External Email - Use Caution 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. [image: Screenshot from 2023-06-20 10-20-03.png] Best, Ruifeng On Tue, Jun 20, 2023 at 9:59 AM Douglas N. Greve <dgr...@mgh.harvard.edu> wrote: > External Email - Use Caution > > 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: > > External Email - Use Caution > 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 <yhuan...@mgh.harvard.edu> > wrote: > >> External Email - Use Caution >> >> Hi Ruifeng, >> >> >> >> You can pass -nc (nochange) flag to mri_convert to keep the original data >> type. >> >> >> >> Best, >> >> >> >> Yujing >> >> >> >> >> >> *From:* freesurfer-boun...@nmr.mgh.harvard.edu < >> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of * >> ruifen...@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? 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