Re: [Freesurfer] about QAtools
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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] mkbrainmask-sess
It could be. It uses fsl only to create a mask of the brain, so it probably does not need a full fsl install, but it might need more than you have. doug On 3/25/12 7:05 AM, Kiley Seymour wrote: Hi again, Could this error be due to the fact that I don't have a full version of fsl installed and configured on my ubuntu virtual machine? i.e. does fsfast require fsl to be installed? Thanks K *From:* Kiley Seymour *To:* "freesurfer@nmr.mgh.harvard.edu" *Sent:* Friday, 23 March 2012 3:04 PM *Subject:* mkbrainmask-sess Dear Freesurfers, I am currently trying to do some retinotopic mapping. I have been successful in running the reconstruction commands and setting everything up for the analysis, but I have run into problems when using the selxavg3-sess command. i.e. selxavg3-sess -a rtopy.self.lh -s IFEE2211 -no-preproc ( -no-preproc since I have co-registered and motion corrected my files in SPM). I was unable to run this command as freesurfer could not find /media/sf_DATA1/RETINOTOPY/IFEE2211/bold/001/global.meanval.dat So I ran mktemplate - sess, which was successfully completed. And then I ran mkbrainmask-sess (see below). Any help with this would be much appreciated. Thanks Kiley FreeSurfer:~/data1/RETINOTOPY> mkbrainmask-sess -s IFEE2211 -d ~/data1/RETINOTOPY /media/sf_DATA1/RETINOTOPY/IFEE2211 Fri Mar 23 09:42:26 EDT 2012 mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -thresh 0.1 -ndil 1 -nerode 0 FSLMATHS fslmaths.fsl Scratch Dir is /tmp/mkbrainmask_7930 /media/sf_DATA1/RETINOTOPY/IFEE2211/bold mri_convert template.nii.gz /tmp/mkbrainmask_7930/in.nii mri_convert template.nii.gz /tmp/mkbrainmask_7930/in.nii $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ reading from template.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998558, -0.0534653, -0.00482299) j_ras = (-0.0536701, 0.992375, 0.110955) k_ras = (0.00114604, -0.111054, 0.993814) writing to /tmp/mkbrainmask_7930/in.nii... # -- Using FSL's BET to Extract Brain-- # /media/sf_DATA1/RETINOTOPY/IFEE2211/bold bet.fsl /tmp/mkbrainmask_7930/in.nii /tmp/mkbrainmask_7930/brain -m -f 0.1 /home/virtualuser/freesurfer/bin/bet.fsl: 150: /bin/remove_ext: not found /home/virtualuser/freesurfer/bin/bet.fsl: 151: /bin/remove_ext: not found /home/virtualuser/freesurfer/bin/bet.fsl: 158: /bin/imtest: not found [: 158: =: unexpected operator /home/virtualuser/freesurfer/bin/bet.fsl: 380: /bin/bet2: not found mri_binarize --i /tmp/mkbrainmask_7930/brain_mask.nii --min .01 --o /tmp/mkbrainmask_7930/brain_mask.nii niiRead(): error opening file /tmp/mkbrainmask_7930/brain_mask.nii $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /media/sf_DATA1/RETINOTOPY/IFEE2211/bold cmdline mri_binarize --i /tmp/mkbrainmask_7930/brain_mask.nii --min .01 --o /tmp/mkbrainmask_7930/brain_mask.nii sysname Linux hostname FreeSurfer machine i686 user virtualuser input /tmp/mkbrainmask_7930/brain_mask.nii frame 0 nErode3d 0 nErode2d 0 output /tmp/mkbrainmask_7930/brain_mask.nii Binarizing based on threshold min0.01 max+infinity binval1 binvalnot 0 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] mkbrainmask-sess
Hi again, Could this error be due to the fact that I don't have a full version of fsl installed and configured on my ubuntu virtual machine? i.e. does fsfast require fsl to be installed? Thanks K From: Kiley Seymour To: "freesurfer@nmr.mgh.harvard.edu" Sent: Friday, 23 March 2012 3:04 PM Subject: mkbrainmask-sess Dear Freesurfers, I am currently trying to do some retinotopic mapping. I have been successful in running the reconstruction commands and setting everything up for the analysis, but I have run into problems when using the selxavg3-sess command. i.e. selxavg3-sess -a rtopy.self.lh -s IFEE2211 -no-preproc ( -no-preproc since I have co-registered and motion corrected my files in SPM). I was unable to run this command as freesurfer could not find /media/sf_DATA1/RETINOTOPY/IFEE2211/bold/001/global.meanval.dat So I ran mktemplate - sess, which was successfully completed. And then I ran mkbrainmask-sess (see below). Any help with this would be much appreciated. Thanks Kiley FreeSurfer:~/data1/RETINOTOPY> mkbrainmask-sess -s IFEE2211 -d ~/data1/RETINOTOPY /media/sf_DATA1/RETINOTOPY/IFEE2211 Fri Mar 23 09:42:26 EDT 2012 mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -thresh 0.1 -ndil 1 -nerode 0 FSLMATHS fslmaths.fsl Scratch Dir is /tmp/mkbrainmask_7930 /media/sf_DATA1/RETINOTOPY/IFEE2211/bold mri_convert template.nii.gz /tmp/mkbrainmask_7930/in.nii mri_convert template.nii.gz /tmp/mkbrainmask_7930/in.nii $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ reading from template.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998558, -0.0534653, -0.00482299) j_ras = (-0.0536701, 0.992375, 0.110955) k_ras = (0.00114604, -0.111054, 0.993814) writing to /tmp/mkbrainmask_7930/in.nii... # -- Using FSL's BET to Extract Brain-- # /media/sf_DATA1/RETINOTOPY/IFEE2211/bold bet.fsl /tmp/mkbrainmask_7930/in.nii /tmp/mkbrainmask_7930/brain -m -f 0.1 /home/virtualuser/freesurfer/bin/bet.fsl: 150: /bin/remove_ext: not found /home/virtualuser/freesurfer/bin/bet.fsl: 151: /bin/remove_ext: not found /home/virtualuser/freesurfer/bin/bet.fsl: 158: /bin/imtest: not found [: 158: =: unexpected operator /home/virtualuser/freesurfer/bin/bet.fsl: 380: /bin/bet2: not found mri_binarize --i /tmp/mkbrainmask_7930/brain_mask.nii --min .01 --o /tmp/mkbrainmask_7930/brain_mask.nii niiRead(): error opening file /tmp/mkbrainmask_7930/brain_mask.nii $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /media/sf_DATA1/RETINOTOPY/IFEE2211/bold cmdline mri_binarize --i /tmp/mkbrainmask_7930/brain_mask.nii --min .01 --o /tmp/mkbrainmask_7930/brain_mask.nii sysname Linux hostname FreeSurfer machine i686 user virtualuser input /tmp/mkbrainmask_7930/brain_mask.nii frame 0 nErode3d 0 nErode2d 0 output /tmp/mkbrainmask_7930/brain_mask.nii Binarizing based on threshold min 0.01 max +infinity binval 1 binvalnot 0___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
