Chris/Ruopeng, you can use https://transfer.partners.org
On 12/17/2021 11:41 AM, Christopher Panks wrote:
External Email - Use Caution
Hi Ruopeng,
I can send the niftis to an individual, but I cannot post them to a
listserv.
Version info:
freesurfer-linux-ubuntu18_x86_64-dev-20211028-42af00d
FreeView Version 3.0 Build Oct 28 2021 08:53:38
I get this warning when I start FreeView:
X server does not support XInput 2
failed to get the current screen resources
QXcbConnection: XCB error: 1 (BadRequest), sequence: 165, resource id:
90, major code: 130 (Unknown), minor code: 47
QXcbConnection: XCB error: 170 (Unknown), sequence: 178, resource id:
90, major code: 146 (Unknown), minor code: 20
QXcbConnection: XCB error: 170 (Unknown), sequence: 178, resource id:
90, major code: 146 (Unknown), minor code: 20
Thank you so much for your help!
Chris Panks
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Wang, Ruopeng
*Sent:* Tuesday, December 14, 2021 6:12 PM
*To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] Freeview Transform Volume tool - output
nifti keeps rotations but loses translations
What version of Freesurfer are you using? Would it be possible to send
us the volume files before and after the rotation?
Best,
Ruopeng
On Dec 14, 2021, at 6:10 PM, Christopher Panks <cpa...@uw.edu> wrote:
* External Email - Use Caution *
I’m trying to get images of post-mortem brains, some from
cadavers, some excised, into standard space. I’m new to Freeview,
so I’m not sure if I’m doing something wrong, or my expectations
are wrong. I find the Transform Volume tool easy to use to get an
image that is correctly rotated, and shifted so that the image is
centered in the frame. The image looks great in the Freeview panes.
Upon saving and then opening the output nifti, I find the
rotational changes have stuck, but the image is as off-center as
the original, with the coronal and axial off towards one side, and
the sagittal not at the midbrain.
When saving the image, I click on ‘Save Volume as…’, leave the
boxes unchecked (‘do not resample’’, and ‘crop to’ ), I modify the
file name, then click OK. I don’t click on ‘Move Center…’, I
don’t check ‘Apply to all…’.
My expectation is that the image would not only be correctly
rotated, but that it would also be centered. Is that the expected
behavior here?
I’ve tried the ‘Move Center to Current Cursor Location’, and the
Apply to all visible volumes, and see no difference. The
off-centeredness is visible in multiple viewers, FSLEyes,
MRIcroGL, and ROIEditor. The directions seem so simple and clear,
I’m just baffled.
Thank you!
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