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 snolin@uab.edu From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@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 snolin@uab.edumailto:snolin@uab.edu
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