When I run this on the command line it seems to be completing the fslroi step fine:
"fslroi /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi_eddy.nii.gz /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/lowb.nii.gz 0 1 ERROR: Unrecognized format of phase map /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/b0pha.nii.gz Linux katelinux.psych.northwestern.edu 2.6.32-642.6.2.el6.x86_64 #1 SMP Mon Oct 24 10:22:33 EDT 2016 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Fri Dec 16 15:38:48 CST 2016 [ksd770@katelinux Temple_Tracula]# fslroi /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi_eddy.nii.gz /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/lowb.nii.gz 0 1 [ksd770@katelinux Temple_Tracula]# trac-all -prep -c dmrirc_10128.txt" What is the next step in the code where it is failing? On Wed, Dec 14, 2016 at 9:19 PM, Katherine Damme <katherine.da...@gmail.com> wrote: > I am now getting this error. I am not sure if this is a new issue or > related. > > fslorient -forceradiological /media/Data/Temple/Temple_ > Tracula/31313422_10128/dmri/b0pha.nii.gz > > mri_probedicom --i //media/Data/Temple/Temple_Tracula/31313422_10128/dti_ > dicom/31313422_10128.MR.Temple.9.1.20140806.182244.xfrp16.dcm > > /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/b0info.dat > > TE: Subscript out of range. > > fslroi /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi_eddy.nii.gz > /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/lowb.nii.gz 0 1 > > ERROR: Unrecognized format of phase map /media/Data/Temple/Temple_ > Tracula/31313422_10128/dmri/b0pha.nii.gz > > Linux katelinux.psych.northwestern.edu 2.6.32-642.6.2.el6.x86_64 #1 SMP > Mon Oct 24 10:22:33 EDT 2016 x86_64 x86_64 x86_64 GNU/Linux > > I check all of these images and I can open them. > > On Tue, Dec 13, 2016 at 7:59 PM, Yendiki, Anastasia < > ayend...@mgh.harvard.edu> wrote: > >> Hi Katherine - Can you please use the attached version and tell me if it >> works? You'll have to copy it into $FREESURFER_HOME/bin, to overwrite the >> version of xfmrot that you have now. If it works, we'll include it in the >> next version. Thanks! >> >> a.y >> >> ------------------------------ >> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [ >> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Katherine Damme [ >> katherine.da...@gmail.com] >> *Sent:* Tuesday, December 13, 2016 9:38 AM >> >> *To:* Freesurfer support list >> *Subject:* Re: [Freesurfer] Tracula Set: No Match >> >> >> >> On Tue, Dec 13, 2016 at 8:34 AM, Yendiki, Anastasia < >> ayend...@mgh.harvard.edu> wrote: >> >>> Ok, if you also send me the first file, /media/Data/Temple/Temple_Trac >>> ula/31313422_10128/dmri/dwi.ecclog, I'll see if I can replicate the >>> error. >>> >>> ------------------------------ >>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [ >>> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Katherine Damme [ >>> katherine.da...@gmail.com] >>> *Sent:* Tuesday, December 13, 2016 9:21 AM >>> >>> *To:* Freesurfer support list >>> *Subject:* Re: [Freesurfer] Tracula Set: No Match >>> >>> Yes. I immediately tried to enter the command in manually, checked the >>> paths, and looked at the command manual for any format errors. >>> >>> [ksd770@katelinux Temple_Tracula]$ xfmrot /media/Data/Temple/Temple_Trac >>> ula/31313422_10128/dmri/dwi.ecclog /media/Data/Temple/Temple_Trac >>> ula/31313422_10128/dmri/bvecs.norot /media/Data/Temple/Temple_Trac >>> ula/31313422_10128/dmri/bvecs >>> >>> set: No match. >>> >>> On Wed, Dec 7, 2016 at 2:41 PM, Yendiki, Anastasia < >>> ayend...@mgh.harvard.edu> wrote: >>> >>>> Thanks. This looks fine. When you run that xfmrot command directly on >>>> the linux command line, do you get the same error? >>>> >>>> ------------------------------ >>>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [ >>>> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Katherine Damme [ >>>> katherine.da...@gmail.com] >>>> *Sent:* Wednesday, December 07, 2016 12:41 PM >>>> *To:* Freesurfer support list >>>> *Subject:* Re: [Freesurfer] Tracula Set: No Match >>>> >>>> >>>> >>>> On Mon, Dec 5, 2016 at 12:00 PM, Yendiki, Anastasia < >>>> ayend...@mgh.harvard.edu> wrote: >>>> >>>>> Hi Katherine - The error occurs when processing this file: >>>>> /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs.norot >>>>> >>>>> Can you send this file? Thanks! >>>>> >>>>> a.y >>>>> ------------------------------ >>>>> *From:* Katherine Damme [katherine.da...@gmail.com] >>>>> *Sent:* Saturday, December 03, 2016 3:42 PM >>>>> *To:* Freesurfer support list; Anastasia Yendiki >>>>> *Subject:* Tracula Set: No Match >>>>> >>>>> Hello! >>>>> >>>>> I have been getting a "set: No match." error. I haven't been able to >>>>> sort out what is causing it. >>>>> >>>>> Attached you will find the configuration file, command, and log files >>>>> associated with this error. >>>>> >>>>> "mv -f /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs >>>>> /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs.norot >>>>> xfmrot /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi.ecclog >>>>> /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs.norot >>>>> /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs >>>>> set: No match." >>>>> >>>>> _______________________________________________ >>>>> 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. >>>> >>>> >>> >>> _______________________________________________ >>> 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. >> >> >
_______________________________________________ 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.
