Dear list,
Sorry to repost it again, but i had rechecked it and found that all the
directories have no permission problems, but qdec could not load this CSD
file. Not sure why it is like this.
Thank you for the help again!
natalia
On Tue, Jul 10, 2012 at 3:20 PM, Natalia h wrote:
> Dear expert
Dear Avi,
thank you for your reply, probably I didn't make my point clear enough. Our
high resolution quantitative T1-maps (derived from multispectral FLASH) have
excellent GM-WM contrast and once autorecon1 (talairach-avi) gets over this
tricky coregistration into standard space all other foll
Dear All,
I am trying to automate ROI creation in freesurfer following the
VolumeRoiCorticalThickness tutorial, based on the AAL defined ROI-s from
MarsBar.
QUESTION
ROI5.nii was originally in the same space as TT_avg152T1.nii (see MORE INFO
below).
I understand that after Step 2 (when TT_
Hi Gari,
When you view the ROI5.nii on fsaverage make sure you include
'-overlay-reg TT_avg152T1_to_fsaverage.dat'. TT_avg152T1_to_fsaverage.dat
is the transformation computed in the previous step which you need to
apply. Nothing was resampled in step 2.
-Louis
On Thu, 12 Jul 2012, Garikoitz
Dear FreeSurfer,
Hello, I am currently working on a project using FreeSurfer (version 5.1.0)
at the Kable Labs at the University of Pennsylvania, and I have come across
a problem when using control points to add incorporate more of the white
matter into the white matter surface. After highlighting
Hi Peter,
This sounds very familiar (including the effect on the opposing
hemisphere) to something I've observed previously under FS v5.1 -- see
the posts titled "control point guidance" from late Jan 2012. This may
be related to a change in how CP's were used in FS v5.1, which I believe
they are
Dear Freesurfers,
I've been looking at the attributes in the '.area.pial' and '.area' (looking to
see how well the area attributes correlate between lh.area and lh.area.pial).
But it seems that the number of attributes in each file is different. Does
anyone know if this is correct and if so, w
Hello,after applying hippocampal subfield segmentation to our sample, we noted that summation of hippocampal subfields (in mm3) differs considerably from hippocampal volume (derived from aseg) in some of our subjects:case 1: 2592 mm3 (aseg hipp. volume) versus 2116 mm3 (summation of hipp. s
Hello,I
got the following error in one of my subjects when running hippocampal
subfields segmentation (only for the left hemisphere). Could you help me
to solve this problem?maximalDeformation: 75.1793 Transforming mesh Done transforming mesh Rasterizing Levenberg-Marquardt... number
Hi all,
I'm running tracula and when doing the step:
trac-all -prior -c single_subject
After some time it gives this error:
MRIalloc(218, 182, 182): could not allocate 158704 bytes for 49th slice
Cannot allocate memory
I' m running tracula on Ubuntu 10.04, with 4GB ram. The diffusion data is
DT
Hi Rui - How many voxels are in your diffusion volume? How many of them
are inside the mask?
a.y
On Thu, 12 Jul 2012, Rui Lavrador wrote:
> Hi all,
> I'm running tracula and when doing the step:
> trac-all -prior -c single_subject
>
> After some time it gives this error:
>
> MRIalloc(218, 18
Hi Peter and Mike
yes, 5.2 will undo those changes, although I still wouldn't expect this
behavior. Peter: are the points brighter (closer to 110) after adding them?
Is the wm.mgz more accurate?
cheers
Bruce
On Thu, 12 Jul 2012, Michael Harms wrote:
>
> Hi Peter,
> This sounds very familiar
Hi Remmelt,
what do you mean by "attributes"? Certainly they actual areas will be
different as the ?h.area is for the ?h.white surfaces and the ?h.area.pial
is for the pial ones.
cheers
Bruce
On Thu, 12 Jul 2012, Schur, Remmelt R.
wrote:
Dear Freesurfers,
I've been looking at the attri
Hi Gabriel,
certainly they won't match as (a) they are different algorithms, and (b)
they are different definitions of what is and is not included. Did you
sum up things like fimbria and fornix in your subfield totals?
cheers
Bruce
On Thu, 12
Jul 2012, Gabriel Gonzalez Escamilla wrote:
>
> H
Hi Peter
because you are adding control points to voxels that are already
accurately segmented (before you added them) I think your problem is a
topological defect that is being fixed incorrectly. You can see this is you
load the ?h.orig and it doesn't follow the wm.mgz. Since you don't know
Hi Bruce,
It appears as if the ?h.orig.nofix file has properly delimited the white
matter surface, where the ?h.orig file has not. What makes me dubious of
there being a topological issue at hand is that I have already tried out
the typical fixes for topological issues, and they've had no positive
PS you can ignore the increase in CP's in the post-fixes version (I had
added them as a bit of experimental troubleshooting yesterday)
On Thu, Jul 12, 2012 at 4:07 PM, Peter McNally wrote:
> Hi Bruce,
>
> It appears as if the ?h.orig.nofix file has properly delimited the white
> matter surface, w
Hi Simon
I'm also puzzled about your "quantitative T1 maps". Are these T1 values
in ms? If so, the image won't have "T1-weighted contrast" as WM will be
darker (shorter T1) than GM, in which case everything would fail. I assume
that what you are going to FreeSurfer (and Avi's code) is instead t
Hi Peter
I can see a bunch of defects immediately. For example, you need to add
voxels such as
155, 162, 145
154 162 146
adding just 3 or 4 voxels to the wm will correct this problem. If you bring
the ?h.orig up over the wm.mgz and they don't match, it means there *must*
be a topological de
p.s. there's another one caused by spurious connections that needs to be
erased, for example voxels such as:
101, 149, 132
and add some around
100, 162, 141
On Thu, 12 Jul 2012, Peter McNally
wrote:
Hi Bruce,
It appears as if the ?h.orig.nofix file has properly delimited the white
matter
Hello
I typed in the command for multiple comparison:
$ mri_glmfit-sim --glmdir rh.tp1_mnp_ltm_age_T1.H.Unp.Int.glmdir
--cwpvalthresh 0.05 --cache 2.0 pos
It starts to process, but there is an error (see below). How do I fix this?
Thanks,
Jenny
mdline mri_glmfit --y rh.tp1_mnp_ltm_age_T1.H.Unp.
Also, in addition to the mri_glmfit-sim command,
I have already run the mris_preproc, mri_surf2surf, and mri_glmfit before
typing mri_glmfit-sim. Did I miss a step? Do I need to update an app?
Thanks,
Jenny
On Thu, Jul 12, 2012 at 3:28 PM, Jenny Liu wrote:
> Hello
>
> I typed in the command fo
Has anyone created an AAL label file for Freesurfer? I've done some
ROI analysis using AAL regions and want to display regional values on
the freesurfer surface.
Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospi
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