Re: [Freesurfer] white matter volume per lobe...
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 200.00 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
Re: [Freesurfer] white matter volume per lobe...
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 200.00 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
Re: [Freesurfer] white matter volume per lobe...
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 200.00 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
Re: [Freesurfer] white matter volume per lobe...
It is probably the region that is more than 5mm away from cortex. In the wmparc it should be labeled as wm-lh-unknown doug On 05/30/2013 11:27 AM, Gonzalo Rojas Costa wrote: Hi Doug: I used the instructions that you told me to get the white matter per each lobule... But, I got the grey colored region (red arrow)... Which neuroanatomical area is ?... Sincerely, Gonzalo Rojas Costa Message: 15 Date: Mon, 27 May 2013 22:41:41 -0400 From: Douglas Greve gr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] white matter volume per lobe... To: freesurfer@nmr.mgh.harvard.edu Message-ID: 51a41965.6050...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed you will need to run mri_annotation2label and specify the output to be an annotation file instead of a segmentation. Then you will have to run mri_aparc2aseg, specifying your lobes annotation as well as --labelwm (look in the recon-all.log file for an example of how wmparc.mgz is created). Then run mri_segstats (you can also get an example from the recon-all.log file). doug -- 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.
Re: [Freesurfer] white matter volume per lobe...
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 On Thu, May 30, 2013 at 12:06 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: It is probably the region that is more than 5mm away from cortex. In the wmparc it should be labeled as wm-lh-unknown doug On 05/30/2013 11:27 AM, Gonzalo Rojas Costa wrote: Hi Doug: I used the instructions that you told me to get the white matter per each lobule... But, I got the grey colored region (red arrow)... Which neuroanatomical area is ?... Sincerely, Gonzalo Rojas Costa Message: 15 Date: Mon, 27 May 2013 22:41:41 -0400 From: Douglas Greve gr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] white matter volume per lobe... To: freesurfer@nmr.mgh.harvard.edu Message-ID: 51a41965.6050...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed you will need to run mri_annotation2label and specify the output to be an annotation file instead of a segmentation. Then you will have to run mri_aparc2aseg, specifying your lobes annotation as well as --labelwm (look in the recon-all.log file for an example of how wmparc.mgz is created). Then run mri_segstats (you can also get an example from the recon-all.log file). doug -- 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
Re: [Freesurfer] white matter volume per lobe...
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 On Thu, May 30, 2013 at 12:06 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: It is probably the region that is more than 5mm away from cortex. In the wmparc it should be labeled as wm-lh-unknown doug On 05/30/2013 11:27 AM, Gonzalo Rojas Costa wrote: Hi Doug: I used the instructions that you told me to get the white matter per each lobule... But, I got the grey colored region (red arrow)... Which neuroanatomical area is ?... Sincerely, Gonzalo Rojas Costa Message: 15 Date: Mon, 27 May 2013 22:41:41 -0400 From: Douglas Greve gr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] white matter volume per lobe... To: freesurfer@nmr.mgh.harvard.edu Message-ID: 51a41965.6050...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed you will need to run mri_annotation2label and specify the output to be an annotation file instead of a segmentation. Then you will have to run mri_aparc2aseg, specifying your lobes annotation as well as --labelwm (look in the recon-all.log file for an example of how wmparc.mgz is created). Then run mri_segstats (you can also get an example from the recon-all.log file). doug -- 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. -- 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
Re: [Freesurfer] white matter volume per lobe...
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 200.00 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 ___ 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.
Re: [Freesurfer] white matter volume per lobe...
what is is labled? On 05/28/2013 01:42 PM, Gonzalo Rojas Costa wrote: Hi Doug: I use the instructions that you told me... But, why I get the gray colored region (red arrow) ?... Sincerely, Gonzalo Rojas Costa Message: 15 Date: Mon, 27 May 2013 22:41:41 -0400 From: Douglas Greve gr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] white matter volume per lobe... To: freesurfer@nmr.mgh.harvard.edu Message-ID: 51a41965.6050...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed you will need to run mri_annotation2label and specify the output to be an annotation file instead of a segmentation. Then you will have to run mri_aparc2aseg, specifying your lobes annotation as well as --labelwm (look in the recon-all.log file for an example of how wmparc.mgz is created). Then run mri_segstats (you can also get an example from the recon-all.log file). doug -- 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.
Re: [Freesurfer] white matter volume per lobe...
Hi Doug: It is labeled as wm-rh-fusiform and wm-lh-fusiform Sincerely, Gonzalo Rojas Costa On Tue, May 28, 2013 at 1:47 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: what is is labled? On 05/28/2013 01:42 PM, Gonzalo Rojas Costa wrote: Hi Doug: I use the instructions that you told me... But, why I get the gray colored region (red arrow) ?... Sincerely, Gonzalo Rojas Costa Message: 15 Date: Mon, 27 May 2013 22:41:41 -0400 From: Douglas Greve gr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] white matter volume per lobe... To: freesurfer@nmr.mgh.harvard.edu Message-ID: 51a41965.6050...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed you will need to run mri_annotation2label and specify the output to be an annotation file instead of a segmentation. Then you will have to run mri_aparc2aseg, specifying your lobes annotation as well as --labelwm (look in the recon-all.log file for an example of how wmparc.mgz is created). Then run mri_segstats (you can also get an example from the recon-all.log file). doug -- 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
Re: [Freesurfer] white matter volume per lobe...
You will need to create a new color table. It is currently referencing FreeSurferColorLUT.txt. If you load the segmentation as both a segmentation and the aux volume, you can see the number associated with the color. You will need to create a table similar to FreeSurferColorLUT.txt doug On 05/28/2013 01:51 PM, Gonzalo Rojas Costa wrote: Hi Doug: It is labeled as wm-rh-fusiform and wm-lh-fusiform Sincerely, Gonzalo Rojas Costa On Tue, May 28, 2013 at 1:47 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: what is is labled? On 05/28/2013 01:42 PM, Gonzalo Rojas Costa wrote: Hi Doug: I use the instructions that you told me... But, why I get the gray colored region (red arrow) ?... Sincerely, Gonzalo Rojas Costa Message: 15 Date: Mon, 27 May 2013 22:41:41 -0400 From: Douglas Greve gr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] white matter volume per lobe... To: freesurfer@nmr.mgh.harvard.edu Message-ID: 51a41965.6050...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed you will need to run mri_annotation2label and specify the output to be an annotation file instead of a segmentation. Then you will have to run mri_aparc2aseg, specifying your lobes annotation as well as --labelwm (look in the recon-all.log file for an example of how wmparc.mgz is created). Then run mri_segstats (you can also get an example from the recon-all.log file). doug -- 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. -- 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
[Freesurfer] white matter volume per lobe...
Hi: I used the following commands to get the cortical volume per each lobe: mri_annotation2label --subject OAS1_0001_MR1 --hemi rh --lobesStrict lobulos --seg lobulos --stat lobulos mri_annotation2label --subject OAS1_0001_MR1 --hemi lh --lobesStrict lobulos --seg lobulos --stat lobulos mris_anatomical_stats -a lobulos -f OAS1_0001_MR1_lobulos_rh -b OAS1_0001_MR1 rh mris_anatomical_stats -a lobulos -f OAS1_0001_MR1_lobulos_lh -b OAS1_0001_MR1 lh Which commands (sintaxis) must I use to compute the white matter volume per each lobe ?... I tested the mri_aparc2aseg and mri_segstats commans with different options, but I couldn't get the volume that I need... Sincerely, -- 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 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.
Re: [Freesurfer] white matter volume per lobe...
you will need to run mri_annotation2label and specify the output to be an annotation file instead of a segmentation. Then you will have to run mri_aparc2aseg, specifying your lobes annotation as well as --labelwm (look in the recon-all.log file for an example of how wmparc.mgz is created). Then run mri_segstats (you can also get an example from the recon-all.log file). doug On 5/27/13 5:53 PM, Gonzalo Rojas Costa wrote: Hi: I used the following commands to get the cortical volume per each lobe: mri_annotation2label --subject OAS1_0001_MR1 --hemi rh --lobesStrict lobulos --seg lobulos --stat lobulos mri_annotation2label --subject OAS1_0001_MR1 --hemi lh --lobesStrict lobulos --seg lobulos --stat lobulos mris_anatomical_stats -a lobulos -f OAS1_0001_MR1_lobulos_rh -b OAS1_0001_MR1 rh mris_anatomical_stats -a lobulos -f OAS1_0001_MR1_lobulos_lh -b OAS1_0001_MR1 lh Which commands (sintaxis) must I use to compute the white matter volume per each lobe ?... I tested the mri_aparc2aseg and mri_segstats commans with different options, but I couldn't get the volume that I need... Sincerely, -- 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 ___ 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.
