Dear guys,
Could I ask which value in the stats/aseg.stats represents the volume of
the cerebrum (including the subcortical structures while excluding the
ventricles and brain stem)? I'm not sure whether the
"SupraTentorialNotVent" can be the value for this measurement, and could it
be a bit bigge
Dear experts,
Could I ask which value in the stats/aseg.stats represents the volume of
the cerebrum (including the subcortical structures while excluding the
ventricles and brain stem)? I'm not sure whether the
"SupraTentorialNotVent" can be the value for this measurement, and could it
be a bit bi
Dear FS experts,
Could I ask which value in the aseg.stats file represent the whole cerebral
volume without ventricles?
Thanks,
Kaiming
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurf
Dear FS guys,
I have run the FS 5.3 and get thickness files e.g. lh.thickness and
rh.thickness, could FSL read these? should we use files like nii instead of
mgz, or is there some options for FSL to read mgz too?
Thanks,
Kaiming
___
Freesurfer mailing l
Hi Bruce,
Yes I get the file rh.thickness.nii.gz, however it seems fs or fsl or
imagej can not open it directly, should I add something?
cheers,
Kaiming
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/
m. What is the aseg like? The
> 3rd one looks ok, but I'm not positive that I understand what you are
> pointing at. The surface will not track subcortical gray matter, only
> cortical
>
>
> On Wed, 4 Dec 2013, Kaiming Yin wrote:
>
> Dear Bruce,
>> that sounds good. H
:
> it's a surface overlay (so one value per vertex), not a volume. You will
> probably want to use mri_surf2vol to sample it into the volume if you want
> fsl to open it
>
> On Wed, 4 Dec 2013, Kaiming Yin wrote:
>
> Hi Bruce,
>> Yes I get the file rh.thickness.nii.g
Hi,
A little confusion here, when I add the control points after edits, should
I run -autorecon2 or -autorecon2-cp?
Another question is about the starting stage of autorecon2-cp, i.e. stage
10+ or stage 12+, which are stated differently on the wikipage and
tutorial.
Happy New Year!
Thanks,
Kaim
Dear FreeSurfer guys,
I am using longitudinal processing stream and with the
RepeatedMeasuresAnova.
I follow the instruction here from
http://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova
my fsgd file is:
GroupDescriptorFile 1
Title k_longitudinal
Class k
Variables TP1-vs-TP2 TP1-vs-T
r data was probably mapped to fsaverage when you call the preproc or
> surf2surf commands? If so you should specify fsaverage as the subject nane.
> Best Martin
>
>
> Sent via my smartphone, please excuse brevity.
>
>
> Original message
> From: Kaiming Yin
he study, because that may introduce a
> processing bias towards that subject (maybe the thickness changes of that
> subject will drive the results or bias it). That is why fsaverage is
> recommended.
>
> Best, Martin
>
>
> On 01/30/2014 06:13 AM, Kaiming Yin wrote:
>
> D
iming
On Thu, Jan 30, 2014 at 6:46 PM, Martin Reuter
wrote:
> Hi Kaiming,
>
> thickness is not a surface, it is a function defined on a surface. Don't
> add it as a surface name to the command line.
>
> Best, Martin
>
>
>
> On 01/30/2014 11:12 AM, Kaiming
Dear guys,
Is there some way to have a more detailed look of the recent changes on the
FreeSurfer Wiki page? I click on the recent changes option but can only see
the latest 13 updates within around 10 days. Could I have a check of that
from further past days?
Thanks a lot,
Kaiming
__
t certain you are right at the medial line and what you are
> seeing is the transition from one hemi to the other. Most likely the brain
> is slightly oblique and so the sagittal slice does not perfectly bisect the
> two hemispheres.
> -Louis
>
>
> On Mon, 10 Mar 2014, Kaim
Dear guys,
I was doing group analysis (command-line) on two groups (patients and
control, no age or other information). The data has been "qcached", and
after following the three steps as "mris_preproc, mri_glmfit and
mri_glmfit-sim" shown in the tutorial on the Freesurfer website, I obtained
the
Dear guys,
I checked one of my subjects file /stats/lh.aparc.stats, in which it said
the commandline as:
mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f
../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c
../label/aparc.annot.ctab subject1 lh white
what does the flag "-t
--C
group_diff.mtx --surf fsaverage rh --cortex --glmdir rh.ad_hv.area.glmdir
mri_glmfit-sim --glmdir rh.ad_hv.area.glmdir --cache 4 neg --cwp 0.05
--2spaces
Their results were all the same.
Thanks,
Kaiming
On Sat, Mar 5, 2016 at 2:01 AM, Kaiming Yin
wrote:
> Dear guys,
>
> I was do
parc.annot.ctab subject1 lh white
mris_anatomical_stats-mgz -cortex ../label/lh.cortex.label -f
../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c
../label/aparc.annot.ctab subject1 lh white
Thanks,
Kaiming
On Sun, Mar 6, 2016 at 7:53 PM, Kaiming Yin
wrote:
> Dear guys,
>
ing, can you include my previous correspondence with your email?
>
>
> On 03/08/2016 05:48 PM, Kaiming Yin wrote:
>
>> Dear Douglas,
>>
>> My command lines were, e.g. right thickness and right white surface
>> (using the same ad_hv.fsgd and group_diff.mtx file
d on Anderson M. Winkler's
srf2vol matlab script.
\params w is white surface, p is pial. Output is an MRI struct of size
nvertices
*/
On Sun, Mar 6, 2016 at 7:53 PM, Kaiming Yin
wrote:
> Dear guys,
>
> I checked one of my subjects file /stats/lh.aparc.stats, in which
@nmr.mgh.harvard.edu
Cc:
Date: Mon, 7 Mar 2016 18:47:11 -0500
Subject: Re: [Freesurfer] group analysis all measures same results
what are your command lines?
On 5 March 2016 at 02:01, Kaiming Yin wrote:
> Dear guys,
>
> I was doing group analysis (command-line) on two groups (patients and
> con
then check whether thickness.fwhm10.fsaverage and
> area.fwhm10.fsaverage are the same in each subject
>
>
> On 3/14/16 10:53 AM, Kaiming Yin wrote:
>
> Dear Douglas,
>
> My command lines were, e.g. right thickness and right white surface (using
> the same ad_hv.fsgd an
Dear guys,
Could I ask in the process of each individual data, are the volumes in the
aseg.stat file or other files in the stats/ folder based on the 001.mgz
data or the nu.mgz data, or others? It seems there is a bit transformation
from the 001.mgz to the nu.mgz, is this true? And will this trans
n of version 6 and things will change.
>
>
> On 03/15/2016 01:56 PM, Kaiming Yin wrote:
>
>> Dear Douglas,
>>
>> Is there anything I can do now to fix this now? I don't want to re-run
>> all the data again.
>>
>> Thanks,
>> Kaiming
>>
&g
ou used. That was a beta version of version 6 and things will change.
>
>
> On 03/15/2016 01:56 PM, Kaiming Yin wrote:
>
>> Dear Douglas,
>>
>> Is there anything I can do now to fix this now? I don't want to re-run
>> all the data again.
>
Dear guys,
Is there a file of "FreeSurferColorLUT.txt" available in the Freesurfer
folders, or should I copy/paste the texts to a .txt file directly from the
FS website?
Also, is there a way to transform this LUT table to enable it to be loaded
into ImageJ, or can it work directly well in ImageJ?
-- Forwarded message --
From: Kaiming Yin
Date: 1 July 2016 at 11:15
Subject: Cerebral (without ventricles) Volume = aseg.stats /
SupraTentorialNotVent ?
To: FreeSurfer Mailing List
Dear guys,
Could I ask which value in the stats/aseg.stats represents the volume of
the
27 matches
Mail list logo
