External Email - Use Caution Thank you Douglas, I tried quickly via correcting my gtmseg.ctab output with standardized for gtmseg only for tissue types, it runs without error, I will create a new look up table and try further.
Thanks again, Kind regards. On Tue, Apr 6, 2021 at 3:53 PM Douglas N. Greve <dgr...@mgh.harvard.edu> wrote: > gtmseg will not give an error, but the color table that gtmseg outputs > will not be right and needs to be fixed. > > On 4/6/2021 9:41 AM, Bahar Hazal Yalçınkaya wrote: > > External Email - Use Caution > Thanks for response, color table and annotations are there "--ctx-annot > Schaefer2018_400Parcels_7Networks_order.annot 1000 2000 --ctab > Schaefer2018_400Parcels_7Networks_order_LUT.txt", gtmseg did not gave an > error, you can see at attachments. (Also I can see 258 Head segmentation in > *gtmseg.ctab > *file) also mri_coreg is working well (see also attachments). The problem > is the "*mri_gtmpvc*" command where it fails while checking tissue types > more precisely it complains about Head segmentation. > > I run with standard options. I checked everything I can think of, each > file and image seems to be similar but still could not find a proper > solution. Is there anything specific I need to check? > Thanks in advance, > Kind regards > > On Tue, Apr 6, 2021 at 3:26 PM Douglas N. Greve <dgr...@mgh.harvard.edu> > wrote: > >> You will need to create a new color table. This is not hard, but not easy >> either. First, there should be a color table already there. I'm not sure >> what that will be like; it might have your segments in it, it might not. It >> might be easier to run gtmseg with the standard options and look at the >> color table, then try to replicate it with your segmentation >> >> On 4/5/2021 6:43 AM, Bahar Hazal Yalçınkaya wrote: >> >> External Email - Use Caution >> Hello Freesurfer"s Developers, >> >> I am trying to follow *PetSurfer* (*MailScanner has detected a possible >> fraud attempt from "secure-web.cisco.com" claiming to be* >> https://secure-web.cisco.com/1B2HO1KM0jnhlHMvubnOYbXX6eMhgWiZ6pFbmY8cJ2rCR2zh7VM-XMlmpKiWAzd5tpEcw6RAupdohvdRKmcJoaAgzRSY1dmGSjgmtdT6CARZGIoZpbZtWPP6y1VMM1fKmi4Psm_C57Invn3aAGEGE0zFpdyHGoW22HTxO2OCOQfY1hc_50vWrBdP468EQW9X5TzK4SepUR_s94d7KIzuv7hfNO_WUMrR3z8qtqTjb0jNNcQDGNKZ5HpdLi9nOSFrkv-V_F731T7DiDbbsXdd1Mw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPetSurfer >> <https://secure-web.cisco.com/1oGyZvXtztP0MX30hKqio2fJStw1wQuIW11p5b1b0CkNwSGz7RCQalhqGZJFfIT2Ob3QQETtldwxv9y8xYVYGSkRdQ_GjplqWAGkIFRP1S40sf8UfJTbg-jdroEwAQvGW-9HmP1fatTZ8h3DhbPvM4MaRIdn-gicol4f85-JI5PjVoycwQ5z0q2oYvFmz9DuRwGJZg7EiKqmfCLYhXNUOPOwhpm1kKKikeaQrRAVCr4-WbYz4Z0GXBVuflZqXa84PEzxVj0uL51CZ_xoDuhu3DA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPetSurfer>) >> to apply PVC to Pet images. >> Default pipeline is working however, whenever i try to use another atlas, >> Schaefer parcellation, mri_gtmpvc command I get following error: >> >> WARNING: LTAconcat(): inverting LTA 1 to match geometry >> >> Replacing 18 >> >> Pruning ctab >> >> tissue type schema >> >> Checking tissue type >> >> ERROR: CheckSegTissueType() tissue type for seg 258 Head-ExtraCerebral >> not set >> >> Failed tissue type check >> >> I have searched to list several people who have issued similar errors but >> unfortunately i could not find any solution that works for me. Below you >> can find commands I used: >> >> $ gtmseg --s subject --o gtmseg.mgz --ctx-annot >> Schaefer2018_400Parcels_7Networks_order.annot 1000 2000 --ctab >> Schaefer2018_400Parcels_7Networks_order_LUT.txt >> $ mri_coreg --s subject --mov AbetaPre.nii.gz --reg AbetaPre.reg.lta >> $ mri_gtmpvc --i AbetaPre.nii.gz --psf 8 --reg AbetaPre.reg.lta >> --regheader --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx >> .01 --km-ref 8 47 --o gtmpvc.output >> Also I checked the run of gtmseg via "*tkmeditfv*" where i can visualise 258 >> Head-ExtraCerebral, and additionally I checked *gtmseg.ctab *file also 258 >> Head-ExtraCerebral in the list. >> I will be happy to hear from you. >> Kind regards. >> -- >> Ph.D. Bahar Hazal Yalçınkaya >> >> >> _______________________________________________ >> Freesurfer mailing listfreesur...@nmr.mgh.harvard.edu*MailScanner has >> detected a possible fraud attempt from "secure-web.cisco.com" claiming to >> be* >> https://secure-web.cisco.com/1bpF6vIi1TzZFN2hZ0kddt70_T6WpYlp2YZzHb5NmkZ84_1QPYWHPFG_xAVTFs0DyiO447A3zVtvA1ojS8Z8JosjVW8f3y0vj30YJkXv-aHu9fuTxZbXYw3yLNG_KcGHo4zuQVTUWWLdS1gC-8ruqQFYpqPr1xcicpcyTesO93J5fcSWFiwz4clzLYUFYIqTZloMS8RZXIBq8rdi8YpSJspibOvtmsyOKwwu0yTASPYGmgQhVxjSWyuVCfdVWPQ8xe0DtRPiILA2jkIQaxvO4aA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> >> <https://secure-web.cisco.com/14cq6eGfvOcpfd9Y3vfBGA7p9Xc5PZeusO6xBxdl8k8go_naRsMxqzInFfDfwXqr6X3L2gvhxFOD1H7AqmaSe25DCQnn5EE763m9AYP-xtv7kA7l2KsaIIGge2I2JmWmriWYx9o0qAbdIELvL7SIJHMSrGrFczppuvppirbL6_AOXcUA8-WmphAP2r5jrHz-jV_ooq3O7ekh6WMvFmVHIz6Bwoy-oRL34X2Yyg55MNnhAJXX5758vDMxC3fx6013vLB7O0-KpYwzWTXm9TMgsRg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> *MailScanner has detected a possible fraud attempt from >> "secure-web.cisco.com" claiming to be* >> https://secure-web.cisco.com/1bpF6vIi1TzZFN2hZ0kddt70_T6WpYlp2YZzHb5NmkZ84_1QPYWHPFG_xAVTFs0DyiO447A3zVtvA1ojS8Z8JosjVW8f3y0vj30YJkXv-aHu9fuTxZbXYw3yLNG_KcGHo4zuQVTUWWLdS1gC-8ruqQFYpqPr1xcicpcyTesO93J5fcSWFiwz4clzLYUFYIqTZloMS8RZXIBq8rdi8YpSJspibOvtmsyOKwwu0yTASPYGmgQhVxjSWyuVCfdVWPQ8xe0DtRPiILA2jkIQaxvO4aA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> <https://secure-web.cisco.com/14cq6eGfvOcpfd9Y3vfBGA7p9Xc5PZeusO6xBxdl8k8go_naRsMxqzInFfDfwXqr6X3L2gvhxFOD1H7AqmaSe25DCQnn5EE763m9AYP-xtv7kA7l2KsaIIGge2I2JmWmriWYx9o0qAbdIELvL7SIJHMSrGrFczppuvppirbL6_AOXcUA8-WmphAP2r5jrHz-jV_ooq3O7ekh6WMvFmVHIz6Bwoy-oRL34X2Yyg55MNnhAJXX5758vDMxC3fx6013vLB7O0-KpYwzWTXm9TMgsRg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> > > > > -- > Ph.D. Bahar Hazal Yalçınkaya > > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1bpF6vIi1TzZFN2hZ0kddt70_T6WpYlp2YZzHb5NmkZ84_1QPYWHPFG_xAVTFs0DyiO447A3zVtvA1ojS8Z8JosjVW8f3y0vj30YJkXv-aHu9fuTxZbXYw3yLNG_KcGHo4zuQVTUWWLdS1gC-8ruqQFYpqPr1xcicpcyTesO93J5fcSWFiwz4clzLYUFYIqTZloMS8RZXIBq8rdi8YpSJspibOvtmsyOKwwu0yTASPYGmgQhVxjSWyuVCfdVWPQ8xe0DtRPiILA2jkIQaxvO4aA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer -- Ph.D. Bahar Hazal Yalçınkaya
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