I m trying to do that! I ll let you know!
thank you again in the mean time Maria Luisa Mandelli, PhD Assistant Professional Researcher University of California, San Francisco 675 Nelson Rising Lane, Suite 190 | San Francisco, CA 94158 Language Neurobiology Lab http://albalab.ucsf.edu/ Memory and Aging Center http://memory.ucsf.edu/ UCSF Dyslexia Center http://dyslexia.ucsf.edu/ ________________________________ From: Glasser, Matthew <glass...@wustl.edu> Sent: Wednesday, June 28, 2017 4:30:28 PM To: Mandelli, Maria Luisa; Brown, Tim; hcp-users@humanconnectome.org Cc: Dierker, Donna Subject: Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found If you were to delete everything and run again do you get the same error? Peace, Matt. From: "Mandelli, Maria Luisa" <marialuisa.mande...@ucsf.edu<mailto:marialuisa.mande...@ucsf.edu>> Date: Wednesday, June 28, 2017 at 6:18 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, "Brown, Tim" <tbbr...@wustl.edu<mailto:tbbr...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Cc: "Dierker, Donna" <do...@wustl.edu<mailto:do...@wustl.edu>> Subject: Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found this is the version freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-HCP and yes I m running the HCP Pipelines Maria Luisa Mandelli, PhD Assistant Professional Researcher University of California, San Francisco 675 Nelson Rising Lane, Suite 190 | San Francisco, CA 94158 Language Neurobiology Lab http://albalab.ucsf.edu/ Memory and Aging Center http://memory.ucsf.edu/ UCSF Dyslexia Center http://dyslexia.ucsf.edu/ ________________________________ From: Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> Sent: Wednesday, June 28, 2017 4:10:27 PM To: Mandelli, Maria Luisa; Brown, Tim; hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Cc: Dierker, Donna Subject: Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found That’s weird as I change the subject directory in the pipelines but don’t normally have this error. FreeSurfer just makes a symlink. What version of FreeSurfer are you using? Are you calling it using the HCP Pipelines? Peace, Matt. From: "Mandelli, Maria Luisa" <marialuisa.mande...@ucsf.edu<mailto:marialuisa.mande...@ucsf.edu>> Date: Wednesday, June 28, 2017 at 6:06 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, "Brown, Tim" <tbbr...@wustl.edu<mailto:tbbr...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Cc: "Dierker, Donna" <do...@wustl.edu<mailto:do...@wustl.edu>> Subject: Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found Hi!thank you for your help! the error is in the log file Invalid argument ERROR reading /mnt/macdata/groups/language/malu-cloud/HCP_project/Pipelines_ExampleData/subjects/hcp350014/T1w/fsaverage/label/lh.BA1.label Linux mmandelli-vm 3.2.0-126-virtual #169-Ubuntu SMP Fri Mar 31 14:47:56 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux So actually it s true I dont have the fsaverage directory in my subject folder but it s in ${FREESURFER_HOME}/subjects/fsaverage Now the my $SUBJECT_DIR is set where are my data not $FREESURFER_HOME.... am I missing a link somewhere? Maria Luisa Mandelli, PhD Assistant Professional Researcher University of California, San Francisco 675 Nelson Rising Lane, Suite 190 | San Francisco, CA 94158 Language Neurobiology Lab http://albalab.ucsf.edu/ Memory and Aging Center http://memory.ucsf.edu/ UCSF Dyslexia Center http://dyslexia.ucsf.edu/ ________________________________ From: Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> Sent: Wednesday, June 28, 2017 4:00:56 PM To: Brown, Tim; hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>; Mandelli, Maria Luisa Cc: Dierker, Donna Subject: Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found Perhaps I missed it but I don’t actually see the error messages you are getting. Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Timothy B. Brown" <tbbr...@wustl.edu<mailto:tbbr...@wustl.edu>> Organization: Washington University in St. Louis Date: Wednesday, June 28, 2017 at 5:00 PM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>, "marialuisa.mande...@ucsf.edu<mailto:marialuisa.mande...@ucsf.edu>" <marialuisa.mande...@ucsf.edu<mailto:marialuisa.mande...@ucsf.edu>> Cc: "Dierker, Donna" <do...@wustl.edu<mailto:do...@wustl.edu>> Subject: Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found Hi Maria, My bet is that the error you are seeing is coming from the last call to recon-all in the FreeSurferPipeline.sh script. This would be in the statements that look like: #Final Recon-all Steps log_Msg "Final Recon-all Steps" recon-all -subjid $SubjectID -sd $SubjectDIR -surfvolume -parcstats -cortparc2 -parcstats2 -cortparc3 -parcstats3 -cortribbon -segstats -aparc2aseg -wmparc -balabels -label-exvivo-ec -openmp ${num_cores} ${seed_cmd_appendix} log_Msg "Completed" In particular, it would be the line that is shown in red above. (Note, depending on the version of the HCP Pipelines you are using, your version of the recon-all command may not have the -openmp ${num_cores} or the ${seed_cmd_appendix} in it.) The -balabels option is asking the recon-all command to "Create Brodmann area labels by mapping from fsaverage". You probably won't have an fsaverage directory in the subject directory which you are processing (in your case the /HCP_project/Pipelines_ExampleData/subjects/hcp350014/T1w directory). In that case, recon-all creates one for you as a symbolic link to the $FREESURFER_HOME/subjects/fsaverage directory. It is in a subdirectory of that created fsaverage directory that files like lh.BA1.label should be found. So, the first things that needs to be determined in your case are: * At the time of this failure, does the /HCP_project/Pipelines_ExampleData/subjects/hcp350014/T1w/fsaverage directory exist at all? * If it does exist, is it a symbolic link to somewhere in your FreeSurfer installation? (I believe it should be a link to the ${FREESURFER_HOME}/subjects/fsaverage directory.) * What is the value of your FREESURFER_HOME environment variable? Can you check into those things and let me know what you find? Best Regards, Tim On 06/28/2017 09:41 AM, Mandelli, Maria Luisa wrote: Hi!I installed the freesurfer-hcp and I got an error in the Freesurfer pipeline here...in the label directory I dont see the file that the script is looking for! (lh.BA1.label) $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ /usr/local/freesurfer/bin/recon-all PWD /HCP_project/Pipelines_ExampleData/subjects/hcp350014/T1w/hcp350014/label CMD mri_label2label --srcsubject fsaverage --srclabel /HCP_project/Pipelines_ExampleData/subjects/hcp350014/T1w/fsaverage/label/lh.BA1.label --trgsubject hcp350014 --trglabel ./lh.BA1.label --hemi lh --regmethod surface Maria Luisa Mandelli, PhD Assistant Professional Researcher University of California, San Francisco 675 Nelson Rising Lane, Suite 190 | San Francisco, CA 94158 Language Neurobiology Lab http://albalab.ucsf.edu/ Memory and Aging Center http://memory.ucsf.edu/ UCSF Dyslexia Center http://dyslexia.ucsf.edu/ ________________________________ From: hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org> <hcp-users-boun...@humanconnectome.org><mailto:hcp-users-boun...@humanconnectome.org> on behalf of Mandelli, Maria Luisa <marialuisa.mande...@ucsf.edu><mailto:marialuisa.mande...@ucsf.edu> Sent: Monday, June 26, 2017 1:52:02 PM To: Dierker, Donna Cc: hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found thank you very much!I have the standard Freesurfer version! I m going to try to the HCP one now! Maria Luisa Mandelli, PhD Assistant Professional Researcher University of California, San Francisco 675 Nelson Rising Lane, Suite 190 | San Francisco, CA 94158 Language Neurobiology Lab http://albalab.ucsf.edu/ Memory and Aging Center http://memory.ucsf.edu/ UCSF Dyslexia Center http://dyslexia.ucsf.edu/ ________________________________ From: Dierker, Donna <do...@wustl.edu><mailto:do...@wustl.edu> Sent: Monday, June 26, 2017 11:54:40 AM To: Mandelli, Maria Luisa Cc: hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found Many of the HCP experts are at OHBM, so replies might take longer. I know from my own experience with HCP output to look here for the Freesurfer subject directories: subject-id/T1w/subject-id/label/* subject-id/T1w/subject-id/mri/* subject-id/T1w/subject-id/surf/* … Also see page 21 here: http://humanconnectome.org/storage/app/media/documentation/s1200/HCP_S1200_Release_Appendix_III.pdf Hopefully there is no problem! :) But I must point out that there is a difference between the Freesurfer v5.3 distribution and Freesurfer 5.3-HCP. The latter uses both T1w & T2w images, which makes a big difference (e.g., for myelin maps). Not sure which you used, but it is an important difference. > On Jun 26, 2017, at 12:27 PM, Mandelli, Maria Luisa > <marialuisa.mande...@ucsf.edu><mailto:marialuisa.mande...@ucsf.edu> wrote: > > Hi! > I m running the structural HCP pipeline and I m using Freesurfer v5.3 > It seems that the job finished without errors but I dont see the files in the > T1w folder of the subject. > For example the wmparc_1mm files > I m not sure where is the problem! > Thank you > > > Maria Luisa Mandelli, PhD > Assistant Professional Researcher > > University of California, San Francisco > 675 Nelson Rising Lane, Suite 190 | San Francisco, CA 94158 > > Language Neurobiology Lab > http://albalab.ucsf.edu/ > Memory and Aging Center > http://memory.ucsf.edu/ > UCSF Dyslexia Center > http://dyslexia.ucsf.edu/ > > _______________________________________________ > 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 _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users -- Timothy B. Brown Business & Technology Application Analyst III Pipeline Developer (Human Connectome Project) tbbrown(at)wustl.edu ________________________________ The material in this message is private and may contain Protected Healthcare Information (PHI). 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 _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
