Dear Freesurfer experts I have some longitudinal data from tp1 and tp2 for three different groups (A,B,C) and 2 different genders (G1,G2).
I followed the longitudinal stream and processed all the images in FS 4.5. For further analysis, I saw the post from Martin and Doug at http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg14266.html in which they suggested to first do the mris_preproc for each time point and then calculate the differences using mris_calc. What I did was instead of doing mris_preproc for each tp separately I made a FSGD file and put all the information about our different classes including baseline (BL) and followup (FU), see below, and then run mris_preproc which gives me ?h_thickness_both_tp_fwhm10.mgh files. GroupDescriptorFile 1 Title diagnosis_gender_glmdir MeasurementName thickness Class A_G1_BL Class A_G1_FU Class A_G2_BL Class A_G2_FU Class B_G1_BL Class B_G1_FU Class B_G2_BL Class B_G2_FU Class C_G1_BL Class C_G1_FU Class C_G2_BL Class C_G2_FU After mris_preproc for example I made the following contrast to compare the changes from BL to FU and then I ran mri_glmfit: contrast to compare (A_BL vs C_BL) vs (A_FU vs C_FU): contarst_AvCBLvAvCFU=[1 -1 1 -1 0 0 0 0 -1 1 -1 1] >> mri_glmfit - - y ?h_thickness_both_tp_fwhm10.mgh - - fsgd diagnosis_gender_BL_FU.fsgd - - C contarst_AvCBLvAvCFU.mtx - - surf fsaverage ?h - - cortex - - glmdir glmdir So using this approach I wanted to compare the difference between the 2 tps using the contrasts and not calculating first the differences using mris_calc and then runnig glm. However, I am not sure if I am doing the right thing. Could you please send me your feedbacks. Thanks in advance, Sima Chalavi. -- Sima Chalavi, Ph.D. student King's College London Institute of Psychiatry (IoP) Box P040, De Crespigny Park London SE5 8AF. Tel:+44-2078485702 BCN Neuroimaging Center (NIC) University Medical Center Groningen Antonius Deusinglaan 2 P.O. Box 196 9713 AW Groningen www.neuroimaging-DID.com
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