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.mgzaparc+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, noproblem found.
- 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.
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer