Dear all
I'm fairly new to Freesufer and have started a cortical thickness group analysis. I had a few doubts/questions which I found most the answers for on previous emails on the FS archives - thank you! But I have a few more questions, I hope one of the FS experts can help me out. I will briefly describe my analysis - I have 2 groups - controls and patients. I am interested in the simple questions - do controls have higher GM thickness than patients and where? Do patients have higher GM thickness than controls and where? I expect controls to have higher GM thickness than the patients in cortical areas, but I expect the patients to have higher volumes of certain subcortical structures.
I am not interested in the effects of age or gender on GM thickness although I would like to control for these as covariates of no interest. In the example below I have not considered gender for simplicity's sake. Because I assume a similar slope among both groups, I decided to go with DOSS and not DODS.
I set out my FSGD file as below:
GroupDescriptorFile 1 Title lh.group_age.glmdir MeasurementName thickness Class Control Class Patient Variables age Input Subject_02 Control 29 Input Subject_04 Control 22 Input Subject_05 Control 23 Input Subject_06 Control 29 Input Subject_07 Control 18 Input Subject_08 Control 20 Input Subject_09 Control 36 Input Subject_10 Control 24 Input Subject_14 Control 29 Input Subject_15 Control 26 Input Subject_16 Control 39 Input Subject_17 Control 40 Input Subject_18 Control 26 Input Subject_19 Control 44 Input Subject_20 Control 34 Input Subject_22 Control 28 Input Subject_23 Control 26 Input Subject_31 Control 46 Input Subject_32 Control 40 Input Subject_41 Control 38 Input Subject_01 Patient 35 Input Subject_03 Patient 28 Input Subject_11 Patient 46 Input Subject_12 Patient 22 Input Subject_21 Patient 32 Input Subject_25 Patient 33 Input Subject_26 Patient 40 Input Subject_27 Patient 30 Input Subject_28 Patient 31 Input Subject_29 Patient 42 Input Subject_30 Patient 39 Input Subject_33 Patient 43 Input Subject_34 Patient 44 Input Subject_35 Patient 36 Input Subject_36 Patient 32 Input Subject_37 Patient 37 Input Subject_38 Patient 27
And my contrast files as: lh-diff-ControlvsPatient.mtx: +1 -1 0 0 lh-diff-PatientvsControl.mtx: -1 1 0 0
For GLM analysis I used the following command: "mri_glmfit --y lh.group_age.10.mgh --fsgd lh.group.fsgd doss --C lh-diff-ControlvsPatient.mtx --surf fsaverage lh --cortex --glmdir lh.group_age.glmdir"
My questions are:
Surface-based group analysis:
1. Can I ignore the error message: 'WARNING: unrecognized mri_glmfit cmd option doss'
2. Do I need 2 contrasts as above or should I be running only the first contrast with the 'abs' thresh-sign in order to obtain a double-sided t-test?
3. If my alternative hypothesis is that Controls>Patients and I specify a 'negative' thresh-sign - does that mean I will only see clusters where Controls<Patients (the reverse of my contrast)? The command I run is "mri_glmfit-sim --glmdir lh.group_age_precachedsim.glmdir--cache 1.3 neg"
4. I'm a bit confused about the vertex-wise threshold - if I specify it to be 3 (p=0.001), is that more or less stringent than specifying it to be 1.3 (p=0.05). I thought that the later (p=0.05) would allow for the consideration of more vertices and therefore would be less stringent, however when I applied both to try and test my theory, no clusters survived multiple comparison correction with p=0.05 but 1 cluster survived when I specified p=0.001. Could someone please shed some light on this?
Subcortical volume group analysis:
1. Can I just perform statistics in a program such as SPSS on the subcortical structure volumes I obtain from the 'aseg.stats' file within each subject's stats sub-directory? Or are there other steps that need to be undertaken in FS beforehand?
I'm sorry about the long email, I really appreciate your advice so thank you in advance
Kind regards Reem
Reem Jan BPharm (Hons), RegPharmNZ
PhD Student / Pharmacist School of Pharmacy, Faculty of Medical & Health Sciences, The University of Auckland, Private Bag 92019, Auckland, New Zealand. Ph: +64 9 373 7599 ext 81138. DDI: +64 9 923 1138 F: +64 9 367 7192