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