Hi Ye,
you would never have two files, as each file represents one image, or
slice from a sequence. So you might have two sequences of files, say
Barba001-1.img, Barba001-2.img... Barba001-256.ima, and Baraba002-1.ima,
Barba002-2.ima.... Barba002-256.ima. Then you would use -i twice, once with
*one* file from each series (it wouldn't matter which one).
cheers
Bruce
On
Mon, 24 Jun 2013, ye tian wrote:
Dear Bruce,
Thank you very much for your suggestion, but I am afraid that I still don't
quite understand you.
In order to make it simple, suppose I have two files, Barba001.IMA and
Barba002.IMA, coming directly from the scanner.
Now if I enter recon-all -s Barba -i Barba001.IMA from the command line, I
am only able to find 001.mgz in the Barba/mri/orig. Aren't I supposed to
to find 001.mgz and 002.mgz?
Thank you so much!
Sincerely,
Ye
On Mon, Jun 24, 2013 at 5:41 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
Hi Ye
you only need to give it a single file from each run and it will
find the rest. The only time you use -i more than once is if you
acquired more than 1 T1-weighted volume. Definitely don't give
it all the files that make up the same volume
cheers
Bruce
On Mon, 24 Jun 2013, ye tian wrote:
Dear David,
I wonder whether there is a short cut for recon-all
-s Barbara -i
/path_to_data/scan1.dicom -i
/path_to_data/scan2.dicom ... -i
/path_to_data/scan100.dicom
Recon-all -i takes only a single file as an input. A
typical user, however,
has hundreds of files for a particular subject. For
example, the directory
Barbara may have 100 scans. Therefore, the above
command is necessary to
include all the scans.
I understand that I can write loops to a text file
and then copy and paste
to command line. However, I wonder whether there is
a simpler way to input
several files or even a directory to recon-all.
Thank you very much!
Sincerely,
Ye
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