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
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