[Freesurfer] Viewing eroded structure after -seg-erode 1

Hi Freesurfer Community, I have performed -seg-erode 1 during mri_segstats on resampled subcortical strutures (T1 to FA/MD). Can I view the eroded masks in T1 anatomical space to visually inspect whether PVE has been adequately accounted for? Thank you. Best Wishes, Elijah __

[Freesurfer] Accuracy of D-K atlas for different age ranges

Hi Freesurfer community, A reviewer has asked how accurate the application of freesurfer regional labels are to different age ranges (specifically our study is between 14 and 24 years old). I'm sure this question has been answered elsewhere so please do forgive me for being lazy and simply asking

Re: [Freesurfer] Group level analysis: Specifying contrasts

Hi Doug, I've attached the fsgd file and the contrast matrix file. Thanks for your help! - Afsana __ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 261

Re: [Freesurfer] Viewing eroded structure after -seg-erode 1

You can load it as an overlay in freeview make sure to specify the registration file as that compted for the DTI. Also make sure to set the threshold to something like 0.5 On 04/11/2016 09:41 AM, Elijah Mak wrote: > Hi Freesurfer Community, > > I have performed -seg-erode 1 during mri_segstats o

Re: [Freesurfer] Group level analysis: Specifying contrasts

What is your source data? It looks like you have two time points per subject, but the names of "offset" and "slope" suggest some preprocessing? Input hc001-lRsk_offset hc001100 Input hc001-lRsk_slope hc001000 Input hc001-mRsk_offset hc0

Re: [Freesurfer] Viewing eroded structure after -seg-erode 1

Thanks Doug. Do you mean loading the structure (i.e. LeftHippocampus2diff.mgz) on the orig.mgz as an overlay? I am able to do that but I can't seem to find an option for thresholding. Sorry if I misunderstood your original email. Best Wishes, Elijah ___

[Freesurfer] TRACULA dev version: Error message

Hi Freesurfer Community, I am running TRACULA on a single subject in the dev version (freesurfer-Darwin-OSX-stable-v6-beta-20151015) #- /Applications/freesurfer6beta/bin/trac-preproc #- #@# Image corrections Mon Apr 11 16:

[Freesurfer] $FREESURFER_HOME/sources.csh

Good morning Doug and all, I am running epidewarp.fsl (using the dev version since I need it to be compatible with the recent versions of FSL; /usr/local/freesurfer/dev/bin/epidewarp.fsl). However, for the first time I see that it complains that it can no longer find /usr/local/freesurfer/stab

Re: [Freesurfer] Accuracy of D-K atlas for different age ranges

Hi Kirstie I can't imagine that there is any serious variability in that age range. The folds are set long before then cheers Bruce On Mon, 11 Apr 2016, Kirstie Whitaker wrote: > Hi Freesurfer community, > > A reviewer has asked how accurate the application of freesurfer regional > labels a

Re: [Freesurfer] $FREESURFER_HOME/sources.csh

That is something we had to put in to be able to run under newer mac OSs. You can remove that line in your version. On 04/11/2016 11:52 AM, Marco Loggia wrote: > Good morning Doug and all, > > I am running epidewarp.fsl (using the dev version since I need it to > be compatible with the recent ve

Re: [Freesurfer] LME for functional data, 3 factors

Dear Martin, Thank you for your quick response. My research question is focused on the group and day effect, so I could simplify the model. From your response, I thought of including in the design matrix the binary code for Condition 2, and for Condition 3 in two columns, like you suggested; h

[Freesurfer] From Talairach to Vertex Index

Hi FS users, I need to check if a specific point in Talairach coordinates is inside a label that I created from a significative cluster of a previous group analysis (the template is fsaverage). How can I do this quickly? Thanks a lot. Best regards. Ilaria __

Re: [Freesurfer] LME for functional data, 3 factors

Hi Laura In the wikihttps://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModelswe recommended to order the columns of the design matrix in thefollowing way: Column 1: theintercept term (which is a column of ones) Colum 2: the timecovariate if it varies across subjects (eg. time from base

[Freesurfer] August FreeSurfer course in Copenhagen, Denmark

There are still some spots available in the Copenhagen FreeSurfer Course which will be held from August 10th to 12th, 2016. The course will be organized by the Neurobiology Research Unit, Copenhagen University Hospital in cooperation with the Laboratory for Computational Neuroimaging of the Ath

[Freesurfer] mri_surfcluster issues

Dear FreeSurfer experts, I am using mri_surfcluster to compare results from PALM and FreeSurfer cluster extent inference. I came across several issues in mri_surfcluster I cannot cope with. 1. I observed that --mask option in mri_surfcluster does not prevent cluster to growing outside the mas

[Freesurfer] TRACULA

Hello Freesurfer Team, I attended the conference last week in Boston and really enjoyed all I learned! But while trying to run through the Tracula tutorial with my own data, I am having an error with my configuration file: ERROR: must specify as many DWI dicoms as subjects. My files are in nifti