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

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

发件人： Louis Nicholas Vinke 发送时间： 2012-03-06 23:50:05 收件人： chenchunhuichina 抄送： freesurfer 主题： 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

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

Got it.

Thanks Louis!

2012-03-27

Chunhui Chen _________________

State Key Laboratory of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China 100875

发件人： Louis Nicholas Vinke 发送时间： 2012-03-26 23:27:09 收件人： chenchunhuichina 抄送： freesurfer 主题： Re: Re: [Freesurfer] about QAtools

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

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.