Hi Chunhui,
The wm-anat-snr missing step is misleading. That file gets created when
QAtools generates the SNR/WM measures using the wm-anat-snr command. It
is not part of the recon-all stream. If you specify the default status
log file included with the scripts you should not get that error (using
the -completeStatusFile flag). This is a slight bug which I need to fix.
I'm not sure about the X error, I'll investigate that.
The gawk command is a dependency issue (http://www.gnu.org/software/gawk/).
-Louis
On Mon, 26 Mar 2012, chenchunhuichina wrote:
Hi Louis and Freesurfers
Last time you helped me fixed the "convert command" problem, and then QATools
can run on my computer smoothly.
But I just realized that this error message is still there,
Received X error!
error code : 1
request code : 148
minor code : 179
Error text: 'BadRequest (invalid request code or no such operation)'
there is also an error message says:
gawk: commond not found
Is this also a dependecy problem?
However, I do get the summary log and the html file with snapshots.
In the log file, it says:
ERROR: Recon-all steps missing in subject sub2 status file wm-anat-snr
I thouhg recon-all run all steps automaticly, what should I do with this
missing step?
Thanks for your help!
2012-03-26
Chunhui Chen
_________________
State Key Laboratory of Cognitive Neuroscience and Learning
Beijing Normal University
Beijing, China 100875
·¢¼þÈË£º Louis Nicholas Vinke
·¢ËÍʱ¼ä£º 2012-03-06 23:50:05
ÊÕ¼þÈË£º chenchunhuichina
³ËÍ£º freesurfer
Ö÷Ì⣺ Re: [Freesurfer] about QAtools
Hi Chunhui,
I believe this is a dependency issue, since the convert command is part of
the ImageMagick Studio. You'll need to download and install the binaries
(http://www.imagemagick.org/). I'll make of note of this on the wiki
page.
-Louis
On Tue, 6 Mar 2012, chenchunhuichina wrote:
Dear Freesurfer experts,
I installed the QAtools and tried a subject with this commond:
$QA_TOOLS/recon_checker -s sub13 -snaps-detailed -gen-asegLUT aseglut.txt
but I encountered the following Error message, can someone help me figure it
out? Any help is appreciated, thanks!
Error message 1:
Received X error!
error code : 1
request code : 148
minor code : 179
Error text: 'BadRequest (invalid request code or no such operation)'
Error message 2:
/opt/fmritools/QAtools/takesnapshotpreset.sh : line 89: convert: command not
found
both of the above two error messages shown in the screen many times, and there
was no figures in the 'QA_check.html'
By the way, I do not have solid anatomical background, is it acceptable that I
only use QAtools for quality control, without manual editing? I am thinking
manual editing by non-experts will induce incorrect data. Any suggestion?
Thanks a lot!
2012-03-06
Chunhui Chen
_________________
State Key Laboratory of Cognitive Neuroscience and Learning
Beijing Normal University
Beijing, China 100875
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