Hi Luca,
I'll leave this for Doug.
Bruce
On Tue, 8 Mar 2005, Luca Roccatagliata wrote:
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
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