External Email - Use Caution As addendum to my message. The full terminal output:
Reading surface /Users/benine/Desktop/PVS_validation_cohort/MyelinMS_MRI_export/Freesurfer_output/REMY001_M0//surf/lh.white Loading annotations from /Users/benine/Desktop/PVS_validation_cohort/MyelinMS_MRI_export/Freesurfer_output/REMY001_M0//label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) CTABwriteFileASCII(/Users/benine/Desktop/PVS_validation_cohort/MyelinMS_MRI_export/Freesurfer_output/avgsubject/label/tmpdir.annot2std.38242/seg.1.REMY001_M0/.ctab): could not open for writing No such file or directory Seg base 0 mghWrite(/Users/benine/Desktop/PVS_validation_cohort/MyelinMS_MRI_export/Freesurfer_output/avgsubject/label/tmpdir.annot2std.38242/seg.1.REMY001_M0/.mgh, -1): could not open file Converting to a segmentation mri_surf2surf --mapmethod nnf --hemi lh --srcsubject REMY001_M0/ --srcsurfreg sphere.reg --sval /Users/benine/Desktop/PVS_validation_cohort/MyelinMS_MRI_export/Freesurfer_output/avgsubject/label/tmpdir.annot2std.38242/seg.1.REMY001_M0/.mgh --trgsubject avgsubject --trgsurfreg sphere.reg --tval /Users/benine/Desktop/PVS_validation_cohort/MyelinMS_MRI_export/Freesurfer_output/avgsubject/label/tmpdir.annot2std.38242/seg.1.REMY001_M0/.std.mgh mghRead(/Users/benine/Desktop/PVS_validation_cohort/MyelinMS_MRI_export/Freesurfer_output/avgsubject/label/tmpdir.annot2std.38242/seg.1.REMY001_M0/.mgh, -1): could not open file Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /Users/benine/Desktop/PVS_validation_cohort/MyelinMS_MRI_export/Freesurfer_output cd /Users/benine/Desktop/PVS_validation_cohort/MyelinMS_MRI_export/Freesurfer_output/avgsubject mri_surf2surf --mapmethod nnf --hemi lh --srcsubject REMY001_M0/ --srcsurfreg sphere.reg --sval /Users/benine/Desktop/PVS_validation_cohort/MyelinMS_MRI_export/Freesurfer_output/avgsubject/label/tmpdir.annot2std.38242/seg.1.REMY001_M0/.mgh --trgsubject avgsubject --trgsurfreg sphere.reg --tval /Users/benine/Desktop/PVS_validation_cohort/MyelinMS_MRI_export/Freesurfer_output/avgsubject/label/tmpdir.annot2std.38242/seg.1.REMY001_M0/.std.mgh sysname Darwin hostname K8WSBENINE machine x86_64 user benine srcsubject = REMY001_M0/ srcval = /Users/benine/Desktop/PVS_validation_cohort/MyelinMS_MRI_export/Freesurfer_output/avgsubject/label/tmpdir.annot2std.38242/seg.1.REMY001_M0/.mgh srctype = trgsubject = avgsubject trgval = /Users/benine/Desktop/PVS_validation_cohort/MyelinMS_MRI_export/Freesurfer_output/avgsubject/label/tmpdir.annot2std.38242/seg.1.REMY001_M0/.std.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 UseDualHemi = 0 Reading source surface reg /Users/benine/Desktop/PVS_validation_cohort/MyelinMS_MRI_export/Freesurfer_output/REMY001_M0//surf/lh.sphere.reg Loading source data ERROR: could not read /Users/benine/Desktop/PVS_validation_cohort/MyelinMS_MRI_export/Freesurfer_output/avgsubject/label/tmpdir.annot2std.38242/seg.1.REMY001_M0/.mgh as type 3 ERROR: make_average_surface Thanks! Am Mi., 26. Feb. 2020 um 10:34 Uhr schrieb Benjamin Ineichen < bv.ineic...@gmail.com>: > Dear Freesurfer experts, > > I want to create a new standard template from my study population. For > this, I thought about using make_average_subject. Thus, I run: > make_average_subject --out avgsubject --subjects REMY001 REMY002 REMY003 > > I get an error message - ERROR: make_average_surface. Please find attached > the error.log. > > Would be very thankful for advice! > > Many thanks! > > /Ben > > -- > ____________________________________ > Benjamin Victor Ineichen, MD PhD > Karolinska Institutet > Center for Molecular Medicine > Stockholm, Sweden > ineic...@protonmail.ch > +41 76 391 04 01 > > Dr. med. et Dr. rer. nat. ETH Benjamin Victor Ineichen > Karolinska Institutet > Center for Molecular Medicine > Stockholm, Sweden > ineic...@protonmail.ch > +41 76 391 04 01 > -- ____________________________________ Benjamin Victor Ineichen, MD PhD Karolinska Institutet Center for Molecular Medicine Stockholm, Sweden ineic...@protonmail.ch +41 76 391 04 01 Dr. med. et Dr. rer. nat. ETH Benjamin Victor Ineichen Karolinska Institutet Center for Molecular Medicine Stockholm, Sweden ineic...@protonmail.ch +41 76 391 04 01
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