Search found 21 matches

by tizianod
Wed Oct 17, 2012 11:14 am
Forum: AIMS
Topic: AIMS 4.3 32bit / 64bit bug
Replies: 3
Views: 4354

Re: AIMS 4.3 32bit / 64bit bug

Thanks. A wolkaround I am using is to use the ascii encoding. At this regard I think it would be nice to have a -e or --ascii option in the command AimsZCat as well.
Thanks
Best
Tiziano
by tizianod
Tue Oct 16, 2012 3:23 pm
Forum: AIMS
Topic: AIMS 4.3 32bit / 64bit bug
Replies: 3
Views: 4354

Re: AIMS 4.3 32bit / 64bit bug

I shall add that the problem occours when we use the default binary output, not if we use ascii output
by tizianod
Tue Oct 16, 2012 3:09 pm
Forum: AIMS
Topic: AIMS 4.3 32bit / 64bit bug
Replies: 3
Views: 4354

AIMS 4.3 32bit / 64bit bug

Hello, I am testing AIMS 4.3 on a 64bit machine but I dicovered something strange: the result of AimsMeshBrain with output in .ply format is different if the command AimsMeshBrain comes from the 32bit or the 64bit distribution. Specifically, the output of the 64bit distribution seems to be wrong sin...
by tizianod
Thu Sep 13, 2012 4:27 pm
Forum: Anatomist
Topic: referential of saved meshes
Replies: 14
Views: 8108

Re: referential of saved meshes

Hi, As I already pointed out some time ago the masks LCortex and RCortex are not in the same space as the original image. As you suggested using the AimsFileConvert command I get the masks back in the correct 'world' space thanks to the Nifti qform transformation. However the voxel orientation in th...
by tizianod
Thu Sep 13, 2012 4:21 pm
Forum: BrainVISA
Topic: T1 bias correction error
Replies: 2
Views: 2150

Re: T1 bias correction error

I think it was because the image was already reformatted to another space (CA-CP). Would this create a problem? what is the best way to send you an image safely?

Thanks
Tiziano
by tizianod
Wed Sep 05, 2012 8:36 pm
Forum: BrainVISA
Topic: non-rigid Tailarach transformation
Replies: 4
Views: 2624

Re: non-rigid Tailarach transformation

I thought it was just an aligment to the CA-CP-IH axes (which is what I need), but if it's not rigid I guess it is actually an affine registration to the Tailarach atlas right?

Thanks a lot ;)
Tiziano
by tizianod
Wed Sep 05, 2012 5:48 pm
Forum: BrainVISA
Topic: non-rigid Tailarach transformation
Replies: 4
Views: 2624

Re: non-rigid Tailarach transformation

Thanks, is there a good reason to have the scaling factors? I Thought that theoretically should be rigid..
by tizianod
Wed Sep 05, 2012 2:09 pm
Forum: BrainVISA
Topic: non-rigid Tailarach transformation
Replies: 4
Views: 2624

non-rigid Tailarach transformation

Hello,

I noticed that, in some cases, Brainvisa computes a Tailarch transformation that is not rigid. Can this be true?
Shouldn't it be just a rigid tranformation?

Thanks
Tiziano
by tizianod
Wed Sep 05, 2012 11:31 am
Forum: BrainVISA
Topic: T1 bias correction error
Replies: 2
Views: 2150

T1 bias correction error

Hello, The Morphologist pipeline stops with the following error: Process Morphologist 2012 started on 2012/09/05 12:29 Skip unselected node: Check SPAM models installation OK, the image seems to be in the correct orientation. ------------------------------ ! VIP Warning: empty volume in VipComputeR...
by tizianod
Mon Sep 03, 2012 5:07 pm
Forum: BrainVISA
Topic: Tailarach transformation
Replies: 1
Views: 1400

Tailarach transformation

Hello, I'd like to use the Tailarach transformation calculated by BrainVisa and I want to understand better what this trasformation maps. Does it maps the i,j,k voxel indexs to Tailarach Space or the AIMS x,y,z coordinates to Tailarach space? I guess it should be the second. In this case, I know tha...
by tizianod
Thu Jun 07, 2012 2:02 pm
Forum: AIMS
Topic: references
Replies: 0
Views: 17180

references

Hello,

We used the commands AimsMesh / AimsMeshBrain for our work. Where can I find reference to the alogorithms used or paper to cite?
Similarly, is there any reference for the VipGetHead command?
by tizianod
Wed May 30, 2012 12:32 pm
Forum: BrainVISA
Topic: runtime error in T1 Bias correction
Replies: 0
Views: 16331

runtime error in T1 Bias correction

The Morpohologist 2012 pipeline stops in the estimation of the bias: Process Morphologist 2012 started on 2012/05/30 13:25 Skip unselected node: Check SPAM models installation OK, the image seems to be in the correct orientation. ------------------------------ ! VIP Warning: empty volume in VipCom...
by tizianod
Wed May 30, 2012 11:27 am
Forum: BrainVISA
Topic: Re-orient transformation
Replies: 3
Views: 1645

Re: Re-orient transformation

I am talking about the case when the initial orientation is not correct: [ [1, 0, 0, 0] [0, 1, 0, 0] [0, 0, -1, 181.99854400000001] [0, 0, 0, 1] ] WARNING: Flipping and re-writing source image voxel size orig : [1, 1, 0.99999199999999999, 1] voxel size final: [1.0, 1.0, 0.99999199999999999] dims ori...
by tizianod
Wed May 30, 2012 9:04 am
Forum: BrainVISA
Topic: Re-orient transformation
Replies: 3
Views: 1645

Re-orient transformation

I have a simple question, it must be a common issue, but I could not find the answare in the forum. When an image is re-oriented in the Morphologist pipeline (after the selection of the points CA-CP) a transformation matrix is applied and it is also displayed in the log. My question is if there is a...
by tizianod
Mon May 07, 2012 8:25 am
Forum: Anatomist
Topic: referential of saved meshes
Replies: 14
Views: 8108

Re: referential of saved meshes

Ok thanks, and yes the brain mask was already OK. Is there a workaround for the other masks in the meanwhile?

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