Freesurfer

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30132 discussions

Tenure track faculty position at UAB
by Visscher, Kristina M 12 Jul '18

12 Jul '18

External Email - Use Caution The UAB Department of Neurobiology is accepting applications for tenure-track faculty positions. Join an excellent and rapidly growing group of colleagues! This is an open-rank, open research topic search and will continue until the positions are filled. Details at: https://jobs.sciencecareers.org/job/482204/department-of-neurobiology-open-…<https://urldefense.proofpoint.com/v2/url?u=https-3A__jobs.sciencecareers.or…> Kristina Visscher, Ph.D. UAB Department of Neurobiology kmv(a)uab.edu<mailto:kmv@uab.edu> | http://labs.uab.edu/visscher/

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Tenure track faculty position at UAB
by Visscher, Kristina M 12 Jul '18

12 Jul '18

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Cortical Thickness at Individual Vertices
by James Gullickson 12 Jul '18

12 Jul '18

External Email - Use Caution All, I am comparing cortical thickness between subjects with and without mild traumatic brain injury (mTBI). So far the contrasts in QDEC have not been significant after correcting for multiple comparisons. I am not necessarily surprised at this due to the heterogeneous nature of mTBI in our sample, i.e. we do not expect any two subjects to have damage in the same area. I am interested in ways to compare cortical thickness that are not dependent on a single ROI having an effect across subjects. One way I have tried is calculating z-scores for the values in the aparc.stats file, and using the number of abnormally low ROIs as a dependant variable to compare between groups. Is there a way to look at thickness differences at an even more general level? E.g. by comparing the number of vertices with abnormally low thickness? If so how would one go about that with Freesurfer data? This paper takes a similar approach with DTI. I'd like to do something analogous to their "number of voxels with low FA" analysis. https://www.sciencedirect.com/science/article/pii/S1053811911012146 Thanks, James

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Regenerate Qcache without Recon-ALL
by Mr. Tass 12 Jul '18

12 Jul '18

External Email - Use Caution Hello just a quick question i didn't run recon-all using the -qcache do i have to start all over ? 😢 the initial run took a week Please advise if there is a way to fix that without having to restart recon-all again thank you

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lazy symbol binding errors
by Davide Momi 12 Jul '18

12 Jul '18

External Email - Use Caution Dear experts, I was running mri2mesh command and I got this error: mris_convert /Users/davidemomi/Desktop/DAVE/sim_fem/fs_subj60/surf/rh.white /Users/davidemomi/Desktop/DAVE/sim_fem/m2m_subj60/tmp/wm.rh.stl dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib dyld: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib So I've tried to source Freesurfer and run sudo -E fs_update But I got another error rsync -zbrlv --progress --suffix=.1531384527_bak rsync:// surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/freesurfer-Darwin-OS… /Applications/freesurfer rsync: failed to connect to surfer.nmr.mgh.harvard.edu: Operation timed out (60) rsync error: error in socket IO (code 10) at /BuildRoot/Library/Caches/com.apple.xbs/Sources/rsync/rsync-52/rsync/clientserver.c(106) [receiver=2.6.9] Could you please help me with both errors? Thanks in advance Davide

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FreeSurfer - Lateral Ventricle Definition
by AKUDJEDU, THEOPHILUS 12 Jul '18

12 Jul '18

External Email - Use Caution Dear FreeSurfer Experts, Can you confirm whether, the volume of the choroid plexus has automatically been added to the laterel ventricle volume or not. Thanks Theo _______________________________ Theophilus Akudjedu BSc, MSc, PhD Candidate Room 202 Comerford Suite, Clinical Science Institute, Department of Psychiatry, National University of Ireland, Galway Phone: +353 838329602 Email: t.akudjedu1(a)nuigalway.ie<mailto:t.akudjedu1@nuigalway.ie> rasningo(a)gmail.com<mailto:rasningo@gmail.com> [https://ci6.googleusercontent.com/proxy/b9-AoNc-V0v85TZ_pj6puJTgX7uWBNlZdoh…]

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make_average_subject error
by Wang, Xiaoyu 12 Jul '18

12 Jul '18

External Email - Use Caution Hello FreeSurfer Developers, I am attempting to perform group analysis on a group of subjects. However, When I am trying to create an average subject I get the following error. mghRead(mri/norm.mgz, -1) could not open file I went into the average folder but I could not find norm.mgz anywhere. Looking further up on the log, it would seem that norm.mgz is supposed to be relabled from aseg.presurf.hypos However, said file is still there. I have looked in the wiki and found a few others who have had similar issues to me however, I can't see the solution or a reply. Does anyone have any Idea what I'm doing wrong? I have attached the recon-all.error as well as the recon-all log if it will be of any help Sincerely Xiaoyu Wang

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Putting results from probabilistic tractography on the surface
by Sims, Sara A 11 Jul '18

11 Jul '18

External Email - Use Caution Hello, I have outputs from FSL probtrackx that I would like to display on Freesurfer surfaces. If I put the volume into freesurfer space how can I get it to sample onto a surface when the values are in white matter and not grey matter? To rephrase, how can I pull data from white matter (just below the grey matter) and display it on a surface? Many thanks, Sara

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Custom color map in Freeview
by Anna Mynick 11 Jul '18

11 Jul '18

Hi all, I’m wondering whether there’s a way to create a custom color map in Freeview that would operate as a alternative to the preset Greyscale, Heatmap, NIH, PET, Jet and GE Color options. Ideally, I could assign each number value a given color, e.g. every “0” value in an .nii file is black, every “1” value is red, every “2” value is blue, every “3" is green and so on. I already have the RGB values worked out for each number value; I just need to know how to format this information and where to put it so that I can my custom colormap as an option in Freeview. For my purposes, there would be no need to adjust the assigned colors based on the overall range of values. For instance, there would be no need to assign a different color value to a “1” value depending on whether the highest value in the overall .nii file is 1 or 100. I did try reading the related conversation here<https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-April/051277.ht…> but I can’t seem to find the file it references, annotval2surfoverlay.m, in the Freesurfer directory. Thanks very much for your help! Anna

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Errors preprocess
by Lee, Seonjoo 11 Jul '18

11 Jul '18

External Email - Use Caution Dear Freesurfer experts, I tried to run preproc-sess but did not have much luck to make it work. I converted resting fmri file into .nii, and I created the following directory structure and it’s stored under /data/sub1/rest/001/fMRI.nii: /data /data/sub1 /data/sub1/rest /data/sub1/rest/001/ /data/sub1/rest/001/fMRI.nii Then I ran preproc-sess -s sub1 -fsd rest -surface $FSAVERAGE_DIR/fsaverage lhrh -mni305 -fwhm 5 -per-run And I kept getting the following error message: ERROR: cound not find session sub1 To run freesurfer I specified SUBEJCTS_DIR as /data (I don’t think it matters, though…) export FREESURFER_HOME=/Applications/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh SUBJECTS_DIR=/data Any suggestion to make it work? Thanks. -Seonjoo

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