Hi@all,
I have a dataset of several MRI T1 images and one Flair. All images of the same subject and were taken in the same session. My goal is to register and segment all those MRI images.
*= A =* In my first try I have used, "recon-all -i image1 -i image2 etc'" for all T1 images (here, I didn't use the Flair images ) . Follow this, I used the " recon-all -all" command. (For about two days...)
Here come Question 1: After all this process, I didn't completely follow the results I got... As I have noticed that I have only one segmentation file (aparc.a2009s+aseg.mgz) ? How can I see the segmentation result with tkmedit in the different brain images ?
*= B =* As I would like the neuroanatomical labels to be inspected for accuracy by a physician. My physician asks to see the segmentation result on top of the Flair images (saying it easier for him to do so on Flair images) So I've used the "recon-all -i image1 -i image2 etc'" command again but this time I've also included the Flair image.
Here come Question 2: However, this time, unfortunately, the "recon-all -iimage1 - i image2 etc'" , failed, saying that: ~~~~~ images have different voxel sizes. Currently not supported, maybe first make conform? Debug info: size(1) = 0.5078, 0.5078, 5.5 size(0) = 0.51, 0.51, 5.5 ~~~~~ Is there something I can do to fix this ?
Thanks for everyone involved in this great project! Highly appreciate your time and efforts.
Best,
Spanier
Hi Spanier
definitely don't invoke recon-all with the FLAIR image. We have some tools in 5.2 for this, but you would call it as a postprocessing step with a different command line in any case. Instead, you can use bbregister to register the flair to the surfaces and resample it.
cheers Bruce
On Sat, 1 Dec 2012, Assaf B. Spanier wrote:
Hi@all, I have a dataset of several MRI T1 images and one Flair. All images of the same subject and were taken in the same session. My goal is to register and segment all those MRI images. = A = In my first try I have used, "recon-all -i image1 -i image2 etc'" for all T1 images (here, I didn't use the Flair images ) . Follow this, I used the "recon-all -all" command. (For about two days...)
Here come Question 1: After all this process, I didn't completely follow the results I got... As I have noticed that I have only one segmentation file (aparc.a2009s+aseg.mgz) ? How can I see the segmentation result with tkmedit in the different brain images ?
= B = As I would like the neuroanatomical labels to be inspected for accuracy by a physician. My physician asks to see the segmentation result on top of the Flair images (saying it easier for him to do so on Flair images) So I've used the "recon-all -i image1 -i image2 etc'" command again but this time I've also included the Flair image.
Here come Question 2: However, this time, unfortunately, the "recon-all -i image1 -i image2 etc'" , failed, saying that:
images have different voxel sizes. Currently not supported, maybe first make conform? Debug info: size(1) = 0.5078, 0.5078, 5.5 size(0) = 0.51, 0.51, 5.5Is there something I can do to fix this ?
Thanks for everyone involved in this great project! Highly appreciate your time and efforts.
Best,
Spanier
Many thanks for the quick response - I would take a look on your suggestion! How about my first question ? About viewing the segmentation results of my first trial ( without the Flair images)
[Please forgive my English :) ]
On Sat, Dec 1, 2012 at 9:53 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Spanier
definitely don't invoke recon-all with the FLAIR image. We have some tools in 5.2 for this, but you would call it as a postprocessing step with a different command line in any case. Instead, you can use bbregister to register the flair to the surfaces and resample it.
cheers Bruce
On Sat, 1 Dec 2012, Assaf B. Spanier wrote:
Hi@all,
I have a dataset of several MRI T1 images and one Flair. All images of the same subject and were taken in the same session. My goal is to register and segment all those MRI images. = A = In my first try I have used, "recon-all -i image1 -i image2 etc'" for all T1 images (here, I didn't use the Flair images ) . Follow this, I used the "recon-all -all" command. (For about two days...)
Here come Question 1: After all this process, I didn't completely follow the results I got... As I have noticed that I have only one segmentation file (aparc.a2009s+aseg.mgz) ? How can I see the segmentation result with tkmedit in the different brain images ?
= B = As I would like the neuroanatomical labels to be inspected for accuracy by a physician. My physician asks to see the segmentation result on top of the Flair images (saying it easier for him to do so on Flair images) So I've used the "recon-all -i image1 -i image2 etc'" command again but this time I've also included the Flair image.
Here come Question 2: However, this time, unfortunately, the "recon-all -i image1 -i image2 etc'" , failed, saying that:
images have different voxel sizes. Currently not supported, maybe first make conform? Debug info: size(1) = 0.5078, 0.5078, 5.5 size(0) = 0.51, 0.51, 5.5Is there something I can do to fix this ?
Thanks for everyone involved in this great project! Highly appreciate your time and efforts.
Best,
Spanier
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.
what different brain images do you mean? You can view them with the surfaces via:
tkmedit <subject name> norm.mgz lh.white -segmentation aparc+aseg.mgz
or
tkmedit <subject name> norm.mgz lh.white -segmentation aparc2009s+aseg.mgz
the tools will be part of FS 5.2 when it comes out in the next month or so. If you really need it before then Nick can get you a beta.
cheers Bruce
On Sat, 1 Dec 2012, Assaf B. Spanier wrote:
Many thanks for the quick response - I would take a look on your suggestion! How about my first question ? About viewing the segmentation results of my first trial ( without the Flair images)
[Please forgive my English :) ]
On Sat, Dec 1, 2012 at 9:53 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Spanier
definitely don't invoke recon-all with the FLAIR image. We have some tools in 5.2 for this, but you would call it as a postprocessing step with a different command line in any case. Instead, you can use bbregister to register the flair to the surfaces and resample it. cheers Bruce On Sat, 1 Dec 2012, Assaf B. Spanier wrote: Hi@all, I have a dataset of several MRI T1 images and one Flair. All images of the same subject and were taken in the same session. My goal is to register and segment all those MRI images. = A = In my first try I have used, "recon-all -i image1 -i image2 etc'" for all T1 images (here, I didn't use the Flair images ) . Follow this, I used the "recon-all -all" command. (For about two days...) Here come Question 1: After all this process, I didn't completely follow the results I got... As I have noticed that I have only one segmentation file (aparc.a2009s+aseg.mgz) ? How can I see the segmentation result with tkmedit in the different brain images ? = B = As I would like the neuroanatomical labels to be inspected for accuracy by a physician. My physician asks to see the segmentation result on top of the Flair images (saying it easier for him to do so on Flair images) So I've used the "recon-all -i image1 -i image2 etc'" command again but this time I've also included the Flair image. Here come Question 2: However, this time, unfortunately, the "recon-all -i image1 -i image2 etc'" , failed, saying that: ~~~~~ images have different voxel sizes. Currently not supported, maybe first make conform? Debug info: size(1) = 0.5078, 0.5078, 5.5 size(0) = 0.51, 0.51, 5.5 ~~~~~ Is there something I can do to fix this ? Thanks for everyone involved in this great project! Highly appreciate your time and efforts. Best, SpanierThe 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.
--
Assaf
We are all - others.
This is exactly the command I've used.
However, as I mentioned my subject has about six or seven T1-MRI images andI have added all of them via the "" recon-all -i image1 -i image2 etc'" command. I can even see those images in the "mri/orig" directory. see: ~~~~~~~~~~ | |-- orig | | |-- 001-iscale.txt | | |-- 001.lta | | |-- 001.mgz | | |-- 002-iscale.txt | | |-- 002.lta | | |-- 002.mgz | | |-- 003-iscale.txt | | |-- 003.lta | | |-- 003.mgz | | |-- 004-iscale.txt | | |-- 004.lta | | `-- 004.mgz ... ... ~~~~~~~~~~
However, I'm not sure how can I used tkmedit to inspect the segmentation of those different MRI images ?
[Hope my question is more clear now]
On Sat, Dec 1, 2012 at 10:31 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
what different brain images do you mean? You can view them with the surfaces via:
tkmedit <subject name> norm.mgz lh.white -segmentation aparc+aseg.mgz
or
tkmedit <subject name> norm.mgz lh.white -segmentation aparc2009s+aseg.mgz
the tools will be part of FS 5.2 when it comes out in the next month or so. If you really need it before then Nick can get you a beta.
cheers Bruce
On Sat, 1 Dec 2012, Assaf B. Spanier wrote:
Many thanks for the quick response - I would take a look on your
suggestion! How about my first question ? About viewing the segmentation results of my first trial ( without the Flair images)
[Please forgive my English :) ]
On Sat, Dec 1, 2012 at 9:53 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Spanier
definitely don't invoke recon-all with the FLAIR image. We have some tools in 5.2 for this, but you would call it as a postprocessing step with a different command line in any case. Instead, you can use bbregister to register the flair to the surfaces and resample it. cheers Bruce On Sat, 1 Dec 2012, Assaf B. Spanier wrote: Hi@all, I have a dataset of several MRI T1 images and one Flair. All images of the same subject and were taken in the same session. My goal is to register and segment all those MRI images. = A = In my first try I have used, "recon-all -i image1 -i image2 etc'" for all T1 images (here, I didn't use the Flair images ) . Follow this, I used the "recon-all -all" command. (For about two days...) Here come Question 1: After all this process, I didn't completely follow the results I got... As I have noticed that I have only one segmentation file (aparc.a2009s+aseg.mgz) ? How can I see the segmentation result with tkmedit in the different brain images ? = B = As I would like the neuroanatomical labels to be inspected for accuracy by a physician. My physician asks to see the segmentation result on top of the Flair images (saying it easier for him to do so on Flair images) So I've used the "recon-all -i image1 -i image2 etc'" command again but this time I've also included the Flair image. Here come Question 2: However, this time, unfortunately, the "recon-all -i image1 -i image2 etc'" , failed, saying that: ~~~~~ images have different voxel sizes. Currently not supported, maybe first make conform? Debug info: size(1) = 0.5078, 0.5078, 5.5 size(0) = 0.51, 0.51, 5.5 ~~~~~ Is there something I can do to fix this ? Thanks for everyone involved in this great project! Highly appreciate your time and efforts. Best, SpanierThe 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.
--
Assaf
We are all - others.
are they different time points or from the same session? What are you trying to achieve? On Sat, 1 Dec 2012, Assaf B. Spanier wrote:
This is exactly the command I've used.
However, as I mentioned my subject has about six or seven T1-MRI images and I have added all of them via the ""recon-all -i image1 -i image2 etc'" command. I can even see those images in the "mri/orig" directory. see:
| |-- orig | | |-- 001-iscale.txt | | |-- 001.lta | | |-- 001.mgz | | |-- 002-iscale.txt | | |-- 002.lta | | |-- 002.mgz | | |-- 003-iscale.txt | | |-- 003.lta | | |-- 003.mgz | | |-- 004-iscale.txt | | |-- 004.lta | | `-- 004.mgz ... ...However, I'm not sure how can I used tkmedit to inspect the segmentation of those different MRI images ?
[Hope my question is more clear now]
On Sat, Dec 1, 2012 at 10:31 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: what different brain images do you mean? You can view them with the surfaces via:
tkmedit <subject name> norm.mgz lh.white -segmentation aparc+aseg.mgz or tkmedit <subject name> norm.mgz lh.white -segmentation aparc2009s+aseg.mgz the tools will be part of FS 5.2 when it comes out in the next month or so. If you really need it before then Nick can get you a beta. cheers Bruce On Sat, 1 Dec 2012, Assaf B. Spanier wrote: Many thanks for the quick response - I would take a look on your suggestion! How about my first question ? About viewing the segmentation results of my first trial ( without the Flair images) [Please forgive my English :) ] On Sat, Dec 1, 2012 at 9:53 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Spanier definitely don't invoke recon-all with the FLAIR image. We have some tools in 5.2 for this, but you would call it as a postprocessing step with a different command line in any case. Instead, you can use bbregister to register the flair to the surfaces and resample it. cheers Bruce On Sat, 1 Dec 2012, Assaf B. Spanier wrote: Hi@all, I have a dataset of several MRI T1 images and one Flair. All images of the same subject and were taken in the same session. My goal is to register and segment all those MRI images. = A = In my first try I have used, "recon-all -i image1 -i image2 etc'" for all T1 images (here, I didn't use the Flair images ) . Follow this, I used the "recon-all -all" command. (For about two days...) Here come Question 1: After all this process, I didn't completely follow the results I got... As I have noticed that I have only one segmentation file (aparc.a2009s+aseg.mgz) ? How can I see the segmentation result with tkmedit in the different brain images ? = B = As I would like the neuroanatomical labels to be inspected for accuracy by a physician. My physician asks to see the segmentation result on top of the Flair images (saying it easier for him to do so on Flair images) So I've used the "recon-all -i image1 -i image2 etc'" command again but this time I've also included the Flair image. Here come Question 2: However, this time, unfortunately, the "recon-all -i image1 -i image2 etc'" , failed, saying that: ~~~~~ images have different voxel sizes. Currently not supported, maybe first make conform? Debug info: size(1) = 0.5078, 0.5078, 5.5 size(0) = 0.51, 0.51, 5.5 ~~~~~ Is there something I can do to fix this ? Thanks for everyone involved in this great project! Highly appreciate your time and efforts. Best, Spanier 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. -- - Assaf We are all - others.--
Assaf
We are all - others.
On Sat, Dec 1, 2012 at 10:47 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
are they different time points or from the same session?
Those are different time points in the same session (10 minute interval between each acquisition)
What are you trying to achieve?
What I would like to achieve ? I would like to get a segmentation for each one of those brain MRI images...
Why? I would like to compare ""the dynamics"" in a different brain region during this one hour MRI session...(Not sure if/how much wise it is... butthis is what I want... for now....) Thanks!!
On Sat, 1 Dec 2012, Assaf B. Spanier wrote:
This is exactly the command I've used.
However, as I mentioned my subject has about six or seven T1-MRI images and I have added all of them via the ""recon-all -i image1 -i image2 etc'" command. I can even see those images in the "mri/orig" directory. see:
| |-- orig | | |-- 001-iscale.txt | | |-- 001.lta | | |-- 001.mgz | | |-- 002-iscale.txt | | |-- 002.lta | | |-- 002.mgz | | |-- 003-iscale.txt | | |-- 003.lta | | |-- 003.mgz | | |-- 004-iscale.txt | | |-- 004.lta | | `-- 004.mgz ... ...However, I'm not sure how can I used tkmedit to inspect the segmentation of those different MRI images ?
[Hope my question is more clear now]
On Sat, Dec 1, 2012 at 10:31 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu
wrote: what different brain images do you mean? You can view them with the surfaces via:
tkmedit <subject name> norm.mgz lh.white -segmentation aparc+aseg.mgz or tkmedit <subject name> norm.mgz lh.white -segmentation aparc2009s+aseg.mgz the tools will be part of FS 5.2 when it comes out in the next month or so. If you really need it before then Nick can get you a beta. cheers Bruce On Sat, 1 Dec 2012, Assaf B. Spanier wrote: Many thanks for the quick response - I would take a look on your suggestion! How about my first question ? About viewing the segmentation results of my first trial ( without the Flair images) [Please forgive my English :) ] On Sat, Dec 1, 2012 at 9:53 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Spanier definitely don't invoke recon-all with the FLAIR image. We have some tools in 5.2 for this, but you would call it as a postprocessing step with a different command line in any case. Instead, you can use bbregister to register the flair to the surfaces and resample it. cheers Bruce On Sat, 1 Dec 2012, Assaf B. Spanier wrote: Hi@all, I have a dataset of several MRI T1 images and one Flair. All images of the same subject and were taken in the same session. My goal is to register and segment all those MRI images. = A = In my first try I have used, "recon-all -i image1 -i image2 etc'" for all T1 images (here, I didn't use the Flair images ) . Follow this, I used the "recon-all -all" command. (For about two days...) Here come Question 1: After all this process, I didn't completely follow the results I got... As I have noticed that I have only one segmentation file (aparc.a2009s+aseg.mgz) ? How can I see the segmentation result with tkmedit in the different brain images ? = B = As I would like the neuroanatomical labels to be inspected for accuracy by a physician. My physician asks to see the segmentation result on top of the Flair images (saying it easier for him to do so on Flair images) So I've used the "recon-all -i image1 -i image2 etc'" command again but this time I've also included the Flair image. Here come Question 2: However, this time, unfortunately, the "recon-all -i image1 -i image2 etc'" , failed, saying that: ~~~~~ images have different voxel sizes. Currently not supported, maybe first make conform? Debug info: size(1) = 0.5078, 0.5078, 5.5 size(0) = 0.51, 0.51, 5.5 ~~~~~ Is there something I can do to fix this ? Thanks for everyone involved in this great project! Highly appreciate your time and efforts. Best, Spanier 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. -- - Assaf We are all - others.--
Assaf
We are all - others.
I see. Call recon-all once for each image with a different subject I'd
On Dec 1, 2012, at 3:58 PM, "Assaf B. Spanier" shpanier@gmail.com wrote:
On Sat, Dec 1, 2012 at 10:47 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: are they different time points or from the same session?
Those are different time points in the same session (10 minute interval between each acquisition)
What are you trying to achieve?
What I would like to achieve ? I would like to get a segmentation for each one of those brain MRI images...
Why? I would like to compare ""the dynamics"" in a different brain region during this one hour MRI session...(Not sure if/how much wise it is... but this is what I want... for now....) Thanks!!
On Sat, 1 Dec 2012, Assaf B. Spanier wrote:
This is exactly the command I've used.
However, as I mentioned my subject has about six or seven T1-MRI images and I have added all of them via the ""recon-all -i image1 -i image2 etc'" command. I can even see those images in the "mri/orig" directory. see:
| |-- orig | | |-- 001-iscale.txt | | |-- 001.lta | | |-- 001.mgz | | |-- 002-iscale.txt | | |-- 002.lta | | |-- 002.mgz | | |-- 003-iscale.txt | | |-- 003.lta | | |-- 003.mgz | | |-- 004-iscale.txt | | |-- 004.lta | | `-- 004.mgz ... ...However, I'm not sure how can I used tkmedit to inspect the segmentation of those different MRI images ?
[Hope my question is more clear now]
On Sat, Dec 1, 2012 at 10:31 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: what different brain images do you mean? You can view them with the surfaces via:
tkmedit <subject name> norm.mgz lh.white -segmentation aparc+aseg.mgz or tkmedit <subject name> norm.mgz lh.white -segmentation aparc2009s+aseg.mgz the tools will be part of FS 5.2 when it comes out in the next month or so. If you really need it before then Nick can get you a beta. cheers Bruce On Sat, 1 Dec 2012, Assaf B. Spanier wrote: Many thanks for the quick response - I would take a look on your suggestion! How about my first question ? About viewing the segmentation results of my first trial ( without the Flair images) [Please forgive my English :) ] On Sat, Dec 1, 2012 at 9:53 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Spanier definitely don't invoke recon-all with the FLAIR image. We have some tools in 5.2 for this, but you would call it as a postprocessing step with a different command line in any case. Instead, you can use bbregister to register the flair to the surfaces and resample it. cheers Bruce On Sat, 1 Dec 2012, Assaf B. Spanier wrote: Hi@all, I have a dataset of several MRI T1 images and one Flair. All images of the same subject and were taken in the same session. My goal is to register and segment all those MRI images. = A = In my first try I have used, "recon-all -i image1 -i image2 etc'" for all T1 images (here, I didn't use the Flair images ) . Follow this, I used the "recon-all -all" command. (For about two days...) Here come Question 1: After all this process, I didn't completely follow the results I got... As I have noticed that I have only one segmentation file (aparc.a2009s+aseg.mgz) ? How can I see the segmentation result with tkmedit in the different brain images ? = B = As I would like the neuroanatomical labels to be inspected for accuracy by a physician. My physician asks to see the segmentation result on top of the Flair images (saying it easier for him to do so on Flair images) So I've used the "recon-all -i image1 -i image2 etc'" command again but this time I've also included the Flair image. Here come Question 2: However, this time, unfortunately, the "recon-all -i image1 -i image2 etc'" , failed, saying that: ~~~~~ images have different voxel sizes. Currently not supported, maybe first make conform? Debug info: size(1) = 0.5078, 0.5078, 5.5 size(0) = 0.51, 0.51, 5.5 ~~~~~ Is there something I can do to fix this ? Thanks for everyone involved in this great project! Highly appreciate your time and efforts. Best, Spanier 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. -- - Assaf We are all - others.--
Assaf
We are all - others.--
- Assaf
We are all - others.
P.s. when they are all done you will want to run the longitudinal stream to create a base, then again on each timepoint
On Dec 1, 2012, at 6:23 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
I see. Call recon-all once for each image with a different subject I'd
On Dec 1, 2012, at 3:58 PM, "Assaf B. Spanier" shpanier@gmail.com wrote:
On Sat, Dec 1, 2012 at 10:47 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: are they different time points or from the same session?
Those are different time points in the same session (10 minute interval between each acquisition)
What are you trying to achieve?
What I would like to achieve ? I would like to get a segmentation for each one of those brain MRI images...
Why? I would like to compare ""the dynamics"" in a different brain region during this one hour MRI session...(Not sure if/how much wise it is... but this is what I want... for now....) Thanks!!
On Sat, 1 Dec 2012, Assaf B. Spanier wrote:
This is exactly the command I've used.
However, as I mentioned my subject has about six or seven T1-MRI images and I have added all of them via the ""recon-all -i image1 -i image2 etc'" command. I can even see those images in the "mri/orig" directory. see:
| |-- orig | | |-- 001-iscale.txt | | |-- 001.lta | | |-- 001.mgz | | |-- 002-iscale.txt | | |-- 002.lta | | |-- 002.mgz | | |-- 003-iscale.txt | | |-- 003.lta | | |-- 003.mgz | | |-- 004-iscale.txt | | |-- 004.lta | | `-- 004.mgz ... ...However, I'm not sure how can I used tkmedit to inspect the segmentation of those different MRI images ?
[Hope my question is more clear now]
On Sat, Dec 1, 2012 at 10:31 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: what different brain images do you mean? You can view them with the surfaces via:
tkmedit <subject name> norm.mgz lh.white -segmentation aparc+aseg.mgz or tkmedit <subject name> norm.mgz lh.white -segmentation aparc2009s+aseg.mgz the tools will be part of FS 5.2 when it comes out in the next month or so. If you really need it before then Nick can get you a beta. cheers Bruce On Sat, 1 Dec 2012, Assaf B. Spanier wrote: Many thanks for the quick response - I would take a look on your suggestion! How about my first question ? About viewing the segmentation results of my first trial ( without the Flair images) [Please forgive my English :) ] On Sat, Dec 1, 2012 at 9:53 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Spanier definitely don't invoke recon-all with the FLAIR image. We have some tools in 5.2 for this, but you would call it as a postprocessing step with a different command line in any case. Instead, you can use bbregister to register the flair to the surfaces and resample it. cheers Bruce On Sat, 1 Dec 2012, Assaf B. Spanier wrote: Hi@all, I have a dataset of several MRI T1 images and one Flair. All images of the same subject and were taken in the same session. My goal is to register and segment all those MRI images. = A = In my first try I have used, "recon-all -i image1 -i image2 etc'" for all T1 images (here, I didn't use the Flair images ) . Follow this, I used the "recon-all -all" command. (For about two days...) Here come Question 1: After all this process, I didn't completely follow the results I got... As I have noticed that I have only one segmentation file (aparc.a2009s+aseg.mgz) ? How can I see the segmentation result with tkmedit in the different brain images ? = B = As I would like the neuroanatomical labels to be inspected for accuracy by a physician. My physician asks to see the segmentation result on top of the Flair images (saying it easier for him to do so on Flair images) So I've used the "recon-all -i image1 -i image2 etc'" command again but this time I've also included the Flair image. Here come Question 2: However, this time, unfortunately, the "recon-all -i image1 -i image2 etc'" , failed, saying that: ~~~~~ images have different voxel sizes. Currently not supported, maybe first make conform? Debug info: size(1) = 0.5078, 0.5078, 5.5 size(0) = 0.51, 0.51, 5.5 ~~~~~ Is there something I can do to fix this ? Thanks for everyone involved in this great project! Highly appreciate your time and efforts. Best, Spanier 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. -- - Assaf We are all - others.--
Assaf
We are all - others.--
- Assaf
We are all - others.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
HI Assaf, Are these 6-7 T1 volumes all collected in the same 1 hour imaging session? If so, it isn't clear what you are trying to do -- brain structure is not going to be changing over the course of 1 hour.
cheers, -MH
On Sun, Dec 2, 2012 at 2:21 AM, Michael Harms mharms@conte.wustl.eduwrote:
HI Assaf, Are these 6-7 T1 volumes all collected in the same 1 hour imaging session?
yes
If so, it isn't clear what you are trying to do -- brain structure is not going to be changing over the course of 1 hour.
ya, I know, I know. - thanks!
Still, I would like to check it out.
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: mharms@wustl.edu
From: Bruce Fischl fischl@nmr.mgh.harvard.edu Date: Saturday, December 1, 2012 5:38 PM To: Bruce Fischl fischl@nmr.mgh.harvard.edu Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu, "Assaf B. Spanier" shpanier@gmail.com Subject: Re: [Freesurfer] Coregister a combination of T1, and Flair images ?
P.s. when they are all done you will want to run the longitudinal stream to create a base, then again on each timepoint
On Dec 1, 2012, at 6:23 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
I see. Call recon-all once for each image with a different subject I'd
On Dec 1, 2012, at 3:58 PM, "Assaf B. Spanier" shpanier@gmail.com wrote:
On Sat, Dec 1, 2012 at 10:47 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
are they different time points or from the same session?
Those are different time points in the same session (10 minute interval between each acquisition)
What are you trying to achieve?
What I would like to achieve ? I would like to get a segmentation for each one of those brain MRI images...
Why? I would like to compare ""the dynamics"" in a different brain region during this one hour MRI session...(Not sure if/how much wise it is... butthis is what I want... for now....) Thanks!!
On Sat, 1 Dec 2012, Assaf B. Spanier wrote:
This is exactly the command I've used.
However, as I mentioned my subject has about six or seven T1-MRI images and I have added all of them via the ""recon-all -i image1 -i image2 etc'" command. I can even see those images in the "mri/orig" directory. see:
| |-- orig | | |-- 001-iscale.txt | | |-- 001.lta | | |-- 001.mgz | | |-- 002-iscale.txt | | |-- 002.lta | | |-- 002.mgz | | |-- 003-iscale.txt | | |-- 003.lta | | |-- 003.mgz | | |-- 004-iscale.txt | | |-- 004.lta | | `-- 004.mgz ... ...However, I'm not sure how can I used tkmedit to inspect the segmentation of those different MRI images ?
[Hope my question is more clear now]
On Sat, Dec 1, 2012 at 10:31 PM, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote: what different brain images do you mean? You can view them with the surfaces via:
tkmedit <subject name> norm.mgz lh.white -segmentation aparc+aseg.mgz or tkmedit <subject name> norm.mgz lh.white -segmentation aparc2009s+aseg.mgz the tools will be part of FS 5.2 when it comes out in the next month or so. If you really need it before then Nick can get you a beta. cheers Bruce On Sat, 1 Dec 2012, Assaf B. Spanier wrote: Many thanks for the quick response - I would take a look on your suggestion! How about my first question ? About viewing the segmentation results of my first trial ( without the Flair images) [Please forgive my English :) ] On Sat, Dec 1, 2012 at 9:53 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Spanier definitely don't invoke recon-all with the FLAIR image. We have some tools in 5.2 for this, but you would call it as a postprocessing step with a different command line in any case. Instead, you can use bbregister to register the flair to the surfaces and resample it. cheers Bruce On Sat, 1 Dec 2012, Assaf B. Spanier wrote: Hi@all, I have a dataset of several MRI T1 images and one Flair. All images of the same subject and were taken in the same session. My goal is to register and segment all those MRI images. = A = In my first try I have used, "recon-all -i image1 -i image2 etc'" for all T1 images (here, I didn't use the Flair images ) . Follow this, I used the "recon-all -all" command. (For about two days...) Here come Question 1: After all this process, I didn't completely follow the results I got... As I have noticed that I have only one segmentation file (aparc.a2009s+aseg.mgz) ? How can I see the segmentation result with tkmedit in the different brain images ? = B = As I would like the neuroanatomical labels to be inspected for accuracy by a physician. My physician asks to see the segmentation result on top of the Flair images (saying it easier for him to do so on Flair images) So I've used the "recon-all -i image1 -i image2 etc'" command again but this time I've also included the Flair image. Here come Question 2: However, this time, unfortunately, the "recon-all -i image1 -i image2 etc'" , failed, saying that: ~~~~~ images have different voxel sizes. Currently not supported, maybe first make conform? Debug info: size(1) = 0.5078, 0.5078, 5.5 size(0) = 0.51, 0.51, 5.5 ~~~~~ Is there something I can do to fix this ? Thanks for everyone involved in this great project! Highly appreciate your time and efforts. Best, Spanier 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. -- - Assaf We are all - others.--
Assaf
We are all - others.--
- Assaf
We are all - others.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ 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.
Okay, I got it...thanks.
Two last questions: (1) After I have this segmentation as a "different subjects". How can I register them all together ? (2) So...what this option "recon-all -i image1 -i image2...." (i.e. Having a several MRI image per subject) is used for ?
Thanks!
On Sun, Dec 2, 2012 at 1:23 AM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
I see. Call recon-all once for each image with a different subject I'd
On Dec 1, 2012, at 3:58 PM, "Assaf B. Spanier" shpanier@gmail.com wrote:
On Sat, Dec 1, 2012 at 10:47 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
are they different time points or from the same session?
Those are different time points in the same session (10 minute interval between each acquisition)
What are you trying to achieve?
What I would like to achieve ? I would like to get a segmentation for each one of those brain MRI images...
Why? I would like to compare ""the dynamics"" in a different brain region during this one hour MRI session...(Not sure if/how much wise it is... butthis is what I want... for now....) Thanks!!
On Sat, 1 Dec 2012, Assaf B. Spanier wrote:
This is exactly the command I've used.
However, as I mentioned my subject has about six or seven T1-MRI images and I have added all of them via the ""recon-all -i image1 -i image2 etc'" command. I can even see those images in the "mri/orig" directory. see:
| |-- orig | | |-- 001-iscale.txt | | |-- 001.lta | | |-- 001.mgz | | |-- 002-iscale.txt | | |-- 002.lta | | |-- 002.mgz | | |-- 003-iscale.txt | | |-- 003.lta | | |-- 003.mgz | | |-- 004-iscale.txt | | |-- 004.lta | | `-- 004.mgz ... ...However, I'm not sure how can I used tkmedit to inspect the segmentation of those different MRI images ?
[Hope my question is more clear now]
On Sat, Dec 1, 2012 at 10:31 PM, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote: what different brain images do you mean? You can view them with the surfaces via:
tkmedit <subject name> norm.mgz lh.white -segmentation aparc+aseg.mgz or tkmedit <subject name> norm.mgz lh.white -segmentation aparc2009s+aseg.mgz the tools will be part of FS 5.2 when it comes out in the next month or so. If you really need it before then Nick can get you a beta. cheers Bruce On Sat, 1 Dec 2012, Assaf B. Spanier wrote: Many thanks for the quick response - I would take a look on your suggestion! How about my first question ? About viewing the segmentation results of my first trial ( without the Flair images) [Please forgive my English :) ] On Sat, Dec 1, 2012 at 9:53 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Spanier definitely don't invoke recon-all with the FLAIR image. We have some tools in 5.2 for this, but you would call it as a postprocessing step with a different command line in any case. Instead, you can use bbregister to register the flair to the surfaces and resample it. cheers Bruce On Sat, 1 Dec 2012, Assaf B. Spanier wrote: Hi@all, I have a dataset of several MRI T1 images and one Flair. All images of the same subject and were taken in the same session. My goal is to register and segment all those MRI images. = A = In my first try I have used, "recon-all -i image1 -i image2 etc'" for all T1 images (here, I didn't use the Flair images ) . Follow this, I used the "recon-all -all" command. (For about two days...) Here come Question 1: After all this process, I didn't completely follow the results I got... As I have noticed that I have only one segmentation file (aparc.a2009s+aseg.mgz) ? How can I see the segmentation result with tkmedit in the different brain images ? = B = As I would like the neuroanatomical labels to be inspected for accuracy by a physician. My physician asks to see the segmentation result on top of the Flair images (saying it easier for him to do so on Flair images) So I've used the "recon-all -i image1 -i image2 etc'" command again but this time I've also included the Flair image. Here come Question 2: However, this time, unfortunately, the "recon-all -i image1 -i image2 etc'" , failed, saying that: ~~~~~ images have different voxel sizes. Currently not supported, maybe first make conform? Debug info: size(1) = 0.5078, 0.5078, 5.5 size(0) = 0.51, 0.51, 5.5 ~~~~~ Is there something I can do to fix this ? Thanks for everyone involved in this great project! Highly appreciate your time and efforts. Best, Spanier 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. -- - Assaf We are all - others.--
Assaf
We are all - others.--
- Assaf
We are all - others.
Re 1) See the Wiki on the longitudinal stream Re 2) That syntax will result in registration and averaging of the input images to yield a single volume that is then run through recon-all
cheers, -MH
Can you please point me to those "tools" ? A link to the relevant website will be highly appreciated. Thanks!
On Sat, Dec 1, 2012 at 9:53 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Spanier
definitely don't invoke recon-all with the FLAIR image. We have some tools in 5.2 for this, but you would call it as a postprocessing step with a different command line in any case. Instead, you can use bbregister to register the flair to the surfaces and resample it.
cheers Bruce
On Sat, 1 Dec 2012, Assaf B. Spanier wrote:
Hi@all,
I have a dataset of several MRI T1 images and one Flair. All images of the same subject and were taken in the same session. My goal is to register and segment all those MRI images. = A = In my first try I have used, "recon-all -i image1 -i image2 etc'" for all T1 images (here, I didn't use the Flair images ) . Follow this, I used the "recon-all -all" command. (For about two days...)
Here come Question 1: After all this process, I didn't completely follow the results I got... As I have noticed that I have only one segmentation file (aparc.a2009s+aseg.mgz) ? How can I see the segmentation result with tkmedit in the different brain images ?
= B = As I would like the neuroanatomical labels to be inspected for accuracy by a physician. My physician asks to see the segmentation result on top of the Flair images (saying it easier for him to do so on Flair images) So I've used the "recon-all -i image1 -i image2 etc'" command again but this time I've also included the Flair image.
Here come Question 2: However, this time, unfortunately, the "recon-all -i image1 -i image2 etc'" , failed, saying that:
images have different voxel sizes. Currently not supported, maybe first make conform? Debug info: size(1) = 0.5078, 0.5078, 5.5 size(0) = 0.51, 0.51, 5.5Is there something I can do to fix this ?
Thanks for everyone involved in this great project! Highly appreciate your time and efforts.
Best,
Spanier
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.
freesurfer@nmr.mgh.harvard.edu
-
Assaf B. Spanier -
Bruce Fischl -
Michael Harms