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Author: Michiru Makuuchi (---.neuro.ki.se)
Date: 10-08-03 12:56
Hi Rick,
> Go ahead and open your
> ROI in an editor. Each line (after the initial comment
> lines)
> has a node index (from your spec file surface), and one or
> more
> values.
Yes, the .roi file is in such format.
# Node_ROI
# ni_type = "SUMA_1D_ROI_DATUMorint,int?"
# ni_dimen = "955"
# ni_datasize = "???"
# idcode_str =
"XYZ_D7exSCC-nzvG3i6X0qlB2A"
# Parent_idcode_str = "XYZ_5hTqkhNSMwSikbZUpjSrzQ"
# Label = "MT"
# >
13177 100
13195 100
14065 100
14078 100
...........
...........
...........
> Hmmm, one question. Does your spec file have two mappable
> surfaces (with "SAME" for MappingRef), or just one?
I cannot understand those things. What I know is that the .spec I have are:
../suma/broulle_lh.scpec
../suma/broulle_rh.spec.
>more broulle_lh.spec
# delimits comments
# Creation information:
# user : makvvci
# date : 2003 10 8 15:15:11 CEST
# machine : shuttlex
# pwd : /mnt/home1/pros/freesurfer_alpha/subjects/broulle/SUMA
# command : @SUMA_Make_Spec_FS -sid broulle
# define the group
Group = broulle
# define various States
StateDef = smoothwm
StateDef = pial
StateDef = inflated
StateDef = occip.patch.3d
StateDef = occip.patch.flat
StateDef = sphere
StateDef = white
StateDef = sphere.reg
NewSurface
SurfaceFormat = ASCII
SurfaceType = FreeSurfer
FreeSurferSurface = lh.smoothwm.asc
MappingRef = SAME
SurfaceState = smoothwm
EmbedDimension = 3
NewSurface
SurfaceFormat = ASCII
SurfaceType = FreeSurfer
FreeSurferSurface = lh.pial.asc
MappingRef = lh.smoothwm.asc
SurfaceState = pial
EmbedDimension = 3
NewSurface
SurfaceFormat = ASCII
SurfaceType = FreeSurfer
FreeSurferSurface = lh.inflated.asc
MappingRef = lh.smoothwm.asc
SurfaceState = inflated
EmbedDimension = 3
NewSurface
SurfaceFormat = ASCII
SurfaceType = FreeSurfer
FreeSurferSurface = lh.occip.patch.3d.asc
MappingRef = lh.smoothwm.asc
SurfaceState = occip.patch.3d
EmbedDimension = 3
NewSurface
SurfaceFormat = ASCII
SurfaceType = FreeSurfer
FreeSurferSurface = lh.occip.patch.flat.asc
MappingRef = lh.smoothwm.asc
SurfaceState = occip.patch.flat
EmbedDimension = 2
NewSurface
SurfaceFormat = ASCII
SurfaceType = FreeSurfer
FreeSurferSurface = lh.white.asc
MappingRef = lh.smoothwm.asc
SurfaceState = white
EmbedDimension = 3
> Once you have 2 mappable surfaces, then this is an example
> of
> the command you might use:
>
> 3dSurf2Vol
> -spec ../suma/broulle_lh.spec \
> -sv ../suma/broulle_SurfVol+orig \
> -grid_parent ../suma/broulle_SurfVol+orig \
> -sdata_1D lh.MT.1D.roi \
> -map_func max \
> -f_steps 10 \
> -prefix lh.MT
When I performed this, I got an error message as follows:
[makvvci@shuttlex broulle_afni]$ 3dSurf2Vol\
? -spec ../suma/broulle_lh.spec \
? -sv ../suma/broulle_SurfVol+orig \
? -grid_parent ../suma/broulle_SurfVol+orig \
? -sdata_1D lh.MT.1D.roi \
? -map_func max \
? -f_steps 10 \
? -prefix lh.MT
Expecting to read 6 surfaces.
vvvvvvvvvvvvvvvvvvvvvvvvvvvvSurface #0 (directly mappable), loading ...
SUMA_FreeSurfer_Read: File ../suma/lh.smoothwm.asc exists and will be read.
Comment: #!ascii version of lh.smoothwm
N_Node 186636
First 2 points [id] X Y Z:
[0] -20.754925 -84.360535 -2.469758
[1] -20.982929 -84.401917 -2.508157
Last 2 points [id] X Y Z:
[186634] -11.211194 30.097889 -26.862423
[186635] -11.689126 30.626593 -26.829609
N_FaceSet 373274
First 2 polygons:
0 1 3
4 3 1
Last 2 polygons:
186397 186635 186399
183291 186635 186397
SUMA_SurfaceMetrics: Calculating surface metrics, please be patient...
SUMA_Make_Edge_List: Min/Max number of edge hosting triangles: [2/3]
Warning SUMA_Make_Edge_List: You have edges that belong to more than two triangles. Bad for analysis assuming surface is a 2-manifold..
Error SUMA_Build_FirstNeighb: Failed in copying neighbor list! jj=8, FN->N_Neighb[91383]=9
If this is a closed surface, the problem is likely due to a tessellation error.
One or more edges may not be part of 2 and only 2 triangles.
Neighbor list for node 91383 will not be ordered as connected vertices.
Further occurences of this error will not be reported.
6 similar occurences of the error above were found in this mesh.
vvvvvvvvvvvvvvvvvvvvvvvvvvvvSurface #1 (mappable via MappingRef), loading ...
SUMA_FreeSurfer_Read: File ../suma/lh.pial.asc exists and will be read.
Comment: #!ascii version of lh.pial
N_Node 186636
First 2 points [id] X Y Z:
[0] -19.950768 -85.455627 -1.342908
[1] -20.286320 -85.487381 -1.429538
Last 2 points [id] X Y Z:
[186634] -8.934763 30.591351 -26.161388
[186635] -9.811653 31.043457 -26.597206
N_FaceSet 373274
First 2 polygons:
0 1 3
4 3 1
Last 2 polygons:
186397 186635 186399
183291 186635 186397
SUMA_SurfaceMetrics: Calculating surface metrics, please be patient...
vvvvvvvvvvvvvvvvvvvvvvvvvvvvSurface #2 (mappable via MappingRef), loading ...
SUMA_FreeSurfer_Read: File ../suma/lh.inflated.asc exists and will be read.
Comment: #!ascii version of lh.inflated
N_Node 186636
First 2 points [id] X Y Z:
[0] 20.231894 -134.274857 -5.566414
[1] 20.045263 -134.202972 -5.563775
Last 2 points [id] X Y Z:
[186634] 42.092793 53.673374 -34.600609
[186635] 42.116638 54.483070 -34.381794
N_FaceSet 373274
First 2 polygons:
0 1 3
4 3 1
Last 2 polygons:
186397 186635 186399
183291 186635 186397
SUMA_SurfaceMetrics: Calculating surface metrics, please be patient...
vvvvvvvvvvvvvvvvvvvvvvvvvvvvSurface #3 (mappable via MappingRef), loading ...
SUMA_FreeSurfer_Read: File ../suma/lh.occip.patch.3d.asc exists and will be read.
Comment: #!ascii version of patch ./lh.orig
N_Node 186515
First 2 points [id] X Y Z:
[0] 20.230000 -134.270004 -5.560000
[1] 20.040001 -134.199997 -5.560000
Last 2 points [id] X Y Z:
[186513] 37.990002 -90.690002 -22.580000
[186514] 37.740002 -90.190002 -21.820000
N_FaceSet 102750
First 2 polygons:
[parent ID:0] 0 1 3
[parent ID:1] 4 3 1
Last 2 polygons:
[parent ID:373030]186514 183486 183481
[parent ID:373031]186514 183481 183100
Warning SUMA_SurfNorm:
(IGNORE for surface patches
134748 nodes (72.245128% of total) are
not members of any FaceSets.
Their normals are set to the
unit vector.
SUMA_SurfaceMetrics: Calculating surface metrics, please be patient...
Warning SUMA_SurfaceMetrics:
(IGNORE for surface patches)
Cannot inherit Edge List
and First Neightbor.
Cause: Node number mismatch.
Independent lists will
be created.
SUMA_Make_Edge_List: Min/Max number of edge hosting triangles: [1/2]
Warning SUMA_Make_Edge_List: You have edges that form a border in the surface.
Error SUMA_Build_FirstNeighb: Failed in copying neighbor list! jj=3, FN->N_Neighb[1500]=6
If this is a closed surface, the problem is likely due to a tessellation error.
One or more edges may not be part of 2 and only 2 triangles.
Neighbor list for node 1500 will not be ordered as connected vertices.
Further occurences of this error will not be reported.
135211 similar occurences of the error above were found in this mesh.
vvvvvvvvvvvvvvvvvvvvvvvvvvvvSurface #4 (mappable via MappingRef), loading ...
SUMA_FreeSurfer_Read: File ../suma/lh.occip.patch.flat.asc exists and will be read.
Comment: #!ascii version of patch ./lh.orig
N_Node 186515
First 2 points [id] X Y Z:
[0] -5.190000 36.200001 0.000000
[1] -5.170000 36.070000 0.000000
Last 2 points [id] X Y Z:
[186513] 58.430000 56.980000 0.000000
[186514] 59.090000 57.759998 0.000000
N_FaceSet 99662
First 2 polygons:
[parent ID:0] 0 1 3
[parent ID:1] 4 3 1
Last 2 polygons:
[parent ID:373030]186514 183486 183481
[parent ID:373031]186514 183481 183100
Warning SUMA_SurfNorm:
(IGNORE for surface patches
136316 nodes (73.085811% of total) are
not members of any FaceSets.
Their normals are set to the
unit vector.
SUMA_SurfaceMetrics: Calculating surface metrics, please be patient...
Warning SUMA_SurfaceMetrics:
(IGNORE for surface patches)
Cannot inherit Edge List
and First Neightbor.
Cause: Node number mismatch.
Independent lists will
be created.
SUMA_Make_Edge_List: Min/Max number of edge hosting triangles: [1/2]
Warning SUMA_Make_Edge_List: You have edges that form a border in the surface.
Error SUMA_Build_FirstNeighb: Failed in copying neighbor list! jj=3, FN->N_Neighb[892]=5
If this is a closed surface, the problem is likely due to a tessellation error.
One or more edges may not be part of 2 and only 2 triangles.
Neighbor list for node 892 will not be ordered as connected vertices.
Further occurences of this error will not be reported.
136706 similar occurences of the error above were found in this mesh.
vvvvvvvvvvvvvvvvvvvvvvvvvvvvSurface #5 (mappable via MappingRef), loading ...
SUMA_FreeSurfer_Read: File ../suma/lh.white.asc exists and will be read.
Comment: #!ascii version of lh.white
N_Node 186636
First 2 points [id] X Y Z:
[0] -20.734705 -84.177246 -2.710882
[1] -21.171965 -84.454140 -2.933572
Last 2 points [id] X Y Z:
[186634] -11.008659 30.225010 -27.733274
[186635] -11.940505 30.429588 -28.349279
N_FaceSet 373274
First 2 polygons:
0 1 3
4 3 1
Last 2 polygons:
186397 186635 186399
183291 186635 186397
SUMA_SurfaceMetrics: Calculating surface metrics, please be patient...
** error: found 1 (of 2) mappable surfaces
Thank you for your patience for reading such a long reply.
I will be very grateful if you could tell me what I should do to get the roi in .BRIK format.
Michiru
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|
Michiru Makuuchi |
10-07-03 12:42 |
|
Fred Dick |
10-07-03 13:06 |
|
rick reynolds |
10-07-03 13:10 |
|
Michiru Makuuchi |
10-08-03 04:06 |
|
rick reynolds |
10-08-03 10:17 |
    |
Re: How to convert surface ROI to volume data new |
|
Michiru Makuuchi |
10-08-03 12:56 |
|
rick reynolds |
10-08-03 13:42 |
|
Michiru Makuuchi |
10-09-03 10:10 |
|
rick reynolds |
10-09-03 11:05 |
|
rick reynolds |
10-08-03 10:24 |
