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
>
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>
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>
>
>
>
>
> _______________________________________________
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--
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
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