As indicated in the error message, bvec and bval files generated from dcm2niix directly are in FSL format, which is not compatible with Freesurfer.

Try to use Freesurfer mri_convert to convert the dicom files.

Yujing

From: Ramesh Babu <mgrameshbabu2013@gmail.com>
Sent: Wednesday, December 10, 2025 6:41 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Dimension mismatch in bvec & bval

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Hello,

I am frequently facing this issue in the dt-recon process. I used dcm2niix to convert the dicom files. Now I facing an issue 

Loading BValues from /mnt/conn_analysis/sr_projects_dti/subjects/subj001/dti/subj001_dti.bvec.fixed2
Found 99 bvalues
Loading BVectors from /mnt/conn_analysis/sr_projects_dti/subjects/subj001/dti/subj001_dti.bval.fixed2
Found 11 bvectors
Detected BVec file as FSL formatted
ERROR: DTIstructFromBFiles(): dimension mismatch
 /mnt/conn_analysis/sr_projects_dti/subjects/subj001/dti/subj001_dti.bvec.fixed2 has 99 rows, /mnt/conn_analysis/sr_projects_dti/subjects/subj001/dti/subj001_dti.bval.fixed2 has 11 rows

$ awk '{print NF; exit}' subj001_dti.bval
33
$ awk '{print NF; exit}' subj001_dti.bvec
33

Could you please provide some suggestions? 

Regards

Ramesh