Now it seams to be working! Thanks a lot! Leah.
> On Apr 14, 2019, at 10:58 AM, Glasser, Matthew <glass...@wustl.edu> wrote: > > Well we don’t support old versions of the HCP Pipelines so you should in fact > upgrade to the current version: from here: > > https://github.com/Washington-University/HCPpipelines/releases > <https://github.com/Washington-University/HCPpipelines/releases> > > This file is where you had the error: > > https://github.com/Washington-University/HCPpipelines/blob/master/MSMAll/scripts/MSMAll.sh > > <https://github.com/Washington-University/HCPpipelines/blob/master/MSMAll/scripts/MSMAll.sh> > > Matt. > > From: Marta Moreno <mmorenoort...@icloud.com > <mailto:mmorenoort...@icloud.com>> > Date: Sunday, April 14, 2019 at 9:49 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>>, "Brown, Tim" > <tbbr...@wustl.edu <mailto:tbbr...@wustl.edu>> > Subject: Re: [HCP-Users] MSMAllPipeline error > > 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 >> <mailto: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. 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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
