On Sun, Dec 2, 2012 at 2:21 AM, Michael Harms <[email protected]>wrote:
> > 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: [email protected] > > From: Bruce Fischl <[email protected]> > Date: Saturday, December 1, 2012 5:38 PM > To: Bruce Fischl <[email protected]> > Cc: "[email protected]" <[email protected]>, > "Assaf B. Spanier" <[email protected]> > 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 <[email protected]> > 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" <[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... > 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. > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ Freesurfer mailing list > [email protected] > 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. > -- - Assaf We are all - others.
_______________________________________________ Freesurfer mailing list [email protected] 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.
