Maybe my email is not clear. Try this to see what you get:
mri_convert aparc+aseg.mgz aparc+aseg1.mgz -odt float
mri_convert aparc+aseg1.mgz aparc+aseg2.mgz -odt int
mris_calc aparc+aseg2.mgz max
I tried 'mris_calc'. The output is in floating format. I have no way to
avoid converting back to int format.
I am using Freesurfer version 5.
Wayne
On 05/10/10 2:33 PM, "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> wrote:
> And when you run
mri_convert aparc+aseg.mgz aparc+aseg2.mgz -odt int
And
> then
mris_calc aparc+aseg2.mgz max
you get that crazy number?
I've tried
> this here with version 5 and cannot replicate. What version
are you
> using?
doug
Wayne Su wrote:
> Here is:
> mris_calc aparc+aseg.mgz max
>
> Max@(index) [ 2035.000000 (7772808) ]
>
>
> On 05/10/10 2:20 PM, "Douglas N
> Greve" <gr...@nmr.mgh.harvard.edu> wrote:
>
>
>> btw, I mean the original
> aparc+aseg.mgz, not the one created after you
>>
> made
>
>> changes
> using those FSL commands.
>>
>
> doug
>
> Douglas N Greve wrote:
>
>>
> And what do
>> you get when you run mris_calc on aparc+aseg.mgz?
>>
>> Wayne
> Su wrote:
>>
>>
>> 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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>>
>>>>>>>>
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>>>>>>>>
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>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>
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>>>>>>
>>>>>
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>>>>>
>>>>>
>>
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>>
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>>>>>
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>>>>>
>>>>>
>>>>>
>>>
>
>>>
>>>
>>
>>
>
>
--
Douglas N. Greve, Ph.D.
MGH-NMR
> Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax:
> 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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