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