Freesurfer February 2017

freesurfer@nmr.mgh.harvard.edu

162 participants
277 discussions

Neurohackweek 2017: a summer school in human neuroscience and data science, September 4th-8th
by Ariel Rokem 18 Feb '17

18 Feb '17

We are happy to announce a call for applications to participate in the Neurohackweek summer school for neuroimaging and data science. This 5 day hands-on workshop, held at the University of Washington eScience Institute in Seattle, will focus on technologies used to analyze human neuroscience data, on methods used to extract information from large datasets of publicly available data (such as the Human Connectome Project, OpenfMRI, etc.), and on tools for making human neuroscience research open and reproducible. Morning sessions will be devoted to lectures and tutorials, and afternoon sessions will be devoted to participant-directed activities: guided work on team projects, hackathon sessions, and breakout sessions on topics of interest. For more details, see: http://neurohackweek.github.io/ We are now accepting applications from trainees and researchers in different stages of their career (graduate students, postdocs, faculty, and research staff) to participate at: https://form.jotformeu.com/70342294106348 Some experience in human neuroscience and at least basic knowledge in programming is desired, but we welcome applications from participants with a variety of relevant backgrounds. Accepted applicants will be asked to pay a fee of $200 upon final registration. This fee will include participation in the course, accommodation in the UW dorms, and two meals a day (breakfast and lunch), for the duration of the course. A limited number of fee waivers and travel grants will be available. We encourage students with financial need and students from groups that are underrepresented in neuroimaging and data science to apply for these grants (see application form for details). Important dates: April 18th: Deadline for applications to participate May 6th: Notification of acceptance June 1st: Final registration deadline On behalf of the instructors, Ariel Rokem, UW eScience Tal Yarkoni, UT Austin

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How to measure hippocampal, ventricle and temporal lobe volume & thickness
by Jing Gu 17 Feb '17

17 Feb '17

Dear FreeSurfer Developers, I am trying to measure hippocampal, ventricle and temporal lobe volume & thickness. Could you let me know the coding? Freesurfer Version : 5.0, unix Have a good weekend. Gina

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Re: [Freesurfer] Running recon-all on external hard-disk?
by Shane Schofield 17 Feb '17

17 Feb '17

Hi Z K, Thanks. I had thought that the recon-all speed will run much slower on the external HD but 10 hours seems to be the average recon-all time so I am pleasantly surprised. Best Wishes, Shane

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Running recon-all on external hard-disk?
by Shane Schofield 17 Feb '17

17 Feb '17

Hello, I am new to image analysis and I have a basic question: is it recommended to run recon-all on external hard-disks (USB3.0) to save space on my laptop? Will there be any issues with regards to the performance of recon-all? I have just finished a recon-all on 1 subject and it took me 10 hours. System spec is Mac Book Pro 13” 2016 model: 2 ghz Intel core i5. 8GB ram. Thank you. Shane

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Stats per region to brain map
by Johannes Klene 17 Feb '17

17 Feb '17

Hi! I've been reading up on tkviewer etc. but can't figure out how to accomplish the following: I calculated some stats (outside Freesurfer) summarizing the relation between cortical thickness and my outcome measure, per region present in the Killiany/Desikan atlas (i.e. running analyses on data obtained from aparcstats2table). Now I'd like to visualize these results, one number per region, by projecting them on the standard brain such that regions that showed a stronger association are more yellow and regions with weaker association are more red. Is there a straightforward way of doing this? I was thinking of maybe adjusting the RGB values in FreeSurferColorLUT.txt file? I'd be very grateful if anyone can provide some tips how to handle this. Kind regards, Johannes

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Parallelization not working as implemented
by Francis Tyson Thomas 17 Feb '17

17 Feb '17

Hi, I have run recon-all with both -parallel enabled (including different openmp threads) and disabled and I'm not able to get processing times same as the information provided in recon-all help. The CPU used is *Dual Intel **Xeon E5-2623 v3* paired with 32GB DDR4 RAM. Is the configuration presented in recon-all help a dual cpu configuration? Following are the runtimes I have obtained, no parallelization : 7 hrs and 58 mins -parallel (coarse parallelization) : 4 hrs and 39 mins -parallel (fine parallelization; -openmp 8) : 4 hrs and 34 mins -parallel (fine parallelization; -openmp 14) : 4 hrs and 37 mins Somehow varying the number of threads is having no effect in the execution time of recon-all as can been seen from the processing times. If you can explain what could be possibly going wrong here, it will help me in speeding it up further. Thanks, Tyson

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recon-all error
by Linette Savage 17 Feb '17

17 Feb '17

Hello, New to freesurfer using Linux (successfully reconstructed several images on a mac) - can you help me determine how to correct the error in this attached attempt at a recon? Many thanks, Linette

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Question regarding comparison image
by Dawn C. Matthews 17 Feb '17

17 Feb '17

In the image comparing the subfield segmentation for versions 5.3 and 6.0 found at https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields, the segmentation by version 6.0 does not capture a gray segment that 5.3 includes, located superior to the other regions. Was it omitted by 6.0 because it is part of a separate anatomical structure, not hippocampus? As a second question, in each case, does the totality of the colored subregions comprise what would be considered to be the total hippocampal volume (at least as represented in the slice shown)? Thanks very much for your time in answering.

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recon_all error on MacOS 10.12.13 Sierra: during mris_smooth. dyld: lazy symbol binding
by Jared Saletin 17 Feb '17

17 Feb '17

Hi Freesurfer gurus: I recently installed 6.0.0 on MacOS 10.12 and recon-all is exiting with an error in mris_smooth. It looks like a library issue. A prior post had the same issue and indicated uninstalling the whole distribution and re-installing 6.0.0 fresh (as opposed to installing over 5.3). I receive the same error however (pasted below). Does anyone have any thoughts? Thanks! Jared > #@# Smooth1 rh Thu Feb 16 16:47:23 EST 2017 > /Users/jared/Desktop/fMRITest/test/scripts > \n mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix \n > Waiting for PID 11130 of (11130 11133) to complete... > /Applications/freesurfer/bin/reconbatchjobs: line 81: 11130 Abort trap: 6 exec $JOB >> $LOG 2>&1 > Waiting for PID 11133 of (11130 11133) to complete... > /Applications/freesurfer/bin/reconbatchjobs: line 81: 11133 Abort trap: 6 exec $JOB >> $LOG 2>&1 > > mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix > > setting seed for random number generator to 1234 > 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 > > > mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix > > setting seed for random number generator to 1234 > 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 > > PIDs (11130 11133) completed and logs appended. > Darwin Jareds-iMac.local 16.4.0 Darwin Kernel Version 16.4.0: Thu Dec 22 22:53:21 PST 2016; root:xnu-3789.41.3~3/RELEASE_X86_64 x86_64 > > recon-all -s test exited with ERRORS at Thu Feb 16 16:47:23 EST 2017 — Jared M. Saletin, PhD Assistant Professor of Psychiatry and Human Behavior Alpert Medical School of Brown University E.P. Bradley Sleep Research Lab 300 Duncan Drive Providence, RI 02906 Email: jared_saletin(a)brown.edu Phone: 401-421-9440 Fax: 401-453-3578

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qdec significancy level
by Eva Wiedemann 17 Feb '17

17 Feb '17

Dear freesurfer-community, I want to compare cortical thickness in a group of Alzheimers patients's to healthy controls. Therefore I ran qdec setting the threshold to Min:1.3, Max:5 (assuming this would give me a significance level of p<=0,05). When I extract the cortical-thickness-data for the ROIs with "aparcstats2table" and perform two-sample-t-tests (assuming unequal variancies) on those, I can see highly significant (p<0,001) differences in many more ROIs, which don't show any significant differences on qdec. Does qdec use any corrections for multiple testing? which statistic test is qdec using? Why do the significancy level and the areas/ROIs showing significant differences differ between qdec and the extracted ROI-Data? I'm using freesurfer v.5.3.0 on Ubuntu 15.10. Thanks for your help in advance! Yours sincerely, Eva Wiedemann

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Freesurfer February 2017