Is this meant to be calculated from the B0 dicoms? On Mon, Dec 19, 2016 at 12:44 PM, Yendiki, Anastasia < ayend...@mgh.harvard.edu> wrote:
> No, it's a separate scan that you provide. > > ------------------------------ > *From:* Katherine Damme [katherine.da...@gmail.com] > *Sent:* Monday, December 19, 2016 1:43 PM > > *To:* Freesurfer support list; Anastasia Yendiki > *Subject:* Re: [Freesurfer] Tracula Set: No Match > > This is being generated by an earlier step in the trac-all -prep right? > > On Fri, Dec 16, 2016 at 4:23 PM, Yendiki, Anastasia < > ayend...@mgh.harvard.edu> wrote: > >> It doesn't recognize the format of your field map. It assumes that the >> field map has either 2 frames (2 phase maps) or 1 frame (a phase difference >> map). >> >> ------------------------------ >> *From:* Katherine Damme [katherine.da...@gmail.com] >> *Sent:* Friday, December 16, 2016 5:18 PM >> *To:* Freesurfer support list; Anastasia Yendiki >> *Subject:* Re: [Freesurfer] Tracula Set: No Match >> >> 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_Trac >> ula/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_Trac >> ula/31313422_10128/dmri/dwi_eddy.nii.gz /media/Data/Temple/Temple_Trac >> ula/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_Trac >>> ula/31313422_10128/dmri/b0pha.nii.gz >>> >>> mri_probedicom --i //media/Data/Temple/Temple_Tra >>> cula/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_Trac >>> ula/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_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. >>>>> >>>>> 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. >> >> > > _______________________________________________ > 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.
