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-bounces@nmr.mgh.harvard.edu on behalf of Jorge Naranjo jn63@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.eduhttp://nyuad.nyu.edu/ Please consider the environment before printing this email.