the results of the monte carlo z-simulation methods produces clusters
where each vertex within a cluster has the same p-value, so in this case
there is no single vertex with the highest value, but the code which is
used to find the vertex with the highest value (which is valid to run in
cases where
Dear Freesurfers,
I'm pre-processing my DTI data with Tracula and i found the following error
while running trac-all -prep -c dmrirc_H_P01:
dtifit -k /home/joana/FIU/H_P01/dmri/dwi.nii.gz -m
/home/joana/FIU/H_P01/dlabel/diff/aparc+aseg_mask.flt.nii.gz -r
/home/joana/FIU/H_P01/dmri/bvecs -b /home/
Hi,
I'm looking for a tool to fill holes of only 1 voxel in size
in a binary mask.
I posted this also to the FSL mailing list but none of the
suggested solutions could do this or were robust enough.
Ed
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Hi Ed,
the dev version of mri_morphology will do this:
mri_morphology fill_holes 26
where the 26 specifies the min # of nbrs that must be on for the output
voxel to be set to 1
cheers
Bruce
On Fri, 30 Sep 2011,
Ed
Gronenschild wrote:
> Hi,
>
> I'm looking for a tool to fill holes of onl
Hi Bruce ,
What do you mean with "dev version"?
Ed
On 30 Sep 2011, at 15:22, Bruce Fischl wrote:
> Hi Ed,
>
> the dev version of mri_morphology will do this:
>
> mri_morphology fill_holes 26
>
> where the 26 specifies the min # of nbrs that must be on for the
> output
> voxel to be set to 1
I mean not the distributed version. If you let us know what
software/hardware environment you are using Krish can get you a binary
On
Fri, 30 Sep 2011, Ed Gronenschild wrote:
> Hi Bruce ,
>
> What do you mean with "dev version"?
>
> Ed
>
> On 30 Sep 2011, at 15:22, Bruce Fischl wrote:
>
>> Hi Ed
Hi Doug,
I believe I got the error for the Abnormal Side R because the fwhm for the
clusters with thresh 2 in QDEC is fwhm = 31.843147 as you can see below: and
when I run mri_glmfit-sim it gives me the error:
and when I run mri_glmfit-sim it gives me the error that cannot find fwhm 32:
ERROR
Dev builds are found here
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/
On Sep 30, 2011, at 9:42 AM, Bruce Fischl wrote:
> I mean not the distributed version. If you let us know what
> software/hardware environment you are using Krish can get you a binary
> On
> Fri, 30 Sep 2011,
when does it get updated? He'll need a new one
On Fri, 30 Sep 2011, MGH wrote:
> Dev builds are found here
>
> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/
>
> On Sep 30, 2011, at 9:42 AM, Bruce Fischl wrote:
>
>> I mean not the distributed version. If you let us know what
>> softwa
Nightly
On Sep 30, 2011, at 9:52 AM, Bruce Fischl wrote:
> when does it get updated? He'll need a new one
>
> On Fri, 30 Sep 2011, MGH wrote:
>
>> Dev builds are found here
>>
>> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/
>>
>> On Sep 30, 2011, at 9:42 AM, Bruce Fischl wrote:
so grab it tomorrow then Ed
On Fri, 30 Sep 2011, MGH wrote:
> Nightly
>
> On Sep 30, 2011, at 9:52 AM, Bruce Fischl wrote:
>
>> when does it get updated? He'll need a new one
>>
>> On Fri, 30 Sep 2011, MGH wrote:
>>
>>> Dev builds are found here
>>>
>>> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/
Hi,
When I ran the QDEC on patients with abnormal side right, the fwhm for the
clusters at thresh 2 is fwhm = 31.843147.
Then, I ran mri_glmfit-sim on the QDEC output and it gives me the following
error (cannot find fwhm 32):
ERROR: cannot find
/usr/local/freesurfer/average/mult-comp-cor/fs
That exceeds the valued for which the tables are cached. What smoothing
level did you use?
doug
Antonella Kis wrote:
>
> Hi,
>
> When I ran the QDEC on patients with abnormal side right, the fwhm for
> the clusters at thresh 2 is fwhm = 31.843147.
> Then, I ran mri_glmfit-sim on the QDEC output
Sorry to ask a trival question: After hippocampus segmentation, how can I
extract the coordinates of each subregion? The general matlab functions seem
unable to read the info.
Thanks in advance,
George
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Hi all - What would be the best way to create ROI masks of the individual
hippo subfields that are generated in Freesurfer?
Thanks!
Shashwath Meda
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Hi Doug,
Thanks for helping me again. I used smoothing level of 20 because I was told
to use this smoothing. If I use the 15 I am not getting the error but I need
to use the 20.Is there a way that I can make it work/correct this error and get
my tables cached in this case?
Please advis
Hi Doug,
Thanks for helping again. I used smoothing level of 20 because I was told to
use this smoothing. If I use the 15 I am not getting the error but I need to
use the 20.Is there a way that I can make it work/correct this error and get my
tables cached in this case?
Is fwhm= 15
There is no one smoothing level that is right. In general, people tend
to just go with a default value. I think that 20 is pretty high, I
usually go with 5-15. You might examine your data to see if you have an
outlier. I think it is unusual for you to get an output fwhm of over 30
when the smo
You can use mri_binarize with the --match option to specify the code for
the subfield you want a mask of. These codes can be found in
$FREESURFER_HOME/FreeSurferColorLUT.txt
doug
Shashwath Meda wrote:
> Hi all - What would be the best way to create ROI masks of the
> individual hippo subfield
Hello Freesurfer team,
I have been running a longitudinal analysis and have just finished
analyzing the data in qdec and running a cluster correction. I would now like
to use the significant cluster annot files to extract the thickness rate stats
for each subject and put them in a table.
Hi Joana - Can you please send your dmrirc file too?
Thanks,
a.y
On Fri, 30 Sep 2011, Joana Braga Pereira wrote:
> Dear Freesurfers,
>
> I'm pre-processing my DTI data with Tracula and i found the following error
> while running trac-all -prep -c dmrirc_H_P01:
>
> dtifit -k /home/joana/FIU/H_
- Forwarded Message -
From: Antonella Kis
To: Douglas N Greve
Sent: Friday, September 30, 2011 12:31 PM
Subject: Re: [Freesurfer] Default for fwhm while running mri_glmfit
I see.I am not sure what exactly you mean by an outlier in my data,but if there
will be an outlier, why the mr
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