Freesurfer

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30063 discussions

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. This e-mail is intended only for the named recipient(s) and may contain confidential, personal and/or health information (information which may be subject to legal restrictions on use, retention and/or disclosure).  No waiver of confidence is intended by virtue of communication via the internet.  Any review or distribution by anyone other than the person(s) for whom it was originally intended is strictly prohibited.  If you have received this e-mail in error, please contact the sender and destroy all copies.   _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1GPP1uq2BjNdWwbt8lH77wbxYBxw9jiZ-OPT_aLlNOqso-… The information in this e-mail is intended only for the person to whom it is addressed. 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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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Issue with FS7.4.1
by Ruifeng Dong 12 Jul '23

12 Jul '23

External Email - Use Caution Hi Freesurfers, I am running the new Freesurfer 7.4.1 on Ubuntu 22.04, but ran into the following error. I tested the same data using FS 6.0.0 and it worked fine. The command I am using is recon-all -3T -all. Thanks. mri_label2vol --defects /qmi08_raid/ruifeng/work_with_project_data_T1/clinical_3dresampled-2-RAI/alltogether/uncompressed/testSub_10_0_h/00_test_dicom/cont_10_0_PRISMA_dicom/rerun_FS741/mriconvert2nii_ASR2PSR_reorientimage3d/surf/lh.orig.nofix /qmi08_raid/ruifeng/work_with_project_data_T1/clinical_3dresampled-2-RAI/alltogether/uncompressed/testSub_10_0_h/00_test_dicom/cont_10_0_PRISMA_dicom/rerun_FS741/mriconvert2nii_ASR2PSR_reorientimage3d/surf/lh.defect_labels /qmi08_raid/ruifeng/work_with_project_data_T1/clinical_3dresampled-2-RAI/alltogether/uncompressed/testSub_10_0_h/00_test_dicom/cont_10_0_PRISMA_dicom/rerun_FS741/mriconvert2nii_ASR2PSR_reorientimage3d/mri/orig.mgz 1000 0 /qmi08_raid/ruifeng/work_with_project_data_T1/clinical_3dresampled-2-RAI/alltogether/uncompressed/testSub_10_0_h/00_test_dicom/cont_10_0_PRISMA_dicom/rerun_FS741/mriconvert2nii_ASR2PSR_reorientimage3d/mri/surface.defects.mgz /qmi08_raid/ruifeng/work_with_project_data_T1/clinical_3dresampled-2-RAI/alltogether/uncompressed/testSub_10_0_h/00_test_dicom/cont_10_0_PRISMA_dicom/rerun_FS741/mriconvert2nii_ASR2PSR_reorientimage3d/label/lh.nofix.cortex.label *** buffer overflow detected ***: terminated Abort (core dumped) ERROR: Command exited with non-zero status 1

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Matrix setup to examine group effect between three groups, one covariate (age) as nuisance variable
by Gavette, Levi William 12 Jul '23

12 Jul '23

External Email - Use Caution Hello FreeSurfer community, I am looking to perform a GLM between three groups with the single covariate of age as the nuisance variable. I am wondering how to set up my matrix design so that the output will be the group difference with age removed? Any help is really appreciated. Thanks, – Levi

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Re: [Freesurfer] FreeSurfer 6 Error On Macbook M2
by fsbuild 12 Jul '23

12 Jul '23

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. This e-mail is intended only for the named recipient(s) and may contain confidential, personal and/or health information (information which may be subject to legal restrictions on use, retention and/or disclosure).  No waiver of confidence is intended by virtue of communication via the internet.  Any review or distribution by anyone other than the person(s) for whom it was originally intended is strictly prohibited.  If you have received this e-mail in error, please contact the sender and destroy all copies.   _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1GPP1uq2BjNdWwbt8lH77wbxYBxw9jiZ-OPT_aLlNOqso-… 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/1OO5E-AvzStCDRVOLkGNp_cSAUjwr46-P7DZchwKVln49I… <https://secure-web.cisco.com/1LNuHEUTKFFf_Ri_TpdBp_TWZjalqBrNtQRx4ex0UDi85sTTSy3TxSFRGQXeKdN-JPnKoj_opy7CIlyoDFVYiIDCB_4QlGm4JtgI4O_WNouLbQbUCLz8AQeOogrhRvdzIfcyEG_Cv16-SGP-d0RHR8iORteRNN8vzUw-6qdHDMktKM4d_Gk-g8sElJkttISoLmxshiIC5ZnNNJGy09LWmSorerJ9KCcghM6dLeDqpSRuUKYzYvns9PerDlR9TKKDCUsgttXK1FGyFd5aYaXRdCHQ3f_c8E_qWI3q9M-uHEsqS-3SViu9S6lzneKLBCKNkBkFutvgV7yAxO6LHRbt9kg/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.

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FreeSurfer 6 Error On Macbook M2
by Prathifkumar, Thuvaragan 12 Jul '23

12 Jul '23

External Email - Use Caution Hello, I recently installed Free Surfer 6, and was following this guide: https://secure-web.cisco.com/1NX-CvThaTKpGd9mog8nONoaeD7OmGTWUDNDqtnOnjVp_e… 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. This e-mail is intended only for the named recipient(s) and may contain confidential, personal and/or health information (information which may be subject to legal restrictions on use, retention and/or disclosure). No waiver of confidence is intended by virtue of communication via the internet. Any review or distribution by anyone other than the person(s) for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and destroy all copies.

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