Re: [HCP-Users] Fwd: Difficulties reading cifti into matlab with ft_read_cifti or ciftiopen

[Glasser, Matthew]

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