Dear Anastasia, Now I understand and it makes perfect sense! Thank you very much for your answers.
Best, Nasia Metoki *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. On Mon, Aug 15, 2016 at 8:49 AM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote: > > Hi Nasia - They both have preprocessing steps because recon-all runs on > the T1 and trac-all runs on the DWIs, so they preprocess different images. > > You cannot skip any of the steps in recon-all and still get a > segmentation. The point of the autorecon schemes is mostly to repeat only > one part of the processing if you change something in between, not to skip > part of the processing entirely. > > Best, > > a.y > > > On Sun, 14 Aug 2016, Athanasia Metoki wrote: > > 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#Outputdir >> ectoriesandfile >> s >> >> 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. 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