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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