[Freesurfer] Freeview_Linux_Subsystem

[Kristian Stefanov]

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Dear developers,
I’m running into an issue using freeview. I have installed freesurfer on a 
Linux subsystem for Windows (Ubuntu 18.04 LTS) according to the guidelines 
(https://surfer.nmr.mgh.harvard.edu/fswiki/WindowsSupport) including Xming. The 
frresurfer commands work without a problem (e.g. recon all), however, freeview 
does not display anything even though I can successfully load volumes and 
surfaces (see attached image). I do not have any problems with FSLeyes or 
tkmedit. Any advise on what could be causing this issue?

Many thanks,
Kristian Stefanov


Kristian Stefanov,

Research Assistant

Imaging Centre of Excellence (ICE)

University of Glasgow

Tel: +44 (0) 0141 541 6859

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[Freesurfer] code for estimating volume

[Kate Marvel]

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Hi Iglesias,

I would like to learn the  two ways for estimating volumes mentioned in
another post, see below. Please send me the codes in Freesurfer to do this.

Thank you,

Kate


-- Forwarded message -
From: Iglesias Gonzalez, Juan E. 
Date: Wed, Apr 8, 2020, 10:43 AM
Subject: Re: [Freesurfer] Hippocampal subfields
To: Freesurfer support list 


Dear Ioana,

This is tricky because the volumes are computed from soft segmentations,
which are not the ones you’re editing. In general, editing outputs is a bad
idea; it may be better to simply discard the cases for which quality
control fails.

Having said that: if you want to use corrected cases, you could compute
volumes by simply summing the number of voxels with each label, and
multiplying by the volume of a voxel (which is 1/27=0.03703703703 cubic
mm). But if you do this, then you need to compute the volume this way for
all cases, including the ones you didn’t edit (you don’t want to mix 2 ways
of estimating volumes).

Cheers,

/Eugenio





Juan Eugenio Iglesias

Senior research fellow

CMIC (UCL), MGH (HMS) and CSAIL (MIT)

http://www.jeiglesias.com







*From: * on behalf of ioana cracana

*Reply-To: *Freesurfer support list 
*Date: *Wednesday, April 8, 2020 at 04:59
*To: *"freesurfer@nmr.mgh.harvard.edu" 
*Subject: *[Freesurfer] Hippocampal subfields



*External Email - Use Caution*

Hello,

I'm doing a study about hippocampal atrophy and I'm using the Segmentation
of Hippocampal subfields tool. There were some minor errors and I edited
them using Freeview, voxel edit tool.  I would like to generate a new
[lr]h.hippoSfVolumes-T1.v10.txt
file using the edited [lr]h.hippoSfLabels-T1.v10.mgz in order to see the
new results. What command do i have to use? Is there another way to edit
the hippocampal subfields?And how do i see the results?

I'm using Freesurfer v6.0.0. on macOS Mojave.



Thanks,

Ioana
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Re: [Freesurfer] Freeview_Linux_Subsystem

[fsbuild]

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Hello Kristian,
I have been looking at this as well, and my understanding is things are not 
configured “out of the box” for an X-Windows client like freeview running under 
the Windows Linux subsystem to work with the 3rd party Xming software running 
on the windows side..  For me, the freeview window is partially drawn in 
the X-window, but its graphics are not entirely drawn or rendered.  I will 
post more information when I know something more.
There is however a virtual machine with Ubuntu linux you can run on windows 
that has been tested and comes installed with both the freesurfer 6 and the new 
freesurfer 7 beta release, 

https://surfer.nmr.mgh.harvard.edu/fswiki/VM_67

- R.

On Apr 11, 2020, at 06:02, Kristian Stefanov 
 
wrote:External Email - Use 
CautionDear developers,I’m 
running into an issue using freeview. I have installed freesurfer on a Linux 
subsystem for Windows (Ubuntu 18.04 LTS) according to the guidelines 
(https://surfer.nmr.mgh.harvard.edu/fswiki/WindowsSupport) including Xming. The 
frresurfer commands work without a problem (e.g. recon all), however, freeview 
does not display anything even though I can successfully load volumes and 
surfaces (see attached image). I do not have any problems with FSLeyes or 
tkmedit. Any advise on what could be causing this issue?  Many 
thanks, Kristian Stefanov Kristian Stefanov,Research AssistantImaging 
Centre of Excellence (ICE)University of GlasgowTel: +44 (0) 0141 541 
6859 ___Freesurfer
 mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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[Freesurfer] Queries on the Function of Freesurfer

[Koustav Chatterjee]

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Dear all,

I am a beginner in FreeSurfer world.
I have 4 questions. It would be kind enough if you could clarify my
confusions.

   - I have came across that 'Freesurfer can reconstruct 2D cortical
   surface from 3D T1 MRI brain image'. However, I know that T1 2D brain
   images are being fed to freesurfer for 'Recon-all...-all' to function all
   its pre-processing steps.

Whether "...reconstruct 2D cortical surface from 3D T1 MRI image"
this *statement
is true*? Is there any step where FreeSurfer make a 3D image from 2D T1
images and again reconstruct them into 2D
cortical surface through preprocessing steps?


   - Can FreeSurfer only recognize 'T1 weighted images' for processing? Why
   only T1, why not T2 or Flair etc?
   - Can we estimate the volume of substantia nigra, pedunculopontine
   nucleus and locus cereleus using FreeSurfer? If so any specific version
   of Freesurfer is required?
   - If I have Freesurfer installed in my PC; I also have T1 and diffusion
   weighted image sequence of a subject. Can I use 'Tracula' to analyse tracts
   of that subject's brain directly? How could I analyse tracts in Freesurfer?

Thank you for your time and effort.
Regards,
Koustav
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[Freesurfer] Trac-all Error

[Hua, Jessica]

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Hi FreeSurfer,

I am running trac-all prepocessing using a configuration file. I tried 
preprocessing a couple of participants, and I keep getting this error:


#-

#@# Tensor fit Sat Apr 11 21:29:36 PDT 2020

dtifit -k /Volumes/HuaExternal/DTI_FS/S11018a_LGI/dmri/dwi.nii.gz -m 
/Volumes/HuaExternal/DTI_FS/S11018a_LGI/dlabel/diff/aparc+aseg_mask.bbr.nii.gz 
-r /Volumes/HuaExternal/DTI_FS/S11018a_LGI/dmri/bvecs -b 
/Volumes/HuaExternal/DTI_FS/S11018a_LGI/dmri/bvals -o 
/Volumes/HuaExternal/DTI_FS/S11018a_LGI/dmri/dtifit

libc++abi.dylib: terminating with uncaught exception of type std::logic_error: 
Mat::operator(): index out of bounds

Abort

This is my configuration file:

set dtroot = /Volumes/HuaExternal/DTI_FS
set subjlist = ( S11018a_LGI )
set dcmroot = /Volumes/HuaExternal/DTI
set dcmlist = ( S11018a.nii )
set bvecfile = /Volumes/HuaExternal/DTI/bvecsSPACE.txt
set bvalfile = /Volumes/HuaExternal/DTI/bvals.txt
set runlist = (1)
set doeddy = 1
set dorotbvecs = 1
set usemaskanat = 1
set thrbet = 0.3
set doregflt = 0
set doregbbr = 1
set doregmni = 1
set doregcvs = 0
set mnitemp = /Volumes/HuaExternal/DTI/MNI152_T1_1mm_brain.nii.gz
set pathlist = ( lh.cst_AS rh.cst_AS \
 lh.ilf_AS rh.ilf_AS \
 lh.unc_AS rh.unc_AS \
 fmajor_PP fminor_PP \
 lh.atr_PP rh.atr_PP \
 lh.cab_PP rh.cab_PP \
 lh.ccg_PP rh.ccg_PP \
 lh.slfp_PP rh.slfp_PP \
 lh.slft_PP rh.slft_PP )
set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5)

Do you know what is going wrong, and how I would fix this issue?

Best,

 Jessica

---

Jessica Hua, M.A.
Cognitive and Emotional Control Lab
Doctoral Candidate Clinical Psychology
University of Missouri
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