Does that file actually exist? It seems to think that the subject name is "unknown", which is probably not right. How did you create suv.reg.lta? That file should have the name of the subject in it. Also, no need to specify the full path to the --seg (so, just --seg gtmseg.mgz is ok).

On 4/26/2019 2:05 AM, Donatienne Van Weehaeghe wrote:

        External Email - Use Caution        

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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