average
>
> cheers
> Bruce
>
>
>
> On Tue, 9 May 2017, james pardon wrote:
>
> Dear All,
>> Apologies in advance for the naive question. Could you please let me know
>> what is the best way of transferring a nifti overlay volume to fsaverage,
>> solely f
Dear All,
Apologies in advance for the naive question. Could you please let me know
what is the best way of transferring a nifti overlay volume to fsaverage,
solely for illustration purposes? I think I should start by registering
with fsaverage volume and then overlay with Freeview, but I'm not s
what pathology these subjects have? Where can I find these?
Thank you,
James Pardon
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The information in this e-mail is intended only
use our conventions (the FreeSurferColorLUT.txt for the aseg,
> or set every wm voxel to the brain.mgz intensity if it is in the white
> matter, and zero otherwise)
>
> cheers
> Bruce
>
> On Thu, 3 Dec 2015, james pardon wrote:
>
> Dear All,
>> I was wondering whe
Dear All,
I was wondering whether there is a simple way to pass T1 segmentations I
have from another software to Freesurfer, in order to do the remaining
recon-all steps?
Thank you in advance,
James
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t;
> On Sat, 22 Aug 2015, james pardon wrote:
>
> > Dear All,
> >
> > I would be grateful if someone could help me to find the correponding
> vertex
> > number on inflated and pial surfaces.
> >
> > Thanks,
> > James
> >
> >
&
Dear All,
I would be grateful if someone could help me to find the correponding
vertex number on inflated and pial surfaces.
Thanks,
James
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I would be grateful if someone could answer my question below from some
time ago.
Dear all,
I need to specify this matrix as my F contrast [1 -1 0; 0 1 -1] ,
however I'm not sure how I can do this. Usually for a matrix like [1 0
0; 0 1 0] i use
mkcontrast-sess -analysis analysis-name -contrast
Dear all,
I need to specify this matrix as my F contrast [1 -1 0; 0 1 -1] ,
however I'm not sure how I can do this. Usually for a matrix like [1 0
0; 0 1 0] i use
mkcontrast-sess -analysis analysis-name -contrast ftest -a 1 -a 2 -nosumconds
I can use -c for -1 in the contrast, but using nosumco
can give you more information
>
> cheers
> Bruce
>
> On Tue, 15 Jul 2014, james pardon wrote:
>
> Hi Bruce,
>> I was wondering whether you have seen my email below?
>>
>> Thanks so much
>>
>> Cheers,
>> James
>>
>>
>> On Sat,
Hi Bruce,
I was wondering whether you have seen my email below?
Thanks so much
Cheers,
James
On Sat, Jul 12, 2014 at 9:18 AM, james pardon
wrote:
> Hi Bruce,
>
> I have sent the link for a problem subject via a private message. Please
> note since MS causes hypointense lesi
, Bruce Fischl
wrote:
> Hi James
>
> if you upload a problem subject we will take a look (the whole subject dir
> please)
> cheers
> Bruce
>
> On Fri, 11 Jul 2014, james pardon wrote:
>
> Hi all,
>> On a few subjects with a specific pathology (MS) I cannot
Hi,
In a subject that I need to edit both wm.mgz and add some control points,
I'm wondering what is the correct recon-all options so that all changes are
applied in on additional run? I noticed that I could overwrite changes made
by one or the other if I run them in tandem (and not simultaneously)
Hi,
I'm working on some subjects with gray matter lesions, where usually these
lesions happen at the boundary of GM and WM (mostly patients with MS). The
problem is that Freesurfer can not follow the cortex past this areas.
I have tried to use control points, white matter edits and even editing t
e Fischl wrote:
>
> Hi James
>>
>> Ruopeng is traveling and may not answer quickly, although Louis might be
>> able to help
>> Bruce
>> On Mon, 23 Jun 2014, james pardon wrote:
>>
>> Sorry if you are receiving this for the second time , not really
Sorry if you are receiving this for the second time , not really sure if
this went through the first time I sent the email:
Dear all,
I'm looking for a way to automate surface on volume visualization, to check
if the surface reconstruction have been successful on a very large number
of subjects.
Dear all,
I'm looking for a way to automate surface on volume visualization, to check
if the surface reconstruction have been successful on a very large number
of subjects. Normally, I would use freeview with -f and -v flags to check
and see if it is necessary to edit controls points, etc.
As an
th -debug as the first option. Pipe
>> the output to a file, eg,
>> recon-all -debug ... |& tee recon-all.log
>> And send me recon-all.log. Note it will likely be very big!
>> doug
>>
>> On 08/03/2012 12:52 PM, james pardon wrote:
>> > works fine. Eve
t/subname/**scripts
> doug
>
>
> On 08/03/2012 12:09 PM, james pardon wrote:
>
>> Nick or Doug could you help us here?
>>
>> On Fri, Aug 3, 2012 at 8:05 PM, Bruce Fischl
>> > fis...@nmr.mgh.**harvard.edu >> wrote:
>>
>> Hi James
>
Nick or Doug could you help us here?
On Fri, Aug 3, 2012 at 8:05 PM, Bruce Fischl wrote:
> Hi James
> can you post to the list so others can answer? I'm not sure what's going
> on, but Nick or Doug might
>
>
> Bruce
>
> On Fri, 3 Aug 2012, james pardon wrote:
Hi Bruce,
subject's folder is empty, there is no scripts folder, or anything else.
Again if I omit -expert everything works fine.
Thanks
On Fri, Aug 3, 2012 at 7:36 PM, james pardon wrote:
> Hi Bruce,
>
> subject's folder is empty, there is no scripts folder, or anything
Dear all,
I'm trying to pass the following flags for mri_normalize through -expert
flag in recon-all, with a file, named expert.opts with the following single
line:
mri_normalize -b 20 -n 5
my command line is:
recon-all -i inputfile -subject subname -all -expert /expert.opts
I receive the follo
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