[Freesurfer] Questions regarding ROI creation for SPM based on FreeSurfer parcellation

External Email - Use Caution Dear FreeSurfer-Experts, I’m in need of your experience to help me with a decision in my current project: I want to use certain areas, that were identified by structural graph theoretical analyses based on the FreeSurfer parcellation and DTI data,

[Freesurfer] Postdoc available at the Central Institute of Mental Health

External Email - Use Caution The Central Institute of Mental Health (CIMH) stands for cutting-edge international research and groundbreaking treatment concepts in psychiatry, psychotherapy, child and adolescent psychiatry, psychosomatics and addiction medicine. The Department of

[Freesurfer] password request for file FS_7_2_0_Ubuntu_18_04_06.ova.7z

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

[Freesurfer] FREESURFER Maintaining vertex Id during transformations

External Email - Use Caution Hi all, I have been able to create my flat map in freesurfer and then do calculations using it to find a point. I then want to map that point back into the 3D space maintaining the coordinates. I was wondering if anyone had done something similar befor

Re: [Freesurfer] FREESURFER Maintaining vertex Id during transformations

Hi Ali We keep track of the vertex index of the flat maps, so you should just be able to use it to look up the coordinate of whatever other (white, pial) surface you want, then see what volumetric coordinates it is at Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Ali

Re: [Freesurfer] FREESURFER Maintaining vertex Id during transformations

External Email - Use Caution Hi Bruce, If I have the coordinate on the flat map how do I get the corresponding vertex ID? And then from that same ID get the 3D coordinates? Ali On Wed, 30 Mar 2022 at 16:09, Fischl, Bruce wrote: > Hi Ali > > > > We keep track of the vertex inde

Re: [Freesurfer] SAMSEG (Lesion Mask Pattern) ... ah, [0 0]

Hi Randy, The default option is 0 for each input scan as no assumption on the MRI contrast and order of the input scans is made. We strongly recommend users to use the value of 1 for both T2w and FLAIR scans and 0 for T1w scans. The mask is reducing false-positive lesions by applying intensity

[Freesurfer] Job opportunity (ResearchAssistant) at Boys Town National Research Hospital

External Email - Use Caution Please apply at https://secure-web.cisco.com/1yo0ekSWIR0Yp45MZ3-6sWQmS9wHjqoQSAfI0CL1kuo7zD1QzqmlDkaj9B1kr2X90yA4Q58HRFrSjAkMk2UTjx1-Q5FXHVZ8WMP2pxkZZtOWtbs3lfjplX4AZzPzOWvEaQ5yy_5CEyALTIAWDE6mT6aJjbFoW-GQA-P0tXPfIHJHWOPwMJ27NuNxG-QXEhHYMbSlgoa1EVA0jVIa

Re: [Freesurfer] password request for file FS_7_2_0_Ubuntu_18_04_06.ova.7z

External Email - Use Caution Hello Roya, Sending the info to your email shortly. - R On Mar 30, 2022, at 09:37, Roya Afshari wrote:External Email - Use CautionHello,I hope this email finds you well.I would like to request for the passwor

[Freesurfer] transitioning from tkmedit to freeview

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

Re: [Freesurfer] FREESURFER Maintaining vertex Id during transformations

Hi Ali If you use read_patch.m I believe it returns a structure that has the original vertex index in it. It’s been a *long* time since I looked at that code, but it looks like we actually store it twice for some reason: for i=1:patch.npts ind = fread(fid, 1, 'int', 0, 'b') ; if (ind <

Re: [Freesurfer] transitioning from tkmedit to freeview

Hi Victor, On Mar 30, 2022, at 4:30 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) mailto:vz...@bidmc.harvard.edu>> wrote: 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 chang