Can you send us an image? The 16 bit shouldn't be a problem
Bruce
On Feb 23, 2011, at 7:28 PM, andrewkra...@ucla.edu wrote:
> The orig.mgz shows up with weird colors (the grey matter is black, the
> background is light gray, and there's a white halo around the brain and in
> the ventricles/CS
If you save it in our ASCII surface format any of our tools should read it,
including mris_convert
Cheers
Bruce
On Feb 22, 2011, at 3:35 PM, Tina Jeon wrote:
> Hello freesurfers,
>
>
>
> I am trying to convert a partially inflated surface .ply file created in afni
> to a freesurfer volum
The orig.mgz shows up with weird colors (the grey matter is black, the
background is light gray, and there's a white halo around the brain
and in the ventricles/CSF).
Another possibility I just thought of is that the original ANALYZE
image is 16-bit, and is 230 x 230 x 230 voxels. Does mri_c
Is there a list of recommended MPRAGE parameters for a Siemens Verio 3T machine?
The structural protocols on this page: MailScanner has detected a possible fraud attempt from "www.nmrmgh.harvard.edu" claiming to be http://www.nmr.mgh.harvard.edu/~andre/ are for a Sonata (1.5T). I'm not sure what
does the orig.mgz show up properly in tkmedit?
On Wed, 23 Feb 2011, Nick
Schmansky wrote:
> add the flag -notal-check to the end of recon-all command to skip the
> check.
>
> if you can make your average using nifti format you're better off as
> analyze doesnt retain orientation (l/r) info.
>
> y
does mri_convert work?
glxgears?
tksurfer?
qdec?
freeview?
your installation should work on ubuntu, as it has for other people, so
i'm a bit at a loss.
n.
On Thu, 2011-02-24 at 07:12 +0800, Liukarl wrote:
> Hello, Nick
>
> the output of uname -a is
>
> "Linux Jie-Liu-Linux 2.6.35-25-gener
Hello, Nick
the output of uname -a is
"Linux Jie-Liu-Linux 2.6.35-25-generic #44-Ubuntu SMP Fri Jan 21 17:40:48 UTC
2011 i686 GNU/Linux"
thanks
Jie
> Subject: Re: [Freesurfer] installation problem
> From: ni...@nmr.mgh.harvard.edu
> To: remembe...@hotmail.com
> CC: freesurfer@nmr.mgh.ha
mri_convert --help has info on specifying orientation, with suitable
warnings about the need for you to make sure you know which way is
correct.
n.
On Wed, 2011-02-23 at 14:55 -0800, andrewkra...@ucla.edu wrote:
> Thanks for the reply. For the orientation, I know from working with
> the sourc
add the flag -notal-check to the end of recon-all command to skip the
check.
if you can make your average using nifti format you're better off as
analyze doesnt retain orientation (l/r) info.
you may have to manually register the brain following this:
http://surfer.nmr.mgh.harvard.edu/fswiki/
Hello,
I'm a complete newbie to FreeSurfer, so I appreciate any and all help
you can provide. I am trying to use FreeSurfer to automatically create
some masks of subcortical structures, but am having trouble getting
the whole process started.
When I run "recon-all -autorecon1 -noskullstrip
Hi all,
We ran mri_surfcluster on our group data (we didn't do montecarlo
simulations), so we used our .mgh file. We used the -ocn flag to make an
output file so we could look at the specific clusters. When we looked at
the data of the ocn file using tksurfer, the most significant cluster
wasn't
Hi Freesurfers,
When conducting ROI analyses in Stable 5, is there a way to generate
a mean functional baseline offset value within the ROI which can be
used to help calculate percent signal change? This would correspond
to the value from row 4 in the output file generated by
roisummary-sess
Hi again.
The orientation looks correct for both volumes (001.mgz and 002.mgz). Does
anyone know what is then going wrong with the registration in Freesurfer?
The average volume (orig.mgz) can be seen here:
http://freesurfer.nikolasborrel.com/bad_registration.tif
Kind regards
Nikolas Borrel-Jense
Dear Pedro,
I would like to start with the tutorials but I don't have permission to copy
the data to the subjects directory, how I can change this?
Best regards,
Carolina
2011/2/22 Pedro Paulo de Magalhães Oliveira Junior
> try the command:
>
> sudo apt-get install tcl
>
> -- PPJ
>
> Please:
Hi,
How can I tell what the tag-control order of collection was for my ASL
images? They were all acquired in Bay 3. I can get you other
parameters if you need...
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what is the output of
uname -a
On Thu, 2011-02-24 at 00:53 +0800, Liukarl wrote:
> Hello, Freesurfer experts:
>
>
>
> I emailed some installation problems a couple days ago, but haven’t
> answered yet. I am new to freesurfer and try to install the newest
> version of freesurfer in Ubuntu sy
Hello, Freesurfer experts:
I emailed some installation problems a couple days ago, but haven’t answered
yet. I am new to freesurfer and try to install the newest version of freesurfer
in Ubuntu system. I closely followed the instructions, and the only difference
is that I installed it in my D
the procedure you followed is correct, although in general you dont need
to run make_average_subject, as the default target subject 'fsaverage'
is fine for most studies. add -target after -qcache
if you did create your own target.
per your questions,
2.2, assuming you imported the group subject
Hi Brian
can you explain more what you mean? We distribute an average subject
(fsaverage) that you could probably use.
cheers
Bruce
On Wed, 23 Feb 2011, Weisinger,
Brian (NIH/NIMH) [F] wrote:
> Is there a way to get a general generic TK_Surfer output without using a
> subject?
>
> Thanks,
> B
hmm, that is large, but the tiny one-voxel border you showed in your image
wouldn't come close to explaining that. Do you want to upload the subject
and we'll take a look?
Bruce
On Wed, 23 Feb 2011, Tetiana Dadakova
wrote:
> Dear Bruce,
>
> The problem is that the volumes I get for hippocampu
Hi Tim,
the one run is okay, but the failure of the Talairach is probably an
indication that the orientation information is incorrect. Because analyze
doesn't specify the orientation, the info you get is just a guess. Bring
the orig.mgz up in tkmedit and see if the anatomical views are correct
Registration is now open.
https://www.epay.ed.ac.uk/browse/extra_info.asp?compid=1&catid=42&modid=2&prodid=453&deptid=24&prodvarid=0
Best regards,
Chris Gorgolewski
On 18 February 2011 17:58, Chris Filo Gorgolewski
wrote:
> Dear all,
>
> I am delighted to invite you to a Neuroimaging Data Proces
Hi Nadia,
the processing steps look OK.
You have several options to analyze the longitudinal data. We do not
have a single tool to do everything automatically but there are many
tools in FreeSurfer that can do the individual steps depending on what
you want to do (as there are many different stat
Is there a way to get a general generic TK_Surfer output without using a
subject?
Thanks,
Brian Weisinger
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The information in this
Hello
I have just started to use FreeSurfer (version 4.5) and have some questions on
the longitudinal stream:
I have started to process cross-sectionally all time points (7 tp) of my
patients with the following script:
recon-all –i tpidN.nii –subjid tpidN* –all*
Then, created an unbiased templa
Dear Bruce,
The problem is that the volumes I get for hippocampus are much larger
than they should be (like 5000 mm^3 for healthy female). Same is for
some other structures.
Best wishes,
Tanja.
On Wed, Feb 23, 2011 at 3:08 PM, Bruce Fischl
wrote:
> Hi Tetiana,
>
> I think what you're seeing ar
Dear Bruce,
Thank you so much for taking care of my stupid questions :)
I searched online regarding the ANALYZE vs Dicom, and I understand
your point now ... The problem is, for this scan, I am afraid the only
data format that I can play with is ANALYZE ... (although there might
be Dicom format
Hi Tetiana,
I think what you're seeing are just the consequences of a voxel-based
segmentation. The borders have to be voxelated. Note that much of this will
be corrected in the volume calculation that performs a partial-volume
correction.
cheers
Bruce
On Wed, 23 Feb 2011, Tetiana Dadakova wr
Hi Freesurfers,
I am currently dealing with some examples of group analysis from
freesurfer-wikipages (see http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G0V).
Could you please give some clarifications in the following scenario:
Assume we have four groups MaleRight, MaleLeft, FemaleRight, and
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