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:

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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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did you look in the suv.reg.lta for the subject name? based on your mri_coreg command, I would NOT expect it to be there. Rather than use --targ, try using --s subjectname

On 4/26/2019 12:43 PM, Donatienne Van Weehaeghe wrote:

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No, there is no unknown folder. I do not understand why he uses unknown instead of the subject names specified in the text file. Also, the muller gartner PVC correction works.

I created the suv.reg.lgta using the following command: mri_coreg --targ /Volumes/DATA_PETMR/data_donatienne/Boston_final_analysis/Donatienne/Analyses_freesurfer/recon_flair/${word}/mri/brainmask.mgz --mov /Volumes/DATA_PETMR/data_donatienne/Boston_final_analysis/VT/Vt_all/${word}.nii --reg /Volumes/DATA_PETMR/data_donatienne/Boston_final_analysis/Donatienne/Analyses_freesurfer/recon_flair/${word}/mri/suv.reg.lta

Thank you for your help.

Op vr 26 apr. 2019 om 17:08 schreef Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu>:

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 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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