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help > RE: Single subject pre/post treatment analysis
Jun 29, 2015 01:06 AM | Alfonso Nieto-Castanon - Boston University
RE: Single subject pre/post treatment analysis
Hi Kaitlin,
You could always load these into Matlab using something like:
filename=sprintf('pFDR_corr_Subject1_Condition001vsCondition002_Source%03d.nii',source);
a = spm_vol(filename);
pvalues = spm_read_vols(a);
but if you are mostly interested in displaying these results perhaps the simplest way would be to first threshold these maps, for example by adding in the original code something like the following (within the for loop):
filename=sprintf('pFDR_thresholded_corr_Subject1_Condition001vsCondition002_Source%03d.nii',source);
V=struct('mat',a(1).mat,'dim',a(1).dim,'fname',filename,'pinfo',[1;0;0],'n',[1,1],'dt',[spm_type('uint8') spm_platform('bigend')]);
spm_write_vol(V,double(p<.05));
and then explore them using the following (or your preferred nifti visualizer)
conn_mesh_display(filename,'');
or
conn_mesh_display('',filename);
to view those suprathreshold clusters using a surface-projected view or a standard 3d-volume view, respectively.
Hope this helps
Alfonso
Originally posted by Kaitlin Cassady:
You could always load these into Matlab using something like:
filename=sprintf('pFDR_corr_Subject1_Condition001vsCondition002_Source%03d.nii',source);
a = spm_vol(filename);
pvalues = spm_read_vols(a);
but if you are mostly interested in displaying these results perhaps the simplest way would be to first threshold these maps, for example by adding in the original code something like the following (within the for loop):
filename=sprintf('pFDR_thresholded_corr_Subject1_Condition001vsCondition002_Source%03d.nii',source);
V=struct('mat',a(1).mat,'dim',a(1).dim,'fname',filename,'pinfo',[1;0;0],'n',[1,1],'dt',[spm_type('uint8') spm_platform('bigend')]);
spm_write_vol(V,double(p<.05));
and then explore them using the following (or your preferred nifti visualizer)
conn_mesh_display(filename,'');
or
conn_mesh_display('',filename);
to view those suprathreshold clusters using a surface-projected view or a standard 3d-volume view, respectively.
Hope this helps
Alfonso
Originally posted by Kaitlin Cassady:
Hello!
I am also interested i comparing seed-to-voxel maps between conditions for a single subject. The script that you provided works very well, but I am wondering how to read the contents of the nifti files to examine the p-values of the between-condition comparison?
Thanks!
I am also interested i comparing seed-to-voxel maps between conditions for a single subject. The script that you provided works very well, but I am wondering how to read the contents of the nifti files to examine the p-values of the between-condition comparison?
Thanks!
Threaded View
Title | Author | Date |
---|---|---|
Helen Carlson | Jun 5, 2014 | |
Alfonso Nieto-Castanon | Jun 7, 2014 | |
Batiah Keissar | Nov 19, 2022 | |
Kaitlin Cassady | Jun 26, 2015 | |
Alfonso Nieto-Castanon | Jun 29, 2015 | |
Nabila BRIHMAT | Nov 21, 2020 | |
Nabila BRIHMAT | Nov 30, 2020 | |
Johann Philipp Zöllner | Jan 24, 2016 | |
Alfonso Nieto-Castanon | Jan 25, 2016 | |
Kaitlin Cassady | Jun 30, 2015 | |
Alfonso Nieto-Castanon | Jul 1, 2015 | |
Kaitlin Cassady | Jul 2, 2015 | |
Alfonso Nieto-Castanon | Jul 4, 2015 | |
Kaitlin Cassady | Jul 6, 2015 | |