Re: [HCP-Users] Regarding: fsl version 5.0.6

[Glasser, Matthew]

I guess I’m still unclear about the difficulty you encountered was—since this all works perfectly for us over here for HCP data (were you trying to use your own data or something?).  If there is an issue with the instructions (something unclear or that lead to a misunderstanding) we’d really like to know what it was so that we can improve the instructions.  Running the volume-based FSL FEAT on HCP data is not recommended and wastes the efforts that were put into acquiring high spatial and temporal resolution HCP data and processing it carefully—you basically lose the benefits of the HCP data over previous approaches.   Otherwise, it’s worth noting that if one is starting from the minimally preprocessed task fMRI HCP packages, one does not need to copy any files around—the task fMRI analysis pipelines will simply run (assuming you set up their input variables correctly).  If one is starting completely from scratch—the raw data—one needs to copy the EV files and .fsf files into the correct locations, as specified in the instructions.   Generally though, one does not actually even need to run this task fMRI analysis pipeline for HCP data, as we provide already analyzed CIFTI grayordinates packages without additional smoothing. Peace, Matt. From: Dr Sampada Sinha <drsampadasi...@gmail.com> Date: Thursday, April 16, 2015 at 4:18 PM To: Matt Glasser <glass...@wusm.wustl.edu> Cc: "tbbr...@wustl.edu" <tbbr...@wustl.edu>, "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] Regarding: fsl version 5.0.6 Dear HCP experts, Thank you very much for your prompt and sincere reply! I did follow all the instructions described in the release notes at: https://github.com/Washington-University/Pipelines/wiki/v3.4.0-Release-Notes,-Installation,-and-Usage#task-analysis . But the process is not running inspite of placing the fsf (level 1) and the EV files in their respective subdirectory and level 2 sf file in the final common pathway. So I started with the feat analysis using fsl instead of using the pipelines (though it did help and saved me a lot of time to go through each process separately otherwise). If I have questions ,I would send email to you again.Thank you so much again! Kind regards! Sampada On Sun, Apr 12, 2015 at 12:22 PM, Glasser, Matthew <glass...@wusm.wustl.edu> wrote: Hi Tim, I thought the packages already have the files in the correct locations?  I don’t do any copying when I pull the data locally. Will be sending you a separate e-mail off list about the pipeline, as additional changes are required and it might be a good time to pull in some new features. Thanks, Matt. From: "Timothy B. Brown" <tbbr...@wustl.edu> Reply-To: "tbbr...@wustl.edu" <tbbr...@wustl.edu> Date: Sunday, April 12, 2015 at 12:20 PM To: Matt Glasser <glass...@wusm.wustl.edu>, Dr Sampada Sinha <drsampadasi...@gmail.com>, "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] Regarding: fsl version 5.0.6 FSL v5.0.6 is currently a specific prerequisite for the pipeline scripts. There is a version of the task analysis scripts that is currently in the review process that should work with both FSL v5.0.6 and FSL v5.0.7 and above. I hope to be able to release it soon.   I may be mistaken, but I believe the file copying that is being referred to is just that necessary to get the FEAT setup files (FSF files) in the right locations to do the Task Analysis as is described in the release notes at:   https://github.com/Washington-University/Pipelines/wiki/v3.4.0-Release-Notes,-Installation,-and-Usage#task-analysis   Best Regards,   Tim   On Sat, Apr 11, 2015, at 12:57, Glasser, Matthew wrote: We do need to get a version of this code compatible with current FSL out, but it is true that the code won’t run properly with FSL version greater than 5.0.6.   All of this copying of files seems concerning, as it should not be necessary.  You should simply be able to run the script if you have downloaded the appropriate package data.     Peace,   Matt.   From: Dr Sampada Sinha <drsampadasi...@gmail.com> Date: Saturday, April 11, 2015 at 11:51 AM To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: [HCP-Users] Regarding: fsl version 5.0.6   Dear HCP experts,   I am trying to run first level Gambling task analysis. I copied and pasted the templates of feat setup files (found in Examples/Scripts) to the MNINonlinear/Results/fMRI_GAMBLING_LR( or _RL) respective directory (number of time points were same as the corresponding scans:253). Next I copied and pasted copy of E-Prime EV files in the MNINonLinear/Results subdirectory. I am getting the following error now (highlighted below):   Last login: Sat Apr 11 09:32:36 on ttys002 rmbp:~ Sampada$ export FREESURFER_HOME=/Applications/freesurfer rmbp:~ Sampada$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-Darwin-lion-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME   /Applications/freesurfer FSFAST_HOME       /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR      /Applications/freesurfer/subjects MNI_DIR           /Applications/freesurfer/mni FSL_DIR           /Applications/fsl rmbp:~ Sampada$ cd /Volumes/HCP_Data/Pipelines-3.4.0/Examples/Scripts/ rmbp:Scripts Sampada$ ./TaskfMRIAnalysisBatch.sh  This script must be SOURCED to correctly setup the environment prior to running any of the other HCP scripts contained here   2   tfMRI_GAMBLING     LS2001 About to use fsl_sub to queue or run /Volumes/HCP_data/Pipelines-3.4.0/TaskfMRIAnalysis/TaskfMRIAnalysis.sh This script, TaskfMRILevel1.sh, assumes fslmaths behavior that is available in version 5.0.6 of FSL. You are using FSL version 5.0.8. Please install FSL version 5.0.6 before continuing. This script, TaskfMRILevel1.sh, assumes fslmaths behavior that is available in version 5.0.6 of FSL. You are using FSL version 5.0.8. Please install FSL version 5.0.6 before continuing. cat: /Volumes/HCP_Data/taskfMRI_Gambling/LS2001/MNINonLinear/Results/tfMRI_GAMBLING/tfMRI_GAMBLING_hp200_s4_level2.fsf: No such file or directory Can't find key fmri(level) set -- --path=/Volumes/HCP_Data/taskfMRI_Gambling         --subject=LS2001         --lvl1tasks=tfMRI_GAMBLING_RL@tfMRI_GAMBLING_LR         --lvl1fsfs=tfMRI_GAMBLING_RL@tfMRI_GAMBLING_LR         --lvl2task=tfMRI_GAMBLING         --lvl2fsf=tfMRI_GAMBLING         --lowresmesh=32         --grayordinatesres=2         --origsmoothingFWHM=2         --confound=NONE         --finalsmoothingFWHM=2         --temporalfilter=200         --vba=NO . /Volumes/HCP_Data/Pipelines-3.4.0/Examples/Scripts/SetUpHCPPipeline.sh rmbp:Scripts Sampada$  …...          …..          …..            …..              …..         ……..            …..   Do I need to download fsl version 5.0.6 now as well to run the task analysis?   Can I get any feedback please about the process which I followed from the HCP site and if I need to put the copied EV files in the respective subdirectories or LINKED_DATA files into the MNINonlinear/Results/taskfMRI directory?   Also, if I can get performance score of Gambling task, based upon which we plan to separate out the regions depending on the score.   Appreciate all your help so far!   Kind regards,   Sampada     P.S.: Sorry about the font last time. I copied and pasted my question from the notes (which has an artsy font by default!)   --  Sampada Sinha Post-Doctoral Associate University of Minnesota (East Bank) Molecular and neuroimaging laboratory Department of Psychiatry Minneapolis-55415                   _______________________________________________ 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 -- Timothy B. Brown Business & Technology Application Analyst III Pipeline Developer (Human Connectome Project) tbbrown(at)wustl.edu ________________________________________ The material in this message is private and may contain Protected Healthcare Information (PHI). 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. -- Sampada Sinha Post-Doctoral Associate University of Minnesota (East Bank) Molecular and neuroimaging laboratory Department of Psychiatry Minneapolis-55415   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