Re: [Freesurfer] Question about mri_convert --conform

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Was that caused by using short? Ie, if you don't use short, is there still a problem?

On 6/20/2023 10:21 AM, Ruifeng Dong wrote:

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Hi Douglas,

Thanks. Out of curiosity, I kept the short data type in the mri_convert --conform by adding options -odt short -ns 1. Freesurfer 6.0 ran well until its default skull stripping, attached below. Screenshot from 2023-06-20 10-20-03.png Best, Ruifeng

On Tue, Jun 20, 2023 at 9:59 AM Douglas N. Greve dgreve@mgh.harvard.edu wrote:

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This was done a long time ago to conserve space/memory. There is a
rescaling that is done, so it should not affect the bias
correction much

On 6/14/2023 3:35 PM, Ruifeng Dong wrote:

...

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Hi Yujing,

Thanks. I am wondering about the reason why Freesurfer converts
data types to uchar. Doesn't this affect the non-uniformity bias
correction that follows?

Best,
Ruifeng

On Tue, Jun 13, 2023 at 9:37 AM Huang, Yujing
<YHUANG43@mgh.harvard.edu> wrote:

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    Hi Ruifeng,

    You can pass -nc (nochange) flag to mri_convert to keep the
    original data type.

    Best,

    Yujing

    *From:*freesurfer-bounces@nmr.mgh.harvard.edu
    <freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of
    *ruifeng14@gmail.com
    *Sent:* Thursday, May 25, 2023 2:45 PM
    *To:* freesurfer@nmr.mgh.harvard.edu
    *Subject:* [Freesurfer] Question about mri_convert --conform

    *        External Email - Use Caution *

    Hi all,

    My input 001.mgz has data type short, but converted to
    unsigned byte. The plot shows the intensity of thee two
    images. How is the data conversion done? Thanks.

    Best,

    Ruifeng

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