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30060 discussions

converting preprecessed functional surface data to gifti
by wangzhiwei3233 26 Jan '24

26 Jan '24

External Email - Use Caution Dear Freesurfer experts, How can I convert the preprecessed functional surface data to gifti format(gii)? I tried mris_convert, but I encountered the following error. error: freadFloat: fread failed Your assistance would be highly appreciated. Best regards, zhiwei ----------------------------------------------- Zhiwei Wang（王志伟), Associate Investigator International Center for Primate Brain Research Center for Excellence in Brain and Intelligence Technology Institute of Neuroscience,Chinese Academy of Sciences Room 215, Building #5, 500 Qiangye Road, Shanghai, 201602,China

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recon-all ends prematurely without error
by Weisholtz, Daniel S.,MD 25 Jan '24

25 Jan '24

Hello FreeSurfer team, I have been using FreeSurfer for some time without difficulty, but I recently encountered a problem that I cannot overcome. When I run recon-all using a command like this: recon-all -s b047test -i /Users/danielweisholtz/Coregistration/raw/b047/b047_MRI_PreAx3DT1MPRAGE_July2022.nii.gz the process terminates in just a few seconds without error. The output reads as follows: fs-check-version --s b047test --o /var/folders/44/ndjzqbx515991v_9vt0j8spr0000gq/T//tmp.IMS2K1 Thu Jan 25 12:35:02 EST 2024 setenv SUBJECTS_DIR /Users/danielweisholtz/Coregistration/subjects cd /Users/danielweisholtz /Applications/freesurfer/7.4.1/bin/fs-check-version --s b047test --o /var/folders/44/ndjzqbx515991v_9vt0j8spr0000gq/T//tmp.IMS2K1 -rwxr-xr-x 1 root wheel 18565 Jun 14 2023 /Applications/freesurfer/7.4.1/bin/fs-check-version freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 $Id$ Darwin i.partners.org<http://i.partners.org> 21.6.0 Darwin Kernel Version 21.6.0: Mon Aug 22 20:19:52 PDT 2022; root:xnu-8020.140.49~2/RELEASE_ARM64_T6000 arm64 pid 6977 Current FS Version freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 Subject does not have a bstampfile, copying /Applications/freesurfer/7.4.1/build-stamp.txt Subject FS Version: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 No constraints on version because REQ=UnSet and FsVerFile=NotThere #@#% fs-check-version match = 1 fs-check-version Done INFO: SUBJECTS_DIR is /Users/danielweisholtz/Coregistration/subjects Actual FREESURFER_HOME /Applications/freesurfer/7.4.1 Darwin i.partners.org<http://i.partners.org> 21.6.0 Darwin Kernel Version 21.6.0: Mon Aug 22 20:19:52 PDT 2022; root:xnu-8020.140.49~2/RELEASE_ARM64_T6000 arm64 /Users/danielweisholtz/Coregistration/subjects/b047test \n mri_convert /Users/danielweisholtz/Coregistration/raw/b047/b047_MRI_PreAx3DT1MPRAGE_July2022.nii.gz /Users/danielweisholtz/Coregistration/subjects/b047test/mri/orig/001.mgz \n mri_convert /Users/danielweisholtz/Coregistration/raw/b047/b047_MRI_PreAx3DT1MPRAGE_July2022.nii.gz /Users/danielweisholtz/Coregistration/subjects/b047test/mri/orig/001.mgz INFO: using NIfTI-1 qform reading from /Users/danielweisholtz/Coregistration/raw/b047/b047_MRI_PreAx3DT1MPRAGE_July2022.nii.gz... INFO: This is an unsigined short. TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, -1, 0) k_ras = (0, 0, 1) writing to /Users/danielweisholtz/Coregistration/subjects/b047test/mri/orig/001.mgz... ~/Coregistration/subjects/b047test/mri/transforms ~/Coregistration/subjects/b047test ~/Coregistration/subjects/b047test Started at Thu Jan 25 12:35:02 EST 2024 Ended at Thu Jan 25 12:35:06 EST 2024 #@#%# recon-all-run-time-hours 0.001 recon-all -s b047test finished without error at Thu Jan 25 12:35:06 EST 2024 done The subject folder is created along with some of the files, but not much is actually there. I had been using FreeSurfer 7.2.0 but I upgraded to 7.4.1, and this did not resolve the problem. Initially, I thought the problem was with the source file I was using, but I tested it with an MRI that I had previously used successfully with recon-all, and I got the same error. So something seems to have changed with my system that is causing this problem. I am running FreeSurfer on a Mac using MacOS 12.6. Many thanks for any assistance you can provide. Sincerely, Dan Weisholtz

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Intensity Representation
by ERNEST KISSI 25 Jan '24

25 Jan '24

External Email - Use Caution Dear Freesurfer Team, I registered a Macromolecular Proton Fraction (MPF) map on T1 image using multimodal registration in FSL and used freesurfer for the parcellation as instructed by one of your colleagues. I want to really confirm that whether the intensity is from the MPF as the T1 just provides the anatomical information and the MPF has the information for the myelination. Upon, a discussion with a colleague. He said that when MPF images are registered on T1 images, the intensity represents the MPF values, not the T1 values. This is because the registration process only transforms the spatial coordinates of the MPF images to match the T1 images, but does not alter the signal intensity or contrast of the MPF images. Therefore, the registered MPF images still reflect the macromolecular proton fraction of the brain tissue. Testing it in fsl, the intensity reflects that of the MPF. And a similar process has been found in a article but in their case they used mri_vol2vol. I want to confirm this since I used your software for the analysis. Thank you for your time.

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Extra Large Defect T1
by Flemister, Abeoseh B. 25 Jan '24

25 Jan '24

External Email - Use Caution Hi Freesurfer team, I have gotten this error message on a successful run before: An extra large defect has been detected... This often happens because cerebellum or dura has not been removed from wm.mgz. This may cause recon-all to run very slowly or crash. if so, see https://secure-web.cisco.com/1kY22AwBCARfSQUY7cjfeplC3gw9EQSf1L_ErLh8Y6XncM… Try following those instructions while running recon-all on a T1.nii.gz structural scan. I read the link and it seems I have to use the wm.mgz file I get from the freesurfer run, but I was wondering if there is any preprocessing I can do to the T1 scan to prevent it? Thanks, Abeoseh Flemister

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File extension .area failures
by James Bartolotti 23 Jan '24

23 Jan '24

External Email - Use Caution The MR data on network drives at our institute were recently migrated to a new server. After the migration, recon-all in freesurfer fails to complete. The issue is that freesurfer generates files with the extension ".area", including lh.area and rh.area, but the .area extension is forbidden on the server and the files will not be created. Has anyone ever had issues with an .area extension? Are there any possible workarounds to change the .area extension used by freesurfer? James Bartolotti, Ph.D. (he/him/his) Senior Scientist Structure and Function Unit, Hoglund Biomedical Imaging Center University of Kansas Medical Center jbartolotti2(a)kumc.edu<mailto:jbartolotti@ku.edu>

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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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