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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
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 list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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 dgreve@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 CautionHello 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 listFreesurfer@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_0wbx5w7luRsMMd4lr... 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_2X... < https://secure-web.cisco.com/1GfMzjyQZs8Re1K1Meh4fVFQOBWZ3sGI6JQ6Yg27rjTb_2X... .
You can, but you need to give mri_glmfit the specific label to use as a mask (eg, --label or --mask). You can extract labels from an annot with mri_annotation2label. Then mri_glmfit-sim will automatically restrict the correction to that label
On 4/6/2023 10:05 AM, John Anderson wrote:
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 dgreve@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 list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1IMIzkVyvWy3tORcOQQLF1TtkCCgy_0wbx5w7luRsMMd4lrtHKWxkROwa6M3fRKd0hZt4fVeMfBG1LjhYqHOfUveFSyvnijbaonYjDLyWMgdpt2qe48Ng6BwmAtimyxO1qyHtmGJwfzSFTWUO8WlCkXnqC5JJQZoGt7LytnfJsZxc9fvYAWWhrZnTqVNcYsKV8-g6yJkIGojLVQ9OePmj7YVtMSBuC9B-yQh1WfJ22Y0uaiUIiyjx0NrDG2aEldH0XOJUi1FLPXrCUs9oSp3fBrPl0xB1HGYvq0988wiG4ggtFjQy-sOb0eDErmabJeNR5GKVTJD1qhVbXIW_SGK1Og/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://www.massgeneralbrigham.org/complianceline <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> <*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://www.massgeneralbrigham.org/complianceline <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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