Freesurfer

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30060 discussions

MRI analysis in Freesurfer
by Le Prieult, Yéléna 11 Sep '23

11 Sep '23

External Email - Use Caution Good afternoon, I have some questions about the analysis of the structural data in Freesurfer, it's the first I use this programm and I'm a bit lost. In order to do the recon-all command, where should I put the T1 weighted images of my subjects (3 different groups with a total of 63 subjects)? Should I put them in the subjects folder of the freesurfer folder (i.e. SUBJECTS_DIR) or should I create a new folder in this subjects folder or should I put them elsewhere? And then should I change the working directory on the terminal so the program can find my subjects? And for the recon-all command itself, once the T1 images are found, should I just write recon-all in the terminal and the preprocessing will start? Thanks a lot in advance for your answer! I really appreciate your help! Have a nice day. Best regards, Yéléna Le Prieult

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Discrepancy in vertex counts between resampled and recon-all generated annot files
by Leonardo Cardoso Saraiva 10 Sep '23

10 Sep '23

External Email - Use Caution Dear Freesurfer Experts, I am using .annot files to extract parcellated vertex-wise morphometric features from surf files (e.g., area value from ?h.area file). For each vertex, I want to determine the parcel it belongs to and its associated morphometric features. During this process, I exclude vertices labeled as ‘unknown’ or ‘medial wall’. In addition to the aparc parcellation, I am also using other parcellations computed on fsaverage. Therefore, I need to resample these parcellations onto native surfaces. To do this, I am using commands such as the one below: mri_surf2surf --srcsubject fsaverage \ --sval-annot ${SUBJECTS_DIR}/fsaverage/label/lh.test\ --trgsubject sub-test \ --trgsurfval ${SUBJECTS_DIR}/sub-test/label/lh.test \ --hemi lh As a sanity check, I used the above command to resample the aparc parcellation onto native surfaces (which is already done by recon-all). However, when I use the .annot files generated by the above command to extract morphometric features from surf files, I get a different number of vertices than when I use the .annot files generated by recon-all. Is this behavior expected? Am I doing something wrong? Thank you for your time and attention. Best, Leo

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Watershed surfaces error
by Srishyla, Diksha 10 Sep '23

10 Sep '23

External Email - Use Caution Hello FreeSurfer Developers, I am attempting to produce watershed surfaces (inner_skull, outer skull, outer skin, brain). I plan to use these for EEG functional connectivity analyses. However, they turn out faulty (image attached). Any insights as to why this might be happening? 1) FreeSurfer version: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b 2) Platform: Ubuntu 22.04.3 LTS 3) recon-all.log: see attached Thank you for your time. Best, Diksha

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Mideface for CT?
by Qian Chu 10 Sep '23

10 Sep '23

External Email - Use Caution Hi all, I have found the mideface algorithm powerful for T1/T2 weighted MRI. I wonder if it has been verified on CT scans as well? Best regards, Qian -------- QIAN CHU (he/him/his) | qian.chu(a){mail.utoronto.ca, ae.mpg.de} | Website<https://secure-web.cisco.com/12Y3Nj0o77aq2uBaYIimnvh3JazrRfhOgPE72E43NgskO5…> PhD Student, Max Planck - University of Toronto Centre for Neural Science and Technology - Neural Circuits, Consciousness, and Cognition Research Group<https://secure-web.cisco.com/1S-QqiisEUAxYPhXulbMb1tJ6yz-Dzcht7kQkp9-6yk1ze…> Max Planck Institute for Empirical Aesthetics - Neuron to Brain laboratory<http://secure-web.cisco.com/1eP4WZTaTyQacINO8HujyxYARwhutNZ1JAL7otbI3HL25Js…> Institute of Biomedical Engineering and Krembil Brain Institute, University of Toronto

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freesurfer data analysis and visualization
by Pukovisa Prawiroharjo 10 Sep '23

10 Sep '23

External Email - Use Caution anyone have suggestion data visualization from freesurfer volumetric. i need visualization of 2 volume before and after of the same individual patient and between 2 groups in a research. i've found some paper use pysurfer, anyone have other suggestions and tutorioal / reading and code about how to use those ? best regards *Pukovisa Prawiroharjo, M.D., Sp.N, Subsp. NGD (K), PhD* Neurobehavior Consultant, Neurology Specialist Neurology Department, Faculty of Medicine, Universitas Indonesia Chair of Bioethics Cluster IMERI UI Chair of International Policy Div, Board of Development Med Services IDI

2 1

keep T1w matrix size during recon-all (without zero-padding)
by Rona Haker 10 Sep '23

10 Sep '23

External Email - Use Caution Hi, Can recon-all be performed without zero-padding the final matrix aparc+aseg in order to keep the original T1w matrix size? This will greatly help me in further analyses. Thank you!

2 1

GLM with multiple nuisance variables
by #NGUYEN THUAN TINH# 10 Sep '23

10 Sep '23

External Email - Use Caution Dear Freesurfer experts, I want to run a GLM to analyze the correlation between a continuous variable Y and a morphometric measure (eg. Cortical thickness). I want to control for some nuisance variables: sex, scan site, age, age squared, age * sex interaction, head size. 1. How should I go about formulating the FSDG file? 2. What should my design matrix be if I am only interested in the relationship between Y and the morphometric measure of interest after controlling for the various nuisance variables? Thank you so much for the help! Yours, Sophia

2 1

SAMSEG choice of the input
by Giulio Siracusano 10 Sep '23

10 Sep '23

External Email - Use Caution Dear Experts, I'm trying to understand what is the best input choice for running SAMSEG --recon in order to have the closest results as possible when compared against ASEG after executing (separately) an instance of recon-all all (and the raw input files in NIFTI format). I'm very well aware that ASEG and SAMSEG are different methods. I'm using the aseg.stats file as a results of the recon-all all command (here renamed as aseg.recon-all.stats for an easier identification). These stats should be my reference. Currently I've run the samseg command using the following input variants: 1) raw input file (brain MP-RAGE sequence) converted into a mgz archive (Raw.mgz). samseg --t1w ./Raw.mgz --s 002_S_0685_DIRECT --recon --refmode t1w The corresponding results are attached into (samseg.direct.stats) 2) This time I've used the file T1.mgz which is one of the intermediate results generated after running recon-all -autorecon 1. Specifically, this is the output of (mri_normalize <https://secure-web.cisco.com/1JV3nYNrViePm1qpOtzuMUtCndnVtCut-gp7OyXxNuXIOk…> -g 1 -mprage nu.mgz T1.mgz). samseg --t1w ./T1W/T1.mgz --s 002_S_0685_DIRECT_T1W --recon --refmode t1w The corresponding samseg.stats file is attached and called (samseg.direct.t1.stats). 3) this time I've used the file brainmask.mgz which is the last intermediate result generated after running recon-all -autorecon 1. Specifically, this is the output of mri_watershed <https://secure-web.cisco.com/1DjG5BDGTEbHYOWKmd4lc63SOmX8IrmziV9_NRWhpCskwO…>. samseg --t1w ./brainmask.mgz --s 002_S_0685_DIRECT_BRAIN --recon --refmode t1w The corresponding samseg.stats file is attached and called (samseg.brain.stats). I've noticed that the SAMSEG stats file (samseg.brain.stats) as obtained when using the brainmask.mgz as input file is the closest with the ASEG statistics (aseg.recon-all.stats). I also observe that the unknown volume is the lowest (# Measure Unknown, 5329.102436, mm^3) when using brainmask.mgz as input for SAMSEG, whereas is higher (Measure Unknown, 325302.894793, mm^3) when using T1.mgz as input file and is the highest (Measure Unknown, 946924.354060, mm^3) for the raw input. I know that for running recon-all we use the raw input files (for example, in NIFTI format), but I wanted to know what is the best possible configuration for SAMSEG in terms of input file in order to have the closest match between SAMSEG and ASEG statistics. Could it be possible to use the intermediate result T1.mgz or brainmask.mgz as input file for running samseg command? Is it a technically correct procedure? Do we need to use only the raw data as input for running samseg --recon command? Hope this is clear Regards GS

3 5

Copy geometry (fov position) from one header to another while keeping voxel and matrix sizes unchanged
by Proulx, Jean Sebastien 08 Sep '23

08 Sep '23

External Email - Use Caution Dear Freesurfers! I have two single-slice images that were acquired with different head positions. Thanks to a fancy AutoAlign-like routine at the scanner (areg by Paul Wighton), the fov of the second image tracked the movement of the head—the brain nicely aligns when overlaying the two untouched image grids with e.g. fslview. To leverage this online registration and properly visualize images in freeview, I need the fov position in header of the second image to be the same as in the header of the first image—basically pretending the head did not move and the two images were acquired with the exact same scanner-space fov position. So far I achieved that in a somewhat inelegant way by loading the first header in matlab with MRIread.m and manually adding the volume data from the second image before saving with MRIwrite.m. That however does not work when the second image have different voxel and matrix sizes—e.g. my second image has twice the resolution of the first and gets blown up to twice the size in freeview after my makeshift header change :-( I suspect a better solution could use mri_vol2vol with an appropriate registration matrix, but I don't know how to get the appropriate matrix. Any suggestions? thanks a lot for the help and Have a very good day! Sébastien

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Re: [Freesurfer] Screen tearing in FreeView on Ubuntu 22.04
by fsbuild 07 Sep '23

07 Sep '23

External Email - Use Caution I’ll suggest a couple of things - (1) you are using a development build of freesurfer which could be unstable.  I would instead try the most recent 7.4.1 release for Ubuntu, and install it via the .deb file installer (system updates may be needed), which you can pick from the downloads available under https://secure-web.cisco.com/1lN9y7zM2gRNbX1ihQ-zCX4n48mKFb2WobA…  Just “sudo apt remove freesurfer” and then “sudo apt install ./<freesurfer deb file>”.  (2)  Perhaps something is going on with OpenGL drivers and graphics hardware.  You could check the latest OpenGL drivers are installed and what you are running is compatible with your version of Ubuntu Linux. - R. On Sep 7, 2023, at 19:40, VINCENT KOPPELMANS <vincent.koppelmans@utah..edu> wrote:        External Email - Use Caution        Hi all, I am encountering the following issue: In FreeView, when I use the mouse to navigate, the crosshair is not under the cursor, but about an inch left and down from it. When I resize the FreeView window, it starts to tear. See the attached screenshot or the Github issue that I opened here: https://secure-web.cisco.com/1nxOyRuDDwSL9nzRXpr6kl-rtPsHnh83mO2… environment:OS: Ubuntu 22.04.3 LTS (but this happened with 20.04 as well)FreeSurfer: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460FreeView: 3.0; Build Jun 14 2023 03:48:54 (but this happened with previous versions as well)Best,Vincent<261422837-033513d0-3922-4a07-95fe-ff30357b5085.png>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh..harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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