Re: [Freesurfer] -conform option in mri_convert produces crazy artefacts

2019-09-04 Thread Bruce Fischl
glad to hear it worked out (and it wasn't our fault!) cheers Bruce On Wed, 4 Sep 2019, Rovai Antonin wrote: External Email - Use Caution Hello I think there is a problem with the dicom files. I could not see it on the images before mri_convert -conform but there’s definitely

Re: [Freesurfer] -conform option in mri_convert produces crazy artefacts

2019-09-04 Thread Rovai Antonin
External Email - Use Caution Hello I think there is a problem with the dicom files. I could not see it on the images before mri_convert -conform but there’s definitely something weird in there. I suspect it comes from some software that misexported the data. Running reconall on

Re: [Freesurfer] -conform option in mri_convert produces crazy artefacts

2019-09-03 Thread Bruce Fischl
hmmm. Can you tar and gzip the whole subject dir and upload it to our ftp site? On Tue, 3 Sep 2019, Rovai Antonin wrote: External Email - Use Caution Hey So opening only the conformed image in freeview, mricro and fsleyes constantly gives me crazy results. Also, the wm segmentation

Re: [Freesurfer] -conform option in mri_convert produces crazy artefacts

2019-09-03 Thread Rovai Antonin
External Email - Use Caution Hey So opening only the conformed image in freeview, mricro and fsleyes constantly gives me crazy results. Also, the wm segmentation is completely wrong so I really think there something wrong in the file…. Best Antonin Hôpital Erasme - ULB

Re: [Freesurfer] -conform option in mri_convert produces crazy artefacts

2019-09-03 Thread Bruce Fischl
Hi Antonin hmmm. Can you try *only* loading the conformed image and seeing how it looks? freeview will use one of the images as the basis for it's display coordinates, which can cause apparent slicing artifacts that are only display issues for other volumes. cheers Bruce On Tue, 3 Sep