Just rerun mris_preproc with the copevar as input instead of the cope. You can also do the same thing with the mask. One thing you have to watch out for is that you set up flame to not try to perform any spatial operations (eg, estimating the fwhm or clustering) as it will try to interpret the surfaces as volumes.

doug

On Tue, 5 Dec 2006, Luetcke, Henry wrote:

Hi all,

I used mris_preproc to generate a surface file from 4 feat directories, as described in the tutorial:

mris_preproc --out lh.cope1.nii.gz --target fsaverage --hemi lh \ --iv fbert1.feat/stats/cope1.nii.gz fbert1.feat/reg/freesurfer/anat2exf.register.dat --iv fbert2.feat/stats/cope1.nii.gz fbert2.feat/reg/freesurfer/anat2exf.register.dat --iv fbert3.feat/stats/cope1.nii.gz fbert3.feat/reg/freesurfer/anat2exf.register.dat --iv fbert4.feat/stats/cope1.nii.gz fbert4.feat/reg/freesurfer/anat2exf.register.dat

I would now like to feed the resulting lh.cope1.nii.gz into fixed-effects analysis with flame and tried the following:

flame -cope=lh.cope1.nii.gz -dm=design.mat -cs=design.grp -tc=design.con -fe

However, flame complains that not all compulsory arguments have been provided. I guess I need a varcope file and a mask file. How can I generate these, given that I am dealing with a surface format file?

Thanks very much in advance for your help.

Best regards,

Henry

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Henry Lütcke Biomedizinische NMR Forschungs GmbH am Max-Planck Institut für Biophysikalische Chemie

Am Fassberg 11 37077 Göttingen Germany

Phone: +49-(0)551-201 1735 Mobile: +49-(0)176-20808069

Mail: hluetck@gwdg.de

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