Hi Doug,
Thanks for your helpful answer (below) with respect to the use of mri_segstats
on functional activation in subject-specific ROIS.
I have a follow-up question, however, regarding the initial creation of the
ROIs. I am basing my ROIs on the Desikan-Killiany atlas, either using existing
labels in the atlas or sometimes splitting them into anterior and posterior. I
tried making the ROis 2 different ways, and found I got different results.
1) If I make an ROI by selecting or drawing D-K atlas regions on fsaverage,
then morph it to each individual’s surface with:
mri_label2label --srcsubject fsaverage --srclabel
/Applications/freesurfer/subjects/fsaverage/label/[ROIname].label --trgsubject
[subj] --trglabel
/Applications/freesurfer/subjects/[subj]/label/[ROIname].label --regmethod
surface --hemi lh
and then – to go from the surface (.label) to the volume (.nii):
mri_label2vol --temp example_func.nii.gz --reg
reg/freesurfer/anat2exf.register.dat --proj frac 0 1 .1 --hemi lh --label
/Applications/freesurfer/subjects/1012/label/[ROIname].label --subject [subj]
--o [output name].nii
then I get a fully contiguous region when I view the ROI on the individual’s
surface or more total voxels when I look at a summary of the ROI
characteristics using mri_segstats.
2) If I instead make the ROI using:
aseg2feat –feat [subj].feat --aseg aparc+aseg
and then
fslmaths [subj].feat/reg/freesurfer/aparc+aseg.nii.gz –thr [label # of
pertinent region] –uthr [label # of pertinent region]
[subj].feat/reg/freesurfer/[ROIname].nii.gz
then I get a chopped up, non-contiguous region with fewer total voxels.
My plan therefore is to use Method #1 above, but I want to make sure this is
OK: that I'm not somehow including spurious voxels that have somehow been
incorrectly generated by going from surface to volume. Am I OK with Method #1
above?
Thanks again,
Susan McLaughlin
Doctoral Candidate
SPACE Lab (Stimulus-Parametric Imaging of Auditory Cortex)
Dept. of Speech and Hearing Sciences
University of Washington
On Mon, 26 Nov 2012, Douglas Greve wrote:
Hi Susan, ok, I see what you are doing now. Let's do it this way:
1. First transfer your label to the volume:
mri_label2vol --temp example_func.nii --reg anat2exf.register.dat
--proj 0 1 .1 --hemi lh --label lh.your.label --o yourlabel.func.nii
2. Then run segstats:
mri_segstats --i cope2.nii --seg yourlabel.func.nii --mask zstat1.nii
--maskthresh 2 --masksign abs --o sum.dat
The cope and the zstat are now volumes.
doug
On 11/26/12 8:26 PM, Susan Alice McLaughlin wrote:
Hi Doug,
Thanks for the quick answer. Sorry to be dense, but does this need
somewhere to include registration matrix, anat2exf.register.dat, to
register to the subject's surface?
And at this point in the analysis, the feat folder does not include
copes and zstats separated out by hemisphere, although there are
zstat[#].surf.lh.w and .rh.w files in the main feat folder.
Again, sorry for my limited understanding of file structure.
Susan
On Mon, 26 Nov 2012, Douglas N Greve wrote:
Hi Susan, you can't use func2roi-sess. You'll have to put together some
commands, but it should not be too hard, something like
mri_segstats --i lh.cope2.nii --slabel subjectname lh your.label --mask
lh.zstat1.nii --maskthresh 2 --masksign abs --o sum.dat
where zstat1 is your all/nothing contrast sampled onto the surface and
cope2 is some other contrast sampled on the surface.
You can do this for each subject, then run asegstats2table giving it
paths to all of your sum.dat files
doug
On 11/26/2012 07:01 PM, Susan Alice McLaughlin wrote:
Hi,
I am hoping do a surface-based functional ROI analysis on
subject-specific ROIs that are both defined structurally and are
masked by an all/nothing functional contrast. func2roi-sess seems
perfect for this except that my data are not in an FS-FAST
data/analysis structure, but are instead pre-processed and
preliminarily analyzed using FSL and mapped to the surface using
reg-feat2anat.
Is there any way to pass my original analysis into func2roi-sess? I
tried using:
func2roi-sess -roidef LH_ant_STG_soundthresh2 -analysis
1012_Run4_featFULLrev.feat/stats/zstat4.nii.gz -anatlabel lh_ant_STG
-maskcontrast 1012_Run4_featFULLrev/stats/zstat16.nii.gz
-maskthreshold 2 -s 1012 -d
but get "ERROR: cannot find any sessions."
Or is there another tool more appropriate for what I am trying to
do? I am looking at mri_segstats, but my hand-drawn ROIs (drawn on
fsaverage in tksurfer and morphed to each subject using
label_2_label) are in .label format and are on the surface.
Thanks in advance for and advice or suggestions.
Susan McLaughlin
Doctoral Candidate
SPACE Lab (Stimulus-Parametric Imaging of Auditory Cortex)
Dept. of Speech and Hearing Sciences
University of Washington
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Susan McLaughlin
Doctoral Candidate
SPACE Lab (Stimulus-Parametric Imaging of Auditory Cortex)
Dept. of Speech and Hearing Sciences
University of Washington
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