t; on behalf of Xin Qi <
> xinqi2...@gmail.com>
> *Date: *Thursday, August 12, 2021 at 12:00 AM
> *To: *Freesurfer support list
> *Subject: *[Freesurfer] about FreeSurfer QA tools errors
>
> *External Email - Use Caution *
>
> Hi Freesurfer Communit
of Xin Qi
Date: Thursday, August 12, 2021 at 12:00 AM
To: Freesurfer support list
Subject: [Freesurfer] about FreeSurfer QA tools errors
External Email - Use Caution
Hi Freesurfer Community Support Team:
We would like to use FreeSurfer QA tools.
After installing it, I tested it on one
Dear Freesurfer list,
As I have used the QA tools on a couple recon-all jobs, I have run into an
error when running recon_checker QA tools. The QA tools are not able to
read many of the output files from recon-all, in the "label" directory. As
I look back into the label directory, this is because
> Falk
>
> Von: freesurfer-boun...@nmr.mgh.harvard.edu
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Antonietta Pepe
> Gesendet: Mittwoch, 23. August 2017 16:47
> An: freesurfer@nmr.mgh.harvard.edu
> Betreff: [Freesurfer] QA tools for FS vs 6.0
>
> Dear FreeSurfer lis
Auftrag von Antonietta Pepe
Gesendet: Mittwoch, 23. August 2017 16:47
An: freesurfer@nmr.mgh.harvard.edu
Betreff: [Freesurfer] QA tools for FS vs 6.0
Dear FreeSurfer list,
is any of you aware of a new version of the QA (quality assessment) tools
<https://surfer.nmr.mgh.harvard.edu/fswiki/QATo
Dear FreeSurfer list,
is any of you aware of a new version of the QA (quality assessment) tools < [
https://surfer.nmr.mgh.harvard.edu/fswiki/QATools |
https://surfer.nmr.mgh.harvard.edu/fswiki/QATools ] > working for FS vs 6.0?
Should I expect a new release in the near feature?
Kind regards,
Dear Freesurfer Experts,
Please excuse my long email yesterday.
Now, I finished code update of the outlier detection part for brainstem
substructures (bs) and Hippocampal Subfields (hc) modules. Code updated in
the similar way as my last email except that I combined the output of both
modules to
Dear Freesurfer Experts,
As one of the new freesurfers, I really appreciate the excellent work of
authors as well as great support of users' forum.
A good guess of mine is that authors, e.g., Vasanth or Louis etc., are busy
updating QA tools after the FSv6 release since the QA Tools v1.2 was
Hi John,
Do tkmedit and tksurfer work by themselves? You can try this by running the
following commands (assuming your SUBJECTS_DIR is set to the location
containinng your subject ALS-0038):
tkmedit ALS-0038 norm.mgz
tksurfer ALS-0038 rh pial
Best,
Lee
On Tue, 13 Sep 2016, John Anderson
Hello, FS experts,
I am trying to use QA tool:
I ran the following command
recon_checker -snaps-only -s-file subjects.txt
The script output the following:
X11 connection rejected because of wrong authentication.
GLUT: Fatal Error in tkmedit.bin: could not open display: localhost:12.0
Dear FS experts,
I tried to run the QA Tools on a subject with the following command:
*${QA_TOOLS}/recon_checker -s 207043_M0_2010-10-07 -outputFOF
${SUBJECTS_DIR}/FOF -gen-outputFOF -gen-asegLUT
${SUBJECTS_DIR}/AsegOutliers*
But I got all errors concerning the detection of Aseg outliers:
Hi Freesurfer users,
I am recently testing the QA Tools in order to identify errors, especially
aseg outliers.
I don''t know if this is the right place to make this question, but I
followed the instructions for download, install and usage, explained on:
Thank you Bruce and MIke!
I was not really looking for something INSTEAD of manual inspection, but
for a measure of the quality of my dataset similarly to what is
reccomended for functional MRI (in that case a SNR below 100 can be
considered a criterion of exclusion).
What are the meaning of these
Hi Mike
I agree! It's really hard to detect e.g. the tip of the nose wrapping
into occipital cortex. I was thinking more of the tools that generate
pages of snapshots so you can quickly scan through datasets to find
dramatic failures
cheers
Bruce
On Mon, 23 Nov 2015, Harms, Michael wrote:
>
Hi all,
I am starting to use QAtools in Freesurfer.
The scripts are working well, but I have two problems:
1. the interpretation of output is the first. Are there ranges of
normality for SNR and intensity? Could you please give me some reference
or link about how to interpret these data? Or do I
Dear experts,
we have a problem with installation of QA-Tools. It seems that it is not
because of ImageMagick and Gawk not being properly installed, but rather there
seems to be some problems with environmental variables. For example, when
changing into QA-Tools directory in the terminal and
Dear freesurfers,
After reading the documentation on freesurfer web site and searching in the
mail archive I wasn't able to find an answer to my question.
I'm trying to perform cerebellar segmentation on 100 subjects.
The recon-all step went well : every t1 image finished without error when
I
' is garbage.
Any ideas on this?
Thanks,
Wil
-Original Message-
From: Irwin, William
Sent: Wednesday, January 09, 2013 6:22 AM
To: Louis Nicholas Vinke
Cc: freesurfer@nmr.mgh.harvard.edu; Irwin, William
Subject: RE: [Freesurfer] QA Tools Snaps Scrambled - Clairification
Hi Louis-
I
,
Wil
-Original Message-
From: Irwin, William
Sent: Wednesday, January 09, 2013 6:22 AM
To: Louis Nicholas Vinke
Cc: freesurfer@nmr.mgh.harvard.edu; Irwin, William
Subject: RE: [Freesurfer] QA Tools Snaps Scrambled - Clairification
Hi Louis-
I was speaking cryptically and/or imprecisely
-contained.
This is a real mystery
-Wil
-Original Message-
From: Louis Nicholas Vinke [mailto:vi...@nmr.mgh.harvard.edu]
Sent: Tuesday, January 08, 2013 6:29 PM
To: Irwin, William
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] QA Tools Snaps Scrambled
Hi Irwin,
It sounds
Nicholas Vinke
Cc: freesurfer@nmr.mgh.harvard.edu; Irwin, William
Subject: RE: [Freesurfer] QA Tools Snaps Scrambled
Hi Louis-
No problem doing command line conversion of an rgb to either jpg or gif in
terms of error messages. However, the converted files are scrambled. Might
there be a dependency
Hi-
I've come across a peculiar behavior with recon_checker, and am hoping someone
can shed some light on this.
I have used it 100's of times in the past, but not for about 2 months. I
recently processed a large set of cases I wanted to QC. When I ran it, some,
but not all, of the snaps were
Hi Irwin,
It sounds like the snapshots from tksurfer are fine, but the ones from
tkmedit are not being generated properly. It may be this peculiar bug
where ImageMagick has trouble reading rgb files. Try converting an rgb
file to a jpg 'convert file.rgb file.jpg'. You may get the error
Hi,
We had never really finalized the QA Tools to feel comfortable distributing
them, and so the permissions on these files are still set so that only the
group of us working with them can use it. In fact, I had thought that the
wiki page associated with it was likewise only available to those
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