Re: [Freesurfer] A mixed effect model approach in within subject dataset {Disarmed}

Hi Jorge and FS experts,I have run again the analysis and still get the convergence problem.I am assuming the issue has to do with the preprocessing steps, as I had doubts on how to follow from the instructions if I am not using qdec and have a cross sectional design. Instructions on lme in the

Re: [Freesurfer] MPRAGE SNR

Dear Jürgen This really helps! I highly appreciate your input on this.   Bests, John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419     Sent: 

Re: [Freesurfer] -hippocampal-subfields-T1T2

Hi Daniel, sorry for the late reply; I was on vacation. It seems that the T1-T2 registration failed. Can you please send me the .log files for the hippocampal subfields? They should be in the following directory:

Re: [Freesurfer] MPRAGE SNR

Hi John there is also a binary called mri_cnr that will compute the contrast-to-noise ratio (CNR), which is really the more interesting metric. It will also spit out the WM means+- std, and the ratio of these two can be used as an SNR measure. cheers Bruce On Mon, 19 Oct 2015, John

Re: [Freesurfer] recon-all stripped brains

Hi John I guess you could run recon-all through to the skull stripping, then copy your skull-stripped volume to brainmask.mgz in the subject's mri dir, then restart recon-all from there. cheers Bruce On Fri, 16 Oct 2015, John Anderson wrote: Dear experts, I want to run recon-all on a

Re: [Freesurfer] MPRAGE SNR

probably similar, although maybe Doug can comment. You probably want to run it on the orig.mgz as the intensity normalization can artificially increase the SNR (which is kind of the point) Bruce On Mon, 19 Oct 2015, John Anderson wrote: Hi Bruce, Thanks a lot!! this is really great! I ran

Re: [Freesurfer] Volumes differ in acquisition paramaters

Hi Kasper, if you use the same file formats and conversion tools across both time points, the images should be identical. Even after conversion to nii. Not sure why they are not. Yes, both warnings are related to the acquisition parameters. The second should better say that header

Re: [Freesurfer] MPRAGE SNR

Hi, FWIW, I've looked at a number of these measures in 500+ subjects from HCP data -- wm-anat-snr, pctsurfcon, G/W cnr, G/CSF cnr -- to see how they relate to each other, and whether they correlate with mean cortical thickness, white matter surface area, or number of SurfaceHoles (prior to

[Freesurfer] BuildYourOwnMonteCarlo

Hi, A question about building your own Monte Carlo. here: https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo it says: "If you want to restrict the correction to a smaller area to reduce the severity of the correction, you can specify a mask or a label and change the output

Re: [Freesurfer] MPRAGE SNR

There is also the issue that grey and white matter are not truly a homogeneous single intensity anatomically. Peace, Matt. On 10/19/15, 9:23 AM, "Harms, Michael" wrote: > >Hi, > >FWIW, I've looked at a number of these

[Freesurfer] Viewing vitamin E capsules?

Dear users, I have been using FreeSurfer for a while now, but am working in a new lab and their goals fall outside of my realm of experience. We are using both MRI imaging as well as FNIRs. We have multiple vitamin E capsules placed during both and would like to be able to view them in

Re: [Freesurfer] Volumes differ in acquisition paramaters

Dear Martin and FS experts.I am having difficulty in loading my qdec.table.dat to Matlab.When I use the [command: Qdec = fReadQdec('qdec.table.dat'); ] Matlab only recognises a matrix of 140x1 cell, whereas instead it should recognise a 140x4.I tried to import the table as 'table' from the gui

Re: [Freesurfer] recon-all stripped brains

It might just work to give recon-all skull stripped brains. I've done it before On 10/19/15 8:38 AM, Bruce Fischl wrote: Hi John I guess you could run recon-all through to the skull stripping, then copy your skull-stripped volume to brainmask.mgz in the subject's mri dir, then restart

Re: [Freesurfer] BuildYourOwnMonteCarlo

In theory that should work. I say "in theory" because there might be something unique to each area in terms of the distribution of the vertices across space. But I'm betting it will be safe to do. But why not run both simulations? On 10/19/15 11:03 AM, Joost Janssen wrote: Hi, A question

Re: [Freesurfer] Viewing vitamin E capsules?

Hi Seth do you really want to include the capsule within the brain mask? You can always view it and find its coordinate by visualizing the orig.mgz. If you really want it in the brainmask.mgz you can clone it back in using freeview or tkmedit cheers Bruce On Mon, 19 Oct 2015, Hutton, Seth

Re: [Freesurfer] Volumes differ in acquisition paramaters

Hi Pablo, maybe your file is not clean and contains strange symbols to separate coumns and rows? Make sure columns are all separated by spaces. You could load the table into exel or openoffice spreadsheet and then export as CSV with space (or you could also try tab) for the separation and

Re: [Freesurfer] MPRAGE SNR

This has been my experience as well. Not much seems to predict which scans will need to be edited. On 10/19/15 10:23 AM, Harms, Michael wrote: > Hi, > > FWIW, I've looked at a number of these measures in 500+ subjects from HCP > data -- wm-anat-snr, pctsurfcon, G/W cnr, G/CSF cnr -- to see how

Re: [Freesurfer] MPRAGE SNR

Hi All, Thank you very much for your comments!   Is it advisable to include SNR as a covariate when we use Qdec to run the final statistics on volumetrics, surfaces and cortical thickness? Does it make sence ?   Bests, John Anderson Senior Research Associate Psychological and Brain Sciences

Re: [Freesurfer] Viewing vitamin E capsules?

Why not just open the T1.mgz and load the FreeSurfer surfaces? Is there a more specific goal? hth d On 10/19/15 10:56 AM, Hutton, Seth wrote: > Dear users, > > I have been using FreeSurfer for a while now, but am working in a new > lab and their goals fall outside of my realm of experience. >

Re: [Freesurfer] MPRAGE SNR

I think you would just be wasting your power Bruce On Mon, 19 Oct 2015, John Anderson wrote: Hi All, Thank you very much for your comments!   Is it advisable to include SNR as a covariate when we use Qdec to run the final statistics on volumetrics, surfaces and cortical thickness? Does it

Re: [Freesurfer] converting surfaces into volumes or integrating them into volumes

In that case, you just need to mri_convert aparc+aseg.mgz aparc+aseg.nii On 10/19/15 3:24 PM, Bruce Fischl wrote: > Hi Boris > > the aparc*aseg.mgz files are probably want you want. They are the surface > parcellations sampled into the volume. Of course you lose resolution when > you sample a

Re: [Freesurfer] converting surfaces into volumes or integrating them into volumes

Hi Boris the aparc*aseg.mgz files are probably want you want. They are the surface parcellations sampled into the volume. Of course you lose resolution when you sample a continuous surface into a discrete volume though. cheers Bruce On Mon, 19 Oct 2015, Boris Shabash wrote: > Hello

[Freesurfer] converting surfaces into volumes or integrating them into volumes

Hello FreeSurfer group How are you? I have currently started working with FS and would like to visualize some of the volume results. I have no issue visualizing the .mgz volumes produced since I can use mri_convert to convert them to .nii format and then visualize them using my software.

Re: [Freesurfer] converting surfaces into volumes or integrating them into volumes

Try mri_surf2vol. Run it with --help to get more docs On 10/19/15 3:09 PM, Boris Shabash wrote: > Hello FreeSurfer group > > How are you? > > I have currently started working with FS and would like to visualize some of > the volume results. I have no issue visualizing the .mgz volumes produced

[Freesurfer] patching 5.1

Hello All Several years ago Freesurfer 5.1 was patched to resolve some issues. I just remember the patch resolved issues plaguing 5.1 and earlier. how does one get the patch version. no where on the FTP server i can see patched versions and instruction on performing a patch. Aaron Tanenbaum

Re: [Freesurfer] MPRAGE SNR

My experience, which appears to be consistent with Doug's, is that there is no substitute for reviewing the images and FS results manually.  Ultimately, it is a bit of a judgement call, and interacts with the goals/purposes of your study. --  Michael Harms, Ph.D.

Re: [Freesurfer] MPRAGE SNR

At best that would probably be harmless (if you have a decent number of subjects), but unless SNR, CNR actually relates to those measures in some fashion, you aren't really accomplishing anything by including it as a covariate.  You certainly wouldn't be able to claim that including SNR as

Re: [Freesurfer] MPRAGE SNR

Thanks MH, Let's say that we have 100 MPRAGEs and we want to include them in a cross sectional analysis. Depending on your experience, do you recommend any criterion to (include/ exclude) these images  in the analysis? As I see visualizing the images alone is not enough to say that the quality