Dear Bruce, thanks for your suggestion. I tried that command (mri_convert slice.dcm $SUBJECTS_DIR/$subject/mri/orig), after entering the folder containing .dcm files, but at first it didn't recognize the file type. I added the option -it dicom, then it looked for a dicom file but it gave this error:
mri_convert -it dicom 001.dcm /binfs/freesurfer_alpha/subjects/DCMsag2/mri/orig reading from 001.dcm... no DICOM files found. Exit Where 001.dcm is my first slice in the series. Have you any suggestion? Best Luca Roccatagliata ----- Original Message ----- From: "Bruce Fischl" <[EMAIL PROTECTED]> To: "Luca Roccatagliata" <[EMAIL PROTECTED]> Cc: <freesurfer@nmr.mgh.harvard.edu> Sent: Monday, March 07, 2005 11:39 AM Subject: Re: [Freesurfer] Convert procedure > if you are reading an analyze file, specify the .img part of it, not the > .hdr. In general though, you're better off using dicom. You can convert > to COR via: > > mri_convert slice.dcm $SUBJECTS_DIR/$subject/mri/orig > > where slice.dcm is one slice in the series you want to convert. > > cheers, > Bruce > > > On Mon, 7 Mar 2005, Luca Roccatagliata wrote: > > > Hi, > > > > > > > > I have problems with the convert/average procedure. > > > > I acquired 124 sagittal slices with a SPGR sequence. Is the conversion from sagittal plane to coronal plane included in this step? > > > > I tried to load .dcm and. img files. First of all, are they both compatible with mri_convert? > > > > I tried with 1 volume file in analyze format, but Freesurfer didn't recognize the header and I had to set it manually. I noted that, even giving the command save, a new file .hdr was not created at this point: the .hdr file created when converting from dcm to analyze was only present in the folder. Then it asked also for .dcm files. > > > > > > > > This is the error it gave me, after starting the volume interpolation: > > > > > > > > > > > > reading /binfs/freesurfer_alpha/subjects/provaANAsag/mri/orig/001/1.2.840.113619.2.1 35.3596.375144.5930.1108451068i00001.hdr... > > > > mri_read(): couldn't determine type of file /binfs/freesurfer_alpha/subjects/provaANAsag/mri/orig/001/1.2.840.113619.2.1 35.3596.375144.5930.1108451068i00001.hdr > > > > /binfs/freesurfer_alpha/bin/Linux/mri_average: MRIread(/binfs/freesurfer_alpha/subjects/provaANAsag/mri/orig/001/1.2.840.11 3619.2.135.3596.375144.5930.1108451068i00001.hdr) failed > > > > > > > > > > > > Thanks in advance, > > > > > > > > Laura Bonzano > > > > Luca Roccatagliata > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
