Dear Dough,

The terminal output: HV_02_11_p2x7

mghRead(/Volumes/DATA_PETMR/data_donatienne/Boston_final_analysis/Donatienne/Analyses_freesurfer/recon_flair/unknown/mri/orig.mgz, -1): could not open file

ERROR: loading /Volumes/DATA_PETMR/data_donatienne/Boston_final_analysis/Donatienne/Analyses_freesurfer/recon_flair/unknown/mri/orig.mgz

This is needed for RBV

The command line: mri_gtmpvc --i /Volumes/DATA_PETMR/data_donatienne/Boston_final_analysis/VT/Vt_all/${word}_lin_T1.nii.gz --reg /Volumes/DATA_PETMR/data_donatienne/Boston_final_analysis/Donatienne/Analyses_freesurfer/recon_flair/${word}/mri/suv.reg.lta --psf 5 --seg /Volumes/DATA_PETMR/data_donatienne/Boston_final_analysis/Donatienne/Analyses_freesurfer/recon_flair/${word}/mri/gtmseg.mgz --default-seg-merge --auto-mask 5 0.01 --rbv --o /DATA_PETMR/data_donatienne/Boston_final_analysis/VT/Vt_all/${word}/PVC/gtmpvc.output.spmreg --no-rescale

Kind regards

Donatienne

Op do 25 apr. 2019 om 17:44 schreef Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu>:

can you send command line and terminal output?

On 4/25/19 10:37 AM, Donatienne Van Weehaeghe wrote:
>
> External Email - Use Caution
>
> Dear freesurfer experts,
>
> I am running the rbv pvc correction on a mac system and encountered
> the following error.
>
> mghRead(/Volumes/DATA_PETMR/data_donatienne/Boston_final_analysis/Donatienne/Analyses_freesurfer/recon_flair/unknown/mri/orig.mgz,
> -1): could not open file
>
> The subjects directory is
> Volumes/DATA_PETMR/data_donatienne/Boston_final_analysis/Donatienne/Analyses_freesurfer/recon_flair,
> the orig files are located in
> Volumes/DATA_PETMR/data_donatienne/Boston_final_analysis/Donatienne/Analyses_freesurfer/recon_flair/$subjectname
>
> Thank you!
>
> Kind regards
> Donatienne
>
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