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Hi experts,
I looked at association between LGI and a behavioural scale on QDEC. after the analysis, to plot the significant clusters/ blobs, I wanted to export LGI values for each subject from each significant blob and based on instructions in previous archives I ran the following command line:
mri_glmfit-sim –glmdir (qdec output directory) --cache 1.3 abs which generated a "cache.th13.abs.y.ocn.dat" file. This file contains 3 columns and 36 rows. I'm assuming the values in the three columns correspond to LGI values for each significant blob for each subject? (I had 3 significant blobs and 36 participants)
Will you please confirm I am doing (and interpreting) this correctly?
Thanks so much,
Avi
Each row is a subject and each column is a cluster. BTW, a threshold of 1.3 is way too low for lGI. If you want to use a threshold that low, you should use permutation instead of monte carlo (in general, permutation is better, but certainly for lGI).
On 8/9/18 1:39 PM, Avi Gharehgazlou wrote:
External Email - Use Caution
Hi experts,
I looked at association between LGI and a behavioural scale on QDEC. after the analysis, to plot the significant clusters/ blobs, I wanted to export LGI values for each subject from each significant blob and based on instructions in previous archives I ran the following command line:
mri_glmfit-sim –glmdir (qdec output directory) --cache 1.3 abs
which generated a "cache.th13.abs.y.ocn.dat" file. This file contains 3 columns and 36 rows. I'm assuming the values in the three columns correspond to LGI values for each significant blob for each subject? (I had 3 significant blobs and 36 participants)
Will you please confirm I am doing (and interpreting) this correctly?
Thanks so much,
Avi
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Thank you for your reply. I chose the 1.3 threshold based on LGI papers in the ASD literature, but I will use 2.0.
1. By permutation do you mean FDR correction?
2. If I use monte carlo at 2.0 (0.01 p-value) would this be okay for LGI, or do you still recommend FDR correction?
Many thanks,
Avi
On Fri, Aug 10, 2018 at 1:53 PM, Douglas Greve dgreve@mgh.harvard.edu wrote:
Each row is a subject and each column is a cluster. BTW, a threshold of 1.3 is way too low for lGI. If you want to use a threshold that low, you should use permutation instead of monte carlo (in general, permutation is better, but certainly for lGI).
On 8/9/18 1:39 PM, Avi Gharehgazlou wrote:
External Email - Use CautionHi experts,
I looked at association between LGI and a behavioural scale on QDEC. after the analysis, to plot the significant clusters/ blobs, I wanted to export LGI values for each subject from each significant blob and based on instructions in previous archives I ran the following command line:
mri_glmfit-sim –glmdir (qdec output directory) --cache 1.3 abs which generated a "cache.th13.abs.y.ocn.dat" file. This file contains 3 columns and 36 rows. I'm assuming the values in the three columns correspond to LGI values for each significant blob for each subject? (I had 3 significant blobs and 36 participants)
Will you please confirm I am doing (and interpreting) this correctly?
Thanks so much,
Avi
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On 8/11/18 12:02 PM, Avi Gharehgazlou wrote:
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Thank you for your reply. I chose the 1.3 threshold based on LGI papers in the ASD literature, but I will use 2.0.
2 is still too low. You'd need at least 3.
- By permutation do you mean FDR correction?
no, permutation and FDR are different
- If I use monte carlo at 2.0 (0.01 p-value) would this be okay for
LGI, or do you still recommend FDR correction?
No, 2 is too low. At least 3, and that may be too low. Permutation will be better.
Many thanks,
Avi
On Fri, Aug 10, 2018 at 1:53 PM, Douglas Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu> wrote:
Each row is a subject and each column is a cluster. BTW, a threshold of 1.3 is way too low for lGI. If you want to use a threshold that low, you should use permutation instead of monte carlo (in general, permutation is better, but certainly for lGI). On 8/9/18 1:39 PM, Avi Gharehgazlou wrote:External Email - Use Caution Hi experts, I looked at association between LGI and a behavioural scale on QDEC. after the analysis, to plot the significant clusters/ blobs, I wanted to export LGI values for each subject from each significant blob and based on instructions in previous archives I ran the following command line: mri_glmfit-sim –glmdir (qdec output directory) --cache 1.3 abs which generated a "cache.th13.abs.y.ocn.dat" file. This file contains 3 columns and 36 rows. I'm assuming the values in the three columns correspond to LGI values for each significant blob for each subject? (I had 3 significant blobs and 36 participants) Will you please confirm I am doing (and interpreting) this correctly? Thanks so much, Avi _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> 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 Partners Compliance HelpLine at http://www.partners.org/complianceline <http://www.partners.org/complianceline> . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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