External Email - Use Caution Dear Doug, Thanks a lot!!! 3t flag helps very much. The data looks fine now. All the best Agnieszka
pon., 19 sie 2019 o 15:59 Greve, Douglas N.,Ph.D. <dgr...@mgh.harvard.edu> napisał(a): > Hi Agnieska, sorry for the delay. It looks like the contrast is slightly > different than FS expects. I ran it with the -3T flag (which changes the > talairach atlas), and it seemed to run fine on that subject. Try it out. > best > doug > > On 8/19/2019 1:23 AM, Agnieszka Sabisz wrote: > > External Email - Use Caution > Dear Doug, > I uploaded the data by ftp in Windows 10 on 1st Aug. 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 > > czw., 1 sie 2019 o 11:44 Agnieszka Sabisz <agnieszkasab...@gmail.com> > napisał(a): > >> 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 >> >> > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://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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