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Hi,
It was my understanding that TRACULA only uses the aparc+aseg segmentation from the standard structural output from FS 7.1.1., and specifically for the relative positions (left, right, anterior, etc.) of each tract with respect to the segmentation labels in the aparc+aseg. Is this correct?
How would we run trac-all if we only had an aprc+aseg from another pipeline that generates FS-compatible outputs? For example, trac-all -preproc -bedp -path -c (where c = dmrirc config file).
Jim
________________________________ 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.
Hi Jim - If the file was called $SUBJECTS_DIR/$subj/mri/aparc+aseg.mgz, included the same labels and followed the same lookup table as the OG aparc+aseg, this could work. Note that, for the new TRACULA (in FS 7.2), we recommend also running the thalamic nuclei segmentation, as it helps with the accuracy of the tracts that terminate or neighbor the thalamus.
Anastasia. ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Alexopoulos, Dimitrios dimitriosalexopoulos@wustl.edu Sent: Wednesday, October 20, 2021 2:54 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Using only a aparc+aseg input file for TRACULA
External Email - Use Caution
External Email - Use Caution
Hi,
It was my understanding that TRACULA only uses the aparc+aseg segmentation from the standard structural output from FS 7.1.1., and specifically for the relative positions (left, right, anterior, etc.) of each tract with respect to the segmentation labels in the aparc+aseg.
Is this correct?
How would we run trac-all if we only had an aprc+aseg from another pipeline that generates FS-compatible outputs?
For example, trac-all -preproc -bedp -path -c (where c = dmrirc config file).
Jim
________________________________
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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Thank you Anastasia.
Jim
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Yendiki, Anastasia Sent: Wednesday, October 20, 2021 2:12 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Using only a aparc+aseg input file for TRACULA
* External Email - Caution * Hi Jim - If the file was called $SUBJECTS_DIR/$subj/mri/aparc+aseg.mgz, included the same labels and followed the same lookup table as the OG aparc+aseg, this could work. Note that, for the new TRACULA (in FS 7.2), we recommend also running the thalamic nuclei segmentation, as it helps with the accuracy of the tracts that terminate or neighbor the thalamus.
Anastasia. ________________________________ 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, October 20, 2021 2:54 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Using only a aparc+aseg input file for TRACULA
External Email - Use Caution
External Email - Use Caution
Hi,
It was my understanding that TRACULA only uses the aparc+aseg segmentation from the standard structural output from FS 7.1.1., and specifically for the relative positions (left, right, anterior, etc.) of each tract with respect to the segmentation labels in the aparc+aseg.
Is this correct?
How would we run trac-all if we only had an aprc+aseg from another pipeline that generates FS-compatible outputs?
For example, trac-all -preproc -bedp -path -c (where c = dmrirc config file).
Jim
________________________________
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.
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Anastasia,
Upon closer inspection the aparc+aseg we have are analogous to the FS labeling, however, the CC is not segmented, it is simply labelled as cortical WM (labels 2/41). Will using Tracula even work at all or will it generate the other tracts but not include the CC minor/major tracts?
Jim
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Yendiki, Anastasia Sent: Wednesday, October 20, 2021 2:12 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Using only a aparc+aseg input file for TRACULA
* External Email - Caution * Hi Jim - If the file was called $SUBJECTS_DIR/$subj/mri/aparc+aseg.mgz, included the same labels and followed the same lookup table as the OG aparc+aseg, this could work. Note that, for the new TRACULA (in FS 7.2), we recommend also running the thalamic nuclei segmentation, as it helps with the accuracy of the tracts that terminate or neighbor the thalamus.
Anastasia. ________________________________ 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, October 20, 2021 2:54 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Using only a aparc+aseg input file for TRACULA
External Email - Use Caution
External Email - Use Caution
Hi,
It was my understanding that TRACULA only uses the aparc+aseg segmentation from the standard structural output from FS 7.1.1., and specifically for the relative positions (left, right, anterior, etc.) of each tract with respect to the segmentation labels in the aparc+aseg.
Is this correct?
How would we run trac-all if we only had an aprc+aseg from another pipeline that generates FS-compatible outputs?
For example, trac-all -preproc -bedp -path -c (where c = dmrirc config file).
Jim
________________________________
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.
Jim, You could run set cmd = (mri_cc -aseg aseg.mgz -o aseg_CCseg.mgz $subj) to get the CC lables. Lilla ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Alexopoulos, Dimitrios dimitriosalexopoulos@wustl.edu Sent: Thursday, October 21, 2021 2:59 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Using only a aparc+aseg input file for TRACULA
External Email - Use Caution
External Email - Use Caution
Anastasia,
Upon closer inspection the aparc+aseg we have are analogous to the FS labeling, however, the CC is not segmented, it is simply labelled as cortical WM (labels 2/41). Will using Tracula even work at all or will it generate the other tracts but not include the CC minor/major tracts?
Jim
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Yendiki, Anastasia Sent: Wednesday, October 20, 2021 2:12 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Using only a aparc+aseg input file for TRACULA
* External Email - Caution *
Hi Jim - If the file was called $SUBJECTS_DIR/$subj/mri/aparc+aseg.mgz, included the same labels and followed the same lookup table as the OG aparc+aseg, this could work. Note that, for the new TRACULA (in FS 7.2), we recommend also running the thalamic nuclei segmentation, as it helps with the accuracy of the tracts that terminate or neighbor the thalamus.
Anastasia.
________________________________
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, October 20, 2021 2:54 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Using only a aparc+aseg input file for TRACULA
External Email - Use Caution
External Email - Use Caution
Hi,
It was my understanding that TRACULA only uses the aparc+aseg segmentation from the standard structural output from FS 7.1.1., and specifically for the relative positions (left, right, anterior, etc.) of each tract with respect to the segmentation labels in the aparc+aseg.
Is this correct?
How would we run trac-all if we only had an aprc+aseg from another pipeline that generates FS-compatible outputs?
For example, trac-all -preproc -bedp -path -c (where c = dmrirc config file).
Jim
________________________________
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.
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Lilla,
But the asegs we're generated using the ABCD-hcp-DCAN infant pipeline, using manually refined ALBERTs atlases, not FS atlases.
Jim .
Get Outlook for Androidhttps://secure-web.cisco.com/1tIdK312nEthYPlHCvhuvt8YzJZqkV1yYDINfxzls_DxVAeI48grjDQy3W67JzwmyA7AmMn54JY_IcABd8GnkbDZWvxa3UtiVM5hxQIRCjvjZlsM1bj6TZwDaJlZ-SotL4KS6p9JsgHnuE_i3rEXdu535xBIzsWsDLuBIIpvReriDArVZYVAFTHQgOnqXpsGySpcQn3R4iujAYVFgkbGJzOr8ypBRhH33BF14uw3LkPNGu-iIJB-Flc0qQRXoSI1Y4pYq45bAT08undfpg6QwPg/https%3A%2F%2Faka.ms%2FAAb9ysg ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Zollei, Lilla,Ph.D. LZOLLEI@mgh.harvard.edu Sent: Thursday, October 21, 2021 3:39:29 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Using only a aparc+aseg input file for TRACULA
* External Email - Caution * Jim, You could run set cmd = (mri_cc -aseg aseg.mgz -o aseg_CCseg.mgz $subj) to get the CC lables. Lilla ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Alexopoulos, Dimitrios dimitriosalexopoulos@wustl.edu Sent: Thursday, October 21, 2021 2:59 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Using only a aparc+aseg input file for TRACULA
External Email - Use Caution
External Email - Use Caution
Anastasia,
Upon closer inspection the aparc+aseg we have are analogous to the FS labeling, however, the CC is not segmented, it is simply labelled as cortical WM (labels 2/41). Will using Tracula even work at all or will it generate the other tracts but not include the CC minor/major tracts?
Jim
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Yendiki, Anastasia Sent: Wednesday, October 20, 2021 2:12 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Using only a aparc+aseg input file for TRACULA
* External Email - Caution *
Hi Jim - If the file was called $SUBJECTS_DIR/$subj/mri/aparc+aseg.mgz, included the same labels and followed the same lookup table as the OG aparc+aseg, this could work. Note that, for the new TRACULA (in FS 7.2), we recommend also running the thalamic nuclei segmentation, as it helps with the accuracy of the tracts that terminate or neighbor the thalamus.
Anastasia.
________________________________
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, October 20, 2021 2:54 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Using only a aparc+aseg input file for TRACULA
External Email - Use Caution
External Email - Use Caution
Hi,
It was my understanding that TRACULA only uses the aparc+aseg segmentation from the standard structural output from FS 7.1.1., and specifically for the relative positions (left, right, anterior, etc.) of each tract with respect to the segmentation labels in the aparc+aseg.
Is this correct?
How would we run trac-all if we only had an aprc+aseg from another pipeline that generates FS-compatible outputs?
For example, trac-all -preproc -bedp -path -c (where c = dmrirc config file).
Jim
________________________________
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.
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Correction Lilla,
I think they are nih atlases in the 21-27mo age group.. We are analyzing the 2yo age group. Could we use the baby FS atlases at that age range since they have the CC segmented to generate the CC on our asegs with the method you suggested below?
Jim
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Alexopoulos, Dimitrios Sent: Thursday, October 21, 2021 5:08 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Using only a aparc+aseg input file for TRACULA
* External Email - Caution *
External Email - Use Caution Lilla,
But the asegs we're generated using the ABCD-hcp-DCAN infant pipeline, using manually refined ALBERTs atlases, not FS atlases.
Jim .
Get Outlook for Androidhttps://secure-web.cisco.com/1tIdK312nEthYPlHCvhuvt8YzJZqkV1yYDINfxzls_DxVAeI48grjDQy3W67JzwmyA7AmMn54JY_IcABd8GnkbDZWvxa3UtiVM5hxQIRCjvjZlsM1bj6TZwDaJlZ-SotL4KS6p9JsgHnuE_i3rEXdu535xBIzsWsDLuBIIpvReriDArVZYVAFTHQgOnqXpsGySpcQn3R4iujAYVFgkbGJzOr8ypBRhH33BF14uw3LkPNGu-iIJB-Flc0qQRXoSI1Y4pYq45bAT08undfpg6QwPg/https%3A%2F%2Faka.ms%2FAAb9ysg ________________________________ 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 Zollei, Lilla,Ph.D. <LZOLLEI@mgh.harvard.edumailto:LZOLLEI@mgh.harvard.edu> Sent: Thursday, October 21, 2021 3:39:29 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Using only a aparc+aseg input file for TRACULA
* External Email - Caution * Jim, You could run set cmd = (mri_cc -aseg aseg.mgz -o aseg_CCseg.mgz $subj) to get the CC lables. Lilla ________________________________ 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: Thursday, October 21, 2021 2:59 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Using only a aparc+aseg input file for TRACULA
External Email - Use Caution
External Email - Use Caution
Anastasia,
Upon closer inspection the aparc+aseg we have are analogous to the FS labeling, however, the CC is not segmented, it is simply labelled as cortical WM (labels 2/41). Will using Tracula even work at all or will it generate the other tracts but not include the CC minor/major tracts?
Jim
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 Yendiki, Anastasia Sent: Wednesday, October 20, 2021 2:12 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Using only a aparc+aseg input file for TRACULA
* External Email - Caution *
Hi Jim - If the file was called $SUBJECTS_DIR/$subj/mri/aparc+aseg.mgz, included the same labels and followed the same lookup table as the OG aparc+aseg, this could work. Note that, for the new TRACULA (in FS 7.2), we recommend also running the thalamic nuclei segmentation, as it helps with the accuracy of the tracts that terminate or neighbor the thalamus.
Anastasia.
________________________________
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, October 20, 2021 2:54 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Using only a aparc+aseg input file for TRACULA
External Email - Use Caution
External Email - Use Caution
Hi,
It was my understanding that TRACULA only uses the aparc+aseg segmentation from the standard structural output from FS 7.1.1., and specifically for the relative positions (left, right, anterior, etc.) of each tract with respect to the segmentation labels in the aparc+aseg.
Is this correct?
How would we run trac-all if we only had an aprc+aseg from another pipeline that generates FS-compatible outputs?
For example, trac-all -preproc -bedp -path -c (where c = dmrirc config file).
Jim
________________________________
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.
________________________________ 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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Lilla,
It worked for the CC into the aseg.
How would I get the CC into the aparc+aseg?
Jim
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Zollei, Lilla,Ph.D. Sent: Thursday, October 21, 2021 3:39 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Using only a aparc+aseg input file for TRACULA
* External Email - Caution * Jim, You could run set cmd = (mri_cc -aseg aseg.mgz -o aseg_CCseg.mgz $subj) to get the CC lables. Lilla ________________________________ 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: Thursday, October 21, 2021 2:59 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Using only a aparc+aseg input file for TRACULA
External Email - Use Caution
External Email - Use Caution
Anastasia,
Upon closer inspection the aparc+aseg we have are analogous to the FS labeling, however, the CC is not segmented, it is simply labelled as cortical WM (labels 2/41). Will using Tracula even work at all or will it generate the other tracts but not include the CC minor/major tracts?
Jim
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 Yendiki, Anastasia Sent: Wednesday, October 20, 2021 2:12 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Using only a aparc+aseg input file for TRACULA
* External Email - Caution *
Hi Jim - If the file was called $SUBJECTS_DIR/$subj/mri/aparc+aseg.mgz, included the same labels and followed the same lookup table as the OG aparc+aseg, this could work. Note that, for the new TRACULA (in FS 7.2), we recommend also running the thalamic nuclei segmentation, as it helps with the accuracy of the tracts that terminate or neighbor the thalamus.
Anastasia.
________________________________
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, October 20, 2021 2:54 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Using only a aparc+aseg input file for TRACULA
External Email - Use Caution
External Email - Use Caution
Hi,
It was my understanding that TRACULA only uses the aparc+aseg segmentation from the standard structural output from FS 7.1.1., and specifically for the relative positions (left, right, anterior, etc.) of each tract with respect to the segmentation labels in the aparc+aseg.
Is this correct?
How would we run trac-all if we only had an aprc+aseg from another pipeline that generates FS-compatible outputs?
For example, trac-all -preproc -bedp -path -c (where c = dmrirc config file).
Jim
________________________________
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 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.
This won't be good for the cc.* tracts for sure (in the new version we have the entire CC covered with 7 subdivisions). TRACULA learns how often the n-th point along tract X falls in or next to label Y from the structural segmentation. If it's learned that a tract goes through label Y=254 half way along its trajectory, and where our segmentation has label 254 yours has something else, it won't a great situation. It could still work though, because other terms of the objective function will drive the fitting (the likelihood term that fits the shape of the tracts to the diffusion orientations, or the anatomical priors in other points along the tract). In general, I'm still surprised by how robust TRACULA turns out to be to various types of snafus. So it's worth trying. ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Alexopoulos, Dimitrios dimitriosalexopoulos@wustl.edu Sent: Thursday, October 21, 2021 2:59 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Using only a aparc+aseg input file for TRACULA
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Anastasia,
Upon closer inspection the aparc+aseg we have are analogous to the FS labeling, however, the CC is not segmented, it is simply labelled as cortical WM (labels 2/41). Will using Tracula even work at all or will it generate the other tracts but not include the CC minor/major tracts?
Jim
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Yendiki, Anastasia Sent: Wednesday, October 20, 2021 2:12 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Using only a aparc+aseg input file for TRACULA
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Hi Jim - If the file was called $SUBJECTS_DIR/$subj/mri/aparc+aseg.mgz, included the same labels and followed the same lookup table as the OG aparc+aseg, this could work. Note that, for the new TRACULA (in FS 7.2), we recommend also running the thalamic nuclei segmentation, as it helps with the accuracy of the tracts that terminate or neighbor the thalamus.
Anastasia.
________________________________
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, October 20, 2021 2:54 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Using only a aparc+aseg input file for TRACULA
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Hi,
It was my understanding that TRACULA only uses the aparc+aseg segmentation from the standard structural output from FS 7.1.1., and specifically for the relative positions (left, right, anterior, etc.) of each tract with respect to the segmentation labels in the aparc+aseg.
Is this correct?
How would we run trac-all if we only had an aprc+aseg from another pipeline that generates FS-compatible outputs?
For example, trac-all -preproc -bedp -path -c (where c = dmrirc config file).
Jim
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We will give 7.2 a try as well. Lilla's suggestion did create/append the CC to the aseg using:
set cmd = (mri_cc -aseg aseg.mgz -o aseg_CCseg.mgz $subj) to get the CC lables.
Thx. Jim
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Yendiki, Anastasia Sent: Thursday, October 21, 2021 6:56 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Using only a aparc+aseg input file for TRACULA
* External Email - Caution * This won't be good for the cc.* tracts for sure (in the new version we have the entire CC covered with 7 subdivisions). TRACULA learns how often the n-th point along tract X falls in or next to label Y from the structural segmentation. If it's learned that a tract goes through label Y=254 half way along its trajectory, and where our segmentation has label 254 yours has something else, it won't a great situation. It could still work though, because other terms of the objective function will drive the fitting (the likelihood term that fits the shape of the tracts to the diffusion orientations, or the anatomical priors in other points along the tract). In general, I'm still surprised by how robust TRACULA turns out to be to various types of snafus. So it's worth trying. ________________________________ 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: Thursday, October 21, 2021 2:59 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Using only a aparc+aseg input file for TRACULA
External Email - Use Caution
External Email - Use Caution
Anastasia,
Upon closer inspection the aparc+aseg we have are analogous to the FS labeling, however, the CC is not segmented, it is simply labelled as cortical WM (labels 2/41). Will using Tracula even work at all or will it generate the other tracts but not include the CC minor/major tracts?
Jim
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 Yendiki, Anastasia Sent: Wednesday, October 20, 2021 2:12 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Using only a aparc+aseg input file for TRACULA
* External Email - Caution *
Hi Jim - If the file was called $SUBJECTS_DIR/$subj/mri/aparc+aseg.mgz, included the same labels and followed the same lookup table as the OG aparc+aseg, this could work. Note that, for the new TRACULA (in FS 7.2), we recommend also running the thalamic nuclei segmentation, as it helps with the accuracy of the tracts that terminate or neighbor the thalamus.
Anastasia.
________________________________
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, October 20, 2021 2:54 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Using only a aparc+aseg input file for TRACULA
External Email - Use Caution
External Email - Use Caution
Hi,
It was my understanding that TRACULA only uses the aparc+aseg segmentation from the standard structural output from FS 7.1.1., and specifically for the relative positions (left, right, anterior, etc.) of each tract with respect to the segmentation labels in the aparc+aseg.
Is this correct?
How would we run trac-all if we only had an aprc+aseg from another pipeline that generates FS-compatible outputs?
For example, trac-all -preproc -bedp -path -c (where c = dmrirc config file).
Jim
________________________________
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
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Alexopoulos, Dimitrios -
Yendiki, Anastasia -
Zollei, Lilla,Ph.D.