Hi Freesurfers,
I did an FIR analysis to get the BOLD response over time, the following way
mkanalysis-sess -analysis Afterimage_FIR2.rh -surface self rh -native -fwhm 5 -paradigm ShapeAE_New.par -event-related -polyfit 1 -mcextreg -TR 1.000 -nconditions 8 -force -fsd bold -fir 4 14
I then generated the relevant contrasts, ran the funcroi-config command, and the func-roi-table-sess command to create 14 files for my ROI, each containing the signal value at 14 different time points.
i.e. funcroi-table-sess -sf sessid -roi Labels/rh.V1 -c condition1 -map cespct -o ROI/frame0 -frame 0
funcroi-table-sess -sf sessid -roi Labels/rh.V1 -c condition1 -map cespct -o ROI/frame1 -frame 1
. . . funcroi-table-sess -sf sessid -roi Labels/rh.V1 -c condition1 -map cespct -o ROI/frame13 -frame 13
My question is this:
To what time point (relative to stimulus onset) does the value in the frame0 file correspond?
As I understand it, the first 4 frame values should correspond to activity pre-stimulus. However, this expectation is not corroborated by the timing and pattern of the BOLD response I am observing.
I would appreciate any guidance on this issue.
Thanks,
Cesar Echavarria
Hi Cesar, for your case, it would correspond to 4sec prior to stimulus onset (the TR that goes from -4 to -3 sec). What seems to be wrong? The last frame would be the TR that goes from +9sec to +10 sec. Not related to your question, but Is 10 sec post stimulus long enough? doug
On 03/05/2013 11:53 AM, Cesar E Echavarria wrote:
Hi Freesurfers,
I did an FIR analysis to get the BOLD response over time, the following way
mkanalysis-sess -analysis Afterimage_FIR2.rh -surface self rh -native -fwhm 5 -paradigm ShapeAE_New.par -event-related -polyfit 1 -mcextreg -TR 1.000 -nconditions 8 -force -fsd bold -fir 4 14
I then generated the relevant contrasts, ran the funcroi-config command, and the func-roi-table-sess command to create 14 files for my ROI, each containing the signal value at 14 different time points.
i.e. funcroi-table-sess -sf sessid -roi Labels/rh.V1 -c condition1 -map cespct -o ROI/frame0 -frame 0
funcroi-table-sess -sf sessid -roi Labels/rh.V1 -c condition1 -map cespct -o ROI/frame1 -frame 1
. . . funcroi-table-sess -sf sessid -roi Labels/rh.V1 -c condition1 -map cespct -o ROI/frame13 -frame 13
My question is this:
To what time point (relative to stimulus onset) does the value in the frame0 file correspond?
As I understand it, the first 4 frame values should correspond to activity pre-stimulus. However, this expectation is not corroborated by the timing and pattern of the BOLD response I am observing.
I would appreciate any guidance on this issue.
Thanks,
Cesar Echavarria
Hi Doug,
As you can see from the attached image (time course on x-axis, normalized BOLD response on y-axis) the signal peak occurs earlier than expected if I were to consider the first frame to be -4 sec relative to stimulus onset. In our experiment we presented a stimulus for 10 seconds, and we wanted to see the time course of the BOLD response while the stimulus was on. We also wanted to see the response of the aftereffect due to the stimulus separately which is why we are interested only in the 10 seconds the stimulus is on.
Thanks,
Cesar
On Tue, Mar 5, 2013 at 12:27 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
Hi Cesar, for your case, it would correspond to 4sec prior to stimulus onset (the TR that goes from -4 to -3 sec). What seems to be wrong? The last frame would be the TR that goes from +9sec to +10 sec. Not related to your question, but Is 10 sec post stimulus long enough? doug
On 03/05/2013 11:53 AM, Cesar E Echavarria wrote:
Hi Freesurfers,
I did an FIR analysis to get the BOLD response over time, the following way
mkanalysis-sess -analysis Afterimage_FIR2.rh -surface self rh -native -fwhm 5 -paradigm ShapeAE_New.par -event-related -polyfit 1 -mcextreg -TR 1.000 -nconditions 8 -force -fsd bold -fir 4 14
I then generated the relevant contrasts, ran the funcroi-config command, and the func-roi-table-sess command to create 14 files for my ROI, each containing the signal value at 14 different time points.
i.e. funcroi-table-sess -sf sessid -roi Labels/rh.V1 -c condition1 -map cespct -o ROI/frame0 -frame 0
funcroi-table-sess -sf sessid -roi Labels/rh.V1 -c condition1 -map cespct -o ROI/frame1 -frame 1
. . . funcroi-table-sess -sf sessid -roi Labels/rh.V1 -c condition1 -map cespct -o ROI/frame13 -frame 13
My question is this:
To what time point (relative to stimulus onset) does the value in the frame0 file correspond?
As I understand it, the first 4 frame values should correspond to activity pre-stimulus. However, this expectation is not corroborated by the timing and pattern of the BOLD response I am observing.
I would appreciate any guidance on this issue.
Thanks,
Cesar Echavarria
-- 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 Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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/**compliancelinehttp://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.
If you presented the stimulus for 10sec, then you should set the time window to include about 12 sec after stimulus offset. If your stimulus is 10 secand you want the time window to start 4 sec prior to onset and go 12 sec after onset, then you will need a time window of 4+10+12=26sec, so it would be --fir 4 22. You have to model the return to baseline even if you are not interested init. Try that and get back to me if it does not work. doug
On 03/05/2013 12:43 PM, Cesar Echavarria wrote:
Hi Doug,
As you can see from the attached image (time course on x-axis, normalized BOLD response on y-axis) the signal peak occurs earlier than expected if I were to consider the first frame to be -4 sec relative to stimulus onset. In our experiment we presented a stimulus for 10 seconds, and we wanted to see the time course of the BOLD response while the stimulus was on. We also wanted to see the response of the aftereffect due to the stimulus separately which is why we are interested only in the 10 seconds the stimulus is on.
Thanks,
Cesar
On Tue, Mar 5, 2013 at 12:27 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Hi Cesar, for your case, it would correspond to 4sec prior to stimulus onset (the TR that goes from -4 to -3 sec). What seems to be wrong? The last frame would be the TR that goes from +9sec to +10 sec. Not related to your question, but Is 10 sec post stimulus long enough? doug On 03/05/2013 11:53 AM, Cesar E Echavarria wrote: Hi Freesurfers, I did an FIR analysis to get the BOLD response over time, the following way mkanalysis-sess -analysis Afterimage_FIR2.rh -surface self rh -native -fwhm 5 -paradigm ShapeAE_New.par -event-related -polyfit 1 -mcextreg -TR 1.000 -nconditions 8 -force -fsd bold -fir 4 14 I then generated the relevant contrasts, ran the funcroi-config command, and the func-roi-table-sess command to create 14 files for my ROI, each containing the signal value at 14 different time points. i.e. funcroi-table-sess -sf sessid -roi Labels/rh.V1 -c condition1 -map cespct -o ROI/frame0 -frame 0 funcroi-table-sess -sf sessid -roi Labels/rh.V1 -c condition1 -map cespct -o ROI/frame1 -frame 1 . . . funcroi-table-sess -sf sessid -roi Labels/rh.V1 -c condition1 -map cespct -o ROI/frame13 -frame 13 My question is this: To what time point (relative to stimulus onset) does the value in the frame0 file correspond? As I understand it, the first 4 frame values should correspond to activity pre-stimulus. However, this expectation is not corroborated by the timing and pattern of the BOLD response I am observing. I would appreciate any guidance on this issue. Thanks, Cesar Echavarria -- 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> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ 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.-- Cesar Echavarria Brain & Cognitive Science MIT 2012
Does the post-stimulus period have to be as long as 12 seconds? With such a long time window I get the following error when running selxavg3-sess:
XCond = 1.47995e+18 (normalized) ERROR: design is ill-conditioned
To clarify: in our design we have 10 seconds of condition 1 followed immediately after with 10 seconds of condition 2 followed by 10 seconds of fixation. Given, this what would be the limit on how much post-stimulus time we should include in our time window?
Thanks again, Cesar
On Tue, Mar 5, 2013 at 1:00 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
If you presented the stimulus for 10sec, then you should set the time window to include about 12 sec after stimulus offset. If your stimulus is 10 secand you want the time window to start 4 sec prior to onset and go 12 sec after onset, then you will need a time window of 4+10+12=26sec, so it would be --fir 4 22. You have to model the return to baseline even if you are not interested init. Try that and get back to me if it does not work. doug
On 03/05/2013 12:43 PM, Cesar Echavarria wrote:
Hi Doug,
As you can see from the attached image (time course on x-axis, normalized BOLD response on y-axis) the signal peak occurs earlier than expected if I were to consider the first frame to be -4 sec relative to stimulus onset. In our experiment we presented a stimulus for 10 seconds, and we wanted to see the time course of the BOLD response while the stimulus was on. We also wanted to see the response of the aftereffect due to the stimulus separately which is why we are interested only in the 10 seconds the stimulus is on.
Thanks,
Cesar
On Tue, Mar 5, 2013 at 12:27 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu>> wrote:
Hi Cesar, for your case, it would correspond to 4sec prior to stimulus onset (the TR that goes from -4 to -3 sec). What seems to be wrong? The last frame would be the TR that goes from +9sec to +10 sec. Not related to your question, but Is 10 sec post stimulus long enough? doug On 03/05/2013 11:53 AM, Cesar E Echavarria wrote: Hi Freesurfers, I did an FIR analysis to get the BOLD response over time, the following way mkanalysis-sess -analysis Afterimage_FIR2.rh -surface self rh -native -fwhm 5 -paradigm ShapeAE_New.par -event-related -polyfit 1 -mcextreg -TR 1.000 -nconditions 8 -force -fsd bold -fir 4 14 I then generated the relevant contrasts, ran the funcroi-config command, and the func-roi-table-sess command to create 14 files for my ROI, each containing the signal value at 14 different time points. i.e. funcroi-table-sess -sf sessid -roi Labels/rh.V1 -c condition1 -map cespct -o ROI/frame0 -frame 0 funcroi-table-sess -sf sessid -roi Labels/rh.V1 -c condition1 -map cespct -o ROI/frame1 -frame 1 . . . funcroi-table-sess -sf sessid -roi Labels/rh.V1 -c condition1 -map cespct -o ROI/frame13 -frame 13 My question is this: To what time point (relative to stimulus onset) does the value in the frame0 file correspond? As I understand it, the first 4 frame values should correspond to activity pre-stimulus. However, this expectation is not corroborated by the timing and pattern of the BOLD response I am observing. I would appreciate any guidance on this issue. Thanks, Cesar Echavarria -- 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>Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> 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.-- Cesar Echavarria Brain & Cognitive Science MIT 2012
-- 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 Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Hi Cesar, you cannot really do the analysis you want to do, it is mathematically impossible. If you do not expect a response from one of the conditions, then you could code it as 0. Alternatively, you can consider both conditions as a single 20 sec event and get the FIR for that event out to 28 sec. If you don't have to have an FIR analysis, you can assume a shape to the HRF and do the usual statistics on it. doug
On 03/05/2013 01:21 PM, Cesar Echavarria wrote:
Does the post-stimulus period have to be as long as 12 seconds? With such a long time window I get the following error when running selxavg3-sess:
XCond = 1.47995e+18 (normalized) ERROR: design is ill-conditioned
To clarify: in our design we have 10 seconds of condition 1 followed immediately after with 10 seconds of condition 2 followed by 10 seconds of fixation. Given, this what would be the limit on how much post-stimulus time we should include in our time window?
Thanks again, Cesar
On Tue, Mar 5, 2013 at 1:00 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
If you presented the stimulus for 10sec, then you should set the time window to include about 12 sec after stimulus offset. If your stimulus is 10 secand you want the time window to start 4 sec prior to onset and go 12 sec after onset, then you will need a time window of 4+10+12=26sec, so it would be --fir 4 22. You have to model the return to baseline even if you are not interested init. Try that and get back to me if it does not work. doug On 03/05/2013 12:43 PM, Cesar Echavarria wrote: Hi Doug, As you can see from the attached image (time course on x-axis, normalized BOLD response on y-axis) the signal peak occurs earlier than expected if I were to consider the first frame to be -4 sec relative to stimulus onset. In our experiment we presented a stimulus for 10 seconds, and we wanted to see the time course of the BOLD response while the stimulus was on. We also wanted to see the response of the aftereffect due to the stimulus separately which is why we are interested only in the 10 seconds the stimulus is on. Thanks, Cesar On Tue, Mar 5, 2013 at 12:27 PM, 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>>> wrote: Hi Cesar, for your case, it would correspond to 4sec prior to stimulus onset (the TR that goes from -4 to -3 sec). What seems to be wrong? The last frame would be the TR that goes from +9sec to +10 sec. Not related to your question, but Is 10 sec post stimulus long enough? doug On 03/05/2013 11:53 AM, Cesar E Echavarria wrote: Hi Freesurfers, I did an FIR analysis to get the BOLD response over time, the following way mkanalysis-sess -analysis Afterimage_FIR2.rh -surface self rh -native -fwhm 5 -paradigm ShapeAE_New.par -event-related -polyfit 1 -mcextreg -TR 1.000 -nconditions 8 -force -fsd bold -fir 4 14 I then generated the relevant contrasts, ran the funcroi-config command, and the func-roi-table-sess command to create 14 files for my ROI, each containing the signal value at 14 different time points. i.e. funcroi-table-sess -sf sessid -roi Labels/rh.V1 -c condition1 -map cespct -o ROI/frame0 -frame 0 funcroi-table-sess -sf sessid -roi Labels/rh.V1 -c condition1 -map cespct -o ROI/frame1 -frame 1 . . . funcroi-table-sess -sf sessid -roi Labels/rh.V1 -c condition1 -map cespct -o ROI/frame13 -frame 13 My question is this: To what time point (relative to stimulus onset) does the value in the frame0 file correspond? As I understand it, the first 4 frame values should correspond to activity pre-stimulus. However, this expectation is not corroborated by the timing and pattern of the BOLD response I am observing. I would appreciate any guidance on this issue. Thanks, Cesar Echavarria -- 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> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ 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. -- Cesar Echavarria Brain & Cognitive Science MIT 2012 -- 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> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/-- Cesar Echavarria Brain & Cognitive Science MIT 2012
Also, did you mean ' fir 4 26' in your previous response? since the TimeWindow parameter should include the 'PreStimulus' time (I just want to double check since this is crucial to my question)
Cesar
On Tue, Mar 5, 2013 at 1:00 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
If you presented the stimulus for 10sec, then you should set the time window to include about 12 sec after stimulus offset. If your stimulus is 10 secand you want the time window to start 4 sec prior to onset and go 12 sec after onset, then you will need a time window of 4+10+12=26sec, so it would be --fir 4 22. You have to model the return to baseline even if you are not interested init. Try that and get back to me if it does not work. doug
On 03/05/2013 12:43 PM, Cesar Echavarria wrote:
Hi Doug,
As you can see from the attached image (time course on x-axis, normalized BOLD response on y-axis) the signal peak occurs earlier than expected if I were to consider the first frame to be -4 sec relative to stimulus onset. In our experiment we presented a stimulus for 10 seconds, and we wanted to see the time course of the BOLD response while the stimulus was on. We also wanted to see the response of the aftereffect due to the stimulus separately which is why we are interested only in the 10 seconds the stimulus is on.
Thanks,
Cesar
On Tue, Mar 5, 2013 at 12:27 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu>> wrote:
Hi Cesar, for your case, it would correspond to 4sec prior to stimulus onset (the TR that goes from -4 to -3 sec). What seems to be wrong? The last frame would be the TR that goes from +9sec to +10 sec. Not related to your question, but Is 10 sec post stimulus long enough? doug On 03/05/2013 11:53 AM, Cesar E Echavarria wrote: Hi Freesurfers, I did an FIR analysis to get the BOLD response over time, the following way mkanalysis-sess -analysis Afterimage_FIR2.rh -surface self rh -native -fwhm 5 -paradigm ShapeAE_New.par -event-related -polyfit 1 -mcextreg -TR 1.000 -nconditions 8 -force -fsd bold -fir 4 14 I then generated the relevant contrasts, ran the funcroi-config command, and the func-roi-table-sess command to create 14 files for my ROI, each containing the signal value at 14 different time points. i.e. funcroi-table-sess -sf sessid -roi Labels/rh.V1 -c condition1 -map cespct -o ROI/frame0 -frame 0 funcroi-table-sess -sf sessid -roi Labels/rh.V1 -c condition1 -map cespct -o ROI/frame1 -frame 1 . . . funcroi-table-sess -sf sessid -roi Labels/rh.V1 -c condition1 -map cespct -o ROI/frame13 -frame 13 My question is this: To what time point (relative to stimulus onset) does the value in the frame0 file correspond? As I understand it, the first 4 frame values should correspond to activity pre-stimulus. However, this expectation is not corroborated by the timing and pattern of the BOLD response I am observing. I would appreciate any guidance on this issue. Thanks, Cesar Echavarria -- 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>Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> 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.-- Cesar Echavarria Brain & Cognitive Science MIT 2012
-- 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 Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
yes, my mistake doug On 03/05/2013 01:30 PM, Cesar Echavarria wrote:
Also, did you mean ' fir 4 26' in your previous response? since the TimeWindow parameter should include the 'PreStimulus' time (I just want to double check since this is crucial to my question)
Cesar
On Tue, Mar 5, 2013 at 1:00 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
If you presented the stimulus for 10sec, then you should set the time window to include about 12 sec after stimulus offset. If your stimulus is 10 secand you want the time window to start 4 sec prior to onset and go 12 sec after onset, then you will need a time window of 4+10+12=26sec, so it would be --fir 4 22. You have to model the return to baseline even if you are not interested init. Try that and get back to me if it does not work. doug On 03/05/2013 12:43 PM, Cesar Echavarria wrote: Hi Doug, As you can see from the attached image (time course on x-axis, normalized BOLD response on y-axis) the signal peak occurs earlier than expected if I were to consider the first frame to be -4 sec relative to stimulus onset. In our experiment we presented a stimulus for 10 seconds, and we wanted to see the time course of the BOLD response while the stimulus was on. We also wanted to see the response of the aftereffect due to the stimulus separately which is why we are interested only in the 10 seconds the stimulus is on. Thanks, Cesar On Tue, Mar 5, 2013 at 12:27 PM, 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>>> wrote: Hi Cesar, for your case, it would correspond to 4sec prior to stimulus onset (the TR that goes from -4 to -3 sec). What seems to be wrong? The last frame would be the TR that goes from +9sec to +10 sec. Not related to your question, but Is 10 sec post stimulus long enough? doug On 03/05/2013 11:53 AM, Cesar E Echavarria wrote: Hi Freesurfers, I did an FIR analysis to get the BOLD response over time, the following way mkanalysis-sess -analysis Afterimage_FIR2.rh -surface self rh -native -fwhm 5 -paradigm ShapeAE_New.par -event-related -polyfit 1 -mcextreg -TR 1.000 -nconditions 8 -force -fsd bold -fir 4 14 I then generated the relevant contrasts, ran the funcroi-config command, and the func-roi-table-sess command to create 14 files for my ROI, each containing the signal value at 14 different time points. i.e. funcroi-table-sess -sf sessid -roi Labels/rh.V1 -c condition1 -map cespct -o ROI/frame0 -frame 0 funcroi-table-sess -sf sessid -roi Labels/rh.V1 -c condition1 -map cespct -o ROI/frame1 -frame 1 . . . funcroi-table-sess -sf sessid -roi Labels/rh.V1 -c condition1 -map cespct -o ROI/frame13 -frame 13 My question is this: To what time point (relative to stimulus onset) does the value in the frame0 file correspond? As I understand it, the first 4 frame values should correspond to activity pre-stimulus. However, this expectation is not corroborated by the timing and pattern of the BOLD response I am observing. I would appreciate any guidance on this issue. Thanks, Cesar Echavarria -- 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> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ 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. -- Cesar Echavarria Brain & Cognitive Science MIT 2012 -- 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> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/-- Cesar Echavarria Brain & Cognitive Science MIT 2012
freesurfer@nmr.mgh.harvard.edu
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Cesar E Echavarria -
Cesar Echavarria -
Douglas N Greve