Hi Anastasia, Found it, I'll replace it right away, thanks :) Best,Elia. Date: Tue, 17 Jun 2014 09:29:14 -0400 From: ayend...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula preprocessing error ( set dob0 = 1 )
Check the email archives for a recent message about epidewarp.fsl from Doug, there is a newer version that works with FSL 5. On Tue, 17 Jun 2014, Elia S. wrote: > > Hi Anastasia, > The epidewarp.fsl gives me the following output: > > FSLVersion 5.0.6 > FSLVerMaj 5 > FSL Version is 5.0.6, must be 3.X or 4.X > > Either from script or command line. > > Best, > Elia. > > > Date: Tue, 17 Jun 2014 09:17:58 -0400 > From: ayend...@nmr.mgh.harvard.edu > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Tracula preprocessing error ( set dob0 = 1 ) > > > Hi Elia - This could very well be the case. Does the epidewarp.fsl command > give you any specific error message, or does it just not create an output? > > a.y > > On Tue, 17 Jun 2014, Elia S. wrote: > > > Hi Anastasia, > > Yes, launching the same command line from terminal produced the same error, > > but at the sa > me > > time we realized we were using the wrong magnetic/phase dicoms.....which > > weren't > > magnetic/phase images at all. > > Could that be the cause of the failure? I would answer the question myself > > but right now > I > > don't have the correct images to test it. > > > > Best, > > Elia. > > > > > > Date: Sun, 15 Jun 2014 07:21:28 -0400 > > From: ayend...@nmr.mgh.harvard.edu > > To: freesurfer@nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] Tracula preprocessing error ( set dob0 = 1 ) > > > > > > Hi Elia - It looks like this file didn't get created: > > /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi.nii.gz > > > > The command that was supposed to create it was epidewarp.fsl. You can find > > the command line that begins with "epidewarp.fsl" in the log file that you > > sent me. When you run that whole line directly from the unix command line, > > do you get any errors? > > > > a.y > > > > On Thu, 12 Jun 2014, Elia S. wrote: > > > > > Dear Freesurfer community, > > > Whenever i try to launch the tracula preprocessing, using "set dob0 = 1 > > > " and the foll > ow > > ing command > > > line: > > > > > > trac-all -prep -no-isrunning -c > > > '/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/tr > ac > > ula.config > > > > > > It stops, giving me errors like these: > > > > > > niiRead(): error opening file > > > /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi.nii.gz > > > > > > ERROR: reading > > > /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_frame0.nii > .g > > z > > > > > > While setting "dob0 = 0" everything runs smoothly. > > > > > > Can you help me please? I'll attach the log + dmrirc (tracula.config) > > > > > > Best, > > > Elia. > > > > > > --------------------------------------------------------------------------------------- > -- > > ---------- > > > ----------- > > > > > > Freesurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 > > > > > > Linux Distribution: Ubuntu 12.04 precise - Ubuntu 12.04.4 LTS > > > > > > Environment/Version: Linux king-ubuntu 3.2.0-56-generic #86-Ubuntu SMP > > > Wed Oct 23 09:20 > :4 > > 5 UTC 2013 > > > x86_64 x86_64 x86_64 GNU/Linux > > > > > > > > > > _______________________________________________ Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurf > er > > The information in this e-mail is intended only for the person to whom it > > is addressed. I > f > > 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. > > _______________________________________________ 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.
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