Freesurfer

freesurfer@nmr.mgh.harvard.edu

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segmentHA_T1.sh Error
by Zachary Miller 21 Dec '20

21 Dec '20

External Email - Use Caution Hello, I am having trouble running segmentHA_T1.sh and I hope that someone will know the solution. Per a similar thread on this mail archive, I have verified that I have writing permissions in the subject directory. My command line and FS output are below. Thank you, Zach Command: segmentHA_T1.sh CDN0001_MSB_10_7.1.1 FStests/CDN0001_MSB Output: #@# Hippocampal Subfields processing (T1) left Fri Dec 18 14:14:40 CST 2020 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/panfs/roc/msisoft/freesurfer/7.1.1/MCRv84//runtime/glnxa64:/panfs/roc/msisoft/freesurfer/7.1.1/MCRv84//bin/glnxa64:/panfs/roc/msisoft/freesurfer/7.1.1/MCRv84//sys/os/glnxa64:/panfs/roc/msisoft/freesurfer/7.1.1/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/panfs/roc/msisoft/freesurfer/7.1.1/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/panfs/roc/msisoft/freesurfer/7.1.1/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/panfs/roc/msisoft/freesurfer/7.1.1/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:/panfs/roc/msisoft/netcdf/4.6.2-gcc8.2.0-serial/lib:/panfs/roc/msisoft/hdf5/hdf5-1.10.4-gcc8.2.0-ompi-4.0.0/lib:/panfs/roc/msisoft/openmpi/el6/4.0.0/gnu-8.2.0.CentOS7/lib:/panfs/roc/msisoft/java/openjdk-11.0.2/lib:/panfs/roc/msisoft/java/openjdk-11.0.2/lib/jli:/panfs/roc/msisoft/java/openjdk-11.0.2/lib/server:/panfs/roc/msisoft/gcc/8.2.0/lib64:/panfs/roc/msisoft/isl/0.19_gcc8.1.0/lib:/panfs/roc/msisoft/mpc/1.1.0_gcc8.1.0/lib:/panfs/roc/msisoft/mpfr/4.0.1_gcc8.1.0/lib:/panfs/roc/msisoft/gmp/6.1.2_gcc8.1.0/lib:/panfs/roc/msisoft/fsl/6.0.1/lib:/panfs/roc/msisoft/matlab/R2014b/runtime/glnxa64:/panfs/roc/msisoft/gcc/8.1.0/lib64 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) @#@FSTIME 2020:12:18:14:14:40 run_segmentSubjectT1_autoEstimateAlveusML.sh N 14 e 26.52 S 1.16 U 7.38 P 32% M 268532 F 598 R 75671 W 0 c 1553 w 10745 I 492960 O 0 L 2.09 8.46 13.64 @#@FSLOADPOST 2020:12:18:14:15:06 run_segmentSubjectT1_autoEstimateAlveusML.sh N 14 2.32 8.00 13.35 Linux cn0224 3.10.0-1160.6.1.el7.x86_64 #1 SMP Tue Nov 17 13:59:11 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux T1 hippocampal subfields exited with ERRORS at Fri Dec 18 14:15:06 CST 2020 -- Zachary Miller Researcher | Institute of Child Development | College of Education and Human Development | cehd.umn.edu University of Minnesota | umn.edu mill5076(a)umn.edu

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mri_watershed error: problem in the COG calcuation
by Julia Yang 21 Dec '20

21 Dec '20

External Email - Use Caution Hi, While running the recon_all, I bumped into this error message below. \n mri_watershed -rusage /Users/Shared/PD-MCI/Freesurfer/PDMCI107/touch/rusage.mri_watershed.dat -T1 -brain_atlas /Applications/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz \n Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... mri_watershed Error: Problem in the COG calculation: T1.mgz may not contain properly normalized white-matter. Confirm that T1.mgz has enough white-matter voxels of value 110. If white-matter contains few if any voxels of value 110, try adding wm control-points to nu.mgz, and re-run recon-all. Darwin med-cr-mtm0xv 18.7.0 Darwin Kernel Version 18.7.0: Thu Jan 23 06:52:12 PST 2020; root:xnu-4903.278.25~1/RELEASE_X86_64 x86_64 recon-all -s PDMCI107 exited with ERRORS at Wed Nov Recon_all failed without creating the brainmask.mgz. I have attached files for possible solution. * Recon-all.log * Nu.mgz * Talairach_with_skull.log * Talairach.xfm Any help would be much appreciated. Kind Regards, Julia Yang

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Autorecon-pial error: freadFloat: fread failed
by Steve Petersen 20 Dec '20

20 Dec '20

External Email - Use Caution Dear Freesurfer experts, After ran the recon-all and correct some pial surface errors in freeview I ran the autorecon-pial command in order to move the pial surface in the right place. All have worked fine in all subjects except in one subject because freesurfer gave to me the following error: [image: imagen.png] How can I fix this problem? Thank you for your time! Best regards,

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Re: [Freesurfer] FS on Ubuntu {Disarmed}
by fsbuild 18 Dec '20

18 Dec '20

External Email - Use Caution Hello Olga, I have not tried the FS 5.3 binaries on an Ubuntu 20 system, but I suspect some shared library references won’t be resolved there.  Even if the FS 5.3 source were to compile on Ubuntu 20, you would likely get some discrepancy in numeric output because of the differences in compilers and libraries.  If you still need to work with FS 5.3 on a newer OS like Ubuntu 20, then you could run the FS 5.3.3 binaries on an older OS like CentOS 6 inside a virtual machine (VM) or container hosted on your Ubuntu 20 system.  VirtualBox is a popular (and free) VM host that runs on most OS's. If you can switch to Freesurfer version 7 then you have some other options. The latest freesurfer 7.1.1 release has installers and binary archives you can download for CentOS 6, 7 and 8.  I believe the CentOS 7 binaries run on Ubuntu 18 (but I have not tried them on Ubuntu 20), Those downloads can be found at, https://secure-web.cisco.com/1fiK2AG75PXa5w6a8FpU6jpBuXQsVUOqz3E0vWVP_aN8fx… We do build the Freesurfer development 7.X.X branch on Ubuntu 18, so you could try those binaries on Ubuntu 20.  Because they are from the development branch, the binaries have not been tested like a release.  But I think binary backwards compatibility should work on Ubuntu 20 for binaries built on Ubuntu 18.  You can download the development archive in a browser via the  link, https://secure-web.cisco.com/1sf6F6d9mG-C6NMXOvnqb9YSyiyXbwrovzLyNphBSIsLhHjAb3VaA6_mniHn_8y35jTdUTeyTW2ur9zbdDhmoMnH-1k2eB_bScdMLCzp5gaJG8e4cpkBkKFSS4e1eEfrX-sQM5g_0LzusgqwolIWDTwH9gte5d5dP1_5KOklAFDrSqgu0pxcoXeLNVrtA_IQFxR7BOzdYp_NhvW6zMgdZFMq8ftTlZqMtg8zysm6CfoYOiaHcwqUAMXJy-RicVC-_zMsHDR7KXzcOR3cuOsbCnA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2Ffreesurfer-linux-ubuntu18_x86_64-dev.tar.gz Or via the wget command from the terminal on your Ubuntu 20 system,$ wget https://secure-web.cisco.com/1sf6F6d9mG-C6NMXOvnqb9YSyiyXbwrovzLyNphBSIsLhH… - R. On Dec 17, 2020, at 10:10, Olga Kepinska <olga.kepinska(a)univie.ac.at> wrote:        External Email - Use Caution        Dear colleagues, I am looking for information about installing FS on Ubuntu 20.04. One concern is that we might need to be able to use an older version of FS (e.g. FS 5.3), and from what we can tell that won't even be compatible with Ubuntu 18.04, see: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall5.3 Cent… is not an option for us as it will not be supported by our institution from 2021. Thank you in advance,Olga Kepinska  -- Olga Kepinska, PhD Postdoctoral ResearcherBrain and Language Lab (http://secure-web.cisco.com/1i423Xj2Jko1XHGoEo0dtinsit1Xj1MNk2m0tu_Z-y3JGMQ… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Regarding MNI152 TEMPLATE
by Rahul Sharma 17 Dec '20

17 Dec '20

External Email - Use Caution Dear All, Hope everyone is safe and well. Did anyone you have MNI152 TEMPLATE mainly required for Alzheimer's Diagnosis. Also can anyone help in recommending any tool other than FREESURFER for preprocessing of sMRI scans for Alzheimer's disease but the only requirement is it should work on windows

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ERROR HC subfield segmentation_FS7.1.1
by alessioproposito＠libero.it 17 Dec '20

17 Dec '20

External Email - Use Caution Dear FreeSurfer Developers, I would like to run the Hippocampus subfields segmentation on Freesurfer 7.1.1. I am working on a HCP cluster with CentOS 7 (Core). Before running the segmentation on my data, I first tried to run the segmentation on your fully recon-ed subject Bert typing 'segmentHA_T1.sh bert'. Unfortunately the process stopped after one minute and it reported the following error: Out of memory. Type HELP MEMORY for your options. Error in segmentSubjectT1_autoEstimateAlveusML (line 210) I've searched the list and no similar errors have been reported. Also, I have attached the hippocampal-subfields-T1.log file in case it's of any use. 1) FreeSurfer version: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 2) Platform: CentOS Linux 7 (Core) 3) Kernel: Linux 4.19.94-300.el7.x86_64 Does anyone have any suggestions on how this can be fixed? Thank very much you in advance! Kind Regards, Alessio

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FS on Ubuntu {Disarmed}
by Olga Kepinska 17 Dec '20

17 Dec '20

External Email - Use Caution Dear colleagues, I am looking for information about installing FS on Ubuntu 20.04. One concern is that we might need to be able to use an older version of FS (e.g. FS 5.3), and from what we can tell that won't even be compatible with Ubuntu 18.04, see: https://secure-web.cisco.com/12yFhpguZQG1d_b4BXMaeOwlINSfTKLpFiTVaH-Gvv3Akk… Centos is not an option for us as it will not be supported by our institution from 2021. Thank you in advance, Olga Kepinska -- Olga Kepinska, PhD  Postdoctoral Researcher Brain and Language Lab (http://secure-web.cisco.com/1dsrrXwsfqJVmxauFjO5Ik59NRfuRWZJmirpH3bWpg4T9dO…) @olgakepinska

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Re: [Freesurfer] Freesurfer Digest, Vol 202, Issue 30 {Disarmed}
by vittal korann 17 Dec '20

17 Dec '20

External Email - Use Caution Hi Douglas, Thanks a lot for your kind explanation! With regards Vittal On Thu, Dec 17, 2020 at 8:12 PM <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://secure-web.cisco.com/1d5gSB-rqVInM6onHMLDbLhUREGgzCvmI5zHvbuwq-S_PJ… > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Re: HCP_1200 parcellation problems (Greve, Douglas N.,Ph.D.) > 2. Re: need assistance to decode QDEC results > (Greve, Douglas N.,Ph.D.) > 3. Re: Cortical thickness volume ROI to surface {Disarmed} > (Greve, Douglas N.,Ph.D.) > 4. Re: Error in selxavg3-sess (Greve, Douglas N.,Ph.D.) > 5. Re: cannot find freesurfer/average/RB_all_2008-03-26.gca with > -use-gpu in v5.3 (Greve, Douglas N.,Ph.D.) > 6. Re: cannot find freesurfer/average/RB_all_2008-03-26.gca with > -use-gpu in v5.3 {Disarmed} (Caspar M. Schwiedrzik) > 7. Re: group analyses {Disarmed} (Greve, Douglas N.,Ph.D.) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 17 Dec 2020 14:28:37 +0000 > From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> > Subject: Re: [Freesurfer] HCP_1200 parcellation problems > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <786b64c3-2d99-06ed-2fe3-812225238514(a)mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > Sorry, I can't tell from your email what the problem is. Can you elaborate? > > On 12/9/2020 2:30 PM, najme soleimani wrote: > > External Email - Use Caution > > Dear FreeSurfer Developers, > I downloaded the HCP_1200 subjects' structural extended data. I am > attempting to have equal sized parcellation on scale 100, so I used > parcellation results of Desikan atlas and increased the parcels from 68 to > 100. > after obtaining split file, I run the following commands on FreeSurfer: > mris_divide_parcellation subj lh aparc.annot splitfile Desikan100 > mris_divide_parcellation subj rh aparc.annot splitfile Desikan100 > mri_aparc2aseg --s subj --annot Desikan100 --old-ribbon --o > $SUBJECTS_DIR/subj/mri/Desikan100.subj.mgz > The interesting part is that after running this command some > disconnectivity were seen in the parcels as it is shown in the picture. In > 3D view, also, when the parcels were loaded on dsi studio, there were some > holes on the parcels which caused disconnected parcels. > I will appreciate if you help me to solve this problem. > > > kind regards, > Najme > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://secure-web.cisco.com/1d5gSB-rqVInM6onHMLDbLhUREGgzCvmI5zHvbuwq-S_PJ… > >

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cannot find freesurfer/average/RB_all_2008-03-26.gca with -use-gpu in v5.3
by Caspar M. Schwiedrzik 17 Dec '20

17 Dec '20

External Email - Use Caution Hi! I am trying to run recon-all in version 5.3 with the -use-gpu flag. I am getting a strange error that I would love to get your input on: cannot find freesurfer/average/RB_all_2008-03-26.gca Neither the file nor the path exist. This is the entire input and output: recon-all -s hum_14600_parallel -i /neuro_tools/freesurfer/subjects/hum_14600/mri/011/mp2rage.nii -all -use-gpu Testing for CUDA device: nvcc: NVIDIA (R) Cuda compiler driver Copyright (c) 2005-2012 NVIDIA Corporation Built on Fri_Sep_21_17:28:58_PDT_2012 Cuda compilation tools, release 5.0, V0.2.1221 Driver : 10.0 Runtime : 5.0 Acquiring CUDA device Using default device CUDA device: Tesla K40m ======= NUMBER OF OPENMP THREADS = 1 ======= stable5 NVIDIA driver version info: NVRM version: NVIDIA UNIX x86_64 Kernel Module 410.79 Thu Nov 15 10:41:04 CST 2018 ERROR: cannot find /neuro_tools/freesurfer/average/RB_all_2008-03-26.gca Is there some documentation on how to set up the environment beyond LD_LIBRARY_PATH? Could that be the issue? Everything works fine without the -use-gpu flag. Thank you! Caspar

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Cortical thickness volume ROI to surface {Disarmed}
by Alina Rojas 17 Dec '20

17 Dec '20

External Email - Use Caution Hello Freesurfer experts, I am attempting to register a ROI (.nii) to the surface of fsaverage to get the statistical output on the cortical thickness. I followed your instructions on https://secure-web.cisco.com/1vMR3HBqveQVdV1izVoGaJ5VcRtbR7HBn6ADoe1ai7ok5u… <https://secure-web.cisco.com/1vMR3HBqveQVdV1izVoGaJ5VcRtbR7HBn6ADoe1ai7ok5u…> but after mri_vol2surf I get this message, I can’t visualize the ROI on the surface. I I’m using Freesurfer 7.0.1. How can I solve this? Thank you, Alina Rojas. srcvol = M1_L.nii.gz srcreg = tmp.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjDist = 0.5 reshape = 0 interp = nearest float2int = round GetProjMax = 1 INFO: float2int code = 0 INFO: using NIfTI-1 qform Done loading volume INFO: This REGISTER_DAT transform is valid only for volumes between COR types with c_(r,a,s) = 0. Input reg is register.dat -------- original matrix ----------- 1.00000 0.00000 0.00000 2.49380; 0.00000 0.00000 1.00000 -22.50500; 0.00000 -1.00000 0.00000 -9.53872; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Reading surface /fsaverage/surf/lh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 0 0 1 using old 2 0.1 0 1 using old 3 0.2 0 1 using old 4 0.3 0 1 using old 5 0.4 0 1 using old 6 0.5 0 1 using old 7 0.6 0 1 using old 8 0.7 0 1 using old 9 0.8 0 1 using old 10 0.9 0 1 using old Done mapping volume to surface Number of source voxels hit = 75073 Writing to lh.fsaverage.M1_L.mgh Dim: 163842 1 1 surfcolor: Subscript out of range.

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