Hi all,
I'd like to run a resting-state fcMRI analysis within the GLM (mri_glmfit), but I'm not completely sure how to set this up in the FSGD file. I've seen the online tutorial of age vs cortical thickness, but I'm not sure how to specify a regressor with a timeseries. Does anyone have an example of an FSGD file for this?
Thanks! Eun Young
We don't usually use mri_glmfit for this kind of thing. If you want to do it this way, then you cannot use an FSGD file. Instead, create a design matrix with the seed time course then pass that to mri_glmfit with the --X option (and no --fsgd option).
On 05/04/2016 10:17 AM, Eun Young Choi wrote:
Hi all,
I'd like to run a resting-state fcMRI analysis within the GLM (mri_glmfit), but I'm not completely sure how to set this up in the FSGD file. I've seen the online tutorial of age vs cortical thickness, but I'm not sure how to specify a regressor with a timeseries. Does anyone have an example of an FSGD file for this?
Thanks! Eun Young
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks, Doug.
I'm still a little unclear about how to set up a timeseries regressor (120 timepoints) in the design matrix while also specifying the # of subjects (500). Would the design matrix be a 500x120 or 120x500?
I should mention that my ultimate goal is to find a statistically sig. threshold for a cortical fcMRI map with 500 subjects. Traditional correction for multiple comparisons, like Bonferroni and FDR, are not sufficient. So I'd now like to find a cluster size-based correction threshold using mri_glm-sim. Hence, my desire to create the cortical fcMRI map using mri_glmfit, so I can get the files needed for mri_glm-sim. Is this an okay approach, or is there a better way to do this?
Thank you so much, Eun Young
On Wed, May 4, 2016 at 3:15 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
We don't usually use mri_glmfit for this kind of thing. If you want to do it this way, then you cannot use an FSGD file. Instead, create a design matrix with the seed time course then pass that to mri_glmfit with the --X option (and no --fsgd option).
On 05/04/2016 10:17 AM, Eun Young Choi wrote:
Hi all,
I'd like to run a resting-state fcMRI analysis within the GLM (mri_glmfit), but I'm not completely sure how to set this up in the FSGD file. I've seen the online tutorial of age vs cortical thickness, but I'm not sure how to specify a regressor with a timeseries. Does anyone have an example of an FSGD file for this?
Thanks! Eun Young
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.
I guess I'm unclear as to what you are trying to do. Are you trying to do a time series analysis of the resting state to extract, eg, correlation with a seed? Or have you already done your time series analysis on each subject, reducing each to a single number at each voxel, and now you are doing a group analysis? doug
On 05/05/2016 11:44 AM, Eun Young Choi wrote:
Thanks, Doug.
I'm still a little unclear about how to set up a timeseries regressor (120 timepoints) in the design matrix while also specifying the # of subjects (500). Would the design matrix be a 500x120 or 120x500?
I should mention that my ultimate goal is to find a statistically sig. threshold for a cortical fcMRI map with 500 subjects. Traditional correction for multiple comparisons, like Bonferroni and FDR, are not sufficient. So I'd now like to find a cluster size-based correction threshold using mri_glm-sim. Hence, my desire to create the cortical fcMRI map using mri_glmfit, so I can get the files needed for mri_glm-sim. Is this an okay approach, or is there a better way to do this?
Thank you so much, Eun Young
On Wed, May 4, 2016 at 3:15 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
We don't usually use mri_glmfit for this kind of thing. If you want to do it this way, then you cannot use an FSGD file. Instead, create a design matrix with the seed time course then pass that to mri_glmfit with the --X option (and no --fsgd option). On 05/04/2016 10:17 AM, Eun Young Choi wrote: > > Hi all, > > I'd like to run a resting-state fcMRI analysis within the GLM > (mri_glmfit), but I'm not completely sure how to set this up in the > FSGD file. I've seen the online tutorial of age vs cortical thickness, > but I'm not sure how to specify a regressor with a timeseries. Does > anyone have an example of an FSGD file for this? > > Thanks! > Eun Young > > > > _______________________________________________ > 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.--
*Eun Young Choi, PhD*
Post-doctoral Associate
University of Rochester Medical Center
601 Elmwood Ave, Box 711
Rochester, NY 14642
cell: 551-580-1572
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
Sorry for the confusion. I currently have individual and group mean fcMRI z-maps from a seed based resting-state analysis (non GLM), but I could also do a GLM-involved analysis for each subject with the seed's timeseries as a regressor. My ultimate goal is have a group z-map that is thresholded at some statistically meaningful threshold. I've tried Bonferroni and FDR corrections, but they're not stringent enough (i.e., even weak correlations are highly significant). So I started looking into doing a cluster size-based correction threshold, which brought me to mri_glmsim and mri_glmfit. But if there's a way to threshold a group zmap without mri_glmsim, I could do that.
Let me know if I can explain further. Thank you! Eun Young
On Thu, May 5, 2016 at 12:22 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
I guess I'm unclear as to what you are trying to do. Are you trying to do a time series analysis of the resting state to extract, eg, correlation with a seed? Or have you already done your time series analysis on each subject, reducing each to a single number at each voxel, and now you are doing a group analysis? doug
On 05/05/2016 11:44 AM, Eun Young Choi wrote:
Thanks, Doug.
I'm still a little unclear about how to set up a timeseries regressor (120 timepoints) in the design matrix while also specifying the # of subjects (500). Would the design matrix be a 500x120 or 120x500?
I should mention that my ultimate goal is to find a statistically sig. threshold for a cortical fcMRI map with 500 subjects. Traditional correction for multiple comparisons, like Bonferroni and FDR, are not sufficient. So I'd now like to find a cluster size-based correction threshold using mri_glm-sim. Hence, my desire to create the cortical fcMRI map using mri_glmfit, so I can get the files needed for mri_glm-sim. Is this an okay approach, or is there a better way to do this?
Thank you so much, Eun Young
On Wed, May 4, 2016 at 3:15 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
We don't usually use mri_glmfit for this kind of thing. If you wantto
do it this way, then you cannot use an FSGD file. Instead, create a design matrix with the seed time course then pass that to mri_glmfit with the --X option (and no --fsgd option). On 05/04/2016 10:17 AM, Eun Young Choi wrote: > > Hi all, > > I'd like to run a resting-state fcMRI analysis within the GLM > (mri_glmfit), but I'm not completely sure how to set this up in the > FSGD file. I've seen the online tutorial of age vs cortical thickness, > but I'm not sure how to specify a regressor with a timeseries. Does > anyone have an example of an FSGD file for this? > > Thanks! > Eun Young > > > > _______________________________________________ > 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.--
*Eun Young Choi, PhD*
Post-doctoral Associate
University of Rochester Medical Center
601 Elmwood Ave, Box 711
Rochester, NY 14642
cell: 551-580-1572
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 just realized there wasn't a question in my email below.
Is there a way to get a group z-map that is thresholded at some statistically meaningful threshold (ie. cluster size p value) without using mri_glmsim and mri_glmfit? If not, how might I specify a timeseries in the design matrix?
Thank you! Eun Young
On Thu, May 5, 2016 at 1:31 PM, Eun Young Choi choiey@gmail.com wrote:
Hi Doug,
Sorry for the confusion. I currently have individual and group mean fcMRI z-maps from a seed based resting-state analysis (non GLM), but I could also do a GLM-involved analysis for each subject with the seed's timeseries as a regressor. My ultimate goal is have a group z-map that is thresholded at some statistically meaningful threshold. I've tried Bonferroni and FDR corrections, but they're not stringent enough (i.e., even weak correlations are highly significant). So I started looking into doing a cluster size-based correction threshold, which brought me to mri_glmsim and mri_glmfit. But if there's a way to threshold a group zmap without mri_glmsim, I could do that.
Let me know if I can explain further. Thank you! Eun Young
On Thu, May 5, 2016 at 12:22 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:
I guess I'm unclear as to what you are trying to do. Are you trying to do a time series analysis of the resting state to extract, eg, correlation with a seed? Or have you already done your time series analysis on each subject, reducing each to a single number at each voxel, and now you are doing a group analysis? doug
On 05/05/2016 11:44 AM, Eun Young Choi wrote:
Thanks, Doug.
I'm still a little unclear about how to set up a timeseries regressor (120 timepoints) in the design matrix while also specifying the # of subjects (500). Would the design matrix be a 500x120 or 120x500?
I should mention that my ultimate goal is to find a statistically sig. threshold for a cortical fcMRI map with 500 subjects. Traditional correction for multiple comparisons, like Bonferroni and FDR, are not sufficient. So I'd now like to find a cluster size-based correction threshold using mri_glm-sim. Hence, my desire to create the cortical fcMRI map using mri_glmfit, so I can get the files needed for mri_glm-sim. Is this an okay approach, or is there a better way to do this?
Thank you so much, Eun Young
On Wed, May 4, 2016 at 3:15 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
We don't usually use mri_glmfit for this kind of thing. If you wantto
do it this way, then you cannot use an FSGD file. Instead, create a design matrix with the seed time course then pass that to mri_glmfit with the --X option (and no --fsgd option). On 05/04/2016 10:17 AM, Eun Young Choi wrote: > > Hi all, > > I'd like to run a resting-state fcMRI analysis within the GLM > (mri_glmfit), but I'm not completely sure how to set this up inthe
> FSGD file. I've seen the online tutorial of age vs cortical thickness, > but I'm not sure how to specify a regressor with a timeseries.Does
> anyone have an example of an FSGD file for this? > > Thanks! > Eun Young > > > > _______________________________________________ > 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.--
*Eun Young Choi, PhD*
Post-doctoral Associate
University of Rochester Medical Center
601 Elmwood Ave, Box 711
Rochester, NY 14642
cell: 551-580-1572
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
--
*Eun Young Choi, PhD*
Post-doctoral Associate
University of Rochester Medical Center
601 Elmwood Ave, Box 711
Rochester, NY 14642
cell: 551-580-1572
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Eun Young Choi