When you use the "-i" flag in recon-all you only need to enter the full path to one of the dicom files for that scan acquisition. mri_convert (which is called by recon-all) will identify all the individual slices from there.

Jenni

On Wed, 2 Aug 2006, Chacko Cherian wrote:

Hello all,

I have 180 slices of a subject in DICOM format.I am trying to run the 'recon-all' procedure for this subject. Are these slices seen by Freesurfer as individual acquisitions or as a single dicom file? In case they are percieved as individual acquisitions,do I need to manually type all the file names(for each slice) for the recon-all procedure or is there a simpler way.

THanks in advance

Chacko Cherian. Arizona State University Graduate Research Assistant

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You only give it the file name from one of the dicoms in the series, eg,

mri_convert onefile.dcm f.mgh

This will look in onefile.dcm, get the series number, then look in all the files in that directory and find the ones that match that series, then unpack them all as a single volume.

doug

Chacko Cherian wrote:

Hello all,

I have 180 slices of a subject in DICOM format.I am trying to run the 'recon-all' procedure for this subject. Are these slices seen by Freesurfer as individual acquisitions or as a single dicom file? In case they are percieved as individual acquisitions,do I need to manually type all the file names(for each slice) for the recon-all procedure or is there a simpler way.

THanks in advance

Chacko Cherian. Arizona State University Graduate Research Assistant

---

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