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 )
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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 . 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.
mri_surfrft_jlbr does not output that kind of information. I'd have to modify it. I'm traveling now. Can you check back in two weeks? doug
On 6/13/14 9:17 AM, kangchengwang0808@gmail.com wrote:
Hi dr Jerome J Maller The analysis I do this research was followed as th_e tutorials https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial _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 <mailto:jerome.maller@monash.edu> *Date:* 2014-06-13 13:50 *To:* ??? <mailto:kangchengwang0808@gmail.com> *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 <mailto:kangchengwang0808@gmail.com>* <kangchengwang0808@gmail.com <mailto: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 <mailto: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 ) _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> 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 . 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. -- *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*
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freesurfer@nmr.mgh.harvard.edu
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Douglas Greve -
kangchengwang0808＠gmail.com