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Hi Gwenaëlle. Sorry to send this again as I don't know whether you could see the attached files (I am unable to).Please see below with the information you have requested.Also snap shot of the template images it looks like the brain extraction is not good how I can correct for this. my_fsl_vbm]> ls design2/ stats/ struc/ template_list.txt~ design_REG_AGE_OUT/ stats_reg_age/ template_list.txt more template_list.txt control_007.nii.gz control_014.nii.gz control_015.nii.gz control_017.nii.gz control_020.nii.gz control_021.nii.gz control_022.nii.gz control_026.nii.gz control_027.nii.gz control_028.nii.gz control_031.nii.gz control_032.nii.gz control_033.nii.gz control_037.nii.gz control_039.nii.gz control_041.nii.gz control_042.nii.gz patient_1030.nii.gz patient_1032.nii.gz patient_1033.nii.gz patient_1035.nii.gz patient_2011.nii.gz patient_2023.nii.gz patient_2035.nii.gz patient_2045.nii.gz patient_3002.nii.gz patient_3005.nii.gz patient_3006.nii.gz patient_3037.nii.gz patient_4019.nii.gz patient_4023.nii.gz patient_4030.nii.gz patient_4032.nii.gz patient_4033.nii.gz ls *_struc_GM_to_T*. control_007_struc_GM_to_T_init.mat control_007_struc_GM_to_T_init.nii.gz control_007_struc_GM_to_T_init_warp.msf control_007_struc_GM_to_T_init_warp.nii.gz control_007_struc_GM_to_T.mat control_007_struc_GM_to_T.nii.gz control_014_struc_GM_to_T_init.mat control_014_struc_GM_to_T_init.nii.gz control_014_struc_GM_to_T_init_warp.msf control_014_struc_GM_to_T_init_warp.nii.gz control_014_struc_GM_to_T.mat control_014_struc_GM_to_T.nii.gz control_015_struc_GM_to_T_init.mat control_015_struc_GM_to_T_init.nii.gz control_015_struc_GM_to_T_init_warp.msf control_015_struc_GM_to_T_init_warp.nii.gz control_015_struc_GM_to_T.mat control_015_struc_GM_to_T.nii.gz control_017_struc_GM_to_T_init.mat control_017_struc_GM_to_T_init.nii.gz control_017_struc_GM_to_T_init_warp.msf control_017_struc_GM_to_T_init_warp.nii.gz control_017_struc_GM_to_T.mat control_017_struc_GM_to_T.nii.gz control_020_struc_GM_to_T_init.mat control_020_struc_GM_to_T_init.nii.gz control_020_struc_GM_to_T_init_warp.msf control_020_struc_GM_to_T_init_warp.nii.gz control_020_struc_GM_to_T.mat control_020_struc_GM_to_T.nii.gz control_021_struc_GM_to_T_init.mat control_021_struc_GM_to_T_init.nii.gz control_021_struc_GM_to_T_init_warp.msf control_021_struc_GM_to_T_init_warp.nii.gz control_021_struc_GM_to_T.mat control_021_struc_GM_to_T.nii.gz control_022_struc_GM_to_T_init.mat control_022_struc_GM_to_T_init.nii.gz control_022_struc_GM_to_T_init_warp.msf control_022_struc_GM_to_T_init_warp.nii.gz control_022_struc_GM_to_T.mat control_022_struc_GM_to_T.nii.gz control_026_struc_GM_to_T_init.mat control_026_struc_GM_to_T_init.nii.gz control_026_struc_GM_to_T_init_warp.msf control_026_struc_GM_to_T_init_warp.nii.gz control_026_struc_GM_to_T.mat control_026_struc_GM_to_T.nii.gz control_027_struc_GM_to_T_init.mat control_027_struc_GM_to_T_init.nii.gz control_027_struc_GM_to_T_init_warp.msf control_027_struc_GM_to_T_init_warp.nii.gz control_027_struc_GM_to_T.mat control_027_struc_GM_to_T.nii.gz control_028_struc_GM_to_T_init.mat control_028_struc_GM_to_T_init.nii.gz control_028_struc_GM_to_T_init_warp.msf control_028_struc_GM_to_T_init_warp.nii.gz control_028_struc_GM_to_T.mat control_028_struc_GM_to_T.nii.gz control_031_struc_GM_to_T_init.mat control_031_struc_GM_to_T_init.nii.gz control_031_struc_GM_to_T_init_warp.msf control_031_struc_GM_to_T_init_warp.nii.gz control_031_struc_GM_to_T.mat control_031_struc_GM_to_T.nii.gz control_032_struc_GM_to_T_init.mat control_032_struc_GM_to_T_init.nii.gz control_032_struc_GM_to_T_init_warp.msf control_032_struc_GM_to_T_init_warp.nii.gz control_032_struc_GM_to_T.mat control_032_struc_GM_to_T.nii.gz control_033_struc_GM_to_T_init.mat control_033_struc_GM_to_T_init.nii.gz control_033_struc_GM_to_T_init_warp.msf control_033_struc_GM_to_T_init_warp.nii.gz control_033_struc_GM_to_T.mat control_033_struc_GM_to_T.nii.gz control_037_struc_GM_to_T_init.mat control_037_struc_GM_to_T_init.nii.gz control_037_struc_GM_to_T_init_warp.msf control_037_struc_GM_to_T_init_warp.nii.gz control_037_struc_GM_to_T.mat control_037_struc_GM_to_T.nii.gz control_039_struc_GM_to_T_init.mat control_039_struc_GM_to_T_init.nii.gz control_039_struc_GM_to_T_init_warp.msf control_039_struc_GM_to_T_init_warp.nii.gz control_039_struc_GM_to_T.mat control_039_struc_GM_to_T.nii.gz control_041_struc_GM_to_T_init.mat control_041_struc_GM_to_T_init.nii.gz control_041_struc_GM_to_T_init_warp.msf control_041_struc_GM_to_T_init_warp.nii.gz control_041_struc_GM_to_T.mat control_041_struc_GM_to_T.nii.gz control_042_struc_GM_to_T_init.mat control_042_struc_GM_to_T_init.nii.gz control_042_struc_GM_to_T_init_warp.msf control_042_struc_GM_to_T_init_warp.nii.gz control_042_struc_GM_to_T.mat control_042_struc_GM_to_T.nii.gz patient_1030_struc_GM_to_T_init.mat patient_1030_struc_GM_to_T_init.nii.gz patient_1030_struc_GM_to_T_init_warp.msf patient_1030_struc_GM_to_T_init_warp.nii.gz patient_1030_struc_GM_to_T.mat patient_1030_struc_GM_to_T.nii.gz patient_1032_struc_GM_to_T_init.mat patient_1032_struc_GM_to_T_init.nii.gz patient_1032_struc_GM_to_T_init_warp.msf patient_1032_struc_GM_to_T_init_warp.nii.gz patient_1032_struc_GM_to_T.mat patient_1032_struc_GM_to_T.nii.gz patient_1033_struc_GM_to_T_init.mat patient_1033_struc_GM_to_T_init.nii.gz patient_1033_struc_GM_to_T_init_warp.msf patient_1033_struc_GM_to_T_init_warp.nii.gz patient_1033_struc_GM_to_T.mat patient_1033_struc_GM_to_T.nii.gz patient_1034_struc_GM_to_T_init.mat patient_1034_struc_GM_to_T_init.nii.gz patient_1034_struc_GM_to_T_init_warp.msf patient_1034_struc_GM_to_T_init_warp.nii.gz patient_1034_struc_GM_to_T.mat patient_1034_struc_GM_to_T.nii.gz patient_1035_struc_GM_to_T_init.mat patient_1035_struc_GM_to_T_init.nii.gz patient_1035_struc_GM_to_T_init_warp.msf patient_1035_struc_GM_to_T_init_warp.nii.gz patient_1035_struc_GM_to_T.mat patient_1035_struc_GM_to_T.nii.gz patient_2001_struc_GM_to_T_init.mat patient_2001_struc_GM_to_T_init.nii.gz patient_2001_struc_GM_to_T_init_warp.msf patient_2001_struc_GM_to_T_init_warp.nii.gz patient_2001_struc_GM_to_T.mat patient_2001_struc_GM_to_T.nii.gz patient_2011_struc_GM_to_T_init.mat patient_2011_struc_GM_to_T_init.nii.gz patient_2011_struc_GM_to_T_init_warp.msf patient_2011_struc_GM_to_T_init_warp.nii.gz patient_2011_struc_GM_to_T.mat patient_2011_struc_GM_to_T.nii.gz patient_2023_struc_GM_to_T_init.mat patient_2023_struc_GM_to_T_init.nii.gz patient_2023_struc_GM_to_T_init_warp.msf patient_2023_struc_GM_to_T_init_warp.nii.gz patient_2023_struc_GM_to_T.mat patient_2023_struc_GM_to_T.nii.gz patient_2035_struc_GM_to_T_init.mat patient_2035_struc_GM_to_T_init.nii.gz patient_2035_struc_GM_to_T_init_warp.msf patient_2035_struc_GM_to_T_init_warp.nii.gz patient_2035_struc_GM_to_T.mat patient_2035_struc_GM_to_T.nii.gz patient_2045_struc_GM_to_T_init.mat patient_2045_struc_GM_to_T_init.nii.gz patient_2045_struc_GM_to_T_init_warp.msf patient_2045_struc_GM_to_T_init_warp.nii.gz patient_2045_struc_GM_to_T.mat patient_2045_struc_GM_to_T.nii.gz patient_3002_struc_GM_to_T_init.mat patient_3002_struc_GM_to_T_init.nii.gz patient_3002_struc_GM_to_T_init_warp.msf patient_3002_struc_GM_to_T_init_warp.nii.gz patient_3002_struc_GM_to_T.mat patient_3002_struc_GM_to_T.nii.gz patient_3005_struc_GM_to_T_init.mat patient_3005_struc_GM_to_T_init.nii.gz patient_3005_struc_GM_to_T_init_warp.msf patient_3005_struc_GM_to_T_init_warp.nii.gz patient_3005_struc_GM_to_T.mat patient_3005_struc_GM_to_T.nii.gz patient_3006_struc_GM_to_T_init.mat patient_3006_struc_GM_to_T_init.nii.gz patient_3006_struc_GM_to_T_init_warp.msf patient_3006_struc_GM_to_T_init_warp.nii.gz patient_3006_struc_GM_to_T.mat patient_3006_struc_GM_to_T.nii.gz patient_3037_struc_GM_to_T_init.mat patient_3037_struc_GM_to_T_init.nii.gz patient_3037_struc_GM_to_T_init_warp.msf patient_3037_struc_GM_to_T_init_warp.nii.gz patient_3037_struc_GM_to_T.mat patient_3037_struc_GM_to_T.nii.gz patient_4019_struc_GM_to_T_init.mat patient_4019_struc_GM_to_T_init.nii.gz patient_4019_struc_GM_to_T_init_warp.msf patient_4019_struc_GM_to_T_init_warp.nii.gz patient_4019_struc_GM_to_T.mat patient_4019_struc_GM_to_T.nii.gz patient_4023_struc_GM_to_T_init.mat patient_4023_struc_GM_to_T_init.nii.gz patient_4023_struc_GM_to_T_init_warp.msf patient_4023_struc_GM_to_T_init_warp.nii.gz patient_4023_struc_GM_to_T.mat patient_4023_struc_GM_to_T.nii.gz patient_4030_struc_GM_to_T_init.mat patient_4030_struc_GM_to_T_init.nii.gz patient_4030_struc_GM_to_T_init_warp.msf patient_4030_struc_GM_to_T_init_warp.nii.gz patient_4030_struc_GM_to_T.mat patient_4030_struc_GM_to_T.nii.gz patient_4031_struc_GM_to_T_init.mat patient_4031_struc_GM_to_T_init.nii.gz patient_4031_struc_GM_to_T_init_warp.msf patient_4031_struc_GM_to_T_init_warp.nii.gz patient_4031_struc_GM_to_T.mat patient_4031_struc_GM_to_T.nii.gz patient_4032_struc_GM_to_T_init.mat patient_4032_struc_GM_to_T_init.nii.gz patient_4032_struc_GM_to_T_init_warp.msf patient_4032_struc_GM_to_T_init_warp.nii.gz patient_4032_struc_GM_to_T.mat patient_4032_struc_GM_to_T.nii.gz patient_4033_struc_GM_to_T_init.mat patient_4033_struc_GM_to_T_init.nii.gz patient_4033_struc_GM_to_T_init_warp.msf patient_4033_struc_GM_to_T_init_warp.nii.gz patient_4033_struc_GM_to_T.mat patient_4033_struc_GM_to_T.nii.gz Thanks Venkat -----Original Message----- From: FSL - FMRIB's Software Library on behalf of Gwenaëlle DOUAUD Sent: Sun 10/7/2012 1:08 PM To: [log in to unmask] Subject: Re: [FSL] FSL VBM template problem Hi Venkat, could you please give me the result of an 'ls' in your main fslvbm directory, a 'more' on your template_list, and of an 'ls *_struc_GM_to_T*.*' in your struc directory? Cheers, Gwenaëlle -------------------------------------------------------------------- Gwenaëlle Douaud, PhD FMRIB Centre, University of Oxford John Radcliffe Hospital, Headington OX3 9DU Oxford UK Tel: +44 (0) 1865 222 523 Fax: +44 (0) 1865 222 717 www.fmrib.ox.ac.uk/~douaud -------------------------------------------------------------------- ________________________________ De : "Rajagopalan, Venkateswaran" <[log in to unmask]> À : [log in to unmask] Envoyé le : Vendredi 5 octobre 2012 21h40 Objet : [FSL] FSL VBM template problem Dear All, I am sorry to post this again. I am running FSLVBM on my structural images and has encountered the following problem. My template list contains only 34 subjects by my result template_4D_GM has 37 images when I go through the movie what am I doing wrong here. Thanks Venkat =================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2012). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. =================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2012). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.