On 08/05/2016 12:33 PM, Vikas Bandalli wrote:
Thank you Doug,
I am very sorry I hadn't explained our subject considered for analysis. The subjects group consists of Patients who are classified into a.Those with Psychosis - Psychotic-pt b. Those without Psychosis - Non-Psychotic-pt
We have Age and sex matched controls for every patient (case control study)
Now,the study was to see the structural variations using freesurfer and qdec, 4 individual 'qdec.dat' files were created such that two groups are considered at a time and analyzed namely
*qdec_1.dat :- Normal vs Patients(Psychotic + Non-Psychotic-pt)* *qdec_2.dat :- Normal vs Psychotic-pt (age and sex matched)* *qdec_3.dat :- Normal vs Non-Psychotic-pt (age and sex matched)* *qdec_4.dat :- Psychotic-pt vs Non-Psychotic-pt
The design was done as with Diagnosis/Psychosis as fixed factors and Age as covariate and ICV as nuisance factor for each 'pair' of analysis
Is the analysis-design appropriately constructed? or is this an inappropriate method.
so you created a new thickness file stack where you subtracted on an individual basis the paired subjects? That is fine.
The qdec GUI crashed with an error 'matrix m1=null' when the ICV values were used as it is (demeaning not done)
ICV definitely needs to be demeaned (and maybe rescaled by the stddev).
1.So,we can retain the negative numbered values for the above design. Also,I would be very interested to know why demeaning is necessary? My understanding is that since the ICV values are huge comapared to other factors
Correct
2.With the above mentioned study design,I wanted to know if the structural changes observed is due to the disease per se and not due to their Lithium intake (Some of the patients {both Psychotic-pt and Non-Psychotic-pt} were put on lithium). How would I have to design the analysis then? Is it possible to analyze this with qdecGUI?
To clarify, two diagnosis groups Psychotic Patients and Non-Psychotic Patients. Some of the patients are on lithium and some are not. Is that right? If so, then you have a two factor design where each factor has two levels, so you can do this analysis in QDEC.
Thank You,
Regards, Vikas Bandalli Raju
On Fri, Aug 5, 2016 at 9:28 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
1. It is not a problem that some of the demeaned ICV values are negative; this is what happens when you demean a set of numbers; you must leave the negative numbers there. Are you doing a paired analysis or do you just have two groups? I don't think you can do a paired analysis in QDEC. 2. would this give you 3 groups (controls, patients with lithium, patients without)? If so, you cannot use QDEC for this. If you can't use QDEC, you'll have to use the command line stream and either set up your own FSGD file or your own design matrix On 08/04/2016 01:36 PM, Vikas Bandalli wrote: Dear Freesurfers, Sorry if the question sounds too basic. 1. I am running an analysis on qdec with paired groups - normal and patients, To control for IntraCranialVolume(ICV),I am adding it as an 'nuisance factor',Is it correct? The suggested mode to add ICV to the tabled was to _demean_ the ICV. But when I subtract the mean values from individual subject ICV values,I noticed that some of the subjects have a negative demeaned ICV value. My question is - How should I proceed to include the data,ignore the negative sign(because I thought a negative ICV makes no sense) and just keep the values or retain the numbers with the sign. Please correct me if I am going wrong in any of the steps. However,I ran two analysis - one with the sign retained and other with sign removed ,I noticed that both have very different results. 2. If I want to see the effect due to lithium within the patient group (Between patients with and without psychosis) how should I design the matrix in GUI. I designed the following format Fixed factor :- Diagnosis - Psychotic-pt Non-Psychotic-pt Co-variate :- Lithium use :- 1 - lithium user 0 - non user Nuisance factor :- ICV Is this design correct? If not how should I construct it ? Also what query would contain the result for anticipated question My intention is to control for Diagnosis and then see effect/change due to lithium use. Thank you very much -- Vikas B. R. Medical student Bangalore Medical College and Research Institute (BMCRI), Bangalore,India, Ph : +918904286825 -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> 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 <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.-- Vikas B. R. Medical student Bangalore Medical College and Research Institute (BMCRI), Bangalore,India, Ph : +918904286825