Hi Freesurer experts,
I’m looking to censor (drop volumes) from my resting state fMRI time series that violate a predetermined motion and signal threshold (FD and DVARS). I've already determined which volumes violate X and Y criteria.
Is there a way to to tell FS to "ignore" these time points in the analysis such as in preproc-sess or mkanalysis-sess?
If there is not and if I were to drop the volumes directly from the 4D file before starting any pre-processing and analysis – would that be a problem for finding and regressing the auto-correlation in the time series?
Thanks! Adam
Yes,you need a time point exclusion file (-tpexclude filename option to mkanalysis-sess). Run mkanalysis with -help to get more info on how to create it.
On 01/25/2018 04:43 PM, Adam Martersteck wrote:
Hi Freesurer experts,
I’m looking to censor (drop volumes) from my resting state fMRI time series that violate a predetermined motion and signal threshold (FD and DVARS). I've already determined which volumes violate X and Y criteria.
Is there a way to to tell FS to "ignore" these time points in the analysis such as in preproc-sess or mkanalysis-sess?
If there is not and if I were to drop the volumes directly from the 4D file before starting any pre-processing and analysis – would that be a problem for finding and regressing the auto-correlation in the time series?
Thanks! Adam
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Just a quick follow-up question, For FD/DVARS or other "censoring" criteria -- using -tpexclusion worked great for surface based analysis with mkanalsysis and selxavg3. Is there a way to do this for seed-to-seed analysis (fcseedcor)?
Thanks!
On Thu, Jan 25, 2018 at 4:00 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Yes,you need a time point exclusion file (-tpexclude filename option to mkanalysis-sess). Run mkanalysis with -help to get more info on how to create it.
On 01/25/2018 04:43 PM, Adam Martersteck wrote:
Hi Freesurer experts,
I’m looking to censor (drop volumes) from my resting state fMRI time series that violate a predetermined motion and signal threshold (FD and DVARS). I've already determined which volumes violate X and Y criteria.
Is there a way to to tell FS to "ignore" these time points in the analysis such as in preproc-sess or mkanalysis-sess?
If there is not and if I were to drop the volumes directly from the 4D file before starting any pre-processing and analysis – would that be a problem for finding and regressing the auto-correlation in the time series?
Thanks! Adam
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/
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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.
Currently there is no way to do this. But it might not be hard to add. If I don't get back in a couple of weeks, send me a reminder.
On 02/14/2018 12:13 PM, Adam Martersteck wrote:
Just a quick follow-up question, For FD/DVARS or other "censoring" criteria -- using -tpexclusion worked great for surface based analysis with mkanalsysis and selxavg3. Is there a way to do this for seed-to-seed analysis (fcseedcor)?
Thanks!
On Thu, Jan 25, 2018 at 4:00 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Yes,you need a time point exclusion file (-tpexclude filename option to mkanalysis-sess). Run mkanalysis with -help to get more info on how to create it. On 01/25/2018 04:43 PM, Adam Martersteck wrote: > Hi Freesurer experts, > > I’m looking to censor (drop volumes) from my resting state fMRI time > series that violate a predetermined motion and signal threshold (FD > and DVARS). I've already determined which volumes violate X and Y > criteria. > > Is there a way to to tell FS to "ignore" these time points in the > analysis such as in preproc-sess or mkanalysis-sess? > > If there is not and if I were to drop the volumes directly from the 4D > file before starting any pre-processing and analysis – would that be > a problem for finding and regressing the auto-correlation in the time > series? > > Thanks! > Adam > > > _______________________________________________ > 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 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 <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/> _______________________________________________ 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> 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 <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 Freesurfer team & Doug,
Just thought I'd check back in as you had asked! Any thoughts on censoring resting state volumes for fcseedcorr?
Thanks, Adam
On Thu, Feb 15, 2018 at 12:57 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
Currently there is no way to do this. But it might not be hard to add. If I don't get back in a couple of weeks, send me a reminder.
On 02/14/2018 12:13 PM, Adam Martersteck wrote:
Just a quick follow-up question, For FD/DVARS or other "censoring" criteria -- using -tpexclusion worked great for surface based analysis with mkanalsysis and selxavg3. Is there a way to do this for seed-to-seed analysis (fcseedcor)?
Thanks!
On Thu, Jan 25, 2018 at 4:00 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Yes,you need a time point exclusion file (-tpexclude filename option to mkanalysis-sess). Run mkanalysis with -help to get more info on howto
create it. On 01/25/2018 04:43 PM, Adam Martersteck wrote: > Hi Freesurer experts, > > I’m looking to censor (drop volumes) from my resting state fMRItime
> series that violate a predetermined motion and signal threshold (FD > and DVARS). I've already determined which volumes violate X and Y > criteria. > > Is there a way to to tell FS to "ignore" these time points in the > analysis such as in preproc-sess or mkanalysis-sess? > > If there is not and if I were to drop the volumes directly from the 4D > file before starting any pre-processing and analysis – would that be > a problem for finding and regressing the auto-correlation in the time > series? > > Thanks! > Adam > > > _______________________________________________ > 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 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 <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/> _______________________________________________ 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> 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 <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
-- 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/
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Hi Freesurfer team & Doug,
Thought I would check in again about censoring volumes and using fcseedcor.
I was thinking about if it hasn't been incorporated yet -- could I create my own first level covariate .dat file and run fcseedcor on a per subject basis and pass the new .dat to xreg? I assume the .dat file would be difference than the one we use for selxavg3 (currently just passing a .dat file with just a single column of a list of volumes that violate criteria).
The new xreg file would have to be *m* rows long (where *m* is the number of TRs). And if frame 119, 120, and 121 where to be excluded: then it would be a *m* by 3 matrix with column 1, row 119 set to 1; row 120 column 2 set to 1; row 121 column 3 set to 1.
Is that all correct?
Thanks, Adam
On Thu, Mar 15, 2018 at 9:47 AM, Adam Martersteck acmarter@gmail.com wrote:
Hi Freesurfer team & Doug,
Just thought I'd check back in as you had asked! Any thoughts on censoring resting state volumes for fcseedcorr?
Thanks, Adam
On Thu, Feb 15, 2018 at 12:57 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:
Currently there is no way to do this. But it might not be hard to add. If I don't get back in a couple of weeks, send me a reminder.
On 02/14/2018 12:13 PM, Adam Martersteck wrote:
Just a quick follow-up question, For FD/DVARS or other "censoring" criteria -- using -tpexclusion worked great for surface based analysis with mkanalsysis and selxavg3. Is there a way to do this for seed-to-seed analysis (fcseedcor)?
Thanks!
On Thu, Jan 25, 2018 at 4:00 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Yes,you need a time point exclusion file (-tpexclude filename option to mkanalysis-sess). Run mkanalysis with -help to get more info on howto
create it. On 01/25/2018 04:43 PM, Adam Martersteck wrote: > Hi Freesurer experts, > > I’m looking to censor (drop volumes) from my resting state fMRItime
> series that violate a predetermined motion and signal threshold(FD
> and DVARS). I've already determined which volumes violate X and Y > criteria. > > Is there a way to to tell FS to "ignore" these time points in the > analysis such as in preproc-sess or mkanalysis-sess? > > If there is not and if I were to drop the volumes directly from the 4D > file before starting any pre-processing and analysis – would that be > a problem for finding and regressing the auto-correlation in the time > series? > > Thanks! > Adam > > > _______________________________________________ > 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 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 <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/> _______________________________________________ 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> 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 <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
-- 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
I think that will work
On 4/23/18 3:08 PM, Adam Martersteck wrote:
Hi Freesurfer team & Doug,
Thought I would check in again about censoring volumes and using fcseedcor.
I was thinking about if it hasn't been incorporated yet -- could I create my own first level covariate .dat file and run fcseedcor on a per subject basis and pass the new .dat to xreg? I assume the .dat file would be difference than the one we use for selxavg3 (currently just passing a .dat file with just a single column of a list of volumes that violate criteria).
The new xreg file would have to be /m/ rows long (where /m/ is the number of TRs). And if frame 119, 120, and 121 where to be excluded: then it would be a /m/ by 3 matrix with column 1, row 119 set to 1; row 120 column 2 set to 1; row 121 column 3 set to 1.
Is that all correct?
Thanks, Adam
On Thu, Mar 15, 2018 at 9:47 AM, Adam Martersteck <acmarter@gmail.com mailto:acmarter@gmail.com> wrote:
Hi Freesurfer team & Doug, Just thought I'd check back in as you had asked! Any thoughts on censoring resting state volumes for fcseedcorr? Thanks, Adam On Thu, Feb 15, 2018 at 12:57 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: Currently there is no way to do this. But it might not be hard to add. If I don't get back in a couple of weeks, send me a reminder. On 02/14/2018 12:13 PM, Adam Martersteck wrote: > Just a quick follow-up question, > For FD/DVARS or other "censoring" criteria -- using -tpexclusion > worked great for surface based analysis with mkanalsysis and selxavg3. > Is there a way to do this for seed-to-seed analysis (fcseedcor)? > > Thanks! > > On Thu, Jan 25, 2018 at 4:00 PM, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > Yes,you need a time point exclusion file (-tpexclude filename > option to > mkanalysis-sess). Run mkanalysis with -help to get more info on how to > create it. > > On 01/25/2018 04:43 PM, Adam Martersteck wrote: > > Hi Freesurer experts, > > > > I’m looking to censor (drop volumes) from my resting state fMRI time > > series that violate a predetermined motion and signal threshold (FD > > and DVARS). I've already determined which volumes violate X and Y > > criteria. > > > > Is there a way to to tell FS to "ignore" these time points in the > > analysis such as in preproc-sess or mkanalysis-sess? > > > > If there is not and if I were to drop the volumes directly from > the 4D > > file before starting any pre-processing and analysis – would > that be > > a problem for finding and regressing the auto-correlation in the > time > > series? > > > > Thanks! > > Adam > > > > > > _______________________________________________ > > 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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <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 > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://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> > <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> > <http://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/> > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>> > > _______________________________________________ > 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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <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 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 <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <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 <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 <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/> _______________________________________________ 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>
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