Hi list,
I have resolved my issue on the previous point 2 by downloading matlab file on: https://sites.google.com/site/kittipat/mvpa-for-brain- fmri/convert_matlab_nifti
after the command that you suggest: fdrthresh = fast_fdrthresh(p,0.05); the script produce p=0.053
Therefore, coming back to my answer I guess that no setting of the FDR threshold to 0.05/3 is requested in order to correct for multiple comparison (right and left hemispheres + subcortical). Is it correct?
On the previous point 4 my answer remains open. I have used this command line:
mri_surfcluster --in sig.nii.gz --hemi rh --sign abs --no-adjust --fdr 0.05
--
minarea 5 --sum summaryfile --subject fsaverage --annot aparc
but I have difficulty to undestand which is the option to visualize the map corrected by mri_surfcluster. Additionally, from --help I do not understand the use of --ocn and --cst options.
Best regards,
Stefano
----Messaggio originale---- Da: stdp82@virgilio.it Data: 7-gen-2016 15.40 A: freesurfer@nmr.mgh.harvard.edu Ogg: [Freesurfer] R: Re: FDR correction
Thanks.
- on question 2:
I have run rh = MRIread('sig.mgh'); but this error occur Undefined function 'MRIread' for input arguments of type 'char'. no help is permitted on MRIread
-on question 3: I'm using this command line to visualize the map describing the functional connectivity form seed to cortex
tksurfer fsaverage rh inflated -aparc -overlay R_seed/my-glm.wls/group. diff/sig.nii.gz -fminmax 1.3 3 tksurfer fsaverage lh inflated -aparc -overlay L_seed/my-glm.wls/group. diff/sig.nii.gz -fminmax 1.3 3
in this way I visualize correctly for right and left hemisphere the connectivity from ipsilateral seed. If I would visualize the the connectivity from contralateral seed, how can I do?
If I use tksurfer fsaverage lh inflated -aparc -overlay R_seed/my-glm.wls/group. diff/sig.nii.gz -fminmax 1.3 3 tksurfer fsaverage rh inflated -aparc -overlay L_seed/my-glm.wls/group. diff/sig.nii.gz -fminmax 1.3 3t
-on question 4: I have resolved with this command line: mri_surfcluster --in sig.nii.gz --hemi rh --sign abs --no-adjust --fdr 0.05
--
minarea 5 --sum summaryfile --subject fsaverage --annot aparc
but I have difficulty to undestand which is the option to visualize the map corrected by mri_surfcluster. Additionally, from --help I do not understand the use of --ocn and --cst options.
Best regards,
Stefano
----Messaggio originale---- Da: greve@nmr.mgh.harvard.edu Data: 7-gen-2016 0.34 A: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] FDR correction
On 01/06/2016 11:00 AM, stdp82@virgilio.it wrote:
Hi list,
I would like to ask you a number of questions regarding the FDR which is performed following seed-based fcMRI using FS-FAST. 1-In the previous mail you have suggested me to use mir_fdr command line (version 6.0). Because I have some problem with new version license (as reported in previous mail) and, overall I have run my data using version 5.3, I would ask you whether FDR integrated in tksurfer (version 5.3) is however reliable as the FDR included in 6.0?
Yes, they call the same code.
2-Becouse the FDR analysis was performed separately for the right and left hemispheres and the subcortical structures, should I set the FDR threshold to 0.05/3 in order to correct for multiple comparison? (I have one group)
I'm not sure. You can try to run both hemispheres in matlab, somethiing like lh = MRIread('sig.lh.mgh'); lhp = 10^-abs(lh.vol); rh = MRIread('sig.rh.mgh'); rlhp = 10^-abs(rh.vol);
p = [lhp rhp]; fdrthresh = fast_fdrthresh(p,fdr);
3- Is easy for me to follow the guidelines and visualize the cortical areas which are functionally connected with the omolateral seed. How can I do to visualize also the the cortical areas which are functionally connected with the controlateral seed? If change only the rh/lh in command line the visualization of the results is wrong.
I don't understand.
4- I'd like to perform mri_surfcluster on a group to eliminate cluster < 5 voxels from sig.nii.gz after FDR correction. I'm running mri_surfcluster --in sig.nii.gz --hemi rh --sign abs --fdr 0.05 --minarea 5 --sum summaryfile --ocn ocnid but --subject ... must be included. How should do I do? I would like to run my analysis on group results, not on a single subject.
If this is from a group analysis, the subject is probablly fsaverage
Thanks for your work. Regards,
Stefano
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