y"
mailto:kathrynmary_wa...@urmc.rochester.edu>>
Reply-To: FS Help
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Thursday, July 9, 2020 at 7:51 PM
To: FS Help
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] QAtools with Freesurfer version 6.0
Ext
r-boun...@nmr.mgh.harvard.edu>>
on behalf of "Wakim, Kathryn-Mary"
mailto:kathrynmary_wa...@urmc.rochester.edu>>
Reply-To: FS Help
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Thursday, July 9, 2020 at 7:51 PM
To: FS Help
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesur
o: FS Help
Subject: [Freesurfer] QAtools with Freesurfer version 6.0
External Email - Use Caution
Hi all,
I’m relatively new to Freesurfer, and I am just beginning to check the output
of my recon-alls using QAtools. However, I’m running into a number of
difficulties and errors with QAtool
External Email - Use Caution
I guess this: https://surfer.nmr.mgh.harvard.edu/fswiki/QATools
But it's outdated, I also gave it a try recently and tried to contact the
author without success. It worked for v5, but is not compatible with v6 output.
(If you search the list archive
Hello Seonjoo,
Could you send along a link to what you ran/tweaked for “QA tools” on
freesurfer ?
- rob
On Oct 4, 2018, at 8:31 PM, Lee, Seonjoo
mailto:sl3...@cumc.columbia.edu>> wrote:
External Email - Use Caution
I tired to use QA tools for freesurfer version6, but did not have mu
External Email - Use Caution
I tired to use QA tools for freesurfer version6, but did not have much success.
Is anyone know how to tweak QA tools for freesurfer version 6?
Thank you.
-Seonjoo Lee
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rom: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Ehsan Adeli
Sent: Thursday, July 26, 2018 7:38 PM
To: freesurfer@nmr.mgh.harvard.edu
Cc: Kilian Pohl
Subject: [Freesurfer] QAtools tkmedit snapshots are black
External Email - Use Caution
Hello,
I tried to create snapshots wi
External Email - Use Caution
Hello,
I tried to create snapshots with tkmedit, but the output snapshot files are
all black. This is the command:
export SUBJECTS_DIR=./
tkmedit blubber norm.mgz
tkmedit shows the image correctly, but when taking a snapshot it is all
black. No error
Dear Sir/Madam,
I found that the QATools is still not updated for the Freesurfer v6.0
yet at https://surfer.nmr.mgh.harvard.edu/fswiki/QATools. Could you please
let me know what't the timeline for the update? or Do you know if anyone
can share the updated QATools with me?
Looking forward to h
Hi,
back in the day Louis mentioned that he was preparing a script for using
the QAtools in Freeview.
(see thread:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg36765.html)
Is there a script like that available by now? It's not yet on
http://surfer.nmr.mgh.harvard.edu/fswiki/
as 35 outliers ...
(With all structures as outliers, and without reporting the SNR/avg/sd for each
segmentation)
When attempting to write out a new segmentation table with the -gen-asegLUT
flag the error I receive is:
gawk: /usr/local/freesurfer/QAtools/QAtools_v1.1/gstd.awk:22: (FILENAME=-
FNR=1)
Everyone,
It would be good if the recon_checker tool would produce separate html pages
for each result type rather than all types for each subject. So you have one
page for all the T1/surfaces, the asegs, the aparc output so that it is easier
to compare between subjects. Is there already an opt
Hi there,
Just trying out the QAtools and I notice that there are a number of
"(standard_in) 1: syntax error" reports for each subcortical label:
checking subcortical label: Endosteum, . +/- .
(standard_in) 1: syntax error
(standard_in) 1: syntax error
(standard_in) 1: syntax error
(standard_in)
Hi,
I am trying to use the QA tools and take some tkmedit snapshots. I can
get everything to work fine in Boston, but when I run on our local Linux
server what tkmedit shows looks correct, but the output gifs of tkmedit
are all black with no content. The tksurfer images show and save fine.
I am
Hi Efrat,
Could you send me the recon-all-status.log file for one of your v4.5
subjects that have completed recon-all without errors? You would find
this file in the scripts sub-directory of the subject.
-Louis
On Mon, 16 Apr 2012, Efrat Kliper wrote:
> Dear FreeSurfer expert,
>
> I am trying
Dear FreeSurfer expert,
I am trying to run QA tools for verifying all steps of the FreeSurfer
recon-all stream.
I am working with FreeSurfer version 4.5.0. I don't see any optional
flagged arguments in which i can specify the version i am working with (the
default version is 5.1.).
I will be grate
Hi Wil,
Sorry about that, the link is now fixed with the most recent version of
the QAtool scripts.
-Louis
On Fri, 20 Jan 2012, Irwin, William wrote:
> Hi -
>
> The link to download the QATools script
> (http://surfer.nmr.mgh.harvard.edu/fswiki/QATools) for non-MGH users is
> broken, and I co
Hi -
The link to download the QATools script
(http://surfer.nmr.mgh.harvard.edu/fswiki/QATools) for non-MGH users is broken,
and I couldn't find it by looking through the ftp download directories.
Regards,
Wil
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Hi,
The QAtools scripts are in the process of being updated and debugged. You
would need to make a new file order file based on one of the subjects in
your data set. See help for the flag to do this. The default file order
file included with the scripts was generated from data which had been
Hi
I have looked at QAtools at
https://surfer.nmr.mgh.harvard.edu/fswiki/QATools.
But there seem to be some trouble. I have fixed up the wrong file issue
but there is problem with my files being in the wrong order. Should I
try to reorder the files to reflect the new situation or is there
somet
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