On Jul 31, 2017, at 8:43 AM, Praful Agrawal <prafulag@cs.utah.edu> wrote:

@Lasthenis: Please use reply to all.

Thanks,

Praful

Begin forwarded message:

From: Lasthenis Angelidakis <lasthenis93@hotmail.com>

Subject: Απ: [shapeworks-users] Question about groom

Date: July 31, 2017 at 3:26:57 AM MDT

To: Praful Agrawal <prafulag@cs.utah.edu>

Hello Shireen,

thank you very much for your help everything works fine with the groom, but when i am running the optimize the program crushes and closes, that is due to the parameters or something else, i changed some of them but with no result, it stills crushes, can you help me?

best regards,

Lasthenis Angelidakis

---

Από: Praful Agrawal <prafulag@cs.utah.edu>
Στάλθηκε: Κυριακή, 30 Ιουλίου 2017 8:11 μμ
Προς: Lasthenis Angelidakis
Κοιν.: shapeworks-users@sci.utah.edu; Shireen Elhabian
Θέμα: Fwd: [shapeworks-users] Question about groom

 

Hi Lasthenis,

Please refer to attached email.

Thanks,

Praful

Begin forwarded message:

From: Shireen Elhabian <shireen@sci.utah.edu>

Subject: Re: [shapeworks-users] Question about groom

Date: July 30, 2017 at 10:50:37 AM MDT

To: Praful Agrawal <prafulag@cs.utah.edu>

Cc: Shireen Elhabian <shireen@sci.utah.edu>

It has to do with the “center” option. This can be disabled when doing grooming (assuming all volumes have the same physical center). However, since I don’t have access to the full dataset, I am not sure if this will hold. 

Also studio does not currently handle joint modeling of anatomical systems. So this data, caudate, sub and thalamus will have to be dealt with as three different studio projects.

Caudate and sub shapes are too thin (occupying small number of voxels), so what I did is reducing the sigma for the gaussian blur and it was a good groomed shape. However I would recommend resampling these structure to a smaller voxel size.

here are some snapshots.

<deghagdjfjpngngk.png>
<heidcejcdggombhb.png>

<ijohnjknjmhdnbme.png>

thanks and best regards

Shireen

------------------------------------------

Shireen Elhabian, M.Sc., Ph.D.
Research Assistant Professor

School of Computing
Scientific Computing and Imaging Institute
University of Utah
WEB 2815
72 Central Campus Drive, Salt Lake City, UT, 84112
Phone (801) 587-3206
Fax (801) 585-6513

On Jul 30, 2017, at 10:03 AM, Praful Agrawal <prafulag@cs.utah.edu> wrote:

<25caudate.nrrd>

<25thalamus.nrrd>

<25sub.nrrd>

On Jul 30, 2017, at 9:51 AM, Shireen Elhabian <shireen@sci.utah.edu> wrote:

I can't open the rar files !!!

Shireen

On 07/26/2017 09:19 AM, Praful Agrawal wrote:

Hi Shireen,

It seems studio is generating incorrect DT for some reason, I think it has to do with some data error but I have not been able to figure it out. Please look at it. Attached are the images provided by the user.

PS: You will need to unzip rar files.

Praful

On Jul 21, 2017, at 5:55 PM, Lasthenis Angelidakis <lasthenis93@hotmail.com> wrote:

The one contiguous block didnt't solve anything the result is the same. 

---

Από: Praful Agrawal <prafulag@cs.utah.edu>
Στάλθηκε: Σάββατο, 22 Ιουλίου 2017 2:43 πμ
Προς: Lasthenis Angelidakis
Κοιν.: shapeworks-users@sci.utah.edu
Θέμα: Re: [shapeworks-users] Question about groom

 

Okay, so I think the issue is that the shape is not one contiguous block. The binary images must have only one connected component.

Hope this helps,

Praful

On Jul 21, 2017, at 5:26 PM, Lasthenis Angelidakis <lasthenis93@hotmail.com> wrote:

---

Από: Praful Agrawal <prafulag@cs.utah.edu>
Στάλθηκε: Σάββατο, 22 Ιουλίου 2017 1:47 πμ
Προς: Lasthenis Angelidakis
Κοιν.: shapeworks-users@sci.utah.edu
Θέμα: Re: [shapeworks-users] Question about groom

 

Please share some of the binary shapes.

Thanks,

Praful

On Jul 21, 2017, at 4:35 PM, Lasthenis Angelidakis <lasthenis93@hotmail.com> wrote:

Yes I am loading binary images.

Στις 22 Ιουλ 2017 12:55 π.μ., ο χρήστης Praful Agrawal <prafulag@cs.utah.ed

okay.. just to confirm.. u are loading binary image volumes as input to shapeworks ?

On Jul 21, 2017, at 2:33 PM, Lasthenis Angelidakis <lasthenis93@hotmail.com> wrote:

Hi Praful,

unfortunately it is not a zoom problem the image is blank, it is saved as DT.nrrd file yes, i imported it and to another program but it was blank all dark.

---

Από: Praful Agrawal <prafulag@cs.utah.edu>
Στάλθηκε: Παρασκευή, 21 Ιουλίου 2017 11:17 μμ
Προς: shapeworks-users@sci.utah.edu; Lasthenis Angelidakis
Θέμα: Re: [shapeworks-users] Question about groom

 

Hi Lasthenis,

Did you try scrolling on the viz windows ? As sometimes the zoom goes beyond display limits, zooming in or out a bit restores the display. Also, did you try to save the project after groom and if it saved *_DT.nrrd files ?

Thanks,

Praful

On Jul 21, 2017, at 2:02 PM, Lasthenis Angelidakis <lasthenis93@hotmail.com> wrote:

Dear Sir or Madam,

I am a postgraduate student at Cyprus University of Technology and I am working my master thesis project, I have a problem with shapeworks studio, I import and display the images nrrd files without a problem, but when I am processing the groom function the images are disappearing, the result is no images at all, but with the given shapes to download for practice from the site, the groom process works fine. Can you give me a hint to solve that?

best regards,

Lasthenis Angelidakis

<25thalamus.rar><25sub.rar><25caudate.rar>

<17caudate_.nrrd><17caudate__DT.nrrd>