selfreqavg has been incorporated into selxavg3.m (called by
selxavg3-sess). But the ideas are still the same, just setting up a sine
and cosine at the fundamental and estimating the amplitude using a GLM.
doug
Michelle Umali wrote:
> Hi Jon,
> Thanks!
>
> I have a question about when selfreqavg.
you need to map your T1 template to fsaverage (probably using
bbregister). Then call tkmedit or tksurfer with a --reg file (see the
multimodal integration tutorial). BTW, you should not confuse this with
doing a surface-based analysis.
doug
Ritobrato Datta wrote:
> Hi Doug,
>
> This email over
Have you tried using mri_annotation2label with the --seg output option?
doug
Michael Waskom wrote:
> If you know Python, you can likely do this pretty easily with tools
> from the PySurfer package: http://pysurfer.github.com/
>
> (Check out surfer.io.read_annotation).
>
> If you're just using th
Yes, that looks correct. Since you have a covariate as a nuisance
variable, you should first run your analysis with a DODS model
(different-offset, different-slope) and look for an interaction between
your group variables and age (the contrasts are similar, swap the first
6 numbers with the las
Hello,
How can I describe the method for WM hypointhensities segmentation and volume calculation?
Can you suggest a reference?
Thank you, Carolina
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I'm using QDEC to analyze cortical thickness differences between groups and
I have a few questions:
1) There are a few variables that I need to control for. First variable is
scanner - I used two different scanners of different field strengths (1.5T
GE and 3T Siemens) so I wanted to control for sc
Hi Carolina,
the one that is the distributed version of freesurfer now uses the same
algorithm as the rest of the aseg labels except that no constraints on
connectivity/topology are applied. We are working on a new method that uses
multispectral (T2/PD/FLAIR) inputs and is considerably more acc
Hi - After upgrading my total RAM to 12 gb (from 6) I am continuing to run into
memory allocation problems running tracula preproc and paths with the error
messages as follows:
1. preproc error
Loading cortex mask from
/usr/local/freesurfer5.1/trctrain/trc010/dlabel/mni/cortex+2m
Hi Ammar - You mentioned that you were able to run things fine on another
computer with 16 Gb of RAM. How much memory was being utilized on that
computer by these processes (dmri_train and dmri_paths)?
a.y
On Tue, 11 Oct 2011, Moiyadi, Ammar wrote:
> Hi - After upgrading my total RAM to 12 gb
Hi:
When I finish white matter editing and try to save the edited main volume
by "Save Main Volume" of the "File" menu on TKMedit Tools window, there is a
dialogue asking me:"Are ou sure you wish to save the changes to the main
volume". When I clicked yes, error message appeared as follows:" Error
what is the main volume you are trying to save? If it's not "conformed"
(i.e. 256^3 and 1mm isotropic, 8 bits/voxel) tkmedit probably isn't the
right tool. In this case, try using freeview
Bruce
On Wed, 12 Oct 2011, Wei-Ta Chen wrote:
Hi:
When I finish white matter editing and try to save
Hello,
I'm having similar issues with a 1.5T data set from here that used a
custom head coil. The talairach transforms are skewed and scaled
incorrectly. Some are not correctable by tkmedit as the movable is too
skewed (almost to a rhomboid shape). I'm fairly new to freesurfer so any
suggestions w
I'm using the labels saved in QDEC to extract cortical thickness values for
certain regions. For example, I've used the lh.v1.label to map onto the
fsaverage brain and then to map this onto each individual subject. When I
load the lh.PALS_B12_Brodmann.annot or the lh.PALS_B12_Visuotopic.annot onto
Hi - dmripaths used about 30 percent of the 16gb at max and than lowered to 6
percent. Dmri train uses about 25 percent of the 16gb throughout its process.
Would running the 32bit version of freesurfer have something to do with the
problem? I have a PAE kernel installed to take advantage of the
What version are you running?
On Oct 11, 2011, at 4:21 PM, "James Sheehan" wrote:
> Hello,
>
> I'm having similar issues with a 1.5T data set from here that used a
> custom head coil. The talairach transforms are skewed and scaled
> incorrectly. Some are not correctable by tkmedit as the mova
I tried converting and recon-all using Freesurfer on a Linux installation and
it works fine.
I have no idea what went wrong with the virtualbox, but it works for me now.
All thanks for the help :)
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Hmmm, can you upload a couple of examples?
On Oct 11, 2011, at 6:44 PM, Warren Winter
wrote:
> Here's one that mislabeled parts of the CC as left cerebral white matter at
> the center slice:
>
>
> Another one mislabels nearly the entire CC at the center slice:
>
>
>
> You can see the l
Glad it worked out, but try to avoid analyze if you can!
Cheers
Bruce
On Oct 11, 2011, at 9:44 PM, "m.vlutters" wrote:
>
> I tried converting and recon-all using Freesurfer on a Linux installation and
> it works fine.
>
> I have no idea what went wrong with the virtualbox, but it works for
Dear Freesurfers,
I've generated individual polar, eccentricity, and fieldsign maps for each
of my subjects. I would like to generate group average maps of these that I
can visualize on the fsaverage brain.
When I ran:
isxconcat-sess -sf sessid -analysis rtopy.self.lh -o group_lh
I got:
ERROR: an
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