Hi Bruce,
I used just mri_binarize, mri_mask and mri_concat and all in mgz format. I
got a 32-bit floating point image with intensity range from 0~2031. Then I
used the mri_convert to convert it to 32-bit integer also both in mgz
format. Here is the message on the screen.
mri_convert aparc+aseg.mgz aparc+aseg2.mgz -odt int
$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $
reading from aparc+aseg.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -1.77636e-15, -1.88564e-15)
j_ras = (0, -4.3715e-16, -1)
k_ras = (0, 1, -3.72529e-09)
changing data type from float to int (noscale = 0)...
MRIchangeType: Building histogram
writing to aparc+aseg2.mgz...
The intensity range of new image is -214783648.00 ~ 214551xxx.00 showed by
DTI_TK Quick Look.
Wayne
On 05/10/10 1:30 PM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote:
> Hi Wayne,
>
> can you check to see whether it's an FSL problem or a FreeSurfer one? If
> you don't use FSL do you still have the problem?
>
> cheers
> Bruce
> On Tue, 5 Oct 2010, Wayne
> Su wrote:
>
>> Well, I tried to avoid FSL, and used only Freesurfer tool to do the same
>> thing. I found there was the same issue when an image with 32-bit float
>> point data type converts to 32-bit integer. No problem for the convertion
>> from 32-bit float point to 8-bit unsigned integer.
>>
>> Wayne
>>
>>
>> On 05/10/10 10:44 AM, "Wayne Su" <w...@interchange.ubc.ca> wrote:
>>
>>> Hello Freesurfer Users,
>>>
>>> I am feeling very bad when I am using mri_convert. There are two problems:
>>> 1. When I converted a file in mgz format to nii.gz format, and did some
>>> volume calculation (mask and addition) by using fslmaths from FSL, then
>>> converted back to mgz. If the image type is uchar, it works fine. If the
>>> image type is int, the intensities changed. The 0¹ value is changed to
>>> 2.1e+09¹, others also in very large number (look like read the data from
>>> wrong place). Here is the code I used:
>>>
>>> ${FREESURFER_HOME}/bin/mri_convert aparc+aseg.mgz aparc+aseg.nii.gz
>>> -odt int
>>> ${FSLDIR}/bin/fslmaths aparc+aseg -mas right_vect_mask_inv -add
>>> right_vect_mask aparc+aseg
>>> ${FREESURFER_HOME}/bin/mri_convert aparc+aseg.nii.gz aparc+aseg.mgz
>>> -odt int
>>>
>>> If no fslmaths calculation, convert back to mgz right way, no
>>> problem
>>> found.
>>>
>>> 2. when the conform is used, some head were rotated a little bit, but not
>>> for
>>> others. I am wondering how to avoid the rotation?
>>>
>>> Regards,
>>> Wayne
>>>
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