Freesurfer

freesurfer@nmr.mgh.harvard.edu

7 participants
30057 discussions

MRInormFindControlPoints
by Shahar Ben Noun 21 Apr '24

21 Apr '24

External Email - Use Caution Dear Freesurfer team, I am attempting to use freesurfer using fmriprep but I get the following error message: error: No such file or directory error: MRInormFindControlPoints: could not find enough control points error: No such file or directory error: MRInormFindControlPoints failed I've searched the archive but couldn't find a solution. Does anyone have any thoughts on how to trouble-shoot this one? I've contacted you before and was asked to look at the input to that step - It seems like the problem is indeed somewhere else in the process, if I understand correctly, at "autorecon1" [Node] Executing "fs_isrunning" <nipype.interfaces.utility.wrappers.Function> 240417-14:16:30,667 nipype.workflow INFO: [Node] Finished "fs_isrunning", elapsed time 0.004s. 240417-14:16:44,30 nipype.workflow INFO: [Node] Setting-up "fmriprep_23_2_wf.sub_01_wf.anat_fit_wf.surface_recon_wf.autorecon1" in "/ems/elsc-labs/benyakov-a/Lab-Shared/fmriprep_work/fmriprep_23_2_wf/sub_01_wf/anat_fit_wf/surface_recon_wf/autorecon1". 240417-14:16:44,70 nipype.workflow INFO: [Node] Executing "autorecon1" <smriprep.interfaces.freesurfer.ReconAll> 240417-14:16:44,77 nipype.interface INFO: resume recon-all : recon-all -autorecon1 -noskullstrip -noT2pial -noFLAIRpial -openmp 8 -subjid sub-01 -sd /ems/elsc-labs/benyakov-a/Lab-Shared/fmriprep_output/sourcedata/freesurfer -nomotioncor -notalairach -nonuintensitycor 240417-14:16:44,78 nipype.interface INFO: resume recon-all : recon-all -autorecon1 -noskullstrip -noT2pial -noFLAIRpial -openmp 8 -subjid sub-01 -sd /ems/elsc-labs/benyakov-a/Lab-Shared/fmriprep_output/sourcedata/freesurfer -nomotioncor -notalairach -nonuintensitycor 240417-14:16:52,329 nipype.workflow INFO: [Node] Finished "autorecon1", elapsed time 8.257549s. 240417-14:16:52,337 nipype.workflow WARNING: [Node] Error on "fmriprep_23_2_wf.sub_01_wf.anat_fit_wf.surface_recon_wf.autorecon1" (/ems/elsc-labs/benyakov-a/Lab-Shared/fmriprep_work/fmriprep_23_2_wf/sub_01_wf/anat_fit_wf/surface_recon_wf/autorecon1) 240417-14:16:52,558 nipype.workflow ERROR: Node autorecon1 failed to run on host benyakov-a.elsc.huji.ac.il. 240417-14:16:52,569 nipype.workflow ERROR: Saving crash info to /ems/elsc-labs/benyakov-a/Lab-Shared/fmriprep_output/sub-01/log/20240417-141555_c3b0815f-caf3-41ba-ab5a-fb57155be490/crash-20240417-141652-shahar.bennoun-autorecon1-682b0086-8863-4f60-9204-6d485fe4a790.txt Also, I've been asked to post "a couple of images of the processing (the orig.mgz, the T1.mgz, the brainmask.mgz, …)", what does that mean? How do I do it? 1) FreeSurfer version: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 2) Platform: Linux 3) PlatformVersion: 5.4.0-159-generic #176-Ubuntu SMP Mon Aug 14 12:04:20 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux Tue Apr 16 13:13:35 IDT 2024 4) recon-all.log 5) autorecon1 command Best regards, Shahar

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Template mapping seems inconsistent
by Dipterix Wang 19 Apr '24

19 Apr '24

External Email - Use Caution Dear FreeSurfer Devs, I'm following the fswiki ( https://secure-web.cisco.com/1W5RqZmGDk4DqrkitgyXA6TeSK5f9Nimf0vTibPbawbImA…) to map sEEG contacts to the template *cvs_avg35_inMNI152*. *I've got MNI305 coordinates for each contact, and I want to plot them on cvs_avg35_inMNI152.* According to the wiki, once I have MNI305 coordinates, I have two choices to calculate the transform from MNI305 to the scanner RAS for this template (instruction 2 and 8b, see below for comparisons). Normally I use instruction 2 since it seems to be more general and can be applied to any template. For MNI152-based templates, instruction 8b seems to be more straightforward. According to your Wiki, these two instructions would yield the identical mapping. *However, a recent case suggested a result of ~5mm difference between these two methods.* My questions are: * Is this error range expected/acceptable in the eyes of FreeSurfer? * Which image defines MNI305 RAS. (For example, MNI152 RAS usually aligns with the scanner RAS of one of ICBM 152 Nonlinear atlases version 2009) * If I need more accurate scanner->MNI305 mapping (instead of using talairach.xfm), what's your recommendations on FreeSurfer templates that are not sitting in MNI152a/b/c space? *Here's my case study:* Here is a screenshot of the native subject's brain. The two contacts (in red) are at the level of thalamus. [image: image.png] Choice 1: Following the instruction 2, > I have an RAS point on the surface (tkrR tkrA tkrS) ("Vertex RAS" from tksurfer) and want to compute the MNI305 RAS that corresponds to this point: > MNI305RAS = TalXFM*Norig*inv(Torig)*[tkrR tkrA tkrS 1]' This is the method that I usually use. I can calculate MNI305 RAS from scanner RAS via talairach.xfm (in mri/transforms/). This transform is 1.0540 0.0028 -0.0071 -0.0761 -0.0105 1.0914 0.0090 1.7791 0.0201 -0.0599 1.1014 *-5.4613* Result: the contacts are at the level of brainstem [image: image.png] Choice 2: instruction 8b However, since the template already aligns with MNI152, as an alternative, I can follow the instruction 8b, > I have an RAS from a voxel in MNI152 space which I want to convert to MNI305 space (fsaverage space). Create a vector of the MNI152 space point like v = [R A S 1]'. Multiply this vector by the matrix below (ie, M*v) 1.0022 0.0071 -0.0177 0.0528 -0.0146 0.9990 0.0027 -1.5519 0.0129 0.0094 1.0027 *-1.2012* *Notice the translation on Z axis is -1.2mm instead of -5.5mm* Result: This mapping seems better [image: image.png] Best, - Dipterix

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editing segmentations from recon-all-clinical
by Agata Wolna 19 Apr '24

19 Apr '24

External Email - Use Caution Hi! I have a question regarding the recon-all-clinical pipeline: is it possible to edit the outputs of the synthseg segmentation run as a part of the pipeline (synthseg.mgz) similarly to editing recons from the standard freesurfer pipeline, and getting updated segmentation estimates (the synthseg.vol.csv files) for these manually updated segmentation? Thanks for your help! Agata

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Postdoc position: MRI of brain networks in developmental neuropsychiatry
by kathrine 19 Apr '24

19 Apr '24

External Email - Use Caution Postdoc position in multimodal imaging of brain structural networks within developmental neuropsychiatry The Danish Research Centre for Magnetic Resonance (DRCMR) at Copenhagen University Hospital Hvidovre (Denmark) is seeking a 3-year postdoc in multimodal imaging and brain structural networks within the field of developmental psychiatry. Together with our strong clinical collaborators at the Child and Adolescent Psychiatry Unit, we run the prospective Danish High Risk and Resilience Study (VIA) (http://secure-web.cisco.com/1uKcGug6sH3c3knXd2pk38v2qWVO5c-s-4U0_J_71ttPxl6…) The VIA study longitudinally follows the largest register-based cohort of children (n=522) in the world born to parents with schizophrenia or bipolar disorder or none of these disorders. Studying children with familial high risk offers a unique opportunity to gain insight into the early disease processes and mechanisms. Children were assessed at the ages of 7, 11, and 15 years. Neuroimaging was included at age 11 and onwards. We are currently finalizing the first longitudinal neuroimaging follow-up at age 15 years and the follow-up at age 19 years starts this summer. The postdoc will mainly be working on the longitudinal VIA data, with a focus on structural and diffusion-weighted image processing. The project includes brain network analysis, such as structural covariance and connectivity analyses, and normative modelling. The postdoc position involves a tight collaboration with Prof. Andrew Zalesky (https://secure-web.cisco.com/15Y6w81JqZebeMycjcQwezkVKOoPmdNX4C3SjM1daiCnTC…) with the possibility to visit Prof. Zalesky’s lab at the University of Melbourne, Australia. The project will be carried out at the DRCMR, which is a leading research centre for biomedical MRI in Europe (http://secure-web.cisco.com/1RTwRU49VmXdDXWeZE53-ZpuUNK4kpiPxlPMWL16ZRslblE…) focusing on the brain. Approx. 75 researchers from more that 20 countries and a diverse range of disciplines are currently pursuing basic and clinically applied MR research of the human brain and its disorders. The DRCMR has a state-of-the-art research infrastructure for preclinical and human medical imaging, which includes six whole-body MR scanners (one 7T, four 3T, and one 1.5T scanners), a preclinical 7T scanner, a High-Performance Computer cluster and several state-of-the-art laboratories for electrophysiology and non-invasive brain stimulation. We see diversity as a strength and encourage all persons regardless of gender, age, ethnicity, disabilities or religion to apply. Starting date: is expected to be August 1st, 2024. Application deadline: May 15th, 2024 at 23:59 (CET) Read more and apply for the position here: https://secure-web.cisco.com/1Y9xzhM3f4cCLewCClC0dv-A8U03yE3-Cu-_88KSRvsuR4… Further information If you have questions concerning the position, you are more than welcome to contact Senior Researcher Kathrine Skak Madsen via e-mail at kathrine(a)drcmr.dk. -- Kathrine Skak Madsen Senior Researcher Danish Research Centre for Magnetic Resonance Copenhagen University Hospital Hvidovre Denmark Email: kathrine(a)drcmr.dk Phone: +45 3862 3323 http://secure-web.cisco.com/14gCCr2Weh29FgbVFb8U15HGbgjmn3Vha5GF5M3WnXLqR4k… http://secure-web.cisco.com/1n2FJ9kZfPAVapgoOAFe6DQLKcu2LwCvn1nx870r1kpeGET…

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250 Voxels Won't Stay Erased from wm.mgz Upon Relaunch
by Smith, Thomas 19 Apr '24

19 Apr '24

External Email - Use Caution Hey FreeSurfer Support, Recently I've been seeing some pial extensions into the subcortical region in FreeSurfer 7.3.2 which cause subcortical segmentation errors in the hippocampus. Turning on wm.mgz, I see erroneous bands of 250 voxels that seem to be causing the extension and subsequent segmentation error. I've tried erasing these bands, but they keep returning upon relaunch. I've also tried treating it like a pial extension into the cerebellum (i.e. editing brain.finalsurfs.manedit.mgz to correct the boundary) and even tried that edit in conjunction with edits on wm.mgz with voxel value 255 for both. Neither method yielded beneficial results. The pial boundary isn't satisfactorily corrected, the hippocampal exclusion remains, and WM hypointensities are introduced. I'm not sure what else to try at this point. Is there any reason as to why the 250 voxels keep returning on wm.mgz? Is there a better way to try editing this type of error? Sincerely, Hunter Smith, MS, BA Neuroimaging Engineer Imaging Core Laboratory (Benzinger) Washington University in St. Louis School of Medicine 4525 Scott Ave., Campus Box 8225 St. Louis, MO 63110 Cell: 502-759-6661 Email: smiththomas(a)wustl.edu ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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[FreeSurfer] Lesion detection at different thresholds
by Krystal Xiwing Yau 18 Apr '24

18 Apr '24

External Email - Use Caution Dear FS experts, I am testing out which threshold works the best for the image. As I tested 0.3 and 0.9, the lesion masks do show the difference but the measurement is the same. Please see below for your information: [cid:abc00aac-cc49-4ef4-9cca-50c4bf72188b] Fig 1. Lesion.mgz with a threshold of 0.3 applied to FLAIR image [cid:7e206b3b-741a-497a-aec8-5bef569267b7] Fig 2. Lesions.mgz with a threshold of 0.7 applied to FLAIR image Do the volume of lesions supposedly different with threshold adjustments? The following code is what I used for running samseg: run_samseg --input $FREESURFER_HOME/${i}.nii $FREESURFER_HOME/${i}_flair_reg.nii --pallidum-separate --lesion --lesion-mask-pattern 0 1 --threshold 0.7 --output $SUBJECTS_DIR/${i}_samsegOutput_thold0.7/ --save-posteriors --threads 8 Thank you for your attention. Regards, Krystal Tel.: +852 2255 5024 Fax: +852 2872 5828 Address: Room 304, 3/F, New Clinical Building, 102 Pokfulam Road, Hong Kong.

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Enorm threshold for dynamic PET images
by Sneha Pandya 18 Apr '24

18 Apr '24

External Email - Use Caution Dear team, I am using mc-afni2 to perform motion correction on dynamic PET images (ref: petsurfer wiki page). I am planning to use an average of un-censored frames as a template to do so. What should the threshold be to estimate these set of un-censored frames? For fMRI we usually use 0.2 or 0.3 for motion. However, for PET data we have values in the enorm file ranges from 0-40. Thank you, Sneha

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GLM Using 2 Surfaces - Thickness and Area
by Tejaswi D. Sudhakar 18 Apr '24

18 Apr '24

External Email - Use Caution Hello Freesurfer team, I am interested in doing one glm analysis using both the thickness and cortical surface area. My question is two-fold: First, is it possible to provide both the thickness and area files to mris_preproc and mri_surf2surf commands or is it only possible to run two separate glms (one for thickness and one for area)? Second, can we consider thickness and area as separate values or are they both correlated? In other words, how correlated are the thickness and area values? Thanks in advances, Tejaswi

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gunzip error in load_mgh.m when file path contains spaces
by Tyler Slouf 18 Apr '24

18 Apr '24

External Email - Use Caution Hello FreeSurfer Developers, I found what I believe to be a bug. Typically I can load mgz files into my Matlab program without any trouble. But if the path containing the mgz file has a space then I get an error. When I run this very short script in Matlab calling the MRIread function (/Applications/freesurfer/7.4.1/matlab/MRIread.m): filepath = char("/Users/user/Documents/folder space test/data/mri.mgz"); mri = MRIread(filepath); I get the following error: gunzip: can't stat: /Users/user/Documents/folder (/Users/user/Documents/folder.gz): No such file or directory gunzip: can't stat: space (space.gz): No such file or directory gunzip: can't stat: test/data/mri.mgz (test/data/mri.mgz.gz): No such file or directory ERROR: problem reading fname SWITCH expression must be a scalar or a character vector. Error in load_mgh (line 163) switch type Error in MRIread (line 90) [mri.vol, M, mr_parms, volsz] = load_mgh(fspec,[],[],headeronly); Error in test_load_mgz (line 2) mri = MRIread(filepath); I traced this down to the function load_mgh.m (/Applications/freesurfer/7.4.1/matlab/load_mgh.m) where a file path string (char array) is dynamically populated with randomly generated folder names to unzip into. It's about line 69 and looks like this: [status,msg] = unix(sprintf('gunzip -c %s > %s', fname, new_fname)); You may notice that potential spaces in the path names fname and new_fname are not escaped with single quotes. I edited the file to escape the parameterized strings like so: [status,msg] = unix(sprintf("gunzip -c '%s' > '%s'", fname, new_fname)); This solved the problem for me. Computer details: OS: MacOS Sonoma (latest) Chipset: Apple M1 (aarch64) Calling Program: Matlab R2023b Freesurfer: 7.4.1 Thank you for your time. Sincerely, Tyler Slouf

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Skin-Skull-Brain segmentation
by XIE Jing 18 Apr '24

18 Apr '24

External Email - Use Caution Hello all, We would like to use FreeSurfer to remodel the head, not only including the detailed brain structural information, but also considering skin and skull. I am wondering if the FreeSurfer is possible to split the skin, skull and brain surfaces at the same time? We tried the syntax "mri_make_bem_surfaces -all" , and the error notes were received as follows: nvertices=2562, nfaces=5120 mri_strip_skull: triangle file /home/customer/Desktop/headmodel/FREESURFER/freesurfer/lib/bem/ic4.tri read trishrink: File /home/customer/Desktop/headmodel/MRI/-all/mri/brain/COR-.info not found Best guess at inner_skull.tri is in inner_skull_tmp.tri What's your suggestions and comments on this question? We appreciate it very much! Thanks in advance! Jing ------------------------------- Jing XIE Associate Professor Mechatronical Engineering Beijing Institute of Technology Beijing 180001, PR China

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