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 > On Apr 13, 2019, at 3:39 PM, Glasser, Matthew <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 >>>>> <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 >>>> <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. 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