Hi Douglas: The file is the OAS1_0001_MR1 case of OASIS-BRAINS database that I re-processed using freesurfer 5.2.0...
Sincerely, Gonzalo Rojas Costa On Fri, May 31, 2013 at 12:12 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > don't know what's going on. Can you upload the subject to our file drop? > 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/ > > > > 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. > -- 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
