Hi Bruce, Doug, and FreeSurfer Team,
We have calculated coregistrations between bold timeseries and T1 images using BBR & distortion correction as implemented in the epi_reg utility in FSL5. We would like to map our functional timeseries to surface space for connectivity analyses (analagous to papers by Yeo & Buckner). Normally, without distortion correction, we would use tkregister tp convert the rigid body coregistration calculated in fsl by flirt(.mat) to a register.dat file, and then use mri_vol2surf to birng the data to surface space. However, with distortion correction, the coregistration between the epi & T1 is represented as a deformation field (_warp.nii.gz).
Is there a way for FreeSurfer to read this warp and use the information? We could of course simply do a two-step registration by moving our epi data into T1 space first using FSL and then use FreeSurfer to get it to the surface, but that would involve an extra interpolation. Are the ways to do this in one step using our already-calculated & QA'd deformation fields from FSL?
Thanks so much for your time & advice.
Best,
Ted Satterthwaite
Hi Ted, can you use epidewarp.fsl to create the warp field (voxel shift map (VSM))? If so, you can then use bbregister and mri_vol2surf with the --vsm option to apply the warp simultaneously with determining or applying the registration. It might work with the warp field that you have (since epidewarp.fsl uses fsl to compute the VSM).
doug
On 11/15/2012 02:35 PM, Ted Satterthwaite wrote:
Hi Bruce, Doug, and FreeSurfer Team,
We have calculated coregistrations between bold timeseries and T1 images using BBR & distortion correction as implemented in the epi_reg utility in FSL5. We would like to map our functional timeseries to surface space for connectivity analyses (analagous to papers by Yeo & Buckner). Normally, without distortion correction, we would use tkregister tp convert the rigid body coregistration calculated in fsl by flirt(.mat) to a register.dat file, and then use mri_vol2surf to birng the data to surface space. However, with distortion correction, the coregistration between the epi & T1 is represented as a deformation field (_warp.nii.gz).
Is there a way for FreeSurfer to read this warp and use the information? We could of course simply do a two-step registration by moving our epi data into T1 space first using FSL and then use FreeSurfer to get it to the surface, but that would involve an extra interpolation. Are the ways to do this in one step using our already-calculated & QA'd deformation fields from FSL?
Thanks so much for your time & advice.
Best,
Ted Satterthwaite
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
Thanks so much for your reply and advice. I may have missed it, but I don't see any information regarding the --vsm option in mri_vol2surf on the command line or wiki help. Can you provide any guidance regarding the use of this option and what the format/units/etc of this vsm should be?
Thanks again for all your help.
Best, t
Re: [Freesurfer] applying distortion correction output from epi_reg in fsl to freesurfer Douglas N Greve Mon, 19 Nov 2012 08:05:18 -0800 Hi Ted, can you use epidewarp.fsl to create the warp field (voxel shift map (VSM))? If so, you can then use bbregister and mri_vol2surf with the --vsm option to apply the warp simultaneously with determining or applying the registration. It might work with the warp field that you have (since epidewarp.fsl uses fsl to compute the VSM). doug
________________________________ From: Ted Satterthwaite ted_satt@yahoo.com To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Sent: Thursday, November 15, 2012 2:35 PM Subject: applying distortion correction output from epi_reg in fsl to freesurfer
Hi Bruce, Doug, and FreeSurfer Team,
We have calculated coregistrations between bold timeseries and T1 images using BBR & distortion correction as implemented in the epi_reg utility in FSL5. We would like to map our functional timeseries to surface space for connectivity analyses (analagous to papers by Yeo & Buckner). Normally, without distortion correction, we would use tkregister tp convert the rigid body coregistration calculated in fsl by flirt(.mat) to a register.dat file, and then use mri_vol2surf to birng the data to surface space. However, with distortion correction, the coregistration between the epi & T1 is represented as a deformation field (_warp.nii.gz).
Is there a way for FreeSurfer to read this warp and use the information? We could of course simply do a two-step registration by moving our epi data into T1 space first using FSL and then use FreeSurfer to get it to the surface, but that would involve an extra interpolation. Are the ways to do this in one step using our already-calculated & QA'd deformation fields from FSL?
Thanks so much for your time & advice.
Best,
Ted Satterthwaite
Happy new year all.
Just wanted to f/u on this as it may have fallen through the cracks-- is there any place to find more info on the vsm function previously suggested?
Thanks again.
Best, t
________________________________ From: Ted Satterthwaite ted_satt@yahoo.com To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Cc: Mark Elliott melliott@mail.med.upenn.edu Sent: Tuesday, December 11, 2012 3:36 PM Subject: Re: applying distortion correction output from epi_reg in fsl to freesurfer
Hi Doug,
Thanks so much for your reply and advice. I may have missed it, but I don't see any information regarding the --vsm option in mri_vol2surf on the command line or wiki help. Can you provide any guidance regarding the use of this option and what the format/units/etc of this vsm should be?
Thanks again for all your help.
Best, t
Re: [Freesurfer] applying distortion correction output from epi_reg in fsl to freesurfer Douglas N Greve Mon, 19 Nov 2012 08:05:18 -0800 Hi Ted, can you use epidewarp.fsl to create the warp field (voxel shift map (VSM))? If so, you can then use bbregister and mri_vol2surf with the --vsm option to apply the warp simultaneously with determining or applying the registration. It might work with the warp field that you have (since epidewarp.fsl uses fsl to compute the VSM). doug
________________________________ From: Ted Satterthwaite ted_satt@yahoo.com To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Sent: Thursday, November 15, 2012 2:35 PM Subject: applying distortion correction output from epi_reg in fsl to freesurfer
Hi Bruce, Doug, and FreeSurfer Team,
We have calculated coregistrations between bold timeseries and T1 images using BBR & distortion correction as implemented in the epi_reg utility in FSL5. We would like to map our functional timeseries to surface space for connectivity analyses (analagous to papers by Yeo & Buckner). Normally, without distortion correction, we would use tkregister tp convert the rigid body coregistration calculated in fsl by flirt(.mat) to a register.dat file, and then use mri_vol2surf to birng the data to surface space. However, with distortion correction, the coregistration between the epi & T1 is represented as a deformation field (_warp.nii.gz).
Is there a way for FreeSurfer to read this warp and use the information? We could of course simply do a two-step registration by moving our epi data into T1 space first using FSL and then use FreeSurfer to get it to the surface, but that would involve an extra interpolation. Are the ways to do this in one step using our already-calculated & QA'd deformation fields from FSL?
Thanks so much for your time & advice.
Best,
Ted Satterthwaite
Hi Ted, the VSM is the voxel shift map created by epidewarp.fsl (this is just a front end script for running the FSL field mapping commands). doug
On 01/01/2013 09:53 AM, Ted Satterthwaite wrote:
Happy new year all.
Just wanted to f/u on this as it may have fallen through the cracks-- is there any place to find more info on the vsm function previously suggested?
Thanks again.
Best, t
*From:* Ted Satterthwaite ted_satt@yahoo.com *To:* "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu *Cc:* Mark Elliott melliott@mail.med.upenn.edu *Sent:* Tuesday, December 11, 2012 3:36 PM *Subject:* Re: applying distortion correction output from epi_reg in fsl to freesurfer
Hi Doug,
Thanks so much for your reply and advice. I may have missed it, but I don't see any information regarding the --vsm option in mri_vol2surf on the command line or wiki help. Can you provide any guidance regarding the use of this option and what the format/units/etc of this vsm should be?
Thanks again for all your help.
Best, t
Re: [Freesurfer] applying distortion correction output from epi_reg in fsl to freesurfer Douglas N Greve Mon, 19 Nov 2012 08:05:18 -0800 Hi Ted, can you use epidewarp.fsl to create the warp field (voxel shift map (VSM))? If so, you can then use bbregister and mri_vol2surf with the --vsm option to apply the warp simultaneously with determining or applying the registration. It might work with the warp field that you have (since epidewarp.fsl uses fsl to compute the VSM). doug
*From:* Ted Satterthwaite ted_satt@yahoo.com *To:* "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu *Sent:* Thursday, November 15, 2012 2:35 PM *Subject:* applying distortion correction output from epi_reg in fsl to freesurfer
Hi Bruce, Doug, and FreeSurfer Team,
We have calculated coregistrations between bold timeseries and T1 images using BBR & distortion correction as implemented in the epi_reg utility in FSL5. We would like to map our functional timeseries to surface space for connectivity analyses (analagous to papers by Yeo & Buckner). Normally, without distortion correction, we would use tkregister tp convert the rigid body coregistration calculated in fsl by flirt(.mat) to a register.dat file, and then use mri_vol2surf to birng the data to surface space. However, with distortion correction, the coregistration between the epi & T1 is represented as a deformation field (_warp.nii.gz).
Is there a way for FreeSurfer to read this warp and use the information? We could of course simply do a two-step registration by moving our epi data into T1 space first using FSL and then use FreeSurfer to get it to the surface, but that would involve an extra interpolation. Are the ways to do this in one step using our already-calculated & QA'd deformation fields from FSL?
Thanks so much for your time & advice.
Best,
Ted Satterthwaite
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Douglas N Greve -
Ted Satterthwaite