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Hi Ruopeng -

Thanks for your reply. As you advised, I used the gradients from the collected data and it gave me an error message which is follows:


--------- Launching dti_recon -----------------


Volume dimension: 173 207 173

Voxel size: 1.050 1.050 1.050

Number of b0's: 1

Number of gradient directions: 143



Reading raw data...99.3%

** nifti_RCI: dims[4] >= nim->dim[4] (143,143)

Process aborted due to error.

Can not read file /autofs/cluster/neuromod/Human_Connectome/Structural_for_7T/126426/dmri/dwi.nii.gz

Process aborted due to error.


I also tried processing with the unpreprocessed data


--------- Launching dti_recon -----------------


Volume dimension: 173 207 173

Voxel size: 1.050 1.050 1.050

Number of b0's: 1

Number of gradient directions: 143



Reading raw data...99.3%

** nifti_RCI: dims[4] >= nim->dim[4] (143,143) Can not read file

Process aborted due to error.

/autofs/cluster/neuromod/Human_Connectome/Structural_for_7T/126426/data.nii.gz

Process aborted due to error.


Could you please help?


Thanks,


Alan


On Thu, May 23, 2019 at 6:27 PM Ruopeng Wang <rpwang@nmr.mgh.harvard.edu> wrote:
You need to use the gradients extracted from the data by FSL (or freesurfer).

Ruopeng

On May 23, 2019, at 5:02 PM, Alan Francis <alandarkenergy@gmail.com> wrote:

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Hi Ruopeng -

I used Diffusion Toolkit to recon DTI data that was preprocessed using FSL. This data is from 7T scanners. I used an Angle threshold of 50. I tried various gradients from 6 - 120, but the images I am getting on trackvis are weird. I have attached a screenshot.

Can you please shed some light on this?

Thank you,

Alan


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Alan N. Francis PhD
Instructor in Psychiatry
Harvard Medical School

Louis V. Gerstner III scholar
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149, 13th street, Charlestown, MA
                                                                                                          
<TrackVis_output.png>_______________________________________________
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_______________________________________________
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Freesurfer@nmr.mgh.harvard.edu
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|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

Alan N. Francis PhD
Instructor in Psychiatry
Harvard Medical School

Louis V. Gerstner III scholar
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149, 13th street, Charlestown, MA