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

You can try running mri_surf2vol to put into a volume, but you're better off with mri_glmfit

Nick Schmansky wrote:

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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