Thanks for your response, and sorry to bother with this issue. I went back to previous MSMAII version not to mix different versions but the problem persists. I have checked --verbose but the only line that includes it with mkdir (or cp) is in line 473 of SingleSubjectConcat.sh. I also checked MSMAllPipeline.sh.
Any other suggestion? Leah. > On Apr 14, 2019, at 10:16 AM, Glasser, Matthew <glass...@wustl.edu> wrote: > > You can delete the --verbose from all the cp lines. All these flags appear > not to be compatible with mac os x built in utilities. > > You certainly should actually download the entire pipelines 4.0.0 release and > follow the instructions there. Running code from multiple versions is likely > to create problems, though the issues with mac that you have encountered thus > far are likely still there. > > Matt. > > From: Marta Moreno <mmorenoort...@icloud.com > <mailto:mmorenoort...@icloud.com>> > Date: Sunday, April 14, 2019 at 2:17 AM > 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>>, > Timothy Coalson <tsc...@mst.edu <mailto:tsc...@mst.edu>> > Subject: Re: [HCP-Users] MSMAllPipeline error > > I downloaded the last version of MSMAll to see if is a version problem. The > script now gives me the following error: > Sun Apr 14 03:11:18 EDT 2019 - MSMAllPipeline.sh - HCPPIPEDIR: > /usr/local/bin/HCP/Connectome_Project_3_22/Pipelines > Sun Apr 14 03:11:18 EDT 2019 - MSMAllPipeline.sh - ABORTING: MSMCONFIGDIR > environment variable must be set > > How should i configure the environment variable: MSMCONFIGDIR? > > Thanks! > > Leah. > >> On Apr 14, 2019, at 2:54 AM, Marta Moreno <mmorenoort...@icloud.com >> <mailto:mmorenoort...@icloud.com>> wrote: >> >> 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.o31773, says: >> (…) >> un Apr 14 02:52:14 EDT 2019 - MSMAll.sh - RSNTargetFile: >> /usr/local/bin/gaurav_folder_new/HCP/Connectome_Project_3_22/Pipelines/global/templates/MSMAll/rfMRI_REST_Atlas_MSMAll_2_d41_WRN_DeDrift_hp2000_clean_PCA.ica_d40_ROW_vn/melodic_oIC.dscalar.nii >> Sun Apr 14 02:52:14 EDT 2019 - MSMAll.sh - File: >> /usr/local/bin/gaurav_folder_new/HCP/Connectome_Project_3_22/Pipelines/global/templates/MSMAll/rfMRI_REST_Atlas_MSMAll_2_d41_WRN_DeDrift_hp2000_clean_PCA.ica_d40_ROW_vn/melodic_oIC.dscalar.nii >> EXISTS >> Sun Apr 14 02:52:14 EDT 2019 - MSMAll.sh - RSNCostWeights: >> /usr/local/bin/gaurav_folder_new/HCP/Connectome_Project_3_22/Pipelines/global/templates/MSMAll/rfMRI_REST_Atlas_MSMAll_2_d41_WRN_DeDrift_hp2000_clean_PCA.ica_d40_ROW_vn/Weights.txt >> Sun Apr 14 02:52:14 EDT 2019 - MSMAll.sh - File: >> /usr/local/bin/gaurav_folder_new/HCP/Connectome_Project_3_22/Pipelines/global/templates/MSMAll/rfMRI_REST_Atlas_MSMAll_2_d41_WRN_DeDrift_hp2000_clean_PCA.ica_d40_ROW_vn/Weights.txt >> EXISTS >> >> Leah. >> >> >>> On Apr 13, 2019, at 4:45 PM, Glasser, Matthew <glass...@wustl.edu >>> <mailto:glass...@wustl.edu>> wrote: >>> >>> https://github.com/Washington-University/HCPpipelines/blob/master/MSMAll/scripts/SingleSubjectConcat.sh >>> >>> <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 <mmorenoort...@icloud.com >>> <mailto:mmorenoort...@icloud.com>> >>> Date: Saturday, April 13, 2019 at 3:32 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 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 - Using named >>> parameters >>> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - Study Folder: >>> /Volumes/data/data3/NTTMS/NTTMS_s002 >>> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - Subject ID: >>> NTTMS_s002_170812 >>> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - fMRI name list: >>> RS_fMRI_MR >>> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - ICA+FIX highpass >>> setting: 0 >>> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - Output fMRI Name: >>> RS_fMRI_MR >>> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - fMRI Proc String: >>> _Atlas_hp0_clean >>> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - Output Proc String: >>> _vn >>> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - Demean: YES >>> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - Variance >>> Normalization: NO >>> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - Compute Variance >>> Normalization: YES >>> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - Revert Bias Field: >>> NO >>> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - MATLAB run mode: 1 >>> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - StudyFolder: >>> /Volumes/data/data3/NTTMS/NTTMS_s002 >>> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - Subject: >>> NTTMS_s002_170812 >>> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - fMRINames: >>> RS_fMRI_MR >>> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - HighPass: 0 >>> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - OutputfMRIName: >>> RS_fMRI_MR >>> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - fMRIProcSTRING: >>> _Atlas_hp0_clean >>> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - OutputProcSTRING: >>> _vn >>> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - Demean: YES >>> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - >>> VarianceNormalization: NO >>> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - >>> ComputeVarianceNormalization: YES >>> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - RevertBiasField: NO >>> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - MatlabRunMode: 1 >>> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - fMRINames: >>> RS_fMRI_MR >>> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - OutputProcSTRING: >>> _vn >>> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - AtlasFolder: >>> /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear >>> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - OutputFolder: >>> /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_MR >>> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - Caret7_Command: >>> /Applications/workbench/bin_macosx64//wb_command >>> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - fMRIName: RS_fMRI_MR >>> Sat Apr 13 16:29:45 EDT 2019 - SingleSubjectConcat.sh - ResultsFolder: >>> /Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_MR >>> Sat Apr 13 16:29:46 EDT 2019 - SingleSubjectConcat.sh - MATH: ((TCS - Mean)) >>> parsed '((TCS - Mean))' as '(TCS-Mean)' >>> >>> Leah. >>> >>>> On Apr 13, 2019, at 4:10 PM, Glasser, Matthew <glass...@wustl.edu >>>> <mailto:glass...@wustl.edu>> wrote: >>>> >>>> You could try setting line 353 to NO: >>>> >>>> https://github.com/Washington-University/HCPpipelines/blob/master/MSMAll/MSMAllPipeline.sh >>>> >>>> <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 >>>>>>>>> <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. 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
