Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30084 discussions

Re: [Freesurfer] Group Analysis Covariates
by Hua, Jessica 17 May '20

17 May '20

External Email - Use Caution Sure, attached are the files again and here is our previous correspondence: Original question: After running the permutation and finding significant clusters, I am trying to calculate the value for each participant for these significant clusters. The perm.th30.abs.y.ocn.dat contain the raw values, and I am trying to get the adjusted values accounting for age, sex, and ICV (this is a three group design). What would be the best way of calculating that? Your response: There is not an easy way to do it, but you can do it in matlab cd glmdir X = load('Xg.dat'); y = load('perm.th30.abs.y.ocn.dat'); beta = inv(X'*X)*X'*y; yhat = X(:,[i j k ...]*beta([i j k ...]) where i j k ... indicate the factors you want keep in your data. Each factor gets a column in the design matrix (and a beta). If you need help figuring this out, send the fsgd file. --- Jessica Hua, M.A. Cognitive and Emotional Control Lab Doctoral Candidate Clinical Psychology University of Missouri

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DTI and T1 AND T2 WEIGHTED IMAGES
by Amar Shukla 17 May '20

17 May '20

External Email - Use Caution Hello Freesurfer, Can we go through the volumetric [surface area and many more ] through DTI images and T1 or t2 weighted images of the same subject. Can we provide common study and can we develop any analysis on these studies. My research is focused on these direction o or any kind of corelation through different Images . basis of diffusion images and T1 or t2 weighted images, so please give suggestions and comment on these. -- With Regards, Amar Shukla

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why fsaverage fold is a "link folder"
by ZhangBo 17 May '20

17 May '20

External Email - Use Caution Hi teams, For recon-all in parallel, why fsaverage fold is a "link folder"? I run recon-all in one computer (Ubuntu), and copy the result to another computer for analysis. And error happened when I need to use data in fsaverage folder. Thanks Bo

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Re: [Freesurfer] Group Analysis Covariates
by Hua, Jessica 16 May '20

16 May '20

External Email - Use Caution Sure, attached is the FSGD file. In case helpful, I have also attached the Xg.dat file. --- Jessica Hua, M.A. Cognitive and Emotional Control Lab Doctoral Candidate Clinical Psychology University of Missouri

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Stanford Postdoc opening: Simultaneous Spinal Cord/Brain fMRI
by Christine Sze Wan Law 15 May '20

15 May '20

External Email - Use Caution The Systems Neuroscience and Pain Laboratory at Stanford University is currently accepting applications for a postdoctoral fellow for neuroimaging research in chronic pain. Funded by NIH (co-PIs Sean Mackey, Gary Glover), this project's overall goal is to characterize pain mechanisms in humans and to develop objective biomarkers of chronic pain. We will be specifically characterizing central sensitization and descending modulation utilizing novel simultaneous neuroimaging technology for spinal cord, brainstem, and brain. The successful candidate will have unique opportunity to engage in simultaneous spinal cord/brain fMRI and to advance spinal cord fMRI acquisition/analysis and biomarker development. Research plans include: 1. Study of functional connectivity between spinal cord and brain 2. Characterization of corticospinal pain signature 3. Physiological noise modeling in spinal cord 4. Refinement of multiecho spinal cord acquisition and analysis pipeline. Applicants should hold a PhD and experience conducting fMRI studies and analysis. Previous experience in spinal cord imaging research is an advantage. The postdoctoral fellow will be responsible for designing experiments, conducting ongoing imaging, analyzing neuroimaging data, planning future studies, searching literature, and writing for publication. The fellow will have opportunity to work within a large group of interdisciplinary Stanford researchers involved with multiple studies ongoing of chronic pain. Additionally, we have a long track record of successfully helping postdoctoral fellows transition to independent grant funding and faculty positions. The Pain Division also has an NIH T32 training program. More information can be found at http://snapl.stanford.edu<http://snapl.stanford.edu/> To apply, submit your (1) CV, (2) NIH Biosketch, and (3) Letter or Research Intent to Dr. Chrsitine Law at cslaw(a)stanford.edu<mailto:cslaw@stanford.edu> Example and Template of biosketch is available here: biosketch formats<https://grants.nih.gov/grants/forms/biosketch.htm#biosketch>. Post-doc applications use non-fellowship template and instructions. Download Letter of Intent template from this link<http://med.stanford.edu/content/dam/sm/pain/documents/research-of-intent-te…>.

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Re: [Freesurfer] Group Analysis Covariates
by Hua, Jessica 15 May '20

15 May '20

External Email - Use Caution After running the permutation and finding significant clusters, I am trying to calculate the value for each participant for these significant clusters. The perm.th30.abs.y.ocn.dat contain the raw values, and I am trying to get the adjusted values accounting for age, sex, and ICV. What would be the best way of calculating that? --- Jessica Hua, M.A. Cognitive and Emotional Control Lab Doctoral Candidate Clinical Psychology University of Missouri

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error in TRACUAL : preprocessing step.
by 안성준(강남)영상의학과) 15 May '20

15 May '20

External Email - Use Caution ________________________________ Hello? Freesurfer developer. I am attempting to run Tracula and follow the tutorial step using my own data but failed in 1st step, preprocessing. I modified configuration file fit to my pathway Command I used : trac-all -prep -c dmrirc.tutorial I think the problem is in the last step,"priors" in the preprocessing. Error message is ERROR: fio_pushd: /Users/ahn/Downloads/9211720/Tracula/freesurfer/dlabel/mini I tried to find the solution but couldn't .. Can you help me out ?? Thank you Ahn 1) FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 2) Platform: macOS mojave 10.14.6 3) log file is attached

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Group Analysis Covariates
by Hua, Jessica 14 May '20

14 May '20

External Email - Use Caution Hi FreeSurfer Experts, I am trying to extract or calculate the adjusted values for each participant in each cluster after accounting for covariates in my permutation analysis. This is a 3 group analysis with 3 covariates (age, sex, and ICV). After navigating to the glmdir folder of interest, I ran the following code: X = load('Xg.dat'); The X matrix was 240x12 (see attached file) * Column 1: 1s for Group 1 and 0s for Group 2 and 0s for Group 3 * Column 2: 0s for Group 1 and 1s for Group 2 and 0s for Group 3 * Column 3: 0s for Group 1 and 0s for Group 2 and 1s for Group 3 * Column 4: Age for Group 1 and 0s for Group 2 and 0s for Group 3 * Column 5: 0s for Group 1 and Age for Group 2 and 0s for Group 3 * Column 6: 0s for Group 1 and 0s for Group 2 and Age for Group 3 * Column 7: Sex for Group 1 and 0s for Group 2 and 0s for Group 3 * Column 8: 0s for Group 1 and Sex for Group 2 and 0s for Group 3 * Column 9: 0s for Group 1 and 0s for Group 2 and Sex for Group 3 * Column 10: zICV for Group 1 and 0s for Group 2 and 0s for Group 3 * Column 11: 0s for Group 1 and zICV for Group 2 and 0s for Group 3 * Column 12: 0s for Group 1 and 0s for Group 2 and zICV for Group 3 beta = MRIread('beta.mgh'); betamat = fast_vol2mat(beta); And I got stuck at this step: yhatmat = X(:,[i j k m n])*betamat([i j k m n],:); I wasn't sure how to modify the code. Is this correct: yhatmat = X(:,[4 5 6 7 8 9 10 11 12])*betamat([4 6 7 8 9 10 11 12],:); Once I figure out the above step, I will finish with this code: yhat = beta; yhat.vol = fast_mat2vol(yhat,yhat.volsize); --- Jessica Hua, M.A. Cognitive and Emotional Control Lab Doctoral Candidate Clinical Psychology University of Missouri

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Re: [Freesurfer] on Ubuntu (was FreeSurfer V 7.0 on Centos 8) {Disarmed}
by fsbuild 14 May '20

14 May '20

External Email - Use Caution Hello Tristan, I can send you an email directly later today with some tests you can try for freeview and some other commands  If the test succeeds, then at least it would mean your environment is good. The original bug report on the Arch Linus page - while listing  a signal 11 - did not look to me like it was not from the same cause as what you subsequently posted.  That error was detecting a divide by zero (before it happened) in the hardware from some calculation which I take to mean the loader had previously found everything it needed to load the binaries into memory and run them. BTW - the 7.1.0 binaries on the download page should work on CentOS8 if you have that OS to try. - R. On May 13, 2020, at 18:09, TRISTAN J PAUTSCH <tpautsch(a)wisc.edu> wrote:        External Email - Use Caution        Just following up to confirm that this issue persists in 7.1..0 in case anyone has any ideas; I've tried everything I can think of at this point.:(From: TRISTAN J PAUTSCH <tpautsch@wisc.edu>Sent: Friday, April 17, 2020 12:21 PMTo: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Cc: ts+ml@rcmd.org <ts+ml@rcmd.org>Subject: Re: [Freesurfer] on Ubuntu (was FreeSurfer V 7.0 on Centos 8) {Disarmed} Just a quick follow up, I've now been able to find my issue in the wild as well (not just on my own machines). I use Arch Linux personally and on a small handful of workstations professionally, and when investigating using FS on Arch, I stumbled upon an AUR build someone had done. While I didn't intend to use this buildfile (still version 6.x), the top comment on the below link alludes to the same PETSC error message with FS as I'm experiencing on my Ubuntu machines:https://aur.archlinux.org/packages/freesurfer-bin/TFrom: TRIS… J PAUTSCH <tpautsch@wisc.edu>Sent: Monday, April 6, 2020 1:32 PMTo: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Cc: ts+ml@rcmd.org <ts+ml@rcmd.org>Subject: Re: [Freesurfer] on Ubuntu (was FreeSurfer V 7.0 on Centos 8) {Disarmed} Apologies for the late reply, hectic times. Please find the requested files here:https://uwmadison.box.com/s/vod1t4vlycd9baom42qqqwkc6unj9auiLet me know how else I can help!TFrom: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard..edu> on behalf of fsbuild(a)contbay.com <fsbuild@contbay.com>Sent: Tuesday, March 31, 2020 6:20 PMTo: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Cc: ts+ml@rcmd.org <ts+ml@rcmd.org>Subject: Re: [Freesurfer] on Ubuntu (was FreeSurfer V 7.0 on Centos 8) {Disarmed}         External Email - Use Caution        Hello Tristan,Going back to that thread, I’d like to try the command you uploaded data for as freesurfer_data.tar.gz on a couple of Ubuntu systems, but either I’m looking in the wrong place or it’s not there anymore.  Is there a shared google drive link or something you point me to for a download link? > freeview -v brainmask.mgz T1.mgz -f lh.white:edgecolor=yellow > lh.pial:edgecolor=magenta rh.white:edgecolor=yellow rh.pial:edgecolor=magenta > > We can also replicate the error by opening freeview and opening all the above > files sequentially through the GUI.- R.On Mar 31, 2020, at 13:41, TRISTAN J PAUTSCH <tpautsch(a)wisc.edu> wrote:        External Email - Use Caution        Thanks for the reply, all.The issues I'm having are the same as they were in my prior thread, found here:MailScanner has detected a possible fraud attempt from "www..mail-archive.com" claiming to be https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg6345… tried everything up to and including compiling everything from scratch (including FS itself, missing libs, PETSC, etc.). The main takeaway is that I pretty convincingly narrowed the issue down to PETSC+Ubuntu 18.04, the most pertinent details for that being in the following post:https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg63702.h… when I was active in that thread, I emailed the PETSC mailing list and got no response, and at the time I was pretty busy with other projects so I had to let it go for the time being; I maintained my old RHEL6 server so people could continue to use FS. Now with everyone in quarantine (and RHEL6 entering ELS this November), it's a decent time to look back into this issue. I wouldn't have reached back out to the FS list, however when I saw that a focus was being placed on Ubuntu (and that there was a working Ubuntu VM), I became hopeful that maybe this issue was resolved?TFrom: fsbuild@contbay.com <fsbuild@contbay.com>Sent: Tuesday, March 31, 2020 3:57 AMTo: freesurfer@nmr.mgh..harvard.edu <freesurfer@nmr.mgh.harvard.edu>Cc: ts+ml@rcmd.org <ts+ml@rcmd.org>; TRISTAN J PAUTSCH <tpautsch@wisc..edu>Subject: Re: [Freesurfer] on Ubuntu (was FreeSurfer V 7.0 on Centos 8) We would also like to know about any issues you are seeing on Ubuntu.I think Ubuntu eliminated some jpeg/png packages from their repos.  Those can be downloaded and installed manually,e.g., libpng12-0_1.2.54-1ubuntu1.1_amd64.deb, libjpeg62_6b2-3_amd64.deb.  That is part of the reason we made an Ubuntu 18 VM available with everything pre-installed. The VM is essentially what has been used for the freesurfer course which runs mostly freeview commands with some mri* commands (though I believe a recon-all also works).  The VM is running binaries built on CentOS7 - as the reference platforms for freesurfer dev are currently CentOS and MacOS.  We are looking at making a .deb installer for freesurfer on Ubuntu though.There is some info on the wiki about packages required to compile the source on Ubuntu - but you don’t need all of these to run (even the CentOS) binaries.MailScanner has detected a possible fraud attempt from "surfer..nmr.mgh.harvard..edu" claiming to behttps://surfer.nmr.mgh.harvard.edu/fswiki/BuildRequirements- R.On Mar 31, 2020, at 02:50, Tim Schäfer <ts+ml(a)rcmd.org> wrote:       External Email - Use Caution        Hi Tristan,I'm about to setup a FreeSurfer installation on an Ubuntu system, and I wondered whether you could elaborate on the kind of issues you are experiencing.Best,Tim--Dr. Tim SchäferPostdoc Computational NeuroimagingDepartment of Child and Adolescent Psychiatry, Psychosomatics and PsychotherapyUniversity Hospital Frankfurt, Goethe University Frankfurt am Main, GermanyOn March 30, 2020 at 11:01 PM TRISTAN J PAUTSCH <tpautsch(a)wisc.edu> wrote:       External Email - Use Caution        Is there going to be an "official" Ubuntu build this time around (as in, built and tested in Ubuntu) that isn't the VM? Both the current CentOS and the dev builds continue to have issues (even when compiled from scratch) on my Ubuntu 18.04 servers.Thanks!T________________________________From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of fsbuild(a)contbay.com <fsbuild(a)contbay.com>Sent: Monday, March 30, 2020 9:40 AMTo: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu>Cc: dr.minafakhry(a)live.com <dr.minafakhry(a)live.com>Subject: Re: [Freesurfer] FreeSurfer V 7.0 on Centos 8       External Email - Use CautionHello Mina,I see from https://www.centosblog.com/centos-eol-dates/ that CentOS 6 will no longer be updated as of 11/2020, and similarly for CentOS 7 in 6/2024.  It looks like CentOS 8 was released around September of 2019.While we do not currently build/test on CentOS8, I am sure it will eventually be supported.   Given some users will continue to use CentOS 6 even after 11/2020 and that many people have been running the freesurfer 6 release on CentOS6, then even the upcoming freesurfer 7 release is targeting CentOS6, CentOS7 and Ubuntu linux (as well as Mac OS).There is also currently an Ubuntu 18 VM with freesurfer 6 and the beta release of freesurfer 7 pre-installed which you can find here, https://surfer.nmr.mgh.harvard.edu/fswiki/VM_67- R.On Mar 30, 2020, at 08:52, Mina Rizkallah <dr.minafakhry(a)live.com> wrote:       External Email - Use CautionGreetings FreeSurfer team,I recently upgraded by workstation from Centos 7 to 8.1 as the support for centos  7 will be over soon.I tried installing freesurfer version 7.0 beta 1 but failed due to some unresolved dependencies (tried on a  virtual centos 7 and worked fine) !!so, when will there be support for centos 8, thank youBest regardsMina_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh..harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh..harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Recon-all Talairach failed error
by Peng Liu 14 May '20

14 May '20

External Email - Use Caution Dear Freesurfer experts, I am trying to run recon-all for a new subject, however I came across with this error 'Talairach failed'. The error log is as following: *talairach done\n cp transforms/talairach.auto.xfm transforms/talairach.xfm \n#--------------------------------------------#@# Talairach Failure Detection Thu May 14 15:11:47 CEST 2020/Users/pliu/Documents/DataAnalysis0512/subjects/Pilot03/mri\n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \nERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0153, pval=0.0000 < threshold=0.0050)\nManual Talairach alignment may be necessary, orinclude the -notal-check flag to skip this test,making sure the -notal-check flag follows -allor -autorecon1 in the command string.See:\nhttp://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach <http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach>\nERROR: Talairach failed!\n* I have read online that I might need to perform a rough coregistration for the input image before running recon-all. But I am a bit lost by which image should it be registered to... Would 'mni305.cor.mgz' be okay as reference image? Any help would be much appreciated. Kindly Regards Peng Liu -------------------------------------------- [image: Otto-von-Guericke University Magdeburg] Peng Liu, PhD Candidate Institut für Kognitive Neurologie und Demenzforschung (IKND) Otto-von-Guericke Universität Magdeburg Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE) Leipziger Str. 44| Haus 64| Raum 217 39120 Magdeburg, Deutschland Email: peng.liu@med.ovgu.de/Peng.Liu@dzne.de Phone: +49 391 67 25074

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