Thank you for replying.
Sorry for this basic question,how can I obtain peak voxel coordiante?
Secodly ,since the "extract ROI" signal yields the average timeseries of that ROI( am I wrong?) shouldn't I apply a threshold as I need the peak voxel time series?
Many thanks in advance.
Generally, we can get the peak coordinate in T map. You may open this map in "viewer" and use the "CI Report" function, and peak value will reported in command window of MATLAB.
As the threshold, you can input the radius when define ROI, and we often use 6mm.
Dear ZHANG and Dear LiXun
Thank you so much for your answers.I tried setting the cluster size before using C.I Report. However,I faced "There is no Cluster !". How should I set the "cluster size" , "volume size" and "rmm" values? I am working on a 3*3*3 functional image and I would like to extract the time series from 5 main regions (i.e,PCC,MPFC...).
Many thanks in advance.
basically, we use overlay function to put an overlay on the underlay image. The overlay image can be a t map, the underlay can be T1 template such as ch2 image. Then we apply a threshold of, for example, p< 0.05 and cluster size > 40 to the overlay image to get "clusters", from which we can get the peak coordinates.
In your case, I think you only want to extract time series from PCC, MPFC, ... i.e., the main nodes of the DMN, don't you? If so, you may refer to classicle DMN paper to find out the peak coordinates from the literature.
Dear Han
Thank you for your detailed answer,it really helped. I have one more question if thats ok...considering the cluster size what does the set volume (mm^3) mean?as my voxel size is 3*3*3 I set it to 27 but automatically it changes to 1080!
I really appreciate your help.
I also tried extracting the timecourses of a predefined ROI. However,I've got "Extracting ROI time courses over, elapsed time: 0.0156001 seconds." in the command window and nothing was showed up in the output directory?
Is there a tutorial available?
Many thanks in advance.
please specify an output directory in the GUI "Extract ROI time course", there will be four files generated in that directory, you can use *ROISignals_*.txt as the mean time course of this ROI.
in your case one voxel's size is 3*3*3 = 27 mm^3, in "cluster size" you should set a number which indicates "how many voxels in a cluster" if this cluster is bigger enough to be displayed in REST sliceviewer (i.e., exceed the "extend" threshold). if you set it as 27, it means only clusters have 27 voxels or more can then be displayed. The cluster volume is then 27*27 = 729, not 1080, please check.
Yes you are right, the first thing is to get a thresholded map using a proper threshold to your resultant map (i.e., t map). By doing so, you will get several clusters, in each of these clusters you will find the peak coordinates. If you use REST toolkits, it's easy to do those steps using REST sliceviewer.
Submitted by LiXun on Tue, 11/25/2014 - 14:11 Permalink
Re: peak voxel time series
You can use peak voxel coordinate as the center to create a sperical ROI, and extract time series by "Extract ROI signals" in rest.
Submitted by ma.shalchy on Tue, 11/25/2014 - 16:31 Permalink
Re: peak voxel time series
Dear LiXun
Thank you for replying.
Sorry for this basic question,how can I obtain peak voxel coordiante?
Secodly ,since the "extract ROI" signal yields the average timeseries of that ROI( am I wrong?) shouldn't I apply a threshold as I need the peak voxel time series?
Many thanks in advance.
Best,
mahsa
Submitted by LiXun on Wed, 11/26/2014 - 16:10 Permalink
Re: peak voxel time series
Generally, we can get the peak coordinate in T map. You may open this map in "viewer" and use the "CI Report" function, and peak value will reported in command window of MATLAB.
As the threshold, you can input the radius when define ROI, and we often use 6mm.
Submitted by ma.shalchy on Sat, 11/29/2014 - 03:40 Permalink
Re: peak voxel time series
Dear ZHANG and Dear LiXun
Thank you so much for your answers.I tried setting the cluster size before using C.I Report. However,I faced "There is no Cluster !". How should I set the "cluster size" , "volume size" and "rmm" values? I am working on a 3*3*3 functional image and I would like to extract the time series from 5 main regions (i.e,PCC,MPFC...).
Many thanks in advance.
Kind Regards,
mahsa
Submitted by ZHANG_RESTadmin on Sat, 11/29/2014 - 13:35 Permalink
Re: peak voxel time series
basically, we use overlay function to put an overlay on the underlay image. The overlay image can be a t map, the underlay can be T1 template such as ch2 image. Then we apply a threshold of, for example, p< 0.05 and cluster size > 40 to the overlay image to get "clusters", from which we can get the peak coordinates.
In your case, I think you only want to extract time series from PCC, MPFC, ... i.e., the main nodes of the DMN, don't you? If so, you may refer to classicle DMN paper to find out the peak coordinates from the literature.
Han
Submitted by ma.shalchy on Sun, 11/30/2014 - 05:25 Permalink
Re: peak voxel time series
Dear Han
Thank you for your detailed answer,it really helped. I have one more question if thats ok...considering the cluster size what does the set volume (mm^3) mean?as my voxel size is 3*3*3 I set it to 27 but automatically it changes to 1080!
I really appreciate your help.
Best,
mahsa
Submitted by ma.shalchy on Mon, 12/01/2014 - 12:57 Permalink
Re: peak voxel time series
I also tried extracting the timecourses of a predefined ROI. However,I've got "Extracting ROI time courses over, elapsed time: 0.0156001 seconds." in the command window and nothing was showed up in the output directory?
Is there a tutorial available?
Many thanks in advance.
Submitted by ZHANG_RESTadmin on Sun, 12/07/2014 - 14:25 Permalink
Re: peak voxel time series
please specify an output directory in the GUI "Extract ROI time course", there will be four files generated in that directory, you can use *ROISignals_*.txt as the mean time course of this ROI.
Submitted by ZHANG_RESTadmin on Sun, 12/07/2014 - 14:22 Permalink
Re: peak voxel time series
in your case one voxel's size is 3*3*3 = 27 mm^3, in "cluster size" you should set a number which indicates "how many voxels in a cluster" if this cluster is bigger enough to be displayed in REST sliceviewer (i.e., exceed the "extend" threshold). if you set it as 27, it means only clusters have 27 voxels or more can then be displayed. The cluster volume is then 27*27 = 729, not 1080, please check.
Submitted by ZHANG_RESTadmin on Fri, 11/28/2014 - 17:53 Permalink
Re: peak voxel time series
Dear Mahsa,
Yes you are right, the first thing is to get a thresholded map using a proper threshold to your resultant map (i.e., t map). By doing so, you will get several clusters, in each of these clusters you will find the peak coordinates. If you use REST toolkits, it's easy to do those steps using REST sliceviewer.