Hi FreeSurfers and Anastasia, TRACULA is working great for me, generating tracts for a sample of 20 subject brains I'm working with. However, for 3 of the brains, I'm receiving incomplete and poorly formed tracts. I've re-run trac-all at least 2x on each subject in case there was a mistake in my original configuration. However, I am reproducing the same results. Does anybody have an idea why I would see these "spotty" tracts?
Thank you for all your help!
Hi Susan - Good to hear that you get good results for most of your subjects. Have you checked the aparc+aseg and the diffusion-to-anatomical registration for the subjects that are failing? I'd check the aparc+aseg_mask (in the dlabel/diff directory) over the FA map to see if there are any holes or misregistration.
a.y
On Mon, 25 Mar 2013, Susan Kuo wrote:
Hi FreeSurfers and Anastasia, TRACULA is working great for me, generating tracts for a sample of 20 subject brains I'm working with. However, for 3 of the brains, I'm receiving incomplete and poorly formed tracts. I've re-run trac-all at least 2x on each subject in case there was a mistake in my original configuration. However, I am reproducing the same results. Does anybody have an idea why I would see these "spotty" tracts?
Thank you for all your help!
-- Susie Kuo NIH
Hi Anastasia, I did as you recommended and checked the diffusion-to-anatomical registration, and the overlay of aparc+aseg_mask on FA, and these views seem to be good. Upon closer inspection, what I find is that there are incipient 'bits' of all the tracts, but they seem to not have 'grown', though they are in the proper space (comparing them to good brains that yielded the full complement of tracts). Is there a configuration in your TRACULA that controls the growing of the tracts specifically? Perhaps I should look into that.
Thank you, btw, for your very prompt reply yesterday- it was much appreciated!
Sincerely, Susie Kuo NIH
On Mon, Mar 25, 2013 at 4:58 PM, Anastasia Yendiki < ayendiki@nmr.mgh.harvard.edu> wrote:
Hi Susan - Good to hear that you get good results for most of your subjects. Have you checked the aparc+aseg and the diffusion-to-anatomical registration for the subjects that are failing? I'd check the aparc+aseg_mask (in the dlabel/diff directory) over the FA map to see if there are any holes or misregistration.
a.y
On Mon, 25 Mar 2013, Susan Kuo wrote:
Hi FreeSurfers and Anastasia, TRACULA is working great for me,
generating tracts for a sample of 20 subject brains I'm working with. However, for 3 of the brains, I'm receiving incomplete and poorly formed tracts. I've re-run trac-all at least 2x on each subject in case there was a mistake in my original configuration. However, I am reproducing the same results. Does anybody have an idea why I would see these "spotty" tracts?
Thank you for all your help!
-- Susie Kuo NIH
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/**compliancelinehttp://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.
Hi Susie - I'm attaching a snapshot from your subject, showing the aparc+aseg overlaid on the FA map. The registration has failed. The frontal lobe has spilled out of the brain, the white matter has spilled into the ventricles.
I strongly recommend using bbregister for the intra-subject registration, which is the default in the latest version of trac-all.
Hope this helps, a.y
On Tue, 26 Mar 2013, Susan Kuo wrote:
Hi Anastasia, I did as you recommended and checked the diffusion-to-anatomical registration, and the overlay of aparc+aseg_mask on FA, and these views seem to be good. Upon closer inspection, what I find is that there are incipient 'bits' of all the tracts, but they seem to not have 'grown', though they are in the proper space (comparing them to good brains that yielded the full complement of tracts). Is there a configuration in your TRACULA that controls the growing of the tracts specifically? Perhaps I should look into that.
Thank you, btw, for your very prompt reply yesterday- it was much appreciated!
Sincerely, Susie Kuo NIH
On Mon, Mar 25, 2013 at 4:58 PM, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:
Hi Susan - Good to hear that you get good results for most of your subjects. Have you checked the aparc+aseg and the diffusion-to-anatomical registration for the subjects that are failing? I'd check the aparc+aseg_mask (in the dlabel/diff directory) over the FA map to see if there are any holes or misregistration. a.y On Mon, 25 Mar 2013, Susan Kuo wrote: Hi FreeSurfers and Anastasia, TRACULA is working great for me, generating tracts for a sample of 20 subject brains I'm working with. However, for 3 of the brains, I'm receiving incomplete and poorly formed tracts. I've re-run trac-all at least 2x on each subject in case there was a mistake in my original configuration. However, I am reproducing the same results. Does anybody have an idea why I would see these "spotty" tracts? Thank you for all your help! -- Susie Kuo NIHThe 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.
-- Susie Kuo
Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle, Sherlock Holmes- Valley of Fear
Hi Anastasia,
I see what you mean. I had previously used the dtifit_FA.nii.gz image and overlaid that with the aparc+aseg+2mm.nii.gz image in /dlabel/diff, using freeview. I didn't end up with the same images as you, however. Can you tell me which images you used to obtain this overlay?
I am going to run bbregister tonight, and I'll let you know how it goes -- I'm hopeful!
Thank you again!
Susie Kuo NIH
On Tue, Mar 26, 2013 at 5:35 PM, Anastasia Yendiki < ayendiki@nmr.mgh.harvard.edu> wrote:
Hi Susie - I'm attaching a snapshot from your subject, showing the aparc+aseg overlaid on the FA map. The registration has failed. The frontal lobe has spilled out of the brain, the white matter has spilled into the ventricles.
I strongly recommend using bbregister for the intra-subject registration, which is the default in the latest version of trac-all.
Hope this helps, a.y
On Tue, 26 Mar 2013, Susan Kuo wrote:
Hi Anastasia, I did as you recommended and checked the
diffusion-to-anatomical registration, and the overlay of aparc+aseg_mask on FA, and these views seem to be good. Upon closer inspection, what I find is that there are incipient 'bits' of all the tracts, but they seem to not have 'grown', though they are in the proper space (comparing them to good brains that yielded the full complement of tracts). Is there a configuration in your TRACULA that controls the growing of the tracts specifically? Perhaps I should look into that.
Thank you, btw, for your very prompt reply yesterday- it was much appreciated!
Sincerely, Susie Kuo NIH
On Mon, Mar 25, 2013 at 4:58 PM, Anastasia Yendiki < ayendiki@nmr.mgh.harvard.edu> wrote:
Hi Susan - Good to hear that you get good results for most of your subjects. Have you checked the aparc+aseg and thediffusion-to-anatomical registration for the subjects that are failing? I'd check the aparc+aseg_mask (in the dlabel/diff directory) over the FA map to see if there are any holes or misregistration.
a.y On Mon, 25 Mar 2013, Susan Kuo wrote: Hi FreeSurfers and Anastasia, TRACULA is working great for me, generating tracts for a sample of 20 subject brains I'm working with. However, for 3 of the brains, I'm receiving incomplete and poorly formed tracts. I've re-run trac-all at least 2x on each subject in case there was a mistake in my original configuration. However, I am reproducing the same results. Does anybody have an idea why I would see these "spotty" tracts? Thank you for all your help! -- Susie Kuo NIHThe 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/**compliancelinehttp://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.
-- Susie Kuo
Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle, Sherlock Holmes- Valley of Fear
Hi Susie - Everything under dlabel/diff is mapped to DWI space (either with flirt or with bbregister, whichever you use). The one in my screenshot was dlabel/diff/aparc+aseg.flt.nii.gz.
a.y
On Wed, 27 Mar 2013, Susan Kuo wrote:
Hi Anastasia, I see what you mean. I had previously used the dtifit_FA.nii.gz image and overlaid that with the aparc+aseg+2mm.nii.gz image in /dlabel/diff, using freeview. I didn't end up with the same images as you, however. Can you tell me which images you used to obtain this overlay?
I am going to run bbregister tonight, and I'll let you know how it goes -- I'm hopeful!
Thank you again!
Susie Kuo NIH
On Tue, Mar 26, 2013 at 5:35 PM, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:
Hi Susie - I'm attaching a snapshot from your subject, showing the aparc+aseg overlaid on the FA map. The registration has failed. The frontal lobe has spilled out of the brain, the white matter has spilled into the ventricles. I strongly recommend using bbregister for the intra-subject registration, which is the default in the latest version of trac-all. Hope this helps, a.y On Tue, 26 Mar 2013, Susan Kuo wrote: Hi Anastasia, I did as you recommended and checked the diffusion-to-anatomical registration, and the overlay of aparc+aseg_mask on FA, and these views seem to be good. Upon closer inspection, what I find is that there are incipient 'bits' of all the tracts, but they seem to not have 'grown', though they are in the proper space (comparing them to good brains that yielded the full complement of tracts). Is there a configuration in your TRACULA that controls the growing of the tracts specifically? Perhaps I should look into that. Thank you, btw, for your very prompt reply yesterday- it was much appreciated! Sincerely, Susie Kuo NIH On Mon, Mar 25, 2013 at 4:58 PM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu> wrote: Hi Susan - Good to hear that you get good results for most of your subjects. Have you checked the aparc+aseg and the diffusion-to-anatomical registration for the subjects that are failing? I'd check the aparc+aseg_mask (in the dlabel/diff directory) over the FA map to see if there are any holes or misregistration. a.y On Mon, 25 Mar 2013, Susan Kuo wrote: Hi FreeSurfers and Anastasia, TRACULA is working great for me, generating tracts for a sample of 20 subject brains I'm working with. However, for 3 of the brains, I'm receiving incomplete and poorly formed tracts. I've re-run trac-all at least 2x on each subject in case there was a mistake in my original configuration. However, I am reproducing the same results. Does anybody have an idea why I would see these "spotty" tracts? Thank you for all your help! -- Susie Kuo NIH 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. -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle, Sherlock Holmes- Valley of Fear-- Susie Kuo
Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle, Sherlock Holmes- Valley of Fear
Hi Anastasia, I'm attaching the graphic I arrived at with the command:
freeview -tv <subjectID>/dlabel/diff/aparc+aseg.flt.nii.gz -v
<subjectID>/dmri/dtifit_FA.nii.gz
Here, I used the subject I send you (Sa69845.5) for the subjectID. I could not detect spill over in these images, mostly because the frontal lobe is a little cut off. Did you perhaps use a different viewer? I'm hoping to be able to detect these mis-registrations better for myself in the future. Thanks for all your help!
Sincerely, Susie Kuo NIH
On Wed, Mar 27, 2013 at 1:32 AM, Anastasia Yendiki < ayendiki@nmr.mgh.harvard.edu> wrote:
Hi Susie - Everything under dlabel/diff is mapped to DWI space (either with flirt or with bbregister, whichever you use). The one in my screenshot was dlabel/diff/aparc+aseg.flt.**nii.gz.
a.y
On Wed, 27 Mar 2013, Susan Kuo wrote:
Hi Anastasia,
I see what you mean. I had previously used the dtifit_FA.nii.gz image and overlaid that with the aparc+aseg+2mm.nii.gz image in /dlabel/diff, using freeview. I didn't end up with the same images as you, however. Can you tell me which images you used to obtain this overlay?
I am going to run bbregister tonight, and I'll let you know how it goes
I'm hopeful!
Thank you again!
Susie Kuo NIH
On Tue, Mar 26, 2013 at 5:35 PM, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:
Hi Susie - I'm attaching a snapshot from your subject, showing the aparc+aseg overlaid on the FA map. The registration has failed. The frontal lobe has spilled out of the brain, the white matter has spilled into the ventricles. I strongly recommend using bbregister for the intra-subject registration, which is the default in the latest version of trac-all. Hope this helps, a.y On Tue, 26 Mar 2013, Susan Kuo wrote: Hi Anastasia, I did as you recommended and checked the diffusion-to-anatomical registration, and the overlay of aparc+aseg_mask on FA, and these views seem to be good. Upon closer inspection, what I find is that there are incipient 'bits' of all the tracts, but they seem to not have 'grown', though they are in the proper space (comparing them to good brains that yielded the full complement of tracts). Is there a configuration in your TRACULA that controls the growing of the tracts specifically? Perhaps I should look into that. Thank you, btw, for your very prompt reply yesterday- it was much appreciated! Sincerely, Susie Kuo NIH On Mon, Mar 25, 2013 at 4:58 PM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu> wrote: Hi Susan - Good to hear that you get good results for most of your subjects. Have you checked the aparc+aseg and the diffusion-to-anatomical registration for the subjects that are failing? I'd check the aparc+aseg_mask (in the dlabel/diff directory) over the FA map to see if there are any holes or misregistration. a.y On Mon, 25 Mar 2013, Susan Kuo wrote: Hi FreeSurfers and Anastasia, TRACULA is working great for me, generating tracts for a sample of 20 subject brains I'm working with. However, for 3 of the brains, I'm receiving incomplete and poorly formed tracts. I've re-run trac-all at least 2x on each subject in case there was a mistake in my original configuration. However, I am reproducing the same results. Does anybody have an idea why I would see these "spotty" tracts? Thank you for all your help! -- Susie Kuo NIH 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<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. -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle, Sherlock Holmes- Valley of Fear-- Susie Kuo
Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle, Sherlock Holmes- Valley of Fear
Hi Susie - The -tv (tract volume) option of freeview is designed specifically to display the merged*.mgz output files of tracula. For a regular volume, use -v or no option at all. For best displaying the aparc+aseg, select it in freeview and choose "Lookup Table" from the Color map menu.
Hope this helps, a.y
On Wed, 27 Mar 2013, Susan Kuo wrote:
Hi Anastasia, I'm attaching the graphic I arrived at with the command:
freeview -tv <subjectID>/dlabel/diff/aparc+aseg.flt.nii.gz -v
<subjectID>/dmri/dtifit_FA.nii.gz
Here, I used the subject I send you (Sa69845.5) for the subjectID. I could not detect spill over in these images, mostly because the frontal lobe is a little cut off. Did you perhaps use a different viewer? I'm hoping to be able to detect these mis-registrations better for myself in the future. Thanks for all your help!
Sincerely, Susie Kuo NIH
On Wed, Mar 27, 2013 at 1:32 AM, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:
Hi Susie - Everything under dlabel/diff is mapped to DWI space (either with flirt or with bbregister, whichever you use). The one in my screenshot was dlabel/diff/aparc+aseg.flt.nii.gz. a.y On Wed, 27 Mar 2013, Susan Kuo wrote: Hi Anastasia, I see what you mean. I had previously used the dtifit_FA.nii.gz image and overlaid that with the aparc+aseg+2mm.nii.gz image in /dlabel/diff, using freeview. I didn't end up with the same images as you, however. Can you tell me which images you used to obtain this overlay? I am going to run bbregister tonight, and I'll let you know how it goes -- I'm hopeful! Thank you again! Susie Kuo NIH On Tue, Mar 26, 2013 at 5:35 PM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu> wrote: Hi Susie - I'm attaching a snapshot from your subject, showing the aparc+aseg overlaid on the FA map. The registration has failed. The frontal lobe has spilled out of the brain, the white matter has spilled into the ventricles. I strongly recommend using bbregister for the intra-subject registration, which is the default in the latest version of trac-all. Hope this helps, a.y On Tue, 26 Mar 2013, Susan Kuo wrote: Hi Anastasia, I did as you recommended and checked the diffusion-to-anatomical registration, and the overlay of aparc+aseg_mask on FA, and these views seem to be good. Upon closer inspection, what I find is that there are incipient 'bits' of all the tracts, but they seem to not have 'grown', though they are in the proper space (comparing them to good brains that yielded the full complement of tracts). Is there a configuration in your TRACULA that controls the growing of the tracts specifically? Perhaps I should look into that. Thank you, btw, for your very prompt reply yesterday- it was much appreciated! Sincerely, Susie Kuo NIH On Mon, Mar 25, 2013 at 4:58 PM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu> wrote: Hi Susan - Good to hear that you get good results for most of your subjects. Have you checked the aparc+aseg and the diffusion-to-anatomical registration for the subjects that are failing? I'd check the aparc+aseg_mask (in the dlabel/diff directory) over the FA map to see if there are any holes or misregistration. a.y On Mon, 25 Mar 2013, Susan Kuo wrote: Hi FreeSurfers and Anastasia, TRACULA is working great for me, generating tracts for a sample of 20 subject brains I'm working with. However, for 3 of the brains, I'm receiving incomplete and poorly formed tracts. I've re-run trac-all at least 2x on each subject in case there was a mistake in my original configuration. However, I am reproducing the same results. Does anybody have an idea why I would see these "spotty" tracts? Thank you for all your help! -- Susie Kuo NIH 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. -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle, Sherlock Holmes- Valley of Fear -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle, Sherlock Holmes- Valley of Fear-- Susie Kuo
Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle, Sherlock Holmes- Valley of Fear
Hi Anastasia, Thank you! I can see that the aparc+aseg spilled over badly. I am going to try bbregister, and then re-betting (Brain Extraction Tool-ing) the original image, since the dtifit_FA looks to include non-brain near the frontal lobe. I'll keep you and the FS community updated on the results, in case anybody is curious.
Sincerely, Susie Kuo NIH
On Wed, Mar 27, 2013 at 10:41 AM, Anastasia Yendiki < ayendiki@nmr.mgh.harvard.edu> wrote:
Hi Susie - The -tv (tract volume) option of freeview is designed specifically to display the merged*.mgz output files of tracula. For a regular volume, use -v or no option at all. For best displaying the aparc+aseg, select it in freeview and choose "Lookup Table" from the Color map menu.
Hope this helps, a.y
On Wed, 27 Mar 2013, Susan Kuo wrote:
Hi Anastasia, I'm attaching the graphic I arrived at with the command:
freeview -tv <subjectID>/dlabel/diff/aparc+**aseg.flt.nii.gz -v
<subjectID>/dmri/dtifit_FA.**nii.gz
Here, I used the subject I send you (Sa69845.5) for the subjectID. I could not detect spill over in these images, mostly because the frontal lobe is a little cut off. Did you perhaps use a different viewer? I'm hoping to be able to detect these mis-registrations better for myself in the future. Thanks for all your help!
Sincerely, Susie Kuo NIH
On Wed, Mar 27, 2013 at 1:32 AM, Anastasia Yendiki < ayendiki@nmr.mgh.harvard.edu> wrote:
Hi Susie - Everything under dlabel/diff is mapped to DWI space(either with flirt or with bbregister, whichever you use). The one in my screenshot was dlabel/diff/aparc+aseg.flt.**nii.gz.
a.y On Wed, 27 Mar 2013, Susan Kuo wrote: Hi Anastasia, I see what you mean. I had previously used the dtifit_FA.nii.gz image and overlaid that with the aparc+aseg+2mm.nii.gz image in /dlabel/diff, using freeview. I didn't end up with the same images as you, however. Can you tell me which images you used to obtain this overlay? I am going to run bbregister tonight, and I'll let you know how it goes -- I'm hopeful! Thank you again! Susie Kuo NIH On Tue, Mar 26, 2013 at 5:35 PM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu> wrote: Hi Susie - I'm attaching a snapshot from your subject, showing the aparc+aseg overlaid on the FA map. The registration has failed. The frontal lobe has spilled out of the brain, the white matter has spilled into the ventricles. I strongly recommend using bbregister for the intra-subject registration, which is the default in the latest version of trac-all. Hope this helps, a.y On Tue, 26 Mar 2013, Susan Kuo wrote: Hi Anastasia, I did as you recommended and checked the diffusion-to-anatomical registration, and the overlay of aparc+aseg_mask on FA, and these views seem to be good. Upon closer inspection, what I find is that there are incipient 'bits' of all the tracts, but they seem to not have 'grown', though they are in the proper space (comparing them to good brains that yielded the full complement of tracts). Is there a configuration in your TRACULA that controls the growing of the tracts specifically? Perhaps I should look into that. Thank you, btw, for your very prompt reply yesterday- it was much appreciated! Sincerely, Susie Kuo NIH On Mon, Mar 25, 2013 at 4:58 PM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu> wrote: Hi Susan - Good to hear that you get good results for most of your subjects. Have you checked the aparc+aseg and the diffusion-to-anatomical registration for the subjects that are failing? I'd check the aparc+aseg_mask (in the dlabel/diff directory) over the FA map to see if there are any holes or misregistration. a.y On Mon, 25 Mar 2013, Susan Kuo wrote: Hi FreeSurfers and Anastasia, TRACULA is working great for me, generating tracts for a sample of 20 subject brains I'm working with. However, for 3 of the brains, I'm receiving incomplete and poorly formed tracts. I've re-run trac-all at least 2x on each subject in case there was a mistake in my original configuration. However, I am reproducing the same results. Does anybody have an idea why I would see these "spotty" tracts? Thank you for all your help! -- Susie Kuo NIH 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<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. -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle, Sherlock Holmes- Valley of Fear -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle, Sherlock Holmes- Valley of Fear-- Susie Kuo
Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle, Sherlock Holmes- Valley of Fear
Actually the brain mask used on the diffusion data *is* the aparc+aseg mapped to diffusion space, so the reason you see that extra non-brain stuff in the FA map is because the aparc+aseg was not aligned well to it.
So you just need to switch on bbregister and switch off flirt in your configuration file, and then rerun trac-all. If the DWI-to-T1 registration is good, then the masking issue will be solved too.
Good luck! a.y
On Wed, 27 Mar 2013, Susan Kuo wrote:
Hi Anastasia, Thank you! I can see that the aparc+aseg spilled over badly. I am going to try bbregister, and then re-betting (Brain Extraction Tool-ing) the original image, since the dtifit_FA looks to include non-brain near the frontal lobe. I'll keep you and the FS community updated on the results, in case anybody is curious.
Sincerely, Susie Kuo NIH
On Wed, Mar 27, 2013 at 10:41 AM, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:
Hi Susie - The -tv (tract volume) option of freeview is designed specifically to display the merged*.mgz output files of tracula. For a regular volume, use -v or no option at all. For best displaying the aparc+aseg, select it in freeview and choose "Lookup Table" from the Color map menu. Hope this helps, a.y On Wed, 27 Mar 2013, Susan Kuo wrote: Hi Anastasia, I'm attaching the graphic I arrived at with the command: > freeview -tv <subjectID>/dlabel/diff/aparc+aseg.flt.nii.gz -v <subjectID>/dmri/dtifit_FA.nii.gz Here, I used the subject I send you (Sa69845.5) for the subjectID. I could not detect spill over in these images, mostly because the frontal lobe is a little cut off. Did you perhaps use a different viewer? I'm hoping to be able to detect these mis-registrations better for myself in the future. Thanks for all your help! Sincerely, Susie Kuo NIH On Wed, Mar 27, 2013 at 1:32 AM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu> wrote: Hi Susie - Everything under dlabel/diff is mapped to DWI space (either with flirt or with bbregister, whichever you use). The one in my screenshot was dlabel/diff/aparc+aseg.flt.nii.gz. a.y On Wed, 27 Mar 2013, Susan Kuo wrote: Hi Anastasia, I see what you mean. I had previously used the dtifit_FA.nii.gz image and overlaid that with the aparc+aseg+2mm.nii.gz image in /dlabel/diff, using freeview. I didn't end up with the same images as you, however. Can you tell me which images you used to obtain this overlay? I am going to run bbregister tonight, and I'll let you know how it goes -- I'm hopeful! Thank you again! Susie Kuo NIH On Tue, Mar 26, 2013 at 5:35 PM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu> wrote: Hi Susie - I'm attaching a snapshot from your subject, showing the aparc+aseg overlaid on the FA map. The registration has failed. The frontal lobe has spilled out of the brain, the white matter has spilled into the ventricles. I strongly recommend using bbregister for the intra-subject registration, which is the default in the latest version of trac-all. Hope this helps, a.y On Tue, 26 Mar 2013, Susan Kuo wrote: Hi Anastasia, I did as you recommended and checked the diffusion-to-anatomical registration, and the overlay of aparc+aseg_mask on FA, and these views seem to be good. Upon closer inspection, what I find is that there are incipient 'bits' of all the tracts, but they seem to not have 'grown', though they are in the proper space (comparing them to good brains that yielded the full complement of tracts). Is there a configuration in your TRACULA that controls the growing of the tracts specifically? Perhaps I should look into that. Thank you, btw, for your very prompt reply yesterday- it was much appreciated! Sincerely, Susie Kuo NIH On Mon, Mar 25, 2013 at 4:58 PM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu> wrote: Hi Susan - Good to hear that you get good results for most of your subjects. Have you checked the aparc+aseg and the diffusion-to-anatomical registration for the subjects that are failing? I'd check the aparc+aseg_mask (in the dlabel/diff directory) over the FA map to see if there are any holes or misregistration. a.y On Mon, 25 Mar 2013, Susan Kuo wrote: Hi FreeSurfers and Anastasia, TRACULA is working great for me, generating tracts for a sample of 20 subject brains I'm working with. However, for 3 of the brains, I'm receiving incomplete and poorly formed tracts. I've re-run trac-all at least 2x on each subject in case there was a mistake in my original configuration. However, I am reproducing the same results. Does anybody have an idea why I would see these "spotty" tracts? Thank you for all your help! -- Susie Kuo NIH 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. -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle, Sherlock Holmes- Valley of Fear -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle, Sherlock Holmes- Valley of Fear -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle, Sherlock Holmes- Valley of Fear-- Susie Kuo
Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle, Sherlock Holmes- Valley of Fear
Hi Anastasia, I saved out some of the completed trac-all.cmds following each TRACULA 'step', and I see where aparc+aseg is mapped to diffusion space. Thank you again for all your help - my project is starting to look a lot better!
Sincerely, Susie Kuo NIH
On Wed, Mar 27, 2013 at 12:02 PM, Anastasia Yendiki < ayendiki@nmr.mgh.harvard.edu> wrote:
Actually the brain mask used on the diffusion data *is* the aparc+aseg mapped to diffusion space, so the reason you see that extra non-brain stuff in the FA map is because the aparc+aseg was not aligned well to it.
So you just need to switch on bbregister and switch off flirt in your configuration file, and then rerun trac-all. If the DWI-to-T1 registration is good, then the masking issue will be solved too.
Good luck!
a.y
On Wed, 27 Mar 2013, Susan Kuo wrote:
Hi Anastasia, Thank you! I can see that the aparc+aseg spilled over
badly. I am going to try bbregister, and then re-betting (Brain Extraction Tool-ing) the original image, since the dtifit_FA looks to include non-brain near the frontal lobe. I'll keep you and the FS community updated on the results, in case anybody is curious.
Sincerely, Susie Kuo NIH
On Wed, Mar 27, 2013 at 10:41 AM, Anastasia Yendiki < ayendiki@nmr.mgh.harvard.edu> wrote:
Hi Susie - The -tv (tract volume) option of freeview is designed specifically to display the merged*.mgz output files of tracula.For a regular volume, use -v or no option at all. For best displaying the aparc+aseg, select it in freeview and choose "Lookup Table" from the Color map menu.
Hope this helps, a.y On Wed, 27 Mar 2013, Susan Kuo wrote: Hi Anastasia, I'm attaching the graphic I arrived at with the command: > freeview -tv <subjectID>/dlabel/diff/aparc+**aseg.flt.nii.gz -v <subjectID>/dmri/dtifit_FA.**nii.gz
Here, I used the subject I send you (Sa69845.5) for the subjectID. I could not detect spill over in these images, mostly because the frontal lobe is a little cut off. Did you perhaps use a different viewer? I'm hoping to be able to detect these mis-registrations better for myself in the future. Thanks for all your help! Sincerely, Susie Kuo NIH On Wed, Mar 27, 2013 at 1:32 AM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu> wrote: Hi Susie - Everything under dlabel/diff is mapped to DWI space (either with flirt or with bbregister, whichever you use). The one in my screenshot was dlabel/diff/aparc+aseg.flt.**nii.gz. a.y On Wed, 27 Mar 2013, Susan Kuo wrote: Hi Anastasia, I see what you mean. I had previously used the dtifit_FA.nii.gz image and overlaid that with the aparc+aseg+2mm.nii.gz image in /dlabel/diff, using freeview. I didn't end up with the same images as you, however. Can you tell me which images you used to obtain this overlay? I am going to run bbregister tonight, and I'll let you know how it goes -- I'm hopeful! Thank you again! Susie Kuo NIH On Tue, Mar 26, 2013 at 5:35 PM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu> wrote: Hi Susie - I'm attaching a snapshot from your subject, showing the aparc+aseg overlaid on the FA map. The registration has failed. The frontal lobe has spilled out of the brain, the white matter has spilled into the ventricles. I strongly recommend using bbregister for the intra-subject registration, which is the default in the latest version of trac-all. Hope this helps, a.y On Tue, 26 Mar 2013, Susan Kuo wrote: Hi Anastasia, I did as you recommended and checked the diffusion-to-anatomical registration, and the overlay of aparc+aseg_mask on FA, and these views seem to be good. Upon closer inspection, what I find is that there are incipient 'bits' of all the tracts, but they seem to not have 'grown', though they are in the proper space (comparing them to good brains that yielded the full complement of tracts). Is there a configuration in your TRACULA that controls the growing of the tracts specifically? Perhaps I should look into that. Thank you, btw, for your very prompt reply yesterday- it was much appreciated! Sincerely, Susie Kuo NIH On Mon, Mar 25, 2013 at 4:58 PM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu> wrote: Hi Susan - Good to hear that you get good results for most of your subjects. Have you checked the aparc+aseg and the diffusion-to-anatomical registration for the subjects that are failing? I'd check the aparc+aseg_mask (in the dlabel/diff directory) over the FA map to see if there are any holes or misregistration. a.y On Mon, 25 Mar 2013, Susan Kuo wrote: Hi FreeSurfers and Anastasia, TRACULA is working great for me, generating tracts for a sample of 20 subject brains I'm working with. However, for 3 of the brains, I'm receiving incomplete and poorly formed tracts. I've re-run trac-all at least 2x on each subject in case there was a mistake in my original configuration. However, I am reproducing the same results. Does anybody have an idea why I would see these "spotty" tracts? Thank you for all your help! -- Susie Kuo NIH 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 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.
-- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle, Sherlock Holmes- Valley of Fear -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle, Sherlock Holmes- Valley of Fear -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle, Sherlock Holmes- Valley of Fear-- Susie Kuo
Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle, Sherlock Holmes- Valley of Fear
freesurfer@nmr.mgh.harvard.edu
-
Anastasia Yendiki -
Susan Kuo