Hello Mohammed, Which data do you already have? If you have HCP data on a hard disk, you might already have the outputs of Level 2 analyses. I would look for them first to verify whether you need to run Level 2 analyses. Edit the following command to find those files on your disk. ls -ld /PATH/TO/SUBJECT/DIRECTORY/MNINonLinear/Results/tfMRI_WM/tfMRI_WM*feat
The error output of the script did tell you what you need to know. You did not provide a fsf file as an argument, so the prepare_level2_feat_analysis.sh script doesn’t know where your analyses are located. If you provide the fsf file as an argument, it should run correctly. If you’re still having troubles, read the script. It is really doing a simple thing, inserting identify matrices where the registration matrices are typically found, to account for the fact that preprocessed HCP data are already registered to MNI space. You can do this manually rather than relying on that very old script, if it is not working for your purposes. --Greg ____________________________________________________________________ Greg Burgess, Ph.D. Staff Scientist, Human Connectome Project Washington University School of Medicine Department of Anatomy and Neurobiology Phone: 314-362-7864 Email: [email protected] > On Jul 27, 2015, at 5:15 AM, mohamad reza <[email protected]> wrote: > > Thanks for your reply > > The problem is i don't have access to high speed internet for downloading the > data right now > I have the data on a hard disk > > regards > > > > > On Sunday, July 26, 2015 9:18 PM, "Glasser, Matthew" > <[email protected]> wrote: > > > Why are you doing it this way instead of just using the already analyzed task > fMRI data? > > Peace, > > Matt. > > From: <[email protected]> on behalf of Mohamad Reza > Khodai <[email protected]> > Reply-To: Mohamad Reza Khodai <[email protected]> > Date: Sunday, July 26, 2015 at 11:00 AM > To: "[email protected]" <[email protected]>, Mohamad > Reza Khodai <[email protected]> > Subject: [HCP-Users] prepare_level2_feat_analysis.sh > > Dear HCP users > > I am trying to perform a 2nd level GLM analyis(using fsl) on fMRI working > memory data. In order to do that,i need to have a registration folder. > I noticed that there is a bash file for this propose. So i downloaded > ''prepare_level2_feat_analysis.sh'' file. > I tried to run this file using commands bellow : > > chmod +x prepare_level2_feat_analysis.sh > > ./prepare_level2_feat_analysis.sh > > > but i got the following results: > > > The input must be a fsf file > Usage: prepare_level2_feat_analysis.sh <Level2_fsf_file> > Prepares lower-level .feat directories for higher-level analyses > > Any ideas? > > regards > Mohammad > _______________________________________________ > 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 > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
