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: > 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 > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > >
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