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To the best of my knowledge, there is not way to tell recon-all about
demographics/subject meta data, and you do not need to worry about this during
recon-all. Instead, you would add age and gender as covariates in your model
later.
Tim
> On August
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Dear freesurfers,
I ran the retinotopy pipline (like preproc-sess, mkanalysis-sess,
Selxavg3-sess) and now I want to view the results with tksurfer.
When I call tksurfer inflated and try to overlay
the reall.nii.gz and imag.nii.gz, I need to choose
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Hi Freesurfer folks,
I'm running Freesurfer's longitudinal pipeline as part of FMRIprep and I've
got two subjects generating similar errors in the mri_robust_template step,
one of which I've copied below. I've defaced these subjects and saved the
worki
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Hello FreeSurfer Developers,
I'm attempting to run some of data with recon-all code, and after some
success run on several data, now I get the following error message even
when I run those data that ran well before:
nu_evaluate: crashed while running e
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Dear all,
my intention is to use the Brainnetome Atlas parcellation/segmentation in
PETSurfer to obtain PVC corrected SUVRs for the atlas ROIs. I used:
gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab
'/media/XYZ/BN_Atlas_freesurfer/
I have not seen that error before. Have you checked the images to make
sure there is nothing strange about them? Eg, some type of artifact?
On 8/13/19 8:12 AM, Z Hessam wrote:
>
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>
> Hello FreeSurfer Developers,
> I'm attempting to run some of data with recon
I don't know that there is much you can do. The PVR is very
computationally intensive, and it does not surprise me that it is taking
a long time. I don't think you need to do 10k permutations. I would
start with 1k. In the output, you will get a confidence interval for the
corrected p-value. Th
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Dear experts,
I have segmented hippocampus into 13 subfields using FS6.0. Then, I want to
study the function connectivity between sibfields. How can I utilize this
template to do this research? Is it possible? Thanks for your reply in advance.
Sinc
I don't know what the Brainnetome is, but it looks like you have it in
annotation form. I think that command should work. Why are you using
--no-xcerseg? This will cause it to not include extracerebral
structures. Also note that you cannot use arbitrarily small segments
when doing PVC.
On 8/13
I think those should be already sampled on the surface, so you should
not need a registration file
On 8/13/19 5:09 AM, Hang Zeng wrote:
>
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>
> Dear freesurfers,
> I ran the retinotopy pipline (like preproc-sess, mkanalysis-sess,
> Selxavg3-sess) and now I wa
You can use mri_surfcluster. That actually has an --fdr flag, so you
should not need to run mri_fdr. When you use --fdr, you do not use
--thmin. Use --sum to get the summary file
On 8/13/19 10:50 AM, miracle ozzoude wrote:
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>
> Thanks a lot doug. I want to
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Thank you for your prompt answer - the command worked. This is the atlas
mentioned: http://atlas.brainnetome.org/brainnetome.html
What is approximately the smallest possible segment when using PVC?
Also, does the exclusion of extracerebral structures ha
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Hi!
I am having difficulties setting the timewindow parameter in
mkanalysis-sess in Freesurfer v5.3.
I am trying to use 80 (data acquired with MION), but the parameter does not
seem to affect analysis.info, where it is always 40.
Is it possible to force
There is no cut off for the minimum size. As it gets smaller, the PVC
noise amplification will become bigger (it also depends on the shape as
well).
I think the --no-xcerseg is the right way to go now
On 8/13/19 11:00 AM, Boris Rauchmann wrote:
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>
> Thank
When you use -gammafit, it automatically sets the time window to 40. If
you really want it at 80, but -timewindow before -gammafit. Do you
really expect the MION hrf to last 80 sec?
On 8/13/19 11:06 AM, Caspar M. Schwiedrzik wrote:
>
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>
> Hi!
> I am having d
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Alright, thanks!
On Tue, Aug 13, 2019 at 5:10 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:
> There is no cut off for the minimum size. As it gets smaller, the PVC
> noise amplification will become bigger (it also depends on the shape as
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Hi,
I am conducting a meta-analysis on papers that have looked at local
gyrification index (lGI) in Autism Spectrum Disorder (ASD) relative to
typically developing (TD) peers.
All lGI papers have used the FreeSurfer software and have reported x,y,z
co
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Hi Doug,
Thanks for the advice.
I think the Leite et al. 2002 NeuroImage paper can be interpreted that way.
See Figure 1 and 2.
http://pop.cerco.ups-tlse.fr/pdf0609/leite_fp_02_283.pdf
Caspar
On Tue, Aug 13, 2019 at 17:12 Greve, Douglas N.,Ph.D. <
dgr
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Ok thank you. Would using the qdec table help in this case?
-Carissa
On Tue, Aug 13, 2019 at 1:03 AM Tim Schäfer wrote:
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>
> To the best of my knowledge, there is not way to tell recon-all about
> demographics/s
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Hi Doug,
All maps were smoothed before starting the analyses. But I think that because
of running some of the analyses in R (incl bootstrapping), they do look a bit
patchy when zooming in.
This resulted in a huge amount of clusters. But I managed to s
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Hello,
The Ohio State Clinical Neuroscience Laboratory directed by Dr. Ruchika
Prakash is seeking to hire a Research Assistant (RA). Please see attached
document for full description.
Best Regards,
The Clinical Neuroscience Laboratory
[image: The Oh
That is in response to a 60 sec stimulus. The time window is the time
needed to account for a very brief stimulus (ie, the impulse response).
fsfast will automatically take into account the duration of the stimulus
as listed in the paradigm file.
On 8/13/19 2:14 PM, Caspar M. Schwiedrzik wrote:
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Hello,
I reached out the other day about if there was a way to specify the data is
from a specific gender or age during the recon all code, such as a tag at
the end. I was told that there is not way to tell recon-all about
demographics/subject meta dat
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Dear Freesurfer experts,
I did find another message with the same error (
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg40379.html)
where you ask if the versions are the same. They are for me. I had also
already run this command, but
Those coordinates are in mni305 space. See this page, case 8
https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
On 8/13/19 1:56 PM, Avi Gharehgazlou wrote:
>
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>
> Hi,
>
> I am conducting a meta-analysis on papers that have looked at local
> gyrifica
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