Hi FS-folks!
I would like to perform a subcortical segmentation only and I am not sure
which preprocessing steps I would have to perform to achieve this goal.
So far I did always the full monty using reconall -all. Which reconall
stages are needed if only the subcortical segmentation is of intere
Hi folks!
Is there any way to convince FS to make use of a high spatial resolution
(better than 1 x 1 x 1 mm3) for subcortical segmentation?
Best wishes,
Luke___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/m
Yup.
http://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon
Depending how far you intend to push it, you might need a
different version of the mri_tesselate function.
Best
Remi Gau
On 10/12/14 08:44, lukas.s
Dear Remi!
Thanks a lot for the fast response. Could comment further on your point
that I might need a different version of mri_tesselate ...
The spatial resolution I am talking about is 0.5x0.5x0.8 mm3.
Best wihes,
Luke
> Yup.
>
> http://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon
>
> Depend
It is in fsaverage.
On Tue, 9 Dec 2014 14:37:43 +0100
pfannmo...@uni-greifswald.de wrote:
> Dear FreeSurfer Experts,
>
> I am puzzeled about the probabilities in the Brodmann area labels. If I take
> the Brodmann areas 1, 2, 3a and 3b and add their probabilities at a certain
> vertex a probab
Hi Pradeep
you can use mri_extract_label to copy just the hippocampal labels out of
the segmentation if that is what you mean. The values for left and right
hippocampus (17 and 53) can be found in
$FREESURFER_HOME/FreeSurferColorLUT.txt
cheers
Bruce
On
Wed, 10 Dec 2014, pradeep mahato wrote:
Hi Luke
you can run -autorecon1 and -autorecon2 if all you care about is the aseg
(although we have tools for editing the cortical aseg labels with the
surfaces that you will not be able to use in this case)
cheers
Bruce
On Wed, 10 Dec 2014,
lukas.sch...@ukb.uni-bonn.de wrote:
>
> Hi FS-folk
hmmm, is it on the boundaries of the labels? And only a bit >1? That can
certainly happen due to resampling and small registration inaccuracies
On Wed, 10 Dec 2014,
pfannmo...@uni-greifswald.de wrote:
> It is in fsaverage.
>
>
> On Tue, 9 Dec 2014 14:37:43 +0100
> pfannmo...@uni-greifswald.de w
Hey,
Someone corrects me if I am wrong, but it seems that the number of vertices currently allowed with freesurfer cannot accomodate more than a certain number of vertices.
I suspect that the new version of Freesurfer should allow for more vertices.
On high res you might get suc
Hi Remi
yes, that's true. The limit is pretty arbitrary and supposed to be bigger
than we would ever want, but if it is limiting we can bump it up
Bruce
On Wed, 10
Dec 2014, Remi Gau wrote:
>
> Hey,
>
> Someone corrects me if I am wrong, but it seems that the number of vertices
> currently a
Hi Bruce,
the mris_thickness was looking for ?h.gray file to run correctly. But no such
file exists. The freesurfer used is 5.3. Any ideas? The command line is:
mris_thickness test_DB48 lh lh.thicknessThe error: reading gray matter surface
/misc/data41/yuex/recon_test/test_DB48/surf/lh.gray
it only looks for that if it can't find lh.pial. Does that exist?
On Wed, 10 Dec 2014, Xiaomin Yue wrote:
Hi Bruce,
the mris_thickness was looking for ?h.gray file to run correctly. But no
such file exists. The freesurfer used is 5.3. Any ideas?
The command line is: mris_thickness test_DB4
Dear Bruce,
if I take BA1, BA2, BA3a and BA3b and sum the probabilities at each vertex
there are 17 % of the vertices which show probabilities > 1. The largest
probability is 1.7778. There is a histogramm of the values attached to this
mail. Is there a possibility to correct those values?
Resp
Hi pfannmoe
that seems reasonable given small registration inaccuracies and
resampling issues
cheers
Bruce
On Wed, 10 Dec 2014, pfannmo...@uni-greifswald.de wrote:
> Dear Bruce,
>
> if I take BA1, BA2, BA3a and BA3b and sum the probabilities at each vertex
> there are 17 % of the vertices whic
On 12/08/2014 09:19 PM, zhang mingxia wrote:
> Hi Doug,
>
> I followed this guide:
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis.
> I used "tksurfer-sess" to view. Does "significant activation in the
> visual cortex" mean the map from"tksurfer-sess -a rtopy.self
No, not for surfaces. Alphasim has to smooth the data which requires
knowledge of the underlying geometry. Alphasim assumes a volume-based
geometry and has no knowledge of surface-based geometry (unless it has
been updated in the last 5 years). We have the ability to do
simulations like alpha
Are you using 1.3 or 1,3 ?
On 12/09/2014 03:10 AM, Milde, Christopher wrote:
> Dear Doug,
>
> I tried to run MCC with cluster-sess but unfortunately I got the same error
> message like when I'm using mri_glmfit-sim.
> It does not recognize the thresh (cluster-forming thresh)
>
> Here is the term
Yes, lh.pial exists
Xiaomin
> On Dec 10, 2014, at 10:33 AM, Bruce Fischl wrote:
>
> it only looks for that if it can't find lh.pial. Does that exist?
>
>> On Wed, 10 Dec 2014, Xiaomin Yue wrote:
>>
>> Hi Bruce,
>> the mris_thickness was looking for ?h.gray file to run correctly. But no
>> s
Yes, lh.pial exists
Xiaomin
> On Dec 10, 2014, at 10:33 AM, Bruce Fischl wrote:
>
> it only looks for that if it can't find lh.pial. Does that exist?
>
>> On Wed, 10 Dec 2014, Xiaomin Yue wrote:
>>
>> Hi Bruce,
>> the mris_thickness was looking for ?h.gray file to run correctly. But no
>> s
what version of FS do you have? You can try runing it with -pial pial but
I wouldn't think that is needed. Is the lh.pial in
/misc/data41/yuex/recon_test/test_DB48/surf/
and is it readable?
On Wed, 10 Dec 2014, Xiaomin Yue wrote:
Yes, lh.pial exists
Xiaomin
On Dec 10, 2014, at 10:33 AM, B
Converting that matrix will not be easy. If you want to try, look at our
wiki page on coordinate systems and see how your coordinate systems
match up. It won't be easy. Your bbregister command is not going to work
for sure, you cannot use --init-header (which should only be used for
two MRIs a
Hi Doug,
Thanks for your response! Please see Josh's follow-up question below.
Thanks again for your help!
Best,
Alex
Original Message
Subject: Re: [Fwd: Re: [Freesurfer] Modeling cortical thickness question]
From:"Roffman, Joshua L.,M
Hi All,
I am using QDEC to run a correlation analysis and I have a lot of large
significant clusters that encompass various different cortical regions. I am
hoping to extract mean thickness' from the significant clusters in order to
create a plot to display the correlations. Can anyone tell me
The problem was solved. I typed the wrong name.
mris_fill had generated wm.mgz correctly, with the problem that a significant
portion of white matter was cutted off. The problem I believe is that the
resolution or the matrix size of wm.mgz is limited to 256 X 256 X 256, but the
high resoluti
Dear FreeSurfer users,
I have a question regarding the link between cortical thickness and
gyrification index: suppose I have a general decrease of cortical thickness
in a lobe of the brain.
Is it correct to suppose that consiquentely the gyrification index will
decrease in the sulci (because of t
Hello all!
I saved clusters as labelfiles with mri_surfcluster (fMRI-Data,
surface = self). The labels seem to hold the following data in each row:
Vertex-No., x-, y-, z-coordinates of some kind (not so sure about
that), and a t-value.
The Label-Vertex-No. and t-value match the output (VtxMax
No, just include "age^3", if the mean function is
E(thickness | X) = B_0 + B_1 * age^3
It's similar to taking the logarithm of one of your predictors. Just
remember that the units for the parameter estimate will be different
than if you were just including age.
On 12/10/2014 12:12 PM, Alexan
They will be the coordinates of the white surface. The coordinate system
is an internal system that we have used for 20 years. See
http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems for more info.
doug
On 12/10/2014 02:29 PM, Philipp Otmar Heinrich Heimbeck wrote:
> Hello all!
>
> I sav
Chris is correct.
On 12/10/2014 02:46 PM, Chris Watson wrote:
> No, just include "age^3", if the mean function is
>
> E(thickness | X) = B_0 + B_1 * age^3
>
> It's similar to taking the logarithm of one of your predictors. Just
> remember that the units for the parameter estimate will be differen
Thanks Doug! Will try the --init-fsl or --init-spm for bbregister.
-Liang
On Wed, Dec 10, 2014 at 10:50 AM, Douglas N Greve wrote:
>
> Converting that matrix will not be easy. If you want to try, look at our
> wiki page on coordinate systems and see how your coordinate systems
> match up. It won
Hi experts,
I have cortical thickness on fsaverage surfaces
(?h.thickness_on_fsaverage.mgh) from a group of individuals. I'd like to
create a volume (.mgh) that represents group mean or sd or other
descriptive statistics. I know mris_calc can do similar job but wonder if
there is more straightforw
You can use mri_concat, something like
mri_concat file1.mgh file2.mgh --mean --o mean.mgh
On 12/10/2014 04:00 PM, Liang Wang wrote:
> Hi experts,
>
> I have cortical thickness on fsaverage surfaces
> (?h.thickness_on_fsaverage.mgh) from a group of individuals. I'd like
> to create a volume (
Cool! Thanks Doug!
-Liang
On Wed, Dec 10, 2014 at 3:05 PM, Douglas N Greve
wrote:
>
> You can use mri_concat, something like
>
> mri_concat file1.mgh file2.mgh --mean --o mean.mgh
>
>
>
> On 12/10/2014 04:00 PM, Liang Wang wrote:
> > Hi experts,
> >
> > I have cortical thickness on fsaverage su
Hi,
I ran our pipeline script that contains DTI_prep and Tracula, and when I
extracted the individual motion data, they are mostly zeros (see below)
Is this normal? If this is a problem, can anyone please let me know if there
any way to fix this (e.g. re-run the motion script..)?
Your help would
ATI/AMD cards with up to date drivers should be fine.
-Zeke
On 12/05/2014 10:00 PM, Chris McNorgan wrote:
> Hi Freesurfers,
>
> I am spec'ing a couple of Linux workstations to run Freesurfer, among
> other software. Complicating matters, our preferred vendor's
> configurations include ATI/AMD vid
the ribbon.mgz isn't part of autorecon2 (or autorecon1) I don't think.
What are you trying to run?
On Thu, 11 Dec 2014, pradeep mahato wrote:
Hi Bruce,
After running autorecon1 and autorecon2, I am getting an error saying
ribbon.mgz file is missing.
Is it that autorecon2 the 23rd function didn
I am running the recon method for oasis
recon-all -autorecon1 -autorecon2 -i ./OAS2_0001_MR1/RAW/mpr-1.nifti.img -i
./OAS2_0001_MR1/RAW/mpr-2.nifti.img -i ./OAS2_0001_MR1/RAW/mpr-3.nifti.img
-s OAS12_1
The program exited saying ribbon.mgz file is missing. Thus I am unable to
get aseg.stats data.
P
There is no documentation or example for mri_extract_label.
What should be the syntax for it. What kernel and xform file should be used.
On Wed, Dec 10, 2014 at 6:50 PM, Bruce Fischl
wrote:
> Hi Pradeep
>
> you can use mri_extract_label to copy just the hippocampal labels out of
> the segmentati
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