Re: [Freesurfer] run preproc-sess with -nomc

Thanks Doug! This indeed worked. (Just had to run mktemplate-sess and mkbrainmask-sess separately.) Evelina On Dec 13, 2011, at 5:48 PM, Douglas N Greve wrote: > You can try specifying the functional stem in mkanalysis-sess with -funcstem > yourfuncstem (assuming your data are yourfuncstem.ni

[Freesurfer] bedpost failure using tracula

Hi, After I run step 2 of tracula (>trac-all -c config_DTI_B.txt -bedp), I am missing multiple bedpost output files (e.g., mergedph1samples.nii). Examining the output, it looks like data from only one slice was written (dmri.bedpostX/diff_slices/data_slice_0002). This issue has replicated across m

[Freesurfer] mri_cc and CC thickness option...

Hi: For example, if I execute the mri_cc command with "-t 2", mri_cc shows me "setting callosum thickness to 5 mm"... Why ?... What exactly specify the -t option ?... Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh

Re: [Freesurfer] mri_cc and CC thickness option...

Hi Gonzalo, it's the distance in mm to extend the cc off the midline. So -t 2 means 1mm at the midline and 2mm in each direction so 5mm total cheers Bruce On Fri, 16 Dec 2011, Gonzalo Rojas Costa wrote: > Hi: > > For example, if I execute the mri_cc command with "-t 2", mri_cc > shows me "se

Re: [Freesurfer] bedpost failure using tracula

Hi Scott - Are there any files created directly under dmri.bedpostX? a.y On Fri, 16 Dec 2011, Scott Hayes wrote: > Hi, > After I run step 2 of tracula (>trac-all -c config_DTI_B.txt -bedp), I > am missing multiple bedpost output files (e.g., mergedph1samples.nii). > Examining the output, it loo

[Freesurfer] Tracula wiki updates & work-around suggestions

Hi Tracula team, I have just successfully processed my first scan through all the Tracula steps! Though, I have to say it could have gone much smoother / quicker if the documentation on the wiki were a little more up-to-date. I realize it's an ongoing struggle to keep documenta

Re: [Freesurfer] Tracula wiki updates & work-around suggestions

Hi Shannon, Thank you for the detailed email, outlining some of the aspects of the tutorial that we could improve. We really appreciate your effort in putting these things together and will definitely try to address your concerns to the best of our ability. Q2. I updated the wiki to correct the t

Re: [Freesurfer] bedpost failure using tracula

Hi, The following files & directories are listed directly under dmri.bedpostX: bvals commands.txtlogs nodif_brain_mask.nii.gz bvecs diff_slices monitor xfms --Scott Anastasia Yendiki Fri, 16 Dec 2011

[Freesurfer] Reliability and accuracy of Freesurfer

I've looked through a number of freesurfer papers, but haven't been able to find the answer to what I am looking for and was hoping someone had the references easily available. (1) What is the reliability of regional volumes generated from freesurfer over time? (2) What is the accuracy of labels

Re: [Freesurfer] bedpost failure using tracula

Hi Scott - Could you try running bedpostx on the dmri/ directory directly and see what if any error you get? a.y On Fri, 16 Dec 2011, Scott Hayes wrote: > Hi, > The following files & directories are listed directly under dmri.bedpostX: > > bvals commands.txtlogs