Run the script 'fixup_mni_perl_path', per the installation instructions. This will correct the faulting mni files in the ${FREESURFER_HOME}/lib/mni/bin directory.

On Thu, 2005-09-29 at 16:10 -0500, Greg Harris wrote:

Dear FreeSurfer maintainers,

When we download FreeSurfer and install it, we end up with files in ${FREESURFER_HOME}/lib/mni/bin that insist that perl be installed in /usr/pubsw/bin with script first lines as follows:

autocrop:#! /usr/pubsw/bin/perl -w field2imp:#!/usr/pubsw/bin/perl -w imp2field:#!/usr/pubsw/bin/perl -w make_template:#!/usr/pubsw/bin/perl -w mritoself:#! /usr/pubsw/bin/perl -w mritotal:#! /usr/pubsw/bin/perl -w nu_correct:#!/usr/pubsw/bin/perl -w nu_estimate:#!/usr/pubsw/bin/perl -w nu_estimate_np_and_em:#!/usr/pubsw/bin/perl -w nu_evaluate:#!/usr/pubsw/bin/perl -w resample_labels:#!/usr/pubsw/bin/perl sharpen_volume:#!/usr/pubsw/bin/perl -w xfmtool:#! /usr/pubsw/bin/perl -w

As it happens, our System Administration authority here is equally adamant that I should shout this complaint at you:

"A LOT OF PEOPLE don't have /usr/pubsw at all."

Of course, I know that these scripts come to you from Montreal Neurological Institute, and they TOLD you to tell all of us that /usr/pubsw is a REQUIREMENT so their scripts will not be sensitive to what version of perl is in use by any others here.

Well, even so, it is our practice to change each of these files to replace '/usr/pubsw/bin' with something acceptable on our installation, '/usr/bin', every time we download an update.

Perhaps, if these scripts are indeed version-specific, the specific version of perl that is required for Intel/Linux should be in the same ${FREESURFER_HOME}/lib/mni/bin directory and referenced as '#!./perl -w' in the MNI scripts.

Or, what would you suggest instead?

Greg Harris Iowa Psychiatry Brain Imaging Lab

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