Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30071 discussions

Confusion about MRI_GLMFIT
by Funk, Quentin 10 Aug '18

10 Aug '18

External Email - Use Caution Freesurfer experts, I'm trying to figure out what values I get from mri_glmfit as in the tutorial.<https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> In particular, I'm interested in how I can compare these values to what I get from QDEC. In that tutorial, the software does a linear regression for each gender and then computes a F_ratio for the two two fits. (How does this relate to the average in the contrast listed?) The F_ratio then gives a way to get P-values (under certain assumptions)--so then from the F_ratio, pvals are computed--this leads to sig.mgh. But what are the other files? The descriptions are a bit too vague for me to understand, unfortunately. The ones I'm interested in primarily are: pcc.mgh -- partial (pearson) correlation coefficient (surface overlay) z.mgh -- z-stat that corresponds to the significance (surface overlay) The z-stat should be some sort of standard score--so a standard score of significance (so p-value?) compared to what distribution? Second, what if I were interested in a different categorical variable--say I had a group of Alzheimer's patients and a group of Healthy patients. In QDEC, I click "diagnosis" as the variable to do the analysis on. What contrast does this correspond to? What type of linear fit is being compared--the slope of the regression with respect to age? If I leave out nuisance variables (like age), I should conceivably get an F-test between the two constant models, which should be more or less similar to a voxelwise t-test? Any help here is appreciated! Quentin Funk, PhD Houston Methodist Research Institute 713-363-9003<tel:713-363-9003> Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & World Report as the No. 1 hospital in Texas for patient care. Houston Methodist is nationally ranked in 8 specialties and is designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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Correlations on QDEC
by Avi Gharehgazlou 10 Aug '18

10 Aug '18

External Email - Use Caution Hi experts, I have examined the relation between LGI and a behavioural continuous scale (SCQ) on QDEC while controlling for sex, age and surface area in my model. When I want to do another analysis, doing exactly this but also controlling for diagnosis as well, QDEC gives the following error: ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 -------------------------------- Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. If you seek help with this problem, make sure to send: 1. Your command line: mri_glmfit.bin --y /d/mjt/9/users/avideh/data/recon/qdec/lh_LGI_RBS_overallscore_NDDs_controlling_SexAgeSA_fhwm0/y.mgh --fsgd /d/mjt/9/users/avideh/data/recon/qdec/lh_LGI_RBS_overallscore_NDDs_controlling_SexAgeSA_fhwm0/qdec.fsgd dods --glmdir /d/mjt/9/users/avideh/data/recon/qdec/lh_LGI_RBS_overallscore_NDDs_controlling_SexAgeSA_fhwm0 --surf fsaverage lh --label /d/mjt/9/users/avideh/data/recon/fsaverage/label/lh.aparc.label --C /d/mjt/9/users/avideh/data/recon/qdec/lh_LGI_RBS_overallscore_NDDs_controlling_SexAgeSA_fhwm0/contrasts/lh-Avg-Intercept-pial_lgi.mat --C /d/mjt/9/users/avideh/data/recon/qdec/lh_LGI_RBS_overallscore_NDDs_controlling_SexAgeSA_fhwm0/contrasts/lh-Avg-pial_lgi-RBS-Cor.mat --C /d/mjt/9/users/avideh/data/recon/qdec/lh_LGI_RBS_overallscore_NDDs_controlling_SexAgeSA_fhwm0/contrasts/lh-Diff-ADHD-ASD-Intercept-pial_lgi.mat --C /d/mjt/9/users/avideh/data/recon/qdec/lh_LGI_RBS_overallscore_NDDs_controlling_SexAgeSA_fhwm0/contrasts/lh-Diff-ADHD-ASD-Cor-pial_lgi-RBS.mat --C /d/mjt/9/users/avideh/data/recon/qdec/lh_LGI_RBS_overallscore_NDDs_controlling_SexAgeSA_fhwm0/contrasts/lh-Diff-M-F-Intercept-pial_lgi.mat --C /d/mjt/9/users/avideh/data/recon/qdec/lh_LGI_RBS_overallscore_NDDs_controlling_SexAgeSA_fhwm0/contrasts/lh-Diff-M-F-Cor-pial_lgi-RBS.mat --C /d/mjt/9/users/avideh/data/recon/qdec/lh_LGI_RBS_overallscore_NDDs_controlling_SexAgeSA_fhwm0/contrasts/lh-X-Dx-Sex-Intercept-pial_lgi.mat --C /d/mjt/9/users/avideh/data/recon/qdec/lh_LGI_RBS_overallscore_NDDs_controlling_SexAgeSA_fhwm0/contrasts/lh-X-Dx-Sex-Cor-pial_lgi-RBS.mat 2. The FSGD file (if using one) 3. And the design matrix above Attempting to diagnose further SumSq: Min=0.488835 (col 11), Max=3.834060 (col 6) ... could not determine the cause of the problem My understanding is that QDEC allows for controlling for 2 discrete variables, thus I don't know what I am doing wrong if I also control for diagnosis (in addition to sex)? I would really appreciate your help, Thanks so much, Avi

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mri_volcluster not recognize --mindistance
by Yagmur Ozdemir 19 10 Aug '18

10 Aug '18

External Email - Use Caution Hello FreeSurfer experts, I am trying to run mri_volcluster with the following command to later create masks of clustered regions from functional data. I get an error saying that the option --mindistance is not recognized, even though this option is shown in mri_volcluster --help and the FS wiki page. Any idea what might be causing this? mri_volcluster --in thresh_highres.nii.gz --sum volcluster.txt --ocn clustered_thresh_highres.nii.gz --thmin 1.5 --sign pos --regheader <subject> --mindistance 10 --minsizevox 800 --fwhm 3 ERROR: Option --mindistance unknown Best Idil

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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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