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You need to understand, you are changing the number of voxels from say 1,000,000 (per volume) to 11,000,000 or more times the number of timepoints (that is a total of 2,000,000,000 or more voxels)! This is a huge amount of voxels, and will be cumbersome for any server (let alone a single PC). i.e. avoid this method! You can share images via google drive or dropbox. I believe it was mentioned earlier that you should register your EPI, keeping them in their native resolution, and do your analysis this way. To reduce the number of slices use fslroi. This way you can get rid of the several z slices of zeros (and neck). Bryson On Wed, Dec 17, 2014 at 1:09 PM, Annelinde Vandenbroucke < [log in to unmask]> wrote: > > Dear readers, > > I have a question regarding registration from functional scans to > anatomical in native space. > I would like to register my functional scans to my structural scan in > native space, because I'm going to draw out retinotopic regions. Fsl seems > like the best program to use for registration. However, when I use epi_reg > or flirt with the bbr option, my functional files become very big (2.6 GB > for 180 volumes, before registration they are around 35 MB). > > One reason might be that the functionals, which are 2.5 mm isotropic, > might be upsampled to 1 mm isotropic to match the structural. However, an > additional problem might arise that I don't understand. I have tried to do > single subject statistics on these big data files. It takes a very long > time, even for one run, and the outcome is strange: a lot of extra 'empty' > data is added to the beginning and end of my functionals. I would like to > add a screenshot here, but I don't know how to do this, since it will only > paste text. > > What it looks like is as follows: normally, on runs that are not aligned > to the structural (small files, 35 MB), I can view the report.html of my > post-stats image in the screen easily: that is, the whole brain fits the > screen and I don't have to scroll down to see all the slices. > When I do my stats on the large, registered, epi, however, the zstat > images cannot be displayed on one screen: if I open report.html, I have to > scroll down to see the whole image. It seems like an additional 20 empty > slices are added to the top and bottom of my functional. > > Does anybody have an idea what is going on and how I might fix this? I am > scripting my whole pipeline, and so would like to avoid using the GUI at > all. Below is the line of script I'm using for registration. Before > registration, functional files are around 35 MB, and structural 2MB. > > Thank you in advance, > Annelinde > > CODE: > epi_reg -v --epi= func_prealign --t1= struct --t1brain = struct_bet > --out=func_align > > flirt gives the same outcome: > flirt -in func_prealign -ref struct_bet -out func_align-interp spline > -wmseg struct_fast_wmseg -cost bbr -dof 6 - applyxfm > > ps. If anybody wants to see the screenshots I'd be happy to email them to > you directly >