Dear all,
Is there a way to output the N3's (non-parametric normalization step) output? I am interested in the bias field that was computed to correct the image intensities.
Thank you for your help, Barbara
Hi Barbara,
I'm not aware of any way that you can do it directly by passing arguments to recon-all (some might correct me on that), but it is possible:
1) As N3 models the bias as a multiplicative effect uncorrected = corrected * bias, the simplest way is to divide each voxel of the volume before and after correction, in order to obtain a volume containing the bias. Note that N3 (by default) works within a mask where low-intensity voxels have been thresholded away. These voxels will contain garbage if you divide all voxels in the volume.
2) Somewhat more complicated: you can specify the -keeptmp flag combined with -tmp SOMEDIR/ (remember the trailing slash) to N3, in order to preserve its working files. This requires you to modify the N3 binary call in the mri_nu_correct.mni script. You also need to convert the mnc files from the tmp dir, so that you can work with the volumes.
3) if you do 2), you also get hold of the low-intensity voxel mask that N3 operates within. You can use this to constrain the division mentioned in 1).
Best, Christian
On 8/27/2014 11:18 PM, Barbara Kreilkamp wrote:
Dear all,
Is there a way to output the N3's (non-parametric normalization step) output? I am interested in the bias field that was computed to correct the image intensities.
Thank you for your help, Barbara _______________________________________________ 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.
Dear Christian,
Thanks a bunch for this answer. I ran all the steps you mentioned (except for the one where I simply do uncorrected/corrected, as these images have different dimensions, it seems nu3 does more than just normalization of intensities, but also image cropping). Do you know anything about the image cropping?
I ended up with the output nu1_mask and nu1_est and I think the last one is the bias field, at least it looks very much like one :). Am I right?
Thanks for your help, Barbara
On 27/08/2014 22:53, Christian Thode Larsen wrote:
Hi Barbara,
I'm not aware of any way that you can do it directly by passing arguments to recon-all (some might correct me on that), but it is possible:
- As N3 models the bias as a multiplicative effect uncorrected =
corrected * bias, the simplest way is to divide each voxel of the volume before and after correction, in order to obtain a volume containing the bias. Note that N3 (by default) works within a mask where low-intensity voxels have been thresholded away. These voxels will contain garbage if you divide all voxels in the volume.
- Somewhat more complicated: you can specify the -keeptmp flag combined
with -tmp SOMEDIR/ (remember the trailing slash) to N3, in order to preserve its working files. This requires you to modify the N3 binary call in the mri_nu_correct.mni script. You also need to convert the mnc files from the tmp dir, so that you can work with the volumes.
- if you do 2), you also get hold of the low-intensity voxel mask that
N3 operates within. You can use this to constrain the division mentioned in 1).
Best, Christian
On 8/27/2014 11:18 PM, Barbara Kreilkamp wrote:
Dear all,
Is there a way to output the N3's (non-parametric normalization step) output? I am interested in the bias field that was computed to correct the image intensities.
Thank you for your help, Barbara _______________________________________________ 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
Hi Barbara what exactly did you divide? If you look at the recon-all.log it will show the exact inputs and outputs of nu_correct.
cheers Bruce
On Thu, 28 Aug 2014, Barbara Kreilkamp wrote:
Dear Christian,
Thanks a bunch for this answer. I ran all the steps you mentioned (except for the one where I simply do uncorrected/corrected, as these images have different dimensions, it seems nu3 does more than just normalization of intensities, but also image cropping). Do you know anything about the image cropping?
I ended up with the output nu1_mask and nu1_est and I think the last one is the bias field, at least it looks very much like one :). Am I right?
Thanks for your help, Barbara
On 27/08/2014 22:53, Christian Thode Larsen wrote:
Hi Barbara,
I'm not aware of any way that you can do it directly by passing arguments to recon-all (some might correct me on that), but it is possible:
- As N3 models the bias as a multiplicative effect uncorrected =
corrected * bias, the simplest way is to divide each voxel of the volume before and after correction, in order to obtain a volume containing the bias. Note that N3 (by default) works within a mask where low-intensity voxels have been thresholded away. These voxels will contain garbage if you divide all voxels in the volume.
- Somewhat more complicated: you can specify the -keeptmp flag combined
with -tmp SOMEDIR/ (remember the trailing slash) to N3, in order to preserve its working files. This requires you to modify the N3 binary call in the mri_nu_correct.mni script. You also need to convert the mnc files from the tmp dir, so that you can work with the volumes.
- if you do 2), you also get hold of the low-intensity voxel mask that
N3 operates within. You can use this to constrain the division mentioned in 1).
Best, Christian
On 8/27/2014 11:18 PM, Barbara Kreilkamp wrote:
Dear all,
Is there a way to output the N3's (non-parametric normalization step) output? I am interested in the bias field that was computed to correct the image intensities.
Thank you for your help, Barbara _______________________________________________ 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Bruce and Christian,
I found the easy way of simply writing 'set cleanup = 0' at the beginning of mri_nu_correct.mni and then I run this command mri_nu_correct.mni --i T2-scic/mri/orig/001.mgz --o nu.mgz --n 2
This way I get all the masks and iterations that were computed.
Now I also see that it generates as many folders as there are iterations, ending with nu2_field and nu2_est if there are two iterations. I see more files now and now I am thinking that the last output is nu2_field, which would be the bias field. So this is why I did not divide anything by hand (also because my 001.mgz and the nu.mgz do not have the same image dimensions) and the info about masked-out voxel would be missing in that case.
All the best and thanks. Barbara
On 28/08/2014 14:46, Bruce Fischl wrote:
Hi Barbara what exactly did you divide? If you look at the recon-all.log it will show the exact inputs and outputs of nu_correct.
cheers Bruce
On Thu, 28 Aug 2014, Barbara Kreilkamp wrote:
Dear Christian,
Thanks a bunch for this answer. I ran all the steps you mentioned (except for the one where I simply do uncorrected/corrected, as these images have different dimensions, it seems nu3 does more than just normalization of intensities, but also image cropping). Do you know anything about the image cropping?
I ended up with the output nu1_mask and nu1_est and I think the last one is the bias field, at least it looks very much like one :). Am I right?
Thanks for your help, Barbara
On 27/08/2014 22:53, Christian Thode Larsen wrote:
Hi Barbara,
I'm not aware of any way that you can do it directly by passing arguments to recon-all (some might correct me on that), but it is possible:
- As N3 models the bias as a multiplicative effect uncorrected =
corrected * bias, the simplest way is to divide each voxel of the volume before and after correction, in order to obtain a volume containing the bias. Note that N3 (by default) works within a mask where low-intensity voxels have been thresholded away. These voxels will contain garbage if you divide all voxels in the volume.
- Somewhat more complicated: you can specify the -keeptmp flag combined
with -tmp SOMEDIR/ (remember the trailing slash) to N3, in order to preserve its working files. This requires you to modify the N3 binary call in the mri_nu_correct.mni script. You also need to convert the mnc files from the tmp dir, so that you can work with the volumes.
- if you do 2), you also get hold of the low-intensity voxel mask that
N3 operates within. You can use this to constrain the division mentioned in 1).
Best, Christian
On 8/27/2014 11:18 PM, Barbara Kreilkamp wrote:
Dear all,
Is there a way to output the N3's (non-parametric normalization step) output? I am interested in the bias field that was computed to correct the image intensities.
Thank you for your help, Barbara _______________________________________________ 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Barbara,
you should just be ble to divide the original image by the nu-corrected one to get the estimated bias field.
cheers Bruce On Wed, 27 Aug 2014, Barbara Kreilkamp wrote:
Dear all,
Is there a way to output the N3's (non-parametric normalization step) output? I am interested in the bias field that was computed to correct the image intensities.
Thank you for your help, Barbara _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Barbara Kreilkamp -
Bruce Fischl -
Christian Thode Larsen