Hi,
I am trying to extract numerical values for BOLD time courses of (a large number of) ROIs. For this purpose I use a tksurfer tcl script. Everything works fine when I only have a small number (~6) of contrasts/stimulus categories (as defined in the paradigm files), but if I increase the number of stimulus categories to 14-18, the script dies without producing anything.
I am able to produce the numerical tables semi-manually with the GUI/tcl shell even for the large number of stimulus categories so I do not quite figure what gives. However, doing this manually for all our data would be impossible. Any suggestions how I could circumvent this problem?
(The visualization part in the script below, that draws the actual time course display, is not necessary for producing the numerical tables, but removing that part of the script does not help - it still dies.)
Any suggestions much appreciated! Also if anyone needs the full script I am happy to send you a copy - however notice that currently one of the command lines only works in the developmental environment (nmr-dev-env).
Cheers,
Tommi
Specs:
on machine ai nmr-dev-env cd /space/cuzco/12/users/raij/avml_fmri_mctogether/ setenv SUBJECTS_DIR /space/cognito/5/users/raij/subjects_mri setenv SUBJECT fsaverage
#Here is the part of the subroutine that does the extraction (to run the whole thing from the master script that sets the variable values, launch run-label-FIR-h.csh in the same directory):
# Set curvature for lh set curv lh.curv read_binary_curv set curvflag 1
# Clear earlier labels labl_remove_all # Clear earlier timecourses func_clear_selection
# Load new label (use actual path to label file instead of $lname if running the script by itself) labl_load $lpath/$lname.label
# Load new timecourse. 3 = No registration needed. # (use actual path to time course file [e.g., bold/<analysisname>/h-lh.bhdr] instead of $timecourse if running the script by itself) func_load_timecourse $timecourse 3
# Set timecourse to show average value across all vertices included in the label set gaLinkedVars(func_graph_avg_mode) 2
# Some draw command, dunno what it does really SendLinkedVarGroup graph
# Select only some of the contrasts for display. Specifically, here turn off contrasts 4-6 # General format: set gGraphSetting(<color>,visible) <0|1> # where <color> is: Red/Green/Blue/Purple/Brown/Pink/Gray/LightBlue/Yellow/Orange # "Red" is condition zero (NULL), "Green" is condition one, etc. set gGraphSetting(Brown,visible) 0 set gGraphSetting(Pink,visible) 0 set gGraphSetting(Gray,visible) 0
# Adjust amplitude (y-axis, % BOLD signal change) scale from -1 to +2 .wwGraph.gwGraph.gwGraph axis config y -min -1 -max 2
# Pre-stimulus baseline correction (to turn OFF, use 0) set gbPreStimOffset 1
# Draw time course display (this command works only in nmr-DEV-env version!) Graph_SelectVerticesFromMode
# Save text file listing the numerical time course values for all categories func_print_timecourse_selection $lpath/$lname-$aname-h.xls
# Save time course display as postscript Graph_SaveToPS $lpath/$lname-$aname-h.ps