Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30055 discussions

Newbie: loading DICOM...
by Bram de Jong 15 Sep '25

15 Sep '25

External Email - Use Caution Hi all, Absolute newbie alert... End goal: 3D printing the brain of my son! After reading through the tutorial, I got stuck. I have a DICOM file, which I looked at with dcmunpack: ❯ dcmunpack -src . -scanonly scan.log if: Empty if. then: Command not found. cd /Users/bram.dejong/Downloads/flux-mri /Applications/freesurfer/8.1.0/bin/dcmunpack -src . -scanonly scan.log -rwxr-xr-x 1 root wheel 50442 Jul 19 01:21 /Applications/freesurfer/8.1.0/bin/dcmunpack --------------------------------------- --------------------------------------- Searching for matching files Thu Sep 11 17:23:02 CEST 2025 Found 1511 total files. Interrogating each and every one of them. Be patient. mri_probedicom --dcm2niix-dicom-dump /Users/bram.dejong/Downloads/flux-mri/. ./log/scan.log Found 1505 DICOM file(s) Found 20 unique series: 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 DICOM Pre-process Summary: 5 t1_vibe_fl3d_sag_0.9mm 0 000009 6 t1_vibe_fl3d_sag_0.9mm_MPR_Tra 0 000171 7 t1_vibe_fl3d_sag_0.9mm_MPR_Cor 0 000331 8 t2_tse_tra_3mm_fss_DRBS 0 001467 9 t2-flair_tir_tra_3mm_DRBS 0 000511 10 dwi-resolve_3scan_trace_tra_p2_160_TRACEW 0 000587 11 dwi-resolve_3scan_trace_tra_p2_160_ADC 0 000549 12 tof_fl3d_tra_CS4 0 000625 13 tof_fl3d_tra_CS4_MIP_SAG 0 001466 14 tof_fl3d_tra_CS4_MIP_COR 0 001426 15 tof_fl3d_tra_CS4_MIP_TRA 0 001427 16 tof_fl3d_tra_CS4_MIP_Radials 0 000761 17 tof_fl3d_tra_CS4 0 000773 18 tof_fl3d_tra_CS4_MIP_SAG 0 001425 19 tof_fl3d_tra_CS4_MIP_COR 0 001069 20 tof_fl3d_tra_CS4_MIP_TRA 0 001424 21 tof_fl3d_tra_CS4_MIP_Radials 0 001412 22 t1_vibe_fl3d_sag_0.9mm+gd 0 001070 23 t1_vibe_fl3d_sag_0.9mm_MPR_Tra 0 000909 24 t1_vibe_fl3d_sag_0.9mm_MPR_Cor 0 001232 Started at Thu Sep 11 17:23:02 CEST 2025 Thu Sep 11 17:23:06 CEST 2025 dcmunpack done I figured out I need to use load series 5, t1_vibe_fl3d_sag_0.9mm into Freesurfer. Looking at the log: ❯ cat log/5-dicomflst.txt /Users/bram.dejong/Downloads/mri/./DICOM/000009 /Users/bram.dejong/Downloads/mri/./DICOM/000010 /Users/bram.dejong/Downloads/mri/./DICOM/000011 /Users/bram.dejong/Downloads/mri/./DICOM/000012 [SNIP] /Users/bram.dejong/Downloads/mri/./DICOM/000170 How do I now direct Freesurf to only pick only series 5 rather than all files in the DICOM? Greetings, Bram

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Re: [+externe Mail+] Re: Recon-all error: synthtrip on Apple M3 Sonoma 14.6.1
by fsbuild 15 Sep '25

15 Sep '25

External Email - Use Caution If you edit the file $FREESURFER_HOME/FreeSurferEnv.csh such that line 183 does not contain the semicolon between the “if” and “then” in your MacOS freesurfer installation, that should eliminate the error you listed before the job was killed.   So you could try running your recon-all again on MacOS (and do not run anything else on the machine during recon-all, e.g., browsers, videos or anything that would consume additional memory). - R.

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Re: [+externe Mail+] Re: Recon-all error: synthtrip on Apple M3 Sonoma 14.6.1
by fsbuild 13 Sep '25

13 Sep '25

External Email - Use Caution  The freesurfer distribution is not currently tested on or supported for Ubuntu 24.  There is however a .deb installer file for Ubuntu 22.https://secure-web.cisco.com/1oNullxLzc9liUdhfga5GqW1fLnd8376FUzplKtAZeU… are instructions about how to create a generic Ubuntu 22 VM, after which you can run the above installerhttps://drive.google.com/file/d/1uNwv29fCeuMHrmTyXw94ZSuroNsPOxu-/… - R.

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Leave
by Andrade Rey René 13 Sep '25

13 Sep '25

External Email - Use Caution Sent from my iPhone

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Re: [+externe Mail+] Re: Recon-all error: synthtrip on Apple M3 Sonoma 14.6.1
by fsbuild 13 Sep '25

13 Sep '25

External Email - Use Caution  Apart from the output about the if statement, it looks like your recon-all command did run and then was killed because mri_synthstrip used too many system resources.   That is unless the command took no time to run and immediately exited.     If the command exited immediately after you entered it on the terminal, then the output about the if statement could indicate there is something not right with your recon-all arguments. Check you can run mri_synthstrip command directly.  A command with actual arguments and processing to do would be a better test, but at least try, $ mri_synthstrip -h You could try reverting recon-all to the old behavior where it will not run the newer mri_* commands as part pf the recon-all pipeline by setting the environment variable FS_V8_XOPTS=0.    That should reduce the chances the system will kill the process because of heavy resource usage. $ export FS_V8_XOPTS=0 && recon-all -s NVR-1 -sd /Volumes/INTENSO/Projects/NeuroVR+/MRI/recon/NVR-1_recon -i /Volumes/INTENSO/Projects/NeuroVR+/MRI/Nifti/NVR-1_nii/5_t1_tfl3d_sag_ti1090_fa9_tr2700_09mm_p2.nii.gz -T2 /Volumes/INTENSO/Projects/NeuroVR+/MRI/Nifti/NVR-1_nii/6_t2_space_sag_081x081x09mm_p2.nii.gz -T2pial -all - R. On Sep 9, 2025, at 08:47, Diedrich, Lukas <lukas.diedrich(a)med.uni-goettingen.de> wrote:        External Email - Use Caution        Thank you for this suggestion. However, changing the shell from zsh to bash did not help as I get the same error.Any other idea? Best wishes and thanks for your helpLukas Dr. rer. nat. Lukas DiedrichPostdoctoral researcherNon-invasive Brain Stimulation (NBS) LabDepartment of NeurologyUniversity Medical Center Göttingen, Germany +49 551 39 64838 | lukas.diedrich(a)med.uni-goettingen.de <NBS_Logo_klein.png> Am 05.09.2025 um 22:35 schrieb fsbuild <fsbuild@contbay.com>:        External Email - Use Caution         If you have not already done so, please try running your commands in the bash shell as shown in the page referenced via the below link (scroll down to MACOS).  So far I've seen no issues running various recon-all tests with 8.0.0 and 8.1.0 on a MacMini running Sequoia 15.5 with an M2 processor and 32GB of RAM using the setups listed on that page.https://secure-web.cisco.com/1rWW9djPvHdA8RjQ5GKcQFsjlPgqBRVuzizVB-1oy… - R. _______________________________________________ Freesurfer mailing list -- freesurfer(a)nmr.mgh.harvard.edu To unsubscribe send an email to freesurfer-leave(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1BLB3A_Aor7vhh4VJU3gnpbq-ikur2FY1421KWRz4gi-EN… 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 https://secure-web.cisco.com/1UwQ7qY2FJsKZtu6W4iR3gRfXytNPCjSCA1LQacPI1mM9V… <https://secure-web.cisco.com/1FUVZMJbmPHEhJ63RzpfI-Ij12fCKYeL0IS5psFW7yVMJoQ0swIh0RiL1KXf0shQPrM9dYDKtSDDIW2ZISxe1kM1eJxagd72qxbBhdC4p6llgdVehhY5x-Wd8L5p30pSdozCPz8Ts-GCXdTiOX9Bcnawg_b098v6GJvmWDKrGpiy34W2g_1Z-SAEf-ISZjGqk0XXRAoLKgGEK-oPQhNUBNtx-vaLBpgNDFY00wjjaQGodQlcev-jZyTWFNhBrjD88CVm5_OfW8IQUJrY6ZzaSKGyhxsEMkAGUgPi28x2xOqA5mRgAuIWfIqJvCOomDpEjOCDGKWfekj0sf1yRjO5cww/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline%26gt; . 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. _______________________________________________ Freesurfer mailing list -- freesurfer(a)nmr.mgh.harvard.edu To unsubscribe send an email to freesurfer-leave(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1BLB3A_Aor7vhh4VJU3gnpbq-ikur2FY1421KWRz4gi-EN…

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Re: RedHat installation
by fsbuild 12 Sep '25

12 Sep '25

External Email - Use Caution  You can try the .rpm installer that matches the RedHat system.  So you could try the CentOS7 rpm on a RedHat7 system, and the Rocky8 rpm on a RedHat8 system.  I’m not sure if the rocky8 installer will work on RedHat 9. - R.On Sep 8, 2025, at 08:48, Gomez-Acebo Ruiz, F. (Fernando) <F.Gomez-AceboRuiz(a)umcutrecht.nl> wrote:        External Email - Use Caution        Hi, I was wondering if FreeSurfer can be installed in Red Hat systems Thank you,FernandoDe informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt.This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197.Please consider the environment before printing this e-mail._______________________________________________Freesurfer mailing list -- freesurfer(a)nmr.mgh.harvard.eduTo unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman3/lists/freesurfer@nmr.mgh.harvard.edu/

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Misaligned datasets with identical headers in Freeview
by Chourrout, Matthieu 12 Sep '25

12 Sep '25

External Email - Use Caution Hi the FreeSurfer team! I have generated two datasets with identical headers, but there is an offset between them when rendering them in Freeview bundled with FreeSurfer 8.0.0 and FreeSurfer 8.1.0 (Ubuntu 22 DEB releases in WSL2 on Windows 11 and on Ubuntu 22). I did the same test on two workstations, and I had no issue when switching back to FreeSurfer 7.4.1 (Ubuntu 22 DEB releases in WSL2 on Windows 11). It's unclear to me if it's only a rendering issue or if the CLI commands such as mri_segstats would also be impacted. I can send a private link to the test data. [cid:faf79ad5-be70-4a9d-bef6-a016ee0f8f50] [cid:2743f6c8-6cf7-4ed3-ae5d-7db33f5b2677] Best regards, Dr Matthieu Chourrout [orcid logo 16px] <https://secure-web.cisco.com/1qcZbiTDh5_TH3_9Rial0Zu9bhFyXywpVaRRTPqKWqPB8G…> Research Fellow on Correlative X-ray Imaging for the Large-scale Imaging of Neural Circuits MXI Lab, UCL Mechanical Engineering Torrington Place, London, WC1E 7JE Bloomsbury Campus, University College London

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PhD positions in neurodevelopmental disorders
by Z S 10 Sep '25

10 Sep '25

External Email - Use Caution Description: Our lab (https://secure-web.cisco.com/1bJ41rR8jEuup-ZfnltW6Mk-VrUnLDy1GAZgmiB_R4Nt4P…) at the University of South Carolina is seeking *PhD students in Neuroscience*. Our lab is affiliated with the Carolina Autism & Neurodevelopment Center, the Institute for Mind & Brain, and working closely with the McCausland Center for Brain Imaging in Columbia, center of SC Metropolitan Statistical Area. Our lab explores the mechanisms of atypical brain development and neurodevelopmental disorders (e.g., autism spectrum disorders) by leveraging statistical modeling to bridge genetic variation, neural circuitry, exposure (e.g., early life adversity) and psychopathological phenotypes, and treatment outcomes. These innovative projects will leverage state-of-the-art machine learning models and neuroimaging, supported by the brand-new Brain Imaging Center (with 3T and high-field 7T MRI scanners) and the Biobehavioral Research Center at the University of South Carolina. This position provides an excellent opportunity for a motivated student to gain hands-on experience with neuroimaging (e.g., MRI) and biomedical research techniques. The candidate will have full access to rich in-house and public datasets, and advanced neuroimaging platforms. Our lab fosters a collaborative and productive environment, and we actively support PhD students in generating high-quality research publications, applying for fellowships and securing their future career paths. Key roles: · Data collection, analysis; present results and publish papers under the PI’s supervision · Collaborate with lab members and international collaborators · Keep up-to-date on relevant studies and methods, and actively discuss them with the PI · Present your work at national and international conferences Requirements: · Bachelor’s or Master’s degree in a relevant field (e.g., neuroscience, psychology, and related area) · Experience with clinical and MRI data analysis is preferred. · Candidates with coding experience are preferred. How to apply: Please submit your CV to Dr. Zhiqiang Sha (zsha(a)mailbox.sc.edu ).

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Postdoctoral position in neuroimaging studies of neurodevelopmental disorders
by Z S 10 Sep '25

10 Sep '25

External Email - Use Caution *Description: * Our lab (https://secure-web.cisco.com/1_T3NvfJuqYnwjO4JZk_Y_pHCobABv2tYSNO634DlMF30W…) at the University of South Carolina is seeking a postdoctoral fellow to lead projects in neurodevelopmental disorders. This position focuses on investigating how genetic factors and environmental factors (e.g., early life stress) influence human brain developmental trajectory and neurodevelopmental disorders (e.g., autism) using computational models. Our lab explores the mechanisms of atypical brain development and neurodevelopmental disorders (e.g., autism) by leveraging in-house (e.g., high-resolution MRI) and public datasets (e.g., ABCD, HBCD, and etc.) to bridge genetic variation, neural circuitry, exposure (e.g., early life adversity) and psychopathological phenotypes, and treatment outcomes. These innovative projects will leverage state-of-the-art deep computational models and neuroimaging, supported by the brand-new Brain Imaging Center (with high-field 7T MRI) and the Biobehavioral Research Center. *Role: * As a postdoctoral fellow, you will lead this interdisciplinary project and benefit from close mentorship and collaborative opportunities in a supportive and productive research environment. You will have full access to (1) rich in-house and public datasets; (2) advanced neuroimaging platforms (3T and 7T MRI); (3) biobehavioral and clinical research resources. You will conduct a range of neuroimaging and genomics-based analyses, design and implement computational models, and lead manuscript preparation. The role also includes: (1) collaborating with international research collaborators; (2) presenting work at international conferences and institutional seminars. *What we offer:* We assist postdoctoral researchers in applying for internal and external grants and provide structured mentorship tailored to each individual's career goals. Our lab fosters a collaborative and productive environment, and we actively support postdocs in building their academic networks, generating high-quality research publications, and securing independent faculty positions. *Requirements: * The ideal candidate will be able to analyze neuroimaging (MRI) data. A strong interest in programming is essential (e.g., Python, R, Matlab, or Linux). The successful applicant will be highly motivated, possess strong analytical and problem-solving skills. Excellent communication skills and the ability to work both independently and collaboratively in an interdisciplinary research environment are also required. How to apply: submit your CV to Dr. Zhiqiang Sha (zsha(a)mailbox.sc.edu) You can also submit your application at https://secure-web.cisco.com/1cGcZDxxsp7m-L8EGTHW8C_jvjHLh1i3TSdKniExuCGuNP…

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Re: Recon-all error: synthtrip on Apple M3 Sonoma 14.6.1
by fsbuild 09 Sep '25

09 Sep '25

External Email - Use Caution  If you have not already done so, please try running your commands in the bash shell as shown in the page referenced via the below link (scroll down to MACOS).  So far I've seen no issues running various recon-all tests with 8.0.0 and 8.1.0 on a MacMini running Sequoia 15.5 with an M2 processor and 32GB of RAM using the setups listed on that page.https://secure-web.cisco.com/1GOFWApQpWTzyWax8ZqPYPCfDLKlE61L1LtFzLl80… - R.

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