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Dear All,
I have used CVS to align around 180 scans to a single, representative subject. I have then used BBR to align the mean b0 image to register the diffusion data to the native space T1 and then apply CVS warps; however, the resulting aligned images for calculated maps from the DWIs are very poor with a great deal of heterogeneity, especially at the boundary but also within white matter. The coefficient of variation of the mean b0 BB registered to the T1 is around 30% globally (excluding the edges of the brain) and 40% or greater for FA. I have reviewed the initial rigid registration of the b0s to the T1s for gross misalignment and found that FLIRT performed pretty well and didn’t fail for any of my subjects and didn’t require manual adjustment; however, the result of after applying the CVS warps is quite poor. The data T1s are 1mm (MPnRAGE) and the b0s are at 2mm. The DWIs were corrected for eddy currents, Gibbs’ ringing, rician noise, and B0 distortions and look pretty great. The DWIs are 70x180x180 at 2mm isotropic and the T1s are 256x256x256 at 1mm isotropic. Are there any suggestions for this issue? I have tried re-aligning the DTI parameter maps to the b0s before applying the CVS warps (although they should be in the same space) and I have tried using both the –t2 and –dti, as well as with/out the –fsl-init flag. Is bbregister shifting the origin for the images at all? Any help would be appreciated.
Cheers, -Austin -- Austin M. Bazydlo, MS PhD Candidate Dept. of Medical Physics University of Wisconsin-Madison
So the B0-to-Anat registration is ok? What command are you using to map the B0s into the CVS space?
On 2/26/2020 3:50 PM, Austin Patrick wrote:
External Email - Use Caution
Dear All,
I have used CVS to align around 180 scans to a single, representative subject. I have then used BBR to align the mean b0 image to register the diffusion data to the native space T1 and then apply CVS warps; however, the resulting aligned images for calculated maps from the DWIs are very poor with a great deal of heterogeneity, especially at the boundary but also within white matter. The coefficient of variation of the mean b0 BB registered to the T1 is around 30% globally (excluding the edges of the brain) and 40% or greater for FA. I have reviewed the initial rigid registration of the b0s to the T1s for gross misalignment and found that FLIRT performed pretty well and didn’t fail for any of my subjects and didn’t require manual adjustment; however, the result of after applying the CVS warps is quite poor. The data T1s are 1mm (MPnRAGE) and the b0s are at 2mm. The DWIs were corrected for eddy currents, Gibbs’ ringing, rician noise, and B0 distortions and look pretty great. The DWIs are 70x180x180 at 2mm isotropic and the T1s are 256x256x256 at 1mm isotropic. Are there any suggestions for this issue? I have tried re-aligning the DTI parameter maps to the b0s before applying the CVS warps (although they should be in the same space) and I have tried using both the –t2 and –dti, as well as with/out the –fsl-init flag. Is bbregister shifting the origin for the images at all? Any help would be appreciated.
Cheers,
-Austin
--
Austin M. Bazydlo, MS
PhD Candidate
Dept. of Medical Physics
University of Wisconsin-Madison
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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The b0-to-anat look fine. I’m using mri_vol2vol with trilinear interpolation to apply the CVS warps.
Thanks, -Austin
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Friday, February 28, 2020 at 3:18 PM To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Issue with BBR and Applying CVS Warps to Diffusion Data
So the B0-to-Anat registration is ok? What command are you using to map the B0s into the CVS space? On 2/26/2020 3:50 PM, Austin Patrick wrote:
External Email - Use Caution
Dear All,
I have used CVS to align around 180 scans to a single, representative subject. I have then used BBR to align the mean b0 image to register the diffusion data to the native space T1 and then apply CVS warps; however, the resulting aligned images for calculated maps from the DWIs are very poor with a great deal of heterogeneity, especially at the boundary but also within white matter. The coefficient of variation of the mean b0 BB registered to the T1 is around 30% globally (excluding the edges of the brain) and 40% or greater for FA. I have reviewed the initial rigid registration of the b0s to the T1s for gross misalignment and found that FLIRT performed pretty well and didn’t fail for any of my subjects and didn’t require manual adjustment; however, the result of after applying the CVS warps is quite poor. The data T1s are 1mm (MPnRAGE) and the b0s are at 2mm. The DWIs were corrected for eddy currents, Gibbs’ ringing, rician noise, and B0 distortions and look pretty great. The DWIs are 70x180x180 at 2mm isotropic and the T1s are 256x256x256 at 1mm isotropic. Are there any suggestions for this issue? I have tried re-aligning the DTI parameter maps to the b0s before applying the CVS warps (although they should be in the same space) and I have tried using both the –t2 and –dti, as well as with/out the –fsl-init flag. Is bbregister shifting the origin for the images at all? Any help would be appreciated.
Cheers, -Austin -- Austin M. Bazydlo, MS PhD Candidate Dept. of Medical Physics University of Wisconsin-Madison
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
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Can you send the mri_vol2vol command line?
On 2/28/2020 4:46 PM, Austin Patrick wrote:
External Email - Use Caution
The b0-to-anat look fine. I’m using mri_vol2vol with trilinear interpolation to apply the CVS warps.
Thanks,
-Austin
*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edu *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Friday, February 28, 2020 at 3:18 PM *To: *"freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] Issue with BBR and Applying CVS Warps to Diffusion Data
So the B0-to-Anat registration is ok? What command are you using to map the B0s into the CVS space?
On 2/26/2020 3:50 PM, Austin Patrick wrote:
* External Email - Use Caution * Dear All, I have used CVS to align around 180 scans to a single, representative subject. I have then used BBR to align the mean b0 image to register the diffusion data to the native space T1 and then apply CVS warps; however, the resulting aligned images for calculated maps from the DWIs are very poor with a great deal of heterogeneity, especially at the boundary but also within white matter. The coefficient of variation of the mean b0 BB registered to the T1 is around 30% globally (excluding the edges of the brain) and 40% or greater for FA. I have reviewed the initial rigid registration of the b0s to the T1s for gross misalignment and found that FLIRT performed pretty well and didn’t fail for any of my subjects and didn’t require manual adjustment; however, the result of after applying the CVS warps is quite poor. The data T1s are 1mm (MPnRAGE) and the b0s are at 2mm. The DWIs were corrected for eddy currents, Gibbs’ ringing, rician noise, and B0 distortions and look pretty great. The DWIs are 70x180x180 at 2mm isotropic and the T1s are 256x256x256 at 1mm isotropic. Are there any suggestions for this issue? I have tried re-aligning the DTI parameter maps to the b0s before applying the CVS warps (although they should be in the same space) and I have tried using both the –t2 and –dti, as well as with/out the –fsl-init flag. Is bbregister shifting the origin for the images at all? Any help would be appreciated. Cheers, -Austin -- Austin M. Bazydlo, MS PhD Candidate Dept. of Medical Physics University of Wisconsin-Madison _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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
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I’d be happy to. This is the call:
mri_vol2vol --targ ${target} \ --m3z $cvsmorph \ --noDefM3zPath --reg ${b0toT1mat_bet} \ --mov ${meanb0_bet} \ --o ${b0_to040_2_t1w} \ --interp trilin
Thanks, -Austin
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Monday, March 2, 2020 at 8:58 PM To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Issue with BBR and Applying CVS Warps to Diffusion Data
Can you send the mri_vol2vol command line? On 2/28/2020 4:46 PM, Austin Patrick wrote:
External Email - Use Caution The b0-to-anat look fine. I’m using mri_vol2vol with trilinear interpolation to apply the CVS warps.
Thanks, -Austin
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Friday, February 28, 2020 at 3:18 PM To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Issue with BBR and Applying CVS Warps to Diffusion Data
So the B0-to-Anat registration is ok? What command are you using to map the B0s into the CVS space? On 2/26/2020 3:50 PM, Austin Patrick wrote:
External Email - Use Caution
Dear All,
I have used CVS to align around 180 scans to a single, representative subject. I have then used BBR to align the mean b0 image to register the diffusion data to the native space T1 and then apply CVS warps; however, the resulting aligned images for calculated maps from the DWIs are very poor with a great deal of heterogeneity, especially at the boundary but also within white matter. The coefficient of variation of the mean b0 BB registered to the T1 is around 30% globally (excluding the edges of the brain) and 40% or greater for FA. I have reviewed the initial rigid registration of the b0s to the T1s for gross misalignment and found that FLIRT performed pretty well and didn’t fail for any of my subjects and didn’t require manual adjustment; however, the result of after applying the CVS warps is quite poor. The data T1s are 1mm (MPnRAGE) and the b0s are at 2mm. The DWIs were corrected for eddy currents, Gibbs’ ringing, rician noise, and B0 distortions and look pretty great. The DWIs are 70x180x180 at 2mm isotropic and the T1s are 256x256x256 at 1mm isotropic. Are there any suggestions for this issue? I have tried re-aligning the DTI parameter maps to the b0s before applying the CVS warps (although they should be in the same space) and I have tried using both the –t2 and –dti, as well as with/out the –fsl-init flag. Is bbregister shifting the origin for the images at all? Any help would be appreciated.
Cheers, -Austin -- Austin M. Bazydlo, MS PhD Candidate Dept. of Medical Physics University of Wisconsin-Madison
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Try this instead set gcam = $SUBJECTS_DIR/$subject/cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z set dstreg = $FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri.2mm/register.lta mri_vol2vol --gcam ${meanb0_bet} ${b0toT1mat_bet} $gcam $dstreg 0 1 ${b0_to040_2_t1w}
This (admittedly cryptic) command should put it into the mri.2mm space of cvs_avg35_inMNI152 0 above means don't use a B0 distortion map 1 above means to use triliinear interp
On 3/2/2020 10:35 PM, Austin Patrick wrote:
External Email - Use Caution
I’d be happy to. This is the call:
mri_vol2vol --targ ${target} \
--m3z $cvsmorph \
--noDefM3zPath --reg ${b0toT1mat_bet} \
--mov ${meanb0_bet} \
--o ${b0_to040_2_t1w} \
--interp trilin
Thanks,
-Austin
*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edu *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Monday, March 2, 2020 at 8:58 PM *To: *"freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] Issue with BBR and Applying CVS Warps to Diffusion Data
Can you send the mri_vol2vol command line?
On 2/28/2020 4:46 PM, Austin Patrick wrote:
* External Email - Use Caution * The b0-to-anat look fine. I’m using mri_vol2vol with trilinear interpolation to apply the CVS warps. Thanks, -Austin *From: *<freesurfer-bounces@nmr.mgh.harvard.edu> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Douglas N. Greve" <dgreve@mgh.harvard.edu> <mailto:dgreve@mgh.harvard.edu> *Reply-To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> *Date: *Friday, February 28, 2020 at 3:18 PM *To: *"freesurfer@nmr.mgh.harvard.edu" <mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> *Subject: *Re: [Freesurfer] Issue with BBR and Applying CVS Warps to Diffusion Data So the B0-to-Anat registration is ok? What command are you using to map the B0s into the CVS space? On 2/26/2020 3:50 PM, Austin Patrick wrote: * External Email - Use Caution * Dear All, I have used CVS to align around 180 scans to a single, representative subject. I have then used BBR to align the mean b0 image to register the diffusion data to the native space T1 and then apply CVS warps; however, the resulting aligned images for calculated maps from the DWIs are very poor with a great deal of heterogeneity, especially at the boundary but also within white matter. The coefficient of variation of the mean b0 BB registered to the T1 is around 30% globally (excluding the edges of the brain) and 40% or greater for FA. I have reviewed the initial rigid registration of the b0s to the T1s for gross misalignment and found that FLIRT performed pretty well and didn’t fail for any of my subjects and didn’t require manual adjustment; however, the result of after applying the CVS warps is quite poor. The data T1s are 1mm (MPnRAGE) and the b0s are at 2mm. The DWIs were corrected for eddy currents, Gibbs’ ringing, rician noise, and B0 distortions and look pretty great. The DWIs are 70x180x180 at 2mm isotropic and the T1s are 256x256x256 at 1mm isotropic. Are there any suggestions for this issue? I have tried re-aligning the DTI parameter maps to the b0s before applying the CVS warps (although they should be in the same space) and I have tried using both the –t2 and –dti, as well as with/out the –fsl-init flag. Is bbregister shifting the origin for the images at all? Any help would be appreciated. Cheers, -Austin -- Austin M. Bazydlo, MS PhD Candidate Dept. of Medical Physics University of Wisconsin-Madison _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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@nmr.mgh.harvard.edu
-
Austin Patrick -
Douglas N. Greve