sdm-help-list > one region, rather than the whole brain
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May 12, 2014 07:05 AM | Nobody
one region, rather than the whole brain
Hi everyone,
I have a general question on meta analysis on neuroimaging studies. If my interest is in differentiation within one region, can we input coordinates of just one region across studies? Can SDM do it with a mask of this region? Just like ROI?
Thanks in advance.
Qian
I have a general question on meta analysis on neuroimaging studies. If my interest is in differentiation within one region, can we input coordinates of just one region across studies? Can SDM do it with a mask of this region? Just like ROI?
Thanks in advance.
Qian
May 13, 2014 12:05 PM | Nobody
RE: one region, rather than the whole brain
Dear Qian, SDM limits its meta-analytic calculations to the voxels
within a mask. Default SDM masks are generic (e.g. gray matter),
but you can use your own mask. To this end, preprocessing must be
called as a command (e.g. using the bottom command line input)
rather than pressing the button.
First copy your mask to the share directory, and change its name so that it begins with "mask_" (for example "mask_myROI.nii.gz"). Afterwards, go to SDM and type the pp command:
pp correlation_template, degree_of_anisotropy, isotropic_fwhm, mask, number_of_randomizations
where correlation_template may be e.g. "gray_matter" (or any other "cor_" file from the share directory), degree_of_anisotropy may be 1, isotropic_fwhm may be 20, and mask may be the name of your mask. For example:
pp gray_matter, 1, 20, myROI, 20
First copy your mask to the share directory, and change its name so that it begins with "mask_" (for example "mask_myROI.nii.gz"). Afterwards, go to SDM and type the pp command:
pp correlation_template, degree_of_anisotropy, isotropic_fwhm, mask, number_of_randomizations
where correlation_template may be e.g. "gray_matter" (or any other "cor_" file from the share directory), degree_of_anisotropy may be 1, isotropic_fwhm may be 20, and mask may be the name of your mask. For example:
pp gray_matter, 1, 20, myROI, 20
May 14, 2014 11:05 AM | Nobody
RE: one region, rather than the whole brain
Hi,
Thanks for the reply and information.
I am interested in task based activation, rather than structural studies such as VBM or DTI. Can I still do the analysis on one region using SDM?
Best,
Qian
Thanks for the reply and information.
I am interested in task based activation, rather than structural studies such as VBM or DTI. Can I still do the analysis on one region using SDM?
Best,
Qian
Dec 7, 2015 04:12 PM | Nobody
RE: one region, rather than the whole brain
Hello! I have a similar question. I am doing a functional MRI meta
analysis and would like to do a ROI analysis, ignoring other areas.
I looked through the tutorial and the manual but could not find the
description on how to perform this analysis. Do I specify ROI
analysis starting from preprocessing? If so, how to do
it?Suggestions are much appreciated.
Thank you
Peggy
Thank you
Peggy
Dec 11, 2015 11:12 AM | Nobody
RE: one region, rather than the whole brain
Dear Peggy,
you should first create a standard, binary mask, name it "mask_roi.nii.gz", and copy it to the sdm share directory. Afterwards, start the pre-processing selecting this mask.
Best,
Joaquim
you should first create a standard, binary mask, name it "mask_roi.nii.gz", and copy it to the sdm share directory. Afterwards, start the pre-processing selecting this mask.
Best,
Joaquim
Dec 11, 2015 04:12 PM | Nobody
RE: one region, rather than the whole brain
Thank you very much! -Peggy
Mar 13, 2017 06:03 PM | Benjamin Smith - Ben Smith
RE: one region, rather than the whole brain
Thank you for your comment. I wonder if this method is applied to
analyze just a single portion of the brain, would that justify a
higher alpha level than the default p=0.005? Or would using a
smaller mask already 'automatically' relax the significance level
an appropriate amount?