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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