Freesurfer May 2021

freesurfer@nmr.mgh.harvard.edu

97 participants
125 discussions

How white matter voxel is represented on the surface ?
by John Gelburg 07 May '21

07 May '21

External Email - Use Caution Dear list, I am sorry for a newbie question: Suppose I analyze the fMRI data in a volumetric way using SPM. I have a voxel that appears in a white matter. Does this mean that this voxel will not appear on the surface? In other words, there would be no corresponding vertex for my voxel ? I would also appreciate any reading suggestions. Thank you, John

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mri_label2vol error
by Melissa Marie Rundle 07 May '21

07 May '21

External Email - Use Caution Hi, I get the following error message when I run mri_label2vol (freesurfer v 6.0) in a jupyter notebook(6.1.4) with python (v3.8.5): dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib However, when I run mri_label2vol directly in a terminal window, the command runs just fine. Nor do I have trouble running similar commands such as mri_vol2vol or mri_convert using the jupyter notebook. I tried running "sudo -E fs_update" as suggested in https://secure-web.cisco.com/1fu8uZTsG4VqEpMIJBtTitHsB5L2G2xXvyt_Drs1gEwm3W… but that didn't solve the problem. Any suggestions would be greatly appreciated. Sincerely, Melissa Rundle

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Freesurfer 7 crashes during mris_fix_topology
by Yakupov, Renat /DZNE 07 May '21

07 May '21

External Email - Use Caution Dear all, I have a subject whose Freesurfer processing crashes during topology fixing step. The last lines in `recon-all.log` are: After retessellation of defect 2 (v0=22890), euler #=-15 (110444,329616,219157) : difference with theory (-18) = -3 CORRECTING DEFECT 3 (vertices=8808, convex hull=2020, v0=31369) Segmentation fault (core dumped) Linux compute-0-2.local 2.6.32-504.16.2.el6.x86_64 #1 SMP Wed Apr 22 06:48:29 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 81489f2bb-M12_T1_01 exited with ERRORS at Tue Apr 27 21:23:59 CEST 2021 For the full `recon-all.log` and `recon-all.error` files please see the attached files. I tried to follow the manual topology fixing instructions from https://secure-web.cisco.com/1CVb3gwDr9GTwil5kr7FQYCZpGmZhLu9ovxhkC6nEa1QhF…, but *.white and *.pial surface files are missing from `surf` directory. It only contains these files: lh.defect_borders lh.defect_labels lh.orig.nofix lh.smoothwm.nofix rh.orig.nofix rh.smoothwm.nofix lh.defect_chull lh.inflated.nofix lh.qsphere.nofix rh.inflated.nofix rh.qsphere.nofix Which files can I use in place of white and pial surface files in order to look for WM segmentation defects? Some additional information about the data: - I am running Freesurfer 7.1 - overall, there are no gross errors in WM segmentation, although the subjects does have significant temporal lobe atrophy - there are two images acquired at different times, and processing fails for both images - interestingly, processing didnt crash with Freesurfer 6. Thank you and have a great weekend, Renat.

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Multiple Freesurfer(s)
by Giulio Degano 07 May '21

07 May '21

External Email - Use Caution Hi all, I am trying to install multiple Freesurfer versions on a Linux server (academic purposes, Linux Ubuntu 20.04). I was able to install 7.1 and 5.3 (I used two different folders) and I also got the licenses. While 7.1 runs with no problem, for 5.3 recon-all keeps giving the "invalid license file error". I am probably missing something. Thanks in advance Best Giulio Degano

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Job ad: MRI physicist
by Keith Schneider 07 May '21

07 May '21

External Email - Use Caution The Center for Biomedical and Brain Imaging (CBBI) is a core imaging facility at the University of Delaware dedicated to scientific research. It is equipped with a Siemens Prisma 3T MRI scanner, Bruker 9.4T small bore MRI scanner, TMS, and MRI-compatible EEG. It supports a wide range of scientific investigations through imaging of humans, animals and materials. Under general direction of the CBBI Manager, the MRI Physicist is responsible for supporting the operations of the Siemens and Bruker MRI scanners. The MRI Physicist is expected to contribute to both research and training efforts that will include pulse sequence programming, parameter and image quality optimization, protocol design, scanner operation, technical support and user training. The candidate will be expected to maintain a broad knowledge of state-of-the-art MRI technology and equipment. The incumbent must have excellent communication and organizational skills, the ability to positively interact with a diverse group of MRI users, and a strong motivation to learn new MRI techniques. MAJOR RESPONSIBILITIES: • Pulse sequence programming on Bruker 9.4T and Siemens 3T MRI scanners • Assist users on appropriate choice and use of coils • Technical liaison for obtaining sequences or protocols for non-standard imaging (e.g. cardiac, musculoskeletal) from Siemens and other sites • File reports as needed for WIP sequences and Siemens MRA • Ensure data quality from the viewpoint of machine fundamentals • Technical support 9.4T and 3T scanners • Protocol design and testing for 9.4T scanner, including imaging of live animals and awake animals; as-needed for 3T • Routine quality assurance for 9.4T and 3T MRI scanners • Train users, including students, on use of 9.4T and 3T MRI scanners • Help users optimize pulse sequence parameters to maximize SNR and avoid imaging artifacts • Consult on image analysis, as needed • Review journals and abstracts to keep abreast of new developments • Collaborate with ongoing research as needed; may have independent research projects if desired • Consult users about imaging details for manuscript preparation and grant applications, as needed • Perform miscellaneous job-related duties as assigned QUALIFICATIONS: • PhD in MR physics or MS with equivalent experience • expert understanding of MR physics, image acquisition, signal processing, imaging processing and image reconstruction • MR pulse sequence programming • Experience with Bruker and Siemens MRI scanners • MRI scanning experience with both humans and animals—willing to handle animals • Ability to design experiments, optimize MRI protocols, troubleshoot image artifacts, analyze data, and interpret results • Knowledge of functional MRI, DTI, MRS, T1/T2 relaxation and perfusion • Siemens IDEA and ICE certification (or ability to obtain) http://careers.udel.edu/cw/en-us/job/493998/mri-physicist-research-office <http://careers.udel.edu/cw/en-us/job/493998/mri-physicist-research-office> For further information, contact me. keith ----- Keith Schneider Director, Center for Biomedical and Brain Imaging Associate Professor Department of Psychological and Brain Sciences University of Delaware

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error at 3d normalization pass 1 of 2 stage with MP2RAGE data
by Corinna Bauer 05 May '21

05 May '21

External Email - Use Caution Hello all, I am trying to run recon-all on MP2RAGE data from Philips and it exits with errors at this point: 3d normalization pass 1 of 2 error: No such file or directory error: MRInormFindControlPoints: could not find enough control points error: No such file or directory error: MRInormFindControlPoints failed Command exited with non-zero status 253 The log file is attached. The input file was the MPRAGE generated on the scanner console (i.e. not the T1 map). I attached a screenshot of orig.mgz viewed in fsleyes. Any thoughts? Thanks! Corinna

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help with SAMSEG
by Alberto Del Cerro Leon 05 May '21

05 May '21

External Email - Use Caution Hello Freesurfer team, my group is interested in using the SAMSEG tool to evaluate white matter lesions in MCI patients. We would like to use a personalized atlas for the measure. We suppose that we need to use the flag --atlas but we don`t know if we need a generic atlas or we need an atlas at each subject' spaces. Thanks in advance for your help.

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Freesurfer version 7 reconall -autorecon2-wm error
by Jewelia K. Yao 05 May '21

05 May '21

External Email - Use Caution Hi Freesurfer Developers, I am trying to run reconall -autorecon2-wm using Freesurfer version 7 after making some minor edits to the wm.mgz file. I've tried it on multiple subjects and still get the same error (recon-all.log attached) when mri_fill starts to run: reading segmented volume aseg.presurf.mgz removing CC from segmentation Looking for area (min, max) = (350, 1400) area[0] = 1276 (min = 350, max = 1400), aspect = 0.46 (min = 0.10, max = 0.75) no need to search using seed (127, 124, 151), TAL = (1.0, 23.0, 4.0) *** Error in `mri_fill': double free or corruption (!prev): 0x0000000001c65070 *** reconall -autorecon2-wm runs well with Freesurfer version 6, but since the data was run through reconall with version 7, I was hoping to to use it for autorecon as well. I couldn't find any similar errors (specific to version 7) in the list. Does anyone know if this error is specific to version 7 and if there's any way to troubleshoot? Thanks! Jewelia

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make_average_subject without Talairach transform
by Trisanna Sprung-Much 05 May '21

05 May '21

External Email - Use Caution Hi there I’d like to know if it is possible to create an average volume and average surface of several subjects without having to incorporate the Talairach transform and no transform at all. Thank you, Trisanna Sprung-Much Research Associate McGill University MD Anderson Cancer Centre --

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Error with mris_convert
by バキット・ムダシル 05 May '21

05 May '21

External Email - Use Caution Hi, I manually made annotation files on an inflated surface of 40 subjects. The labels that makes these annotfiles are 13 in total but not present in all subjects every time, some can be missing depending on the brains surface morphology. I made the ctab files manually in the label folder in eluding an unknown label in the first line. I tried to convert one of the annotfiles into gii format and got the following error: mris_convert --annot $SUBJECTS_DIR/spl_01/label/lh.par.annot $SUBJECTS_DIR/spl_01/surf/lh.white ~/Desktop/spl_01/lh.par.gii reading colortable from annotation file... colortable with 14 entries read (originally none) Segmentation fault: 11 What this error exactly means, and how I can solve this issue. Thanks Mudathir

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Freesurfer May 2021