Hi Bram, try using mris_surfseg2vol. Look in the recon-all log file for an example usage doug
On 3/10/2024 12:43 PM, Bram Diamond wrote:
External Email - Use Caution
Hello FreeSurfer Experts!
I’m having trouble projecting the Yeo 17n annotation to volume space. I’ve tried on FS v7.4.1 on Mac OS (14.3.1) and FS v7.3.2 on Linux (7.9).
I’ve tried the following two methods:
---- 1. aparc2aseg ----
cd $FREESURFER_HOME/subjects/fsaverage/label
mri_aparc2aseg \
--s fsaverage \
--o Yeo2011_17Networks_N1000.mgz \
--annot Yeo2011_17Networks_N1000
---- Output ----
SUBJECTS_DIR /Applications/freesurfer/7.4.1/subjects
subject fsaverage
outvol Yeo2011_17Networks_N1000.mgz
useribbon 0
baseoffset 0
RipUnknown 0
Reading lh white surface
/Applications/freesurfer/7.4.1/subjects/fsaverage/surf/lh.white
Reading lh pial surface
/Applications/freesurfer/7.4.1/subjects/fsaverage/surf/lh.pial
Loading lh annotations from /Applications/freesurfer/7.4.1/subjects/fsaverage/label/lh.Yeo2011_17Networks_N1000.annot
Have color table for lh white annotation
Building hash of lh white
Building hash of lh pial
Reading rh white surface
/Applications/freesurfer/7.4.1/subjects/fsaverage/surf/rh.white
Reading rh pial surface
/Applications/freesurfer/7.4.1/subjects/fsaverage/surf/rh.pial
Loading rh annotations from /Applications/freesurfer/7.4.1/subjects/fsaverage/label/rh.Yeo2011_17Networks_N1000.annot
Have color table for rh white annotation
Building hash of rh white
Building hash of rh pial
Loading ribbon segmentation from /Applications/freesurfer/7.4.1/subjects/fsaverage/mri/ribbon.mgz
Loading aseg from /Applications/freesurfer/7.4.1/subjects/fsaverage/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 = 332584
Used brute-force search on 0 voxels
Writing output aseg to Yeo2011_17Networks_N1000.mgz
error: mghWrite(Yeo2011_17Networks_N1000.mgz, -1): could not open file
#VMPC# mri_aparc2aseg VmPeak 0
mri_aparc2aseg done
---- 2. label2vol ----
cd $FREESURFER_HOME/subjects/fsaverage/label
mri_label2vol \
--annot lh.Yeo2011_17Networks_N1000.annot \
--o lh.Yeo2011_17Networks_N1000.mgz \
--hemi lh \
--fill-ribbon \
--identity \
--subject fsaverage
---- Output ----
Number of labels: 0
Annot File: lh.Yeo2011_17Networks_N1000.annot
Template Volume: (null)
Outut Volume: lh.Yeo2011_17Networks_N1000.mgz
Registration File: (null)
Fill Threshold: 0
Label Vox Vol: 1
ProjType: (null)
ProjTypeId: 0
ProjStart: 0
ProjStop: 0
ProjDelta: 0.1
Subject: fsaverage
Hemi: lh
UseNewASeg2Vol: 0
DoLabelStatVol 0
LabelCodeOffset 0
setenv SUBJECTS_DIR /Applications/freesurfer/7.4.1/subjects
7.4.1
INFO: loading surface /Applications/freesurfer/7.4.1/subjects/fsaverage/surf/lh.white
nvertices = 163842
Reading thickness /Applications/freesurfer/7.4.1/subjects/fsaverage/surf/lh.thickness
Loading annotations from lh.Yeo2011_17Networks_N1000.annot
annotidmax = 18
nlabels = 18
Loading /Applications/freesurfer/7.4.1/subjects/fsaverage/mri/ribbon.mgz
Mapping
error: mghWrite(lh.Yeo2011_17Networks_N1000.mgz, -1): could not open file
I’ve done this before, so I feel like I must be doing something wrong. Any ideas?
Cheers,
Bram
*Bram R. Diamond, MS*
Clinical Psychology Doctoral Candidate
Northwestern University Feinberg School of Medicine
Mesulam Center for Cognitive Neurology & Alzheimer’s Disease
300 E. Superior Street | Tarry 8 | Chicago, IL 60611
www.brain.northwestern.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer