Re: [Freesurfer] Volume analysis in native space vs. mni305 space

2016-02-07 Thread Douglas Greve 


Right. FSFAST uses "three spaces": lh (surface), rh (surface), and 
subcortical (volume). To prevent voxels from being counted twice, we 
mask cortical voxels out of the volume-based analysis.


On 2/5/16 11:29 AM, Rodriguez-Thompson, Anais wrote:

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

On Feb 1, 2016, at 12:40 PM, Rodriguez-Thompson, Anais 
> wrote:



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

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Re: [Freesurfer] Volume analysis in native space vs. mni305 space

2016-02-05 Thread Rodriguez-Thompson, Anais 
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

On Feb 1, 2016, at 12:40 PM, Rodriguez-Thompson, Anais 
mailto:arodriguez-thomp...@mgh.harvard.edu>>
 wrote:

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

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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.