Re: [Freesurfer] Coregister a combination of T1, and Flair images ?

-- 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.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 >>>> 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.