Dear HCP developers, Could you elaborate more on this segment of Freesurferpipeline script:
It is noted because of being compatible with freesurfer we have to downsample our submilimeter data to 1mm resolution. The scripts uses the following commands: flirt -interp spline -in "$T1wImage" -ref "$T1wImage" -applyisoxfm 1 -out "$T1wImageFile"_1mm.nii.gz applywarp --rel --interp=spline -i "$T1wImage" -r "$T1wImageFile"_1mm.nii.gz --premat=$FSLDIR/etc/flirtsch/ident.mat -o "$T1wImageFile"_1mm.nii.gz applywarp --rel --interp=nn -i "$T1wImageBrain" -r "$T1wImageFile"_1mm.nii.gz --premat=$FSLDIR/etc/flirtsch/ident.mat -o "$T1wImageBrainFile"_1mm.nii.gz What is the purpose of those two "applywarp" commands? can't we use sometning like the below command to get around the 1mm resolution issue (assuming that data size is less than 255x255x255)? *mri_convert -i <invol> -o <outvol> -iis 1 -ijs 1 -iks 1* Also right after the applywarp commands, this line follows: fslmaths "$T1wImageFile"_1mm.nii.gz -div $Mean -mul 150 -abs "$T1wImageFile"_1mm.nii.gz Is this for image normalization ? and from where that "150" comes ? Thank you! Mahmoud _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
