Freesurfer January 2024

freesurfer@nmr.mgh.harvard.edu

70 participants
111 discussions

Re: [Freesurfer] EasyReg question
by Èlia Pedregosa 22 Jan '24

22 Jan '24

External Email - Use Caution Thanks for your answer. We resolve the problem using another computer. In our project we perform MRI registration of different subjects to create a template. After that we use a segmentation of the template to get some parts of the brain. However the segmentation result has some problems due to: 1. poor registration that creates a template with artefacts. 2. the registration is fine, but we are not segmenting correctly. Do you think EasyReg is a good tool to do intersubject registration to segment afterwards? Thanks for your time. Best regards, Èlia Pedregosa Sandoval BIOREM_biomedical engineering Madrazo 68, bxs. 08006 BARCELONA Telf. 934 186 129 http://secure-web.cisco.com/1gQtA56pXeIhA3rGpVB0S3YxxEwqCyfzAZYcWHbQMsmdNFq…<http://secure-web.cisco.com/1poW64X4mxi-hsqO28iU-InDnGU--KgayklsjY39BL4hYRv…> [cid:2f424f3f-1f4e-4e8e-b674-f53b9a89bf7c]<http://secure-web.cisco.com/1poW64X4mxi-hsqO28iU-InDnGU--KgayklsjY39BL4hYRv…>[cid:5f0d10d4-e87a-4f82-a482-406856b8b5b9]<https://secure-web.cisco.com/1ph5sx1pVTRGKELOTQHj6UWuSTR001PMh8iuE9sYyoz8Em…> ________________________________ De: Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ(a)mgh.harvard.edu> Enviat el: divendres, 19 de gener de 2024 15:49 Per a: Èlia Pedregosa <eliapedregosa(a)biorem.cat> Tema: Re: EasyReg question Thanks for the interest in our work! It depends on the size of the images, but yeah it’s very memory hungry (a few dozen GBs) Cheers, /Eugenio -- Juan Eugenio Iglesias http://secure-web.cisco.com/1NZI7VBYYnBjWA-boNgos16_ad9rPYbyRvaQIw19pT1vV0c… From: Èlia Pedregosa <eliapedregosa(a)biorem.cat> Date: Friday, January 19, 2024 at 7:47 AM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Cc: Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ(a)mgh.harvard.edu> Subject: EasyReg question External Email - Use Caution Dear Juan Eugenio Iglesias, We are a biomedical engineering company (BIOREM) in Barcelona, and we are collaborating in a research and innovation project with the University of Barcelona. For this project we use EasyReg to do brain registrations. However, we have some problems with the necessary memory to run the program. In that sense, we ask you which computational requirements we need. If it is possible, could you provide us this information? Thanks, best regards. Èlia Pedregosa Sandoval BIOREM_biomedical engineering Madrazo 68, bxs. 08006 BARCELONA Telf. 934 186 129 http://secure-web.cisco.com/1gQtA56pXeIhA3rGpVB0S3YxxEwqCyfzAZYcWHbQMsmdNFq…<http://secure-web.cisco.com/1mKlCVTT8GFIj7hRcUnfvI5dXY9xqjHL4uFc1ixqYh8JELP…> [cid:2c4df705-8b32-4ee8-8018-7e8bb8586820]<http://secure-web.cisco.com/1mKlCVTT8GFIj7hRcUnfvI5dXY9xqjHL4uFc1ixqYh8JELP…>[cid:aa04d6f8-7841-41ff-853f-54f95dfc75b9]<https://secure-web.cisco.com/1bzv5HYJB4wHoi0afMXmVtUOkKVAlTyAOUkC6iJ_VsAh7q…> Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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Re: [Freesurfer] recon-all cannot execute: required file not found
by fsbuild 19 Jan '24

19 Jan '24

External Email - Use Caution I don’t see what FREESURFER _HOME is set to, but if you used the .deb package installer, it would be /usr/local/freesurfer/7.4.0, i.e. $ wget  https://secure-web.cisco.com/1vzo5wK6ItFFFMnllsCMKRTIzcqYXDSETeXibiyz78VEk_TVHkbVLtjlltPd0g0Uvd8x0WK89GE8gU1KWFMzKnfwwgiI7LxjmgavQJ6CRuDKNdbu69lRngmJXHI_jT7Apzbthify1jBVr0Rl4tHRLO59uiYFLhP5xVv4FxnW-1brLM5t_f80dYxYqxS-tDJmUcSQBJ26bUuIwdNXHT49QU9R4-QLIUjxabN7pBG7dNNvYjk6etULRIlRTmLlKSxZ11x1M0Be8QDGN-sL353J66YtQqcu9Ew-9KlI2nYNXikCfbW-0PZolvzHu35pUzJw_8zpHpyEpfdmLOKtTKWv0Iw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.0%2Ffreesurfer_ubuntu22-7.4.0_amd64.deb%24 sudo apt-get install ./freesurfer_ubuntu22-7.4.0_amd64.deb… answer yes to all queries ….,.. output deleted ... $ export FREESURFER_HOME=/usr/local/freesurfer/7.4.0$ source $FREESURFER_HOME/SetUpFreeSurfer.sh … output deleted … $ which recon-all /usr/local/freesurfer/7.4.0/bin/recon-all $ recon-all -version  freesurfer-linux-ubuntu22_x86_64-7.4.0-20230510-e558e6e If you used the tar file instead, then some permissions might not be correct depending upon how/where it was unarchived (and some dependencies might be missing). - R. On Jan 19, 2024, at 15:20, Peled, Noam,PhD <NPELED(a)mgh.harvard.edu> wrote:I'm just trying now to run the "recon-all -version", also without any arguments. Both produce the same error.Thanks!NoamFrom: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@mgh.harvard.edu>Sent: Friday, January 19, 2024 3:10 PMTo: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>Subject: Re: [Freesurfer] recon-all cannot execute: required file not found I’m wondering how you ran recon-all.  Do you see the error even running it w/o any arguments? From: freesurfer-bounces@nmr..mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> On Behalf Of Peled, Noam,PhDSent: Friday, January 19, 2024 2:59 PMTo: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>Subject: Re: [Freesurfer] recon-all cannot execute: required file not found Thanks Yujing,Yes, I looked for the file permissions using ls -l. It does have execute permissions.I also tried running chmod which didn't help.. Thanks,NoamFrom: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@mgh.harvard.edu>Sent: Friday, January 19, 2024 2:54 PMTo: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>Subject: Re: [Freesurfer] recon-all cannot execute: required file not found After sourcing Freesurfer, $FREESURFER_HOME is added to the front of your $PATH. 1. ‘ls -l $FREESURFER_HOME/bin/recon-all’ to check if your recon-all has the execute permissions?2. use ‘chmod +x $FREESURFER_HOME/bin/recon-all’ to grant the permission  Best, Yujing From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Peled, Noam,PhDSent: Friday, January 19, 2024 2:42 PMTo: freesurfer@nmr.mgh.harvard.eduSubject: [Freesurfer] recon-all cannot execute: required file not found Dear group,I'm trying to run Freesurfer on digitalOcean server running Ubuntu 22.10 (GNU/Linux 5.19.0-46-generic x86_64)I Downloaded freesurfer 7.4.0 (freesurfer-linux-ubuntu22_x86_64-7.4.0-20230510-e558e6e)After sourcing Freesurfer, recon-all gives following error:.../freesurfer/bin/recon-all: cannot execute: required file not found Other functions, e.g. freeview, mri_info, all seem to work as expected Would love some help.Thanks,Noam  _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Issue with mri_glmfit-sim
by Douglas N. Greve 19 Jan '24

19 Jan '24

Sorry, I already forgot what the problem was. Can you include our previous correspondence? Also, make sure to reply to the list. Thanks! On 1/19/2024 10:07 AM, O'Neill, Alexandra Grace wrote: > > Hi Doug, > > Thank you for getting back to me. Unfortunately, the issue is > persisting, and the command is still running but with no output files. > Is there anything else that could potentially be the problem? I’m > attaching the most recent log file (as a txt file) from the command I > ran. Please let me know if any other information would be helpful! > > Thank you so much, > > Alexandra >

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recon-all cannot execute: required file not found
by Peled, Noam,PhD 19 Jan '24

19 Jan '24

Dear group, I'm trying to run Freesurfer on digitalOcean server running Ubuntu 22.10 (GNU/Linux 5.19.0-46-generic x86_64) I Downloaded freesurfer 7.4.0 (freesurfer-linux-ubuntu22_x86_64-7.4.0-20230510-e558e6e) After sourcing Freesurfer, recon-all gives following error: .../freesurfer/bin/recon-all: cannot execute: required file not found Other functions, e.g. freeview, mri_info, all seem to work as expected Would love some help. Thanks, Noam

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Re: [Freesurfer] conversion of D-K atlas
by Fischl, Bruce R.,PHD 19 Jan '24

19 Jan '24

Maybe you can give us more details about what you are trying to do? Generate an fMRI time-series that is the average response in each cortical parcel? And subcortical structure? The subcortical segmentation is not Talairach, although I'm not sure that is relevant. Generating the average time series should be pretty straightforward if that is what you want (although Doug will know the commands better than I do) Cheers Bruce From: Arkhipova Anna, MUDr. <Anna.Arkhipova(a)fnol.cz> Sent: Friday, January 19, 2024 10:08 AM To: Fischl, Bruce R.,PHD <BFISCHL(a)mgh.harvard.edu>; Freesurfer(a)nmr.mgh.harvard.edu; fischl <fischl(a)nmr.mgh.harvard.edu> Cc: phlustik(a)upol.cz; Jasenská Monika, Ing. <Monika.Jasenska(a)fnol.cz> Subject: Re: conversion of D-K atlas External Email - Use Caution Hi Bruce, thank you a lot for your kind reply. Unfortunately, we've got further question, since we tried the following command: recon-all -sd $PWD/surf -all -i ./Mprage.nii.gz -s $PWD -parallel -openmp $num_cores and acquired a cortical-level parcellation according to the D-K atlas, but the subcortical parcellation was produced (we think) automatically according to the Talairach atlas (see attached). Actually, we would like to get time-series in 82 brain regions as per D-K atlas, which should generate a vector of size 82x1 according to the methodology of Poudel et al. J Neural Eng. 2021. However, as you wrote that D-K atlas is only cortical, would you think that it is possible at all (to get cortical + subcortial via D-K)? Or have we proceeded wrongly? We are sorry for repeatedly bothering you.. (We have tried to contact for the atlas both prof. Killiany and dr. Desikan, who sadly passed away, and also asked dr. Poudel himself, but he suggested a different atlas (we are not sure why) without subcortical regions.) Thank you very much again! Best regards, Anna and lab team ________________________________ From: Fischl, Bruce R.,PHD <BFISCHL(a)mgh.harvard.edu<mailto:BFISCHL@mgh.harvard.edu>> Sent: January 9, 2024 3:48:23 PM To: Arkhipova Anna, MUDr.; Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>; fischl Cc: phlustik(a)upol.cz<mailto:phlustik@upol.cz> Subject: RE: conversion of D-K atlas Upozornění: Tento e-mail přišel z externí e-mailové adresy. Dbejte zvýšené opatrnosti při otvírání příloh a odkazů v textu mailu, nezadávejte svoje přihlašovací údaje. 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<mailto:Anna.Arkhipova@fnol.cz>> Sent: Tuesday, January 9, 2024 6:14 AM To: Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>; fischl <fischl(a)nmr.mgh.harvard.edu<mailto:fischl@nmr.mgh.harvard.edu>> Cc: phlustik(a)upol.cz<mailto:phlustik@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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/complianceline<https://secure-web.cisco.com/1Jks6aGDbVRK45MXX_bng2dSYKT5jA6CUTif0iwWA4-fH6…> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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Applying Wang Atlas to Group Analysis Results in FreeSurfer
by Sujeevini Sujanthan 19 Jan '24

19 Jan '24

External Email - Use Caution Hi, I would like to apply the wang atlas over the group activation maps produced from Freesurfer analysis. I would appreciate any guidance/instructions you can offer for how I can do that. Thank you for your time!

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EasyReg question
by Èlia Pedregosa 19 Jan '24

19 Jan '24

External Email - Use Caution Dear Juan Eugenio Iglesias, We are a biomedical engineering company (BIOREM) in Barcelona, and we are collaborating in a research and innovation project with the University of Barcelona. For this project we use EasyReg to do brain registrations. However, we have some problems with the necessary memory to run the program. In that sense, we ask you which computational requirements we need. If it is possible, could you provide us this information? Thanks, best regards. Èlia Pedregosa Sandoval BIOREM_biomedical engineering Madrazo 68, bxs. 08006 BARCELONA Telf. 934 186 129 http://secure-web.cisco.com/1_MkzRbqyiH66KINd6uLPW_76jujv3qAzV1ApABqrJsjeA5…<http://secure-web.cisco.com/1hwvnraVglmADsDEbkSqMeXsjPrZJpioumEzOxIWUrmWh2G…> [cid:f6917007-7636-4b37-be0a-010ab3bd281d]<http://secure-web.cisco.com/1hwvnraVglmADsDEbkSqMeXsjPrZJpioumEzOxIWUrmWh2G…>[cid:c6b9a427-fbb1-4f20-986e-499840b7bfe5]<https://secure-web.cisco.com/1usD7oypvISKxz1aQD5yWVstXVJ4ILSB42PJyvh6B-AJ8H…>

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Issue with mri_brainvol_stats for only some participants
by Carly McIntyre-Wood 18 Jan '24

18 Jan '24

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Re: [Freesurfer] SUBJECTS_DIR writing permissions to run hippocampal/amygdala subfields
by Heese, E. van (Eva) 18 Jan '24

18 Jan '24

External Email - Use Caution Hi all, Thanks again for your help. We fixed the issue by adding user write permissions for the owner-user in the installation folder (note that the owner of the file in the installation folder is different from the users that we used for testing). : -rw-r--r--. 1 admin admin 366711 Sep 21 2017 /installationfolder/7.3.2-centos8_x86_64/average/HippoSF/atlas/AtlasDump.mgz The fix was necessary for the other AtlasDump.mgz files. Best, Eva ______________________________________________________ AmsterdamUMC disclaimer : http://secure-web.cisco.com/1wlx9tXYYUIMj_Rg1KZxU9HYTynqYvQ9dJZEYbomVrvzBlz…

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Ex-vivo adult brain MRI segmentation and surface analysis
by K Eswar 18 Jan '24

18 Jan '24

External Email - Use Caution Dear FS community I have an ex-vivo human adult brain MRI, both in T1 MPRAGE and Fiesta. I have recently come across a paper on MRI segmentation using a function called- samseg. From the webpage( https://secure-web.cisco.com/1AJdw_iZ93Ctl2bXUM-tS9sQoJ_9a6-0RHBNEGqz7c8Pz8…) I realized that there is a different approach altogether to processing these fixative brains. However, as a first step, when I tried the samseg function, I noticed that the function exited with errors. The steps where it fails are: Read mesh collection: /home/sgbc/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz Transforming points Transforming points Read mesh collection: /home/sgbc/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz Read mesh collection: /home/sgbc/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz Killed I am using the Ubuntu 22.04 version with RAM 32GB Freesurver version: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 I would greatly appreciate it if you could help me with MRI segmentation and cortical surface analysis on these brains. Thanks for your time and consideration. Regards K Eswar Project Scientist Sudha Gopalakrishnan Brain Centre IIT Madras, India

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Freesurfer January 2024