Hi! Has someone used retroicor (retroactive correction of physiological noise; Glover at al. 2000) with Freesurfer? I would like to create nuisance regressors for EPI data based on cardiac and respiratory signals. The AFNI version of retroicor produces slice-based regressors, and I am not sure how to use them in Freesurfer. Suggestions for alternative implementations would also be appreciated. Thanks! Caspar
Hi Caspar, I don't have anything that is plug-and-play for RETROICOR. You will need a text file to use as an external regressor with one column for each regressor and one row for each time point. You can play with my matlab functions. First, pass the waveform (cardiac or respiration) to peakfinder.m, then call fast_retroicor.m passing it the peaks and returning the regressors. Then save the regressors you want in a text file and specify them using -nuisreg option to mkanalysis-sess. doug
On 07/18/2012 11:28 AM, Caspar M. Schwiedrzik wrote:
Hi! Has someone used retroicor (retroactive correction of physiological noise; Glover at al. 2000) with Freesurfer? I would like to create nuisance regressors for EPI data based on cardiac and respiratory signals. The AFNI version of retroicor produces slice-based regressors, and I am not sure how to use them in Freesurfer. Suggestions for alternative implementations would also be appreciated. Thanks! Caspar
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug, thanks for your advice. I am using freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0-full, while I have a copy of peakfinder.m, fast_retroicor.m does not seem to be part of the package. Could you let me know where to download it? Thanks, Caspar
2012/7/18 Douglas N Greve greve@nmr.mgh.harvard.edu
Hi Caspar, I don't have anything that is plug-and-play for RETROICOR. You will need a text file to use as an external regressor with one column for each regressor and one row for each time point. You can play with my matlab functions. First, pass the waveform (cardiac or respiration) to peakfinder.m, then call fast_retroicor.m passing it the peaks and returning the regressors. Then save the regressors you want in a text file and specify them using -nuisreg option to mkanalysis-sess. doug
On 07/18/2012 11:28 AM, Caspar M. Schwiedrzik wrote:
Hi! Has someone used retroicor (retroactive correction of physiological noise; Glover at al. 2000) with Freesurfer? I would like to create nuisance regressors for EPI data based on cardiac and respiratory signals. The AFNI version of retroicor produces slice-based regressors, and I am not sure how to use them in Freesurfer. Suggestions for alternative implementations would also be appreciated. Thanks! Caspar
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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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.
Try this ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fast_retroicor.m
On 07/18/2012 01:25 PM, Caspar M. Schwiedrzik wrote:
Hi Doug, thanks for your advice. I am using freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0-full, while I have a copy of peakfinder.m, fast_retroicor.m does not seem to be part of the package. Could you let me know where to download it? Thanks, Caspar
2012/7/18 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>
Hi Caspar, I don't have anything that is plug-and-play for RETROICOR. You will need a text file to use as an external regressor with one column for each regressor and one row for each time point. You can play with my matlab functions. First, pass the waveform (cardiac or respiration) to peakfinder.m, then call fast_retroicor.m passing it the peaks and returning the regressors. Then save the regressors you want in a text file and specify them using -nuisreg option to mkanalysis-sess. doug On 07/18/2012 11:28 AM, Caspar M. Schwiedrzik wrote: > Hi! > Has someone used retroicor (retroactive correction of physiological > noise; Glover at al. 2000) with Freesurfer? > I would like to create nuisance regressors for EPI data based on > cardiac and respiratory signals. > The AFNI version of retroicor produces slice-based regressors, and I > am not sure how to use them in Freesurfer. > Suggestions for alternative implementations would also be appreciated. > Thanks! > Caspar > > > > > _______________________________________________ > 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 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.
great! one more question: how do I choose fmin and fmax? thanks, caspar
2012/7/18 Douglas N Greve greve@nmr.mgh.harvard.edu
Try this ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/fast_retroicor.mftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fast_retroicor.m
On 07/18/2012 01:25 PM, Caspar M. Schwiedrzik wrote:
Hi Doug, thanks for your advice. I am using freesurfer-Linux-centos4_x86_**64-stable-pub-v5.1.0-full, while I have a copy of peakfinder.m, fast_retroicor.m does not seem to be part of the package. Could you let me know where to download it? Thanks, Caspar
2012/7/18 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto: greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu>>
Hi Caspar, I don't have anything that is plug-and-play for RETROICOR. You will need a text file to use as an external regressor with one column for each regressor and one row for each time point. You can play with my matlab functions. First, pass the waveform (cardiac or respiration) to peakfinder.m, then call fast_retroicor.m passing it the peaks and returning the regressors. Then save the regressors you want in a text file and specify them using -nuisreg option to mkanalysis-sess. doug On 07/18/2012 11:28 AM, Caspar M. Schwiedrzik wrote: > Hi! > Has someone used retroicor (retroactive correction of physiological > noise; Glover at al. 2000) with Freesurfer? > I would like to create nuisance regressors for EPI data based on > cardiac and respiratory signals. > The AFNI version of retroicor produces slice-based regressors, and I > am not sure how to use them in Freesurfer. > Suggestions for alternative implementations would also be appreciated. > Thanks! > Caspar > > > > > ______________________________**_________________ > 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/**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<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> <http://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> <http://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 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.-- 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
and some more questions: in fast_retroicor(t,indpeak,M,peakamp,troughamp) what is t / M? how do I get peakamp and throughamp? thanks again, caspar
2012/7/18 Caspar M. Schwiedrzik cschwiedrz@rockefeller.edu
great! one more question: how do I choose fmin and fmax? thanks, caspar
2012/7/18 Douglas N Greve greve@nmr.mgh.harvard.edu
Try this ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/fast_retroicor.mftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fast_retroicor.m
On 07/18/2012 01:25 PM, Caspar M. Schwiedrzik wrote:
Hi Doug, thanks for your advice. I am using freesurfer-Linux-centos4_x86_**64-stable-pub-v5.1.0-full, while I have a copy of peakfinder.m, fast_retroicor.m does not seem to be part of the package. Could you let me know where to download it? Thanks, Caspar
2012/7/18 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto: greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu>>
Hi Caspar, I don't have anything that is plug-and-play for RETROICOR. You will need a text file to use as an external regressor with one column for each regressor and one row for each time point. You can play with my matlab functions. First, pass the waveform (cardiac or respiration) to peakfinder.m, then call fast_retroicor.m passing it the peaks and returning the regressors. Then save the regressors you want in a text file and specify them using -nuisreg option tomkanalysis-sess. doug
On 07/18/2012 11:28 AM, Caspar M. Schwiedrzik wrote: > Hi! > Has someone used retroicor (retroactive correction of physiological > noise; Glover at al. 2000) with Freesurfer? > I would like to create nuisance regressors for EPI data based on > cardiac and respiratory signals. > The AFNI version of retroicor produces slice-based regressors, andI > am not sure how to use them in Freesurfer. > Suggestions for alternative implementations would also be appreciated. > Thanks! > Caspar > > > > > ______________________________**_________________ > 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/**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<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> <http://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> <http://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 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.-- 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
M is the number of regressor pairs. Leave out the others and it will figure them out.
On 07/18/2012 01:43 PM, Caspar M. Schwiedrzik wrote:
and some more questions: in fast_retroicor(t,indpeak,M,peakamp,troughamp) what is t / M? how do I get peakamp and throughamp? thanks again, caspar
2012/7/18 Caspar M. Schwiedrzik <cschwiedrz@rockefeller.edu mailto:cschwiedrz@rockefeller.edu>
great! one more question: how do I choose fmin and fmax? thanks, caspar 2012/7/18 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> Try this ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fast_retroicor.m On 07/18/2012 01:25 PM, Caspar M. Schwiedrzik wrote: Hi Doug, thanks for your advice. I am using freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0-full, while I have a copy of peakfinder.m, fast_retroicor.m does not seem to be part of the package. Could you let me know where to download it? Thanks, Caspar 2012/7/18 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>>> Hi Caspar, I don't have anything that is plug-and-play for RETROICOR. You will need a text file to use as an external regressor with one column for each regressor and one row for each time point. You can play with my matlab functions. First, pass the waveform (cardiac or respiration) to peakfinder.m, then call fast_retroicor.m passing it the peaks and returning the regressors. Then save the regressors you want in a text file and specify them using -nuisreg option to mkanalysis-sess. doug On 07/18/2012 11:28 AM, Caspar M. Schwiedrzik wrote: > Hi! > Has someone used retroicor (retroactive correction of physiological > noise; Glover at al. 2000) with Freesurfer? > I would like to create nuisance regressors for EPI data based on > cardiac and respiratory signals. > The AFNI version of retroicor produces slice-based regressors, and I > am not sure how to use them in Freesurfer. > Suggestions for alternative implementations would also be appreciated. > Thanks! > Caspar > > > > > _______________________________________________ > 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 -- 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> FileDrop: 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> _______________________________________________ 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. -- 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug, I think M is automatically computed, but t needs to be given (in addition to indpeak). What is t? Thanks, Caspar
2012/7/18 Douglas N Greve greve@nmr.mgh.harvard.edu
M is the number of regressor pairs. Leave out the others and it will figure them out.
On 07/18/2012 01:43 PM, Caspar M. Schwiedrzik wrote:
and some more questions: in fast_retroicor(t,indpeak,M,peakamp,troughamp) what is t / M? how do I get peakamp and throughamp? thanks again, caspar
2012/7/18 Caspar M. Schwiedrzik <cschwiedrz@rockefeller.edu mailto:cschwiedrz@rockefeller.edu>
great! one more question: how do I choose fmin and fmax? thanks, caspar 2012/7/18 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> Try thisftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fast_retroicor.m
On 07/18/2012 01:25 PM, Caspar M. Schwiedrzik wrote: Hi Doug, thanks for your advice. I am using freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0-full, while I have a copy of peakfinder.m, fast_retroicor.m does not seem to be part of the package. Could you let me know where to download it? Thanks, Caspar 2012/7/18 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>>> Hi Caspar, I don't have anything that is plug-and-play for RETROICOR. You will need a text file to use as an external regressor with one column for each regressor and one row for each time point. You can play with my matlab functions. First, pass the waveform (cardiac or respiration) to peakfinder.m, then call fast_retroicor.m passing it the peaks and returning the regressors. Then save the regressors you want in a text file and specify them using -nuisreg option to mkanalysis-sess. doug On 07/18/2012 11:28 AM, Caspar M. Schwiedrzik wrote: > Hi! > Has someone used retroicor (retroactive correction of physiological > noise; Glover at al. 2000) with Freesurfer? > I would like to create nuisance regressors for EPI data based on > cardiac and respiratory signals. > The AFNI version of retroicor produces slice-based regressors, and I > am not sure how to use them in Freesurfer. > Suggestions for alternative implementations would also be appreciated. > Thanks! > Caspar > > > > > _______________________________________________ > 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
-- 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> FileDrop: 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 _______________________________________________ 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. -- 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 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
t is time of pulse or respiration acquisition (eg, .02*[0:1000]). indpeak is the list of indices in t where the peaks were found. doug
On 07/19/2012 09:24 AM, Caspar M. Schwiedrzik wrote:
Hi Doug, I think M is automatically computed, but t needs to be given (in addition to indpeak). What is t? Thanks, Caspar
2012/7/18 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>
M is the number of regressor pairs. Leave out the others and it will figure them out. On 07/18/2012 01:43 PM, Caspar M. Schwiedrzik wrote: > and some more questions: in fast_retroicor(t,indpeak,M,peakamp,troughamp) > what is t / M? > how do I get peakamp and throughamp? > thanks again, caspar > > 2012/7/18 Caspar M. Schwiedrzik <cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>>> > > great! > one more question: how do I choose fmin and fmax? > thanks, caspar > > 2012/7/18 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>>> > > Try this > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fast_retroicor.m > > > > On 07/18/2012 01:25 PM, Caspar M. Schwiedrzik wrote: > > Hi Doug, > thanks for your advice. I am using > freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0-full, > while I have a copy of peakfinder.m, fast_retroicor.m does > not seem to be part of the package. > Could you let me know where to download it? > Thanks, Caspar > > > 2012/7/18 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>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> > > > Hi Caspar, I don't have anything that is plug-and-play > for RETROICOR. > You will need a text file to use as an external > regressor with one > column for each regressor and one row for each time > point. You can > play > with my matlab functions. First, pass the waveform > (cardiac or > respiration) to peakfinder.m, then call > fast_retroicor.m passing > it the > peaks and returning the regressors. Then save the > regressors you > want in > a text file and specify them using -nuisreg option to > mkanalysis-sess. > doug > > On 07/18/2012 11:28 AM, Caspar M. Schwiedrzik wrote: > > Hi! > > Has someone used retroicor (retroactive correction of > physiological > > noise; Glover at al. 2000) with Freesurfer? > > I would like to create nuisance regressors for EPI data > based on > > cardiac and respiratory signals. > > The AFNI version of retroicor produces slice-based > regressors, and I > > am not sure how to use them in Freesurfer. > > Suggestions for alternative implementations would also be > appreciated. > > Thanks! > > Caspar > > > > > > > > > > _______________________________________________ > > 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>> > <mailto: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 > > -- > 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>> > <mailto: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>> > <tel: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>> <tel: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: > 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> > > _______________________________________________ > 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>> > <mailto: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. > > > > -- > 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> > FileDrop: 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> > > > > > > _______________________________________________ > 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
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If you don't specify them, I think it tries to figure them out.
On 07/18/2012 01:36 PM, Caspar M. Schwiedrzik wrote:
great! one more question: how do I choose fmin and fmax? thanks, caspar
2012/7/18 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>
Try this ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fast_retroicor.m On 07/18/2012 01:25 PM, Caspar M. Schwiedrzik wrote: Hi Doug, thanks for your advice. I am using freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0-full, while I have a copy of peakfinder.m, fast_retroicor.m does not seem to be part of the package. Could you let me know where to download it? Thanks, Caspar 2012/7/18 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>>> Hi Caspar, I don't have anything that is plug-and-play for RETROICOR. You will need a text file to use as an external regressor with one column for each regressor and one row for each time point. You can play with my matlab functions. First, pass the waveform (cardiac or respiration) to peakfinder.m, then call fast_retroicor.m passing it the peaks and returning the regressors. Then save the regressors you want in a text file and specify them using -nuisreg option to mkanalysis-sess. doug On 07/18/2012 11:28 AM, Caspar M. Schwiedrzik wrote: > Hi! > Has someone used retroicor (retroactive correction of physiological > noise; Glover at al. 2000) with Freesurfer? > I would like to create nuisance regressors for EPI data based on > cardiac and respiratory signals. > The AFNI version of retroicor produces slice-based regressors, and I > am not sure how to use them in Freesurfer. > Suggestions for alternative implementations would also be appreciated. > Thanks! > Caspar > > > > > _______________________________________________ > 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 -- 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> FileDrop: 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> _______________________________________________ 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. -- 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>
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Douglas N Greve