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