Freesurfer October 2014

freesurfer@nmr.mgh.harvard.edu

129 participants
187 discussions

Brainhack EDT - Boston Updates and Registration Details
by MCLAREN, Donald 13 Oct '14

13 Oct '14

*October 18th and 19th, Boston* *McGovern Institute for Brain Research @ MIT - * *http://whereis.mit.edu/?go=46* <http://whereis.mit.edu/?go=46> *3rd floor Atrium * *Doors will be locked, so we will have to let you in. If you are the door, please call 4-3544 or (617-324-3544) or send a chat message here: * *https://gitter.im/satra/brainhackEDT* <https://gitter.im/satra/brainhackEDT> *BRAINHACK EDT - BOSTON NEWS/UPDATES:* · Siemens is providing funds to help host Brainhack EDT - Boston. · The Brainhack EDT - Boston organizing committee is excited to announce that we will be providing lunch to attendees who register/confirm their attendance and food choices by 6PM on October 15th (see instructions below; http://goo.gl/tMfwa2) · The Brainhack EDT - Boston organizing committee is working on organizing a group dinner (attendee pays) on Saturday night in Cambridge. · Amazon will provide credits for cloud computing ($100 per person) · NeuroElectrics will be bringing a couple of their wireless EEG headsets for interested parties to hack on. Please check the column if you are interested. · All attendees must confirm their registration by following the registration instructions below. *REGISTRATION DETAILS:* With the generous support from Siemens, we will be providing lunch to attendees of Brainhack Boston. In order to receive lunch, you must confirm your registration (indicate YES/NO) and food choices by Noon on October 15th, 2014. Please click here to register: http://goo.gl/tMfwa2 When you are registering please provide us with your lunch choices along with whether or not you plan to attend the organized dinner on Saturday Night (attendees pay for their own dinner). If you do not provide us with your lunch choices, you will not get free lunch. In addition, please indicate whether you are interested in working with/on the Neuroelectrics headset. *PROJECT PROPOSALS:* We've heard rumors of several projects for Brainhack EDT - Boston. In order to spread the word of these projects, we request that you add your project(s) on the following page: http://goo.gl/fSMgc3 Project proposal introductions will be 1 minute. If you want to use a slide to introduce your project, please send the powerpoint slide to mclaren.donald-a(a)t-gmail.com *BRAINHACK EDT - BOSTON SCEHDULE:* *Saturday, October 18, 2014* 08:30 Attendee Arrival (with coffee) 09:00 Welcome reception 09:15 Ignite Talk with icebreaker 09:45 Project Pitch 10:00 Open Hacking 12:00 Onsite Lunch (Mexicali) 13:00 Crowd Annotation Projects (Dolphin Brain) 13:45 Unconference Session 15:00 Coffee Break 15:30 Open Hacking 18:30 Organized dinner (pay your own way) 20:30 Open Hacking *Sunday, October 19, 2014* 08:30 Attendee Arrival 09:00 Ignite Session II 09:30 Unconference Session 10:30 Open Hacking 12:30 Onsite Lunch (Mexicali) 13:30 Open Hacking 15:00 Coffee Break 15:30 Open Hacking 17:00 Project Summaries and Wrap-up 18:30 Adjournment 19:00 Optional Dinner or Open Hacking *The Boston Brainhack Committee* Donald G McLaren, MGH/HMS Satra Ghosh, MIT Matt Hutchison, Harvard University

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Image normalization and pial/wm error
by Sneha Pandya 13 Oct '14

13 Oct '14

Dear all, I am running recon-all on few SPGR T1s and few MPRAGE T1s. However most of my dataset, may it be SPGR or MPRAGE has some artifacts and poor wm/gm contrast. Have attached a screen shot of bad pial and wm error (going beyond dura). Even gcut did not do a good job of cutting of all the dura, and I had to manually edit voxels in all the slices. I feel even after that if I run recon-all, it will not give me any reliable cortical thickness measures. Can anyone please suggest me if I should still manually edit all other subjects for all the slices throughout the volume or exclude them from analysis? PS: attached image FOV is 260 and I used -cw256 flag to restrict FOV to 256. For other images FOV is within 256, but still there is lot of dura in the brainmask. Thanks, Sneha

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v5.1 control point mri_ca_normalize bug
by Marx, Gabe 13 Oct '14

13 Oct '14

Hello Freesurfer experts, I had a question regarding the v5.1 control point mri_ca_normalize bug. I read the release notes and know that this bug can be worked around by adding the -nocanorm flag to my recon-all however I have become worried about the ramifications of skipping mri_ca_normalize in my pipeline. Would someone be able to give me a better description as to what mri_ca_normalize is doing and what I am sacrificing by taking it out of my pipeline? Furthermore, in regards to the patch for the recon-all script to fix this bug, what is the patch doing exactly? If I had some data in which I used the -nocanorm flag and other data in which I used the patch would I still be able to make valid analysis if I merged them? Would there be significant inconsistencies? Thanks! Best, Gabe

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Talairach transformation
by Roberta Santoro 13 Oct '14

13 Oct '14

Dear list, I am new to Freesurfer and I have a doubt about the Talairach transformation. As far I understand, the Talairach transformation is applied to compute the surface representations. However, this seems to be a “hidden“ step, i.e. no volume is saved as Talairach transformed. Is this correct? Do the final surfaces (and parcellations) show the brain before or after Talairach transformation? I am asking this because I need to extract ROIs in the original space, i.e. before Talairach transform. Thanks a lot for your help Roberta

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no-octave
by elahe' yargholi 12 Oct '14

12 Oct '14

Dears, Mkanalysis-sess does not accept -per-run and It looks like mkcontrast-sess cannot initiate Matlab in the terminal. I have installed octave and addpath and save path both /home/fsl/Desktop/freesurfer/matlab /home/fsl/Desktop/freesurfer/fsfast/toolbox I will appreciate in advance if you possibly could help me to solve the problem. Best Regards, Elahe' Windows 7 and vmware10 Linux version: ------- freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /home/fsl/Desktop/freesurfer FSFAST_HOME /home/fsl/Desktop/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /home/fsl/Desktop/freesurfer/subjects MNI_DIR /home/fsl/Desktop/freesurfer/mni FSL_DIR /usr/local/fsl Current working directory: *pwd* */home/fsl* *which freesurfer* */home/fsl/Desktop/freesurfer/**bin/freesurfer* *which mkanalysis-sess* */home/fsl/Desktop/freesurfer/fsfast/bin/mkanalysis-sess* *which mkcontrast-sess* */home/fsl/Desktop/freesurfer/fsfast/bin/mkcontrast-sess* Command lines: *mkdir FIVA* *cd FIVA* *mkdir MT_Localizer* *cd MT_Localizer* *mkdir subj1sess1 * *cd subj1sess1* *unpacksdcmdir -src /home/fsl/Desktop/MTLocalizer/IMAGES -targ . -run 2 bold nii f.nii -run 3 bold nii f.nii -run 4 bold nii f.nii -run 5 bold nii f.nii -run 6 bold nii f.nii -run 7 bold nii f.nii -run 8 bold nii f.nii -run 9 bold nii f.nii -run 10 bold nii f.nii -run 11 bold nii f.nii* Within subj1sess1, made a text file named subjectname, and wrote subj001 (the name of my anatomical subject). *cd ..* *preproc-sess -s subj1sess1 -fsd bold -surface self lhrh -mni305 -fwhm 5 -per-run* *plot-twf-sess -s subj1sess1 -fsd bold -mc* *tkregister-sess -s subj1sess1 -fsd bold -per-run -bbr-sum* *tkregister-sess -s subj1sess1 -fsd bold -per-run* For each run, a paradigm file (paradigm.par) is included. *mkanalysis-sess -a MT.lh -surface self lh -fsd bold -fwhm 5 -event-related -paradigm paradigm.par -nconditions 2 -refeventdur 16 -TR 2 **-nskip 4 **-polyfit 2 -spmhrf 0 -mcextreg -per-run* *'ERROR flag -per-run unrecognized'* It does not accept -per-run so I omitted that. *mkanalysis-sess -a MT.lh -surface self lh -fsd bold -fwhm 5 -event-related -paradigm paradigm.par -nconditions 2 -refeventdur 16 -TR 2 -nskip 4 -polyfit 2 -spmhrf 0 -mcextreg* *mkanalysis-sess -a MT.rh -surface self rh -fsd bold -fwhm 5 -event-related -paradigm paradigm.par -nconditions 2 -refeventdur 16 -TR 2 -nskip 4 -polyfit 2 -spmhrf 0 -mcextreg * *mkcontrast-sess -analysis MT.lh -contrast M_S -a 2 -c 1 * Non-Null Conditions INFO: Found 1 Delays Condition Weights: -1.00000000000000000000 1.00000000000000000000 mkcontrast -anadir MT.lh -wcond -1.00000000000000000000 1.00000000000000000000 -sumconds -o MT.lh/12.mat -wdelay 1 -no-octave $Id: mkcontrast,v 1.10 2010/07/16 16:20:10 greve Exp $ cmtxfile MT.lh/12.mat nconds 2, wcond -1.00000000000000000000 1.00000000000000000000 ndelays 1, wdelay 1 ndelays 1, wpsa sumconds 1 sumdelays 0 nircorr 0 TER 0.050000 rdelta rtau ERROR running mkcontrast mkcontrast -anadir MT.lh -wcond -1.00000000000000000000 1.00000000000000000000 -sumconds -o MT.lh/12.mat -wdelay 1 -no-octave

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Registering a parcellation from MNI_2mm space to subject native space
by Marcelo Gomes Mattar 11 Oct '14

11 Oct '14

Hello, I'm new to freesurfer, and I'm lost in something that I believe is very basic. I have a parcellation of the brain in .nii format that is currently in MNI space (2mm). I would like to move this parcellation to subject native space, so that I can extract the BOLD timeseries from each region of the parcellation. I understand that an option I have is to simply use FSL tools such as FLIRT or FNIRT and move the parcellation file to subject space (using nearest neighbor interpolation). However, given that I have reconstructed the subject's anatomy to the surface space, I believe I can do a better job that an affine transformation. What should I do in this case? 1) Is there any freesurfer tool that would allow me to register a volume to another volume, but aided by surface information? 2) If so, what steps should I follow? Thank you very much, -- Marcelo Mattar University of Pennsylvania

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Method development for coupled EEG-fMRI (1x Full EPSRC studentship)
by Etienne B. Roesch 10 Oct '14

10 Oct '14

Method development for coupled EEG-fMRI (1x Full EPSRC studentship) The goal of the project is to develop novel methods for the joint analysis of signals from electroencephalography (EEG) and functional magnetic resonance imaging (fMRI), when they are obtained concurrently. Technological advances of the last 10 years make it possible for scientists to record both modalities concurrently, in what is now known as coupled EEG-fMRI. By simultaneously recording these two modalities, scientists can potentially say where and when neural activity is occurring, whereas previously researchers had to settle for one or the other. This engineering feat, however, has not yet been met with the ability to make use of the combination of these signals to infer more knowledge than would otherwise be gathered in separate experiments. Filling this gap is the ambition of the present project. This is a method project, which requires skills and knowledge in applied mathematics/statistics/physics and programming. One studentship is available, to join a research group in the remit of this project. Prior exposure to either/or EEG and fMRI is preferred, but training on both modalities will be provided. The emphasis of the studentship is on the development of novel analysis methods, but the successful candidate will have opportunities to join empirical work using EEG-fMRI. The student will be supervised by Dr. Etienne Roesch and receive support from Dr. Michael Lindner and Prof. Tom Johnstone, with R&D support from Brain Products. The CINN is host to a research-dedicated 3T Siemens TRIO, with a full license for sequence development, and a full suite of MR-compatible systems. Additionally, the student will be granted access to the cluster of NVIDIA Tesla GPUs and other facilities at CINN, as well as at the School of Systems Engineering. The University of Reading is ranked as one of the UK’s 20 most research-intensive universities and as one of the top 200 universities in the world (Times Higher Education 2013). Our campus was voted first in the Times Higher Education Student Experience survey and has a Green Flag Award. It is situated 25 minutes West of London. Reading University Students’ Union was voted the 6th best in the UK (National Student Survey 2012). Essentials: Commitment to academic research and personal development; Ability to work collaboratively; Effective interpersonal and communication skills, including writing to a high standard, document preparation for technical notes and journal papers; Experience of work in interdisciplinary settings; Attention to details. Desirables: Self-guided work in developing statistical designs and approaches in research; Creative approach to problem solving; Ability to work independently; Experience in giving presentations and conveying complex ideas clearly. Eligibility: Applicants should hold a minimum of a UK Honours Degree at 2:1 level or equivalent in a relevant subject. Please note that due to restrictions on the funding this studentship is for UK/EU applicants only. Funding Details: Studentship will cover Home/EU Fees, pay the Research Council minimum stipend (£13,863 in 2014/15) for up to 3 years and include funding for international conferences. How to apply: To apply for this studentship please submit an application for a PhD in Cybernetics (full time) to the University – see http://www.reading.ac.uk/Study/apply/pg-applicationform.aspx . In the section ‘Research proposal’, please upload or copy-paste your covering letter. When prompted as part of your online application, you should provide details of the funding you are applying for, quoting the reference GS14-68. Once you have submitted your application, you should receive an email to confirm receipt of your online application. Please forward this email, along with your covering letter and CV (as pdf), to Dr. Etienne B. Roesch, e.b.roesch(a)reading.ac.uk, by the application deadline. Application Deadline: Monday November 10th, 2014 (interviews on November 21st, 2014, Skype or in Reading) Further Enquiries: Please contact Dr. Etienne B. Roesch, e.b.roesch(a)reading.ac.uk. Kind regards, Etienne Save the world from email! http://emailcharter.org ––– Dr. Etienne B. Roesch Lecturer (Assistant Professor) in Cognitive Science University of Reading, UK http://doodle.com/MeetWithEtienne

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WM & Pial Segmentation Errors
by Smith, Michael 10 Oct '14

10 Oct '14

Hi, I’ve been having trouble on a few of our subjects with getting the white matter and pial surface files to “line up” correctly with the volume files. I’ve attached a screenshot of what is happening: the pial surface is in red and the white matter surface file is in yellow. I have also attached an example of a “good” subject for comparison. I’ve tried looking through the tutorials online but didn’t see anything that was really related to my issue and I was wondering what the best way to correct this. We have T2 weighted images for several subjects is well if that helps. Not sure if Freesurfer can use T2 images instead of T1 in the –reconall script but I thought I would mention it. Thank you very much in advance! Best, Michael S.

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Re: [Freesurfer] rawfunc2surf-sess with a limited set of surface files
by Reza Rajimehr 10 Oct '14

10 Oct '14

Thanks Doug! I got it to work. The outputs are like fmc.sm2.F99.lh.iter05.nii.gz Should I still specify stem as fmc.iter05 in mkanalysis-sess? Reza Try added something like "-expkey iter05". When you make the analysis you will have to spec "-stem fmc.iter05" doug On 10/09/2014 12:12 AM, Reza Rajimehr wrote: > Hi Doug, > > Removing -i fmc did not help, and I still get the same error. > > By looking at the rawfunc2surf-sess script, it looks like specifying an > argument for -surfreg makes ExpKeyNeeded = 1. Can I just specify something > for -expkey? Is this something that is used only in the name of log file? > > Thanks, > Reza > > > Try it without -i fmc > > > On 10/08/2014 04:38 AM, Reza Rajimehr wrote: >> One more question: >> >> I tried to run: >> >> rawfunc2surf-sess -s oz_fparc -i fmc -trgsubject F99 -surfreg >> iter05.sphere.reg -fwhm 2 -per-session >> >> And I got this: >> >> ERROR: experts key needed (-expkey) >> >> Not sure what this flag is. >> >> Reza

2 1

Image normalization and pial/wm error
by Sneha Pandya 09 Oct '14

09 Oct '14

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Freesurfer October 2014