Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30130 discussions

Inter-rater reliability
by Taylor, Lisa 10 Jan '24

10 Jan '24

External Email - Use Caution Hi there, Has anyone in this community used a form of inter-rater reliability measure for multiple people editing for one project? I have some PIs who are interested in doing this for a project where several labs will be editing Freesurfer for a project. I am a bit stumped as I have always just used visual review to ensure reliability/validity between editors. Also, would a inter-rater reliability measure be more effective than visual reviewing? Thank you for any insight you can provide! Lisa

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Re: [Freesurfer] Freeview keeps aborting.
by fsbuild 10 Jan '24

10 Jan '24

External Email - Use Caution  I would check with your IT support staff about the error including asking if the machines in your cluster are setup to display X Windows sessions with image viewing applications like Freeview.   If the machines support remote graphics, they should be able to tell you what you need to set in your terminal session for it to work.   But it could be they expect programs like freeview to run on your local client machine and read the image files/data over the network via NFS, etc. - R. On Jan 9, 2024, at 18:52, Dong, Yilei <yid025(a)health.ucsd.edu> wrote:        External Email - Use Caution        Dear freesurfer help, I have freesurfer installed on UCSD's Expanse HPC, which is on the Rocky Linux 8 operating system. Every time I try to open freeview, it always keeps aborting. How should I fix this so that freeview's GUI can be shown? I have included the screenshot for reference on the error. Thank you. Sincerely,Yilei <Screen Shot 2024-01-09 at 3.47.14 PM.png>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh..harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freeview keeps aborting.
by Dong, Yilei 09 Jan '24

09 Jan '24

External Email - Use Caution Dear freesurfer help, I have freesurfer installed on UCSD's Expanse HPC, which is on the Rocky Linux 8 operating system. Every time I try to open freeview, it always keeps aborting. How should I fix this so that freeview's GUI can be shown? I have included the screenshot for reference on the error. Thank you. Sincerely, Yilei

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Scratch Directory Permissions Denied
by Michael Ruvalcaba 09 Jan '24

09 Jan '24

External Email - Use Caution Hello, I am trying to run the recon -all function in my MATLAB pipeline using Freesurfer 6.0.0 and I have no issues with it. However, when I run the recon -all step using Freesurfer 7.2.0 and run the following command (the recon -all step finishes without error by the way): ft_read_mri([subdir '3D_Images/freesurfer_pre-op/freesurfer/mri/T1.mgz']); I get the following error: /bin/bash: /scratch/tp746feb5d_1e83_4141_b25d_1824a1cb209e.load_mgh.m.mgh: Permission denied The issue is there is no scratch file and it looks like between version 6.0.0 and 7.2.0 there is some extra lines of code that uses a scratch directory (which 6.0.0 doesn't) Does anyone have any input on this? I hope this made sense! Best, Michael Ruvalcaba

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[WARNING: ATTACHMENT UNSCANNED]FreeSurfer Error
by ERNEST KISSI 09 Jan '24

09 Jan '24

External Email - Use Caution Dear Freesurfer Developers, I am a graduate student working on Macromolecular Proton Fraction (MPF) and I need to generate parcellation for it using Freesurfer. I have read several articles that reported successful results with this method. However, I have encountered some errors when I tried to run Freesurfer on my data. Some of the errors are related to transformation at the talairach, and some are related to missing brain mask. I have been struggling with these issues for four days and I have not been able to process any of my data. I have an urgent deadline for my thesis presentation on Friday and I would appreciate your assistance. I have subscribed to the mailing list but I have not received a confirmation email yet. I have attached a screenshot of my registration and two examples of my T1 MPF images. Could you please test them on your end and let me know what the problem is and how to fix it? Thank you for your time and support. Sincerely,

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recon-all vs. recon-all-clinical: missing ROIs
by Biondo, Francesca 09 Jan '24

09 Jan '24

External Email - Use Caution Hi, recon-all generates these volumes, amongst others: "Left-vessel", "Left-choroid-plexus", "Right-vessel", "Right-choroid-plexus" recon-all-clinical does not generate these volumes. Or at least that I am able to detect. Any ideas how to extract or calculate them? Regarding the choroid plexus, would it be correct to use this formula? Estimated choroid plexus volume (both left and right) = "VentricleChoroidVol" - "left lateral ventricle" - "right lateral ventricle" Thank you very much for your support - Francesca

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Re: [Freesurfer] Infant fs
by fsbuild 09 Jan '24

09 Jan '24

External Email - Use Caution  Looks like you need to fill out the request form, https://secure-web.cisco.com/1Zztv_hv2CHwkWkqDcQ75P0iZ5m3guJnkq6OOGA_AuaX-I… - R. On Jan 8, 2024, at 18:12, Amrita Pal <palamritaorama(a)gmail.com> wrote:        External Email - Use Caution        HelloI am trying to use the infant fs for processing my pediatric data. Where can I download the package?Thanks and Regards Amrita_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] conversion of D-K atlas
by Fischl, Bruce R.,PHD 09 Jan '24

09 Jan '24

Hi Anna Parcellation is more than just format conversion - you need to map it onto the details of an individual subject's anatomy. In addition, the DKT atlas is only cortical. If you want subcortical regions in addition you should run recon-all as it will produce both. Cheers Bruce From: Arkhipova Anna, MUDr. <Anna.Arkhipova(a)fnol.cz> Sent: Tuesday, January 9, 2024 6:14 AM To: Freesurfer(a)nmr.mgh.harvard.edu; fischl <fischl(a)nmr.mgh.harvard.edu> Cc: phlustik(a)upol.cz Subject: conversion of D-K atlas External Email - Use Caution Dear prof. Fischl, We would like to kindly ask a question, if there is a way to convert Fressurfer Atlas Desikan-Killiany (lh and rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs) to Nifti file for parcellation of our resting-state fMRI data. Although we have tried script mri_convert, we obtained only cortical regions, but we need also subcortical regions. Would it be anyhow possible? Thank you so much in advance. Sincerely yours, Anna Arkhipova, MD fMRI laboratory Department of Neurology, Faculty of Medicine and Dentistry Palacky University and University hospital Olomouc Czech Republic

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SynthSR for T2-weighted images
by hmarzban＠student.ubc.ca 09 Jan '24

09 Jan '24

External Email - Use Caution Hello Eugenio, I wanted to inquire whether you have plans to create a tool for synthesizing T2-weighted low-field MRI images similar to SynthSR, which was developed for T1-weighted images. I'm in need of synthesizing T2-weighted images for Hyperfine, and I'm curious if there is a suitable method available for this purpose. Because, as I understand it, SynthSR transforms T2-weighted images into T1-weighted ones, and it is not designed for handling T2-weighted images. Is my understanding correct? Regards Hengameh

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Subject does not have a bstampfile
by Joanna Kidoń 09 Jan '24

09 Jan '24

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to compute Segmentation of hippocampal subfields and nuclei of the amygdala (cross-sectional and longitudinal), as described on the https://secure-web.cisco.com/1thysYb_zO3z1vpgSTaPhhhrJHE6mFgjDwcJg3vFCVfZAw…, but I get the following error when I run the recon-all -all -s command: Subject does not have a bstampfile, copying /usr/local/freesurfer/7.3.2/build-stamp.txt Subject FS Version: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 No constraints on version because REQ=UnSet and FsVerFile=NotThere #@#% fs-check-version match = 1 fs-check-version Done INFO: SUBJECTS_DIR is /mnt/c/Users/GCM/Desktop/subjects Actual FREESURFER_HOME /usr/local/freesurfer/7.3.2 Linux LAP-LKP 5.15.133.1-microsoft-standard-WSL2 #1 SMP Thu Oct 5 21:02:42 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux #-------------------------------------------- #@# MotionCor Sun Jan 7 20:48:46 CET 2024 ERROR: no run data found in /mnt/c/Users/GCM/Desktop/subjects/NowakG/mri. Make sure to have a volume called 001.mgz in /mnt/c/Users/GCM/Desktop/subjects/NowakG/mri/orig. If you have a second run of data call it 002.mgz, etc. See also: http://secure-web.cisco.com/1YoN1A69KdRcMav_4NI9T7PYgKG5FAtbmkvQ7vxtAUykGwu… Linux LAP-LKP 5.15.133.1-microsoft-standard-WSL2 #1 SMP Thu Oct 5 21:02:42 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux recon-all -s NowakG exited with ERRORS at Sun Jan 7 20:48:46 CET 2024 I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the scripts/recon-all.log in case it's of any use. Best regards, Joanna -- ---------------------------------------------------------------------------------- dr n.med., specjalista fizyki medycznej, neurobiolog Przewodnicząca Sekcji Diagnostyki Obrazowej Polskiego Towarzystwa Fizyki Medycznej Zakład Kardiologii Inwazyjnej i Elektrokardiologii, III Katedra Kardiologii Śląski Uniwersytet Medyczny w Katowicach Kierownik Działu Fizyki Medycznej, Koordynator ds. Ochrony Radiologicznej Z-ca Kierownika Zakładu Diagnostyki Obrazowej Górnośląskie Centrum Medycznego im. prof. L. Gieca SUM w Katowicach PhD, specialist in medical physics, neurobiologist Chairwoman of the Diagnostic Imaging Section of the Polish Society of Medical Physics Department of Invasive Cardiology and Electrocardiology, 3rd Department of Cardiology, Medical University of Silesia in Katowice Head of the Medical Physics Department, Coordinator for Radiological Protection, Deputy Head of the Department of Diagnostic Imaging Leszek Giec Upper-Silesian Medical Centre of the Medical University of Silesia in Katowice

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