Freesurfer July 2023

freesurfer@nmr.mgh.harvard.edu

93 participants
130 discussions

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

2 1

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

2 1

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.

1 0

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.

1 0

Pass code
by Farner Lynn 12 Jul '23

12 Jul '23

External Email - Use Caution To whom it may concern, Would you please send me the pass code for opening the archive of FS 7.2.0? Thank you for your help. Best regards, Lynn Farner

1 0

[FreeSurfer] Talairach Failure Detection
by Krystal Xiwing Yau 12 Jul '23

12 Jul '23

External Email - Use Caution Dear Freesurfer experts, I would like to seek for help regarding talairach error. I have browsed through the forum about it but still not solving my problem... The following steps are the solutions I have tried: * Re-run recon-all with -notal-check * Re-run recon-all with -notalairach * The above flags gave the same error message as follow: * WARNING2: gca.c::GCAhistoScaleImageIntensities: h_mri->nbins=100, mri_peak=108 after smoothing, mri peak at 0, scaling input intensities by inf error: Numerical result out of range error: GCAhistoScaleImageIntensities: could not find wm peak Command exited with non-zero status 252 * Ran the command to fix the registration: tkregisterfv --s Sub-108 --fstal --no-surfs * The view for this subject is weird because it shows the axial view when the coronal view is selected * [cid:49cf1b63-a35e-4003-8f38-a1def3b7bd64] * The correct view showed up when the coronal view is selected * [cid:abd68344-6bc3-489a-9eef-20569a419c02] When I viewed 001.mgz in Freeview, there was no such problem. However, some artifact (i.e. the weird lines) occurred in certain slices, as circled in pink: [cid:0c0b2ea4-3b3e-4361-ad0c-c5dec191c85c] [cid:eadbe192-c57a-48db-b429-b162b0154d0f] [cid:229941cf-2005-44c6-a979-0bf60c03da18] I am not sure how to fix it with tkregisterfv and what are the standards for it. It would be so much appreciated if someone could help out with this issue. Regards, Krystal Tel.: +852 2255 5024 Fax: +852 2872 5828 Address: Room 304, 3/F, New Clinical Building, 102 Pokfulam Road, Hong Kong.

3 7

LMW and missing timepoints
by Lara Foland-Ross 11 Jul '23

11 Jul '23

External Email - Use Caution Hi there, We have a longitudinal structural neuroimaging dataset with anywhere between 1 and 4 timepoints collected for each participant. How does LME handle missing data when analyzing longitudinal trends? Thanks, Lara Lara Foland-Ross, Ph.D. Senior Research Associate and Imaging Lab Manager Center for Interdisciplinary Brain Sciences Research Stanford University School of Medicine 401 Quarry Road, Room 1356 Stanford, CA 94305-5795

2 2

wm-hypointensities
by Andrew Dedinas Geoly 11 Jul '23

11 Jul '23

External Email - Use Caution Hi Freesurfer experts! I am hoping to extract the wm-hypointensity data from some recon-all-clinical runs. I was able to extract aseg.stats information correctly but noticed there was no information regarding the wm-hypointensities. Is this supported by recon-all-clinical? Best, Andrew --- Andrew D. Geoly, MS Research Data Analyst 1 Brain Stimulation Lab Department of Psychiatry and Behavioral Sciences Stanford University School of Medicine

1 0

WM-hypointensities
by Andrew Dedinas Geoly 11 Jul '23

11 Jul '23

1 0

Preserving original T1w space coordinate
by parsatad＠student.ubc.ca 11 Jul '23

11 Jul '23

External Email - Use Caution Hello, Hope you are doing well. I was wondering if the parcellation process recenters the coordinates and if so, is there a way to not recenter and preserve original T1w space coordinates? Thanks, Parsa

2 1

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer July 2023