Wouldn't that occur by using the MNI tools anyway?
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wed 5/18/2005 9:39 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] WMFilll and talairach coordinates
just that you have sacrificed resolution. On Wed, 18 May 2005, Fornito, Alexander wrote: > Other than that though, should there be any problem if I align my images prior to starting with freesurfer? > Provided I align to the MNI 152 brain, it should still be in talaraich space... > > -----Original Message----- > From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] > Sent: Wed 5/18/2005 10:55 AM > To: Fornito, Alexander > Cc: peggy christidis; freesurfer@nmr.mgh.harvard.edu > Subject: RE: [Freesurfer] WMFilll and talairach coordinates > > > > 1. to report talairach coords. > 2. To get cutting planes to separate the hemispheres when the head is at an > angle. > 3. To find the callosum if other heuristics fail. > 4. To pick some control points in the white matter for intensity > normalization. > > cheers, > Bruce > > > On Wed, 18 May 2005, Fornito, Alexander > wrote: > > > Hi, > > Just to toss my hat into the ring, can I ask why the transform is kept. Is it used later on? > > I've also been having trouble with the MNI tools, and was thinking of using FLIRT or AIR to align the images first. What is th point of having the .xfm? > > Thanks, > > Alex > > > > -----Original Message----- > > From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] > > Sent: Wed 5/18/2005 6:00 AM > > To: peggy christidis > > Cc: freesurfer@nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] WMFilll and talairach coordinates > > > > > > > > Hi Peggy, > > > > we don't apply the transform, just keep it around, so blurring isn't a > > problem. I don't know if AFNI knows how to write out .xfm files (the mni > > transform format), but that would be the best solution. > > > > > > Bruce > > > > On Tue, 17 May 2005, > > peggy christidis wrote: > > > > > Hello, > > > > > > I'm having a bit of trouble with the "Create Surface" step in FreeSurfer. I > > > have a single mprage scan that creates a decent first pass surface, but > > > there's still some brainstem and cerebellum attached to it. I followed the > > > troubleshooting guidelines in the FreeSurfer manual regarding Failure of > > > Automatic Cutting Planes. I went to Expert Preferences --> WMFill, and > > > inputed the appropriate coordinates to separate the brainstem and cerebellum. > > > The coordinates I used were not in Talairach space, but I assumed this was > > > okay because the manual says to use original coordinates if you don't have > > > Talairach coordinates. However, when I re-ran "Create Surface", nothing > > > happened (i.e., filled volume and surface both still show the > > > pons/cerebellum/brainstem attached). I read through the FreeSurfer mailing > > > list archives and read that Talairach coordinates are indeed needed. > > > > > > Here's my question: The volume I'm using shows a head that's slightly tilted > > > about 10 degrees to the left, so I should probably do the Taliarach > > > transformation anyway. However, I don't have the mni_tools installed on my > > > computer (I had major installation problems with them). Anyway, could I do a > > > taliarach transformation outside of Freesurfer (like in AFNI) and then > > > tranfer that talairached volume to FreeSurfer? My concern is that the > > > transformation will blur the volume, making segmentation difficult. What > > > should I do? > > > > > > Thanks, > > > Peggy > > > _______________________________________________ > > > 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 > > > > > > > > >
no, because we just keep the transform around, but only apply it for either reporting purposes, or apply the inverse to find anatomical features (e.g. the callosum)
On Thu, 19 May 2005, Fornito, Alexander wrote:
Wouldn't that occur by using the MNI tools anyway?
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wed 5/18/2005 9:39 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] WMFilll and talairach coordinates
just that you have sacrificed resolution.
On Wed, 18 May 2005, Fornito, Alexander wrote:
Other than that though, should there be any problem if I align my images prior to starting with freesurfer? Provided I align to the MNI 152 brain, it should still be in talaraich space...
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wed 5/18/2005 10:55 AM To: Fornito, Alexander Cc: peggy christidis; freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] WMFilll and talairach coordinates 1. to report talairach coords. 2. To get cutting planes to separate the hemispheres when the head is at an angle. 3. To find the callosum if other heuristics fail. 4. To pick some control points in the white matter for intensity normalization. cheers, Bruce On Wed, 18 May 2005, Fornito, Alexander wrote: > Hi, > Just to toss my hat into the ring, can I ask why the transform is kept. Is it used later on? > I've also been having trouble with the MNI tools, and was thinking of using FLIRT or AIR to align the images first. What is th point of having the .xfm? > Thanks, > Alex > > -----Original Message----- > From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] > Sent: Wed 5/18/2005 6:00 AM > To: peggy christidis > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] WMFilll and talairach coordinates > > > > Hi Peggy, > > we don't apply the transform, just keep it around, so blurring isn't a > problem. I don't know if AFNI knows how to write out .xfm files (the mni > transform format), but that would be the best solution. > > > Bruce > > On Tue, 17 May 2005, > peggy christidis wrote: > > > Hello, > > > > I'm having a bit of trouble with the "Create Surface" step in FreeSurfer. I > > have a single mprage scan that creates a decent first pass surface, but > > there's still some brainstem and cerebellum attached to it. I followed the > > troubleshooting guidelines in the FreeSurfer manual regarding Failure of > > Automatic Cutting Planes. I went to Expert Preferences --> WMFill, and > > inputed the appropriate coordinates to separate the brainstem and cerebellum. > > The coordinates I used were not in Talairach space, but I assumed this was > > okay because the manual says to use original coordinates if you don't have > > Talairach coordinates. However, when I re-ran "Create Surface", nothing > > happened (i.e., filled volume and surface both still show the > > pons/cerebellum/brainstem attached). I read through the FreeSurfer mailing > > list archives and read that Talairach coordinates are indeed needed. > > > > Here's my question: The volume I'm using shows a head that's slightly tilted > > about 10 degrees to the left, so I should probably do the Taliarach > > transformation anyway. However, I don't have the mni_tools installed on my > > computer (I had major installation problems with them). Anyway, could I do a > > taliarach transformation outside of Freesurfer (like in AFNI) and then > > tranfer that talairached volume to FreeSurfer? My concern is that the > > transformation will blur the volume, making segmentation difficult. What > > should I do? > > > > Thanks, > > Peggy > > _______________________________________________ > > 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 > > >
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Fornito, Alexander