Hi Kristina
can you please post to the list so others can answer? If you add control
points to the temporal WM where you are missing gm it should recover most
if not all of it. Hippocampus is not neocortical and isn't supposed to be
included. The surfaces are somewhat arbitrary there, and excl
Oh, I see. So in the calculation of total GM in aseg.stats does it include the
hippocampus, although it is not showing on the masks for surface of GM or PIAL?
I also tried to calculate total intracranial CSF (ventricles + outer liquor
spaces). Is following calculation correct:
e T
Hi Kristina,
This page has the details I believe you are looking for:
https://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats
-Louis
On Tue, 27 May 2014, Mayer Kristina wrote:
Oh, I see. So in the calculation of total GM in aseg.stats does it include the
hippocampus, although it is not s
Dear Louis,
I got my information from the same page. As eTIV is a totally different
algorithm, I am not sure if it is faisible to calculate total CSF from this
parameters.
As eTIV isn't representing voxels should I rather use the following:
eTIV - BrainSegNotVentSurf = total intracrani
Hi Michael,
I had a similar problem a while ago. Maybe this might help.
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg31152.html
Best,
Franz
Am 23.05.2014 um 05:38 schrieb Harms, Michael:
>
> Hi,
> I converted a surface to GIFTI
> e.g.,
> mris_convert lh.white lh.white.gii
>
Hi Jon
definitely not control points. I guess you would have to draw stuff in,
but that kind of intensity patch is so far from our expectations it may
be hard. Any idea where it comes from?
Bruce
On Tue, 27 May
2014, Jonathan Holt wrote:
Hi all,
this is a recurring issue that I'm hoping I
No idea, I think it’s due to the scanner, but could be wrong. Drawing in WM
voxels?
On May 27, 2014, at 10:20 AM, Bruce Fischl wrote:
> Hi Jon
>
> definitely not control points. I guess you would have to draw stuff in, but
> that kind of intensity patch is so far from our expectations it may
yes, that's what I meant. It looks too far in the interior to be a B0
effect. Do you see it in all your subjects? What sequence/scanner are you
using?On Tue, 27 May 2014, Jonathan Holt wrote:
No idea, I think it’s due to the scanner, but could be wrong. Drawing in WM
voxels?
On May 27, 2014,
Thank you Bruce,
I convert the fsaverage flat map into a ascii file, using: mris_convert -p
lh.cortex.patch.flat lh.cortex.patch.flat.asc.
Now I need to read these two files.
(1) I used read_patch.m to read lh.cortex.patch.flat. But an error came out, it
said ‘ Error using ==> read_patch a
Yes the HCP pipelines have to take care of this as well so that the
surfaces and volume align outside of FreeSurfer.
Peace,
Matt.
On 5/27/14, 8:35 AM, "Franz Liem" wrote:
>Hi Michael,
>
>I had a similar problem a while ago. Maybe this might help.
>http://www.mail-archive.com/freesurfer%40nmr.m
Hi Qiongmin
why are you trying to read the patches into matlab?
Also, can you send us your full matlab command that generated the error?
Sounds like you passed the incorrect file name
cheers
Bruce
On Tue, 27 May 2014,
Caka wrote:
Thank you Bruce,
I convert the fsaverage flat map into a
Hi FreeSurfer Team,
Please help out a FreeSurfer newbie! We are having an issue with mapping our
functional data onto the inflated brain. When we finish the mapping, it seems
that much of the data is showing up in white-matter space, and therefore,
cannot be seen on the external surface of th
we used an SPGR sequence on a GE 3T, it was 7-10 years old at the time. it’s
not on every subject, but on the handful of subjects that do present this
issue, it’s definitely stubborn and I’ve been unable to fix it as of yet.
On May 27, 2014, at 10:28 AM, Bruce Fischl wrote:
> yes, that's what
Hi Sherryse
you only need to register the anatomicals to the funtionals once, then
sample the functional data onto the surface using mri_vol2surf. This will
create a surface overlay that can be visualized on any of the surfaces
for that subject (e.g. lh.white, lh.pial, lh.inflated)
cheers
Br
Hi Lucette,
Are you saying that the label file saved by freeview can not be loaded
by other tools in freesurfer? Can you post the complete commands and
output that did not work?
Best,
Ruopeng
On 05/27/2014 02:03 AM, Lucette Cysique wrote:
Dear Ruopeng and colleagues,
I am interested in fol
Hi all,
I have been trying to work with DTI data in FreeSurfer for the first time. We
acquire our data on a 4T Varian and reconstruct into AFNI format (BRIK/HEAD
files). I set up the bval and bvec files successfully and ran the "dt_recon"
script. It seemed to run fine until I got an fslregist
Hi Freesurfers,
I was wondering if the SurferOutput files for the average subject's brain were
somewhere tobe downloaded on the wiki or within the toolbox?
Thanks,
m
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Freesurfer mailing list
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https://mail.nmr.mgh.harvar
What is the model of the scanner? I think there is an error in there
because it can' find the parameters it needs. You can also try something
like
mri_convert 160 11147SACC000.MR.RESEARCH_NEURO. test.mgh
this might print something more informative to the terminal. You can
also try
mri_probed
Why not just use the wmparc.mgz created by recon-all?
doug
On 05/22/2014 12:04 PM, Andrea Tateo wrote:
> Hi FreeSurfer expert,
>
> after that I have used the command "recon-all"
>
> I would like to obtain wm-lh and wm-rh information ( for example
> wm-lh-bankssts,wm-lh-caudalanteriorcingulate,w
Hi Martin,
Wasn't sure whether you'd seen my reply below, look forward to hear back
your thoughts, thanks!
Tudor
On 25 May 2014 21:40, "Tudor Popescu" wrote:
> Thanks very much Martin and Bruce. I guess I'd misread the Wiki (my own
> fault, not the text's), and am glad to hear that the longitudin
Hi Kayle, can you try the following
bbregister --s SLOTS007 --mov flair.mgz --init-header --reg reg.test.dat
--t2 --lta reg.test.lta
this should hopefully generate a good registration. If it does, then I
can find a work-around for you
doug
On 05/23/2014 03:05 PM, Kayle Sawyer wrote:
> Hello,
Are they siemens dicoms? If not, use dcmunpack. If so, what is the
command you ran and terminal output?
On 05/26/2014 11:34 AM, Caroline Lewis wrote:
> Hi,
>
> I am trying to use the unpacksdcmdir command to convert my dicom files
> to mgz/nifti, and when i run the command:
>
> unpacksdcmdir -
Does it print out anything else? An alternative is to use the command
line stream (create your own fsgd file, run mris_preproc, smooth,
mri_glmfit, mri_glmfit-sim)
doug
On 05/27/2014 06:38 AM, Saloni Sharma wrote:
> I am attaching a screen shot of the error, if it helps!
>
>
> On 26 May 2014
recon-all will not produce the registration file you are looking for. It
should be produced by reg-feat2anat. Try running it with --debug as the
first argument and post the terminal output to the list
doug
On 05/27/2014 12:10 PM, Sherryse Corrow wrote:
> Hi FreeSurfer Team,
>
> Please help ou
Did it actually fail? If not, does the registration look ok? That msg
should just be a warning
doug
On 05/27/2014 02:06 PM, Weber, Wade (weberw) wrote:
>
> Hi all,
>
> I have been trying to work with DTI data in FreeSurfer for the first
> time. We acquire our data on a 4T Varian and reconstruct
It prints out fine and gives results if I only use it to analyse two
groups(differentiated on stress levels) but if I add gender as a discrete
variable or even as a continuous one along with the groups it shows this error.
Sent from my iPhone
> On 27 May 2014, at 23:40, Douglas N Greve wrote:
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