This is a bug in mris_preproc. A work-around is to add --srcfmt mgh as the last argument. In the mean time I'll fix mris_preproc
doug
On 09/18/2014 11:32 AM, Lars M. Rimol wrote:
Hi,
I get the following error message when running mris_preproc, and I'm wondering what file is it looking for?:
Reading curvature file /usit/abel/u1/rimol/subjects/long/long_v0v2_amd/007v2.long.007_base/surf/lh.(null) MRISreadCurvature: could not open /usit/abel/u1/rimol/subjects/long/long_v0v2_amd/007v2.long.007_base/surf/lh.(null) No such file or directory ERROR: reading curvature file
This subject, 007, seems to have all the files it should:
[rimol @ ~/subjects/long/long_v0v2_amd]$ ls /usit/abel/u1/rimol/subjects/long/long_v0v2_amd/007v2.long.007_base/surf lh.area lh.inflated.H lh.pial_lgi lh.smoothwm.K1.crv lh.thickness rh.avg_curv rh.orig rh.smoothwm.BE.crv rh.smoothwm.S.crv rh.white lh.area.mid lh.inflated.K lh.pial-outer-smoothed lh.smoothwm.K2.crv lh.volume rh.curv rh.orig_pial rh.smoothwm.C.crv rh.sphere lh.area.pial lh.jacobian_white lh.smoothwm lh.smoothwm.K.crv lh.w-g.pct.mgh rh.curv.pial rh.orig_white rh.smoothwm.FI.crv rh.sphere.reg lh.avg_curv lh.orig lh.smoothwm.BE.crv lh.smoothwm.S.crv lh.white rh.inflated rh.pial rh.smoothwm.H.crv rh.sulc lh.curv lh.orig_pial lh.smoothwm.C.crv lh.sphere rh.area rh.inflated.H rh.pial_lgi rh.smoothwm.K1.crv rh.thickness lh.curv.pial lh.orig_white lh.smoothwm.FI.crv lh.sphere.reg rh.area.mid rh.inflated.K rh.pial-outer-smoothed rh.smoothwm.K2.crv rh.volume lh.inflated lh.pial lh.smoothwm.H.crv lh.sulc rh.area.pial rh.jacobian_white rh.smoothwm rh.smoothwm.K.crv rh.w-g.pct.mgh
Here's the entire output:
[rimol @ ~/subjects/long/long_v0v2_amd]$ mris_preproc --qdec-long ~/long_qdec_FINAL2_w33_model1.dat --target fsaverage --hemi lh --meas area --area pial --out test_pial.mgh nsubjects = 172 INFO: turning on jacobican correction tmpdir is ./tmp.mris_preproc.11745 /cluster/home/rimol/subjects/long/long_v0v2_amd Log file is test_pial.mris_preproc.log Thu Sep 18 17:23:19 CEST 2014 setenv SUBJECTS_DIR /usit/abel/u1/rimol/subjects/long/long_v0v2_amd cd /cluster/home/rimol/subjects/long/long_v0v2_amd /cluster/software/VERSIONS/freesurfer-5.3.0/bin/mris_preproc --qdec-long /usit/abel/u1/rimol/long_qdec_FINAL2_w33_model1.dat --target fsaverage --hemi lh --meas area --area pial --out test_pial.mgh
Linux login-0-1.local 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.59.2.4 2012/12/06 16:06:52 mreuter Exp $ freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 tmpdir is ./tmp.mris_preproc.11745 Src lh sphere.reg Trg lh sphere.reg
#@# 1/172 007v2.long.007_base Thu Sep 18 17:23:19 CEST 2014 --------------
mri_surf2surf --srcsubject 007v2.long.007_base --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.11745/007v2.long.007_base.1.mgh --sval-area pial --jac --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = 007v2.long.007_base srcval = (null) srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.11745/007v2.long.007_base.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /usit/abel/u1/rimol/subjects/long/long_v0v2_amd/007v2.long.007_base/surf/lh.sphere.reg Loading source data Reading curvature file /usit/abel/u1/rimol/subjects/long/long_v0v2_amd/007v2.long.007_base/surf/lh.(null) MRISreadCurvature: could not open /usit/abel/u1/rimol/subjects/long/long_v0v2_amd/007v2.long.007_base/surf/lh.(null) No such file or directory ERROR: reading curvature file
-- yours,
Lars M. Rimol, PhD St. Olavs Hospital Trondheim, Norway
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