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Mar 20, 2017 12:03 AM | Larissa
Comparing ROI timeseries in two conditions
Hi Alfonso,
I have 10 subjects with two resting state conditions each. I want to plot the mean original BOLD timeseries within the significant ROI clusters I get from the 2nd-level seed-to-voxel analysis in REX for both resting state conditions separately for comparison. I understand that REX only displays the timeseries from the first-level analysis. To try this in REX, for Sources I selected 10 subject files from the 1st resting state condition in the ~/results/firstlevel/ANALYSIS_01 folder that were labeled (se_Subject001_Condition001.nii, se_Subject002_Condtion001.nii ..... se_Subject010_Condition001.nii), under ROIs I selected the significant cluster from ~/results/secondlevel/ANALYSIS_01/AllSubjects/rest_condition1(1).rest_condition2(-1)/Putamen_r/sigclusterROI.nii , and when I went to extract the data, nothing was plotted. My rationale was if this worked, I would then select the 10 subjects from Condition 2 from the first-level analysis, extract the mean time series of the significant ROI cluster and have the plots to compare. This did not work.
However, if I select my 10 subjects under Sources from the second-level analysis (irrespective of condition contrast (i.e., the subjects labeled as CON_Subject011_compA001_001.nii, CON_Subject002_compA001_001.nii etc) and keep the ROI cluster selected, hit extract mean, I get the resulting time series plotted for the significant cluster. How can I now extract the mean timeseries for this significant ROI cluster separated by condition?
Any advice?
Larissa
I have 10 subjects with two resting state conditions each. I want to plot the mean original BOLD timeseries within the significant ROI clusters I get from the 2nd-level seed-to-voxel analysis in REX for both resting state conditions separately for comparison. I understand that REX only displays the timeseries from the first-level analysis. To try this in REX, for Sources I selected 10 subject files from the 1st resting state condition in the ~/results/firstlevel/ANALYSIS_01 folder that were labeled (se_Subject001_Condition001.nii, se_Subject002_Condtion001.nii ..... se_Subject010_Condition001.nii), under ROIs I selected the significant cluster from ~/results/secondlevel/ANALYSIS_01/AllSubjects/rest_condition1(1).rest_condition2(-1)/Putamen_r/sigclusterROI.nii , and when I went to extract the data, nothing was plotted. My rationale was if this worked, I would then select the 10 subjects from Condition 2 from the first-level analysis, extract the mean time series of the significant ROI cluster and have the plots to compare. This did not work.
However, if I select my 10 subjects under Sources from the second-level analysis (irrespective of condition contrast (i.e., the subjects labeled as CON_Subject011_compA001_001.nii, CON_Subject002_compA001_001.nii etc) and keep the ROI cluster selected, hit extract mean, I get the resulting time series plotted for the significant cluster. How can I now extract the mean timeseries for this significant ROI cluster separated by condition?
Any advice?
Larissa
Mar 23, 2017 03:03 PM | Alfonso Nieto-Castanon - Boston University
RE: Comparing ROI timeseries in two conditions
Hi Larissa,
What I would suggest just for simplicity would be to export your second-level results mask with your clusters of interest, then re-import that as a new ROI in Setup.ROIs (select the newly created file named something like [yourmaskfile].ROIs.nii) and then re-run Setup and Denoising steps (selecting the do not overwrite option) just to have those new ROIs processed. After this you will have in the conn*/results/preprocessing/ folder your new ROI_Subject*_Condition*.mat files containing the BOLD timeseries (after denoising) within each of your ROIs, including your new clusters.
Hope this helps
Alfonso
Originally posted by Larissa :
What I would suggest just for simplicity would be to export your second-level results mask with your clusters of interest, then re-import that as a new ROI in Setup.ROIs (select the newly created file named something like [yourmaskfile].ROIs.nii) and then re-run Setup and Denoising steps (selecting the do not overwrite option) just to have those new ROIs processed. After this you will have in the conn*/results/preprocessing/ folder your new ROI_Subject*_Condition*.mat files containing the BOLD timeseries (after denoising) within each of your ROIs, including your new clusters.
Hope this helps
Alfonso
Originally posted by Larissa :
Hi Alfonso,
I have 10 subjects with two resting state conditions each. I want to plot the mean original BOLD timeseries within the significant ROI clusters I get from the 2nd-level seed-to-voxel analysis in REX for both resting state conditions separately for comparison. I understand that REX only displays the timeseries from the first-level analysis. To try this in REX, for Sources I selected 10 subject files from the 1st resting state condition in the ~/results/firstlevel/ANALYSIS_01 folder that were labeled (se_Subject001_Condition001.nii, se_Subject002_Condtion001.nii ..... se_Subject010_Condition001.nii), under ROIs I selected the significant cluster from ~/results/secondlevel/ANALYSIS_01/AllSubjects/rest_condition1(1).rest_condition2(-1)/Putamen_r/sigclusterROI.nii , and when I went to extract the data, nothing was plotted. My rationale was if this worked, I would then select the 10 subjects from Condition 2 from the first-level analysis, extract the mean time series of the significant ROI cluster and have the plots to compare. This did not work.
However, if I select my 10 subjects under Sources from the second-level analysis (irrespective of condition contrast (i.e., the subjects labeled as CON_Subject011_compA001_001.nii, CON_Subject002_compA001_001.nii etc) and keep the ROI cluster selected, hit extract mean, I get the resulting time series plotted for the significant cluster. How can I now extract the mean timeseries for this significant ROI cluster separated by condition?
Any advice?
Larissa
I have 10 subjects with two resting state conditions each. I want to plot the mean original BOLD timeseries within the significant ROI clusters I get from the 2nd-level seed-to-voxel analysis in REX for both resting state conditions separately for comparison. I understand that REX only displays the timeseries from the first-level analysis. To try this in REX, for Sources I selected 10 subject files from the 1st resting state condition in the ~/results/firstlevel/ANALYSIS_01 folder that were labeled (se_Subject001_Condition001.nii, se_Subject002_Condtion001.nii ..... se_Subject010_Condition001.nii), under ROIs I selected the significant cluster from ~/results/secondlevel/ANALYSIS_01/AllSubjects/rest_condition1(1).rest_condition2(-1)/Putamen_r/sigclusterROI.nii , and when I went to extract the data, nothing was plotted. My rationale was if this worked, I would then select the 10 subjects from Condition 2 from the first-level analysis, extract the mean time series of the significant ROI cluster and have the plots to compare. This did not work.
However, if I select my 10 subjects under Sources from the second-level analysis (irrespective of condition contrast (i.e., the subjects labeled as CON_Subject011_compA001_001.nii, CON_Subject002_compA001_001.nii etc) and keep the ROI cluster selected, hit extract mean, I get the resulting time series plotted for the significant cluster. How can I now extract the mean timeseries for this significant ROI cluster separated by condition?
Any advice?
Larissa