Re: [Freesurfer] mri_convert Siemens .IMA error

Hi Paul, I was finally able to track down the bug. You can get a new version from here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/mri_convert.macos copy it to $FREESURFER_HOME/bin/mri_convert doug On 12/08/2013 06:28 PM, prasser wrote: > Hi Doug, > > Sorry for the dela

Re: [Freesurfer] mri_convert Siemens .IMA error

Can you upload a single dicom file to me? One should be enough On 12/06/2013 04:02 PM, Paul Rasser wrote: >> >> We are using Freesurfer5.3 on os x 10.8. >> > > > On 6 Dec 2013, at 2:19 pm, Douglas Greve > wrote: > >> >> This may be a known problem. What

Re: [Freesurfer] mri_convert Siemens .IMA error

> We are using Freesurfer5.3 on os x 10.8. > > On 6 Dec 2013, at 2:19 pm, Douglas Greve wrote: > > > This may be a known problem. What version of FS are you using and what is > your platform? > doug > > > > >> On 12/5/13 3:26 PM, prasser wrote: >> Thanks, but the orientation shift appear

Re: [Freesurfer] mri_convert Siemens .IMA error

This may be a known problem. What version of FS are you using and what is your platform? doug On 12/5/13 3:26 PM, prasser wrote: Thanks, but the orientation shift appears as a skew. Also, we don't have any fiducial markers for this group of scans so it would be a little tricky to confirm

Re: [Freesurfer] mri_convert Siemens .IMA error

Thanks, but the orientation shift appears as a skew. Also, we don't have any fiducial markers for this group of scans so it would be a little tricky to confirm the correct application of -out_orientation. I would rather let mri_convert handle this from the .IMAs. Is there any additional inform

Re: [Freesurfer] mri_convert Siemens .IMA error

Not sure if this helps, but you can alter the output orientation using the flag "--out_orientation" followed by LIA (for example). Maybe the input file needs to be in a specific orientation before it can be converted properly. On Wed, Dec 4, 2013 at 9:56 PM, prasser wrote: > Hi, > > I'm curren

[Freesurfer] mri_convert Siemens .IMA error

Hi, I'm currently having problems converting .IMA files collected from a Siemens Skyra to .mgz format using mri_convert from Freesurfer5.3 on os x. Using: mri_convert -it siemens -ot mgz 1.IMA test.mgz I get the error message: does not contain a Siemens ASCII header has this file been anon