External Email - Use Caution Thank you for your response! Here the commands:
#register image to MNIspace flirt -in mydata_T1.nii.gz -ref fsl/data/standard/MNI152_T1_1mm -out mydata_T1_MNI.nii.gz -omat mydata_T1_MNI.mat #Create a registration from the ROI-anatomical volume to a freesurfer template subject fslregister --s fsaverage --mov mydata_T1_MNI.nii.gz --reg tmp.dat #Map the ROI-mask to the fsaverage surface, to create an fsaverage-ROI surface overlay. mri_vol2surf --mov ROI_MNI.nii.gz --reg tmp.dat --projdist-max 0 1 0.1 --interp nearest --hemi lh --out lh.fsaverage.ROI_MNI.mgh —noreshape tkmeditfv fsaverage lh inflated -overlay lh.fsaverage.M1_L.mgh -fthresh 0.5 I tried with another threshold, and to change it while in Freeview and it’s either the whole surface with the overlay or none. Thank you for your help! Alina Rojas > Am 16.11.2020 um 17:04 schrieb Douglas N. Greve <[email protected]>: > > please send the command line > > On 11/16/2020 7:20 AM, Alina Rojas wrote: >> External Email - Use Caution >> >> Hello Freesurfer experts, >> >> I am attempting to register a ROI (.nii) to the surface of fsaverage to get >> the statistical output on the cortical thickness. I followed your >> instructions on MailScanner has detected a possible fraud attempt from >> "secure-web.cisco.com" claiming to >> behttps://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness >> <https://secure-web.cisco.com/1vMR3HBqveQVdV1izVoGaJ5VcRtbR7HBn6ADoe1ai7ok5utz9wmCB_PLEjDtsOmyziziVBQRSmBgczrdyk56eX0vaBWBNP1iIevBdxOho3o-JJ64DuVK1J6XpzIFNVqqzBDHDrU6O2cYjWTNnglb4Ow4OIdXr5Qq28eboicyUSvLl2KmB0P0lQY9abQIfjX6hs_1Q1FvwX1Tx7YnGwsbJIgqcpDRG0dkvqZc0pgeiBQbnNjLadwozbHME2Ale8Kt0-V-I2Urmgq5zbEhzlAPvCA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVolumeRoiCorticalThickness> >> but after mri_vol2surf I get this message, I can’t visualize the ROI on the >> surface. I I’m using Freesurfer 7.0.1. How can I solve this? Thank you, >> Alina Rojas. >> >> srcvol = M1_L.nii.gz >> srcreg = tmp.dat >> srcregold = 0 >> srcwarp unspecified >> surf = white >> hemi = lh >> ProjDist = 0.5 >> reshape = 0 >> interp = nearest >> float2int = round >> GetProjMax = 1 >> INFO: float2int code = 0 >> INFO: using NIfTI-1 qform >> Done loading volume >> INFO: This REGISTER_DAT transform is valid only for volumes between COR >> types with c_(r,a,s) = 0. >> Input reg is register.dat >> -------- original matrix ----------- >> 1.00000 0.00000 0.00000 2.49380; >> 0.00000 0.00000 1.00000 -22.50500; >> 0.00000 -1.00000 0.00000 -9.53872; >> 0.00000 0.00000 0.00000 1.00000; >> -------- original matrix ----------- >> Reading surface /fsaverage/surf/lh.white >> Done reading source surface >> Mapping Source Volume onto Source Subject Surface >> 1 0 0 1 >> using old >> 2 0.1 0 1 >> using old >> 3 0.2 0 1 >> using old >> 4 0.3 0 1 >> using old >> 5 0.4 0 1 >> using old >> 6 0.5 0 1 >> using old >> 7 0.6 0 1 >> using old >> 8 0.7 0 1 >> using old >> 9 0.8 0 1 >> using old >> 10 0.9 0 1 >> using old >> Done mapping volume to surface >> Number of source voxels hit = 75073 >> Writing to lh.fsaverage.M1_L.mgh >> Dim: 163842 1 1 >> surfcolor: Subscript out of range. >> >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> [email protected] <mailto:[email protected]> >> https://secure-web.cisco.com/182BqfOmZHFfN-HXG0WKcZl1t7mCNEi6craJT61YlVMJ8c1BoYM9RlZhjXTzA4TeZ05e3OGT-xSV3Uin7CmBt_0BPg_0i1AWtJU1vZn2DKlHVGhyXp5WKXs1Q8ReIzK9xXEDa8NUDM3gsQVJpynhZD0gBj8FZlLEe9wNRv_4oDjFKtbqnX17Bqp5oWazA3LmrSeY0WMS-oVyt6_TjHFXCvvRLqx34lzCC8Be07NxJdDYc7K9_JaqoorFJc4KzIlIupp0UXZJiXV-VI33g3W95uw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> >> <https://secure-web.cisco.com/182BqfOmZHFfN-HXG0WKcZl1t7mCNEi6craJT61YlVMJ8c1BoYM9RlZhjXTzA4TeZ05e3OGT-xSV3Uin7CmBt_0BPg_0i1AWtJU1vZn2DKlHVGhyXp5WKXs1Q8ReIzK9xXEDa8NUDM3gsQVJpynhZD0gBj8FZlLEe9wNRv_4oDjFKtbqnX17Bqp5oWazA3LmrSeY0WMS-oVyt6_TjHFXCvvRLqx34lzCC8Be07NxJdDYc7K9_JaqoorFJc4KzIlIupp0UXZJiXV-VI33g3W95uw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> > _______________________________________________ > Freesurfer mailing list > [email protected] <mailto:[email protected]> > https://secure-web.cisco.com/182BqfOmZHFfN-HXG0WKcZl1t7mCNEi6craJT61YlVMJ8c1BoYM9RlZhjXTzA4TeZ05e3OGT-xSV3Uin7CmBt_0BPg_0i1AWtJU1vZn2DKlHVGhyXp5WKXs1Q8ReIzK9xXEDa8NUDM3gsQVJpynhZD0gBj8FZlLEe9wNRv_4oDjFKtbqnX17Bqp5oWazA3LmrSeY0WMS-oVyt6_TjHFXCvvRLqx34lzCC8Be07NxJdDYc7K9_JaqoorFJc4KzIlIupp0UXZJiXV-VI33g3W95uw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > <https://secure-web.cisco.com/182BqfOmZHFfN-HXG0WKcZl1t7mCNEi6craJT61YlVMJ8c1BoYM9RlZhjXTzA4TeZ05e3OGT-xSV3Uin7CmBt_0BPg_0i1AWtJU1vZn2DKlHVGhyXp5WKXs1Q8ReIzK9xXEDa8NUDM3gsQVJpynhZD0gBj8FZlLEe9wNRv_4oDjFKtbqnX17Bqp5oWazA3LmrSeY0WMS-oVyt6_TjHFXCvvRLqx34lzCC8Be07NxJdDYc7K9_JaqoorFJc4KzIlIupp0UXZJiXV-VI33g3W95uw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
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