Freesurfer July 2023

freesurfer@nmr.mgh.harvard.edu

93 participants
130 discussions

Freesurfer installation issue
by Ramesh Babu 15 Jul '23

15 Jul '23

External Email - Use Caution Dear Expert, I am trying to install Freesurfer-7.2 .deb package. I had this package earlier, and after formatting my system now, I am trying to install Freesurfer again. But I am facing the following issues. 'freesurfer_7.2.0_amd64.deb' is not a Debian format archive dpkg: error processing archive freesurfer_7.2.0_amd64.deb (--install): dpkg-deb --control subprocess returned error exit status 2 Errors were encountered while processing: freesurfer_7.2.0_amd64.deb Kindly request you to provide a solution to solve this issue. Thanks in advance Ramesh

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Partnership Proposal for Freesurfer Expert Training with Universitas Indonesia
by Pukovisa Prawiroharjo 15 Jul '23

15 Jul '23

External Email - Use Caution Dear Freesurfer Team, Greetings. My name is dr. Pukovisa Prawiroharjo, Sp.S(K), PhD. I am a lecturer and researcher at the Department of Neurology Faculty of Medicine Universitas Indonesia (UI) in Indonesia. I am pleased to inform you that we have been awarded a grant from the UI Incubate program. This program is aimed at promoting growth in university startups that focus on innovative solutions. Our project revolves around the concept of a "Brain Analysis Consultation Service." Our primary goal is to democratize access to predictive analytics for neurodegenerative diseases, making such advanced techniques more available to the general public. The business model is to build a clinic for brain analysis using Freesurfer as a core element of our service. The data given by the MRI will be used to analyze and predict neurodegenerative diseases from our patients. The service we aim to offer will allow patients to consult with us about their Freesurfer results for our team to analyze. Through this, we hope to give them a clearer understanding of their condition, helping predict the trajectory of their neurodegenerative disease more accurately. With this in mind, we would like to invite your team to conduct an expert class on Freesurfer for us. This class will surely boost our understanding of the software and improve the efficiency and effectiveness of our work. We sincerely hope this proposal interests you and aligns with your mission to further knowledge and research in neuroscience. If so, we would be delighted to discuss this further and provide you with any more details you may need. Thank you for considering our proposal. We look forward to the potential of working together for a common goal. Best regards, *Pukovisa Prawiroharjo, M.D., Sp.N, Subsp. NGD (K), PhD* Neurobehavior Consultant, Neurology Specialist Neurology Department, Faculty of Medicine, Universitas Indonesia Chair of Bioethics Cluster IMERI UI Chair of International Policy Div, Board of Development Med Services IDI

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(no subject)
by Pukovisa Prawiroharjo 15 Jul '23

15 Jul '23

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Longitudinal pipeline for FreeSurfer (v7.3.2)
by Jackson Lee 13 Jul '23

13 Jul '23

External Email - Use Caution Hi there, I am hoping to process some longitudinal data using the longitudinal recon-all pipeline available in FreeSurfer: https://secure-web.cisco.com/1Y9uqixBqGC2B0XHSMg2zr4QS96oUVSkkZcMdhRqdEkVD1… Will this pipeline work for FreeSurfer v7.3.2? I cannot see any resources to suggest this is the case. Additionally, I am hoping to conduct some longitudinal analysis using the hippocampal subfield pipeline: https://secure-web.cisco.com/1ILqdmv74otr5LeRS7UQz83p5UDddkh5pv-Luvs5PHnW-6… Would the best course of action be to run recon-all with the longitudinal pipeline first (assuming it is applicable for freeSurfer v7.3.2) and then use the longitudinal command for post-hoc subfield analysis?: segmentHA_T1_long.sh <baseID> [SUBJECTS_DIR] Thank you, Jack

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Basal Ganglia in brain.mgz denoted as WM
by AmirHussein Abdolalizadeh 13 Jul '23

13 Jul '23

External Email - Use Caution Hi Freesurfer users/experts, I accidentally noticed a bizarre behavior -in my opinion- in the FreeSurfer 7.3.2 in which there were large regions of the basal ganglia changed to the WM value (value = 110). Both the original T1 and the brain.mgz screenshots are attached. I haven't tried it with the latest FreeSurfer versions but it seems quite odd. Any comments are appreciated. Best, Amir

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How to segment the visual cortex?
by 周乐晴 13 Jul '23

13 Jul '23

External Email - Use Caution Dear Sir, I can find Visual_v3_d cortex area in FreeSurferColorLUT.txt. but I was confused that where I can find the result file of the visual cortex, or it needs more process?                                                                         Sincerely                                                                        Rosie Zhou  

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Pass code
by yuanyuelunar 13 Jul '23

13 Jul '23

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Postdoc Position for Human Intracranial EEG Lab
by Winfield, Jalen 12 Jul '23

12 Jul '23

External Email - Use Caution Dear all, Please find enclosed Post-Doctoral position that may be of interest. * Funding Duration: 4-5 years * Start Date: As soon as possible * Research Team: Laboratory for Human Brain Mapping at the Feinstein Institute for Medical Research - Hofstra Northwell School of Medicine, NY, USA * Application: Interested candidate should send CV, names and contact info of 2-3 references, and any questions to Stephan Bickel, MD PhD (sbickel(a)northwell.edu<mailto:sbickel@northwell.edu>) This post-doc position is part of a large, recently funded NIH multi-center project to investigate the functional role of slow fluctuating cortical activity. These slow fluctuations are a ubiquitous and fascinating feature of brain activity and is thought to play a crucial role in many cognitive functions from attention, interoception, state switching, etc. This is an extremely collaborative project among a large amount (>25 PIs) of international leaders in the field using scalp EEG, fMRI, iEEG, and single unit recordings in humans and animal models, electrical stimulation, and computational modeling. The candidate will have ample opportunities to work closely with these collaborators. Additionally, the candidate is encouraged to help mentor/supervise research assistants. See attached for more information. The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.

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Re: [Freesurfer] Freesurfer Digest, Vol 233, Issue 12
by Jacoby, John 12 Jul '23

12 Jul '23

External Email - Use Caution Hi Yujing, sure thing. Thanks for taking a look. rawavg.mgz Volume information for rawavg.mgz type: MGH dimensions: 208 x 300 x 320 voxel sizes: 0.800001, 0.800000, 0.800000 type: SHORT (4) fov: 256.000 dof: 1 xstart: -83.2, xend: 83.2 ystart: -120.0, yend: 120.0 zstart: -128.0, zend: 128.0 TR: 2500.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = 0.9972, y_r = 0.0478, z_r = 0.0572, c_r = 4.2108 : x_a = -0.0268, y_a = 0.9456, z_a = -0.3241, c_a = 13.0358 : x_s = -0.0696, y_s = 0.3217, z_s = 0.9443, c_s = -19.3591 talairach xfm : Orientation : RAS Primary Slice Direction: axial voxel to ras transform: 0.7978 0.0383 0.0457 -91.8157 -0.0214 0.7565 -0.2593 -56.7298 -0.0556 0.2573 0.7554 -173.0404 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant 0.512001 ras to voxel transform: 1.2465 -0.0335 -0.0869 97.5046 0.0598 1.1821 0.4021 142.1226 0.0714 -0.4051 1.1804 187.8310 0.0000 0.0000 0.0000 1.0000 orig.mgz Volume information for rawavg.mgz type: MGH dimensions: 208 x 300 x 320 voxel sizes: 0.800001, 0.800000, 0.800000 type: SHORT (4) fov: 256.000 dof: 1 xstart: -83.2, xend: 83.2 ystart: -120.0, yend: 120.0 zstart: -128.0, zend: 128.0 TR: 2500.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = 0.9972, y_r = 0.0478, z_r = 0.0572, c_r = 4.2108 : x_a = -0.0268, y_a = 0.9456, z_a = -0.3241, c_a = 13.0358 : x_s = -0.0696, y_s = 0.3217, z_s = 0.9443, c_s = -19.3591 talairach xfm : Orientation : RAS Primary Slice Direction: axial voxel to ras transform: 0.7978 0.0383 0.0457 -91.8157 -0.0214 0.7565 -0.2593 -56.7298 -0.0556 0.2573 0.7554 -173.0404 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant 0.512001 ras to voxel transform: 1.2465 -0.0335 -0.0869 97.5046 0.0598 1.1821 0.4021 142.1226 0.0714 -0.4051 1.1804 187.8310 0.0000 0.0000 0.0000 1.0000 nu.mgz Volume information for nu.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.000000, 1.000000, 1.000000 type: UCHAR (0) fov: 256.000 dof: 1 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 2500.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = -0.0000, z_r = 0.0000, c_r = 4.2108 : x_a = 0.0000, y_a = -0.0000, z_a = 1.0000, c_a = 13.0358 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -19.3591 talairach xfm : /autofs/space/yoda_002/users/datasets/HCA/data/derivatives/FreeSurfer_failed/HCA6429272_V1_MR/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1.0000 -0.0000 0.0000 132.2108 0.0000 -0.0000 1.0000 -114.9642 0.0000 -1.0000 0.0000 108.6409 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000 0.0000 0.0000 132.2108 0.0000 0.0000 -1.0000 108.6409 0.0000 1.0000 -0.0000 114.9643 -0.0000 -0.0000 -0.0000 1.0000 T1.mgz? Volume information for T1.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.000000, 1.000000, 1.000000 type: UCHAR (0) fov: 256.000 dof: 1 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 2500.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = -0.0000, z_r = 0.0000, c_r = 4.2108 : x_a = 0.0000, y_a = -0.0000, z_a = 1.0000, c_a = 13.0358 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -19.3591 talairach xfm : /autofs/space/yoda_002/users/datasets/HCA/data/derivatives/FreeSurfer_failed/HCA6429272_V1_MR/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1.0000 -0.0000 0.0000 132.2108 0.0000 -0.0000 1.0000 -114.9642 0.0000 -1.0000 0.0000 108.6409 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000 0.0000 0.0000 132.2108 0.0000 0.0000 -1.0000 108.6409 0.0000 1.0000 -0.0000 114.9643 -0.0000 -0.0000 -0.0000 1.0000 ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of freesurfer-request(a)nmr.mgh.harvard.edu <freesurfer-request(a)nmr.mgh.harvard.edu> Sent: Wednesday, July 12, 2023 12:16 PM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: Freesurfer Digest, Vol 233, Issue 12 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://secure-web.cisco.com/12tqMvVwMoVIkiryXwUMd2vYtmGrMUQNIE7L1lW6FZX-AS… or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: FreeSurfer 6 Error On Macbook M2 (fsbuild) 2. Issue with FS7.4.1 (Ruifeng Dong) 3. Matrix setup to examine group effect between three groups, one covariate (age) as nuisance variable (Gavette, Levi William) 4. Re: Matrix setup to examine group effect between three groups, one covariate (age) as nuisance variable (Huang, Yujing) 5. Re: Issue with FS7.4.1 (Huang, Yujing) 6. Re: Indices out of bounds error during mri_watershed (Huang, Yujing) ---------------------------------------------------------------------- Message: 1 Date: Wed, 12 Jul 2023 15:57:21 +0200 From: fsbuild <fsbuild(a)contbay.com> Subject: Re: [Freesurfer] FreeSurfer 6 Error On Macbook M2 To: freesurfer(a)nmr.mgh.harvard.edu Cc: thuvaragan.prathifkumar(a)sri.utoronto.ca Message-ID: <c47171311e8871740213347438567e50(a)trashmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution The graphics packages used in Freeview have changed since the Freesurfer 6 release, and also how they and the other Intel binaries are compiled for current versions of MacOS.   So a run time error, e.g., segfault, could occur when running under Rosetta on a silicon Mac. Please try one of the current MacOS Freesurfer 7 releases from the download page, surfer.nmr.mgh.harvard.edu/fswiki/rel7downloads - R. On 7/12/23 08:35, Prathifkumar, Thuvaragan (thuvaragan.prathifkumar(a)sri.utoronto.ca) wrote:         External Email - Use Caution         Hello, I recently installed Free Surfer 6, and was following this guide: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1NRP4tsM45lW3UFB3Jf_X6qXB5GUcDVNjcJDXPLcS2Shw2… I got till Example 3, and Example 3 works perfectly. As attached as an image in this email.  For some reason, in Example 4, to open the GUI (freeview) based on the fully recon-ed subject bert in Example 3, I get an error and I'm not sure why. Why does that happen? Is it due to compatibility issues with the apple silicon chip? The error message is attached as an image in this email as well. Any help is appreciated. Thank you. 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Indices out of bounds error during mri_watershed
by Jacoby, John 12 Jul '23

12 Jul '23

External Email - Use Caution Hi all, I am running into an error running recon-all and I can't figure out what's going on just from the error messages. I'm hoping someone here can help. I'm using FreeSurfer 7.2 and this is the command I'm trying to run: recon-all -subjid HCA6429272_V1_MR -i /autofs/space/yoda_002/users/datasets/HCA/data/as_downloaded/HCA6429272_V1_MR/scans/110-T1w/resources/NIFTI/files/HCA6429272_V1_MR_T1w_MPR_vNav_4e_RMS.nii.gz -all build stamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b operating system: cat /etc/centos-release Rocky Linux release 8.8 (Green Obsidian) I've run about 1200 recons in the last few weeks from the same dataset using analogous commands for the other T1s, but this is the only one that failed. The T1 isn't great quality, but not terrible either (screenshot below). The error happens during the watershed step: "mri_watershed Error: indices out of bounds". I've attached the log and error file from the recon. Thanks for any help you can provide. Best, John Screenshot of the input T1: [cid:173163e6-208e-4800-a256-55aed18f186d]

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Freesurfer July 2023