Question about ICA-FIX

[zhi chi]

Hi experts,

I'm performing ICA-FIX, and I got the error:

>FIX Classifying components in Melodic directory: rfMRI_hp200.ica using training file: >/home/fix/training_files/NHPHCP_Macaque_RIKEN30SRFIX.RData and threshold 10

>FIX Applying cleanup using cleanup file: >rfMRI_hp200.ica/fix4melview_NHPHCP_Macaque_RIKEN30SRFIX_thr10.txt and motion >cleanup set to 1

>Could not find a supported file with prefix "rfMRI_hp200.ica/filtered_func_data_clean"

I checked the logMatlab.txt,  log.txt, and the .fix_2b_predict.log, there is no error, and follows are errors in the .fix.log, can anyone help me to figure out the potential reasons? I actually ran it successfully before, but when I ran it again, it failed. 

                                                                              < M A T L A B (R) >

                                                                    Copyright 1984-2020 The MathWorks, Inc.

                                                                    R2020b (9.9.0.1467703) 64-bit (glnxa64)

                                                                                August 26, 2020

 

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aggressive = 0

domot = 1

hp = 200.000000

DOvol = 1

TR = 1.600000

{ Error using xml_parser>compile (line 127)

[XML] Unknown data at the end of the XML file.

Error in xml_parser>tag_element (line 224)

            contents = compile(contents);

Error in xml_parser>compile (line 175)

                            frag = tag_element(frag);

Error in xml_parser>tag_element (line 224)

            contents = compile(contents);

Error in xml_parser>compile (line 175)

                            frag = tag_element(frag);

Error in xml_parser>tag_element (line 224)

            contents = compile(contents);

Error in xml_parser>compile (line 175)

                            frag = tag_element(frag);

Error in xml_parser>tag_element (line 224)

            contents = compile(contents);

Error in xml_parser>compile (line 175)

                            frag = tag_element(frag);

Error in xml_parser>tag_element (line 224)

            contents = compile(contents);

Error in xml_parser>compile (line 175)

                            frag = tag_element(frag);

Error in xml_parser (line 103)

    compile(tree);

Error in xmltree (line 37)

        tree.tree = xml_parser(varargin{1});

Error in cifti_parse_xml (line 8)

    tree = xmltree(bytes);

Error in cifti_read (line 28)

        outstruct = cifti_parse_xml(hdr.extensions(ciftiextindex).edata, filename);

Error in ciftiopen (line 9)

    cifti = cifti_read(filename, 'wbcmd', wbcmd);

Error in fix_3_clean (line 62)

  BO=ciftiopen('Atlas.dtseries.nii',WBC);

}  

[Glasser, Matt]

Did you make some change to the GIFTI toolbox (e.g., including sourcing it from a new source like SPM)?

Matt.

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[zhi chi]

Thank you so much Matt! You are right, after I removed the GIFTI path in MATLAB and rerun the script, the problem was solved. 

[Coalson, Timothy Scott (S&T-Student)]

As another option, you can try the cifti-matlab master branch or its v2.0.1 release, where I renamed my version of xmltree, which should avoid this issue.  This change hasn't been added to the master branch of the HCP pipelines yet, we are working on it along with a new pipeline.

Tim

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From: zhi chi <ccllzz...@gmail.com>
Sent: Monday, November 29, 2021 1:14 AM
To: HCP-Users <hcp-...@humanconnectome.org>
Cc: glas...@wustl.edu <glas...@wustl.edu>
Subject: Re: [hcp-users] Question about ICA-FIX

 

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