Hi,
We are measuring BOLD % signal change levels (from cespct maps) across separate analyses and the issue of whether the cespct values are pre-stimulus baseline corrected - or not - obviously would be expected to effect the results.
We use a FIR group analysis of a rapid event-related design with a - mkanalysis-sess -prestim = 2 TRs - mkcontrast-sess -rmprestim
We then use a tcl script to plot the numerical values in a table - here we use set gbPreStimOffset 1 func_print_timecourse_selection $lpath/<table-of-time-course-values>.txt
Visually, when we use tksurfer to view the time course results from the bold/<analysisname>/h-lh.bhdr file, then all contrasts included in the analysis are showed at the same time (nice) and the two prestimulus values are included in the display. So far so good. However there is no option to view the results as BOLD % signal change (cespct). A minor annoyance is that the time courses are not baseline corrected despite that we used the -rmprestim option as explained above (they change to be baseline corrected only after we push the View/Configure/Time Course putton Remove prestim).
The only way we have found to visually view (or plot with the tcl script) the cespct values is to look at the time course results inside the folders for specific contrasts (e.g., bold/<analysisname>/A-REST/cespct-lh.bhdr). However here we never see any prestimulus values (otherwise the same full analysis time window as above is shown), so we do not know if the mean of the two prestim points has been subtracted from the amplitudes (= baseline correction).
Below please find the detailed commands for looking at the h-lh.bhdr and cespct curves.
We would appreciate any advice how to get the pre-stim values visible even for cespct and/or double check that the cespct values (when plotted using the tcl script) are baseline corrected.
Thanks!!!
-Tommi
Details:
On machine cuzco nmr-dev-env (or nmr-std-env, does not seem to make a difference in this case) cd /space/cuzco/7/users/raij/avml_fmri_mctogether setenv SUBJECTS_DIR /space/cognito/5/users/raij/subjects_mri setenv SUBJECT fsaverage
Load the h-lh.bhdr curves (prestim baseline are visible, no cespct option): tksurfer fsaverage lh inflated -timecourse fegroup/bold/group_ISI1TR_BERT_ERFIRsm5pf5tpefsub/sphsm10-ffx/h-lh.bhdr
Load the cespct-lh.bhdr curves, no prestim baseline data points visible: tksurfer fsaverage lh inflated -timecourse fegroup/bold/group_ISI1TR_BERT_ERFIRsm5pf5tpefsub/sphsm10-ffx/A-REST/cespct-lh.bhdr
--- Tommi Raij, MD., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.