Freesurfer

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16 participants
30098 discussions

Different significant clusters: qdec vs mri_glmfit-sim
by Cassandra Wannan 13 Apr '16

13 Apr '16

Hi Freesurfer experts, Qdec does not appear to allow me to automatically extract mean values for significant clusters for each participant, so I have been doing this using command line after running the original analysis in Qdec. However, I have found that there are some differences in the significant clusters between the two. The command line I am using is: mri_glmfit-sim --glmdir TRSCtrl_Vocab_DODS --cache 2 abs --cwp 0.01 I believe that this should correspond to analysis in Qdec using the preset threshold of 2 and Monte-Carlo Null-Z Simulation value of 2.0 (0.01). The significant clusters from Qdec are: # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP CWPLow CWPHi NVtxs Annot 1 7.740 109023 669.23 -6.1 -12.5 47.0 0.00120 0.00080 0.00170 1618 paracentral 2 5.854 63055 1542.69 -19.0 -73.2 -3.6 0.00010 0.00000 0.00020 1913 lingual 3 5.393 127437 1063.38 -23.4 -6.9 -28.0 0.00010 0.00000 0.00020 2069 entorhinal 4 5.026 112833 788.05 -13.9 -45.3 38.9 0.00010 0.00000 0.00020 1660 precuneus 5 4.726 141529 523.23 -34.4 -5.7 10.9 0.00760 0.00650 0.00870 1456 insula 6 4.413 23898 863.24 -13.4 25.1 26.4 0.00010 0.00000 0.00020 1495 superiorfrontal 7 3.819 21492 874.38 -17.8 -72.7 29.0 0.00010 0.00000 0.00020 1321 precuneus Whereas from the command line: # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs Annot 1 7.740 109023 668.36 56.9 -11.3 35.0 0.00050 0.00020 0.00080 1618 postcentral 2 5.854 63055 1328.30 52.2 -58.3 -8.8 0.00010 0.00000 0.00020 1913 inferiortemporal 3 5.393 127437 1004.26 32.5 -2.8 -38.4 0.00010 0.00000 0.00020 1950 fusiform 4 5.026 112833 782.44 54.3 -41.2 42.3 0.00010 0.00000 0.00020 1660 supramarginal 5 4.413 23898 780.09 56.5 2.1 6.1 0.00010 0.00000 0.00020 1495 precentral 6 3.819 21492 673.28 46.3 -59.1 31.8 0.00050 0.00020 0.00080 1321 inferiorparietal When I view the glmfit clusters in free view they do appear very similar to the ones in Qdec, but there is one less significant clusters and obviously the cluster names are different. Am I using the correct command line to extract this information? Many thanks, Cassie

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missing baseline in longitudinal analysis
by Mihaela Stefan 13 Apr '16

13 Apr '16

Hello FreeSurfers, We are conducting a longitudinal analysis and we have a subject who is missing the structural at baseline (it has fMRI data though). That subject returned for the 1st and the 2nd follow-up. Can we process the longitudinal pipeline the usual way and account for the missing baseline in the LME analysis? The other option would be to treat the 1st follow-up as baseline but we would like to be consistent with the fMRI analyses and keep the baseline time point. Thanks! Mihaela

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Freesurfer v6 beta
by Francis Tyson Thomas 13 Apr '16

13 Apr '16

Hi, I was wondering when would the new Freesurfer v6 beta be available? Also I have been using the old beta for my hippocampal segmentation and I wanted to know if this new beta will affect the results of that? Thanks, Tyson

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How to view entire brain results in Freeview for LME data
by Jennifer Legault 13 Apr '16

13 Apr '16

Dear Freesurfer Experts, I have run my participants' longitudinal sMRI data through the preprocessing longitudinal pipeline, ran the LME multivariate analysis, cluster-thresholded the data, and am now trying to visualize those results in Freeview (for some reason tksurfer is very, very slow to run on my computer). I am interested in the Fs volume (thickness*area) measure. I noticed in the FsFast Tutorial <https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastGroupLev…>, that all the corrected results were able to be merged into one file using the vlrmerge command. In the beginning of the tutorial, it states that fMRI and structuraI group analyses run similarly. * I was therefore wondering if I can use the vlrmerge command (or some similar command) for my LME data, such that I can view the following information all in one file: both hemispheres, aparc and aseg. * Currently I can only view the aparc results for each of the hemispheres separately (and I haven't found a way to visualize the aseg data). Thank you for taking the time to read this email. Best, Jennifer Legault Ph.D candidate, Neuroscience Brain, Language, and Computation Lab The Pennsylvania State University

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Oblique Slice Acquisition
by Katherine Reiter 13 Apr '16

13 Apr '16

Hello freesurfer experts, I am working with a dataset that was acquired with oblique slices aligned to each participant's ac-pc line. 1) I've run a handful of subjects through mri_convert and the recon stream and each subject has a slight abnormality in the ventral temporal regions. It's subtle but apparent in each acquisition (image attached and the abnormality is apparent at the red cross). We believed it to be an alignment issue due to the oblique slices. Is there any way to fix this abnormality? 2) Are there any different preprocessing steps that should be added to mri_convert or the recon stream? Thanks much in advance! Kate Katherine Reiter, M.S. Clinical Psychology Doctoral Student Marquette University Phone: (414) 288-3807 Email: katherine.reiter(a)marquette.edu

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Open Research Assistant position at the VA
by Leslie Nordstrom 13 Apr '16

13 Apr '16

Hi FreeSurfers, There is a research assistant position opening at the VA Boston Healthcare System in neuroimaging and aging (job announcement is attached). This would be a great position for someone who is interested in both the technical aspects of MRI data processing/analysis as well as in neuropsychology and aging research. Interested applicants should send a resume and contact information for two references via email to Leslie Nordstrom: lesliekn(a)bu.edu with RESEARCH ASSISTANT as the subject line. Please forward this message to anyone you think might be interested in the position!

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.license and tksurfer
by stdp82＠virgilio.it 13 Apr '16

13 Apr '16

Hi list, please see the error reported below. It occurs when I invoke tksurfer.Of note, I have completed without problem fs-fast analysis without error.The .license file is well placed and written.Thanks Stefano tksurfer fsaverage rh inflated -aparc -overlay subj/rest/fc.ROI.surf.rh/ROI/sig.nii.gz -fminmax 1.3 3 thresholds min=1.3 max=3 slope=0.588235 mid=2.15 subject is fsaverage hemi is rh surface is inflated surfer: current subjects dir: /Applications/freesurfer/subjects/subject_prova surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /Applications/freesurfer/subjects/fMRI/con_run1 checking for nofix files in 'inflated' Reading image info (/Applications/freesurfer/subjects/subject_prova/fsaverage) Reading /Applications/freesurfer/subjects/subject_prova/fsaverage/mri/orig.mgz surfer: Reading header info from /Applications/freesurfer/subjects/subject_prova/fsaverage/mri/orig.mgz -------------------------------------------------------------------------- ERROR: FreeSurfer license file /Applications/freesurfer/.license not found. If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment.

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Re: [Freesurfer] TRACULA
by Alan Francis 13 Apr '16

13 Apr '16

Hi Jasmin - When replying please cc the FS group so that they may weigh in on the situation. Looking at the log, they key problem appears to be this: niiRead(): error opening file Users/jasminalves/Desktop/data/DTI/40/DTI.nii.gz Tracula is not able to open your DTI.nii.gz Please check this file or pathway. best, Alan On Tue, Apr 12, 2016 at 11:17 AM, Jasmin Alves <jalves(a)usc.edu> wrote: > Hi Alan, > > Thank you for your reply. I changed the pathway but now have stumbled upon > a new error. I tried looking through the feeds and couldn't really find a > relevant solution. > > Jasmins-MacBook-Pro:data jasminalves$ trac-all -prep -c dmrirc.txt > > INFO: SUBJECTS_DIR is /Users/jasminalves/Desktop/data/FREESURFER > > INFO: Diffusion root is /Users/jasminalves/Desktop/data/FREESURFER > > Actual FREESURFER_HOME /Applications/freesurfer > > trac-preproc -c > /Users/jasminalves/Desktop/data/FREESURFER/40/scripts/dmrirc.local -log > /Users/jasminalves/Desktop/data/FREESURFER/40/scripts/trac-all.log -cmd > /Users/jasminalves/Desktop/data/FREESURFER/40/scripts/trac-all.cmd > > #------------------------------------- > > /Applications/freesurfer/bin/trac-preproc > > #------------------------------------- > > #@# Image corrections Tue Apr 12 08:04:37 PDT 2016 > > mri_convert Users/jasminalves/Desktop/data/DTI/40/DTI.nii.gz > /Users/jasminalves/Desktop/data/FREESURFER/40/dmri/dwi_orig.nii.gz > > mri_convert Users/jasminalves/Desktop/data/DTI/40/DTI.nii.gz > /Users/jasminalves/Desktop/data/FREESURFER/40/dmri/dwi_orig.nii.gz > > niiRead(): error opening file > Users/jasminalves/Desktop/data/DTI/40/DTI.nii.gz > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > > reading from Users/jasminalves/Desktop/data/DTI/40/DTI.nii.gz... > > Darwin Jasmins-MacBook-Pro.local 14.5.0 Darwin Kernel Version 14.5.0: Tue > Sep 1 21:23:09 PDT 2015; root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64 > > trac-preproc exited with ERRORS at Tue Apr 12 08:04:37 PDT 2016 > > Your help would be appreciated. > > Thank you, > > Jasmin > > On Tue, Apr 12, 2016 at 7:26 AM, Alan Francis <alandarkenergy(a)gmail.com> > wrote: > >> Hi Jasmin - >> >> In your dmrirc file , the dcmlist refers to the dicom list. You have put >> the BVEC/BVAL files there. That is not correct. You need to place the >> actual pathway to your niftis in this position. >> >> set subjlist = (40 39 36) >> >> # Input diffusion DICOMs (file names relative to dcmroot) >> # If original DICOMs don't exist, these can be in other image format >> # but then bvecfile and bvalfile must be specified >> # >> set dcmroot = Users/jasminalves/Desktop/data/DTI >> set dcmlist = (40/DTI.nii.gz DTI.bvec DTI.bval 39/DTI.nii.gz DTI.bvec >> DTI.bval 36/DTI.nii.gz DTI.bvec DTI.bval) *<- Pathway to NIFTIS HERE* >> >> Hope this helps, >> >> best, >> >> Alan >> >> >> -- >> |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| >> >> *Alan N. Francis PhD* >> Instructor - Imaging Neuroscience >> Brain Imaging Center >> McLean Hospital >> Harvard Medical School >> 115 Mill Street, Belmont, MA 02478 >> alanf(a)bwh.harvard.edu <ezra_wegbreit(a)brown.edu> >> afrancis(a)mclean.harvard.edu >> >> >> |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| >> > > > > -- > Jasmin Alves > Predoctoral Student > Medical Biology Graduate Program > University of Southern California > jalves(a)usc.edu > > -- |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| *Alan N. Francis PhD* Instructor - Imaging Neuroscience Brain Imaging Center McLean Hospital Harvard Medical School 115 Mill Street, Belmont, MA 02478 alanf(a)bwh.harvard.edu <ezra_wegbreit(a)brown.edu> afrancis(a)mclean.harvard.edu |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

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DODS vs DOSS for correlation analysis
by Cassandra Wannan 13 Apr '16

13 Apr '16

Hi Doug, I am carrying out some correlations between cortical thickness and cognitive ability, and had a question about the use of DODS vs DOSS for my analysis with Qdec. From reading some of the forums, it seems as though DOSS should be used when there are no interactions present. I am including gender as a covariate (fixed factor) and age as a nuisance variable in my model. When I run this with DODS, it shows that the correlation between thickness and cognition does not differ between males and females - does this mean that I should run the correlation using DOSS? I only seem to find significant correlations using DOSS, however I do not want to report these if the analysis is not correct. Thanks, Cassie Cassandra Wannan *PhD Candidate/Research Assistant/Psychology Tutor* Melbourne Neuropsychiatry Centre -------------------------------------------- 0433 339 839 cwannan(a)student.unimelb.edu.au

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Summer School "Advanced Scientific Programming in Python" in Reading, UK, September 5--11, 2016
by Etienne B. Roesch 13 Apr '16

13 Apr '16

*Advanced Scientific Programming in Python* a Summer School by the G-Node, and the Centre for Integrative Neuroscience and Neurodynamics, School of Psychology and Clinical Language Sciences, University of Reading, UK Scientists spend more and more time writing, maintaining, and debugging software. While techniques for doing this efficiently have evolved, only few scientists have been trained to use them. As a result, instead of doing their research, they spend far too much time writing deficient code and reinventing the wheel. In this course we will present a selection of advanced programming techniques and best practices which are standard in the industry, but especially tailored to the needs of a programming scientist. Lectures are devised to be interactive and to give the students enough time to acquire direct hands-on experience with the materials. Students will work in pairs throughout the school and will team up to practice the newly learned skills in a real programming project — an entertaining computer game. We use the Python programming language for the entire course. Python works as a simple programming language for beginners, but more importantly, it also works great in scientific simulations and data analysis. We show how clean language design, ease of extensibility, and the great wealth of open source libraries for scientific computing and data visualization are driving Python to become a standard tool for the programming scientist. This school is targeted at Master or PhD students and Post-docs from all areas of science. Competence in Python or in another language such as Java, C/C++, MATLAB, or Mathematica is absolutely required. Basic knowledge of Python and of a version control system such as git, subversion, mercurial, or bazaar is assumed. Participants without any prior experience with Python and/or git should work through the proposed introductory material before the course. We are striving hard to get a pool of students which is international and gender-balanced. You can apply online: https://python.g-node.org *Application deadline: 23:59 UTC, May 15, 2016. Be sure to read the FAQ before applying. * Participation is for free, i.e. no fee is charged! Participants however should take care of travel, living, and accommodation expenses by themselves. Travel grants may be available. *Date & Location * September 5—11, 2016. Reading, UK *Program * - Best Programming Practices • Best practices for scientific programming • Version control with git and how to contribute to open source projects with GitHub • Best practices in data visualization - Software Carpentry • Test-driven development • Debugging with a debugger • Profiling code - Scientific Tools for Python • Advanced NumPy - Advanced Python • Decorators • Context managers • Generators - The Quest for Speed • Writing parallel applications • Interfacing to C with Cython • Memory-bound problems and memory profiling • Data containers: storage and fast access to large data - Practical Software Development • Group project *Preliminary Faculty * • Francesc Alted, freelance consultant, author of PyTables, Spain • Pietro Berkes, Enthought Inc., Cambridge, UK • Zbigniew Jędrzejewski-Szmek, Krasnow Institute, George Mason University, Fairfax, VA, USA • Eilif Muller, Blue Brain Project, École Polytechnique Fédérale de Lausanne, Switzerland • Juan Nunez-Iglesias, Victorian Life Sciences Computation Initiative, University of Melbourne, Australia • Rike-Benjamin Schuppner, Institute for Theoretical Biology, Humboldt-Universität zu Berlin, Germany • Bartosz Teleńczuk, European Institute for Theoretical Neuroscience, CNRS, Paris, France • Stéfan van der Walt, Berkeley Institute for Data Science, UC Berkeley, CA, USA • Nelle Varoquaux, Centre for Computational Biology Mines ParisTech, Institut Curie, U900 INSERM, Paris, France • Tiziano Zito, freelance consultant, Germany *Organizers * For the German Neuroinformatics Node of the INCF (G-Node) Germany: • Tiziano Zito, freelance consultant, Germany • Zbigniew Jędrzejewski-Szmek, Krasnow Institute, George Mason University, Fairfax, USA • Jakob Jordan, Institute of Neuroscience and Medicine (INM-6), Forschungszentrum Jülich GmbH, Germany For the Centre for Integrative Neuroscience and Neurodynamics, School of Psychology and Clinical Language Sciences, University of Reading UK: • Etienne Roesch, Centre for Integrative Neuroscience and Neurodynamics, University of Reading, UK *Website*: https://python.g-node.org *Contact*: python-info(a)g-node.org Kind regards, Etienne ----- Dr. Etienne B. Roesch Lecturer in Cognitive Science University of Reading

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