Hi,
This also happened to me using -cifti-label-import with discard others, the
resulting file is not empty, it contains the 0s and 1s in the right place,
but it doesn't contain the information about the names and colors from the
text file. To fix this I rerun the same command using the output fro
Hi - it sounds like maybe it's working fine within the limits of slight
differences in mathematical precision between the C++ vs matlab parts of the
processing - so the main question would be - have you looked in a viewer at the
difference image - e.g. are the voxels with large differences isola
I think this is more of a question for the FSL list, but I don't know fsl_glm
well enough to say if what you are doing is equivalent or not.
Peace,
Matt.
From: "Ely, Benjamin" mailto:benjamin@mssm.edu>>
Date: Tuesday, September 27, 2016 at 7:20 PM
To: Matt Glasser mailto:glass...@wustl.edu>
Hi Matt and Greg,
Thanks for the feedback! I've looked at the various fix .m files from the
current release; based on fix_3_clean.m, I tried the following for a single
resting-state run:
# highpass filter; sigma of 1000.08 = FWHM of 2355 per Smith et al 2013
NeuroImage, also consistent with c
Actually, -cifti-math will output a dlabel file with an improper label
table, which will look empty (it is not a proper dlabel file, but it does
have the ROI you want in it). You should then use -cifti-change-mapping
with -scalar on that output to make it into a viewable ROI file (you could
also d
If you already have a dlabel file that excludes the things you aren't
interested in, you don't need to bother with the -cifti-reduce I
described. Since "unlabeled" is generally represented as 0, you can use
-cifti-math with 'x > 0' to generate a combined binary ROI from that
restricted dlabel file
To me, a mask is a binary ROI (1 where the stuff you want is, 0
elsewhere). This is quite different from a label file (lots of different
integers). I did not mean for you to run -cifti-reduce on a dlabel file.
I was suggesting that you use -cifti-label-to-roi to make a binary ROI from
each label
The command I was using was :
wb_command -cifti-reduce Brodmann_Bilateral_IFG.dlabel.nii MAX
Brodmann_Bilateral_IFG_Merged.dscalar.nii
Where Brodmann_Bilateral_IFG.dlabel.nii contains two labels.
Again, this command does not seem to the production of a label file directly.
Thanks
On Sep 27, 2
I’m sorry, but this is still not clear to me. It seems this function is meant
to perform an operation to produce a scalar file, but what is produced when I
use MAX for example is just a scalar file where the value for the key each
labeled region had in the label file is not the value in that sca
http://www.humanconnectome.org/software/workbench-command.php?function=-cifti-reduce
It is a simple reduction across columns (by default, anyway) in the file.
For these kinds of files, that means it isn't reducing across space. MAX
is one of the options it can calculate, and for binary ROIs, that
How would this work with -cifti-reduce? If I have a cifti with BA44 and BA45
for example and I want those two regions to be merged into one, how would
-cifti-reduce do that? Wouldn’t it be more suited to calculating something
(i.e. mean, mode, etc.) within each of those parcels?
Thank you
On S
The easier way is to use -cifti-merge (or wb_shortcuts -cifti-concatenate
for simpler syntax), then -cifti-reduce. It is possible to do with
-cifti-math, but not as convenient.
Tim
On Tue, Sep 27, 2016 at 4:37 PM, Michael F.W. Dreyfuss <
mid2...@med.cornell.edu> wrote:
> Thank you, that works.
Thank you, that works. Then if I want multiple parcels to be collapsed into a
single ROI to make a mask spanning several ROIs that are not considered
separate keys, which command would do that.
Thank you,
Michael
On Sep 27, 2016, at 5:26 PM, Timothy Coalson
mailto:tsc...@mst.edu>> wrote:
The
The easiest way to deal with this is probably to use -cifti-separate to get
them as gifti label files, which are each single-hemisphere. The use of
the same key/name for both hemispheres was an unfortunate choice, which we
intended to avoid in the future.
Tim
On Tue, Sep 27, 2016 at 4:15 PM, Mi
Thank you,
The problem was that the computer I was using before had an older version of
workbench. It works on my current computer.
As far as using
-cifti-label-to-roi
How would that work with files like Human.Brodmann09.32k_fs_LR.dlabel.nii where
the ROIs in both hemispheres are under the
That is supposed to work the way you expected it to. Are you using
workbench version 1.2.3? If you can point me to that dlabel file (perhaps
off-list), I'll check if there is a bug that needs fixing.
Tim
On Tue, Sep 27, 2016 at 1:19 PM, Michael F.W. Dreyfuss <
mid2...@med.cornell.edu> wrote:
For that, you want -cifti-separate, splitting into hemispheres (resulting
in left and right label.gii files in this case) is exactly what it does.
See my response in the other thread for pulling individual areas out of a
parcellation and combining their ROIs.
Tim
On Tue, Sep 27, 2016 at 2:44 PM,
The surface structures in -cifti-separate are much coarser, they represent
the cifti file organization, not the parcellation areas. You want
CORTEX_LEFT and CORTEX_RIGHT for that command to work. However, the
outputs are gifti files, not cifti files - it is a format conversion
command, and probab
In a related question, if I want to treat hemispheres separately, how can I
create a simple hemispheric label file, or split a file like
Human.Brodmann09.32k_fs_LR.dlabel.nii into two hemispheres to treat the
Brodmann areas of each area separately?
Essentially, all of my questions are directed
Hello, I have been trying to make a file containing the parcellations for BA44
and BA45 using the Broadmann using the following command:
wb_command -cifti-label-import Human.Brodmann09.32k_fs_LR.dlabel.nii
BrodmannLabels.txt Brodmann_IFG.dlabel.nii -discard-others
Where BrodmannLabels.txt con
I can get separate the volumetric part of cifti files with a command like:
wb_command -cifti-separate
ToyNogo_fdr_palm/ToyNogo_results_merged_tstat.dscalar.nii COLUMN -volume
ACCUMBENS_RIGHT R_Acc_Beta.nii.gz -roi R_NAcc_ROI.nii.gz
But when I try that on surface data I get the error:
wb_command
Thank you,
Yes, I wasn’t necessarily looking for one parcel, but any set of parcels that
may be implicated in response inhibition or considered to be part of IFG,
although the fewer the better for fewer comparisons.
If I want to follow the following steps, can you please recommend which
wb_com
HCP did not have a task that was geared toward response inhibition.
Furthermore, although it’s alluring to believe that a single parcel will
encapsulate all of response inhibition, it’s doubtful.
Why not select a set of parcels in and near IFG, and correct for multiple
comparisons? Use a meta-a
I agree, that’s why I was checking in to see if there was a sub parcel you had
identified as being involved in response inhibition from your tasks, such as
flanker. There is a lot of background of IFG being involved in response
inhibition, particularly on go/nogo tasks,, so I was wondering if yo
Hi Michael,
Just a reminder to be careful here to avoid issues of circularity/double-dipping. You indicated that you had a priori hypotheses about IFG involvement, but that doesn’t allow you to then select a particular IFG parcel based on your task activation map.
Ideally, you would
I clicked in a corresponding location and your activation appears to fall
within area IFSp. The inferior frontal gyrus contains multiple areas, as does
the inferior frontal sulcus. We have only directly commented on the function
of the areas in relation to the 7 HCP acquired tasks (See the sup
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