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> 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. _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
