Re: [Freesurfer] unknown option in new brainstem segmentation

[Marmaduke]

On March 10, 2016 10:41:12 AM GMT+01:00, Claudia Testa  
wrote:
>
>Dear Freesurfers,
>I've installed Freesurfer 6.0 beta in a virtual machine,
>and run the -brainstem-structures option to recon-all.
>
>The process stopped with an error:  "ERROR: Option --DKTatlas40
>unknown"
>
>In the following, all the information:
>_
>FREESURFER_HOME: /usr/local/freesurfer
>
>Build stamp: freesurfer_Linux_centos6_x86_64-dev-20160229
>
>RedHat release: CentOS release 6.7 (Final)
>
>Kernel info: Linux 2.6.32-573.el6.x86_64 x86_64
>
>__
>
>1) subject name is 11960
>2) the command line is:
>recon-all -all -i /usr/local/freesurfer/input/11960_3D_lf.nii.gz  -s
>11960 -brainstem-structures
>3) mri_aparc2aseg --s 11960 --volmask --aseg aseg.presurf.hypos
>--DKTatlas40
>
>ERROR: Option --DKTatlas40 unknown
>Linux freesurfer-fabio 2.6.32-573.el6.x86_64 #1 SMP Thu Jul 23 15:44:03
>UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
>
>recon-all -s 11960 exited with ERRORS at Wed Mar  9 23:53:10 CET 2016
>
>4) in attach the recon-all.log file
>
>
>Thank you for your help
>
>Claudia
>
>
>
>
>
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hi

I had this as well, you have to rerun the last step manually with the correct 
atlas flag.


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[Freesurfer] License on fsaverage datasets

[Marmaduke Woodman]

hi

As part of developing some tools [1] partly on the FreeSurfer ecosystem,
we'd like to use the fsaverage5 dataset as a test data. In our workflow
that would mean committing those files to our Git repo, pushing to GitHub,
testing on Travis CI etc which makes them public in our repo. We have,
however, no intention of otherwise redistributing the data.

If we place the FreeSurfer license file next to the fsaverage5 folder in
our repo, is this OK? or would you have a strong preference against this?


Thanks,
Marmaduke


[1] The project in question is here

https://github.com/ins-amu/bnm-recon-tools

though not well developed at its current stage.
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[Freesurfer] Problem checking out sources

[Marmaduke Woodman]

hi

I followed the instructions for checking out the sources, by logging in
first and then trying to checkout

~/src/fs$ cvs -d :pserver:anonym...@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot
co -P -r stable5 dev
cvs server: cannot find module `dev' - ignored
cvs [checkout aborted]: cannot expand modules

alas I am a CVS n00b and have no idea what this means.. am I missing
something obvious?

Thanks,
Marmaduke
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[Freesurfer] Slim down FS6

[Marmaduke Woodman]

Hi

I'm using just the standard structural recon-all pipeline, nothing else. FS6's 
directory totals just over 9 GiB. Is there a way to slim that down, or is it 
all required for the structural pipeline? 

I'm using Docker containers, hence trying to slim down the image size. 

Thanks,
Marmaduke



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Re: [Freesurfer] Slim down FS6 (Marmaduke Woodman)

[Marmaduke Woodman]

> On 5 Feb 2017, at 19:07, Alex Cohen  wrote:
> 
> Have you looked at the modifications for the BIDS App version:
> 
> https://github.com/BIDS-Apps/freesurfer 
> 
No, I admittedly didn't Google hard before asking, but this is a great example 
to work from. Thanks!___
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[Freesurfer] Deflate surface

[marmaduke woodman]

Hi

I would like to resample the cortical surface on the sphere at a lower 
resolution, and then deflate the surface to its folded form.

Is this something which can be done using the inflated surface that FS 
generates?

Thank you,
Marmaduke
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Re: [Freesurfer] Deflate surface

[marmaduke woodman]

Hi

On 03/04/2016 07:06 PM, Bruce Fischl wrote:

> I think there are some tools around for downsampling the surfaces like
> mris_decimate. Have you tried any of them?

Yes, indeed mris_decimate works well for the downsampling.

However, I'd like to recover the cortical parcellation for the 
downsampled surface. Is there a shortcut to do this, or does it need to 
go through the same steps of inflation, registration and parcellation as 
the original surface?

Thanks for answering my somewhat naive questions..

Marmaduke
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Re: [Freesurfer] Deflate surface

[marmaduke woodman]

On 03/04/2016 09:10 PM, marmaduke woodman wrote:

> However, I'd like to recover the cortical parcellation for the
> downsampled surface.

I tried to decimate the pial & white surfaces, generate a corresponding 
thickness file and then

mris_sample_parc -ct /opt/freesurfer/FreeSurferColorLUT.txt tvb lh 
aparc+aseg.mgz decim.annot

but this seems not to generate a proper annot file. The same procedure 
works for the original pial & white surfaces.


The alternative, it appears to me, would be to generate decimated white, 
smoothwm, inflated, sphere, curv & sulc surfaces, apply mris_register to 
obtain decimated sphere.reg and then mris_ca_label to obtain a proper 
annot file for the decimation.


I will try this, but any insight would be appreciated.

cheers,
Marmaduke
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Re: [Freesurfer] Deflate surface

[marmaduke woodman]

On 03/04/2016 10:06 PM, Bruce Fischl wrote:
> what are you trying to achieve?

A per-subject ~10k vertex pial surface with a corresponding annot. We 
use it as a spatial domain for simulating neural activity; 150k vertices 
is too many for this purpose.

 > It might be easiest to use something like
> fsaverage5 as the downsampled surface. Then you would just map your
> subjects to fsaverage5 using the existing sphere.reg files

If I understand correctly, different subjects would then have identical 
cortical geometry, which isn't sufficient for our use case, as we are 
calculating the forward solution for EEG/MEG which can depend on the 
individual's cortical geometry.

Sorry if I've misunderstood your suggestion, I'm still a freesurfer noob.


Thanks,
Marmaduke




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Re: [Freesurfer] Deflate surface

[marmaduke woodman]

On 03/04/2016 10:19 PM, Bruce Fischl wrote:
> I think you can map it to fsaverage5 then use mri_surf2surf with
> -sval-xyz to map the fsaverage5 surface back to each subject

This seems to generate a surface with the number of vertices in the 
subject, (160k) not fsaverage5 (10k), though perhaps I've not got the 
flags correct. I tried the command


mri_surf2surf --srcsubject fsaverage5 --trgsubject tvb --hemi lh 
--sval-xyz pial --tval ./fsaverage5-xyz-in-tvb --tval-xyz tvb/mri/T1.mgz


If I reverse the subjects, I get a surface with 10k vertices, but then 
the cortical geometry is that of fsaverage, no?
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Re: [Freesurfer] Deflate surface

[marmaduke woodman]

On 03/04/2016 10:50 PM, marmaduke woodman wrote:
> On 03/04/2016 10:19 PM, Bruce Fischl wrote:
>> I think you can map it to fsaverage5 then use mri_surf2surf with
>> -sval-xyz to map the fsaverage5 surface back to each subject

Sorry for the noise, fwiw, this seems to do the trick:


mri_surf2surf --srcsubject tvb --trgsubject fsaverage5 --hemi lh 
--sval-xyz pial --tval pial.tvb --tval-xyz tvb/mri/T1.mgz

produces the 10k vertex surface in fsaverage5/surf/lh.pial.tvb, and


mri_surf2surf --srcsubject tvb --trgsubject fsaverage5 --hemi lh 
--sval-annot tvb/label/lh.aparc.annot --tval ./tvb-annot-on-fsaverage5.annot

produces a corresponding annotation.



thanks for your help!
Marmaduke
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[Freesurfer] mri_surf2surf dev vs stable

[marmaduke woodman]

Hi

The command

mri_surf2surf --srcsubject tvb --trgsubject fsaverage5 --hemi lh 
--sval-xyz pial --tval pial.tvb --tval-xyz ./tvb/mri/T1.mgz

works on dev (mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve), but on 
stable fails with

ERROR: Option ./tvb/mri/T1.mgz unknown


Is there a simple workaround or do I need to upgrade from stable to dev?


thanks,
Marmaduke
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Re: [Freesurfer] mri_surf2surf dev vs stable

[marmaduke woodman]

On 03/06/2016 08:23 PM, marmaduke woodman wrote:

> mri_surf2surf ...--tval-xyz ./tvb/mri/T1.mgz

just to follow up, it seems --tval-xyz is a flag (no argument) on 
stable, but on dev takes an argument.

So, on stable, just

mri_surf2surf ... --tval-xyz

will run, but the resulting surface doesn't have the source subject's 
volume geometry info.

How can this be embedded in the surface to achieve the same effect as 
the --tval-xyz mri/T1.mgz flag in the dev version?


thanks,
Marmaduke
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[Freesurfer] Embed vol geom in surf file

[marmaduke woodman]

hi

Is it possible to embed a volume geometry in a surface file explicitly? 
I'm unable to find a mri_ or mris_ command which seems to do this. Is 
there any workaround via the GUI tools?


Thanks,
Marmaduke
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Re: [Freesurfer] Embed vol geom in surf file

[marmaduke woodman]

On 03/07/2016 08:34 PM, dgw wrote:
> Marmaduke,
>
> Could you describe what it is you want to do? What do you mean by
> volume geometry? What type of information do you want to put on the
> surface?

I wish to approximate the effect of the  --tval-xyz vol  argument to 
mris_surf2surf in the dev version, which is not present in the stable 
version, where --tval-xyz is just a flag taking no arguments.

thanks,
Marmaduke
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