Hi. I think this looks right, yes. Though, also, I am hoping that before
the next release in a week or two we will get time to put this
functionality into Featquery proper.
Cheers, Steve.
On Wed, 1 Sep 2004, Zach Supalla wrote:
> A week or two ago, I asked a question about using featquery together with
> the effect.sh script he posted. Since then, I've written my own script that
> does exactly this, and it seems to give me good data. I am, however,
> concerned that, since I don't really understand the inner workings of FSL, I
> am only leading myself to believe this is good data, and in fact this method
> is flawed. To anyone who understands exactly what featquery does: is this
> going to give me the adjusted % BOLD signal change that I want?
>
>
>
> #!/bin/ksh
>
> #
> # This script runs a Featquery analysis on your data,
> # and then corrects it for tests that are event-related.
> #
>
> #
> # Specify the path for the subject directories
> #
> ORIG_PATH=/net/lurch3/RetMap/AttLoad/3T/
>
> #
> # Specify the subject directories
> #
> DIRS="s2 s3"
>
> #
> # Specify the sessions
> #
> SESS="run1 run2 run3 run4"
>
> #
> # Specify the pes you want to retrieve.
> #
> FILES="pe1 pe2"
>
> #
> # Specify the name of the directory or directories in which the
> # region of interest masks you want to use are located.
> # These masks should be in standard space for the following
> # code to work without modification.
> #
> MASK_DIRECTORY="run5 run6"
>
> #
> # Give a name for an output report file.
> #
> REPORT="report"
>
> #
> # Adjust the header to reflect your individual conditions
> #
> print "subject session mask PE value" > $REPORT
>
> #
> # Don't worry about this
> #
> for D in $DIRS; do
> for S in $SESS; do
> for M in $MASK_DIRECTORY; do
> for F in $FILES; do
> print -n "${D} ${S} ${M} ${F} " >> $REPORT
>
> #
> # This should be the full directory path of the data.
> # The $D is your directory, and the $S is your subject.
> # If it is wrong, either adjust your directory structure
> # or change this path.
> #
> DATA_PATH=$ORIG_PATH/$D/functional/$S.feat
>
> #
> # Similarly, this should be the full directory path of your mask.
> # Again, if it is wrong, change it.
> #
> MASK=$ORIG_PATH/$D/functional/$M.feat/ROI_reg.hdr
>
> #------------------------------------------------------------------------------------------
> # Shouldn't need to change anything below this point
> #------------------------------------------------------------------------------------------
>
> #
> # Runs featquery on the data, then parses the report
> # for the useful information (the mean)
> #
> featquery 1 $DATA_PATH 1 stats/$F -p $MASK
>
> PE=$(awk 'BEGIN { FS="\t" ; RS="" } { printf($15) }' \
> $DATA_PATH/featquery/report.txt)
>
> #
> # Adjust the signal to reflect percent signal change
> #
> COLUMN=${F#pe}
> DESIGN=$(awk 'BEGIN { column = '"$COLUMN"' ; mn = 0; mx = 0 } \
> matrix == 1 { if ($column < mn) mn=$column; \
> if ($column > mx) mx=$column }\
> /Matrix/ { matrix = 1 }\
> END { printf("%0.3f\n", mx-mn ) }' $DATA_PATH/design.mat)
>
> awk 'BEGIN {printf("%0.3f ", '$PE' * '"$DESIGN"') } ' \
> $DATA_PATH/design.mat >> $REPORT
>
> print " " >> $REPORT
>
> rm $DATA_PATH/featquery/*
> rmdir $DATA_PATH/featquery/
> done
> done
> done
> done
>
Stephen M. Smith DPhil
Associate Director, FMRIB and Analysis Research Coordinator
Oxford University Centre for Functional MRI of the Brain
John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
