Dear Anastasia, Thank you so much for responding so fast! I see what you're saying and thank you for your input.
I have one more question if you don't mind taking a moment to respond. I noticed that both trac-all and recon-all include some preprocessing steps (eg. motion correction, eddy current correction, skull stripping). How come and they both have these steps if one is supposed to run both commands? My understandind is, if someone wants to run TRACULA from scratch, they would need to run *both* recon-all (first) and trac-all (second). One would have to run recon-all in order to get the cortical parcellation and subcortical segmentation (mri/aparc+aseg.mgz) file which will be used from trac-all in the mask creation step. In my case where I have some preprocessed data, is there a particular -autorecon# command which only does some of the recon steps that would help me get the cortical parcellation and subcortical segmentation (mri/aparc+aseg.mgz) file that I am missing? I understand I may be asking a lot! Once more thank you very much for your initial response and your time! Best, Nasia Metoki On Sat, Aug 13, 2016 at 8:03 PM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote: > > Hi Athanasia - TRACULA expects certains files named a certain way to be > there at the end of each preprocessing step. These are described here: > > https://surfer.nmr.mgh.harvard.edu/fswiki/trac-all# > Outputdirectoriesandfiles > > If you are using pre-existing files, you have to make sure that they > follow the same file/directory naming convention. > > You just run recon-all with the default settings. The aparc+aseg is > created in one of the last steps of recon-all, so all the previous steps > have to run as well. > > Hope this helps! > > a.y > > On Sat, 13 Aug 2016, Athanasia Metoki wrote: > > > Dear Freesurfer Developers, > > > > I am fairly new to image analysis and this is the first time I use > > Freesurfer. > > > > I have some DTI data and I have already preprocessed them and ran > bedpostX > > using FSL. I ran probabilistic tractography on FSL as well to get the > > connectivity between two distinct brain areas. > > > > I am also interested in getting the probability distribution for the > > uncinate fasciculi so I am trying to use TRACULA. > > My question is: Can I use TRCULA without doing preprocessing and dedpostX > > again? If so, will I need to do the cortical parcelation and subcortical > > segmentation with recon-all and get the aparc+aseg.mgz file in order to > use > > TRACULA? Which argument would I need to use when I run recon-all? > > > > Thank you! > > > > Athanasia Metoki > > Psychology Doctoral Student - Brain and Cognitive Sciences Program > > Cognitive Neuroscience Laboratory > > Temple University > > Department of Psychology > > 1701 N 13th St. > > Philadelphia, PA 19122 > > Email: athanasia.met...@temple.edu > > > > ____________________________________________________________ > _______________ > > ____ > > The contents of this email message and any attachments are intended > solely > > for the addressee(s) and may contain confidential and/or privileged > > information and may be legally protected from disclosure. If you are not > the > > intended recipient of this message or their agent, or if this message has > > been addressed to you in error, please immediately alert the sender by > reply > > email and then delete this message and any attachments. If you are not > the > > intended recipient, you are hereby notified that any use, dissemination, > > copying, or storage of this message or its attachments is strictly > > prohibited. > > > > > _______________________________________________ > 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. > >
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