Hi Mandy, you don't need an fsgd file in this case because you used --osgm. Otherwise you can just list the first session. The glmfit command is correct.

doug

On 8/2/11 12:51 PM, Mandy Nagy wrote:

One of our volume analyses does not look as it should after we perform the mri_glmfit.

Our block design paradigm has 2 separate sessions for each subject with alternating periods of task and rest. We did individual analyses for task-rest for each session. We then concatenated the data into 2 files: one for each session. Then we ran fscalc to add the 2 concatenated files. Up until this point, the data looked like it should.

subjects dir: /cluster/manoach/milton/subjects freesurfer 5

However, when we then ran the group analysis using mri_glmfit, we got results that looked abnormal. Our command:

mri_glmfit --y mstmct_v_base.nii --glmdir group_analysis/volume/mstmct_v_base/ --osgm

We were unsure if we should put in the fsgd file, because we weren't sure which subjects should be included because we added the two sessions using fscalc. (Each subject has two sessions and 2 subject IDS).

We realize it could be a problem that arose before the mri_glmfit , but we aren't sure if there was anything else we should consider when running the mri_glmfit itself.

Thank you!

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