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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>>>>
>>>>
>>
>>
>>
>>
>
>
--
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
FileDrop:
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