Dear FreeSurfer and SPM experts,
I am trying to calculate functional connectivity maps using FreeSurfer pipeline: http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthr... .
After defining a seed region on raw anatomical image, I co-registered functional data with anatomical data (as reference) and made sure that the seed is at correct place on both anatomical (top left in attached image) and functional (top right) data. Using SPM, I confirmed co-registration was fine.
But after running all the steps of FC, looks like the FC maps are not correct: sig.nii.gz at -fthresh 2 3 (shown at bottom left) because I am not getting significant FC at seed location. Here, bottom right shows the seed location on surface after I convert the seed to fsaverage space (for visualization purpose).
Any thoughts, ideas or tips on what went wrong here, would be really appreciated.
Thanks.
what was your mkanalysis-sess command?
On 06/08/2016 02:10 PM, Martin Juneja wrote:
Dear FreeSurfer and SPM experts,
I am trying to calculate functional connectivity maps using FreeSurfer pipeline: http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthr....
After defining a seed region on raw anatomical image, I co-registered functional data with anatomical data (as reference) and made sure that the seed is at correct place on both anatomical (top left in attached image) and functional (top right) data. Using SPM, I confirmed co-registration was fine.
But after running all the steps of FC, looks like the FC maps are not correct: sig.nii.gz at -fthresh 2 3 (shown at bottom left) because I am not getting significant FC at seed location. Here, bottom right shows the seed location on surface after I convert the seed to fsaverage space (for visualization purpose).
Any thoughts, ideas or tips on what went wrong here, would be really appreciated.
Thanks.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Dr. Greve,
I used following command for this:
mkanalysis-sess -analysis LH_XY.surf.lh -surface fsaverage lh -fwhm 5 -notask -taskreg LH_XYZ.dat 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -mcextreg -polyfit 5 -nskip 4 -fsd bold -TR 3.
Thanks.
On Wed, Jun 15, 2016 at 3:07 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
what was your mkanalysis-sess command?
On 06/08/2016 02:10 PM, Martin Juneja wrote:
Dear FreeSurfer and SPM experts,
I am trying to calculate functional connectivity maps using FreeSurfer pipeline:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthr... .
After defining a seed region on raw anatomical image, I co-registered functional data with anatomical data (as reference) and made sure that the seed is at correct place on both anatomical (top left in attached image) and functional (top right) data. Using SPM, I confirmed co-registration was fine.
But after running all the steps of FC, looks like the FC maps are not correct: sig.nii.gz at -fthresh 2 3 (shown at bottom left) because I am not getting significant FC at seed location. Here, bottom right shows the seed location on surface after I convert the seed to fsaverage space (for visualization purpose).
Any thoughts, ideas or tips on what went wrong here, would be really appreciated.
Thanks.
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.
Have you verified that the Anat-Func registration in FreeSurfer is correct? You can view it with tkregister-sess.
On 06/16/2016 10:26 AM, Martin Juneja wrote:
Hi Dr. Greve,
I used following command for this:
mkanalysis-sess -analysis LH_XY.surf.lh -surface fsaverage lh -fwhm 5 -notask -taskreg LH_XYZ.dat 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5
-mcextreg -polyfit 5 -nskip 4 -fsd bold -TR 3.
Thanks.
On Wed, Jun 15, 2016 at 3:07 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
what was your mkanalysis-sess command? On 06/08/2016 02:10 PM, Martin Juneja wrote: > Dear FreeSurfer and SPM experts, > > I am trying to calculate functional connectivity maps using FreeSurfer > pipeline: > http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough. > > After defining a seed region on raw anatomical image, I co-registered > functional data with anatomical data (as reference) and made sure that > the seed is at correct place on both anatomical (top left in attached > image) and functional (top right) data. Using SPM, I confirmed > co-registration was fine. > > But after running all the steps of FC, looks like the FC maps are not > correct: sig.nii.gz at -fthresh 2 3 (shown at bottom left) because I > am not getting significant FC at seed location. Here, bottom right > shows the seed location on surface after I convert the seed to > fsaverage space (for visualization purpose). > > Any thoughts, ideas or tips on what went wrong here, would be really > appreciated. > > Thanks. > > > _______________________________________________ > 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: 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 <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
freesurfer@nmr.mgh.harvard.edu
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Martin Juneja