On Sat, Dec 1, 2012 at 10:47 PM, Bruce Fischl <[email protected]>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... 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 <[email protected] >> > >> 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 >> <[email protected]> >> 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.
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