Can you send the terminal output that includes the error?
On 11/06/2018 06:36 PM, James Michael Roe wrote:
> External Email - Use Caution
>
> Hi Bruce
>
> I realise that my last message made it sound as though the problem was fixed.
> However, I was only confirming that the files load fine in freeview (are not
> corrupted) as asked.
> The issue of many subs area and volume files failing to register when using
> --jac is still unsolved
>
> Appreciate the support.
>
> Thanks
>
> James
>
> ________________________________________
> From: James Michael Roe
> Sent: 31 October 2018 19:45
> To: Freesurfer support list
> Subject: Re: [Freesurfer] mris_apply_reg failing for area/volume
>
> 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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