Hi! I am having some troubles converting MNC files to NII while preserving the exact values in the MNC file. I have tried to use mri_convert and mnc2nii, but in both cases, the values in the file output get changed. The help of mri_convert mentions that the output for MNC files may not work. Is there a workaround or a recommended procedure to convert MNC into NII? Thanks, Caspar
Hi Caspar
hmm, I don't know why that would be the case. Can you send the full command line and screen output? cheers Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote:
Hi! I am having some troubles converting MNC files to NII while preserving the exact values in the MNC file. I have tried to use mri_convert and mnc2nii, but in both cases, the values in the file output get changed. The help of mri_convert mentions that the output for MNC files may not work. Is there a workaround or a recommended procedure to convert MNC into NII? Thanks, Caspar
Hi Bruce, I have tried the two following commands, and various flags on mri_convert: mnc2nii -nii -int paxinos-MNI.mnc paxinos-MNI.nii mri_convert -i paxinos-MNI.mnc -o paxinos-MNI.nii
Yhe output of the latter would be: mri_convert -i paxinos-MNI.mnc -o paxinos-MNI.nii $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from paxinos-MNI.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to paxinos-MNI.nii...
for mri_convert, --nochange, -odt float/int/uchar, --no_scale 1 all do not make a difference.
It could be that the problem arises once I call mri_binarize afterwards. I know that there are values between 1 and 256 in the MNC file, but when I call mri_binarize with -match on the MNC file or on any of the converted NIFTI files, it does not find any values lower than 53 or so.
Caspar
2014/1/22 Bruce Fischl fischl@nmr.mgh.harvard.edu
Hi Caspar
hmm, I don't know why that would be the case. Can you send the full command line and screen output? cheers Bruce
On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote:
Hi!
I am having some troubles converting MNC files to NII while preserving the exact values in the MNC file. I have tried to use mri_convert and mnc2nii, but in both cases, the values in the file output get changed. The help of mri_convert mentions that the output for MNC files may not work. Is there a workaround or a recommended procedure to convert MNC into NII? Thanks, Caspar
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.
how do you know that the values were there before? Try running mri_diff on the .nii and the .mnc and see if it finds any differences Bruce
On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote:
Hi Bruce, I have tried the two following commands, and various flags on mri_convert: mnc2nii -nii -int paxinos-MNI.mnc paxinos-MNI.nii mri_convert -i paxinos-MNI.mnc -o paxinos-MNI.nii
Yhe output of the latter would be: mri_convert -i paxinos-MNI.mnc -o paxinos-MNI.nii $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from paxinos-MNI.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to paxinos-MNI.nii...
for mri_convert, --nochange, -odt float/int/uchar, --no_scale 1 all do not make a difference.
It could be that the problem arises once I call mri_binarize afterwards. I know that there are values between 1 and 256 in the MNC file, but when I call mri_binarize with -match on the MNC file or on any of the converted NIFTI files, it does not find any values lower than 53 or so.
Caspar
2014/1/22 Bruce Fischl fischl@nmr.mgh.harvard.edu Hi Caspar
hmm, I don't know why that would be the case. Can you send the full command line and screen output? cheers Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi! I am having some troubles converting MNC files to NII while preserving the exact values in the MNC file. I have tried to use mri_convert and mnc2nii, but in both cases, the values in the file output get changed. The help of mri_convert mentions that the output for MNC files may not work. Is there a workaround or a recommended procedure to convert MNC into NII? Thanks, CasparThe 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.
Hi Bruce, mri_diff does not return any differences. However, when I load the MNC file into Matlab using loadminc ( http://www.mathworks.com/matlabcentral/fileexchange/32644-loadminc), I do retain all the values between 0 and 255. Also, I have something like an annotation file for the MNC file that lists values between 0 and 255. The MNC is unsigned byte. Caspar
2014/1/22 Bruce Fischl fischl@nmr.mgh.harvard.edu
how do you know that the values were there before? Try running mri_diff on the .nii and the .mnc and see if it finds any differences
Bruce
On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote:
Hi Bruce,
I have tried the two following commands, and various flags on mri_convert: mnc2nii -nii -int paxinos-MNI.mnc paxinos-MNI.nii mri_convert -i paxinos-MNI.mnc -o paxinos-MNI.nii
Yhe output of the latter would be: mri_convert -i paxinos-MNI.mnc -o paxinos-MNI.nii $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from paxinos-MNI.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to paxinos-MNI.nii...
for mri_convert, --nochange, -odt float/int/uchar, --no_scale 1 all do not make a difference.
It could be that the problem arises once I call mri_binarize afterwards. I know that there are values between 1 and 256 in the MNC file, but when I call mri_binarize with -match on the MNC file or on any of the converted NIFTI files, it does not find any values lower than 53 or so.
Caspar
2014/1/22 Bruce Fischl fischl@nmr.mgh.harvard.edu Hi Caspar
hmm, I don't know why that would be the case. Can you send the full command line and screen output? cheers Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi! I am having some troubles converting MNC files to NII while preserving the exact values in the MNC file. I have tried to use mri_convert and mnc2nii, but in both cases, the values in the file output get changed. The help of mri_convert mentions that the output for MNC files may not work. Is there a workaround or a recommended procedure to convert MNC into NII? Thanks, CasparThe 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.
Hi Caspar
now, I'm confused. So it sounds like mri_convert is doing the conversion properly then? Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote:
Hi Bruce, mri_diff does not return any differences. However, when I load the MNC file into Matlab using loadminc (http://www.mathworks.com/matlabcentral/fileexchange/32644-loadminc), I do retain all the values between 0 and 255. Also, I have something like an annotation file for the MNC file that lists values between 0 and 255. The MNC is unsigned byte. Caspar
2014/1/22 Bruce Fischl fischl@nmr.mgh.harvard.edu how do you know that the values were there before? Try running mri_diff on the .nii and the .mnc and see if it finds any differences Bruce
On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi Bruce, I have tried the two following commands, and various flags on mri_convert: mnc2nii -nii -int paxinos-MNI.mnc paxinos-MNI.nii mri_convert -i paxinos-MNI.mnc -o paxinos-MNI.nii Yhe output of the latter would be: mri_convert -i paxinos-MNI.mnc -o paxinos-MNI.nii $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from paxinos-MNI.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to paxinos-MNI.nii... for mri_convert, --nochange, -odt float/int/uchar, --no_scale 1 all do not make a difference. It could be that the problem arises once I call mri_binarize afterwards. I know that there are values between 1 and 256 in the MNC file, but when I call mri_binarize with -match on the MNC file or on any of the converted NIFTI files, it does not find any values lower than 53 or so. Caspar 2014/1/22 Bruce Fischl <fischl@nmr.mgh.harvard.edu> Hi Caspar hmm, I don't know why that would be the case. Can you send the full command line and screen output? cheers Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi! I am having some troubles converting MNC files to NII while preserving the exact values in the MNC file. I have tried to use mri_convert and mnc2nii, but in both cases, the values in the file output get changed. The help of mri_convert mentions that the output for MNC files may not work. Is there a workaround or a recommended procedure to convert MNC into NII? Thanks, Caspar 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.
Hi Bruce, I am confused, too. If the conversion is proper, why does mri_binarize not find values below ~53? when I call mri_binarize with -match on the MNC file or on any of the converted NIFTI files? Caspar
2014/1/22 Bruce Fischl fischl@nmr.mgh.harvard.edu
Hi Caspar
now, I'm confused. So it sounds like mri_convert is doing the conversion properly then?
Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote:
Hi Bruce,
mri_diff does not return any differences. However, when I load the MNC file into Matlab using loadminc (http://www.mathworks.com/matlabcentral/fileexchange/32644-loadminc), I do retain all the values between 0 and 255. Also, I have something like an annotation file for the MNC file that lists values between 0 and 255. The MNC is unsigned byte. Caspar
2014/1/22 Bruce Fischl fischl@nmr.mgh.harvard.edu how do you know that the values were there before? Try running mri_diff on the .nii and the .mnc and see if it finds any differences Bruce
On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi Bruce, I have tried the two following commands, and various flags on mri_convert: mnc2nii -nii -int paxinos-MNI.mnc paxinos-MNI.nii mri_convert -i paxinos-MNI.mnc -o paxinos-MNI.nii Yhe output of the latter would be: mri_convert -i paxinos-MNI.mnc -o paxinos-MNI.nii $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from paxinos-MNI.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to paxinos-MNI.nii... for mri_convert, --nochange, -odt float/int/uchar, --no_scale 1 all do not make a difference. It could be that the problem arises once I call mri_binarize afterwards. I know that there are values between 1 and 256 in the MNC file, but when I call mri_binarize with -match on the MNC file or on any of the converted NIFTI files, it does not find any values lower than 53 or so. Caspar 2014/1/22 Bruce Fischl <fischl@nmr.mgh.harvard.edu> Hi Caspar hmm, I don't know why that would be the case. Can you send the full command line and screen output? cheers Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi! I am having some troubles converting MNC files to NII while preserving the exact values in the MNC file. I have tried to use mri_convert and mnc2nii, but in both cases, the values in the file output get changed. The help of mri_convert mentions that the output for MNC files may not work. Is there a workaround or a recommended procedure to convert MNC into NII? Thanks, Caspar 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.
can you send us the full command line and screen output of the mri_binarize command? On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote:
Hi Bruce, I am confused, too. If the conversion is proper, why does mri_binarize not find values below ~53? when I call mri_binarize with -match on the MNC file or on any of the converted NIFTI files? Caspar
2014/1/22 Bruce Fischl fischl@nmr.mgh.harvard.edu Hi Caspar
now, I'm confused. So it sounds like mri_convert is doing the conversion properly then? Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi Bruce, mri_diff does not return any differences. However, when I load the MNC file into Matlab using loadminc (http://www.mathworks.com/matlabcentral/fileexchange/32644-loadminc), I do retain all the values between 0 and 255. Also, I have something like an annotation file for the MNC file that lists values between 0 and 255. The MNC is unsigned byte. Caspar 2014/1/22 Bruce Fischl <fischl@nmr.mgh.harvard.edu> how do you know that the values were there before? Try running mri_diff on the .nii and the .mnc and see if it finds any differences Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi Bruce, I have tried the two following commands, and various flags on mri_convert: mnc2nii -nii -int paxinos-MNI.mnc paxinos-MNI.nii mri_convert -i paxinos-MNI.mnc -o paxinos-MNI.nii Yhe output of the latter would be: mri_convert -i paxinos-MNI.mnc -o paxinos-MNI.nii $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from paxinos-MNI.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to paxinos-MNI.nii... for mri_convert, --nochange, -odt float/int/uchar, --no_scale 1 all do not make a difference. It could be that the problem arises once I call mri_binarize afterwards. I know that there are values between 1 and 256 in the MNC file, but when I call mri_binarize with -match on the MNC file or on any of the converted NIFTI files, it does not find any values lower than 53 or so. Caspar 2014/1/22 Bruce Fischl <fischl@nmr.mgh.harvard.edu> Hi Caspar hmm, I don't know why that would be the case. Can you send the full command line and screen output? cheers Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi! I am having some troubles converting MNC files to NII while preserving the exact values in the MNC file. I have tried to use mri_convert and mnc2nii, but in both cases, the values in the file output get changed. The help of mri_convert mentions that the output for MNC files may not work. Is there a workaround or a recommended procedure to convert MNC into NII? Thanks, Caspar 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.
mri_binarize --i paxinos-MNI.nii --match 1 --o labels/1.nii
$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /rdata3/space3/data/cschwiedrz/cooked/anatomicals/mni_macaque cmdline mri_binarize --i paxinos-MNI.nii --match 1 --o labels/1.nii sysname Linux hostname wiener machine x86_64 user cschwiedrz
input paxinos-MNI.nii frame 0 nErode3d 0 nErode2d 0 output labels/1.nii Binarizing based on matching values nMatch 1 0 1 binval 1 binvalnot 0 Found 0 values in range Counting number of voxels Found 0 voxels in final mask mri_binarize done
2014/1/22 Bruce Fischl fischl@nmr.mgh.harvard.edu
can you send us the full command line and screen output of the mri_binarize command?
On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote:
Hi Bruce,
I am confused, too. If the conversion is proper, why does mri_binarize not find values below ~53? when I call mri_binarize with -match on the MNC file or on any of the converted NIFTI files? Caspar
2014/1/22 Bruce Fischl fischl@nmr.mgh.harvard.edu Hi Caspar
now, I'm confused. So it sounds like mri_convert is doing the conversion properly then? Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi Bruce, mri_diff does not return any differences. However, when I load the MNC file into Matlab using loadminc (http://www.mathworks.com/matlabcentral/fileexchange/32644-loadminc), I do retain all the values between 0 and 255. Also, I have something like an annotation file for the MNC file that lists values between 0 and 255. The MNC is unsigned byte. Caspar
2014/1/22 Bruce Fischl <fischl@nmr.mgh.harvard.edu> how do you know that the values were there before? Try running mri_diff on the .nii and the .mnc and see if it finds any differences Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi Bruce, I have tried the two following commands, and various flags on mri_convert: mnc2nii -nii -int paxinos-MNI.mnc paxinos-MNI.nii mri_convert -i paxinos-MNI.mnc -o paxinos-MNI.nii Yhe output of the latter would be: mri_convert -i paxinos-MNI.mnc -o paxinos-MNI.nii $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from paxinos-MNI.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to paxinos-MNI.nii... for mri_convert, --nochange, -odt float/int/uchar, --no_scale 1 all do not make a difference. It could be that the problem arises once I call mri_binarize afterwards. I know that there are values between 1 and 256 in the MNC file, but when I call mri_binarize with -match on the MNC file or on any of the converted NIFTI files, it does not find any values lower than 53 or so. Caspar 2014/1/22 Bruce Fischl <fischl@nmr.mgh.harvard.edu> Hi Caspar hmm, I don't know why that would be the case. Can you send the full command line and screen output? cheers Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi! I am having some troubles converting MNC files to NII while preserving the exact values in the MNC file. I have tried to use mri_convert and mnc2nii, but in both cases, the values in the file output get changed. The help of mri_convert mentions that the output for MNC files may not work. Is there a workaround or a recommended procedure to convert MNC into NII? Thanks, Caspar 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.
and what if you run it on the mnc? On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote:
mri_binarize --i paxinos-MNI.nii --match 1 --o labels/1.nii
$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /rdata3/space3/data/cschwiedrz/cooked/anatomicals/mni_macaque cmdline mri_binarize --i paxinos-MNI.nii --match 1 --o labels/1.nii sysname Linux hostname wiener machine x86_64 user cschwiedrz
input paxinos-MNI.nii frame 0 nErode3d 0 nErode2d 0 output labels/1.nii Binarizing based on matching values nMatch 1 0 1 binval 1 binvalnot 0 Found 0 values in range Counting number of voxels Found 0 voxels in final mask mri_binarize done
2014/1/22 Bruce Fischl fischl@nmr.mgh.harvard.edu can you send us the full command line and screen output of the mri_binarize command? On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote:
Hi Bruce, I am confused, too. If the conversion is proper, why does mri_binarize not find values below ~53? when I call mri_binarize with -match on the MNC file or on any of the converted NIFTI files? Caspar 2014/1/22 Bruce Fischl <fischl@nmr.mgh.harvard.edu> Hi Caspar now, I'm confused. So it sounds like mri_convert is doing the conversion properly then? Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi Bruce, mri_diff does not return any differences. However, when I load the MNC file into Matlab using loadminc (http://www.mathworks.com/matlabcentral/fileexchange/32644-loadminc), I do retain all the values between 0 and 255. Also, I have something like an annotation file for the MNC file that lists values between 0 and 255. The MNC is unsigned byte. Caspar 2014/1/22 Bruce Fischl <fischl@nmr.mgh.harvard.edu> how do you know that the values were there before? Try running mri_diff on the .nii and the .mnc and see if it finds any differences Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi Bruce, I have tried the two following commands, and various flags on mri_convert: mnc2nii -nii -int paxinos-MNI.mnc paxinos-MNI.nii mri_convert -i paxinos-MNI.mnc -o paxinos-MNI.nii Yhe output of the latter would be: mri_convert -i paxinos-MNI.mnc -o paxinos-MNI.nii $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from paxinos-MNI.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to paxinos-MNI.nii... for mri_convert, --nochange, -odt float/int/uchar, --no_scale 1 all do not make a difference. It could be that the problem arises once I call mri_binarize afterwards. I know that there are values between 1 and 256 in the MNC file, but when I call mri_binarize with -match on the MNC file or on any of the converted NIFTI files, it does not find any values lower than 53 or so. Caspar 2014/1/22 Bruce Fischl <fischl@nmr.mgh.harvard.edu> Hi Caspar hmm, I don't know why that would be the case. Can you send the full command line and screen output? cheers Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi! I am having some troubles converting MNC files to NII while preserving the exact values in the MNC file. I have tried to use mri_convert and mnc2nii, but in both cases, the values in the file output get changed. The help of mri_convert mentions that the output for MNC files may not work. Is there a workaround or a recommended procedure to convert MNC into NII? Thanks, Caspar 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.
same thing
2014/1/22 Bruce Fischl fischl@nmr.mgh.harvard.edu
and what if you run it on the mnc?
On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote:
mri_binarize --i paxinos-MNI.nii --match 1 --o labels/1.nii
$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /rdata3/space3/data/cschwiedrz/cooked/anatomicals/mni_macaque cmdline mri_binarize --i paxinos-MNI.nii --match 1 --o labels/1.nii sysname Linux hostname wiener machine x86_64 user cschwiedrz
input paxinos-MNI.nii frame 0 nErode3d 0 nErode2d 0 output labels/1.nii Binarizing based on matching values nMatch 1 0 1 binval 1 binvalnot 0 Found 0 values in range Counting number of voxels Found 0 voxels in final mask mri_binarize done
2014/1/22 Bruce Fischl fischl@nmr.mgh.harvard.edu can you send us the full command line and screen output of the mri_binarize command? On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote:
Hi Bruce, I am confused, too. If the conversion is proper, why does mri_binarize not find values below ~53? when I call mri_binarize with -match on the MNC file or on any of the converted NIFTI files? Caspar 2014/1/22 Bruce Fischl <fischl@nmr.mgh.harvard.edu> Hi Caspar now, I'm confused. So it sounds like mri_convert is doing the conversion properly then? Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi Bruce, mri_diff does not return any differences. However, when I load the MNC file into Matlab using loadminc (http://www.mathworks.com/matlabcentral/fileexchange/32644-loadminc), I do retain all the values between 0 and 255. Also, I have something like an annotation file for the MNC file that lists values between 0 and 255. The MNC is unsigned byte. Caspar
2014/1/22 Bruce Fischl <fischl@nmr.mgh.harvard.edu> how do you know that the values were there before? Try running mri_diff on the .nii and the .mnc and see if it finds any differences Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi Bruce, I have tried the two following commands, and various flags on mri_convert: mnc2nii -nii -int paxinos-MNI.mnc paxinos-MNI.nii mri_convert -i paxinos-MNI.mnc -o paxinos-MNI.nii Yhe output of the latter would be: mri_convert -i paxinos-MNI.mnc -o paxinos-MNI.nii $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from paxinos-MNI.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to paxinos-MNI.nii... for mri_convert, --nochange, -odt float/int/uchar, --no_scale 1 all do not make a difference. It could be that the problem arises once I call mri_binarize afterwards. I know that there are values between 1 and 256 in the MNC file, but when I call mri_binarize with -match on the MNC file or on any of the converted NIFTI files, it does not find any values lower than 53 or so. Caspar 2014/1/22 Bruce Fischl <fischl@nmr.mgh.harvard.edu> Hi Caspar hmm, I don't know why that would be the case. Can you send the full command line and screen output? cheers Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi! I am having some troubles converting MNC files to NII while preserving the exact values in the MNC file. I have tried to use mri_convert and mnc2nii, but in both cases, the values in the file output get changed. The help of mri_convert mentions that the output for MNC files may not work. Is there a workaround or a recommended procedure to convert MNC into NII? Thanks, Caspar 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.
then is seems like the problem is with your mnc, not with anything we are doing, right? On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote:
same thing
2014/1/22 Bruce Fischl fischl@nmr.mgh.harvard.edu and what if you run it on the mnc? On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote:
mri_binarize --i paxinos-MNI.nii --match 1 --o labels/1.nii $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /rdata3/space3/data/cschwiedrz/cooked/anatomicals/mni_macaque cmdline mri_binarize --i paxinos-MNI.nii --match 1 --o labels/1.nii sysname Linux hostname wiener machine x86_64 user cschwiedrz input paxinos-MNI.nii frame 0 nErode3d 0 nErode2d 0 output labels/1.nii Binarizing based on matching values nMatch 1 0 1 binval 1 binvalnot 0 Found 0 values in range Counting number of voxels Found 0 voxels in final mask mri_binarize done 2014/1/22 Bruce Fischl <fischl@nmr.mgh.harvard.edu> can you send us the full command line and screen output of the mri_binarize command? On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi Bruce, I am confused, too. If the conversion is proper, why does mri_binarize not find values below ~53? when I call mri_binarize with -match on the MNC file or on any of the converted NIFTI files? Caspar 2014/1/22 Bruce Fischl <fischl@nmr.mgh.harvard.edu> Hi Caspar now, I'm confused. So it sounds like mri_convert is doing the conversion properly then? Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi Bruce, mri_diff does not return any differences. However, when I load the MNC file into Matlab using loadminc (http://www.mathworks.com/matlabcentral/fileexchange/32644-loadminc), I do retain all the values between 0 and 255. Also, I have something like an annotation file for the MNC file that lists values between 0 and 255. The MNC is unsigned byte. Caspar 2014/1/22 Bruce Fischl <fischl@nmr.mgh.harvard.edu> how do you know that the values were there before? Try running mri_diff on the .nii and the .mnc and see if it finds any differences Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi Bruce, I have tried the two following commands, and various flags on mri_convert: mnc2nii -nii -int paxinos-MNI.mnc paxinos-MNI.nii mri_convert -i paxinos-MNI.mnc -o paxinos-MNI.nii Yhe output of the latter would be: mri_convert -i paxinos-MNI.mnc -o paxinos-MNI.nii $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from paxinos-MNI.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to paxinos-MNI.nii... for mri_convert, --nochange, -odt float/int/uchar, --no_scale 1 all do not make a difference. It could be that the problem arises once I call mri_binarize afterwards. I know that there are values between 1 and 256 in the MNC file, but when I call mri_binarize with -match on the MNC file or on any of the converted NIFTI files, it does not find any values lower than 53 or so. Caspar 2014/1/22 Bruce Fischl <fischl@nmr.mgh.harvard.edu> Hi Caspar hmm, I don't know why that would be the case. Can you send the full command line and screen output? cheers Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi! I am having some troubles converting MNC files to NII while preserving the exact values in the MNC file. I have tried to use mri_convert and mnc2nii, but in both cases, the values in the file output get changed. The help of mri_convert mentions that the output for MNC files may not work. Is there a workaround or a recommended procedure to convert MNC into NII? Thanks, Caspar 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.
or, since the correct values display if I load the same MNC file with Matlab, it could be a problem with mri_binarize?
2014/1/22 Bruce Fischl fischl@nmr.mgh.harvard.edu
then is seems like the problem is with your mnc, not with anything we are doing, right?
On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote:
same thing
2014/1/22 Bruce Fischl fischl@nmr.mgh.harvard.edu and what if you run it on the mnc? On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote:
mri_binarize --i paxinos-MNI.nii --match 1 --o labels/1.nii $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /rdata3/space3/data/cschwiedrz/cooked/anatomicals/mni_macaque cmdline mri_binarize --i paxinos-MNI.nii --match 1 --o labels/1.nii sysname Linux hostname wiener machine x86_64 user cschwiedrz input paxinos-MNI.nii frame 0 nErode3d 0 nErode2d 0 output labels/1.nii Binarizing based on matching values nMatch 1 0 1 binval 1 binvalnot 0 Found 0 values in range Counting number of voxels Found 0 voxels in final mask mri_binarize done 2014/1/22 Bruce Fischl <fischl@nmr.mgh.harvard.edu> can you send us the full command line and screen output of the mri_binarize command? On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi Bruce, I am confused, too. If the conversion is proper, why does mri_binarize not find values below ~53? when I call mri_binarize with -match on the MNC file or on any of the converted NIFTI files? Caspar 2014/1/22 Bruce Fischl <fischl@nmr.mgh.harvard.edu> Hi Caspar now, I'm confused. So it sounds like mri_convert is doing the conversion properly then? Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi Bruce, mri_diff does not return any differences. However, when I load the MNC file into Matlab using loadminc (http://www.mathworks.com/matlabcentral/fileexchange/32644-loadminc), I do retain all the values between 0 and 255. Also, I have something like an annotation file for the MNC file that lists values between 0 and 255. The MNC is unsigned byte. Caspar
2014/1/22 Bruce Fischl <fischl@nmr.mgh.harvard.edu> how do you know that the values were there before? Try running mri_diff on the .nii and the .mnc and see if it finds any differences Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi Bruce, I have tried the two following commands, and various flags on mri_convert: mnc2nii -nii -int paxinos-MNI.mnc paxinos-MNI.nii mri_convert -i paxinos-MNI.mnc -o paxinos-MNI.nii Yhe output of the latter would be: mri_convert -i paxinos-MNI.mnc -o paxinos-MNI.nii $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from paxinos-MNI.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to paxinos-MNI.nii... for mri_convert, --nochange, -odt float/int/uchar, --no_scale 1 all do not make a difference. It could be that the problem arises once I call mri_binarize afterwards. I know that there are values between 1 and 256 in the MNC file, but when I call mri_binarize with -match on the MNC file or on any of the converted NIFTI files, it does not find any values lower than 53 or so. Caspar 2014/1/22 Bruce Fischl <fischl@nmr.mgh.harvard.edu> Hi Caspar hmm, I don't know why that would be the case. Can you send the full command line and screen output? cheers Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi! I am having some troubles converting MNC files to NII while preserving the exact values in the MNC file. I have tried to use mri_convert and mnc2nii, but in both cases, the values in the file output get changed. The help of mri_convert mentions that the output for MNC files may not work. Is there a workaround or a recommended procedure to convert MNC into NII? Thanks, Caspar 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.
Can you describe the potential problem with mri_binarize more fully?
On 01/22/2014 12:50 PM, Caspar M. Schwiedrzik wrote:
or, since the correct values display if I load the same MNC file with Matlab, it could be a problem with mri_binarize?
2014/1/22 Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>
then is seems like the problem is with your mnc, not with anything we are doing, right? On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: same thing 2014/1/22 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> and what if you run it on the mnc? On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: mri_binarize --i paxinos-MNI.nii --match 1 --o labels/1.nii $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /rdata3/space3/data/cschwiedrz/cooked/anatomicals/mni_macaque cmdline mri_binarize --i paxinos-MNI.nii --match 1 --o labels/1.nii sysname Linux hostname wiener machine x86_64 user cschwiedrz input paxinos-MNI.nii frame 0 nErode3d 0 nErode2d 0 output labels/1.nii Binarizing based on matching values nMatch 1 0 1 binval 1 binvalnot 0 Found 0 values in range Counting number of voxels Found 0 voxels in final mask mri_binarize done 2014/1/22 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> can you send us the full command line and screen output of the mri_binarize command? On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi Bruce, I am confused, too. If the conversion is proper, why does mri_binarize not find values below ~53? when I call mri_binarize with -match on the MNC file or on any of the converted NIFTI files? Caspar 2014/1/22 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> Hi Caspar now, I'm confused. So it sounds like mri_convert is doing the conversion properly then? Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi Bruce, mri_diff does not return any differences. However, when I load the MNC file into Matlab using loadminc (http://www.mathworks.com/matlabcentral/fileexchange/32644-loadminc), I do retain all the values between 0 and 255. Also, I have something like an annotation file for the MNC file that lists values between 0 and 255. The MNC is unsigned byte. Caspar 2014/1/22 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> how do you know that the values were there before? Try running mri_diff on the .nii and the .mnc and see if it finds any differences Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi Bruce, I have tried the two following commands, and various flags on mri_convert: mnc2nii -nii -int paxinos-MNI.mnc paxinos-MNI.nii mri_convert -i paxinos-MNI.mnc -o paxinos-MNI.nii Yhe output of the latter would be: mri_convert -i paxinos-MNI.mnc -o paxinos-MNI.nii $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from paxinos-MNI.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to paxinos-MNI.nii... for mri_convert, --nochange, -odt float/int/uchar, --no_scale 1 all do not make a difference. It could be that the problem arises once I call mri_binarize afterwards. I know that there are values between 1 and 256 in the MNC file, but when I call mri_binarize with -match on the MNC file or on any of the converted NIFTI files, it does not find any values lower than 53 or so. Caspar 2014/1/22 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> Hi Caspar hmm, I don't know why that would be the case. Can you send the full command line and screen output? cheers Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi! I am having some troubles converting MNC files to NII while preserving the exact values in the MNC file. I have tried to use mri_convert and mnc2nii, but in both cases, the values in the file output get changed. The help of mri_convert mentions that the output for MNC files may not work. Is there a workaround or a recommended procedure to convert MNC into NII? Thanks, Caspar 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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Hi Doug, when I try to use mri_binarize with -match, certain values, especially ones smaller than about 50, are not found. This happens with the original MNC file as well as with NIFTI files that I converted from the MNC file. When I load the MNC file in Matlab, all the values that mri_binarize did not find show up. The data type of the MNC file is unsigned byte; it is read as 32bit integer in Matlab. Caspar
2014/1/22 Douglas N Greve greve@nmr.mgh.harvard.edu
Can you describe the potential problem with mri_binarize more fully?
On 01/22/2014 12:50 PM, Caspar M. Schwiedrzik wrote:
or, since the correct values display if I load the same MNC file with Matlab, it could be a problem with mri_binarize?
2014/1/22 Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>
then is seems like the problem is with your mnc, not with anything we are doing, right? On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: same thing 2014/1/22 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> and what if you run it on the mnc? On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: mri_binarize --i paxinos-MNI.nii --match 1 --o labels/1.nii $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /rdata3/space3/data/cschwiedrz/cooked/anatomicals/mni_macaque cmdline mri_binarize --i paxinos-MNI.nii --match 1 --o labels/1.nii sysname Linux hostname wiener machine x86_64 user cschwiedrz input paxinos-MNI.nii frame 0 nErode3d 0 nErode2d 0 output labels/1.nii Binarizing based on matching values nMatch 1 0 1 binval 1 binvalnot 0 Found 0 values in range Counting number of voxels Found 0 voxels in final mask mri_binarize done 2014/1/22 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> can you send us the full command line and screen output of the mri_binarize command? On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi Bruce, I am confused, too. If the conversion is proper, why does mri_binarize not find values below ~53? when I call mri_binarize with -match on the MNC file or on any of the converted NIFTI files? Caspar 2014/1/22 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> Hi Caspar now, I'm confused. So it sounds like mri_convert is doing the conversion properly then? Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi Bruce, mri_diff does not return any differences. However, when I load the MNC file into Matlab using loadminc (http://www.mathworks.com/matlabcentral/fileexchange/32644-loadminc),
I do retain all the values between 0 and 255. Also, I have something like an annotation file for the MNC file that lists values between 0 and 255. The MNC is unsigned byte. Caspar 2014/1/22 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> how do you know that the values were there before? Try running mri_diff on the .nii and the .mnc and see if it finds any differences Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi Bruce, I have tried the two following commands, and various flags on mri_convert: mnc2nii -nii -int paxinos-MNI.mnc paxinos-MNI.nii mri_convert -i paxinos-MNI.mnc -o paxinos-MNI.nii Yhe output of the latter would be: mri_convert -i paxinos-MNI.mnc -o paxinos-MNI.nii $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from paxinos-MNI.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to paxinos-MNI.nii... for mri_convert, --nochange, -odt float/int/uchar, --no_scale 1 all do not make a difference. It could be that the problem arises once I call mri_binarize afterwards. I know that there are values between 1 and 256 in the MNC file, but when I call mri_binarize with -match on the MNC file or on any of the converted NIFTI files, it does not find any values lower than 53 or so. Caspar 2014/1/22 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> Hi Caspar hmm, I don't know why that would be the case. Can you send the full command line and screen output? cheers Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi! I am having some troubles converting MNC files to NII while preserving the exact values in the MNC file. I have tried to use mri_convert and mnc2nii, but in both cases, the values in the file output get changed. The help of mri_convert mentions that the output for MNC files may not work. Is there a workaround or a recommended procedure to convert MNC into NII? Thanks, Caspar 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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I've looked at the volume you sent. One problem may be that the minc file might have a scale factor which we are not properly reading. When I use mnc2nii it produces a nifti file that has a slope of 1.00392. Not much, but it is there. The values that come out are not integer and there is nothing in the range of 0-73. Using loadminc.m I can see values in the range of 0-73. The datafile has slice-dependent scaling (based on what loadminc is doing). We don't rescale by slice when loading minc. I would suggest finding a program that does the correct rescaling. One possibility is to first do the conversion with mri_convert to create junk.nii the in matlab
a = MRIread('junk.nii'); [imaVOL,scaninfo] = loadminc('paxinos-MNI.mnc'); a.vol = imaVOL; MRIwrite(a,'myvol.nii');
doug
On 01/22/2014 01:09 PM, Caspar M. Schwiedrzik wrote:
Hi Doug, when I try to use mri_binarize with -match, certain values, especially ones smaller than about 50, are not found. This happens with the original MNC file as well as with NIFTI files that I converted from the MNC file. When I load the MNC file in Matlab, all the values that mri_binarize did not find show up. The data type of the MNC file is unsigned byte; it is read as 32bit integer in Matlab. Caspar
2014/1/22 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>
Can you describe the potential problem with mri_binarize more fully? On 01/22/2014 12:50 PM, Caspar M. Schwiedrzik wrote: > or, since the correct values display if I load the same MNC file with > Matlab, it could be a problem with mri_binarize? > > > 2014/1/22 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> > > then is seems like the problem is with your mnc, not with anything > we are doing, right? > > On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: > > same thing > > > 2014/1/22 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> > and what if you run it on the mnc? > On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: > > mri_binarize --i paxinos-MNI.nii --match 1 --o > labels/1.nii > > $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 > greve Exp $ > cwd > > /rdata3/space3/data/cschwiedrz/cooked/anatomicals/mni_macaque > cmdline mri_binarize --i paxinos-MNI.nii --match 1 > --o labels/1.nii > sysname Linux > hostname wiener > machine x86_64 > user cschwiedrz > > input paxinos-MNI.nii > frame 0 > nErode3d 0 > nErode2d 0 > output labels/1.nii > Binarizing based on matching values > nMatch 1 > 0 1 > binval 1 > binvalnot 0 > Found 0 values in range > Counting number of voxels > Found 0 voxels in final mask > mri_binarize done > > > > 2014/1/22 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> > can you send us the full command line and > screen output of the > mri_binarize command? > On Wed, 22 Jan 2014, Caspar M. Schwiedrzik > wrote: > > Hi Bruce, > I am confused, too. > If the conversion is proper, why does > mri_binarize > not find values below > ~53? when I call mri_binarize with > -match on the MNC > file or on any of the > converted NIFTI files? > Caspar > > > > > 2014/1/22 Bruce Fischl > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> > Hi Caspar > > now, I'm confused. So it sounds > like > mri_convert is doing the > conversion properly then? > Bruce > On Wed, 22 Jan 2014, Caspar M. > Schwiedrzik > wrote: > > Hi Bruce, > mri_diff does not return any > differences. However, > when I load the MNC file > into Matlab using loadminc > > > > (http://www.mathworks.com/matlabcentral/fileexchange/32644-loadminc), > I do > retain all the values > between 0 and 255. > Also, I > have something like an > annotation file for the MNC > file that > lists values > between 0 and 255. > The MNC is unsigned byte. > Caspar > > > 2014/1/22 Bruce Fischl > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> > how do you know that > the values > were there > before? Try running > mri_diff on the .nii > and the .mnc > and see if > it finds any > differences > Bruce > > > On Wed, 22 Jan 2014, > Caspar M. > Schwiedrzik > wrote: > > Hi Bruce, > I have tried the > two > following commands, > and various > flags on > mri_convert: > mnc2nii -nii > -int > paxinos-MNI.mnc > paxinos-MNI.nii > mri_convert -i > paxinos-MNI.mnc -o > paxinos-MNI.nii > > Yhe output of > the latter > would be: > mri_convert -i > paxinos-MNI.mnc -o > paxinos-MNI.nii > $Id: > mri_convert.c,v > 1.179.2.2 > 2011/05/16 20:53:47 > greve Exp $ > reading from > paxinos-MNI.mnc... > TR=0.00, > TE=0.00, TI=0.00, > flip > angle=0.00 > i_ras = (1, 0, > 0) > j_ras = (0, 1, > 0) > k_ras = (0, 0, > 1) > writing to > paxinos-MNI.nii... > > for mri_convert, > --nochange, > -odt > float/int/uchar, > --no_scale 1 all > do not > make a > difference. > > It could be that > the problem > arises once > I call > mri_binarize > afterwards. I > know that there > are values > between 1 and > 256 in the > MNC file, but > when I > call > mri_binarize with > -match on the MNC > file or on > any of the > converted > NIFTI files, it > does not > find any values > lower than > 53 or so. > > Caspar > > > > > 2014/1/22 Bruce > Fischl > > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> > Hi Caspar > > hmm, I > don't know why > that would > be the case. > Can you send the > full > command line and > screen > output? > cheers > Bruce > On Wed, 22 > Jan 2014, > Caspar M. > Schwiedrzik > wrote: > > Hi! > I am > having some > troubles > converting MNC > files to > NII > while > preserving the > > exact values in > the MNC > file. I have > tried to use > > mri_convert and > mnc2nii, > but > in both > cases, the > values in the > file output get > > changed. The > help of > > mri_convert > mentions that > the output for > MNC files > may > not work. > Is > there a > workaround or a > recommended > procedure to > > convert MNC into > NII? > > Thanks, Caspar > > > > > > > > > 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 <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug, your suggestion to go via Matlab with loadminc worked perfectly. Thank you very much! Caspar
2014/1/22 Douglas N Greve greve@nmr.mgh.harvard.edu
I've looked at the volume you sent. One problem may be that the minc file might have a scale factor which we are not properly reading. When I use mnc2nii it produces a nifti file that has a slope of 1.00392. Not much, but it is there. The values that come out are not integer and there is nothing in the range of 0-73. Using loadminc.m I can see values in the range of 0-73. The datafile has slice-dependent scaling (based on what loadminc is doing). We don't rescale by slice when loading minc. I would suggest finding a program that does the correct rescaling. One possibility is to first do the conversion with mri_convert to create junk.nii the in matlab
a = MRIread('junk.nii'); [imaVOL,scaninfo] = loadminc('paxinos-MNI.mnc'); a.vol = imaVOL; MRIwrite(a,'myvol.nii');
doug
On 01/22/2014 01:09 PM, Caspar M. Schwiedrzik wrote:
Hi Doug, when I try to use mri_binarize with -match, certain values, especially ones smaller than about 50, are not found. This happens with the original MNC file as well as with NIFTI files that I converted from the MNC file. When I load the MNC file in Matlab, all the values that mri_binarize did not find show up. The data type of the MNC file is unsigned byte; it is read as 32bit integer in Matlab. Caspar
2014/1/22 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto: greve@nmr.mgh.harvard.edu>
Can you describe the potential problem with mri_binarize more fully? On 01/22/2014 12:50 PM, Caspar M. Schwiedrzik wrote: > or, since the correct values display if I load the same MNC file with > Matlab, it could be a problem with mri_binarize? > > > 2014/1/22 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> > > then is seems like the problem is with your mnc, not with anything > we are doing, right? > > On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: > > same thing > > > 2014/1/22 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> > and what if you run it on the mnc? > On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: > > mri_binarize --i paxinos-MNI.nii --match 1 --o > labels/1.nii > > $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 > greve Exp $ > cwd > > /rdata3/space3/data/cschwiedrz/cooked/anatomicals/mni_macaque > cmdline mri_binarize --i paxinos-MNI.nii --match 1 > --o labels/1.nii > sysname Linux > hostname wiener > machine x86_64 > user cschwiedrz > > input paxinos-MNI.nii > frame 0 > nErode3d 0 > nErode2d 0 > output labels/1.nii > Binarizing based on matching values > nMatch 1 > 0 1 > binval 1 > binvalnot 0 > Found 0 values in range > Counting number of voxels > Found 0 voxels in final mask > mri_binarize done > > > > 2014/1/22 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> > can you send us the full command line and > screen output of the > mri_binarize command? > On Wed, 22 Jan 2014, Caspar M. Schwiedrzik > wrote: > > Hi Bruce, > I am confused, too. > If the conversion is proper, why does > mri_binarize > not find values below > ~53? when I call mri_binarize with > -match on the MNC > file or on any of the > converted NIFTI files? > Caspar > > > > > 2014/1/22 Bruce Fischl > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> > Hi Caspar > > now, I'm confused. So it sounds > like > mri_convert is doing the > conversion properly then? > Bruce > On Wed, 22 Jan 2014, Caspar M. > Schwiedrzik > wrote: > > Hi Bruce, > mri_diff does not return any > differences. However, > when I load the MNC file > into Matlab using loadminc > > > > (http://www.mathworks.com/matlabcentral/fileexchange/32644-loadminc), > I do > retain all the values > between 0 and 255. > Also, I > have something like an > annotation file for the MNC > file that > lists values > between 0 and 255. > The MNC is unsigned byte. > Caspar > > > 2014/1/22 Bruce Fischl > <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu
<mailto:fischl@nmr.mgh.harvard.edu>>> > how do you know that > the values > were there > before? Try running > mri_diff on the .nii > and the .mnc > and see if > it finds any > differences > Bruce > > > On Wed, 22 Jan 2014, > Caspar M. > Schwiedrzik > wrote: > > Hi Bruce, > I have tried the > two > following commands, > and various > flags on > mri_convert: > mnc2nii -nii > -int > paxinos-MNI.mnc > paxinos-MNI.nii > mri_convert -i > paxinos-MNI.mnc -o > paxinos-MNI.nii > > Yhe output of > the latter > would be: > mri_convert -i > paxinos-MNI.mnc -o > paxinos-MNI.nii > $Id: > mri_convert.c,v > 1.179.2.2 > 2011/05/16 20:53:47 > greve Exp $ > reading from > paxinos-MNI.mnc... > TR=0.00, > TE=0.00, TI=0.00, > flip > angle=0.00 > i_ras = (1, 0, > 0) > j_ras = (0, 1, > 0) > k_ras = (0, 0, > 1) > writing to > paxinos-MNI.nii... > > for mri_convert, > --nochange, > -odt > float/int/uchar, > --no_scale 1 all > do not > make a > difference. > > It could be that > the problem > arises once > I call > mri_binarize > afterwards. I > know that there > are values > between 1 and > 256 in the > MNC file, but > when I > call > mri_binarize with > -match on the MNC > file or on > any of the > converted > NIFTI files, it > does not > find any values > lower than > 53 or so. > > Caspar > > > > > 2014/1/22 Bruce > Fischl > > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> > Hi Caspar > > hmm, I > don't know why > that would > be the case. > Can you send the > full > command line and > screen > output? > cheers > Bruce > On Wed, 22 > Jan 2014, > Caspar M. > Schwiedrzik > wrote: > > Hi! > I am > having some > troubles > converting MNC > files to > NII > while > preserving the > > exact values in > the MNC > file. I have > tried to use > > mri_convert and > mnc2nii, > but > in both > cases, the > values in the > file output get > > changed. The > help of > > mri_convert > mentions that > the output for > MNC files > may > not work. > Is > there a > workaround or a > recommended > procedure to > > convert MNC into > NII? > > Thanks, Caspar > > > > > > > > > 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 <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Caspar M. Schwiedrzik -
Douglas N Greve