AUTOMATING THE OPERATION OF FSL VIA SCRIPTS.
Hi,
I am a postdoc student at Florida International University; I have been using fsl for 3 years by now. I have tried to automate the operation of fsl via scripting. I have been succesful in automating the processing of 1 contrast model, but I have not been able to automate 2 or more contrasts.
I have written the script to mimic the structure of the desing.fsf used in the operation of fsl so I can automate the processing of several datsets with one single contrast, but I have failed to aautomate 2 or more contarst design in fsl (modifying designTemplateFEAT.fsf ).
I have executed manually fsl to process a RH-LH finger tapping paradigm to compare to the file generated by my script. On runing my script with multi contrasts, fsl performs the prestat part but it stops after a while generating the error message ERRORS OCURED DURING THE ANALYSIS.
I have noticed that there is a file called:
design.com
Which has:
/ContrastName1 rh
/ContrastName2 lh
/NumWaves 2
/NumContrasts 2
/PPheights 1.279210e+00 1.279210e+00
/RequiredEffect 1.285 1.285
/Matrix
1.000000e+00 0.000000e+00
-1.000000e+00 0.000000e+00
The same file is generated when I run my script whit the following content:
/ContrastName1
/ContrastName2
I would appreciate any reference or hint to write a script that generates a model with more than 1 contrast. I thought it was only needed to write these lines on the design.fsf file but I was wrong.
# Number of contrasts
set fmri(ncon_orig) 2
set fmri(ncon_real) 2
Any help is deeply appreciated.
--
Magno R. Guillen, PhD
Office: 2220 ECE Building
Phone: (305) 348 - 4106
College of Engineering
Center of Advanced Education & Technology - CATE
Florida International University - FIU
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