Try removing the mask and funcstem flags

On 11/29/2021 12:49 PM, Hiersche, Kelly J. wrote:

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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-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/FsFastFirstLeve... https://secure-web.cisco.com/1HFp-P1BTuyECuoTw5lESlfUSHFqQVIQ7RnEtbQVSkdXbpD-BfoerQdUofRq8zxycV-sMFVktqvvCs5P_Mthp0ei03z26Z_2h7KCtGVPba0CVNO9D-5WQuAfeUqgD4HL5xcF1Fe8K6YWlh0KzdrrgH8TrDz9hZNuHO37ueFOfk9peom7pNHaQ9fDt3tBhoXnOpvncAZksWT3s-wcah9miCOcHshdEGg8bnKkNn6EssitUzo5clWc2GC_oQSrOGYytJH3GRwXmyBJ6mr0F-sbTITXvDzK-cBVl1BPhkO3RY6FNTDQDwGy_wampkiMON8bpAVgaVNNyi850U-kFDVLIPQ/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fsecure-web.cisco.com%2F1i0LcvXc_pWxYrG0y8LzlZO7IfvmC_UpV6cd9EBpLiYz691LC8ZZxenFAFLThZDwWA9B3gqr427fuo4gIW_UApRZ4HnhyE--4n1riYpxVkN51_HSluoN7RvhScv1DHFw7bSCJ0zsqXSx9101qhpJCaDVO6iIRiJSWf539hQDEXUv0GRQj5G5pJxWWZkHuaNaJjK8tH-3_N09V9VHNplUH_00QltaR2DYkF533lkMSxJ_21ufiyfdkpYimByzPbHE4bVWAWNZ0Vy4A0e4ZiEjRKLjfrLejQ08R-VuM6jxUMIKn7IgT-ICmWdfQrIOzL_2vYY4e9sMGddb5z3vdRMj_XA%2Fhttps%2A3A%2A2F%2A2Fsurfer.nmr.mgh.harvard.edu%2A2Ffswiki%2A2FFsFastTutorialV5.1%2A2FFsFastFirstLevel__%3BJSUlJSUl%21%21KGKeukY%21jamAwe2rt9bV25rNVEsM7VSsLUSIPCyV1NstcH4IqS--ZWFujG5xPHSm-_QRuI2N8heSkM9-PNg%24 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/1duUZ-b0HBTRM5eUwLlK9AjyO1XBuaA6zcZkb6cg2sWPD2jh0oDWRQj7f1MaQkqr3XjUFkZc_FyNxaIV89ynqi1_W7QR2ZMh28J5t-XJK3QuuE2iSq86AMU7AiizRJsEbi7vebZ8Hlh5ZaheXQNuty2wFV78NnPsoProftQvvD-somPwaSzSKO6FtabuwBdE50C3fCSF5MJoemEZRmhoD57BWTkrqaS0aOgyWhmI6U3i--kPHS21a3un_CkDWPszEo8oV5x4nyoZnQI2eN0VGp3QtXWXOw7WbG1hD6W0A2O7AcsohzhTw53HPVdtkgcYGw96Oj2kEm7sz3FXIQDRcdA/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fsecure-web.cisco.com%2F1Sor7-h_gxGA_NBXCIF2cnCakBuzWn-uVbkP71hrF-15-uN-yPZMZmi3kEC7J04gY__hv7B9nXr3WBKeUKxOm2ARABA3qbbXeq_UCQP6kYpAlwRN1Lmjs4LDQzWIvmqwpbuLNUdAopRjQRoR0TIdvr8VV-G4exusT4txcHYaHojYOsyNUW_3md9vLAoF0m-ujmr_Rr0EuurR5bAmw6rwn87kGNQPpVJJ52hOxpUHpxX63dkNnzfH2OOcXR3Js60fj98Rub3VqUXKmU9KYBQAVgOKng5ytmCjF1v6PYw5mROgvvlEAXnT5DXrqtnaNluG0owlDYiSfrY-MTokGuBeLCQ%2Fhttps%2A3A%2A2F%2A2Fsurfer.nmr.mgh.harvard.edu%2A2Ffswiki%2A2FFsFastTutorialV5.1%2A2FFsFastPreProc__%3BJSUlJSUl%21%21KGKeukY%21jamAwe2rt9bV25rNVEsM7VSsLUSIPCyV1NstcH4IqS--ZWFujG5xPHSm-_QRuI2N8heS9sHIeh8%24

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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