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 <[email protected]> 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" <[email protected]> > Reply-To: "[email protected]" <[email protected]> > Date: Sunday, April 12, 2015 at 12:20 PM > To: Matt Glasser <[email protected]>, Dr Sampada Sinha < > [email protected]>, "[email protected]" < > [email protected]> > 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 <[email protected]> > Date: Saturday, April 11, 2015 at 11:51 AM > To: "[email protected]" <[email protected]> > 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 > [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 > > -- > 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 _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
