Hi Ornaith,

Regarding your freeview question - you can use shift + Ctrl + left button to select vertex for filling uncut area. But I just found out there is a glitch on macOS that prevent that from working. A workaround is to uncheck the Cut button, which will quit Cut mode and return to normal viewing mode, then just left mouse button to move the 3D cursor to the vertex you want, then check Cut button again and finish filling uncut area. I’ll fix this issue asap. May also drop the shift + ctrl requirement to make the whole process more intuitive.

Best, Ruopeng

On Oct 23, 2020, at 5:03 AM, Ornaith O Reilly <oreillor@tcd.iemailto:oreillor@tcd.ie> wrote:

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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 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 <Image 4 -patch created.png><Image 2 - Geometry for patch.png>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer