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 >>>> >>
dwi.ecclog
Description: dwi.ecclog
trac-all.log
Description: trac-all.log
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