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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 https://secure-web.cisco.com/1KKgvfrXJGjQJ5zjq_uJgVI7FZF_1Yms747_s_N5YKZgNCG... 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: https://secure-web.cisco.com/1R3ca-_kZlKG6UMHW-K0XesdEmNb2A3RSqg26YdNzjZ-Rhq...
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