Hi Matt,
I am very grateful for your kindness. After looked through files in working directory by fslinfo, I found a image, named T1_store.2.nii.gz, which I think is the first file be generated in wrong space (91x108x91). Given the name of the file, I traced back the command line in the fMRIvolume script. Finally, I found Line 126 in OneStepResampling.sh which is the command line to generate the file. #---------------- ${FSLDIR}/bin/flirt -interp spline -in ${T1wImage} -ref ${T1wImage} -applyisoxfm ${FinalfMRIResolution} -out ${WD}/${T1wImageFile}.${FinalfMRIResolution} #--------------- So I tested this command line independently using the image in its log file. Repeatedly, the result file was also generated in 91x108x91 space. I noticed that in this script, the fMRI image would be resampled reference to T1_store.2.nii.gz. I think because of the wrong space of T1_store.2.nii.gz, it also effected the fMRI resampling image. However, I notice a comment above Line 126 in OneStepResampling.sh. #------ NB: don't use FLIRT to do spline interpolation with -applyisoxfm for the 2mm and 1 mm cases because it dosen't know the peculiarities of the MNI template FOVs #------ I wonder if it give a cue to the problem? Sincerely, Qunjun _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users