Re: [Freesurfer] Clarification about "Per-Run" Motion Correction and Registration in Preproc-Sess
yes and yes On 12/07/2017 02:23 PM, Taylor, Johnmark wrote: > Thanks once again for all the help on this. I am running the GLM in > native space, typically so that I can get the beta values to use in an > MVPA analysis. So it sounds like if you specify per-run > motion-correction and registration, and don't tell it to resample to > anything (e.g., the MNI brain or the surface), then there's no > guarantee that the voxels will properly line up if you want to do, for > instance, a single-subject GLM in the subject's native space? So in > this case, per-session motion correction would be better so that all > the functional volumes in the session are registered properly? > > > > Thank you, this is very helpful! A few quick followup questions: > > > > 1) If you don't specifically tell preproc-sess what space to resample > > too (e.g., by using the "-surface" or "-mni305" flags), does it > > automatically resample to the subject's anatomical volume, then? > I don't think it will do anything if you don't specify > > > > 2) If fmc.nii.gz is already registered to the subject's volume, then > > how come a registration file has to be specified when visualizing GLM > > results using tksurfer? If fmc.nii.gz is already resampled to > > anatomical space, then surely any GLM contrasts should be as well, no? > fmc is not registered to the anatomical, it is registered to the > template. The template is registered to the anat through the > registration file. The data are still in the native functional space. > > > > 3) If per-run motion correction and registration is specified in > > pre-proc sess, then there will be a different functional-->structural > > transformation for each run, correct? > Correct > > If this is the case, then when visualizing session-wide GLM results > > using tksurfer, which registration file should be specified when > > loading up the overlay, since there'll be a different registration > > file for each run? > In what space are you doing the GLM? Usually, the raw data are resampled > onto the surface (eg, fmc.fsaverage.lh.sm05.nii.gz), and the GLM is done > in this spae.so no registration is needed. > > > > Apologies for these (probably basic) questions, I just want to make > > sure I am crystal-clear on what preproc-sess is doing. > > > > Cheers, and many thanks, > > > > JohnMark > > > ___ > 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 gr...@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.
[Freesurfer] Clarification about "Per-Run" Motion Correction and Registration in Preproc-Sess
Thanks once again for all the help on this. I am running the GLM in native space, typically so that I can get the beta values to use in an MVPA analysis. So it sounds like if you specify per-run motion-correction and registration, and don't tell it to resample to anything (e.g., the MNI brain or the surface), then there's no guarantee that the voxels will properly line up if you want to do, for instance, a single-subject GLM in the subject's native space? So in this case, per-session motion correction would be better so that all the functional volumes in the session are registered properly? > Thank you, this is very helpful! A few quick followup questions: > > 1) If you don't specifically tell preproc-sess what space to resample > too (e.g., by using the "-surface" or "-mni305" flags), does it > automatically resample to the subject's anatomical volume, then? I don't think it will do anything if you don't specify > > 2) If fmc.nii.gz is already registered to the subject's volume, then > how come a registration file has to be specified when visualizing GLM > results using tksurfer? If fmc.nii.gz is already resampled to > anatomical space, then surely any GLM contrasts should be as well, no? fmc is not registered to the anatomical, it is registered to the template. The template is registered to the anat through the registration file. The data are still in the native functional space. > > 3) If per-run motion correction and registration is specified in > pre-proc sess, then there will be a different functional-->structural > transformation for each run, correct? Correct > If this is the case, then when visualizing session-wide GLM results > using tksurfer, which registration file should be specified when > loading up the overlay, since there'll be a different registration > file for each run? In what space are you doing the GLM? Usually, the raw data are resampled onto the surface (eg, fmc.fsaverage.lh.sm05.nii.gz), and the GLM is done in this spae.so no registration is needed. > > Apologies for these (probably basic) questions, I just want to make > sure I am crystal-clear on what preproc-sess is doing. > > Cheers, and many thanks, > > JohnMark ___ 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.
Re: [Freesurfer] Clarification about "Per-Run" Motion Correction and Registration in Preproc-Sess
; Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > 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 > <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/ > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > > > -- > > Message: 2 > Date: Mon, 4 Dec 2017 12:32:00 -0500 > From: Douglas N Greve <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > Subject: Re: [Freesurfer] Clarification about "Per-Run" Motion > Correction and Registration in Preproc-Sess > To: freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <813a5a08-d27e-a2a6-8472-66f998aaa...@nmr.mgh.harvard.edu > <mailto:813a5a08-d27e-a2a6-8472-66f998aaa...@nmr.mgh.harvard.edu>> > Content-Type: text/plain; charset=utf-8; format=flowed > > > > On 12/03/2017 06:35 PM, Taylor, Johnmark wrote: > > Hello, > > > > A few quick questions about the "Per-Run" option in preproc-sess. I > > understand that in this option, each run's images are registered to > > the middle timepoint of that run, rather than the first timepoint of > > the first run. I was wondering, though: > > > > 1) Why is this the preferred option instead of per-session? > The interpolation is less if it is done on a per-run basis, and the > registration might be better > > 2) If motion-correction is only done internally to each run, then > > wouldn't between-run motion throw things off if you wanted to do > a GLM > > spanning the whole scanning session (although I assume it'd be fine > > for single-run GLMs)? What ensures that the images line up properly > > between runs? > That is why we resample into the group atlas space (eg, fsaverage) or > the self anatomical space so that all the runs are aligned. > > > > Thank you very much, > > > > JohnMark > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > 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 > <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/ > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > > > -- > > Message: 3 > Date: Mon, 4 Dec 2017 12:33:46 -0500 > From: Douglas N Greve <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > Subject: Re: [Freesurfer] freesurfer design > To: freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <daca7a06-f2e5-09a1-f05b-7e24204bc...@nmr.mgh.harvard.edu > <mailto:daca7a06-f2e5-09a1-f05b-7e24204bc...@nmr.mgh.harvard.edu>> > Content-Type: text/plain; charset=windows-1252; format=flowed > > In theory, this is just a two "group" analysis. Search the wiki > for FSGD > to get examples. You can include covariates, but you must use a DOSS > model when running m
Re: [Freesurfer] Clarification about "Per-Run" Motion Correction and Registration in Preproc-Sess
Thank you, this is very helpful! A few quick followup questions: 1) If you don't specifically tell preproc-sess what space to resample too (e.g., by using the "-surface" or "-mni305" flags), does it automatically resample to the subject's anatomical volume, then? 2) If fmc.nii.gz is already registered to the subject's volume, then how come a registration file has to be specified when visualizing GLM results using tksurfer? If fmc.nii.gz is already resampled to anatomical space, then surely any GLM contrasts should be as well, no? 3) If per-run motion correction and registration is specified in pre-proc sess, then there will be a different functional-->structural transformation for each run, correct? If this is the case, then when visualizing session-wide GLM results using tksurfer, which registration file should be specified when loading up the overlay, since there'll be a different registration file for each run? Apologies for these (probably basic) questions, I just want to make sure I am crystal-clear on what preproc-sess is doing. Cheers, and many thanks, JohnMark On Mon, Dec 4, 2017 at 3:20 PM, <freesurfer-requ...@nmr.mgh.harvard.edu> wrote: > Send Freesurfer mailing list submissions to > freesurfer@nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-requ...@nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-ow...@nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > >1. Re: mri_binarize (Douglas N Greve) >2. Re: Clarification about "Per-Run" Motion Correction and > Registration in Preproc-Sess (Douglas N Greve) >3. Re: freesurfer design (Douglas N Greve) >4. Re: subcortical structures volume (Douglas N Greve) >5. Re: mri_vol2surf wrong hemisphere (Douglas N Greve) >6. Re: Concatenating .mgh surface space functional MRI runs > (Douglas N Greve) >7. Re: QDEC and comparing two conditions (Douglas N Greve) >8. Re: Combining parcellated regions within an atlas? > (Douglas N Greve) >9. Re: Overlaying multiple results onto one surface (Douglas N Greve) > 10. recon edit error (Nicole Orme) > > > -- > > Message: 1 > Date: Mon, 4 Dec 2017 12:30:33 -0500 > From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] mri_binarize > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: <9d91f7ea-a55b-cd78-2b55-687cf2078...@nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=utf-8; format=flowed > > you can do it in two steps. First, use mri_binarize to create a mask of > the structutures you want. Then use mri_mask to apply the mask to the > aparc.DKT file > > > On 12/03/2017 07:44 AM, John Anderson wrote: > > Dear FS experts, > > I want to use mri_binarize to create (binarized and free of CSF and > > ventricles) mask from "aparc.DKTatlas+aseg". How can I substract CSF > > and ventricles from teh atlas using mri_binarize? > > > > Thanks > > John > > > > > > ___ > > 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 > gr...@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/ > > > > -- > > Message: 2 > Date: Mon, 4 Dec 2017 12:32:00 -0500 > From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Clarification about "Per-Run" Motion > Correction and Registration in Preproc-Sess > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: <813a5a08-d27e-a2a6-8472-66f998aaa...@nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=utf-8; format=flowed > > > > On 12/03/2017 06:35 PM, Taylor, Johnmark wrote: > > Hello, > > > > A few quick questions about the "Per-Run" option in preproc-sess. I > > understand that in this option, each run's images are registered to > > the middle timepoint of that run, rather than the first
Re: [Freesurfer] Clarification about "Per-Run" Motion Correction and Registration in Preproc-Sess
On 12/03/2017 06:35 PM, Taylor, Johnmark wrote: > Hello, > > A few quick questions about the "Per-Run" option in preproc-sess. I > understand that in this option, each run's images are registered to > the middle timepoint of that run, rather than the first timepoint of > the first run. I was wondering, though: > > 1) Why is this the preferred option instead of per-session? The interpolation is less if it is done on a per-run basis, and the registration might be better > 2) If motion-correction is only done internally to each run, then > wouldn't between-run motion throw things off if you wanted to do a GLM > spanning the whole scanning session (although I assume it'd be fine > for single-run GLMs)? What ensures that the images line up properly > between runs? That is why we resample into the group atlas space (eg, fsaverage) or the self anatomical space so that all the runs are aligned. > > Thank you very much, > > JohnMark > > > ___ > 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 gr...@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.
[Freesurfer] Clarification about "Per-Run" Motion Correction and Registration in Preproc-Sess
Hello, A few quick questions about the "Per-Run" option in preproc-sess. I understand that in this option, each run's images are registered to the middle timepoint of that run, rather than the first timepoint of the first run. I was wondering, though: 1) Why is this the preferred option instead of per-session? 2) If motion-correction is only done internally to each run, then wouldn't between-run motion throw things off if you wanted to do a GLM spanning the whole scanning session (although I assume it'd be fine for single-run GLMs)? What ensures that the images line up properly between runs? Thank you very much, JohnMark ___ 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.
