Thank you, Bruce. That solved my problem.
Wayne
On 05/10/10 3:21 PM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote:
> you want noscale to be 1 (-ns 1) otherwise it will rescale the image
> "intensities" in teh aparc+aseg and you'll got nonsense
> On Tue, 5 Oct 2010,
> Douglas N Greve wrote:
>
>> I've never heard of DTI_TK Quick Look. Does it actually read mgz files? What
>> value does it give for aparc+aseg.mgz? Try loading the file into matlab with
>> the FreeSurfer MRIread.m function and see what it gives for the max. Or just
>> run
>>
>> mris_calc aparc+aseg2.mgz max
>>
>> doug
>>
>> Wayne Su wrote:
>>> 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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