Hi
In monkey fmri, we usually have to do the functional-anatomical
registration manually since bbregister doesn't work very well.
It was easy in version 4.5 since we usually used just one run for
registration. In version 5.1 we can use per-run option to improve
registration but I am wonderi
Hi Wil,
Sorry about that, the link is now fixed with the most recent version of
the QAtool scripts.
-Louis
On Fri, 20 Jan 2012, Irwin, William wrote:
> Hi -
>
> The link to download the QATools script
> (http://surfer.nmr.mgh.harvard.edu/fswiki/QATools) for non-MGH users is
> broken, and I co
you can just rerun the mris_sphere command that is in the recon-all.log
(or recon-all.cmd)
cheers
Bruce
On Fri, 20 Jan 2012, Arno Klein wrote:
dear bruce,
you're right -- i am able to view the pial surface, but when i try to view
the spherical surface with tksurfer i get the same memory error
dear bruce,
you're right -- i am able to view the pial surface, but when i try to view
the spherical surface with tksurfer i get the same memory error.
is there any way to fix the sphere without affecting anything else?
neuromorphometrics has painstakingly manually edited the freesurfer labels
g
can you load the lh.sphere in tksurfer? I'm not sure it is the mgz file
that is the problem. Maybe your partition filled up and the sphere file
isn't complete?
On Fri, 20 Jan
2012, Arno Klein wrote:
dear doug,
sadly, no dice.
cheers,
@rno
On Fri, Jan 20, 2012 at 4:45 PM, Douglas N Grev
Hi Arno,
Please give these matlab commands a shot.
[v,M, mr] = load_mgh('orig.mgz');
save_mgh(v, 'orig.mgz', M, mr);
-Louis
On Fri, 20 Jan 2012, Arno Klein wrote:
> dear doug,
>
> sadly, no dice.
>
> cheers,
> @rno
>
>
>
> On Fri, Jan 20, 2012 at 4:45 PM, Douglas N Greve
> wrote:
>
>> Try doin
dear doug,
sadly, no dice.
cheers,
@rno
On Fri, Jan 20, 2012 at 4:45 PM, Douglas N Greve
wrote:
> Try doing it in matlab, so
> a = MRIread('orig.mgz');
> MRIwrite(a,'orig.mgz');
>
> doug
>
> Arno Klein wrote:
>
>>
>> dear doug,
>>
>> i am using FS v5.1 now but ran the 20 oasis subjects throug
Try doing it in matlab, so
a = MRIread('orig.mgz');
MRIwrite(a,'orig.mgz');
doug
Arno Klein wrote:
>
> dear doug,
>
> i am using FS v5.1 now but ran the 20 oasis subjects through FS v5.0.
> i am only having this trouble for one of the subjects.
>
> after the mri_convert workaround i am still ge
Hi Frank, I think this problem is only spm related when using bbregister
with the --init-spm option. This will in no way affect the anatomical
analysis. According to my notes, this happens with spm8 when it uses
analyze format. analyze is the default format used intermediate files by
spmregis
dear doug,
i am using FS v5.1 now but ran the 20 oasis subjects through FS v5.0. i am
only having this trouble for one of the subjects.
after the mri_convert workaround i am still getting the same memory
allocation error.
cheers,
@rno
On Fri, Jan 20, 2012 at 4:23 PM, Douglas N Greve
wrote:
Hi Cat,
first create and save a label of your cluster.
In a terminal, cd to the GLM directory inside qdec directory and then cd
to the folder of the contrast of interest and run
mri_segstats --id 1 --slabel fsaverage lh yourlabel --i gamma.mgh --sum
yourlabel.sum
the output yourlabel.sum will h
This is a strange problem we've been having with some mgz files that
were generated during a short period of time last summer when there was
a bug in the mgz writing code. What version of FS are you using? In the
current dev version, this should not be a problem. A work-around is to
convert the
Hello Experts:
In qdec, I would like to analyze if the thickness- entorhinal volume
correlation differs between APOE positive and negative subjects accounting for
age.
I have chosen age as a nuisance variable and entorhinal volume as a covartiate.
( hope this is correct)
Results show me several
i get the following memory allocation error for only one out of 20 oasis
subjects that i processed with freesurfer 5.1 on an ubuntu 11.10 machine
with 24gb memory:
mris_register -curv subjects/OAS1_0061_MR1/surf/lh.sphere
templates_freesurfer/lh.KKI_2.tif
subjects/OAS1_0061_MR1/surf/lh.sphere_to_K
Hi -
The link to download the QATools script
(http://surfer.nmr.mgh.harvard.edu/fswiki/QATools) for non-MGH users is broken,
and I couldn't find it by looking through the ftp download directories.
Regards,
Wil
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Hi Rudolph, try
recon-all -sphere -s subject
or run mris_sphere
doug
Rudolph Pienaar wrote:
> Hi all --
>
> If I make changes to a subject's ?h.smoothwm, how do I re-generate the
> ?h.sphere surfaces? I'd like to reduce the number of mesh vertices using
> 'mris_decimate' on a given hemisphe
Hi all --
If I make changes to a subject's ?h.smoothwm, how do I re-generate the
?h.sphere surfaces? I'd like to reduce the number of mesh vertices using
'mris_decimate' on a given hemisphere, and then (re)generate a
corresponding spherical surface.
Thanks
--
Rudolph Pienaar, M.Eng, D.Eng /
Hi everyone,
Just a quick word of warning (plus two follow-up questions): there are more
instances where your brain can get flipped. For example, I just regenerated my
surface, using the correct orientation, certain about that. If I then do
bbregister afterwards using the structural I convert b
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