Freesurfer September 2016

freesurfer@nmr.mgh.harvard.edu

133 participants
200 discussions

[FreeSurfer] aparc.a2009s.stats, MeanCurv, GausCurv
by Hanbyul Cho 22 Sep '16

22 Sep '16

Dear FreeSurfer Team, I heard that the processed subjects/stats/?h.aparc.a2009s.stats included the integrated rectified mean curvature value (MeanCurv) and integrated rectified Gaussian curvature value (GausCurv). I wonder that whether the integrated rectified curvature values are about pial surface or white matter surface. Thank you. Best wishes, Han

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freesurfer longitudinal data
by Gabor Perlaki 22 Sep '16

22 Sep '16

Dear all, Is it possible to get simple ROI data (such as aseg.stats or aparc.stats in case of cross-sectional analysis) as the result of the longitudinal analysis, which can be further analyzed by SPSS? Best Regards, Gabor <petzinger.gabor(a)gmail.com>

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cluster feature extraction from qdec output
by Damien MARIE 22 Sep '16

22 Sep '16

Dear experts, I would like to know what is the best and simplest way to extract cortical surface area and thickness from clusters obtained after a Monte Carlo correction. This is a group comparison I did with qdec including gender as discrete variable + age and mean thickness or whole hemispheric surface area as nuisance factors, so I would like to get the feature residuals after the removal of the covariate effects. I am sorry, I saw several posts about that but for me it’s not completely clear what command line I should use to get tables for this… Thank you and best, Damien

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optseq2 question
by Yoed Kenett 21 Sep '16

21 Sep '16

hello i am trying to use optseq2 to design a study. I have a new mac book pro with El Capitan installed. I have tried downloading all different optseq2 versions but each time when i try to run it through the terminal i get the same exact error: -bash: optseq2: command not found what am i doing wrong here? which version should i use and how do i get it to work? thanks so much Yoed

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combining epi dewarping and motion correction w/ mri_vol2vol
by Nathan Tardiff 21 Sep '16

21 Sep '16

Hello, I am attempting to combine my motion correction and b0 unwarping steps. I have .lta files produced by registering every volume of a BOLD run to the first volume using mri_robust_register and a vsmap for dewarping produced by epidewarp.fsl. Is it sufficient to input them both into mri_vol2vol to combine these steps? Something like: The command I was thinking of trying was: mri_vol2vol --mov inFile --targ dstFile --o outFile --lta ltafile --vsm vsmap --cubic Or would something about the creation of the .lta files also need to be changed? Thanks, Nathan

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Failure in testing newly installed FreeSurfer
by Saeed mahdizadeh bakhshmand 21 Sep '16

21 Sep '16

Hello FreeSurfer Developers, I'm trying to test a very basic command (recon-all) according to this page(https://surfer.nmr.mgh.harvard.edu/fswiki/TestingFreeSurfer) after installing FreeSurfer and I receive following error after a few seconds: ERROR:recon-all -s bert exited with ERRORS at Sun Sep 4 17:18:51 EDT 2016 I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 2) Platform: x86_64 3) uname -a: Linux saeed-CDS-Custom-Configuration 4.4.0-36-generic #55-Ubuntu SMP Thu Aug 11 18:01:55 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached Saeed

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Research Fellow or Research Associate Position
by Lili He 21 Sep '16

21 Sep '16

Cincinnati Children’s Hospital Medical Center (CCHMC) is a premier pediatric research institution. We are driven by our mission to improve child health and transform the delivery of care through fully integrated, globally recognized research, education and innovation. Post-doctoral research fellows at Cincinnati Children’s are valued for their unique interests and strengths, and are supported by our institution’s strong programming for post-docs through the Office of Postdoctoral Affairs and the Office of Academic Affairs and Career Development. Mentoring, support for international students and an emphasis on crafting high-quality grant proposals are only a few of the features that set our program apart. Dr. Lili He’s research focuses on developing objective MRI methods for neonates; developing multimodal MRI neuroimaging biomarkers to predict long-term cognitive, behavioral and sensorimotor deficits. We are now seeking a creative and highly motivated individual with good writing skills and training in MRI image processing data analysis. Previous experience on machine learning will be plus. The major duties of this opening are: to develop quantitative method for use in advanced neuroimaging and brain mapping involving structure MRI, functional MRI and DTI; to analyze brain image data using existing commercial and publicly available image analysis programs (such as SPM, FSL, CONN, Freesurfer). Candidates for either Postdoctoral Research Fellow or Research Associate (commensurate with previous experiences) must hold a PhD with a background in any of the following disciplines: computer science, biomedical engineering, bioinformatics, electrical engineering and neuroscience. Emphasis on programming expertise in Matlab, C/C++ and in UNIX environment. The work promises to be challenging and presents a highly exciting opportunity to utilize resources available at Cincinnati Children's Hospital Medical Center (CCHMC) and collaborations from the Department of Pediatrics, Division of Neonatology and with the Pediatric Neuroimaging Research Consortium (PNRC) faculty. Contact: Lili He, PhD Address: Lili.He(a)cchmc.org

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Configuration question for unbuntu
by Thomas Beaudry 21 Sep '16

21 Sep '16

Hi, I installed freesurfer and followed all of the configuration steps. I am now doing the sample tests, and noticed that it can't find libjpeg.so.62. According to this resource: https://surfer.nmr.mgh.harvard.edu/fswiki/Download I should do the following: cd /usr/lib (/usr/lib/i386 or /usr/lib/x86_64 on some Ubuntu distros) sudo ln -s libjpeg.so.8 libjpeg.so.62 sudo ln -s libtiff.so.4 libtiff.so.3? After doing this is, it works, and I no longer get any errors. However, I am maintaining a cluster, and would prefer not doing this for every machine. Is there a place in the install directory or a parth/variable that I could modify to have it work without having to do the fix mentioned above? Thanks, and have a nice day, Thomas Beaudry

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Recon hires 7T {Disarmed}
by Köbe, Theresa 21 Sep '16

21 Sep '16

Dear FreeSurfer Developers, I am attempting to run recon-all on 7T MP2RAGE images (resolution 0.7x0.7x0.7mm³) with hippocampus subfield segmentation. I use the freesurfer version 5.3 so that I expect an automatic down-sampling to 1x1x1mm³. I used the data directly from the scanner (without reorientation to standard etc.) and used the following command: recon-all -s $subject.freesurfer -hires -i $subject.mp2rage.nii -expert /media/NeuroMet_Project/scripts/expert.opts -all -hippo-subfields" As expert option I used only: mris_inflate -n 15 The processing starts fine but ends with the following error: ERROR: dimension mismatch between input volume and seg input 321 321 321 seg 322 322 322 Could you please help me dealing with this problem? I attached also the log-file Thank you so much. Best Theresa ------------------------------------------------------------------------- Charité – Universitätsmedizin Berlin NeuroCure Clinical Research Center NCRC Dipl.-Biol. Theresa Köbe AG Kognitive Neurologie Wiss. Mitarbeiter Charitéplatz 1, D-10117 Berlin Tel +49 30 450 560 185 Fax +49 30 450 7 560 280 Interne Besuchsadresse: CCM, Sauerbruchweg 5, E2 http://www.charite.de/service/lageplan/plan/map/ccm_sauerbruchweg_5/<redir.aspx?REF=mc29RH9tIXK9qgoNB0UJ6dmsQ-pCBih_Q7so140WG76sl9oBFOLTCAFodHRwOi8vd3d3LmNoYXJpdGUuZGUvc2VydmljZS9sYWdlcGxhbi9wbGFuL21hcC9jY21fc2F1ZXJicnVjaHdlZ181Lw..>

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fmri pipeline
by A Nunes 20 Sep '16

20 Sep '16

Hi, I am getting a bit confused from the mailing archive on how to properly map volume fmri data into surface fsaverage5. 1. Should I map the volume fmri into individual surface first and then to fsaverage, or I won't loose data if I map it directly to fsaverage5? 2. Should I smooth the data when mapping into the individual surface or from individual surface to fasaverage5? Thanks Adonay

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Freesurfer September 2016