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
