Hi Anastasia,
A question I had about the gradient tables for Tracula - I recently came across this passage from Hui Zhang:
"To correct for any errors that you identify, you need to first modify the gradient table, then repeat the tensor reconstruction. The modification of the gradient table typically involves flipping the signs of the x or y component of all gradient vectors. To determine the correct flipping of the signs in a systematic way, it is necessary to understand why this happens. The reason is that the gradient directions are always defined with respect to some right-handed frame of reference, while the frame of reference of the acquired image data is typically NOT right-handed. This mismatch is the cause of the problem. The sign flipping intends to fix this mismatch and the key is to identify the difference between the two frames of reference in question. In our experience, if the data is acquired on SIEMENS scanners, the signs of x gradient components need to be flipped; for GE scanners, it is usually the y components." (from http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Documentation.Visualizatio... ).
Does this mean that the gradient tables i get from dcm2nii need to have the Y component flipped for my GE acquisitions or is this adjusted in the tracula processing?
Thank you.
Hi Sal - Sorry but I don't know what the interaction of dcm2nii and GE dicom headers is. If anyone else on the list uses dcm2nii on GE dicoms, they can chime in.
To make sure the gradient table is right, I'd always check the primary eigenvector directions (overlaying dmri/dtifit_V1.nii.gz on dmri/dtifit_FA.nii.gz and viewing the former as lines). You just need to do this on one of the data sets from your sequence just to make sure they're oriented correctly. Also, if the gradient vectors need flipping, the tracts from tracula will come out looking visibly wrong. So you'll know that something went wrong.
Hope this helps, a.y
On Thu, 22 Aug 2013, Salil Soman wrote:
Hi Anastasia, A question I had about the gradient tables for Tracula - I recently came across this passage from Hui Zhang:
"To correct for any errors that you identify, you need to first modify the gradient table, then repeat the tensor reconstruction. The modification of the gradient table typically involves flipping the signs of the x or y component of all gradient vectors. To determine the correct flipping of the signs in a systematic way, it is necessary to understand why this happens. The reason is that the gradient directions are always defined with respect to some right-handed frame of reference, while the frame of reference of the acquired image data is typically NOT right-handed. This mismatch is the cause of the problem. The sign flipping intends to fix this mismatch and the key is to identify the difference between the two frames of reference in question. In our experience, if the data is acquired on SIEMENS scanners, the signs of x gradient components need to be flipped; for GE scanners, it is usually the y components."(from http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Documentation.Visua lizationTool).
Does this mean that the gradient tables i get from dcm2nii need to have the Y component flipped for my GE acquisitions or is this adjusted in the tracula processing?
Thank you.
-- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System
I have GE data and never had to make any changes to the gradient table.
On 08/22/2013 01:05 PM, Anastasia Yendiki wrote:
Hi Sal - Sorry but I don't know what the interaction of dcm2nii and GE dicom headers is. If anyone else on the list uses dcm2nii on GE dicoms, they can chime in.
To make sure the gradient table is right, I'd always check the primary eigenvector directions (overlaying dmri/dtifit_V1.nii.gz on dmri/dtifit_FA.nii.gz and viewing the former as lines). You just need to do this on one of the data sets from your sequence just to make sure they're oriented correctly. Also, if the gradient vectors need flipping, the tracts from tracula will come out looking visibly wrong. So you'll know that something went wrong.
Hope this helps, a.y
On Thu, 22 Aug 2013, Salil Soman wrote:
Hi Anastasia, A question I had about the gradient tables for Tracula - I recently came across this passage from Hui Zhang:
"To correct for any errors that you identify, you need to first modify the gradient table, then repeat the tensor reconstruction. The modification of the gradient table typically involves flipping the signs of the x or y component of all gradient vectors. To determine the correct flipping of the signs in a systematic way, it is necessary to understand why this happens. The reason is that the gradient directions are always defined with respect to some right-handed frame of reference, while the frame of reference of the acquired image data is typically NOT right-handed. This mismatch is the cause of the problem. The sign flipping intends to fix this mismatch and the key is to identify the difference between the two frames of reference in question. In our experience, if the data is acquired on SIEMENS scanners, the signs of x gradient components need to be flipped; for GE scanners, it is usually the y components."(from http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Documentation.Visua lizationTool).
Does this mean that the gradient tables i get from dcm2nii need to have the Y component flipped for my GE acquisitions or is this adjusted in the tracula processing?
Thank you.
-- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
-
Anastasia Yendiki -
Chris Watson -
Salil Soman