thanks, but we are using qdec to do the inital analysis , not mri_glmfit Jon

________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu Sent: Thursday, September 11, 2014 9:54 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_glmfit-sim montecarlo analysis with mask

You do this by specifying a mask or label to mri_glmfit, then mri_glmfit-sim will automatically use this mask. Note that you have to run the simulation (ie, you cannot use --cache). In this case you may want to run mri_mcsim. See http://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo

doug

On 09/11/2014 10:49 AM, Jon Alan Wieser wrote:

HI freesurfer experts

We were wondering if it is possible to restrict the Monte Carlo analysis run by mri_glmfit-sim to a specific region fo the surface , instead of the whole surface, by using a mask or label to specify the ROI?

I didn't see a --mask or --label option in mri_glmfit-sim

Thank

Jon

---

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-- 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 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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thanks, I'll try that Jon

________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu Sent: Thursday, September 11, 2014 10:03 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_glmfit-sim montecarlo analysis with mask

You'll have to use mri_glmfit to do this. QDEC is very limited when it comes to doing something special. QDEC will generate the fsgd file and contrast files for you. You can even look in the QDEC output folder for the mri_glmfit.log file which gives the mri_glmfit command. You'll just need to add a label to that.

doug

On 09/11/2014 10:59 AM, Jon Alan Wieser wrote:

thanks, but we are using qdec to do the inital analysis , not mri_glmfit Jon

---

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu Sent: Thursday, September 11, 2014 9:54 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_glmfit-sim montecarlo analysis with mask

You do this by specifying a mask or label to mri_glmfit, then mri_glmfit-sim will automatically use this mask. Note that you have to run the simulation (ie, you cannot use --cache). In this case you may want to run mri_mcsim. See http://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo

doug

On 09/11/2014 10:49 AM, Jon Alan Wieser wrote:

...

HI freesurfer experts

We were wondering if it is possible to restrict the Monte Carlo analysis run by mri_glmfit-sim to a specific region fo the surface , instead of the whole surface, by using a mask or label to specify the ROI?

I didn't see a --mask or --label option in mri_glmfit-sim

Thank

Jon

---

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 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 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

---

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.

---

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 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 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer