Hi Doug Thanks for your email. I gave your suggestion a try - reduced the dPSD to 0.5 (as well as adjusted the PSDMAX, and no. of volumes to reflect the new TR - see full command line below). Unfortunately the efficiency is way down (0.03) and the VRF you previously suggested should be between 20-40 is 4.5! I now wonder if Optseq is trying to tell me this is now a bad design!!
Would be very grateful for any ideas for improvement?
optseq2 --ntp 240 --tr 2.5 --psdwin 0 20 0.5 --ev hf 3 50 --ev lf 3 50 --ev nf 3 50 --nkeep 3 --o test14 --nsearch 10000 --focb 100
many thanks Ella
Date: Sun, 28 Jul 2013 23:33:07 -0400 From: greve@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] dPSD and ev duration
Hi Ella, it has an internal clock that events have to be syncrhonized to. Try setting the dPSD to 0.5
doug
On 7/28/13 4:05 PM, Ella Hinton wrote:
Hi
Quick question - why must the duration of the EVs be an integer multiple of the dPSD, which is also tied to the TR? I have event duration of 3 seconds, but would like to reduce my TR from 3 down to 2.5, but I can't seem to input the correct numbers for optseq to help me.
thanks in advance
Ella
_______________________________________________ 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 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 Ella, sorry for the delay. The VRF gets reduced by a factor roughly equal to TR/dPSD, so 5 in your case. Whether this matters depends on how you eventually want to analyze the data. If you are going to assume a shape to the HRF (eg, using SPM or FSL), then it won't make much difference since the realized VRF will be 5 times your 4.5 which puts you in a good range. If you plan to analyze using an FIR (ie, don't assume a shape), then you might want to add some runs to boost the power.
doug
On 7/29/13 4:06 PM, Ella Hinton wrote:
Hi Doug Thanks for your email. I gave your suggestion a try - reduced the dPSD to 0.5 (as well as adjusted the PSDMAX, and no. of volumes to reflect the new TR - see full command line below). Unfortunately the efficiency is way down (0.03) and the VRF you previously suggested should be between 20-40 is 4.5! I now wonder if Optseq is trying to tell me this is now a bad design!!
Would be very grateful for any ideas for improvement?
optseq2 --ntp 240 --tr 2.5 --psdwin 0 20 0.5 --ev hf 3 50 --ev lf 3 50 --ev nf 3 50 --nkeep 3 --o test14 --nsearch 10000 --focb 100
many thanks Ella
Date: Sun, 28 Jul 2013 23:33:07 -0400 From: greve@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] dPSD and ev duration
Hi Ella, it has an internal clock that events have to be syncrhonized to. Try setting the dPSD to 0.5 doug
On 7/28/13 4:05 PM, Ella Hinton wrote:
Hi Quick question - why must the duration of the EVs be an integer multiple of the dPSD, which is also tied to the TR? I have event duration of 3 seconds, but would like to reduce my TR from 3 down to 2.5, but I can't seem to input the correct numbers for optseq to help me. thanks in advance Ella _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 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
-
Douglas Greve -
Ella Hinton