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: [email protected]
To: [email protected]; [email protected]
CC: [email protected]; [email protected]
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 <[email protected]>
Date: Wednesday, April 30, 2014 at 3:15 AM
To: Matt Glasser <[email protected]>, Timothy Coalson <[email protected]>
Cc: Donna Dierker <[email protected]>, "[email protected]"
<[email protected]>
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: [email protected]
To: [email protected]
CC: [email protected];
[email protected]; [email protected]
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 <[email protected]>
Date: Tuesday, April 29, 2014 at 1:19 PM
To: Matt Glasser <[email protected]>
Cc: Donna Dierker <[email protected]>, "Luo,Yishan"
<[email protected]>, "[email protected]"
<[email protected]>
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
<[email protected]> 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
<[email protected]> 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" <[email protected]> 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" <[email protected]> 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
>> [email protected]
>>
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>
>
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