Freesurfer May 2016

freesurfer@nmr.mgh.harvard.edu

135 participants
197 discussions

2nd announcement, Summer School "Advanced Scientific Programming in Python" in Reading, UK, September 5--11, 2016
by Etienne B. Roesch 10 May '16

10 May '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 • 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

1 0

mri_glmfit-sim error
by Govindarajan, Koushik Athreya 09 May '16

09 May '16

Dear FS experts, I ran into an error with one of my mri_glmfit-sim execution and was not sure what was going on. The same simulation is currently running for the left hemisphere without any hiccups but I get this following error for the right hemisphere: ----------------------------------------------------------------------------------------------------------------------- cd /home/adits123/Desktop/projectoutputdata /usr/local/freesurfer/bin/mri_glmfit-sim --glmdir /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir --sim mc-z 10000 1.3 mc-z.pos.1.3 --sim-sign pos --cwpvalthresh 0.05 $Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $ Thu May 5 13:16:51 CDT 2016 Linux localhost.localdomain 2.6.32-250.el6.x86_64 #1 SMP Tue Mar 6 23:00:19 EST 2012 x86_64 x86_64 x86_64 GNU/Linux adits123 setenv SUBJECTS_DIR /home/adits123/Desktop/projectoutputdata FREESURFER_HOME /usr/local/freesurfer Original mri_glmfit command line: cmdline mri_glmfit --glmdir rh.paired-diff.glmdir --y rh.paired-diff.thickness.sm05.mgh --fsgd paireddifftp1tp2.txt --C contrastpaired.mtx --surf fsaverage rh DoSim = 1 UseCache = 0 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = -nan nSimPerJob = 10000 1/1 Thu May 5 13:16:51 CDT 2016 mri_glmfit --y /home/adits123/Desktop/projectoutputdata/rh.paired-diff.thickness.sm05.mgh --C /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/tmp.mri_glmfit-sim-931/contrastpaired.mtx --mask /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/mask.mgh --sim mc-z 10000 1.3 /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/csd/mc-z.pos.1.3.j001 --sim-sign pos --fwhm -nan --fsgd /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/y.fsgd dods --surf fsaverage rh white simbase /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/csd/mc-z.pos.1.3.j001 FWHM = -nan ERROR: input FWHM is NaN (not a number). Check the mask in the glm directory. Thu May 5 13:16:51 CDT 2016 ERROR: cannot find any csd files -------------------------------------------------------------------------------------------------------------------------------- I am not sure what the fwhm is NaN error is and also why it is only showing up for one hemisphere. Any help is appreciated. Thanks Koushik Govindarajan

3 7

Confirming the FC steps
by Martin Juneja 09 May '16

09 May '16

Dear FS experts, I just finished calculating functional connectivity maps using FreeSurfer. I just want to confirm if the following steps I used are correct: (1). I defined configured seed regions parameters using fcseed-config command, say R01.config and R02.config and created seeds using fcseed-sess command to generate R01.dat and R02.dat files. (2). Created nuisance vaiables: wm.config and vcsf.config files using fcseed-config and -sess: this step is independent of seeds and is done only once independent of seeds (3). For mkanalysis-sess command for each seed using R0*.dat file, I used '-notask' argument because I am performing resting-state analysis. (4). For subject level analysis, I used selxavg3 for each seed (5). For 2nd level analysis: isxconcat-sess -all-contrasts -map sig.nii.gz I can process all these steps without any error. If these steps are correct, can some one please confirm again that for RSFC, I am correctly using -notask in step (3) and -all-contrast in step (5). Also, in the instructions, it's mentioned to use -map pcc if interested in calculating partial correlation coefficient, but I am interested in using sig to get group level significant maps, would that be OK to use in this command as -map sig? Thanks for your help. Regards, MJ

2 5

Correcting defect
by Katarina Trojacanec 09 May '16

09 May '16

Dear FreeSurfer Team, I have been trying to run creation of template with FreeSurfer. However, for two cases for one patient (case 1: template based on TP1 and TP4, case 2: template based on TP2 and TP4), the correcting defect step is running too long. According to the information in the mail archive, the defects are probably too big, and that is the reason for the long processing. May I send you via ftp the subjects directories so you can help me to proceed with this subject, because I am not able to figure out and correct the problem? Should I send you the base directories in their current state or the cross-sectionally processed time points as well? Best Regards, Katarina Trojacanec, M.Sc. Teaching and research assistant Faculty of Computer Science and Engineering Ss. Cyril and Methodius University - Skopje, Republic of Macedonia

2 6

LME parpool matlabpool update
by Seán Froudist Walsh 09 May '16

09 May '16

Hey, Not sure if this could save someone else the trouble. The LME fitting software wasn't working for me since I updated Matlab, which has now switched from matlabpool to parpool for parallel processing, so I switched the call in the scripts to parpool, which seems to be working fine. Please find the updated scripts attached, for anyone interested. Best wishes, Sean Sean Froudist-Walsh Postdoctoral Fellow Friedman Brain Institute Icahn School of Medicine at Mount Sinai

2 1

Volumetric measurments and difference between results from "recon_all" and "mri_segstats"
by Saeed Mahdizadeh Bakhshmand 09 May '16

09 May '16

Hello Folks, I used the recon-all -i -all -segmentation for the structural image. FreeSurfer makes several folder and one of them is "stats". In this folder, there is aseg.stats that includes volume of different brain regions. Also, I found "mri_segstats" command line that gives us the volume of the same brain regions. But, there is significant difference between reported numbers from these two methods . I would say the difference is approximately 200 mm3 for each brain region. Do you know what is correct way to measure volume of segmented brain regions using FreeSurfer? Cheers, Saeed

4 3

Free surfer Gray Matter
by Limachia, Gaurang (NIH/NINDS) [F] 09 May '16

09 May '16

Hello Dr. Fischl, I had question about Freesurfer, I am trying to correct the gray matter volume. So I made changes by adding pixels to the contour, and ran recon-all. Subsequently, when I opened up the file after performing recon-all I saw were the pixels (which are white) that I added when I was making the changes. How do you make changes to the gray matter, and what type of recon command should I run after making the changes. I searched through the various tutorials, but that further confused me. I am attaching a screen shot of the brain as well as the tool that I used to add the pixel, and you will be able to see the white pixels I am mentioning above. Thank you for your time. Best Regards, Gaurang Shyam Limachia

2 1

Freesurfer for other species
by Daya P 09 May '16

09 May '16

Hi all, I was wondering if anybody else is using Freesurfer on non-human subjects? Thank you, Daiana

2 1

Re: [Freesurfer] Cortical Thickness of a Volume-defined ROI
by Mahtab Farahbakhsh 09 May '16

09 May '16

Dear FreeSurfer, I am trying to find the cortical thickness of my ROI which is the perisylvian region of the left hemisphere. What I did was to define a label based on the anatomical area of this region and tried to define a ROI based on this label and the command -mri_label2volume. Howevere, I am using freeview and the tutorial that I found about this issue was based on tkmedit. Would you please guide me how I should get this done? Best Regards, Mahtab Farahbakhsh.

2 2

Manual correction for brainstem module
by Jacky Lee 09 May '16

09 May '16

Hi freesurfer experts, I have successfully run the brainstem module for some subjects. On visual checking, I can see there are voxels with T1 hypointense lesions mislabelled as non-brainstem tissue. I manually corrected them on the brainstemSsLabels.v10.mgz on Freeview. Then how do I obtain this new corrected volume of the brainstem substructures? Thanks. Regards, Jacky

2 1

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Freesurfer May 2016