Hi Chris, thanks for the heads up on the documentation. I have updated it to read:

--avgwf textfile For each segmentation, computes the average waveform across all the voxels in the segmentation (excluding voxels masked out). The results are saved in an ascii text file with number of rows equal to the number of frames and number of columns equal to the number of segmentations reported. The order of segmentations is the same order as in the summary file.

doug

On 12/04/2012 09:39 PM, Chris McNorgan wrote:

Thanks, Doug

That was quite helpful, and I have just extracted the mean timeseries from one of my parcellations. I just wanted to note a discrepancy between the mri_segstats output and what is indicated in the mri_segstats --help output. According to the program help:

--avgwf textfile For each segmentation, compute an average waveform across all the voxels in the segmentation (excluding voxels masked out). The results are saved in an ascii text file with number of rows equal to the number of frames and number of columns equal to the number of segmentations reported plus 2. The first row is -1 -1 then all of the segid numbers. After that, the first two columns are: (1) 0-based frame number and (2) 0-based frame number times TR.

However when I open the textfile, the average timeseries data appears to be there, but the column and row data indicating the segid and frame numbers and timings are missing. In other words, according to the --help description, there should be TR rows and SEGIDs+2 columns, but I instead have a TR x SEGID matrix (also, I would have thought that there should be TR+1 rows, to allow for the first row to contain the SEGIDs, followed by TR rows of signal data; is that a typo in the help information?). "-1 -1" doesn't appear anywhere in the output. I assume that the columns are written in ascending SEGID order, but I cannot be certain because the first row does not contain the SEGIDs. These problems don't seem insurmountable so long as I am clear as to which matrix entry corresponds to which SEGID at which timepoint. Any idea why the header row and two leftmost frame number and timing columns were omitted from the output?

Thanks

Hi Chris, you're almost there. There are a few mods I'd make to your stream:

1. You can run preproc-sess -s subXX -fsd rest -surface self lhrh -fwhm 0
(without the -mni305 since you are working in the subject's anatomy)
2. mri_segstats \
--annot subXX lh myaparcPXXXXXX \
--i $FUNCTIONALS_DIR/subXX/rest/001/fmcpr.lh.self.nii.gz \
--sum lh_1_16.sum.txt \
--avgwf lh_1_16.wav.txt

So you pass mri_segstats the surface data and the annotation

doug

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