can you tell us the details of the acquisition? The contrast is intrinsic, and it has to be sufficient for g/w segmentation.

On Wed, 14 Feb 2007, Anil Roy wrote:

Nick,

The files were acquired axially(120 slices) on a GE scanner. These scans are a couple of years old. I should also inform you that I converted the orginal 120 slices into afni brik format (afni was able to read them) and then used mri_convert to convert the BRIK to cor. Freesurfer then used this cor to run the recon-all pipeline.

The original files could not be read by Freesurfer which is why I did that.

Also, this may be obvious to you but cannot the contrast be simply changed by Freesurfer. In tkmedit, the brightness and contrast can be adjusted so isn't there a way that recon-all can use this change while running the brain.

Thanks - Anil

On 2/14/07, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote:

...

Anil,

The image has almost no contrast. I've attached a TIFF of one slice. How was this acquired? Bruce, any idea why it would be so white?

Nick

On Wed, 2007-02-14 at 16:10 -0500, aroy85@gmail.com wrote:

...

The following files have been uploaded to the Martinos Center FileDrop

site

...

by Anil Roy for you to download:

(1) orig.mgz

These files will expire in 30 days.

To view or download these files, go in your web browser to:

https://www.nmr.mgh.harvard.edu/facility/filedrop/showgroup/5010/426/7389dc7...

...

DO NOT SHARE this web address with anyone else. It is your personal

access key to the files.

...

Overall Comment about files from Anil Roy:

Hi,

Attached is the orig.mgz file for the subject that quits at the

watershed step.

...

Thanks,

Anil.

Anil,

I was able to successfully run -autorecon1 (after performing my own tal alignment). This included the skullstrip.

How much memory does your machine have? It needs to have at least 2GB.

Nick

On Wed, 2007-02-14 at 15:49 -0600, Anil Roy wrote:

Nick,

The files were acquired axially(120 slices) on a GE scanner. These scans are a couple of years old. I should also inform you that I converted the orginal 120 slices into afni brik format (afni was able to read them) and then used mri_convert to convert the BRIK to cor. Freesurfer then used this cor to run the recon-all pipeline.

The original files could not be read by Freesurfer which is why I did that.

Also, this may be obvious to you but cannot the contrast be simply changed by Freesurfer. In tkmedit, the brightness and contrast can be adjusted so isn't there a way that recon-all can use this change while running the brain.

Thanks - Anil

On 2/14/07, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote: Anil,

    The image has almost no contrast.  I've attached a TIFF of one
    slice.
    How was this acquired?  Bruce, any idea why it would be so
    white?

    Nick


    On Wed, 2007-02-14 at 16:10 -0500, aroy85@gmail.com wrote:
    > The following files have been uploaded to the Martinos
    Center FileDrop site
    > by Anil Roy for you to download:
    >
    > (1) orig.mgz
    >
    >
    >
    > These files will expire in 30 days. 
    >
    > To view or download these files, go in your web browser to:
    >
    >
    https://www.nmr.mgh.harvard.edu/facility/filedrop/showgroup/5010/426/7389dc72a7ad03d19b7736c8a7adff69
    >
    > DO NOT SHARE this web address with anyone else.  It is your
    personal access key to the files.
    >
    > Overall Comment about files from Anil Roy:
    >
    > Hi,
    >
    > Attached is the orig.mgz file for the subject that quits at
    the watershed step.
    >
    > Thanks,
    >
    > Anil.
    >
    >

---

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