External Email - Use Caution

Several things:

1) The FreeSurfer list is probably not the best place for support for the HCP Pipelines as there is a dedicated user list hcp-users@humanconnectome.org for this. Folks who support the HCP Pipelines may not monitor the FreeSurfer list as closely. 2) It is very difficult to follow these threads across multiple days when the prior replies are not included in each e-mail. 3) it is correct that PreFreeSurfer does not use matlab. It does use python however, which you have gotten a bunch of python errors. It would appear that there is some incompatibility between Python and your mac¹s installed libraries, which is used for gradient nonlinearity correction and several FSL scripts. Because of how your libraries are configured, it appears to be looking for them in your matlab install, rather than in your system libraries folders. This library "/Applications/MATLAB_R2017b.app/sys/os/maci64/libgfortran.3.dylib² is not compatible with your scipy python 3.6 install. Perhaps there is another version of libgfortran.3 and you have defaulted your system to look for this in matlab¹s folders before anywhere else. This could occur if trying to run the HCP Pipelines from inside matlab, which is not recommended.

Based on the above, you might get actually best get help on the FSL list for this specific issue (entitled something like ³cannot run FSL python code like /usr/local/fsl/bin/imcp on my mac, please see these errors below²).

Matt.

On 2/17/19, 3:20 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Shachar Gal" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of gal.shachar@gmail.com> wrote:

   External Email - Use Caution

Actually Im not really sure why Matlab pops up here.. this is ran there is nothing that is Matlab dependent in the PreFreesurfer Pipeline...

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.