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. > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
