Hi Torsten,
ad 1.:
yes. Just no space inbetween "filtered_func_warp" and ".txt".
ad 2.:
yes, before. But I would try without (as you are motion correcting your
data).
Cheers,
Andreas
Am 17.10.11 14:12 schrieb "Torsten Ruest" unter <[log in to unmask]>:
>Hi Steve,
>
>sorry for the confusion, I may not have been writing out things properly,
>will do this now:
>
>1.I first use feat to pre-process the subjects data, ie. Motion
>correction, B0 unwarping, smoothing and high-pass filtering. I also do
>the linear/nonlinear registration to highres and then to standard space.
>
>2.Then I bring the individuals filtered_func data into standard space:
>applywarp --ref=${FSLDIR}/data/standard/MNI152_T1_2mm --in=$filtered_func
>--warp=$warp --premat=$premat out=$output
>
>3.I apply command-line melodic in temporal concatenation mode on standard
>space data. Note I run it on all subjects (patients and controls) without
>specifying any contrasts:
>melodic -i filtered_func_warp .txt -o melodic -a concat --nomask --nobet
>--mmthresh=0.5 --tr=3 --report -v Oall
>
>4.Then I run dual_regression, specifying the groups. Note I included a
>3rd EV column to account for slightly different acquisition parameters
>(ie there are a several subjects where the acquisition matrix was
>slightly different from the majority of subjects, I attach the simple
>design)
>dual_regression melodic_ados/melodic_IC 1 design.mat design.con 5000
>melodic_dual_reg `cat filtered_func_warp .txt `
>
>So my questions:
>1. Does this procedure look OK to you? Particularly the simple design...
>2. If I wanted to include the motion parameters, I'd need to use fsl_glm
>before? Is this generally recommended to do?
>
>Thank you so much in advance for your patience.
>
>All the best,
>
>Torsten
>
