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Postdoctoral position at Northwestern University
by Derin J Cobia 15 Sep '14

15 Sep '14

(Posted on behalf of a colleague) ======================== A postdoc position is available immediately in the Neuroimaging and Applied Computational Anatomy Lab, Department of Psychiatry and Behavioral Sciences at the Northwestern University Feinberg School of Medicine. Our laboratory aims to develop multidimensional and multimodal neuroimaging biomarkers using the tools of computational anatomy. Working with collaborators from engineering, mathematics, psychology and clinical specialties, our research is focused on the following major areas: automated pipelines for mapping of brain structures using MRI, development of complex neuroimaging biomarkers, clinical applications in dementia, psychosis, mood disorders and genetics, neuroinformatics, and neuroimaging of animal models. This position is initially limited to two years with the possibility of extension. It will be partially funded by a new 5-year NIH study (PI Greg Miller, PhD) of the relationship between socioeconomic status and maturation patterns in the corticolimbic and corticostriatal circuitries of school-age youths. The successful applicant will work primarily on T1, DTI and resting-state fMRI analysis in this and various other clinical populations with a particularly emphasis on multimodal approaches. The position will be integrated closely with the existing collaborative environment. Additionally, supervision of graduate and medical students will be required. Candidates should hold a Ph.D. in neuroscience, psychology, engineering or related fields. A strong publication record and background on structural neuroimaging research should be demonstrated. Experience with fMRI analysis is highly desirable. Applicants should have strong analytical skills and experience with existing tools for large-scale analysis of neuroimaging data (i.e., FreeSurfer, 3D Slicer, SPM, FSL, AFNI, etc.). Proficiency in relevant programming languages (e.g. MATLAB, Python) and statistical analysis (R, SAS, SPSS) is required. Working experience in epidemiological research or large-scale clinical studies is highly desirable. The successful candidate must be capable of working independently and taking initiatives. The candidate is expected to be a team-player with excellent communication and writing skills. Please send a letter of research interest, CV, and names of 3 references to Dr. Lei Wang (leiwang1(a)northwestern.edu) Northwestern University is an Equal Opportunity, Affirmative Action Employer of all protected classes, including veterans and individuals with disabilities. Women and minorities are encouraged to apply. Hiring is contingent upon eligibility to work in the United States.

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Cortical gray matter surface area
by will brown 15 Sep '14

15 Sep '14

Hi all, I messed up this question recently so just want to clarify and try again. We want to know the cortical gray matter surface area of our subjects but are unclear about how to get this info. ?.aparc.stats reports: Measure Cortex, WhiteSurfArea, White Surface Total Area, XXXX, mm^2 How about the gray matter? Thanks, Will

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fsfast: using an empirically derived HRF with mkanalysis-sess
by Alex Kell 14 Sep '14

14 Sep '14

hi freesurfers, i would like to use an empirically derived HRF with mkanalysis-sess. i have derived the HRF i want [via an FIR model], but it's not obvious how i can use my custom HRF with mkanalysis-sess. one option, it seems, is to feed in my own regressors with the -taskreg flag and then not supply the model with any other regressors of interest. i'd just convolve stick regressors that have the appropriate timing with my own HRF. but this would only work if selxavg3-sess does NOT convolve task regressors with the HRF. so two questions: 1. is the -taskreg flag the best way to do this? is there another, better way? 2. does selxavg3-sess convolve task regressors with the HRF? thanks, alex

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how to shrink wm surface
by Andrea Horváth 13 Sep '14

13 Sep '14

Dear Freesurfers, After running recon-all, the wm surfaces are too close to the pial surface, some gray matter is segmented as white matter as seen in the attached picture (red cross: a bigger cortical part is included in the white matter). How can I shrink the wm surface? Thank you for your help! Andrea

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trac-all exited with errors
by BigBen2293＠web.de 12 Sep '14

12 Sep '14

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trac-all exited with errors
by BigBen2293＠web.de 12 Sep '14

12 Sep '14

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Qdec "create stats tables" error
by Markus Gschwind 12 Sep '14

12 Sep '14

Dear all, I am trying to make work Qdec on my system ubuntu 12.04. freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 After I have loaded my qdec.table.dat and renamed the analysis folder , when I then try to create the "stats tables", I get an error and it blocks at 20% of the waiting bar. Data table loading completed successfully. > > SUBJECTS_DIR is '~/Documents/ARNAUD/' > > mkdir -p /usr/local/freesurfer/subjects/qdec/stats_tables/ > > mkdir: cannot create directory `/usr/local/freesurfer/subjects/qdec': >> Permission denied > > ERROR: In >> /usr/pubsw/packages/KWWidgets/CVS-vtk560/KWWidgets/vtkKWTkUtilities.cxx, >> line 230 > > vtkKWQdecApp (0x289a94e0): > > Script: > > vtkTemp2 GenerateStatsDataTables > > Returned Error on line 1: > > Uncaught exception: command failed: mkdir -p >> /usr/local/freesurfer/subjects/qdec/stats_tables/ > > >> Stack trace: > > Uncaught exception: command failed: mkdir -p >> /usr/local/freesurfer/subjects/qdec/stats_tables/ > > >> while executing > > "vtkTemp2 GenerateStatsDataTables" > > > It seems that it tries to write into the default SUBJECT_DIR, thing that I do not understand as I put the actual SUBJECT_DIR in the top line of qdec.table.dat (and it is correctly recognized in the qdec window SUBJECTS_DIR). How could I come around that problem? Thanks in advance! Markus

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FsFast Functional Connectivity Analysis
by Jiahe Zhang 12 Sep '14

12 Sep '14

Hi Doug, I was trying to run functional connectivity analysis following instructions on the FreeSurferWiki ( http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkth…) I was able to successfully run the following commands (nothing errored as far as I can tell) but the resulting partial correlation and significance maps turned out to be empty. Could you take a look at the commands and let me know if anything can be improved? 1. PREPROC preproc-sess -s subject_001 -fwhm 6 -surface fsaverage lhrh -mni305-2mm -fsd bold -per-run -stc up 2. SEED CONFIG fcseed-config -segid 1010 -fcname L_Posteriorcingulate.dat -fsd bold -mean -cfg mean.L_Posteriorcingulate.config 3. SEED TIMECOURSE fcseed-sess -s subject_001 -cfg mean.L_Posteriorcingulate.config (wm.dat and vcsf.dat were similarly created) 4. ANALYSIS CONFIG mkanalysis-sess -analysis fc.lpccseed.surf.lh.lpf -surface fsaverage lh -fwhm 6 -notask -taskreg L_Posteriorcingulate.dat 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -mcextreg -polyfit 5 -nskip 4 -fsd bold -TR 5 -per-run -lpf .1 5. ANALYSIS selxavg3-sess -analysis fc.lpccseed.surf.lh.lpf -s subject_001 Thanks, Jiahe -- Jiahe Zhang Ph.D. Student Department of Psychology Northeastern University 617-373-4789

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FW: Most recent/complete FreeSurfer + Patches?
by Gurney, Jenny 12 Sep '14

12 Sep '14

Hi guys! We would like to install the latest and greatest FreeSurfer on the processing cluster used by the CNDA at Washington University. We're thinking about installing the 5.3.0-HCP, and then over that, the released 5.3.0 patches. We're looking for verification that doing the install this way makes sense and that these two code sets don't conflict in any way. We know that the 5.3.0-HCP version updates the mris_make_surfaces, however, the patches do not include that update, which is why we are thinking about starting with 5.3.0-HCP as the base install. Note that this is being done on CentOS 6.x The currently available patches seem to include: mni152reg mri_mcsim mri_segstats recon-all tksurfer-sess tksurferfv Is that a complete list or did we miss some binaries/scripts? Also, it seems that the 'patch' binaries are dynamically linked, while the release binaries are statically linked. Besides dependency issues, could this cause an issue with results consistency, etc. if other system libraries get updated? Thanks, guys. Hope all is well. Matt House, Jenny Gurney and John Flavin @WU in STL ________________________________ The material in this message is private and may contain Protected Healthcare Information (PHI). If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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WM segmentation
by Shengwei Zhang 12 Sep '14

12 Sep '14

Hi FreeSurfer list members, I'm working on a white matter hyper-intensity study, and trying to group the segmented WM labels in lobes based on the wmparc.mgz file made by recon. But I found that there's a large part of "unsegmented WM" near ventricles, and wonder if such labels are consistently assigned among subjects, because most of the WM hyperintensity voxels are located within these locations. Or is there other way to segment the 'unsegmented WM' in more details? I'd appreciate any help related to this topic. Shengwei

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