[Freesurfer] mri_volcluster in single direction
Hello All, I've been using fslstats to create a mask of voxels reaching a certain threshold and then using mri_volcluster to reduce the mask down to just clusters above 3 voxels. Now we're trying to filter them down to just those clusters that have more than 3 contiguous voxels in a single direction, rather than total volume. I can't find anything in the help file on this, but I was wondering if there's possibly an undocumented flag in mri_volcluster that would do this? Thanks! - G. William Chapman IV ENG BME 2012 wchap...@bu.edu (617) 383-9042 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mri_convert PD
The files have been dropped.
https://www.nmr.mgh.harvard.edu/facility/filedrop/showgroup/24787/1/d2a16267b417faa9da6f7cff3c36228a
On Wed, Jun 22, 2011 at 13:21, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote:
if you file drop these volumes we'll take a look
Bruce
On Wed, 22 Jun 2011, G. William Chapman IV wrote:
Hello all,
I'm attempting to use mri_convert in order to match the slice size and
thickness of T2 and PD images to the Freesurfer T1 images, after
converting
the norm.mgz and the T2/PD images to .nii.gz. For the T2 I'm using:
mri_convert ${SUBJECT}/T2/T2.nii.gz -rl ${SUBJECT}/mri/norm.nii.gz
--like
${SUBJECT}/mri/norm.nii.gz ${**SUBJECT}/T2/T2_like_norm.nii.**gz
And having no problems. However, using the same code for the PD images I'm
arriving at a bus error each time (output below). Is there any possible
work
around for this?
(freesurfer-Darwin-leopard-**i686-stable-pub-v5.0.0)
---
bash-3.2$ mri_convert ${SUBJECT}/PD/PD.nii.gz -rl
${SUBJECT}/mri/norm.nii.gz
--like ${SUBJECT}/mri/norm.nii.gz ${SUBJECT}/PD/PD_like_norm.**nii.gz
mri_convert 003_S_0907_M00/PD/PD.nii.gz -rl 003_S_0907_M00/mri/norm.nii.gz
--like 003_S_0907_M00/mri/norm.nii.gz 003_S_0907_M00/PD/PD_like_**
norm.nii.gz
$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $
reading from 003_S_0907_M00/PD/PD.nii.gz...
TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 2.05103e-10, 0)
j_ras = (-2.05103e-10, -1, 0)
k_ras = (-0, -0, 1)
reading template info from volume 003_S_0907_M00/mri/norm.nii.**gz...
INFO: transform src into the like-volume: 003_S_0907_M00/mri/norm.nii.gz
Bus error
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Re: [Freesurfer] mri_convert PD
I'm not sure why the PD would be two frames -- the files were downloaded as
dcm from the ADNI database. After looking through them though, there was a
repeat of the slices, so I removed the second frame. Seems to have solved
the problem, as the reslice is working now.
On Thu, Jun 23, 2011 at 09:28, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote:
p.s. also, why are you specifying --like and -rl?
On Thu, 23 Jun 2011, G. William Chapman IV wrote:
The files have been dropped.https://www.nmr.mgh.**
harvard.edu/facility/filedrop/**showgroup/24787/1/**
d2a16267b417faa9da6f7cff3c3622**8ahttps://www.nmr.mgh.harvard.edu/facility/filedrop/showgroup/24787/1/d2a16267b417faa9da6f7cff3c36228a
On Wed, Jun 22, 2011 at 13:21, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:
if you file drop these volumes we'll take a look
Bruce
On Wed, 22 Jun 2011, G. William Chapman IV wrote:
Hello all,
I'm attempting to use mri_convert in order to match the slice size
and
thickness of T2 and PD images to the Freesurfer T1 images, after
converting
the norm.mgz and the T2/PD images to .nii.gz. For the T2 I'm using:
mri_convert ${SUBJECT}/T2/T2.nii.gz -rl ${SUBJECT}/mri/norm.nii.gz
--like
${SUBJECT}/mri/norm.nii.gz ${**SUBJECT}/T2/T2_like_norm.nii.**gz
And having no problems. However, using the same code for the PD
images I'm
arriving at a bus error each time (output below). Is there any
possible work
around for this?
(freesurfer-Darwin-leopard-**i686-stable-pub-v5.0.0)
---
bash-3.2$ mri_convert ${SUBJECT}/PD/PD.nii.gz -rl
${SUBJECT}/mri/norm.nii.gz
--like ${SUBJECT}/mri/norm.nii.gz ${SUBJECT}/PD/PD_like_norm.**
nii.gz
mri_convert 003_S_0907_M00/PD/PD.nii.gz -rl
003_S_0907_M00/mri/norm.nii.gz
--like 003_S_0907_M00/mri/norm.nii.gz 003_S_0907_M00/PD/PD_like_**
norm.nii.gz
$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $
reading from 003_S_0907_M00/PD/PD.nii.gz...
TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 2.05103e-10, 0)
j_ras = (-2.05103e-10, -1, 0)
k_ras = (-0, -0, 1)
reading template info from volume 003_S_0907_M00/mri/norm.nii.**
gz...
INFO: transform src into the like-volume:
003_S_0907_M00/mri/norm.nii.gz
Bus error
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is
addressed. If you believe this e-mail was sent to you in error and the
e-mail
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HelpLine at
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
[Freesurfer] mri_convert PD
Hello all,
I'm attempting to use mri_convert in order to match the slice size and
thickness of T2 and PD images to the Freesurfer T1 images, after converting
the norm.mgz and the T2/PD images to .nii.gz. For the T2 I'm using:
mri_convert ${SUBJECT}/T2/T2.nii.gz -rl ${SUBJECT}/mri/norm.nii.gz --like
${SUBJECT}/mri/norm.nii.gz ${SUBJECT}/T2/T2_like_norm.nii.gz
And having no problems. However, using the same code for the PD images I'm
arriving at a bus error each time (output below). Is there any possible work
around for this?
(freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0)
---
bash-3.2$ mri_convert ${SUBJECT}/PD/PD.nii.gz -rl ${SUBJECT}/mri/norm.nii.gz
--like ${SUBJECT}/mri/norm.nii.gz ${SUBJECT}/PD/PD_like_norm.nii.gz
mri_convert 003_S_0907_M00/PD/PD.nii.gz -rl 003_S_0907_M00/mri/norm.nii.gz
--like 003_S_0907_M00/mri/norm.nii.gz 003_S_0907_M00/PD/PD_like_norm.nii.gz
$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $
reading from 003_S_0907_M00/PD/PD.nii.gz...
TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 2.05103e-10, 0)
j_ras = (-2.05103e-10, -1, 0)
k_ras = (-0, -0, 1)
reading template info from volume 003_S_0907_M00/mri/norm.nii.gz...
INFO: transform src into the like-volume: 003_S_0907_M00/mri/norm.nii.gz
Bus error
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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