It is definitely possible to display time courses in tksurfer, but I
usually load them from the cmd line with -timecourse. I don't think I've
ever done it from the gui. Kevin will have to look into that error.
If you'd like to try loading from the cmd line then:
cd fegroup/bold/ISI1TR_BERT_ERFIRsm5pf5tpefsub/sph
You will need to paint the HDRs onto fsaverage:
mri_surf2surf --hemi lh --sval h-lh.bhdr --tval h-lh-fsaverage.mgh
--srcsubject ico --trgsubject fsaverage --noreshape
Do the same thing for sig:
cd AV-REST
mri_surf2surf --hemi lh --sval sig-lh.bhdr --tval sig-lh-fsaverage.mgh
--srcsubject ico --trgsubject fsaverage --noreshape
This will create: h-lh-fsaverage.mgh
You can then:
tksurfer fsaverage lh inflated -overlay AV-REST/sig-lh-fsaverage.bhdr
-timecourse h-lh-fsaverage.mgh
doug
[EMAIL PROTECTED] wrote:
Dear Fellow Freesurfers,
I am trying to display HDR waveforms (time courses) for group level FIR
analyses in tksurfer.
When opening the group analysis data with tkmedit and a functional
overlay, obviously some sort of time course data is loaded, because I can
scroll back and forth between the different time points/frames of the
functional overlay (for the specific contrast that I loaded).
However the load timecourse function does not seem to be working.
When attempting to load a hemodynamic waveform, I receive either an error
(func_load_timecourse: error in FunD_New) without opening the HDR window,
or then the time course volume is "interpreted as encoded scalar volume"
and only one time point, of only one contrast, is shown in the HDR window.
I have tried downloading all possible and impossible files related to the
group analysis (.hdr/.bhdr/.bfloat/.dat/.mat/.w) from both within the
specific contrast directory or the one higher level, but they all fail in
either of the two ways above. The wiki, in this case, was not very helpful
in trying to discover which file to load:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial_2fVisualization
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial_2fVisualization
Is this function currently functional? If so, which file should I load?
Details:
group brain = fsaverage
STUDY_DIR = /space/cognito/21/users/raij/avml_fmri_mctogether/
SUBJECTS_DIR = /space/cognito/5/users/raij/subjects_mri/
environment = nmr-std-env on machine ai (FreeSurfer vs >3)
group analysis name = fegroup,
analysis = ISI1TR_BERT_ERFIRsm5pf5tpefsub
example contrast: AV-REST
Thanks for your help!
Tommi
---
Tommi Raij, M.D., Ph.D.
MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging
Bldg 149, 13th St
Charlestown, MA 02129
U.S.A.
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358
Fax: 617-726-7422
In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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