hi everyone
i have run recon-all on somme subjects and i want to make
build a masque containing somme geri (pre and post central for example) andÂ
with some color, to load on a pial surface (as overlay). i tried to understand
the commands like mri_annotation2label and
Dear all,
I think I figured out the contrasts (I'm using [0 0 0 0 0.5 0.5 0 0]...is
that correct?) but I've come across an error when trying to do the next
step in the tutorial.
I didn't cache the data during recon-all, so I ran the following:
mris_preproc --fsgd MMSE-AD.fsgd --target fsaverage
Hello Anastasia!
Thank you very much for your response!
My bvecs and bvals were created by saving excel spreadsheet as a tab
delimited file on mac. I reformated my bvecs manually using nano and
reran the preprocessing. Unfortunately, it exited with the same error.
I'm providing you my reformated
Dear all,
in the process of understanding freesurfer I like to see/inspect the created
transforms visually. However, so far I am not able to see all the data that is
stored in the transforms folder.
So is it possible to see files like /transforms/lh.curv or /transfroms/lh.sulc?
And if yes,
Hi Maria,
those files don't live in the transforms dir, they live in the surf dir.
Further, pial, inflated and orig are surfaces with geometry and topology
information, but sulc and curv are just scalar fields over the surface.
You can display them on any of the surfaces using file-load
Dear Bruce,
thanks again for your quick help. And sorry for mixing up the directories.
Best,
Maria
- Original Message -
From: Bruce Fischl fis...@nmr.mgh.harvard.edu
To: Maria Felber fel...@cbs.mpg.de
Cc: freesurfer@nmr.mgh.harvard.edu
Sent: Friday, December 2, 2011 4:25:10 PM
Subject:
no problem, it happens
On Fri, 2 Dec 2011, Maria Felber wrote:
Dear Bruce,
thanks again for your quick help. And sorry for mixing up the directories.
Best,
Maria
- Original Message -
From: Bruce Fischl fis...@nmr.mgh.harvard.edu
To: Maria Felber fel...@cbs.mpg.de
Cc:
Hi Linda, you have two class varibles (M and F) and three continuous
variables (Age, MMSE, and ED), so you'll have 2*(3+1)=8 regressors, so
your contrast will have 6 elements. The order of the elements will be:
1. M-offset
2. F-offset
3. M-AgeSlope
4. F-AgeSlope
5. M-MMSE-Slope
6. F-MMSE-Slope
Hi Jeff, it's going to be tricker than that to get the exact value. For
the WM volume computation, there's yet another routine that is used.
This one creates a high-resolution volume to determine which voxels are
withing the WM surface. It then loops through the voxels within the WM
surface
Is this volume data? If so, then use --grf with mri_glmfit-sim instead
of --cache.
doug
Antonella Kis wrote:
Dear Doug,
Can you please advise me how I can do a multiple comparison for my DTI
group analysis?
I tried and I ran:
mri_glmfit --y group-fa-tal.nii
--fsgd
What exactly is your question? Run mri_annotation2label to convert the
annotation with pre and postcentral gyri to labels. Then re-combine just
those two labels into an annotation with mris_label2annot. You can
supply a color table to control what colors the labels have in the new
annotation.
does /home/virtualuser/freesurfer/subjects/lh.MMSE-AD.thickness.00.mgh
exist?
doug
Linda Zhang wrote:
Dear all,
I think I figured out the contrasts (I'm using [0 0 0 0 0.5 0.5 0
0]...is that correct?) but I've come across an error when trying to do
the next step in the tutorial.
I
Thanks Doug. And good question that I've wondered about myself Jeff.
The part about the high-resolution volume that is created under the
hood explains why mris_wm_volume takes substantially longer to complete
than would be expected relative to just running `mris_volume Xh.white`
and then
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