On May 2, 2018, at 6:51 PM, Dicamillo, Robert <RDICAMILLO@mgh.harvard.edu> wrote:

Hello Ruy,

Do you mean the mri_train binary that gets built under ./freesurfer/mri_train ?

(I see a ./freesurfer/dmri_poistats, ./freesurfer/dmri_tensroreig but not a ./freesurfer/dmri_train).

Things are not necessarily setup so you can cd to ./freesurfer/<subdir> and just build

what is there in isolation from the rest of the tree.

But for ./freesiurfer/mri_train, you could try the following, which worked for me on a Mac, e.g.,

after changing mri_train.c,

$ cd ./freesurfer/mri_train

$ rm -f mri_train mri_train.o

$ make -r mri_train

- rob

On May 2, 2018, at 5:37 PM, Ricardo Valle <ruyvallem@gmail.com> wrote:

        External Email - Use Caution        

Hello,

I need help recompiling dmri_train for Mac. It seems like the instructions in the Mac Developer’s don’t work.

When I cd to the trc subdirectory and run make, I am told there is nothing to do. I tried editing the Makefile, adding bin_PROGRAMS = dmri_train, at which point I got a different error. I then uncommented some other lines in the Makefile and managed to start compiling dmri_train, but I’ve been getting a never-ending sequence of errors, essentially telling me that the compiler can’t find various dependencies (boost/program_options.h, itk*.h, etc.). I’ve tried running ./configure with various flags that disable or enable various build options, copying over .h files from other locations, adding -I <path> directives for the compiler in the Makefile, etc. etc. to no avail.

Thank you,

Ruy

On Apr 30, 2018, at 5:19 PM, Ricardo Valle <ruyvallem@gmail.com> wrote:

Dear Freesurfer community,

I am trying to recompile Freesurfer in order to get a binary of the latest version of dmri_train. I have been following the instructions in the Freesurfer Mac Developer’s page and am stuck at the following:

git annex get --metadata fstags=makeinstall .

I am attaching the output (stdout and stderr) from this command to this email. Please note that I called the git-annex repository mgh rather than datasrc. The purpose of running this is so I can run make install.

Is there a way of recompiling only dmri_train or only the dmri_* programs? If not, do you know why git-annex might be giving me problems and how to solve this?

Thank you,

Ruy

<fs-annex-get.txt>

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