External Email - Use Caution Hi Doug
Here is the output file
James Michael Roe
PhD. Candidate
Center for Lifespan Changes in Brain and Cognition
Department of Psychology
University of Oslo
PB 1094 Blindern
0317 Oslo
Mobile: 958 49 437
________________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D.
<dgr...@mgh.harvard.edu>
Sent: 07 November 2018 19:02
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_apply_reg failing for area/volume
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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subexample_slurm.log
Description: subexample_slurm.log
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