Sorry, is this related to the earlier question about how to remove non-wm labels or is this a new submission? If a new subj, can you describe the problem you are having?
On 02/05/2018 01:23 PM, Sims, Sara A wrote: > > This is the whole process output from a rerun on a subject that didn’t > work the first time or with the rerun: > > Reading ctab > /data/user/snolin/Scripts/Labelmaker/color_tables/clut.8lhV1.ctab > > Number of ctab entries 2 > > $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ > > cwd /data/user/snolin/Scripts/Labelmaker > > cmdline mris_label2annot --ctab > /data/user/snolin/Scripts/Labelmaker/color_tables/clut.8lhV1.ctab --s > 211215 --h lh --l > /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/label/8_LH_V1.label > > --a 8V1 > > sysname Linux > > hostname c0039 > > machine x86_64 > > user snolin > > subject 211215 > > hemi lh > > SUBJECTS_DIR /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon > > ColorTable > /data/user/snolin/Scripts/Labelmaker/color_tables/clut.8lhV1.ctab > > AnnotName 8V1 > > nlables 1 > > LabelThresh 0 0.000000 > > ERROR: > /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/label/lh.8V1.annot > > already exists > > Reading ctab > /data/user/snolin/Scripts/Labelmaker/color_tables/clut.8rhV1.ctab > > Number of ctab entries 2 > > $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ > > cwd /data/user/snolin/Scripts/Labelmaker > > cmdline mris_label2annot --ctab > /data/user/snolin/Scripts/Labelmaker/color_tables/clut.8rhV1.ctab --s > 211215 --h rh --l > /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/label/8_RH_V1.label > > --a 8V1 > > sysname Linux > > hostname c0039 > > machine x86_64 > > user snolin > > subject 211215 > > hemi rh > > SUBJECTS_DIR /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon > > ColorTable > /data/user/snolin/Scripts/Labelmaker/color_tables/clut.8rhV1.ctab > > AnnotName 8V1 > > nlables 1 > > LabelThresh 0 0.000000 > > ERROR: > /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/label/rh.8V1.annot > > already exists > > SUBJECTS_DIR /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon > > subject 211215 > > outvol > /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1+aseg.mgz > > useribbon 0 > > baseoffset 0 > > labeling wm > > dmaxctx 5.000000 > > RipUnknown 0 > > Reading lh white surface > > > /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/surf/lh.white > > Reading lh pial surface > > > /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/surf/lh.pial > > Loading lh annotations from > /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/label/lh.8V1.annot > > Reading rh white surface > > > /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/surf/rh.white > > Reading rh pial surface > > > /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/surf/rh.pial > > Loading rh annotations from > /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/label/rh.8V1.annot > > Loading ribbon segmentation from > /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/ribbon.mgz > > Building hash of lh white > > Building hash of lh pial > > Building hash of rh white > > Building hash of rh pial > > Loading aseg from > /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/aseg.mgz > > ASeg Vox2RAS: ----------- > > -1.00000 0.00000 0.00000 128.00000; > > 0.00000 0.00000 1.00000 -128.00000; > > 0.00000 -1.00000 0.00000 128.00000; > > 0.00000 0.00000 0.00000 1.00000; > > ------------------------- > > 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 = > 1124316 > > Used brute-force search on 0 voxels > > Fixing Parahip LH WM > > Found 0 clusters > > Fixing Parahip RH WM > > Found 0 clusters > > Writing output aseg to > /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1+aseg.mgz > > $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ > > cwd /data/user/snolin/Scripts/Labelmaker > > cmdline mri_binarize.bin --i > /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1+aseg.mgz > > --o > /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1_bin.mgz > > --match 4001 3001 > > sysname Linux > > hostname c0039 > > machine x86_64 > > user snolin > > input > /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1+aseg.mgz > > frame 0 > > nErode3d 0 > > nErode2d 0 > > output > /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1_bin.mgz > > Binarizing based on matching values > > nMatch 2 > > 0 4001 > > 1 3001 > > binval 1 > > binvalnot 0 > > fstart = 0, fend = 0, nframes = 1 > > Found 0 values in range > > Counting number of voxels in first frame > > Found 0 voxels in final mask > > Count: 0 0.000000 16777216 0.000000 > > mri_binarize done > > mri_convert.bin > /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1_bin.mgz > > /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1_bin.nii > > > > $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ > > reading from > /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1_bin.mgz... > > TR=2400.00, TE=0.00, TI=0.00, flip angle=0.00 > > i_ras = (-1, 0, 0) > > j_ras = (0, 0, -1) > > k_ras = (0, 1, 0) > > writing to > /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1_bin.nii... > > Matrix from regfile: > > 1.00000 -0.00055 0.00091 -0.38465; > > -0.00091 0.00095 1.00000 0.38039; > > -0.00055 -1.00000 0.00095 -0.14575; > > 0.00000 0.00000 0.00000 1.00000; > > movvol > /data/project/vislab/raw/HCP_900sub/HCP_diff_data/211215/data.nii.gz > > targvol > /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1_bin.nii > > outvol > /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1_diffROI.nii > > regfile > /data/user/snolin/HCP_registration/HCP_BBR/HCP_registration_new/211215/register_edit.dat > > invert 1 > > tal 0 > > talres 2 > > regheader 0 > > noresample 0 > > interp nearest (0) > > precision float (3) > > Gdiag_no -1 > > Synth 0 > > SynthSeed 1518108582 > > Invert! > > Inverting registration > > Final tkRAS-to-tkRAS Matrix is: > > 1.00000 -0.00091 -0.00055 0.38491; > > -0.00055 0.00095 -1.00000 -0.14632; > > 0.00091 1.00000 0.00095 -0.37990; > > 0.00000 0.00000 0.00000 1.00000; > > Vox2Vox Matrix is: > > 1.25000 -0.00069 0.00114 36.96743; > > 0.00114 0.00118 -1.25000 218.81943; > > 0.00069 1.25000 0.00118 18.96824; > > 0.00000 0.00000 0.00000 1.00000; > > Resampling > > Output registration matrix is identity > > mri_vol2vol done > > Sara Sims > > Graduate Research Fellow > > University of Alabama at Birmingham > > Department of Psychology > > 205-975-4060 > > sno...@uab.edu > > *From: *<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas > Greve <gr...@nmr.mgh.harvard.edu> > *Reply-To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > *Date: *Saturday, February 3, 2018 at 1:12 PM > *To: *"freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > *Subject: *Re: [Freesurfer] mri_aparc2aseg labelwm not labelling wm > > Can you send the terminal output of one of the runs that fails? > > On 1/31/18 4:10 PM, Sims, Sara A wrote: > > Freesurfers, > > I am trying to use a cortical label to label wm. I am using the > following command line: > > mri_aparc2aseg --s $patient --annot 8V1 –labelwm > > And most of the time in most subjects this works, however > sometimes the output file doesn’t label any wm with the 3000+N or > 4000+N like it usually does. I have tried changing the > -wmparc-dmax, -hypo-as-wm, -smooth_normals. Basically everything I > could find but it won’t budge even though doing other labels in > the same person works fine. Fyi: The original cortical label is > also correctly place in the cortical ribbon. > > Any ideas? > > Please! > > Thanks, > > Sara Sims > > Graduate Research Fellow > > University of Alabama at Birmingham > > Department of Psychology > > 205-975-4060 > > sno...@uab.edu<mailto:sno...@uab.edu> > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu<mailto: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 -- 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.
