Freesurfer June 2004

freesurfer@nmr.mgh.harvard.edu

24 participants
25 discussions

Re: [Freesurfer] scatter plot of multiple subjects thickness data in tksurfer
by Robert D Twomey 03 Jun '04

03 Jun '04

Thanks for your prompt response. > Is this the most current version of FreeSurfer? We have the 07-24-2003 version, however I am sure that we saw this working with this version of Freesurfer last summer. If possible we would prefer to stick with our current version and avoid updating and re-installation. > What input are you giving to load the bfloat? In tksurfer File->Load Overlay, we specified the file y_doss-thickness-250lh_000.bfloat Robert ----- Original Message ----- From: Kevin Teich <kteich(a)nmr.mgh.harvard.edu> Date: Thursday, June 3, 2004 3:10 pm Subject: Re: [Freesurfer] scatter plot of multiple subjects thickness data in tksurfer > > > On Thu, 3 Jun 2004, Robert D Twomey wrote: > > > Hi Brian, > > > > Thanks for the e-mail. Unfortunately we are still having > problems getting the graph window to appear. Here is what we have: > > > > 1) > > > load the y values into tksurfer to see scatter plots. > > We tried to load the .bfloat file as an overlay, and got this > message in the log window: > > > > sclv_read_bfloat_values: error in FunD_New > > > > Not a directory > > > > > > 2) Here are the messages I get in the log window when loading > y_doss-thickness-250lh.fsgd file (No graph window appears): > > > > INFO: ignoring tag Creator > > INFO: ignoring tag SmoothSteps > > INFO: ignoring tag SUBECTS_DIR > > INFO: ignoring tag SynthSeed > > Read one slice only. Did you put all the slices in the same > directory?> WARNING: Could not get the graph title. > > WARNING: Could not get the measurement label. > > WARNING: Could not get the subject name. > > WARNING: Could not get the data file name. > > ERROR: Could not get number of classes. > > > > > > Thanks for your help, > > > > Robert > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > Kevin Teich > > > >

2 1

Re: [Freesurfer] scatter plot of multiple subjects thickness data in tksurfer
by Robert D Twomey 03 Jun '04

03 Jun '04

Hi Brian, Thanks for the e-mail. Unfortunately we are still having problems getting the graph window to appear. Here is what we have: 1) > load the y values into tksurfer to see scatter plots. We tried to load the .bfloat file as an overlay, and got this message in the log window: sclv_read_bfloat_values: error in FunD_New Not a directory 2) Here are the messages I get in the log window when loading y_doss-thickness-250lh.fsgd file (No graph window appears): INFO: ignoring tag Creator INFO: ignoring tag SmoothSteps INFO: ignoring tag SUBECTS_DIR INFO: ignoring tag SynthSeed Read one slice only. Did you put all the slices in the same directory? WARNING: Could not get the graph title. WARNING: Could not get the measurement label. WARNING: Could not get the subject name. WARNING: Could not get the data file name. ERROR: Could not get number of classes. Thanks for your help, Robert

2 1

tkmedit cpu usage
by Jason Bacon 03 Jun '04

03 Jun '04

Hi all, Is it normal for tkmedit to saturate the cpu when freesurfer is idle? We have two researchers running the tutorial, and the tkmedit process never stops crunching the cpu, no matter how long it's been since they initiated something. We're running the latest snapshot for Linux and OS/X. Thanks, Jason

2 1

scatter plot of multiple subjects thickness data in tksurfer
by Robert D Twomey 02 Jun '04

02 Jun '04

Hello, I would like to be able to click on a vertex in tksurfer and see a scatter plot of all individual subject's thickness at that vertex--to see what went into our between group comparison (implemented w/ mris_glm) and the resulting sigt value at that point. I saw a display that looked like this before, but I do not remember how to create it. Is this possible, and how do I create the plot? Thank you for your help, Robert Twomey Center for the Study of Learning Georgetown University

2 1

func2roi
by Tamara Knutsen 01 Jun '04

01 Jun '04

i do not yet have any anatomically defined area labels, and i have a functional comparison that activates the area i want as my ROI, but some other areas as well. is it possible to manually edit the functionally thresholded mask to have only the ROI i want, by somehow deleting the undesired voxels (or changing their value to 0)? let me know. thanks, t

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 June 2004