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 <agnieszkasabisz@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. <DGREVE@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.
> <DGREVE@mgh.harvard.edu <mailto:DGREVE@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
>>
>>
>>
>>
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