Hello,
I am using FreeSurfer 5.1.0. When running recon-all -label_v1 -s $SUBJECT It could not find the rh.white and lh.white surfaces. Subsequently, there was no data in the rh.v1.predict.label. % tksurfer.bin: no data in label file /cluster/haru/uni/1/users/nap_study/struct/nap_01/label/rh.v1.predict.label
Additionally, no <subjid>/label/?h.v1.prob.label was created. I am using the V1_average found on the NMR servers (see output of ls -l below run in $SUBJECTS_DIR):
V1_average -> /usr/local/freesurfer/stable5_1_0/subjects/V1_average
Am I using the wrong V1_average? Do I need to provide any further details?
Thanks, Dan
Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-v5.1.0-20110514 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-v5.1.0-20110514 INFO: SUBJECTS_DIR is /autofs/cluster/haru/uni/1/users/nap_study/struct Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos4.0_x86_64/stable5_1_0 -rw-rw-r-- 1 dwakeman pls 385906 Mar 28 16:00 /autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/scripts/recon-all.log Linux gobo 2.6.18-238.9.1.el5 #1 SMP Tue Apr 12 18:10:13 EDT 2011 x86_64 x86_64 x86_64 GNU/Linux #----------------------------------------- #@# Label V1 lh Wed Mar 28 17:05:43 EDT 2012 /autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/label
predict_v1.sh -h lh nap_01
/autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/surf/lh.inflated.H already exists, skipping.
mris_register -inflated -a 4096 -dist 10.0 -parea 1.0 /autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/surf/lh.sphere /autofs/cluster/haru/uni/1/users/nap_study/struct/V1_average/label/lh.v1.invivo.tif /autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/surf/lh.v1.invivo.reg
using inflated surface for initial alignment using n_averages = 4096 l_dist = 10.000 using l_parea = 1.000 $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from /autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/surf/lh.sphere... reading template parameterization from /autofs/cluster/haru/uni/1/users/nap_study/struct/V1_average/label/lh.v1.invivo.tif... curvature mean = 0.000, std = 1.000 curvature mean = 0.018, std = 0.041 curvature mean = 0.006, std = 0.891 curvature mean = 0.018, std = 0.043 curvature mean = 0.002, std = 0.959 curvature mean = 0.018, std = 0.045 curvature mean = 0.001, std = 0.981 curvature mean = 0.018, std = 0.049 curvature mean = 0.000, std = 0.991 writing registered surface to /autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/surf/lh.v1.invivo.reg... curvature mean = 0.000, std = 0.604 curvature mean = 0.004, std = 0.952 curvature mean = 0.037, std = 0.807 curvature mean = -0.011, std = 0.957 curvature mean = 0.012, std = 0.930 curvature mean = -0.020, std = 0.961 curvature mean = 0.006, std = 0.967 curvature mean = -0.024, std = 0.961 curvature mean = 0.002, std = 0.985 curvature mean = -0.026, std = 0.286 curvature mean = 0.002, std = 0.068 curvature mean = 0.065, std = 0.336 curvature mean = 0.002, std = 0.081 curvature mean = 0.039, std = 0.522 curvature mean = 0.002, std = 0.087 curvature mean = 0.019, std = 0.665 curvature mean = 0.002, std = 0.090 curvature mean = 0.007, std = 0.771 expanding nbhd size to 1 mris_spherical_average -osurf v1.invivo.reg -n -o nap_01 label lh.v1.invivo.label lh v1.invivo.reg V1_average /autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/label/lh.v1.prob.label
output surface = v1.invivo.reg painting output onto subject nap_01. processing subject V1_average... MRISreadVertexPosition(white): could not open file /autofs/cluster/haru/uni/1/users/nap_study/struct/V1_average/surf/lh.white No such file or directory MRISreadOriginalProperties: could not read surface file white No such file or directory could not read surface positions from white No such file or directory threshold_labelfile_at_0p8 /autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/label/lh.v1.prob.label /autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/label/lh.v1.predict.label
thresholding the label...cat: /autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/label/lh.v1.prob.label: No such file or directory done #----------------------------------------- #@# Label V1 rh Wed Mar 28 18:47:58 EDT 2012 /autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/label
predict_v1.sh -h rh nap_01
/autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/surf/rh.inflated.H already exists, skipping.
mris_register -inflated -a 4096 -dist 10.0 -parea 0.4 /autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/surf/rh.sphere /autofs/cluster/haru/uni/1/users/nap_study/struct/V1_average/label/rh.v1.invivo.tif /autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/surf/rh.v1.invivo.reg
using inflated surface for initial alignment using n_averages = 4096 l_dist = 10.000 using l_parea = 0.400 $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from /autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/surf/rh.sphere... reading template parameterization from /autofs/cluster/haru/uni/1/users/nap_study/struct/V1_average/label/rh.v1.invivo.tif... curvature mean = -0.000, std = 1.000 curvature mean = 0.014, std = 0.039 curvature mean = 0.007, std = 0.894 curvature mean = 0.015, std = 0.037 curvature mean = 0.003, std = 0.935 curvature mean = 0.015, std = 0.039 curvature mean = 0.001, std = 0.966 curvature mean = 0.015, std = 0.042 curvature mean = 0.000, std = 0.984 writing registered surface to /autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/surf/rh.v1.invivo.reg... curvature mean = 0.000, std = 0.598 curvature mean = -0.003, std = 0.935 curvature mean = 0.032, std = 0.805 curvature mean = -0.004, std = 0.942 curvature mean = 0.012, std = 0.925 curvature mean = -0.008, std = 0.944 curvature mean = 0.005, std = 0.965 curvature mean = -0.010, std = 0.943 curvature mean = 0.001, std = 0.984 curvature mean = -0.027, std = 0.279 curvature mean = 0.004, std = 0.070 curvature mean = 0.065, std = 0.345 curvature mean = 0.004, std = 0.084 curvature mean = 0.041, std = 0.531 curvature mean = 0.004, std = 0.090 curvature mean = 0.021, std = 0.675 curvature mean = 0.004, std = 0.093 curvature mean = 0.006, std = 0.787 mris_spherical_average -osurf v1.invivo.reg -n -o nap_01 label rh.v1.invivo.label rh v1.invivo.reg V1_average /autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/label/rh.v1.prob.label
output surface = v1.invivo.reg painting output onto subject nap_01. processing subject V1_average... MRISreadVertexPosition(white): could not open file /autofs/cluster/haru/uni/1/users/nap_study/struct/V1_average/surf/rh.white No such file or directory MRISreadOriginalProperties: could not read surface file white No such file or directory could not read surface positions from white No such file or directory threshold_labelfile_at_0p8 /autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/label/rh.v1.prob.label /autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/label/rh.v1.predict.label
thresholding the label...cat: /autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/label/rh.v1.prob.label: No such file or directory done
#------------------------------------------
recon-all -s nap_01 finished without error at Wed Mar 28 20:28:12 EDT 2012 done