Hi dr Jerome J Maller
  
   The analysis I do this research was followed as the tutorials of freesurfer group analysis (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis). The detailed was followed:
   (1) recon-all <subject> autorecon-all; (2)   recon-all -s <subject> -localLGI; (3) recon-all -s <subject> -qcache/recon-all -s <subject> -qcache -measure pial_lgi ; (4) mris_preproc --fsgd --catch-in thickness --target --out ;(5) mri_glmfit --y --fsgd --C --surf --cortex --glmdir ;(6) using matlab to do clusterwise correction for multiple comparisons with mri_surfrft_jlbr.

In the result file, there are files (sig.cw.neg.mgh,sig.cw.pos.mgh,sig.vw.neg.mgh.sig.vw.pos.mgh). Lastly, I look the result with command of mri_surfcluster. I want to extract the data of each subject in the regions of significant.


Thank you

Wang Kangcheng

Faculty of Psychology, Southwest University, China

Email: kangchengwang0808@gmail.com / wangkangcheng.001@163.com

Address:  No.2 Tiansheng Road, BeiBei District, Chongqing, 400715,P.R.China 

 
From: Jerome Maller
Date: 2014-06-13 13:50
To: 王康程
Subject: Fwd: [Freesurfer] How to extract significant result for each subject
Hi Wang,

Here are my instructions for extracting data from Freesurfer:

How to export the data from Freesurfer into SPSS

 

1.      After you have conducted a QDEC analysis, a new directory will have been created in the “qdec” directory called “stats_tables”. Navigate to this directory

2.      Copy all of the files in the directory (they will all have a .dat extension) onto a Windows computer

3.      Open MS Excel

4.      Select on a .dat file (although it may appear with a .stats extension) and then open it (you may have to select “delimited”, then “tab”)

5.      Save the file in Excel 97-2003 format

6.      Close Excel

7.      Open SPSS

8.      Change the option in the navigation window to show “All files”

9.      Select the Excel file which you have just saved

10.  The Excel file will now open in SPSS.

11.  Save As

12.  Complete this process for all of the .dat files

13.  Once all .dat files have been converted to SPSS format, merge them (using the merge feature in SPSS: Data à Merge Files à Add variables)


Regards,


Jerome Maller


---------- Forwarded message ----------
From: kangchengwang0808@gmail.com <kangchengwang0808@gmail.com>
Date: 13 June 2014 12:53
Subject: [Freesurfer] How to extract significant result for each subject
To: freesurfer <freesurfer@nmr.mgh.harvard.edu>


Dear freesurfers,
   I contrast depression and control and find that patients have a lower thickness in region of inferior frontal gyrus. Now, I want to extract the data of thickness for each subject. Could you tell which command could do this?
Thank you

Wang Kangcheng ( New learner of freesurfer )



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--

Dr Jerome J Maller   BSc,GradDipPsych,MSc,PhD

Neuroscientist

NHMRC Industry Career Development Fellow (CDF)

CETBIR (Centre for Excellence in Traumatic Brain Injury) Postdoctoral Research Fellow

Monash Alfred Psychiatry Research Centre (MAPrc)

Central Clinical School, Monash University and Alfred Hospital

4th Floor, 607 St Kilda Rd, Melbourne VIC

 

Adjunct Associate Professor

Centre for Research on Ageing, Health and Wellbeing, Research School of Population Health, ANU College of Medicine, Biology and Environment at the Australian National University.

 

Phone: +61 3 9076 2404

Fax: +61 3 9076 6588

Mobile: +61 419 221 454