[Freesurfer] mri_robust_template- Segmentation Fault

2012-06-28 Thread Usman Khan
Hi there Freesurfer,
I am running into a seg fault while running mri_robust_template on
freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 on a Centos6.2 build.

Thinking that this may perhaps be an OS-related issue, I tried to download
FS binaries from
http://www.freesurfer.net/pub/dist/freesurfer/misc/linux-centos6_x86_64/
but the link is dead

Any help would be appreciated

Usman

$Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $

--satit: Will estimate SAT iteratively!
--mov: Using 191_0001.nii.gz as movable/source volume.
--mov: Using 192_0001.nii.gz as movable/source volume.
Total: 2 input volumes
--template: Using test.nii.gz as template output volume.
reading source '191_0001.nii.gz'...
reading source '192_0001.nii.gz'...
Segmentation fault (core dumped)
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[Freesurfer] Combining linear transformations

2012-07-10 Thread Usman Khan
Hi FreeSurfer,
I have two images. One MPRAGE (1x1x1mm) and a T1-weighted (0.682x0.682x3mm)
image used for CBV mapping. We have run FS, with hippocampal subfields on
the MPRAGE and would now like to transform the posterior probability maps
to the T1-weighted CBV space.

I have been using
1) mri_vol2vol with --regheader to map the posterior_* subfield files to
nu.mgz space
2) mri_robust_register to coregister the nu.mgz file to the T1-weighted CBV
image

Is there any way to combine the .reg and .lta files from (1) and (2) to
transform the subfield posterior probability maps directly from their
0.5mm^3 space to the T1-weighted CBV space? I have been reluctant to create
an intermediate volume between steps 1 and 2, as resampling the subfield
probability maps into 1x1x1mm nu.mgz space will result in loss of
resolution to the 0.68x0.68 (coronal) space in the T1-weighted CBV scan.

Any help would be appreciated

Usman
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Re: [Freesurfer] Combining linear transformations

2012-07-10 Thread Usman Khan
Hi Martin,
Thanks for the quick reply. I tried the following commands, but it looks
like the volumes are still out of line. Is there something I am missing?


to get from hc_subfield --> nu.mgz --> t1_cbv
#register and create transforms
1) mri_vol2vol --mov hc_subfield.mgz --targ nu.mgz --reg-final *
xfm_hcsubfield_to_nu.dat* --regheader
2) mri_robust_register --mov nu.mgz --dst t1_cbv.mgz --lta *xfm_nu_to_t1.lta
* --satit

#convert output from (1) from reg-final.dat to .lta
3) tkregister2 --noedit --mov hc_subfield.mgz --targ nu.mgz --reg
*xfm_hcsubfield_to_nu.dat
--ltaout test.lta*
4) mri_concatenate_lta test.lta xfm_nu_to_t1.lta *final.lta*

#apply lta file, using t1_cbv as target and hc_subfield as --mov file
5) mri_vol2vol --mov subfield --targ t1_cbv.mgz --reg *final.lta* --out
test.mgz


On Tue, Jul 10, 2012 at 6:10 PM, Martin Reuter
wrote:

> Hi Usman,
>
> you need to convert the reg to lta (using tkregister2) and then you can
> use mri_concatenate_lta .
>
> Cheers, Martin
>
>
>
> On Tue, 2012-07-10 at 17:36 -0400, Usman Khan wrote:
> > Hi FreeSurfer,
> > I have two images. One MPRAGE (1x1x1mm) and a T1-weighted
> > (0.682x0.682x3mm) image used for CBV mapping. We have run FS, with
> > hippocampal subfields on the MPRAGE and would now like to transform
> > the posterior probability maps to the T1-weighted CBV space.
> >
> >
> > I have been using
> > 1) mri_vol2vol with --regheader to map the posterior_* subfield files
> > to nu.mgz space
> > 2) mri_robust_register to coregister the nu.mgz file to the
> > T1-weighted CBV image
> >
> >
> > Is there any way to combine the .reg and .lta files from (1) and (2)
> > to transform the subfield posterior probability maps directly from
> > their 0.5mm^3 space to the T1-weighted CBV space? I have been
> > reluctant to create an intermediate volume between steps 1 and 2, as
> > resampling the subfield probability maps into 1x1x1mm nu.mgz space
> > will result in loss of resolution to the 0.68x0.68 (coronal) space in
> > the T1-weighted CBV scan.
> >
> >
> > Any help would be appreciated
> >
> >
> > Usman
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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Re: [Freesurfer] Combining linear transformations

2012-07-11 Thread Usman Khan
Hi Martin,
Thanks for the suggestion. I resolved the issue by using the --regheader
flag in tkmregister, and --reg as the default output by mri_vol2vol (even
though I did supply a reg-final flag). It seems like I mixed up the
difference between reg-final and the default registration matrix. would you
mind explaining the difference? in any event, here is my script:

for i in $(ls posterior_left_* posterior_Left-Hippocampus.mgz
posterior_right_* posterior_Right-Hippocampus.mgz); do
fname=$(basename $i); fname=${fname%%.*};
echo "$fname"
tkregister2 --noedit --reg hc_subfields/xfm_"$fname".mgz.reg --regheader
--targ nu.mgz --mov "$i" --ltaout hc_subfields/xfm_"$fname".lta
mri_concatenate_lta hc_subfields/xfm_"$fname".lta xfm_nu_to_pre.lta
hc_subfields/xfm_"$fname"_to_pregado.lta
mri_convert -at hc_subfields/xfm_"$fname"_to_pregado.lta "$i"
hc_subfields/final/final_"$fname".mgz;
done

Thanks,

Usman


On Jul 10, 2012, at 10:40 PM, Martin Reuter 
wrote:

Hi Usman ,

Try validating each step by applying each transform. I usually use
mri_convert -at
For it.

Best Martin

Usman Khan  wrote:
Hi Martin,
Thanks for the quick reply. I tried the following commands, but it looks
like the volumes are still out of line. Is there something I am missing?


to get from hc_subfield --> nu.mgz --> t1_cbv
#register and create transforms
1) mri_vol2vol --mov hc_subfield.mgz --targ nu.mgz --reg-final *
xfm_hcsubfield_to_nu.dat* --regheader
2) mri_robust_register --mov nu.mgz --dst t1_cbv.mgz --lta *xfm_nu_to_t1.lta
* --satit

#convert output from (1) from reg-final.dat to .lta
3) tkregister2 --noedit --mov hc_subfield.mgz --targ nu.mgz --reg
*xfm_hcsubfield_to_nu.dat
--ltaout test.lta*
4) mri_concatenate_lta test.lta xfm_nu_to_t1.lta *final.lta*

#apply lta file, using t1_cbv as target and hc_subfield as --mov file
5) mri_vol2vol --mov subfield --targ t1_cbv.mgz --reg *final.lta* --out
test.mgz


On Tue, Jul 10, 2012 at 6:10 PM, Martin Reuter
wrote:

> Hi Usman,
>
> you need to convert the reg to lta (using tkregister2) and then you can
> use mri_concatenate_lta .
>
> Cheers, Martin
>
>
>
> On Tue, 2012-07-10 at 17:36 -0400, Usman Khan wrote:
> > Hi FreeSurfer,
> > I have two images. One MPRAGE (1x1x1mm) and a T1-weighted
> > (0.682x0.682x3mm) image used for CBV mapping. We have run FS, with
> > hippocampal subfields on the MPRAGE and would now like to transform
> > the posterior probability maps to the T1-weighted CBV space.
> >
> >
> > I have been using
> > 1) mri_vol2vol with --regheader to map the posterior_* subfield files
> > to nu.mgz space
> > 2) mri_robust_register to coregister the nu.mgz file to the
> > T1-weighted CBV image
> >
> >
> > Is there any way to combine the .reg and .lta files from (1) and (2)
> > to transform the subfield posterior probability maps directly from
> > their 0.5mm^3 space to the T1-weighted CBV space? I have been
> > reluctant to create an intermediate volume between steps 1 and 2, as
> > resampling the subfield probability maps into 1x1x1mm nu.mgz space
> > will result in loss of resolution to the 0.68x0.68 (coronal) space in
> > the T1-weighted CBV scan.
> >
> >
> > Any help would be appreciated
> >
> >
> > Usman
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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Re: [Freesurfer] A question about hippocampal subfield segmentation

2012-08-30 Thread Usman Khan
Hi Lijie (cc to mailing list),

I wrote a script to do just this in July. Here is a link to a tar file. It
requires knowledge of matlab and bash, but is pretty straight forward. It

https://www.dropbox.com/s/s1f78j2ozv1gw8q/subfield_to_ROI.tar.gz

a) transforms the subfield probabilities to nu.mgz space (bash, using
mri_label2vol)
b) applies a threshold to the maps (Koen suggested 50% of max probability,
hence 128 of 255) to avoid over-estimation of the subfield volumes (bash)
c) comparing the probabilities of individual subfields in IJK space and
assigning a unique label to each subfield

We can continue this discussion off-line if you like
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