Freesurfer May 2020

freesurfer@nmr.mgh.harvard.edu

111 participants
208 discussions

Coordinate Transformation
by Hye Bin Yoo 04 May '20

04 May '20

External Email - Use Caution Dear Freesurfer Developers, How are you? We have been using Freesurfer Freeview for localizing implanted electrodes for human brains, and the coordinate system of choice was "Talairach". However, we are trying to utilize MNI152 coordinate system for advanced analyses. How could we transform between the coordinate systems between Talairach and MNI152 using Freesurfer commands? We do realize there are formulae available, but we would like to make sure WHAT coordinates Freeview is actually referring to. For your information, please find the attached picture. The red squares are on RAS and Talairach, and we assume these correspond to MNI305 and Talairach in MNI space, respectively. Is there an internal formulae we can utilize to obtain the RAS values given Talairach coordinates only? Thank you very much for your help in advance!

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longitudinal trac-all -path exited with error
by Zeng, Qi 04 May '20

04 May '20

External Email - Use Caution Hi, My trac-all -path exited with error after trying to load BEDPOST parameter samples from SUBJ.long.SUBJ_base/dmri.bedpostX. So is there something wrong with my bedpostX from trac-all -bedp? Should I run bedpostX separately again without trac-all. Though my last step '-bedp' didn't prompt 'finished without error' log message as preproc did, expected files were created. BTW, which log script should I look into? the one follows SUBJ_base/script or SUBJ_ses-1.long.SUBJ_base/script? Here attached the trac-all -path log. Thank you so much! Best, Qi -- Ph.D. candidate Icahn School of Medicine at Mount Sinai

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recon-all and fMRI coordinates mismatch
by Peled, Noam 04 May '20

04 May '20

Hello, After running recon-all on a patient, the resulting T1.mgz coordinates system turned to be LIA. Can I guarantee the recon-all output will be in RAS? I also would like to run FS-FAST on this patient's fMRI task dataset, which is in LSA. Any recommendation what should I do to make sure both are in the same coordinates system (I preferred RAS)? Thanks, Noam

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Hippocampus subfields ROI
by Muhammad Naveed Iqbal Qureshi 04 May '20

04 May '20

External Email - Use Caution Hi FreeSurfer experts, I ran developmental version of freesurfer to get the hippocampus subfields ROI and volume. I can see in the hipposubfields.lh.T1.v21.stats and lh.hippoSfVolumes-T1.v21.txt fils with separate information for the head and tail volumes of each subfield. May I know what is the file name containing the corresponding separate 21 head and tail ROIs? I can only find full subfield in all the ROI files. Thank you. Regards, Naveed

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Re: [Freesurfer] Longitudinal Hippocampal Subfields Module, existed with errors
by Zeng, Qi 04 May '20

04 May '20

External Email - Use Caution Hi Eugenio, Thank you so much for the prompt reply ! Here attached the log file. The files generated: SUBJ/SUBJ_base/tmp/hippoSF_T1_long.v21_left SUBJ/SUBJ_base/scripts/long-hippocampal-subfields-T1 Best, Qi On Wed, Apr 29, 2020 at 5:22 PM Zeng, Qi <qi.zeng(a)icahn.mssm.edu> wrote: > Hi Eugenio, > > Thank you so much for the prompt reply ! > Here attached the output error and log file. > The files generated: > SUBJ/SUBJ_base/tmp/hippoSF_T1_long.v21_left > SUBJ/SUBJ_base/scripts/long-hippocampal-subfields-T1 > > Best, > Qi > > On Wed, Apr 29, 2020 at 3:23 PM Iglesias Gonzalez, Juan E. < > JIGLESIASGONZALEZ(a)mgh.harvard.edu> wrote: > >> Dear Qi, >> >> The correct syntax is that of your First try, but I’m very surprised you >> got that error, as we fixed this a while ago… Can you please send me the >> complete output? >> >> Cheers, >> >> /Eugenio >> >> >> >> >> >> Juan Eugenio Iglesias >> >> Senior research fellow >> >> CMIC (UCL), MGH (HMS) and CSAIL (MIT) >> >> http://www.jeiglesias.com >> >> >> >> >> >> >> >> *From: *<freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Zeng, Qi" >> <qi.zeng(a)icahn.mssm.edu> >> *Reply-To: *Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> >> *Date: *Wednesday, April 29, 2020 at 04:44 >> *To: *"freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> >> *Subject: *[Freesurfer] Longitudinal Hippocampal Subfields Module, >> existed with errors >> >> >> >> * External Email - Use Caution * >> >> Hi, >> >> I am trying to use the longitudinal pipeline of the “hippocampal >> subfields and nuclei of amygdala”. Keep getting error messages when running >> it longitudinal but with no error message running it cross-sectional. I >> want to know if there is any way to fix the error and to run a longitudinal >> pipeline successfully. >> >> I am using Freesurfer/dev and matlab_runtime/2014b. >> >> I got two timepoints for each subject and finished recon-all longitudinal >> with no errors. >> >> 1) First Try >> >> segmentHA_T1_long.sh SUBJ_base >> >> >> run for about 15 mins and exited with error message: >> >> “Error using kvlGEMSMatlab >> >> >> /autofs/space/panamint_005/users/iglesias/software/freesurfer/GEMS2/kvlAtlasMeshDeformationOptimizer.cxx:327: >> >> itk::ERROR: AtlasMeshDeformationLBFGSOptimizer(0x2ac1fead7740): search >> direction is not a descent direction! >> >> Error in kvlStepOptimizer (line 11) >> >> Error in SegmentSubfieldsT1Longitudinal” >> >> >> no mri/lh.amygNucVolumes-T1.v21 and mri/lh.hippoSfVolumes-T1.v21 >> generated. >> >> >> >> 2) Second Try >> >> segmentHA_T1.sh SUBJ1_timepoint1.long.SUBJ1_base >> >> segmentHA_T1.sh SUBJ1_timepoint2.long.SUBJ1_base >> >> >> run for about 16 mins, most successful but a few with errors: >> >> “Error in segmentSubjectT1_autoEstimateAlveusML (line 1539)” >> >> Or >> >> >> >> >> “Open file failed because file >> '/tmp/MCR_2841219388/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlSetMeshCollectionPositions.m' >> has invalid content. Details: 'file is closed.failbit is set.' >> >> The file >> >> >> "/tmp/MCR_2841219388/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlSetMeshCollectionPositions.m" >> >> cannot be executed. >> >> Error in segmentSubjectT1_autoEstimateAlveusML (line 538)” >> >> >> >> >> successful done subject or hemisphere generated >> mri/lh.amygNucVolumes-T1.v21 and mri/lh.hippoSfVolumes-T1.v21. >> >> >> >> 3) Third Try cross-sectional >> >> segmentHA_T1.sh SUBJ1_timepoint1 >> >> segmentHA_T1.sh SUBJ1_timepoint2 >> >> >> run for about 15 mins, all successful with no errors: >> >> >> all subjects have mri/lh.amygNucVolumes-T1.v21 and >> mri/lh.hippoSfVolumes-T1.v21 generated. >> >> >> >> Manual inspection with freeview, it seems fine with all successful >> longitudinal and cross sectional subfield segmentation outputs mgz. >> >> >> >> I wonder if I can fix first try and second try errors so that >> longitudinal output can be generated. >> >> >> >> Thank you for your help! >> >> Best, >> >> Qi >> >> >> >> -- >> >> >> >> Ph.D. candidate >> >> Icahn School of Medicine at Mount Sinai >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > > Ph.D. candidate > Icahn School of Medicine at Mount Sinai > > -- Ph.D. candidate Icahn School of Medicine at Mount Sinai

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Recon-all exited WITH errors
by Mason Wells 04 May '20

04 May '20

External Email - Use Caution Hi Experts, I appear to be having some issues with recon-all. I ran the command from a bash script (see attached), and it appears to work fine for the left hemisphere as the correct files are in the surf folder. However, there are no right hemisphere surf files. I have attached the log and error log for PPT01 and PPT02. Any advice on as to why this has happened would be great. Thanks in advance, Mason Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: WellsMT1(a)cardiff.ac.uk<mailto:WellsMT1@cardiff.ac.uk> Tel: 02920 879628 Web: Cardiff University webpage<https://www.cardiff.ac.uk/people/research-students/view/974214-> Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau’r Golwg & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: WellsMT1(a)caerdydd.ac.uk<mailto:WellsMT1@caerdydd.ac.uk> Ffôn: 02920 879628

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Files generate in the process of "recon-all -autorecon3" are all missing
by Frank Chau 04 May '20

04 May '20

External Email - Use Caution Dear Freesurfer experts, I ran recon-all on a batch of subjects on the Linux CentOS virtual machine base on Windows 10. I found all files which should be generated in the "recon-all<https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all> -autorecon3" are all missing in this batch of subjects. ( "recon-all<https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all> -autorecon3"refer to the page of FreeSurfer Tutorial: Process Flow: https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV5.1)<https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV5.1> However, this problem did not appear on the MAC platform. I wonder that why this problem only appear on Linux platform. I attached the recon-all.log of a subject which the "recon-all<https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all> -autorecon3" files were missing. Could you kindly help me to speculate the cause of this problem. Thank you. Regards Frank --------------------------- FRANK C Y CHAU Research assistant Division of Neurology Department of Medicine Tel: +852 6340 2553 Fax: 2872 5828 E-mail : cyfrank(a)hku.hk<mailto:cyfrank@hku.hk> Rm 304, 3/F, New Clinical building, Queen Mary Hospital, 102 Pokfulam Road, Hong Kong

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recon-all
by jiahui 04 May '20

04 May '20

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to compare two groups' cortex, but for some of my subjects I get the following error when I run mri_glmfit \ --y rh.thickness.10.mgz \ --fsgd g3v1.fsgd dods\ --C group.mtx \ --surf fsaverage rh \ --cortex \ --glmdir g3v1.rh ERROR: DOF=0(this is error?) g3v1h.rh only 4 files(should have beta.mgh sig.mgz files...) I've searched the list and no similar errors have been reported. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: ubuntu 16.04.6 LTS 3) mri_glmfit.log and figure01 figure02 figure03: see attached

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Question regarding design matrix/fsgd/resulting statistical tests
by s7675854＠stud.uni-frankfurt.de 04 May '20

04 May '20

External Email - Use Caution Dear Freesurfer experts, I have a beginner question regarding fsgd and mtx files. For example, if I have one group and am interested in the correlation between some test score and cortical thickness/surface area, controlling for age and intracranial volume. I would have 1 group and 3 covariates, e.g. class 1 score age icv subj1 1 55 20 3333 subj2 1 43 24 3333 Now if I am interested in the correlation between the test score and an anatomical parameter, I would go with the design matrix: 0 1 0 0 (doss). My question is, why does this calculate an F test, if I am only interested in one group? (I would understand a t-test with test-score slope >0, but where does the F come from?) I am drawing a mental blank here and would appreciate your help! Thanks a lot, Dorothee

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segmentHA_T1.sh fails with "Error in myMRIread: temporary directory does not exist"
by Soichi Hayashi 04 May '20

04 May '20

External Email - Use Caution Hello. I am trying to run segmentHA_T1.sh right after successfully completing recon-all -all I have a freesurfer output directory under my currently working directory inside ./output. So I ran this command. $ segmentHA_T1.sh output . When I do I run into the following error message. #-------------------------------------------- > #@# Hippocampal Subfields processing (T1) left Mon May 4 09:16:43 EDT 2020 > ------------------------------------------ > Setting up environment variables > --- > LD_LIBRARY_PATH is > .:/lib64:/usr/local/freesurfer/MCRv84//runtime/glnxa64:/usr/local/freesurfer/MCRv84//bin/glnxa64:/usr/local/freesurfer/MCRv84//sys/os/glnxa64:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:/.singularity.d/libs > 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) > > > > Linux elogin2 4.4.180-94.103-default #1 SMP Mon Aug 19 15:06:57 UTC 2019 > (62f4295) x86_64 x86_64 x86_64 GNU/Linux > T1 hippocampal subfields exited with ERRORS at Mon May 4 09:16:58 EDT 2020 > For more details, see the log file > ./output/scripts/hippocampal-subfields-T1.log How can I correct this problem? Soichi

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Freesurfer May 2020