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" greve@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" greve@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" fischl@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" wsu@interchange.ubc.ca wrote:
> > > > > >> Hello Freesurfer Users, >> >> I am >>
feeling very bad when I am using mri_convert. There are two problems:
- 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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