Which version of FS are you using? I don't think it was in 5.3, so you might have to use 6.0 version of mri_glmfit. Also, before you compute and report the mean correlation inside of a significant cluster, you might want to read this paper:

Puzzlingly High Correlations in fMRI Studies of Emotion, Personality, and Social Cognition

https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&a...

On 6/5/18 10:24 AM, jahanvi patel wrote:

Hello together,

We used the following command to perform correlation analysis. But we didn't obtain the "pcc.mgh" file which we want to extract the correlation coefficient from the significant cluster.

Is there a command or way to generate the pcc.mgh file?

Thank you in advance

mri_glmfit \ --glmdir GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2 \ --y lh.testretest_only_TP2.thickness-pc1.stack.fwhm15.mgh \ --label lh.testretest.fsaverage.cortex.label \ --fsgd GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2/TP1_TP2.fsgd \ --C GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2/contrasts/main.mtx \ --C GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2/contrasts/Delta_age.mtx \ --C GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2/contrasts/Delta_CesD_score.mtx \ --C GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2/contrasts/Delta_STATI_state.mtx \ --C GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2/contrasts/Delta_STATI_trait.mtx \ --C GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2/contrasts/Delta_total_medi_min.mtx \ --C GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2/contrasts/Delta_FFMQ_f1.mtx \ --C GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2/contrasts/Delta_FFMQ_f2.mtx \ --surf fsaverage lh

Best, Jahanvi

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