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We have acquired data on a few kids and have generated nice surfaces, however, the diffusion data we acquired (102 directions and AP/PA distortion maps) were suspect due to motion and results from Tracula were not ideal.
We have since brought these kids back for a repeat scan, but only acquired the diffusion sequences, and no structural T1. Can we use the original surfaces/output as input to tracula with the DTI data from the repeat MR session?
Jim
"The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution 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 email."
________________________________ 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.
Yes, you can. The only thing that TRACULA uses from the structural is the aparc+aseg, and specifically the relative positions (left, right, anterior, etc.) of each tract with respect to the segmentation labels in the aparc+aseg. It's safe to assume that those positions will not have changed between sessions. If the sessions are not too far apart, the registration between the diffusion and structural within-subject across sessions will probably be OK, but that's something to check.
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Alexopoulos, Dimitrios dimitriosalexopoulos@wustl.edu Sent: Wednesday, May 2, 2018 3:02:16 PM To: Freesurfer support list Subject: [Freesurfer] using diffusion for tracula, but with surfaces from a different MR sessions
External Email - Use Caution
We have acquired data on a few kids and have generated nice surfaces, however, the diffusion data we acquired (102 directions and AP/PA distortion maps) were suspect due to motion and results from Tracula were not ideal.
We have since brought these kids back for a repeat scan, but only acquired the diffusion sequences, and no structural T1.
Can we use the original surfaces/output as input to tracula with the DTI data from the repeat MR session?
Jim
“The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution 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 email.”
________________________________
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.
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The MR sessions were a few weeks apart on 9-10 year olds.
How would I go about confirming the registration between the diffusion and structural data across sessions?
Jim
"The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution 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 email."
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia Sent: Wednesday, May 02, 2018 2:10 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] using diffusion for tracula, but with surfaces from a different MR sessions
Yes, you can. The only thing that TRACULA uses from the structural is the aparc+aseg, and specifically the relative positions (left, right, anterior, etc.) of each tract with respect to the segmentation labels in the aparc+aseg. It's safe to assume that those positions will not have changed between sessions. If the sessions are not too far apart, the registration between the diffusion and structural within-subject across sessions will probably be OK, but that's something to check.
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Alexopoulos, Dimitrios <dimitriosalexopoulos@wustl.edumailto:dimitriosalexopoulos@wustl.edu> Sent: Wednesday, May 2, 2018 3:02:16 PM To: Freesurfer support list Subject: [Freesurfer] using diffusion for tracula, but with surfaces from a different MR sessions
External Email - Use Caution
We have acquired data on a few kids and have generated nice surfaces, however, the diffusion data we acquired (102 directions and AP/PA distortion maps) were suspect due to motion and results from Tracula were not ideal.
We have since brought these kids back for a repeat scan, but only acquired the diffusion sequences, and no structural T1.
Can we use the original surfaces/output as input to tracula with the DTI data from the repeat MR session?
Jim
"The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution 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 email."
________________________________
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.
________________________________ 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.
You should be OK. After running the preprocessing, you can look at the structural segmentation that's been mapped to diffusion space (dlabel/diff/aparc+aseg.bbr.nii.gz) on the FA map (dmri/dtifit_FA.nii.gz).
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Alexopoulos, Dimitrios dimitriosalexopoulos@wustl.edu Sent: Wednesday, May 2, 2018 3:15:38 PM To: Freesurfer support list Subject: Re: [Freesurfer] using diffusion for tracula, but with surfaces from a different MR sessions
External Email - Use Caution
The MR sessions were a few weeks apart on 9-10 year olds.
How would I go about confirming the registration between the diffusion and structural data across sessions?
Jim
“The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution 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 email.”
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia Sent: Wednesday, May 02, 2018 2:10 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] using diffusion for tracula, but with surfaces from a different MR sessions
Yes, you can. The only thing that TRACULA uses from the structural is the aparc+aseg, and specifically the relative positions (left, right, anterior, etc.) of each tract with respect to the segmentation labels in the aparc+aseg. It's safe to assume that those positions will not have changed between sessions. If the sessions are not too far apart, the registration between the diffusion and structural within-subject across sessions will probably be OK, but that's something to check.
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Alexopoulos, Dimitrios <dimitriosalexopoulos@wustl.edumailto:dimitriosalexopoulos@wustl.edu> Sent: Wednesday, May 2, 2018 3:02:16 PM To: Freesurfer support list Subject: [Freesurfer] using diffusion for tracula, but with surfaces from a different MR sessions
External Email - Use Caution
We have acquired data on a few kids and have generated nice surfaces, however, the diffusion data we acquired (102 directions and AP/PA distortion maps) were suspect due to motion and results from Tracula were not ideal.
We have since brought these kids back for a repeat scan, but only acquired the diffusion sequences, and no structural T1.
Can we use the original surfaces/output as input to tracula with the DTI data from the repeat MR session?
Jim
“The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution 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 email.”
________________________________
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.
________________________________
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.
External Email - Use Caution
Anastasia, Thank you for the input.
Jim
"The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution 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 email."
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia Sent: Wednesday, May 02, 2018 2:22 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] using diffusion for tracula, but with surfaces from a different MR sessions
You should be OK. After running the preprocessing, you can look at the structural segmentation that's been mapped to diffusion space (dlabel/diff/aparc+aseg.bbr.nii.gz) on the FA map (dmri/dtifit_FA.nii.gz).
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Alexopoulos, Dimitrios <dimitriosalexopoulos@wustl.edumailto:dimitriosalexopoulos@wustl.edu> Sent: Wednesday, May 2, 2018 3:15:38 PM To: Freesurfer support list Subject: Re: [Freesurfer] using diffusion for tracula, but with surfaces from a different MR sessions
External Email - Use Caution
The MR sessions were a few weeks apart on 9-10 year olds.
How would I go about confirming the registration between the diffusion and structural data across sessions?
Jim
"The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution 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 email."
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia Sent: Wednesday, May 02, 2018 2:10 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] using diffusion for tracula, but with surfaces from a different MR sessions
Yes, you can. The only thing that TRACULA uses from the structural is the aparc+aseg, and specifically the relative positions (left, right, anterior, etc.) of each tract with respect to the segmentation labels in the aparc+aseg. It's safe to assume that those positions will not have changed between sessions. If the sessions are not too far apart, the registration between the diffusion and structural within-subject across sessions will probably be OK, but that's something to check.
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Alexopoulos, Dimitrios <dimitriosalexopoulos@wustl.edumailto:dimitriosalexopoulos@wustl.edu> Sent: Wednesday, May 2, 2018 3:02:16 PM To: Freesurfer support list Subject: [Freesurfer] using diffusion for tracula, but with surfaces from a different MR sessions
External Email - Use Caution
We have acquired data on a few kids and have generated nice surfaces, however, the diffusion data we acquired (102 directions and AP/PA distortion maps) were suspect due to motion and results from Tracula were not ideal.
We have since brought these kids back for a repeat scan, but only acquired the diffusion sequences, and no structural T1.
Can we use the original surfaces/output as input to tracula with the DTI data from the repeat MR session?
Jim
"The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution 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 email."
________________________________
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.
________________________________
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.
________________________________ 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@nmr.mgh.harvard.edu
-
Alexopoulos, Dimitrios -
Yendiki, Anastasia