Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30099 discussions

Brainhack Eastern Standard Time - Boston October 18-19, 2014
by MCLAREN, Donald 23 Sep '14

23 Sep '14

*Do you have a great idea for collaboration or want to collaborate on great ideas?* *!!!!THEN BRAINHACK IS THE PLACE FOR YOU!!!!* Brainhack is a unique conference that convenes researchers, artists, and members of industry from across the globe and a myriad of disciplines to work together on innovative projects broadly related to neuroscience. Year after year, global Brainhack events have brought together researchers to participate in open collaboration resulting in new ideas, relationships, and publications. Brainhack Eastern Daylight Time (EDT; http://brainhack.org/brainhack-edt/) will unite several regional Brainhack events during October 18 & 19, 2014. Having several simultaneous events will help build a critical mass for the regional Brainhack movement and provide opportunities for inter-Brainhack collaboration. The Boston Brainhack will be held at the McGovern Institute for Brain Research at MIT and is additionally supported by Siemens and Amazon. The Boston Brainhack aims to foster local collaborations across the diverse neuroscience interests and institutions in the Boston area. The three most common questions: *Q. What happens at a brainhack?* A. Think of it as a maker space for neuroscientists. Neuroscience is a complex, multidisciplinary field with many unknowns. It is often the case that no individual's expertise is enough to tackle research questions that can encompass physics, mathematics, modeling, statistics, art, etc. These events serve to catalyze collaboration across individuals from different disciplines, create local connections, and promote "thinking outside the box". The events also increase awareness of new and changing technologies around us as neuroscience move towards data and computationally intensive approaches. Most importantly it is the social human spirit that brings together people to share in efforts to solve problems together. If you have a scientific problem, then the Boston Brainhack can help you solve it. Think of it like a conference, but instead of talking about solutions, actually sitting down and implementing them. *Q. I am new to the field or don't know how to code, can I still come?* A. Yes! At any level or from any discipline you can make significant contributions. At Brainhack you will both learn and contribute. If you want to know how to code in a specific program, please let us know and we'll do our best to facilitate the learning process. If you are in a different field and want to hear about neuroscience problems, come on over. *Q. What do I need to do to prepare?* A. Here are a few tips 1. To help us get a rough headcount, please sign up at: http://goo.gl/tMfwa2 2. Consider questions or ideas you would like to work on at Brainhack 3. Post project ideas or become a member of a project: http://brainhack.org/brainhack-edt/ 4. Bring tools, data or just enthusiasm on October 18th and 19th. 5. Start chatting at: https://gitter.im/satra/brainhackEDT/~chat#initial <https://gitter.im/satra/brainhackEDT/~chat%22%20%5Cl%20%22initial> or posting questions at: http://neurostars.org <%22> (tag with Brainhack) We look forward to seeing everyone at the McGovern Institute. Sincerely, The Boston Brainhack Committee Donald G McLaren, MGH/HMS Satra Ghosh, MIT Matt Hutchison, Harvard University

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Re: [Freesurfer] Converting GIFTI files to Freesurfer files
by Reza Rajimehr 23 Sep '14

23 Sep '14

Hi, I tested this with mris_convert provided by Nick in the link below, and it worked fine. ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos6_x86… However, mris_convert in dev version gave me the segmentation fault (core dumped). Just FYI! Best, Reza Hi, To convert GIFTI files to the Freesurfer files, I just need to do something like this? mris_convert F99.R.inflated.74k_f99.surf.gii rh.inflated Thanks, Reza

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missing time point and longitudinal analysis
by Emma Thompson 22 Sep '14

22 Sep '14

Hi Freesurfers, I'm conducting a longitudinal analysis but have several subjects with a few missing time points. The paradigm contained 4 time points in total, a baseline that occurred prior to any treatment and 3 post-treatment time points. All my subjects have baseline time points. However, a few subjects have a missing post-treatment time point. Can I still use these subjects in my longitudinal analysis even though 1 of the 3 post-treatment time points are missing? Thanks in advance for your help!

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talairach coordinates
by ri 19 Sep '14

19 Sep '14

Hi all I was wondering whether it’s possible to get the talairach coordinates associated with each label in the segmentation. I would like to use Freesurfer’s segmentation for analysis in Matlab.How to create a text file with the talairach coordinates of each label (or of a specific label, by label number), Thanks

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Question about Voxel Quantification with Thresholds
by Karishma Smart 19 Sep '14

19 Sep '14

Dear all, Is there a way to get a count of the voxels in a manually drawn ROI while retaining each voxel's intensity value? *In particular, I would like to get a count of how many voxels in this manually drawn ROI fall above and below an assigned intensity threshold.* I have used mri_segstats to quantify the number of voxels in a particular ROI that I have drawn manually (i.e. not using aseg). However, in doing so (I created a label for the ROI and used mri_segstats to count the number of voxels in the label), I assigned each voxel the intensity of the label, thus losing the intensity information. Any guidance or assistance would be greatly appreciated. Preferably, it would be helpful if anybody knows a way to do this that is not modality-dependent. Thank you in advance for your help, Karishma -- Karishma Smart B.A. Biological Sciences Cornell University Class of 2013 Boston University School of Graduate Medical Sciences Class of 2015

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Converting GIFTI files to Freesurfer files
by Reza Rajimehr 19 Sep '14

19 Sep '14

Hi, To convert GIFTI files to the Freesurfer files, I just need to do something like this? mris_convert F99.R.inflated.74k_f99.surf.gii rh.inflated Thanks, Reza

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ERROR reading /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label
by Mahmoud 19 Sep '14

19 Sep '14

Dear all, After running "recon-all -i $SUBJECTS_DIR/Case018/case018_tp2/22-1.dcm -subject case018_tp2 -all" I'm always getting the following error and really don't know how to fix. Could anybody please help me. The recon-all.log file is attached. Thank you, Mahmoud Reporting on 70 segmentations mri_segstats done /usr/local/freesurfer/subjects/case018_tp2/label #-------------------------------------------- #@# BA Labels lh Thu Sep 18 20:23:27 EDT 2014 INFO: fsaverage subject does not exist in SUBJECTS_DIR INFO: Creating symlink to fsaverage subject... cd /usr/local/freesurfer/subjects; ln -s /usr/local/freesurfer/subjects/fsaverage; cd - mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label --trgsubject case018_tp2 --trglabel ./lh.BA1.label --hemi lh --regmethod surface Too many levels of symbolic links mri_label2label: could not open label file /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label srcsubject = fsaverage trgsubject = case018_tp2 trglabel = ./lh.BA1.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Invalid argument ERROR reading /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label Linux ubuntu 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s case018_tp2 exited with ERRORS at Thu Sep 18 20:23:27 EDT 2014 For more details, see the log file /usr/local/freesurfer/subjects/case018_tp2/scripts/recon-all.log

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HCP pipelines: fMRIVolume --> correction of gradient-nonlinearity-induced distortion
by Matthieu Vanhoutte 19 Sep '14

19 Sep '14

Dear Freesurfer's experts, I'm trying to follow fMRI Volume pipeline from "The minimal preprocessing pipelines for the Human Connectome Project" (NeuroImage, 2013) on HCP data. The first step has to be the correction of gradient-nonlinearity-induced distortion. The correction is then done with a customized version of the gradient_nonlin_unwarp package available in FreeSurfer (Jovicich et al., 2006). I couldn't manage to find this package on internet, the only things I've found is the freesurfer grad_unwarp command and a webpage ( https://surfer.nmr.mgh.harvard.edu/fswiki/GradientUnwarping) with no download link... Where can I find this package and how to use it ? Many thanks ! Best, ------------------------------------- Matthieu Vanhoutte, MSc Research Engineer - Department of Neuroradiology Regional University Hospital, Lille, France

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segmentation fault mri_convert Ubuntu 14.04
by Alessandra Griffa 19 Sep '14

19 Sep '14

Dear all, I am running FreeSurfer version [recon-all,v 1.313.2.6 2010/08/04] on an Ubuntu machine. After updating my system from Ubuntu 12.04 to Ubuntu 14.04 I get a segmentation fault when I try to resample images using mri_convert: /mri_convert -vs 1 1 1 /folder/original_image.nii.gz /folder/resampled image.nii.gz // //$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $// //reading from /folder/original_image.nii.gz...// //Segmentation fault (core dumped)/ Any help on this? (for consistency with an on-going study I would like not to install a newer FreeSurfer version) Thank you very much! Alessandra -- ------------------------------ Alessandra Griffa Doctoral assistant Signal Processing Laboratory 5 EPFL STI IEL LTS5 ELD 233 (Bâtiment ELD) Station 11 CH-1015 Lausanne Tel.: +41216934807 web: http://lts5www.epfl.ch/ personal page: http://people.epfl.ch/alessandra.griffa?lang=en ------------------------------

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Freeview screenshot automation questions
by Eric Xiuming ZHANG 19 Sep '14

19 Sep '14

Dear FreeSurfer experts, I understand that > freeview -v brain.nii.gz -ss screenshot takes the screenshots and quits the freeview. Regarding this, I have the following two questions. (1) Is it possible to suppress the redundant GUI flashing? It is really a pain when many images are batch-processed, because the GUI keeps flashing up and closing. (2) Is it possible to take multiple screenshots with one session? I wish to screenshot multiple slices of one image. I have tried > freeview -v brain.nii.gz\ > -viewport sagittal -slice 80 127 127 -ss sag1 \ > -viewport sagittal -slice 127 127 127 -ss sag2 \ > -viewport sagittal -slice 156 127 127 -ss sag3 \ However, the session ends right after the first -ss, producing only one screenshot (sag1.png). I can surely do freeview -v brain.nii.gz 3 times to get these 3 screenshots, but that is very inefficient. Thank you very much for your help in advance! Best regards, Xiuming ZHANG (Eric) Xiuming ZHANG (Mr.) :: Department of Electrical & Computer Engineering (ECE) :: National University of Singapore (NUS)

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