Hi,
Ok, I will look into inverting the image as Martin suggested. Is there
some background info available on how to put the segmentation input into
the surface-based analysis. In case the inversion doesn't work. I'm
particularly wondering if I need to have the images in *.mgz file format
or w
Thank you Martin,
I only wanted know if there is a way to do this without using an
external program. I will try using a standard tool.
Tommaso
Martin Reuter wrote:
Hi Tommaso,
I am not sure about freesurfer, but why don't you simply use a standard
tool for mesh simplification e.g. qslim
htt
Hey Krish,
Thanks for your input. Good idea too, never thought about doing that.
Tried this in command line and worked without a hitch. Then i realized if
you just use command line what I did before works as well. The error must
somehow be resulting from issues with tcsh or something. But I fo
Also, in case anyone is interested -- if you have a brik volume in the
subject folder, specifying mri/orig/001.mgz gives the same error as
specifying orig/001.mgz, at least for me. So that wasn't the cause of the
problem.
John
On Thu, Oct 23, 2008 at 7:44 AM, John Sheppard <
[EMAIL PROTECTED]> w
Hi, groups,
I noticed the updates of longitudinal analysis in the new version of
Freesurfer. However, I still have a couple of questions about the goal of
longitudinal analysis.
1. The goal of longitudinal analysis is to detect the atrophy (thinning), but
the transformation in the registration
Hi Wang,
1. An affine transform from tp1 to tp2 would only remove global atrophy,
but not the region effects we are interested in.
2. For intra-subject registration the surface-based is not needed as we
expect the changes to be small.
cheers,
Bruce
On Thu, 23 Oct 2008, Wang, Xin wrote:
Hi Nick,
After I run recon-all, the files I get are not in mgz format and I would
like to convert them into img format to view them in FSL view. How can I do
that?
Thanks,
Regards,
Sameer
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mri_convert file.mgz file.img should do the trick (or file.nii for nifti)
On
Thu, 23 Oct 2008, sameer kumar wrote:
Hi Nick,
After I run recon-all, the files I get are not in mgz format and I would
like to convert them into img format to view them in FSL view. How can I do
that?
Thanks,
Rega
and how do you get it into FSL?
On Wed, 22 Oct 2008, Juranek, Jenifer
wrote:
yes, the correct Sgmtn label is displayed in the TkMedit Tools
-Original Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Wednesday, October 22, 2008 4:30 PM
To: Juranek, Jenifer
Cc: freesurfer@nmr
Hi all,
It says .mgz file not found. I am new to FS so please help me out with this.
Thanks,
Regards,
Sameer
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what file are you trying to convert?
On Thu, 23 Oct 2008, sameer kumar
wrote:
Hi all,
It says .mgz file not found. I am new to FS so please help me out with this.
Thanks,
Regards,
Sameer
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The output files of recon-all
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which ones? There are many, some of them are surfaces, which I don't
think FSL can show, and some are volume that you could import into FSL
(e.g. $SUBJECTS_DIR/$subject/mri/aseg.mgz, which is the whole-brain
segmentation)
cheers,
Bruce
On Thu, 23 Oct 2008, sameer kumar wrote:
The output file
Hi all -
Is there a way to create "intermediate" surfaces in FreeSurfer? By
intermediate I mean "some fraction" between gray/white and pial.
Cheers
-=R
--
Rudolph Pienaar, M.Eng, D.Eng / email: [EMAIL PROTECTED]
MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging
149 (2301) 13th St
yes, mris_expand will do it.
cheers
Bruce
On Thu, 23 Oct 2008, Rudolph Pienaar wrote:
Hi all -
Is there a way to create "intermediate" surfaces in FreeSurfer? By
intermediate I mean "some fraction" between gray/white and pial.
Cheers
-=R
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Hello,
Not sure if this bug has been mentioned before, but there is a bug with
using aparcstats2table for the aparc.a2005s parcellation map. If some of
the subjects in the group have missing values of a certain type,
aparcstats2table fails to designate a 0 for them. So for instance, it's
often
Hi,
I have 2 questions.
1) How do I calculate psd min, max, and dpsd. Is there a formula for
calculating these values? I have 4 kinds of stimuli, stim duration = 3s,
stim repetition = 25, TR =2 so:
optseq2 --ntp 180 --tr 2 --psdwin [?] --ev A 3 25 --ev B 3 25 --ev C 3 25
--ev D 3 25 --o 4type
Does anybody know how to convert a series of Analyze files into a single nii
file? Each analyze file is a single 3D volume at a time point; the nii file
would be 4d.
Thanks,
Xu
--
Xu Cui
Department of Psychiatry and Behavioral Sci
The body of my email was lost because of the attachments: here it is
again for those who are curious. Sorry about that, I didn't know a text
file attachment would do that.
Not sure if this bug has been mentioned before, but there is a bug with
using aparcstats2table for the aparc.a2005s parcell
Victor,
We are aware of this bug. Unfortunately, there is no 'quick fix', which
is why it has not been repaired yet. But yes, I agree its an ugly one
which creates havoc with automated scripts. Hopefully a fix will appear
in the next release.
Nick
On Thu, 2008-10-23 at 13:19 -0700, Laluz, Vic
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