Freesurfer

freesurfer@nmr.mgh.harvard.edu

12 participants
30081 discussions

GM Volumes
by Nils B. 10 May '21

10 May '21

External Email - Use Caution Dear Freesurfer developers, I'm hoping you can help me once again. Right now I'm working on how to extract certain measurements out of my data set. I have two groups and MRI data from one time point in elderly people. The data quality is pretty bad but for pilot analysis I want to analyze the gray matter volume difference in some ROI's. I've already found the total GM volume in the aseg-stats as well as the hippocampal volumes but I couldn't find any of these ROI's: subiculum, parahippocampal gyrus,Central sulcus, Cingulate cortex, left frontal cortex, central premotor cortex, ventral premotor cortex. Are any of these regions found in the Freesurfer output or is there a way to generate them? Has Freesurfer even a way to automatically identify these regions? My Set-up: Freesurfer Version: 7.1 Plattform: Ubuntu 18.04 Thank you in advance for the help! Best regards, Nils -- Nils Böer Research Assistant with Bachelor Degree (WHB) *Psychology and Movement Science* University of Paderborn Department of Sports and Health Warburger Str. 100 33098 Paderborn Room: Sp 1.401 Email: nils.tobias94(a)gmail.com / nboeer(a)mail.uni-paderborn.de <nils.tobias94(a)gmail.com> Web: https://secure-web.cisco.com/1WVj0EcABQ4b3chjPYhYGhDOux-whaYVbSMnsWR9otFaBI… https://secure-web.cisco.com/1KCbyE0u2DHoajFIXnQlic2g_jJy0p9EnLmzpN0VFe-d7c… <https://secure-web.cisco.com/1WVj0EcABQ4b3chjPYhYGhDOux-whaYVbSMnsWR9otFaBI…>

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Extract ROI cortical thickness with mri_segstat
by LIN, Yezhe 10 May '21

10 May '21

External Email - Use Caution Dear Freesurfer experts, My name is Yezhe Lin. I am trying to extract the thickness in an area we found significant in group analysis. However, when we did a t-test on the extracted values, the significance was not obtained. I wonder something could go wrong somewhere and what possibly caused the difference. I attached my scripts for the adjusted pipeline FYI. steps #make a 3x3x3 ROI using the peak coordinate obtained in group analysis in standard space (MNI152) by fslview #check ROI location tkmedit -f /usr/local/fsl/data/standard/MNI152_T1_2mm_brain.nii.gz -overlay MNI152_T1_2mm_rh.thickness.CBPHCagesexeTIVmask.nii -fthresh 0.5   # register to fsaverage of the dataset cd ../fsaverage/surf/ (Freesurfer_Home fsaverage) fslregister --s fsaverage --mov /mnt/backup2/restore-2021/CBPFreesurfer/FreesurferResults/TP1/FS/mask/MNI152_T1_2mm_brain.nii --reg MNI2mm_to_fsaverage.dat   #To check results, run: tkregister2 --mov /mnt/backup2/restore-2021/CBPFreesurfer/FreesurferResults/TP1/FS/mask/MNI152_T1_2mm_brain.nii --reg MNI2mm_to_fsaverage.dat --surf orig   #view your ROI in the fsaverage subject volume to ensure that it is located where you expect it to be: (two pials clear) cd $SUBJECTS_DIR/fsaverage/surf  tkmedit fsaverage T1.mgz \   -overlay /mnt/backup2/restore-2021/CBPFreesurfer/FreesurferResults/TP1/FS/mask/MNI152_T1_2mm_rh.thickness.CBPHCagesexeTIVmask.nii \   -overlay-reg MNI2mm_to_fsaverage.dat \   -fthresh 0.5 \   -surface lh.white -aux-surface rh.white #register ROI to fsaverage space cd $SUBJECTS_DIR/fsaverage/surf mri_vol2surf \   --mov /mnt/backup2/restore-2021/CBPFreesurfer/FreesurferResults/TP1/FS/mask/MNI152_T1_2mm_rh.thickness.CBPHCagesexeTIVmask.nii \   --reg MNI2mm_to_fsaverage.dat \ --projdist-max 0 1 0.1 \   --interp nearest \   --hemi rh \   --out rh.fsaverage.thickness.CBPHCagesexeTIVmask.mgh   #view the ROI registration (on the peak center of significant cluster) tksurfer fsaverage rh inflated -overlay rh.fsaverage.thickness.CBPHCagesexeTIVmask.mgh -fthresh 0.5 # extract values from rh.XXX.CBPvsHC_age_sex_eTIV.10.mgh mri_segstats --i ../rh.thickness.CBPvsHC_age_sex_eTIV.10.mgh --seg rh.fsaverage.thickness.CBPHCagesexeTIVmask.mgh --excludeid 0 --avgwf CBPHC_th_results.dat Hope my questions is clear! Appreciate your kind help and time! ------------------ Best regards, Yezhe Yezhe Lin, MD MMed  (she/her/hers) Postdoctoral Associate, Department of Psychiatry University of Rochester Medical Center yezhe.lin.bee(a)gmail.com Twitter: @LinYezhe | LinkedIn | Researchgate  

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average thickness lobe stats
by Agurne Sampedro Calvete 10 May '21

10 May '21

External Email - Use Caution Dear Freesurfer experts, I am trying to obtain the average thickness of the brain lobes. I am particularly interested in the temporal lobe. I have run "mri_annotation2label" (--lobeStrict) and "mris_anatomical_stats" commands and I have obtained the average thickness of the different lobes in each hemisphere. However, I am interested in obtaining data of both hemispheres together, that is, a single thickness average for example for the temporal lobe. Is there a way to calculate it? Could I just sum both averages from each hemisphere? Thank you very much in advance. Kind regards, Agurne

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Question about hippocampal sub-volume extraction
by Wei Shao 07 May '21

07 May '21

External Email - Use Caution Hello,Dear Freesurfer exports I have a question about the pipeline of hippocampal sub-volume extraction: quantifyHAsubregions.sh hippoSf <T1>-<analysisID> <output_file> <OPTIONAL_SUBJECTS_DIR> Let's say I have two different groups of analysisID such as sub-AVP???? and sub-BAY???? I can pass a wildcard to extract the data of T2 scan from all sub-BAY???? subjects by quantifyHAsubregions.sh hippoSf BAY*-T2 result.txt But Is there any way that I can extract the sub-volume from all the two different group subjects at one time? Thanks. Best, Wei

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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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