Hi FS experts and users
I have done the each subjects' surface regestration on fsaverage surface, and
merge all of them into a *.mgh. Group analysis is also completed.
Now I have two questions:
1,I want to extract the VtxMax vertex number thickness for all subjects. The
VtxMax vertex number can
You should try to run recon_all command with -all flag to run on the
structural T1 dataset. After that you can use the tutorials from the
freesurfer wiki to do a Feat analysis.
For recon_all you need to specify only the subject and the script
automatically does the rest. Segmentation and parcellat
Hi Sampada
the recon-all script is designed to analyze T1-weighted structural data.
Once that has been done, it can be used to facilitate fMRI analysis. Is
that what you are trying to do? What are the 8 volumes?
cheers
Bruce
On Fri, 9 May 2014, Dr Sampada Sinha wrote:
Hello Freesurfer,
Th
Hello Freesurfer,
Thanks Shantanu I was able to convert the .nii to .mgz files . However,
about the recon-all command do I run it separately for each .mgz file or
run it one time for all .mgz file(which are eight in numbers)? And what
command do I use for recon-all? I have tried many but none is w
Hi Gabor,
sorry, I still don't know what you mean. The volume estimates in aseg.stats
do include partial volume estimates. Do you mean to include only the volume
of a structure that comes from partial volume voxels? Would that really be
useful? For something like the hippocampus it will be a lo
Hi Jodie,
'years' should contain the real time between time points (usually,
unless you have test-retest where time is irrelevant, or different task
that can be ordered as you like). For what you are trying to do you
should use linear mixed effects models with a piecewise linear setup.
This wi
Dear Bruce,
I think of a file which also shows the partial volume estimates for
the segmented structures.
Thanks,
Gabor
2014-05-07 22:31 GMT+02:00 Gabor Perlaki :
> Dear Bruce,
>
> Is there a file generated by freesurfer which stores the subcortical
> segmentations together with the information
Hi Tudor,
the longitudinal pipeline in FS is actually one of the best on the
planet as far as I know :-). If there is any contradictory information
on the wiki, can you point me to that so I can see what causes the
misconception. Really: compared to independent processing, it
significantly in
Doug,
Thank you for the response. You are correct in that it was originally in
native EPI space. I'll try out your suggestions.
Cheers
On Fri, May 9, 2014 at 1:51 PM, Douglas N Greve
wrote:
>
> What space is the RS data in? If native functional space, I would
> register to the anatomical (bbre
What space is the RS data in? If native functional space, I would
register to the anatomical (bbregister), then use mri_vol2vol with the
--fstal option
On 05/08/2014 04:31 PM, Paul Beach wrote:
>> Hi Freesurfers,
>>
>> I have several processed resting time series files (processed through
>> AF
Thanks, it works fine now, i missed that update.
Best,Elia.
Date: Fri, 9 May 2014 11:24:02 -0400
From: ayend...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Freesurfer-Tracula Error
Hi Elia - This issue was fixed in the last update:
http://surfer.nmr
Hi Elia - This issue was fixed in the last update:
http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula/#Updates
FYI, there will be another tracula update soon (after ISMRM) that will
further improve the longitudinal stream specifically.
a.y
On Fri, 9 May 2014, Elia S. wrote:
Dear Free
Probably Emil¹s current example would be best because it is failing in
your recon-all setup.
Matt.
On 5/9/14, 9:31 AM, "Bruce Fischl" wrote:
>Hi Matt
>
>if you can send me an example I'll try to find time to take a look
>Bruce
>On Fri, 9
>May 2014, Matt Glasser wrote:
>
>> Hi Bruce,
>>
>> For
Hi Greg
I would probably say the reverse. In general mprage is optimal for
CNR/unit time in terms of gray/white contrast. Flash has some advantage
for e.g. distinguishing pallidum from putamen, but you would need to modify
our recon stream to take advantage of them
cheers
Bruce
On Thu, 8 May
Hi Peng
the flat maps are stored in a different format than the surfaces, called
a "patch" format (since they are only a piece of the whole surface - not
the entire thing). You can load them with file->load patch in tksurfer. Not
sure about freeview, perhaps Ruopeng can comment?
cheers
Bruce
Hi all,
I am trying to run 2x3 factorial model correcting for age, sex and intracranial
volume. Just to give you insight in my data I have my fsgd file as
GroupDescriptorFile 1
Title DODS analysis 2x3 factorial
Class MaleGroup1Low
Class MaleGroup1Medium
Class MaleGroup1High
Class MaleGroup2Low
Cl
Hi Bruce,
For whatever reason, sometimes the T2w surface adjustment will be way off.
Adjusting the -nsigma_above <#> -nsigma_below <#> even a little bit up and
down can get it out of the minimum and make it work, so there might be a
bug.
Peace,
Matt.
From: "Emil H.J. Nijhuis"
Reply-To: Fre
Hi Matt
if you can send me an example I'll try to find time to take a look
Bruce
On Fri, 9
May 2014, Matt Glasser wrote:
Hi Bruce,
For whatever reason, sometimes the T2w surface adjustment will be way off.
Adjusting the -nsigma_above <#> -nsigma_below <#> even a little bit up and
down can g
Dear Doug,
I have read this post(
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg25218.html)
regarding
extracting Mean Cth of each hemisphere and I just get insula as the last
and totally 34 numbers, I use
aparcstats2table --hemi lh --subjects bert -m thickness --tablefile
lh.Cth.be
Dear Freesurfer Staff,
I encountered the following error while running tracula - longitudinal:
ERROR: flag ; unrecognized
The exact command line i ran is the following one:
trac-all -prep -c
'/home/elia/scripts/Tracula/LCL/dcmTimePoints_tar-2/tracula.config'
I will attach the complete erro
More information, error from tksurfer is as following:
MRISalloc(16711682, 480): could not allocate vertices
Cannot allocate memory
-- Forwarded message --
From: peng
Date: Fri, May 9, 2014 at 1:01 PM
Subject: a question on flat surface
To:
Hi Freesurfers,
I have tried to obtain a flat surface as described by the upper part
(full cortex) of the following page:
http://freesurfer.net/fswiki/FreeSurferOccipitalFlattenedPatch
However, I failed to load the results in freeview (it took forever), nor
can I read in matlab with rea
Dear all,
For the evaluation of the subcortical volumes we executed ‘mri_segstats’ on
‘aseg.mgz’ and for comparison on ‘aparc+aseg.mgz’ in a number of individuals.
Apparently the volume of subcortical structures, like the hippocampus, is
calculated as the same values if calculated (without part
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