Hi Alex, mris_preproc produces a stack images (27 in the first case and 16 in the 2nd case). For some reason the first two images are the same in both stacks. This is the way that you have run the program because both calls to mris_preproc use
NNC0035_pet_lh.mgh and NNC0045_pet_lh.mgh as the first two inputs doug On 03/27/2015 02:32 PM, Alexandra Tanner wrote: > Hi Doug and Freesurfers, > > Our group has PET data for 27 subjects that we are hoping to combine to > generate surface group average maps. We would also like to generate > average maps for 3 subsets of subjects based on genotype. I ran > mris_preproc to combine my individual subject PET surface maps to generate > a concatenated map for my N=27 subjects and 3 separate subgroups based on > genotype (N=16, N=9, N=2), with the commands below. We viewed the > concatenated maps generated by mris_preproc in tksurfer and the N=27 and > N=16 maps are identical, which we find puzzling (please see images > attached). > > We are curious 1) what the output map of the mris_preproc command actually > is (ex. a sum, an average, etc), and 2) if anyone knows why our outputs > would be identical for our 27 subjects and our 16 subjects. > > Any help or explanation would be greatly appreciated! > > Best, > Alex > > > mris_preproc commands run: > > setenv SUBJECTS_DIR /cluster/roffman/users/Stable5_PerRun > cd > /autofs/cluster/roffman/users/Stable5_PerRun/NNC_PMOD_LoganRef_BPnd/PET_analyses > /usr/local/freesurfer/stable5_0_0/bin/mris_preproc --target fsaverage > --hemi lh --is NNC0035_pet_lh.mgh --is NNC0045_pet_lh.mgh --is > NNC0047_pet_lh.mgh --is NNC0065_pet_lh.mgh --is NNC0078_pet_lh.mgh --is > NNC0089_pet_lh.mgh --is NNC0095_pet_lh.mgh --is NNC0101_pet_lh.mgh --is > NNC0102_pet_lh.mgh --is NNC0114_pet_lh.mgh --is NNC0118_pet_lh.mgh --is > NNC0119_pet_lh.mgh --is NNC0901_pet_lh.mgh --is NNC0902_pet_lh.mgh --is > NNC0906_pet_lh.mgh --is NNC0908_pet_lh.mgh --is NNC0915_pet_lh.mgh --is > NNC0916_pet_lh.mgh --is NNC0917_pet_lh.mgh --is NNC0918_pet_lh.mgh --is > NNC0919_pet_lh.mgh --is NNC0924_pet_lh.mgh --is NNC0926_pet_lh.mgh --is > NNC0928_pet_lh.mgh --is NNC0930_pet_lh.mgh --is NNC0931_pet_lh.mgh --is > NNC0932_pet_lh.mgh --f > /cluster/roffman/users/Stable5_PerRun/Subject_Files/27_NNC_Subjects --out > /cluster/roffman/users/Stable5_PerRun/NNC_PMOD_LoganRef_BPnd/PET_analyses/27_NNC_removed_bad_PET_fMRI/lh.pet.mgh > > setenv SUBJECTS_DIR /cluster/roffman/users/Stable5_PerRun/ > cd > /autofs/cluster/roffman/users/Stable5_PerRun/NNC_PMOD_LoganRef_BPnd/PET_analyses > /usr/local/freesurfer/stable5_0_0/bin/mris_preproc --target fsaverage > --hemi lh --is NNC0035_pet_lh.mgh --is NNC0045_pet_lh.mgh --is > NNC0065_pet_lh.mgh --is NNC0089_pet_lh.mgh --is NNC0118_pet_lh.mgh --is > NNC0901_pet_lh.mgh --is NNC0902_pet_lh.mgh --is NNC0908_pet_lh.mgh --is > NNC0915_pet_lh.mgh --is NNC0916_pet_lh.mgh --is NNC0917_pet_lh.mgh --is > NNC0924_pet_lh.mgh --is NNC0928_pet_lh.mgh --is NNC0930_pet_lh.mgh --is > NNC0931_pet_lh.mgh --is NNC0932_pet_lh.mgh --f > /cluster/roffman/users/Stable5_PerRun/Subject_Files/16_NNC_AGCarrier_COMT_27NNC > --out > /cluster/roffman/users/Stable5_PerRun/NNC_PMOD_LoganRef_BPnd/PET_analyses/16_AG_Carrier_COMT_27NNC/lh.pet.mgh -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
