Freesurfer

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30070 discussions

trac-all with or without sub-thalamic nuclei segmentation
by Woo-Suk Tae 02 Jul '23

02 Jul '23

External Email - Use Caution Dear FreeSurfer developer. I successfully completed the tracula trac-all analysis using freesurfer 7.4.1. ThalamicNuclei.v13.T1.FSvoxelSpace.mgz images were obtained using segmentThalamicNuclei.sh, and trac-all analyses results were obtained using both set usethalnuc = 0 and 1 in the tracula config option. The tracts obtained from the two analyzes were similar in general, but slightly different in detail. Can you elaborate a bit more on what the usethalnuc option does to the results? Sincerely yours. Woo-Suk, Tae Seoul, Korea ---------------------------------------------------------------------------------------- Woo-Suk, Tae Ph.D. Research Professor Brain Convergence Research Center, Medical Research Center Anam Hospital, Korea University Medical Center, Seoul, Korea mobile: 82-10-9120-4629 office: 82-2-920-6831 email: wstae(a)korea.ac.kr, woosuk.tae(a)gmail.com, wo <woostae(a)naver.com>ostae(a)gmail.com ----------------------------------------------------------------------------------------

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Cluster summary table
by Maria Czarnecka 02 Jul '23

02 Jul '23

External Email - Use Caution Dear Experts, I calculated a conjunction using "mri_concat". I have a beautiful map but I need a cluster summary table for it. How can I get that? Best, Maria Czarnecka

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Re: [Freesurfer] mris_label2annot
by Maria Czarnecka 02 Jul '23

02 Jul '23

External Email - Use Caution Dear Yujing, Thank you so much for your answer. My ctab looks like this: 11100 Unknown 0 0 0 0 11102 G_and_S_occipital_inf 0 0 0 0 11111 G_cuneus 0 0 0 0 11119 G_occipital_middle 221 60 60 0 11120 G_occipital_sup 0 0 0 0 11121 G_oc-temp_lat-fusifor 0 0 0 0 11122 G_oc-temp_med-Lingual 0 0 0 0 11130 G_precuneus 0 0 0 0 11143 Pole_occipital 221 60 60 0 11145 S_calcarine 221 60 60 0 11158 S_oc_middle_and_Lunatus 0 0 0 0 11160 S_occipital_ant 0 0 0 0 11161 S_oc-temp_lat 20 180 140 0 11162 S_oc-temp_med_and_Lingual 0 0 0 0 11166 S_parieto_occipital 221 60 60 0 a sample of one of my label files: #!ascii label , from subject fsaverage vox2ras=TkReg 1630 139 -4.532 -75.888 20.953 0.0000000000 300 -15.423 -72.840 16.348 0.0000000000 301 -15.452 -76.689 23.049 0.0000000000 571 -15.631 -67.683 9.887 0.0000000000 573 -4.258 -84.880 12.147 0.0000000000 version of FreeSurfer: freesurfer-linux-centos7_x86_64-7.3.2-20220804-6354275

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Excellent results from recon-all-clinical
by Michael Mc Laughlin 30 Jun '23

30 Jun '23

External Email - Use Caution Hi, I just wanted to say how impressed I am by the Freesurfer brain analysis software in general and to share some results of a comparison of the new *recon-all-clinical *option with various contrast types and resolutions. This is only one subject, a healthy 62 year old male, so it's a very small study indeed, but the recon-all clinical does a great job in finding the correct volume of gray and white matter with some very low resolution clinical MRIs with non-ideal contrast MRI settings. As you can see below, the T2 and T2 FLAIR gray and white volumes results with 0.72mm x 0.72mm x 6.5mm get very close to the correct volumes as measured by recon-all on the T1-MPRAGE scan. When I look at the actual detail of the slices it looks good too. Obviously it can't do magic and it has to basically "guess" where the information is completely missing when there is 6.5mm between slices. The cortex tissue volumes for the T1 headscout, which is 1.6mm cubic voxels and has very low contrast between white and gray is also very good, considering the data it has to work with. The standard recon-all is not designed to work with a clinical T1 SE scan and naturally, does a much poorer GM/WM segmentation job. Here are the results I got: [image: image.png] [image: image.png] [image: image.png] [image: image.png] So, well done to the whole Freesurfer crew and especially to the volunteers who devote so much time to this support list. Michael McLaughlin, 2019 Parsons Medal Holder

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recon-all ends with error
by Justin Kasowski 29 Jun '23

29 Jun '23

External Email - Use Caution Writing masked volume to brain.finalsurfs.mgz...done. @#@FSTIME 2023:06:28:16:19:10 mri_mask N 5 e 0.51 S 0.01 U 0.44 P 89% M 74240 F 0 R 2972 W 0 c 3 w 760 I 0 O 0 L 0.13 0.04 0.01 @#@FSLOADPOST 2023:06:28:16:19:11 mri_mask N 5 0.13 0.04 0.01 #-------------------------------------------- #@# Fill Wed Jun 28 16:19:11 PDT 2023 /mnt/c/Users/BigBrain/documents/Subjects/sub-049/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.presurf.mgz -ctab /usr/local/freesurfer/7.2.0/SubCorticalMassLUT.txt -auto-man filled.auto.mgz filled.mgz ../tmp/filled.edits.txt wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.presurf.mgz... error: volume size must be greater than 0 in every dimension Command exited with non-zero status 1 The error implies aseg.presurf.mgz or talairach.lta have a 0 dimension, but neither do. mri_info for aseg.presurf is below, I've attached the log and talairach.lta files: bigbrain@DESKTOP-EDQPTKK:/mnt/c/Users/BigBrain/Documents/Subjects/sub-049/mri$ mri_info aseg.presurf.mgz Volume information for aseg.presurf.mgz type: MGH dimensions: 256 x 256 x 256

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Longitudinal structural analysis in FreeSurfer ???
by Hamied Haroon 29 Jun '23

29 Jun '23

External Email - Use Caution Hello, I've run recon-all on patient T1s acquired at different timepoints after a neurological insult, in FreeSurfer v7.3.2 I want to analyse any change in the volume, surface area and average thickness of specific regions across time in each patient. Can I do this in FreeSurfer? Many thanks. Best wishes, Hamied Dr Hamied A Haroon, MSc, PhD, MInstP Research Associate in Biomedical Magnetic Resonance Imaging The University of Manchester

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Re: [Freesurfer] Freesurfer Digest, Vol 232, Issue 12 - data not displayed
by Haley O Higginbotham 28 Jun '23

28 Jun '23

External Email - Use Caution I've re-enabled the gpu and updated the drivers, and now glxgears runs properly and freeview opens and displays data. I am still unable to click on anything in the popup editing menus though, and the cursor appears greyed out when hovering over these popup windows. I also tried MobaXterm with the same results. (Interestingly the device manager and Intel Driver and Support Assistant incorrectly suggested that the graphics driver was up-to-date and I had to manually search the Intel driver database to find the actual most current driver: 31.0.101.4502) Update: I have also had to switch to a new computer and am running Ubuntu 22.04.2 with freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 through wsl2 Thanks, Haley

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Recon-all v.7.1.1 and TRACULA 7.3.2 compatible?
by Blujus, Jenna 28 Jun '23

28 Jun '23

External Email - Use Caution Hi all, I am using TRACULA for a longitudinal analysis of WM integrity. I used the longitudinal stream from freesurfer v7.1.1 to process the T1w images via recon-all. I'd like to use TRACULA v7.3.2 to process the DWI data and generate 42 WM tracts. Can I feed in the recon-all outputs from v7.1.1 to v7.3.2 or should they be reprocessed with v7.3.2? Thank you, Jenna

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mris_label2annot
by Maria Czarnecka 28 Jun '23

28 Jun '23

External Email - Use Caution Dear Sisters and Brothers in neuroscience, I am trying to make my own annotation file that will include only occipital cortex labels from the a2009s atlas. Is it possible? I am trying to do that with: mris_label2annot --ctab lh.my-color-table.txt --a my-annot-name --h lh --s fsaverage --l lh.S_calcarine.label --l lh.S_parieto_occipita.label --l lh.G_cuneus.label --l lh.G_oc-temp_med-Lingual.label --l lh.S_collat_transv_post.label --l lh.G_and_S_occipital_inf.label --l lh.Pole_occipital.label --l lh.G_occipital_middle.label --l lh.S_oc_middle_and_Lunatus.label --l lh.S_oc_sup_and_transversal.label --l lh.G_occipital_sup.label --l lh.S_oc-temp_med_and_Lingual.label --l lh.G_oc-temp_lat-fusifor.label --l lh.S_oc-temp_lat.label If i run it i get: 0 0 1 -1 NOT_FOUND 2 -1 NOT_FOUND 3 -1 NOT_FOUND 4 -1 NOT_FOUND 5 -1 NOT_FOUND 6 -1 NOT_FOUND 7 -1 NOT_FOUND 8 -1 NOT_FOUND 9 -1 NOT_FOUND 10 -1 NOT_FOUND 11 -1 NOT_FOUND 12 -1 NOT_FOUND 13 -1 NOT_FOUND Writing annot to... The file is saved and it is empty. Where is my mistake? I will be grateful for your help, Best, Maria Czarnecka

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Re: [Freesurfer] Error running hippocampus subfields and amygdala nuclei segmentation pipeline
by Mengjie Huang 27 Jun '23

27 Jun '23

External Email - Use Caution Hi FreeSurfer experts, I am writing to follow up on the ‘invalidMEXFile’ error. I have tried to run the segmentation pipeline with both 7.1.1 and the dev version, but the problem persists. Unfortunately I don't have access to the Python version. Could you please provide any guidance on how to resolve the error? Many thanks for your time and help. Best regards, Mengjie > On 14 Jun 2023, at 2:56 am, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > > Message: 8 > Date: Tue, 13 Jun 2023 16:07:34 +0000 > From: "Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ(a)mgh.harvard.edu> > Subject: Re: [Freesurfer] Error running hippocampus subfields and > amygdala nuclei segmentation pipeline > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <BL0PR04MB65315BAA0800424C60740C87FD55A(a)BL0PR04MB6531.namprd04.prod.outlook.com> > > Content-Type: text/plain; charset="windows-1252" > > External Email - Use Caution > > I?ll defer to our software engineering experts, but in the meantime, you could maybe try the Python version? > https://secure-web.cisco.com/1Cv_49AxchVd_2vIYynJ4qP6kfmnE5Dy5Tw3AuuGeUNzzO… > Cheers, > /E > > -- > Juan Eugenio Iglesias > http://secure-web.cisco.com/1QfGfcEcTkVF9fEP1hlZPh1BIK3eVs0WEnf3b34X1Z7TR0_… > > From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Mengjie Huang <mhua0773(a)uni.sydney.edu.au> > Date: Tuesday, June 13, 2023 at 8:12 AM > To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> > Subject: [Freesurfer] Error running hippocampus subfields and amygdala nuclei segmentation pipeline > > External Email - Use Caution > Hello FreeSurfer developers, > > I am writing to seek help regarding an issue I encountered when trying to run the hippocampus subfields and amygdala nuclei segmentation pipeline (please see the error message attached below). > I am running FreeSurfer V.7.1.1 on my university?s high performance computing (HPC) system. I have Matlab R2014b installed in '/usr/local/freesurfer/MCRv84?). I greatly appreciate any suggestions on how to resolve this issue. Many thanks for your time and help. > > > ------------------------------ > USER mhua0773 > HOST hpc008 > PROCESSID 3344 > PROCESSOR x86_64 > OS Linux > ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS 1 > Linux hpc008 2.6.32-696.16.1.el6.x86_64 #1 SMP Wed Nov 15 16:51:15 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux > pbsjob 6889001.pbsserver > ------------------------------ > > freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 > > setenv SUBJECTS_DIR /scratch/Amy_FTD/controls_2_base/Preprocessing > cd /scratch/RDS-FSC-Amy_FTD-RW/controls_2_base/Preprocessing > /usr/local/freesurfer/7.1.1//bin/segmentHA_T1.sh 501_MRI1 > > #-------------------------------------------- > #@# Hippocampal Subfields processing (T1) left Tue Jun 13 13:59:28 AEST 2023 > ------------------------------------------ > Setting up environment variables > --- > LD_LIBRARY_PATH is .:/usr/local/freesurfer/7.1.1//MCRv84//runtime/glnxa64:/usr/local/freesurfer/7.1.1//MCRv84//bin/glnxa64:/usr/local/freesurfer/7.1.1//MCRv84//sys/os/glnxa64:/usr/local/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:/usr/local/freesurfer/7.1.1//lib/vtk/lib > Invalid MEX-file '/tmp/MCR_65032579/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64': /tmp/MCR_65032579/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64: failed to map segment from shared object: Operation not permitted > > Error in kvlClear (line 11) > > > > Error in segmentSubjectT1_autoEstimateAlveusML (line 115) > > > > MATLAB:invalidMEXFile > @#@FSTIME 2023:06:13:13:59:28 run_segmentSubjectT1_autoEstimateAlveusML.sh N 14 e 6.47 S 0.57 U 4.19 P 73% M 201140 F 0 R 61507 W 0 c 189 w 3872 I 0 O 84184 L 18.03 17.42 13.59 > @#@FSLOADPOST 2023:06:13:13:59:34 run_segmentSubjectT1_autoEstimateAlveusML.sh N 14 18.03 17.43 13.61 > Linux hpc008 2.6.32-696.16.1.el6.x86_64 #1 SMP Wed Nov 15 16:51:15 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux > > T1 hippocampal subfields exited with ERRORS at Tue Jun 13 13:59:34 AEST 2023 > > Best regards, > Mengjie > >

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