Re: [HCP-Users] CIFTIOPEN: NaN values in .dscalar.nii not read
I am feeling confused. If brainordinate is what is shown in the
information box when you click on a vertex, then mine does match the 96484
grayordinates. I also have brainordinates on the medial wall (e.g.,
VERTEX CortexRight 433 is on the medial wall). Let me know if I should look
elsewhere for the brainordinates.
Thanks,
Cherry
On Sun, Mar 22, 2015 at 5:24 PM, Glasser, Matthew glass...@wusm.wustl.edu
wrote:
I’m pretty sure that wb_view indices match ciftiopen if you use
“Identify Brainordinate.” As I said, the medial wall is not defined in any
of the dense timeseries files you might wish to use in your analysis (even
if it was, the data inside it wouldn’t be valid as it wouldn’t be cerebral
cortex). Let me know if you don’t follow the instructions below for
converting your dlabel files into 91282 grayordinates space.
Peace,
Matt.
From: Yizhou Ma maxxx...@umn.edu
Date: Sunday, March 22, 2015 at 5:19 PM
To: Matt Glasser glass...@wusm.wustl.edu, hcp-users@humanconnectome.org
hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] CIFTIOPEN: NaN values in .dscalar.nii not read
Another thing is that when I look at a grayordinate in wb_view, it
gives the index of that grayordinate and its statistics. I can use the
index number to find the corresponding grayordinate easily if I am using
96484 grayordiantes from ft_read_cifti, but not as easy if I am using
ciftiopen.
On Sun, Mar 22, 2015 at 5:05 PM, Glasser, Matthew glass...@wusm.wustl.edu
wrote:
Yes, ciftiopen gives the correct number of grayordinates. If you need
to correct your dlabel files, you can use wb_command -cifti-separate to get
out the GIFTI label files and then use wb_command -cifti-create-label with
the correct medial wall ROIs—any subject’s
${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.${Hemisphere}.atlasroi.32k_fs_LR.shape.gii
will do. If you also want to put zeros in the subcortical structures, you
can additionally use as the parcel-volume any subject’s
${StudyFolder}/${Subject}/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz and as the
label volume the same volume where you’ve set all voxels to zero.
Peace,
Matt.
From: Yizhou Ma maxxx...@umn.edu
Date: Sunday, March 22, 2015 at 4:56 PM
To: Matt Glasser glass...@wusm.wustl.edu
Subject: Re: [HCP-Users] CIFTIOPEN: NaN values in .dscalar.nii not read
Hi Matthew,
I am trying to calculate the correspondence between the HCP ICA
parcellations with other parcellations (e.g. Yeo 2011, Power 2011).
It is ciftiopen that is giving me 91282 grayordinates.
Best,
Cherry
On Sun, Mar 22, 2015 at 4:52 PM, Glasser, Matthew
glass...@wusm.wustl.edu wrote:
For ft_read_cifti, that sounds like a bug, as there are only a total
of 91282 grayordinates at 2mm spacing (the medial wall is not defined in
the CIFTI standard grayordinates space). As far as matching the dlabel
files with the rest of the CIFTI files, it is true that you need to remove
the medial wall (and they don’t include any subcortical structures
either). What is it that you are trying to do with the dlabel files?
Peace,
Matt.
From: Yizhou Ma maxxx...@umn.edu
Date: Sunday, March 22, 2015 at 4:44 PM
To: hcp-users@humanconnectome.org hcp-users@humanconnectome.org
Subject: [HCP-Users] CIFTIOPEN: NaN values in .dscalar.nii not read
Dear HCP experts,
I'd like to report what seems to me a problem with ciftiopen. When I
opened a .dscalar.nii file with ft_read_cifti, I got 96854 grayordinates.
Yet when I used ciftiopen, I got 91282 grayordiantes. It seems to me that
ciftiopen automatically left out where there is a NaN in the .dscalar
file. This has been a problem for me since I've been trying to use some of
the .dlabel files offered by HCP, which come with 64984 surface
grayordinates when opened with ciftiopen, medial wall included. It took me
a while to realize that my results are not matching up because the
discorrespondence in indices.
Given that ciftiopen does not read the labelnames and label values
from cifti files, I think it can be confusing when it left out NaN values
on the medial wall when reading .dscalar files.
Best,
Cherry
___
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.
--
The materials in this message are private and may contain Protected
Healthcare Information or other information
Re: [HCP-Users] CIFTIOPEN: NaN values in .dscalar.nii not read
I see. In my WB 1.0 the information window offers Select Brainordinates
function. Yet I can only select the surface vertices there.
On Sun, Mar 22, 2015 at 5:40 PM, Glasser, Matthew glass...@wusm.wustl.edu
wrote:
Those are vertex IDs that don’t match grayordinate Ids (even in your
space they won’t match for the right hemisphere). There should be a select
brainordinate option somewhere in that window that you can use to get a
specific brainordinate. The whole information window needs a bit of a
rewrite though and the development version of wb_view I have in front of me
has already had some of the changes made to it so I cannot tell you exactly
where to look.
Peace,
Matt.
From: Yizhou Ma maxxx...@umn.edu
Date: Sunday, March 22, 2015 at 5:33 PM
To: Matt Glasser glass...@wusm.wustl.edu
Cc: hcp-users@humanconnectome.org hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] CIFTIOPEN: NaN values in .dscalar.nii not read
I am feeling confused. If brainordinate is what is shown in the
information box when you click on a vertex, then mine does match the 96484
grayordinates. I also have brainordinates on the medial wall (e.g.,
VERTEX CortexRight 433 is on the medial wall). Let me know if I should look
elsewhere for the brainordinates.
Thanks,
Cherry
On Sun, Mar 22, 2015 at 5:24 PM, Glasser, Matthew glass...@wusm.wustl.edu
wrote:
I’m pretty sure that wb_view indices match ciftiopen if you use
“Identify Brainordinate.” As I said, the medial wall is not defined in any
of the dense timeseries files you might wish to use in your analysis (even
if it was, the data inside it wouldn’t be valid as it wouldn’t be cerebral
cortex). Let me know if you don’t follow the instructions below for
converting your dlabel files into 91282 grayordinates space.
Peace,
Matt.
From: Yizhou Ma maxxx...@umn.edu
Date: Sunday, March 22, 2015 at 5:19 PM
To: Matt Glasser glass...@wusm.wustl.edu,
hcp-users@humanconnectome.org hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] CIFTIOPEN: NaN values in .dscalar.nii not read
Another thing is that when I look at a grayordinate in wb_view, it
gives the index of that grayordinate and its statistics. I can use the
index number to find the corresponding grayordinate easily if I am using
96484 grayordiantes from ft_read_cifti, but not as easy if I am using
ciftiopen.
On Sun, Mar 22, 2015 at 5:05 PM, Glasser, Matthew
glass...@wusm.wustl.edu wrote:
Yes, ciftiopen gives the correct number of grayordinates. If you need
to correct your dlabel files, you can use wb_command -cifti-separate to get
out the GIFTI label files and then use wb_command -cifti-create-label with
the correct medial wall ROIs—any subject’s
${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.${Hemisphere}.atlasroi.32k_fs_LR.shape.gii
will do. If you also want to put zeros in the subcortical structures, you
can additionally use as the parcel-volume any subject’s
${StudyFolder}/${Subject}/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz and as the
label volume the same volume where you’ve set all voxels to zero.
Peace,
Matt.
From: Yizhou Ma maxxx...@umn.edu
Date: Sunday, March 22, 2015 at 4:56 PM
To: Matt Glasser glass...@wusm.wustl.edu
Subject: Re: [HCP-Users] CIFTIOPEN: NaN values in .dscalar.nii not read
Hi Matthew,
I am trying to calculate the correspondence between the HCP ICA
parcellations with other parcellations (e.g. Yeo 2011, Power 2011).
It is ciftiopen that is giving me 91282 grayordinates.
Best,
Cherry
On Sun, Mar 22, 2015 at 4:52 PM, Glasser, Matthew
glass...@wusm.wustl.edu wrote:
For ft_read_cifti, that sounds like a bug, as there are only a total
of 91282 grayordinates at 2mm spacing (the medial wall is not defined in
the CIFTI standard grayordinates space). As far as matching the dlabel
files with the rest of the CIFTI files, it is true that you need to remove
the medial wall (and they don’t include any subcortical structures
either). What is it that you are trying to do with the dlabel files?
Peace,
Matt.
From: Yizhou Ma maxxx...@umn.edu
Date: Sunday, March 22, 2015 at 4:44 PM
To: hcp-users@humanconnectome.org hcp-users@humanconnectome.org
Subject: [HCP-Users] CIFTIOPEN: NaN values in .dscalar.nii not read
Dear HCP experts,
I'd like to report what seems to me a problem with ciftiopen. When I
opened a .dscalar.nii file with ft_read_cifti, I got 96854 grayordinates.
Yet when I used ciftiopen, I got 91282 grayordiantes. It seems to me that
ciftiopen automatically left out where there is a NaN in the .dscalar
file. This has been a problem for me since I've been trying to use some of
the .dlabel files offered by HCP, which come with 64984 surface
grayordinates when opened with ciftiopen, medial wall included. It took me
a while to realize that my results are not matching up because the
discorrespondence in indices.
Given that ciftiopen does not read
