Jim,
I haven't used SPM so I can't comment on what SPM likes, but the
utilities asegstats2table and aparcstats2table will create text-file
tables of the aseg and aparc data for one or more subjects, which I
would think could be easily imported into SPM.
If you use mri_glmfit directly, there is a little bit of info on
creating a contrast matrix here:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/CreateContrastVectors
Nick
On Wed, 2008-02-27 at 22:17 -0600, James N Porter wrote:
Hi Nick-
I've run into the same problem recently and am looking at piping my FreeSurfer data out to another stats program. There is all sorts of info on the list about sending FS data out to Matlab, but are there any tips for getting it into a format that SPM will agree with? My other option is to just use mri_glmfit, but I'm having problems there, too, with setting up my desired contrasts.
Any tips to tide us over until qdec mark 2 comes out?
---------
Jim Porter
Graduate Student
Clinical Science & Psychopathology Research
University of Minnesota
Nick Schmansky wrote:
I see that group.levels has four levels. Unfortunately, right now qdec
only supports two levels for a discrete factor. One the features in the
works is to increase this.
On Wed, 2008-02-27 at 14:04 -0500, Cameron B. Ellis wrote:
Hi,
I pasted an error that I am receiving in qdec below. SUBJECTS_DIR is
/space/lightning/2/users/NEAA-freesurfer. If you need any more information
from me I will be happy to provide it. Any help is much appreciated.
Thanks,
troy:cameo[87] ERROR: QdecGlmDesign::GenerateContrasts: factor 1 must
have 2 levels
ninputs = 48
Checking inputs
nframestot = 48
Allocing output
Writing to /autofs/space/lightning_002/users/NEAA-freesurfer/qdec/NEA
A-freesurfer/y.mgh
gdfReadHeader: reading /autofs/space/lightning_002/users/NEAA-freesur
fer/qdec/NEAA-freesurfer/qdec.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 txt-untxt 1.01875
Class Means of each Continuous Variable
1 groupPH-gendermale 2.8400
2 groupPL-gendermale 0.5333
3 groupVH-gendermale 0.6000
4 groupVL-gendermale -0.4667
5 groupPH-genderfemale 1.0857
6 groupPL-genderfemale 0.0833
7 groupVH-genderfemale 3.1167
8 groupVL-genderfemale 0.6500
INFO: gd2mtx_method is dods
Reading source surface /autofs/space/lightning_002/users/NEAA-freesur
fer/fsaverage/surf/lh.white
reading group avg surface area 822 cm^2 from file
Reading in average area /autofs/space/lightning_002/users/NEAA-freesu
rfer/fsaverage/surf/lh.white.avg.area.mgh
ERROR: no contrasts specified
Error in Analyze: command failed: mri_glmfit --y /autofs/space/lightn
ing_002/users/NEAA-freesurfer/qdec/NEAA-freesurfer/y.mgh --fsgd /auto
fs/space/lightning_002/users/NEAA-freesurfer/qdec/NEAA-freesurfer/qde
c.fsgd --glmdir /autofs/space/lightning_002/users/NEAA-freesurfer/qde
c/NEAA-freesurfer --surf fsaverage lh --label /autofs/space/lightning
_002/users/NEAA-freesurfer/fsaverage/label/lh.cortex.label
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