Freesurfer March 2023

freesurfer@nmr.mgh.harvard.edu

104 participants
154 discussions

Password for Zip file
by Technology Kishoge 13 Mar '23

13 Mar '23

External Email - Use Caution Hello, I am trying to set up the software using Virtual Box but require the password for the zip file? Thanks

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Along- tract multiple comparison result visualisation and summary interpretation
by miracle ozzoude 13 Mar '23

13 Mar '23

External Email - Use Caution Hello, Please, can someone answer my questions regarding the along-tract stats using mri_glmfit and mri_glmfit-sim with permutation for version 7.2. 1) I ran it and I found a significant negative association between FA and clinical score (see attached summary file). how do I know the entire length of the tract and how much was affected based on the summary file; should I be interpreting the results from the summary file differently? 2) Also when performing clusterwise correction for multiple comparison for along-tract analyses, should the bonferroni flag (--2spaces) be included? This is because it wasn't mentioned/included in the tracula statistics tutorial nor the publication "Using diffusion MRI data acquired with ultra-high gradient strength to improve tractography in routine-quality data". 3) Lastly, is it appropriate to embed the perm.th13.neg.sig.cluster.mgh from mri_glmfit-sim in dmri_trk2trk? Many thanks, Paul

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how the variance calculated for t-value in the first level GLM in fsfast
by haoran.x＠gmail.com 13 Mar '23

13 Mar '23

External Email - Use Caution Hi, I have a naïve question. When I use GLM for a single subject timeseries data, how the variance is evaluated to get the t value? I know the beta values and contrast matrix make the numerator for the t value. How is the denominator made? Is it through the fitting residual ie std(residual), or is it from session by session or run by run variance? Can I find the formula somewhere? I was not able to find the answer in tutorial or the existing mailing list. Thanks a lot! Best, Haoran

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mri_glmfit with age-squared
by Triebswetter, Curtis 13 Mar '23

13 Mar '23

External Email - Use Caution Hello Freesurfer experts, I am attempting to run the command mri_glmfit --y lh.RBS_ADRC_N0_control.10.mgh --fsgd RBS_ADRC_APOE_age22.fsgd dods --C APOE_ageINT.mtx --surf fsaverage lh --cortex --glmdir lh.RBS_ADRC_N0.glmdir On this .fsgd file: “RBS_ADRC_APOE_age22.txt” Using the following design matrix: “lh.RBS_ADRC_N0.txt” I am receiving the error message: -------------------------------- ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 -------------------------------- Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. I would appreciate your insights into what may be the likely cause of this error and apologize that the files are in text format. If need be, I can convert these to their proper formats. misc information: Freesurfer 6.00 CentOS v7 Best, Curtis

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How to find topological defects
by KennethSPrice 13 Mar '23

13 Mar '23

External Email - Use Caution Hello Freesurfers, I've found the tutorial for editing wm.mgz (https://secure-web.cisco.com/1_VE6Du8jnccjig75E4hpWkJh1_YR3uP_xPzMfYusO6K01…) I'm curious if there is a way to find the topological defects easily? Is there a text file in the stats folder, for example, which locates the coordinates of topological defects? Thanks, Ken Sent with [Proton Mail](https://secure-web.cisco.com/1KF2a2rKWu_5CevMXrlKZAUb4EzG3VQGOQnGyxhP… secure email.

2 3

mri_segstats
by John Anderson 13 Mar '23

13 Mar '23

External Email - Use Caution Dear Freesurfer community, Please forgive me for the basic nature of my question. I was wondering whether there is an argument that can be included in mri_segstats to display the results in cubic centimeters (cm^3) instead of cubic millimeters (mm^3). thanks for any suggestions. Thank you, John

2 1

Apply a nonlinear transform to a surface.
by Aaron Tanenbaum 13 Mar '23

13 Mar '23

External Email - Use Caution I am working on a project that will involve applying nonlinear work to a freesurfer surface. This project is in its infancy. I have not figured out all the details. The nonlinear transform will be in either FNIRT or ANTS format. Does anyone know how to do this?

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Freeview error
by Estephan Moana Filho 13 Mar '23

13 Mar '23

External Email - Use Caution Hi, I'm trying to open freeview in a linux node in my institution's computing cluster and an error is coming up consistently - see below. Can you please advise? Thank you. agc01:~ moana004$ module list > No Modulefiles Currently Loaded. > agc01:~ moana004$ module load freesurfer/6.0.0 > agc01:~ moana004$ > study_sharedfolder=/home/moanae/shared/project_K99_ChrTMDHCP_qunex02; \ > > subjID_list="20005 10015 11012"; \ > > for subjID in ${subjID_list}; do freeview > ${study_sharedfolder}/sessions/${subjID}/hcp/${subjID}/T1w/${subjID}/mri/brainmask.gcuts.mgz:colormap=heat > ${study_sharedfolder}/sessions/${subjID}/hcp/${subjID}/T1w/${subjID}/mri/T1.mgz:opacity=0.5; > done > libGL error: unable to load driver: swrast_dri.so > libGL error: failed to load driver: swrast > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, > probably memory access out of range > [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > [0]PETSC ERROR: or see > http://secure-web.cisco.com/1Bgfp-85Thmw5Xhnu5rrkPFwya2Y3o-Kg07_nIggSZ9oXXb… ERROR: > or try http://secure-web.cisco.com/1JsIV3v6H8VSyBNnbIppnqmNOkuk-noOC5m-VFsDLuqNWwP… on linux or man libgmalloc on Apple to find > memory corruption errors > [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and > run > [0]PETSC ERROR: to get more information on the crash. > [0]PETSC ERROR: --------------------- Error Message > ------------------------------------ > [0]PETSC ERROR: Signal received! > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 > CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 > [0]PETSC ERROR: See docs/changes/index.html for recent updates. > [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > [0]PETSC ERROR: See docs/index.html for manual pages. > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: Unknown Name on a linux-gnu named agc01 by moana004 Fri > Mar 10 11:22:48 2023 > [0]PETSC ERROR: Libraries linked from > /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt > [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010 > [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc > --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 > --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: User provided function() line 0 in unknown directory > unknown file > [unset]: aborting job: > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 > libGL error: unable to load driver: swrast_dri.so > libGL error: failed to load driver: swrast > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, > probably memory access out of range > [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > [0]PETSC ERROR: or see > http://secure-web.cisco.com/1Bgfp-85Thmw5Xhnu5rrkPFwya2Y3o-Kg07_nIggSZ9oXXb… ERROR: > or try http://secure-web.cisco.com/1JsIV3v6H8VSyBNnbIppnqmNOkuk-noOC5m-VFsDLuqNWwP… on linux or man libgmalloc on Apple to find > memory corruption errors > [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and > run > [0]PETSC ERROR: to get more information on the crash. > [0]PETSC ERROR: --------------------- Error Message > ------------------------------------ > [0]PETSC ERROR: Signal received! > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 > CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 > [0]PETSC ERROR: See docs/changes/index.html for recent updates. > [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > [0]PETSC ERROR: See docs/index.html for manual pages. > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: Unknown Name on a linux-gnu named agc01 by moana004 Fri > Mar 10 11:22:50 2023 > [0]PETSC ERROR: Libraries linked from > /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt > [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010 > [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc > --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 > --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: User provided function() line 0 in unknown directory > unknown file > [unset]: aborting job: > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 > libGL error: unable to load driver: swrast_dri.so > libGL error: failed to load driver: swrast > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, > probably memory access out of range > [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > [0]PETSC ERROR: or see > http://secure-web.cisco.com/1Bgfp-85Thmw5Xhnu5rrkPFwya2Y3o-Kg07_nIggSZ9oXXb… ERROR: > or try http://secure-web.cisco.com/1JsIV3v6H8VSyBNnbIppnqmNOkuk-noOC5m-VFsDLuqNWwP… on linux or man libgmalloc on Apple to find > memory corruption errors > [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and > run > [0]PETSC ERROR: to get more information on the crash. > [0]PETSC ERROR: --------------------- Error Message > ------------------------------------ > [0]PETSC ERROR: Signal received! > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 > CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 > [0]PETSC ERROR: See docs/changes/index.html for recent updates. > [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > [0]PETSC ERROR: See docs/index.html for manual pages. > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: Unknown Name on a linux-gnu named agc01 by moana004 Fri > Mar 10 11:22:51 2023 > [0]PETSC ERROR: Libraries linked from > /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt > [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010 > [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc > --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 > --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: User provided function() line 0 in unknown directory > unknown file > [unset]: aborting job: > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 > agc01:~ moana004$ > -- Estephan J. Moana-Filho, DDS, MS, PhD Assistant Professor Division of TMD, Orofacial Pain and Dental Sleep Medicine Graduate Faculty in Oral Biology Department of Diagnostic and Biological Sciences UMN School of Dentistry moana004(a)umn.edu 6-320d Moos Tower 515 Delaware St. SE Minneapolis, MN 55455-0329 Office: (612) 624-3338 Clinic: (612) 626-0140 Fax: (612) 626-0138 Clinical referrals: z.umn.edu/TMDrefer UMN profile: https://secure-web.cisco.com/1qDzqxV8A0saK5iVzOb_YFpj8bFrtMnaV7PlkTYT0_-gJx… ORCID ID: http://secure-web.cisco.com/1_aaPiXWbc5YByvuEhM2gYDWPGPbSIFVNqn8PmXWXc3hUEs… Publons: https://secure-web.cisco.com/1xpdcvUYZasLT9y5HJGpNs2tmC4cot__gVR6i_BeYNss6z… My Bibliography (NCBI): https://secure-web.cisco.com/107k1mETeQHnb4m4TKKH4M_6g4tY9rwD3cvRPnRFwNezv_… The information transmitted in this e-mail is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material, including "protected health information." If you are not the intended recipient, you are hereby notified that any review, retransmission, dissemination, distribution, or copying of this message is strictly prohibited. If you have received this communication in error, please destroy and delete this message from any computer and contact us immediately by return e-mail.

2 1

Error using chol
by Caspar M. Schwiedrzik 13 Mar '23

13 Mar '23

External Email - Use Caution Hi! I am running into an issue with fast_selxavg3b. I am attempting a first level PPI analysis. The command is mkanalysis-sess -fsd bold -native -delay -2/2 -notask -TR 2 -polyfit 6 -analysis [xxx] -funcstem [xxx] -runlistfile mooneyppi.list -nuisreg motion.dat 6 -tpef tpef_dvars.dat -acfbins 5 -acffwhm 0 -mask [xxx] -force -nuisreg juice.dat 1 -nuisreg fixation.dat 1 -taskreg ppi.dat 4 I get the following error: GLS Residual Pass run 1 t= 0.0 Error using chol Matrix must be positive definite. Error in fast_selxavg3b (line 942) Wseg = inv(chol(toeplitz(acfrun))'); Before that, I am getting several warnings of this kind: > In fast_selxavg3b (line 895) Warning: Matrix is singular, close to singular or badly scaled. Results may be inaccurate. A few of them, but not run 1, have RCOND = NaN. This is with versions 7.2 and 5.3. I found one previous conversation on the mailing list regarding this error in the context of a resting state analysis, but no conclusion. Any advice would be appreciated. Thanks! Caspar

2 1

white and pial surfaces of the hippocampus
by Khazar Ahmadi 13 Mar '23

13 Mar '23

External Email - Use Caution Dear FS experts, Id like to delineate WM and pial surfaces in the hippocampus and subsequently bin GM layers of it (like the approach that is commonly used for laminar analyses in V1 or other sensory cortices). I think the current output of recon-all does not contain WM/pial surfaces in subcortical regions. Have tried running the FS hippocampal module. It generates subfields (in .mgz format) and volume estimates but I cannot find any surface-based output. Is there a way to obtain pial and WM surfaces in this region? I have another question regarding surface-based representation of the subfields. Based on the paper by Sämann et al., 2020 (see the link below; Figure 6), I think it is possible to have surface-based visualization of the subfields using ENIGMA, but I could not find additional documentation on that. Any ideas on how to obtain surface-based segmentation of the hippocampus would be greatly appreciated. Thanks a lot, and best wishes, Khazar https://secure-web.cisco.com/162vGALDRGyKKidOcJ8MJ6vwNqV2G11ikgdRoQJk8awcbY… -- Khazar Ahmadi, PhD Postdoctoral Researcher, Institute of Cognitive Neuroscience, Department of Neuropsychology, Ruhr University Bochum, Bochum,Germany

2 1

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Freesurfer March 2023