In this regard I've decided to change the dataset. We're going for ADNI Dataset http://adni.loni.usc.edu/ where I can find data in various format(nifti, mnc).
Is there any other dataset I can find labeled dataset for Hippocampus segmentation.
Thank you for helping me!
Dilip
On Mon, Apr 10, 2017 at 6:31 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
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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