Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30135 discussions

Re: [Freesurfer] Freesurfer Digest, Vol 147, Issue 4
by Domenico Zacà 10 May '16

10 May '16

Hi Bruce, thank you for your reply. Indeed that's the way to do it. However how can I automatically build an updated color code scale for the new annotation/label file? The analysis I'm running clusters together the ROIs from the old annotation file based on the network analysis results. I have done it manually because I had only 13 clusters to take care of but I'd prefer to find an automated way if possible also to be consistent if I'm comparing the cluster algorithm results between different groups. Cheers, Domenico Domenico Zacà, PhD MR Lab Research Fellow Center for Mind/Brain Sciences University of Trento, Italy Via delle Regole, 101 38100 Mattarello (TN) Italy Telephone: +39-0461-28 3069 Fax: +39-0461-28-3066 Email: domenico.zaca(a)unitn.it MRI Methods Group: http://r.unitn.it/en/cimec/mri On Mon, May 2, 2016 at 8:59 PM, <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. no recon button (Burke,Sarah E) > 2. Brainstem segmentation (Haque, Muhammad E) > 3. Re: import ROI analysis results from Matlab into FreeSurfer > (Bruce Fischl) > 4. Re: no recon button (Douglas Greve) > 5. Re: no recon button (Burke,Sarah E) > 6. Re: no recon button (Douglas Greve) > 7. Re: no recon button (Burke,Sarah E) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 2 May 2016 16:14:28 +0000 > From: "Burke,Sarah E" <saraheburke(a)ufl.edu> > Subject: [Freesurfer] no recon button > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > < > BLUPR0801MB155544A9C1E2604C95B3B8DCB8790(a)BLUPR0801MB1555.namprd08.prod.outlook.com > > > > Content-Type: text/plain; charset="iso-8859-1" > > Hello, > > > I searched the mail list and saw that others have had this problem, but I > see no answers to their queries. I have version 1.0 (5/13/2013) of Freeview > for Linux. I have no recon button. What should I do? > > > Thank you >

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[Vacancy] Postdoc Position to Study Brain and Behavioral Plasticity Occurring with Spaceflight and Analog Environments.
by Vincent Koppelmans 10 May '16

10 May '16

A funded postdoctoral position is available immediately (with start date in summer 2016) to work in Dr. Rachael Seidler’s laboratory at the University of Michigan studying brain and behavioral plasticity occurring with spaceflight and analog environments. As one of the world’s leading research institutions, the University of Michigan provides an exceptionally supportive environment for research. University support includes integrated and state of the art computer technology, exceptional students and staff, and a network of world-renowned scientists. The Neuromotor Behavior Laboratory (directed by Dr. Seidler) is an interdisciplinary, productive, and dynamic group of students and staff researching the neurocognitive control of movement. The post-doctoral researcher will study cognitive, sensory, and motor behavioral plasticity and their neural correlates using functional MRI and resting state connectivity. The candidate will be expected to work collaboratively with a research team to collect and analyze data, prepare manuscripts for publication, and participate at national and international level meetings. The candidate must be willing and able to travel internationally for data collection. Interested applicants should submit a cover letter, curriculum vita, and the names and contact information for two referees to Rachael D. Seidler, Ph.D. via e-mail (rseidler(a)umich.edu <mailto:rseidler@umich.edu>). Review of applications will begin immediately. Necessary Qualifications: Ph.D. in psychology, neuroscience, kinesiology or related field and experience with MRI techniques including structural MRI, DTI, and / or functional MRI. The candidate must possess excellent verbal and written communication skills, be strongly motivated, and work well in a team setting. Experience with computer programming a plus (MATLAB, LabView, and / or E-Prime). The position is initially available for one year and may be renewable. Questions regarding the position can be emailed to rseidler(a)umich.edu <mailto:rseidler@umich.edu>. The University of Michigan is an Equal Opportunity, Affirmative Action Employer.

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Freesurfer 6.0 -qcache vs mris_fwhm
by Ajay Kurani 10 May '16

10 May '16

Hi Freesurfer Experts, I am trying to understand the difference between qcache option and mris_fwhm and which is appropriate for a cortical thickness analysis. I processed my files with qcache and have lh.thickness.fsaverage.fwhm15.gii (converted) files. I used an afni tool SurfFWHM to estimate the smoothness of a subject at when looking at the fwhm0 image it iwas 5.5 and for 10, 15 and 20mm it was approximately 9.3-9.9 smoothness level. I also used mris_fwhm --hemi lh --s fsaverage --smooth-only --i lh.thickness.fsaverage.mgz --fwhm 15 --cortex --o test_15.gii and when using SurfFWHM on the smae subject the smoothness was estimated at 11.25. 1) I am not sure if the qcache or the mris_fwhm file is more appropriate to use for a cortical thickness analysis. 2) For qdec if I select the 15mm option does it assume the smoothness is 15mm when calculating monte carlo corrections? Would there be a different way to estimate this since my smoothness at 15mm is closer to 10mm? Thanks, Ajay

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Pediatric longitudinal processing
by Hawks, Zoe 10 May '16

10 May '16

I'm looking to use FS for longitudinal processing in a pediatric population ranging from 6-18 years. From what I've read, the longitudinal stream isn't appropriate because our data violate the assumption of fixed head size. Any advice on how to account for increases in head size would be appreciated. Thank you!

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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

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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

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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

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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

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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

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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

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