Hi Eileen - In b0plist you can give files that contain either 2 phase maps (a volume with 2 frames), or the difference of 2 phase maps (a volume with only 1 frame). Depending on whether the volume that you specified has 2 or 1 frame, trac-all will assume which of the above you're giving it.
Your error seems to be that mri_convert doesn't recognize the format of your volume:
mri_convert /home/image/FASD/call1285/call1285_dti_021210/proc/b0pha.nii /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII _T1_021210/dmri/b0pha.nii.gz niiRead(): unsupported datatype 32 (with scl_slope != 0) in /home/image/FASD/call1285/call1285_dti_021210/proc/b0pha.nii
Can you view the volume in freeview, for example? If freesurfer tools can't recognize the format of your file, then it's not a tracula-specific problem. In that case, it's best to send a new email on the list about the mri_convert error, so that you get responses from the appropriate experts.
a.y
On Wed, 27 Aug 2014, Eileen Moore wrote:
Anastasia, I'm not sure how I can give tracula the phase difference maps, can you provide an example?
As a reminder, I've run a wrapper script around epidewarp which takes our dicom images and converts them into a phase difference map (it is based on the script that was authored by Doug Greve for the fBIRN consortium).
In the tutorial dmrirc example I see only the 'set b0mlist' and 'set b0plist' options, and am unsure where I could give it the phase difference map.
I've also tried converting the dicom magnitude and phase maps to nifti format and inputting these into the dmrirc file but I am still getting an error. (See attached log file).
Thanks, Eileen.
------------------------------ Message: 10 Date: Thu, 17 Jul 2014 04:14:16 -0400 (EDT) From: Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] trac-all -prep error field map error To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Message-ID: <alpine.LRH.2.03.1407170411110.12767@nmr.mgh.harvard.edu> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Hi Eileen - All image formats that mri_convert (and thus any freesurfer program) can read will do, you don't need dicom. Try giving trac-all the phase difference maps you have and let's see what happens. Best, a.y On Wed, 16 Jul 2014, Eileen Moore wrote: > Hi Anastasia, > > OK - our imaging physicists had developed a wrapper script around epidewarp > which takes our dicom images and converts them into the phase difference map > (it is based on the script that was authored by Doug Greve for the fBIRN > consortium). It looks like the tracula script requires dicom images. Is > there a way for me to do epidewarp manually and then follow through with the > remaining steps using trac-all? > > Thanks, > Eileen. > > > Date: Mon, 14 Jul 2014 11:23:47 -0400 (EDT) > From: Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] trac-all -prep error field map error > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <alpine.LRH.2.03.1407141119560.23459@nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > > Hi Eileen - That step is run with the program epidewarp.fsl, > which you can > run on the command line to see the available options. The input > phase map > volume is expected to have either 2 frames (2 separate phase > maps) or 1 > frame (the difference phase map). This error from trac-all means > that it > found that your input phase map has something other than 1 or 2 > frames, so > it doesn't know how to handle it. > > Hope this helps, > a.y > > On Sat, 12 Jul 2014, Eileen Moore wrote: > > > Hi - I'm using freesurfer 5.3 on an Ubuntu operating system. > I'm tyring to > > run tracula on some? images acquired from a GE scanner. I am > running into > > problems when I try to perform the registration-based > B0-inhomogeneity > > compensation, getting an error in the terminal output: "ERROR: > Unrecognized > > format of phase map". However, trac-all -prep runs fine when I > skip the > > B0-inhomogeneity compensation step. Is there something else I > need to do to > > use field map correction? > > > > I've attached the trac-all.log and a copy of the terminal > output. > > > > Thanks, > > Eileen. > > > > > > > > > > > >