help > Single subject analysis
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Nov 13, 2014 09:11 AM | Conny McCormick
Single subject analysis
Hello,
I would like to perform a single subject analysis with conn. I know that it is possible to visualize the ROI-voxel connectivity in a single subject but no nifti images are stored. Is there a way of extracting the correlation information for single subjects in an image format?
Cheers,
Conny
I would like to perform a single subject analysis with conn. I know that it is possible to visualize the ROI-voxel connectivity in a single subject but no nifti images are stored. Is there a way of extracting the correlation information for single subjects in an image format?
Cheers,
Conny
Nov 14, 2014 12:11 AM | Alfonso Nieto-Castanon - Boston University
RE: Single subject analysis
Hi Conny,
The files named "BETA_Subject#_Condition#_Source#.nii" in the conn*/results/firstlevel/ANALYSIS_01/ folder contain the Fisher-transformed correlation values between each seed/source and the rest of the brain (for each subject, condition, and seed/source). You can also select the "Create seed-to-voxel first-level r-maps/p-maps/FDR-p-maps" options in Setup.Options if you want the corresponding additional image files to be created during the first-level analysis step. Let me know if this is what you were looking for.
Best
Alfonso
Originally posted by Conny McCormick:
The files named "BETA_Subject#_Condition#_Source#.nii" in the conn*/results/firstlevel/ANALYSIS_01/ folder contain the Fisher-transformed correlation values between each seed/source and the rest of the brain (for each subject, condition, and seed/source). You can also select the "Create seed-to-voxel first-level r-maps/p-maps/FDR-p-maps" options in Setup.Options if you want the corresponding additional image files to be created during the first-level analysis step. Let me know if this is what you were looking for.
Best
Alfonso
Originally posted by Conny McCormick:
Hello,
I would like to perform a single subject analysis with conn. I know that it is possible to visualize the ROI-voxel connectivity in a single subject but no nifti images are stored. Is there a way of extracting the correlation information for single subjects in an image format?
Cheers,
Conny
I would like to perform a single subject analysis with conn. I know that it is possible to visualize the ROI-voxel connectivity in a single subject but no nifti images are stored. Is there a way of extracting the correlation information for single subjects in an image format?
Cheers,
Conny
Nov 14, 2014 07:11 PM | Conny McCormick
RE: Single subject analysis
Dear Alfonso,
Thanks for the fast reply. Yes, that's what I am looking for but unfortunately, these files are not created if you only have one subject in your set up file. Is there a chance of creating these files for one subject only?
Thanks,
Conny
Thanks for the fast reply. Yes, that's what I am looking for but unfortunately, these files are not created if you only have one subject in your set up file. Is there a chance of creating these files for one subject only?
Thanks,
Conny
Nov 14, 2014 08:11 PM | fred Sampedro
RE: Single subject analysis
Hi Alfonso,
Thanks a lot, that was useful to me too. By the way, how can I add that condition within a batch_conn script? e.g. "batch.Setup.Options.computeR??? = 1"
Thanks a lot in advance.
Fred
Thanks a lot, that was useful to me too. By the way, how can I add that condition within a batch_conn script? e.g. "batch.Setup.Options.computeR??? = 1"
Thanks a lot in advance.
Fred
Nov 15, 2014 12:11 AM | Alfonso Nieto-Castanon - Boston University
RE: Single subject analysis
Dear Conny,
Those files should be created during the first-level analysis step (when pressing Done on the first-level analyses tab), irrespective of the number of subjects in your analyses (the analyses that cannot be performed with only one subject are all of those in the second-level results tab, which involve population-level inferences). Could you please check whether when running your first-level analyses you get any error message that may indicate why these files are not being created?
Thanks
Alfonso
Originally posted by Conny McCormick:
Those files should be created during the first-level analysis step (when pressing Done on the first-level analyses tab), irrespective of the number of subjects in your analyses (the analyses that cannot be performed with only one subject are all of those in the second-level results tab, which involve population-level inferences). Could you please check whether when running your first-level analyses you get any error message that may indicate why these files are not being created?
Thanks
Alfonso
Originally posted by Conny McCormick:
Dear Alfonso,
Thanks for the fast reply. Yes, that's what I am looking for but unfortunately, these files are not created if you only have one subject in your set up file. Is there a chance of creating these files for one subject only?
Thanks,
Conny
Thanks for the fast reply. Yes, that's what I am looking for but unfortunately, these files are not created if you only have one subject in your set up file. Is there a chance of creating these files for one subject only?
Thanks,
Conny
Nov 15, 2014 12:11 AM | Alfonso Nieto-Castanon - Boston University
RE: Single subject analysis
Hi Fred,
The field in question is batch.Setup.outputfiles. This is a six-value vector with 1/0's indicating which of the 6 types of files you want created (e.g. to create seed-to-voxel r maps set the third value to 1, e.g. batch.Setup.outputfiles=[0 0 1 0 0 0]). Please see help batch or the batch manual for some additional info.
Hope this helps
Alfonso
Originally posted by fred Sampedro:
The field in question is batch.Setup.outputfiles. This is a six-value vector with 1/0's indicating which of the 6 types of files you want created (e.g. to create seed-to-voxel r maps set the third value to 1, e.g. batch.Setup.outputfiles=[0 0 1 0 0 0]). Please see help batch or the batch manual for some additional info.
Hope this helps
Alfonso
Originally posted by fred Sampedro:
Hi Alfonso,
Thanks a lot, that was useful to me too. By the way, how can I add that condition within a batch_conn script? e.g. "batch.Setup.Options.computeR??? = 1"
Thanks a lot in advance.
Fred
Thanks a lot, that was useful to me too. By the way, how can I add that condition within a batch_conn script? e.g. "batch.Setup.Options.computeR??? = 1"
Thanks a lot in advance.
Fred
Nov 17, 2014 12:11 PM | Conny McCormick
RE: Single subject analysis
Dear Alfonso,
Thanks a lot for your response! It's now running fine.
Cheers,
Conny
Thanks a lot for your response! It's now running fine.
Cheers,
Conny
Jan 22, 2016 07:01 PM | Johann Philipp Zöllner - Goethe University Frankfurt
RE: Single subject analysis
Dear all,
Is there a way to display first level connectivity maps analogous to the way second level results can be displayed by the "results explorer" of the conn toolbox? I am simply looking for a way to render first level connectivity analyses on a surface brain map. Going through Mricon, the BETA.../conn... images seem rather different from within conn. I was wondering what the thresholding is for the BETA... and corr... Nifit-images that are produced by conn during the first level analysis?
Thank you!
Johann Philipp
Is there a way to display first level connectivity maps analogous to the way second level results can be displayed by the "results explorer" of the conn toolbox? I am simply looking for a way to render first level connectivity analyses on a surface brain map. Going through Mricon, the BETA.../conn... images seem rather different from within conn. I was wondering what the thresholding is for the BETA... and corr... Nifit-images that are produced by conn during the first level analysis?
Thank you!
Johann Philipp
Jun 22, 2017 10:06 PM | Stephen L. - Coma Science Group, GIGA-Consciousness, Hospital & University of Liege
RE: Single subject analysis
To get something similar to CONN's first-level previsualization in
a nifti mask: get the BETA*.nii file as pointed by Alfonso, then
use SPM ImageCalc (or something similar) to filter the voxels. Use
two filters:
1. generate positive mask: use equation (i1.*(i1>0.25)) to get the positive thresholded mask (with similar threshold as CONN, can Alfonso confirm if this is how CONN calculates the thresholded map?)
2. generate the negative mask: use equation (i1.*(i1<0.25))
Bonus: if you have a viewer that supports a bidirectional color scheme (with positive and negative colors), then you can generate one combined mask with one equation: (i1.*(abs(i1)>0.25))
Then you can use these two masks as overlays on your subject's normalized structural image in your favorite nifti viewer.
But it would be great to have this implemented in CONN directly! We also often want to explore (and sometimes even publish) 1st-level results. Isn't it possible to port the 2nd-level visualizations on 1st-level? At least the brain surface viewer? That would be awesome!
1. generate positive mask: use equation (i1.*(i1>0.25)) to get the positive thresholded mask (with similar threshold as CONN, can Alfonso confirm if this is how CONN calculates the thresholded map?)
2. generate the negative mask: use equation (i1.*(i1<0.25))
Bonus: if you have a viewer that supports a bidirectional color scheme (with positive and negative colors), then you can generate one combined mask with one equation: (i1.*(abs(i1)>0.25))
Then you can use these two masks as overlays on your subject's normalized structural image in your favorite nifti viewer.
But it would be great to have this implemented in CONN directly! We also often want to explore (and sometimes even publish) 1st-level results. Isn't it possible to port the 2nd-level visualizations on 1st-level? At least the brain surface viewer? That would be awesome!
Dec 18, 2017 01:12 PM | Kasia Siuda - Institut du Cerveau et de la Moelle Epiniere
RE: Single subject analysis
Dear Steven,
According to what Alfonso wrote, :"The files named "BETA_Subject#_Condition#_Source#.nii" (...) contain the Fisher-transformed correlation values between each seed/source and the rest of the brain (for each subject, condition, and seed/source).". I was wondering why would you suggest thresholding the results on Fisher transformed r of 0.25? Shouldn't we threshold it by the p-value (FDR corrected) to take under account the significance of correlation in each voxel?
Thanks! Kasia
According to what Alfonso wrote, :"The files named "BETA_Subject#_Condition#_Source#.nii" (...) contain the Fisher-transformed correlation values between each seed/source and the rest of the brain (for each subject, condition, and seed/source).". I was wondering why would you suggest thresholding the results on Fisher transformed r of 0.25? Shouldn't we threshold it by the p-value (FDR corrected) to take under account the significance of correlation in each voxel?
Thanks! Kasia
Jan 8, 2018 12:01 PM | Stephen L. - Coma Science Group, GIGA-Consciousness, Hospital & University of Liege
RE: Single subject analysis
Dear Katarzyna,
Using the corrected p-value would indeed be better, but I think CONN by default simply threshold with an absolute value (as shown in the GUI, if you hover the mouse on the 1st-level previsualization there is a "0.1" or "0.25" value appearing, which you can modify).
But if you have a script to threshold based on p-value I guess it would be better :-)
Using the corrected p-value would indeed be better, but I think CONN by default simply threshold with an absolute value (as shown in the GUI, if you hover the mouse on the 1st-level previsualization there is a "0.1" or "0.25" value appearing, which you can modify).
But if you have a script to threshold based on p-value I guess it would be better :-)