Re: [Freesurfer] How to run part of TRACULA
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.
[Freesurfer] How to run part of TRACULA
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.
Re: [Freesurfer] TRACULA tract endpoints on cortical surface
Thank you Anastasia, I'll try this. Best wishes, Barbara On 12/08/2016 23:19, Anastasia Yendiki wrote: > Hi Barbara - This can be done with mri_vol2surf. The projection that's > described in that passage can be done with --projdist-max -6 6 1, and the > surface smoothing with --surf-fwhm 6. There are other options in > mri_vol2surf, I'd recommend playing with the settings to see what works > better for your data. > > Best, > > a.y > > > On Fri, 5 Aug 2016, Barbara Kreilkamp wrote: > >> Dear Freesurfers and TRACULA experts, >> >> Thank you for your help so far. I am trying to map the endpoints of the >> tract probability distributions onto the cortical surface (as mentioned >> in Solsnes et al. 2016 NI and Storsve et al. 2016 PLos). >> >> I've somehow gathered that I need to do this (example one endpoint): >> >> flirt -ref /mri/orig/T1.nii.gz -in >> dpath/rh.ilf_AS_avg33_mni_bbr/endpt2.pd.nii.gz -applyxfm -init >> /dmri/xfms/diff2anat.bbr.mat >> >> I then loaded the images in Freeview and they look reasonable together >> with the lh.white and lh.pial surfaces: freeview -v /mri/brain -tv >> dapth/rh.ilf_AS_agv33_mni_bbr/endpt2_anat.pd.nii.gz >> >> What I don't get is how to do this: >> >> "we projected the tract endpoints onto the gray/white matter surface by >> sampling along the surface normal vector, anywhere within 6 mm (3 >> DWI-space voxels) of the gray/white junction and then smoothing along >> the surface with a 2D Gaussian kernel of 6mm full width at half max." >> (Solsnes et al. 2016) >> >> Any help would be greatly appreciated. >> >> Best wishes, >> Barbara >> >> ___ >> 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. 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. > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
