OK, I understand now. That is not currently possible with tkmedit/tksurfer. Kevin would have to add something to do that, and it will probably not be that easy. There are some other things I want to add in terms of graphing in tkmedit/surfer, and I'll keep this in mind.

doug

On Mon, 13 Nov 2006 raij@nmr.mgh.harvard.edu wrote:

Ok Doug, I guess I should have talked about time courses instead of overlays. Let me clarify:

on machine stim (via remote VNC): nmr-dev-env cd /space/cuzco/7/user/raij/avml_fmri_mctogether setenv SUBJECTS_DIR /space/cognito/5/users/raij/subjects_mri setenv SUBJECT fsaverage

Launch tksurfer: tksurfer fsaverage lh inflated

Load first set of time courses from the first experiment ("ISI1TR") using the tcl shell: func_load_timecourse fegroup/bold/group_ISI1TR_BERT_ERFIRsm5pf5tpefsub/sphsm10-ffx/h-lh.bhdr 3

Now, as expected, when I click on the brain, I will see 6 waveforms, one for each contrast ("Condition") for the vertex point I selected. (Actually I load a ROI from the tcl shell and set the waveform display to show the mean value within the ROI, but this should not make any difference to the current question.)

Now for the interesting part. I want to overlay more waveforms from another experiment ("ISI2TR") usingthe tcl shell for the same vertex point (or ROI): func_load_timecourse fegroup/bold/group_ISI2TR_BERT_ERFIRsm5pf5tpefsub/sphsm10-ffx/h-lh.bhdr 3

However, instead of getting 6 more waveforms to add to a total of 12 waveforms, the earlier 6 waveforms disappear and I get only the new 6 waveforms.

The question is, how do I get to keep all 12 waveforms on the display?

(Eventually I will even want to load a third experiment to get 6 more waveforms, and finally, switch off all other waveforms except Condition 3 in each of the three experiments, but once the above problem is sorted out then I think I can manage the rest - we already have working tcl scripts for the rest of this).

Thanks,

Tommi

...

Not sure what you mean. tksurfer/tkmedit do not plot overlays, per se. Rather, you pass a timecourse file to it, and is plots the values in the time course file.

raij@nmr.mgh.harvard.edu wrote:

...

Hi Surfers,

To facilitate comparison of ROI BOLD waveforms across different experiments we are trying to find a way to plot time courses of *** multiple overlays *** simultaneously in the tksurfer time course window.

Is there a way to do this using the tcl script? Usually the time course window shows the multiple contrasts for a single overlay, but as soon as I change the overlay, the old time courses are erased and the time courses change to the new overlay. I guess what I am saying is that we would like to avoid erasing the old stuff in the time course window and just keep adding more waveforms from new overlays (with the possibility of still selecting which waveforms will be visible).

We are trying to do this within tksurfer.

Any suggestions are much appreciated!

Thanks,

Tommi

---

Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 USA _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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