Re: [HCP-Users] MSMAllPipeline error

2019-04-13 Thread Marta Moreno
Thanks for your response! Sorry to bother you but still I am getting an error. Now it says: cp: illegal option -- - usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvX] source_file target_file cp [-R [-H | -L | -P]] [-fi | -n] [-apvX] source_file … target_directory In cat MSMAllPipeline.sh.o31

Re: [HCP-Users] MSMAllPipeline error

2019-04-13 Thread Glasser, Matthew
https://github.com/Washington-University/HCPpipelines/blob/master/MSMAll/scripts/SingleSubjectConcat.sh Line 473 apparently has to be -p on a mac Matt. From: Marta Moreno mailto:mmorenoort...@icloud.com>> Date: Saturday, April 13, 2019 at 3:32 PM To: Matt Glasser mailto:glass...@wustl.edu>> Cc:

Re: [HCP-Users] MSMAllPipeline error

2019-04-13 Thread Marta Moreno
Thanks for your response. I changed line 353 to NO. Now I am getting a different error: mkdir: illegal option -- - usage: mkdir [-pv] [-m mode] directory … In cat MSMAllPipeline.sh.o9037, it stops in: (…) Operating System: Apple OSX Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - Usin

Re: [HCP-Users] MSMAllPipeline error

2019-04-13 Thread Glasser, Matthew
You could try setting line 353 to NO: https://github.com/Washington-University/HCPpipelines/blob/master/MSMAll/MSMAllPipeline.sh For more recent versions of FIX and MR+FIX, variance normalization is always already computed. That said, it isn’t clear to me why it is failing to compute it again.

Re: [HCP-Users] MSMAllPipeline error

2019-04-13 Thread Marta Moreno
Thanks for your response. I am using now the concatenated name, called “RS_fMRI_MR” when I run MR ICA+FIX: fMRINames="RS_fMRI_MR" OutfMRIName=“RS_fMRI_MR" (…) but still getting same error: While running: /Applications/workbench/bin_macosx64/../macosx64_apps/wb_command.app/Contents/MacOS/wb_comman

Re: [HCP-Users] MSMAllPipeline error

2019-04-13 Thread Glasser, Matthew
If you ran MR+FIX, your data are already concatenated for MSMAll, so just provide the concatenated fMRIName from the MR+FIX run. It should work then. Matt. From: Marta Moreno mailto:mmorenoort...@icloud.com>> Date: Saturday, April 13, 2019 at 2:37 PM To: Matt Glasser mailto:glass...@wustl.edu>>

Re: [HCP-Users] MSMAllPipeline error

2019-04-13 Thread Marta Moreno
Thanks for your response! I changed the set up as follow: fMRINames="RS_fMRI_1@RS_fMRI_2" OutfMRIName="RS_fMRI_1@RS_fMRI_2" HighPass="0" fMRIProcSTRING="_Atlas_hp0_clean" MSMAllTemplates="${HCPPIPEDIR}/global/templates/MSMAll" RegName="MSMAll_InitalReg" HighResMesh="164" LowResMesh="32" InRegName=

Re: [HCP-Users] MSMAllPipeline error

2019-04-13 Thread Glasser, Matthew
You can just put your MR+FIX concatenated name in for the fMRIName and OutfMRIName. Matt. From: Marta Moreno mailto:mmorenoort...@icloud.com>> Date: Saturday, April 13, 2019 at 2:15 PM To: Matt Glasser mailto:glass...@wustl.edu>> Cc: "Harms, Michael" mailto:mha...@wustl.edu>>, HCP Users mailto:

Re: [HCP-Users] MSMAllPipeline error

2019-04-13 Thread Marta Moreno
Thanks for your response! I am running the following script MSMAllPipelineBatch.sh from ${StudyFolder}/${Subject}/scripts after running MR ICA+FIX with success I set up the script as follow: fMRINames="RS_fMRI_MR" OutfMRIName="RS_fMRI_MR_REST" HighPass=“0" fMRIProcSTRING="_Atlas_hp0_clean" MSMAl

Re: [HCP-Users] MSMAllPipeline error

2019-04-13 Thread Glasser, Matthew
I guess specify how you called the MSMAll pipeline and perhaps that will provide a clue to the error if there are no other errors. Matt. From: Marta Moreno mailto:mmorenoort...@icloud.com>> Date: Saturday, April 13, 2019 at 1:58 PM To: "Harms, Michael" mailto:mha...@wustl.edu>> Cc: Matt Glasser

Re: [HCP-Users] MSMAllPipeline error

2019-04-13 Thread Marta Moreno
Dear Experts, I re-run MR ICA+FIX with hp=0 without errors but I am getting same error as before when running MSMAll; i.e. the file “*vn_tempcompute.dscalar.nii" does not exist. Please advice. ERROR: failed to open file '/Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Resul

Re: [HCP-Users] MSMAllPipeline error

2019-04-13 Thread Marta Moreno
Thanks for your response. I am re-running MR ICA+FIX with hp=0. Will confirm if problem running MSMAll with hp=0 is solved. Leah. > On Apr 13, 2019, at 12:33 PM, Harms, Michael wrote: > > > We extended that feature such that it should be an accepted option for all > the "ICAFIX"-related s

Re: [HCP-Users] MSMAllPipeline error

2019-04-13 Thread Harms, Michael
We extended that feature such that it should be an accepted option for all the "ICAFIX"-related scripts, but we haven't had a chance yet to extend it to the context of MSMAll and TaskAnalysis. Hopefully in the near future... -- Michael Harms, Ph.D.

Re: [HCP-Users] MSMAllPipeline error

2019-04-13 Thread Glasser, Matthew
I wouldn¹t use hp=pd2 unless you know what you are doing, as that option has not been fully tested. I run with hp=0. Matt. On 4/13/19, 10:41 AM, "hcp-users-boun...@humanconnectome.org on behalf of Marta Moreno" wrote: >Dear Experts, > >I am running the following script MSMAllPipelineBatch.sh f

[HCP-Users] MSMAllPipeline error

2019-04-13 Thread Marta Moreno
Dear Experts, I am running the following script MSMAllPipelineBatch.sh from ${StudyFolder}/${Subject}/scripts after running MR ICA+FIX with success, and I am getting the following error: ERROR: failed to open file '/Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_