External Email - Use Caution
Hi Bruce
Can confirm that both files (rh.area & rh.volume) load fine in freeview
Thanks for the help!
James
________________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl
<fis...@nmr.mgh.harvard.edu>
Sent: 29 October 2018 15:43
To: Freesurfer support list
Subject: Re: [Freesurfer] mris_apply_reg failing for area/volume
Hi James
can you verify that the various files (e.g.
/cluster/projects/p23/projects/Memory_Project/James/AgeSym/long_recons_FXhemi/010_NDev/1000409_02_10_02_11.long.base_1000409_11/surf/rh.area)
are intact by loading them into freeview? For the area file you will of
course have to load it as an overlay not as a surface (since it isn't a
surface)
cheers
Bruce
On Mon, 29 Oct 2018, James Michael Roe wrote:
>
> External Email - Use Caution
>
>
> Dear freesurfer experts
>
>
>
> I’m running the following commands to register RH area and volume files per
> sub to both hemispheres
> of a symmetrical template following Xhemi routines.
>
> The commands have already worked for many subs, but are failing to write the
> target file for a
> number of others (and all run fine without the –-jac flag)
>
>
> #right to left
>
> mris_apply_reg \
>
> --src $SUBJECTS_DIR/$sub/surf/rh.area \
>
> --trg $concatdir/rh.lh.area.${sub}.${template}.nii.gz \
>
> --streg $SUBJECTS_DIR/$sub/xhemi/surf/lh.${template}.sphere.reg
> $SUBJECTS_DIR/${template}/surf/lh.sphere.reg \
>
> --jac
>
>
>
> #right to right
>
> mris_apply_reg \
>
> --src $SUBJECTS_DIR/$sub/surf/rh.area \
>
> --trg $concatdir/rh.rh.area.${sub}.${template}.nii.gz \
>
> --streg $SUBJECTS_DIR/$sub/surf/rh.${template}.sphere.reg
> $SUBJECTS_DIR/${template}/surf/rh.sphere.reg \
>
> --jac
>
>
>
>
> The error is not template-specific as the output is the same using
> fsaverage_sym
>
> Attached is the log file.
>
>
>
> Thanks in advance!
>
>
>
>
> - James
>
>
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