Hi Ornaith

Can you please send us the commands and outputs as text, not as images? Then we can search, copy, paste, etc….

Why do you have -w 10 in your command line? That will generate interim snapshots of the integration, which you probably don’t care about. It also tries to open a log file, and I think that is failing as you probably don’t have write permission to wherever you are running it from

Cheers

Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Ornaith O Reilly
Sent: Friday, October 23, 2020 12:45 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Help to create flattened images of a whole hemisphere

        External Email - Use Caution        

Hi Ruopeng,

Thanks so much for getting back to me, that worked! However after saving the patch as lh.full.patch.3d and running the line  mris_flatten -w 10 lh.full.patch.3d lh.full.flat.patch.3d i got the error attached in the image.  Do you have any idea why that's happening?

Your help is greatly appreciated.

Kind regards,

Ornaith

On Fri 23 Oct 2020 at 17:21, Wang, Ruopeng <RWANG4@mgh.harvard.edu> wrote:

Hi Ornaith,

Regarding your freeview question - you need to move the current cursor (the 3d red cross hair) to a valid surface vertex. Supposedly you can do that using shift + Ctrl + left button in Cut/Path edit mode. But I just found out there is a glitch on macOS that prevent it from working. A workaround is to uncheck the Cut button, which will quit Cut mode and return to normal viewing mode, then just use 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 4:56 AM, Ornaith O Reilly <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 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

<Image 1 - tksurferfv not working.png><Image 2 - Geometry for patch.png><Image 3  Patch - Error.png><Image 4 -patch created.png>_______________________________________________
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