Hi FreeSurfer experts,
I'm writing to follow up on an email I sent on Monday.
I'm working in 5.3 and switching over to running my 1st level
analysis in fsaverage. I noticed that when visualizing the
volume output from the mni305 analysis in tkmedit, there is only
activation in subcortical regions and none in cortical regions.
I read in the FreeSurfer release notes for 5.1 that fsfast "now masks
the volume-based analysis to include only subcortical areas."
I
just wanted to confirm that we are not seeing cortical
activation in the volume due to it being masked out.
Again,
my commands are:
Pre-processing:
preproc-sess -s GDDA001 -surface fsaverage lhrh -mni305
-fwhm 5 -per-run -d $SUBJECTS_DIR -fsd bold -so siemens
Mkanalysis: mkanalysis-sess -analysis
SIRP_LoadRegression_Stable5.3_012616_sm5_mni305 -mni305 2
-fwhm 5 -paradigm slopepar -event-related -fsd bold
-runlistfile runlistfile -tpef tpef_1.5mm.txt -timewindow
20 -TER 2 -nconditions 9 -gammafit 2.25 1.25 -refeventdur
2 -per-run -TR 2 -stc siemens -force
Thanks,
Anais
Hi FreeSurfer experts,
I'm in the process of switching over our first-level
analyses from being run in native space to being run in
fsaverage/mni305 space. Looking at the first-levels on an
individual subject level, the volume analyses look fairly
different (cortical signal especially is lost in the mni305
analysis). I've attached a couple of slides with images
comparing the two volume analyses.
My commands for the mni305 analysis are...
Pre-processing: preproc-sess -s GDDA001 -surface
fsaverage lhrh -mni305 -fwhm 5 -per-run -d $SUBJECTS_DIR
-fsd bold -so siemens
Mkanalysis: mkanalysis-sess -analysis
SIRP_LoadRegression_Stable5.3_012616_sm5_mni305 -mni305 2
-fwhm 5 -paradigm slopepar -event-related -fsd bold
-runlistfile runlistfile -tpef tpef_1.5mm.txt -timewindow 20
-TER 2 -nconditions 9 -gammafit 2.25 1.25 -refeventdur 2
-per-run -TR 2 -stc siemens -force
Mkcontrast: mkcontrast-sess -analysis
SIRP_LoadRegression_Stable5.3_012616_sm5_mni305 -contrast
2vFix -a 2 -c 0
My commands for the native space analysis are...
Preprocessing: preproc-sess -s GDDA001 -fwhm 5 -per-run
-d $SUBJECTS_DIR -fsd bold
Mkanalysis: mkanalysis-sess -analysis
SIRP_LoadRegression_Stable5_050514 -TR 2 -paradigm slopepar
-event-related -runlistfile runlistfile -tpef tpef_1.5mm.txt
-native -fwhm 5 -timewindow 20 -TER 2 -nconditions 9
-gammafit 2.25 1.25 -refeventdur 2
Mkcontrast: mkcontrast-sess -analysis
SIRP_LoadRegression_Stable5_050514 -contrast 2vFix -a 2 -c 0
I have a couple of questions regarding the differences
between the two analyses. First, why is so much of the
signal robustness from the native space volume analysis lost
in the mni305 analysis? Second, why are the voxel sizes so
different between the two analyses (with the native space
analysis having a much larger voxel size)?
Thanks,
Anais
<Volume_analysis_discrepancies.pdf>
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