As a further comment, you mentioned way back in the thread that you wanted
to get average time courses for parcels. Have you looked at wb_command
-cifti-parcellate, as I suggested?
Tim
On Wed, Aug 24, 2016 at 11:08 AM, Glasser, Matthew <glass...@wustl.edu>
wrote:
> If the goal is to analyze the CIFTI file in matlab, there is no need to
> used CIFTI separate.
>
> Peace,
>
> Matt.
>
> From: <hcp-users-boun...@humanconnectome.org> on behalf of "Harms,
> Michael" <mha...@wustl.edu>
> Date: Wednesday, August 24, 2016 at 11:04 AM
> To: Ferdaus Kawsar <ferdaus.kaw...@gmail.com>, Timothy Coalson <
> tsc...@mst.edu>
>
> Cc: "hcp-users@humanconnectome.org" <HCP-Users@humanconnectome.org>
> Subject: Re: [HCP-Users] Extract average time-course from cortical parcels
>
>
> A .nii or .nii.gz is not a CIFTI file (it is a NIFTI file), and
> consequently ciftiopen doesn’t work with it.
>
> If you want to load a NIFTI file in matlab, there are a number of tools
> out there, including load_nifti.m that comes with FreeSurfer, and
> read_avw.m that comes with FSL. I’m sure there are other dedicated NIFTI
> matlab readers as well.
>
> cheers,
> -MH
>
> --
> Michael Harms, Ph.D.
> -----------------------------------------------------------
> Conte Center for the Neuroscience of Mental Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave. Tel: 314-747-6173
> St. Louis, MO 63110 Email: mha...@wustl.edu
>
> From: <hcp-users-boun...@humanconnectome.org> on behalf of Ferdaus Kawsar
> <ferdaus.kaw...@gmail.com>
> Date: Wednesday, August 24, 2016 at 10:46 AM
> To: Timothy Coalson <tsc...@mst.edu>
> Cc: "hcp-users@humanconnectome.org" <HCP-Users@humanconnectome.org>
> Subject: Re: [HCP-Users] Extract average time-course from cortical parcels
>
> Hi Tim,
> I used -cifti-separate and created the files. However, even
> though I can load the data in Matlab for left_data.func.gii and
> right_data.func.gii,
> I cannot load the volume files in Matlab. I could not load out_vol.nii.gz
> and out_vol_structs.nii.gz , files in matlab.(I unzipped them first) I
> tried both ft_read_cifti and ciftiopen and none of them works.
>
> They can both be viewed by workbench.
>
> Here is the error message I see when I use ciftiopen to load out_vol.nii
>
> out_vol_cft_open=ciftiopen('/home/fkawsar/HCP_Data/
> Experimental/MNI3.17/out_vol.nii','/home/fkawsar/Downloads/
> workbench/exe_linux64/wb_command');
>
> While running:
> /home/fkawsar/Downloads/workbench/exe_linux64/wb_command -cifti-convert
> -to-gifti-ext /home/fkawsar/HCP_Data/Experimental/MNI3.17/out_vol.nii
> /tmp/tp5ece90ba_3f9e_4d81_aec6_2b19c0f950c2.gii
>
> ERROR: no cifti extension found in file '/home/fkawsar/HCP_Data/
> Experimental/MNI3.17/out_vol.nii'
>
> /home/fkawsar/Downloads/workbench/exe_linux64/wb_command -cifti-convert
> -to-gifti-ext /home/fkawsar/HCP_Data/Experimental/MNI3.17/out_vol.nii
> /tmp/tp5ece90ba_3f9e_4d81_aec6_2b19c0f950c2.gii: Signal 127
> Error using read_gifti_file_standalone (line 20)
> [GIFTI] Loading of XML file /tmp/tp5ece90ba_3f9e_4d81_aec6_2b19c0f950c2.gii
> failed.
>
> Error in gifti (line 71)
> this = read_gifti_file_standalone(
> varargin{1},giftistruct);
>
> Error in ciftiopen (line 31)
> cifti = gifti([tmpfile '.gii']);
>
> Hope you can help.
>
> Best,
> -Ferdaus
>
>
> On Thu, Aug 11, 2016 at 5:39 PM, Timothy Coalson <tsc...@mst.edu> wrote:
>
>> -cifti-separate creates nifti and gift files from parts of the cifti
>> file. That output is a volume file, and should have been named ending in
>> .nii.gz, such that it would be compressed on-disk. However, I would not
>> recommend doing it this way for all subcortical structures, as that is a
>> lot of volume files, all of which will have the full original FOV from the
>> volume preprocessing output.
>>
>> If the only thing you want to do with them is average them into per-area
>> timeseries, I suggest you try -cifti-parcellate before anything else. You
>> may need to first make a dlabel file that combines your chosen surface and
>> subcortical parcellations.
>>
>> If you want all the individual timeseries separately, then you might try
>> the -volume-all option of -cifti-separate, and possibly the -crop options,
>> as well as the -roi options to tell you which voxels have data in them.
>> The -metric option will get you the surface data. Note that you can
>> specify these options simultaneously to a single command:
>>
>> wb_command -cifti-separate <input> COLUMN -volume-all out_vol.nii.gz
>> -crop -label out_vol_structs.nii.gz -metric CORTEX_LEFT left_data.func.gii
>> -roi left_roi.func.gii -metric CORTEX_RIGHT right_data.func.gii -roi
>> right_roi.func.gii
>>
>> Tim
>>
>>
>> On Thu, Aug 11, 2016 at 3:35 PM, Ferdaus Kawsar <ferdaus.kaw...@gmail.com
>> > wrote:
>>
>>> Hi Tim,
>>> Thanks for your reply. I used cifti-separate as you suggested
>>> to create volumes from *.dtseries.nii file I have. However, I am having
>>> difficulty to read the resultant file. Is it a cifti file? I cannot read
>>> this file using either ft_read_cifti() or ciftiopen(). Also the file is
>>> huge (1.8 GB). How do I extract time-course from this file?
>>>
>>> I created the file using following command:
>>> wb_command -cifti-separate '*.dtseries.nii' COLUMN -volume
>>> PUTAMEN_RIGHT 'out_putament_right'
>>>
>>>
>>> Best
>>> -Ferdaus
>>>
>>> On Wed, Aug 10, 2016 at 5:42 PM, Timothy Coalson <tsc...@mst.edu> wrote:
>>>
>>>> You might want to use "wb_command -cifti-parcellate" to do this for
>>>> you, it has some extra options to do things like weighted means according
>>>> to vertex area.
>>>>
>>>> Manually matching things up in matlab from loaded cifti files may be
>>>> difficult, as some .dlabel.nii files don't exclude the medial wall, and may
>>>> not include the subcortical voxels that the .dtseries.nii files do. You
>>>> can use -cifti-separate on cifti files to make simpler single-hemisphere
>>>> full-surface gifti files, and a nifti volume file for the subcortical stuff
>>>> (though doing this on the timeseries will result in a fairly large volume
>>>> file when loaded in memory).
>>>>
>>>> Tim
>>>>
>>>>
>>>> On Wed, Aug 10, 2016 at 2:48 PM, Ferdaus Kawsar <
>>>> ferdaus.kaw...@gmail.com> wrote:
>>>>
>>>>> Hi HCP Team,
>>>>> I was wondering if someone could help regarding a
>>>>> task I am trying to do. I need to extract average time-course for both
>>>>> cortical and sub-cortical parcels.
>>>>> I was able to extract average time-courses for sub-cortical parcels.
>>>>>
>>>>> After I loaded my *dtseries.nii cifti files (using ft_read_cifti()) in
>>>>> matlab, I could access all the time-courses for sub-cortical regions.
>>>>> There
>>>>> are 19 sub-cortical regions. After I got all the time -courses for a
>>>>> sub-cortical region, a simple mean() method in matlab gave me the average
>>>>> time-course. I am curious if this approach is right?
>>>>>
>>>>> Also, how do I get the time-courses for a cortical parcel? My eventual
>>>>> goal is to extract average time course for each of 180 parcels in each
>>>>> hemisphere.
>>>>>
>>>>> Best regards,
>>>>> -Ferdaus
>>>>> --
>>>>> Ferdaus A. Kawsar, PhD
>>>>> Research Scientist II
>>>>> Department of Neurology
>>>>> Medical College of Wisconsin
>>>>> Milwaukee, WI
>>>>>
>>>>> _______________________________________________
>>>>> HCP-Users mailing list
>>>>> HCP-Users@humanconnectome.org
>>>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>>>>
>>>>
>>>>
>>>
>>>
>>> --
>>> Ferdaus A. Kawsar, PhD
>>> Research Scientist II
>>> Department of Neurology
>>> Medical College of Wisconsin
>>> Milwaukee, WI
>>>
>>
>>
>
>
> --
> Ferdaus A. Kawsar, PhD
> Research Scientist II
> Department of Neurology
> Medical College of Wisconsin
> Milwaukee, WI
>
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