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!
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 <cpanks@uw.edumailto:cpanks@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! _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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 <cpanks@uw.edumailto:cpanks@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! _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1zCeTGEn_BzD6-TmBO9sK1X2H_Ociuz8cE8p3onS1KHffP_...
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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 <cpanks@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! _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1zCeTGEn_BzD6-TmBO9sK1X2H_Ociuz8cE8p3onS1KHffP_orF_uFj6Os_grP12FmyHDdl3ea8vTRf0uxMJ-7qEJ8p4M2Sm2vwjyk0nGmArLZiBzHiFnDc4544371QghqdGjcu3vQ9LWKpK89tzwCUuCwG_Sm3O8Fa9tWppR2Kku8cojpu8hO6Bz1HlO1Et0D7Ch1_AQEoXIJ9WKz9x129wF3DjvyaTJqG5TI0Sy4QZP1ZnFMyIjgIG2oza1i_6i8SFy0nro4yEye61CEKbkNXzvdm8kRgixmmbf9NB0tICR5RQkS1zvx-K1E_uKT5JdAxg7I0aHjC4d9qJyAoC9KXg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
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Wang, Ruopeng