Freesurfer

freesurfer@nmr.mgh.harvard.edu

5 participants
30076 discussions

Clusters and significance maps
by Laura Willers de Souza 04 Apr '22

04 Apr '22

External Email - Use Caution Hello FreeSurfer Developers, I would like to know if there is any way to visualize the clusters that survive correction for multiple comparisons with a color gradient corresponding to the corrected significance level? As in this image below (article link https://secure-web.cisco.com/1qOoEvjPnK_m3u0z_SOdGWxN5T-4Pz-fU8mFBd-TCs-_nQ…) [cid:04a0dc7a-9b96-4922-ada8-1337d936f1b0] Thanks in advance! Laura Willers de Souza Master Student in Biochemistry Zimmer Lab - Federal University of Rio Grande do Sul - Porto Alegre/RS - Brazil

2 3

lh.white surface co-registration
by Salar Dini, Elaheh 04 Apr '22

04 Apr '22

External Email - Use Caution Dear Freesurfer experts, Is there a way to move lh.white of a subject to a new coordinate? Something quite similar as volumetric co-registration but for surfaces. To be exact, I have moved a subject's brainmask.mgz, orig.mgz, aparc+aseg.mgz, and T1 mgz to a new coordinate using mri_coreg and subsequently vol2vol, but the surfaces are still in the original coordinate and doesn't match the volumes. Is there a way to move the surface files to the new coordinate? OS: Centos 7, Freesurfer version: 7.2.0 Thank you for your time and help. Kindly, Ela

2 3

repeated measures ANOVA 2x2 covariate
by Agurne Sampedro Calvete 04 Apr '22

04 Apr '22

External Email - Use Caution Dear FreeSurfer experts, I am doing a repeated measures ANOVA 2x2 (2 groups and 2 time points) and I would like to include in the analysis a covariate that is constant over the 2 times (e.g., baseline medication). I would like to see a "group x time x covariate" interaction. What should the design look like? I know that without covariate the design is as follows: GroupDescriptorFile 1 Class Subject1 Class Subject2 Variables Tp1vsTp2.Group1 Tp1vsTp2.Grroup2 Input Subject1_time1 Subject1 1 0 Input Subject1_time2 Subject1 -1 0 Input Subject2_time1 Subject2 0 1 Input Subject2_time2 Subject02 0 -1 Design matrix: 1 0 1 0 1 0 -1 0 0 1 0 1 0 1 0 -1 Contrasts (.mtx files): Tp1vsTp2.Group1 0 0 1 0 Tp1vsTp2.Group2 0 0 0 -1 Interaction (timexgroup) 0 0 1 -1 However, I do not know how I could include the interaction with that covariate. Thank you very much in advance. Kind regards, Agurne

2 4

password request for file FS_7_2_0_Ubuntu_18_04_06.ova.7z
by Anouck Matthijs 04 Apr '22

04 Apr '22

External Email - Use Caution Hello, I hope this email finds you well. I would like to request for the password to FS_7_2_0_Ubuntu_18_04_06.ova.7z<https://secure-web.cisco.com/1uT35qjETx2PBJuQg2agRxnXoPV7XDxnsMIStfOfoxzdC5…> file to be able to expand it. Thank you for your time. Anouck Matthijs PhD student Movement control & Neuroplasticity Research Group KU Leuven University Leuven, Belgium

1 0

Beta values
by Laura Willers de Souza 03 Apr '22

03 Apr '22

External Email - Use Caution Hello FreeSurfer Developers, I'm extracting beta values from some analyzes and I would like to know if I'm extracting and interpreting these values correctly. To extract the beta values I used this command: mri_segstats --seg lh.cortisol_CSF.glmdir/cortisol_CSF_slope/perm.th20.neg.sig.ocn.mgh --i lh.cortisol_CSF.glmdir/beta.mgh --excludeid 0 --avgwf lh.cortisol_CSF.beta.clusters.dat The model consists of 1 group and 1 covariate. I used the contrasts for intercept and slope. The beta values extraction file contains 2 lines (image below). [cid:c5a3c332-10fc-4726-b15e-672b02ded1fa] * Would the first line be the beta value for the intercept and the second line for the slope? * Thus the glm equation for the 1st cluster would be: cortical thickness = 2.57 - 0.12X + n Is this correct? Thanks in advance! Laura Willers de Souza Master Student in Biochemistry Zimmer Lab - Federal University of Rio Grande do Sul - Porto Alegre/RS - Brazil

2 1

transitioning from tkmedit to freeview
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 03 Apr '22

03 Apr '22

External Email - Use Caution Hi, My lab has been using tkmedit, although it is deprecated, for pial edits. We resist transitioning towards freeview due to changed functionality, which I understand because freeview is used for more than just pial edits but - Are there any tools that can I am not aware of that makes freeview similar to tkmedit? 1. the main thing is the removal of keyboard shortcuts. Being able to press ctrl-G to turn on/off segmentation rapidly, and ctrl-1/2 to turn on/off the T1.mgz rapidly makes quality checking a lot faster rather than having to manually click on the volume you want to turn off. 2. likewise, being able to press x/y/z to easily switch between views (sagittal, axial etc) 3. tkmedit in my lab was configured so that right click replaced voxel intensity to zero, and wheel click replaced voxel intensity to voxel intensity of the T1.mgz (essentially restoring the original voxel intensity). Can you configure the options so that it readily does that (I understand that instead of right click it would probably be left click now) Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --

3 2

Re: [Freesurfer] “Illegal instruction (core dumped)” in mri_synthseg and mri_synthsr
by fsbuild 01 Apr '22

01 Apr '22

External Email - Use Caution Hello Gonzalo, We’re aware that some binaries will not run on older Intel processors that do not support AVX instructions.  You could try running it on a different machine with a newer intel CPU.  We’ve also has some reports about this on Apple hardware with M1 processors and are looking into it. - R. On Apr 1, 2022, at 17:00, Gonzalo Rojas Costa <gonzalo.rojas.costa(a)gmail.com> wrote:       External Email - Use Caution        Hi: I tried to use mri_synthseg and mri_synthsr commands, but I got theerror message "Illegal instruction (core dumped)". Any solution? Ihave the March 31st, 2022 version. Sincerely,Gonzalo Rojas CostaDepartment of RadiologyClínica las CondesLo Fontecilla 441, Las Condes, Santiago, Chile.Tel: 56-2-2105170Cel: 56-9-97771785https://secure-web.cisco.com/1A3UQ11G-wOv-3pW2zSaWtZKG8SS328lgaqQXucSvEjh6odB-KDmWxYXm4OCFP3VTPEYF9hixnewYKSlG7U33uk7GWkTJW6hJiGRkhdV_vDr7AMoQ_fDtCehpAMSERscngsF_9sVywi05i9ZSVyFj92rhbO080hMC0i6fHZ_MZg69OILUh5UpP4_dEkx1qnSe2RZRG9FibNQxe9UsmqWHfXxwUZplkELriSfTXkcGJJBKRE0sIKnqxcf9cJaaCAIILk8QvhuDqeQXsDu_ZEj0ydi__kwRkHsgw9bZW2-o-G4eMML6GiZG0eV9lroWlpGJPlz_nblO3Gn1tZkXPPRe-g/https%3A%2F%2Fscholar.google.com%2Fcitations%3Fuser%3DLO7LZ3oAAAAJhttps://secure-web.cisco.com/1mvpNMRQKSP8FkYyfvVpb7eLS9lj8kZfszgSu9oRJQ8X5gT1o5EbOPN9_w0I95lz3bmOOhFKTa2yoVqxi7B3ZxSiDoHdeWmAqnJ6H2C4zZ0V-Dryb5Fpf5HJAloFFnAPsltFLGzloThFZvs6eFlGeVt7cSS1vWQsIhhM1FylufIpPjPqlNUy1L4AaJ6HlQtupYff3l2933LsgOOn6hPtplYjxT35EZg2jWOhSoBoJqYbI6T5McFyGjNG6_xmplW_nWwnr2nGkwIP7R2THKOSbB2oi_XpvElIQbTLyxgEOSjJaSbVmrbfjwXlAdkK5xx5iyvuPMc7Ki0qOdzWHpNM0Ew/https%3A%2F%2Fwww.researchgate.net%2Fprofile%2FGonzalo_Rojas2https://secure-web.cisco.com/1BSQzDFZczyH2KnRdF2ICVDpUxz6g0ttdU0u-j9PVXo7bIp_PAiaidUZgqXnba0vu5Bcu80MTlDSLj_H7drSSmjw9o-ApoFWbGvavQaIPYZkWqEeyYHXffZDlBqPAfGOKiijJqECUGZQ0ZkgMjioihhpc_46unYRzJwP_Olaq_uOLxoBnFiOk7RIEOQOrq4m6ogPai73zS4t5-NWaw-Mn-m-7R5KlfS9by8_FWZHpa8Er7-QUKcjE38ltkwFIVoarGW9OvPw0N-crWzU8IYfcTPNe5bDV_hl0-6p7OS4tpeaMilAitHaZVfbxHEjfdo0qXAT3CbbKH9FEWORrybZ44Q/https%3A%2F%2Fcvn.fecyt.es%2F0000-0002-6228-2678http://secure-web.cisco.com/1dOFt7henxwABk7hXay_AiRKApZWkzldFKpSeFu7YZA9mXuuq9U_88R1YuXngvPpHdu4VYrPFXW8qpV_t3rjlxPDrWmJNKmo7DIqMAcaKYwVd34QHt8Vu2frhBEQ5zp0hhEKyySjNS26mVbfna1FwRR2qFoO4GLoa0O-CUfmtFcpmQp1ZS5tB3IIIooNFaP9ioUIuL6frrXyXTu8HtC7ofXbWJekLulscwlodKoWS9-0rO63GYRLbZPq7ezoZNSITVOB6XKri_qCiUi8hy6OQd2arca-LWXt0BwR65j3RHAX2DYtTHt-hFCsLj9gxEGZppeokmXXZGI__MKC2zTaPkw/http%3A%2F%2Fwww.researcherid.com%2Frid%2FB-2036-2013https://secure-web.cisco.com/1Th1b2nsH7DOoOS75firwrxXGmPTRXXCJK7nGZMWtY8MELWqNmHiJIS9tMuuGkwnYTZ9aJ15O9a5OeCMYTkOBAPIwIDNZjyO4qlCxeP18bVZa0AvP26wB6Qkdew8E7SeIKlwzJWNlh6zOfjaJO3m5Z-4JtKJdxdQGlOCiylUc1b9uoVLu836jxV38np5BFFUBTUXiqXiPHMJ4c-zCdHzMc2cH0X2THYKZG7S39ZW0lJvDZHwg7dYeDZZ6o4Xx08zkRjVR00HM35JJbEavZAQ2orYZuhSCzBQl4JG4DH-xQwa1qsm_N_RKSzTcQ26dMv7fiNbb3_KBGtQBzOCM8yU5aw/https%3A%2F%2Fcl.linkedin.com%2Fin%2Fgonzalorojascosta_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

“Illegal instruction (core dumped)” in mri_synthseg and mri_synthsr
by Gonzalo Rojas Costa 01 Apr '22

01 Apr '22

External Email - Use Caution Hi: I tried to use mri_synthseg and mri_synthsr commands, but I got the error message "Illegal instruction (core dumped)". Any solution? I have the March 31st, 2022 version. Sincerely, Gonzalo Rojas Costa Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 https://secure-web.cisco.com/1A3UQ11G-wOv-3pW2zSaWtZKG8SS328lgaqQXucSvEjh6o… https://secure-web.cisco.com/1mvpNMRQKSP8FkYyfvVpb7eLS9lj8kZfszgSu9oRJQ8X5g… https://secure-web.cisco.com/1BSQzDFZczyH2KnRdF2ICVDpUxz6g0ttdU0u-j9PVXo7bI… http://secure-web.cisco.com/1dOFt7henxwABk7hXay_AiRKApZWkzldFKpSeFu7YZA9mXu… https://secure-web.cisco.com/1Th1b2nsH7DOoOS75firwrxXGmPTRXXCJK7nGZMWtY8MEL…

1 0

Re: [Freesurfer] Password for virtual machine
by fsbuild 01 Apr '22

01 Apr '22

External Email - Use Caution Sending the info to your email shortly. - R. On Apr 1, 2022, at 13:03, Ogier, Stephen E. (Assoc) <stephen.ogier(a)nist.gov> wrote:        External Email - Use Caution        Hi, I’m getting started with FreeSurfer, and I was wondering if I could be sent the passcode to unzip the virtual machine? Thanks,Stephen Stephen Ogier, PhDPostdoctoral Associate, Magnetic Imaging Group, Applied Physics DivisionNational Institute of Standards and Technology_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Seeking beta testers for new Freesurfer help forum
by Sennott, Liam Ricker 01 Apr '22

01 Apr '22

Hello, FreeSurfer community, The FreeSurfer administrative team is working on transitioning the current FreeSurfer mailing list infrastructure to a new, more user-friendly platform called Discourse. We’re still finalizing the website, so we’re looking for potential beta testers for this new platform. As a beta tester, you will post your questions to Discourse and interact with the FreeSurfer staff in discussion board format. Please email lsennott(a)mgh.harvard.edu<mailto:lsennott@mgh.harvard.edu> if you are interested in helping us test this new system! Thank you, Liam Sennott FreeSurfer Admin

1 0

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer