Sorry about that. I attached the previous conversation below. Yes - I am interested in applying the monte carlo sim to my own model fit. Doug can you walk me through the steps I need to get this part done? When you say residuals, I am assuming that I need to supply a vector file of residuals after I fit my model to the smoothed data (eg. using mri_surf2surf --sval [concat thickness] --fwhm-trg [smooth level] etc. ) - correct? Since I don't have the --glmdir to supply, what are the other files or options that I need to manually supply for mri_glmfit-sim to run the correction? Thank you in advance!

That looks fine. If you are going to use the monte carlo sim, then you'll need an estimate of the FWHM. In mri_glmfit, we get that by running mris_fwhm on the residuals. So, assuming that your analysis has residuals, then you should save those out too.

On 05/24/2016 01:55 PM, Chung, Yoonho wrote:

Hi - If I would like to try to perform mass-univariate statistics at the vertex level (thickness, area, vol at each vertex) without using the mri_glmfit, is this order a sound step (in general) for mapping stats parameter of choice (p-val or t s or weights for example) to the surface?

1. Use mris_preproc and surf2surf to get the data to common space and

smooth.

2. Load the data to matlab using fs_read_Y() or MRIread

3. Perform stats at each vertex using stats toolbox to apply modeling

approach of your choice (e.g., machine learning, linear mixed model etc.)

4. Extract P-values (or other parameters) for each vertex for the

variable of primary interest

5. Use MRIwrite to create mgh file

6. Perform multiple comparison using freesurfer functions (e.g.,

FDR or monte carlo sim)

7. view corrected maps using tksufer?

Any steps I should consider adding or avoid?

Thank you!

________________________________ From: Douglas N Greve greve@nmr.mgh.harvard.edu Sent: Wednesday, June 1, 2016 12:47:53 PM To: Chung, Yoonho; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Using customized stats code for mass-univariate approach in freesurfer for structural data

Please include previous correspondence

On 06/01/2016 11:39 AM, Chung, Yoonho wrote:

Yes - I am interested in applying the monte carlo sim to my own model fit. Doug can you walk me through the steps I need to get this part done? When you say residuals, I am assuming that I need to supply a vector file of residuals after I fit my model to the smoothed data (eg. using mri_surf2surf --sval [concat thickness] --fwhm-trg [smooth level] etc. ) - correct? Since I don't have the --glmdir to supply, what are the other files or options that I need to manually supply for mri_glmfit-sim to run the correction? Thank you in advance!

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 FileDrop v2.0 - Martinos Center for Biomedical Imaginghttps://gate.nmr.mgh.harvard.edu/filedrop2 gate.nmr.mgh.harvard.edu Filedrop is for sending files work-related files up to 2GiB; For files over 2GiB, please use the Accellion File Transfer from Partners; Filedrop is not a secure ...

www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: 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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complia... . 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.