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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 in Image 1.
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 and image 3 shows the error that I get when I attempt to press the Press Fill Uncut Area button (I tried this many times and got the same result).
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
