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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
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
-- |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
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 alanf@bwh.harvard.edu mailto:ezra_wegbreit@brown.edu afrancis@mclean.harvard.edu mailto:afrancis@mclean.harvard.edu
<TrackVis_output.png>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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:
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
-- *|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|*
*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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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Alan Francis -
Ruopeng Wang