Hi Doug,
I have pasted the correspondences below. My question is, if I want to identify
the PCs in a group for a single modality (PET), how should I run the
mri_glmfit? A single group design with A contrast of 1 0 (for a nuisance
covariate)?
Thanks !
Elijah
Doug:
For within modality, y
sorry, can you repost with previous correspondence?
On 12/01/2016 06:30 PM, Foo Keat Mak wrote:
> Thanks Doug. Does that mean that a one group design? With a contrast
> of 1 0 (adjusting for one variable)?
>
>
>
>
> ___
> Freesurfer mailing list
> Free
Thanks Doug. Does that mean that a one group design? With a contrast of 1 0
(adjusting for one variable)?
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this
sure, good luck
Bruce
On Thu, 1 Dec 2016, Rizvi, Batool wrote:
> Sounds great, thanks again for your help and will try out your
> recommendations.
> Have a great day!
>
> B
>
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.h
Sounds great, thanks again for your help and will try out your recommendations.
Have a great day!
B
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
[fis...@nmr.mgh.harvard.edu]
Sent: Thursda
yes, you can remove the control.dat file and run autorecon2-cp and
autorecon3. Should only take a couple of hours depending on your
processor
On Thu, 1 Dec 2016, Rizvi, Batool wrote:
>
> Hi Bruce,
> Thanks so much for the feedback, that is very helpful. We'll try deleting the
> control points t
Hi Bruce,
Thanks so much for the feedback, that is very helpful. We'll try deleting the
control points then. Is there a quick way to rerun recon-all without having it
take up to 5-8 hours?
Also, a separate question, when running autorecon, after edits to the white
matter and pial surfaces, sho
the problme is that you have several control points in voxels that aren't
entirely wm. For example, 129, 134, 173 is a control point and it has no wm
in it. This causes the intensity in that region to go up way too high, as
we will normalize the control points to the desired wm intensity (110).
I mean to tar and gzip the entire subject dir, which will be too big to
email. You can put it on our ftp site:
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
On Thu, 1 Dec 2016, Rizvi, Batool wrote:
> Hi Bruce,
> Thanks for your reply. It is actually brighter on the brainmask.mgz tha
Hi Bruce,
Thanks for your reply. It is actually brighter on the brainmask.mgz than the
orig.mgz when I checked. I'm uploading the freesurfer subject here.
Thanks!
BR
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] o
hmmm, that's awfully bright. Is it also bright on the orig.mgz? It's not
really possible to diagnose from a single slice from a single subject. If
you tar, gzip and upload the subject one of us will take a look
cheers
Bruce
On Thu, 1
Dec 2016, Rizvi, Batool wrote:
Hi FreeSurfer experts,
For within modality, you can add --pca to mri_glmfit (run it with --help
to get more info). We do not have ICA tools in FS.
On 12/01/2016 02:04 PM, Foo Keat Mak wrote:
> Hi Freesurfer Team,
>
> For a given group, I want to look at the covariance patterns between
> thickness and PET. Within Fre
Hi Freesurfer Team,
For a given group, I want to look at the covariance patterns between thickness
and PET. Within Freesurfer, what are some general workflow tips on how I could
go about performing PCA (within modality) or joint ICA analyses looking at the
covariance patterns across modalities
If you want to find the effect of group regressing out the effect of age
and there is truly a difference in the age slopes, then you have a
problem. Imagine a scatter plot of thickness vs age. Each group gets
it's own best fit line (offset and slope). If the slopes are the same,
then the two li
Dear FS's experts,
Could you answer me about questions from below inline precedent mail ?
Best regards,
Matthieu
2016-11-22 21:31 GMT+01:00 Matthieu Vanhoutte :
> Hi Martin,
>
> Please see inline below:
>
> Le 22 nov. 2016 à 17:04, Martin Reuter a
> écrit :
>
> Hi Matthieu,
> (also inline)
>
Thanks a lot Dr. Harms and Dr. Wakeman for the help. This is really helpful.
On Wed, Nov 30, 2016 at 10:24 AM, Harms, Michael wrote:
>
> That would be yet another way.
> For those that are curious, the field is “MosaicRefAcqTimes”.
>
> cheers,
> -MH
> --
> Michael Harms, Ph.D.
>
> --
If you want to use the FA map, it's dmri/dtifit_FA.nii.gz
From: Knut J Bjuland [knutjor...@outlook.com]
Sent: Wednesday, November 30, 2016 4:40 PM
To: Yendiki, Anastasia
Cc: Freesurfer support list
Subject: Re: [Freesurfer] obtain fa FA data from the white matter R
Hi,
Somewhat off-topic, but are there Freesurfer users on this list who might use
the Pegasus WMS for executing workflows? If so, I’d like to hear about your use
cases. I’m part of an NSF-funded project to incorporate data integrity and
security assurances into Pegasus for scientific workflows.
Dear All,
At the NORMENT – K.G. Jebsen Research Centre for Psychosis Research, a Centre
of Excellence, Institute of Clinical Medicine, University of Oslo, Norway,
there is a position available as a postdoctoral student funded by the Research
Council of Norway. The research area is psychiatric ne
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