no, you'll need to figure out which series to give an a file from, but it will figure out the other files in the same series.
Also, please cc the list so that others can answer Bruce
On Wed, 11 Sep 2013, Pedro Rosa wrote:
Hi, Thanks for your help. Is freesurfer able to select T1-w dicoms among dicoms from other acquisitions (dwi, t2w)? I ask this because I have dicoms from all acquisitions in a single folder, and I believe that the process of sorting them may be leading to these problems.
Pedro Rosa
On 11 Sep 2013, at 03:17 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Pedro
you are *far* better off avoiding the analyze format. If you must convert, try nifti, but in general we prefer starting with the dicoms directly. If you give recon-all a *single* image file in the correct (T1-weighted) dicom series we will figure out the other ones
cheers Bruce On Wed, 11 Sep 2013, Pedro Rosa wrote:
Hi, I am finding a warning at recon-all when creating the folders: INFO: could not find /Path/subject.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 1, coronal unflipped. INFO: if not valid, please provide the information in /Path/subject.mat file
What are the consequences of this to image orientation or to registration in further steps? I have sorted the DICOMs using MRIcron (generates .img and .hdr for T1 acquisition). Regards, Pedro.
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