How do i convert dicom into mgz files.
tried using recon-all
what does subject id refer to and what is its significance.
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The
Thanks for your quick reply. It seems that we have some other problems now
with the machine, but 'll let you know whether the new mri_tessellate
works ;-).
On Fri, Sep 6, 2013 at 5:16 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote:
here you go. Let us know if it works
cheers
Bruce
On
Dear SIr,
I made some analysis based on FS v.2.0.
Does the Deprecated version means that the results generated by FSv.2 can't be
published???
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Dear Sir,
I'd like to know the command lines for running recon-all for multiple datasets.
Can you please help me on that?
I've tried using the following command lines
cd /home/john/Anu (where I kept all the .nii files)
for x in *
do
recon-all -i SZ*.nii -s $x -all
done
But this is not
I really meant FS5.2..
Sorry for the lack of clarity of my prev. mail
From: Anupa AV av.an...@yahoo.com
To: Freesurfer freesurfer@nmr.mgh.harvard.edu; Bruce Fischl
fis...@nmr.mgh.harvard.edu
Sent: Saturday, September 7, 2013 3:14 PM
Subject: version 2 FS
subject id is the identifier you pick for that subject. It is arbirtary but
needs to be unique (at least in that SUBJECTS_DIR). recon-all will read
dicom fine and create .mgz files from it. Try it and if it fails send us
your full command line and screen output and we will tell you what was
Hi Anupa
it means that for some acquisition types the pial surfaces in 5.2 had
substantial errors. We recommend rerunning with 5.3. Note that this should
just involve compute time as all manual interventions will be retained
cheers
Bruce
On
Sat, 7 Sep 2013, Anupa AV wrote:
Dear SIr,
I
Hi Anupa
in general recon-all only processes a single dataset at a time. You can run
multiple versions of recon-all if you have the processors and memory to
support it. Something like:
foreach x ( *)
recon-all -i SZ.${x}.nii -s $x -all
end
assuming that you had already converted your
The problem here is that SZ*.nii presumably refers to a list of files due to
shell expansion. I don't know how recon-all handles that (e.g. if it will take
only the first file in the list, or all files), but that command probably won't
do what you want it to.
it won't handle it. If you gave it multiple inputs each with it's own -i it
would assume that they are different images of the same subject and perform
motion correction and averaging. I don't think that is the case here - you
want to give each instance of recon-all a single nifti volume as
Note that this does not apply to HCP-style FreeSurfer runs or the HCP
released data.
Peace,
Matt.
On 9/7/13 8:26 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:
Hi Anupa
it means that for some acquisition types the pial surfaces in 5.2 had
substantial errors. We recommend rerunning with
Anupa,
If you want to run several subjects at the same time just open different
command windows. On each you can run a recon all. You can also run a list
of recon on each window. Just put the commands in a text file, name it
something like i.e. group1.sh and run the command sh group1.sh. Each
Hi FreeSurfer Experts,
On this page
(https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecMultipleComparisons),
it says: In particular, thresholds of 1.3, 2, 2.3, 3, 3.3 and 4, corresponding
to p-values of 0.05, 0.01, 0.005, 0.001, 0.0005 and 0.0001, which are common
thresholds.
I am
mri_convert dicomfile file.mgz
where dicomfile is a single file from the series (it will find the rest)
On 9/7/13 3:28 AM, swathy p.s wrote:
How do i convert dicom into mgz files.
tried using recon-all
what does subject id refer to and what is its significance.
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