Hi HCP Experts:
I have some resting data collected by my group that has been "minimally
preprocessed" with the HCP pipeline, up through ICA-FIX. The data collection
parameters were chosen to mimic those of the actual 3T HCP subjects, including
a TR of 0.72 secs, but with AP/PA encoding directions rather than LR/RL.
The problem: I want to create seed maps with this data using Feat. (So the
inputs to Feat would have names like "rfMRI_3T_REST_AP_hp2000_clean.nii.gz") To
this end, I'm using a first-level design file that does Stats only, but it
aborts while doing setup processes in Prestats. The Feat log contains:
Prestats
/usr/local/opt/fsl-5.0.6-centos5_64/bin/fslmaths prefiltered_func_data
filtered_func_data
/usr/local/opt/fsl-5.0.6-centos5_64/bin/fslmaths filtered_func_data -Tmin
-bin mask -odt char
/usr/local/opt/fsl-5.0.6-centos5_64/bin/fslstats filtered_func_data -k
mask -R | awk '{ print }' -
0.000000
ERROR:: Empty mask image
ERROR:: Empty mask image
ERROR:: Empty mask image
....
I tried manually running the different phases of the second statement above
(ie, first the fslmaths -Tmin operation, then fslmaths -bin, then -odt). The
-Tmin operation appears to yield a reasonable file, but the -bin operation
results in an empty mask. It looks like the -Tmin results may all be negative,
but I'm not sure why this might be a problem. In fact, since Tmin is getting
the lowest value in a timecourse, wouldn't all negatives be likely? I confess I
don't exactly know what the -Tmin operation is trying to accomplish here.
I have contacted the FSL listserv about this, but so far no answer. I'm
assuming Feat is unhappy with input from ICA-FIX, but on inspection in FSLview,
the cleaned file looks ok. Also, ICA-AROMA-cleaned data (not processed with HCP
pipeline) appears to run through Feat correctly.
Would you have any insight as to why this is happening? Also are there other
issues involved in using HCP-pipeline-processed data in Feat that I should be
aware of? (For the moment I have chosen to avoid the MSMAll and
DeDriftAndResample steps.)
Thanks for any help.
-Christina Fales
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