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Hello,

I was adapting existing code in my lab that was used for doing a volume-based analysis, so I tried to keep the inputs the same. 

Do you think removing the mask flag would be helpful?

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From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu>
Sent: Monday, November 29, 2021 12:28 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Errors with mkanalysis-sess: missing file fmcpr.brainmask.fsaverage.lh

 

In your mkanalysis command, why are you specifying the mask and the funcstem? These are tricky options to get right ...

On 11/29/2021 9:50 AM, 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/FsFastFirstLevel 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 

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:

 

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

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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