Freesurfer August 2018

freesurfer@nmr.mgh.harvard.edu

104 participants
167 discussions

coregistering with bbregister
by Ben M 10 Aug '18

10 Aug '18

External Email - Use Caution Hi, I'm trying to coregister the strucural image to the mean functional image using bbregister, so after reconall I did: bbregister --t2 --init-fsl --reg /data/bbregister/reg.dat --mov /data/mean_func.nii.gz --s 001 bet /data/structural.nii.gz /data/bet_structural.nii.gz #brain.nii.gz is the brain.mgz from reconall output (in freesurfer space) mri_vol2vol --mov /data/bet_structural.nii.gz --targ /data/brain.nii.gz --o /data/coregistered_structural.nii.gz --reg /data/bbregister/reg.dat --inv –-nearest But when I load the coregistered_structural.nii.gz and the mean_func.nii.gz they are not aligned. I'm sure I'm doing something wrong, could someone help me figure it out please? Thanks in advance, Ben

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Viewing the output of mris_preproc in Freeview + export to Matlab
by Alon Baram 10 Aug '18

10 Aug '18

External Email - Use Caution Hello, I want to overlay the .mgh file which is the output of mris_preproc in freeview on the fsaverage surface. This file has (according to mri_info) the dimensions Nverteces x 1 x 1 x Nsubjects: my data in fsaverage space for each of my subjects. But when I load it in freeview I can only see one value in each vertex. Is there a way to view "4D" (it's actually 2D: Nverteces x Nsubjects) data in Freeview? If not, what is the single value (per vertex) that freeview chooses to show me? is it just the data from the first subject? I tried to look in the documentation for any clues about viewing time-series data in Freeview, but failed. I would also be very happy to understand what is the best way to save this 4D .mgh file in a format that I can then import it into Matlab. Thanks for the help!

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Hippocampal subfield registration question.
by Jamie Hanson 10 Aug '18

10 Aug '18

External Email - Use Caution Dear FS List, I was just started to run hippocampal subfield segmentation and had a question about registration (and a related output warning). In the ~5 test subjects I've tried the SF routine, I get a warning early on that says-- ********************************************************** * * WARNING: Registration did not converge in 5 steps! * Problem might be ill posed. * Please inspect output manually! * ********************************************************** Two questions-- 1) Is that anything to be concerned about? 2) If so, are there relevant documents regarding checking the outputs to flag potential poor registration/segmentation? Any information or thoughts are greatly appreciated! Thanks much! All the best, Jamie. -- Jamie Hanson Assistant Professor, Psychology Research Scientist, Learning Research and Development Center University of Pittsburgh Personal website: jamiehanson.org

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New segmentation of thalamic nuclei
by Iglesias Gonzalez, Eugenio 10 Aug '18

10 Aug '18

External Email - Use Caution Dear FreeSurfer users, It is my pleasure to announce that our new tool to segment the thalamic nuclei from structural MR scans is available in the development version of FreeSurfer. The tool relies on an atlas derived from manual annotations made on histological sections. The module can analyze the main FreeSurfer T1 scan, but also supports MR images with contrasts other than T1 – as long as the corresponding T1 has been processed with recon-all. If you’ve got images processed with an earlier version of FreeSurfer, you don’t need to process them again with the development version; you can directly run the new module on your existing processed subjects. You can find the documentation, including a link to a preprint of the paper, in the wiki: https://surfer.nmr.mgh.harvard.edu/fswiki/ThalamicNuclei As with any other FreeSurfer tool (particularly those that have been recently released), we appreciate any feedback that you might have. Kind regards, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/

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Q & A Forum in neuroimaging techniques
by James Brown 09 Aug '18

09 Aug '18

External Email - Use Caution Dear Colleagues, We would like to create Q & A forum about issues in neuroimaging techniques. Experts from the Martinos Center and Oxford FMRIB will be invited to build this forum and to answer questions and provide plans for critical technical issues. This forum will serve as a reference for our colleagues who would like to learn about neuroimaging (analyses pipelines, methodologies, tools development..... etc) as well as a library and repository that can benefit any one who is interested in this field. The forum will include chat rooms and live discussions with an experts in the field. We are looking forward for your support and contributions. Please follow us here: https://area51.stackexchange.com/proposals/119504/neuroimaging?referrer=JC-… Sincerely, James Brown

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Mailing List Submission
by Maurisa Major 09 Aug '18

09 Aug '18

External Email - Use Caution Hi, I would like to post the following to the mailing list: Freesurfer experts, We are a small medical practice in California and are looking for someone who works with Freesurfer to help us visualize MRI's with DTI so we can show the images to our patients. If you or someone you know is willing to do some freelancing with us, please contact us at maurisa(a)tsmdinc.com with the subject line "Freesurfer Freelancer." Thank you. -- Best, Maurisa

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Using Freesurfer for unconventional group analysis
by Alon Baram 09 Aug '18

09 Aug '18

External Email - Use Caution Hi! (tl:dr - I have a few questions listed at the end of this message. most of the message is just details about these questions). I have a volumetric map of values for each subject, which you can think of as a contrast (it is actually a contrast of distances from a Representational Similarity Analysis (RSA) calculated in Matlab using the RSA toolbox, but that’s irrelevant to my questions). I did my preprocessing in FSL. These maps are currently in a downsampled (2x2x2) version of the anatomical image (see next paragraph for details). I used FSL’s FLIRT to move my functional images to that space, using the examplefunc2highres.mat transformation matrix, highres (the anatomical image) as the reference image, and the flag -applyisoxfm 2 to ensure the resolution stays 2x2x2. (( **Less relevant to my Freesurfer questions so feel free to skip**: the reason I chose to run my RSA analyses in this 2x2x2 anatomical space is that I have 8 runs (EPI sequences), with a structural scan after 4 runs. Since I need to align all my runs to one template image to do the RSA analysis with conditions across runs, it seemed like a natural choice: I first run FEAT preprocessing on each run separately, and use a the middle image from run X as the motion correction template for run X (as is the default). I then transform the filtered_func_data.nii.gz file of each run to the 2x2x2 anatomical space. If this seems like a mistake to you, please let me know! )) I would like to project these contrast maps to a common surface, and to do group analysis on the surface. I think I need to use the command mris_preproc or mri_vol2surf (see next paragraph), but both need a registration file which I’m not sure how to get. given that my contrast images are already in the “correct” (anatomical space) orientation, I thought the transformation matrix should just be the identity matrix. I tried using bbregister with the brain extracted structural image as the --mov template (the resolution in the resulting register.dat file will be 1x1x1, and not 2x2x2 like the transformed functional images, but the resolution lines in the register.dat file are anyway being ignored. The transformation matrix should be correct). I tried this and the transformation matrix was not the identity matrix, but rather: 9.999998211860657e-01 5.568005726672709e-04 -6.800168921472505e-05 5.548541247844696e-02 1.512142625870183e-04 -1.508450955152512e-01 9.885573387145996e-01 -3.581156954169273e-02 5.401717498898506e-04 -9.885571599006653e-01 -1.508451700210571e-01 3.751721233129501e-02 when I look at this registration with tkregisterfv it looks fine (both for the structural image and for the examplefunc after transformed to the 2x2x2 structural space) - so this seems to be working. If anybody has an explanation why the transformation matrix between the skull-striped anatomical image from FSL to orig.mgz is not the identity matrix I would appreciate it. I’m not sure how to get the maps into a common surface and not subject surface. The register.dat file I will obtain will be the registration from the functional space (in my case the downsampled anatomical space) to the subject’s anatomical space. If I give that as input to mri_vol2surf, but use "--trgsubject fsaverage", will Freesurfer automatically know to apply the registration from the subject’s surface to fsaverage (if I'm correct it uses the sphere registration - is that the right thing to do?)? If I only want to do surface group analysis and I’m not interested in viewing the individual subject’s contrasts on the surface, do I even need to use mri_vol2surf? or is it enough to just use mris_preproc and use the --iv flags to specify the volumetric contrast images and the register.dat files? I would like to run a one-sided Wilcoxon sign-rank test on these contrasts across subjects (and not a GLM - I want to know if my contrasts are different from 0 across subjects, but the contrast maps are not necessarily normally distributed) . so I can’t use mri_glmfit. Is there any way of doing that in Freesurfer? If not, is there an easy way to export the output of mris_preproc (stacked contrasts of different subjects, already sampled to fsaverage) into Matlab? After doing the analysis in Matlab, can i just write the result (a vector of p-values of size nNodes x 1) into a csv file or something like that, and then load it in Freeview as an overlay on the fsaverage surface? Is there a particular way in which this conversion from freesurfer to Matlab and back to freesurfer should be done? Finally, I will need to correct for multiple comparisons. Is there any way for me to still do that with the Freesurfer machinery for cluster correction, even though I am not running mri_glmfit, but rather doing a non-parametric statistical test? To summarise, my questions are: 1) How to create a registration.dat file with registration from my weird 2x2x2 anatomical space, where my (functional) contrasts currently are, to the anatomical space (same orientation, different resolution). 2) How to use those registration.dat files correctly to prepare the contrasts for group analysis - do I need to use mri_vol2surf or should I use mris_preproc? 3) Is there a way of running a one-sided Wilcoxon sign-rank test in Freesurfer? 4) What is the best way to export .mgh files to Matlab, and save them from Matlab in formats that are Freesurfer-compatible? 5) If I am not running a GLM, is it possible to still use Freesurfer for multiple comparisons? If so, how? Thanks very much for any help!

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Mismatching hippocampal output
by Dean, Sophie 08 Aug '18

08 Aug '18

External Email - Use Caution Dear FreeSurfer developers, As I understand it is recommended data is processed using the same OS. However, it also states on the FreeSurfer webpage that there is an exception for some post-processing tools. Recon-all was first done with: FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Platform: Darwin Kernel Version 17.4.0 Post-processing for hippocampal segmentation was done separately on two different machines with different operating systems: 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Platform: Linux Version 2.6.32-696.23.1.el6.x86_64 2) FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Platform: Darwin Kernel Version 17.7.0 Both have slightly different volume outputs. Is this difference due to software/OS differences? Which output would you recommend using? I have attached recon-all logs in case they are of use for my inquest. With thanks and kind regards, Sophie

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paradigm file for functional block design
by Desch, Simon 08 Aug '18

08 Aug '18

External Email - Use Caution Dear Freesurfer experts, I have a mapping paradigm with block design. Each off-block has a jittered length of 12-14s. Each on-block belongs to 1 out of 5 conditions (in this case stimulation sites). When creating the paradigm-file (like here: https://surfer.nmr.mgh.harvard.edu/fswiki/SensMotOddEvenPar) is it necessary to include each off-block as a separate line? Or is it sufficient to include only on-blocks and silently assume all the rest of the sequence to be of kind „NULL event“ coded with 0 (i.e. similar to what FSL does)? Thank you in advance! Sincerely, Simon Desch Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c _____________________________________________ Simon Desch Department of Cognitive and Clinical Neuroscience Central Institute of Mental Health Square J5, 68159 Mannheim Germany Phone: +49 (0) 621 1703 6304

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structure of project directory for longitudinal functional analysis
by Desch, Simon 08 Aug '18

08 Aug '18

External Email - Use Caution Dear Freesurfer experts, I’m very new to Freesurfer and I’m struggling to setup my project directory for a functional analysis. I’m running a study with each subject doing two MRI sessions, i.e. before and after they perform a perceptional training at home for three month. In each session (i.e. before and after training) they do a sensory mapping task and I want to compare mapping pre- and post-training. If possible I’d like to run this analysis contrasting two groups (who performed different kinds of training). I’m about to setup the project directory structure as depicted here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV4.5. The first issue I stumbled across is if to put data of all pre-training measurements of all subjects in a different „Session“ ( it says "All the data collected in one functional session (or visit) are placed under the folder (the "session directory").). As far as I can see the tutorial does neither cover longitudinal within subject comparisons nor between group comparisons (using mri_glmfit). Thus, any help is highly appreciated! Thank you! Sincerely, Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c _____________________________________________ Simon Desch Department of Cognitive and Clinical Neuroscience Central Institute of Mental Health Square J5, 68159 Mannheim Germany Phone: +49 (0) 621 1703 6304

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Freesurfer August 2018