Hi Doug,
Is it possible to use the bbregister parameters to resample a functional image such that it is in register with the anatomical image but retains the epi geometry? I actually don't care so much about the epi-anat registration, but what I would like to be able to do is motion correct and otherwise preprocess my timeserieses within session* and then move different sessions into a common volumetric space for analysis. As I have great faith in bbregister, ideally the transformation would be determined with this method (I suspect it is superior to picking a slice from one of the sessions to use as a motion correction target across all sessions). Additionally, I would prefer not to upsample the source voxels either into 1x1x1 anatomical geometry or to surface vertices. Unfortunately, my affine understanding isn't deep enough for me to figure this out myself.
Does that make sense, and (if so) do you have any ideas?
Thanks! Michael
* Here i use "session" in the sense of "run", which is different I think from FSFast terminology so apologies for any confusion.
hey mike,
take a look at:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mc-bbr
cheers,
satra
On Mon, Dec 19, 2011 at 2:04 AM, Michael Waskom mwaskom@stanford.eduwrote:
Hi Doug,
Is it possible to use the bbregister parameters to resample a functional image such that it is in register with the anatomical image but retains the epi geometry? I actually don't care so much about the epi-anat registration, but what I would like to be able to do is motion correct and otherwise preprocess my timeserieses within session* and then move different sessions into a common volumetric space for analysis. As I have great faith in bbregister, ideally the transformation would be determined with this method (I suspect it is superior to picking a slice from one of the sessions to use as a motion correction target across all sessions). Additionally, I would prefer not to upsample the source voxels either into 1x1x1 anatomical geometry or to surface vertices. Unfortunately, my affine understanding isn't deep enough for me to figure this out myself.
Does that make sense, and (if so) do you have any ideas?
Thanks! Michael
- Here i use "session" in the sense of "run", which is different I think
from FSFast terminology so apologies for any confusion.
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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.
That may or may not do what you want. I think that version keeps the functional data in the functional space. It would be better to register each TR to the anat, then simply sample each TR to the anatomical space (volume or surface) rather than going back into functional space. doug
Satrajit Ghosh wrote:
hey mike,
take a look at:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mc-bbr
cheers,
satra
On Mon, Dec 19, 2011 at 2:04 AM, Michael Waskom <mwaskom@stanford.edu mailto:mwaskom@stanford.edu> wrote:
Hi Doug, Is it possible to use the bbregister parameters to resample a functional image such that it is in register with the anatomical image but retains the epi geometry? I actually don't care so much about the epi-anat registration, but what I would like to be able to do is motion correct and otherwise preprocess my timeserieses within session* and then move different sessions into a common volumetric space for analysis. As I have great faith in bbregister, ideally the transformation would be determined with this method (I suspect it is superior to picking a slice from one of the sessions to use as a motion correction target across all sessions). Additionally, I would prefer not to upsample the source voxels either into 1x1x1 anatomical geometry or to surface vertices. Unfortunately, my affine understanding isn't deep enough for me to figure this out myself. Does that make sense, and (if so) do you have any ideas? Thanks! Michael * Here i use "session" in the sense of "run", which is different I think from FSFast terminology so apologies for any confusion. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 Satra and Doug,
That script is good to know about. But, from what I can tell, it looks like it will output a timeseries in the same space as the original template (each frame gets transformed with a combination of the matrix specifying its registration to the anatomical and the inverse of the matrix specifying the registration from the template to the anatomical). So this might give me somewhat better motion correction, but it won't give me a common space across runs.
Best, Michael
On Mon, Dec 19, 2011 at 7:26 AM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
That may or may not do what you want. I think that version keeps the functional data in the functional space. It would be better to register each TR to the anat, then simply sample each TR to the anatomical space (volume or surface) rather than going back into functional space. doug
Satrajit Ghosh wrote:
hey mike,
take a look at:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mc-bbr
cheers,
satra
On Mon, Dec 19, 2011 at 2:04 AM, Michael Waskom <mwaskom@stanford.edu mailto:mwaskom@stanford.edu> wrote:
Hi Doug, Is it possible to use the bbregister parameters to resample a functional image such that it is in register with the anatomical image but retains the epi geometry? I actually don't care so much about the epi-anat registration, but what I would like to be able to do is motion correct and otherwise preprocess my timeserieses within session* and then move different sessions into a common volumetric space for analysis. As I have great faith in bbregister, ideally the transformation would be determined with this method (I suspect it is superior to picking a slice from one of the sessions to use as a motion correction target across all sessions). Additionally, I would prefer not to upsample the source voxels either into 1x1x1 anatomical geometry or to surface vertices. Unfortunately, my affine understanding isn't deep enough for me to figure this out myself. Does that make sense, and (if so) do you have any ideas? Thanks! Michael * Here i use "session" in the sense of "run", which is different I think from FSFast terminology so apologies for any confusion. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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.
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-- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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It will output a register.dat for each frame. You can extract the frame from the time series (mri_convert --frame ), apply the reg with mri_vol2vol or mri_vol2surf, then concatenate the results back into a time series (mri_concat) doug
Michael Waskom wrote:
Hi Satra and Doug,
That script is good to know about. But, from what I can tell, it looks like it will output a timeseries in the same space as the original template (each frame gets transformed with a combination of the matrix specifying its registration to the anatomical and the inverse of the matrix specifying the registration from the template to the anatomical). So this might give me somewhat better motion correction, but it won't give me a common space across runs.
Best, Michael
On Mon, Dec 19, 2011 at 7:26 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
That may or may not do what you want. I think that version keeps the functional data in the functional space. It would be better to register each TR to the anat, then simply sample each TR to the anatomical space (volume or surface) rather than going back into functional space. doug Satrajit Ghosh wrote: > hey mike, > > take a look at: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mc-bbr > > cheers, > > satra > > > > On Mon, Dec 19, 2011 at 2:04 AM, Michael Waskom <mwaskom@stanford.edu <mailto:mwaskom@stanford.edu> > <mailto:mwaskom@stanford.edu <mailto:mwaskom@stanford.edu>>> wrote: > > Hi Doug, > > Is it possible to use the bbregister parameters to resample a > functional image such that it is in register with the anatomical > image but retains the epi geometry? I actually don't care so much > about the epi-anat registration, but what I would like to be able > to do is motion correct and otherwise preprocess my timeserieses > within session* and then move different sessions into a common > volumetric space for analysis. As I have great faith in > bbregister, ideally the transformation would be determined with > this method (I suspect it is superior to picking a slice from one > of the sessions to use as a motion correction target across all > sessions). Additionally, I would prefer not to upsample the source > voxels either into 1x1x1 anatomical geometry or to surface > vertices. Unfortunately, my affine understanding isn't deep enough > for me to figure this out myself. > > Does that make sense, and (if so) do you have any ideas? > > Thanks! > Michael > > * Here i use "session" in the sense of "run", which is different I > think from FSFast terminology so apologies for any confusion. > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto: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 <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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Sorry, I guess it's not clear what I'm hoping to do.
Because I'm going to use this data for mvpa, I don't want to resample into 1x1x1 voxels or go onto the surface. But I have multiple runs that I want to use, so I need there to be a voxel-to-brain correspondence across the different runs.
Michael
On Mon, Dec 19, 2011 at 12:46 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
It will output a register.dat for each frame. You can extract the frame from the time series (mri_convert --frame ), apply the reg with mri_vol2vol or mri_vol2surf, then concatenate the results back into a time series (mri_concat) doug
Michael Waskom wrote:
Hi Satra and Doug,
That script is good to know about. But, from what I can tell, it looks like it will output a timeseries in the same space as the original template (each frame gets transformed with a combination of the matrix specifying its registration to the anatomical and the inverse of the matrix specifying the registration from the template to the anatomical). So this might give me somewhat better motion correction, but it won't give me a common space across runs.
Best, Michael
On Mon, Dec 19, 2011 at 7:26 AM, Douglas N Greve < greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu>> wrote:
That may or may not do what you want. I think that version keeps the functional data in the functional space. It would be better to register each TR to the anat, then simply sample each TR to the anatomical space (volume or surface) rather than going back into functional space. doug
Satrajit Ghosh wrote:
hey mike,
take a look at:
ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**
greve/mc-bbrftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mc-bbr
cheers,
satra
On Mon, Dec 19, 2011 at 2:04 AM, Michael Waskom
<mwaskom@stanford.edu mailto:mwaskom@stanford.edu
<mailto:mwaskom@stanford.edu mailto:mwaskom@stanford.edu>**>
wrote:
Hi Doug, Is it possible to use the bbregister parameters to resample a functional image such that it is in register with the anatomical image but retains the epi geometry? I actually don't care somuch
about the epi-anat registration, but what I would like to beable
to do is motion correct and otherwise preprocess my timeserieses within session* and then move different sessions into a common volumetric space for analysis. As I have great faith in bbregister, ideally the transformation would be determined with this method (I suspect it is superior to picking a slicefrom one
of the sessions to use as a motion correction target across all sessions). Additionally, I would prefer not to upsample thesource
voxels either into 1x1x1 anatomical geometry or to surface vertices. Unfortunately, my affine understanding isn't deepenough
for me to figure this out myself. Does that make sense, and (if so) do you have any ideas? Thanks! Michael * Here i use "session" in the sense of "run", which isdifferent I
think from FSFast terminology so apologies for any confusion. ______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> The information in this e-mail is intended only for theperson to
whom it is addressed. If you believe this e-mail was sent to you inerror and
the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. If the e-mail wassent 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
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422
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-- 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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
hi michael,
so for each frame of every session you get a bbreg file and the script ends up aligning the volumes to some reference. all you need to do is propagate that reference across your sessions. you might for example want this to be the middle volume of your entire experiment.
cheers,
satra
On Mon, Dec 19, 2011 at 10:18 PM, Michael Waskom mwaskom@stanford.eduwrote:
Sorry, I guess it's not clear what I'm hoping to do.
Because I'm going to use this data for mvpa, I don't want to resample into 1x1x1 voxels or go onto the surface. But I have multiple runs that I want to use, so I need there to be a voxel-to-brain correspondence across the different runs.
Michael
On Mon, Dec 19, 2011 at 12:46 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:
It will output a register.dat for each frame. You can extract the frame from the time series (mri_convert --frame ), apply the reg with mri_vol2vol or mri_vol2surf, then concatenate the results back into a time series (mri_concat) doug
Michael Waskom wrote:
Hi Satra and Doug,
That script is good to know about. But, from what I can tell, it looks like it will output a timeseries in the same space as the original template (each frame gets transformed with a combination of the matrix specifying its registration to the anatomical and the inverse of the matrix specifying the registration from the template to the anatomical). So this might give me somewhat better motion correction, but it won't give me a common space across runs.
Best, Michael
On Mon, Dec 19, 2011 at 7:26 AM, Douglas N Greve < greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu>> wrote:
That may or may not do what you want. I think that version keeps the functional data in the functional space. It would be better to register each TR to the anat, then simply sample each TR to the anatomical space (volume or surface) rather than going back into functional space. doug
Satrajit Ghosh wrote:
hey mike,
take a look at:
ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**
greve/mc-bbrftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mc-bbr
cheers,
satra
On Mon, Dec 19, 2011 at 2:04 AM, Michael Waskom
<mwaskom@stanford.edu mailto:mwaskom@stanford.edu
<mailto:mwaskom@stanford.edu mailto:mwaskom@stanford.edu>**>
wrote:
Hi Doug, Is it possible to use the bbregister parameters to resample a functional image such that it is in register with the anatomical image but retains the epi geometry? I actually don't care somuch
about the epi-anat registration, but what I would like to beable
to do is motion correct and otherwise preprocess my timeserieses within session* and then move different sessions into a common volumetric space for analysis. As I have great faith in bbregister, ideally the transformation would be determined with this method (I suspect it is superior to picking a slicefrom one
of the sessions to use as a motion correction target across all sessions). Additionally, I would prefer not to upsample thesource
voxels either into 1x1x1 anatomical geometry or to surface vertices. Unfortunately, my affine understanding isn't deepenough
for me to figure this out myself. Does that make sense, and (if so) do you have any ideas? Thanks! Michael * Here i use "session" in the sense of "run", which isdifferent I
think from FSFast terminology so apologies for any confusion. ______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for theperson to
whom it is addressed. If you believe this e-mail was sent to you inerror and
the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. If the e-mail wassent 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.eduFreesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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.**edugreve@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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.** harvard.edu Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
OK, cool, I'll look into this for the future.
But back to my original question. If I already have data preprocessed with several runs, each run motion-corrected within-session, and an affine registration from each run's space to the anatomical determined by bbregister, is there any way to use those transformation parameters to take the function scans into a common space that retains the original voxel size?
Michael
On Mon, Dec 19, 2011 at 1:34 PM, Satrajit Ghosh satra@mit.edu wrote:
hi michael,
so for each frame of every session you get a bbreg file and the script ends up aligning the volumes to some reference. all you need to do is propagate that reference across your sessions. you might for example want this to be the middle volume of your entire experiment.
cheers,
satra
On Mon, Dec 19, 2011 at 10:18 PM, Michael Waskom mwaskom@stanford.eduwrote:
Sorry, I guess it's not clear what I'm hoping to do.
Because I'm going to use this data for mvpa, I don't want to resample into 1x1x1 voxels or go onto the surface. But I have multiple runs that I want to use, so I need there to be a voxel-to-brain correspondence across the different runs.
Michael
On Mon, Dec 19, 2011 at 12:46 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:
It will output a register.dat for each frame. You can extract the frame from the time series (mri_convert --frame ), apply the reg with mri_vol2vol or mri_vol2surf, then concatenate the results back into a time series (mri_concat) doug
Michael Waskom wrote:
Hi Satra and Doug,
That script is good to know about. But, from what I can tell, it looks like it will output a timeseries in the same space as the original template (each frame gets transformed with a combination of the matrix specifying its registration to the anatomical and the inverse of the matrix specifying the registration from the template to the anatomical). So this might give me somewhat better motion correction, but it won't give me a common space across runs.
Best, Michael
On Mon, Dec 19, 2011 at 7:26 AM, Douglas N Greve < greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu>> wrote:
That may or may not do what you want. I think that version keeps the functional data in the functional space. It would be better to register each TR to the anat, then simply sample each TR to the anatomical space (volume or surface) rather than going back into functional space. doug
Satrajit Ghosh wrote:
hey mike,
take a look at:
ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**
greve/mc-bbrftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mc-bbr
cheers,
satra
On Mon, Dec 19, 2011 at 2:04 AM, Michael Waskom
<mwaskom@stanford.edu mailto:mwaskom@stanford.edu
<mailto:mwaskom@stanford.edu mailto:mwaskom@stanford.edu>**>
wrote:
Hi Doug, Is it possible to use the bbregister parameters to resample a functional image such that it is in register with theanatomical
image but retains the epi geometry? I actually don't care somuch
about the epi-anat registration, but what I would like to beable
to do is motion correct and otherwise preprocess mytimeserieses
within session* and then move different sessions into a common volumetric space for analysis. As I have great faith in bbregister, ideally the transformation would be determined with this method (I suspect it is superior to picking a slicefrom one
of the sessions to use as a motion correction target across all sessions). Additionally, I would prefer not to upsample thesource
voxels either into 1x1x1 anatomical geometry or to surface vertices. Unfortunately, my affine understanding isn't deepenough
for me to figure this out myself. Does that make sense, and (if so) do you have any ideas? Thanks! Michael * Here i use "session" in the sense of "run", which isdifferent I
think from FSFast terminology so apologies for any confusion. ______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu
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ah in that case you need to multiply the affine stored in one session's bbreg with the inverse of the other bbreg from the target session and then use mri_vol2vol with the composite transform. note: only nearest or trilinear interp
cheers,
satra
On Tue, Dec 20, 2011 at 12:07 AM, Michael Waskom mwaskom@stanford.eduwrote:
OK, cool, I'll look into this for the future.
But back to my original question. If I already have data preprocessed with several runs, each run motion-corrected within-session, and an affine registration from each run's space to the anatomical determined by bbregister, is there any way to use those transformation parameters to take the function scans into a common space that retains the original voxel size?
Michael
On Mon, Dec 19, 2011 at 1:34 PM, Satrajit Ghosh satra@mit.edu wrote:
hi michael,
so for each frame of every session you get a bbreg file and the script ends up aligning the volumes to some reference. all you need to do is propagate that reference across your sessions. you might for example want this to be the middle volume of your entire experiment.
cheers,
satra
On Mon, Dec 19, 2011 at 10:18 PM, Michael Waskom mwaskom@stanford.eduwrote:
Sorry, I guess it's not clear what I'm hoping to do.
Because I'm going to use this data for mvpa, I don't want to resample into 1x1x1 voxels or go onto the surface. But I have multiple runs that I want to use, so I need there to be a voxel-to-brain correspondence across the different runs.
Michael
On Mon, Dec 19, 2011 at 12:46 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:
It will output a register.dat for each frame. You can extract the frame from the time series (mri_convert --frame ), apply the reg with mri_vol2vol or mri_vol2surf, then concatenate the results back into a time series (mri_concat) doug
Michael Waskom wrote:
Hi Satra and Doug,
That script is good to know about. But, from what I can tell, it looks like it will output a timeseries in the same space as the original template (each frame gets transformed with a combination of the matrix specifying its registration to the anatomical and the inverse of the matrix specifying the registration from the template to the anatomical). So this might give me somewhat better motion correction, but it won't give me a common space across runs.
Best, Michael
On Mon, Dec 19, 2011 at 7:26 AM, Douglas N Greve < greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu>> wrote:
That may or may not do what you want. I think that version keeps the functional data in the functional space. It would be better to register each TR to the anat, then simply sample each TR to the anatomical space (volume or surface) rather than going back into functional space. doug
Satrajit Ghosh wrote:
hey mike,
take a look at:
ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**
greve/mc-bbrftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mc-bbr
cheers,
satra
On Mon, Dec 19, 2011 at 2:04 AM, Michael Waskom
<mwaskom@stanford.edu mailto:mwaskom@stanford.edu
<mailto:mwaskom@stanford.edu mailto:mwaskom@stanford.edu>**>
wrote:
Hi Doug, Is it possible to use the bbregister parameters to resample a functional image such that it is in register with theanatomical
image but retains the epi geometry? I actually don't care somuch
about the epi-anat registration, but what I would like to beable
to do is motion correct and otherwise preprocess mytimeserieses
within session* and then move different sessions into a common volumetric space for analysis. As I have great faith in bbregister, ideally the transformation would be determinedwith
this method (I suspect it is superior to picking a slicefrom one
of the sessions to use as a motion correction target acrossall
sessions). Additionally, I would prefer not to upsample thesource
voxels either into 1x1x1 anatomical geometry or to surface vertices. Unfortunately, my affine understanding isn't deepenough
for me to figure this out myself. Does that make sense, and (if so) do you have any ideas? Thanks! Michael * Here i use "session" in the sense of "run", which isdifferent I
think from FSFast terminology so apologies for any confusion. ______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu
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Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422
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