Re: [caret-users] negative values displayed positive

2015-06-23 Thread Frédéric Roux
Hi Dona,

thank you very much for looking into this.

The Volume I sent contained values that were thresholded for
significance. This is why some values were zero.

The blob probably results from the cluster-permutation approach
that I applied in order to compute the significance.

I should also say that the data comes from MEG source reconstruction
and that I interpolated the data onto the SPM template brain (T1.nii).

Based on your response I assume that the problem does not come from
Caret but from the data that contains positive values. The problem must
thus occur while I am exporting the data to a volume file. 

Thanks for the quick help! I know where to search now.

Fred
--
FR

- Original Message -
From: Donna Dierker do...@brainvis.wustl.edu
To: SureFit Caret, and SuMS software users caret-users@brainvis.wustl.edu
Sent: Monday, June 22, 2015 4:36:09 PM
Subject: Re: [caret-users] negative values displayed positive

Hi FR,

This is rather an odd file.  I did 3dhistog on it and got this output:

http://brainmap.wustl.edu/pub/donna/SPAIN/BCBL/your_file.3dhistog.txt
login pub
password download

Mostly zeroes, but 14184 voxels set to 32766 (and no voxels set to any values 
in between 0 and 32766).

And when I map this to the PALS atlas, I get nothing on most vertices, but 
solid yellow over a perisylvian blob.  And when I click in the yellow, sure 
enough the ID window confirms the vertex is set to 32766 intensity.

Working as expected, but data a bit off the beaten path.

Donna


On Jun 21, 2015, at 4:55 PM, Frédéric Roux f.r...@bcbl.eu wrote:

 Hi Dona,
 
 thanks for getting back on this.
 I am using NIFTI, so nothing rare from that side.
 
 Just uploaded the file via the link you sent me.
 
 Thanks for looking into this.
 
 --
 FR
 
 - Original Message -
 From: Donna Dierker do...@brainvis.wustl.edu
 To: SureFit Caret, and SuMS software users caret-users@brainvis.wustl.edu
 Sent: Sunday, June 21, 2015 6:37:50 PM
 Subject: Re: [caret-users] negative values displayed positive
 
 I'm not sure what would do this.  What format is your volume?  NIFTI?  Older 
 .hdr/.img pairs sometimes got x-flipped upon opening under some 
 circumstances, but nothing I know of (except explicit *(-1) using volume 
 math) does this.
 
 You can use something AFNI 3dinfo or 3dhistog to double-check your volume's 
 values, or you can upload your volume here and I can do so tomorrow:
 
 http://brainvis.wustl.edu/cgi-bin/upload.cgi
 
 You can also have a look at the palette format, and just make sure it's not 
 the palette that is making your values appear to be flipped:
 
 http://brainvis.wustl.edu/CaretHelpAccount/caret5_help/file_formats/file_formats.html#paletteFile
 
 Caret has some built-in palettes (see D/C: Metric Settings menu).
 
 
 On Jun 21, 2015, at 3:55 AM, Frédéric Roux f.r...@bcbl.eu wrote:
 
 Dear all,
 
 I'm trying to map a functional volume to the PLAS-B12
 surface but the sign of the values gets flipped so that
 negative values appear as positive ones.
 
 Does anyone know what could be wrong?
 
 Many thanks.
 
 Fred
 
 --
 FR
 
 - Original Message -
 From: Matt Glasser m...@ma-tea.com
 To: SureFit Caret, and SuMS software users caret-users@brainvis.wustl.edu
 Sent: Saturday, June 20, 2015 11:37:53 PM
 Subject: Re: [caret-users] Missing parts in MyelinMap+Different number of 
 nodes!
 
 Yes please use the HCP pipelines for myelin mapping.
 
 Peace,
 
 Matt.
 
 On 6/19/15, 4:17 AM, Donna Dierker do...@brainvis.wustl.edu wrote:
 
 Hi Xara,
 
 Because you are in the enviable position of having high res T1 AND T2,
 you may be able to use the Human Connectome Project pipelines on your
 data, rather than this (older generation) caret-based myelin mapping
 script:
 
 http://www.humanconnectome.org/documentation/HCP-pipelines/
 
 This also has the advantage of writing output files in workbench formats,
 rather than older caret formats.  I have a hunch that Matt Glasser will
 point you in that direction (he is probably at OHBM conference or on his
 way home).
 
 I confess I am not as familiar with this script as Matt is, but from what
 I read at the link you sent, it appears the maps are on the native mesh,
 rather than 164k.  And I don't see myelin represented in the list of
 freesurfer_to_fs_LR output files here:
 
 http://brainvis.wustl.edu/wiki/index.php/Caret:Operations/Freesurfer_to_fs
 _LR/Output
 
 (These were independent efforts going on at roughly the same time.)
 
 You may already have considered the HCP pipeline route, but if not, it is
 worth a look -- you've got the T2's at the right res, which is often a
 hitch.  I suspect myelin maps on 164k won't be your only benefit.
 
 Donna
 
 
 On Jun 19, 2015, at 8:58 AM, Shams, Z. z.sh...@donders.ru.nl wrote:
 
 Dear users,
 
 
 
 I just started working with Caret for creating myelin maps. I used HCP
 imaging protocols for data acquisition, both T1 and T2 data have the
 voxel size of 0.7mm isotropic.
 
 I followed the instructions in
 http

[caret-users] negative values displayed positive

2015-06-21 Thread Frédéric Roux
Dear all,

I'm trying to map a functional volume to the PLAS-B12
surface but the sign of the values gets flipped so that
negative values appear as positive ones.

Does anyone know what could be wrong?

Many thanks.

Fred

--
FR

- Original Message -
From: Matt Glasser m...@ma-tea.com
To: SureFit Caret, and SuMS software users caret-users@brainvis.wustl.edu
Sent: Saturday, June 20, 2015 11:37:53 PM
Subject: Re: [caret-users] Missing parts in MyelinMap+Different number of nodes!

Yes please use the HCP pipelines for myelin mapping.

Peace,

Matt.

On 6/19/15, 4:17 AM, Donna Dierker do...@brainvis.wustl.edu wrote:

Hi Xara,

Because you are in the enviable position of having high res T1 AND T2,
you may be able to use the Human Connectome Project pipelines on your
data, rather than this (older generation) caret-based myelin mapping
script:

http://www.humanconnectome.org/documentation/HCP-pipelines/

This also has the advantage of writing output files in workbench formats,
rather than older caret formats.  I have a hunch that Matt Glasser will
point you in that direction (he is probably at OHBM conference or on his
way home).

I confess I am not as familiar with this script as Matt is, but from what
I read at the link you sent, it appears the maps are on the native mesh,
rather than 164k.  And I don't see myelin represented in the list of
freesurfer_to_fs_LR output files here:

http://brainvis.wustl.edu/wiki/index.php/Caret:Operations/Freesurfer_to_fs
_LR/Output

(These were independent efforts going on at roughly the same time.)

You may already have considered the HCP pipeline route, but if not, it is
worth a look -- you've got the T2's at the right res, which is often a
hitch.  I suspect myelin maps on 164k won't be your only benefit.

Donna


On Jun 19, 2015, at 8:58 AM, Shams, Z. z.sh...@donders.ru.nl wrote:

 Dear users,
 
  
 
 I just started working with Caret for creating myelin maps. I used HCP
imaging protocols for data acquisition, both T1 and T2 data have the
voxel size of 0.7mm isotropic.
 
 I followed the instructions in
http://brainvis.wustl.edu/wiki/index.php/Caret:Operations/MyelinMapping.
 
 Actually I managed to display the four outputs, but some parts of the
maps are missing when overlaying on a surface(they¹re not complete maps:
either raw or corrected myelin maps).
 
 Another problem is that I used the freesurfer to fs LR script to
convert all my freesurfer files to the 164k_fs_LR mesh,
 
 but when I try  to show the myelin maps on e.g. very-inflated 164k fs
LR, It fails with the error of containing a different number of nodes
thanŠ .
 
  
 
 I¹d appreciate any help and instructions.
 
  
 
 Thanks,
 
 
 Xara
 
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Re: [caret-users] negative values displayed positive

2015-06-21 Thread Frédéric Roux
Hi Dona,

thanks for getting back on this.
I am using NIFTI, so nothing rare from that side.

Just uploaded the file via the link you sent me.

Thanks for looking into this.

--
FR

- Original Message -
From: Donna Dierker do...@brainvis.wustl.edu
To: SureFit Caret, and SuMS software users caret-users@brainvis.wustl.edu
Sent: Sunday, June 21, 2015 6:37:50 PM
Subject: Re: [caret-users] negative values displayed positive

I'm not sure what would do this.  What format is your volume?  NIFTI?  Older 
.hdr/.img pairs sometimes got x-flipped upon opening under some circumstances, 
but nothing I know of (except explicit *(-1) using volume math) does this.

You can use something AFNI 3dinfo or 3dhistog to double-check your volume's 
values, or you can upload your volume here and I can do so tomorrow:

http://brainvis.wustl.edu/cgi-bin/upload.cgi

You can also have a look at the palette format, and just make sure it's not the 
palette that is making your values appear to be flipped:

http://brainvis.wustl.edu/CaretHelpAccount/caret5_help/file_formats/file_formats.html#paletteFile

Caret has some built-in palettes (see D/C: Metric Settings menu).


On Jun 21, 2015, at 3:55 AM, Frédéric Roux f.r...@bcbl.eu wrote:

 Dear all,
 
 I'm trying to map a functional volume to the PLAS-B12
 surface but the sign of the values gets flipped so that
 negative values appear as positive ones.
 
 Does anyone know what could be wrong?
 
 Many thanks.
 
 Fred
 
 --
 FR
 
 - Original Message -
 From: Matt Glasser m...@ma-tea.com
 To: SureFit Caret, and SuMS software users caret-users@brainvis.wustl.edu
 Sent: Saturday, June 20, 2015 11:37:53 PM
 Subject: Re: [caret-users] Missing parts in MyelinMap+Different number of 
 nodes!
 
 Yes please use the HCP pipelines for myelin mapping.
 
 Peace,
 
 Matt.
 
 On 6/19/15, 4:17 AM, Donna Dierker do...@brainvis.wustl.edu wrote:
 
 Hi Xara,
 
 Because you are in the enviable position of having high res T1 AND T2,
 you may be able to use the Human Connectome Project pipelines on your
 data, rather than this (older generation) caret-based myelin mapping
 script:
 
 http://www.humanconnectome.org/documentation/HCP-pipelines/
 
 This also has the advantage of writing output files in workbench formats,
 rather than older caret formats.  I have a hunch that Matt Glasser will
 point you in that direction (he is probably at OHBM conference or on his
 way home).
 
 I confess I am not as familiar with this script as Matt is, but from what
 I read at the link you sent, it appears the maps are on the native mesh,
 rather than 164k.  And I don't see myelin represented in the list of
 freesurfer_to_fs_LR output files here:
 
 http://brainvis.wustl.edu/wiki/index.php/Caret:Operations/Freesurfer_to_fs
 _LR/Output
 
 (These were independent efforts going on at roughly the same time.)
 
 You may already have considered the HCP pipeline route, but if not, it is
 worth a look -- you've got the T2's at the right res, which is often a
 hitch.  I suspect myelin maps on 164k won't be your only benefit.
 
 Donna
 
 
 On Jun 19, 2015, at 8:58 AM, Shams, Z. z.sh...@donders.ru.nl wrote:
 
 Dear users,
 
 
 
 I just started working with Caret for creating myelin maps. I used HCP
 imaging protocols for data acquisition, both T1 and T2 data have the
 voxel size of 0.7mm isotropic.
 
 I followed the instructions in
 http://brainvis.wustl.edu/wiki/index.php/Caret:Operations/MyelinMapping.
 
 Actually I managed to display the four outputs, but some parts of the
 maps are missing when overlaying on a surface(they¹re not complete maps:
 either raw or corrected myelin maps).
 
 Another problem is that I used the freesurfer to fs LR script to
 convert all my freesurfer files to the 164k_fs_LR mesh,
 
 but when I try  to show the myelin maps on e.g. very-inflated 164k fs
 LR, It fails with the error of containing a different number of nodes
 thanŠ .
 
 
 
 I¹d appreciate any help and instructions.
 
 
 
 Thanks,
 
 
 Xara
 
 ___
 caret-users mailing list
 caret-users@brainvis.wustl.edu
 http://brainvis.wustl.edu/mailman/listinfo/caret-users
 
 
 ___
 caret-users mailing list
 caret-users@brainvis.wustl.edu
 http://brainvis.wustl.edu/mailman/listinfo/caret-users
 
 
 
 ___
 caret-users mailing list
 caret-users@brainvis.wustl.edu
 http://brainvis.wustl.edu/mailman/listinfo/caret-users
 
 ___
 caret-users mailing list
 caret-users@brainvis.wustl.edu
 http://brainvis.wustl.edu/mailman/listinfo/caret-users


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Re: [caret-users] blacking out subcortical regions

2014-11-10 Thread Frédéric Roux
thanks Donna!

Frédéric Roux

- Original Message -
From: Donna Dierker do...@brainvis.wustl.edu
To: SureFit Caret, and SuMS software users caret-users@brainvis.wustl.edu
Sent: Monday, November 10, 2014 4:52:53 PM
Subject: Re: [caret-users] blacking out subcortical regions

There is a paint file that comes with many of the PALS-B12 datasets (e.g., Sept 
2006 tutorial) that has a medial wall column.  Use that as the primary overlay 
with your metric or other overlay as the secondary overlay.  This grays out the 
medial wall.


On Nov 9, 2014, at 10:43 AM, Frédéric Roux f.r...@bcbl.eu wrote:

 Hi there,
 
 I've finally managed to get to visualize my MEG source-reconstruction data 
 using caret !!!
 So far I am very satisfied with the way everything looks.
 
 The only thing that's missing is a way to black out the sub-cortical areas? 
 I've seen
 people do this regularly in their publications and I would like to do the 
 same as from
 what I understand the PALS-B12 surface is only meant for cortical 
 representations?
 
 I could basically try to null all the values which lie below a certain 
 coordinate of
 the Z-axis in my data, but I was wondering if there is a simple and easier 
 way to do
 it in in Caret.
 
 Any help or suggestions would be highly appreciated.
 
 Thanks.
 
 Fred
 ---
 
 
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