cortical surface-based functional analysis

[MSh]

Hi

After replacing the file FunctionalProjection.py with the one attached to the previous post, now I get a new error message (attached) right after pressing the run button in the "projection of functional volumes" process.

MSh

[Grégory Operto]

Did you give a look to the log to get more info on what might have caused the error ? (BrainVisa menu -> log, in the process window)
If not, could you send me a copy of the log (maybe in a private message)... Please send especially the log info related to the process in particular.

[MSh]

Hi Grégory

I just e-mailed you the log file (couldn't attach the log file to this post because it was too big).

Thanks
MSh

[MSh]

Hi

I managed to do the “projection of functional volumes” step by converting the files with “Aims converter” and registering functional volumes to the structural image using “Rigid registration with mutual information” (as explained in the post: http://brainvisa.info/forum/viewtopic.php?f=2&t=1367). For the next steps, however, I don't know how to fill in these fields:

1.protocol_text
2.timetexture
3.projection_texture (is this the output of “concatenate texture” or “projection of functional volumes” process?)
4.contrast (how can the contrast of interest be inserted?)
5.What are “beta” and “spm_texture” (the outputs of the “surface-based statistical parametric map” process)

Any comments?

Thanks
MSh

[faillenot]

no ... sorry !

[Grégory Operto]

Hi MSh,

Here are some hints about filling-in the process fields :

- you must give a projection_texture which is the concatenation of all the textures resulting from the projection of every functional volume.
This concatenation process can be found in the general Tools toolbox.

- for protocol_text, you must provide a text file respecting the following xml structure :

Code: Select all

    <doc>
    <tr>24</tr>
    <time>0</time><time>2400</time><time>5700</time>
    <type>1</type><type>2</type><type>1</type>
    </doc>

where <tr> sets the acquisition time one volume in .10^-1 s (here it is tr=2.4 s), <time> sets every stimulus time onset in ms, and <type> sets the type of stimulus (i.e. an integer, according to a custom matching table of yours such as "1->right motor", "2->checkboard" ...). In the end, you must have as many <time> tags as <type>. This text file is used for computing the expected activated node time course, and therefore the linear model regressors.

- beta is an optional parameter which allows to write a texture with the beta after the regression.

- spmt_texture is the resulting t-map, corresponding to the given contrast (see following field).

- contraste is a vector of integers describing the conditions of interest : this vector depends on your protocol_text file. For instance, a contrast vector like 0 0 1 -1 means that you are interested in the contrast between the type 3 stimulation minus type 4.

Basically, this process consists in computing a GLM on the surface from a nodes matrix instead of a voxel matrix. This user interface still needs some improvement : furthermore, it has not been tested for various configurations, so its execution might not be straightforward. Just in case, you might find it easier to compute this GLM by any other method of your choice, while waiting for the next release.
You probably noticed that this process is User Level 2, which means still under development and not really yet supported.

Grégory