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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?
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@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
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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:
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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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