External Email - Use Caution Dear experts,
I created a loop for mri_surf2surf so that it would run for 300+ subjects. For most of them, it ran successfully. However, it did not work for 30 subjects. I then went to investigate one by one and I am getting a Permission denied error for some reason. I confirm that recon-all has been performed and also that I have read/write/execute permissions. See below for the log. Any ideas why this could be happening to specific subjects? mri_surf2surf \ --srcsubject fsaverage_sym \ --trgsubject SPN01_CMH_0079_01 \ --hemi lh \ --sval-annot fsaverage_sym/label/lh.500_sym.aparc.annot \ --tval SPN01_CMH_0079_01/label/lh.500_sym.aparc.annot Setting mapmethod to nnf 7.1.0 setenv SUBJECTS_DIR /home/eji/projects/spins/preproc/freesurfer/subjects/w0 cd /home/eji/projects/spins/preproc/freesurfer/subjects/w0 mri_surf2surf --srcsubject fsaverage_sym --trgsubject SPN01_CMH_0079_01 --hemi lh --sval-annot fsaverage_sym/label/lh.500_sym.aparc.annot --tval SPN01_CMH_0079_01/label/lh.500_sym.aparc.annot sysname Linux hostname nu2 machine x86_64 user eji srcsubject = fsaverage_sym srcval = (null) srctype = trgsubject = SPN01_CMH_0079_01 trgval = SPN01_CMH_0079_01/label/lh.500_sym.aparc.annot 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 UseDualHemi = 0 Reading source surface reg /home/eji/projects/spins/preproc/freesurfer/subjects/w0/fsaverage_sym/surf/lh.sphere.reg Loading source data Reading surface file /home/eji/projects/spins/preproc/freesurfer/subjects/w0/fsaverage_sym/surf/lh.orig reading colortable from annotation file... colortable with 161 entries read (originally /scratch/tmpdir.annot2std.28231/seg.1.073.xhemi.ctab) Reading target surface reg /home/eji/projects/spins/preproc/freesurfer/subjects/w0/SPN01_CMH_0079_01/surf/lh.sphere.reg Done Using surf2surf_nnfr() Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (123600) Surf2Surf: Dividing by number of hits (123600) INFO: nSrcLost = 61776 nTrg121 = 123600, nTrgMulti = 0, MnTrgMultiHits = 0 nSrc121 = 85136, nSrcLost = 61776, nSrcMulti = 78706, MnSrcMultiHits = 0.488705 Saving target data Converting to target annot Saving to target annot SPN01_CMH_0079_01/label/lh.500_sym.aparc.annot error: Permission denied error: could not write annot file SPN01_CMH_0079_01/label/lh.500_sym.aparc.annot _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
