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://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
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>> 
>> 
>> 
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> 
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