Hi again,
Sorry, I didn't list all the commands I have been using:
preproc-sess -s $subj -fsd bold -sliceorder odd -surface fsaverage lhrh -mni305
-fwhm 3 -per-run -force (and with -no-subcort-mask in v5.3.0 on snowleopard)
mkanalysis-sess -fsd bold -stc odd -mni305 2 -fwhm 3 -paradigm para.para
-nconditions 5 -gammafit 2.25 1.25 -TR 2 -analysis analysis-sm3.mni
-event-related -refeventdur 2 -polyfit 1 -mcextreg -per-run -rlf runlist
-timeoffset -1.0 -refeventdur 2 -force
mkcontrast-sess -analysis analysis-sm3.mni -contrast visresp -a 1 -c 2
selxavg3-sess -s $subj -analysis analysis-sm3.mni
Then I look at the mask.nii created in bold/analysis-sm3.mni overlaid on
mni305.cor.mgz (I view the overlay with freeview).
The overlaid mask.nii from v5.3.0 looks the same as mask.nii from v5.2.0 only
if I use -no-subcort-mask in v5.3.0.
Leila
________________________________
Hi,
I would like to verify (as a sanity check and to make sure that I'm on the
right track in my analysis) that preproc-sess runs with -no-subcort-mask by
default in freesurfer-Darwin-lion-stable-pub-v5.2.0, but with -no-subcort-mask
turned off by default in stablev5.3.0 on snowleopard.
I first did an MNI305 analysis in v5.2.0 (mountain lion) and was able to see my
slices very nicely overlaid on the average/mni305.cor.mgz brain. However, the
same analysis in v5.3.0 (snowleopard) didn't overlay on
the brain in a sensible way, and only after I searched the mailing list did I
realize that I needed to use -no-subcort-mask. Using this option gave me the
same results as with v.5.2.0. Searching through
freesurfer/fsfast/bin/preproc-sess I don't see where this flag is set by
default to -no-subcort-mask in v5.2.0 (in fact, it seems that ApplySubCortMask
= 1; by default). So I'm pretty confused, and I'm just not sure that I'm doing
things the right way...
Thanks in advance,
Leila
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
