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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