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Hello,
I am analyzing my DTI scans in Ubuntu 22 LTS with FreeSurfer 8.1. I am facing a registration issue when I run the following script.
# Setting Up Environment BASE_DIR="/mnt/data_analysis/freesurfer_data/sr_dti_analysis/subj02" SUBJECTS_DIR="$BASE_DIR" SUBJECT="subj02_fs" export SUBJECTS_DIR SUBJECT
# Define Input and Output Subfolders T1_DICOM="$BASE_DIR/t1_SPGR" DTI_DICOM="$BASE_DIR/epi_dti" T1_NIFTI="$BASE_DIR/t1_nifti" DTI_NIFTI="$BASE_DIR/dti_nifti" DTI_DIR="$BASE_DIR/$SUBJECT/dtrecon" MRI_DIR="${SUBJECTS_DIR}/${SUBJECT}/mri" OUTDIR="$DTI_DIR"
# Resampling subject's wmparc, aparc+aseg, and brain volumes to diffusion space for vol in wmparc aparc+aseg brain; do vol_file="${SUBJECTS_DIR}/${SUBJECT}/mri/${vol}.mgz" vol2diff="${OUTDIR}/${vol}2diff.mgz"
cmd=(mri_vol2vol --mov "${OUTDIR}/lowb.nii" \ --targ "$vol_file" \ --inv \ --interp nearest \ --o "$vol2diff" \ --reg "${OUTDIR}/register.dat" \ --no-save-reg) echo "${cmd[@]}" "${cmd[@]}" done
# Mask FA, ADC, ICV volumes using wmparc2diff.mgz for vol in fa adc ivc; do cmd=(mri_mask "${OUTDIR}/${vol}.nii" \ "${SUBJECTS_DIR}/${SUBJECT}/mri/wmparc2diff.mgz" \ "${OUTDIR}/${vol}-masked.mgz") echo "${cmd[@]}" "${cmd[@]}" done
# Resampling masked volumes to MNI space interp="trilin" template="$FREESURFER_HOME/average/mni152/mri/brain.mgz" # MNI template morph="${SUBJECTS_DIR}/${SUBJECT}/mri/transforms/${SUBJECT}_to_mni.m3z" # Example morph
for vol in fa adc ivc; do vol_file="${OUTDIR}/${vol}-masked.mgz" outvol="${OUTDIR}/${vol}-masked_MNI.mgz"
cmd=(mri_vol2vol --targ "$template" \ --m3z "$morph" \ --noDefM3zPath \ --reg "${OUTDIR}/register.dat" \ --mov "$vol_file" \ --o "$outvol" \ --interp "$interp" \ --no-save-reg) echo "${cmd[@]}" "${cmd[@]}" done
Error: INFO: This REGISTER_DAT transform is valid only for volumes between COR types with c_(r,a,s) = 0. /mnt/data_analysis/freesurfer_data/sr_dti_analysis/subj02/subj02_fs/dtrecon/lowb.nii.gz /mnt/data_analysis/freesurfer_data/sr_dti_analysis/subj02/subj02_fs/mri/wmparc.mgz error: File exists error: LTAchangeType: src geometry must be valid
Then I did the BB registration separately. bbregister --s subj02_fs \ --mov $DTI_DIR/lowb.nii.gz \ --dti \ --init-fsl \ --reg $DTI_DIR/register.dat
Still, I am facing the same issue. Please provide some solutions.
Best Ramesh