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. Perhaps you are not reporting the first error that occurs. Matt. From: Marta Moreno <mmorenoort...@icloud.com<mailto:mmorenoort...@icloud.com>> Date: Saturday, April 13, 2019 at 2:55 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Cc: "Harms, Michael" <mha...@wustl.edu<mailto:mha...@wustl.edu>>, HCP Users <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] MSMAllPipeline error 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_command -cifti-math '((TCS - Mean)) / max(VN,0.001)' /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_MR/RS_fMRI_MR_Atlas_hp0_clean_vn.dtseries.nii -var TCS /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_MR/RS_fMRI_MR_Atlas_hp0_clean.dtseries.nii -var Mean /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_MR/RS_fMRI_MR_Atlas_hp0_clean_mean.dscalar.nii -select 1 1 -repeat -var VN /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_MR/RS_fMRI_MR_Atlas_hp0_clean_vn_tempcompute.dscalar.nii -select 1 1 -repeat ERROR: failed to open file '/Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_MR/RS_fMRI_MR_Atlas_hp0_clean_vn_tempcompute.dscalar.nii', file does not exist, or folder permissions prevent seeing it Leah. ******************************************* Leah Moreno, PhD Research Scientist Division of Experimental Therapeutics Department of Psychiatry Columbia University Medical Center 1051 Riverside Drive, Unit 21 New York, NY 10032 phone: (914) 218-7311 email: mm4...@cumc.columbia.edu<mailto:mm4...@cumc.columbia.edu> On Apr 13, 2019, at 3:39 PM, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: 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 <mmorenoort...@icloud.com<mailto:mmorenoort...@icloud.com>> Date: Saturday, April 13, 2019 at 2:37 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Cc: "Harms, Michael" <mha...@wustl.edu<mailto:mha...@wustl.edu>>, HCP Users <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] MSMAllPipeline error 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="MSMSulc" MatlabMode="1" #Mode=0 compiled Matlab, Mode=1 interpreted Matlab but still getting same error: While running: /Applications/workbench/bin_macosx64/../macosx64_apps/wb_command.app/Contents/MacOS/wb_command -cifti-math '((TCS - Mean)) / max(VN,0.001)' /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_1/RS_fMRI_1_Atlas_hp0_clean_vn.dtseries.nii -var TCS /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_1/RS_fMRI_1_Atlas_hp0_clean.dtseries.nii -var Mean /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_1/RS_fMRI_1_Atlas_hp0_clean_mean.dscalar.nii -select 1 1 -repeat -var VN /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_1/RS_fMRI_1_Atlas_hp0_clean_vn_tempcompute.dscalar.nii -select 1 1 -repeat ERROR: failed to open file '/Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_1/RS_fMRI_1_Atlas_hp0_clean_vn_tempcompute.dscalar.nii', file does not exist, or folder permissions prevent seeing it Leah. On Apr 13, 2019, at 3:22 PM, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: You can just put your MR+FIX concatenated name in for the fMRIName and OutfMRIName. Matt. From: Marta Moreno <mmorenoort...@icloud.com<mailto:mmorenoort...@icloud.com>> Date: Saturday, April 13, 2019 at 2:15 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Cc: "Harms, Michael" <mha...@wustl.edu<mailto:mha...@wustl.edu>>, HCP Users <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] MSMAllPipeline error 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" MSMAllTemplates="${HCPPIPEDIR}/global/templates/MSMAll" RegName="MSMAll_InitalReg" HighResMesh="164" LowResMesh="32" InRegName="MSMSulc" MatlabMode="1" #Mode=0 compiled Matlab, Mode=1 interpreted Matlab In "cat MSMAllPipeline.sh.o3905", it does not complete the following step: Sat Apr 13 15:09:36 EDT 2019 - SingleSubjectConcat.sh - OutputVN: /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_MR/RS_fMRI_MR_Atlas_hp0_clean_vn_tempcompute.dscalar.nii (…) And stops in: >> Sat Apr 13 15:09:44 EDT 2019 - SingleSubjectConcat.sh - >> ComputeVN('/Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_MR/RS_fMRI_MR_Atlas_hp0_clean.dtseries.nii','NONE','/Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_MR/RS_fMRI_MR_hp0.ica/filtered_func_data.ica/melodic_mix','/Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_MR/RS_fMRI_MR_hp0.ica/.fix','/Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_MR/RS_fMRI_MR_Atlas_hp0_clean_vn_tempcompute.dscalar.nii','/Applications/workbench/bin_macosx64//wb_command'); Sat Apr 13 15:09:44 EDT 2019 - SingleSubjectConcat.sh - MATH: ((TCS - Mean)) / max(VN,0.001) Leah. On Apr 13, 2019, at 3:02 PM, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: 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 <mmorenoort...@icloud.com<mailto:mmorenoort...@icloud.com>> Date: Saturday, April 13, 2019 at 1:58 PM To: "Harms, Michael" <mha...@wustl.edu<mailto:mha...@wustl.edu>> Cc: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, HCP Users <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] MSMAllPipeline error 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/Results/RS_fMRI_MR/RS_fMRI_MR_Atlas_hp0_clean_vn_tempcompute.dscalar.nii', file does not exist, or folder permissions prevent seeing it The file that exists is: RS_fMRI_MR_Atlas_hp0_clean_vn.dscalar.nii Thanks!, Leah. On Apr 13, 2019, at 12:33 PM, Harms, Michael <mha...@wustl.edu<mailto:mha...@wustl.edu>> wrote: 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. ----------------------------------------------------------- Associate Professor of Psychiatry Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu<mailto:mha...@wustl.edu> On 4/13/19, 11:28 AM, "hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org> on behalf of Glasser, Matthew" <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org> on behalf of glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: 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<mailto:hcp-users-boun...@humanconnectome.org> on behalf of Marta Moreno" <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org> on behalf of mmorenoort...@icloud.com<mailto:mmorenoort...@icloud.com>> wrote: 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/Resul ts/RS_fMRI_MR/RS_fMRI_MR_Atlas_hppd2_clean_vn_tempcompute.dscalar.nii', file does not exist, or folder permissions prevent seeing it I set up the script as follow: fMRINames="RS_fMRI_MR" OutfMRIName="RS_fMRI_MR_REST" HighPass="pd2" fMRIProcSTRING="_Atlas_hppd2_clean" MSMAllTemplates="${HCPPIPEDIR}/global/templates/MSMAll" RegName="MSMAll_InitalReg" HighResMesh="164" LowResMesh="32" InRegName="MSMSulc" MatlabMode="1" #Mode=0 compiled Matlab, Mode=1 interpreted Matlab I checked and the file called: *tempcompute.dscalar.nii¹, is not there. What am I doing wrong? Something went wrong in the previous step while running MR ICA+FIX that I am not aware of? Thanks a lot! Leah. _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto: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<mailto: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. ________________________________ 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. ________________________________ 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. ________________________________ 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. ________________________________ 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
