External Email - Use Caution Dear Freesurfer experts:
I am having trouble processing with recon-all the file I obtain with presurfer from an MP2RAGE. I don’t know if you have any experience with this. The data I obtained from this https://secure-web.cisco.com/1DoAeFvUHnYto_t5xoLbWcFtbuOwQtmlS1ENoWBmeeHffDpNErW4_gUBNrL5wbRsqdn8Lvt8o-hftAn4O3mHZlavh98oBX5sjSMs6gyoyT47B4jGytWCy0opSP505tXZd0usKIHMHIWlSmIqHKG6eDzK-1hhavHJFtmcsFeyidS8mPmaHdP-KpuCotmuwqgIPCppobf5sCRfNWndHYDvrfUWS7cnm05Gepyhhd9wWDL3SOx7eMSw78OvBAoGp4jAtzA51dgT22RZWjsiDkVkZhxVB65cvL3d0EEIQEb3b-Pvc_aXfazlGDtAv_BN8ebkALkCERCl8XVgThOSIi-yo1DOledDb39I-AMQQIyh_XeQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsmData Then I use subject “fsm08un”. I run presurfer as in https://secure-web.cisco.com/1avsRdF8F2mgWmm0OUulJTd3eZF6z9U3j9ezKhlvZi12HC0IpY4Nah1yM9zPdaEgn4XgbjeONuQbMGr9DrUl1ib_zBmc-EE50cnExQ7r-SquKETECpYIH8FI2PNE_wseQcG9IdIgbmgUS28z8SgosW5HOBtqPlBxbH_624ZNh7HPzc7i6nPoue8uM5ePZ_Ro_AHX9ld3OtrW6lwse45wPv2u3LUCxXJvzjGyuTogJ0vKoxfw65J2DT-hcJs3sC5VIZfVWiyxjgoy6-5P7oV--mxBJYd5c4h4nKHW3xfcLKzdKMl2UZTYYHtCxqY-E4Hgw7yh-06jF6j9eVH3-h8Qkv97Kmur_vXvB1bBLBTy21Jo/https%3A%2F%2Fgithub.com%2Fsrikash%2Fpresurfer Then I run recon-all -all -i MPRAGEised_stripped.nii.gz -s fsm08un_MPRAGEised -openmp 8 . . . ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=130,y=125, z=130, r=124102 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1447023003 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1862269955 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -230683617 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1409286624 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 943723776 OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 943755195 mri_watershed Error: GLOBAL region of the brain empty ! Darwin Renes-MacBook-Air.local 22.5.0 Darwin Kernel Version 22.5.0: Thu Jun 8 22:22:19 PDT 2023; root:xnu-8796.121.3~7/RELEASE_ARM64_T8103 arm64 recon-all -s fsm08un_MPRAGEised exited with ERRORS at Tue Aug 1 15:40:57 CEST 2023 For more details, see the log file /Applications/freesurfer/7.3.2/subjects/fsm08un_MPRAGEised/scripts/recon-all.log To report a problem, see http://secure-web.cisco.com/1t6IHvg5_DeUlvFUHchBUPV_vqGqDEzbhHz1e6IOApGryD_Xrrkklep8jgVlZe9fJKNdDSOe6dvXPcqeE6olUXH6XkwRpSbUcCq_CYo0eJB7QJX1x8157w6wuaeu9PxMFRxj9l6U7_YsLyJ3W4BkntY5GeVn75rbX4VT9y4EqfPy4_WPODDMhEjDbZCEiiAMiUSQHDjaJvTtL1piF4w-tYrD_HViPkWHDc5wKiwkS6i1HfUcAqZBC-q2Vuz_Y1F4DL521hE0ls6V1llkejmlhXJE191JBHRwAJluOe4DF6n3DFAN7b2GGf1zrBWBiyozzxImlnLVnx11viFmCh-qC9ksePIwjrMFh0B-vMaSzS0E/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting If you need the recon-all.log I can send it. Best, Rene Andrade.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
