I noticed that you are explicitly setting the mask and funcstem in mkanalysis-sess. Is there a reason for that? Also, I'd set -poly to 5.

On 11/21/2021 1:11 PM, Hiersche, Kelly J. wrote:

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Hello FreeSurfer Developers,

First, I am new to using Freesurfer, so I apologize if any information is unclear.

I am attempting to use the following tutorial *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastFirstLeve... https://secure-web.cisco.com/1KKgvfrXJGjQJ5zjq_uJgVI7FZF_1Yms747_s_N5YKZgNCGOMeS-uBP8-XyfvGQqxNQ2kNRGpMdVD-l4SP5CiEic9c_tI35GMoJE6Sb491sj-H31iaM-POIUms_Q0s7FHOD2YRT1S9f6rjulYbuOUBL9xxRNRhcK19SgzXAbUPJCM_zmItcZr7pBo3wqHy7IvkxPcZUHHu2qSGURpFsZtpoev0-WE5zGzv7gV_gSisXAPLRyzOFnS-FUhNnf6WkJ4aDshlD1YgdAFvaSof0Q7EdzgPMmTsek__sdyr7qIcKRNn3Vl3g6ARaRHDXMvSsFsesmqvIgyBJKDX-8AWaifiQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsFastTutorialV5.1%2FFsFastFirstLevel to do a surface based GLM in an individual subject (using my own data, not the tutorial data), but I am getting the following error:

Error using MRIread (line 76) ERROR: cannot determine format of /*subnum/bold/runnum/masks*/fmcpr.brainmask.fsaverage.lh (MRIread)

I am getting that error because the fmcpr.brainmask.fsaverage.lh does not exist. To fix this error, I re-ran preprocessing using the following tutorial: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastPreProc https://secure-web.cisco.com/1R3ca-_kZlKG6UMHW-K0XesdEmNb2A3RSqg26YdNzjZ-RhqmPe-x1ag2VCykMD2zftJadwRyd02YgL1xqEuuo5BSxT6PCdIkNNWUylmMkbaDnk6thb22V1RZQKgXY4xp_r3V7CQ5srW_gt2Lr7hQ3XVEReDCipXQQhcYb6EoCKwknBoPDp0kLj2UL7t85-F8m-Bm2lTwCm4H3QNBdErXl7_KaiEN9_ZYzyU44xXnkEY1MgoXenRnSyLkm2TozNiCMkxQSw2HtBjFstXLvSOFjamEwyooDK2Xv3_t3o_UfyclzKzBt055kbDZw2bp9XBHBGcGhs3ARdDmpbjaNl4atow/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsFastTutorialV5.1%2FFsFastPreProc

After preprocessing, I still got the same error.

*Here are the files that do exist in that path: *subnum/bold/run-num/masks* * brain.e3.nii.gz            brain.fsaverage.lh.pr.nii.gz  brain.fsaverage.rh.pr.nii.gz  brain.mni305.2mm.pr.nii.gz  brain.nii.gz.mkbrainmask.log brain.fsaverage.lh.nii.gz  brain.fsaverage.rh.nii.gz brain.mni305.2mm.nii.gz       brain.nii.gz

*There are some fmcpr files in this folder: subnum/bold/run-num* fmcpr.brainmask.norm.2x2x2.nii.gz     fmcpr.mcdat fmcpr.norm.nii.gz              fmcpr.sm5.fsaverage.rh.nii.gz fmcpr.brainmask.normtmp.2x2x2.nii.gz  fmcpr.nii.gz  fmcpr.sm0.norm.nii.gz          fmcpr.sm5.mni305.2mm.nii.gz fmcpr.mat.aff12.1D                    fmcpr.nii.gz.mclog  fmcpr.sm5.fsaverage.lh.nii.gz  fmcpr.sm5.norm.nii.gz

*Here are the commands I am running:* *These commands work: * *mkanalysis-sess* -fsd bold -rlf $analysis_stem-$run_set.rlf -surface fsaverage $hemi -event-related -paradigm $PARA_NAME -refeventdur 18 -nconditions $nconditions -mask $func_stem.brainmask -gammafit 2.25 1.25 -nuisreg mcprextreg 6 -TR 1.0000 -polyfit 1 -analysis $analysis_stem-$run_set-$func_stem-$tpe.sm5.$hemi.$REG_STEM -tpexclude $tpe$TPE_STEM -funcstem $func_stem.sm$kernel$REG_STEM -per-run

*mkcontrast-sess* -analysis $analysis_stem-$run_set-$func_stem-$tpe.sm5.$hemi.$REG_STEM -contrast Con1-Con2 -a 1 -c 2

*preproc-sess* -fsd bold -rlf $analysis_stem-$run_set.rlf -surface fsaverage lhrh -mni305 -fwhm 5 -per-run

*This command errors * mkanalysis-sess -fsd bold -rlf $analysis_stem-$run_set.rlf -surface fsaverage $hemi -event-related -paradigm $PARA_NAME -refeventdur 18 -nconditions $nconditions -gammafit 2.25 1.25 -nuisreg mcprextreg 6 -TR 1.0000 -polyfit 1 -analysis $analysis_stem-$run_set-$func_stem-$tpe.sm5.$hemi.$REG_STEM -tpexclude $tpe$TPE_STEM -funcstem $func_stem.sm$kernel$REG_STEM -per-run

1. I am running freesurfer through matlab on the Ohio Supercomputer; freesurfer/6.0.0

Thank you for all your troubleshooting help!

Kelly

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