Is it possible to run tracula with out a phase mapping MRI scan? All I have in this data is a MPRAGE and DWI images weighted at either 0 or 1000.
Thank you. On Tue, Jan 3, 2017 at 1:07 PM, Yendiki, Anastasia <ayend...@mgh.harvard.edu > wrote: > Hi Katherine - You need to have an appropriate field mapping MRI scan. > > Best, > 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:* Sunday, January 01, 2017 5:16 PM > > *To:* Freesurfer support list > *Subject:* Re: [Freesurfer] Tracula Set: No Match > > Sorry the phase map. How do I generate an appropriately formatted phase > map? > > On Sun, Jan 1, 2017 at 4:15 PM, Katherine Damme <katherine.da...@gmail.com > > wrote: > >> How do I generate a field map? >> >> On Mon, Dec 19, 2016 at 10:09 PM, Yendiki, Anastasia < >> ayend...@mgh.harvard.edu> wrote: >> >>> No - there is no relation between B0 field inhomogeneities (measured by >>> a field map) and b=0 volumes. The capital B refers to the magnetic field in >>> the scanner, the small b is the b-value (diffusion weighting). >>> >>> ------------------------------ >>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [ >>> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Katherine Damme [ >>> katherine.da...@gmail.com] >>> *Sent:* Monday, December 19, 2016 11:01 PM >>> >>> *To:* Freesurfer support list >>> *Subject:* Re: [Freesurfer] Tracula Set: No Match >>> >>> 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_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_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 $FREESURFER_HOME/bin, to >>>>>>> overwrite >>>>>>> the version of xfmrot that you have now. If it works, we'll include it >>>>>>> in >>>>>>> the next version. Thanks! >>>>>>> >>>>>>> a.y >>>>>>> >>>>>>> ------------------------------ >>>>>>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [ >>>>>>> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Katherine >>>>>>> Damme [katherine.da...@gmail.com] >>>>>>> *Sent:* Tuesday, December 13, 2016 9:38 AM >>>>>>> >>>>>>> *To:* Freesurfer support list >>>>>>> *Subject:* Re: [Freesurfer] Tracula Set: No Match >>>>>>> >>>>>>> >>>>>>> >>>>>>> On Tue, Dec 13, 2016 at 8:34 AM, Yendiki, Anastasia < >>>>>>> ayend...@mgh.harvard.edu> wrote: >>>>>>> >>>>>>>> Ok, if you also send me the first file, >>>>>>>> /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi.ecclog, >>>>>>>> I'll see if I can replicate the error. >>>>>>>> >>>>>>>> ------------------------------ >>>>>>>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [ >>>>>>>> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Katherine >>>>>>>> Damme [katherine.da...@gmail.com] >>>>>>>> *Sent:* Tuesday, December 13, 2016 9:21 AM >>>>>>>> >>>>>>>> *To:* Freesurfer support list >>>>>>>> *Subject:* Re: [Freesurfer] Tracula Set: No Match >>>>>>>> >>>>>>>> Yes. I immediately tried to enter the command in manually, checked >>>>>>>> the paths, and looked at the command manual for any format errors. >>>>>>>> >>>>>>>> [ksd770@katelinux Temple_Tracula]$ 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_Trac >>>>>>>>>> ula/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. >>> >>> >> > > _______________________________________________ > 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.
