I'm a bit late on this, but the error messages in the original post are consistent with an incorrect header on the file being opened, please try a different cifti file and see if that works.
Tim On Sun, Mar 8, 2015 at 4:01 AM, jan-mathijs schoffelen < [email protected]> wrote: > > Hi Cherry, > > Could you tell us where you got the copy from ft_read_cifti? It sounds as > if the error you reported is due to me screwing up the code, and somehow > this buggy function made it to a location where you obtained it from. As > far as I am aware the most recent version that you can obtain from the > fieldtrip package (fieldtrip.fcdonders.nl; if you download the software > and unzip it, the function is in fieldtrip/fileio/ft_read_cifti) should be > OK. A way to quickly try this, would be to grab the code from google code: > https://code.google.com/p/fieldtrip/source/browse/trunk/fileio/ft_read_cifti.m > Could you give it a try and report back whether this version of the code > works for your purposes? > > Thanks and best wishes, > > > Jan-Mathijs > > > Jan-Mathijs Schoffelen, MD PhD > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > [email protected] > Telephone: +31-24-3614793 > > http://www.hettaligebrein.nl > > > On Mar 8, 2015, at 7:38 AM, Yizhou Ma <[email protected]> wrote: > > Indeed. I look forward to their reply. > > On Sun, Mar 8, 2015 at 12:37 AM, Glasser, Matthew <[email protected] > > 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 <[email protected]> >> Date: Sunday, March 8, 2015 at 12:34 AM >> To: Matt Glasser <[email protected]> >> Cc: "[email protected]" <[email protected]> >> 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 <[email protected]> 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 < >>> [email protected]> 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 <[email protected]> >>>> Date: Sunday, March 8, 2015 at 12:07 AM >>>> To: "[email protected]" <[email protected]> >>>> Subject: [HCP-Users] Fwd: Difficulties reading cifti into matlab with >>>> ft_read_cifti or ciftiopen >>>> >>>> >>>> ---------- Forwarded message ---------- >>>> From: Yizhou Ma <[email protected]> >>>> 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" <[email protected]> >>>> >>>> >>>> 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 < >>>> [email protected]> wrote: >>>> >>>>> Are you not including the directory path to the file? >>>>> >>>>> Peace, >>>>> >>>>> Matt. >>>>> >>>>> From: Yizhou Ma <[email protected]> >>>>> Date: Saturday, March 7, 2015 at 10:47 PM >>>>> To: "[email protected]" <[email protected]> >>>>> 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 >>>>> [email protected] >>>>> 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 >>>> [email protected] >>>> 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. 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