does the mri folder exist? do you have write permission to it? is the disk out of space?

On 7/23/2020 11:04 AM, Ellen Ji wrote:

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Yes, exactly, I am running it from /home/eji/projects/spins/preproc/freesurfer/subjects/w0.

(using a virtual machine, but ran mri_aparc2aseg a few weeks ago with no problem)

On 7/23/2020 4:56 PM, Douglas N. Greve wrote:

...

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:

...

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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;

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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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