Hi Ansgar,

If you have your own bvals and bvecs, you should add the following extra lines to your dmrirc file.

set bvalfile = /path/to/bvals.txt set bvecfile = /path/to/bvecs.txt set nb0 = *No. of low-b images* (In your case you can set nb0 to 5 and tracula will use the first 5 images to get an average lowb image.)

set dcmroot = /path/to/diffusion_data set dcmlist = Diffusion file (relative to dcmroot) //you can specify any image format if you have given th bvals,bvecs info from the paragraph above.

The training dataset that is distributed as a part of freesurfer consists of 33 subjects. For the purposes of the tutorial we used the first 10 subjects for demonstration and hence used the remaining 23 as training subjects.

Hope that helps,

Please let us know if you have any questions, Priti

Dear Anastasia and Team FreeSurfer, First of all thanks so much for developing TRACULA. I think it has a lot of potential! Here is my question: I'm trying to modify "dmrirc_single_subject" file in order to reflect our local sequence and wondered how you are dealing with DTI repeat sequences for the same subject. We acquire 5 B0s and 30 directional scans twice in a row. So our *Diffusion bvalue Table would look like this: ==================================================================

• 0 0 0 0 0 1000 1000 1000 1000 1000 1000 1000 1000 1000

1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 0 0 0 0 0 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 Now I wonder how I would modify the below default settings from the tutorial data to reflect this: ===================================================================== set subjlist = (Diff001)

set runlist = (1)

# Input diffusion DICOMs (file names relative to dcmroot)

set dcmroot = /usr/local/freesurfer/TUTORIAL_DATA/diffusion_tutorial/

set dcmlist = (Diff001/orig/6-1.dcm)

=====================================================================

Oh also, I noticed that in the wiki you have the following settings:

set trainfile = $TUTORIAL_DATA/diffusion_tutorial/subj,train,difftutorial23.txt

=============================================================================================== In the latest version of the freesurfer distribution I counted 33 subjects for the training algorithm and therefore use:

"subj,train,difftutorial33.txt" pointing to

/usr/local/freesurfer/trctrain/trc001 /usr/local/freesurfer/trctrain/trc002 /usr/local/freesurfer/trctrain/trc003 /usr/local/freesurfer/trctrain/trc004 /usr/local/freesurfer/trctrain/trc005 /usr/local/freesurfer/trctrain/trc006 /usr/local/freesurfer/trctrain/trc007 /usr/local/freesurfer/trctrain/trc008 /usr/local/freesurfer/trctrain/trc009 /usr/local/freesurfer/trctrain/trc010 /usr/local/freesurfer/trctrain/trc011 /usr/local/freesurfer/trctrain/trc012 /usr/local/freesurfer/trctrain/trc013 /usr/local/freesurfer/trctrain/trc014 /usr/local/freesurfer/trctrain/trc015 /usr/local/freesurfer/trctrain/trc016 /usr/local/freesurfer/trctrain/trc017 /usr/local/freesurfer/trctrain/trc018 /usr/local/freesurfer/trctrain/trc019 /usr/local/freesurfer/trctrain/trc020 /usr/local/freesurfer/trctrain/trc021 /usr/local/freesurfer/trctrain/trc022 /usr/local/freesurfer/trctrain/trc023 /usr/local/freesurfer/trctrain/trc024 /usr/local/freesurfer/trctrain/trc025 /usr/local/freesurfer/trctrain/trc026 /usr/local/freesurfer/trctrain/trc027 /usr/local/freesurfer/trctrain/trc028 /usr/local/freesurfer/trctrain/trc029 /usr/local/freesurfer/trctrain/trc030 /usr/local/freesurfer/trctrain/trc031 /usr/local/freesurfer/trctrain/trc032 /usr/local/freesurfer/trctrain/trc033

Does that make sense?

Thanks so much for your help!

Ansgar _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer