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
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