External Email - Use Caution Dear Dr Greve, Apologize for not providing a clear explanation earlier. The file lh.all.suvr.sm05.proj0.5.nii.gz is the result of combining all SUVR maps, using mri_concat, after projecting them onto the brain surface with mri_vol2surf. I would like to know if it is possible to use mri_glmfit-sim to correct for specific regions of interest (such as lobes) instead of correcting the entire brain. I am using the following command: mri_glmfit-sim --glmdir lh.suvr.glmdir --cache 4 pos --cwp 0.05 --2spaces
When I include the "--annot lobes" option in my command (mri_glmfit-sim --glmdir lh.suvr.glmdir --cache 4 pos --cwp 0.05 --2spaces --annot lobes), the resulting statistical output is similar, but the annotations are replaced with their corresponding lobes. However, p-values are not adjusted for the number of regions of interest specified in the "--annot" option. Thanks again On Wed, Apr 5, 2023 at 10:46 PM Douglas N. Greve <dgr...@mgh.harvard.edu> wrote: > What is h.all.suvr.sm05.proj0.5.nii.gz? Where did it come from? The name > looks like it might be a voxel-wise map, but you say something about ROIs. > mri_glmfit does not correct for multiple comparisons. For ROI-based > analyses, you can use bonferroni or FDR. For maps you can use > mri_glmfit-sim. > > On 4/4/2023 4:53 PM, John Anderson wrote: > > External Email - Use Caution > Hello Freesurfer, > Currently, I am using the Petsurfer manual, which is easily understandable > and clear. Nonetheless, I have a question regarding the "mri_glmfit" step. > As far as I know, this command is used to correct data for multiple > comparisons among all the ROIs in the aparc+aseg.mgz file. Can you please > confirm if my understanding is correct? > > mri_glmfit.bin --y lh.all.suvr.sm05.proj0.5.nii.gz --fsgd 2G0C.fsgd --C > patients_vs_controls.mtx --surf fsaverage lh --cortex --glmdir > lh.patinets_vs_controls > > In particular, I am interested in correcting data across lobes instead of > across all ROIs. I followed the steps mentioned in the FS forum to create > lobes, and I can observe lobe annotations in the wmparc.mgz file. I am > curious to know whether using the "--annot" flag will adjust the p-values > across different lobe ROIs instead of all ROIs in the aparc+aseg.mgz file. > I have attempted this, but it appears to only change the name of the > annotation in the final statistics file, and the p-value remains the same. > Do I need to include any additional arguments in the command? > > Thanks for your help > John > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1IMIzkVyvWy3tORcOQQLF1TtkCCgy_0wbx5w7luRsMMd4lrtHKWxkROwa6M3fRKd0hZt4fVeMfBG1LjhYqHOfUveFSyvnijbaonYjDLyWMgdpt2qe48Ng6BwmAtimyxO1qyHtmGJwfzSFTWUO8WlCkXnqC5JJQZoGt7LytnfJsZxc9fvYAWWhrZnTqVNcYsKV8-g6yJkIGojLVQ9OePmj7YVtMSBuC9B-yQh1WfJ22Y0uaiUIiyjx0NrDG2aEldH0XOJUi1FLPXrCUs9oSp3fBrPl0xB1HGYvq0988wiG4ggtFjQy-sOb0eDErmabJeNR5GKVTJD1qhVbXIW_SGK1Og/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > The information in this e-mail is intended only for the person to whom it > is addressed. If you believe this e-mail was sent to you in error and the > e-mail contains patient information, please contact the Mass General > Brigham Compliance HelpLine at > https://secure-web.cisco.com/1GfMzjyQZs8Re1K1Meh4fVFQOBWZ3sGI6JQ6Yg27rjTb_2XL-Xq9M0s68042r4bT1U9mBl9Ceax-SZohzKmWtx-58MM6FhbsoPzb1l17vIY1-dgwz8Z3x_euf1tLp7DvPHmqjC2qEQ6f3n_XHmV9KqNfEZsNlYfOQhVLpL3VZK7GUc5uD-RF3654z18VETZF-995LwQJbqXR3MOHOr7ngoF0idSgW8ssrAIIoixEFOzd-_UAtNZ26EZn_-uAt39Lw2MZyqYMViDuCQpiCtJ8Wj-gmXmKkgti53E469mg6IGI_xYn50bYRlKSXo4TRwhfj7riR3vQXnBIIg3M7A8B8DQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > < > https://secure-web.cisco.com/1GfMzjyQZs8Re1K1Meh4fVFQOBWZ3sGI6JQ6Yg27rjTb_2XL-Xq9M0s68042r4bT1U9mBl9Ceax-SZohzKmWtx-58MM6FhbsoPzb1l17vIY1-dgwz8Z3x_euf1tLp7DvPHmqjC2qEQ6f3n_XHmV9KqNfEZsNlYfOQhVLpL3VZK7GUc5uD-RF3654z18VETZF-995LwQJbqXR3MOHOr7ngoF0idSgW8ssrAIIoixEFOzd-_UAtNZ26EZn_-uAt39Lw2MZyqYMViDuCQpiCtJ8Wj-gmXmKkgti53E469mg6IGI_xYn50bYRlKSXo4TRwhfj7riR3vQXnBIIg3M7A8B8DQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> > . >
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