I think eroding the region makes sense in general - you just have to be careful
to exclude subjects who end up with no data (as you discovered!)
You could also look into why these three subjects had such small wm regions
under entorhinal cortex. My (still) suspicious mind wonders if there is a b
Hi Sampada
the problem isn't the oblique orientation it is the resolution (too low!)
and contrast (not enough!). Can you give us the details of the scan?
Resolution, type, etc?
cheers
Bruce
On Fri, 25 Mar 2016, Dr Sampada Sinha wrote:
Hello Bruce,
Please find enclosed snapshots of actu
mri_concat subject1/lh.thickness.fsaverage.mgh subect2/lh ... --mean --o
lh.thickness.fsaverage.mean.mgh
On 03/24/2016 07:24 PM, Sahil Bajaj wrote:
> Hello FreeSurfer community,
>
> I calculated cortical thickness for 100 controls following the
> instructions described here:
> https://surfer.n
I'm new to FreeSurfer. Trying to do volumetric analysis on MPRAGE data but
on half of the studies the results are poor. Specifically, the gray matter
volume is very small due to a poor segmentation of the white matter which
includes much of the cortical gray matter. The contrast to noise is good
Hello Bruce and Douglas,
This is what my design looks like.
GroupDescriptorFile 1
Class Group1
Class Group2
Variables Age Firstsessionscore
Input subj1 Group1 72 0.76
Input subj2 Group1 67 0.43
Input subj3 Group2 80 1.23
The contrast matrix i used was [0 0 0 0 0.5 0.5]. I am writing to investigat
what was your mri_glmfit-sim command line?
On 03/25/2016 02:00 PM, Miracle Ozzoude wrote:
> Hello Bruce and Douglas,
> This is what my design looks like.
> GroupDescriptorFile 1
> Class Group1
> Class Group2
> Variables Age Firstsessionscore
> Input subj1 Group1 72 0.76
> Input subj2 Group1 67 0.4
mri_glmfit-sim --glmdir lh.firstsessionscore1.glmdir --cache 3 pos
--cwpvalthresh 0.05 --2spaces
From: Douglas N Greve
Sent: March 25, 2016 6:05 PM
To: Miracle Ozzoude; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] whole hemisphere is yellow
not sure what is happening. Can you tar up the glmfit folder and send it to me
at our file drop?
https://gate.nmr.mgh.harvard.edu/filedrop2
On 03/25/2016 02:09 PM, Miracle Ozzoude wrote:
> mri_glmfit-sim --glmdir lh.firstsessionscore1.glmdir --cache 3 pos
> --cwpvalthresh 0.05 --2spaces
>
On 03/24/2016 07:37 PM, Joseph Dien wrote:
> Doug, I see now what your concern was with just adjusting the beta
> weights. Since FSFAST is using a pseudo-mixed effects model, there is
> also a need to pass the cesvar statistics up to the second level. How
> that might accommodate the derivat
this is the contrast file with the corrected and uncorrected map right?
miracle
From: Douglas N Greve
Sent: March 25, 2016 6:11 PM
To: Miracle Ozzoude; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] whole hemisphere is yellow
not sure what is
also, i do require a username and password in order to send you the folder.
From: Douglas N Greve
Sent: March 25, 2016 6:11 PM
To: Miracle Ozzoude; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] whole hemisphere is yellow
not sure what is happe
Hi Freesurfers,
I'd like to use mris_make_face_parcellation to downsample an individual
subject's surface mesh to a resolution similar to fsaverage6.
My understanding is that mris_make_face_parcellation should let me do this,
and it does what I expect with ic3-5. However when I run it with ic6 as
Hi Michael,
I think this is a problem that crops up periodically for us in the
MEEG world, where we use these downsampling
as calculated in MNE. If my memory serves, as you go to higher
resolutions you end up with multiple points
being mapped to the same location, which I don't believe we have eve
Hello Douglas,
I have sent the files to you. Thank you.
Best,
Miracle
From: Douglas N Greve
Sent: March 25, 2016 6:11 PM
To: Miracle Ozzoude; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] whole hemisphere is yellow
not sure what is happenin
Hi Randy
we need significantly more information from you if you want our help.
What kind of scan are you talking about? Have you tried any intervention
such as control points? Can you post an image or email us an example of one
that fails?
cheers
Bruce
On Fri, 25 Mar 2016, Dr. Benson
wrot
Hi,
Can you say a bit more about what you mean?
> If my memory serves, as you go to higher resolutions you end up with
multiple points being mapped to the same location,
Do you mean multiple icosahedron vertices being mapped to the same native
mesh vertex, or the other way around?
In any case,
first caveat, I could be wrong:
On Fri, Mar 25, 2016 at 3:18 PM, Michael Waskom wrote:
> Hi,
>
> Can you say a bit more about what you mean?
>
>> If my memory serves, as you go to higher resolutions you end up with
>> multiple points being mapped to the same location,
>
> Do you mean multiple ico
I meant the glmfit folder, which is
lh.firstsessionscore1.glmdir
On 03/25/2016 02:29 PM, Miracle Ozzoude wrote:
> Hello Douglas,
> I have sent the files to you. Thank you.
> Best,
> Miracle
>
>
> From: Douglas N Greve
> Sent: March 25, 2016 6:11 PM
> T
Hello Douglas,
I just sent you the current file. Thank you.
Best,
Miracle
From: Douglas N Greve
Sent: March 25, 2016 9:35 PM
To: Miracle Ozzoude; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] whole hemisphere is yellow
I meant the glmfit fo
Hi Freesurfer experts,
We'd like to begin a cortical thickness and hippocampal subfield analysis in
the most recent devel version of FS. Can you please confirm that we will we be
able to run the analysis of these data in the final stable release of 6.0?
Thanks,
Lara
Lara Foland-Ross, Ph.D.
Re
Hello all,
We have run recon -all on some healthy control subjects T1 images but we
found out that the gray-white segmentation on half our subjects is bad and it
leads to increased white matter volumes and decreased gray matter volumes. I
have included a snap shot showing the difference in
Good. Thanks.
On Fri, Mar 25, 2016 at 9:59 PM, Ramtilak Gattu
wrote:
> Hello all,
>
>
> We have run recon -all on some healthy control subjects T1 images but we
> found out that the gray-white segmentation on half our subjects is bad and
> it leads to increased white matter volumes and decre
eek, that's terrible! SO it's a standard FLASH scan? The TE is a bit
long, but not terribly so. If you upload one of the subjects that did
poorly I'll take a look. We try hard to be agnositc to many things, but if
you know the sequence is fixed you can specifiy some of the contrast
parameters o
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