External Email - Use Caution

Thank you for your answer!

I actually found a .gcs version of the atlas here https://secure-web.cisco.com/1DEIqPvOjJClzmnD0pPJe4KUO0ZGfQXNibFw42NNAFdce7z.... 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 https://secure-web.cisco.com/1ryL0fLjnek4Tnqkk8ASdgyohf1OqhYaYARM-aoRqIgHHa4... 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/12IAK5Ur9fuEvwqrpoWlUXGX8RuQFwflXSttKHeTA5fQnqm4nJcuvEExXAh-_8q-X63npS9CdJA5UzNkezBoAgTJ-D6KPKgUHZ44hpprXUyyhnc77GTmQLfgcwW4LT0hTnWNGRNeDAXGX3gshheanPM1sKrtU76YXL2WbYmjEJqfMQ4oToGgCD1UkuzBbfz2mD25AXF43quxrJu8sqchS75zlbQq-q3rhK781bxzspUO8vtxcOiT2AichIxGhU6KXDp8c3EMwsobkntLOFBxfbQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fmris_ca_label -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/1QV93h4cOkPnD7_nSX85-sjhRWrFz-fWNKvA_Z7YUYnKkTEhFskry8y3P2x2mNczBxaXayY0UU2w-92vHrmfJWZtqHgWL7pZY7tuKCLLNRWG9fNoH_wsanPDbl3s5p7zLmwU7lrIo0EvwgWaQGWC4YAbwcCtK1R01UZJQmveyCPTn6oWKrwva46GU5UzI7BBcW4d6Z6rZaM0MIb6UxKL_Untmvp0qxq8Qw3PJr6pzWQEtmBm0mC9Lgig0uwmrrgrxluk0JEQc92CfZctNtBHeaA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fmris_anatomical_stats -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:

External Email - Use Caution

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/1RRyd6xMtrNJXVyY1JWC4jbWTyhI_rynylHQX17eQ6cV_6-...https://secure-web.cisco.com/1znEOm2w0dQV4t0t9QyQq7Ma3ojLFRlolC2Oal0YVkqOJUodCGVKTnRhr2D_9LDr7Bw7iaWRhwkh0iGvCegJR-qeHO5rV2l0x6SGbUSAzOVPBfpmzZ3s9GF6p5csqj5AYgfCeCoeKqKv5VyR5Ap7_saXFW2aFBNdgpSojzgSl56sfLda9uEim7_l2sn7OuAgmSQfgY3EJAX2UwhhKIDD3pe1605a_oc_KECBg8LgzuQ2bmPWz_fVd8E1_Rr6BAzPFKmxPaoCqONmC9whx7c5X8Q/https%3A%2F%2Ffra01.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1st38nLf-34KvmX5j8oNCBRhTI_Ki20PWEfeEACfqaaGqdiXjkdA--goU3B6IkaTck3uXUFW9PmxiYWxWNPST5LUGFFTaUlKadBruD6A0SMedSCRFTzDENaGqJqlV34SDvtILiz55CiWkiCY7mgnZGga2VfWgyBqq8eGOtGYAHFCl78eI1uoxy7uER0ZQuKi0_lg1e5SY3Esympi07huCo4yNWH2ilL0M2AeBJJEIROQSy4Ya9blgPiWIQnsqIOEKBYcIOqmyH5WrcQ_-hDuHtg%252Fhttps%25253A%25252F%25252Fwww.gin.cnrs.fr%25252Fen%25252Ftools%25252Faicha%25252F%26data%3D04%257C01%257Celina.thibeausutre%2540icm-institute.org%257Cbc41ab0f3f894166b77208d8d805febc%257C9df7cf1718fa41508b00dc5e754777d8%257C0%257C0%257C637496867552962843%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3Dl%252BJSnlrxooSAkkhXwLjNjxnvLyNPwlJl5axMVfDdMCg%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

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1HK_cgze3en9ZI2Qm8wMRPOStuZRcsQlsySHKA9riOjZBDl...https://secure-web.cisco.com/123VMFQTy2tuEvDEaL12fdFZ31Ec4fBre242Z0sfX10W9Wt9TjagpdwPkJaic1I2__QFfUdrBlh4dPBuQ2xIaJ9NzndKtqZie-_UnxKHk9AWKIg6bUEsFkddW3jJCb294FT_e5XHUgZ8eKs6qHjAN8gVv5XYklCnPkHfp-L5kbEG5snlznXbZS2hHO_-QdRCtSrxBI2b7-JLP13rN4Y7fDxjCdMXXLxTiAFcUSnIV5Mkf1skb2d_WMK2Cy6V_Iu38AKVFR42IqNDvuOrnhQiFdQ/https%3A%2F%2Ffra01.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fmail.nmr.mgh.harvard.edu%252Fmailman%252Flistinfo%252Ffreesurfer%26data%3D04%257C01%257Celina.thibeausutre%2540icm-institute.org%257Cbc41ab0f3f894166b77208d8d805febc%257C9df7cf1718fa41508b00dc5e754777d8%257C0%257C0%257C637496867552972836%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3DjPylHdSi8ZUpstj%252BRR0Elak%252B43mLFHDhsbYzhBbhqfA%253D%26reserved%3D0

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1HK_cgze3en9ZI2Qm8wMRPOStuZRcsQlsySHKA9riOjZBDl...

Look for those commands in the subject/scripts/recon-all.cmd to verify. It is possible that the table is not up-to-date

On 2/23/2021 10:52 AM, THIBEAU SUTRE Elina wrote:

External Email - Use Caution

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://figshare.com/articles/dataset/multiAtlasTT_data/5998583 https://secure-web.cisco.com/1DEIqPvOjJClzmnD0pPJe4KUO0ZGfQXNibFw42NNAFdce7z3wfEYEHkLr6hUVsVtT49h6keiOEtxdoM54OmnAKuttOm_uXHUzlLXqsnBvAgInmXl1-XvcPJ28TR2wnfF8ZQjNRniz_OW04Uf_LYdUS7_wKdXxqdbZXiKtYejiwKOhqtGkCxXD2aY0K8duznwGNsMMLGj1IzpCUoSQxy_Km-8CtuxPK4WRfXyhIEJ_3QnSfFNJc3ElrSxZ-I1JCmVKr6YpQxqzIabA4i_rJ50-Mg/https%3A%2F%2Ffigshare.com%2Farticles%2Fdataset%2FmultiAtlasTT_data%2F5998583.

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://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV6.0 https://secure-web.cisco.com/1ryL0fLjnek4Tnqkk8ASdgyohf1OqhYaYARM-aoRqIgHHa4KMvcpBqGYD1SkRwj59xoxgBZGZu8HbsRTqDUPo3wdzMY3Zl4GBq4zQiiTlcGE2qkr553kCi0Nx2TQG5p5VrWJFITVb1II2aF344_5DGTQGtCCXkdaLpuuwg-vS-7XmKpTg_EoqLOmYdN_sn1Kapk9KLNy6gT0EqgCqrSBUI-CqZkqtpAktc98SlWC3c_NV3HGeO-QD1Z7ZL025sNnH_Zzg9Xz8HeI9QVlqkjxTVA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReconAllTableStableV6.0 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_label https://secure-web.cisco.com/12IAK5Ur9fuEvwqrpoWlUXGX8RuQFwflXSttKHeTA5fQnqm4nJcuvEExXAh-_8q-X63npS9CdJA5UzNkezBoAgTJ-D6KPKgUHZ44hpprXUyyhnc77GTmQLfgcwW4LT0hTnWNGRNeDAXGX3gshheanPM1sKrtU76YXL2WbYmjEJqfMQ4oToGgCD1UkuzBbfz2mD25AXF43quxrJu8sqchS75zlbQq-q3rhK781bxzspUO8vtxcOiT2AichIxGhU6KXDp8c3EMwsobkntLOFBxfbQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fmris_ca_label -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_stats https://secure-web.cisco.com/1QV93h4cOkPnD7_nSX85-sjhRWrFz-fWNKvA_Z7YUYnKkTEhFskry8y3P2x2mNczBxaXayY0UU2w-92vHrmfJWZtqHgWL7pZY7tuKCLLNRWG9fNoH_wsanPDbl3s5p7zLmwU7lrIo0EvwgWaQGWC4YAbwcCtK1R01UZJQmveyCPTn6oWKrwva46GU5UzI7BBcW4d6Z6rZaM0MIb6UxKL_Untmvp0qxq8Qw3PJr6pzWQEtmBm0mC9Lgig0uwmrrgrxluk0JEQc92CfZctNtBHeaA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fmris_anatomical_stats -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.edu mailto: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:

...

External Email - Use Caution

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://www.gin.cnrs.fr/en/tools/aicha/ https://secure-web.cisco.com/1znEOm2w0dQV4t0t9QyQq7Ma3ojLFRlolC2Oal0YVkqOJUodCGVKTnRhr2D_9LDr7Bw7iaWRhwkh0iGvCegJR-qeHO5rV2l0x6SGbUSAzOVPBfpmzZ3s9GF6p5csqj5AYgfCeCoeKqKv5VyR5Ap7_saXFW2aFBNdgpSojzgSl56sfLda9uEim7_l2sn7OuAgmSQfgY3EJAX2UwhhKIDD3pe1605a_oc_KECBg8LgzuQ2bmPWz_fVd8E1_Rr6BAzPFKmxPaoCqONmC9whx7c5X8Q/https%3A%2F%2Ffra01.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1st38nLf-34KvmX5j8oNCBRhTI_Ki20PWEfeEACfqaaGqdiXjkdA--goU3B6IkaTck3uXUFW9PmxiYWxWNPST5LUGFFTaUlKadBruD6A0SMedSCRFTzDENaGqJqlV34SDvtILiz55CiWkiCY7mgnZGga2VfWgyBqq8eGOtGYAHFCl78eI1uoxy7uER0ZQuKi0_lg1e5SY3Esympi07huCo4yNWH2ilL0M2AeBJJEIROQSy4Ya9blgPiWIQnsqIOEKBYcIOqmyH5WrcQ_-hDuHtg%252Fhttps%25253A%25252F%25252Fwww.gin.cnrs.fr%25252Fen%25252Ftools%25252Faicha%25252F%26data%3D04%257C01%257Celina.thibeausutre%2540icm-institute.org%257Cbc41ab0f3f894166b77208d8d805febc%257C9df7cf1718fa41508b00dc5e754777d8%257C0%257C0%257C637496867552962843%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3Dl%252BJSnlrxooSAkkhXwLjNjxnvLyNPwlJl5axMVfDdMCg%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

---

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

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer