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:
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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.edumailto: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 CautionDear 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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