Hi Jorge,
Some v6.0 binary data must have been pruned from the public server. I just
synced it all back, so now you should be able to download the extra files with:
git fetch datasrc
git annex get .
Sorry about that. Glad to see you got everything else working – compiling 6.0
externally is not an easy task nowadays!
best
Andrew
From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Jorge Naranjo
<j...@nyu.edu>
Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, April 8, 2020 at 6:18 AM
To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Compiling Freesurfer 6 on Centos7 Install not working due
to annex files missing
External Email - Use Caution
Hi all
I’m building Freesurfer version 6 (stable6 branch) in a fresh centos7 OS
git clone https://github.com/freesurfer/freesurfer.git
cd freesurfer
git checkout stable6
git remote add datasrc
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/repo/annex.git
git fetch datasrc
git annex get --metadata fstags=makeinstall .
I do this since the options in the wiki using CMAKE and everything don’t work
for this version and BTW I can’t find the instruction to build it in Linux
anymore. I don’t know if this instructions were removed or what
After some small tweaks in the configure and packages I do:
./setup_configure
./configure --with-cuda=/usr/local/cuda/lib64 --enable-openmp --disable-Wall
--disable-Werror --enable-emu LDFLAGS=-lQt5X11Extras CFLAGS=-fpermissive
CXXFLAGS=-fpermissive --disable-Werror
--with-pkgs-dir=/opt/freesurfer/packages
--prefix=/share/apps/NYUAD4/freesurfer/6/ --with-cppunit-dir=/usr
--with-itk-dir=/opt/freesurfer/packages/itk/3.16.0/
--with-vtk-dir=/opt/freesurfer/packages/vtk/5.6.0/
--with-gts-dir=/opt/freesurfer/packages/gts/0.7.6/
--with-ann-dir=/opt/freesurfer/packages/ann/1.1.2/
--with-petsc-dir=/opt/freesurfer/packages/petsc/2.3.3/
--with-mni-dir=/opt/freesurfer/packages/mni/current/
--with-mpi-dir=/usr/lib64/openmpi/
--with-vxl-dir=/opt/freesurfer/packages/vxl/1.14.0
--with-kwwidgets-dir=/opt/freesurfer/packages/KWWidgets/5.6.0
make
Up to this point, everything goes OK!
Now the "make install" fails:
/bin/install: cannot stat ‘face.gca’: No such file or directory
/bin/install: cannot stat ‘talairach_mixed_with_skull.gca’: No such file or
directory
/bin/install: cannot stat ‘wmsa_new_eesmith.gca’: No such file or directory
/bin/install: cannot stat ‘aseg+spmhead.ixi.gca’: No such file or directory
/bin/install: cannot stat ‘aseg+spmhead+vermis+pons.ixi.gca’: No such file or
directory
/bin/install: cannot stat ‘pons.mni152.2mm.mgz’: No such file or directory
/bin/install: cannot stat ‘lh.atlas2002_simple.gcs’: No such file or directory
/bin/install: cannot stat ‘lh.atlas2005_simple.gcs’: No such file or directory
/bin/install: cannot stat
‘lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs’: No such file
or directory
/bin/install: cannot stat ‘lh_trans_toSulc.gcs’: No such file or directory
/bin/install: cannot stat ‘lh.destrieux.simple.2009-07-29.gcs’: No such file or
directory
/bin/install: cannot stat ‘rh.atlas2002_simple.gcs’: No such file or directory
/bin/install: cannot stat ‘rh.atlas2005_simple.gcs’: No such file or directory
/bin/install: cannot stat
‘rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs’: No such file
or directory
/bin/install: cannot stat ‘rh_trans_toSulc.gcs’: No such file or directory
/bin/install: cannot stat ‘rh.destrieux.simple.2009-07-29.gcs’: No such file or
directory
/bin/install: cannot stat ‘rh.DKTatlas40.gcs’: No such file or directory
/bin/install: cannot stat ‘lh.DKTatlas40.gcs’: No such file or directory
/bin/install: cannot stat ‘rh.DKTatlas100.gcs’: No such file or directory
/bin/install: cannot stat ‘lh.DKTatlas100.gcs’: No such file or directory
/bin/install: cannot stat ‘lh.average.curvature.filled.buckner40.tif’: No such
file or directory
/bin/install: cannot stat ‘lh.average.CURVATURE.tif’: No such file or directory
/bin/install: cannot stat ‘lh.average.tif’: No such file or directory
/bin/install: cannot stat ‘rh.average.curvature.filled.buckner40.tif’: No such
file or directory
/bin/install: cannot stat ‘rh.average.CURVATURE.tif’: No such file or directory
/bin/install: cannot stat ‘rh.average.tif’: No such file or directory
/bin/install: cannot stat ‘rigidly_aligned_brain_template.tif’: No such file or
directory
/bin/install: cannot stat ‘label_scales.dat’: No such file or directory
/bin/install: cannot stat ‘mni305.cor.mgz’: No such file or directory
/bin/install: cannot stat ‘mni305.mask.cor.mgz’: No such file or directory
/bin/install: cannot stat ‘mni305.cor.subfov1.mgz’: No such file or directory
/bin/install: cannot stat ‘mni305.cor.subfov2.mgz’: No such file or directory
/bin/install: cannot stat ‘mni305.cor.subfov1.reg’: No such file or directory
/bin/install: cannot stat ‘mni305.cor.subfov2.reg’: No such file or directory
/bin/install: cannot stat ‘mni152.register.dat’: No such file or directory
/bin/install: cannot stat ‘mni152.mni305.cor.subfov1.dat’: No such file or
directory
/bin/install: cannot stat ‘mni152.mni305.cor.subfov2.dat’: No such file or
directory
make[2]: *** [install] Error 1
The problem arises when moving to the stable6 branch, and I need that one.
I tried what suggested here:
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51895.html
$> git annex get distribution/average/mult-comp-cor.tar.gz
$> make install
But didn’t work either
Any help??
Thanks in advance
Jorge A. Naranjo
Senior HPC Computational Specialist
NYU Abu Dhabi
Office Tel (UAE): +971 2 628 4750
Mobile (UAE): +971 56 319 2814
New York University - Abu Dhabi (NYUAD)
Saadiyat Campus - A2, Room-131
P.O. Box 129188
Abu Dhabi, United Arab Emirates
http://nyuad.nyu.edu<http://nyuad.nyu.edu/>
Please consider the environment before printing this email.
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