Freesurfer April 2022

freesurfer@nmr.mgh.harvard.edu

97 participants
155 discussions

Using Glaser Atlas (HCP-MMP1) on Standard Recon-All
by Ruben sn:: RMO2cmZlbA== 07 Apr '22

07 Apr '22

External Email - Use Caution Hi all, I'm trying to use the Glaser atlas (HCP-MMP1) to get thickness, volume, and area measures for an existing fs-subject, meaning that the standard recon-all was already performed. I was able to extract some measures, but it would be nice to get verified that my approach is valid. I'm using FreeSurfer 7.1 and have already applied standard recon-all to all my subjects. The following variables are used: $subjid = folder name of the recon-all output for a specific subject $hcpdir = the directory where I stored the annotation files for the hcp-atlas I got annotation files with the atlas projected onto fsaverage from here https://secure-web.cisco.com/1I7iKyRV6ybWIIhCzcBweKSPq9s7w7SmrhQN_FfL8XYj8j…. Then I applied the annotation files to get the statistics file using: mris_anatomical_stats -th3 -mgz -cortex $subjid/label/lh.cortex.label -f lh.hcp.stats -b -a $hcpdir/lh.HCP-MMP1.annot f475 lh white Subsequently, I used the following commands to extract measures in CSV files. aparcstats2table --delimiter comma --subjects $subjid --parc hcp --hemi lh --meas area --transpose --tablefile lh_hpc_area_stats.csv aparcstats2table --delimiter comma --subjects $subjid --parc hcp --hemi lh --meas volume --transpose --tablefile lh_hpc_volume_stats.csv aparcstats2table --delimiter comma --subjects $subjid --parc hcp --hemi lh --meas thickness --transpose --tablefile lh_hpc_thickness_stats.csv Is this a valid approach, and would I get meaningful values, or would I have to run some other additional steps? Kind regards, Ruben Dörfel.

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Hippocampal Segmentation issue on Freesurfer 7.2.0 on MacOS Monterey 12.2
by Ashwati Vipin (Dr) 06 Apr '22

06 Apr '22

External Email - Use Caution Dear Freesurfer developers, The hip segmentation starts running and the matlab icon pops up as well but it stops abruptly and shows this error instead: #-------------------------------------------- #@# Hippocampal Subfields processing (T1) left Wed Apr 6 13:44:29 +08 2022 ------------------------------------------ Setting up environment variables --- DYLD_LIBRARY_PATH is .:/Applications/freesurfer/7.2.0/MCRv84//runtime/maci64:/Applications/freesurfer/7.2.0/MCRv84//bin/maci64:/Applications/freesurfer/7.2.0/MCRv84//sys/os/maci64:/Applications/freesurfer/7.2.0/lib/gcc/lib: Registering imageDump.mgz to hippocampal mask from ASEG Error using images.internal.morphmex Invalid MEX-file '/tmp/MCR_3070620170/.mcrCache8.4/segmen0/toolbox/images/images/+images/+internal/morphmex.mexmaci64': dlopen(/tmp/MCR_3070620170/.mcrCache8.4/segmen0/toolbox/images/images/+images/+internal/morphmex.mexmaci64, 0x0006): Library not loaded: @rpath/libmwimages_res.dylib Referenced from: /private/tmp/MCR_3070620170/.mcrCache8.4/segmen0/toolbox/images/images/+images/+internal/morphmex.mexmaci64 Reason: tried: './libmwimages_res.dylib' (no such file), '/Applications/freesurfer/7.2.0/MCRv84//runtime/maci64/libmwimages_res.dylib' (no such file), '/Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwimages_res.dylib' (no such file), '/Applications/freesurfer/7.2.0/MCRv84//sys/os/maci64/libmwimages_res.dylib' (no such file), '/Applications/freesurfer/7.2.0/lib/gcc/lib/libmwimages_res.dylib' (no such file), '/libmwimages_res.dylib' (no such file), '/private/tmp/MCR_3070620170/.mcrCache8.4/segmen0/toolbox/images/images/+images/+internal/libmwimages_res.dylib' (no such file), '/private/tmp/MCR_3070620170/.mcrCache8.4/segmen0/toolbox/images/images/+images/+internal/./libmwimages_res.dylib' (no such file), '/private/tmp/MCR_3070620170/.mcrCache8.4/segmen0/toolbox/images/images/+images/+internal/../../../../../bin/maci64/libmwimages_res.dylib' (no such file), '/private/tmp/MCR_3070620170/.mcrCache8.4/segmen0/toolbox/images/images/+images/+internal/../../../../../sys/os/maci64/libmwimages_res.dylib' (no such file), '/private/tmp/MCR_3070620170/.mcrCache8.4/segmen0/toolbox/images/images/+images/+internal/libmwimages_res.dylib' (no such file), '/private/tmp/MCR_3070620170/.mcrCache8.4/segmen0/toolbox/images/images/+images/+internal/./libmwimages_res.dylib' (no such file), '/private/tmp/MCR_3070620170/.mcrCache8.4/segmen0/toolbox/images/images/+images/+internal/../../../../../bin/maci64/libmwimages_res.dylib' (no such file), '/private/tmp/MCR_3070620170/.mcrCache8.4/segmen0/toolbox/images/images/+images/+internal/../../../../../sys/os/maci64/libmwimages_res.dylib' (no such file), '/Applications/MATLAB_R2014b.app/bin/maci64/libmwimages_res.dylib' (no such file), '/Applications/MATLAB_R2014b.app/bin/maci64/./libmwimages_res.dylib' (no such file), '/Applications/MATLAB_R2014b.app/bin/maci64/../../sys/os/maci64/libmwimages_res.dylib' (no such file), '/Applications/freesurfer/7.2.0/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/libmwimages_res.dylib' (no such file), '/Applications/freesurfer/7.2.0/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/./libmwimages_res.dylib' (no such file), '/Applications/freesurfer/7.2.0/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/../../sys/os/maci64/libmwimages_res.dylib' (no such file), '/usr/local/lib/libmwimages_res.dylib' (no such file), '/usr/lib/libmwimages_res.dylib' (no such file) Error in images.internal.morphop (line 99) Error in imerode (line 122) Error in segmentSubjectT1_autoEstimateAlveusML (line 188) MATLAB:invalidMEXFile Darwin Ashwatis-MacBook-Pro.local 21.3.0 Darwin Kernel Version 21.3.0: Wed Jan 5 21:37:58 PST 2022; root:xnu-8019.80.24~20/RELEASE_ARM64_T8101 arm64 T1 hippocampal subfields exited with ERRORS at Wed Apr 6 13:44:48 +08 2022 For more details, see the log file /Users/ashwativipin/Desktop/Freesurfer/Stats//BIOC_0001_v01_T1_FS/scripts/hippocampal-subfields-T1.log I’ve attached the logfile as well. ls /Applications/freesurfer/7.2.0/MCRv84/ gives me the following output: [cid2539829440*image001.png(a)01D849BC.F5AB1960] Please help. Best, Ashwati -- Ashwati Vipin (PhD) Research Fellow - Dementia Research Centre Lee Kong Chian School of Medicine Nanyang Technological University, Singapore [signature_1222593402] ________________________________ CONFIDENTIALITY: This email is intended solely for the person(s) named and may be confidential and/or privileged. If you are not the intended recipient, please delete it, notify us and do not copy, use, or disclose its contents. Towards a sustainable earth: Print only when necessary. Thank you.

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Re: [Freesurfer] FreeSurfer VirtualBox Image
by fsbuild 06 Apr '22

06 Apr '22

External Email - Use Caution Sending the info to your email shortly. - R. On Apr 5, 2022, at 21:56, Marc <mddirisi(a)lakeheadu.ca> wrote:        External Email - Use Caution        Hi there!I was following the FreeSurfer VirtualBox installation tutorial on the wiki (https://secure-web.cisco.com/1_udjFHwPLIJrynuPi7juHksX6N9r5hAnQtEydx919pNax…) and was wondering if I could get the password for the encrypted archive.Thanks in advance! _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Mri Convert Brucker MGRE files dicom to nii error
by Mateo Jean 06 Apr '22

06 Apr '22

External Email - Use Caution Hello FreeSurfer Developers I need to convert 512 dicom files from Bruker into .nii . I firstly add .dcm to my Bruker multi gradient echo phase files then enter the following command : mri_convert MRIm001.dcm phaseMGE.nii Here is the first message : reading from MRIm001.dcm... Starting DICOMRead2() dcmfile = /mnt/c/Users/Sahadatou/Documents/Stage_JEAN_2022/data/fantomes/tests/bug_test2/MRIm001.dcm dcmdir = /mnt/c/Users/Sahadatou/Documents/Stage_JEAN_2022/data/fantomes/tests/bug_test2 ERROR: don't know how to get DWI parameters from --Bruker BioSpin MRI GmbH -- ERROR: GetDICOMInfo(): dcmGetDWIParams() 1 DICOM File: /mnt/c/Users/Sahadatou/Documents/Stage_JEAN_2022/data/fantomes/tests/bug_test2/MRIm001.dcm break /home/rd521/space_freesurfer/build/docker_ubuntu18/trunk/rd521-7.2.0/utils/DICOMRead.cpp:4930 Ref Series No = 4 Found 514 files, checking for dicoms ERROR: don't know how to get DWI parameters from --Bruker BioSpin MRI GmbH -- ERROR: GetDICOMInfo(): dcmGetDWIParams() 1 DICOM File: /mnt/c/Users/Sahadatou/Documents/Stage_JEAN_2022/data/fantomes/tests/bug_test2/MRIm001.dcm break /home/rd521/space_freesurfer/build/docker_ubuntu18/trunk/rd521-7.2.0/utils/DICOMRead.cpp:4930 ERROR: don't know how to get DWI parameters from --Bruker BioSpin MRI GmbH -- ERROR: GetDICOMInfo(): dcmGetDWIParams() 1 Then 508 error messages like the three last lines appear. It ends with : First Sorting Computing Slice Direction Vs: 0 0 1 Vs: 0 0 1 Second Sorting IsDWI = 0, IsPhilipsDWI = 0 Counting frames nframes = 8 nslices = 63 ndcmfiles = 508 ERROR: the number of frames * number of slices does not equal the number of dicom files. I did a test with only 448 files (I just copy-paste the first 448 files = 7 TE * 64 slices) and I obtained the same error messages but the nifti files are created and seem usable (quick test with Fiji). Here are the last lines : First Sorting Computing Slice Direction Vs: 0 0 1 Vs: 0 0 1 Second Sorting IsDWI = 1, IsPhilipsDWI = 0 Counting frames nframes = 7 nslices = 64 ndcmfiles = 448 INFO: rescale not needed PE Dir = COL (dicom read) Loading pixel data TR=50.00, TE=3.10, TI=0.00, flip angle=15.00 i_ras = (-1, -0, 0) j_ras = (-0, -1, 0) k_ras = (-0, -0, 1) writing to phaseMGR.nii... Saving bvals and bvecs I'm pretty new with mri convert and I don't understand why it stops converting to nii with 512 files (8 TE) but not 448 files for Brucker files. Best Regards, Mateo Version: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b

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FreeSurfer VirtualBox Image
by Marc 05 Apr '22

05 Apr '22

1 0

MCRv84 issue on Freesurfer 7.2.0 on MacOS Monterey 12.2
by Ashwati Vipin (Dr) 05 Apr '22

05 Apr '22

External Email - Use Caution Dear Freesurfer Developers, I have recently downloaded Freesurfer 7.2.0 and am trying to run the hippocampal segmentation. I tried installing the Matlab 2014b compiler but when I run the command: sudo FREESURFER_HOME=$FREESURFER_HOME fs_install_mcr 2014b it repeatedly gives me the error: ./install: line 334: /var/folders/zz/zyxvpxvq6csfxvn_n0000000000000/T/tmp.6Gemf2Ah/bin/unknown/install_unix: No such file or directory ls: /var/folders/zz/zyxvpxvq6csfxvn_n0000000000000/T/tmp.6Gemf2Ah/install-target/v*: No such file or directory Following this I am unable to run the hippocampal subfield segmentation. Additionally, I also tried downloading the compiler separately and copying the bin/maci64 folder into a new directory under the freesurfer root directory labelled “MCRv84”. When I do this, it starts running for a second but then gives me the following error: Setting up environment variables --- DYLD_LIBRARY_PATH is .:/Applications/freesurfer/7.2.0/MCRv84//runtime/maci64:/Applications/freesurfer/7.2.0/MCRv84//bin/maci64:/Applications/freesurfer/7.2.0/MCRv84//sys/os/maci64:/Applications/freesurfer/7.2.0/lib/gcc/lib: dyld[85643]: Library not loaded: @rpath/libmwmclmcrrt.8.4.dylib Referenced from: /Applications/freesurfer/7.2.0/MCRv84/bin/maci64/libmwlaunchermain.dylib Reason: tried: './libmwmclmcrrt.8.4.dylib' (no such file), '/Applications/freesurfer/7.2.0/MCRv84//runtime/maci64/libmwmclmcrrt.8.4.dylib' (no such file), '/Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwmclmcrrt.8.4.dylib' (no such file), '/Applications/freesurfer/7.2.0/MCRv84//sys/os/maci64/libmwmclmcrrt.8.4.dylib' (no such file), '/Applications/freesurfer/7.2.0/lib/gcc/lib/libmwmclmcrrt.8.4.dylib' (no such file), '/libmwmclmcrrt.8.4.dylib' (no such file), '/Applications/freesurfer/7.2.0/MCRv84/bin/maci64/libmwmclmcrrt.8.4.dylib' (no such file), '/Applications/freesurfer/7.2.0/MCRv84/bin/maci64/./libmwmclmcrrt.8.4.dylib' (no such file), '/Applications/freesurfer/7.2.0/MCRv84/bin/maci64/../../sys/os/maci64/libmwmclmcrrt.8.4.dylib' (no such file), '/Applications/freesurfer/7.2.0/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/libmwmclmcrrt.8.4.dylib' (no such file), '/Applications/freesurfer/7.2.0/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/./libmwmclmcrrt.8.4.dylib' (no such file), '/Applications/freesurfer/7.2.0/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/../../sys/os/maci64/libmwmclmcrrt.8.4.dylib' (no such file), '/Applications/freesurfer/7.2.0/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/libmwmclmcrrt.8.4.dylib' (no such file), '/Applications/freesurfer/7.2.0/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/./libmwmclmcrrt.8.4.dylib' (no such file), '/Applications/freesurfer/7.2.0/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/../../sys/os/maci64/libmwmclmcrrt.8.4.dylib' (no such file), '/usr/local/lib/libmwmclmcrrt.8.4.dylib' (no such file), '/usr/lib/libmwmclmcrrt.8.4.dylib' (no such file) /Applications/freesurfer/7.2.0/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 33: 85643 Abort trap: 6 /Applications/freesurfer/7.2.0/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML BIOC_0001_v01_T1_FS /Users/ashwativipin/Desktop/Freesurfer/Stats/ 0.333333333333333333333333333333333333 /Applications/freesurfer/7.2.0/average/HippoSF/atlas/AtlasMesh.gz /Applications/freesurfer/7.2.0/average/HippoSF/atlas/AtlasDump.mgz /Applications/freesurfer/7.2.0/average/HippoSF/atlas/compressionLookupTable.txt 0.05 left L-BFGS v21 '/Applications/freesurfer/7.2.0/bin/fs_run_from_mcr /Applications/freesurfer/7.2.0/bin/' 0 Darwin Ashwatis-MacBook-Pro.local 21.3.0 Darwin Kernel Version 21.3.0: Wed Jan 5 21:37:58 PST 2022; root:xnu-8019.80.24~20/RELEASE_ARM64_T8101 arm64 T1 hippocampal subfields exited with ERRORS at Mon Apr 4 12:11:15 +08 2022 For more details, see the log file /Users/ashwativipin/Desktop/Freesurfer/Stats//BIOC_0001_v01_T1_FS/scripts/hippocampal-subfields-T1.log I have also attached the log file for you. Could you please help? I’m not sure what I’m doing wrong since the above steps worked just fine a few months ago. I also have matlab 2022 installed and am wondering if that could be interfering with this? Thanks so much! Hope to hear from you soon. Best, Ashwati ________________________________ CONFIDENTIALITY: This email is intended solely for the person(s) named and may be confidential and/or privileged. If you are not the intended recipient, please delete it, notify us and do not copy, use, or disclose its contents. Towards a sustainable earth: Print only when necessary. Thank you.

2 5

Re: [Freesurfer] VM pass code request
by fsbuild 05 Apr '22

05 Apr '22

External Email - Use Caution Sending the info to your email shortly. - R. On Apr 5, 2022, at 18:34, Nathan Bolander <nathan.bolander(a)gmail.com> wrote:        External Email - Use Caution        I am sending email to the list to request the pass code to extract the VM archive, as instructed in the Wiki. Best regards,Nathan _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Freesurfer 7.2.0 release in Ubuntu 18d // .ova.7z password
by fsbuild 05 Apr '22

05 Apr '22

External Email - Use Caution Sending the info to your private email shortly. - R On Apr 5, 2022, at 07:44, ΑΙΚΑΤΕΡΙΝΗ ΝΑΛΕΝΤΖΗ-ΜΑΡΙΑΝΟΥ <biomed_rad20010(a)uniwa.gr> wrote:        External Email - Use Caution        Greetings team Freesurfer,Following the instructions in your wiki page, I’m sending you to kindly provide me with the .7z password for the said file (Freesurfer 7.2.0 release in Ubuntu 18.04.06: FS_7_2_0_Ubuntu_18_04_06.ova.7z).Thanks a lot in advance,Katerina Nalentzi _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

VM pass code request
by Nathan Bolander 05 Apr '22

05 Apr '22

External Email - Use Caution I am sending email to the list to request the pass code to extract the VM archive, as instructed in the Wiki. Best regards, Nathan

1 0

Still seeking Beta Testers for new FreeSurfer discussion platform
by Sennott, Liam Ricker 05 Apr '22

05 Apr '22

Hello again, FreeSurfer community, I’m reaching out to you again today because we are still in search of people who are willing to test our new FreeSurfer help platform. Thank you to those who have already responded; we will be reaching out to you shortly. The FreeSurfer administrative team is working on transitioning the current FreeSurfer mailing list infrastructure to a new, more user-friendly platform called Discourse. We’re still finalizing the website, so we’re looking for potential beta testers for this new platform. As a beta tester, you will post your questions to Discourse and interact with the FreeSurfer staff in discussion board format. Please email lsennott(a)mgh.harvard.edu<mailto:lsennott@mgh.harvard.edu> if you are interested in helping us test this new system! Thank you, Liam Sennott FreeSurfer Admin

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Freesurfer April 2022