Okay we will look into it. Matt.
From: "Theis, Nicholas" <[email protected]<mailto:[email protected]>> Date: Thursday, May 10, 2018 at 2:35 PM To: Matt Glasser <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] Missing MSMAll input spatial maps I do not recall moving around any scripts. I just did a quick search, and all the scripts I was "missing" (the ciftiopen.m, demean.m, etc) are in the HCP_Pipelines/global/matlab directory (this, I assume, is their default location)... I should have searched my code directories for these earlier. Anyway, the scripts are there, it seems I just failed to notice them. If a path needs to be edited manually in order for MSMall to find these scripts then I am not sure where that path is supposed to be modified (i.e. which .sh script to edit). Thank you for the quick responses, Nick ________________________________ From: Glasser, Matthew <[email protected]<mailto:[email protected]>> Sent: Thursday, May 10, 2018 1:51:08 PM To: Theis, Nicholas; [email protected]<mailto:[email protected]> Subject: Re: [HCP-Users] Missing MSMAll input spatial maps There already is such a line in the code, had you moved those scripts to a new location? Peace, Matt. From: "Theis, Nicholas" <[email protected]<mailto:[email protected]>> Date: Thursday, May 10, 2018 at 11:38 AM To: Matt Glasser <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] Missing MSMAll input spatial maps Sorry, I'm not sure what settings you are referring to, but when I added the directory containing... ciftiopen.m ciftisave.m demean.m ss_svds.m ...to Matlab's path with "addpath('the/directory');" in the MSMAll/scripts/MSMregression.m script (I had to add an "addpath()" line into that .m script), the MSMall.sh script was able to find the files I was previously missing. So that specific error has been resolved. Perhaps there is a way to include these Matlab scripts in the path for MSMregression in a more obvious manner, such as via a settings file? If so I must have missed those instructions. ________________________________ From: Glasser, Matthew <[email protected]<mailto:[email protected]>> Sent: Thursday, May 10, 2018 11:56:57 AM To: Theis, Nicholas; [email protected]<mailto:[email protected]> Subject: Re: [HCP-Users] Missing MSMAll input spatial maps What are the settings? Peace, Matt. From: "Theis, Nicholas" <[email protected]<mailto:[email protected]>> Date: Thursday, May 10, 2018 at 10:20 AM To: Matt Glasser <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] Missing MSMAll input spatial maps Matt- I'm calling it from the terminal using the following command: $HCPscriptsDirectory/MSMAllPipelineBatch.sh --StudyFolder=$HcpDir --Subjlist=$Subject It runs for a few minutes, then crashes during MSMregression (line 41): B0=ciftiopen(inputspatialmaps,wbcommand); OUTB0=B0; GM=B0.cdata; clear B0; GMorig=GM. ...I just noticed that the "ciftiopen" function is undefined- that is the error Matlab is throwing. I should have noticed this before! I added the path to my cifti reader/writer directory into MSMregression.m script, along with the path to "demean.n" and "ss_sdvs.m" and now it is generating those input spatial maps. Seems to be working fine now. Best, Nick ________________________________ From: Glasser, Matthew <[email protected]<mailto:[email protected]>> Sent: Thursday, May 10, 2018 10:12:09 AM To: Theis, Nicholas; [email protected]<mailto:[email protected]> Subject: Re: [HCP-Users] Missing MSMAll input spatial maps How did you call the MSMAll pipeline? Peace, Matt. From: <[email protected]<mailto:[email protected]>> on behalf of "Theis, Nicholas" <[email protected]<mailto:[email protected]>> Date: Thursday, May 10, 2018 at 9:03 AM To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: [HCP-Users] Missing MSMAll input spatial maps Dear HCP experts, I'm currently working on the MSMall stage of the HCP pipeline (using interpreted Matlab), but have encountered the following error: ERROR: failed to open file '.../MNINonLinear/fsaverage_LR32k/sub-1508.individual_RSNs_d40_MSMSulc.32k_fs_LR.dscalar.nii' file does not exist (I've abbreviated the parent directories with "...", our subject is called 'sub-1508') It seems like that missing file is the output of MSMregression.m, and an input file is also missing here. Specifically, the Matlab script is looking for: inputspatialmaps: .../MNINonLinear/fsaverage_LR32k/sub-1508.atlas_RSNs_d40_MSMSulc.32k_fs_LR.dscalar But in the fsaverage_LR32k directory I only have "sub-1508.atlas_RSNs_d40.32k_fs_LR.dscalar" I believe I've run all the necessary earlier stages of the pipeline (FreeSurfer, GenericSurfaceProcessing in MSMsulc mode, and the ICA Fix steps). Any ideas why this "inputspatialmaps" file would be missing? Is it produced in the MSMall stage, or is it supposed to be there before running MSMall? Thank you, Nick Theis _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
