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.


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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