Thanks for such a prompt reply, Nick!

I realize now that the root issue is probably that I did not use the --fsgd flag when I ran mri_glmfit (because it conflicted with the --X flag, which I used to specify a custom design matrix). So, the y.fsgd file was not created in the glmdir. The y.fsgd file contains quite a few more lines than the original fsgd (including PlotFile and DesignMatFile). So I would like to know if any other lines need to be included in my original fsgd to visualize plots in tksurfer.

Thanks, - Jerry

On Sun, Apr 13, 2008 at 4:17 PM, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote:

Jerry,

Your .fsgd file is probably missing a PlotFile line. Add this before the DesignMatFile line:

PlotFile /path/to/my/y.mgh

where the y.mgh file is the one containing the concatenation of your input data (in qdec, its automatically generated and called y.mgh).

The fsgdPlot.tcl problem is (was) unrelated to this.

Nick

On Sun, 2008-04-13 at 16:08 -0400, Jerry Yeou-Wei Chen wrote:

...

Hello,

I am getting the following error when I try to load an FSGD file in tksurfer. The stats were processed using a custom design matrix without error and I am able to view the results.

FSGD file doesn't contain a PlotFile entry. Error loading GDF

/scratch/freesurfer/subjects/adina/descic39_allSubjects_readyForStats/oldStats_vbmDesign/vbmDesign_fsgd.txt

...

I understand that others have encountered a similar problem with an earlier release due to a missing file (fsgdfPlot.tcl). However, if I understand correctly, this was updated in the current release (4.0.3)

Thanks,

• Jerry

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