External Email - Use Caution
Hi Douglas,
This is for a lGI analysis. I used a fwhm of 10 and not 38:
mri_surf2surf --hemi lh --s fsaverage --sval lh.lgi.mgh --fwhm 10 --cortex --tval lh.lgi.10B.mgh
So why am I getting this error? cannot find
/usr/local/freesurfer/average/mult-comp-cor/fsaverage/rh/cortex/fwhm38/abs/th13/mc-z.csd
When I run : mri_glmfit-sim --glmdir rh.project.glmdir --cache 2 abs --cwpvalthresh .05 --2spaces??
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of freesurfer-request@nmr.mgh.harvard.edu Sent: 05 November 2020 11:29 To: freesurfer@nmr.mgh.harvard.edu Subject: [EXTERNAL] Freesurfer Digest, Vol 201, Issue 6
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Today's Topics:
1. LGI quality control {Disarmed} (Nelson, Eric) 2. Re: Meta-analysing brain measure statistics across multiple cohorts using different versions of Freesurfer (Stephanie K) 3. Re: Meta-analysing brain measure statistics across multiple cohorts using different versions of Freesurfer (Ammon, William) 4. Re: aparcstats2table {Disarmed} (Kiyotaka Nemoto) 5. Fwd: Welcome to the "Freesurfer" mailing list {Disarmed} (Nicholas BH NG (NUHS)) 6. Fwd: using CAT12 segmentation for PVC (Donatienne Van Weehaeghe) 7. aparcstats2table (Saman Fouladi) 8. Join the Brainhack donostia (Vicente Ferrer) 9. repeated measures ANOVA 2x2 two groups two times {Disarmed} (Agurne Sampedro Calvete) 10. Re: .mgh file unknown, GLM paired analysis {Disarmed} (Agurne Sampedro Calvete) 11. Re: mri_glmfit_sim error (Douglas N. Greve) 12. Re: mri_convert error (Douglas N. Greve) 13. Re: Extract he value of area and volume in the fsaverage for every subject {Disarmed} {Disarmed} (Douglas N. Greve) 14. Re: Question about smoothing for extracting anatomical stats {Disarmed} (Douglas N. Greve) 15. Re: Troubleshooting -parallel flag for Freesurfer, error in the cortical ribbon mask stage during recon-all {Disarmed} (Douglas N. Greve) 16. Re: Fixing error with pial surface {Disarmed} (Douglas N. Greve) 17. Re: mris_anatomical_stats error: stating file (Douglas N. Greve) 18. Re: (no subject) (Douglas N. Greve) 19. Re: Fwd: using CAT12 segmentation for PVC (Douglas N. Greve) 20. Re: repeated measures ANOVA 2x2 two groups two times {Disarmed} (Douglas N. Greve) 21. Re: LGI quality control {Disarmed} (Douglas N. Greve) 22. Re: repeated measures ANOVA 2x2 two groups two times {Disarmed} (Agurne Sampedro Calvete) 23. Re: trac-preproc error (Hasimoglu, Yasemin) 24. Re: mris_anatomical_stats error: stating file (Chan, Shi Yu)
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Message: 1 Date: Wed, 4 Nov 2020 19:12:50 +0000 From: "Nelson, Eric" eanelson@uab.edu Subject: [Freesurfer] LGI quality control {Disarmed} To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Message-ID: DM6PR07MB791577DA3BB61700D9F42BE5C7EF0@DM6PR07MB7915.namprd07.prod.outlook.com Content-Type: text/plain; charset="us-ascii"
External Email - Use Caution
Hello,
I am using FreeSurfer 7.1.1 to run LGI and have done so successfully. I am now trying to quality check my data using tksurfer as described on the wiki tksurfer my_subject_id lh inflated -overlay lh.pial_lgi However the LGI overlay is not covering the entirety of the inflated brain. Specifically the medial frontal surface and some subcortical are not measured for LGI. Here is a link of the overlay images for a few subjects: https://secure-web.cisco.com/1y5I8DUvRNOHPY2e1TIaZl17tWS96xMg81U_dq63kxl7l6A... . I<https://secure-web.cisco.com/1Hod0xhqjDXliu4d6GvJjLlbNiHOsmMLOvn77883QuHzRrG... >. I haven't been able to find any images of what this overlay should look like so I don't know if this is expected or if som ething has gone wrong with the processing. Any feedback would be greatly appreciated
Best,
Eric