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
