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 <hcp-users-boun...@humanconnectome.org> on behalf of Mandelli, Maria Luisa <marialuisa.mande...@ucsf.edu> Sent: Monday, June 26, 2017 1:52:02 PM To: Dierker, Donna Cc: 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> Sent: Monday, June 26, 2017 11:54:40 AM To: Mandelli, Maria Luisa Cc: 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> 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 > 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 http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
