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" <[email protected]> wrote: > > > > > 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... 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 <[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 . 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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