Hi all,
I have a nifti file f.nii whose size is 80*80*60*266, (266 is the TRs).
Using "mri_info f.nii", I can see that its orientation is is PIL. I want to
change it to RPI.
I do the following:
"mri_conver --in_orientation PIL --out_orientation RPI -i f.nii -o
f.rpi.nii"
It give me f.rpi.nii, wh
Hi Myriam
we are continually working to improve accuracy and robustness. Amygdala
is of course pretty difficult. Did you look at the discrepant case? If so,
which one was visually more accurate?
And yes, we expect that somewhat less editing is required in 5.1. There is
also an array of new f
Hello Freesurfer users and experts,
We already run 55 subjects with Freesurfer 5.0 and wish now to increase our
sample size up to 200 and are now deciding whether to run everybody again
with Freesurfer 5.1 or just go on with the previous version.
We are doing subcortical analysis (amygdala) and ho
this page has some notes on a particular tksurfer problem:
https://surfer.nmr.mgh.harvard.edu/fswiki/TksurferDisplayProblems
not sure if this is what you are encountering.
n.
On Mon, 2011-07-11 at 15:41 -0400, Bruce Fischl wrote:
> Hi Antonella,
>
> usually we run everything then go back and c
Hi Wang,
you can use mris_divide_parcellation.
cheers
Bruce
On Fri, 8 Jul 2011, ??? wrote:
Hi,freesurfers:
Recently,I read a paper which used freesurfer to processed their data,this
is the paper's
link:http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.0060159
In thi
Dear all,
I am delighted to announce release of Nipype version 0.4.
Nipype, an open-source, community-developed initiative under the
umbrella of NiPy, is a Python project that provides a uniform
interface to existing neuroimaging software and facilitates
interaction between these packages within a
Hi Antonella,
usually we run everything then go back and check. I'll leave 1) for Nick
and Krish.
cheers
Bruce
On Mon, 11 Jul 2011, Antonella Kis wrote:
Hi Bruce,
I
1). My LNX3 the only one which is working is a Fedora Linux, Kernel Linux
2.6.32.23-170.fc12.x86_64, GENOME 2.28.2
LNX2 wh
HiBruce,
I
1). My LNX3 the only one which is working is a Fedora Linux, Kernel Linux
2.6.32.23-170.fc12.x86_64, GENOME 2.28.2
LNX2 where I get the weird surface display is a Linux CENTOS x86_64, GENOME
2.16.0
The Analyst computer where I got the multiple frames error is a Linux, Kernel
Li
Hi Doug,
Do you have any comment regarding the easiest way to prevent
interpolation of oblique acquisitions at the conform step of the FS
pipeline?
thanks,
-MH
On Thu, 2011-06-16 at 21:21 -0400, Bruce Fischl wrote:
> Hi Mike,
>
> the intent was to be independent of the prescription of the slice
Hello All,
Is there a way to calculate the length and breadth of V1 in mm defined by the
Fischl method ? How do I do it ?
Thanks
Ri
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Fellow FreeSurfers,
How do you calculate Brain Volume in FS5.1? In 4.5 there was the
BrainSegNotVent statistic in aseg.stats, but I'm not seeing that in 5.1. I
did find something about the SupraTentorialVol, but that would exclude the
brainstem and cerebellum. I'm not sure if that also includes
what happens when the Load Project selection is run?
when it is being saved, i expect it to exist in the tmp dir while it is
being created, then it is deleted. when it is loaded, it should extract
it to that directory.
n.
On Thu, 2011-07-07 at 09:59 +0200, Tetiana Dadakova wrote:
> Hi Nick,
>
Would the best solution be to average the frames of the first file or can I
specify just one frame?
Corinna
On Mon, Jul 11, 2011 at 1:17 PM, Corinna Bauer wrote:
> Looks like it is because one of the files has multiple frames.
>
> mri_info first file:
>
> Volume information for wm.reg.pet.mgz
>
Looks like it is because one of the files has multiple frames.
mri_info first file:
Volume information for wm.reg.pet.mgz
type: MGH
dimensions: 256 x 256 x 256 x 6
voxel sizes: 1., 1., 1.
type: FLOAT (3)
fov: 256.000
dof: 0
xsta
(forgot to cc the list)...
In general, that error means the number of elements in your first input
is not equal to the number of element in your second.
Can you run the command and copy-paste the output into an email? Also,
run 'mris_calc' with '--verbosity 10'. That will print out additional
Hi Corinna,
can you run mri_info on the two volumes and see what sizes they are?
Bruce
On Mon,
11 Jul 2011, Corinna Bauer wrote:
When running fscalc, I get the following error on some of my subjects but not
all of them,
mris_calc:
Sorry, but I seem to have encountered an error.
if you export it as an annotation then all the labels will be combined in
one file. I think you are probably editing the ?h.aparc.annot, so you could
overwrite that one if you want. The correct mri_segstats command could then
be found in the subject's recon-all.log or recon-all.cmd file in the
When running fscalc, I get the following error on some of my subjects but
not all of them,
mris_calc:
Sorry, but I seem to have encountered an error.
While checking on input filetype sizes,
I found a size mismatch, i.e. len(input1)!=len(input2)
Any suggestions?
Thanks,
Co
Hi Timothy
you should be able to. You can use the -nth switch to convert
each frame individually
cheers
Bruce
On Mon, 11 Jul 2011, Timothy Brown wrote:
> Hi All,
>
> Can mri_convert be used with multiframe dicom?
>
> In attempting to use the command that was successful on non-multiframe
> di
Hi Bruce, Doug, and All:
Questions on a continuing problem:
When I run tksurfer, the caudalanteriorcingulate is invaded by the
corpuscallosum.
I edited the boundary using the instructions at:
https://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer_labeledit
I'm then instructed to "Save the annotat
Hi All,
Can mri_convert be used with multiframe dicom?
In attempting to use the command that was successful on non-multiframe
dicom I receive the following error:
/usr/local/freesurfer/bin/mri_convert -it dicom -ot analyze
401/GL.MR.Project.401.1.20100923.103636.ench9
h.0502265032.dcm ANALYZ
Good morning Bruce,
1). My LNX3 the only one which is working is a Fedora Linux, Kernel Linux
2.6.32.23-170.fc12.x86_64, GENOME 2.28.2
LNX2 where I get the weird surface display is a Linux CENTOS x86_64, GENOME
2.16.0
The Analyst computer where I got the multiple frames error is a Linux, Ker
Hi Adil - These are books that I've found useful:
http://www.amazon.com/Handbook-Pulse-Sequences-Matt-Bernstein/dp/0120928612
http://www.amazon.com/Principles-Magnetic-Resonance-Imaging-Perspective/dp/0780347234
Analysis past the image reconstruction stage is difficult to find in a
single book s
Hi Jixin
mris_divide_parcellation should do the trick. You can give it the max area
of a parcellation and it will keep subdividing along the primary eigen-axis
until no units are above that surface area.
cheers
Bruce
On Mon, 11 Jul 2011, ???
wrote:
Hellow,
Freesurfer could provide
Hellow,
Freesurfer could provide for every participant a
standardized partition of the cortex into 66 regional areas. I do not know how
to use freesurfer to subdivide these regional areas into a set of small and
compact regions of about 1.5 cm2, resulting in high resolution atlas covering the
Hi,
Is there any good MRI book that teaches the basics of MRI acquisition and
various types of sequences or maybe another that teaches basics of image
analysis?
Thanks,
AJ
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.m
26 matches
Mail list logo
