Hi,
You can use the flameo command. I have an example below that makes the inputs to flameo and then runs it.
Best,
David
fslmerge -t mask ${MAINDIR}/FSL/2*/L2_m12_action.gfeat/mask.nii.gz
fslmaths mask -Tmin mask
fslmerge -t mean_func ${MAINDIR}/FSL/2*/L2_m12_action.gfeat/mean_func.nii.gz
fslmaths mean_func -Tmean mean_func
fslmerge -t cope${i} ${MAINDIR}/FSL/2*/L2_m12_action.gfeat/stats/cope${i}.nii.gz
fslmaths cope${i} -mas mask cope${i}
fslmerge -t varcope${i} ${MAINDIR}/FSL/2*/L2_m12_action.gfeat/stats/varcope${i}.nii.gz
fslmaths varcope${i} -mas mask varcope${i}
fslmerge -t tdof_t${i} ${MAINDIR}/FSL/2*/L2_m12_action.gfeat/stats/tdof_t${i}.nii.gz
fslmaths tdof_t${i} -mas mask tdof_t${i}
cp ${MAINDIR}/FSL/design.* .
fslmerge -t bg_image ${MAINDIR}/FSL/2*/prestats1.feat/reg/highres.nii.gz
fslmaths bg_image -inm 1000 -Tmean bg_image -odt float
flameo --cope=cope${i} --vc=varcope${i} --dvc=tdof_t${i} --mask=mask --ld=stats --dm=design.mat --cs=design.grp --tc=design.con --runmode=flame1
easythresh stats/zstat1 mask 3.1 0.05 mean_func grot_3p1
> On Mar 30, 2016, at 12:40 PM, Yaroslav Halchenko <[log in to unmask]> wrote:
>
> Please pardon my possibly basic question (but I guess then the answer
> could be obvious): how could I run 2nd level analysis across subjects
> if I have copes (already in MNI space at 2mm)?
>
> Specifying cope files (output by nipype pipeline) as "Inputs are
> 3D cope images from FEAT directories" with a simplistic (mean effect)
> design in Feat GUI or feeding generated .fsf to feat cmdline just leads
> to a somewhat mis-instructed
>
> "Registration has not been run for all of the FEAT directories that you
> have selected for group analysis."
>
> since Feat seems to check reg/examples_func2standard.mat,
> example_func2standard.mat, and design.lev files in the cope
> directories.
>
> What could be the GUI/.fsf/cmdline invocation to provide *eat with all
> necessary information?
>
> Thanks in advance for the clarification
> --
> Yaroslav O. Halchenko
> Center for Open Neuroscience http://centerforopenneuroscience.org
> Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
> Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419
> WWW: http://www.linkedin.com/in/yarik
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