_seg >> /home/umii/kanex161/Documents/Thesis/data/outputs/easyreg/ref_seg.nii.gz >> --flo_seg >> /home/umii/kanex161/Documents/Thesis/data/outputs/easyreg/flo_seg.nii.gz >> --flo_reg >> /home/umii/kanex161/Documents/Thesis/data/outputs/easyreg/flo_reg.nii.gz >> --fwd_field >> /home/umii/kanex161/Documents/Thesis/data/outputs/easyreg/fwd_field.nii.gz >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://secure-web.cisco.com/1qLYsybXokH6Mlxb8os-fUiQrVWsq1OzULGrXVfJlbxVUl… >> 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 Mass General >> Brigham Compliance HelpLine at >> https://secure-web.cisco.com/18OkIo0E19u0EW3GOeaBwKtwYz9l3ug2q-32ZwtKUCzioC… < >> https://secure-web.cisco.com/18OkIo0E19u0EW3GOeaBwKtwYz9l3ug2q-32ZwtKUCzioC…> . >> Please note that this e-mail is not secure (encrypted). If you do not >> wish to continue communication over unencrypted e-mail, please notify the >> sender of this message immediately. Continuing to send or respond to >> e-mail after receiving this message means you understand and accept this >> risk and wish to continue to communicate over unencrypted e-mail. >> >

1 0

Cerebellum + Subcortical models extraction
by Nathan Santana Schunk 15 May '23

15 May '23

External Email - Use Caution Hi, I would like to know about the acquisitions of the cerebellum and subcortical areas. I ask if you, Freesurfer developers, could recommend any software script that allows me to extract the cerebellum in a high enough quality? Does Freesurfer offers the best known (by you) tool to do so or does somewhere else has a more specialized script for this purpose? Also, just to confirm, does the current recon-all_clinical register all the subcortical areas? Or do I need to perform an specific command to properly get them? I want to connect all the intracranial neuro matter (Cortex + Subcortical area + cerebellum) in a single volume, for this purpose I pretend to place the structures in the exact coordinates they're supposed to be, according to each other positions. If there's any suggestion on how I could do it accuratelly, I ask for your assistance. One last thing, could you inform me of the existence of programs that allows me to analyse my brain data, and through that get outputs showing me possible indications? (I won't use these for clinical purposes, these won't I search for that and

2 2

mri_synthmorph
by Nadia Kane 15 May '23

15 May '23

External Email - Use Caution Hi, I tried using mri_synthmorph in FreeSurfer on synthetic mouse brain data, but my output moved image is just black pixels. Thanks, Nadia Nadia Kane Junior Imaging Specialist University Imaging Centers | University of Minnesota https://secure-web.cisco.com/1-_2xu5FXwci4r2dOLiyNlYk4-xv-fvNQHJ5NU5FNen836…

2 1

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Freesurfer May 2023