Re: [Freesurfer] Question regarding conversion to mgz

2012-02-16 Thread Hemant Bokil
Thanks, Bruce, Doug, I will check how to do that. Hemant On Thu, Feb 16, 2012 at 11:21 AM, Douglas N Greve wrote: > Hi Hemant, sorry for the delay in getting back to you. I'm not sure what > could be causing the problem. FreeSurfer definitely reads the direction > cosines from the dicom. If you

Re: [Freesurfer] Question regarding conversion to mgz

2012-02-16 Thread Douglas N Greve
Hi Hemant, sorry for the delay in getting back to you. I'm not sure what could be causing the problem. FreeSurfer definitely reads the direction cosines from the dicom. If you upload the dicom volume to our file drop, I'll take a look. filedrop url is at the end of this email. doug Hemant Bokil

Re: [Freesurfer] Question regarding conversion to mgz

2012-02-10 Thread Bruce Fischl
hmmm, I'll wait for Doug to comment as he knows far more about the dicom stuff than I do Bruce On Fri, 10 Feb 2012, Hemant Bokil wrote: Hi Bruce, Thanks very much for your prompt reply. I am puzzled that freesurfer doesn't get the direction cosines. Which fields is it looking for in the dicom

Re: [Freesurfer] Question regarding conversion to mgz

2012-02-10 Thread Hemant Bokil
Hi Bruce, Thanks very much for your prompt reply. I am puzzled that freesurfer doesn't get the direction cosines. Which fields is it looking for in the dicom metadata ? When I load the slices in Matlab, I can see ImagePositionPatient and ImageOrientationPatient and SliceLocation and they all seem r

Re: [Freesurfer] Question regarding conversion to mgz

2012-02-10 Thread Bruce Fischl
Hi Hemant sorry for missing your previous post. I'm not sure what to tell you though, if the direction cosines are nans that's going to be trouble. You could still visualize your data in a slice viewer, but you may never be able to tell left from right. Where did you get the dicoms? Are they r

[Freesurfer] Question regarding conversion to mgz

2012-02-10 Thread Hemant Bokil
Hello, I had posted this question earlier but no one picked it up so I am trying again. Briefly, I have been having difficulties with the very first step of the recon-all pipeline, namely, in conversion of my dicom datasets to freesurfer's mgz format. The error message (attached below) suggests tha