Dear Freesufers,
I want to run: mri_normalize gentle,
And
mris_make_surfaces min_border_white 85 -min_gray_at_white_border 80
In as few steps as possible as I will run around 800 images. So far I only
managed to this by braking up the process several subparts (like doing
autorecon1 before m
Hi Erik
you can do this with the expert options in recon-all. Run recon-all -help
and see if it is clear, otherwise post and someone here who has used it can
walk you through it.
cheers
Bruce
On Tue, 11 Feb 2014, Erik Lindberg wrote:
Dear Freesufers,
I want to run: mri_normalize gentle,
Ciao Anastasia, I checked and I'm using the latest version of Freesurfer,
version 5.3.0. It seems like that the command trac-all path while working
on the bvecs table and doing the corrections makes some errors and you can
see it from the bvecs file I found in the dmri directory which is only 4
row
Is this okay to do even if I've done a coregistration, nothing will be deleted?
Also, are the pial surfaces necessary for plotting? I'm wondering if I can just
use the files that I have to create a plot without having to rerun anything.
Thanks,
Mia
> On Feb 10, 2014, at 4:31 PM, "Bruce F
if they are zero length there is nothing there now
On Tue, 11 Feb 2014,
Borzello, Mia wrote:
> Is this okay to do even if I've done a coregistration, nothing will be
> deleted? Also, are the pial surfaces necessary for plotting? I'm wondering if
> I can just use the files that I have to create
Dear Freesurfers,
I want to run: mri_normalize gentle,
And
mris_make_surfaces min_border_white 85 -min_gray_at_white_border 80
in MY recon-all script. I understand that I have to put the flag -expert
to do this - but I seem to make errors in my command
It would be greatly apprecia
Okay and is there a way to check if the files I currently have are sufficient
to plot with?
Thanks,
m
> On Feb 11, 2014, at 9:58 AM, "Bruce Fischl"
> wrote:
>
> if they are zero length there is nothing there now
>> On Tue, 11 Feb 2014, Borzello, Mia wrote:
>>
>> Is this okay to do even i
Hi All,
I have a few questions about wmparc:
What rule is used to determine what grey matter structure corresponds to a
white matter point?
What exactly has to be the case when UnsegmentedWhiteMatter is reported?
Is there a reference you could point me to?
Thanks,
Sujith
__
what kind of plotting do you mean?
On Tue, 11 Feb 2014, Borzello, Mia wrote:
> Okay and is there a way to check if the files I currently have are sufficient
> to plot with?
>
> Thanks,
> m
>
>
>
>> On Feb 11, 2014, at 9:58 AM, "Bruce Fischl"
>> wrote:
>>
>> if they are zero length there is noth
Dear freesurfer experts,
I am trying to compute the differences in subcortical volumes between
two groups. I have read previous mail,
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg17597.html , and
in this mail, your answer was 'you can do a subcortical volume analysi
Hi again Anastasia,
I tried also to convert my three row bvecs file in a three column one but I
still got the same "bvecs and bvals don't have the same number of entries"
error. I then tried also to change the dot to comma as the decimal
separator but still nothing
Francesco Baldacchini
2014-02
woops- sorry meant to include everyone. The name of the file I use to plot is
"lh.pial-outer-smoothed." So I either want to create this file or figure out
another way to plot. Do i need lh.pial to make lh.pial-outer-smoothed?
From: Bruce Fischl [fis...@nm
Another question- will I need to re-coregister if I rerun a reconstruction?
Thanks,
m
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Borzello, Mia
Sent: Tuesday, February 11, 2014 11:05 AM
To: Bruce Fisc
What is in lh.volume.average.fwhm10.mgh? It is named as if it is a file
with surface data in it.
On 02/11/2014 11:04 AM, Wang, Guoying wrote:
>
> Dear freesurfer experts,
>
> I am trying to compute the differences in subcortical volumes between
> two groups. I have read previous mail,
> https
Sorry, for the delay...
1. You can use mri_surfcluster with the --fdr option.
2. I'm not sure I understand. Are you really setting the FDR to .88?
Usually it is some thing like .05
doug
On 02/10/2014 03:28 PM, pfot...@nmr.mgh.harvard.edu wrote:
> Hi FS community,
>
> I was wondering if anyon
Hi Panos,
also the LME tools (matlab) have tools for FDR correction:
/lme_mass_FDR/ (Original Benjamini and Hochberg FDR procedure)
/lme_mass_FDR2/ (A more powerful two-stage FDR procedure:
"Adaptive Linear Step-up Procedures that control the False
Discovery Rate" Benjamini, Krieger, Yekutiel
Hello all,
I have run bedpostx on a series of DTI scans over ~1 year, the earlier
ones in stable 5.1 and later ones in 5.3. I'm seeing quite a lot of
variability in intensity from the earlier to later versions - re-running
bedpostx in 5.3 on an older scan and comparing with 5.1 yields up to 10%
Hi Mia,
while that is possible, it may be smarter to re-run those subjects from
scratch. It is unclear why those files are empty. Maybe there are files
that have been partially written etc. Those would not be re-created. I'd
be very reluctant re-using data even partially that I know has been
Hi Doug and Martin,
Thanks both for your replies!
Doug, I would normally set the FDR to something close to .05 but when this
value didn't give me any significant clusters for my analysis, I was
trying to find which value was the min one that gave significant clusters
just out of curiosity, and th
Hi Mia
I don't know where that file comes from - I don't think it's one we
typically generate, but I would imagine it does need the ?h.pial surface as
input
cheers
Bruce
On Tue, 11 Feb 2014, Borzello, Mia wrote:
> woops- sorry meant to include everyone. The name of the file I use to plot is
you shouldn't
On Tue, 11 Feb 2014, Borzello, Mia wrote:
> Another question- will I need to re-coregister if I rerun a reconstruction?
>
> Thanks,
> m
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of B
FYI
-- Forwarded message --
Date: Tue, 11 Feb 2014 16:50:15 +
From: "Babcock, Debra (NIH/NINDS) [E]"
To: "Babcock, Debra (NIH/NINDS) [E]"
Subject: Program Director job opening at the NINDS
Dear Colleagues,
The NINDS is currently seeking to hire several program directo
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
__
There may be an easier wqay to do this but a simple hack that appears to
work is to use the "max_days" parameter in the url. For example:
https://surfer.nmr.mgh.harvard.edu/fswiki/RecentChanges?max_days=100
-Zeke
On 02/11/2014 12:57 PM, Kaiming Yin wrote:
> Dear guys,
>
> Is there some way to h
HI! All,
I got an error when I ran dt_recon
WARNING: file /Users/gnchen/tmp/3011_DTI/orig/MR01.dcm does not contain a
Siemens ASCII header
has this file been anonymized?
ERROR: cannot unpack mosiacs without ASCII header
I can confirm it is Siemens mosaics format. Any idea how to by pass
Dear Freesurfers,
Is there anyway to get a compiled list of all the significant clusters with
information about their maximum thickness value, x/y/z vertices, t
statistic etc on QDEC? Does this have anything to do with a SaveClusterFile
command? All of this information must be stored somewhere for
Look in the QDEC output folder. In each contrast folder, you should see
a summary file. I think the info you want is in that file.
doug
On 02/11/2014 03:08 PM, Natasha Haris wrote:
> Dear Freesurfers,
>
> Is there anyway to get a compiled list of all the significant clusters
> with information
Hi
I have a dataset of children who have had hemispherectomy surgery to treat
epilepsy. I want to be able to run recon-all on these children. I have
masked out the remaining tissue from the excised side so that only tissue
from the healthy hemisphere remains, and aligned this single hemisphere t
Hi Kristian
Can you send us an image to illustrate what you mean?
Thanks
Bruce
> On Feb 11, 2014, at 8:31 PM, Kristian Eschenburg
> wrote:
>
> Hi
>
> I have a dataset of children who have had hemispherectomy surgery to treat
> epilepsy. I want to be able to run recon-all on these children.
Hi Anastasia and freesurfer experts,
I am trying to get DTI values along the tracts as in the pathstatbyvoxel
file, but excluding inflammatory WM lesions. I have masks of the WM
lesions that I could apply on the DTI maps, but then how could I compute
the DTI metrics along the tract with the exclusi
Hello Free surfer Expert ,
I am kooking for the exact value of voxel / pixel which represent White
,Grey and CSF fluid matter in brain.
I am trying to draw contour, and to measure the count...or How to count the
pixel for particular region...?
Thanks in advance for your timely advise.
cheers
Sa
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