Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30076 discussions

cluster failing on HCP freesurfer script
by Sanchez, Juan (NYSPI) 26 Oct '18

26 Oct '18

External Email - Use Caution Dear community, My group is using the latest version of condor clustering to process our data on OS X. We have a bash script that calls freesurfer to run our HCP pipelines. I can run the script to completion when running it locally on each of the clustered machines, however when submitting the job I get the following error Can’t locate MNI/Startup.pm in @INC (you may need to install the MNI::Startup module) (@INC contains: /Applications/freesurfer/mni/lib/../System/Library/Perl/5.8.6 /Library/Perl/5.18/darwin-thread-multi-2level /Library/Perl/5.18 /Network/Library/Perl/5.18/darwin-thread-multi-2level /Network/Library/Perl/5.18 /Library/Perl/Updates/5.18.2 /System/Library/Perl/5.18/darwin-thread-multi-2level /System/Library/Perl/5.18 /System/Library/Perl/Extras/5.18/darwin-thread-multi-2level /System/Library/Perl/Extras/5.18 .) at /Applications/freesurfer/mni/bin/nu_correct line 37. BEGIN failed--compilation aborted at /Applications/freesurfer/mni/bin/nu_correct line 37. (standard_in) 2: comparison in expression Can anyone suggest a solution? Thanks J

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Re: [Freesurfer] Error in segmentHA_T1.sh
by Scheffler, F, Mev [fredas＠sun.ac.za] 26 Oct '18

26 Oct '18

External Email - Use Caution Sorry, scratch that. Apparently it just didn’t realise that my subjects were in a subdirectory in the subjects directory. Running now. Note to self: “Think before you click send” Kind regards, FREDA SCHEFFLER Research Assistant / PhD Candidate [email.jpg] MA Research Psychology Faculty of Medicine and Health Sciences Fakulteit Geneeskunde en Gesondheidswetenskappe Universiteit Stellenbosch University PO Box | Posbus 241, Cape Town | Kaapstad, 8000 Francie van Zijl Drive | -rylaan, Tygerberg, 7505 South Africa | Suid-Afrika Tel: +27 21 938 9771 Email | E-pos: fredas(a)sun.ac.za From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Scheffler, F, Mev [fredas(a)sun.ac.za]" <fredas(a)sun.ac.za> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Friday, 26 October 2018 at 18:24 To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Error in segmentHA_T1.sh External Email - Use Caution Dear Freesurfer Developers I’ve run recon-all -all on a batch of 20 subjects on a linux based high performance computing setup and am now trying to run the segmentHA_T1 on them as well. It sets up the environment and then complains about myMRIread and Error in segmentSubjectT1_autoEstimateAlveusML (line 157) Here is the command line output: #-------------------------------------------- #@# Hippocampal Subfields processing (T1) left Fri Oct 26 18:06:27 SAST 2018 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is <redacted, because I’m paranoid> Error using myMRIread (line 16) Error in myMRIread: temporary directory does not exist Error in segmentSubjectT1_autoEstimateAlveusML (line 157) @#@FSTIME 2018:10:26:18:06:27 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 e 107.33 S 6.58 U 8.77 P 14% M 145072 F 14363 R 298922 W 0 c 179 w 32314 I 33416 O 0 L 0.02 5.50 14.86 @#@FSLOADPOST 2018:10:26:18:08:14 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 0.78 4.16 13.38 Linux cnode0070 3.10.0-514.6.1.el7.x86_64 #1 SMP Wed Jan 18 13:06:36 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux T1 hippocampal subfields exited with ERRORS at Fri Oct 26 18:08:15 SAST 2018 What am I doing wrong here? Thanks very much. Kind regards, FREDA SCHEFFLER Research Assistant / PhD Candidate [email.jpg] MA Research Psychology Faculty of Medicine and Health Sciences Fakulteit Geneeskunde en Gesondheidswetenskappe Universiteit Stellenbosch University PO Box | Posbus 241, Cape Town | Kaapstad, 8000 Francie van Zijl Drive | -rylaan, Tygerberg, 7505 South Africa | Suid-Afrika Tel: +27 21 938 9771 Email | E-pos: fredas(a)sun.ac.za [http://cdn.sun.ac.za/100/ProductionFooter.jpg]<http://www.sun.ac.za/english/about-us/strategic-documents> The integrity and confidentiality of this email are governed by these terms. Disclaimer<http://www.sun.ac.za/emaildisclaimer%20> Die integriteit en vertroulikheid van hierdie e-pos word deur die volgende bepalings bereël. Vrywaringsklousule<http://www.sun.ac.za/emaildisclaimer%20>

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Segmentation fault
by Whitney, Jon 26 Oct '18

26 Oct '18

External Email - Use Caution Hey Freesurfer team, I'm working on running Tracula, and have been running into segmentation fault issues. We have consistently been running into segmentation fault issues. * The data we are working with comes from children*, and I'm concerned that differences in MRI image brightness and mapping between adult and children's brains may be throwing Tracula off. In many cases the typical pathlist of files ( lh.cst_AS, rh.cst_AS, etc) are not fully populated in the bedp step. We have therefore started submitting the job with the set pathlist and set ncpts to only point to files which are generated during the bedp step. Nonetheless, we are still getting segmentation fault errors during the final path step. I'm using freesurfer version 6.0.0-2beb96c, but I'm not sure what version of Tracula I'm using. This is a log of the error: Initial proposal SD file: /data/Abeona/W4WUM/dlabel/diff/lh.cst_AS_avg33_mni_bbr_cpts_6_std.txt /data/Abeona/W4WUM/dlabel/diff/rh.cst_AS_avg33_mni_bbr_cpts_6_std.txt /data/Abeona/W4WUM/dlabel/diff/lh.ilf_AS_avg33_mni_bbr_cpts_5_std.txt /data/Abeona/W4WUM/dlabel/diff/rh.ilf_AS_avg33_mni_bbr_cpts_5_std.txt /data/Abeona/W4WUM/dlabel/diff/lh.unc_AS_avg33_mni_bbr_cpts_5_std.txt /data/Abeona/W4WUM/dlabel/diff/rh.unc_AS_avg33_mni_bbr_cpts_5_std.txt /data/Abeona/W4WUM/dlabel/diff/fmajor_PP_avg33_mni_bbr_cpts_7_std.txt /data/Abeona/W4WUM/dlabel/diff/fminor_PP_avg33_mni_bbr_cpts_5_std.txt /data/Abeona/W4WUM/dlabel/diff/lh.atr_PP_avg33_mni_bbr_cpts_5_std.txt /data/Abeona/W4WUM/dlabel/diff/rh.atr_PP_avg33_mni_bbr_cpts_5_std.txt /data/Abeona/W4WUM/dlabel/diff/lh.ccg_PP_avg33_mni_bbr_cpts_5_std.txt /data/Abeona/W4WUM/dlabel/diff/rh.ccg_PP_avg33_mni_bbr_cpts_5_std.txt /data/Abeona/W4WUM/dlabel/diff/lh.cab_PP_avg33_mni_bbr_cpts_4_std.txt /data/Abeona/W4WUM/dlabel/diff/rh.cab_PP_avg33_mni_bbr_cpts_4_std.txt /data/Abeona/W4WUM/dlabel/diff/lh.slfp_PP_avg33_mni_bbr_cpts_5_std.txt /data/Abeona/W4WUM/dlabel/diff/rh.slfp_PP_avg33_mni_bbr_cpts_5_std.txt /data/Abeona/W4WUM/dlabel/diff/lh.slft_PP_avg33_mni_bbr_cpts_5_std.txt /data/Abeona/W4WUM/dlabel/diff/rh.slft_PP_avg33_mni_bbr_cpts_5_std.txt Loading DWIs from /data/Abeona/W4WUM/dmri/dwi.nii.gz Loading mask from /data/Abeona/W4WUM/dlabel/diff/aparc+aseg_mask.bbr.nii.gz Loading BEDPOST parameter samples from /data/Abeona/W4WUM/dmri.bedpostX Loading b-values from /data/Abeona/W4WUM/dmri/bvals Loading gradients from /data/Abeona/W4WUM/dmri/bvecs INFO: Found 1 baseline images (b = 0) out of a total of 31 frames Segmentation fault (core dumped) Linux ip-10-0-0-222 4.4.0-137-generic #163-Ubuntu SMP Mon Sep 24 13:14:43 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux trac-paths exited with ERRORS at Wed Oct 24 01:22:16 UTC 2018 The Freesurfer help I've looked at previous suggested that it could be a memory error, but we're using a remote drive that has lots of disk space and 26 GB RAM, so I doubt that's it. Checked the LANG, we are using en_US.UTF-8. I've run this on at least 8 different patients so far, and only one of them has not had this kind of error. Some of the different patients have different numbers of the normal path files exported into /dlabel/diff/, so it seems like there is patient-to-patient variability in how well the bedp phase is able to map things out. Thanks for your help! -Jon -- Notice: This e-mail message, together with any attachments, contains information of ERT that may be confidential, proprietary copyrighted and/or legally privileged, and is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please immediately return this by e-mail and then delete it.

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Error in segmentHA_T1.sh
by Scheffler, F, Mev [fredas＠sun.ac.za] 26 Oct '18

26 Oct '18

External Email - Use Caution Dear Freesurfer Developers I’ve run recon-all -all on a batch of 20 subjects on a linux based high performance computing setup and am now trying to run the segmentHA_T1 on them as well. It sets up the environment and then complains about myMRIread and Error in segmentSubjectT1_autoEstimateAlveusML (line 157) Here is the command line output: #-------------------------------------------- #@# Hippocampal Subfields processing (T1) left Fri Oct 26 18:06:27 SAST 2018 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is <redacted, because I’m paranoid> Error using myMRIread (line 16) Error in myMRIread: temporary directory does not exist Error in segmentSubjectT1_autoEstimateAlveusML (line 157) @#@FSTIME 2018:10:26:18:06:27 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 e 107.33 S 6.58 U 8.77 P 14% M 145072 F 14363 R 298922 W 0 c 179 w 32314 I 33416 O 0 L 0.02 5.50 14.86 @#@FSLOADPOST 2018:10:26:18:08:14 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 0.78 4.16 13.38 Linux cnode0070 3.10.0-514.6.1.el7.x86_64 #1 SMP Wed Jan 18 13:06:36 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux T1 hippocampal subfields exited with ERRORS at Fri Oct 26 18:08:15 SAST 2018 What am I doing wrong here? Thanks very much. Kind regards, FREDA SCHEFFLER Research Assistant / PhD Candidate [email.jpg] MA Research Psychology Faculty of Medicine and Health Sciences Fakulteit Geneeskunde en Gesondheidswetenskappe Universiteit Stellenbosch University PO Box | Posbus 241, Cape Town | Kaapstad, 8000 Francie van Zijl Drive | -rylaan, Tygerberg, 7505 South Africa | Suid-Afrika Tel: +27 21 938 9771 Email | E-pos: fredas(a)sun.ac.za [http://cdn.sun.ac.za/100/ProductionFooter.jpg]<http://www.sun.ac.za/english/about-us/strategic-documents> The integrity and confidentiality of this email are governed by these terms. Disclaimer<http://www.sun.ac.za/emaildisclaimer> Die integriteit en vertroulikheid van hierdie e-pos word deur die volgende bepalings bereël. Vrywaringsklousule<http://www.sun.ac.za/emaildisclaimer>

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smoothwm.H vs curv
by Chris Adamson 26 Oct '18

26 Oct '18

External Email - Use Caution Freesurfer devs, I want to be able to compute mean curvature in a compatible way to ?h.curv with existing tools but not within the recon-all pipeline. I notice that ?h.curv is written in mris_make_surfaces. I want to just use mris_curvature. This is used to write smoothwm.H. So seemingly I can use mris_curvature to write out the same output as ?h.curv. However, why is ?h.smoothwm.H different to ?h.curv? It seems to be produced with exactly the same code, i.e. MRISComputeMetricProperties, MRISComputeSecondFundamentalForm, MRISuseMeanCurvature, MRISaverageCurvatures ... Thanks in advance, Chris Adamson. Disclaimer This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Children’s Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication.

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Freesurfer commands not found - unable to install
by Thaker, Ashesh A 25 Oct '18

25 Oct '18

External Email - Use Caution Dear Freesurfer team, Surely there is a simple fix to my problem, but I've been unable to succesfully run Freesurfer commands after many attempts (with my very basic bash knowledge) and searching prior archives. I'm running Freesurfer on a 64-bit machine, Ubuntu 18.04 LTS. No Freesurfer commands work (files not found), except the "freesurfer" command. I've included some pertinent output below. All of the installation files seem to be in the right place and the path seems to be correct, so I'm perplexed. Any help very much appreciated. Kind regards, Ashesh Thaker, MD | Assistant Professor School of Medicine, Department of Radiology University of Colorado Anschutz Medical Campus  720 848 6568 (office) | ashesh.thaker(a)ucdenver.edu ------------------- ashesh@ashesh-gpu:~$ export FREESURFER_HOME=/usr/local/freesurfer ashesh@ashesh-gpu:~$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni FSL_DIR /usr/local/fsl ashesh@ashesh-gpu:~$ recon-all bash: /usr/local/freesurfer/bin/recon-all: /bin/tcsh: bad interpreter: No such file or directory ashesh@ashesh-gpu:~$ freeview bash: /usr/local/freesurfer/bin/freeview: /bin/tcsh: bad interpreter: No such file or directory ashesh@ashesh-gpu:~$ freesurfer FreeSurfer is a set of tools for the analysis and visualization of structural and functional brain imaging data. FreeSurfer also refers to the structural imaging stream within the FreeSurfer suite. Users should consult the online documentation available at: http://surfer.nmr.mgh.harvard.edu Alternatively, the 'recon-all' command help-text provides adequate information to begin processing subject data, such as the sample subject 'bert' found in the 'freesurfer/subjects' directory. Type 'recon-all --help' to view this help-text. Direct comments and questions to: freesurfer(a)nmr.mgh.harvard.edu You are running this version of FreeSurfer: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c ashesh@ashesh-gpu:~$ echo $PATH /usr/local/freesurfer/bin:/usr/local/freesurfer/fsfast/bin:/usr/local/freesurfer/tktools:/usr/local/fsl/bin:/usr/local/freesurfer/mni/bin:/usr/local/fsl/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin

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Thalamic Nuclei Parcellation Label Files Problem
by zhac looch 25 Oct '18

25 Oct '18

External Email - Use Caution Hello Freesurfer team, I just run code 'Recon-all -all' on my analyzed data. Then, I run the code down below; segmentThalamicNuclei.sh bert [SUBJECTS_DIR] That gave me 3 files named; 'ThalamicNuclei.v10.T1.FSvoxelSpace' 'ThalamicNuclei.v10.T1' and 'ThalamicNuclei.v10.T1.volumes' but I need different label files for each parcels. The thing is I don't know how to do it. Can anyone give an idea to do it? Sorry for my ignorance, as step by step guidance through setting up the parcellation would be much appreciated. Thank you...

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Cortical Parcellations in individual space using Yeo et al 2011
by Bailin, Emma 24 Oct '18

24 Oct '18

Hello, I'm preparing to do resting state analyses and I'd like to use the Yeo 2011 network atlas for the cortical parcellations. Looking through the archive, I know that mri_surf2surf with the -sval-annot flag can be used to convert the fsaverage from the Yeo et al 2011 study to an individual subject space, but I noticed a caveat to this when I called mri_surf2surf -help. The caveat is on example 5: "this is not a substitute for running the cortical parcellation! The parcellations that it maps to the new subject may not be appropriate for that subject." Given this information, I've got a few questions: 1) How accurate is the mapping using mri_surf2surf? That is, is it good for preliminary data, but not for the final analysis? 2) How do you run the cortical parcellation using the Yeo 2011 atlas? [I know that mris_ca_train and mris_ca_label exist, but I'm unsure if they are the right commands to run when I'm not building my own atlas] 3) If I do the cortical parcellations using the Yeo 2011 atlas, will the edits/labels I've done using the Desikan atlas remain accurate? This goes back to the second question, as I'm not sure where in the general processing stage I need to go. Thank you! Sincerely, Emma Bailin Emma Bailin Research Coordinator Laboratory for Visual Neuroplasticity Schepens Eye Research Institute Mass. Eye and Ear Infirmary Harvard Medical School Mass. Eye and Ear Confidentiality Notice: This e-mail and any files transmitted with it are confidential and are intended solely for the use of the individual(s) addressed in the message above. This communication may contain sensitive or confidential information. If you are not an intended recipient, dissemination, forwarding, printing, or copying of this e-mail is strictly prohibited. If you believe you have received this e-mail in error and the email contains patient information, please contact the Mass. Eye and Ear Compliance Line at 844-815-4401. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and delete the e-mail.

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Yeo 2011 Functional Cortical Parcellations
by Bronwyn Overs 24 Oct '18

24 Oct '18

Hi Mailing List, I am attempting to apply the Yeo 2011 7-network fucntional parcellations to a set of fs MRIs processed with v5.1.0. Below are listed the first three steps I plan to take and I am seeking advice as to: A) Whether this approach is valid. B) Steps to take next. * Steps 1-3: * *1. Run MNI152 1mm template through recon-all* recon-all -i FSL_MNI152_FreeSurferConformed_1mm.nii -subjid Yeo2011_MNI152_FS recon-all -all -subjid Yeo2011_MNI152_FS *2. Warp the Yeo_atlas1mm.nii.gz to freesurfer nonlinear volumetric space* mri_vol2vol --mov Yeo2011_7Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii --s Yeo2011_MNI152_FS --targ $FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z --o Yeo2011_atlas_FSI.nii.gz --nearest *3. warp the Yeo_atlas_freesurfer_internal_space.nii.gz to each subject:* mri_vol2vol --mov $SUBJECTS_DIR/subjID/mri/norm.mgz --s subjID --targ Yeo2011_atlas_FSI.nii.gz --m3z talairach.m3z --o Yeo2011_atlas_subjID.nii.gz --nearest --inv-morph When previously mapping the Choi 2012 straital parcellations, steps 4 and 5 were: 4. *Creating a striatal mask in the native subject's space from freesurfer segmented Caudate (11 & 50), Putamen (12 & 51), and Accumbens (26 & 58)*: mri_binarize --i subjID/mri/aparc+aseg.mgz --match 11 --match 12 --match 26 --match 50 --match 51 --match 58 --o striatum_mask.nii.gz *5. **Using this mask to mask the choi striatal parcellations* fslmaths Choi2012_atlas_subjID.nii.gz -mas striatum_mask_subjID.nii.gz Yeo_atlas_subjID_mask.nii.gz Do I need to do a similar thing for the Yeo cortical parcellations and if so what regions should I include in the cortical mask? -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 neura.edu.au <http://neura.edu.au> Follow @neuraustralia on twitter <https://twitter.com/neuraustralia>Follow NeuRA on facebook <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe>

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Is the cortical thickness calculated using Hausdorff distance in FreeSurfer?
by Zhiliang Long 24 Oct '18

24 Oct '18

External Email - Use Caution Dear FS experts: I'm doing a project about the changes of cortical thickness after sleep deprivation. I know that cortical thickness is calculated as the closest distance from the gray/white boundary to the gray/CSF boundary at each vertex. Is the thickness calculated using the Hausdorff distance? Best Zhiliang Long

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