Hi,
I was wondering if we can compare "functional connectivity" between blocks within a run as we do for BOLD signal using freesurfer. Current documentation of freesurfer is for resting state and does not consider conditions that experiment is Blocked Design.
Similar question has been asked previous but nobody answered (see the link below) https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-June/024394.html
Regards
Hi Shahin, you can do seed-based analysis. In principle you can do this with task data, you just need to adjust your conclusions accordingly. There is no easy to way to only do the analysis on the resting epochs of a blocked design, if that is what you mean. doug
On 10/24/2012 12:55 AM, SHAHIN NASR wrote:
Hi,
I was wondering if we can compare "functional connectivity" between blocks within a run as we do for BOLD signal using freesurfer. Current documentation of freesurfer is for resting state and does not consider conditions that experiment is Blocked Design.
Similar question has been asked previous but nobody answered (see the link below) https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-June/024394.html
Regards
-- Shahin Nasr
PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School
Thanks doug But I am not sure if it was the answer. To be more specific, my subjects did two different tasks within one fmri run. I want to see their functional connectivity during task 1 and task 2 separately.
If it was resting state, I didn't need to separate my data and a simple fcseed-config like below was enough:
fcseed-config -roi Labels/rh.V1 -fcname mean.R_V1.dat -fsd rest -mean -cfg CFG_Files/mean.R_V1.config
But now, I don't know how to modify my fcseed-config to say I have had two conditions (task) within one run and I need to measure the seed for each task separately.
On Wed, Oct 24, 2012 at 1:00 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
Hi Shahin, you can do seed-based analysis. In principle you can do this with task data, you just need to adjust your conclusions accordingly. There is no easy to way to only do the analysis on the resting epochs of a blocked design, if that is what you mean. doug
On 10/24/2012 12:55 AM, SHAHIN NASR wrote:
Hi,
I was wondering if we can compare "functional connectivity" between blocks within a run as we do for BOLD signal using freesurfer. Current documentation of freesurfer is for resting state and does not consider conditions that experiment is Blocked Design.
Similar question has been asked previous but nobody answered (see the link below) https://mail.nmr.mgh.harvard.**edu/pipermail/freesurfer/2012-** June/024394.htmlhttps://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-June/024394.html
Regards
-- Shahin Nasr
PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School
-- 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
Sorry, this type of analysis is not possible with FSFAST. You could possibly create a new functional volume by extracting the relevant frames for a condition, then run the functional connectivity on that. doug
On 10/24/2012 01:23 PM, SHAHIN NASR wrote:
Thanks doug But I am not sure if it was the answer. To be more specific, my subjects did two different tasks within one fmri run. I want to see their functional connectivity during task 1 and task 2 separately.
If it was resting state, I didn't need to separate my data and a simple fcseed-config like below was enough:
fcseed-config -roi Labels/rh.V1 -fcname mean.R_V1.dat -fsd rest -mean -cfg CFG_Files/mean.R_V1.config
But now, I don't know how to modify my fcseed-config to say I have had two conditions (task) within one run and I need to measure the seed for each task separately.
On Wed, Oct 24, 2012 at 1:00 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Hi Shahin, you can do seed-based analysis. In principle you can do this with task data, you just need to adjust your conclusions accordingly. There is no easy to way to only do the analysis on the resting epochs of a blocked design, if that is what you mean. doug On 10/24/2012 12:55 AM, SHAHIN NASR wrote: Hi, I was wondering if we can compare "functional connectivity" between blocks within a run as we do for BOLD signal using freesurfer. Current documentation of freesurfer is for resting state and does not consider conditions that experiment is Blocked Design. Similar question has been asked previous but nobody answered (see the link below) https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-June/024394.html Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School -- 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>-- Shahin Nasr
PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School
freesurfer@nmr.mgh.harvard.edu
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Douglas N Greve -
SHAHIN NASR