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