Thank you for the thorough response Steve.
Best,
Krista
On Thu, Jul 14, 2011 at 3:32 AM, Stephen Smith <[log in to unmask]> wrote:
> Hi - I strongly recommend that unless you really understand the details of
> the scripts/programs and GUIs, it is safest and simplest to carry out
> "standard" and "complete" analyses and not try to move single files around
> and perform part-analyses - hope that makes sense?
>
> filtered_func_data does not know anything about the spatial transformations
> that were used to get it into the space it is currently in.
>
> In general it's not good to re-feed preprocessed data again into the main
> processes such as registration, because it probably has (e.g.) been
> spatially smoothed, which would then reduce the quality of further
> registrations.
>
> Hope this helps,
> Cheers, Steve.
>
>
>
> On 13 Jul 2011, at 06:26, Krista Wisner wrote:
>
> Hi,
>
> This may seem like a rudimentary topic/question, but I have not been able
> to find a clear answer and wanted to check before running my analyses.
>
> Context:
> I completed all of my preprocessing steps (motion correction, slice timing
> correction, BET, smoothing, high pass filtering, B0 unwarping; FLIRT for
> linear reg of func to structural; FNIRT for non-linear reg of structural to
> standard) in FEAT first so that I could check that these steps were
> completed successfully before moving into my analysis.
>
> Question:
> If I were to copy just the filtered_func_data.nii.gz files into a new
> directory somewhere else in order to run my group analysis on a different
> server, would all of the FLIRT/FNIRT efforts be lost? Or is this
> information somehow embedded in the filtered_func_data.nii.gz file? {I ask
> this since (1) upon loading the filtered_func_data.nii.gz into fslview, I
> see that this image file clearly shows no evidence of the transformations
> actually being performed ... and since (2) the /reg folder created in the
> .feat directory during the preprocessing in FEAT would no longer be found
> with the filtered_func_data.nii.gz once it has been copied to it's new
> location on a different server.}
>
> Follow-up Question.
> - If indeed the FLIRT/FNIRT efforts are lost after copying the
> filtered_func_data.nii.gz files into a new directory, if I were to copy the
> required structurals into the same directory, could this registration
> (FLIRT/FNIRT) be completed "again" during the group level analysis in
> MELODIC?
> - Or more simply, while copying the filtered_func_data.nii.gz for each
> person into the new directory, I could copy the /reg directory created
> during the FEAT preprocessing along with the it into the new location. Would
> this take care of making sure the registration completed correctly during
> the group-level analysis?
>
> Thank you in advance,
>
> Krista Wisner
>
>
>
> ---------------------------------------------------------------------------
> Stephen M. Smith, Professor of Biomedical Engineering
> Associate Director, Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
> ---------------------------------------------------------------------------
>
>
>
>
--
Krista Wisner
Graduate Student
Clinical Science and Psychopathology Research Program
University of Minnesota
N427 Elliott Hall, 75 E. River Rd.
Minneapolis, MN 55455
