Hello Freesurfer developers,

I am new to Freesurfer and I'm hoping that someone can help me; I'm attempting to get a flattened patch of an entire hemisphere. Below is a page outlining how to use mris_flatten to achieve this:

https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOccipitalFlattenedPatch

I am just trying to achieve this with the tutorial data to start with.

1. First problem is that when I run the command 'tksurferfv bert lh inflated'; I am getting the error outlined below:

Ornaiths-MacBook-Air-3:subjects ornaithoreilly$ tksurferfv bert lh inflated

freeview -f /Applications/freesurfer/7.1.1/subjects/bert/surf/lh.inflated:curvature=/Applications/freesurfer/7.1.1/subjects/bert/surf/lh.curv -viewport 3d

/Applications/freesurfer/7.1.1/bin/fsvglrun: line 20: conditional binary operator expected

/Applications/freesurfer/7.1.1/bin/fsvglrun: line 20: syntax error near `FS_ALLOW_VGLRUN'

/Applications/freesurfer/7.1.1/bin/fsvglrun: line 20: `if [[ ! -v FS_ALLOW_VGLRUN ]]; then'

Ornaiths-MacBook-Air-3:subjects ornaithoreilly$

2. I realised that I could create a patch using freeview instead of tksurfer. However I attempted to follow the instructions on the page above to do this and ran into some problems. Image 2 shows an example of the patch that I created but when I attempt to press the Press Fill Uncut Area button (I tried this many times and got the same result) a pop up appeared saying "please move cursor to a valid vertex".

3. However one time I did succeed in making a patch (I don't know what I did differently this time?) - see image 4 attached. I saved it as lh.full.patch.3d. When I tried to run the command mris_flatten :

mris_flatten -w 10 lh.full.patch.3d lh.full.flat.patch.3d

I got the output:

Ornaiths-MacBook-Air-3:surf ornaithoreilly$ mris_flatten -w 10 lh.full.patch.3d lh.full.flat.patch.3d

using write iterations = 10

reading new surface format patch lh.full.patch.3d with 125717 vertices (94.1% of total)

reading original vertex positions...

minimizing metric distortion induced by projection...

MRISunfold() max_passes = 1 -------

tol=2.0e-01, sigma=0.0, host=unkno, nav=1024, nbrs=2, l_nlarea=1.000, l_dist=1.000

using quadratic fit line minimization

complete_dist_mat 0

rms 0

smooth_averages 0

remove_neg 0

ico_order 0

which_surface 0

target_radius 0.000000

nfields 0

scale 0.000000

desired_rms_height -1.000000

momentum 0.900000

nbhd_size 7

max_nbrs 12

niterations 40

nsurfaces 0

SURFACES 3

flags 0 (0)

use curv 0

no sulc 0

no rigid align 0

mris->nsize 2

mris->hemisphere 0

randomSeed 0

--------------------

/Users/developer/space_freesurfer/build/tulum/trunk/developer-7.1.1/utils/mrisurf_metricProperties.cpp:9034 Error opening parms.fp using filename lh.full.flat.patch.3d.out mode w

The version of Freesurfer and the platform that I'm using is outlined below:

1) FreeSurfer version: freesurfer-darwin-macOS-7.1.1-20200811-8b40551

2) Platform: macOS High Sierra 10.13.6 (17G7024)

If anyone could shed some light on any of these errors or suggest an alternative method it would be greatly appreciated.

Thanks a lot.

Kind Regards

Ornaith O'Reilly