Re: [Freesurfer] Why does nii2mnc fail with a neck-cropped-structural Image?

[Usman Ayub]

Hi,

Writing this question helped me find my own mistake. I have been using
output_better.nii.gz instead of output_better.nii. Running gunzip
extraction before nii2mnc solves the problem.

Thanks alot,
Usman Ayub Sheikh

On Thu, Sep 7, 2017 at 4:32 PM, Usman Ayub  wrote:

> Hi Freesurfer People,
>
> The aim is get ROI masks for my functional images and to achieve that for
> each of the subjects in my data, I am:
>
> 1. Running freesurfer for segmentation of structural scan,
> 2. Running feat analysis that would give me transformation matrices
> including structural2functional and then,
> 3. I am transforming my masks from step 1 to functional space using flirt.
>
> The first step requires me to use the actual structural image and the
> second step won't produce good results if I don't do brain extraction on
> the structural image.
>
> Now the problem is, for structural image of one of the subjects, I cannot
> get good brain extraction unless I use fslroi to crop the neck out first.
> And if I do that, the transformation matrices that I get using resulting
> bet image won't be usable with the freesurfer masks that I have obtained
> using the uncropped structural image.
>
> And if I try to use fslroi-cropped-structural-image with freesurfer, the
> nii2mnc command would produce this error:
>
> $ nii2mnc output_better.nii.gz
>> ** ERROR: nifti_image_read(output_better.nii.gz): bad dim[0]
>> Segmentation fault (core dumped)
>>
>
> I don't know how am I supposed to fix this issue.
>
> Thanks,
> Usman Ayub Sh
>
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[Freesurfer] Why does nii2mnc fail with a neck-cropped-structural Image?

[Usman Ayub]

Hi Freesurfer People,

The aim is get ROI masks for my functional images and to achieve that for
each of the subjects in my data, I am:

1. Running freesurfer for segmentation of structural scan,
2. Running feat analysis that would give me transformation matrices
including structural2functional and then,
3. I am transforming my masks from step 1 to functional space using flirt.

The first step requires me to use the actual structural image and the
second step won't produce good results if I don't do brain extraction on
the structural image.

Now the problem is, for structural image of one of the subjects, I cannot
get good brain extraction unless I use fslroi to crop the neck out first.
And if I do that, the transformation matrices that I get using resulting
bet image won't be usable with the freesurfer masks that I have obtained
using the uncropped structural image.

And if I try to use fslroi-cropped-structural-image with freesurfer, the
nii2mnc command would produce this error:

$ nii2mnc output_better.nii.gz
> ** ERROR: nifti_image_read(output_better.nii.gz): bad dim[0]
> Segmentation fault (core dumped)
>

I don't know how am I supposed to fix this issue.

Thanks,
Usman Ayub Sh
___
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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.