Hi Michelle

can you cc the list so others can answers? I'm also no longer sure which thread this is - were you trying to use the skull stripping from another package? If so, convert that file to be named brainmask.mgz, then do *not* include the -noskullstrip in your command line. Let us do the skull strippping, which will create a brainmask.auto.mgz, but should preserve the brainmask.mgz (since it is different than the .auto file)

cheers
Bruce

On Tue, 18 Jul 2017, Michelle VanTieghem wrote:

Hi Bruce, 


Thanks for the information. Sorry I had changed my mail settings so I wasn’t
seeing your responses until now. I had tried to run all, but just skip skull
strip step, as well as the talaraich check step since we saw errors with
that too.

The command I used is follows:

recon-all -all -3T -mprage -notal-check -noskullstrip -i/vega/psych/users/mrv2115/fsdata/ORIG_AFNI_SKULLSTRIP/SB001/mprage_deobliqu
e_brain.nii -s SB001

However, I am getting the following error during the registration step (see
below). It looks like the mask volume brainmask.mgz hasn't been generated,
but i don't know why. You suggested to convert my afni skull stripped brain
to brain mask.mgz and place in the MRI folder. but am I still going to run
the steps of autorecon-1 ? (intensity normalization, etc)? Does recon-all
take inputs of already existing mri/brainmask.mgz files? It seems like it
just needs one file and then re-generates a new directory with mri, scripts,
ect. I would appreciate more detail on how to implement this! 

Thank you,

Michelle 


ERROR:



 ======= NUMBER OF OPENMP THREADS = 1 =======

aligning to atlas containing skull, setting unknown_nbr_spacing = 3

using MR volume brainmask.mgz to mask input volume...

reading 1 input volumes...

logging results to talairach.log

reading '/vega/psych/app/freesurfer/average/RB_all_2008-03-26.gca'...

average std = 6.9   using min determinant for regularization = 4.7

0 singular and 1812 ill-conditioned covariance matrices regularized

reading 'nu.mgz'...

mghRead(/vega/psych/users/mrv2115/fsdata/processed/SB001/mri/brainmask.mgz,
-1): could not $

mri_em_register: could not open mask volume brainmask.mgz.


Linux bogota.cc.columbia.edu 2.6.32-696.el6.x86_64 #1 SMP Tue Feb 21
00:53:17 EST 2017 x86_$


recon-all -s SB001 exited with ERRORS at Tue Jul 18 11:50:24 EDT 2017


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