External Email - Use Caution        

Dear Freesurfer experts,

I’ve just completed a GLM analysis in Freesurfer and I’d like to be sure that all the steps I’ve performed are the right ones.

My analysis is looking at age related changes in cortical thickness in one group of patients, after regressing out the effects of disease duration. I obviously assume an inverse relationship between age and cortical thickness so that older age would be associated with cortical thickness reductions in specific brain regions.

To test this hypothesis with Freesurfer I’ve used a GLM DOSS design. 
I’ve generated a fsgd file with the first column being the list of patients, the second column the age of patients, and the third column the disease duration.
Then I’ve run the mris_preproc command.

Afterward,  I’ve generated 2 contrast matrices (one for the left and one for the right hemisphere) with the following structure: 0 -1 0.

1 question. Is the contrast matrices structure I’ve chosen the most appropriate one for the hypothesis I’d like to test?

Then, I’ve run the glm analysis using the mri_glmfit command.

To visualize the results I’ve used the freeview -f command and set the overlay_threshold to 1,5 instead of 4, cause I was interested in looking at all results significant at p < 0.05.

2 question. Is the overlay_threshold I’ve used the correct one?

Lastly, I was interested in looking at my results after Montecarlo correction, so I’ve run the simulation using the mri_glmfit-sim command.
However, here I’ve changed few options:

 

mri_glmfit-sim \
  --glmdir lh.dur.glmdir \
  --cache 4 neg \ (here I’ve changed to 1,5 since I was interested again at a P value < 0,05 and not < 0.0001 and I’ve changed the neg option with abs since I was interested in absolute values identified through the previously run analysis)
  --cwp  0.05\
  --2spaces

3 question. Are the edits I made to the command correct? It is not perfectly clear to me which one should be the preferred sign for the analysis (neg, pos or abs?).

In the end, in order to visualize the Montecarlo corrected results I’ve used again the Freeview -f command and again I’ve sent the overlay threshold to 1,5 since I was interested in all significant clusters at P < 0,05.

4 question. Again, this threshold is the correct one for my purpose?

I have one last question concerning the Montecarlo simulation. Are there any cases in which you would suggest to do not use it since it would not be an appropriate correction?

Sorry for the long email but I needed to report all the steps in order to get an answer.
Many thanks for all the help you’ll be able to provide.

Best,

Pilar Ferraro



Il giorno 16 feb 2020, alle ore 6:00 PM, freesurfer-request@nmr.mgh.harvard.edu ha scritto:

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Today's Topics:

  1. Re: Apply transformation (Adam Rytina)
  2. A couple of questions (Zvi Baratz)


----------------------------------------------------------------------

Message: 1
Date: Sat, 15 Feb 2020 18:52:43 +0000
From: Adam Rytina <adam.rytina@outlook.cz>
Subject: Re: [Freesurfer] Apply transformation
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<AM0PR0602MB33773F725E71511D519EA0409A140@AM0PR0602MB3377.eurprd06.prod.outlook.com>

Content-Type: text/plain; charset="iso-8859-2"

       External Email - Use Caution        

Thanks, unfortunately, I am making some mistake but I don?t know where.

First of all I run autorecon1 on my anatomical T1 data (the orig.mgz image is saved in /usr/local/freesurfer/subjects/anatomical).
Then in the /usr/local/freesurfer/data I run mri_robust register command of the T1 and diffusion DWI data. The registration.lta file is saved here.

Now I add an anatomical mask "3D_T1_brain_mask.nii" to the same folder /usr/local/freesurfer/data that I want to transform to the anatomical T1 space.

In the same /usr/local/freesurfer/data I run : "mri_vol2vol --lta registration.lta --mov 3D_T1_brain_mask.nii --o f-in-anat3.nii --s anatomical --fstarg"

To sum up, I am aiming to apply a transformation matrix on the T1 anatomical brain mask and transform it to the T1 space defined by 3D T1 image.
The problem is this command transforms orig.mgz file (a skull stripped T1 image) instead of 3D_T1_brain_mask.nii.

Please, do you know where I make mistake?

Thanks a lot
________________________________
Od: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> za u?ivatele Douglas Greve <dgreve@mgh.harvard.edu>
Odesl?no: sobota 15. ?nora 2020 17:15
Komu: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
P?edm?t: Re: [Freesurfer] Apply transformation

Yes, mri_vol2vol

On 2/15/20 11:07 AM, Adam Rytina wrote:

       External Email - Use Caution

Hello all,

I want to apply the saved transformation (a transformation matrix 4x4 acquired by registration of an anatomical and a diffusion image) on my input anatomical mask and change a final FOV by specifying a diffusion reference image (its voxels size). It means to apply the same command as the command ApplyXFM in FSL FLIRT. Does this option exist also in Freesurfer?

Thanks a lot
Regards
Adam




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Message: 2
Date: Sun, 16 Feb 2020 14:07:05 +0200
From: Zvi Baratz <z.baratz@gmail.com>
Subject: [Freesurfer] A couple of questions
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<CANJsFRZEX1H9D_9mTgP5mYh2Lfdr-GJQv69cvQh4=TS9p3e4Eg@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

       External Email - Use Caution        

Hi all,

Thank you for all your amazing work!
I started using FreeSurfer recently and there are a couple of questions I
was hoping someone here might be able to help me with:

  1. Does anyone know of any way to silence recon-all's output or redirect
  it to stdout when called programmatically through nipype? I tried a couple
  of different approaches (using python's os.devull and creating a fake
  file-handle that does nothing on write() calls), but I can't seem to be
  able to get rid of it. Also, and I apologize if it exists and I simply
  missed it, I think it would be great to simply add a --quiet flag or
  something of the sort, considering the output is anyhow saved to a log
  file.
  2. Is there any more documentation on recon-all's output other that the
  ReconAllOutputFiles
  <https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllOutputFiles> page?
  I've noticed a lot of info is missing there. I would be more than happy to
  contribute to it myself but I'm not sure what resources I can use to gather
  more information, and also I'm having trouble finding the corresponding
  documentation files on GitHub.

Thanks again and all the best!
Zvi
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