Hi all,

I am missing functional data (specifically left hemisphere) from my preprocessed (untalaraiched) data. The data, however, is still present in my time series data.

It seems that up until my 3ddeconvolve step (which creates my functional bucket), my data is still there. However, when I use afni to look at my bucket functional file, only one hemisphere activity is there, even at the lowest thresholds.

Has anyone encountered this problem? I have used the script below for all my subjects and only on this particular subject has it not worked.

Thanks!

#!/bin/bash

protocol=1195
subject=E\-07\-195
anatvol=0004
funcvol=0008

cd $subject
mkdir Results

## do anatomical volume
echo "*** RENDERING ANATOMICAL VOLUME ***"
to3d -session Results -prefix Volume $protocol\-$anatvol*

## Automatically discard the first volume from each functional run:
echo "*** DISCARDING FIRST FUNCTIONAL VOLUMES ***"
mkdir Discard_First_Volume
mv $protocol\-$funcvol*-00001.dcm ./Discard_First_Volume

echo "*** RENDERING FUNCTIONAL RUN ***"
to3d -session Results -prefix TS -epan -time:zt 38 210 2000 alt+z2 $protocol\-$funcvol*

cd Results

## align each functional volume to the first volume of TS
echo "*** PERFORMING MOTION CORRECTION ***"
3dvolreg -dfile motion -base TS+orig\[1\] -tshift -Fourier -prefix TS_reg TS+orig

## movment plots need to be checked
1dplot -volreg -xlabel 'Time Point' 'motion[1-6]' &

echo "*** PERFORMING SPATIAL SMOOTHING ***"
3dmerge -prefix TS_reg_blur6mm -1blur_fwhm 6 -doall TS_reg+orig

echo "*** PERFORMING BANDPASS FILTERING ***"
#3dFourier -prefix TS_reg_blur6mm_bpf -lowpass .5 -highpass .009 -retrend TS_reg_blur6mm+orig

echo "*** ANALYZING CLIP LEVELS ***"
#3dClipLevel TS_reg_blur6mm+orig
cliplevel=`3dClipLevel TS_reg_blur6mm+orig`

echo "*** CALCULATING BASELINE ACTIVATION ***"
#3dTstat -prefix TS_reg_blur6mm_bpf_mean TS_reg_blur6mm_bpf+orig
3dTstat -prefix TS_reg_blur6mm_mean TS_reg_blur6mm+orig


echo "*** CALCULATING PERCENT SIGNAL CHANGE ***"
#3dcalc -a TS_reg_blur6mm_bpf+orig -b TS_reg_blur6mm_bpf_mean+orig -expr "(a/b * 100) * step (b-$cliplevel)" -prefix TS_reg_blur6mm_bpf_scaled (must change clip level)
3dcalc -a TS_reg_blur6mm+orig -b TS_reg_blur6mm_mean+orig -expr "(a/b * 100) * step (b-$cliplevel)" -prefix TS_reg_blur6mm_scaled


echo "*** DETRENDING ***"
#3dDetrend -prefix TS_reg_blur6mm_bpf_scaled_detrended -polort 2 TS_reg_blur6mm_bpf_scaled+orig
3dDetrend -prefix TS_reg_blur6mm_scaled_detrended -polort 2 TS_reg_blur6mm_scaled+orig


echo "RESAMPLING VOXEL SIZE"
#3dresample -dxyz 3 3 3 -prefix TS_reg_blur6mm_bpf_scaled_detrended_resample3 -inset TS_reg_blur6mm_bpf_scaled_detrended+orig
3dresample -dxyz 3 3 3 -prefix TS_reg_blur6mm_scaled_detrended_resample3 -inset TS_reg_blur6mm_scaled_detrended+orig


echo "PERFORMING THE GENERAL LINEAR MODEL"
3dDeconvolve \
-input TS_reg_blur6mm_scaled_detrended_resample3+orig \
-automask \
-polort 2 \
-num_stimts 9 \
-stim_file 1 ../../QuietTrials.1D \
-stim_label 1 Quiet \
-stim_file 2 ../../NoiseTrials.1D \
-stim_label 2 Noise \
-stim_file 3 ../../LoudTrials.1D \
-stim_label 3 Loud \
-stim_file 4 'motion[1]' \
-stim_label 4 roll \
-stim_file 5 'motion[2]' \
-stim_label 5 pitch \
-stim_file 6 'motion[3]' \
-stim_label 6 yaw \
-stim_file 7 'motion[4]' \
-stim_label 7 IS \
-stim_file 8 'motion[5]' \
-stim_label 8 RL \
-stim_file 9 'motion[6]' \
-stim_label 9 AP \
-tout \
-fout \
-bucket MWIN4_bucket \
-num_glt 3 \
-glt 1 ../../Noise-Quiet.mat \
-glt_label 1 Noise-Quiet \
-glt 1 ../../Loud-Quiet.mat \
-glt_label 2 Loud-Quiet \
-glt 1 ../../Loud-Noise.mat \
-glt_label 3 Loud-Noise \

echo "*** DONE!!! ***"
echo "*** NOW REMEMBER TO NUDGE THE ANATOMICAL DATASET ***"
echo "*** THEN RUN THE TALAIRACHING + CLEANUP SCRIPT ***"