External Email - Use Caution
Hello Freesurfer team,
I tried to use SAMSEG-long to deal with my longitudinal data with paired MPRAGE and FLAIR images. But when I checked the original FLAIR images I have, I found that they have a voxel resolution of 1.333333 x 1.333333 x 2.000000. When I view it on Freeview, although the axial view is fine, only a rectangular portion of the sagittal and coronal brain is available, with the top and the bottom cut off. I guess it’s probably due to resampling issue that assumes isotropic voxels which we do not have. Is there any way to fix this problem?
Best, Jin
External Email - Use Caution
Hi Jin,
To me it doesn't sound like a resolution issue: samseg will happily "eat" whatever resolution you have in your images, although for multicontrast data such as yours you'd need to resample all contrasts to the image grid of one contrast (typically T1 since it's higher resolution). I'm guessing top/bottom axial slices in the FLAIR were simply not acquired?
Koen
On Mon, Oct 21, 2024 at 4:32 PM Jin Liu jin.liu@stonybrook.edu wrote:
External Email - Use CautionHello Freesurfer team,
I tried to use SAMSEG-long to deal with my longitudinal data with paired MPRAGE and FLAIR images. But when I checked the original FLAIR images I have, I found that they have a voxel resolution of 1.333333 x 1.333333 x 2.000000. When I view it on Freeview, although the axial view is fine, only a rectangular portion of the sagittal and coronal brain is available, with the top and the bottom cut off. I guess it’s probably due to resampling issue that assumes isotropic voxels which we do not have. Is there any way to fix this problem?
Best,
Jin _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1cfIOVcvsOAkcEjMFX3ns4ly-wND2ILPYTPEAvEF6PQQZ12... The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1UeKRSqsr0QNHsWJ67NZYw5DSFzN2YFpNuI9IyqgceH_VnI... < https://secure-web.cisco.com/1UeKRSqsr0QNHsWJ67NZYw5DSFzN2YFpNuI9IyqgceH_VnI... .
Is this just a visualization issue? What is your freeview command?
On 11/12/2024 3:55 AM, Koen Van Leemput wrote:
External Email - Use Caution
Hi Jin,
To me it doesn't sound like a resolution issue: samseg will happily "eat" whatever resolution you have in your images, although for multicontrast data such as yours you'd need to resample all contrasts to the image grid of one contrast (typically T1 since it's higher resolution). I'm guessing top/bottom axial slices in the FLAIR were simply not acquired?
Koen
On Mon, Oct 21, 2024 at 4:32 PM Jin Liu jin.liu@stonybrook.edu wrote:
External Email - Use Caution Hello Freesurfer team, I tried to use SAMSEG-long to deal with my longitudinal data with paired MPRAGE and FLAIR images. But when I checked the original FLAIR images I have, I found that they have a voxel resolution of 1.333333 x 1.333333 x 2.000000. When I view it on Freeview, although the axial view is fine, only a rectangular portion of the sagittal and coronal brain is available, with the top and the bottom cut off. I guess it’s probably due to resampling issue that assumes isotropic voxels which we do not have. Is there any way to fix this problem? Best, Jin _______________________________________________ Freesurfer mailing list 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/1cfIOVcvsOAkcEjMFX3ns4ly-wND2ILPYTPEAvEF6PQQZ128mAXtM_aWUsy8iUDEjaJDjmrW2lDFdgXrxxW7_7UjK_CvUH_esAWpeQGAAkpeTw5gsUZhdeEDwA_t5L_VlfLdM3qypeYqfiYZ9ULPQpwW4WoLzxno0418vj3UAaEWGfq5LVqIF0tZTgG3eM4rKqYRGIUJ-YRiZzv_UWW3UffgzrhoaN4ioItitXIDQ2voylh_yZi-kTTL5HpdYj1QRcqiKCCBVRfZ_C6DfCHJjAJR9d3bylnSmEY6JPYxH2MqWvcxIh3wrzhLJ8dZzy9QxStBcWeEq9j-Ij2wjbGBmGA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://www.massgeneralbrigham.org/complianceline <https://secure-web.cisco.com/1UeKRSqsr0QNHsWJ67NZYw5DSFzN2YFpNuI9IyqgceH_VnImiy-621jXoFb19wkXGfyMPjYdwUTM4SewniZQDjfe_hIqz_NvPJDu_frottOXqL4yg9cE_6dtrQQiMjjxoFlxuUB0pGXeLZ0KNr01z2p3vz0CaFFi7e6wy2WuAIh1g22_q_wzEbdHIycpQLs6NYUTe2Ykr8ZRsdGv9BpXCmLytDvcqP-NxfVloCXXxxDf_SujRBCR0PK_kv16th6bfy9J5NfBtmz1Pu47WKd_VrzKcvyUu_igCAsLvKWByF9rOiVPMyM4IUkImtse5GapF6st3jBiQ8SxrhVA9UFIgmg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> <*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://www.massgeneralbrigham.org/complianceline <https://secure-web.cisco.com/1UeKRSqsr0QNHsWJ67NZYw5DSFzN2YFpNuI9IyqgceH_VnImiy-621jXoFb19wkXGfyMPjYdwUTM4SewniZQDjfe_hIqz_NvPJDu_frottOXqL4yg9cE_6dtrQQiMjjxoFlxuUB0pGXeLZ0KNr01z2p3vz0CaFFi7e6wy2WuAIh1g22_q_wzEbdHIycpQLs6NYUTe2Ykr8ZRsdGv9BpXCmLytDvcqP-NxfVloCXXxxDf_SujRBCR0PK_kv16th6bfy9J5NfBtmz1Pu47WKd_VrzKcvyUu_igCAsLvKWByF9rOiVPMyM4IUkImtse5GapF6st3jBiQ8SxrhVA9UFIgmg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>> .
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N. Greve -
Jin Liu -
Koen Van Leemput