Hi Gonzalo, the segmentation that you are seeing is paired with the insula parcellation. doug
On 05/30/2013 04:36 PM, Gonzalo Rojas Costa wrote: > Hi Doug: > > The command is: > > mri_aparc2aseg --s OAS1_0001_MR1 --labelwm --hypo-as-wm --rip-unknown > --volmask --o mri/lobulitos.mgz --annot lobulos --wmparc-dmax 200 > > and the terminal output is: > > mri_aparc2aseg --s OAS1_0001_MR1 --labelwm --hypo-as-wm --rip-unknown > --volmask --o mri/lobulitos_2.mgz --annot lobulos --wmparc-dmax 200 > > SUBJECTS_DIR /usr/local/freesurfer/subjects > subject OAS1_0001_MR1 > outvol mri/lobulitos_2.mgz > useribbon 0 > baseoffset 0 > labeling wm > labeling hypo-intensities as wm > dmaxctx 200.000000 > RipUnknown 1 > > Reading lh white surface > /usr/local/freesurfer/subjects/OAS1_0001_MR1/surf/lh.white > > Reading lh pial surface > /usr/local/freesurfer/subjects/OAS1_0001_MR1/surf/lh.pial > > Loading lh annotations from > /usr/local/freesurfer/subjects/OAS1_0001_MR1/label/lh.lobulos.annot > reading colortable from annotation file... > colortable with 8 entries read (originally none) > > Reading rh white surface > /usr/local/freesurfer/subjects/OAS1_0001_MR1/surf/rh.white > > Reading rh pial surface > /usr/local/freesurfer/subjects/OAS1_0001_MR1/surf/rh.pial > > Loading rh annotations from > /usr/local/freesurfer/subjects/OAS1_0001_MR1/label/rh.lobulos.annot > reading colortable from annotation file... > colortable with 8 entries read (originally none) > Have color table for lh white annotation > Have color table for rh white annotation > Loading ribbon segmentation from > /usr/local/freesurfer/subjects/OAS1_0001_MR1/mri/ribbon.mgz > Loading filled from > /usr/local/freesurfer/subjects/OAS1_0001_MR1/mri/filled.mgz > Ripping vertices labeled as unkown > Ripped 7659 vertices from left hemi > Ripped 7544 vertices from right hemi > > Building hash of lh white > > Building hash of lh pial > > Building hash of rh white > > Building hash of rh pial > > Loading aseg from /usr/local/freesurfer/subjects/OAS1_0001_MR1/mri/aseg.mgz > ASeg Vox2RAS: ----------- > -1.000 0.000 0.000 128.000; > 0.000 0.000 1.000 -128.000; > 0.000 -1.000 0.000 128.000; > 0.000 0.000 0.000 1.000; > ------------------------- > > Labeling Slice > 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 > 19 > 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 > 39 > 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 > 59 > 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 > 79 > 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 > 99 > 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 > 119 > 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 > 139 > 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 > 159 > 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 > 179 > 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 > 199 > 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 > 219 > 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 > 239 > 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 688931 > Used brute-force search on 139 voxels > Fixing Parahip LH WM > Found 0 clusters > Fixing Parahip RH WM > Found 0 clusters > Writing output aseg to mri/lobulitos_2.mgz > > Sincerely, > > > Gonzalo Rojas Costa > > > On Thu, May 30, 2013 at 4:10 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu> wrote: >> can you send me your full command line as well as the terminal output? >> >> On 05/30/2013 02:26 PM, Gonzalo Rojas Costa wrote: >>> Hi Doug: >>> >>> But, in the mri_aparc2aseg command, I test with the "--wmparc-dmax >>> 200" option... I put that big value to test it, but I got the image >>> that I sent you... >>> >>> Sincerely, >>> >>> >>> Gonzalo Rojas Costa > -- > Gonzalo Rojas Costa > Laboratory for Advanced Medical Image Processing > Department of Radiology > Clínica las Condes > Lo Fontecilla 441, Las Condes, Santiago, Chile. > Tel: 56-2-2105170 > Cel: 56-9-97771785 > www.clc.cl > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
