Hi
I have proceed my data and produced a significance map across all my subjects
and this looks fine on the fsaverage inflated brain. To compare to some other
results, I really need to wrap this map into standard MNI152 space.
To do this, I have used the following commands but with a problem at
Hi FS experts,
I want to extract time course from sig.mgh. But the *.y.ocn.mgh cannot be
created. So I want to view it in other formats, such as nii. So how to convert
it into nii format.
Thanks.
All the best.
Rujing Zha
2014-03-11
charujing123___
F
Hi FS experts,
For the sig.mgh, can I see the time course vertex by vertex in freeview?
Thanks.
All the best.
Rujing Zha___
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The informati
Hello Freesurfer Expert,
Can anyone help me with histogram plotting of different surfaces in
tksurfer.
I looking to calculate the thickness of cortex.
Thanks in advance,
Saurabh Thakur,
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Dear FS experts,
I have a serial study in which I have run cross-sectional and
longitudinal analysis on 5 time points. Now, I want to add a 6th time point to
my dataset. Do I have to rerun my base template creation step from scratch or
is there a way to just add further time points t
what is it that you want to histogram? If the thickness, tksurfer will do
this for you if you load it as an overlay. Or you can read it into matlab
and show it there
On Tue, 11 Mar 2014, Saurabh Thakur
wrote:
> Hello Freesurfer Expert,
>
> Can anyone help me with histogram plotting of differe
Hi Louis,
Thanks, so should this be amended or can be simply left there which may not
influence the stats results and further comparison?
Great thanks,
Kaiming
On Mon, Mar 10, 2014 at 8:01 PM, Louis Nicholas Vinke <
vi...@nmr.mgh.harvard.edu> wrote:
> Hi Kaiming,
> I'm almost certain you are r
Hi Kaiming,
I can't say for certain looking at that one slice, but I'm pretty sure
it's fine. What you can do is make the surfaces for one hemi a different
color than the other hemi, then pan through in the sagittal view and you
should see one set of surfaces go out as the other comes in. Als
Hello-
I'm having a consistent problem running multiple subjects through tracula.
I am able to run single subjects through all steps but whenever I try to
run it on multiple subjects I get the same error about a syntax error and
one of the items it wants to copy being a directory so its not being
If you're asking whether we have tools that do myelination-based
segmentation from T1, the answer is no. I've found from fMRI that the
transversetemporal label does pretty well.
doug
On 03/10/2014 11:34 AM, Ritobrato Datta wrote:
> Hi Doug, Wow, telepathy…Just resent my email and got this repl
Hi Peng, there's a lot going on there, and it is not specific enough for
me to make recommendations. Take a look at the docs we have on our
coordinate systems
http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems?action=AttachFile&do=get&target=fscoordinates.pdf
you might get the answer y
Almost right. Try this command (reversed mov and targ and added --inv):
mri_vol2vol --inv –targ SIG.fsspace.mgz –mov
/$FSL_DIR$/data/standard/MNI152_T1_2mm.nii.gz –o SIG_MNI.nii –interp
nearest –reg /$FS_DIR$/average/mni152.register.dat
I know, it is a little confusing
doug
On 03/11/2014 04
mri_convert file.mgh file.nii
doug
On 03/11/2014 05:55 AM, charujing123 wrote:
> Hi FS experts,
> I want to extract time course from sig.mgh. But the *.y.ocn.mgh cannot
> be created. So I want to view it in other formats, such as nii. So how
> to convert it into nii format.
> Thanks.
> All the
the time course of what?
On 03/11/2014 07:18 AM, charujing123 wrote:
> Hi FS experts,
> For the sig.mgh, can I see the time course vertex by vertex in freeview?
> Thanks.
> All the best.
> Rujing Zha
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mg
Hello,
I would like to conduct an analysis using mri_glmfit but I'm getting this
error:
ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08
My command was:
mri_glmfit --y lh.area.fwhm10.fsaverage.mgh --fsgd finalgroupanalysis.fsgd
dods --C group_effect.mtx --surf fsaverage lh --corte
Hi Sarah - The best way to troubleshoot the configuration file is to
source it, make sure that there are no errors, and then echo each variable
to make sure it contains what you intended.
For example once you run "source Tracula_config" you'll get an error, and
you'll find that you have to c
The fsgd file appears to have been created using a windows program (or
mac program that saves in windows format). Is that correct? I've
attached a linux-compatible version. Let me know if that works.
doug
On 03/11/2014 12:19 PM, Wanda Truong wrote:
Hello,
I would like to conduct an analys
try configure->functional overlay or something like that after loading
the thickness into a functional overlay
On Tue, 11 Mar 2014, Saurabh Thakur
wrote:
> I am referring one paper.
> It mentioned about the freesurfer and cortical thickness they hv got in
> tksurfer.
>
> I m just want to know h
what template? When discussing coordinate systems you have to be very
specific. A template could be a volume template or a surface template.
If a volume template it could be MNI305 or MNI152. If MNI152 it could be
the 1mm version or the 2mm version. All of these things are important
and the qu
Hi Doug,
Thanks for the new fsgd file - it solved the error. However, now I get a
different error:
ERROR: dimension mismatch between y and X.
y has 46 inputs, X has 71 rows.
which is similar to the error I got when I tried to do this analysis in
QDEC. I've attached my Xg.dat. I'm not sure what
how did you create the input lh.area.fwhm10.fsaverage.mgh? How many
subjects does it have in it? The error means that the FSGD file has a
different number of Input lines than the lh.area file has subjects
On 03/11/2014 02:45 PM, Wanda Truong wrote:
> Hi Doug,
>
> Thanks for the new fsgd file -
Hi Doug,
Thanks for your reply. Just to be clear, I need to ask some trivial
questions:
1) I need to do that subtraction in the fsgd file right? (In which case
there will be negative numbers as well)
2) I ran the analysis and the resulting significant clusters when looking
at the results of [1 -
Thanks for your reply. I am using *ICBM 2009a Nonlinear Asymmetric 1×1x1mm
template. *I did not expect that it will make much difference in the
algorithm. Does freesurfer favor certain template than others?
btw: the individual mri is also 1 mm resolution.
On Tue, Mar 11, 2014 at 8:46 PM, peng wr
Hi Doug,
With the terminology in the document you provided, I can summarize what
I want to do exactly as part of the flow chart in page 7. I listed it as
between==. As described in the document, I can get Ta, Tb by ; and R from a file ; am I right?
Practically, I may put my template as a subjec
Hi guys,
I was wondering if someone could take a look at a subject that I just uploaded (L217_100908.zip).
An RA was editing wm.mgz to attempt to fix a topology problem in the LH visual cortex. The edited wm.mgz that she created looks fine to me, but after re-running FS, the surfaces still ar
Hi Mike
mri_pretess that is causing this behavior. I guess we delete the pretess
output after ceating the surfaces, which makes it harder to diagnose this
kind of thing. I ran (which I got from the recon-all.log):
mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz
Hi doug,
sig.mgh is my result for two group t-test on pial thickness of whole brain. So
I want to see the time course of thickness of rh.ttest.thickness.10.mgh vertex
by vertex.
Thanks.
All the best.
Rujing Zha
2014-03-12
charujing123
发件人:Douglas N Greve
发送时间:2014-03-12 00:16
主题:Re: [Frees
Hi,
I'm interested in comparing CT differences between 2 different groups, and
in order to increase my sample size I'm contemplating combining 3 datasets
with different scanning parameters.
Some scans were collected with a 3T1 with fmri head coil, while others were
collected with a 3T2 magnet wit
Hi Bruce,
Thanks Bruce.
I knew that code, but I have no idea to deal with my problem after reading the
help. Would you please tell me how to use mri_surf2vol after I describe my
problem details?
I have a file named rh.36sb.score.thickness.10.mgh which is created from the
"mris_preproc --fsgd $FS
Hi Ashley
that is probably trouble unless your groups are perfectly balanced across
the datasets (that is, the same # in each group were scanned on each
configuration).
cheers
Bruce
On Tue, 11 Mar 2014,
Ashley Shurick wrote:
Hi,
I'm interested in comparing CT differences between 2 diffe
try mri_surf2vol with the output volume named .nii
cheers
Bruce
On Wed, 12 Mar 2014,
charujing123 wrote:
Hi doug,
Thanks doug.
I try this code, but it represent two dimension for each subject data when
loaded in the AFNI. Is there any code to volume-based conversion from mgh to
nii?
All the b
Hi doug,
Thanks doug.
I try this code, but it represent two dimension for each subject data when
loaded in the AFNI. Is there any code to volume-based conversion from mgh to
nii?
All the best.
Rujing Zha
2014-03-12
charujing123
发件人:Douglas N Greve
发送时间:2014-03-12 00:16
主题:Re: [Freesurfer]
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