freesurfers,
we've acquired fMRI data from [slightly different] slice prescriptions, all partial brain slices. we want to analyze this data all together, but we also want to have the best registration possible [i.e., use bbregister]. what's the best way to do this? here are the ideas we have:
1. analyze these data on the individual subject's surface with selxavg3-sess. the one problem is that we don't see how to pass the registration file for each run. [there are different registrations for distortion-corrected or not]
2. run glms for each run independently and then combine the subject's data together with a FFX analysis. what's the easiest way to run a FFX analysis with fsfast?
3. upsample these functional data to the subject's anatomy [either volume or surface] and then run the analysis there. however, this will take a good chunk of memory and compute time.
what's the best thing to do here?
thanks in advance, rosa
Hi Rosa, let me see if I have this straight. For a single subject (in a single session?) you have multiple runs. Each run only covers a part of the brain (do the different runs overlap?). In the end, you want to have a full brain analysis by combining the different parts. Is that right?
doug
On 12/18/2013 03:57 PM, Rosa Lafer-Sousa wrote:
freesurfers,
we've acquired fMRI data from [slightly different] slice prescriptions, all partial brain slices. we want to analyze this data all together, but we also want to have the best registration possible [i.e., use bbregister]. what's the best way to do this? here are the ideas we have:
- analyze these data on the individual subject's surface with
selxavg3-sess. the one problem is that we don't see how to pass the registration file for each run. [there are different registrations for distortion-corrected or not]
- run glms for each run independently and then combine the subject's
data together with a FFX analysis. what's the easiest way to run a FFX analysis with fsfast?
- upsample these functional data to the subject's anatomy [either
volume or surface] and then run the analysis there. however, this will take a good chunk of memory and compute time.
what's the best thing to do here?
thanks in advance, rosa
--
210-325-3185 rlaferso@wellesley.edu mailto:rlaferso@wellesley.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
I collected all the runs in the same subject in one session for the same brain region (roughly the same slice window) but I collected a field map for each run and undistorted each run independently. I also motion corrected each run independently. Each run covers roughly the same part of the brain, but I took the subject out partway between the session, so the slice perscription is slightly off across the before and after runs (it's as if they were separate sessions).
Is that more clear?
Thanks! Rosa
On Wednesday, December 18, 2013, Douglas N Greve wrote:
Hi Rosa, let me see if I have this straight. For a single subject (in a single session?) you have multiple runs. Each run only covers a part of the brain (do the different runs overlap?). In the end, you want to have a full brain analysis by combining the different parts. Is that right?
doug
On 12/18/2013 03:57 PM, Rosa Lafer-Sousa wrote:
freesurfers,
we've acquired fMRI data from [slightly different] slice prescriptions, all partial brain slices. we want to analyze this data all together, but we also want to have the best registration possible [i.e., use bbregister]. what's the best way to do this? here are the ideas we have:
- analyze these data on the individual subject's surface with
selxavg3-sess. the one problem is that we don't see how to pass the registration file for each run. [there are different registrations for distortion-corrected or not]
- run glms for each run independently and then combine the subject's
data together with a FFX analysis. what's the easiest way to run a FFX analysis with fsfast?
- upsample these functional data to the subject's anatomy [either
volume or surface] and then run the analysis there. however, this will take a good chunk of memory and compute time.
what's the best thing to do here?
thanks in advance, rosa
--
210-325-3185 rlaferso@wellesley.edu javascript:; <mailto:rlaferso@wellesley.edujavascript:;
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu javascript:; https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu javascript:; 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/
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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.
I would just treat them as separate runs and analyze them as "normal" (ie, with -per-run alignment). bbregister should be able to do the registration properly. Do you foresee problems with that?
doug
On 12/18/13 6:17 PM, Rosa Lafer-Sousa wrote:
Hi Doug,
I collected all the runs in the same subject in one session for the same brain region (roughly the same slice window) but I collected a field map for each run and undistorted each run independently. I also motion corrected each run independently. Each run covers roughly the same part of the brain, but I took the subject out partway between the session, so the slice perscription is slightly off across the before and after runs (it's as if they were separate sessions).
Is that more clear?
Thanks! Rosa
On Wednesday, December 18, 2013, Douglas N Greve wrote:
Hi Rosa, let me see if I have this straight. For a single subject (in a single session?) you have multiple runs. Each run only covers a part of the brain (do the different runs overlap?). In the end, you want to have a full brain analysis by combining the different parts. Is that right? doug On 12/18/2013 03:57 PM, Rosa Lafer-Sousa wrote: > freesurfers, > > we've acquired fMRI data from [slightly different] slice > prescriptions, all partial brain slices. we want to analyze this data > all together, but we also want to have the best registration possible > [i.e., use bbregister]. what's the best way to do this? here are the > ideas we have: > > 1. analyze these data on the individual subject's surface with > selxavg3-sess. the one problem is that we don't see how to pass the > registration file for each run. [there are different registrations > for distortion-corrected or not] > > 2. run glms for each run independently and then combine the subject's > data together with a FFX analysis. what's the easiest way to run a > FFX analysis with fsfast? > > 3. upsample these functional data to the subject's anatomy [either > volume or surface] and then run the analysis there. however, this will > take a good chunk of memory and compute time. > > what's the best thing to do here? > > thanks in advance, > rosa > > > -- > > > 210-325-3185 > rlaferso@wellesley.edu <javascript:;> <mailto:rlaferso@wellesley.edu <javascript:;>> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <javascript:;> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <javascript:;> Phone Number: 617-724-2358 Fax: 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 <javascript:;> 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.-- Rosa Lafer-Sousa Lab Manager, Conway Lab Wellesley College - Neuroscience 106 Central Street Wellesley, MA
Harvard Medical School -Neurobiology 220 Longwood Ave WAB Rm 215 Boston, MA 02115
210-325-3185 rlaferso@wellesley.edu mailto:rlaferso@wellesley.edu
Thanks Doug, I have a registration file for each run (for both the undistorted and not) and am curious how to pass that reg file for each run when I call either mkanalysis-ess or selxavg3-sess. It would seem I need to indicate the appropriate registration file during at least one of those calls, but I can't find a flag for that in the documentation.
rosa
On Wed, Dec 18, 2013 at 11:12 PM, Douglas Greve greve@nmr.mgh.harvard.eduwrote:
I would just treat them as separate runs and analyze them as "normal" (ie, with -per-run alignment). bbregister should be able to do the registration properly. Do you foresee problems with that?
doug
On 12/18/13 6:17 PM, Rosa Lafer-Sousa wrote:
Hi Doug,
I collected all the runs in the same subject in one session for the same brain region (roughly the same slice window) but I collected a field map for each run and undistorted each run independently. I also motion corrected each run independently. Each run covers roughly the same part of the brain, but I took the subject out partway between the session, so the slice perscription is slightly off across the before and after runs (it's as if they were separate sessions).
Is that more clear?
Thanks! Rosa
On Wednesday, December 18, 2013, Douglas N Greve wrote:
Hi Rosa, let me see if I have this straight. For a single subject (in a single session?) you have multiple runs. Each run only covers a part of the brain (do the different runs overlap?). In the end, you want to have a full brain analysis by combining the different parts. Is that right?
doug
On 12/18/2013 03:57 PM, Rosa Lafer-Sousa wrote:
freesurfers,
we've acquired fMRI data from [slightly different] slice prescriptions, all partial brain slices. we want to analyze this data all together, but we also want to have the best registration possible [i.e., use bbregister]. what's the best way to do this? here are the ideas we have:
- analyze these data on the individual subject's surface with
selxavg3-sess. the one problem is that we don't see how to pass the registration file for each run. [there are different registrations for distortion-corrected or not]
- run glms for each run independently and then combine the subject's
data together with a FFX analysis. what's the easiest way to run a FFX analysis with fsfast?
- upsample these functional data to the subject's anatomy [either
volume or surface] and then run the analysis there. however, this will take a good chunk of memory and compute time.
what's the best thing to do here?
thanks in advance, rosa
--
210-325-3185 rlaferso@wellesley.edu mailto:rlaferso@wellesley.edu
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
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.
-- Rosa Lafer-Sousa Lab Manager, Conway Lab Wellesley College - Neuroscience 106 Central Street Wellesley, MA
Harvard Medical School -Neurobiology 220 Longwood Ave WAB Rm 215 Boston, MA 02115
210-325-3185 rlaferso@wellesley.edu
This will be a little tricky. Copy the registration file to bold/RRR/register.dof6.dat (RRR is the run number). Then run preproc-sess with -no-reg. When you run selxavg3-sess use -no-prepproc. If you run preproc-sess without -no-reg or your run selxavg3-sess without -no-preproc it might try to regenerate the registration and overwrite your registration file. To prevent this, you can make the register.dof6.dat non-writable.
doug
On 12/19/2013 11:51 AM, Rosa Lafer-Sousa wrote:
Thanks Doug, I have a registration file for each run (for both the undistorted and not) and am curious how to pass that reg file for each run when I call either mkanalysis-ess or selxavg3-sess. It would seem I need to indicate the appropriate registration file during at least one of those calls, but I can't find a flag for that in the documentation.
rosa
On Wed, Dec 18, 2013 at 11:12 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
I would just treat them as separate runs and analyze them as "normal" (ie, with -per-run alignment). bbregister should be able to do the registration properly. Do you foresee problems with that? doug On 12/18/13 6:17 PM, Rosa Lafer-Sousa wrote:Hi Doug, I collected all the runs in the same subject in one session for the same brain region (roughly the same slice window) but I collected a field map for each run and undistorted each run independently. I also motion corrected each run independently. Each run covers roughly the same part of the brain, but I took the subject out partway between the session, so the slice perscription is slightly off across the before and after runs (it's as if they were separate sessions). Is that more clear? Thanks! Rosa On Wednesday, December 18, 2013, Douglas N Greve wrote: Hi Rosa, let me see if I have this straight. For a single subject (in a single session?) you have multiple runs. Each run only covers a part of the brain (do the different runs overlap?). In the end, you want to have a full brain analysis by combining the different parts. Is that right? doug On 12/18/2013 03:57 PM, Rosa Lafer-Sousa wrote: > freesurfers, > > we've acquired fMRI data from [slightly different] slice > prescriptions, all partial brain slices. we want to analyze this data > all together, but we also want to have the best registration possible > [i.e., use bbregister]. what's the best way to do this? here are the > ideas we have: > > 1. analyze these data on the individual subject's surface with > selxavg3-sess. the one problem is that we don't see how to pass the > registration file for each run. [there are different registrations > for distortion-corrected or not] > > 2. run glms for each run independently and then combine the subject's > data together with a FFX analysis. what's the easiest way to run a > FFX analysis with fsfast? > > 3. upsample these functional data to the subject's anatomy [either > volume or surface] and then run the analysis there. however, this will > take a good chunk of memory and compute time. > > what's the best thing to do here? > > thanks in advance, > rosa > > > -- > > > 210-325-3185 <tel:210-325-3185> > rlaferso@wellesley.edu <mailto:rlaferso@wellesley.edu> > > > _______________________________________________ > 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 <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 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. -- Rosa Lafer-Sousa Lab Manager, Conway Lab Wellesley College - Neuroscience 106 Central Street Wellesley, MA Harvard Medical School -Neurobiology 220 Longwood Ave WAB Rm 215 Boston, MA 02115 210-325-3185 rlaferso@wellesley.edu <mailto:rlaferso@wellesley.edu>-- Rosa Lafer-Sousa Lab Manager, Conway Lab Wellesley College - Neuroscience 106 Central Street Wellesley, MA
Harvard Medical School -Neurobiology 220 Longwood Ave WAB Rm 215 Boston, MA 02115
210-325-3185 rlaferso@wellesley.edu mailto:rlaferso@wellesley.edu
freesurfer@nmr.mgh.harvard.edu
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Douglas Greve -
Douglas N Greve
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Rosa Lafer-Sousa