Dear All,
I wanted to check that corrections to a Long pial surface through edits to
brainmask.mgz and brain.finalsurfs.manedit.mgz are followed by the command:
recon-all -long tpN1 templateID -autorecon2-pial -autorecom3
Is this correct?
Also, after editing the Long aseg.mgz to correct the vo
Hi experts,
I've used the command mri_vol2surf with the --projfrac 0.5 flag to sample a
volume halfway between the pial and white matter surfaces.
I was wondering if there was a way to visualise where this surface lay on
the volume? Ideally I'd like to show a figure with the pial, white and this
Dear all,
I’d like to know if there are any differences in the way that the auditory
cortex regions of interest are segmented between freesurfer versions 5.0 to
5.3. Do all version provide output for the below three ROIs, and are the
atlases used for this (both the default and the Destrieux) u
Dear Freesurfer experts,
I am working with the longitudinal stream and have come across medially
crossing pial surfaces in the base of a few participants. I tried editing the
aseg.mgz file and then running the process again with the -noaseg flag but that
didn't help. It also seems that in the a
No, if you don't explicitly pass it the --wls flag, then a standard
random effects (ordinary least squares) is used.
doug
On 4/20/15 12:43 AM, ye tian wrote:
Dear Doug,
I don't understand what you mean by "the variance of the fMRI time
series". I fed Freesurfer only structural MRI data. Does
I'll leave the first question for Martin but it looks right to me
(except for the typo in what should be "-autorecon3"). For the second one I
think you want to rerun the mri_segstats and mris_anatomical_stats
commands, which should be done by autorecon3
cheers
Bruce
On Mon, 20 Apr 2015, pras
Hi Kirstie
you can do this with mris_expand. For example:
mris_expand -thickness lh.white 0.5 lh.graymid
will generate a surface halfway between white and pial. Using that surface
to sample is probably a better method than using profrac, although I expect
the differences will be small unless
Yes
doug
On 4/19/15 7:23 PM, Bronwyn Overs wrote:
Hi Doug,
Sorry I am not sure that I understand. Does the --y file contain all
of the values for each individuals subject, mapped to the fsaverage image?
Kind regards,
Bronwyn Overs
Research Assistant
Neuroscience Research Australia
Neurosc
Hi Narly
I don't think any of those labels changes, but the surface-based
registration has changed a bit which will change how they are mapped onto
individuals
cheers
Bruce
On Mon, 20 Apr 2015, Narly Golestani wrote:
Dear all,
I’d like to know if there are any differences in the way tha
I can't remember for afni. For BBR, it is the center of the anatomical
volume.
On 4/17/15 5:54 AM, pfannmo...@uni-greifswald.de wrote:
> Hello Doug,
>
> just a very last question. Where ist the origin of the coordinate system if
> the motion parameters are calculated using mc-afni2 and where is
Try something like this. Run mri_vol2vol with --help to get info about
each of the flags
mri_vol2vol --mov $invol --reg $reg \
--tal --talres $res --talxfm $talxfm --interp $interp \
--no-save-reg --o $outvol
On 4/15/15 10:03 AM, Xiaomin Yue wrote:
Because resampling from 1.5 to
That is what the --seg-erode is supposed to help with.
On 4/15/15 10:05 AM, Thomas Potrusil wrote:
thanks, it´s working like you suggested!
I´m wondering if you have any idea how I can minimize this effect
within subcortical areas since, you´re right, DTI space has bigger
voxels. I´m thankful
Hi Sara
For those analysis Iwent through the following steps:
First considered afull model for both the mean and the covariance and selected
the bestmodel for the covariance:
1- Fitted a fullmodel (model1) including intercept, time and time squared as
bothfixed effects and random effects.2- Sepa
Hello,
I am having a problem with optseq2, where the final NULL event is given a
much longer duration than the rest of the events. This happens even if I
set tnullmax to a lower number- for example, I set tnullmax to 10 seconds,
and the final interval came out at 48 seconds. Do you know how to res
Can you try using this version of optseq?
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/optseq2
I changed some things that might fix this problem. I ran the command
line below with it, and it gave reasonable results for the last null.
On 4/20/15 1:22 PM, Dan Goldman wrote:
H
Hi Douglas,
Thank you for the quick response.
Could you tell me which version of optseq this is? Are there multiple
versions of optseq2?
On Mon, Apr 20, 2015 at 1:31 PM, Douglas Greve
wrote:
>
> Can you try using this version of optseq?
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/
This is the most recent version, the one that will be part of FS version 6.
On 4/20/15 1:40 PM, Dan Goldman wrote:
Hi Douglas,
Thank you for the quick response.
Could you tell me which version of optseq this is? Are there multiple
versions of optseq2?
On Mon, Apr 20, 2015 at 1:31 PM, Dougl
I am having some trouble using this version- when I try to use it in
Terminal, it returns "Permission denied." Is there something I need to do
to be able to use it on my computer?
Thanks for your help.
On Mon, Apr 20, 2015 at 1:50 PM, Douglas Greve
wrote:
>
> This is the most recent version, the
chmod a+x optseq2
On 4/20/15 2:13 PM, Dan Goldman wrote:
I am having some trouble using this version- when I try to use it in
Terminal, it returns "Permission denied." Is there something I need to
do to be able to use it on my computer?
Thanks for your help.
On Mon, Apr 20, 2015 at 1:50 PM,
When I try that I get the error "cannot execute binary file".
On Mon, Apr 20, 2015 at 2:46 PM, Douglas Greve
wrote:
> chmod a+x optseq2
>
>
>
>
> On 4/20/15 2:13 PM, Dan Goldman wrote:
>
> I am having some trouble using this version- when I try to use it in
> Terminal, it returns "Permission de
Nevermind, I got it to work! Thanks for your help.
On Mon, Apr 20, 2015 at 2:51 PM, Dan Goldman wrote:
> When I try that I get the error "cannot execute binary file".
>
> On Mon, Apr 20, 2015 at 2:46 PM, Douglas Greve
> wrote:
>
>> chmod a+x optseq2
>>
>>
>>
>>
>> On 4/20/15 2:13 PM, Dan Goldm
It seems that I am unable to run the file that you sent on a mac- is it a
different version from the one available for MacOSX here?
https://surfer.nmr.mgh.harvard.edu/optseq/
On Mon, Apr 20, 2015 at 2:53 PM, Dan Goldman wrote:
> Nevermind, I got it to work! Thanks for your help.
>
> On Mon, Apr
Hi P,
usually edits to surfaces should not be required in the long. The
surfaces there get initialized from the base, so you need to make sure
the base surface is as accurate as possible. Several edits also get
transferred automatically from the cross sectional runs. See this
http://freesurfe
Dear Doug,
Does that mean that an OLS is automatically performed for sMRI images?
Thank you very much!
Sincerely,
Ye
On Mon, Apr 20, 2015 at 8:44 AM, Douglas Greve
wrote:
> No, if you don't explicitly pass it the --wls flag, then a standard
> random effects (ordinary least squares) is used.
Hi Rachel
looks like the intensity normalization failed, although there might have
been an earlier failure that caused it. Have you checked the
talairach.xfm? If you can't figure it out, upload the subject dir and we
will take a look
cheers
Bruce
On Mon, 20 Apr 2015, Rachel Jonas wrote:
> Hi
Yes
On 4/20/15 3:38 PM, ye tian wrote:
Dear Doug,
Does that mean that an OLS is automatically performed for sMRI images?
Thank you very much!
Sincerely,
Ye
On Mon, Apr 20, 2015 at 8:44 AM, Douglas Greve
mailto:gr...@nmr.mgh.harvard.edu>> wrote:
No, if you don't explicitly pass it the
Hi
so take a look at
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData
where the entry points are described ( for brainmask and finalsurfs
-autorecon-pial should be OK, for aseg it says to use
-autorecon2-noaseg )
Also this page
https://surfer.nmr.mgh.harvard.edu/fswiki
Thanks Jorge!
In our case, at step 4, an F-test does show significant evidence for a
quadratic term, but not across the whole brain. We have a strong hypothesis
that there should be a time effect (linear or quadratic) across most of the
brain, and it makes sense that some regions will show line
Hello,
I have a question re: calculations of efficiency and vrf in optseq2.
We are running two tasks. One is a reasoning tasks, with trial lengths of
12 seconds. The other is an embedded figures task with trial lengths of 10
seconds. For both tasks, we have set a minimum ISI of 4 seconds and a
maxi
Thank you for your reply.
Yes, I'm finding that it is only small edits that are required in the Long for
the case of pial surface errors. It is usually in areas where no editing was
required in the cross and base, but the pial surface in the Long extends to
include dura or cerebellum. I was ho
Thank you again for your reply.
For editing aseg.mgz, as mentioned in
https://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide/TkMeditWorkingWithData/FreeviewSegmentations
it does suggest using -autorecon2-noaseg, but from what I can see this does
not update the aparc+aseg.mgz and associated .sta
On 4/20/15 5:45 PM, Dan Goldman wrote:
Hello,
I have a question re: calculations of efficiency and vrf in optseq2.
We are running two tasks. One is a reasoning tasks, with trial lengths
of 12 seconds. The other is an embedded figures task with trial
lengths of 10 seconds. For both tasks, we h
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