Hello Doug, it worked perfectly, thanks !
Marcel
2013/6/16 Douglas Greve greve@nmr.mgh.harvard.edu
Oh, I see what the problem is. You can try replacing this line in the script:
set cmd = (mri_concat --sum $surfvol $involmasked --o $outvol)
with
set cmd = (fscalc $surfvol add $involmasked -o $outvol)
let me know if that works
doug
On 6/15/13 12:17 PM, Marcel Falkiewicz wrote:
Hello Doug, my command line is:
vlrmerge --o f_vol.nii.gz --v fmcpr.sm8.mni305.2mm.nii.gz --lh fmcpr.sm8.fsaverage.lh.nii.gz --rh fmcpr.sm8.fsaverage.rh.nii.gz --subcortmask masks/brain.mni305.2mm.nii.gz
I think it does work with multiple frames correctly, but has summing over the frames hardcoded :
Allocing output Done allocing nframes = 1702 Computing sum across frames Writing to f_vol.nii.gz sob, 15 cze 2013, 21:04:20 CEST vlrmerge done
Full log is attached.
Marcel
2013/6/15 Douglas Greve greve@nmr.mgh.harvard.edu
Hi Marcel, vlrmerge should handle multiple frames. what is your command line? Can you send the log file? doug
On 6/14/13 10:32 AM, Marcel Falkiewicz wrote:
Hello, I would like to perform some Bayesian analyses implemented in SPM, but with the data normalized with FreeSurfer. I would like to merge together surface and subcortal normalized timeseries into a single 4d timeseries in volumetric space, which could be used as an input to spm. I tried using vlrmerge, but it produces only a single volume. One method would be splitting the timeseries for each space into single volumes, using vlrmerge on each triplet and then merging the results. However, this would take enourmous ammout of time. Do you know any quicker workarounds?
Thanks in advance, Marcel
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