Freesurfer

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30070 discussions

Calculating subject-level voxelwise % change in cortical thickness across timepoints
by Elijah Mak 04 Jun '18

04 Jun '18

External Email - Use Caution Hi Freesurfer Experts, I have a question about calculating voxelwise % change. We have collected T1-MRI across 3 time points in a couple of subjects and the aim is to produce individual surfaces/maps showing the % of cortical thinning with respect to the baseline data. Each time point has been processed using the standard recon-all. Next, the base template was created using data from all 3 time points. The longs were processed accordingly. I am thinking of using something like FSCALC to get the new surface, showing the % difference compared to T1. Would all of these steps be correct? Many thanks for your help in advance. Best Wishes, Elijah

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Question on MRI_surf2vol
by Nicholas Heugel 03 Jun '18

03 Jun '18

External Email - Use Caution I have some questions regarding how MRI_vol2surf works. More specifically, how does it handle the vertices when performing the process. If the same vertex is the closest to multiple locations on the surface file, is it projected to all those locations? If so, is there any limit? or will it project that activity to every location it can? Or, is the activity at each vertex only allowed to be projected to a single location on the inflated surface? Thank you for your time. Nicholas Heugel Biomedical Engineering Ph.D Candidate Marquette University

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Fwd: FW: Resting-State and Brain Connectivity, 2018, in Montreal: programs are available
by Kelvin Mok 01 Jun '18

01 Jun '18

External Email - Use Caution Dear Community, *The Sixth Biennial Conference on Resting-State and Brain Connectivity* *Conference**:** September 26 - 28, 2018* *Educational workshop: September 24 - 25, 2018* *Montreal, QC, Canada* - Early abstract submission deadline: June 10, 2018 - For those who submit by June 10, notice of acceptance will be sent on a rolling basis no later than June 30, 2018. - Early registration rate until July 10, 2018 - Late abstract submission can be made until August 1, 2018 See the program: *http://restingstate.com/2018/ <http://restingstate.com/2018/>* *Amir Shmuel* *Chair of the organizing committee* *[image: http://restingstate.com/2018/wp-content/uploads/2017/06/resting-state-logo-…

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Vertex-wise Cortical Thickness BA_exvivo.thresh label
by sarah.kloeppig＠web.de 01 Jun '18

01 Jun '18

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Subfields Development Version MATLAB:scriptNotAFunction
by Lachlan Strike 01 Jun '18

01 Jun '18

External Email - Use Caution Hi I’m attempting to run the hippocampal/amygdala subfields segmentation in the most recent daily build of FreeSurfer (Centos7). The T1 only and multispectral variations run fine, but attempting the segmentation without the T1 (USE_T1=0) produces the following error: Attempt to execute SCRIPT segmentSubjectT2_autoEstimateAlveusML as a function: /tmp/MCR_3555778206/.mcrCache8.4/segmen0/segmentSubje/segmentSubjectT2_autoEstimateAlveusML.m MATLAB:scriptNotAFunction Error:Attempt to execute SCRIPT segmentSubjectT2_autoEstimateAlveusML as a function: /tmp/MCR_3555778206/.mcrCache8.4/segmen0/segmentSubje/segmentSubjectT2_autoEstimateAlveusML.m Linux vagrant 4.4.0-75-generic #96-Ubuntu SMP Thu Apr 20 09:56:33 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Any ideas? I am running this within a singularity container, but as the T1 and multispec versions ran without error I’m hoping it’s not related to that. Thanks Lachlan Queensland Brain Institute The University of Queensland, Australia

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Re: [Freesurfer] FSGD design for multi-centre study
by C.P.E. Rollins 01 Jun '18

01 Jun '18

External Email - Use Caution I thought that I could not remove the class since this would mean that the contrast positive and negative values would no longer add up to 0. For instance if I remove only class "patient_centre2_female", then my contrast would have 11 (-1) and 12 (1) as opposed to 12 and 12. Could you please clarify? Thanks again, Colleen -------- Original Message -------- Subject: Re: [Freesurfer] FSGD design for multi-centre study Date: 2018-04-20 11:19 From: "C.P.E. Rollins" <cper2(a)cam.ac.uk> To: Freesurfer <freesurfer(a)nmr.mgh.harvard.edu> Thanks a lot for the explanation. The issue is that I don't think Freesurfer will run a design for which there are no subjects for a given class. So if I keep the classes (24 classes since 6 centres x 2 gender x 2 groups (patient vs. control), and have the contrast with 12 (-1) and 12 (1), -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 1 1 1 1 1 1 1 1 1 1 1 0 I get the error: -------------------------------- 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'm assuming this is because there are no participants in, for example, patient_centre2_female Is there any way to get around this issue, or should I remove those centres from my analysis (since I can't only remove "patient_centre2_female", as this would make the contrast unbalanced (positives and negatives would not add to the same number). I hope this was clear but please let me know if it was not. Thanks again, Colleen

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white matter and grey matter
by Ritesh Mahajan 01 Jun '18

01 Jun '18

External Email - Use Caution Hello Team, 1) How can i just get the white matter and grey matter together? 2) At what stage of free-surfer i can get this? I tried looking at the brainmask.mgz at the end of recon-all -autorecon1 stage. But, it looks like it has CSF and other parts of brain as well. Can you please help me out with this? Thanks, Ritesh Mahajan

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Cortical thickness and cortical stroke
by Guillaume Bellanger 31 May '18

31 May '18

External Email - Use Caution Hi Freesurfers users, I am looking on cortical thickness after ischemic stroke, especially stroke with cortical involvment. Freesurfer is validated in this population, Li, Q. (2015). When I check the surfaces on Freeview, cortical infarcts are excluded (which is great because of the major anatomy distorsion) but the pial and white surfaces (in contact to the area excluded) are different from zero. It seems that Free-surfer still calculates the cortical thickness as an average measure of the surfaces in contact to the area excluded (which doesn't have any grey matter !). I send you a picture to illustrate my question. I am wondering: how does Freesurfer calculate the surfaces in contact to a cortical area excluded ? If the areas are excluded does it have any consequences on the GLM with QDEC ? Thanks a lot Guillaume

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hippocampal subfield segmentation error (fsv6.0)
by miracle ozzoude 31 May '18

31 May '18

External Email - Use Caution Hello, I am using v6.0 installed on a linux server (via PUTTY) to segment hippocampal subfields. I downloaded the runtime from this link ( https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime) and followed the instructions on how to install it ( it was installed on the same server as v6.0). The installation process worked fine. However, when I wanted to run recon-all on already processed FS data ( e.g. recon-all -s ${SUBJECTS_DIR}/$session -hippocampal-subfields-T1 -parallel -openmp 6 -bigventricles -3T -time), I encountered an error. I have attached the log for your viewing. Thank you. Best, Miracle

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SIP disabled, fs_update run, still getting "dyld: lazy symbol binding failed" from within MATLAB
by Frederick Barrett 31 May '18

31 May '18

External Email - Use Caution Greetings freesurfer folk, Following previous posts here, as well as the freesurfer v6.0 release notes, I have disabled SIP (I'm in Mac High Sierra 10.13.4), updated my installation ($> sudo -E fs_update), and rebooted my computer, but I still get this problem. I am trying to run mri_vol2surf using the 'unix' command from within MATLAB (2017b), and upon doing so, I receive the dreaded "dyld: lazy symbol binding failed" error. I can run mri_vol2surf just fine on the command line (outside of MATLAB), and I've made sure the unix path accessible within MATLAB matches the unix path on the command line, and that freesurfer environment variables are all accessible within MATLAB. Does anyone have any ideas on how I might fix this problem? Thank you very much for your time. Best, Fred ---------------------------------------------------------- Frederick Barrett, Ph.D Assistant Professor of Psychiatry and Behavioral Sciences Behavioral Pharmacology Research Unit Johns Hopkins School of Medicine 5510 Nathan Shock Dr / Rm 3048 Baltimore, MD 21224 Voice/mail: (410) 550-9777 Email: fbarret2(a)jhmi.edu<mailto:fbarret2@jhmi.edu> | frederick.barrett(a)gmail.com<mailto:frederick.barrett@gmail.com> Google Scholar: http://goo.gl/vjrrsl<http://scholar.google.com/citations?user=KCtXPmAAAAAJ>

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