Thanks Doug and Bruce for your response.
Here is the result of the command Doug requested:
$ mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a ./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab C02DL_t1 rh white
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot.
reading volume /home/quadrellis/civ_ptsd/structural_fs/C02DL_t1/mri/wm.mgz...
reading input surface /home/quadrellis/civ_ptsd/structural_fs/C02DL_t1/surf/rh.white...
Using TH3 vertex volume calc
Total face volume 229272
Total vertex volume 224839 (mask=0)
reading input pial surface /home/quadrellis/civ_ptsd/structural_fs/C02DL_t1/surf/rh.pial...
reading input white surface /home/quadrellis/civ_ptsd/structural_fs/C02DL_t1/surf/rh.white...
reading colortable from annotation file...
colortable with 15 entries read (originally /usr/local/freesurfer/6.0.beta/average/colortable_BA.txt)
Saving annotation colortable ./BA_exvivo.thresh.ctab
table columns are:
number of vertices
total surface area (mm^2)
total gray matter volume (mm^3)
average cortical thickness +- standard deviation (mm)
integrated rectified mean curvature
integrated rectified Gaussian curvature
folding index
intrinsic curvature index
structure name
atlas_icv (eTIV) = 1539395 mm^3 (det: 1.265500 )
lhCtxGM: 216981.653 216526.000 diff= 455.7 pctdiff= 0.210
rhCtxGM: 224488.981 223971.000 diff= 518.0 pctdiff= 0.231
lhCtxWM: 221893.625 222489.000 diff= -595.4 pctdiff=-0.268
rhCtxWM: 224605.205 224852.000 diff= -246.8 pctdiff=-0.110
SubCortGMVol 51078.000
SupraTentVol 967354.464 (965462.000) diff=1892.464 pctdiff=0.196
SupraTentVolNotVent 940904.464 (939012.000) diff=1892.464 pctdiff=0.201
BrainSegVol 1111453.000 (1108301.000) diff=3152.000 pctdiff=0.284
BrainSegVolNotVent 1080460.000 (1080411.464) diff=48.536 pctdiff=0.004
BrainSegVolNotVent 1080460.000
CerebellumVol 141268.000
VentChorVol 26450.000
3rd4th5thCSF 4543.000
CSFVol 1413.000, OptChiasmVol 158.000
MaskVol 1614399.000
663 321 1164 2.414 0.317 0.126 0.029 10 0.7 BA1_exvivo
1878 1200 2522 2.055 0.423 0.096 0.018 13 1.5 BA2_exvivo
846 653 728 1.608 0.324 0.159 0.035 9 1.3 BA3a_exvivo
1782 1155 1902 1.588 0.371 0.089 0.018 9 1.5 BA3b_exvivo
930 539 1396 2.423 0.439 0.108 0.030 8 1.4 BA4a_exvivo
1048 718 1669 2.480 0.403 0.093 0.021 4 1.0 BA4p_exvivo
6264 3392 9732 2.494 0.482 0.103 0.030 66 7.5 BA6_exvivo
951 631 1818 2.403 0.428 0.123 0.027 16 1.1 BA44_exvivo
915 650 1780 2.212 0.349 0.139 0.031 16 1.0 BA45_exvivo
3074 2189 3724 1.675 0.473 0.134 0.035 33 4.8 V1_exvivo
4690 2886 4907 1.698 0.528 0.151 0.041 79 8.3 V2_exvivo
324 198 535 2.216 0.477 0.135 0.036 5 0.5 MT_exvivo
285 170 847 3.400 0.783 0.132 0.036 4 0.4 perirhinal_exvivo
245 177 522 2.386 0.732 0.126 0.020 2 0.2 entorhinal_exvivo
The annotation seems to be fine, I have attached a screenshot of the second command.
The initial command I ran was: "recon-all -all -s bert -hippocampal-subfields-T1”
However I noticed there was no [lr]h.hippoSfLabels-T1.v10.mgz output. When I tried to run the just the hippocampal segmentation I got an error that the matlab dependencies weren’t installed, so presumably that is why I received the original message ?!
Cheers,
Scott
From: "quadrellis@me.com" quadrellis@me.com Date: Tuesday, 8 December 2015 8:57 am To: freesurfer@nmr.mgh.harvard.edu Subject: Freesurfer 6 - exited with errors
Hi All,
I am trying to track down the source of an error on one of my first runs using freesurfer 6.
I have attached the relevant logs. Any help would be much appreciated.
Cheers,
Scott
You may need to download the Matlab Compiler Runtime (MCR) for Matlab 2012b. To do so, please run the following commands (you might need root permissions):
LINUX:
cd $FREESURFER_HOME curl "http://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&..." -o "runtime2012b.tar.gz" tar xvf runtime2012b.tar.gz
MAC:
cd $FREESURFER_HOME curl "http://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&..." -o "runtime2012b.tar.gz" tar xvf runtime2012b.tar.gz
On 12/08/2015 05:52 AM, Scott Quadrelli wrote:
Thanks Doug and Bruce for your response.
Here is the result of the command Doug requested:
*$ mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a ./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab C02DL_t1 rh white*
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot.
reading volume /home/quadrellis/civ_ptsd/structural_fs/C02DL_t1/mri/wm.mgz...
reading input surface /home/quadrellis/civ_ptsd/structural_fs/C02DL_t1/surf/rh.white...
Using TH3 vertex volume calc
Total face volume 229272
Total vertex volume 224839 (mask=0)
reading input pial surface /home/quadrellis/civ_ptsd/structural_fs/C02DL_t1/surf/rh.pial...
reading input white surface /home/quadrellis/civ_ptsd/structural_fs/C02DL_t1/surf/rh.white...
reading colortable from annotation file...
colortable with 15 entries read (originally /usr/local/freesurfer/6.0.beta/average/colortable_BA.txt)
Saving annotation colortable ./BA_exvivo.thresh.ctab
table columns are:
number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure nameatlas_icv (eTIV) = 1539395 mm^3 (det: 1.265500 )
lhCtxGM: 216981.653 216526.000 diff= 455.7 pctdiff= 0.210
rhCtxGM: 224488.981 223971.000 diff= 518.0 pctdiff= 0.231
lhCtxWM: 221893.625 222489.000 diff= -595.4 pctdiff=-0.268
rhCtxWM: 224605.205 224852.000 diff= -246.8 pctdiff=-0.110
SubCortGMVol 51078.000
SupraTentVol 967354.464 (965462.000) diff=1892.464 pctdiff=0.196
SupraTentVolNotVent 940904.464 (939012.000) diff=1892.464 pctdiff=0.201
BrainSegVol 1111453.000 (1108301.000) diff=3152.000 pctdiff=0.284
BrainSegVolNotVent 1080460.000 (1080411.464) diff=48.536 pctdiff=0.004
BrainSegVolNotVent 1080460.000
CerebellumVol 141268.000
VentChorVol 26450.000
3rd4th5thCSF 4543.000
CSFVol 1413.000, OptChiasmVol 158.000
MaskVol 1614399.000
663 321 1164 2.414 0.317 0.126 0.029 10 0.7 BA1_exvivo
1878 1200 2522 2.055 0.423 0.096 0.018 13 1.5 BA2_exvivo
846 653 728 1.608 0.324 0.159 0.035 9 1.3 BA3a_exvivo
1782 1155 1902 1.588 0.371 0.089 0.018 9 1.5 BA3b_exvivo
930 539 1396 2.423 0.439 0.108 0.030 8 1.4 BA4a_exvivo
1048 718 1669 2.480 0.403 0.093 0.021 4 1.0 BA4p_exvivo
6264 3392 9732 2.494 0.482 0.103 0.030 66 7.5 BA6_exvivo
951 631 1818 2.403 0.428 0.123 0.027 16 1.1 BA44_exvivo
915 650 1780 2.212 0.349 0.139 0.031 16 1.0 BA45_exvivo
3074 2189 3724 1.675 0.473 0.134 0.035 33 4.8 V1_exvivo
4690 2886 4907 1.698 0.528 0.151 0.041 79 8.3 V2_exvivo
324 198 535 2.216 0.477 0.135 0.036 5 0.5 MT_exvivo
285 170 847 3.400 0.783 0.132 0.036 4 0.4 perirhinal_exvivo
245 177 522 2.386 0.732 0.126 0.020 2 0.2 entorhinal_exvivo
The annotation seems to be fine, I have attached a screenshot of the second command.
The initial command I ran was: "recon-all -all -s bert -hippocampal-subfields-T1” However I noticed there was no /[lr]h.hippoSfLabels-T1.v10.mgz /output. When I tried to run the just the hippocampal segmentation I got an error that the matlab dependencies weren’t installed, so presumably that is why I received the original message ?!
Cheers,
Scott
From: "quadrellis@me.com mailto:quadrellis@me.com" <quadrellis@me.com mailto:quadrellis@me.com> Date: Tuesday, 8 December 2015 8:57 am To: <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Freesurfer 6 - exited with errors
Hi All,
I am trying to track down the source of an error on one of my first runs using freesurfer 6.
I have attached the relevant logs. Any help would be much appreciated.
Cheers,
Scott
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Scott Quadrelli