[Freesurfer] Cortical thickness (spc) extraction

External Email - Use Caution Dear FreeSurfer, I used QDEC for the longitudinal two‐stage model analyses, where temporal data within each subject was reduced to a symmetrised percent rate of change (spc) maps using the long_mris_slopes function for data acquired at two time-point

[Freesurfer] Longitudinal QDEC

External Email - Use Caution Dear All, I am running a longitudinal (2-time points) group cortical analysis in Freesurfer 5.3 with Qdec. After shrinking the longitudinal QDEC table into a cross-sectional form, I added a text file containing the lines MEASURE1 = long.thickness-av

[Freesurfer] Longitudinal QDEC

External Email - Use Caution Dear All, I am running a longitudinal (2-time points) group cortical analysis in Freesurfer 5.3 with Qdec. After shrinking the longitudinal QDEC table into a cross-sectional form, I added a text file containing the lines MEASURE1 = long.thickness-av

[Freesurfer] FreeSurfer - Lateral Ventricle Definition

External Email - Use Caution Dear FreeSurfer Experts, Can you confirm whether, the volume of the choroid plexus has automatically been added to the laterel ventricle volume or not. Thanks Theo ___ Theophilus Akudjedu BSc, MSc, PhD Candidate Ro

Re: [Freesurfer] Freesurfer Digest, Vol 168, Issue 54

ugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: on behalf of "AKUDJEDU, THEOPHILUS" Reply-To: Freesurfer support list Date: Tuesday, 27 February 2018

[Freesurfer] Hippocampal Subfield Error

Hi All, I tried to run a subject through FreeSurfer 6.0 for hippocampal Subfield segmentation but exited with errors. The content of the recon-all.error file is below. SUBJECT CHRM2001 DATE Sun Feb 25 00:34:13 GMT 2018 USER 15233963 HOST psych-sl03 PROCESSOR x86_64 OS Linux Linux psych-sl03

[Freesurfer] MNI Coordinates

Hi All, I am trying to visualise nodes of a brain network reconstructed using FreeSurfer Desikan-Killiany Atlas parcellation scheme (aparc+aseg.mgz) on Brain Net Viewer and Network Based Statistics software. In order to do so, I need to upload a .txt file listing Freesurfer labels coordinates

[Freesurfer] How to obtain MNI coordinates

Hi All, I am trying to visualise nodes of a brain network reconstructed using FreeSurfer Desikan-Killiany Atlas parcellation scheme (aparc+aseg.mgz) on Brain Net Viewer and Network Based Statistics software. In order to do so, I need to upload a .txt file listing Freesurfer labels coordinates i

[Freesurfer] Subcortical Segmentation

Hi FreeSurfers, Are we able to correct the anatomical boundaries of subcortical structures delineated with FreeSurfer? On which output file do we do this if it's possible? Thank you Theo ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu h

[Freesurfer] Longitudinal Pipeline

From: AKUDJEDU, THEOPHILUS Sent: Tuesday, June 13, 2017 3:19:00 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Longitudinal Pipeline Hi All, Is it standard practice to conduct reliability when corrections are made in freesurfer for subcortical structure volumes? Also, are you able to

[Freesurfer] Longitudinal Pipeline

Hi All, Is it standard practice to conduct reliability when corrections are made in freesurfer for subcortical structure volumes? Also, are you able to analyse data acquired (1.5T - time point one) with time-point two (3T) in the longitudinal pipeline? Thanks Theo _

Re: [Freesurfer] Freesurfer Digest, Vol 152, Issue 22

Dear All, I want to know the freesurfer anatomical definition for the caudate and the hippocampus. Thank you. Theo From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of freesurfer-requ...@nmr.mgh.harvard.edu Sent: 16 October 2016 17:00:01 To: free

[Freesurfer] FreeSurfer Atlas

Hi All, Which default atlas does FreeSurfer 5.3 use for the segmentation of subcortical structures? Thanks Theo ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The informat