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Finally I found why I could not reproduce the results, the atlas used for cortical parcellisation changed and are not the ones written in the documentation. The Desikan atlas is actually DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs and not curvature.buckner40.filled.desikan_killiany.2007-06-20.gcs anymore.
Le 23 févr. 2021 à 16:52, THIBEAU SUTRE Elina <elina.thibeausutre@icm-institute.orgmailto:elina.thibeausutre@icm-institute.org> a écrit :
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Thank you for your answer!
I actually found a .gcs version of the atlas here MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1GmKT3Pr0kzZX8jesiVyn29E2cuTEtHGX5wM-qb27JmnW1K...https://secure-web.cisco.com/1TPDae69tXL0YhSBozrk1N7tGtE3GXe2a1yGFBoxgjwLfrCvksskOQZymx-eN_b2tErfw7WWLxnOfVM0_94moU0hTgdCHZRoxNFm6V5RZvl6R4oIrsZF35HkuvLX4tUYDsZr3Kpw4CXoV4KwdYrzpjgZ9aYHcZD5nlHc_YJQf32UjtOSt-IRsT7rfLyQ_4ss3NW1c9HwILFPO79DiowdIXZZJ2WbC6l6fGXl8ZLLdaF2zZFfGwTmDeXKFf0Ad1GzZ/https%3A%2F%2Ffra01.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1DEIqPvOjJClzmnD0pPJe4KUO0ZGfQXNibFw42NNAFdce7z3wfEYEHkLr6hUVsVtT49h6keiOEtxdoM54OmnAKuttOm_uXHUzlLXqsnBvAgInmXl1-XvcPJ28TR2wnfF8ZQjNRniz_OW04Uf_LYdUS7_wKdXxqdbZXiKtYejiwKOhqtGkCxXD2aY0K8duznwGNsMMLGj1IzpCUoSQxy_Km-8CtuxPK4WRfXyhIEJ_3QnSfFNJc3ElrSxZ-I1JCmVKr6YpQxqzIabA4i_rJ50-Mg%252Fhttps%25253A%25252F%25252Ffigshare.com%25252Farticles%25252Fdataset%25252FmultiAtlasTT_data%25252F5998583%26data%3D04%257C01%257Celina.thibeausutre%2540icm-institute.org%257Ce43a570b7e2c4e81beca08d8d81316eb%257C9df7cf1718fa41508b00dc5e754777d8%257C0%257C0%257C637496924728217586%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%26sdata%3Dnynp5FR02zjX1gppkk4dMOempplMBwVqlH39%252BSKBk0E%253D%26reserved%3D0. I now try to reproduce the steps done in freesurfer recon-all with this atlas.
I now have another problem: when I try to reproduce the steps based on MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1-cKffH_pDrVfcWaSKtbQUnXtwY-xaNNTXr2qAEJq2kcF9w...https://secure-web.cisco.com/1Rap1myL0Tv6l1BJFKg53EXKX9EWfJ-4OhgrdVbMb46TThKNs1tFTxXULIW6tWYmk68Vy9PtVQD1SyBqep1I4J7rBbkW9ttgY7OwkbnDEjMNJP7UCkOYiSYx-BZMIO6UUjUnoqFyNXe4aNhZ3FKPvjCT2s9Af2cGbCYKB7eBx3yX9dxkpzADE0PYijMmDxvvEcA4J0XAImyW9IIgWOIQvZbkpcWzs30DYmxjEVMq1HR3HWApoiFMBoHZQojU4V5gC/https%3A%2F%2Ffra01.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1ryL0fLjnek4Tnqkk8ASdgyohf1OqhYaYARM-aoRqIgHHa4KMvcpBqGYD1SkRwj59xoxgBZGZu8HbsRTqDUPo3wdzMY3Zl4GBq4zQiiTlcGE2qkr553kCi0Nx2TQG5p5VrWJFITVb1II2aF344_5DGTQGtCCXkdaLpuuwg-vS-7XmKpTg_EoqLOmYdN_sn1Kapk9KLNy6gT0EqgCqrSBUI-CqZkqtpAktc98SlWC3c_NV3HGeO-QD1Z7ZL025sNnH_Zzg9Xz8HeI9QVlqkjxTVA%252Fhttps%25253A%25252F%25252Fsurfer.nmr.mgh.harvard.edu%25252Ffswiki%25252FReconAllTableStableV6.0%26data%3D04%257C01%257Celina.thibeausutre%2540icm-institute.org%257Ce43a570b7e2c4e81beca08d8d81316eb%257C9df7cf1718fa41508b00dc5e754777d8%257C0%257C0%257C637496924728227577%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%26sdata%3DYcAJRU2715SmWl0VC7h3GLeFDt0uvowRmGx8NviEKzE%253D%26reserved%3D0 with an atlas used by the pipeline (for example ?h.curvature.buckner40.filled.desikan_killiany.2007-06-20.gcs) I do not obtain the same result than with recon-all.
My freesurfer version is 6.0.0 and I tried to do the two steps leading to the creation of statistics for one particular subject:
mris_ca_labelhttps://secure-web.cisco.com/1Ve1LvaGvrLWGQ_Zr7ZmIMI0UciCyi15YkpsibVTCfLnbC2Ehn84kLCMeCLRtnEG3YOUPhf1yGnO0y7VwvZ1NDqlmkFDJVaG8-NKhoyTiRQNbj4CsqKPf52n6YECNCjJrOlM7RaR2rgTMrx39bdTYDGw3xktY10XG08sIoKv4egFpmp6ET-9UrEPahtg9f_8BlI_sj-WMk1JkGV2rxJmttztXBdpIFxMWJPrTW7OKMlpxLJ8CiOyBow5sbqFeTBPy/https%3A%2F%2Ffra01.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F12IAK5Ur9fuEvwqrpoWlUXGX8RuQFwflXSttKHeTA5fQnqm4nJcuvEExXAh-_8q-X63npS9CdJA5UzNkezBoAgTJ-D6KPKgUHZ44hpprXUyyhnc77GTmQLfgcwW4LT0hTnWNGRNeDAXGX3gshheanPM1sKrtU76YXL2WbYmjEJqfMQ4oToGgCD1UkuzBbfz2mD25AXF43quxrJu8sqchS75zlbQq-q3rhK781bxzspUO8vtxcOiT2AichIxGhU6KXDp8c3EMwsobkntLOFBxfbQ%252Fhttps%25253A%25252F%25252Fsurfer.nmr.mgh.harvard.edu%25252Ffswiki%25252Fmris_ca_label%26data%3D04%257C01%257Celina.thibeausutre%2540icm-institute.org%257Ce43a570b7e2c4e81beca08d8d81316eb%257C9df7cf1718fa41508b00dc5e754777d8%257C0%257C0%257C637496924728237579%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%26sdata%3D%252B4t2Ol3wK%252BHBY8Finn8%252BDfCC8oMkAiPqoz6oIY25TcI%253D%26reserved%3D0 -l ../label/?h.cortex.label -aseg aseg.presurf.mgz <subjid> ?h ?h.sphere.reg $FREESURFER_HOME/average/?h.curvature.buckner40.filled.desikan_killiany.2007-06-20.gcs ?h.aparc.annot
mris_anatomical_statshttps://secure-web.cisco.com/1kM2N-dozPnvnd_mmUSWE9LIs-SWUUwDyW0FHKuhm0D8lhf7dnfxPbe4IbPcwD9Az1wmmkz06TdeOuhYYy0AlwwNK0A2vREqk9E-887rcSLFLyDvRkbJnCUp1eDtv-GkXu7PY09cq7lA3gto6kT2cJ7D34dl2gGUvyTvHyj-7to7Rd8y8UJcc_XUv6ndowAnDKv808eH2WX7c96UBakgtvTYywhFRHD_rAz-n_E5J2RsnYmCtPZdBomYrwlgVNEZZ/https%3A%2F%2Ffra01.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1QV93h4cOkPnD7_nSX85-sjhRWrFz-fWNKvA_Z7YUYnKkTEhFskry8y3P2x2mNczBxaXayY0UU2w-92vHrmfJWZtqHgWL7pZY7tuKCLLNRWG9fNoH_wsanPDbl3s5p7zLmwU7lrIo0EvwgWaQGWC4YAbwcCtK1R01UZJQmveyCPTn6oWKrwva46GU5UzI7BBcW4d6Z6rZaM0MIb6UxKL_Untmvp0qxq8Qw3PJr6pzWQEtmBm0mC9Lgig0uwmrrgrxluk0JEQc92CfZctNtBHeaA%252Fhttps%25253A%25252F%25252Fsurfer.nmr.mgh.harvard.edu%25252Ffswiki%25252Fmris_anatomical_stats%26data%3D04%257C01%257Celina.thibeausutre%2540icm-institute.org%257Ce43a570b7e2c4e81beca08d8d81316eb%257C9df7cf1718fa41508b00dc5e754777d8%257C0%257C0%257C637496924728237579%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%26sdata%3DI1hXZMEztNGpwgZJEe%252B18%252Fj0hA4QZ7%252FpGQBxST4tJWI%253D%26reserved%3D0 -th3 -mgz -cortex ../label/?h.cortex.label -f stats/?h.aparc.stats -b -a label/?h.aparc.annot -c label/aparc.annot.ctab <subjid> ?h
Can you confirm that these are the correct steps to perform ? And that the root directory here is $SUBJECTS_DIR/<subjid> /mri?
Le 23 févr. 2021 à 15:07, Douglas N. Greve <dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu> a écrit :
depends on the nature of AICHA. Are these labels on a group of subjects? If so, you can build your own gcs file with train-gcs-atlas. If it is just a label set, then you should run recon-all on the template subject, sample the labels onto the surface (mri_vol2surf), then convert the resulting surface segmentation to an annotation (mris_seg2annot), then map the annot to other subjects with mris_apply_reg
On 2/22/2021 8:59 AM, THIBEAU SUTRE Elina wrote:
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Hello freesurfer experts,
I would like to use freesurfer recon-all to obtain the regional cortical thicknesses of subjects of ADNI dataset. I launched freesurfer recon-all and obtained the parcellations according to Destrieux and Desikan-Killiany atlases. I would like to know how to obtain the same parcellations with another atlas, AICHA (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1XEWG1hSkbalsFB0I9ErSgcWhYrJEwa4mSLdh1UyKBjHAJC...https://secure-web.cisco.com/12Nbh4ssHC35lblXxHoeZuZQGAWJehEKBaApFn8eMO6WuWLsUrmyHdbI0WU49i_kY8s38aiRwwyg_CShp7Gd84ycLVjHOCad9zr9IetQUIzE3DMbrH-8XpzFAjahCVIn3QerecxfTHIZ1t5cZmNGJphXm9f4fa2H_F0cLkPJ79deFZ-rShX06i7Gng9HDd3Pj6a5rmgK-w4ksgNb65G3MHQ/https%3A%2F%2Ffra01.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1znEOm2w0dQV4t0t9QyQq7Ma3ojLFRlolC2Oal0YVkqOJUodCGVKTnRhr2D_9LDr7Bw7iaWRhwkh0iGvCegJR-qeHO5rV2l0x6SGbUSAzOVPBfpmzZ3s9GF6p5csqj5AYgfCeCoeKqKv5VyR5Ap7_saXFW2aFBNdgpSojzgSl56sfLda9uEim7_l2sn7OuAgmSQfgY3EJAX2UwhhKIDD3pe1605a_oc_KECBg8LgzuQ2bmPWz_fVd8E1_Rr6BAzPFKmxPaoCqONmC9whx7c5X8Q%252Fhttps%25253A%25252F%25252Ffra01.safelinks.protection.outlook.com%25252F%25253Furl%25253Dhttps%2525253A%2525252F%2525252Fsecure-web.cisco.com%2525252F1st38nLf-34KvmX5j8oNCBRhTI_Ki20PWEfeEACfqaaGqdiXjkdA--goU3B6IkaTck3uXUFW9PmxiYWxWNPST5LUGFFTaUlKadBruD6A0SMedSCRFTzDENaGqJqlV34SDvtILiz55CiWkiCY7mgnZGga2VfWgyBqq8eGOtGYAHFCl78eI1uoxy7uER0ZQuKi0_lg1e5SY3Esympi07huCo4yNWH2ilL0M2AeBJJEIROQSy4Ya9blgPiWIQnsqIOEKBYcIOqmyH5WrcQ_-hDuHtg%2525252Fhttps%252525253A%252525252F%252525252Fwww.gin.cnrs.fr%252525252Fen%252525252Ftools%252525252Faicha%252525252F%252526data%25253D04%2525257C01%2525257Celina.thibeausutre%25252540icm-institute.org%2525257Cbc41ab0f3f894166b77208d8d805febc%2525257C9df7cf1718fa41508b00dc5e754777d8%2525257C0%2525257C0%2525257C637496867552962843%2525257CUnknown%2525257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%2525253D%2525257C1000%252526sdata%25253Dl%2525252BJSnlrxooSAkkhXwLjNjxnvLyNPwlJl5axMVfDdMCg%2525253D%252526reserved%25253D0%26data%3D04%257C01%257Celina.thibeausutre%2540icm-institute.org%257Ce43a570b7e2c4e81beca08d8d81316eb%257C9df7cf1718fa41508b00dc5e754777d8%257C0%257C0%257C637496924728247572%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%26sdata%3Dl7aTUQVIffuzjsl%252BjF1GW2EKYMJyu6I33VBi9aHOaTs%253D%26reserved%3D0), which is only available in nifti format.
I understood that I should create a .gcs file from the nifti version but I am not sure how. I saw that mris_ca_train could be used to create such a file from a a manually labelled dataset but I don’t know how to create these labelled subjects from the nifti atlas.
If anyone has already this kind of conversion .nii -> .gcs I would be really interested to know how you have done that!
Best regards, Elina
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