Hello FreeSurfers,
I want to compare cortical thickness differences between my two groups. Is this the correct pipeline?
I ran make_average_subject on each group.
To get the study thickness file in control space, I did this: mri_surf2surf --srcsubject study --srcsurfval study/surf/lh.thickness --trgsubject control --trgsurfval control/surf/study.thickness.mgh --hemi lh
And then to calculate the differences, I used: mris_thickness_diff -out diff.mgh control/surf/pial control/surf/lh.thickness control/surf/pial control/surf/study.thickness.mgh. Is this the right way to do this? mris_thickness_diff says it should only be used on the same subject. mris_diff says it is still being tested. I also see mris_thickness_comparison. Which command is the best to use to get a thickness difference map?
Thank you very much, Jeff Sadino
Hi Jeff,
I think you want to use Doug's tools for this (mri_glm and such). He'll probably comment in an hour or two
cheers Bruce
On Mon, 13 Feb 2012, Jeff Sadino wrote:
Hello FreeSurfers, I want to compare cortical thickness differences between my two groups. Is this the correct pipeline?
I ran make_average_subject on each group.
To get the study thickness file in control space, I did this: mri_surf2surf --srcsubject study --srcsurfval study/surf/lh.thickness --trgsubject control --trgsurfval control/surf/study.thickness.mgh --hemi lh
And then to calculate the differences, I used: mris_thickness_diff -out diff.mgh control/surf/pial control/surf/lh.thickness control/surf/pial control/surf/study.thickness.mgh. Is this the right way to do this? mris_thickness_diff says it should only be used on the same subject. mris_diff says it is still being tested. I also see mris_thickness_comparison. Which command is the best to use to get a thickness difference map?
Thank you very much, Jeff Sadino
Hi Jeff, you should use mris_preproc to stack the subjects into one file, mri_surf2surf to smooth them, and mri_glmfit to analyze them (including computing the difference between groups and other stats). See the group tutorial on the web page. You could probably do what you are suggesting, but it takes you off the usual pipeline and would be a dead end in the case that you wanted to take the next step such as computing p-values.
doug
On 2/14/12 9:15 AM, Bruce Fischl wrote:
Hi Jeff,
I think you want to use Doug's tools for this (mri_glm and such). He'll probably comment in an hour or two
cheers Bruce
On Mon, 13 Feb 2012, Jeff Sadino wrote:
Hello FreeSurfers, I want to compare cortical thickness differences between my two groups. Is this the correct pipeline?
I ran make_average_subject on each group.
To get the study thickness file in control space, I did this: mri_surf2surf --srcsubject study --srcsurfval study/surf/lh.thickness --trgsubject control --trgsurfval control/surf/study.thickness.mgh --hemi lh
And then to calculate the differences, I used: mris_thickness_diff -out diff.mgh control/surf/pial control/surf/lh.thickness control/surf/pial control/surf/study.thickness.mgh. Is this the right way to do this? mris_thickness_diff says it should only be used on the same subject. mris_diff says it is still being tested. I also see mris_thickness_comparison. Which command is the best to use to get a thickness difference map?
Thank you very much, Jeff Sadino
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Freesurfers,
this question may be naive - I somewhat new to freesurfer. What is the difference between analyzing data with QDEC or just using aparc-aseg.txt values in other statistical program (besides being able to "visualize" the results).
Many thanks Alfredo Damasceno
Hi Alfredo,
the stats files are summary measures over the ROIs, whereas QDEC lets you make statistical maps and obtain p-values for every point in the cortex.
cheers Bruce
On Thu, 3 May 2012, Alfredo Damasceno wrote:
Dear Freesurfers,
this question may be naive - I somewhat new to freesurfer. What is the difference between analyzing data with QDEC or just using aparc-aseg.txt values in other statistical program (besides being able to "visualize" the results).
Many thanks Alfredo Damasceno
Hi Jeff, make_average_subject is just if you want to visualize results on a surface presenting the average of your own subjects, rather than using the provided 'fsaverage'. It is not necessary (and not related) to performing group statistical comparisons per se.
You can use the 'qdec' utility to do compute maps of groupwise statisical differences on the surface, after first running recon-all with the -qcache flag.
cheers, -MH
On Mon, 2012-02-13 at 20:06 -1000, Jeff Sadino wrote:
Hello FreeSurfers,
I want to compare cortical thickness differences between my two groups. Is this the correct pipeline?
I ran make_average_subject on each group.
To get the study thickness file in control space, I did this: mri_surf2surf --srcsubject study --srcsurfval study/surf/lh.thickness --trgsubject control --trgsurfval control/surf/study.thickness.mgh -- hemi lh
And then to calculate the differences, I used: mris_thickness_diff - out diff.mgh control/surf/pial control/surf/lh.thickness control/surf/pial control/surf/study.thickness.mgh. Is this the right way to do this? mris_thickness_diff says it should only be used on the same subject. mris_diff says it is still being tested. I also see mris_thickness_comparison. Which command is the best to use to get a thickness difference map?
Thank you very much, Jeff Sadino _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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