Re: [Freesurfer] Multiple inputs into recon-all -i

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 fischl@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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