[FIX] preproc now mri_converts moco file to match orig

pwighton · Oct 10, 2023 · dd0ebe2 · dd0ebe2
1 parent 9dd31c0
commit dd0ebe2
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/cox1-preproc.bash b/cox1-preproc.bash
@@ -67,8 +67,8 @@ do
     echo "cp ${IMG_REF_DIR}/${PET_IMG_FILE} ${PETSURFER_DIR}/pet.nii.gz"
     cp ${IMG_REF_DIR}/${PET_IMG_FILE} ${PETSURFER_DIR}/pet.nii.gz
 
-    echo "cp ${MOCO_REF_DIR}/${PET_MOCO_FILE} ${PETSURFER_DIR}/pet.mn.nii.gz"
-    cp ${MOCO_REF_DIR}/${PET_MOCO_FILE} ${PETSURFER_DIR}/pet.mn.nii.gz
+    echo "mri_convert --reslice_like ${PETSURFER_DIR}/pet.nii.gz ${MOCO_REF_DIR}/${PET_MOCO_FILE} ${PETSURFER_DIR}/pet.mn.nii.gz"
+    mri_convert --reslice_like ${PETSURFER_DIR}/pet.nii.gz ${MOCO_REF_DIR}/${PET_MOCO_FILE} ${PETSURFER_DIR}/pet.mn.nii.gz
 
     echo "${CALC_FRAMEWISE_AIF_PY} -a ${BLOOD_REF_DIR}/${BLOODSTREAM_FILE} -b ${IMG_REF_DIR}/${PET_JSON_FILE} -o ${PETSURFER_DIR}/aif.bloodstream.dat"
     ${CALC_FRAMEWISE_AIF_PY} -a ${BLOOD_REF_DIR}/${BLOODSTREAM_FILE} -b ${IMG_REF_DIR}/${PET_JSON_FILE} -o ${PETSURFER_DIR}/aif.bloodstream.dat