Thank you Daniel.
This is very helpful.

On 6/29/07, Daniel Glen <[log in to unmask] > wrote:
Freesurfer's mri_convert could be used on a Mac. In AFNI, the DICOM data can be ordered without Osirix by using the Dimon program:

  Dimon -dicom_org -GERT_Reco -infiles_pattern EP/*

The script created by this command uses the to3d program to convert the DICOM files. You can edit this script, GERT_Reco, or use the default output file name provided. to3d can write NIFTI datasets directly by adding .nii or .nii.gz to the prefix specification. You can also use the 3dAFNItoNIFTI program or 3dcopy to create a NIFTI dataset from an AFNI dataset. The bvecs equivalent is a somewhat transposed version of the one used in AFNI's 3dDWItoDT, but you're not using that, so you should create one for FSL directly.

Daniel Glen

On Jun 28, 2007, at 4:53 AM, Agnieszka Burzynska wrote:

Dear all,
I have to switch on working with Mac only. In this case MRIconvert does not work. My idea is to use Afni, convert data to 4D head and Briks files, then to Analyze or niftii type.

  1. Does it work smoothly for DW data?

My friend ordered my dicoms with Osirix and then converted them to niftii, but there is no file like bevcs or bvals.

2. Did we do something wrong or it will simply not work for DTIfit in FSL?


On 28.06.2007 2:58 Uhr, "Marc Dubin" <[log in to unmask]> wrote:

Thanks Dianne. It will give it a try!

On 6/27/07, Dianne Patterson < [log in to unmask]> wrote:

is an excellent converter...


On 6/27/07, Marc Dubin < [log in to unmask]> wrote:
Dear FSL Users:

I have a directory with 2016 DICOM files from one DTI run and was wondering if it is possible to load
these in to FSL and then to save as a single 4D NIFTI file.



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