The FWHM 38 values is the final smoothness that includes applied and inherent. with lGI, you get a lot of inherent smoothing. You can try not smoothing at all, but I would probably go for permutation rather than MCZ

On 11/5/2020 12:39 PM, Basavaraju, Rakshathi wrote:

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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

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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... NoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3D7wiCSt92CUigLhdzg8LhducfMTfDwOdJhAfgtnz4h3s%26e%3D . I<https://secure-web.cisco.com/1Hod0xhqjDXliu4d6GvJjLlbNiHOsmMLOvn77883QuHzRrG... D >. 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