Hi FreeSurfer users, I have some resting state data that I preprocessed and conducted first level analyses using the flag -no-con-ok. Since no ces.nii.gz or sig.nii.gz is createdcomes up because there is no contrast, I'm wondering if it's possible to conduct functional ROI analyses with the data processed this way. Or would I have to do ROI analyses with the data processed in a seed-based manner where the seed is the "contrast"? Best, Talia
Don't include the -no-con-ok flag. For resting state, you don't need to run mkcontrast-sess because a contrast will automatically be created for you.
On 06/01/2016 02:24 PM, Raney, Talia L. wrote:
Hi FreeSurfer users, I have some resting state data that I preprocessed and conducted first level analyses using the flag -no-con-ok. Since no ces.nii.gz or sig.nii.gz is createdcomes up because there is no contrast, I'm wondering if it's possible to conduct functional ROI analyses with the data processed this way. Or would I have to do ROI analyses with the data processed in a seed-based manner where the seed is the "contrast"? Best, Talia _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Okay, the thing is that when I remove the no-con flag I get this error "ERROR: the design type of this analysis is notask selxavg-sess can only be used to analyse event-related and blocked", which means I have to change the analysis.info using mkanalysis-sess,correct? Which flag would I use then? Does this mean then that I have to use the seed as a task regressor? Thank you! Best, Talia
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Wednesday, June 01, 2016 2:42 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Selxavg3-sess with no-con-ok and ROI analyses
Don't include the -no-con-ok flag. For resting state, you don't need to run mkcontrast-sess because a contrast will automatically be created for you.
On 06/01/2016 02:24 PM, Raney, Talia L. wrote:
Hi FreeSurfer users, I have some resting state data that I preprocessed and conducted first level analyses using the flag -no-con-ok. Since no ces.nii.gz or sig.nii.gz is createdcomes up because there is no contrast, I'm wondering if it's possible to conduct functional ROI analyses with the data processed this way. Or would I have to do ROI analyses with the data processed in a seed-based manner where the seed is the "contrast"? Best, Talia _______________________________________________ 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
Are you using selxavg-sess or selxavg3-sess. you should be using selxavg3-sess
On 06/01/2016 03:45 PM, Raney, Talia L. wrote:
Okay, the thing is that when I remove the no-con flag I get this error "ERROR: the design type of this analysis is notask selxavg-sess can only be used to analyse event-related and blocked", which means I have to change the analysis.info using mkanalysis-sess,correct? Which flag would I use then? Does this mean then that I have to use the seed as a task regressor? Thank you! Best, Talia
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Wednesday, June 01, 2016 2:42 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Selxavg3-sess with no-con-ok and ROI analyses
Don't include the -no-con-ok flag. For resting state, you don't need to run mkcontrast-sess because a contrast will automatically be created for you.
On 06/01/2016 02:24 PM, Raney, Talia L. wrote:
Hi FreeSurfer users, I have some resting state data that I preprocessed and conducted first level analyses using the flag -no-con-ok. Since no ces.nii.gz or sig.nii.gz is createdcomes up because there is no contrast, I'm wondering if it's possible to conduct functional ROI analyses with the data processed this way. Or would I have to do ROI analyses with the data processed in a seed-based manner where the seed is the "contrast"? Best, Talia _______________________________________________ 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
That's my bad. I tried with selxavg3-sess and I get a different error saying no contrasts and to create contrasts with mkcontrast-sess or run with -no-con-ok. Is it possible I did mkanalysis-sess wrong? Thanks! Talia
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Wednesday, June 01, 2016 5:21 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Selxavg3-sess with no-con-ok and ROI analyses
Are you using selxavg-sess or selxavg3-sess. you should be using selxavg3-sess
On 06/01/2016 03:45 PM, Raney, Talia L. wrote:
Okay, the thing is that when I remove the no-con flag I get this error "ERROR: the design type of this analysis is notask selxavg-sess can only be used to analyse event-related and blocked", which means I have to change the analysis.info using mkanalysis-sess,correct? Which flag would I use then? Does this mean then that I have to use the seed as a task regressor? Thank you! Best, Talia
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Wednesday, June 01, 2016 2:42 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Selxavg3-sess with no-con-ok and ROI analyses
Don't include the -no-con-ok flag. For resting state, you don't need to run mkcontrast-sess because a contrast will automatically be created for you.
On 06/01/2016 02:24 PM, Raney, Talia L. wrote:
Hi FreeSurfer users, I have some resting state data that I preprocessed and conducted first level analyses using the flag -no-con-ok. Since no ces.nii.gz or sig.nii.gz is createdcomes up because there is no contrast, I'm wondering if it's possible to conduct functional ROI analyses with the data processed this way. Or would I have to do ROI analyses with the data processed in a seed-based manner where the seed is the "contrast"? Best, Talia _______________________________________________ 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
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
freesurfer@nmr.mgh.harvard.edu
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Douglas N Greve -
Raney, Talia L.