Hi Das

when you give mri_ca_label the option:

-l 100307/label/lh.cortex.label

you are telling it to mask out what it thinks are non-cortical areas and assign them unknown. Is this a problem?

cheers Bruce

On Fri, 14 Apr 2017, Das S. wrote:

Hi, I have created an .annot file from label files using mris_label2annot command.

mris_label2annot --s 100307 --h lh --no-unknown --ctab 100307/label/eq_parcellation_ label/MyColorLUTnew.txt --a eqnew40aparc --ldir 100307/label/eq_parcellation_label/

Then I have created a .gcs file from the above .annot file.

mris_ca_train -t 100307/label/eq_parcellation_label/MyColorLUT.txt lh 100307/surf/lh.sphere.reg 100307/label/lh.left40aparc.annot 100307 100307/label/lh.reg40aparc.gcs

Then from the .gcs file I have another .annot file.

mris_ca_label -l 100307/label/lh.cortex.label -aseg 100307/mri/aseg.presurf.mgz 100307 lh 100307/surf/lh.sphere.reg 100307/label/lh.eqnew40aparc.gcs 100307/label/lh.aparc.annot

The 2nd annot file is corrupted and showing a big gray patch.While checking the annotation file in matlab, found that the those vertex on the .annot file were not assigned any colorcode from colortable. Here is the content of MyColorLUTnew.txt:

0 unknown 1 1 1 0 1 node1 70 130 180 0 2 node2 245 245 245 0 3 node3 205 62 78 0 4 node4 120 18 134 0 5 node5 196 58 250 0 6 node6 0 148 0 0 7 node7 220 248 164 0 8 node8 230 148 34 0 9 node9 0 118 14 0 10 node10 70 118 14 0 11 node11 122 186 220 0 12 node12 236 13 176 0 13 node13 12 48 255 0 14 node14 204 182 142 0 15 node15 42 204 164 0 16 node16 119 159 176 0 17 node17 220 216 20 0 18 node18 103 255 255 0 19 node19 80 196 98 0 20 node20 60 58 210 0 21 node21 160 58 210 0 22 node22 120 58 210 0 23 node23 40 58 210 0 24 node24 60 120 60 0 25 node25 255 100 0 0 26 node26 250 165 0 0 27 node27 0 255 127 0 28 node28 165 42 42 0 29 node29 135 206 235 0 30 node30 160 32 240 0 31 node31 0 200 200 0 32 node32 100 50 100 0 33 node33 135 50 74 0 34 node34 122 135 50 0 35 node35 51 50 135 0 36 node36 74 155 60 0 37 node37 120 62 43 0 38 node38 74 155 60 0 39 node39 122 135 50 0 40 node40 70 130 180 0

Any help will be much appreciated, why the file is getting corrupted in the 2nd step?

Thanks Sarbani