Hi all,
I just would like to comment that I receive the exact same error message
when I try to open one of the CIFTI test data examples available in NITRC:
>> x = ft_read_cifti('Conte69.parcellations_VGD11b.32k_fs_LR.dlabel.nii');
reading CORTEX_LEFT surface from Conte69.L.inflated.32k_fs_LR.surf.gii
reading CORTEX_RIGHT surface from Conte69.R.inflated.32k_fs_LR.surf.gii
Dot name reference on non-scalar structure.
Error in ft_read_cifti (line 930)
key = NamedMap.LabelTable.Key;
I'm using what it seems is most recent version available in GitHub.
Thanks.
All the best,
Anderson
On 9 March 2015 at 00:57, Yizhou Ma <maxxx...@umn.edu> wrote:
> Hi Dr. Schoffelen,
>
> I have just submitted the bug. I also searched the script for
> ft_write_cifti and found nothing about .dlabel there. Does that mean that
> .dlabel is not supported for that command either?
>
> Best,
> Cherry
>
> On Sun, Mar 8, 2015 at 2:24 PM, jan-mathijs schoffelen <
> jm.schoffe...@gmail.com> wrote:
>
>> Hi Cherry,
>>
>> Sorry about this. Could you go to the following URL and follow the
>> instructions in order to create a 'bug' on FieldTrip's bug tracking
>> website: http://fieldtrip.fcdonders.nl/bugzilla ?
>> It would be great if you could create this bug and also upload the dense
>> label file that is giving you problems. If file size is a problem, please
>> send the file (preferably off-list) to me.
>>
>> Best wishes,
>> Jan-Mathijs
>>
>>
>> On Mar 8, 2015, at 7:37 PM, Yizhou Ma <maxxx...@umn.edu> wrote:
>>
>> 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 <maxxx...@umn.edu> 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 <maxxx...@umn.edu> wrote:
>>>
>>>> Indeed. I look forward to their reply.
>>>>
>>>> On Sun, Mar 8, 2015 at 12:37 AM, Glasser, Matthew <
>>>> glass...@wusm.wustl.edu> 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 <maxxx...@umn.edu>
>>>>> Date: Sunday, March 8, 2015 at 12:34 AM
>>>>> To: Matt Glasser <glass...@wusm.wustl.edu>
>>>>> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>>>>> 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 <maxxx...@umn.edu> 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 <
>>>>>> glass...@wusm.wustl.edu> 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 <maxxx...@umn.edu>
>>>>>>> Date: Sunday, March 8, 2015 at 12:07 AM
>>>>>>> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>>>>>>> Subject: [HCP-Users] Fwd: Difficulties reading cifti into matlab
>>>>>>> with ft_read_cifti or ciftiopen
>>>>>>>
>>>>>>>
>>>>>>> ---------- Forwarded message ----------
>>>>>>> From: Yizhou Ma <maxxx...@umn.edu>
>>>>>>> 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" <glass...@wusm.wustl.edu>
>>>>>>>
>>>>>>>
>>>>>>> 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 <
>>>>>>> glass...@wusm.wustl.edu> wrote:
>>>>>>>
>>>>>>>> Are you not including the directory path to the file?
>>>>>>>>
>>>>>>>> Peace,
>>>>>>>>
>>>>>>>> Matt.
>>>>>>>>
>>>>>>>> From: Yizhou Ma <maxxx...@umn.edu>
>>>>>>>> Date: Saturday, March 7, 2015 at 10:47 PM
>>>>>>>> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>>>>>>>> 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
>>>>>>>> HCP-Users@humanconnectome.org
>>>>>>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>>>>>>>
>>>>>>>>
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>>>>>>>> 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.
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> HCP-Users mailing list
>>>>>>> HCP-Users@humanconnectome.org
>>>>>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>>>>>>
>>>>>>>
>>>>>>> ------------------------------
>>>>>>>
>>>>>>> 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.
>>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> ------------------------------
>>>>>
>>>>> 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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