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 snolin@uab.edu
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
snolin@uab.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 snolin@uab.edu From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@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 snolin@uab.edumailto:snolin@uab.edu
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
snolin@uab.edu
*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@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 snolin@uab.edu<mailto:snolin@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
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 snolin@uab.edu On 2/5/18, 12:31 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of greve@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 > > snolin@uab.edu > > *From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas > Greve greve@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 $patient --annot 8V1 –labelwm > > And most of the time in most subjects this works, however > sometimes the output file doesn’t label any wm with the 3000+N or > 4000+N like it usually does. I have tried changing the > -wmparc-dmax, -hypo-as-wm, -smooth_normals. Basically everything I > could find but it won’t budge even though doing other labels in > the same person works fine. Fyi: The original cortical label is > also correctly place in the cortical ribbon. > > Any ideas? > > Please! > > Thanks, > > Sara Sims > > Graduate Research Fellow > > University of Alabama at Birmingham > > Department of Psychology > > 205-975-4060 > > snolin@uab.edumailto:snolin@uab.edu > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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Doug,
I have attached a picture of what the error looks like. As you can see all the values in the volume are all zero (blue) and there is nothing next to the cortical label (red). If it helps this the code I use to create it. subjects=/data/user/snolin/Scripts/Freesurfer_scripts/partial_recon; unset SUBJECTS_DIR SUBJECTS_DIR=$subjects export SUBJECTS_DIR patient=211215
#Label 8 conversion
mris_label2annot --ctab /data/user/snolin/Scripts/Labelmaker/color_tables/clut.8lhV1.ctab --s $patient --h lh --l $subjects/$patient/label/8_LH_V1.label --a 8V1
mris_label2annot --ctab /data/user/snolin/Scripts/Labelmaker/color_tables/clut.8rhV1.ctab --s $patient --h rh --l $subjects/$patient/label/8_RH_V1.label --a 8V1
mri_aparc2aseg --s $patient --annot 8V1 --labelwm
mri_binarize --i $subjects/$patient/mri/8V1+aseg.mgz --o $subjects/$patient/mri/8V1_bin.mgz --match 4001 3001
mri_convert $subjects/$patient/mri/8V1_bin.mgz $subjects/$patient/mri/8V1_bin.nii
mri_vol2vol --mov /data/project/vislab/raw/HCP_900sub/HCP_diff_data/$patient/data.nii.gz --targ $subjects/$patient/mri/8V1_bin.nii --reg /data/user/snolin/HCP_registration/HCP_BBR/HCP_registration_new/$patient/register_edit.dat --o $subjects/$patient/mri/8V1_diffROI.nii --inv --nearest
I would appreciate any help!
Sara Sims Graduate Research Fellow University of Alabama at Birmingham Department of Psychology 205-975-4060 snolin@uab.edu On 2/5/18, 5:02 PM, "Sims, Sara A" snolin@uab.edu 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 snolin@uab.edu On 2/5/18, 12:31 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of greve@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 > > snolin@uab.edu > > *From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas > Greve greve@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 > > snolin@uab.edumailto:snolin@uab.edu > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edumailto: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 greve@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/
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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 snolin@uab.edu On 2/5/18, 12:31 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of greve@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 > > snolin@uab.edu > > *From: *<freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas > Greve <greve@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 > > snolin@uab.edu<mailto:snolin@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 greve@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.
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Douglas Greve -
Douglas N Greve
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Sims, Sara A