Hi Sara, can you repost with just the new issue? I'm having problems differentiating them just looking through the email
On 2/5/18 6:02 PM, Sims, Sara A wrote: > Doug, > > This is a new problem. I figured out my earlier issue. This makes a > 8V1+aseg.mgz file there are just no 4001 and 3001's in the file so when I > binarize there is nothing there. So my question is why is it not identifying > the wm next to my label? This is happening in multiple subjects on varying > labels. > > Sara Sims > Graduate Research Fellow > University of Alabama at Birmingham > Department of Psychology > 205-975-4060 > sno...@uab.edu > On 2/5/18, 12:31 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of > Douglas N Greve" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of > gr...@nmr.mgh.harvard.edu> wrote: > > 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. > > > > _______________________________________________ > 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
