Hi Reem, #1. Is this from mri_glmfit-sim? If so, you can ignore it #2. You do not need both contrasts. Use abs to get a double sided test #3. The first contrast will be positive for Control>Patient. If you specify neg, it will only show clusters where Control<Patient #4. Depends on what you mean by "stringent". There is nothing more or less conservative about any particular voxel-wise threshold since you are not drawing conclusions based on the voxel-wise threshold but on the cluster-wise p-value. In general, the clusterwise correction is probably more reliable at higher voxel-wise thresholds.
Subcortical: yes, just create a table and load it into SPSS. The only other thing is that you may want to normalize the volumes for ICV or brain volume, depending upon your hypothesis. doug On 05/09/2012 08:44 PM, Reem Jan wrote: > > 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 > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
