Hi Ruopeng,
I agree that the options are treated as part of the file path in my command
line.
Thank you for the support.
Best,
Ikbeom
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Ruopeng Wang
Sent: Wednesday, October 16, 2019 4:27 PM
To:
Hi Ikbeom,
I think this is because the added options at the end of file path are
treated as part of the path by the shell and thus returns no match. I
will try to put a fix on that.
Best,
Ruopeng
On 10/16/19 4:09 PM, Jang, Ikbeom wrote:
Dear FreeSurfer community:
I am a beginner and
Dear FreeSurfer community:
I am a beginner and tying to load multiple volumes in Freeview with a single
option applied to all the volumes.
For example, I would like to set grayscale window as min=0 and max=100 for all
volumes. Is there a simple command line which does that efficiently?
The
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Dear FS List,
My group was trying to look at the overlap between cortical labels in the
longitudinal processing stream and I had a question re: use of transform
files. In brief, we followed the commands for the longitudinal
processing stream, creating
it will figure out the input and output for you
On Wed, 16 Oct 2019,
Inglese, Marianna wrote:
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Hi Bruce,
shall I do that with my original T1 as input or the T1.mgz?
Thank you.
BW
Marianna
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Hi Bruce,
shall I do that with my original T1 as input or the T1.mgz?
Thank you.
BW
Marianna
Da: freesurfer-boun...@nmr.mgh.harvard.edu
per conto di Bruce Fischl
Inviato: mercoledì 16 ottobre 2019 17:58
A:
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Postdoctoral Research Associate
Waisman Center, University of Wisconsin–Madison, Madison WI
The Waisman Laboratory for Brain Imaging & Behavior at the Waisman Center,
University of Wisconsin–Madison, is seeking highly motivated postdoctoral
Hi Marianna
I think you can just run recon-all -s -skullstrip and it will
run it for you as it normally does
cheers
Bruce
On Wed, 16 Oct 2019, Inglese, Marianna
wrote:
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Dear all,
from this:
(...) Removes the skull from mri/T1.mgz and stores
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Dear all,
from this:
(...) Removes the skull from mri/T1.mgz and stores the result in
mri/brainmask.auto.mgz and mri/brainmask.mgz. Runs the mri_watershed program.
If the strip fails, users can specify seed points (-wsseed) or change the
threshold
that will do a bit more than just the skullstripping
On Wed, 16 Oct 2019,
Krieger, Donald N. wrote:
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Please pardon me for jumping in here.
I looks like recon-all -autorecon1 will do it, yes?
Best - Don
-Original Message-
From:
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Please pardon me for jumping in here.
I looks like recon-all -autorecon1 will do it, yes?
Best - Don
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Bruce Fischl
Sent: Wednesday, October 16, 2019 12:48 PM
To:
oh, sure, you can just run that part of recon-all. You don't need to
rerun the whole thing
cheers
Bruce
On Wed, 16 Oct 2019, Inglese, Marianna wrote:
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Hi Bruce,
what I mean is that, two of the main outputs of recon-all are T1.mgz (which
has the
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Hi Bruce,
what I mean is that, two of the main outputs of recon-all are T1.mgz (which has
the skull) and brain.mgz (which has been skull stripped). For a group of
patients, I lost the brain.mgz file and I still have the T1.mgz. I was
wondering if
Hi Marianna
I'm not sure what you mean by "replicate". The procedure should be the
same for all inputs unless you change something explicitly
cheers
Bruce
On Wed, 16 Oct 2019,
Inglese, Marianna wrote:
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Thank you Bruce.
I thought it was
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Thank you Bruce.
I thought it was something similar to the FSL bet function, which extracts the
brain using a fractional intensity threshold (0.5 for example).
So I guess I won't be able to replicate the same exact skull stripping of
freesurfer's
Hi Marianna
the skull stripping is a hybrid procedure that uses both a watershed
algorithm and a deformable surface. There is no single intensity threshold
in it. Maybe I'm misunderstanding your question? There are parameters you
can change (for example the preflooding height), but there is
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To whom it may concern,
I am using recon-all to segment many T1s. As I can see, one of the automatic
step performed by recon-all is the skull stripping. Would it be possible to
know the threshold used for the stripping? I guess it is the same
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Dear Bruce,
Thanks for the reply. I have uploaded my data through the Martinos Center
FileDrop, here is the link:
+ Data_Xiaoqian.zip (169.46 MiB) <
http://gate.nmr.mgh.harvard.edu/filedrop2/?p=6wbctqzrzh1>
I explained my problems in that link, but
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Postdoctoral Fellowship in Pediatric Neuroimaging at the University of
Pennsylvania
Drs. Allyson Mackey and Dylan Tisdall are seeking a postdoctoral fellow for an
NIH-funded study on early childhood brain development. The goals of the study
are to
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Hi,
I'm designing an analysis that will have 6 groups (two factors/three
levels). I was wondering if I could get some input regarding my contrast
for the group effect. Based on the group effect contrast under the FSGD
examples for 3 groups I've
Hi Xiaoqian
it's pretty hard to tell what's going on from these images. If you tar/gzip
your whole subject dir and upload it with an email telling us the specific
voxel coords that you want us to examine
cheers
Bruce
On Wed, 16 Oct 2019, Xiaoqian Yan wrote:
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Thanks.
On Tue, Oct 15, 2019 at 5:00 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:
> Correct
>
> On 10/15/2019 9:38 AM, Keri Woods wrote:
>
> External Email - Use Caution
> Hi Doug
>
> Thank you very much for the very helpful
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