Here is the output from mris_calc:
mris_calc aparc+aseg2.mgz max
Max@(index) [ 2145516800.000000 (6400402) ]
Wayne
On 05/10/10 2:05 PM, "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> 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 Œ0¹ value is changed to
>>>>> Œ2.1e+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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