Freesurfer August 2017

freesurfer@nmr.mgh.harvard.edu

145 participants
233 discussions

mri_glmfit-sim annotations
by Van Der Deijl, Rosanne 21 Aug '17

21 Aug '17

Dear Freesurfer team, I was wondering how the annotations for the clusters that came out of mri_glmfit are picked. I am wondering because I have a cluster which visually seems to cover mostly the insula (and with a previous set of subjects this same cluster was annotated as the insula), but it is now annotated as the superiortemporal (which it indeed also partly covers). Is just the region in which the largest part of the cluster lies picked for annotation, or is it done p-value-wise or in some other way? Thank you in advance! Kind regards, Rose

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Cortical gyrification findings
by Martin Juneja 21 Aug '17

21 Aug '17

Hello FS experts, I am correlating some of the behavioral measures with cortical thickness (CT) and cortical gyrification (CG) measures. - For CT-behavioral: I have some expected results after correcting for multiple comparisons using mri_glmfit-sim - For CG-behavioral: Again, I have some expected results (more expected that CT-behavioral results) - only 3 clusters (sig.mgh result) but none of those survived after correcting for multiple comparisons using PALM, I can't use mri_glmfit-sim because my design is non-orthogonal. I also learnt from FS discussion forum and literature that CG is already extremely smooth so it would require large area to survive multiple comparisons correction. I was wondering if I can report my CG results based on this argument. If yes, then any more suggestions/references which I can use as arguments to justify my CG findings, that would really help. Thanks.

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mri_mcsim error
by Zhiliang Long 21 Aug '17

21 Aug '17

Dear FS experts: I am writting to ask for help about mri_mcsim. I would like to run mri_mcsim with only one FWHM (e.g. --fwhm 13) instead of FWHM=1:fwhm-max (the default is FWHM=1:30). Thus i tried: mri_mcsim --o $FREESURFER_HOME/average/mult-comp-cor/fsaverage/lh/mask --base mc-z --surface fsaverage lh --nreps 100 --mask mask.mgh --fwhm 13 However, i got errors: ERROR: Option 13 unknown. Is there any information that i missed ? Thanks in advance for any suggestions. Best Zhiliang Long

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Problem opening freeview
by Micah Rhodes 21 Aug '17

21 Aug '17

Hello, I am having a problem opening up freeview in MobaXterm (a bash terminal) on my windows 7 machine. Although freesurfer is working, when I attempt to open freeview, it tells me that "XWin_Moba.exe has stopped working." Have you ever come across this issue? Thanks

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Freeview in FreeSurfer 6.0
by Wu Jianxiao (Jadecci) 21 Aug '17

21 Aug '17

Dear FreeSurfer team, I was viewing MNI152 template from FSL in freeview using FreeSurfer 6.0, and somehow there was a shift between 1mm and 2mm template. The problem does not show in FreeSurfer 5.3. Is there an error with freeview in FS6 or did the command change? The command I used is as follow: freeview $FSL_DIR/data/standard/MNI152_?mm_brain.nii.gz Thank you! Wu Jianxiao Department of Physiology & Department of Electrical and Computer Engineering National University of Singapore

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Custom intensities in aparc+aseg
by Martin Kavec 20 Aug '17

20 Aug '17

Dear all, I ran my subjects through recon-all successfully. I am in a need to have custom intensities for segmentation and parcellation in aparc+aseg. Say, 10 - ventricles, 20 - amygdala, 30 - putamen, ... I would appreciate advice on how I could achieve that. Thanks in advance, Martin

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Freesurfer manual edit problems
by Chethana Kishore 19 Aug '17

19 Aug '17

sir/maam, i request your help in solving in a query of mine. while the manual edit is being done , and we use the "save the main volume" button to save the progress. but subsequently on opening the image to further our edits it appears as a very brightly intense image and difficulty in differentiating the grey/white matter leading it to be unuseable. can u please suggest how to solve this problem? Thanks and regards Chethana K

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pet surfer
by John Anderson 18 Aug '17

18 Aug '17

Hi Dr Greve, I followed the steps in WIKI to do SUV-surface based analyses + PVC. I have the following questions and I highly appreciate your input: 1. Why the dimension of the images (mgx.gm, mgx.ctx.gm and mgx.ctx.subgm) is not like the original SUV image that has been fed to the pipeline. i.e. I start with image-dimensions 128X128X128 : 2X2X2 and end up with 79X113X102 : 2X2X2 Also FOV is different as well between the original SUV image /256/ and the output mgx images /158/. How this happen? I am I doing something wrong? 2. Some voxels in the mgx images has negative signal intensity. is this normal? Thank you for any clarification. John

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Solution found for: recon_all error on MacOS 10.12.13 Sierra
by Alissa Stafford 18 Aug '17

18 Aug '17

Hi, I was having the same problem as described here: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-March/050544.ht… when I was trying to run selxavg3-sess. I realize that this error was mentioned in the release notes and that the potential fix was sourcing freesurfer and then typing "sudo -E fs_update” into terminal. fs_update seemed to run without any problems, but did not fix the lazy symbol binding error. I did end up fixing the problem after many hours. My fix: I went to http://hpc.sourceforge.net/, downloaded gcc-7.1-bin.tar.gz and followed the instructions on the webpage. I found this error and solution described for another software package here: https://www.ncl.ucar.edu/Download/macosx.shtml#InstallCompilers. I wish I understood compilers enough to figure out exactly what is going on, but I only know that this fixed my error. I subscribe to the freesurfer emails, but don’t think I am able to add to an old thread or anything so wanted to contact you two directly. I am hoping you could add this to the original thread or the release notes so that others can use this if fs_update does not work for them either. Best, Alissa

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Curvature in FreeSurfer
by Kasper Jessen 18 Aug '17

18 Aug '17

Dear FreeSurfer, We have been discussing the mean curvature provided by FreeSurfer software. As i understand the mean curvature is measured as 1/r and has a unit of 1/mm. But a) What is the curvature an expression of? Is it the degree of folding of the brain and is it the white matter surface or pial surface? b) An increased value of mean curvature - does that mean an increase in folding of the brain? c) What is the expected association between the mean curvature; and cortical thickness and surface area? Any suggestions of litterature? I have read through two webpages below, but unfortunately the confusion still exist :-) http://mathworld.wolfram.com/MeanCurvature.html http://mathworld.wolfram.com/GaussianCurvature.html I am aware that this may be a simple question but the different measures of curvature (fx. gaussian vs mean curvature) made us discuss the differences and what it is an expression of. Best regards, Kasper

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Freesurfer August 2017