Freesurfer September 2023

freesurfer@nmr.mgh.harvard.edu

71 participants
88 discussions

Follow up question on group analysis (mri_glmfit)
by inbal paran 23 Sep '23

23 Sep '23

External Email - Use Caution Thanks for the quick response. So I followed the steps of the tutorial and performed group analysis by running mris_preproc, then mri_surf2surf and then mri_glmfit. Is that the correct way to do that? and in this case, can I include multiple continuous variables in my analysis (in the fsgd file)? Thanks again Inbal -------- It is worse -- we do not support qdec anymore On 8/5/2023 6:04 AM, inbal paran wrote: External Email - Use Caution Hello FreeSurfer Developers, I have a question regarding group analysis: When I followed the instructions on how to build my FSGD file, it said that:"FSGD files are created automatically by qdec, but qdec is currently (12/9/08) limited to two continuous variables and two discrete variables with two levles. Is this still the case, or is it possible to include more than 2 continuous variables? The freesurfer version I am using: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 Thank you Inbal -- *Inbal Paran, M.PT <http://secure-web.cisco.com/1w6eByVfQtHP57lPYq2r_KIYGKXnqPLFlDOaO0p2X1WZmr0…>.* Schwartz Movement analysis & Rehabilitation Laboratory, Physical Therapy Department, Recanati School for Community Health Professions. Faculty of Health Sciences at Ben-Gurion University of the Negev.

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lta_convert does not produce ITK transforms that are correctly applied by antsApplyTransforms
by Yazdan Rezaee Jouryabi 23 Sep '23

23 Sep '23

External Email - Use Caution Dear all, Hi for checking registration i used fsl applyxfm on an Image(1)(Called Image.nii ) with specific Registration Matrice (Which we suppose to receive when we apply registration Methods) and Generate the "fsl_resampled.nii.gz" (Note: Image Orientations were LAS and in one other Experiment with also the same problem PSR) for our case i will attach the "fsl.mat" (Desired Matrix) using, fsl, freesurfer, and ants i got the correct results (let's call them "fslregistered.mat" and "freesurfer.mat" the converted lta to fsl-liked Matrix) Everything is OK till now But the converted lta-like and fsl-like matrix for ANTs (Which are called ants.lta, and ants.mat) using the lines below: - ConvertTransformFile 3 ./ANTS/ants_0GenericAffine.mat ./ANTS/ants.txt - lta_convert --initk ./ANTS/ants.txt --outlta ./ANTS/ants.lta --src ./Image.nii --trg ./fsl_resampled.nii.gz --ltavox2vox - lta_convert --inlta ./ANTS/ants.lta --outfsl ./ANTS/ants.mat --src ./Image.nii --trg ./fsl_resampled.nii.gz As All Results Images (Registered Image of all Methods) are aligned perfectly i think that there might be some issues with lta_convert Best Regards Yazdan Rezaee J *P.S. *" I've checked the one similar mail one this topic and the conclusion on that was about (sform, qform) incompatibility but the affine matrices of S-form and q-form are equivalent in my case."

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Convert Freesurfer segmentations to OBJ files
by Byripudi Naveen Kumar ed20d402 21 Sep '23

21 Sep '23

External Email - Use Caution Dear experts, I am trying to convert freesurfer segmentations to obj files for visualization in virtual reality. How to do this without losing any segmentation label names and colors. I tried to import the surfaces into 3d slicer but I could not do it. Also can you guide me on how to combine the tractography segments from tracula with the anatomical segmentations from recon-all? Thank you in advance Yours sincerely Naveen Kumar

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Training in Advanced Statistical Methods in Neuroimaging and Genetics, April 15 - 26, 2024
by ROBERT CARY WELSH 20 Sep '23

20 Sep '23

External Email - Use Caution Hi Folks, Our NIH-funded course, “Training in Advanced Statistical Methods in Neuroimaging and Genetics”, will be held in-person in Salt Lake City, UT, from April 15 - 26, 2024. This is a course geared to advanced undergraduate students graduate students, postdocs, and junior faculty. Topics include (see website for more details): Bayesian methods of functional connectivity and activation, longitudinal modeling, network neuroscience, polygenic risk scores, multimodal modeling and predictive modeling. The course is a mix of lectures and hands-on computer labs. Our main lecturers include: Martin Lindquist, Johns Hopkins University Mandy Mejia, Indiana University Rick Betzel, Indiana University Anna Docherty, University of Utah To read more about the course and to apply please see: neurostatsbootcamp.org<http://secure-web.cisco.com/1WGCNO64hrsDRKsP26U8raRZJtaEs4uG-nIYndj55ZcaHIY…> The application (which is multi-part, so please read the detailed instructions) deadline is November 1, 2023. We also offer a limited number of need-based tuition-reduction awards. This is a not-for-profit course and faculty are supported by NIH R25NS117281. Prior testimonials, “This course changed my life”, “I truly learned a lot!”, “This was an excellently planned course.” For more information email us at neurostats(a)g.ucla.edu Best, Robert and Anna ----------- Robert Welsh Professor-in-Residence UCLA Anna Docherty Associate Professor University of Utah

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Re: [Freesurfer] mri_convert: Segmentation fault (core dumped) synthsr scan
by fsbuild 19 Sep '23

19 Sep '23

External Email - Use Caution Hello Ken, The output from your linux shell limits in the log show the following, cputime      unlimitedfilesize     unlimiteddatasize     unlimitedstacksize    8192 kbytescoredumpsize 0 kbytesmemoryuse    unlimitedvmemoryuse   unlimiteddescriptors  1024 memorylocked 64 kbytesmaxproc      7823 maxlocks     unlimitedmaxsignal    7823 maxmessage   819200 maxnice      0 maxrtprio    0 maxrttime    unlimited I would set at least coredumpsize to something non-zero so you can at least get a core file saved that could be looked at.   By default the limits on my Ubuntu 22 system are: $ ulimit -areal-time non-blocking time  (microseconds, -R) unlimitedcore file size              (blocks, -c) unlimiteddata seg size               (kbytes, -d) unlimitedscheduling priority                 (-e) 0file size                   (blocks, -f) unlimitedpending signals                     (-i) 378881max locked memory           (kbytes, -l) 64max memory size             (kbytes, -m) unlimitedopen files                          (-n) 1048576pipe size                (512 bytes, -p) 8POSIX message queues         (bytes, -q) 819200real-time priority                  (-r) 0stack size                  (kbytes, -s) 8192cpu time                   (seconds, -t) unlimitedmax user processes                  (-u) unlimitedvirtual memory              (kbytes, -v) unlimitedfile locks                          (-x) unlimited You can try setting the core file size to unlimited with, $ ulimit -c unlimited... then check the value was changed to something > 0 ...$ ulimit -a You could increase memory size (and as many shell limits as possible) to unlimited to get the max size allowed by the system in the script you use to run recon-all, and then try running recon-all  again to see if you can retrieve a core dump file. - R. On Sep 16, 2023, at 09:55, KennethSPrice <KennethSPrice(a)protonmail.com> wrote:        External Email - Use Caution        OK, I've attached the log file. ------- Original Message -------On Friday, September 15th, 2023 at 2:59 PM, fsbuild <fsbuild(a)contbay.com> wrote:        External Email - Use Caution         It might help if you could send along the crash report as an attachment..-R.On Sep 15, 2023, at 14:36, KennethSPrice <KennethSPrice(a)protonmail.com> wrote:        External Email - Use Caution        Update: I tried running recon-all (5.1, ubuntu 18) on a sample MPRAGE scan and got the "mri_convert: segmentation fault (core dumped)" error again. Any clarity on this issue would be appreciated. Thanks,K------- Original Message -------On Thursday, September 14th, 2023 at 10:41 PM, KennethSPrice <KennethSPrice(a)protonmail.com> wrote:Howdy yall,I ran a subject through synthsr (freesurfer 7.4) and am trying to run the output through the freesurfer 5.1 pipeline (the rest of my dataset was processed with 5.1). I am getting the error "Segmentation fault (core dumped)" during the mri_convert step. Any suggestions? Thanks,Ken_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<recon-all.log>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] freeview upgrade isn’t working/library issue
by fsbuild 19 Sep '23

19 Sep '23

External Email - Use Caution  I don't think we can guarantee upgrading freeview will work with the existing libraries in a sufficiently old freeview distribution.  I’m not sure what version of Ubuntu is running from the kernel listed below, but you could create a backup of your existing freesurfer tree (if you need to keep it), and then run the .deb freesurfer 7.4.1 installer matching your system (Ubuntu 18, 20, 22) which you can download from,  https://secure-web.cisco.com/1W5Z7do8RHfQJIQIHZ9EbWhe5GYVhLQ8shO8lqEwhsAE6g… - R. On Sep 19, 2023, at 15:33, Hoptman, Matthew (NKI) <Matthew.Hoptman(a)nki.rfmh.org> wrote:        External Email - Use Caution        TO: freesurfer@nmr.mgh.harvard.eduFROM: matthew.hoptman@nki.rfmh.orgSUBJECT: freeview upgrade isn’t working/library issue Hello FreeSurfer Developers, I followed the instructions here to upgrade freeview:MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeviewI am now getting the error: freeview: error while loading shared libraries: libvtkDomainsChemistry-7.1.so.1: cannot open shared object file: No such file or directory I saw that it was recommended to install the package libvtk7.1, but that isn’t working:E: Unable to locate package libvtk7.1E: Couldn't find any package by glob 'libvtk7.1' Any help is appreciated. I am using:5.4.0-122-generic #138-Ubuntu SMP Wed Jun 22 15:00:31 UTC 2022 x86_64 x86_64 x86_64 GNU/LinuxThanks, Matt  IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail.PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Recall: freeview upgrade isn’t working/library issue
by Hoptman, Matthew (NKI) 19 Sep '23

19 Sep '23

External Email - Use Caution Hoptman, Matthew (NKI) would like to recall the message, "freeview upgrade isn’t working/library issue". ________________________________ IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation.

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freeview upgrade isn’t working/library issue
by Hoptman, Matthew (NKI) 19 Sep '23

19 Sep '23

External Email - Use Caution TO: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> FROM: matthew.hoptman(a)nki.rfmh.org SUBJECT: freeview upgrade isn’t working/library issue Hello FreeSurfer Developers, I followed the instructions here to upgrade freeview: https://secure-web.cisco.com/1Fr1m43dMDo6PfZjwvbGiKtV6gtUUqAq08NIpRJf8nkhbp… I am now getting the error: freeview: error while loading shared libraries: libvtkDomainsChemistry-7.1.so.1: cannot open shared object file: No such file or directory I saw that it was recommended to install the package libvtk7.1, but that isn’t working: E: Unable to locate package libvtk7.1 E: Couldn't find any package by glob 'libvtk7.1' Any help is appreciated. I am using: 5.4.0-122-generic #138-Ubuntu SMP Wed Jun 22 15:00:31 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux Thanks, Matt IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. ________________________________ IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation.

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TRACULA cluster visualization - mri_glmfit-sim issue?
by Goeckner, Bryna 18 Sep '23

18 Sep '23

External Email - Use Caution Hi Freesurfer Developers, I am having an issue similar to two posted earlier this year with the visualization of significant clusters from tracula not seeming to match the data. (link to first posting here: https://secure-web.cisco.com/1YIyp3Yo44Yjw3sCRGiQdzImJfJAVEC8lOoyUpu2pWJi9R…) Specifically, when mri_glmfit is first run, the data and initial visualization of the significant voxels along the lh cingulum bundle (dorsal) make it appear that the area with the most significant effect is in the anterior part of the tract (see sig_overlay.png). When mri_glmfit-sim is run, the text file of the significance values masked by clusters that survive correction also makes it appear that the significant effects would be in the anterior portion of the tract because they are at the top of the text file (see perm.th13.abs.sig.masked.txt), and earlier data, in agreement with information on the tracula page, is given anteriror to posterior along this tract. This matched what I would expect given the data before clusterwise correction. However, the visualization of the masked significance values seems to show only posterior areas with effects (see sigmasked_overlay.png) I am wondering if there is something in the mri_glmfit-sim process that woucl be causing this apparent flip in the visualization or if there is something I need to be doing differently. Please let me know if you need any additional information and thanks in advance for your help! My code: mri_glmfit --y ${STATDIR}/${TRACT}.avg16_syn_bbr.${MET}.nii.gz --fsgd ${STATDIR}/${STUDY}/inputs/${FSGD}.fsgd doss --C ${STATDIR}/${STUDY}/inputs/${C}.mtx --o ${STATDIR}/${STUDY}/${C}/${TRACT}.${MET}.glmdir --save-eres mri_glmfit-sim --glmdir ${STATDIR}/${STUDY}/${C}/${TRACT}.${MET}.glmdir --cwp 0.05 --perm 1000 1.3 abs To create visualizations: dmri_trk2trk --in /opt/freesurfer/trctrain/hcp/syn/${TRACT}.display.trk --out ${STATDIR}/${STUDY}/${C}/${ResFol}/${TRACT}.${MET}.maskedoverlay.trk --over ${STATDIR}/${STUDY}/${C}/${TRACT}.${MET}.glmdir/${C}/perm.th13.abs.sig.masked.mgh To create text file from mri_glmfit-sim makes output: mri_convert --ascii perm.th13.abs.sig.masked.mgh perm.th13.abs.sig.masked.txt Bryna Goeckner (she/her) Graduate Student Meier Lab<https://secure-web.cisco.com/1L0DdRAsArvZ7gyFkPi0YnO8htwQ03fLvWrtjVgm-rwoJR…> Medical College of Wisconsin Neuroscience Doctoral Program

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Re: [Freesurfer] mri_convert: Segmentation fault (core dumped) synthsr scan
by fsbuild 16 Sep '23

16 Sep '23

External Email - Use Caution  It might help if you could send along the crash report as an attachment. -R. On Sep 15, 2023, at 14:36, KennethSPrice <KennethSPrice(a)protonmail.com> wrote:        External Email - Use Caution        Update: I tried running recon-all (5.1, ubuntu 18) on a sample MPRAGE scan and got the "mri_convert: segmentation fault (core dumped)" error again. Any clarity on this issue would be appreciated. Thanks,K------- Original Message -------On Thursday, September 14th, 2023 at 10:41 PM, KennethSPrice <KennethSPrice(a)protonmail.com> wrote:Howdy yall,I ran a subject through synthsr (freesurfer 7.4) and am trying to run the output through the freesurfer 5.1 pipeline (the rest of my dataset was processed with 5.1). I am getting the error "Segmentation fault (core dumped)" during the mri_convert step. Any suggestions? Thanks,Ken_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer September 2023