Hi all,
I have BOLD data from a breathhold task that I want to analyze using 3dDeconvolve, but I'm not sure how to proceed. I will begin by providing some context for my question.
The scan length was 5 minutes and 24 seconds (including 12s of scanner warm-up. There were a total of 78 TRs, with each TR = 4s (to accomodate BOLD and ASL scanning; I'm focusing on the BOLD piece right now).
The timing of the breathhold task was as follows:
0 = 1st rest onset
47 = 2nd rest onset
94 = 3rd rest onset
141 = 4th rest onset
188 = 5th rest onset
235 = 6th rest onset
282 = final rest onset
30 = breathe out onset
77 = breathe out onset
124 = breathe out onset
171 = breathe out onset
218 = breathe out onset
265 = breathe out onset
312 = final rest offset
32 = breathhold onset
79 = breathhold onset
126 = breathhold onset
173 = breathhold onset
220 = breathhold onset
267 = breathhold onset
From there, the BOLD and ASL data were isolated. The EPI was aligned to the anatomical in native space. I did not extract the brain or warp to MNI, as the superior sagittal sinus is a region of interest. Physiological correction and a lowpass filter was applied. Using the mean time series, a mean delay value was generated in MATLAB by calculating the average time required for the BOLD signal to peak after each breathhold (not including the first breath hold).
I want to remove the first 11 volumes (including the first BH) from the analysis, and to incorporate the mean delay value for each subject. So, I removed the first BH from the .1D stim_times file. Then, for each stimulus time, I subtracted 44 (11TRs x 4s) and added the mean delay value for the subject. Then, I used 3dTcat to remove the first 11TRs from the input data file. Does this make sense?
From here, I'm trying to run the individual-level regression analysis using 3dDeconvolve. But when I run the script I have copy/pasted below (3dDeconvolve_BLOCK.sh), I don't get the expected output files. Do I have this correctly set up? I have also copy/pasted the terminal output below. Any thoughts are greatly appreciated.
Cheers,
Alain
3dDeconvolve_BLOCK.sh
### run the regression analysis
3dDeconvolve -input 101.breathhold.BOLD.nophymotcorr.nii \
-polort 2 \
-num_stimts 1 \
-stim_times 1 breathhold_stimulus.1D 'BLOCK(15,1)' \
-stim_label 1 BH \
-iresp 1 BH.101 \
-jobs 2 \
-fout -tout -rout -bout -x1D X.xmat.1D -xjpeg X.jpg \
-fitts fitts.101 \
-errts errts.101 \
-bucket stats.101
Script started on Sun Apr 24 21:44:00 2016
-------- freesurfer-Darwin-lion-stable-pub-v5.3.0 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /Users/Alain/freesurfer
FSFAST_HOME /Users/Alain/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /Users/Alain/freesurfer_data
MNI_DIR /Users/Alain/freesurfer/mni
FSL_DIR /Users/Alain/fsl
[?1034hbash-3.2$ 3d bash 3d dDeconvolve_BLOCK.sh
++ 3dDeconvolve: AFNI version=AFNI_2011_12_21_1014 (Sep 23 2014) [64-bit]
++ Authored by: B. Douglas Ward, et al.
++ loading dataset 101.breathhold.BOLD.nophymotcorr.nii
++ STAT automask has 15206 voxels (out of 65536 = 23.2%)
++ Skipping check for initial transients
*+ WARNING: Input polort=2; Longest run=308.0 s; Recommended minimum polort=3
++ -stim_times using TR=4 s for stimulus timing conversion
++ -stim_times using TR=4 s for any -iresp output datasets
++ [you can alter the -iresp TR via the -TR_times option]
++ ** -stim_times NOTE ** guessing GLOBAL times if 1 time per line; LOCAL otherwise
++ ** GUESSED ** -stim_times 1 using LOCAL times
++ Number of time points: 77 (no censoring)
+ Number of parameters: 4 [3 baseline ; 1 signal]
++ total shared memory needed = 43,515,904 bytes (about 44 million [mega])
++ mmap() memory allocated: 43,515,904 bytes (about 44 million [mega])
++ Memory required for output bricks = 43,515,904 bytes (about 44 million [mega])
++ Wrote matrix image to file X.jpg
++ Wrote matrix values to file X.xmat.1D
++ ========= Things you can do with the matrix file =========
++ (a) Linear regression with ARMA(1,1) modeling of serial correlation:
3dREMLfit -matrix X.xmat.1D -input 101.breathhold.BOLD.nophymotcorr.nii \
-fout -tout -rout -Rbuck stats.101_REML -Rvar stats.101_REMLvar \
-Rfitts fitts.101_REML -Rerrts errts.101_REML -verb
++ N.B.: 3dREMLfit command above written to file stats.REML_cmd
++ (b) Visualization/analysis of the matrix via ExamineXmat.R
++ (c) Synthesis of sub-model datasets using 3dSynthesize
++ ==========================================================
++ ----- Signal+Baseline matrix condition [X] (77x4): 1.4143 ++ VERY GOOD ++
++ ----- Signal-only matrix condition [X] (77x1): 1 ++ VERY GOOD ++
++ ----- Baseline-only matrix condition [X] (77x3): 1 ++ VERY GOOD ++
++ ----- polort-only matrix condition [X] (77x3): 1 ++ VERY GOOD ++
++ +++++ Matrix inverse average error = 4.47315e-16 ++ VERY GOOD ++
++ Matrix setup time = 0.43 s
++ Voxels in dataset: 65536
++ Voxels per job: 32768
++ Job #1: processing voxels 32768 to 65535; elapsed time=0.559
++ Job #0: processing voxels 0 to 32767; elapsed time=0.570
++ voxel loop:0123456789.0123456789.0123456789.0123456789.012345678++ Job #1 finished; elapsed time=0.806
9.
++ Job #0 waiting for children to finish; elapsed time=0.809
++ Job #0 now finishing up; elapsed time=0.809
++ Wrote bucket dataset into ./stats.101+orig.BRIK
+ created 8 FDR curves in bucket header
++ Wrote iresp 3D+time dataset into ./BH.101+orig.BRIK
++ Wrote 3D+time dataset into ./fitts.101+orig.BRIK
++ Wrote 3D+time dataset into ./errts.101+orig.BRIK
++ Program finished; elapsed time=1.588
bash-3.2$ exit
exit
Script done on Sun Apr 24 21:44:13 2016
