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 >>>>>>> >>>>>>> >>>>>>> ------------------------------ >>>>>>> >>>>>>> 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. >>>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> 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. >>>> >>> >>> >> > > _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
