Sorry, it should be from
/home/eji/projects/spins/preproc/freesurfer/subjects/w0
(without the /mri)
On 7/23/2020 8:37 AM, Ellen Ji wrote:
External Email - Use Caution
Dear experts,
I am running mri_aparc2aseg and, based on the output, it seems to run
through successfully until the very end where it does not actually
write the file (I receive "error: niiWrite(): error opening file
mri/aparc.500+2mm.nii.gz"). However, I am 100% sure that I have
writing access in the directory. Below you will see the details. Do
you know why I am having this issue? Thank you for your time, Ellen
mri_aparc2aseg \
> --s SPN01_CMH_0001_01 \
> --annot 500_sym.aparc \
> --wmparc-dmax 2 \
> --labelwm \
> --hypo-as-wm \
> --o mri/aparc.500+2mm.nii.gz
SUBJECTS_DIR /home/eji/projects/spins/preproc/freesurfer/subjects/w0
subject SPN01_CMH_0001_01
outvol mri/aparc.500+2mm.nii.gz
useribbon 0
baseoffset 0
labeling wm
labeling hypo-intensities as wm
dmaxctx 2.000000
RipUnknown 0
8 avail.processors, using 1
Reading lh white surface
/home/eji/projects/spins/preproc/freesurfer/subjects/w0/SPN01_CMH_0001_01/surf/lh.white
Reading lh pial surface
/home/eji/projects/spins/preproc/freesurfer/subjects/w0/SPN01_CMH_0001_01/surf/lh.pial
Loading lh annotations from
/home/eji/projects/spins/preproc/freesurfer/subjects/w0/SPN01_CMH_0001_01/label/lh.500_sym.aparc.annot
reading colortable from annotation file...
colortable with 161 entries read (originally
/scratch/tmpdir.annot2std.28231/seg.1.073.xhemi.ctab)
Have color table for lh white annotation
Building hash of lh white
Building hash of lh pial
Reading rh white surface
/home/eji/projects/spins/preproc/freesurfer/subjects/w0/SPN01_CMH_0001_01/surf/rh.white
Reading rh pial surface
/home/eji/projects/spins/preproc/freesurfer/subjects/w0/SPN01_CMH_0001_01/surf/rh.pial
Loading rh annotations from
/home/eji/projects/spins/preproc/freesurfer/subjects/w0/SPN01_CMH_0001_01/label/rh.500_sym.aparc.annot
reading colortable from annotation file...
colortable with 161 entries read (originally
/scratch/tmpdir.annot2std.12874/seg.1.073.xhemi.ctab)
Have color table for rh white annotation
Building hash of rh white
Building hash of rh pial
Loading ribbon segmentation from
/home/eji/projects/spins/preproc/freesurfer/subjects/w0/SPN01_CMH_0001_01/mri/ribbon.mgz
Loading filled from
/home/eji/projects/spins/preproc/freesurfer/subjects/w0/SPN01_CMH_0001_01/mri/ribbon.mgz
Loading aseg from
/home/eji/projects/spins/preproc/freesurfer/subjects/w0/SPN01_CMH_0001_01/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 (256)
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 = 906029
Used brute-force search on 0 voxels
Fixing Parahip LH WM
Found 1 clusters
0 k 791.000000
Fixing Parahip RH WM
Found 3 clusters
0 k 751.000000
1 k 1.000000
2 k 2.000000
Writing output aseg to mri/aparc.500+2mm.nii.gz
error: niiWrite(): error opening file mri/aparc.500+2mm.nii.gz
#VMPC# mri_aparc2aseg VmPeak 1376092
mri_aparc2aseg done
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