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Dear Yujing, I rerun it again by giving the full path in the script. Now it's working well. It accepts the files converted by dcm2niix.

Thank you Ramesh

On Wed, Dec 10, 2025, 9:45 PM Huang, Yujing YHUANG43@mgh.harvard.edu wrote:

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 _______________________________________________ Freesurfer mailing list -- freesurfer@nmr.mgh.harvard.edu To unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.edu

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