Aha, Ok, I will try to get my hands on that data and give it a go. Thanks for the help! Heidi
On 6/1/16, 4:01 AM, "Anastasia Yendiki" <ayend...@nmr.mgh.harvard.edu> wrote: > >The input needs to be the diffusion-weighted images, not the FA, MD, etc. >There should be as many volumes in this input nifti as there are b-values >in bval file and gradient vectors in the bvec file. The image >registration, tractography, etc etc is performed on the >diffusion-weighted >images, not on the FA, MD, etc. The FA, MD, etc are used only in the very >end, to extract FA, MD, etc for each tract. But to get the tracts in the >first place, you need the images. > >On Tue, 31 May 2016, Jacobs H (NP) wrote: > >> 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 >> >> _______________________________________________ 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. 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