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Hello, thank you, we are using FS 5.3 virtual box, is there a version of 6.0 for the virtual box too?

About the correlation, we meant to obtain the r-value (pearson correlation coef) from each significant cluster we got after running Monte Carlo simulation. So we didn't want to correlate only one cluster because we had correlate the whole brain thickness with the scores first, and we got the results from freesurfer, but it shows only the p-value, there was no r-value shown in the files. Hope it is correct to do in this way?

Best, Jahanvi

Message: 2 Date: Tue, 5 Jun 2018 12:55:23 -0400 From: Douglas Greve dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] pcc.mgh file missing To: freesurfer@nmr.mgh.harvard.edu Message-ID: 4a311f78-3567-8817-f500-8bac737fa1af@mgh.harvard.edu Content-Type: text/plain; charset="utf-8" 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... cd=2&cad=rja&uact=8&ved=0ahUKEwj6wuqb_rzbAhVnslQKHa4tAAkQFggzMAE& url=https%3A%2F%2Fwww.edvul.com%2Fpdf%2FVulHarrisWinkielmanPashler- PPS-2009.pdf&usg=AOvVaw0C6XKQkj4hypGKRIaZFLc0

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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