Update: I can not open .dlabel.nii files with ft_read_cifti. Error message
is:
Dot name reference on non-scalar structure.
Error in ft_read_cifti (line 930)
key = NamedMap.LabelTable.Key;
On Sun, Mar 8, 2015 at 12:49 PM, Yizhou Ma <[email protected]> wrote:
> Hi Dr. Schoffelen,
>
> Thanks for your reply. I downloaded the fieldtrip package you listed and I
> can now open all kinds of cifti files.
>
> The initial package I installed is from this page:
> https://github.com/Washington-University/cifti-matlab
> and I was linked from here:
> https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-2.HowdoyougetCIFTIfilesintoMATLAB
>
> Also just to mention that both yours and Timothy's email never got into my
> mailbox. I wouldn't have seen them if I did not read the HCP digest.
>
> Thanks,
> Cherry
>
>
> On Sun, Mar 8, 2015 at 12:38 AM, Yizhou Ma <[email protected]> wrote:
>
>> Indeed. I look forward to their reply.
>>
>> On Sun, Mar 8, 2015 at 12:37 AM, Glasser, Matthew <
>> [email protected]> wrote:
>>
>>> Is that the function from the MEG part of the HCP consortium? If so,
>>> I hope they will see and comment on this. It’s probably a bug in their
>>> CIFTI reader/writer (which aims to be much more than mine does and will
>>> hopefully end up being the replacement).
>>>
>>> Peace,
>>>
>>> Matt.
>>>
>>> From: Yizhou Ma <[email protected]>
>>> Date: Sunday, March 8, 2015 at 12:34 AM
>>> To: Matt Glasser <[email protected]>
>>> Cc: "[email protected]" <[email protected]>
>>> Subject: Re: [HCP-Users] Fwd: Difficulties reading cifti into matlab
>>> with ft_read_cifti or ciftiopen
>>>
>>> Also to add some info on using "ft_read_cifti" just so it may be
>>> helpful for developers of this command:
>>>
>>> It worked perfectly for the .dtseries files I tried.
>>> For .dscalar files, be it ICA groups maps or individual
>>> thickness/curvature/... files, I got the error:
>>> Reference to non-existent field 'LabelTable'.
>>>
>>> Best,
>>> Cherry
>>>
>>> On Sun, Mar 8, 2015 at 12:27 AM, Yizhou Ma <[email protected]> wrote:
>>>
>>>> Hi,
>>>>
>>>> Since "melodic_IC.dscalar.nii" for d=25 seemed to be the only file
>>>> that I could not open, I just unzipped all my group ICA maps and now the
>>>> new "melodic_IC.dscalar.nii" can be opened.
>>>>
>>>> I am confused as the freshly unzipped "melodic_IC.dscalar.nii" is much
>>>> smaller than the one I have been working on. I indeed have been viewing
>>>> this file in wb_view and may have applied thresholds and clicked on
>>>> coordinates for display purposes. But I don't think I could have done any
>>>> significant change to a cifti file in wb_view, to the point that it can no
>>>> longer be read by ciftiopen.
>>>>
>>>>
>>>> Best,
>>>> Cherry
>>>>
>>>> On Sun, Mar 8, 2015 at 12:18 AM, Glasser, Matthew <
>>>> [email protected]> wrote:
>>>>
>>>>> I’m puzzled by that as well, unless you don’t have write permission
>>>>> to the location which can mess things up.
>>>>>
>>>>> Peace,
>>>>>
>>>>> Matt.
>>>>>
>>>>> From: Yizhou Ma <[email protected]>
>>>>> Date: Sunday, March 8, 2015 at 12:07 AM
>>>>> To: "[email protected]" <[email protected]>
>>>>> Subject: [HCP-Users] Fwd: Difficulties reading cifti into matlab with
>>>>> ft_read_cifti or ciftiopen
>>>>>
>>>>>
>>>>> ---------- Forwarded message ----------
>>>>> From: Yizhou Ma <[email protected]>
>>>>> Date: Sun, Mar 8, 2015 at 12:07 AM
>>>>> Subject: Re: [HCP-Users] Difficulties reading cifti into matlab with
>>>>> ft_read_cifti or ciftiopen
>>>>> To: "Glasser, Matthew" <[email protected]>
>>>>>
>>>>>
>>>>> Hi Dr. Glasser,
>>>>>
>>>>> I moved everything I need to open under the /bin just to make sure
>>>>> that I did not mess up with the path.
>>>>>
>>>>> An update: I am now able to use most .dscalar and .dtseries files for
>>>>> participants with ciftiopen. Yet I don't know what I did to get it right.
>>>>> I
>>>>> also succeeded in open "melodic_IC.dscalar.nii" for ICA d=50, yet I got
>>>>> the
>>>>> same error for "melodic_IC.dscalar.nii" for ICA d=25. This inconsistency
>>>>> confuses me.
>>>>>
>>>>>
>>>>> Best,
>>>>> Cherry
>>>>>
>>>>> On Sun, Mar 8, 2015 at 12:01 AM, Glasser, Matthew <
>>>>> [email protected]> wrote:
>>>>>
>>>>>> Are you not including the directory path to the file?
>>>>>>
>>>>>> Peace,
>>>>>>
>>>>>> Matt.
>>>>>>
>>>>>> From: Yizhou Ma <[email protected]>
>>>>>> Date: Saturday, March 7, 2015 at 10:47 PM
>>>>>> To: "[email protected]" <[email protected]>
>>>>>> Subject: [HCP-Users] Difficulties reading cifti into matlab with
>>>>>> ft_read_cifti or ciftiopen
>>>>>>
>>>>>> Dear HCP experts,
>>>>>>
>>>>>> I am experiencing difficulties reading cifti into matlab.
>>>>>>
>>>>>> For the ICA maps (melodic_IC.dscalar.nii). I used:
>>>>>>
>>>>>> cifti=ft_read_cifti('melodic_IC.dscalar.nii')
>>>>>>
>>>>>> The error I got was:
>>>>>> Error using read_nifti2_hdr (line 56)
>>>>>> cannot open melodic_IC.dscalar.nii as nifti file, hdr size =
>>>>>> 1684628319, should be 348 or 540
>>>>>>
>>>>>> I also tried:
>>>>>> cifti=ciftiopen('melodic_IC.dscalar.nii','wb_command')
>>>>>>
>>>>>> and I got
>>>>>> ERROR: error reading NIfTI file
>>>>>> /workbench/bin_rh_linux64/melodic_IC.dscalar.nii:
>>>>>> /workbench/bin_rh_linux64/melodic_IC.dscalar.nii is not a valid NIfTI
>>>>>> file
>>>>>> wb_command -cifti-convert -to-gifti-ext melodic_IC.dscalar.nii
>>>>>> /tmp/tpe16b84a6_70fd_4d0b_80c7_1daf1d5c79b7.gii: Signal 127
>>>>>> Error using read_gifti_file (line 17)
>>>>>> [GIFTI] Loading of XML file
>>>>>> /tmp/tpe16b84a6_70fd_4d0b_80c7_1daf1d5c79b7.gii failed.
>>>>>>
>>>>>> Error in gifti (line 71)
>>>>>> this = read_gifti_file(varargin{1},giftistruct);
>>>>>>
>>>>>> Error in ciftiopen (line 31)
>>>>>> cifti = gifti([tmpfile '.gii']);
>>>>>>
>>>>>> Errors when opening other cifti files are different, for example
>>>>>>
>>>>>>
>>>>>> cifti=ciftiopen('rfMRI_REST1_LR_Atlas_hp2000_clean.dtseries.nii','wb_command')
>>>>>> Undefined function 'file_array' for input arguments of type 'char'.
>>>>>>
>>>>>> I run all commands in workbench's bin. My workbench is v1.0. My gifti
>>>>>> library was just downloaded so no reason to believe that it is not
>>>>>> up-to-date.
>>>>>>
>>>>>> Any help is appreciated.
>>>>>>
>>>>>> Best,
>>>>>> Cherry
>>>>>>
>>>>>> _______________________________________________
>>>>>> HCP-Users mailing list
>>>>>> [email protected]
>>>>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>>>>>
>>>>>>
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>>>>>> contents
>>>>>> of this information is strictly prohibited. If you have received this
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>>>>>> in error, please immediately notify the sender via telephone or return
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>>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> HCP-Users mailing list
>>>>> [email protected]
>>>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>>>>
>>>>>
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>>>>>
>>>>> 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.
>>>>>
>>>>
>>>>
>>>
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>>>
>>> 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.
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>>
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>
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