Hi Michelle
they have to overlap unless the classification was 100% accurate with no
variability. You can just pick the label with the highest probability at
each vertex
cheers
Bruce
On Tue, 16 Aug 2011, Michelle Umali wrote:
> Hi Doug,
> So I did the additional smoothing and the map looks bet
can you send a pic?
Michelle Umali wrote:
> Hi Doug,
> So I did the additional smoothing and the map looks better.. It's
> still hard to interpret though. I was expecting alternating red and
> blue bands to signify V1/V2/V3 boundaries, but it's very irregular
> with red curves running ever
Hi Tapsya,
If you want to supply a registration to bbregister, then use --init-reg
(and don't use --init-fsl). The xopts should give you the same result as
the first command.
doug
tap...@nmr.mgh.harvard.edu wrote:
> Hi Doug,
>
> As mentioned below (by Dr. Tommi), bbregister with the flag --t1 do
Hi Doug,
As mentioned below (by Dr. Tommi), bbregister with the flag --t1 does
provide better results. i.e.
>>bbregister --init-fsl --s avml07 --bold --mov bold/template.nii.gz --reg
bold/register.dof6.dat --init-reg-out bold/init.register.dof6.dat --t1
However, supplying register.dat (from old
Hi Doug,
So I did the additional smoothing and the map looks better.. It's
still hard to interpret though. I was expecting alternating red and
blue bands to signify V1/V2/V3 boundaries, but it's very irregular
with red curves running every which way into blue splotches. Do you
have any s
That should work, but it should not register anyway (unless the raw data
or template change).
doug
r...@nmr.mgh.harvard.edu wrote:
> Hi Doug,
>
> You are absolutely right - I should have noticed the T1 warning in the
> bbregister logs. I guess funny things can happen when scanning with a
> short
Hi Doug,
You are absolutely right - I should have noticed the T1 warning in the
bbregister logs. I guess funny things can happen when scanning with a
short (1.15 sec) TR without fat suppression (also this was Trio before the
Tim upgrade and multichannel arrays).
We tried bbregister with t1 weight
Thanks Bruce. You are right. mri_diff gave nothing on the Shell. So, i don't
have to worry.
Cheers, Forrest
On Mon, Aug 15, 2011 at 8:47 PM, Bruce Fischl wrote:
> try running mri_diff on them. The image data should be the same. It's
> probably the difference between the command line gunzip and t
Hi Dear All,
Does anyone knows how do I run a benchmark test on GPU with FreeSurfer and CUDA?
Thanks,
Leo Souza
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This email message is for the sole use of the intended recipient(s) and may
contain
confidential inf
Hi Carolina - There's info on the new release and how to install it here:
https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
a.y
On Tue, 16 Aug 2011, Carolina Valencia wrote:
Hi FS'users,
I'm trying to do the Tracula tutorial but after set the configuration file I
run the command trac-all
Hi Carolina,
Tracula is a part of Stable v5.1.0 not Stable v5.0.0, so you need to
update your version.
-Priti
> Hi FS'users,
>
> I'm trying to do the Tracula tutorial but after set the configuration file
> I
> run the command trac-all
> cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects
Hi Bruce, Doug, and All,
I have corrected a boundary between lh corpuscallosum and
caudalanteriorcingulate.
I have overwritten the label/lh.aparc.annot as per Bruce's email below.
However, doesn't this leave a number of files with incorrect information now in
the stats directory?
Do I need t
Hi FS'users,
I'm trying to do the Tracula tutorial but after set the configuration file I
run the command trac-all
cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/Tracula_Tutorial_Public/diffusion_tutorial>
trac-all -help
trac-all: Command not found.
I have the version: freesurfer-Linu
Antonella Kis wrote:
> Dear Freesurfer experts,
>
> I am doing a thickness-age correlation group difference study (patients
> versus controls. I would like to know if:
>
> 1) my contrast vector defined as 0 0 0.5 0.5 is correct in order to test the
> change in thickness with age
>
Yes.
> 2)w
Hi Corey,
You may be interested in the recent thread on the SPM list discussing
similar issues about why one shouldn't put too much stock in Brodman
area labels unless they are derived from actual histology (e.g., the
work of Julich/Amunts/Zilles et al).
https://www.jiscmail.ac.uk/cgi-bin/webadmi
Hi Corey
for much of the brain these are just guesses as we don't have human
architectonic info. It's what we have now, but we don't even really know
what the error bars are on a lot of the areas.
cheers
Bruce
On Tue, 16 Aug 2011, Corey Keller wrote:
> Thanks for the response Bruce. It seems
wow, that's interesting. Your data is actually T1 weighted! There are a
couple of things you can do. First, you can copy your register.dat over
the register.dof6.dat. An alternative is to run register-sess
(bbregister) with t1 weighting. You can do this by creating a file with
the line "--t1" i
Hi Rajeev,
Usually, this type of error is produced if stats file is missed, check if aseg.
stats file is there in directory "/usr/local/freesurfer/subjects/140/stats"
directory.
If this file is missed in some subjects, you can add "--skip" to command line
like;
asegstats2table --subjects 01 0
Thanks for the response Bruce. It seems that the WFU pick atlas
(http://fmri.wfubmc.edu/software/PickAtlas) has linked each talairach
coordinate with a Brodmann area. Is it not possible (or accurate) to
first convert the subject's RAS to talairach coordinates to link each
coordinate to the associat
Thanks Doug and Bruce!
On Tue, Aug 16, 2011 at 10:58 AM, Douglas N Greve wrote:
> Supratentorial is GM+WM+Ventricles+**WMHypointensities+Thalamus+**
> VentralDC
>
>
> Bruce Fischl wrote:
>
>> Hi Alan
>>
>> the ICV we compute is from the det of the talairach xform using Randy
>> Buckner's method
Supratentorial is GM+WM+Ventricles+WMHypointensities+Thalamus+VentralDC
Bruce Fischl wrote:
> Hi Alan
>
> the ICV we compute is from the det of the talairach xform using Randy
> Buckner's method (see his paper on this topic). It includes everything
> inside the skull implicitly.
>
> I'll leave
btw, the intracranial volume is an estimate based on the talairach
transform (it is not computed by counting voxels in the cranium).
doug
Bruce Fischl wrote:
> it includes all of those
>
> cheers
> Bruce
> On Tue, 16 Aug 2011, carolina.mr wrote:
>
>
>> Hi, all,
>>
>> Does anybody know what the
Hi Adam, you'll need to add AFNI into your path (this is a recent
change). You can do that in your .cshrc file with something like:
setenv AFNIDIR /usr/pubsw/packages/AFNI/current/
set path = ($path $AFNIDIR/bin)
doug
Adam Nitenson wrote:
> Hi Doug and Freesurfers,
>
> I encountered an err
Michelle Umali wrote:
> Hi Doug,
> I've already smoothed by 5 during preproc-sess, so does this mean I
> should do additional smoothing during fieldsign-sess step?
>
Try the additional one now to see if it fixes the map.
> Also, is this the correct command to use the sphere and not the patch
Hi Alan
the ICV we compute is from the det of the talairach xform using Randy
Buckner's method (see his paper on this topic). It includes everything
inside the skull implicitly.
I'll leave Supratentorial for someone else, as I don't remember.
cheers
Bruce
On Tue, 16 Aug
2011, Alan Francis
Hi Corey,
sorry, there is no such thing, although wouldn't it be nice if there were
:)
Bruce
On Tue, 16 Aug 2011, Corey Keller wrote:
> Hi Freesurfers,
>
> I was wondering if you have come across a method to automatically
> parcellate the whole brain into Brodmann areas. I know the newest
> fre
Hi Bruce:
Following up on Carolina's question, if I understand correctly,
Is ICV = GM+WM+Ventricular Volume ?
and
Supratentorial Volume = GM+WM ?
thanks,
Alan
On Tue, Aug 16, 2011 at 10:03 AM, Bruce Fischl
wrote:
> it includes all of those
>
> cheers
> Bruce
> On Tue, 16 Aug 2011, carolina
Hi Freesurfers,
I was wondering if you have come across a method to automatically
parcellate the whole brain into Brodmann areas. I know the newest
freesurfer version does this for several BAs but not all BAs have been
incorporated. I was wondering if anyone knows of an existing Brodmann
atlas (fo
no, the CSF label by itself is kind of useless. It pretty much impossible
to distinguish bone from CSF on just a T1, so we don't label sulcal CSF.
Mostly just the ventricles, which are explicitly labeled.
Bruce
On Tue, 16 Aug 2011, carolina.mr wrote:
> Hi, all,
>
> One more thing about the aseg
it includes all of those
cheers
Bruce
On Tue, 16 Aug 2011, carolina.mr wrote:
> Hi, all,
>
> Does anybody know what the intracranial volume and supratentorial volume
> include? Does it include only the parenquima volume (white matter / gray
> matter volumes) or it
> includes the ventricules an
This fixed everything! Thank you!
Christopher Luna
MIT Brain and Cognitive Sciences, Class of 2012
Desimone Lab, McGovern Institute for Brain Research
MIT Archery Club
Alpha Kappa Psi Colony at MIT
On Wed, Aug 10, 2011 at 2:43 PM, Douglas N Greve
wrote:
> One thing you can try is to look at th
Hi, all,One more thing about the aseg: what does the CSF volume includes (the supratentorial arachnoid space? suprat + infrat?).Thank you, Carolina
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Hi, all,Does anybody know what the intracranial volume and supratentorial volume include? Does it include only the parenquima volume (white matter / gray matter volumes) or it includes the ventricules and CSF? What about the WM hhypointensities? Are they included in the WM Volume measurement or in
Hi all,
I am new to this, and wonder if you could help me set this up please.
OS: Ubuntu 10.10 ; 64 bit (a complete newbie with linux)
I am going through buckner - tutorial for the group analysis with Qdec.
I am at the step where I have to import the aseg and aparc data. I clicked
on the "genera
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