Freesurfer

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30132 discussions

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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Postdoctoral Fellowship in Neuroimaging (MRI & DWI)
by Meaghan Perdue 08 Aug '18

08 Aug '18

External Email - Use Caution Dear Freesurfer Community, Please consider the job opportunity below and pass along to colleagues who may be interested. *POSTDOCTORAL FELLOWSHIP IN NEUROIMAGING (MRI and DTI)* The LandiLab (PI: Nicole Landi, PhD *https://landi.lab.uconn.edu/ <https://urldefense.proofpoint.com/v2/url?u=https-3A__landi.lab.uconn.edu_&d…>*) at Haskins Laboratories *https://haskinslabs.org/ <https://haskinslabs.org/>* (which is closely affiliated with Yale and the University of Connecticut) is seeking to hire a postdoctoral research fellow. This postdoc will join a project investigating the neurobiological basis (brain structure, genetics) of reading. The successful applicant will be responsible for conducting and interpreting analyses of neuroimaging data (structural and diffusion imaging data). This position is part of a multi-site project (Haskins Laboratories, University of Houston, Baylor College of Medicine) that is aggregating and analyzing neuroimaging and genotyping data from multiple locations to explore gene-brain-behavior relationships. Applicants must have a background conducting research using MRI. The ideal candidate will also have experience with diffusion weighted imaging (DWI) and experience with advanced statistical analysis of imaging data (e.g. imaging-genetic analyses, Bayesian methods, machine learning). *For details regarding required qualifications and application procedure, please visit: https://haskinslabs.org/postdoctoral-fellowship-neuroimaging-mri-and-dti <https://haskinslabs.org/postdoctoral-fellowship-neuroimaging-mri-and-dti>* Best regards, Meaghan Perdue -- Meaghan Perdue PhD Student Developmental Psychology Neurobiology of Language University of Connecticut Bousfield A302

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surface arithmetic?
by Rockers, Elijah D. 07 Aug '18

07 Aug '18

External Email - Use Caution Hello, I have a subject with two MRIs and surface reconstructions, several years apart. I would like to directly compare these surfaces if possible, for instance, to subtract (new - old) to see a "difference surface" or something similar. Is there a way to A) Get the surfaces into the same space so they can be combined mathematically, and B) performs operations with the surfaces, a la fslmaths? Many thanks, - Eli 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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WM segmentation
by Ben M 07 Aug '18

07 Aug '18

External Email - Use Caution Hi, I would like to create a mask of the WM for fMRI analysis. I read a previous post in which it was suggested to get the wm segmentation and erode it, since the result will be exclusively WM. My question is why is this so? Why can I assume that getting the WM mask from the aseg file will almost certainly get me high probability WM, >0.9 for example? In most segmentation algorithms we get posterior probabilities at each voxel, so that we can then select voxels with posterior probabilities >0.90 for example. Why is freesurfer's WM segmentation so accurate that we do not need posterior probabilities? Are these very high probabilities somehow already coded in freesurfer's segmentation algorithm? Thanks, Ben

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mris_register segmentation fault while running recon-all with -cm option on a scan with .6mm isotropic voxels
by Lalonde, Francois (NIH/NIMH) [E] 07 Aug '18

07 Aug '18

External Email - Use Caution Hello FreeSurfer Developers, I am trying to run the hippocampal and amygdala subfield segmentation and take advantage of the .6mm resolution of the scan. I was able to run recon-all successfully on the scan without the -cm option. I get the following error: ------------------------------ SUBJECT nomove_xpace_06mm_tr3bcm DATE Fri Aug 3 11:58:33 EDT 2018 USER flalonde HOST cn0638 PROCESSOR x86_64 OS Linux Linux cn0638 3.10.0-693.2.2.el7.x86_64 #1 SMP Tue Sep 12 22:26:13 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux $Id: recon-all,v 1.601 2017/02/08 21:17:33 greve Exp $ /data/flalonde/freesurfer_dev/bin/recon-all PWD /gpfs/gsfs4/users/CPB/3TD/6mm/subjects/nomove_xpace_06mm_tr3bcm/scripts CMD mris_register -curv -rusage /gpfs/gsfs4/users/CPB/3TD/6mm/subjects/nomove_xpace_06mm_tr3bcm/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /data/flalonde/freesurfer_dev/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg I’ve attached a copy of the recon-all.log 1) Freesurfer version: freesurfer-linux-centos7_x86_64-dev-20180723-7bf4760 2) Platform: CentOS Linux release 7.5.1804 (Core) 3) uname -a: Linux felix.nimh.nih.gov 3.10.0-693.2.2.el7.x86_64 #1 SMP Tue Sep 12 22:26:13 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached The list mentions running a post-hoc surface deformation (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg47309.html) using mris_make_surfaces as a workaround but I’m not sure if this is applies in my case or what the full command might be (e.g. mris_make_surfaces subjectname lh). Thanks, François M. Lalonde, Ph.D. DNU / HGB / DIRP / NIMH 10 Center Drive, Room 4N244 Bethesda, MD 20892-1600

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Getting error while extracting hippocampus volume in dev version of freesurfer
by Yubraj Gupta 07 Aug '18

07 Aug '18

External Email - Use Caution Hello Freesurfer Developers, While extracting the Hippocampus volume from the subject folder, I'm getting the following error. This file does not contain MRI parameters This file does not contain MRI parameters In an assignment A(:) = B, the number of elements in A and B must be the same. Error in segmentSubjectT1_autoEstimateAlveusML (line 1856) MATLAB:subsassignnumelmismatch @#@FSTIME 2018:08:08:01:27:03 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 e 868.58 S 607.16 U 8388.47 P 1035% M 3765176 F 0 R 23295004 W 0 c 1773466 w 3380046 I 0 O 847496 L 19.31 35.64 36.84 @#@FSLOADPOST 2018:08:08:01:41:31 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 28.36 47.98 45.74 Linux tars 3.10.0-693.11.1.el7.x86_64 #1 SMP Mon Dec 4 23:52:40 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux T1 hippocampal subfields exited with ERRORS at Wed Aug 8 01:41:31 KST 2018 I've searched the list and no similar errors have been reported. Does anyone have any thought on how to troubleshoot this one? Also, I've attached the Hippo_T1.log in case it's of any use. 1) Freesurfer version: freesurfer-linux-centos7_x86_64-dev- 20180725-1793f7a 2) platform: centos-release 7centos 3) unmae -a: Linux tars 3.10.0-693.11.1.el7.x86_64 #1 SMP Mon Dec 4 23:52:40 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux 4) Hippo_T1.log: see attached

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XL Defect Detected
by Rockhill, Alexander P. 07 Aug '18

07 Aug '18

Hi all, I am running recon-all and the command is stuck on the output CORRECTING DEFECT 31 (vertices=8161, convex hull=3290, v0=29848) XL defect detected... It has been on that step overnight. Is there some way to ignore the defect or correct it without taking so long? This is using freesurfer 6. Thanks, Alex Rockhill Translational NeuroEngineering Laboratory Division of Neurotherapeutics, Department of Psychiatry Massachusetts General Hospital, Martinos Center 149 13th St Charlestown #2301, Boston, MA 02129

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