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Hi Sheena,

Please, see below:

On 13 July 2016 at 03:14, Sheena Sharma <[log in to unmask]> wrote:

Hello all,

I am trying to understand the values reported in the mean_mask_ts.txt file after running Featquery on a higher level feat directory. I understand from a previous post that this txt file contains the COPE value for the filtered_func_data for each subject.

These are the average values within the ROI from the filtered_func_data. They may represent COPEs from lower levels or simply the FMRI timeseries, depending on what the filtered_func_data contains.

My confusion is the units of the values in the text file. At first I thought these may be % signal change values as I had selected the option to "Convert PE/COPE values to %" on the Featquery gui. However the numbers are quite large (see below) and I wouldn't expect a signal change greater than 0.5-1.5% . If these are not percentages, then are they just the COPE values?

They are in the same units as in the filtered_func_data.

To extract the mean and max % signal change for each individual in a ROI would I need to input first level FEAT directories rather than the higher level cope*.feat directories?

The %BOLD signal change would have to be computed at the lower levels, using the signal intensities for that level for each subject. I don't think Featquery will give this as a full time series, but this can be done with a script (i.e., for each subject, compute the %signal change, producing one 3D file, then use fslstats with the ROI as a mask to obtain the cross subject timeseries in percentages).

All the best,

Anderson

Example mean_mask_ts.txt:
55.91312166
70.1213331
29.2250837
40.60217899
25.99467156
54.61878798
-73.20141583
-31.39513564
10.07220322
27.77939051
12.27284728
-1.009457075
-10.67031771
46.3296817
80.98639609
10.13387873
-4.281710488
-18.84343454

Thank you very much for your help!
Sheena