Hello Carissa,

There have been some changes to the files related to the “—make all” option. You can try downloading an updated version of the recon-all.makefile from the list of files under,

ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev_binaries/centos7_x86_64/

and replace the existing one in $FREESURFER_HOME/bin with the downloaded one.

One way to do this from the terminal would be,

… move aside the old recon-all.makefile.OLD ...

$ mv $FREESURFER_HOME/bin/recon-all.makefile $FREESURFER_HOME/bin/recon-all.makefile.OLD

… and if you downloaded the new one into your home directory downloads folder, then you would copy it in from the path, e.g., if saved to $HOME/Downloads,

$ cp -f $HOME/Downloads/recon-all.makefile $FREESURFER_HOME/bin/recon-all.makefile

… check they files now the same - you should get no output from the diff command …

$ diff $HOME/Downloads/recon-all.makefile $FREESURFER_HOME/bin/recon-all.makefile

The try running your rein-all again.

- rob

On Apr 11, 2018, at 11:53 AM, Carissa Nicole Weis <cnweis@uwm.edumailto:cnweis@uwm.edu> wrote:

Hello,

I am running recon-all for several subjects’ 7T data using Freesurfer version 6.0 and currently trying to ensure appropriate skull stripping and pial/wm surface generation. For a few participants that needed some control points added and for which I reran them through the –autorecon2-cp option, I was unable to open the pial surfaces for review. I’ve seen on some of the other posts that you guys recommend running “recon-all –make all” to rebuild the files. I’ve tried to run the -make all command but have been running into the same error in the “Jacobian white lh” step:

#@# Jacobian white lh Wed Apr 4 12:07:37 CDT 2018 /bigraid-03/LS/Data/7T_fall2017/6315/6315_fs/scripts

mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white

reading surface from ../surf/lh.white.preaparc… mrisReadTriangleFile(../surf/lh.sphere.reg): surface doesn’t match ../surf/lh.white.preaparc

No such file or directory mrisReadTriangleFile failed.

No such file or directory mris_jacobian: could not read target surface ../surf/lh.sphere.reg No such file or directory

recon-all –s 6315_fs exited with ERRORS at Wed Apr 4 12:07:40 CDT 2018

All of the output in the log file up until this point appears to have finished without error. I can now open the surfaces for review, but am wondering what is affected by –make all not finishing completely.

Carissa N. Weis, B.S. Graduate Student Affective Neuroscience Laboratory University of Wisconsin-Milwaukee cnweis@uwm.edumailto:cnweis@uwm.edu

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