[Freesurfer] Unpacking DWI Data

Hello Freesurfer Experts, Our research team has recently collected data from Martinos Center. The entire scanning protocol (including anatomical, functional runs, DWI) is in one directory. Therefore I have been using unpacksdcmdir to tell me what runs go with each scanning sequence. I have h

Re: [Freesurfer] Unpacking DWI Data

ou to read in a dicom folder and save a new folder with subfolders according to the sequences that were run. At the same time you can also anonymize your data. Does this help? Best wishes, Barbara On 17/09/2016 22:17, Emily Louise Belleau wrote: Hello Freesurfer Experts, Our research tea

Re: [Freesurfer] Unpacking DWI Data

, Osirix Lite should be sufficient, I think it works by picking File-import and then File-export-export DICOMs (decompression is sometimes helpful). It should be straightforward, just have a go at it. Hope it helps. Best wishes, Barbara On 19/09/2016 00:36, Emily Louise Belleau wrote: Hi Barbara

[Freesurfer] Tracula Missing Statistics

Hello Tracula Experts, I noticed that for a few of my subjects, I am missing all "Center" statistics for FA, MD etc. for certain tracts like the left uncinate fasciculus for example. I am assuming this means that an optimal pathway was unable to be foun

[Freesurfer] DTI Statistics

?Hello all, I was just wondering if in publications/papers it is more common to report the average FA statistics, the weighted average statistics, or the center statistics (the average of the highest probability pathway). These are the statistics provided by Tracula. Thanks, Emily __

[Freesurfer] Tracula

Hello, I did all of my DTI preprocessing through tracula. I now am using FSL probtractx (which utilizes the bedpost stage output) to explore pathways from the amygdala to the ventromedial prefontal cortex. When I used FSL's probtractx, when I viewed the tract. The tract was in the wrong area

Re: [Freesurfer] Tracula

.y On Wed, 3 Sep 2014, Emily Louise Belleau wrote: > Hello, > > I did all of my DTI preprocessing through tracula. I now am using FSL > probtractx (which utilizes the bedpost stage output) to explore pathways from > the amygdala to the ventromedial prefontal cortex. > > When

Re: [Freesurfer] Tracula

. On Thu, 4 Sep 2014, Emily Louise Belleau wrote: > Hi Anastasia, > > Yes my amygdala seed is in MNI space. When I used the MNI to diffusion.mat > file in the dmri folder and placed it into FSL's probtractx, I developed a > track that was in the wrong area of the br

Re: [Freesurfer] Tracula

f the other inputs > that you're giving probtrackx (e.g. a volume from the bedpostx directory) > to make sure they look right in fslview. > > > On Thu, 4 Sep 2014, Emily Louise Belleau wrote: > >> Hi Anastasia, >> >> Yes my amygdala seed is in MNI space. When I use

[Freesurfer] Tracula Question

?Hello, I was wondering what the difference was between the dwi.nii.gz and thd data.nii.gz files. I know based on the website description that the dwi.nii.gz file is the DWI after all corrections have been made but I was unsure about the data.nii.gz file. I am