Re: [Freesurfer] Phase Encoding Direction and epidewarp.fsl

Hi Doug, All other things being equal, if you switch from AP to RL phase encoding in an axial acquisition, then the PE direction will switch from the y-axis to the x-axis in the images. It doesn't really have anything to do with Siemens, since the images are written out in a standard anatomical o

Re: [Freesurfer] Phase Encoding Direction and epidewarp.fsl

I guess it is possible that Siemens is doing something funny with the images. I've never used sagittal before. On 11/13/2012 12:51 PM, Clark Fisher wrote: > I'm using a script that calls unpacksdcmdir. Maybe there is some setting in > our config file that forces the orientation? Nothing obviou

Re: [Freesurfer] Phase Encoding Direction and epidewarp.fsl

Hi Clark, hi Doug fugue has an option that might help here. Here is the relevant excerpt rom calling fugue on the command line (as in fugue of fsl 5.0.1 but I am sure this was also present in fsl 4.1.n): "--unwarpdirspecifies direction of warping [x/y/z/x-/y-/z-] (default y)" it seems that t

Re: [Freesurfer] Phase Encoding Direction and epidewarp.fsl

I'm using a script that calls unpacksdcmdir. Maybe there is some setting in our config file that forces the orientation? Nothing obvious though. On Nov 13, 2012, at 12:03 PM, Douglas N Greve wrote: > I'm a little confused as to why the rows are not the phase encode direction > to begin with.

Re: [Freesurfer] Phase Encoding Direction and epidewarp.fsl

I'm a little confused as to why the rows are not the phase encode direction to begin with. What did you use to convert the dicoms to nifti? doug On 11/13/2012 11:59 AM, Clark Fisher wrote: > Thanks Doug, > > Would the proper way to handle this then be to switch the rows and columns > before unwa

Re: [Freesurfer] Phase Encoding Direction and epidewarp.fsl

Thanks Doug, Would the proper way to handle this then be to switch the rows and columns before unwarping, then switch them back before the further processing steps? -Clark ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.

Re: [Freesurfer] Phase Encoding Direction and epidewarp.fsl

actually, I have no idea:). This is a wrapper around the FSL programs. I wrote the code always assuming that the phase encode direction was the row direction. Usually, it gets unpacked that way. Is the data getting reoriented along the way? doug On 11/13/2012 11:34 AM, Satrajit Ghosh wrote: > h

Re: [Freesurfer] Phase Encoding Direction and epidewarp.fsl

hi doug, just to follow up on this. if i had the phase encode direction (we currently store various dicom attributes in a nifti header extension), where would i provide it? cheers, satra On Tue, Nov 13, 2012 at 11:27 AM, Douglas N Greve wrote: > Hi Clark, the phase encode direction is always

Re: [Freesurfer] Phase Encoding Direction and epidewarp.fsl

Hi Clark, the phase encode direction is always lost since that information is not represented in the nifti header. epidewarp.fsl always assumes that the phase encode direction is in the row direction. doug On 11/13/2012 07:32 AM, Clark Fisher wrote: > Hi everyone, > > I recently switched the pha

[Freesurfer] Phase Encoding Direction and epidewarp.fsl

Hi everyone, I recently switched the phase encoding direction of the functional sequence I've been using from F >> H to R >> L and ran into a problem with epidewarp.fsl (in version 4). The unwarping was still happening along the F >> H axis in the new images where phase encoding was R >> L.