Anderson,
We are aware of the problem. If you want to be kept in the loop as to the
resolution of this issue, please follow the instruction below and sign up on
our bugzilla bug tracking website.
Best,
Jan-Mathijs
On Apr 4, 2015, at 11:13 PM, Anderson M. Winkler <wink...@fmrib.ox.ac.uk> wrote:
> 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
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>> The materials in this message are private and may contain Protected
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>> of this information is strictly prohibited. If you have received this email
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