What is the aseg label for them?
On Nov 13, 2012, at 4:30 PM, Nikhil Chandra wrote:
> Hello,
>
> After completing the FreeSurfer Recommended Reconstruction, we have noticed
> that in aparc+aseg, many subjects exhibit small clusters of voxels in the
> medial temporal lobe that are labeled a
-- Forwarded message --
From: youngmin huh
Date: 2012/11/14
Subject: Re: bad acquisition and noise problem.
To: Bruce Fischl
Thanks for your comment.
I would appreciate if you could take a look.
Do you want a whole folder of the subjects, or just 001.mgz and log file?
Thanks,
it's not a question of SNR, the problem appears to me to be that the B0
distortions are so bad that a bunch of the temporal lobe is piled up on top
of itself. There's no way to fix that posthoc. If you upload the full
volume I'm happy to take a look
On Wed, 14 Nov 2012, youngmin huh wrote:
I
I'm not engaged in obtaining images, so I don't have any details about the
images.
I wonder the method which you commented can be applied to images I already
earned.
If it's not, is there any way to recover SNR after image scanning?
Thanks,
Youngmin Huh.
2012/11/13 Bruce Fischl
> what is the
Hi Martin,
Yes, that's it, I wasn't changing the "Measure" in the "Design" tab !
Thank you very much for the advice and support !
Sincerely,
Alex
Le 13/11/2012 3:41 PM, Martin Reuter a écrit :
> Hi Alex,
>
> just tested it with our dev version and it works for me. When you setup
> the subje
Rahul?
On Tue, 13 Nov 2012, Amanda Schlesinger wrote:
> Hello all -
>
> I'm unclear on whether the subgenual ACC gets included in the rostral
> ACC when running parcellations from the Desikan atlas. From the
> Desikan paper's description and images, it appears to me that the rACC
> area curves und
Hello all -
I'm unclear on whether the subgenual ACC gets included in the rostral
ACC when running parcellations from the Desikan atlas. From the
Desikan paper's description and images, it appears to me that the rACC
area curves under the genu of the CC and that the caudal boundary
there at the ge
Hi Doug,
All other things being equal, if you switch from AP to RL phase encoding
in an axial acquisition, then the PE direction will switch from the y-axis
to the x-axis in the images. It doesn't really have anything to do with
Siemens, since the images are written out in a standard anatomical
o
I guess it is possible that Siemens is doing something funny with the
images. I've never used sagittal before.
On 11/13/2012 12:51 PM, Clark Fisher wrote:
> I'm using a script that calls unpacksdcmdir. Maybe there is some setting in
> our config file that forces the orientation? Nothing obviou
Hi Alex,
just tested it with our dev version and it works for me. When you setup
the subjectsdir and have the file in $SUBJECT_DIR/qdec/.Qdecrc then
after starting qdec you should be able to select e.g.
long.thickness-rate under 'Measure' in the 'Design' tab.
Best, Martin
On Tue, 2012-11-13 at 1
Hi Alex,
the .Qdecrc (with captial Q) needs to be in the qdec directory within
the $SUBJECTS_DIR. Can you check if that is the case?
Thanks, Martin
On Tue, 2012-11-13 at 13:51 -0500, Alex Hanganu wrote:
> Hello Martin,
>
> thanks again for your help. We created the .Qdecrc file in the qdec
>
Hi Vincent,
sorry, I'm not sure. This is an area that Ron Killiany and Marilyn Albert
had found sizable effects in prodromal AD patients, which is why Ron
included it in his parcellation, but I'm not sure how they decided the
extent and location of it. You could email Rahul Desikan and ask him
Hello Martin,
thanks again for your help. We created the .Qdecrc file in the qdec
directory. It still gives the same error. Also we made some changes to
the .Qdecrc file, for example we changed the ...long.thickness.. to
...long-thickness..., but the error remaines the same.
We performed addit
Hi Clark, hi Doug
fugue has an option that might help here. Here is the relevant excerpt rom
calling fugue on the command line (as in fugue of fsl 5.0.1 but I am sure this
was also present in fsl 4.1.n):
"--unwarpdirspecifies direction of warping [x/y/z/x-/y-/z-] (default y)"
it seems that t
I'm using a script that calls unpacksdcmdir. Maybe there is some setting in
our config file that forces the orientation? Nothing obvious though.
On Nov 13, 2012, at 12:03 PM, Douglas N Greve wrote:
> I'm a little confused as to why the rows are not the phase encode direction
> to begin with.
The terminal output looks ok. Do you mean that there is something wrong
with the output volume? What?
doug
On 11/12/2012 11:30 AM, Yangmei LUO wrote:
> Hi Douglas,
>
> It appeared the same error as before. The picture of the results is
> the same. I am so sorry.
> Thanks again!
>
> Best,
> Yangm
Yes, the problem is rawavg.mgz. When was it created? How many runs do
you have in this data set? You can also try using your input volume
subject/mri/orig/001.mgz (or what ever it is called). If you only have
one run, then rawavg.mgz should just be a copy of 001.mgz
doug
On 11/12/2012 11:54 AM
I'm a little confused as to why the rows are not the phase encode
direction to begin with. What did you use to convert the dicoms to nifti?
doug
On 11/13/2012 11:59 AM, Clark Fisher wrote:
> Thanks Doug,
>
> Would the proper way to handle this then be to switch the rows and columns
> before unwa
Thanks Doug,
Would the proper way to handle this then be to switch the rows and columns
before unwarping, then switch them back before the further processing steps?
-Clark
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Hi Azeez,
try using mris_fill.
cheers
Bruce
On Tue, 13 Nov 2012, Azeez Adebimpe wrote:
Hi Freesurferers or Experts,
I have been trying to convert the watershed bem brain surfaces to vol with
mri_fill and mri_surf2vol but not succeed.
My main aim is to create mask for outer_skull, inner_skul
actually, I have no idea:). This is a wrapper around the FSL programs. I
wrote the code always assuming that the phase encode direction was the
row direction. Usually, it gets unpacked that way. Is the data getting
reoriented along the way?
doug
On 11/13/2012 11:34 AM, Satrajit Ghosh wrote:
> h
That contrast will do what you want but a more general one would be
[1 -1 0 0 0 0 0 0 0 0 0 0]
[0 0 0 1 -1 0 0 0 0 0 0 0]
[1 0 -1 0 0 0 0 0 0 0 0 0]
[0 0 0 1 0 -1 0 0 0 0 0 0]
This will return positive if there is any difference between the
genotypes regardless of gender. In your contrast, you c
hi doug,
just to follow up on this. if i had the phase encode direction (we
currently store various dicom attributes in a nifti header extension),
where would i provide it?
cheers,
satra
On Tue, Nov 13, 2012 at 11:27 AM, Douglas N Greve wrote:
> Hi Clark, the phase encode direction is always
Hi Stan, can you run that mri_concat command from the terminal command line and
send me the resulting terminal output? I've put the command below
doug
mri_concat
/data1/projects/ysbrand-vumc/pddatabase-freesurfer/0050/surf/lh.volume.fwhm10.fsaverage.mgh
/data1/projects/ysbrand-vumc/pddatabase
Hi Clark, the phase encode direction is always lost since that
information is not represented in the nifti header. epidewarp.fsl always
assumes that the phase encode direction is in the row direction.
doug
On 11/13/2012 07:32 AM, Clark Fisher wrote:
> Hi everyone,
>
> I recently switched the pha
Hi Freesurferers or Experts,
I have been trying to convert the watershed bem brain surfaces to vol with
mri_fill and mri_surf2vol but not succeed. My main aim is to create mask for
outer_skull, inner_skull and other from their respective surfaces. Is there any
other method to use?
Azeez
Azeez
what is the bandwidth? The typical way to fix it is to increase the
bandwidth. You can probably recover some of the SNR you will lose by
reducing your flip angle, which is pretty far from the Ernst angle.
Also, minimize your TE (if 4ms is not already the min)
cheers
Bruce
On Tue, 13 Nov 2012, y
the intensity normalization has a region growing component that is bounded
by intensity gradients. In images like MPRAGE, where SNR is traded for CNR
it can help to raise the threshold for stopping so that more white matter
is included (that's what the -b 20 does, I think the default it 10 or 15
Hi Freesurfer experts,
I'm very sorry to bother you, but I am very confused with the following
questions:
My experimental design includes two discrete factors: genotype with three
levels (GG,GA,AA ); gender (F, M), and one covariate.
So I can get 6 classes: MGG, MGA,MAA, FGG,FGA,FAA.
1) I wa
Dear Freesurfers,
Does anyone know why sometimes the "bankssts" (banks of the superior temporal
sulcus) is only found in the sulcus, and sometimes occupies a sizeable part of
an adjacent gyrus (superior temporal / inferior parietal)?
The dark-green area is generally only visible in the inflated
Hi everyone,
I recently switched the phase encoding direction of the functional sequence
I've been using from F >> H to R >> L and ran into a problem with
epidewarp.fsl (in version 4). The unwarping was still happening along the F >>
H axis in the new images where phase encoding was R >> L.
Hello Freesurfer experts,
I have got some problems with qdec. For testing my data i make an design with
age, sexe and right and left hippocampus. The same design as the tutorial on
the freesurfer wiki. When starting anlalyze i get an Error in Analyze: command
failed: mri_concat
/data1/project
Hi Freesurfer experts,
I'm very sorry to bother you, but I am very confused with the following
questions:
My experimental design includes two discrete factors: genotype with three
levels (GG,GA,AA ); gender (F, M), and one covariate.
So I can get 6 classes: MGG, MGA,MAA, FGG,FGA,FAA.
1)
Hi Freesurfer experts,
I'm very sorry to bother you, but I am very confused with the following
questions:
My experimental design includes two discrete factors: genotype with three
levels (GG,GA,AA ); gender (F, M), and one covariate.
So I can get 6 classes: MGG, MGA,MAA, FGG,FGA,FAA.
1) I wa
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