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Hi all
Regarding hippocampal subfield segmentation in FS7- how can I move the segmentation result to native T2w space? I plan to compare the result with a manual segmentation which was done in this space, using scripts which require nifti inputs.
I have run FS7 specifying with the -cm flag that this takes place in my T1 (MP2RAGE) 0.65mm isotropic resolution: recon-all -all -s <subject> -i T1w.nii -T2 T2w.nii -T2pial -gcut -cm
Then I ran the Hc subfield segmentation, specifying that my T2w volume (3D-SPACE, 0.55mm isotropic) should be used for this: segmentHA_T2.sh <subject> T2w.nii 3DT2 0
The output that I want to move back to native 3DT2 space is the labelled volume lh.hippoAmygLabels-3DT2.v21.mgz (or the nifti of this which of course I can create using mri_convert). However this volume is 0.333mm isotropic and has a limited field of view - from the documentation: "Note that [lr]h.hippoAmygLabels-T1.v21.mgz and [lr]h.hippoAmygLabels-T1.v21.[hierarchy].mgz cover only a patch around the hippocampus, at a higher resolution than the input image."
The most relevant guidance I can find in the documentation is "[lr]h.hippoAmygLabels-T1.v21.FSvoxelSpace.mgz live in the same voxel space as the other Freesurfer volumes (e.g., orig.mgz, nu.mgz, aseg.mgz), so you can use it directly to produce masks for further analyses, but its resolution is lower (1 mm vs 0.333 mm)." In my case FSvoxelSpace is at 0.65mm resolution, but this is still lower than my T2w volume (0.55mm) and so would involve some downsampling (0.333mm --> 0.65mm --> 0.55mm) which I would like to avoid.
I have tried various linear registration approaches but I always end up with a result which, although in 0.55mm space, is clearly not aligned with the hippocampus when viewed together with my T2w.nii in ITK-SNAP.
Any suggestions would be much appreciated!
Many thanks
Mike
Dear Michael,
Your code will create 3DT2.FSspace.mgz which is at 0.55mm resolution but with a rotation/translation in the header to overlap the T1 in RAS space.
You can now run mri_convert [lr]h.hippoAmygLabels-T1.v21.[hierarchy].mgz [lr]h.hippoAmygLabels-T1.v21.[hierarchy].resampled.mgz -rl 3DT2.FSspace.mgz -rt nearest -odt float to produce a volume in the same space as 3DT2.FSspace.mgz (also at 0.55mm). The flat -rl stands for “replace like”.
At that point, if the rotation between the original T2 and 3DT2.FSspace.mgz bothers you, you can combine the voxels from [lr]h.hippoAmygLabels-T1.v21.[hierarchy].resampled.mgz and combine them with the header of the original T2 to undo the rotation ;-)
Cheers,
/E
Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com
On Dec 8, 2021, at 04:33, Eyre, Michael <michael.eyre@kcl.ac.ukmailto:michael.eyre@kcl.ac.uk> wrote:
External Email - Use Caution
Hi all
Regarding hippocampal subfield segmentation in FS7- how can I move the segmentation result to native T2w space? I plan to compare the result with a manual segmentation which was done in this space, using scripts which require nifti inputs.
I have run FS7 specifying with the -cm flag that this takes place in my T1 (MP2RAGE) 0.65mm isotropic resolution: recon-all -all -s <subject> -i T1w.nii -T2 T2w.nii -T2pial -gcut -cm
Then I ran the Hc subfield segmentation, specifying that my T2w volume (3D-SPACE, 0.55mm isotropic) should be used for this: segmentHA_T2.sh <subject> T2w.nii 3DT2 0
The output that I want to move back to native 3DT2 space is the labelled volume lh.hippoAmygLabels-3DT2.v21.mgz (or the nifti of this which of course I can create using mri_convert). However this volume is 0.333mm isotropic and has a limited field of view - from the documentation: "Note that [lr]h.hippoAmygLabels-T1.v21.mgz and [lr]h.hippoAmygLabels-T1.v21.[hierarchy].mgz cover only a patch around the hippocampus, at a higher resolution than the input image."
The most relevant guidance I can find in the documentation is "[lr]h.hippoAmygLabels-T1.v21.FSvoxelSpace.mgz live in the same voxel space as the other Freesurfer volumes (e.g., orig.mgz, nu.mgz, aseg.mgz), so you can use it directly to produce masks for further analyses, but its resolution is lower (1 mm vs 0.333 mm)." In my case FSvoxelSpace is at 0.65mm resolution, but this is still lower than my T2w volume (0.55mm) and so would involve some downsampling (0.333mm --> 0.65mm --> 0.55mm) which I would like to avoid.
I have tried various linear registration approaches but I always end up with a result which, although in 0.55mm space, is clearly not aligned with the hippocampus when viewed together with my T2w.nii in ITK-SNAP.
Any suggestions would be much appreciated!
Many thanks
Mike _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Dear Juan
Thanks, this worked perfectly!
best wishes
Mike ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Iglesias Gonzalez, Juan E. JIGLESIASGONZALEZ@mgh.harvard.edu Sent: 08 December 2021 16:24 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Propagating hippocampal subfield segmentation to native T2w space
You don't often get email from jiglesiasgonzalez@mgh.harvard.edu. Learn why this is importanthttp://secure-web.cisco.com/1gczV1S--jbZutCtaIg9qq-lvPdLHcLY74Q_icZExDzYDet2apFwcKRaD9VUP--NUPQFIP5luS4nPJV7L2PgoDgfByNbjRByLhB9KecXzXhoat0tD24tA63Jap-hoLaaJJjb0HkgGuWpbDd79ZY-mb_fxox3A0KhIUjiY-bwWnF3bl8LdsSF6fkYROTddk0xTTvYT4BsvXGH_S70WAprp4xgqgvLdxAinya_wPSFpzaiH-qTOXo6L4x4-0Vr0k25JJEyeBDWHklS7IOhCFpti9CIIejrP2JQc0rbnOkZ4bkt8IISHszKxP7iObBviuhV_/http%3A%2F%2Faka.ms%2FLearnAboutSenderIdentification Dear Michael,
Your code will create 3DT2.FSspace.mgz which is at 0.55mm resolution but with a rotation/translation in the header to overlap the T1 in RAS space.
You can now run mri_convert [lr]h.hippoAmygLabels-T1.v21.[hierarchy].mgz [lr]h.hippoAmygLabels-T1.v21.[hierarchy].resampled.mgz -rl 3DT2.FSspace.mgz -rt nearest -odt float to produce a volume in the same space as 3DT2.FSspace.mgz (also at 0.55mm). The flat -rl stands for “replace like”.
At that point, if the rotation between the original T2 and 3DT2.FSspace.mgz bothers you, you can combine the voxels from [lr]h.hippoAmygLabels-T1.v21.[hierarchy].resampled.mgz and combine them with the header of the original T2 to undo the rotation ;-)
Cheers,
/E
Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://secure-web.cisco.com/1E1XL9kwKPTpVCde-QcmIE3ny24irr5U-TWrQrV4Y1latdsO...https://secure-web.cisco.com/17SPp2UFyVXgNi8YzVezcuWO5E-1RP0KSlPseHX04J4gvAt_qU6NVQcmbMNYOf11Nr9RYBwlMDNTFy82jWpqG0gr0-sOsBi6loGJI2zfMkkDHerpo1HwFKU3poYMR-jP0YOzNSylE7FSDHEtRvS9KXaENLQVJxu91SkPFU9J6l4ot8kdFUQTaINW4v7zrPk8T15EZQOWiCBA_hV9NPxOynjjHjevseQ8C6F9MBIFMCOrlYV8tLEZ5uWN-DEzZ_fq5gL9evGTo43Zigzyggs9Z2KN09_ejcY1sBXucBqegiwwZjtmXNbOCcFsBpLHAa1K-/https%3A%2F%2Feur03.safelinks.protection.outlook.com%2F%3Furl%3Dhttp%253A%252F%252Fwww.jeiglesias.com%252F%26data%3D04%257C01%257Cmichael.eyre%2540kcl.ac.uk%257Cbfb6066500b3423edf0108d9ba6783aa%257C8370cf1416f34c16b83c724071654356%257C0%257C0%257C637745776037823403%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%26sdata%3DJd%252BE4FTrHFHgtWiZMUqfsAqMvrCM1r5quJVCeKIZ93U%253D%26reserved%3D0
On Dec 8, 2021, at 04:33, Eyre, Michael <michael.eyre@kcl.ac.ukmailto:michael.eyre@kcl.ac.uk> wrote:
External Email - Use Caution
Hi all
Regarding hippocampal subfield segmentation in FS7- how can I move the segmentation result to native T2w space? I plan to compare the result with a manual segmentation which was done in this space, using scripts which require nifti inputs.
I have run FS7 specifying with the -cm flag that this takes place in my T1 (MP2RAGE) 0.65mm isotropic resolution: recon-all -all -s <subject> -i T1w.nii -T2 T2w.nii -T2pial -gcut -cm
Then I ran the Hc subfield segmentation, specifying that my T2w volume (3D-SPACE, 0.55mm isotropic) should be used for this: segmentHA_T2.sh <subject> T2w.nii 3DT2 0
The output that I want to move back to native 3DT2 space is the labelled volume lh.hippoAmygLabels-3DT2.v21.mgz (or the nifti of this which of course I can create using mri_convert). However this volume is 0.333mm isotropic and has a limited field of view - from the documentation: "Note that [lr]h.hippoAmygLabels-T1.v21.mgz and [lr]h.hippoAmygLabels-T1.v21.[hierarchy].mgz cover only a patch around the hippocampus, at a higher resolution than the input image."
The most relevant guidance I can find in the documentation is "[lr]h.hippoAmygLabels-T1.v21.FSvoxelSpace.mgz live in the same voxel space as the other Freesurfer volumes (e.g., orig.mgz, nu.mgz, aseg.mgz), so you can use it directly to produce masks for further analyses, but its resolution is lower (1 mm vs 0.333 mm)." In my case FSvoxelSpace is at 0.65mm resolution, but this is still lower than my T2w volume (0.55mm) and so would involve some downsampling (0.333mm --> 0.65mm --> 0.55mm) which I would like to avoid.
I have tried various linear registration approaches but I always end up with a result which, although in 0.55mm space, is clearly not aligned with the hippocampus when viewed together with my T2w.nii in ITK-SNAP.
Any suggestions would be much appreciated!
Many thanks
Mike _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1ZbTEmiPTaEFDpgx887E6Pw5veto26-W0tC_gwv7rYgKtVE...https://secure-web.cisco.com/1zPPfNPwJtSWr58Pbntufzk_Vz0MBOadxPFTsAWxjkrrECP1xtx-iCJ4qzo4PR1YCK3djBstGYbEiazeqBvrB5xUcjhlnWf9Xo4LosoP1xpZHiUXl8PuhhpC5zoOcUaO4boZUSFCuHQHapgPetmhXYa5XW4mc5pA_WbnPeqB9XyofP1m494pMLL9y8PYfW8hH-UYVuwTlJ2X_jELvu70CYmmB6X-Z9oWs_9c4GKzFP64-ozzmOQIWe4g_8Pyk7e4pUs6ztKI4QLPxoAKNk7FM5CWWehD1Zb9swtIwc4J0f26RD3T00M-EBaM2CfUUQtzl/https%3A%2F%2Feur03.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fmail.nmr.mgh.harvard.edu%252Fmailman%252Flistinfo%252Ffreesurfer%26data%3D04%257C01%257Cmichael.eyre%2540kcl.ac.uk%257Cbfb6066500b3423edf0108d9ba6783aa%257C8370cf1416f34c16b83c724071654356%257C0%257C0%257C637745776037823403%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%26sdata%3DhoAhnrsmNQVztPQsWfnZFYRG517Vh8U1a7e1ozESPzQ%253D%26reserved%3D0
freesurfer@nmr.mgh.harvard.edu
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Eyre, Michael -
Iglesias Gonzalez, Juan E.