External Email - Use Caution
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
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 REMY003I 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 PhDKarolinska InstitutetCenter for Molecular MedicineStockholm, Sweden+41 76 391 04 01Dr. med. et Dr. rer. nat. ETH Benjamin Victor IneichenKarolinska InstitutetCenter for Molecular MedicineStockholm, Sweden+41 76 391 04 01