you can also just give them to recon-all directly. Analyze is a dangerous format to use however as it doesn't allow you to determine left from right. Hopefully you have some type of fiducial marker in the image (e.g. a vitamin E tablet)

cheers
Bruce
On Mon, 10 Apr 2017, Nina Jacobsen wrote:

Hi Dilip,
Try the mri_convert function to convert your images, so recon-all can read
them:
https://surfer.nmr.mgh.harvard.edu/pub/docs/html/mri_convert.help.xml.html

____________________________________________________________________________
Fra: freesurfer-bounces@nmr.mgh.harvard.edu
[freesurfer-bounces@nmr.mgh.harvard.edu] på vegne af Dilip Puri
[dilippuripuri@gmail.com]
Sendt: 10. april 2017 10:02
Til: Freesurfer support list
Emne: Re: [Freesurfer] segmentation help

Hi all,

Actually I've images in Analyze7.5 format(.img/.hdr).
Can anyone help me to reconstruct('recon-all') for this format.

Thanks
Dilip

On Mon, Apr 10, 2017 at 12:14 PM, Nina Jacobsen <njacob12@student.aau.dk>
wrote:
      Hi Dilip.
You have to place your files where the subject-directory points. If
you dont change the directory yourself, this is under
freesurfer/subjects.

For more info about recon all,see https://surfer.nmr.mgh.harvard.edu/fswiki/recon-allhttps://surfer.nmr.m
gh.harvard.edu/fswiki/recon-all

Nina.

____________________________________________________________________________

Fra: freesurfer-bounces@nmr.mgh.harvard.edu
[freesurfer-bounces@nmr.mgh.harvard.edu] på vegne af Dilip Puri
[dilippuripuri@gmail.com]
Sendt: 10. april 2017 07:46
Til: Freesurfer support list
Emne: Re: [Freesurfer] segmentation help

Hi,

To-do "recon-all" where should I keep all the files. I mean in which
directory. What are the command lines?


Hope for response.


Thanks
Dilip

On Sun, Apr 9, 2017 at 7:18 PM, Bruce Fischl
<fischl@nmr.mgh.harvard.edu> wrote:
      Hi Dilip

      you need to run your image through recon-all.

      cheers
      Bruce

      On Sun, 9 Apr 2017, Dilip Puri
      wrote:

      > Hi all,
      >
      > I've 200 analyze7.5 format images(OASIS Dataset) and I
      want to segment
      > HippoCampus.
      >
      > My input file xyz.img and output file will be like
      xyz_seg.img which
      > contains only hippocampus image it like Grond Truth
      image for my original
      > input image.
      >
      > Here is sample files including original and segmented
      mask link.
      >
      > Even I am very new to FREESURFER so I don't know the
      procedure to
      > reconstruct the images.
      >
      >
      > Kindly help me.
      >
      >
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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
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