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. 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
