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:
External Email - Use Caution
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/${word}/mri/suv.reg.lta
Thank you for your help.
Op vr 26 apr. 2019 om 17:08 schreef Greve, Douglas N.,Ph.D.
<dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>>:
Does that file actually exist? It seems to think that the subject name is
"unknown", which is probably not right. How did you create suv.reg.lta? That
file should have the name of the subject in it. Also, no need to specify the
full path to the --seg (so, just --seg gtmseg.mgz is ok).
On 4/26/2019 2:05 AM, Donatienne Van Weehaeghe wrote:
External Email - Use Caution
Dear Dough,
The terminal output: HV_02_11_p2x7
mghRead(/Volumes/DATA_PETMR/data_donatienne/Boston_final_analysis/Donatienne/Analyses_freesurfer/recon_flair/unknown/mri/orig.mgz,
-1): could not open file
ERROR: loading
/Volumes/DATA_PETMR/data_donatienne/Boston_final_analysis/Donatienne/Analyses_freesurfer/recon_flair/unknown/mri/orig.mgz
This is needed for RBV
The command line: mri_gtmpvc --i
/Volumes/DATA_PETMR/data_donatienne/Boston_final_analysis/VT/Vt_all/${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/${word}/PVC/gtmpvc.output.spmreg
--no-rescale
Kind regards
Donatienne
Op do 25 apr. 2019 om 17:44 schreef Greve, Douglas N.,Ph.D.
<dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>>:
can you send command line and terminal output?
On 4/25/19 10:37 AM, Donatienne Van Weehaeghe wrote:
>
> External Email - Use Caution
>
> Dear freesurfer experts,
>
> I am running the rbv pvc correction on a mac system and encountered
> the following error.
>
> mghRead(/Volumes/DATA_PETMR/data_donatienne/Boston_final_analysis/Donatienne/Analyses_freesurfer/recon_flair/unknown/mri/orig.mgz,
> -1): could not open file
>
> The subjects directory is
> Volumes/DATA_PETMR/data_donatienne/Boston_final_analysis/Donatienne/Analyses_freesurfer/recon_flair,
> the orig files are located in
> Volumes/DATA_PETMR/data_donatienne/Boston_final_analysis/Donatienne/Analyses_freesurfer/recon_flair/$subjectname
>
> Thank you!
>
> Kind regards
> Donatienne
>
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