Yes, each nifti contains one volume. I have different nifti’s for the different metrics (FA, MD,..) Is there a way I can use the trac-all on these files?
On 5/31/16, 9:26 PM, "Anastasia Yendiki" <ayend...@nmr.mgh.harvard.edu> wrote: > >Some of the errors make me suspect that your input DWI files contain only >one volume. Could this be the case? > >On Tue, 31 May 2016, Jacobs H (NP) wrote: > >> Hmm, weird, as I put a # in front of it. Putting the eddy current to 0 >> gives the same error. Enclosed is the config file. >> Thank you so much >> Heidi >> >> On 5/31/16, 8:13 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf >>of >> Anastasia Yendiki" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of >> ayend...@nmr.mgh.harvard.edu> wrote: >> >>> >>> Hi Heidi - It knows where to find the freesurfer recons of the T1's >>>from >>> SUBJECTS_DIR (see example config file). Based on your log file, it >>>looks >>> like you haven't turned off the eddy current compensation, because it's >>> trying to run it. If you attach your config file, I'll take a look. >>> >>> Best, >>> a.y >>> >>> On Tue, 31 May 2016, Jacobs H (NP) wrote: >>> >>>> Thanks! I tried to adapt the configuration file and it got a bit >>>> further, >>>> but then crashes again. Not sure why? I have added the log file, so >>>>that >>>> maybe you could have a look at what is happening? >>>> Also, how does the trac-all command knows where to find the T1 data? >>>> Thanks >>>> Heidi >>>> >>>> On 5/31/16, 5:07 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf >>>> of >>>> Anastasia Yendiki" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf >>>>of >>>> ayend...@nmr.mgh.harvard.edu> wrote: >>>> >>>>> >>>>> No, it should be pointed to the DWI data, which can be corrected >>>>>niftis >>>>> instead of the original dicoms. I would recommend turning off all the >>>>> corrections in the configuration file, and then running everything >>>>> without >>>>> skipping steps. This will create all the files that are expected to >>>>>be >>>>> there for the registration. >>>>> >>>>> On Tue, 31 May 2016, Jacobs H (NP) wrote: >>>>> >>>>>> Dear Anastasia, >>>>>> >>>>>> Thanks for the feedback. So, does this mean that the dcm root should >>>>>> be >>>>>> pointed towards the T1¹s? I have the FreeSurfer recon-all output in >>>>>>a >>>>>> different folder. >>>>>> Enclosed is the log file (of one subject) and the configuration >>>>>>file. >>>>>> You >>>>>> will see that I tried the inter and intra option, because I thought >>>>>> that >>>>>> for the inter it would not need anything else than the MNI template >>>>>> and >>>>>> the DTI images. >>>>>> >>>>>> Thanks >>>>>> >>>>>> Best >>>>>> Heidi >>>>>> >>>>>> On 5/31/16, 4:01 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on >>>>>>behalf >>>>>> of >>>>>> Anastasia Yendiki" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf >>>>>> of >>>>>> ayend...@nmr.mgh.harvard.edu> wrote: >>>>>> >>>>>>> >>>>>>> Hi Heidi - The intra-subject registration step that you're trying >>>>>>>to >>>>>>> run >>>>>>> registers your subject's DWI and T1 images. It expects to find >>>>>>>those >>>>>>> images. It doesn't use the FA, MD, etc in any way. >>>>>>> >>>>>>> Did the log file get created in scripts/trac-all.log? If so, can >>>>>>>you >>>>>>> please send that file and your configuration file? Thanks! >>>>>>> >>>>>>> a.y >>>>>>> >>>>>>> On Tue, 31 May 2016, Jacobs H (NP) wrote: >>>>>>> >>>>>>>> Dear FreeSurfers, >>>>>>>> >>>>>>>> The data I have is preprocessed, so I have the all the metrics >>>>>>>>(FA, >>>>>>>> MD, >>>>>>>> L1, L2, L3,..) in nifti format. >>>>>>>> On this data I would like to start tracula starting from step 1.3. >>>>>>>> >>>>>>>> I have organized the data as mentioned on the wiki: >>>>>>>> For example: >>>>>>>> <subjID>/<dmri> dtifit_FA.nii.gz >>>>>>>> >>>>>>>> I have also filled in the configuration file, canceling out the >>>>>>>> things >>>>>>>> I don¹t need and then I tried to run: >>>>>>>> Trac-all intra c <configuration file> >>>>>>>> >>>>>>>> Unfortunately, it does not work, it says: dcmlist: subscript out >>>>>>>>of >>>>>>>> range >>>>>>>> >>>>>>>> I do not have the original filesŠ is there a way that I can get >>>>>>>>the >>>>>>>> script working? >>>>>>>> >>>>>>>> Many thanks. >>>>>>>> Heidi >>>>>>>> >>>>>> >>>> >> _______________________________________________ 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.
