Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30071 discussions

Trouble figuring out error
by Reyes, Nicholas 21 Sep '25

21 Sep '25

External Email - Use Caution Hello! I cannot seem to figure out the problem with this patient. I am newer to using freesurfer, so I am a little lost trying out what I've read in the documentation. Could you help give me some insight on figuring this out? Thank you in advance, Nicholas K. Reyes | B.S. in Neuroscience Neural Signals Processing and Modeling Lab The University of Alabama at Birmingham nkreyes(a)uab.edu<mailto:nkreyes@uab.edu> || 205-937-3421 Nicholas K. Reyes | UNP Major & BME Minor College of Arts and Sciences The University of Alabama at Birmingham nkreyes(a)uab.edu<mailto:nkreyes@uab.edu> || 205-937-3421

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Issue with Skull Strip when Original Volume is Cut at the Nose
by 이준혁 21 Sep '25

21 Sep '25

External Email - Use Caution Environment - OS: Ubuntu 22.04.5 LTS - FreeSurfer: 7.4.1 I'm running FreeSurfer (Ubuntu 22.04 version 7.4.1), and during the Autorecon1 preprocessing, I noticed that the result depends on whether the original 3D volume includes the full face or the nose part is cut. When you run a truncated picture rather than a full face as input, the Skull strip results are completely different. In this case, do you have any official recommendations for normal preprocessing? How should I proceed I will attach the original picture and the pre-processing result picture.

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hippocampal subfield segmentation
by Zehua Cui 21 Sep '25

21 Sep '25

External Email - Use Caution Hi all, We want to use Freesurfer's automatic hippocampal subfield segmentation flag using a T1 and T2 (high resolution hippocampal T2 sequence that is focused on the Medial Temporal Lobe and does not have full coverage of the brain). We previously ran recon-all with just the T1. Is it essential for us to re-run recon-all with both the T1 and the T2 as input or can we simply run the subfields flag and specify the T1 and T2 (which we copied over into the recon-all output directory) there? Will it make a big difference for the resulting subfield volumes? Thank you very much! -- Zehua Cui|崔泽华, Ph.D. Post-Doctoral Fellow Neurocognitive Development Lab 4094 Campus Drive, Biology/Psychology Building University of Maryland, College Park, MD 20742 Zoom Meeting ID: https://secure-web.cisco.com/1_DD2JIMsdFxT6lsQdL9CaK--HcIDgdBd5U8PGauw5NHp6…

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PhD position available - Sensory perception in autism
by Katharina von Kriegstein 19 Sep '25

19 Sep '25

We are seeking an enthusiastic PhD student with a strong interest in understanding sensory mechanisms and their alteration in autism. The project builds on our recent finding of visual thalamus alterations in autism (Schelinksi et al., 2024; https://secure-web.cisco.com/19hZK5bwvYmG0GYg8OAwj8JKBulM6Pe5bEGEX8XO8SMYKz…) The position is fully funded for three years with possible extension. Starting date is flexible. The official advertisement and description on how to apply is available here: https://secure-web.cisco.com/1YP8enc7jCos91K-mxZsvR-WbI15w-6MhBvFytQrDuMENd… _ _ Katharina von Kriegstein Professor of Cognitive and Clinical Neuroscience Vice-Dean Faculty of Psychology Technische Universität Dresden Chemnitzer Str. 48b, 01187 Dresden, Germany Phone +49 (0) 351-463-43145 https://secure-web.cisco.com/1my-8zoYy1bkEhOy2_N-cN9onZBYycalJJ2Nh3jeaPylT6… https://secure-web.cisco.com/1S6HIFEtSj3TSK5TiFBdONX6NjOP8Lz-NUrQZw5Nx2DtAr… External Email - Use Caution

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Support Alert: MacOS 2026 Tahoe and Freesurfer
by fsbuild 15 Sep '25

15 Sep '25

External Email - Use Caution  Apple released MacOS 26, Tahoe, to the general public today in advance of the typical release date.  We recommend that Freesurfer MacOS users do not upgrade to or use Tahoe since the current 8.1.0 release and previous releases were not tested on Tahoe.    Please check this list for future updates. - R.

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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   Please try running your recon-all command without the -T2pial option. - R.

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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.

1 0

Leave
by Andrade Rey René 13 Sep '25

13 Sep '25

External Email - Use Caution Sent from my iPhone

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