Hi Elizabeth - From your log file, I see that you're using FreeSurfer 6. Please use the latest version (7.2), as TRACULA has undergone a drastic overhaul in this version. The TRACULA tutorials and documentation on the wiki apply to this new version.

To use field maps, you need one more acquisition parameter: the TE difference between the phase maps of the field mapping sequence. If the field map is in DICOM format, this parameter can be read from the header. If the field map is in NIfTI format, you have to specify this parameter manually in the config file (set dTE = ...)

BTW, if your data are in BIDS format, there is a new script that can figure all this stuff out and auto-generate the TRACULA config file: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg71565.html

Hope this helps, Anastasia. ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Kaplan, Elizabeth elizabeth_kaplan@brown.edu Sent: Thursday, December 9, 2021 11:27 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Fieldmap Images in Nifti Format

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Hi All,

I am working on processing diffusion data with Tracula and am running into an error when attempting to use fieldmaps to compensate for B0 inhomogeneity distortions. The error that I run into reads "ERROR: must specify as many gradient vector tables as DWI scans ". I am able to completely run Tracula processing when specifying dob0 = 0.

Is it possible to use fieldmap images that are in Nifti format or is DICOM format required for this input? Any other guidance is greatly appreciated!