External Email - Use Caution
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:
External Email - Use CautionHi 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 PhDInstructor in PsychiatryHarvard Medical School*
*Louis V. Gerstner III scholarMartinos Center for Biomedical Imaging*
*Massachusetts General Hospital*
*149, 13th street, Charlestown, MA*
*alanf@bwh.harvard.edu ezra_wegbreit@brown.edu * *afrancis@mclean.harvard.edu afrancis@mclean.harvard.edu*
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