date:20180228

Re: [HCP-Users] wbsparse

2018-02-28 Thread Timothy Coalson

The fiberTemp.nii file doesn't contain the specific data that probtrackx
needs, so no.  It contains orientation distribution parameters suitable for
visualization, while probtrackx expects many precomputed direction samples
- the visualization distribution is an approximation based on those.

Tim


On Wed, Feb 28, 2018 at 6:25 PM, Shadi, Kamal 
wrote:

> Is there anyway I can do the surface-to-surface tractography myself given
> the data provided in https://balsa.wustl.edu/study/show/W336. I can see
> there is a fiberTEMP.nii file there but I do not know if I can run
> probtrackx using it.
>
> Regards,
> Kamal
>
> From: Timothy Coalson 
> Date: Wednesday, February 28, 2018 at 6:56 PM
> To: "Glasser, Matthew" 
> Cc: "Shadi, Kamal" , "
> hcp-users@humanconnectome.org" 
> Subject: Re: [HCP-Users] wbsparse
>
> Also beware, since one of the dimensions is white matter voxels, the dconn
> from -convert-matrix4-to-matrix2 will be larger than a standard 91k dconn
> (78GB based on the information you posted, versus ~30GB for a 91k dconn).
>
> Surface-to-surface tractography would normally be done with a different
> output format.  You may be able to approximate it with a hack by generating
> a volume ROI just inside the white matter surface, but that will be
> somewhat angle-dependent in its response, so I wouldn't trust it much.
>
> Tim
>
>
> On Wed, Feb 28, 2018 at 5:04 PM, Glasser, Matthew 
> wrote:
>
>> wb_command -convert-matrix4-to-matrix2 will convert wbsparse to a dense
>> connectome file.  I’m not sure you can actually do what you are asking,
>> because all that is stored are counts of streamlines that use a particular
>> fiber orientation in a voxel.
>>
>> Peace,
>>
>> Matt.
>>
>> From: "Shadi, Kamal" 
>> Date: Wednesday, February 28, 2018 at 5:00 PM
>> To: Matt Glasser , "hcp-users@humanconnectome.org" <
>> hcp-users@humanconnectome.org>
>> Subject: Re: [HCP-Users] wbsparse
>>
>> Yes, It’s in https://balsa.wustl.edu/study/show/W336.
>>
>> From: "Glasser, Matthew" 
>> Date: Wednesday, February 28, 2018 at 5:28 PM
>> To: "Shadi, Kamal" , "
>> hcp-users@humanconnectome.org" 
>> Subject: Re: [HCP-Users] wbsparse
>>
>> Did you get that from BALSA?
>>
>> Peace,
>>
>> Matt.
>>
>> From:  on behalf of "Shadi,
>> Kamal" 
>> Date: Wednesday, February 28, 2018 at 4:25 PM
>> To: "hcp-users@humanconnectome.org" 
>> Subject: [HCP-Users] wbsparse
>>
>> Hi All,
>>
>> Is there anyway I can use trajTemp.wbsparse file to extract connectivity
>> information between a vertex on a surface and an ROI in gift label file
>> (streamline count in particular)? The information of trajTemp file is as
>> follows:
>>
>> Name: pm1.trajTEMP.wbsparse
>>
>> Type: Connectivity - Fiber Trajectory
>> TEMPORARY
>>
>> Structure:CortexLeft CortexRight Cerebellum
>> AccumbensLeft AccumbensRight AllGreyMatter AllWhiteMatter AmygdalaLeft
>> AmygdalaRight BrainStem CaudateLeft CaudateRight CerebellarWhiteMatterLeft
>> CerebellarWhiteMatterRight CerebellumLeft CerebellumRight
>> CerebralWhiteMatterLeft CerebralWhiteMatterRight Cortex
>> DiencephalonVentralLeft DiencephalonVentralRight HippocampusLeft
>> HippocampusRight Invalid Other OtherGreyMatter OtherWhiteMatter
>> PallidumLeft PallidumRight PutamenLeft PutamenRight ThalamusLeft
>> ThalamusRight
>>
>> Maps to Surface:  false
>>
>> Maps to Volume:   true
>>
>> Maps with LabelTable: false
>>
>> Maps with Palette:false
>>
>> CIFTI Dim[0]: 650534
>>
>> CIFTI Dim[1]: 32492
>>
>> ALONG_ROW map type:   BRAIN_MODELS
>>
>> Has Volume Data:  true
>>
>> Volume Dims:  225,293,186
>>
>> Volume Space: -0.43,0,0,48;0,0.43,0,-64;0,0,0.43,-48
>>
>> AccumbensLeft:591 voxels
>>
>> AccumbensRight:   575 voxels
>>
>> AmygdalaLeft: 1894 voxels
>>
>> AmygdalaRight:1669 voxels
>>
>> BrainStem:22490 voxels
>>
>> CaudateLeft:  3433 voxels
>>
>> CaudateRight: 3293 voxels
>>
>> CerebellarWhiteMatterLeft:4665 voxels
>>
>> CerebellarWhiteMatterRight:   4685 voxels
>>
>> CerebellumLeft:   22753 voxels
>>
>> CerebellumRight:  27627 voxels
>>
>> CerebralWhiteMatterLeft:  92543 voxels
>>
>> CerebralWhiteMatterRight: 93079 voxels
>>
>> CortexLeft:   159552 voxels
>>
>> CortexRight:  161301 voxels
>>
>>

Re: [HCP-Users] Pittsburgh Sleep Quality Index Component Scores

2018-02-28 Thread Ely, Benjamin

Hi Greg and co,

What’s the status on the planned release of PSQI component scores? Also, are 
there plans to release the MMSE (aka Mini) component scores?

Thank you!
-Ely

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Re: [HCP-Users] wbsparse

2018-02-28 Thread Shadi, Kamal

Is there anyway I can do the surface-to-surface tractography myself given the 
data provided in https://balsa.wustl.edu/study/show/W336. I can see there is a 
fiberTEMP.nii file there but I do not know if I can run probtrackx using it.

Regards,
Kamal

From: Timothy Coalson >
Date: Wednesday, February 28, 2018 at 6:56 PM
To: "Glasser, Matthew" >
Cc: "Shadi, Kamal" >, 
"hcp-users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] wbsparse

Also beware, since one of the dimensions is white matter voxels, the dconn from 
-convert-matrix4-to-matrix2 will be larger than a standard 91k dconn (78GB 
based on the information you posted, versus ~30GB for a 91k dconn).

Surface-to-surface tractography would normally be done with a different output 
format.  You may be able to approximate it with a hack by generating a volume 
ROI just inside the white matter surface, but that will be somewhat 
angle-dependent in its response, so I wouldn't trust it much.

Tim


On Wed, Feb 28, 2018 at 5:04 PM, Glasser, Matthew 
> wrote:
wb_command -convert-matrix4-to-matrix2 will convert wbsparse to a dense 
connectome file.  I’m not sure you can actually do what you are asking, because 
all that is stored are counts of streamlines that use a particular fiber 
orientation in a voxel.

Peace,

Matt.

From: "Shadi, Kamal" >
Date: Wednesday, February 28, 2018 at 5:00 PM
To: Matt Glasser >, 
"hcp-users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] wbsparse

Yes, It’s in https://balsa.wustl.edu/study/show/W336.

From: "Glasser, Matthew" >
Date: Wednesday, February 28, 2018 at 5:28 PM
To: "Shadi, Kamal" >, 
"hcp-users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] wbsparse

Did you get that from BALSA?

Peace,

Matt.

From: 
>
 on behalf of "Shadi, Kamal" 
>
Date: Wednesday, February 28, 2018 at 4:25 PM
To: "hcp-users@humanconnectome.org" 
>
Subject: [HCP-Users] wbsparse

Hi All,

Is there anyway I can use trajTemp.wbsparse file to extract connectivity 
information between a vertex on a surface and an ROI in gift label file 
(streamline count in particular)? The information of trajTemp file is as 
follows:


Name: pm1.trajTEMP.wbsparse

Type: Connectivity - Fiber Trajectory TEMPORARY

Structure:CortexLeft CortexRight Cerebellum 
AccumbensLeft AccumbensRight AllGreyMatter AllWhiteMatter AmygdalaLeft 
AmygdalaRight BrainStem CaudateLeft CaudateRight CerebellarWhiteMatterLeft 
CerebellarWhiteMatterRight CerebellumLeft CerebellumRight 
CerebralWhiteMatterLeft CerebralWhiteMatterRight Cortex DiencephalonVentralLeft 
DiencephalonVentralRight HippocampusLeft HippocampusRight Invalid Other 
OtherGreyMatter OtherWhiteMatter PallidumLeft PallidumRight PutamenLeft 
PutamenRight ThalamusLeft ThalamusRight

Maps to Surface:  false

Maps to Volume:   true

Maps with LabelTable: false

Maps with Palette:false

CIFTI Dim[0]: 650534

CIFTI Dim[1]: 32492

ALONG_ROW map type:   BRAIN_MODELS

Has Volume Data:  true

Volume Dims:  225,293,186

Volume Space: -0.43,0,0,48;0,0.43,0,-64;0,0,0.43,-48

AccumbensLeft:591 voxels

AccumbensRight:   575 voxels

AmygdalaLeft: 1894 voxels

AmygdalaRight:1669 voxels

BrainStem:22490 voxels

CaudateLeft:  3433 voxels

CaudateRight: 3293 voxels

CerebellarWhiteMatterLeft:4665 voxels

CerebellarWhiteMatterRight:   4685 voxels

CerebellumLeft:   22753 voxels

CerebellumRight:  27627 voxels

CerebralWhiteMatterLeft:  92543 voxels

CerebralWhiteMatterRight: 93079 voxels

CortexLeft:   159552 voxels

CortexRight:  161301 voxels

DiencephalonVentralLeft:  4361 voxels

Re: [HCP-Users] Neighbors of a vertex

2018-02-28 Thread Timothy Coalson

Workbench does this internally, but it doesn't currently have a command to
output it (the number of neighbors varies per vertex, so it could be hard
to make efficient use of in something like matlab).  The .surf.gii file has
this information in it, in the triangles array, so if you load it, you just
have to build a lookup based on that.  Each triple in the triangles array
is the vertices of a single triangle.

When we use neighbor information (things like gradient, where it needs to
respond to as small a local neighborhood as possible), we also take the
length of each edge and/or coordinates of each neighbor into account, since
the triangles don't have to be close to equilateral.  If we are doing
something that uses larger spatial extent (smoothing), we instead use
geodesic distances rather than single-hop neighbors, so that we get
circular ROIs with distance information, regardless of the mesh topology.
This is exposed for a single vertex at a time via wb_command
-surface-geodesic-distance (the full matrix would be large and takes a
while to compute, but it can be added if it would be sufficiently useful).

Tim


On Wed, Feb 28, 2018 at 1:22 PM, Shankar Tumati 
wrote:

> Hello experts,
>
> I would like to get a list of neighbors of each vertex in a 32k surface
> file. How can I do this with workbench? If not with workbench, is there
> another way to get this info?
>
> Thank you.
>
> Best,
> Shankar
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Re: [HCP-Users] Neighbors of a vertex

2018-02-28 Thread Yaroslav Halchenko

On Wed, 28 Feb 2018, Shankar Tumati wrote:

> Hello experts,

> I would like to get a list of neighbors of each vertex in a 32k surface file. 
> How can I do this with workbench? If not with workbench, is there another way 
> to get this info?

quick one:  we rely on neighborhood information in PyMVPA while 
doing surface-based or surface-guided (selects neighboring voxels)
searchlight in PyMVPA. See e.g.
http://www.pymvpa.org/generated/mvpa2.support.nibabel.surf.Surface.html?highlight=surface#mvpa2.support.nibabel.surf.Surface.neighbors
http://www.pymvpa.org/examples/searchlight_surf.html?highlight=surface

-- 
Yaroslav O. Halchenko
Center for Open Neuroscience http://centerforopenneuroscience.org
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834   Fax: +1 (603) 646-1419
WWW:   http://www.linkedin.com/in/yarik
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Re: [HCP-Users] wbsparse

2018-02-28 Thread Timothy Coalson

Also beware, since one of the dimensions is white matter voxels, the dconn
from -convert-matrix4-to-matrix2 will be larger than a standard 91k dconn
(78GB based on the information you posted, versus ~30GB for a 91k dconn).

Surface-to-surface tractography would normally be done with a different
output format.  You may be able to approximate it with a hack by generating
a volume ROI just inside the white matter surface, but that will be
somewhat angle-dependent in its response, so I wouldn't trust it much.

Tim


On Wed, Feb 28, 2018 at 5:04 PM, Glasser, Matthew 
wrote:

> wb_command -convert-matrix4-to-matrix2 will convert wbsparse to a dense
> connectome file.  I’m not sure you can actually do what you are asking,
> because all that is stored are counts of streamlines that use a particular
> fiber orientation in a voxel.
>
> Peace,
>
> Matt.
>
> From: "Shadi, Kamal" 
> Date: Wednesday, February 28, 2018 at 5:00 PM
> To: Matt Glasser , "hcp-users@humanconnectome.org" <
> hcp-users@humanconnectome.org>
> Subject: Re: [HCP-Users] wbsparse
>
> Yes, It’s in https://balsa.wustl.edu/study/show/W336.
>
> From: "Glasser, Matthew" 
> Date: Wednesday, February 28, 2018 at 5:28 PM
> To: "Shadi, Kamal" , "
> hcp-users@humanconnectome.org" 
> Subject: Re: [HCP-Users] wbsparse
>
> Did you get that from BALSA?
>
> Peace,
>
> Matt.
>
> From:  on behalf of "Shadi, Kamal"
> 
> Date: Wednesday, February 28, 2018 at 4:25 PM
> To: "hcp-users@humanconnectome.org" 
> Subject: [HCP-Users] wbsparse
>
> Hi All,
>
> Is there anyway I can use trajTemp.wbsparse file to extract connectivity
> information between a vertex on a surface and an ROI in gift label file
> (streamline count in particular)? The information of trajTemp file is as
> follows:
>
> Name: pm1.trajTEMP.wbsparse
>
> Type: Connectivity - Fiber Trajectory TEMPORARY
>
> Structure:CortexLeft CortexRight Cerebellum
> AccumbensLeft AccumbensRight AllGreyMatter AllWhiteMatter AmygdalaLeft
> AmygdalaRight BrainStem CaudateLeft CaudateRight CerebellarWhiteMatterLeft
> CerebellarWhiteMatterRight CerebellumLeft CerebellumRight
> CerebralWhiteMatterLeft CerebralWhiteMatterRight Cortex
> DiencephalonVentralLeft DiencephalonVentralRight HippocampusLeft
> HippocampusRight Invalid Other OtherGreyMatter OtherWhiteMatter
> PallidumLeft PallidumRight PutamenLeft PutamenRight ThalamusLeft
> ThalamusRight
>
> Maps to Surface:  false
>
> Maps to Volume:   true
>
> Maps with LabelTable: false
>
> Maps with Palette:false
>
> CIFTI Dim[0]: 650534
>
> CIFTI Dim[1]: 32492
>
> ALONG_ROW map type:   BRAIN_MODELS
>
> Has Volume Data:  true
>
> Volume Dims:  225,293,186
>
> Volume Space: -0.43,0,0,48;0,0.43,0,-64;0,0,0.43,-48
>
> AccumbensLeft:591 voxels
>
> AccumbensRight:   575 voxels
>
> AmygdalaLeft: 1894 voxels
>
> AmygdalaRight:1669 voxels
>
> BrainStem:22490 voxels
>
> CaudateLeft:  3433 voxels
>
> CaudateRight: 3293 voxels
>
> CerebellarWhiteMatterLeft:4665 voxels
>
> CerebellarWhiteMatterRight:   4685 voxels
>
> CerebellumLeft:   22753 voxels
>
> CerebellumRight:  27627 voxels
>
> CerebralWhiteMatterLeft:  92543 voxels
>
> CerebralWhiteMatterRight: 93079 voxels
>
> CortexLeft:   159552 voxels
>
> CortexRight:  161301 voxels
>
> DiencephalonVentralLeft:  4361 voxels
>
> DiencephalonVentralRight: 3784 voxels
>
> HippocampusLeft:  4503 voxels
>
> HippocampusRight: 4413 voxels
>
> PallidumLeft: 2183 voxels
>
> PallidumRight:2320 voxels
>
> PutamenLeft:  8039 voxels
>
> PutamenRight: 7422 voxels
>
> ThalamusLeft: 6502 voxels
>
> ThalamusRight:6857 voxels
>
> ALONG_COLUMN map type:BRAIN_MODELS
>
> Has Volume Data:  false
>
> CortexLeft:   32492 out of 32492 vertices
>
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Re: [HCP-Users] wbsparse

2018-02-28 Thread Glasser, Matthew

wb_command -convert-matrix4-to-matrix2 will convert wbsparse to a dense 
connectome file.  I’m not sure you can actually do what you are asking, because 
all that is stored are counts of streamlines that use a particular fiber 
orientation in a voxel.

Peace,

Matt.

From: "Shadi, Kamal" >
Date: Wednesday, February 28, 2018 at 5:00 PM
To: Matt Glasser >, 
"hcp-users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] wbsparse

Yes, It’s in https://balsa.wustl.edu/study/show/W336.

From: "Glasser, Matthew" >
Date: Wednesday, February 28, 2018 at 5:28 PM
To: "Shadi, Kamal" >, 
"hcp-users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] wbsparse

Did you get that from BALSA?

Peace,

Matt.

From: 
>
 on behalf of "Shadi, Kamal" 
>
Date: Wednesday, February 28, 2018 at 4:25 PM
To: "hcp-users@humanconnectome.org" 
>
Subject: [HCP-Users] wbsparse

Hi All,

Is there anyway I can use trajTemp.wbsparse file to extract connectivity 
information between a vertex on a surface and an ROI in gift label file 
(streamline count in particular)? The information of trajTemp file is as 
follows:


Name: pm1.trajTEMP.wbsparse

Type: Connectivity - Fiber Trajectory TEMPORARY

Structure:CortexLeft CortexRight Cerebellum 
AccumbensLeft AccumbensRight AllGreyMatter AllWhiteMatter AmygdalaLeft 
AmygdalaRight BrainStem CaudateLeft CaudateRight CerebellarWhiteMatterLeft 
CerebellarWhiteMatterRight CerebellumLeft CerebellumRight 
CerebralWhiteMatterLeft CerebralWhiteMatterRight Cortex DiencephalonVentralLeft 
DiencephalonVentralRight HippocampusLeft HippocampusRight Invalid Other 
OtherGreyMatter OtherWhiteMatter PallidumLeft PallidumRight PutamenLeft 
PutamenRight ThalamusLeft ThalamusRight

Maps to Surface:  false

Maps to Volume:   true

Maps with LabelTable: false

Maps with Palette:false

CIFTI Dim[0]: 650534

CIFTI Dim[1]: 32492

ALONG_ROW map type:   BRAIN_MODELS

Has Volume Data:  true

Volume Dims:  225,293,186

Volume Space: -0.43,0,0,48;0,0.43,0,-64;0,0,0.43,-48

AccumbensLeft:591 voxels

AccumbensRight:   575 voxels

AmygdalaLeft: 1894 voxels

AmygdalaRight:1669 voxels

BrainStem:22490 voxels

CaudateLeft:  3433 voxels

CaudateRight: 3293 voxels

CerebellarWhiteMatterLeft:4665 voxels

CerebellarWhiteMatterRight:   4685 voxels

CerebellumLeft:   22753 voxels

CerebellumRight:  27627 voxels

CerebralWhiteMatterLeft:  92543 voxels

CerebralWhiteMatterRight: 93079 voxels

CortexLeft:   159552 voxels

CortexRight:  161301 voxels

DiencephalonVentralLeft:  4361 voxels

DiencephalonVentralRight: 3784 voxels

HippocampusLeft:  4503 voxels

HippocampusRight: 4413 voxels

PallidumLeft: 2183 voxels

PallidumRight:2320 voxels

PutamenLeft:  8039 voxels

PutamenRight: 7422 voxels

ThalamusLeft: 6502 voxels

ThalamusRight:6857 voxels

ALONG_COLUMN map type:BRAIN_MODELS

Has Volume Data:  false

CortexLeft:   32492 out of 32492 vertices

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Re: [HCP-Users] wbsparse

2018-02-28 Thread Shadi, Kamal

Yes, It’s in https://balsa.wustl.edu/study/show/W336.

From: "Glasser, Matthew" >
Date: Wednesday, February 28, 2018 at 5:28 PM
To: "Shadi, Kamal" >, 
"hcp-users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] wbsparse

Did you get that from BALSA?

Peace,

Matt.

From: 
>
 on behalf of "Shadi, Kamal" 
>
Date: Wednesday, February 28, 2018 at 4:25 PM
To: "hcp-users@humanconnectome.org" 
>
Subject: [HCP-Users] wbsparse

Hi All,

Is there anyway I can use trajTemp.wbsparse file to extract connectivity 
information between a vertex on a surface and an ROI in gift label file 
(streamline count in particular)? The information of trajTemp file is as 
follows:


Name: pm1.trajTEMP.wbsparse

Type: Connectivity - Fiber Trajectory TEMPORARY

Structure:CortexLeft CortexRight Cerebellum 
AccumbensLeft AccumbensRight AllGreyMatter AllWhiteMatter AmygdalaLeft 
AmygdalaRight BrainStem CaudateLeft CaudateRight CerebellarWhiteMatterLeft 
CerebellarWhiteMatterRight CerebellumLeft CerebellumRight 
CerebralWhiteMatterLeft CerebralWhiteMatterRight Cortex DiencephalonVentralLeft 
DiencephalonVentralRight HippocampusLeft HippocampusRight Invalid Other 
OtherGreyMatter OtherWhiteMatter PallidumLeft PallidumRight PutamenLeft 
PutamenRight ThalamusLeft ThalamusRight

Maps to Surface:  false

Maps to Volume:   true

Maps with LabelTable: false

Maps with Palette:false

CIFTI Dim[0]: 650534

CIFTI Dim[1]: 32492

ALONG_ROW map type:   BRAIN_MODELS

Has Volume Data:  true

Volume Dims:  225,293,186

Volume Space: -0.43,0,0,48;0,0.43,0,-64;0,0,0.43,-48

AccumbensLeft:591 voxels

AccumbensRight:   575 voxels

AmygdalaLeft: 1894 voxels

AmygdalaRight:1669 voxels

BrainStem:22490 voxels

CaudateLeft:  3433 voxels

CaudateRight: 3293 voxels

CerebellarWhiteMatterLeft:4665 voxels

CerebellarWhiteMatterRight:   4685 voxels

CerebellumLeft:   22753 voxels

CerebellumRight:  27627 voxels

CerebralWhiteMatterLeft:  92543 voxels

CerebralWhiteMatterRight: 93079 voxels

CortexLeft:   159552 voxels

CortexRight:  161301 voxels

DiencephalonVentralLeft:  4361 voxels

DiencephalonVentralRight: 3784 voxels

HippocampusLeft:  4503 voxels

HippocampusRight: 4413 voxels

PallidumLeft: 2183 voxels

PallidumRight:2320 voxels

PutamenLeft:  8039 voxels

PutamenRight: 7422 voxels

ThalamusLeft: 6502 voxels

ThalamusRight:6857 voxels

ALONG_COLUMN map type:BRAIN_MODELS

Has Volume Data:  false

CortexLeft:   32492 out of 32492 vertices

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Re: [HCP-Users] wbsparse

2018-02-28 Thread Glasser, Matthew

Did you get that from BALSA?

Peace,

Matt.

From: 
>
 on behalf of "Shadi, Kamal" 
>
Date: Wednesday, February 28, 2018 at 4:25 PM
To: "hcp-users@humanconnectome.org" 
>
Subject: [HCP-Users] wbsparse

Hi All,

Is there anyway I can use trajTemp.wbsparse file to extract connectivity 
information between a vertex on a surface and an ROI in gift label file 
(streamline count in particular)? The information of trajTemp file is as 
follows:


Name: pm1.trajTEMP.wbsparse

Type: Connectivity - Fiber Trajectory TEMPORARY

Structure:CortexLeft CortexRight Cerebellum 
AccumbensLeft AccumbensRight AllGreyMatter AllWhiteMatter AmygdalaLeft 
AmygdalaRight BrainStem CaudateLeft CaudateRight CerebellarWhiteMatterLeft 
CerebellarWhiteMatterRight CerebellumLeft CerebellumRight 
CerebralWhiteMatterLeft CerebralWhiteMatterRight Cortex DiencephalonVentralLeft 
DiencephalonVentralRight HippocampusLeft HippocampusRight Invalid Other 
OtherGreyMatter OtherWhiteMatter PallidumLeft PallidumRight PutamenLeft 
PutamenRight ThalamusLeft ThalamusRight

Maps to Surface:  false

Maps to Volume:   true

Maps with LabelTable: false

Maps with Palette:false

CIFTI Dim[0]: 650534

CIFTI Dim[1]: 32492

ALONG_ROW map type:   BRAIN_MODELS

Has Volume Data:  true

Volume Dims:  225,293,186

Volume Space: -0.43,0,0,48;0,0.43,0,-64;0,0,0.43,-48

AccumbensLeft:591 voxels

AccumbensRight:   575 voxels

AmygdalaLeft: 1894 voxels

AmygdalaRight:1669 voxels

BrainStem:22490 voxels

CaudateLeft:  3433 voxels

CaudateRight: 3293 voxels

CerebellarWhiteMatterLeft:4665 voxels

CerebellarWhiteMatterRight:   4685 voxels

CerebellumLeft:   22753 voxels

CerebellumRight:  27627 voxels

CerebralWhiteMatterLeft:  92543 voxels

CerebralWhiteMatterRight: 93079 voxels

CortexLeft:   159552 voxels

CortexRight:  161301 voxels

DiencephalonVentralLeft:  4361 voxels

DiencephalonVentralRight: 3784 voxels

HippocampusLeft:  4503 voxels

HippocampusRight: 4413 voxels

PallidumLeft: 2183 voxels

PallidumRight:2320 voxels

PutamenLeft:  8039 voxels

PutamenRight: 7422 voxels

ThalamusLeft: 6502 voxels

ThalamusRight:6857 voxels

ALONG_COLUMN map type:BRAIN_MODELS

Has Volume Data:  false

CortexLeft:   32492 out of 32492 vertices

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Re: [HCP-Users] Concatenate sessions from Emotion task

2018-02-28 Thread David Hofmann

Alright, thanks a bunch :)

greetings

David

2018-02-28 18:05 GMT+01:00 Harms, Michael :

>
>
> Just compute the length of the run implied by the number of frames (#
> frames * TR), and check if any events in the .txt files from the first run
> have an onset later than that!
>
>
>
> --
>
> Michael Harms, Ph.D.
>
> ---
>
> Conte Center for the Neuroscience of Mental Disorders
>
> Washington University School of Medicine
>
> Department of Psychiatry, Box 8134
>
> 660 South Euclid Ave
> .
> Tel: 314-747-6173 <(314)%20747-6173>
>
> St. Louis, MO  63110  Email:
> mha...@wustl.edu
>
>
>
> *From: *David Hofmann 
> *Date: *Wednesday, February 28, 2018 at 11:03 AM
>
> *To: *"Harms, Michael" 
> *Cc: *"Glasser, Matthew" , hcp-users <
> hcp-users@humanconnectome.org>
> *Subject: *Re: [HCP-Users] Concatenate sessions from Emotion task
>
>
>
> Hey again,
>
>
>
> how can I check for this?
>
>
>
> 2018-02-28 15:52 GMT+01:00 Harms, Michael :
>
>
>
> Also, there may (very rarely) be cases where the first emotion run was
> aborted (or recon stopped/crashed), while the EPRIME script itself
> continued to completion.  I’m not sure if we edited those condition .txt
> files to ensure that there were no events listed beyond the actual
> available number of frames, because it wouldn’t have mattered in our model
> framework (when modeling each run separately).  But it would matter in your
> situation, so you probably need to add some additional checks for that
> situation.
>
>
>
> --
>
> Michael Harms, Ph.D.
>
> ---
>
> Conte Center for the Neuroscience of Mental Disorders
>
> Washington University School of Medicine
>
> Department of Psychiatry, Box 8134
>
> 660 South Euclid Ave
> .
> Tel: 314-747-6173 <(314)%20747-6173>
>
> St. Louis, MO  63110  Email:
> mha...@wustl.edu
>
>
>
> *From: *David Hofmann 
> *Date: *Wednesday, February 28, 2018 at 8:45 AM
>
>
> *To: *"Harms, Michael" 
> *Cc: *"Glasser, Matthew" , hcp-users <
> hcp-users@humanconnectome.org>
> *Subject: *Re: [HCP-Users] Concatenate sessions from Emotion task
>
>
>
> Ok, there were some rounding inaccuracies, get the same onsets as you now!
>
>
>
> Thanks for the hint, I will make sure to check the number of frames for
> each file.
>
>
>
> Thanks again,
>
>
>
> David
>
>
>
> 2018-02-28 15:05 GMT+01:00 Harms, Michael :
>
>
>
> Sure, that’s close.  (I get 158.787, 200.93, and 243.073).
>
>
>
> Make sure you use the actual number of frames in the first run (to
> properly determine the correct offset in the case that the first emotion
> run was aborted a little early).  i.e., don’t assume that the first emotion
> run will **always** have 176 frames.
>
>
>
> Cheers,
>
> -MH
>
>
>
>
>
> --
>
> Michael Harms, Ph.D.
>
> ---
>
> Conte Center for the Neuroscience of Mental Disorders
>
> Washington University School of Medicine
>
> Department of Psychiatry, Box 8134
>
> 660 South Euclid Ave
> .
> Tel: 314-747-6173 <(314)%20747-6173>
>
> St. Louis, MO  63110  Email:
> mha...@wustl.edu
>
>
>
> *From: *David Hofmann 
> *Date: *Wednesday, February 28, 2018 at 7:50 AM
> *To: *"Harms, Michael" 
> *Cc: *"Glasser, Matthew" , hcp-users <
> hcp-users@humanconnectome.org>
>
>
> *Subject: *Re: [HCP-Users] Concatenate sessions from Emotion task
>
>
>
> Hi Michael,
>
>
>
> there is an SPM function that handles the concatenation by adding session
> regressors and adjusting the high-pass filter. I'm still pondering if I
> want to include a regressor that accounts for the transition between
> sessions, but not sure how it would look like. Any ideas on that?
>
>
>
> Ok, that sounds easy :).
>
>
>
> TR=0.72
>
> and number of volumes in the emotion task is: 176
>
>
>
> My onsets of session 2 are:
>
>
>
> 32.067
>
> 74.21
>
> 116.353
>
>
>
> So I will just add: 0.72*176=126,72 to all onsets and get:
>
>
>
> 158,800
>
> 200,943
>
> 243,085
>
>
>
> Can you confirm I got this right?
>
>
>
>
>
> greetings
>
>
>
> David
>
>
>
>
>
> 2018-02-27 16:01 GMT+01:00 Harms, Michael :
>
>
>
> Well, you know the TR, and the number of frames in the first run, so just
> add the product of those two to the times in the 2nd run (unless you are
> manually deleting additional frames at the start of either run).
>
>
>
> Cheers,
>
> -MH
>
>
>
> --
>
> Michael Harms, Ph.D.
>
>

[HCP-Users] Neighbors of a vertex

2018-02-28 Thread Shankar Tumati

Hello experts,

I would like to get a list of neighbors of each vertex in a 32k surface file. 
How can I do this with workbench? If not with workbench, is there another way 
to get this info?

Thank you.

Best,
Shankar
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[HCP-Users] FreeSurfer processing in Structural preprocessing

2018-02-28 Thread Pubuditha Abeyasinghe

Hi all,

I am trying to adopt the HCP pipeline to preprocess our data.
As the first step I am trying the execution of the pipeline with the example 
data that is given in the tutorial. The first part which is the PreFreeSurfer 
processing was completed successfully.

But I am having a problem with the second part, the FreeSurfer processing. When 
I start it, the process instantly comes to an end giving me the following error;

~/Pipelines/FreeSurfer/FreeSurferPipeline.sh: line 41: recon-all.v6.hires: 
command not found

I double check the freesurfer installation and I source it as explained as 
well. Does this error has something to do with the installation? How can I fix 
it? Thank you very much for your help!

Regards,
Pubuditha



[Western University]
Pubuditha Abeyasinghe
PhD Candidate
Department of Physics and Astronomy
Brain and Mind Institute
Western University
London, ON, Canada
email: pabey...@uwo.ca

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Re: [HCP-Users] Concatenate sessions from Emotion task

2018-02-28 Thread Harms, Michael


Just compute the length of the run implied by the number of frames (# frames * 
TR), and check if any events in the .txt files from the first run have an onset 
later than that!

--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110  Email: 
mha...@wustl.edu

From: David Hofmann 
Date: Wednesday, February 28, 2018 at 11:03 AM
To: "Harms, Michael" 
Cc: "Glasser, Matthew" , hcp-users 

Subject: Re: [HCP-Users] Concatenate sessions from Emotion task

Hey again,

how can I check for this?

2018-02-28 15:52 GMT+01:00 Harms, Michael 
>:

Also, there may (very rarely) be cases where the first emotion run was aborted 
(or recon stopped/crashed), while the EPRIME script itself continued to 
completion.  I’m not sure if we edited those condition .txt files to ensure 
that there were no events listed beyond the actual available number of frames, 
because it wouldn’t have mattered in our model framework (when modeling each 
run separately).  But it would matter in your situation, so you probably need 
to add some additional checks for that situation.

--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid 
Ave.  
  Tel: 314-747-6173
St. Louis, MO  63110  Email: 
mha...@wustl.edu

From: David Hofmann >
Date: Wednesday, February 28, 2018 at 8:45 AM

To: "Harms, Michael" >
Cc: "Glasser, Matthew" >, 
hcp-users >
Subject: Re: [HCP-Users] Concatenate sessions from Emotion task

Ok, there were some rounding inaccuracies, get the same onsets as you now!

Thanks for the hint, I will make sure to check the number of frames for each 
file.

Thanks again,

David

2018-02-28 15:05 GMT+01:00 Harms, Michael 
>:

Sure, that’s close.  (I get 158.787, 200.93, and 243.073).

Make sure you use the actual number of frames in the first run (to properly 
determine the correct offset in the case that the first emotion run was aborted 
a little early).  i.e., don’t assume that the first emotion run will *always* 
have 176 frames.

Cheers,
-MH


--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid 
Ave.  
  Tel: 314-747-6173
St. Louis, MO  63110  Email: 
mha...@wustl.edu

From: David Hofmann >
Date: Wednesday, February 28, 2018 at 7:50 AM
To: "Harms, Michael" >
Cc: "Glasser, Matthew" >, 
hcp-users >

Subject: Re: [HCP-Users] Concatenate sessions from Emotion task

Hi Michael,

there is an SPM function that handles the concatenation by adding session 
regressors and adjusting the high-pass filter. I'm still pondering if I want to 
include a regressor that accounts for the transition between sessions, but not 
sure how it would look like. Any ideas on that?

Ok, that sounds easy :).

TR=0.72
and number of volumes in the emotion task is: 176

My onsets of session 2 are:

32.067
74.21
116.353

So I will just add: 0.72*176=126,72 to all onsets and get:

158,800
200,943
243,085

Can you confirm I got this right?


greetings

David


2018-02-27 16:01 GMT+01:00 Harms, Michael 
>:

Well, you know the TR, and the number of frames in the first run, so just add 
the product of those two to the times in the 2nd run (unless you are manually 
deleting additional frames at the start of either run).

Cheers,
-MH

--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid

Re: [HCP-Users] Concatenate sessions from Emotion task

2018-02-28 Thread David Hofmann

Hey again,

how can I check for this?

2018-02-28 15:52 GMT+01:00 Harms, Michael :

>
>
> Also, there may (very rarely) be cases where the first emotion run was
> aborted (or recon stopped/crashed), while the EPRIME script itself
> continued to completion.  I’m not sure if we edited those condition .txt
> files to ensure that there were no events listed beyond the actual
> available number of frames, because it wouldn’t have mattered in our model
> framework (when modeling each run separately).  But it would matter in your
> situation, so you probably need to add some additional checks for that
> situation.
>
>
>
> --
>
> Michael Harms, Ph.D.
>
> ---
>
> Conte Center for the Neuroscience of Mental Disorders
>
> Washington University School of Medicine
>
> Department of Psychiatry, Box 8134
>
> 660 South Euclid Ave
> .
> Tel: 314-747-6173 <(314)%20747-6173>
>
> St. Louis, MO  63110  Email:
> mha...@wustl.edu
>
>
>
> *From: *David Hofmann 
> *Date: *Wednesday, February 28, 2018 at 8:45 AM
>
> *To: *"Harms, Michael" 
> *Cc: *"Glasser, Matthew" , hcp-users <
> hcp-users@humanconnectome.org>
> *Subject: *Re: [HCP-Users] Concatenate sessions from Emotion task
>
>
>
> Ok, there were some rounding inaccuracies, get the same onsets as you now!
>
>
>
> Thanks for the hint, I will make sure to check the number of frames for
> each file.
>
>
>
> Thanks again,
>
>
>
> David
>
>
>
> 2018-02-28 15:05 GMT+01:00 Harms, Michael :
>
>
>
> Sure, that’s close.  (I get 158.787, 200.93, and 243.073).
>
>
>
> Make sure you use the actual number of frames in the first run (to
> properly determine the correct offset in the case that the first emotion
> run was aborted a little early).  i.e., don’t assume that the first emotion
> run will **always** have 176 frames.
>
>
>
> Cheers,
>
> -MH
>
>
>
>
>
> --
>
> Michael Harms, Ph.D.
>
> ---
>
> Conte Center for the Neuroscience of Mental Disorders
>
> Washington University School of Medicine
>
> Department of Psychiatry, Box 8134
>
> 660 South Euclid Ave
> .
> Tel: 314-747-6173 <(314)%20747-6173>
>
> St. Louis, MO  63110  Email:
> mha...@wustl.edu
>
>
>
> *From: *David Hofmann 
> *Date: *Wednesday, February 28, 2018 at 7:50 AM
> *To: *"Harms, Michael" 
> *Cc: *"Glasser, Matthew" , hcp-users <
> hcp-users@humanconnectome.org>
>
>
> *Subject: *Re: [HCP-Users] Concatenate sessions from Emotion task
>
>
>
> Hi Michael,
>
>
>
> there is an SPM function that handles the concatenation by adding session
> regressors and adjusting the high-pass filter. I'm still pondering if I
> want to include a regressor that accounts for the transition between
> sessions, but not sure how it would look like. Any ideas on that?
>
>
>
> Ok, that sounds easy :).
>
>
>
> TR=0.72
>
> and number of volumes in the emotion task is: 176
>
>
>
> My onsets of session 2 are:
>
>
>
> 32.067
>
> 74.21
>
> 116.353
>
>
>
> So I will just add: 0.72*176=126,72 to all onsets and get:
>
>
>
> 158,800
>
> 200,943
>
> 243,085
>
>
>
> Can you confirm I got this right?
>
>
>
>
>
> greetings
>
>
>
> David
>
>
>
>
>
> 2018-02-27 16:01 GMT+01:00 Harms, Michael :
>
>
>
> Well, you know the TR, and the number of frames in the first run, so just
> add the product of those two to the times in the 2nd run (unless you are
> manually deleting additional frames at the start of either run).
>
>
>
> Cheers,
>
> -MH
>
>
>
> --
>
> Michael Harms, Ph.D.
>
> ---
>
> Conte Center for the Neuroscience of Mental Disorders
>
> Washington University School of Medicine
>
> Department of Psychiatry, Box 8134
>
> 660 South Euclid Ave
> .
> Tel: 314-747-6173 <(314)%20747-6173>
>
> St. Louis, MO  63110  Email:
> mha...@wustl.edu
>
>
>
> *From: * on behalf of David
> Hofmann 
> *Date: *Tuesday, February 27, 2018 at 7:48 AM
> *To: *"Glasser, Matthew" 
> *Cc: *hcp-users 
> *Subject: *Re: [HCP-Users] Concatenate sessions from Emotion task
>
>
>
> Hi Matthew,
>
>
>
> I basically want to have one file, that is the concatenation of the RL and
> LR files and one file with the onsets for the fear and neut conditions for
> both sessions. For example, subject 100206 has one fear.txt file for each
> session with the following block onsets:
>
>
>
> 32.08 18  1
>
> 74.223 18
>
> 1
>
> 116.365 18
>
> 1
>
>
>
> for the first session

Re: [HCP-Users] rerunning FreeSurferPipelineBatch script

2018-02-28 Thread Darko Komnenić

Thanks a lot!

On Wed, Feb 28, 2018 at 3:51 PM, Glasser, Matthew 
wrote:

> I think it will be okay to just rerun the FreeSurferPipeline if you delete
> the FreeSurfer folder
>
> ${StudyFolder}/${Subject}/T1w/${Subject}
>
> Peace,
>
> Matt.
>
> From:  on behalf of Darko Komnenić
> 
> Date: Wednesday, February 28, 2018 at 8:16 AM
> To: "hcp-users@humanconnectome.org" 
> Subject: [HCP-Users] rerunning FreeSurferPipelineBatch script
>
> Dear HCP experts,
> if the PreFreeSurferPipelineBatch script finished successfully, and then
> the FreeSurfer one finished with errors, but made some new output files
> before stopping, is it OK to just simply rerun FreeSurferPipeline script on
> the same participants? Or should I first delete all the new files that were
> added by this script, and leave only the ones that were there after the
> PreFreeSurfer script finished?
>
> Thanks,
> Darko
>
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>

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Re: [HCP-Users] Concatenate sessions from Emotion task

2018-02-28 Thread Harms, Michael


Also, there may (very rarely) be cases where the first emotion run was aborted 
(or recon stopped/crashed), while the EPRIME script itself continued to 
completion.  I’m not sure if we edited those condition .txt files to ensure 
that there were no events listed beyond the actual available number of frames, 
because it wouldn’t have mattered in our model framework (when modeling each 
run separately).  But it would matter in your situation, so you probably need 
to add some additional checks for that situation.

--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110  Email: 
mha...@wustl.edu

From: David Hofmann 
Date: Wednesday, February 28, 2018 at 8:45 AM
To: "Harms, Michael" 
Cc: "Glasser, Matthew" , hcp-users 

Subject: Re: [HCP-Users] Concatenate sessions from Emotion task

Ok, there were some rounding inaccuracies, get the same onsets as you now!

Thanks for the hint, I will make sure to check the number of frames for each 
file.

Thanks again,

David

2018-02-28 15:05 GMT+01:00 Harms, Michael 
>:

Sure, that’s close.  (I get 158.787, 200.93, and 243.073).

Make sure you use the actual number of frames in the first run (to properly 
determine the correct offset in the case that the first emotion run was aborted 
a little early).  i.e., don’t assume that the first emotion run will *always* 
have 176 frames.

Cheers,
-MH


--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid 
Ave.  
  Tel: 314-747-6173
St. Louis, MO  63110  Email: 
mha...@wustl.edu

From: David Hofmann >
Date: Wednesday, February 28, 2018 at 7:50 AM
To: "Harms, Michael" >
Cc: "Glasser, Matthew" >, 
hcp-users >

Subject: Re: [HCP-Users] Concatenate sessions from Emotion task

Hi Michael,

there is an SPM function that handles the concatenation by adding session 
regressors and adjusting the high-pass filter. I'm still pondering if I want to 
include a regressor that accounts for the transition between sessions, but not 
sure how it would look like. Any ideas on that?

Ok, that sounds easy :).

TR=0.72
and number of volumes in the emotion task is: 176

My onsets of session 2 are:

32.067
74.21
116.353

So I will just add: 0.72*176=126,72 to all onsets and get:

158,800
200,943
243,085

Can you confirm I got this right?


greetings

David


2018-02-27 16:01 GMT+01:00 Harms, Michael 
>:

Well, you know the TR, and the number of frames in the first run, so just add 
the product of those two to the times in the 2nd run (unless you are manually 
deleting additional frames at the start of either run).

Cheers,
-MH

--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid 
Ave.  
  Tel: 314-747-6173
St. Louis, MO  63110  Email: 
mha...@wustl.edu

From: 
>
 on behalf of David Hofmann 
>
Date: Tuesday, February 27, 2018 at 7:48 AM
To: "Glasser, Matthew" >
Cc: hcp-users 
>
Subject: Re: [HCP-Users] Concatenate sessions from Emotion task

Hi Matthew,

I basically want to have one file, that is the concatenation of the RL and LR 
files and one file with the onsets for the fear and neut conditions for both 
sessions. For example, subject 100206 has one fear.txt file for each session 
with the following block onsets:

32.08 18  1
74.223 18
1
116.365 18
1

for the first session and

32.067 18
1
74.21 18  1
116.353 18
1

for the second session

Now, after concatenation of the data files, I have to adjust the onsets of the 
second session, such that all onsets are now greater

Re: [HCP-Users] rerunning FreeSurferPipelineBatch script

2018-02-28 Thread Glasser, Matthew

I think it will be okay to just rerun the FreeSurferPipeline if you delete the 
FreeSurfer folder

${StudyFolder}/${Subject}/T1w/${Subject}

Peace,

Matt.

From: 
>
 on behalf of Darko Komnenić >
Date: Wednesday, February 28, 2018 at 8:16 AM
To: "hcp-users@humanconnectome.org" 
>
Subject: [HCP-Users] rerunning FreeSurferPipelineBatch script

Dear HCP experts,
if the PreFreeSurferPipelineBatch script finished successfully, and then the 
FreeSurfer one finished with errors, but made some new output files before 
stopping, is it OK to just simply rerun FreeSurferPipeline script on the same 
participants? Or should I first delete all the new files that were added by 
this script, and leave only the ones that were there after the PreFreeSurfer 
script finished?

Thanks,
Darko

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Re: [HCP-Users] Concatenate sessions from Emotion task

2018-02-28 Thread David Hofmann

Ok, there were some rounding inaccuracies, get the same onsets as you now!

Thanks for the hint, I will make sure to check the number of frames for
each file.

Thanks again,

David

2018-02-28 15:05 GMT+01:00 Harms, Michael :

>
>
> Sure, that’s close.  (I get 158.787, 200.93, and 243.073).
>
>
>
> Make sure you use the actual number of frames in the first run (to
> properly determine the correct offset in the case that the first emotion
> run was aborted a little early).  i.e., don’t assume that the first emotion
> run will **always** have 176 frames.
>
>
>
> Cheers,
>
> -MH
>
>
>
>
>
> --
>
> Michael Harms, Ph.D.
>
> ---
>
> Conte Center for the Neuroscience of Mental Disorders
>
> Washington University School of Medicine
>
> Department of Psychiatry, Box 8134
>
> 660 South Euclid Ave
> .
> Tel: 314-747-6173 <(314)%20747-6173>
>
> St. Louis, MO  63110  Email:
> mha...@wustl.edu
>
>
>
> *From: *David Hofmann 
> *Date: *Wednesday, February 28, 2018 at 7:50 AM
> *To: *"Harms, Michael" 
> *Cc: *"Glasser, Matthew" , hcp-users <
> hcp-users@humanconnectome.org>
>
> *Subject: *Re: [HCP-Users] Concatenate sessions from Emotion task
>
>
>
> Hi Michael,
>
>
>
> there is an SPM function that handles the concatenation by adding session
> regressors and adjusting the high-pass filter. I'm still pondering if I
> want to include a regressor that accounts for the transition between
> sessions, but not sure how it would look like. Any ideas on that?
>
>
>
> Ok, that sounds easy :).
>
>
>
> TR=0.72
>
> and number of volumes in the emotion task is: 176
>
>
>
> My onsets of session 2 are:
>
>
>
> 32.067
>
> 74.21
>
> 116.353
>
>
>
> So I will just add: 0.72*176=126,72 to all onsets and get:
>
>
>
> 158,800
>
> 200,943
>
> 243,085
>
>
>
> Can you confirm I got this right?
>
>
>
>
>
> greetings
>
>
>
> David
>
>
>
>
>
> 2018-02-27 16:01 GMT+01:00 Harms, Michael :
>
>
>
> Well, you know the TR, and the number of frames in the first run, so just
> add the product of those two to the times in the 2nd run (unless you are
> manually deleting additional frames at the start of either run).
>
>
>
> Cheers,
>
> -MH
>
>
>
> --
>
> Michael Harms, Ph.D.
>
> ---
>
> Conte Center for the Neuroscience of Mental Disorders
>
> Washington University School of Medicine
>
> Department of Psychiatry, Box 8134
>
> 660 South Euclid Ave
> .
> Tel: 314-747-6173 <(314)%20747-6173>
>
> St. Louis, MO  63110  Email:
> mha...@wustl.edu
>
>
>
> *From: * on behalf of David
> Hofmann 
> *Date: *Tuesday, February 27, 2018 at 7:48 AM
> *To: *"Glasser, Matthew" 
> *Cc: *hcp-users 
> *Subject: *Re: [HCP-Users] Concatenate sessions from Emotion task
>
>
>
> Hi Matthew,
>
>
>
> I basically want to have one file, that is the concatenation of the RL and
> LR files and one file with the onsets for the fear and neut conditions for
> both sessions. For example, subject 100206 has one fear.txt file for each
> session with the following block onsets:
>
>
>
> 32.08 18  1
>
> 74.223 18
>
> 1
>
> 116.365 18
>
> 1
>
>
>
> for the first session and
>
>
>
> 32.067 18
>
> 1
>
> 74.21 18  1
>
> 116.353 18
>
> 1
>
>
>
> for the second session
>
>
>
> Now, after concatenation of the data files, I have to adjust the onsets
> of the second session, such that all onsets are now greater than the last
> onset of the first session (116.365). Basically, just add some value to the
> onsets of the second session.  This will depend on the number of "dummy
> volumes" at the end of the first session and begin of the second session
> asf.
>
>
>
> I'm using SPM so I don't think concatenating the design files will work
> here.
>
>
>
> Hope it became clear what I mean.
>
>
>
> Thanks!
>
>
>
> 2018-02-27 14:01 GMT+01:00 Glasser, Matthew :
>
> Is this a question of what to do with the images? Presumably for the
> design you could just concatenate the design files after generation and the
> image files after demean and hp200 or detrend.
>
>
>
> Peace,
>
>
>
> Matt.
>
>
>
> *From: * on behalf of David
> Hofmann 
> *Date: *Tuesday, February 27, 2018 at 4:52 AM
> *To: *hcp-users 
> *Subject: *[HCP-Users] Concatenate sessions from Emotion task
>
>
>
> Hi all,
>
>
>
> I would like to concatenate the RL and LR files from the Emotion task
> (modelling the sessions separately is not an option for the analysis I want
> to do later on) and thus have to change the onsets in fear.txt and

Re: [HCP-Users] path to bbregister .dat file for REST call

2018-02-28 Thread Hodge, Michael


Hi Olivia,

You can use a script similar to this to iterate over all the experiments and 
preprocessing resources and pull down these files for all subjects:

#!/bin/bash
#
# ITERATE OVER 3T EXPERIMENTS
#
for CSVROW in $(curl -s -k --cookie JSESSIONID=$JSESSIONID 
https://db.humanconnectome.org/data/projects/HCP_1200/experiments?xsiType=xnat:mrSessionData\=ID,label,URI\=csv
 | grep "_3T"); do
  LABEL=$(echo $CSVROW | cut -d, -f3)
  SUBJ=$(echo $LABEL | sed -e "s/_.*$//")
  URI=$(echo $CSVROW | cut -d, -f4)
  #
  # ITERATE OVER PIPELINE RESOURCES FOR EACH EXPERIMENT
  #
  for RESOURCEROW in $(curl -s -k --cookie JSESSIONID=$JSESSIONID 
https://db.humanconnectome.org${URI}/resources?xsiType=xnat:resourceCatalog\=csv);
 do
   RESOURCE=$(echo ${RESOURCEROW} | cut -d, -f2)
   #
   # DOWNLOAD FILES FROM FMRI PREPROC RESOURCES
   #
   if [[ $RESOURCE =~ ^.*fMRI.*_preproc ]]; then
 SERIES=$(echo "$RESOURCE" | sed -e 
"s/_preproc//")
 echo $SUBJ $LABEL $URI $RESOURCE 
$SERIES
   
DIRECTORY="$SUBJ/MNINonLinear/Results/${SERIES}/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased"
 mkdir -p $DIRECTORY/FieldMap
 curl -s -k --cookie 
JSESSIONID=$JSESSIONID 
https://db.humanconnectome.org${URI}/resources/${RESOURCE}/files/${SERIES}/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased/fMRI2str.mat
 -o $DIRECTORY/fMRI2str.mat
 curl -s -k --cookie 
JSESSIONID=$JSESSIONID 
https://db.humanconnectome.org${URI}/resources/${RESOURCE}/files/${SERIES}/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased/FieldMap/SBRef_dc_jac.nii.gz
 -o $DIRECTORY/FieldMap/SBRef_dc_jac.nii.gz
   fi
  done
done

You can set the JSESSIONID with this call:

read -s -p "ENTER PASSWORD: " PW;JSESSIONID=`curl -s -k -u 
YOUR_USERNAME_HERE:$PW https://db.humanconnectome.org/REST/JSESSIONID`;export 
JSESSIONID;echo $JSESSIONID

I hope this helps.  Note, I didn't include the file Tim mentioned that you 
would already in your download folders.

Regards,

Mike

From: hcp-users-boun...@humanconnectome.org 
[mailto:hcp-users-boun...@humanconnectome.org] On Behalf Of Viessmann, Olivia M.
Sent: Tuesday, February 27, 2018 9:48 AM
To: NEUROSCIENCE tim 
Cc: hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] path to bbregister .dat file for REST call

Dear Tim,

thanks a lot for the detailed explanation, this is all tremendously helpful and 
is indeed what I am looking for.
I hope someone on this list knows where the transforms are stored. As soon as I 
know from where to download it I will give it a try and let you know if it 
worked.

Thanks
Olivia




On 26 Feb 2018, at 18:22, Timothy Coalson 
> wrote:

0307_3T/RESOURCES/rfMRI_REST1_LR_preproc/rfMR


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The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.

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[HCP-Users] rerunning FreeSurferPipelineBatch script

2018-02-28 Thread Darko Komnenić

Dear HCP experts,
if the PreFreeSurferPipelineBatch script finished successfully, and then
the FreeSurfer one finished with errors, but made some new output files
before stopping, is it OK to just simply rerun FreeSurferPipeline script on
the same participants? Or should I first delete all the new files that were
added by this script, and leave only the ones that were there after the
PreFreeSurfer script finished?

Thanks,
Darko

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Re: [HCP-Users] Concatenate sessions from Emotion task

2018-02-28 Thread Harms, Michael


Sure, that’s close.  (I get 158.787, 200.93, and 243.073).

Make sure you use the actual number of frames in the first run (to properly 
determine the correct offset in the case that the first emotion run was aborted 
a little early).  i.e., don’t assume that the first emotion run will *always* 
have 176 frames.

Cheers,
-MH


--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110  Email: 
mha...@wustl.edu

From: David Hofmann 
Date: Wednesday, February 28, 2018 at 7:50 AM
To: "Harms, Michael" 
Cc: "Glasser, Matthew" , hcp-users 

Subject: Re: [HCP-Users] Concatenate sessions from Emotion task

Hi Michael,

there is an SPM function that handles the concatenation by adding session 
regressors and adjusting the high-pass filter. I'm still pondering if I want to 
include a regressor that accounts for the transition between sessions, but not 
sure how it would look like. Any ideas on that?

Ok, that sounds easy :).

TR=0.72
and number of volumes in the emotion task is: 176

My onsets of session 2 are:

32.067
74.21
116.353

So I will just add: 0.72*176=126,72 to all onsets and get:

158,800
200,943
243,085

Can you confirm I got this right?




greetings


David



2018-02-27 16:01 GMT+01:00 Harms, Michael 
>:

Well, you know the TR, and the number of frames in the first run, so just add 
the product of those two to the times in the 2nd run (unless you are manually 
deleting additional frames at the start of either run).

Cheers,
-MH

--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid 
Ave.  
  Tel: 314-747-6173
St. Louis, MO  63110  Email: 
mha...@wustl.edu

From: 
>
 on behalf of David Hofmann 
>
Date: Tuesday, February 27, 2018 at 7:48 AM
To: "Glasser, Matthew" >
Cc: hcp-users 
>
Subject: Re: [HCP-Users] Concatenate sessions from Emotion task

Hi Matthew,

I basically want to have one file, that is the concatenation of the RL and LR 
files and one file with the onsets for the fear and neut conditions for both 
sessions. For example, subject 100206 has one fear.txt file for each session 
with the following block onsets:

32.08 18  1
74.223 18
1
116.365 18
1

for the first session and

32.067 18
1
74.21 18  1
116.353 18
1

for the second session

Now, after concatenation of the data files, I have to adjust the onsets of the 
second session, such that all onsets are now greater than the last onset of the 
first session (116.365). Basically, just add some value to the onsets of the 
second session.  This will depend on the number of "dummy volumes" at the end 
of the first session and begin of the second session asf.

I'm using SPM so I don't think concatenating the design files will work here.

Hope it became clear what I mean.

Thanks!

2018-02-27 14:01 GMT+01:00 Glasser, Matthew 
>:
Is this a question of what to do with the images? Presumably for the design you 
could just concatenate the design files after generation and the image files 
after demean and hp200 or detrend.

Peace,

Matt.

From: 
>
 on behalf of David Hofmann 
>
Date: Tuesday, February 27, 2018 at 4:52 AM
To: hcp-users 
>
Subject: [HCP-Users] Concatenate sessions from Emotion task

Hi all,

I would like to concatenate the RL and LR files from the Emotion task 
(modelling the sessions separately is not an option for the analysis I want to 
do later on) and thus have to change the onsets in fear.txt and neu.txt for the 
second session accordingly. I'm not quite sure how to do this properly and hope 
for some guidance.

Many thanks in advance

David



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___

Re: [HCP-Users] Concatenate sessions from Emotion task

2018-02-28 Thread David Hofmann

Hi Michael,

there is an SPM function that handles the concatenation by adding session
regressors and adjusting the high-pass filter. I'm still pondering if I
want to include a regressor that accounts for the transition between
sessions, but not sure how it would look like. Any ideas on that?

Ok, that sounds easy :).

TR=0.72
and number of volumes in the emotion task is: 176

My onsets of session 2 are:

32.067

74.21

116.353


So I will just add: 0.72*176=126,72 to all onsets and get:


158,800

200,943

243,085


Can you confirm I got this right?



greetings


David



2018-02-27 16:01 GMT+01:00 Harms, Michael :

>
>
> Well, you know the TR, and the number of frames in the first run, so just
> add the product of those two to the times in the 2nd run (unless you are
> manually deleting additional frames at the start of either run).
>
>
>
> Cheers,
>
> -MH
>
>
>
> --
>
> Michael Harms, Ph.D.
>
> ---
>
> Conte Center for the Neuroscience of Mental Disorders
>
> Washington University School of Medicine
>
> Department of Psychiatry, Box 8134
>
> 660 South Euclid Ave
> .
> Tel: 314-747-6173 <(314)%20747-6173>
>
> St. Louis, MO  63110  Email:
> mha...@wustl.edu
>
>
>
> *From: * on behalf of David
> Hofmann 
> *Date: *Tuesday, February 27, 2018 at 7:48 AM
> *To: *"Glasser, Matthew" 
> *Cc: *hcp-users 
> *Subject: *Re: [HCP-Users] Concatenate sessions from Emotion task
>
>
>
> Hi Matthew,
>
>
>
> I basically want to have one file, that is the concatenation of the RL and
> LR files and one file with the onsets for the fear and neut conditions for
> both sessions. For example, subject 100206 has one fear.txt file for each
> session with the following block onsets:
>
>
>
> 32.08 18  1
>
> 74.223 18
>
> 1
>
> 116.365 18
>
> 1
>
>
>
> for the first session and
>
>
>
> 32.067 18
>
> 1
>
> 74.21 18  1
>
> 116.353 18
>
> 1
>
>
>
> for the second session
>
>
>
> Now, after concatenation of the data files, I have to adjust the onsets
> of the second session, such that all onsets are now greater than the last
> onset of the first session (116.365). Basically, just add some value to the
> onsets of the second session.  This will depend on the number of "dummy
> volumes" at the end of the first session and begin of the second session
> asf.
>
>
>
> I'm using SPM so I don't think concatenating the design files will work
> here.
>
>
>
> Hope it became clear what I mean.
>
>
>
> Thanks!
>
>
>
> 2018-02-27 14:01 GMT+01:00 Glasser, Matthew :
>
> Is this a question of what to do with the images? Presumably for the
> design you could just concatenate the design files after generation and the
> image files after demean and hp200 or detrend.
>
>
>
> Peace,
>
>
>
> Matt.
>
>
>
> *From: * on behalf of David
> Hofmann 
> *Date: *Tuesday, February 27, 2018 at 4:52 AM
> *To: *hcp-users 
> *Subject: *[HCP-Users] Concatenate sessions from Emotion task
>
>
>
> Hi all,
>
>
>
> I would like to concatenate the RL and LR files from the Emotion task
> (modelling the sessions separately is not an option for the analysis I want
> to do later on) and thus have to change the onsets in fear.txt and neu.txt
> for the second session accordingly. I'm not quite sure how to do this
> properly and hope for some guidance.
>
>
>
> Many thanks in advance
>
>
>
> David
>
>
>
>
>
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>
>
>
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>
>
> --
>
> The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If you
> are not the intended recipient, be advised that any unauthorized use,
> disclosure, copying or the taking of any action in reliance on the contents
> of this information is strictly prohibited. If you have received this email
> in error, please immediately notify the sender via telephone or return mail.
>

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
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Re: [HCP-Users] wbsparse

Re: [HCP-Users] Pittsburgh Sleep Quality Index Component Scores

Re: [HCP-Users] wbsparse

Re: [HCP-Users] Neighbors of a vertex

Re: [HCP-Users] Neighbors of a vertex

Re: [HCP-Users] wbsparse

Re: [HCP-Users] wbsparse

Re: [HCP-Users] wbsparse

Re: [HCP-Users] wbsparse

Re: [HCP-Users] Concatenate sessions from Emotion task

[HCP-Users] Neighbors of a vertex

[HCP-Users] FreeSurfer processing in Structural preprocessing

Re: [HCP-Users] Concatenate sessions from Emotion task

Re: [HCP-Users] Concatenate sessions from Emotion task

Re: [HCP-Users] rerunning FreeSurferPipelineBatch script

Re: [HCP-Users] Concatenate sessions from Emotion task

Re: [HCP-Users] rerunning FreeSurferPipelineBatch script

Re: [HCP-Users] Concatenate sessions from Emotion task

Re: [HCP-Users] path to bbregister .dat file for REST call

[HCP-Users] rerunning FreeSurferPipelineBatch script

Re: [HCP-Users] Concatenate sessions from Emotion task

Re: [HCP-Users] Concatenate sessions from Emotion task

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