Re: [Freesurfer] mri_concat error

[Mateus Aranha]

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Hi Douglas!

Thanks for the reply. Apparently, this error was due to a lack of license
file in freesurfer folder. I downloaded a license, put it in the right
place. When I try to process a subject, it works well, but when I try to
analyze my data with qdec, the analysis starts, but then qdec crashes and I
hot the following error in the terminal:

[image: image.png]

I could not solve or move around this problem...

Thanks!
Mateus

On Fri, Feb 4, 2022 at 2:26 PM Douglas N. Greve 
wrote:

> Hard to say. This is one reason we are not supporting qdec anymore. Was
> there anything printed to the terminal?
>
> On 2/3/2022 8:27 AM, Mateus Aranha wrote:
>
> External Email - Use Caution
> Dear all,
>
> I'm constantly getting the following error and I have no idea where the
> problem is...
>
> [image: image.png]
>
> Thanks for your help,
> Mateus
>
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[Freesurfer] mri_concat error

[Mateus Aranha]

External Email - Use Caution

Dear all,

I'm constantly getting the following error and I have no idea where the
problem is...

[image: image.png]

Thanks for your help,
Mateus
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[Freesurfer] Compute geometric mean of 32 b1000 images (DTI)

[Mateus Aranha]

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Dear all,

I have 32 directions DTI images and I need to compute DWI and ADC maps from
these images. As far as I know the DWI is obtained by calculating the
geometric mean of the 32 b1000 images. Can it be done with mri_concat
--gmean Ng?

Many thanks,
Mateus
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[Freesurfer] Error in qdec

[Mateus Aranha]

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Hello,

Iḿ trying to perform a group analysis using qdec, but the analysis stops at
70% and the following error message is shown:

[image: Screenshot from 2020-06-29 13-03-27.png]

How should I proceed?

Thanks,
Mateus
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[Freesurfer] Error with -qcache

[Mateus Aranha]

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Dear FS team,

I'm running -qcache on my subjects before group analysis and I get the
following error for 2 of the subjects:

ERROR: number of vertices in
/home/neuroimagen7/Desktop/SoccerPlayers/ReconFiles/recon_T1/edits/ANON0266_recon_T1/surf/lh.thickness
does not match surface (139424,138940)
ERROR: reading curvature file

The remaining subjects are fine!

Thank you!
Mateus
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[Freesurfer] Custom color lookup table

[Mateus Aranha]

Hi all,

I recently installed freesurfer on my mac, and I'm having a small problem with 
freeview. If I load a segmentation file, and then try to associate it with a 
custom color lookup table, freeview stops responding. Even if I was to use an 
exact copy of /Applications/freesurfer/FreeSurferColorLUT.txt, the problem 
still persists:

cp -i /Applications/freesurfer/FreeSurferColorLUT.txt \ 
~/Documents/CustomColor.txt

I will try to re-install the program, but I first wanted to check if anyone has 
ever encountered issues with custom color tables.

See info below:

> MacBook Air (13")
> OS X Yosemite (Version 10.10)
> Processor: 1,4 GHz Intel Core i5; x86_64)
> Memory: 4GB 1600 MHz DDR3

I first downloaded XQuartz 2.7.6 and then downloaded/installed latest versions 
of freesurfer and freeview:

http://xquartz.macosforge.org/downloads/SL/XQuartz-2.7.6.dmg 

ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Darwin-lion-stable-pub-v5.3.0.dmg
 

ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/freeview/lion/Freeview 


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