Add " --cwsig cwsig.mgh", then load cwsig.mgh as an overlay in tksurfer. Set the threshold to 1.3 (cluster p < .05). doug

On 03/28/2012 07:48 AM, Tetiana Dadakova wrote:

Hello Doug,

I cancel my first question, I realized CWP values are in the same file.

Regarding second question, my cluster is quite big, so it goes beyond just one atlas region. I would like to see what regions it cover, but for this I need to overlay atlas at the surface (desirably the same as I overlay cluster) in tksurfer. Can I somehow do it?

Thank you for your time, Tanja.

On Tue, Mar 27, 2012 at 9:55 AM, Tetiana Dadakovatetiana.d@gmail.com wrote:

...

Hello Doug,

thank you so much for your reply.

Could you please answer two more questions:

I used the following line mri_surfcluster --in conjunction_sig.mgh --thmin 1.3 --thmax 5 --sign abs --subject fsaverage --hemi lh --annot aparc --minarea 0 --csd /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm10/abs/th13/mc-z.csd --cwsig summary_sig.mgh --sum summary_sig.txt

I get a table summary_sig.txt with all the clusters uncorrected for multiple comparisons. Also, I get the corrected clusters summary_sig.mgh, which I can visualize with tksurfer.

My questions are:

1. Can I get a txt file with corrected (for multiple comparisons) clusters?
2. Can I overlay a Desikan-Killiany Atlas in tksurfer?

Thank you again for your help. Tanja.

On Mon, Mar 26, 2012 at 8:38 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:

...

You can view it with tksurfer (instead of qdec). You can run the clustering program (mri_surfcluster) to determine the location, max value, and cluster-wise significance. You can run mri_surfcluster with --help to get details, but you'll need to run it something like:

mri_surfcluster --in conjunction_sig.mgh --thmin 2 --sign abs --subject fsaverage --hemi lh --annot aparc --csd path/to/csdfile --sum sum.dat

where --thmin 2 means to use p<.01 as the voxel-wise cluster-forming threshold, --sign abs means to consider pos or negative values when forming the threshold, sum.dat is the output. The tricky part will be to get the right CSD file. The path will be something like

$FREESURFER_HOME/average/mult-comp-cor/fsaverage/lh/cortex/fwhm12/abs/th20/mc-z.cdf

where "th20" corresponds to "--thmin 2", and "abs" corresponds to "--sign abs" and "fwhm12" means that the fwhm.dat file in the qdec output directory has a value between 11 and 12.

doug

On 03/21/2012 11:00 AM, Tetiana Dadakova wrote:

...

Thank you, Doug, for your explanation about conjunction analysis in FreeSurfer.

I did everything as you said using sig maps, and now I have a conjunction_sig.mgh, which I don't know how to look at. Is it possible to load it in qdec (my purpose is to see where the conjunction clusters are located and what is their size, max value, significance)?

Best wishes, Tanja

On Mon, Aug 29, 2011 at 7:01 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:

...

For #1, Donald is right about FS -- you have to exclude the subject. For #2, you can use mri_concat with the --conjunct option (using sig or t or z maps as input).

the Conjunction option takes the min of the abs across frames at each voxel. The output value at the voxel is the min, including the true sign of the min. Eg, if the two frames are: +2.1 and +3.4 --> +2.1 -2.1 and -3.4 --> -2.1 +2.1 and -3.4 --> +2.1 -2.1 and +3.4 --> -2.1 See: Nichols, Brett,Andersson, Wager, and Poline NeuroImage, Volume 25, Issue 3, 15 April 2005, 653-660.

doug

MCLAREN, Donald wrote:

...

See inline responses.On Wed, Aug 24, 2011 at 7:35 AM, Tetiana Dadakova <tetiana.d@gmail.commailto:tetiana.d@gmail.com> wrote:

Dear FS experts,

I have two questions:

1. In qdec.table.dat file I am specifying several continuous factors,
e.g factor1 and factor2. For some subjects factor2 is missing,
therefore I leave empty space in those cells. When I load a
qdec.table.dat into qdec, the whole line of the subject with missing
factor2 is omitted.
I was wondering if I can make some input into the empty cell, so that
qdec recognizes that for this subject the value is missing only for
factor2, and the value for factor1 is present.

I'm not sure about Freesurfer, but in all my work with neuroimaging data across platforms, missing data in X requires that the subject to be excluded. The reason is the Y=X1*B+X2*B. Since you don't know X2, you can't find predicted Y and thus you can't find the error associated with that subject. Programs that all allow you to keep the subject often impute the value of the missing data to get the full X matrix or do not use the General Linear Model to find the solution. The GLM approach inverts the X matrix and you can't invert a matrix with an empty cell, as far as I know.

2. Is it possible to do conjunction analysis in FreeSurfer, I mean
looking at common differences in two groups as compared to the third
group?

When I do conjunctions, I use a logical AND. There are other ways, but there are statistical issues. The logical AND will show where group A> group C and where group B> group C. To do this, I load the thresholded surfaces into matlab, make them both binary, multiply one of them by 2, then add the two datasets together. Then write the data back out to the surface. The new values will be 0 for no difference in either group, 1 or 2 for a difference in one of the group comparison, 3 where both groups are different from the third.

Thank you for your time and help,
Tanja.
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