The argument to the --s flag should be the name of the subject as was specified when you ran recon-all, eg
recon-all -i t1_SPGR.nii  -s subjectname -all
Then use dt_rcon -s subjectname ...

On 9/12/2024 7:45 AM, Ramesh Babu wrote:

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Dear All,

I am new to dti analysis. I am trying analysis in a single subject. I set the environment as mentioned below.

export DTI_DATA=export DTI_DATA=/mnt/data_analysis/mchp_projects/sneha/dti_analysis/FS_DTI_analysis
export SUBJECTS_DIR=$DTI_DATA/subjects/t1_data/

In the last step, I received this error.
dt_recon --i dti_data.nii --b bvals.txt bvecs.txt --s $SUBJECTS_DIR/t1_SPGR.nii --o dtioutput2

error: mghRead(/mnt/data_analysis/mchp_projects/sneha/dti_analysis/FS_DTI_analysis/subjects/t1_data//t1_SPGR.nii/mri/brainmask.mgz, -1): could not open file

How to get this brain mask? Should it be from subject T1 image or bo map?

I attached the full error report as a text file.

I kindly request you to provide me with a solution.

Thanks in advance

Ramesh

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