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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 $DTI_DIR/register.dat
Still, I am facing the same issue. Please provide some solutions.
Best Ramesh
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Gentle reminder.
On Sat, Nov 1, 2025 at 7:16 PM Ramesh Babu mgrameshbabu2013@gmail.com wrote:
Hello,
I am analyzing my DTI scans in Ubuntu 22 LTS with FreeSurfer 8.1. I am facing a registration issue when I run the following script.
# Setting Up Environment BASE_DIR="/mnt/data_analysis/freesurfer_data/sr_dti_analysis/subj02" SUBJECTS_DIR="$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 $DTI_DIR/register.dat
Still, I am facing the same issue. Please provide some solutions.
Best Ramesh
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Dear Experts, Sorry repeating the question. I am expecting to get some reply. My question may be lengthier but need for clarity.
I am analyzing my DTI scans in Ubuntu 22 LTS with FreeSurfer 8.1. I am facing a registration issue when I run the following script.
# Setting Up Environment BASE_DIR="/mnt/data_analysis/freesurfer_data/sr_dti_analysis/subj02" SUBJECTS_DIR="$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 $DTI_DIR/register.dat
Still, I am facing the same issue. Please provide some solutions.
Best Ramesh
Try to convert the register.dat to lta using the following command, and replace register.dat in mri_vol2vol with the converted lta lta_convert --inreg register.dat --outlta register.lta --src <> --trg <>
Yujing
From: Ramesh Babu mgrameshbabu2013@gmail.com Sent: Wednesday, November 19, 2025 6:25 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Re: DTI Registration issue
External Email - Use Caution Dear Experts, Sorry repeating the question. I am expecting to get some reply. My question may be lengthier but need for clarity.
I am analyzing my DTI scans in Ubuntu 22 LTS with FreeSurfer 8.1. I am facing a registration issue when I run the following script.
# Setting Up Environment BASE_DIR="/mnt/data_analysis/freesurfer_data/sr_dti_analysis/subj02" SUBJECTS_DIR="$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 $DTI_DIR/register.dat
Still, I am facing the same issue. Please provide some solutions.
Best Ramesh
External Email - Use Caution
Dear Huang,
After a gap, I started working on DTI. Thank you for providing a script. It modified it as follows lta_convert --inreg "${OUTDIR}/register.dat" \ --outlta "${OUTDIR}/register.lta" \ --src "${OUTDIR}/lowb.nii.gz" \ --trg "$SUBJECTS_DIR/${SUBJECT}/mri/rawavg.mgz" This script has generated generated .lta file.
Then I resampled structural data in the diffusion space by using the script given below. $ mri_vol2vol \ --mov dti/dti_output_folder/lowb.nii.gz \ --targ subj001/mri/wmparc.mgz \ --inv --interp nearest \ --o subj001/mri/wmparc2diff2.mgz \ --reg dti/dti_output_folder/register.lta \ --no-save-reg I got a weird output. Please see the attached file and give your suggestions.
Regards Ramesh
On Thu, Nov 20, 2025 at 8:25 PM Huang, Yujing YHUANG43@mgh.harvard.edu wrote:
Try to convert the register.dat to lta using the following command, and replace register.dat in mri_vol2vol with the converted lta
lta_convert --inreg register.dat --outlta register.lta--src <> --trg <>
Yujing
*From:* Ramesh Babu mgrameshbabu2013@gmail.com *Sent:* Wednesday, November 19, 2025 6:25 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Re: DTI Registration issue
External Email - Use Caution *Dear Experts,
Sorry repeating the question. I am expecting to get some reply. My question may be lengthier but need for clarity.
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 $DTI_DIR/register.dat
Still, I am facing the same issue. Please provide some solutions.
Best
Ramesh
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Hello, I found a solution for what I mentioned in an earlier email. In this line --trg "$SUBJECTS_DIR/${SUBJECT}/mri/rawavg.mgz" I used rawavg. Instead of it, replaced with --trg "$SUBJECTS_DIR/${SUBJECT}/mri/orig.mgz" Now its working well.
On Tue, Dec 9, 2025 at 4:56 PM Ramesh Babu mgrameshbabu2013@gmail.com wrote:
Dear Huang,
After a gap, I started working on DTI. Thank you for providing a script. It modified it as follows lta_convert --inreg "${OUTDIR}/register.dat" \ --outlta "${OUTDIR}/register.lta" \ --src "${OUTDIR}/lowb.nii.gz" \ --trg "$SUBJECTS_DIR/${SUBJECT}/mri/rawavg.mgz" This script has generated generated .lta file.
Then I resampled structural data in the diffusion space by using the script given below. $ mri_vol2vol \ --mov dti/dti_output_folder/lowb.nii.gz \ --targ subj001/mri/wmparc.mgz \ --inv --interp nearest \ --o subj001/mri/wmparc2diff2.mgz \ --reg dti/dti_output_folder/register.lta \ --no-save-reg I got a weird output. Please see the attached file and give your suggestions.
Regards Ramesh
On Thu, Nov 20, 2025 at 8:25 PM Huang, Yujing YHUANG43@mgh.harvard.edu wrote:
Try to convert the register.dat to lta using the following command, and replace register.dat in mri_vol2vol with the converted lta
lta_convert --inreg register.dat --outlta register.lta--src <> --trg <>
Yujing
*From:* Ramesh Babu mgrameshbabu2013@gmail.com *Sent:* Wednesday, November 19, 2025 6:25 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Re: DTI Registration issue
External Email - Use Caution *Dear Experts,
Sorry repeating the question. I am expecting to get some reply. My question may be lengthier but need for clarity.
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
Freesurfer mailing list -- freesurfer@nmr.mgh.harvard.edu To unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.edu
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Ramesh Babu