I tried -label option and OTHER as my structure name, it gives me the same
error message.I am wondering is there any wrong with my labellist file?
because i specify my label to be named OTHER, there is nor CORTEX_LEFT
CORTEX_RIGHT in my label file.
Lisa
Date: Thu, 1 May 2014 22:00:41 -0500
Subject: Re: [HCP-Users] activation region mask
From: tsc...@mst.edu
To: lys84...@hotmail.com
CC: glass...@wusm.wustl.edu; do...@brainvis.wustl.edu;
hcp-users@humanconnectome.org
Structures are not labels, you need to use CORTEX_LEFT and CORTEX_RIGHT with
-cifti-separate, that error says the structure you specified isn't a structure
contained in the cifti file. However, it outputs gifti files, and if those
don't work in your tractography program, you may need to do some additional
conversion.
Also, if you want gifti label files from a cifti dlabel file, use -label
instead of -metric with -cifti-separate.
Tim
On Thu, May 1, 2014 at 9:47 PM, Luo,Yishan <lys84...@hotmail.com> wrote:
I am using dsistudio for fiber tracking. It doesn't accept gifti file.
I tried -cifti-separte -metric, but it reports: ERROR: getSurfaceMap called for
nonexistant structure
I used -cifti-label-import to create the dlabel filemy labellist is "OTHER
1 255 0 0 100"
So for -metric <structure> I use OTHER for structure.
But happens for this error?
Thanks very much for your help.
Lisa
From: glass...@wusm.wustl.edu
To: lys84...@hotmail.com; tsc...@mst.edu
CC: do...@brainvis.wustl.edu; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] activation region mask
Date: Wed, 30 Apr 2014 14:38:45 +0000
What fiber tracking software are you using? probtrackx accepts GIFTI labels on
the surface. wb_command -cifti-separate -volume-all only separates out the
subcortical data. To get the surface data you need to specify the -metric
outputs.
Peace,
Matt.
From: <Luo>, Yishan <lys84...@hotmail.com>
Date: Wednesday, April 30, 2014 at 3:15 AM
To: Matt Glasser <glass...@wusm.wustl.edu>, Timothy Coalson <tsc...@mst.edu>
Cc: Donna Dierker <do...@brainvis.wustl.edu>, "hcp-users@humanconnectome.org"
<hcp-users@humanconnectome.org>
Subject: RE: [HCP-Users] activation region mask
Thanks all for your answers. The problem was solved by using
-cifti-label-import.
Sorry for bothering. Here I have another question:
I have a label file *.dlabel.nii (created by thresholding the
*tfMRI_MOTOR_level2_hp200_s4.dscalar file, in my previous question)
I print the information of this file to a txt file, and find there are 14326
nonzero labels.
I'd like to change this file into a normal nifti file in mni space, so that I
can use it as a roi region for fiber tracking,
I use the command "-cifti-separate -volume-all "
and change it into a *.nii file, but when I read the file, I find there are
only 3256 labels.
I dont know why some labels are discarded.
Best Regards,
Lisa
From: glass...@wusm.wustl.edu
To: tsc...@mst.edu
CC: do...@brainvis.wustl.edu;
lys84...@hotmail.com; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] activation region mask
Date: Tue, 29 Apr 2014 18:20:19 +0000
That command needs a -cifti-roi flag added to it for it to be usable in this
case I think (and I think it should be added).
Matt.
From: Timothy Coalson <tsc...@mst.edu>
Date: Tuesday, April 29, 2014 at 1:19 PM
To: Matt Glasser <glass...@wusm.wustl.edu>
Cc: Donna Dierker <do...@brainvis.wustl.edu>, "Luo,Yishan"
<lys84...@hotmail.com>, "hcp-users@humanconnectome.org"
<hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] activation region mask
Sorry, didn't get the URL right:
http://www.humanconnectome.org/software/workbench-command.php?function=-cifti-average-dense-roi
Tim
On Tue, Apr 29, 2014 at 1:18 PM, Timothy Coalson
<tsc...@mst.edu> wrote:
If you have only one ROI, you could also look at the -cifti-average-dense-roi
command: http://www.humanconnectome.org/software/workbench-command.php
Tim
On Tue, Apr 29, 2014 at 10:11 AM, Glasser, Matthew
<glass...@wusm.wustl.edu> wrote:
To convert the output of -cifti-math to a label file, use wb_command
-cifti-label-import. You can use wb_command -cifti-merge to extract
frames, though it is not as convenient as something like fslroi would be
as you have to specify each frame.
Peace,
Matt.
On 4/29/14, 8:19 AM, "Donna Dierker" <do...@brainvis.wustl.edu> wrote:
>Hi Lisa,
>
>While there is a -volume flag (e.g., for subcortical structures), it is
>not mandatory. This command works for me:
>
>wb_command -cifti-create-label $OUTPUT_DLABEL_1 \
> -left-label $INPUT_LABEL_LH -right-label $INPUT_LABEL_RH
>
>I'm sorry I don't know how to extract the frames.
>
>Donna
>
>
>On Apr 29, 2014, at 2:48 AM, "Luo,Yishan" <lys84...@hotmail.com> wrote:
>
>> Dear all,
>>
>> I would like to do the following things with task fMRI.
>>
>> I threshold the file
>>HCP_Q1-2_R120_tfMRI_ALLTASKS_level3_hp200_s4.dscalar.nii to get the
>>activation region
>> using -cifti-math "x>5"
>>
>> I want to extract the average timeseries from the roi region.
>> But it seems that -cifti-parcellate requires a label file as input. And
>>-cifti-create-label requires a volume file as input to create a label.
>> But my output from -cifti-math is in cifti format, it is neither a
>>volume nor a label.
>>
>> How can I do to transform it?
>>
>> Another question is how can I extract several frames from
>>"tfMRI_MOTOR_LR_Atlas.dtseries.nii" file, such as from frame 10 to 20?
>>
>>
>> Thanks a lot!
>>
>> Best Regards,
>> Lisa
>>
>>
>>
>>
>>
>> _______________________________________________
>> HCP-Users mailing list
>> HCP-Users@humanconnectome.org
>>
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>
>
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taking of any action in reliance on the contents of this information is
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