hello, i'm struggling with how to specify a schedule and then ask optseq2 to identify an optimal timing schedule. specifically i have a conditioned cue and an unconditioned stimulus. the high threat CS always needs to follow with a high pain US and low threat CS with a low pain CS. how can i specify such a schedule in optseq2? i've been trying a number of combinations of below, but am failing miserably with lots of varying warnings and error messages and inability to read files or 'Bus error'
what should the --in input schedule file format look like? that might be the missing link .. although that's hard to say for sure.
many thanks, claire
Hi Claire, you can't do this type of design in optseq because optseq requires that there be no constraints of which stimulus can follow itself or another stimulus (obviously this does not work for your design). If you take a CS-US pair as a stimulus, then that should work. Also, you could spec just one condition and randomly recode stimuli as CS and US. It is not perfect, but you'd get the random timing, and it is probably good enough.
doug
On 8/1/13 6:44 PM, Claire Wilcox wrote:
hello, i'm struggling with how to specify a schedule and then ask optseq2 to identify an optimal timing schedule. specifically i have a conditioned cue and an unconditioned stimulus. the high threat CS always needs to follow with a high pain US and low threat CS with a low pain CS. how can i specify such a schedule in optseq2? i've been trying a number of combinations of below, but am failing miserably with lots of varying warnings and error messages and inability to read files or 'Bus error'
what should the --in input schedule file format look like? that might be the missing link .. although that's hard to say for sure.
many thanks, claire
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Freesurfers,
I ran a Monte Carlo analysis to identify significant clusters of activated voxels in a between-group comparison of fMRI data I've collected.
I was wondering if there was any way to limit what tksurfer displays to only the significant clusters based on the Monte Carlo -- i.e., those with a corrected cluster wise p < .05.
I know that you can display those clusters using the sig.cluster.mgh image file that is generated with the Monte Carlo analysis. But, the blobs in that map dont have any color variation and don't look the same way that activation does when typically using sig.nii (i.e., some are all yellow, orange or red).
Any help or suggestions would be much appreciated.
Thanks!
Ben Benjamin Brent, M.D., M.S. Massachusetts Mental Health Center 75 Fenwood Road, Room 618 Boston, MA 02115 617-754-1262
This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.
Hi Ben, if you look at the help for mri_glmfit-sim (run with --help) it will detail the various outputs. one of them is csdbase.sig.masked.mgh which I think is what you want. best doug
On 8/1/13 9:09 PM, bbrent@bidmc.harvard.edu wrote:
Dear Freesurfers,
I ran a Monte Carlo analysis to identify significant clusters of activated voxels in a between-group comparison of fMRI data I've collected.
I was wondering if there was any way to limit what tksurfer displays to only the significant clusters based on the Monte Carlo -- i.e., those with a corrected cluster wise p < .05.
I know that you can display those clusters using the sig.cluster.mgh image file that is generated with the Monte Carlo analysis. But, the blobs in that map dont have any color variation and don't look the same way that activation does when typically using sig.nii (i.e., some are all yellow, orange or red).
Any help or suggestions would be much appreciated.
Thanks!
Ben Benjamin Brent, M.D., M.S. Massachusetts Mental Health Center 75 Fenwood Road, Room 618 Boston, MA 02115 617-754-1262
This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
I analyzed my data using freesurfer 4.5, so I don't get the csdbase.sig.masked.mgh output.
Apart from re-analyzing my data using the up to date version of freesurfer, is there a way to get the csdbase.sig.masked output file using freesurfer 4.5?
Thanks for any suggestions.
Ben
Benjamin Brent, M.D., M.S. Massachusetts Mental Health Center 75 Fenwood Road, Room 618 Boston, MA 02115 617-754-1262 ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Thursday, August 01, 2013 10:55 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] limiting display to significant clusters with tksurfer
Hi Ben, if you look at the help for mri_glmfit-sim (run with --help) it will detail the various outputs. one of them is csdbase.sig.masked.mgh which I think is what you want. best doug
On 8/1/13 9:09 PM, bbrent@bidmc.harvard.edu wrote:
Dear Freesurfers,
I ran a Monte Carlo analysis to identify significant clusters of activated voxels in a between-group comparison of fMRI data I've collected.
I was wondering if there was any way to limit what tksurfer displays to only the significant clusters based on the Monte Carlo -- i.e., those with a corrected cluster wise p < .05.
I know that you can display those clusters using the sig.cluster.mgh image file that is generated with the Monte Carlo analysis. But, the blobs in that map dont have any color variation and don't look the same way that activation does when typically using sig.nii (i.e., some are all yellow, orange or red).
Any help or suggestions would be much appreciated.
Thanks!
Ben Benjamin Brent, M.D., M.S. Massachusetts Mental Health Center 75 Fenwood Road, Room 618 Boston, MA 02115 617-754-1262
This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.
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
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.
Hi Ben, you can do your group analysis using 5.3 even though your individual data was done with 4.5. That may be the easiest way to get the results you need. I can't remember what 4.5 has and does not have.
doug
On 08/13/2013 01:26 PM, bbrent@bidmc.harvard.edu wrote:
Hi Doug,
I analyzed my data using freesurfer 4.5, so I don't get the csdbase.sig.masked.mgh output.
Apart from re-analyzing my data using the up to date version of freesurfer, is there a way to get the csdbase.sig.masked output file using freesurfer 4.5?
Thanks for any suggestions.
Ben
Benjamin Brent, M.D., M.S. Massachusetts Mental Health Center 75 Fenwood Road, Room 618 Boston, MA 02115 617-754-1262 ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Thursday, August 01, 2013 10:55 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] limiting display to significant clusters with tksurfer
Hi Ben, if you look at the help for mri_glmfit-sim (run with --help) it will detail the various outputs. one of them is csdbase.sig.masked.mgh which I think is what you want. best doug
On 8/1/13 9:09 PM, bbrent@bidmc.harvard.edu wrote:
Dear Freesurfers,
I ran a Monte Carlo analysis to identify significant clusters of activated voxels in a between-group comparison of fMRI data I've collected.
I was wondering if there was any way to limit what tksurfer displays to only the significant clusters based on the Monte Carlo -- i.e., those with a corrected cluster wise p < .05.
I know that you can display those clusters using the sig.cluster.mgh image file that is generated with the Monte Carlo analysis. But, the blobs in that map dont have any color variation and don't look the same way that activation does when typically using sig.nii (i.e., some are all yellow, orange or red).
Any help or suggestions would be much appreciated.
Thanks!
Ben Benjamin Brent, M.D., M.S. Massachusetts Mental Health Center 75 Fenwood Road, Room 618 Boston, MA 02115 617-754-1262
This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.
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
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@nmr.mgh.harvard.edu
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bbrent＠bidmc.harvard.edu -
Claire Wilcox -
Douglas Greve -
Douglas N Greve