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30099 discussions

Displaying labels in FreeView
by Mohammed Goryawala 16 Sep '14

16 Sep '14

Hello All, I am doing a study and I have determined some regionals volumes in the Aparc and Aseg files which are significant. I would like to show these in Freeview while hiding the other insignificant ones. Please advice if its possible in Freeview. Thank you Mohammed Goryawala, PhD University of Miami Miller School of Medicine

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how to choose the best random effect in LME models
by Bernardoni, Fabio 16 Sep '14

16 Sep '14

Dear Freesurfer Users, I am trying different LME models to describe the time evolution of cortical thickness in anorexia patients. The LME tools provide a function (lme_mass_LR) to test whether a model with q+1 random effects is better (fits the data better) than one with q random effects, eg whether a model with random intercept and slope is better than one with only intercept random. I have two questions: 1- is there a similar function to test whether the model with intercept as a random effect is better than the model with slope as a random effect (ie two models with the same number of random effects)? In another thread I read one should judge which random effect is to be chosen from the percentage of voxels where one has convergence. It sounds reasonable, but an explanation of why this should be so would be welcome. 2- does it make sense to use lme_mass_LR to test whether a model with 1 random effect is better than one with 0 random effects? I have it with something like: LR_pval = lme_mass_LR(lhstats_0RE,lhstats_1RE,0); And I get as a result LR_pval= 0.3 (a constant vector) which I do not know how to interpret: something wrong, this test does not make any sense, choose the 0 random effect model ... Thanks in advance for your help. Cheers, Fabio Dr. Fabio Bernardoni wiss. Mitarbeiter Klinik und Poliklinik für Kinder- und Jugendpsychiatrie und -psychotherapie Tel. +49 (0)351 458-5245 Fax +49 (0)351 458-7206 Universitätsklinikum Carl Gustav Carus an der Technischen Universität Dresden Anstalt des öffentlichen Rechts des Freistaates Sachsen Fetscherstraße 74, 01307 Dresden http://www.uniklinikum-dresden.de Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer Vorsitzender des Aufsichtsrates: Prof. Dr. med. Peter C. Scriba USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113

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Re: [Freesurfer] problems with tracula pre-processing (bvecs)
by lshih＠bidmc.harvard.edu 15 Sep '14

15 Sep '14

Hi, I was having similar errors as Michele Cavallari regarding "error reading /path/to/subject/dmri/dwi_frame," but I'm not sure it's related to my bvecs file. I did try reconfiguring my bvecs file into columns instead of row just in case, but that didn't solve the problem. It really just looks like it can't find the dwi_frame file after the mri_concat command. I am attaching my trac-all.log and config file. Running Freesurfer 5.3 on Macbook OS 10.7.5. The bvecs files were generated after I converted my dicoms to nifti using dcm2niigui (GE scanner). Can anyone tell me how dwi_frame is generated? Ludy This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

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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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