From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Haley O Higginbotham
Sent: Friday, June 23, 2023 1:28 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Freesurfer Digest, Vol 232, Issue 12 - data not displayed

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Today's Topics:

   1. Re: Size of overlap between a label and a volume (John Anderson)
   2. Freeview: data not displayed (Haley O Higginbotham)
   3. Re: Freeview: data not displayed (Fischl, Bruce R.,PHD)
   4. [FreeSurfer] Talairach Failure Detection (Krystal Xiwing Yau)


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Message: 1
Date: Sat, 17 Jun 2023 07:45:35 -0400
From: John Anderson <jb19790001@gmail.com>
Subject: Re: [Freesurfer] Size of overlap between a label and a volume
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <CABPMGjnBVnozT=1BcLNrXPe5fmciy4=7iisRTJ3xbXyVXY4Ctg@mail.gmail.com>
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Let's say the red spot is overlay.nii.gz
1) convert aparc+aseg from mgz to nii.gz using:
mri_convert aparc+aseg.mgz aparc+aseg.nii.gz
2) create mask between overlay and the atlas using fslmaths:
fslmaths aparc+aseg.nii.gz -mas overlay.nii.gz overlay_overlap.nii.gz
3) use fslstats (or mris_cacl) to compute volume:
fslstats   aparc+aseg.nii.gz -k overlay_overlap.nii.gz -V
this output #voxels and volume

Alternatively, you might consider mri_seg_overlap
https://secure-web.cisco.com/1yEdORqlIEup_8SwhRxwcP4XoV0QdvHT3rxvRNSBm4KwTJa8GFaC4IypTfW6sCwqLkCV8-04lx4IwpYw1bloRw_V6dP7ZHDGcAKW_GxvmcPnNpEDrGOUP0_IOqBySvJcnPNi6vhkSVi10dToaEBiERpqDFz-EnxCjEgNGIJ3XNt-k3tKuVVXCHwRVILgioT9OGbo6ypjpXFGP3ZXbaHEcno4FQfRfil7Daqyt9jtk6hu7MV49cAA-kVltRnz0XNs6FPf7MtEN0eemFGiV1vvMIp5rjRfhyA2LWaKuhK4F6Eq2uHqE_n9TYs6AsXPSvtrmL8vi3cGm-6XyMKJwBQAM1Q/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fmri_overlap


On Fri, Jun 16, 2023 at 10:37?PM parsatad@student.ubc.ca <
parsatad@student.ubc.ca> wrote:

>         External Email - Use Caution
>
> Hello,
>
> Hope you are doing well. I'm new to freesurfer so I was wondering if you
> could help me out with something please.
>
> I'm looking for a simple way to find the size (i.e. volume in mm3) of
> overlap between a particular label (1027 ctx-lh-rostalmiddlefrontal) ) in
> an aparc+aseg file and a NIfTI volume file that can be overlayed on the
> aparc+aseg file. Please look at the attached file for a better
> visualization of what I'm describing.
>
> I'd really appreciate it if you could point me in the right direction.
>
> Thank you,
>
> Parsa
>
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> https://secure-web.cisco.com/1QOro1Z2r3HL9t5oIefcbPfQTo4oxpIuIeCBs3Tp0a1yEDSnWFtnDs4dDxmZ0KAaurt7X2ksh15CPKyMoFG1e_bLBE1T_ymhu-QUAx4_yJt_1k-rAAQN4ZiVDIg4Y_tN7C1oy_6FBjRoalfTUF3bw8gpxFTQgq2CkCi1aG7mPoXG2pttMvKyTe22pGcV-hg-84orMuAyku6C8FYMYvBx2wvn9egPVJBsDqGreYKUcqBi-_1Uwrahua-8-GNZRSxA7lkKttOaKGrG44K8d-XZbWzrEmOKseNEhdxJYbTkJ1qa6s-uE-1odtnhsORP79OWVcMhivoexZwjx_N4wT3CvjA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> .
>
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Message: 2
Date: Sun, 18 Jun 2023 00:13:40 +0000
From: Haley O Higginbotham <hhigginb@mit.edu>
Subject: [Freesurfer] Freeview: data not displayed
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <AA577D2C-2C58-423C-8AB4-B92F3E74BE53@mit.edu>
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?
Hi FreeSurfer Developers,

I've just installed Freesurfer and am trying to view a sample subject's data in Freeview (bert T1.mgz) but nothing is displayed (blank black screen - see attached screenshot). Xming is running and I've confirmed graphics function with xeyes. The progress bar in Freeview also completes and zooming in/out hasn't helped. I've also tested other volumes, surfaces, and patients with the same results.
I'm running freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 on Ubuntu 20.04.6 LTS via WSL2
Has anyone experienced something like this before or have any clue what might be going on? Sorry if it's a simple solution - I'm new here

Thanks in advance,
Haley

[cid:71a16993-26fc-4e0c-b21c-e03609ba5b22]
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Message: 3
Date: Sun, 18 Jun 2023 01:17:07 +0000
From: "Fischl, Bruce R.,PHD" <BFISCHL@mgh.harvard.edu>
Subject: Re: [Freesurfer] Freeview: data not displayed
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <CH0PR04MB79726387219F05E5EBB92D6CEF5EA@CH0PR04MB7972.namprd04.prod.outlook.com>
       
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The voxel coordinate shown at the bottom  is -59, so for some reason the cursor is outside the FOV. Try clicking there and typing in 100,100,100 or something like that

Cheers
Bruce



From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Haley O Higginbotham
Sent: Saturday, June 17, 2023 8:14 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Freeview: data not displayed


        External Email - Use Caution
?
Hi FreeSurfer Developers,

I've just installed Freesurfer and am trying to view a sample subject's data in Freeview (bert T1.mgz) but nothing is displayed (blank black screen - see attached screenshot). Xming is running and I've confirmed graphics function with xeyes. The progress bar in Freeview also completes and zooming in/out hasn't helped. I've also tested other volumes, surfaces, and patients with the same results.
I'm running freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 on Ubuntu 20.04.6 LTS via WSL2
Has anyone experienced something like this before or have any clue what might be going on? Sorry if it's a simple solution - I'm new here

Thanks in advance,
Haley

[cid:image001.png@01D9A161.116FCEA0]
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Message: 4
Date: Mon, 19 Jun 2023 07:50:57 +0000
From: Krystal Xiwing Yau <krystaly@hku.hk>
Subject: [Freesurfer] [FreeSurfer] Talairach Failure Detection
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <7bc4fde85b5e41469fb369a18589c0ce@hku.hk>
Content-Type: text/plain; charset="iso-8859-1"

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Dear Freesurfer experts,


I would like to seek for help regarding talairach error. I have browsed through the forum about it but still not solving my problem...


The following steps are the solutions I have tried:


  *   Re-run recon-all with -notal-check
  *   Re-run recon-all with -notalairach
     *   The above flags gave the same error message as follow:
     *   WARNING2: gca.c::GCAhistoScaleImageIntensities: h_mri->nbins=100, mri_peak=108
after smoothing, mri peak at 0, scaling input intensities by inf
error: Numerical result out of range
error: GCAhistoScaleImageIntensities: could not find wm peak
Command exited with non-zero status 252
  *   Ran the command to fix the registration: tkregisterfv --s Sub-108 --fstal --no-surfs
     *   The view for this subject is weird because it shows the axial view when the coronal view is selected
     *   [cid:49cf1b63-a35e-4003-8f38-a1def3b7bd64]
     *   The correct view showed up when the coronal view is selected
     *   [cid:abd68344-6bc3-489a-9eef-20569a419c02]



When I viewed 001.mgz in Freeview, there was no such problem. However, some artifact (i.e. the weird lines) occurred in certain slices, as circled in pink:

[cid:0c0b2ea4-3b3e-4361-ad0c-c5dec191c85c]

[cid:eadbe192-c57a-48db-b429-b162b0154d0f]

[cid:229941cf-2005-44c6-a979-0bf60c03da18]


I am not sure how to fix it with tkregisterfv and what are the standards for it.


It would be so much appreciated if someone could help out with this issue.


Regards,
Krystal

Tel.: +852 2255 5024
Fax: +852 2872 5828
Address: Room 304, 3/F, New Clinical Building, 102 Pokfulam Road, Hong Kong.
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