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 > > > _______________________________________________ > 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 gr...@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. 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