Re: [Freesurfer] Diffusion analysis qs
the unflipped vectors because, instead of flipping vectors, we convert both vectors and images to LAS orientation. This ensures that they work both for FSL and for us, and that you can view things correctly in both freeview and fslview, without the subject looking like it's hanging upside down from its bat cave or some such awkward arrangement. In the end, the best way of knowing that the gradient table is correct is to run one example subject through and view the eigenvectors of the tensors as lines to see if they're pointing in the right direction. (Even though the tensors themselves aren't used for tractography, they're good for troubleshooting.) On Mon, 21 Jul 2014, Harms, Michael wrote: FS uses FSL tools under the hood, so you want to use the bvecs that are rotated into the axes of the scan. cheers, -MH --? Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO ?63110 Email:?mha...@wustl.edu From: Rotem Saar saar.ro...@gmail.com Reply-To:?Freesurfer?support list freesurfer@nmr.mgh.harvard.edu Date: Monday, July 21, 2014 1:54 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Diffusion analysis qs - gradient matrix Dear?freesurfer?experts, For diffusion analysis in?freesurfer?- I want to know which gradient matrix ?freesurfer?expects. The thing is - when I look at the gradient matrix created using a MATLAB script that reads the directions from the dicom header - I get one table, but the bvecs file created in MRIconvert (for converting dicoms to nifti) looks different. This is the situation when an angle is applied during the acquisition of the dMRI scans, which means that each subject has its own gradient matrix. So my question is which table should I use for diffusion analysis in ?freesurfer? The one that was created from the dicom header or the one created for NIFTI format using MRIconvert ?? Rotem Saar-Ashkenazy Department of Brain and Cognitive Science Ben Gurion University of the Negev, Beer-Sheva, 84105 School of Social Work Ashkelon Academic College, Ashkelon, 78211 Israel ___ 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] Diffusion analysis qs
the subject looking like it's hanging upside down from its bat cave or some such awkward arrangement. In the end, the best way of knowing that the gradient table is correct is to run one example subject through and view the eigenvectors of the tensors as lines to see if they're pointing in the right direction. (Even though the tensors themselves aren't used for tractography, they're good for troubleshooting.) On Mon, 21 Jul 2014, Harms, Michael wrote: FS uses FSL tools under the hood, so you want to use the bvecs that are rotated into the axes of the scan. cheers, -MH --? Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO ?63110 Email:?mha...@wustl.edu From: Rotem Saar saar.ro...@gmail.com Reply-To:?Freesurfer?support list freesurfer@nmr.mgh.harvard.edu Date: Monday, July 21, 2014 1:54 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Diffusion analysis qs - gradient matrix Dear?freesurfer?experts, For diffusion analysis in?freesurfer?- I want to know which gradient matrix ?freesurfer?expects. The thing is - when I look at the gradient matrix created using a MATLAB script that reads the directions from the dicom header - I get one table, but the bvecs file created in MRIconvert (for converting dicoms to nifti) looks different. This is the situation when an angle is applied during the acquisition of the dMRI scans, which means that each subject has its own gradient matrix. So my question is which table should I use for diffusion analysis in ?freesurfer? The one that was created from the dicom header or the one created for NIFTI format using MRIconvert ?? Rotem Saar-Ashkenazy Department of Brain and Cognitive Science Ben Gurion University of the Negev, Beer-Sheva, 84105 School of Social Work Ashkelon Academic College, Ashkelon, 78211 Israel ___ 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] Diffusion analysis qs
660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO ?63110 Email: mha...@wustl.edu From: Rotem Saar saar.ro...@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Monday, July 21, 2014 1:54 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Diffusion analysis qs - gradient matrix Dear freesurfer experts, For diffusion analysis in freesurfer - I want to know which gradient matrix freesurfer expects. The thing is - when I look at the gradient matrix created using a MATLAB script that reads the directions from the dicom header - I get one table, but the bvecs file created in MRIconvert (for converting dicoms to nifti) looks different. This is the situation when an angle is applied during the acquisition of the dMRI scans, which means that each subject has its own gradient matrix. So my question is which table should I use for diffusion analysis in freesurfer? The one that was created from the dicom header or the one created for NIFTI format using MRIconvert ?? Thanks Rotem Saar-Ashkenazy Department of Brain and Cognitive Science Ben Gurion University of the Negev, Beer-Sheva, 84105 School of Social Work Ashkelon Academic College, Ashkelon, 78211 Israel ___ 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.
Re: [Freesurfer] Diffusion analysis qs
the hood, so you want to use the bvecs that are rotated into the axes of the scan. cheers, -MH --? Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO ?63110 Email: mha...@wustl.edu From: Rotem Saar saar.ro...@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Monday, July 21, 2014 1:54 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Diffusion analysis qs - gradient matrix Dear freesurfer experts, For diffusion analysis in freesurfer - I want to know which gradient matrix freesurfer expects. The thing is - when I look at the gradient matrix created using a MATLAB script that reads the directions from the dicom header - I get one table, but the bvecs file created in MRIconvert (for converting dicoms to nifti) looks different. This is the situation when an angle is applied during the acquisition of the dMRI scans, which means that each subject has its own gradient matrix. So my question is which table should I use for diffusion analysis in freesurfer? The one that was created from the dicom header or the one created for NIFTI format using MRIconvert ?? Thanks Rotem Saar-Ashkenazy Department of Brain and Cognitive Science Ben Gurion University of the Negev, Beer-Sheva, 84105 School of Social Work Ashkelon Academic College, Ashkelon, 78211 Israel ___ 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] Diffusion analysis qs - gradient matrix
Dear freesurfer experts, For diffusion analysis in freesurfer - I want to know which gradient matrix freesurfer expects. The thing is - when I look at the gradient matrix created using a MATLAB script that reads the directions from the dicom header - I get one table, but the bvecs file created in MRIconvert (for converting dicoms to nifti) looks different. This is the situation when an angle is applied during the acquisition of the dMRI scans, which means that each subject has its own gradient matrix. So my question is which table should I use for diffusion analysis in freesurfer? The one that was created from the dicom header or the one created for NIFTI format using MRIconvert ? Thanks Rotem Saar-Ashkenazy Department of Brain and Cognitive Science Ben Gurion University of the Negev, Beer-Sheva, 84105 School of Social Work Ashkelon Academic College, Ashkelon, 78211 Israel ___ 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.
Re: [Freesurfer] Diffusion analysis qs - gradient matrix
FS uses FSL tools under the hood, so you want to use the bvecs that are rotated into the axes of the scan. cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: Rotem Saar saar.ro...@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Monday, July 21, 2014 1:54 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Diffusion analysis qs - gradient matrix Dear freesurfer experts, For diffusion analysis in freesurfer - I want to know which gradient matrix freesurfer expects. The thing is - when I look at the gradient matrix created using a MATLAB script that reads the directions from the dicom header - I get one table, but the bvecs file created in MRIconvert (for converting dicoms to nifti) looks different. This is the situation when an angle is applied during the acquisition of the dMRI scans, which means that each subject has its own gradient matrix. So my question is which table should I use for diffusion analysis in freesurfer? The one that was created from the dicom header or the one created for NIFTI format using MRIconvert ? Thanks Rotem Saar-Ashkenazy Department of Brain and Cognitive Science Ben Gurion University of the Negev, Beer-Sheva, 84105 School of Social Work Ashkelon Academic College, Ashkelon, 78211 Israel The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ 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.
Re: [Freesurfer] Diffusion analysis qs - gradient matrix
It'd be nice if things were that simple, but! Although the pre-processing is done with FSL tools, tractography is done with locally written code. Some gradient sets may appear to work with FSL, but they won't work for us. For example, some dicom converters may perform a L-R flip as preparation for feeding the gradient vectors into FSL. We need the unflipped vectors because, instead of flipping vectors, we convert both vectors and images to LAS orientation. This ensures that they work both for FSL and for us, and that you can view things correctly in both freeview and fslview, without the subject looking like it's hanging upside down from its bat cave or some such awkward arrangement. In the end, the best way of knowing that the gradient table is correct is to run one example subject through and view the eigenvectors of the tensors as lines to see if they're pointing in the right direction. (Even though the tensors themselves aren't used for tractography, they're good for troubleshooting.) On Mon, 21 Jul 2014, Harms, Michael wrote: FS uses FSL tools under the hood, so you want to use the bvecs that are rotated into the axes of the scan. cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: Rotem Saar saar.ro...@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Monday, July 21, 2014 1:54 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Diffusion analysis qs - gradient matrix Dear freesurfer experts, For diffusion analysis in freesurfer - I want to know which gradient matrix freesurfer expects. The thing is - when I look at the gradient matrix created using a MATLAB script that reads the directions from the dicom header - I get one table, but the bvecs file created in MRIconvert (for converting dicoms to nifti) looks different. This is the situation when an angle is applied during the acquisition of the dMRI scans, which means that each subject has its own gradient matrix. So my question is which table should I use for diffusion analysis in freesurfer? The one that was created from the dicom header or the one created for NIFTI format using MRIconvert ? Thanks Rotem Saar-Ashkenazy Department of Brain and Cognitive Science Ben Gurion University of the Negev, Beer-Sheva, 84105 School of Social Work Ashkelon Academic College, Ashkelon, 78211 Israel The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ 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.
