Freesurfer March 2022

freesurfer@nmr.mgh.harvard.edu

86 participants
124 discussions

Linear mixed model for longitudinal data
by Julian Macoveanu 14 Mar '22

14 Mar '22

External Email - Use Caution Dear Kersten, Thank you for your answer, I have some follow-up questions to the first two points before I can move on. 1) Regarding family-relation, since three random effects may not work, did you mean that a simpler model with 2 random effects (intercept and family ID, thus leaving out slope which I assume is time from baseline) would work? While forgetting family ID is an option, it would be a model that may attract criticism. 2) Regarding multiple comparison correction, I understand how to perform the procedure you suggested (second option) to simply calculate the corrected p threshold using pcor = -log10(pth) and then use pcor as threshold for the sig.mgh. However after running FDR2: [detvtx,sided_pval,pth] = lme_mass_FDR2(F_lhstats.pval,F_lhstats.sgn,lhcortex,0.05,0); While detvtx is not empty (a few vertexes survived) and the pth value is calculated to 1.00000e-30 and therefore pcor to 30. This doesn’t seem right. What is also strange is that I saw a few times a more reasonable pth in the range of e-5 using the exact same data and procedure. I cannot replicate this in the same analysis in R2021, now I only get the e-30 (I only tried left cortex thickness so far). Best, Julian

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recon-all outpputs for deep learning
by REEM ABU BAKR BAHATHIQ 13 Mar '22

13 Mar '22

External Email - Use Caution Hello Freesurfer experts I want to apply deep learning to structural brain images processed by Recon-all. My goal is to demonstrate the morphological variation(e.g., gray matter volumes or cortical thickness) of brain regions in structural magnetic resonance imaging using convolutional neural networks (CNN). Then interpret those models on the basis of the region of interest. But I'm still distracted by the model input . I searched before but still couldn't decide which Recon-all output I should use to perform the task. I think I'll use the folder(mri) but I'm not sure which file. can any one guide me . Thanks,

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Re: [Freesurfer] Ubuntu VM Developer Password request?
by fsbuild 12 Mar '22

12 Mar '22

External Email - Use Caution Sending the info to your email shortly. - R. On Mar 12, 2022, at 09:52, Dean, Owen <Owen_Dean(a)urmc.rochester.edu> wrote:        External Email - Use Caution        Dear the Freesurfer Team, I am writing to request the Ubuntu VM Developer password for the Freesurfer version? Thank you!Sincerely, OwenOwen DeanUniversity of Rochester School of Medicine and Dentistryhe, him, his_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Ubuntu VM Developer Password request?
by Dean, Owen 12 Mar '22

12 Mar '22

External Email - Use Caution Dear the Freesurfer Team, I am writing to request the Ubuntu VM Developer password for the Freesurfer version? Thank you! Sincerely, Owen Owen Dean University of Rochester School of Medicine and Dentistry he, him, his

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Research Assistant Position Available at the Ohio State University Department of Psychology (MINDSET Lab)
by Shell, Abby 11 Mar '22

11 Mar '22

External Email - Use Caution Research Assistant Position Available at the Ohio State University Department of Psychology. Looking for someone with prior experience in MRI. Familiar with structural preprocessing and/or other modalities. Comfortable with coding. More details below and at the following link: https://secure-web.cisco.com/1Ew4JKXvwVU2ux2rMVVo8xQZAYM4_HBG8Cs5i1y-L-yuc_… The MINDSET lab Department of Psychology, within the College of Arts and Sciences, seeks a Research Assistant 1-Social to join our team. The College of Arts and Sciences is the largest college and the academic heart of the university. The College hosts 81 majors. With 38 departments, 20+ world-class research centers, and more than 2,000 faculty and staff members, students have the unique opportunity to study with the best artists, scholars, and scientists in their field. The College values diversity and offers a supportive, open, and inclusive community. The MINDSET lab is directed by Dr. Jasmeet Hayes. The MINDSET lab studies relationships among physical and psychological trauma, cognition and the brain [using Magnetic Resonance Imaging (MRI) metrics]. We also examine neural correlates of memory in healthy and clinical populations. The Research Assistant 1 assists in the general coordination and conduct of research in the MINDSET lab, including administration of neuropsychological tests and/or questionnaires to young and older adults; recruits, screens, and schedules human subjects, including coordination of subject appointments (cognitive, MRI, and physical fitness assessments), subject payments, and submission of IRB amendments; assists with participant recruitment efforts between the laboratory and community partners; assists with research lab purchases and maintains lab supplies; assists with cognitive, MRI, and medical history data collection, including obtaining informed consent, cognitive testing (computer and paper and pencil based testing), MRI data acquisition, and record keeping; assists with cognitive and MRI data processing and analyses, including analyses of behavioral data and MRI data using openly available software like FSL, AFNI, or SPM and/or UNIX or MATLAB; supervises undergraduate research assistants. Position available for one year with the possibility of extension for additional years based on satisfactory performance and availability of funds. Required Education Bachelor's degree in psychology or related field or an equivalent combination of education and experience. [The Ohio State University] Abby Shell Research Assistant The MINDSET Lab Department of Psychology 1835 Neil Avenue, Columbus, OH 43210 6149497868 Office shell.73(a)buckeyemail.osu.edu<mailto:shell.73@osu.edu> / osu.edu<http://secure-web.cisco.com/17n3otLadud0JP4E4Ze6BBYSds4smQaxEvWETdy8i1BIt6g…> Pronouns: she/her/hers

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Re: [Freesurfer] SAMSEG Lesion images not written
by Cerri, Stefano 11 Mar '22

11 Mar '22

Hi Randy, "seg.mgz" is the "hard segmentation", with lesion labeled as 99. You have all the volumes in "samseg.stats". If you want segmentation maps (values between 0 and 1), you should add the flag --save-posteriors to run_samseg. They will be saved in the samseg output directory under the "posteriors" folder. You can get a lesion segmentation mask by binarizing the lesion probability map with mri_binarize. Best, Stefano Dear experts I was able to get SAMSEG --lesion to work on WSL (did not crash once I used float images instead of 16bit usign), but all that's being written out are listed below: Folder: D:\0007_Subjects-FS\T1T2-lesion-float\ Files: cost.txt gaussians.rescaled.txt mode01_bias_corrected.mgz mode01_bias_field.mgz mode01_scaling.txt mode02_bias_corrected.mgz mode02_bias_field.mgz mode02_scaling.txt samseg.stats samseg.talairach.lta sbtiv.stats seg.mgz template.lta template_coregistered.mgz template_transforms.mat Since this is the first time got --lesion to run, I have no idea what the output "should" be.? Shouldn't some sort "lesion mask" be written out? Thanks in advance for any insights/comments you might have -Randy XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX SNIPPET FROM THE END OF THE "SUCCESSFUL" SAMSEG --lesion run XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX run_samseg -o $SUBJECTS_DIR/T1T2-lesion-float -i o_ADNI_002_S_4654__MRI-m072_float.nii rT1_o_ADNI_002_S_4654__MRI-m072_FLAIR_float.nii --pallidum-separate --lesion --lesion-mask-pattern 0 1 --threshold 0.7 .................................... .................................... Sample 44 times Sample 45 times Sample 46 times Sample 47 times Sample 48 times Sample 49 times Sample 50 times thresholding posterior of? Lesions with threshold: 0.7 Constructing image-to-world transform from header information (o_ADNI_002_S_4654__MRI-m072_float.nii) Read image: o_ADNI_002_S_4654__MRI-m072_float.nii using default intracranial structures to compute sbtiv measure run_samseg complete: 0:34:36.159030 daedalus@DESKTOP-TILLA3B:/usr/local/freesurfer/7-dev/subjects$ .................................... YAY! .................................... XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

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SAMSEG Lesion images not written
by daedalus39＠aol.com 10 Mar '22

10 Mar '22

External Email - Use Caution Dear experts I was able to get SAMSEG --lesion to work on WSL (did not crash once I used float images instead of 16bit usign), but all that's being written out are listed below: Folder: D:\0007_Subjects-FS\T1T2-lesion-float\ Files: cost.txt gaussians.rescaled.txt mode01_bias_corrected.mgz mode01_bias_field.mgz mode01_scaling.txt mode02_bias_corrected.mgz mode02_bias_field.mgz mode02_scaling.txt samseg.stats samseg.talairach.lta sbtiv.stats seg.mgz template.lta template_coregistered.mgz template_transforms.mat Since this is the first time got --lesion to run, I have no idea what the output "should" be. Shouldn't some sort "lesion mask" be written out? Thanks in advance for any insights/comments you might have -Randy XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX SNIPPET FROM THE END OF THE "SUCCESSFUL" SAMSEG --lesion run XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX run_samseg -o $SUBJECTS_DIR/T1T2-lesion-float -i o_ADNI_002_S_4654__MRI-m072_float.nii rT1_o_ADNI_002_S_4654__MRI-m072_FLAIR_float.nii --pallidum-separate --lesion --lesion-mask-pattern 0 1 --threshold 0.7 .................................... .................................... Sample 44 times Sample 45 times Sample 46 times Sample 47 times Sample 48 times Sample 49 times Sample 50 times thresholding posterior of Lesions with threshold: 0.7 Constructing image-to-world transform from header information (o_ADNI_002_S_4654__MRI-m072_float.nii) Read image: o_ADNI_002_S_4654__MRI-m072_float.nii using default intracranial structures to compute sbtiv measure run_samseg complete: 0:34:36.159030 daedalus@DESKTOP-TILLA3B:/usr/local/freesurfer/7-dev/subjects$ .................................... YAY! .................................... XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

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SAMSEG Lesion images not written
by daedalus39＠aol.com 10 Mar '22

10 Mar '22

1 0

Re: [Freesurfer] MACBOOK PRO M1 Monterey
by fsbuild 10 Mar '22

10 Mar '22

External Email - Use Caution Hello Zaenab, The package you highlighted, freesurfer-darwin-macOS-dev.pkg, is the one to install on the Mac to use the development build with the latest updates.  If you’ve run other Mac package installers, then the steps should be familiar to you when you install it.  I think you could also run the more stable 7.2.0 Freesurfer (with an installer named freesurfer-darwin-7.2.0-dev.pkg) if you are not using a 2nd monitor to display graphics with an M1 machine running MacOS Monterey. - R. On Mar 10, 2022, at 15:58, Dhari, Zaenab S <zaenab.dhari(a)gmail.com> wrote:       External Email - Use Caution        Hello,For downloading the development version of FS which package of theones available you recommend (attached screen shot), Since the newcomputer I have is Macbook Pro M1 Monterey ( brand new with no otherOS installed other than its built in MacOS), I am not sure howcompatible it with these Linux/Centos OS. I just have been readingpeople posts on random tech websites and it seems a bit tricky, anysuggestions will be much appreciated.Thanks<screen shot of versions.PNG>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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MACBOOK PRO M1 Monterey
by Dhari, Zaenab S 10 Mar '22

10 Mar '22

External Email - Use Caution Hello, For downloading the development version of FS which package of the ones available you recommend (attached screen shot), Since the new computer I have is Macbook Pro M1 Monterey ( brand new with no other OS installed other than its built in MacOS), I am not sure how compatible it with these Linux/Centos OS. I just have been reading people posts on random tech websites and it seems a bit tricky, any suggestions will be much appreciated. Thanks

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Freesurfer March 2022