Freesurfer June 2018

freesurfer@nmr.mgh.harvard.edu

105 participants
154 discussions

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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Freesurfer June 2018