Freesurfer March 2024

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by 이예린/융합의과학과 08 Mar '24

08 Mar '24

External Email - Use Caution Hi, I would like to be deleted from the mailing list. Thanks

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ascii: bad interpreter: No such file or directory
by Kavanaugh, Brian 07 Mar '24

07 Mar '24

External Email - Use Caution Hello everyone, I am new to freesurfer so I apologize if this is a simple answer. i'm running mris_ca_label to get the BN atlas parcellation: mris_ca_label -1 /users/bkavanau/data/bkavanau/temp/derivatives/fmriprep/sourcedata/freesurfer/sub-004/label/lh.cortex.label 001 lh /users/bkavanau/data/bkavanau/temp/derivatives/fmriprep/sourcedata/freesurfer/sub-004/surf/lh.sphere.reg /users/bkavanau/data/bkavanau/temp/derivatives/fmriprep/sourcedata/freesurfer/lh.BN_Atlas.gcs /users/bkavanau/data/bkavanau/temp/derivatives/fmriprep/sourcedata/freesurfer/sub-004/label/lh.BN_Atlas.annot But it seems freesurfer is having an issue reading my lh.cortex.label file: /users/bkavanau/data/bkavanau/temp/derivatives/fmriprep/sourcedata/freesurfer/sub-004/label/lh.cortex.label: ascii: bad interpreter: No such file or directory Might anyone have thoughts on how to resolve? I've seen adjacent errors before, but none related to ascii specifically. thank you! brian Brian Kavanaugh, PsyD, ABPP Board Certified Pediatric Neuropsychologist, E. P. Bradley Hospital Assistant Professor, Warren Alpert Medical School of Brown University

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Cortical parcellation showing dots
by Hyunchul Lee 07 Mar '24

07 Mar '24

External Email - Use Caution Hello, I'm using Freesurfer recon-all to create reconstructions to use with MNE-python for source estimation of SEEG data. My work relies on having correct labeling of segmentation data. For most cases, there has been no trouble but I am having trouble where the cortical parcellation shows up as dots in one hemisphere. Please see image attached. I also noticed that the lh.ribbon.mgz is also 'dotty' (also attached). There is no issue with the right hemisphere. This reconstruction was not manually edited, but only recon-all was used. I have tried using mris_volmask --label_left_ribbon, setting the argument to various values. That didn't work that great - reducing to 0 basically whites everything out except for the white matter on the ipsilateral hemisphere and anything 1 or more produces the same 'dots'. Interestingly the pial and wm surfaces all look ok. Also, I am not sure if creating the correct ribbon.mgz is going to fix the aparc.a2009+aseg file. I would really appreciate your advice. Best regards, *Hyunchul Lee* MBBS PhD

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xhemi
by Joost Janssen 06 Mar '24

06 Mar '24

External Email - Use Caution Dear Doug, The objective is to have _regional_ laterality index for thickness for aparc mapped to the left hemisphere. The following commands work without error but are they correct for meeting my objective? Thanks. surfreg --s $subject --t fsaverage_sym --lh --no-annot surfreg --s $subject --t fsaverage_sym --lh --no-annot --xhemi mri_convert $subject/surf/lh.thickness $subject/surf/lh.thickness.mgh mri_convert $subject/surf/rh.thickness $subject/surf/rh.thickness.mgh mris_apply_reg --src $subject/surf/lh.thickness.mgh --trg $subject/surf/lh.thickness.lh.fsaverage_sym.mgh --streg $subject/surf/lh.fsaverage_sym.sphere.reg fsaverage_sym/surf/lh.sphere.reg mris_apply_reg --src $subject/surf/rh.thickness.mgh --trg $subject/surf/rh.thickness.lh.fsaverage_sym.mgh --streg $subject/xhemi/surf/lh.fsaverage_sym.sphere.reg fsaverage_sym/surf/lh.sphere.reg fscalc $subject/surf/lh.thickness.lh.fsaverage_sym.mgh pctdiff0 $subject/surf/rh.thickness.lh.fsaverage_sym.mgh div 200 -o $subject/surf/li.thickness.lh.fsaverage_sym.mgh mri_segstats --annot fsaverage lh aparc --i $subject/surf/li.thickness.lh.fsaverage_sym.mgh --sum $subject/stats/li.thickness.aparc.stats -joost

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Hi
by Farzaneh, Hana 06 Mar '24

06 Mar '24

Hfarzaneh(a)mgh.harvard.edu Get Outlook for iOS<https://aka.ms/o0ukef>

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Spring 2024 FreeSurfer course
by Sennott, Liam Ricker 06 Mar '24

06 Mar '24

Hello all, The next virtual FreeSurfer course will be held on April 29th, 30th, and May 1st. Registration for this virtual FreeSurfer course is opening on Monday, March 11th at 12pm Eastern Daylight Time. Visit our course website to find out more information: https://surfer.nmr.mgh.harvard.edu/fswiki/VirtualCourse Specific questions about the course can be sent to fscourse(a)mgb.org<mailto:fscourse@mgb.org>

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remote access to freesurfer installation...
by Gonzalo Rojas Costa 06 Mar '24

06 Mar '24

External Email - Use Caution Hi: Is there a freesurfer facility where an MRI study can be processed remotely? Sincerely, Gonzalo Rojas Costa

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Unexpected skull shape after wraped to MNI
by GOFFINET Sara 06 Mar '24

06 Mar '24

External Email - Use Caution Hello, I ran freesurfer recon_all on a T1 MRI sequence (you can find the orig T1 in Screenshtot1) and my participant's brain warped to MNI (worig.nii) looks deformed (Screenshot2). Do you know why is there a bump (the worig file does not overlay well on MNI) while the reconstruction of the pial surface (lh.pial, rh.pial) shows no abnormality? Thanks in advance, Sara Goffinet

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TRACULA GLM output question
by Hoskinson, Kristen 05 Mar '24

05 Mar '24

External Email - Use Caution We’re working on a project where we ran 3 groups, 1 covariate, and ran a glm looking at white matter at cross-sections from TRACULA output, covarying for functional activation. We’re now wanting to plot out the interaction/slopes per group, but are having trouble locating the data that would allow that step. Could anyone direct us? Thank you! -- Kristen R. Hoskinson, Ph.D. (she/her) Associate Professor of Pediatrics The Ohio State University College of Medicine Principal Investigator, Social Cognition, Adjustment, and Neurodevelopment (SCAN) Lab Center for Biobehavioral Health The Abigail Wexner Research Institute at Nationwide Children's Hospital 700 Children's Drive Columbus, Ohio 43205 (614) 722-3021 kristen.hoskinson(a)nationwidechildrens.org<mailto:kristen.robinson@nationwidechildrens.org>

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Citing the bert dataset
by Shounak Nandi 05 Mar '24

05 Mar '24

External Email - Use Caution Hi, I have used the bert<https://secure-web.cisco.com/1iRXfF4vATaFfKjWoBFscMdP724sTiLA-ialN9LArN1Wnu…> <https://secure-web.cisco.com/1iRXfF4vATaFfKjWoBFscMdP724sTiLA-ialN9LArN1Wnu…> dataset in one of the scientific works and was curious how I cite it? I am eager to know your thoughts. Thanks, Shounak Nandi Radiology Trainee, Department of Radiology and Radiological Science, Division of Cancer Imaging Research, Johns Hopkins School of Medicine, Baltimore, MD

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Freesurfer March 2024