Freesurfer June 2020

freesurfer@nmr.mgh.harvard.edu

91 participants
130 discussions

Freesurfer statement
by Juranek, Jenifer 07 Jun '20

07 Jun '20

External Email - Use Caution I pledge to do better. I pledge to pursue systemic change as passionately as I pursue research questions. Thank you Freesurfer Team for speaking up so eloquently with your signed statement. Jenifer Juranek

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flirt.fsl error (NEWMAT::SingularException) when running bbregister in Freesurfer 7.0.0
by julienbesle 06 Jun '20

06 Jun '20

External Email - Use Caution Hi, I just installed freesurfer v7 and I'm getting an error in a script that calls bbregister with the --fslmat and --init-fsl options. This error does not occur in freesurfer v6 even when using exactly the same data, but it does also occur with a development version of freesurfer I downloaded in Sept 2019 (exact same error). The call is: DEBUG : 2020-05-06 12:07:12,816 : runCmd : Running: bbregister --s HLOSS_p5 --mov /home/julien/data/HLOSS/pilot05_B/DWI/B0_corrected_mean_resampled_MPRAGE.nii --reg /home/julien/data/HLOSS/pilot05_B/DWI/easy_lausanne_test/b0-TO-orig.dat --fslmat /home/julien/data/HLOSS/pilot05_B/DWI/easy_lausanne_test/b0-TO-orig.mat --init-fsl --dti The error occurs when bbregister calls fsl.flirt: INFO : 2020-05-06 12:08:24,560 : main : flirt.fsl -ref /home/julien/data/HLOSS/pilot05_B/DWI/easy_lausanne_test/tmp.bbregister.8331/fslregister/refvol.fslregister.nii -in /home/julien/data/HLOSS/pilot05_B/DWI/easy_lausanne_test/tmp.bbregister.8331/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /home/julien/data/HLOSS/pilot05_B/DWI/easy_lausanne_test/tmp.bbregister.8331/fslregister/fslmat0.trans.mat -schedule /usr/local/freesurfer/bin/fsl.5.0.2.xyztrans.sch -init /home/julien/data/HLOSS/pilot05_B/DWI/easy_lausanne_test/tmp.bbregister.8331/reg.init.dat.fsl.mat0 INFO : 2020-05-06 12:08:55,102 : main : Wed May 6 12:08:54 EEST 2020 INFO : 2020-05-06 12:08:55,603 : main : /mnt/f/data/HLOSS INFO : 2020-05-06 12:08:56,105 : main : flirt.fsl -ref /home/julien/data/HLOSS/pilot05_B/DWI/easy_lausanne_test/tmp.bbregister.8331/fslregister/refvol.fslregister.nii -in /home/julien/data/HLOSS/pilot05_B/DWI/easy_lausanne_test/tmp.bbregister.8331/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /home/julien/data/HLOSS/pilot05_B/DWI/easy_lausanne_test/tmp.bbregister.8331/reg.init.dat.fsl.mat -init /home/julien/data/HLOSS/pilot05_B/DWI/easy_lausanne_test/tmp.bbregister.8331/fslregister/fslmat0.trans.mat -schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch INFO : 2020-05-06 12:09:15,632 : main : terminate called after throwing an instance of 'NEWMAT::SingularException' INFO : 2020-05-06 12:09:15,633 : main : Abort (core dumped) INFO : 2020-05-06 12:09:15,634 : main : ERROR: flirt CRITICAL : 2020-05-06 12:09:15,634 : runCmd : Return Value: 1 It looks like the first time flirt.fsl is called everything goes fine, but the second time, the error occurs. Unfortunately this is not a script I wrote myself, so I'm not sure what this particular call to bbregister is supposed to achieve. I'm not sure the call to fsl.flirt depends on which version of FSL I have installed, but just in case, I used the FSL v6 and didn't change anything to the FSL installation between trying Freesurfer v6, dev or v7. I run everything on Ubuntu 16.04 running on WSL on Windows 10. Any idea what could be going wrong? Thanks Julien -- ------------------------------------- Julien Besle Lagos Center, Apt 9A Sadat Street Beirut Lebanon tel: +961 78 980 317 -------------------------------------

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Permutation simulation cluster include vertices below cluster-forming threshold
by Fengdan Ye 05 Jun '20

05 Jun '20

External Email - Use Caution Hello Freesurfers, I am using mri_glmfit-sim to find significant clusters using permutation simulation. My command is as follows: mri_glmfit-sim \ --glmdir lh.cn_ad.glmdir \ --perm 1000 3.0 pos \ --cwp 0.05 \ --2spaces \ --bg 1 When I opened the *.sig.masked.mgh, I noticed that some vertices below the cluster forming threshold (3.0) were also included (the lowest value I found in the cluster was around 2.5). These vertices also seem to be on the edge of the cluster. Based on the FsTutorial, the permutation simulation should exclude all vertices below the cluster forming threshold. Is there any sort of smoothing done on the clusters that could have caused the vertices below CFT to be included? I checked the mail archive and found this thread that have exactly the same question, but with no answer: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15375.html <https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15375.html> Thank you, Fengdan

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mri_watershed
by Edoardo Pinzuti 05 Jun '20

05 Jun '20

External Email - Use Caution Dear Freesurfer community, I have a question regarding the mri_watershed. Is the inner_skull extracted from the brain.mgz which gets masked by the brainmask.mgz automatically? Thanks

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dura edits .mgz~ file?
by KennethSPrice 05 Jun '20

05 Jun '20

External Email - Use Caution Hello Freesurfers, I edited the brainmask.mgz file after running recon-all but no changes were saved. Instead I have a mysterious 'brainmask.mgz~' file that I cannot open with freeview. What is this file and does it contain my edits? If so how do I convert it? Already tried mri_convert. Thanks, Ken Sent with [ProtonMail](https://protonmail.com) Secure Email.

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mri_glmfit masking strategy
by Barletta, Valeria 05 Jun '20

05 Jun '20

Hello Freesurfers, I need to perform a GLM in 25 patients versus 19 controls but I need the comparison to be done only on normal appearing cortex (in patients), thus excluding cortical lesions. * Is it possible to concatenate binary masks projected to surface? What command shall I use? * If I use the option --mask for mri_glmfit, will I obtain the same type of output with the only difference that clusters are looked for in the concatenated masks? Thank you, Valeria Barletta, MD Massachusetts General Hospital 149 13th Street, Charlestown MA 02129 (617)-724-8823

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Thalamic nuclei segmentation
by Quentin Devignes 05 Jun '20

05 Jun '20

External Email - Use Caution Dear Doctor Iglesias, Thanks for your previous reply. As agreed, I post my question on the Freesurfer list. We are doing shape analyses on thalamus in order to determine whether distinct cognitive profiles in Parkinson’s disease have different deformation fiels of the thalamic surface. We used SPHARM-PDM tool (shape analysis module in Slicer4) to obtain deformation fields and p-values map (cf. attached file; vectors represent the magnitude of deformation between two groups).We are not developing a new method, we used an existing one (SPHARM-PDM). However, to be more accurate, we would like to delineate thalamic nuclei on the surface of our meshes (because the nuclei have different functional role). Existing atlases (such as yours) are usable on volumes but not on surfaces. Do you have any idea how we could project your atlas onto a surface? We did not find any method in the scientific literature. Hope you could help us, Best regards, Quentin DEVIGNES PhD candidate in neurosciences Neuropsychologist UMR-S 1172 - Lille Neuroscience and Cognition - FRANCE

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Fwd: Postdoctoral fellowship Innis lab NIH start 2021
by Douglas N. Greve 05 Jun '20

05 Jun '20

-------- Forwarded Message -------- Subject: Postdoctoral fellowship Innis lab NIH start 2021 Date: Fri, 5 Jun 2020 14:12:26 +0000 From: Innis, Robert (NIH/NIMH) [E] <innisr(a)mail.nih.gov> To: Innis, Robert (NIH/NIMH) [E] <innisr(a)mail.nih.gov> External Email - Use Caution A postdoctoral position will be available in my lab starting in spring/summer 2021. Please forward the attached advertisement to anyone who may be interested. Although immodest of me to say, the lab’s research projects are at a very exciting and productive stage. The two major goals are translational studies of neuroinflammation (i.e., COX-1, COX-2, and TSPO) and indirect markers of cAMP signaling (via PDE4B and PDE4D). The studies extend from transgenic mice to monkeys and to patients, especially with depression or dementia. Stay safe and many thanks, Bob Innis ************************************ Robert B. Innis, MD, PhD Chief, Molecular Imaging Branch National Institute of Mental Health 10 Center Drive, MSC-1026 Bldg. 10, Rm. B1D43 Bethesda, MD 20892-1026 Tel: 301-594-1368 Fax: 301-480-3610 Email: robert.innis(a)nih.gov <mailto:robert.innis@nih.gov> Branch Administrative Manager: Elizabeth Alzona Tel: 301-594-1089 Email: alzonae(a)irp.nimh.nih.gov <mailto:alzonae@irp.nimh.nih.gov> Molecular Imaging Branch website<https://www.nimh.nih.gov/labs-at-nimh/research-areas/clinics-and-labs/mib/m…> ************************************ ____________________________________ LEGAL CONFIDENTIALITY NOTICE: This email message (including all attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure, copying or distribution is strictly prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message.

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BRAIN Initiative postdoc position available at LCN (FreeSurfer team)
by Iglesias Gonzalez, Juan E. 04 Jun '20

04 Jun '20

Dear all, The Laboratory for Computational Neuroimaging (LCN) is seeking to fill a postdoctoral position in image analysis as part of an exciting NIH project titled: “Open-source software for multi-scale mapping of the human brain”, awarded to Drs. J. Eugenio Iglesias and Bruce Fischl as part of the BRAIN Initiative. The project aims to create tools for ex vivo brain MRI analysis, laminar analysis, MRI-histology integration, and surface-based sampling, using machine learning techniques. The ultimate goal is to make these tools available to other BRAIN Initiative sites and the research community in general, by integrate them tools into FreeSurfer, the open-source suite distributed by the LCN, which has nearly 50,000 worldwide licenses. We are seeking a talented and enthusiastic postdoctoral researcher to develop machine learning and image analysis methods for this project. The postholder will work with Drs. Iglesias and Fischl to develop the new tools, and also closely collaborate with a software engineer to integrate them with FreeSurfer. The postholder will also interact with our collaborators at the Allen Institute for Brain Science, which will play the role of use case for the tools. This project provides an exciting opportunity for a postdoctoral researcher at the interface between machine learning, medical image analysis and neuroscience, with a huge potential impact on the neuroimaging field. Applicants should have: - A Ph.D. degree in computer vision, neuroimaging, or biomedical engineering/image analysis. Applicants with degrees in related areas (e.g., Engineering, Physics, Applied Mathematics) will also be considered. Applicants close to submission of their PhD thesis will be considered as well. - Strong mathematical and problem solving abilities. - Expertise in programming, at least with high-level languages / packages. - An established publication track record. - Ideally, experience with one/some of the following: neuroimaging, deep learning, image registration. The position is available in summer 2020, and applications will be reviewed as they arrive. The duration of the contract is two years, with possibility of further extension. For applications, please send the following documents to jiglesiasgonzalez(a)mgh.harvard.edu: - A cover letter (maximum 1 page) - CV (maximum 4 pages) - List of publications Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com

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freeview command for displaying selected labels
by Schranzer René 03 Jun '20

03 Jun '20

External Email - Use Caution Hello FreeSurfer Developers, is there a way to display only selected labels from the aseg.mgz file using the freeview command line (with FreeSurfer V. 7.1). I know that it is possible to manually turn individual labels on and off in the 2D slice view, but I haven't found a command to do so. Is there a way or workaround? Thanks, René

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Freesurfer June 2020