External Email - Use Caution Dear Doug, I uploaded the data by ftp in Windows 10. I hope You can see a tar file. The file's name is HTN_Con_096 and it contains the subject's folder after recon_all. Do You need any other data? All the best Agnieszka
pon., 29 lip 2019 o 22:44 Greve, Douglas N.,Ph.D. <dgr...@mgh.harvard.edu> napisał(a): > That is a little strange. Can you tar up the data and upload it to > ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming > Let me know when it is there and what the file name is > > On 7/24/19 4:53 AM, Agnieszka Sabisz wrote: > > > > External Email - Use Caution > > > > Dear Freesurfer Team, > > I checked skull stripping and I think it's all right. (see in attachment) > > The registration looks all right in translational directions but not > > in scaling. In the attachment you can see the comparison between > > tkregister view and freeview of the same patient. > > What may be the reason and how to cope with that? We cannot normalize > > the volume data to eTIV (as it is not proper), what value should we > > use instead? > > Best regards, > > Agnieszka > > > > sob., 22 cze 2019 o 02:15 Greve, Douglas N.,Ph.D. > > <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> napisał(a): > > > > If the registration looks ok then it probably means that the skull > > stripping was too aggressive. Have you looked at the skull stripping? > > > > On 6/14/2019 1:40 PM, Agnieszka Sabisz wrote: > >> > >> External Email - Use Caution > >> > >> Hi all! > >> > >> We are running FS v.6.0. on a supercomputer operating on Linux. > >> We have two sets of data - one from 1.5T Aera Siemens, second > >> from 3.0T Achieva TX Philips. The T1 images on both scanners have > >> comparable CNR, with an isotropic resolution of 1mm3 each. The > >> recon-all finished with no errors, but in approximately half of > >> the Philips data there is a significant (up to 40%) difference > >> between the brain mask volume and eTIV (no such problem on > >> Siemens). We inspected the Talairach registration (as is pointed > >> that eTIV is calculated upon it) in the mismatched data with: > >> tkregister2 --mgz --s <subject> --fstal --surf orig > >> and in the corrupted data the brain mask and the WM-GM borders > >> align in terms of placement but are of a wrong scale > >> (proportionate to the "brainmask-to-eTIV" difference). > >> > >> What may be the reason and how to cope with that? We cannot > >> normalize the volume data to eTIV (as it is not proper), what > >> value should we use instead? > >> > >> Attached you will find example tkregister2 output screenshots. > >> > >> Best regards, > >> Agnieszka Sabisz > >> > >> > >> > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu <mailto: > Freesurfer@nmr.mgh.harvard.edu> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto: > Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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