Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30070 discussions

Reminder: FSurf webinar tomorrow
by Suchandra Thapa 12 Apr '17

12 Apr '17

Dear FreeSurfer Community, The Open Science Grid consortium (http://www.opensciencegrid.org) offers a service “FSurf” which allows large scale batch processing of MRI scans using FreeSurfer. FSurf supports the standard FreeSurfer workflow (autorecon-all) or workflows with arbitrary FreeSurfer options. FSurf currently uses FreeSurfer 5.3 but support for FreeSurfer 6.0 will be added in the near future. Note that no proposal for an allocation is required to use the service. We are hosting a 30 minute webinar on Thursday, April 13th, 2pm CDT to cover the basics of batch processing using FSurf. The webinar will be accessible from a PC, Mac, Linux, iOS, or Android device at https://IU.zoom.us/j/644966220. Instructions for getting started with FSurf can be found here: http://bit.ly/freesurferopensciencegrid. We hope to see you there, and best regards. The OSG FSurf support team Suchandra Thapa sthapa(a)ci.uchicago.edu Computation Institute Searle Chemistry Laboratory #201A 5735 South Ellis Avenue Chicago, IL 60637

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Survey on inputs for surface-based analysis pipelines
by Christopher Markiewicz 12 Apr '17

12 Apr '17

Hi list, We're working on FMRIPREP <https://fmriprep.readthedocs.io/en/stable/>, a pipeline aimed at performing baseline preprocessing, and producing cleaned structural and functional data which can be fed into any of a number of analysis pipelines. We've recently begun incorporating surface reconstruction and surface-mapped functionals, and we'd like to get feedback on what outputs would be most valuable to people, in terms of formats, spaces and sampling strategies. 1) What surfaces do you use for sampling functional data and visualization? If you use down-sampled surfaces, do you have a preferred down-sampling strategy or target mesh? 2) What statistical analyses and model-fitting tools do you use for surface-based analyses? And are there any particular considerations you have for preparing your data for use by these tools? I appreciate your time and any input you may have to help us build a tool that fits the needs of the community. Thanks, -- Chris Markiewicz Center for Reproducible Neuroscience Stanford University

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correlation coefficient R
by tom parker 12 Apr '17

12 Apr '17

Dear Freesurfers, I made some correlations between cortical thickness and age in qdec. Is it possible to get the correlation coefficient value of this analysis? I just need to put it in a table with the significant results. Thank you so much!

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Fwd: wm edits not incorporated
by Octavian Lie 12 Apr '17

12 Apr '17

Dear All, Regarding wm.mgz edits not incorporated into wm surface, which seems to have been reported on by several of us with FS 6.00. I followed Antonin's idea of editing 001.mgz by switching wm-intensity voxels clearly not wm (mostly in the subtemporal regions, at times close to bright dural portions in the crown) to gm intensities and ran recon-all -all, and this time all was OK. So it seems that the problem is that on re-initializing during -autorecon2-wm rerun, the routine does not edit out high intensity voxels even if manually excluded in wm.mgz. This seems to be different to some extent with how FS 5.3 was reacting, although I did not look at this systematically. There may be a reason that manual editing is just part of the story during rerun and does not automatically override the recon stream, but I do not know it. Octavian ---------- Forwarded message ---------- From: Octavian Lie <octavian.lie(a)gmail.com> Date: Sun, Apr 2, 2017 at 7:59 PM Subject: wm edits not incorporated To: octavian lie <octavian.lie(a)gmail.com> Dear Bruce, I just transferred subject r02.tar.gz. Again, wm.mgz edits (all deleted voxels, no additions) are not incorporated on reruns using any of the recon-all -autorecon-wm -aitorecon3 recon-all -autorecon2 -autorecon3 recon-all -make all FOr example, the complete command line for a rerun is recon-all -autorecon2-wm -autorecon3 -3T -bigventricles -cw256 -subjid r02 -parallel > output.txt & Here are some of the edited voxels which are not excluded from the wm on rerun: -40.14, -2.67, 116.29 coronal slice 132 12.73, -23.67, 126.16 coronal slice 171 14.05, 12.33, 11.61 coronal slice 147 I mention this is not the only subject where I have this problem. Thank you for your help. Octavian

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Cerebellum for PetSurfer, edit aseg or brainmask?
by Shane S 12 Apr '17

12 Apr '17

Hello Experts, I want to use the cerebellum as the reference region for PET analysis using the PetSurfer. Unfortunately in very few cases, the segmentation is not good. I have attached some pictures. In this case, should I be editing the aseg or the brainmask.mgz? Thank you for your help. -- Shane Schofield

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mri_concat pet images into 1 template image
by Shane S 12 Apr '17

12 Apr '17

Hello Freesurfer, I have 3 PET images per individual. I am learning PetSurfer based on the Greve et al., 2014 paper. On the PetSurfer link, there are 2 methods. mri_convert pet.nii.gz —frame frameno template.nii.gz or mri_concat pet.nii.gz --mean —0 template.nii.gz What are the differences? My files are listed as subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz Is "mri_concat subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz —mean —o template.nii.gz” correct? Thank you for helping. Best Wishes, S -- Shane Schofield

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Manual edits
by John Anderson 12 Apr '17

12 Apr '17

Dear Freesurfer experts, I am not an expert in manual edits, so I highly appreciate any feedback regarding the issues in my questions below. I ran the following command line “recon-all -s subjid -all” on T1 image for one of the subjects. when reviewing the output images (i.e. wm.mgz, brainmask.mgz) I found issues as attached. Attached is an output of the command: "Freeveiw orig.mgz wmparc.mgz wm.mgz" 1. When I reviewed “wm.mgz” I see interactions between the white matter (wm), and the cortex (yellow arrows). To fix this, I edited “wm.mgz” by removing the wm voxels from the cortex, and the data was saved in the file “wm.seg.mgz” 2. I found many holes in many slices similar to the (black arrow). I filled all these holes. The data saved in “wm.seg.mgz” 3. I fixed some issues related to dura and bad skullstipping Then I ran the command: “recon-all -autorecon2-wm -autorecon3 -subjid <subject>” which output the file “brain.finalsurfs.mgz” and the command “recon-all -autorecon-pial -subjid <subject>” Now, I want to understand where Freesurfer implement the new edits? Which files will be used as the main files that include the new edits. Logically, the edits must be implemented in "wm.mgz" and "brainmask.mgz". What confuses me is when I open orig.mgz wm.mgz and brainmask.mgz in freesview. I see the original non-edited files. I am not sure what I am doing wrong so I highly appreciate any help. John

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glmfit mismatch between X and C with same no of columns
by Clara Kühn 12 Apr '17

12 Apr '17

Dear Freesurfer experts, I'm trying to run a repeated measures anova as described here: https://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova I have 40 subjects with 2 time points each, so it's quite a large matrix. When running the mri_glmfit command I get the following error: ERROR: dimension mismatch between X and contrast /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/C-pre-vs-post.mtx X has 41 cols, C has 81 cols I'm not sure what to do as the matrix and the contrast (see attachments) actually have the same amount of columns... Any help would be much appreciated, thank you! Clara -- Clara Kühn, Phd Student Max-Planck-Institute for Human Cognitive and Brain Science Department of Neuropsychology Stephanstrasse 1A 04103 Leipzig, Germany Phone: +49 341 - 9940 2271 Fax: +49 341 - 9940 2260 Web: www.cbs.mpg.de E-Mail: ckuehn(a)cbs.mpg.de

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R package for graph theory analysis of MRI data {Disarmed}
by Chris Watson 11 Apr '17

11 Apr '17

Dear Freesurfer users, (apologies for cross-post) I am pleased to announce the first major release of my R package "brainGraph" (v1.0.0), a collection of functions for performing graph theory analyses of brain MRI data. I chose R because it is free and is, in my opinion, the best choice for just about any statistical analysis. It is available on CRAN at https://cran.r-project.org/web/packages/brainGraph/index.html and development versions will be on my Github page (link below). You can use it for gray matter covariance networks (cortical thickness, volume, surface area, or LGI), DTI tractography data (FSL's "probtrackx2", PANDA, TrackVis, etc.), and for resting-state fMRI (the Matlab toolbox DPABI/DPARSF). It is very heavily dependent on the fantastic R package "igraph" (see igraph.org) which is based on C code and is quite a bit faster than many other R applications. My Github page for the package is https://github.com/cwatson/brainGraph <https://email.tch.harvard.edu/owa/redir.aspx?REF=AuYw-ae9TnjtRShTO7f-UJbUR6…>. At the bottom is the "README.md" file which provides some basic information. Most important is the link to the User Guide, which has extensive installation and usage information (warning: it is a direct PDF link). It is very long but should be helpful. You will find code for getting your data into R, and I have documented many analysis steps and include multiple figures. I hope this is intuitive for both veteran and novice R users. Additionally, there are links for help learning R, and links to other R packages relevant to neuroimaging applications. Some features that should be of interest include: * calculation of a large number of graph/vertex/edge measures (particularly those most common in neuroimaging) * between-group vertex-wise analysis using the GLM * implementation of the network-based statistic (NBS) * bootstrapping & permutation testing * random graph generation, small-worldness, and global/local/nodal efficiency * rich-club calculations * robustness ("targeted attack" or "random failure") & vulnerability * a basic GUI to explore your networks (up to 2 groups/subject at a time) Please see the NEWS.md file ( https://github.com/cwatson/brainGraph/blob/master/NEWS.md) for the changelog. This remains a work-in-progress, so I am very happy to receive bug reports, feature requests, general questions asking for help with code, (constructive) criticism, etc. Please join the Google Group that I set up for those purposes: https://groups.google.com/forum/?hl=en#!forum/brainGraph-help Chris Watson

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mri_convert defaults to trilinear interpolation if "--like" option is used, regardless of "-rt nearest"
by Harris Hoke 11 Apr '17

11 Apr '17

I’m currently running freesurfer 6.0.0, and I’ve run into the same problem described in this thread on the archives <http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg43697.html> . Does anyone know if a fix exists? I'm trying to move binary parcel files from the SPM default MNI152 space to Freesurfer cvs_avg35_MNI152 space. ~Harris

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