looks like the freesurfer wiki is down.
cheers,
satra
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thanks Satra,
it's back up now.
Bruce
On Tue, 28 Aug 2012, Satrajit Ghosh wrote:
> looks like the freesurfer wiki is down.
> cheers,
>
> satra
>
>
>
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Hi,
I'm not sure if this is a bug report or a feature request. I have been
using mri_convert to convert dicoms to nii.gz and mgz files, and I
have noticed some discrepancies when reading the volumes in with
MRIread in either matlab or octave. The volumes differ in their
support of the flip angle,
does NIFTI support the MR parameters? I'm not sure it does. I suspect
that 50 is correct and not 50.00745058060 (can you imagine setting
that on the console)?
On Tue, 28 Aug 2012, dgw wrote:
> Hi,
>
> I'm not sure if this is a bug report or a feature request. I have been
> using mri_convert
On most (all?) scanners TR is stored as an integer. For example, on siemens
it's in microseconds and then stored as a long. (this is the value in the
protocol, not the actual execution TR, but when/if there are no bugs, then this
is correct). When you convert a long to float (single or double
Hi Souheil,
does NIFTI store the MR parameters?
thanks
Bruce
On Tue, 28 Aug 2012, Inati, Souheil (NIH/NIMH) [E] wrote:
> On most (all?) scanners TR is stored as an integer. For example, on
siemens it's in microseconds and then stored as a long. (this is the value
in the protocol, not the ac
Hi Bruce and Freesurfers,
The standard part of the nifti_1 header specifies that the first three
dimensions are space and the fourth dimension is time and you can store
dX,dY,dZ,dT and units. This page has a nice description of that part of the
standard:
http://nifti.nimh.nih.gov/nifti-1/docum
thanks Souheil
Bruce
On Tue, 28 Aug 2012, Inati, Souheil (NIH/NIMH) [E] wrote:
> Hi Bruce and Freesurfers,
>
> The standard part of the nifti_1 header specifies that the first three
> dimensions are space and the fourth dimension is time and you can store
> dX,dY,dZ,dT and units. This page ha
Ok, so I guess my problem is that the formats don't support it. Sorry
for the run around.
D
On Tue, Aug 28, 2012 at 1:46 PM, Inati, Souheil (NIH/NIMH) [E]
wrote:
> Hi Bruce and Freesurfers,
>
> The standard part of the nifti_1 header specifies that the first three
> dimensions are space and the
You have to be clear when you say support. I don't know what you're trying to
do, but you can put anything you like in the extension part of the nifti
header. If you want to store TR, TE, flip angle, mother's date of birth, you
can. You just have to write the code to handle it. Other program
Ok, maybe I'm making this question too intricate. Here's the short version:
How can I FDR correct painted surface significance maps when I have no talraich
.xfm file and no cortical segmentation?
Thanks again,
Clark
Hi Freesurfers,
I have another monkey-specific question. I'd like to output
Hi Clark
you shouldn't need either. Load your overlays then click the button to
compute the FDR threshold in the tksurfer configure overlay interface.
cheers
Bruce
On
Tue, 28 Aug 2012, Clark Fisher wrote:
> Ok, maybe I'm making this question too intricate. Here's the short version:
> How can I
Hi Bruce,
Thanks. I actually have used this function of tksurfer, but am looking for a
way to save the corrected maps, so that they could be manipulated by other
tools (for instance, viewed by PySurfer). I recognize that this may not be an
officially supported functionality, but is there some
I'll leave that for Doug.
Bruce
On Tue, 28 Aug 2012, Clark Fisher wrote:
> Hi Bruce,
>
> Thanks. I actually have used this function of tksurfer, but am looking for a
> way to save the corrected maps, so that they could be manipulated by other
> tools (for instance, viewed by PySurfer). I recog
Hi Clark,
On Aug 28, 2012, at 11:15 AM, Clark Fisher wrote:
> Hi Bruce,
>
> Thanks. I actually have used this function of tksurfer, but am looking for a
> way to save the corrected maps, so that they could be manipulated by other
> tools (for instance, viewed by PySurfer).
Does it
Hello,
When running the mri_ca_train I am getting a Bus error near the beginning of
it.
'bash-3.2$ mri_ca_train -parc_dir Alloybrain_mask_LUTComplete_float.mgz -T1
norm.mgz Alloy single_oneAlloy.gcareading segmentation from subject's
mri/Alloybrain_mask_LUTComplete_float.mgz directoryreading
how did you change the type to float? Make sure it doesn't scale the
inputs if that is the segmentation volume. rebuild_gca_atlas.csh uses our
compute cluster queueing system which is what the pbsubmit script is.
You'll need to modify it to use whatever cluster you are using or to run
them in s
To change to type Float I used: fslmaths
Alloybrain_mask_LUTComplete.nii.gz -thr 0
Alloybrain_mask_LUTComplete_float.nii.gz -odt float
I will try some other methods for changing the data type, but if that isn't the
issue are there other cases of getting similar errors from mri_ca_train?
does that scale the values? Hopefully not. It sounds like things don't fail
after you changed to float until you get the pbsubmit problem, correct?
On Tue, 28 Aug 2012, Jeff Thompson wrote:
To change to type Float I used:
fslmaths Alloybrain_mask_LUTComplete.nii.gz -thr 0
Alloybrain_mask
Thanks a lot Nick.
It worked like a charm:
"recon-all -s struct_FS finished without error at Thu Aug 23 03:52:39
PDT 2012
done"
For other users whose OS automatically unzips the .gz,
the command to type is:
sudo tar xvf freesurfer-Darwin-tiger-ppc-stable-pub-v5.1.0.tar
Thanks!
Fidel
On
Hopefully that doesn't scale the values I will make sure it doesn't.
When running mri_ca_train by itself after changing to float the next error was
the Bus error.
When running rebuild_gca_atlas.csh I was having problems with pbsubmit, but
after avoiding that it seems to be stuck with mri_ca_tra
Oh, so you still got a bus error? I didn't realize that. Make sure the seg
volumes are ok
On Aug 28, 2012, at 6:10 PM, Jeff Thompson wrote:
> Hopefully that doesn't scale the values I will make sure it doesn't.
>
> When running mri_ca_train by itself after changing to float the next error
Looks like the careg died, probably because you ran out of memory. Was
anything else running on the machine?
On Aug 28, 2012, at 10:17 PM, Hugh Pemberton wrote:
> Hi Freesurfers,
>
> Have had this error come up after recon-all for a number of subjects and was
> wondering if you know what t
Yeah had 4/5 other processes going together, shall I just sort memory and
re-do? Thanks for such a speedy response!
Hugh
On 29 Aug 2012, at 12:35, Bruce Fischl wrote:
> Looks like the careg died, probably because you ran out of memory. Was
> anything else running on the machine?
>
>
>
> On
That's my best guess.
Good luck
Bruce
On Aug 28, 2012, at 11:07 PM, Hugh Pemberton wrote:
> Yeah had 4/5 other processes going together, shall I just sort memory and
> re-do? Thanks for such a speedy response!
> Hugh
>
> On 29 Aug 2012, at 12:35, Bruce Fischl wrote:
>
>> Looks like the c
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