Re: [Freesurfer] talairach.xfm error frequency

Would you recommend subjects through autorecon1 in freesurfer 5.0 and then through autorecon2 and autorecon3 in 5.1? Thanks, -Eric On Wed, Oct 10, 2012 at 4:35 PM, Eric Cunningham wrote: > Hi all, > Ah, good to know that there is a Talairach accuracy problem. What have > other groups been doing

Re: [Freesurfer] talairach.xfm error frequency

Hi all, Ah, good to know that there is a Talairach accuracy problem. What have other groups been doing about this? Do you think it makes sense to manually edit much of our data? From what we've seen so far (registering to ages 3-9 so more errors expected) about 25% of our data have the registrat

Re: [Freesurfer] talairach.xfm error frequency

I think 5.1 specifically has a problem with Talairach accuracy (is that right Nick?). Should be much better with the next release On Wed, 10 Oct 2012, Eric Cunningham wrote: Hi Bruce, I am running version 5.10 Thanks, -Eric On Wed, Oct 10, 2012 at 3:13 PM, Bruce Fischl wrote: Hi Eric

Re: [Freesurfer] talairach.xfm error frequency

Hi Bruce, I am running version 5.10 Thanks, -Eric On Wed, Oct 10, 2012 at 3:13 PM, Bruce Fischl wrote: > Hi Eric > > what version are you running? > Bruce > > On Wed, 10 Oct 2012, Eric Cunningham wrote: > > Greetings, >> >> I am trying to determine how bad a talairach.xfm registration has to be

Re: [Freesurfer] talairach.xfm error frequency

Hi Eric what version are you running? Bruce On Wed, 10 Oct 2012, Eric Cunningham wrote: Greetings, I am trying to determine how bad a talairach.xfm registration has to be to warrant a manual edit.  I have found that even minor edits can have noticable (9%) effects on major subcortical volumes

[Freesurfer] talairach.xfm error frequency

Greetings, I am trying to determine how bad a talairach.xfm registration has to be to warrant a manual edit. I have found that even minor edits can have noticable (9%) effects on major subcortical volumes (such as thalamus or hippocampus). Very few registrations seem to have completely failed, b

Re: [Freesurfer] talairach.xfm

Hi Darshan no, resection is probably trouble depending on how big it is. The talairach_afd is the automated failure detection. I can see why it would give a warning for the resected dataset, but Vincent: you should visually inspect your registration. It's not usually wrong when it warns, and f

Re: [Freesurfer] talairach.xfm

I am having the same error with one of my datasets . This subject has a good part of the brain resected . Does Freesurfer have problems dealing with partially resected brain datasets? - Original Message - I am having trouble with 2 scans that exit with errors. Both have the same error:

[Freesurfer] talairach.xfm

I am having trouble with 2 scans that exit with errors. Both have the same error: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** This is actually preceded by a message stating that talairach.xfm already exists and will not be copied. If I use the --clean-tal option

Re: [Freesurfer] talairach.xfm empty

that should do it. Make sure that the partition isn't full Bruce On Wed, 30 Nov 2011, Christine Smith wrote: > Hello, > > I have a subject whose talairach.xfm file is present, but has no size (0 kb). > > I reran recon-all -talairach -s . It does not fix the > problem. The only error in that outpu

[Freesurfer] talairach.xfm empty

Hello, I have a subject whose talairach.xfm file is present, but has no size (0 kb). I reran recon-all -talairach -s . It does not fix the problem. The only error in that output was: error loading transform from //mri/transforms/talairach.xfm After rerunning the -talairach part of recon-all the

Re: [Freesurfer] talairach.xfm and talairach_avi

Hi Martin, Thanks for the detailed explanation! I think I've got it down now. Best, Lisa __ Lisa F. Akiyama Research Study Assistant Institute for Learning & Brain Sciences (I-LABS) University of Washington P Please consider the environment before printing this e-

Re: [Freesurfer] talairach.xfm and talairach_avi

Basically yes, but the 3x3 submatrix can be more than just rotation and scaling (there can be shearing in a 9 degree of freedom linear transform). So the 12 DOFs are 3 rotation, 3scaling,3 shearing,3 translation. Only the translation parameters can be read directly from the matrix (as you corre

Re: [Freesurfer] talairach.xfm and talairach_avi

Hi Lisa, this is an affine transformation. Usually there is a 4th row containing 0 0 0 1 A point at position x,y,z is mapped to the target location via M * (x,y,z,1)^t where M is the 4x4 matrix and (x,y,z,1)^T is the column vector of the coordinates of the point with a 1 in the 4th row. The top

Re: [Freesurfer] talairach.xfm and talairach_avi

Hello, Could someone inform me what each value of the 3x4 talairach transformation matrix signifies (e.g. translation, rotation in specific directions)? Here's an example of an talairach.xfm output. MNI Transform File > % tkregister2 > > Transform_Type = Linear; > Linear_Transform = >1.055506

[Freesurfer] talairach.xfm and talairach_avi

Hello, Are there any documentations on the details of the talairach_avi command and the 3x4 matrix (talairach.xfm) output? Thank you. Best, Lisa Akiyama __ Lisa F. Akiyama Research Study Assistant Institute for Learning & Brain Sciences (I-LABS) University of Washi

Re: [Freesurfer] talairach.xfm p=0.0000 error, brainmask.mgz not created

Hi Prantik, do you process the data directly from dicoms? If you bring up the orig.mgz in tkmedit does it orient properly? cheers Bruce On Tue, 11 Aug 2009, Prantik Kundu wrote: > Hello > > In default FS usage, all of the MPRAGE's from this particular study > that I'm analyzing are dying with

[Freesurfer] talairach.xfm p=0.0000 error, brainmask.mgz not created

Hello In default FS usage, all of the MPRAGE's from this particular study that I'm analyzing are dying with the error shown below. MPRAGE's from other studies appear to be processed just fine. The MPRAGEs from the experiment that FS is failing on are generally of higher quality than those