Freesurfer

freesurfer@nmr.mgh.harvard.edu

5 participants
30091 discussions

fix topology problem
by miracle ozzoude 19 Apr '17

19 Apr '17

Hello freesurfer, I am running recon-all on a scan and for the past 4 days, it hasn't finished the fix topology step of recon-all. I have attached the recon.log in the email. Thanks Best, Paul

2 6

R: Re: FSGD file FS-FAST
by stdp82＠virgilio.it 19 Apr '17

19 Apr '17

I did not find it for for 4 Groups (1 Factor, 4 Levels), Zero Covariates. I need for check to avoid error on my analysis.Please could you say me whether the followed codes are correct. A) Group effect1 -1 0 01 0 -1 01 0 0 -1 B) 0.5 0.5 -0.5 -0.5 Many thanks. Stefano ----Messaggio originale---- Da: "Douglas Greve" <greve(a)nmr.mgh.harvard.edu> Data: 19-apr-2017 3.50 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] FSGD file FS-FAST Have you looked at https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples ? On 4/17/17 5:32 PM, stdp82(a)virgilio.it wrote: Hi list, please could you suggest me the group.effect.mtx and the file.mtx relative to Null Hypothesis for 4 Groups (1 Factor, 4 Levels), Zero Covariates. DODS or DOSS. Thanks Stefano _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

2 1

Error for Surface-based Group analysis in Freesurfer
by Hyeong-Cheol Moon 18 Apr '17

18 Apr '17

대용량 첨부파일 1개(293MB)대용량 첨부 파일은 30일간 보관 / 100회까지 다운로드 가능 20160906_SGJ_7T_TN.zip 293MB 다운로드 기간: 2017/04/17 ~ 2017/05/17Hello~ Freesurfer Developers. I am hyeong Cheol Moon from South of Korea. I took a your class few days ago, It was very help for me. I am mainly research Brain Anatomy data using high resolution images at 7 Tesla I am attempting to compute for Recon-all -qcache to Model and Contrasts GLM I was recon-all using high-resolution tutorial from "http://freesurfer.net/fswiki/HiResRecon" But In my recon file, there is no surf/lh.white. K. ERROR: cannot find /Applications/freesurfer/subjects/2_20160816_PTE_7T_TN/surf/lh.white.K Darwin munhyeongcheol-ui-MacBook-Pro.local 16.4.0 Darwin Kernel Version 16.4.0: Thu Dec 22 22:53:21 PST 2016; root:xnu-3789.41.3~3/RELEASE_X86_64 x86_64 I have questions 1) Can not be Normalization in High-resolution data? 2) If I compared to between Patients and Control in volume or thickness, could simply compare using stats information(individual)? 3) This is personal questions. I am master course students and beginner for neuroimaging analysis. Could you recommend to study methods? Someday Hope to study in your group, Phd course or Post doc course. Thanks !! 1) Freesurfer version : freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 2)Platform : MacOS Sierra 10.12.3 3)I attached a Recon-all file(that is patients with Trigeminal neuralgia) -------------------------------------------------------------------------------------- Hyeong Cheol Moon, 문형철 Graduate student, College of Medicine, Chungbuk National University B.S. Dept of Electronic and wireless engineering M.S. Dept of Medical neuroscience and neurosurgery Address : 404, e7-3, 1 Chungdae-ro, Seowon-gu, Cheongju, Chungbuk 28644, South of Korea E-mail : jimmun(a)naver.com, jimmun(a)chungbuk.ac.kr Mobile : +82-10-4536-5434

2 1

FSGD file FS-FAST
by stdp82＠virgilio.it 18 Apr '17

18 Apr '17

Hi list,please could you suggest me the group.effect.mtx and the file.mtx relative to Null Hypothesis for 4 Groups (1 Factor, 4 Levels), Zero Covariates. DODS or DOSS.ThanksStefano

2 1

Re: [Freesurfer] Selxavg3-sess Looking for (and can't find) "fmc.sm0"
by Taylor, Johnmark 18 Apr '17

18 Apr '17

Apologies for delayed response--here is the full terminal output. (error in bold) -------------------------------------------------------------- selxavg3-sess logfile is /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/scripts/glm/log/selxavg3-sess-bold-glm_double_all_ps_0-170417150715.log -------------------------------------------------------------- preproc-sess -s 170322_xu_binding01_sub01 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -a glm_double_all_ps_0 -nolog -------------------------------------------------------------- preproc-sess logfile is /dev/null -------------------------------------------------------------- $Id: preproc-sess,v 1.45.2.3 2013/01/22 22:09:10 greve Exp $ jtaylor setenv FREESURFER_HOME /ncf/nrg/sw/apps/freesurfer/5.3.0 setenv SUBJECTS_DIR /ncf/vcn/jtaylor/mri-space/subjects Linux ncf2705.rc.fas.harvard.edu 2.6.32-642.6.2.el6.x86_64 #1 SMP Wed Oct 26 06:52:09 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/scripts/glm /ncf/vcn/jtaylor/programs/batch_edits/preproc-sess -s 170322_xu_binding01_sub01 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -a glm_double_all_ps_0 -nolog Mon Apr 17 15:07:18 EDT 2017 instem f mc 1 f fmc stc 0 fmc sm 0 fmc mask 1 brain 170322_xu_binding01_sub01 Template ----------------------------- mktemplate-sess -s 170322_xu_binding01_sub01 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -fsd bold -rlf runlist_double.txt -nolog -update Session: /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170322_xu_binding01_sub01 ---------------- Mon Apr 17 15:07:18 EDT 2017 Detected input format at nii.gz 170322_xu_binding01_sub01 Update not needed Run: 008 ---------------- Mon Apr 17 15:07:19 EDT 2017 170322_xu_binding01_sub01 008 Update not needed Run: 010 ---------------- Mon Apr 17 15:07:19 EDT 2017 170322_xu_binding01_sub01 010 Update not needed Run: 012 ---------------- Mon Apr 17 15:07:19 EDT 2017 170322_xu_binding01_sub01 012 Update not needed Run: 020 ---------------- Mon Apr 17 15:07:19 EDT 2017 170322_xu_binding01_sub01 020 Update not needed Run: 022 ---------------- Mon Apr 17 15:07:19 EDT 2017 170322_xu_binding01_sub01 022 Update not needed Run: 024 ---------------- Mon Apr 17 15:07:19 EDT 2017 170322_xu_binding01_sub01 024 Update not needed Run: 034 ---------------- Mon Apr 17 15:07:19 EDT 2017 170322_xu_binding01_sub01 034 Update not needed Run: 036 ---------------- Mon Apr 17 15:07:19 EDT 2017 170322_xu_binding01_sub01 036 Update not needed Run: 038 ---------------- Mon Apr 17 15:07:19 EDT 2017 170322_xu_binding01_sub01 038 Update not needed Run: 046 ---------------- Mon Apr 17 15:07:19 EDT 2017 170322_xu_binding01_sub01 046 Update not needed Run: 048 ---------------- Mon Apr 17 15:07:19 EDT 2017 170322_xu_binding01_sub01 048 Update not needed Run: 050 ---------------- Mon Apr 17 15:07:19 EDT 2017 170322_xu_binding01_sub01 050 Update not needed Mon Apr 17 15:07:19 EDT 2017 mktemplate-sess completed 170322_xu_binding01_sub01 Mask ------------------------ mkbrainmask-sess -maskstem brain -fsd bold -s 170322_xu_binding01_sub01 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -rlf runlist_double.txt -nolog -update ------------------------------------------------ /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170322_xu_binding01_sub01 Mon Apr 17 15:07:19 EDT 2017 170322_xu_binding01_sub01 Update not needed for session-level mask 170322_xu_binding01_sub01 Update not needed for run 008 mask 170322_xu_binding01_sub01 Update not needed for run 008 meanval 170322_xu_binding01_sub01 Update not needed for run 010 mask 170322_xu_binding01_sub01 Update not needed for run 010 meanval 170322_xu_binding01_sub01 Update not needed for run 012 mask 170322_xu_binding01_sub01 Update not needed for run 012 meanval 170322_xu_binding01_sub01 Update not needed for run 020 mask 170322_xu_binding01_sub01 Update not needed for run 020 meanval 170322_xu_binding01_sub01 Update not needed for run 022 mask 170322_xu_binding01_sub01 Update not needed for run 022 meanval 170322_xu_binding01_sub01 Update not needed for run 024 mask 170322_xu_binding01_sub01 Update not needed for run 024 meanval 170322_xu_binding01_sub01 Update not needed for run 034 mask 170322_xu_binding01_sub01 Update not needed for run 034 meanval 170322_xu_binding01_sub01 Update not needed for run 036 mask 170322_xu_binding01_sub01 Update not needed for run 036 meanval 170322_xu_binding01_sub01 Update not needed for run 038 mask 170322_xu_binding01_sub01 Update not needed for run 038 meanval 170322_xu_binding01_sub01 Update not needed for run 046 mask 170322_xu_binding01_sub01 Update not needed for run 046 meanval 170322_xu_binding01_sub01 Update not needed for run 048 mask 170322_xu_binding01_sub01 Update not needed for run 048 meanval 170322_xu_binding01_sub01 Update not needed for run 050 mask 170322_xu_binding01_sub01 Update not needed for run 050 meanval Mon Apr 17 15:07:21 EDT 2017 mkbrainmask-sess done 170322_xu_binding01_sub01 Registration ----------------------------- register-sess -s 170322_xu_binding01_sub01 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -fsd bold -dof 6 -rlf runlist_double.txt -per-session -nolog -update -------------------------------------------------------------- register-sess logfile is /dev/null -------------------------------------------------------------- Mon Apr 17 15:07:22 EDT 2017 setenv SUBJECTS_DIR /ncf/vcn/jtaylor/mri-space/subjects cd /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/scripts/glm /ncf/nrg/sw/apps/freesurfer/5.3.0/fsfast/bin/register-sess -s 170322_xu_binding01_sub01 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -fsd bold -dof 6 -rlf runlist_double.txt -per-session -nolog -update freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux ncf2705.rc.fas.harvard.edu 2.6.32-642.6.2.el6.x86_64 #1 SMP Wed Oct 26 06:52:09 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux Session: /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170322_xu_binding01_sub01 ---------------- Mon Apr 17 15:07:22 EDT 2017 /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170322_xu_binding01_sub01 Mon Apr 17 15:07:22 EDT 2017 register-sess completed 170322_xu_binding01_sub01 MC ----------------------------- mc-sess -fstem f -fmcstem fmc -s 170322_xu_binding01_sub01 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -fsd bold -rlf runlist_double.txt -per-session -nolog -update Logfile is /dev/null ------------------------------------------- /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170322_xu_binding01_sub01 RunList: 008 010 012 020 022 024 034 036 038 046 048 050 170322_xu_binding01_sub01 008 Update not needed 170322_xu_binding01_sub01 010 Update not needed 170322_xu_binding01_sub01 012 Update not needed 170322_xu_binding01_sub01 020 Update not needed 170322_xu_binding01_sub01 022 Update not needed 170322_xu_binding01_sub01 024 Update not needed 170322_xu_binding01_sub01 034 Update not needed 170322_xu_binding01_sub01 036 Update not needed 170322_xu_binding01_sub01 038 Update not needed 170322_xu_binding01_sub01 046 Update not needed 170322_xu_binding01_sub01 048 Update not needed 170322_xu_binding01_sub01 050 Update not needed Mon Apr 17 15:07:22 EDT 2017 mc-sess completed SUCCESSFULLY ---------------------------------------- Started at Mon Apr 17 15:07:18 EDT 2017 Ended at Mon Apr 17 15:07:22 EDT 2017 preproc-sess done preproc-sess -s 170329_xu_binding01_sub02 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -a glm_double_all_ps_0 -nolog -------------------------------------------------------------- preproc-sess logfile is /dev/null -------------------------------------------------------------- $Id: preproc-sess,v 1.45.2.3 2013/01/22 22:09:10 greve Exp $ jtaylor setenv FREESURFER_HOME /ncf/nrg/sw/apps/freesurfer/5.3.0 setenv SUBJECTS_DIR /ncf/vcn/jtaylor/mri-space/subjects Linux ncf2705.rc.fas.harvard.edu 2.6.32-642.6.2.el6.x86_64 #1 SMP Wed Oct 26 06:52:09 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/scripts/glm /ncf/vcn/jtaylor/programs/batch_edits/preproc-sess -s 170329_xu_binding01_sub02 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -a glm_double_all_ps_0 -nolog Mon Apr 17 15:07:23 EDT 2017 instem f mc 1 f fmc stc 0 fmc sm 0 fmc mask 1 brain 170329_xu_binding01_sub02 Template ----------------------------- mktemplate-sess -s 170329_xu_binding01_sub02 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -fsd bold -rlf runlist_double.txt -nolog -update Session: /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170329_xu_binding01_sub02 ---------------- Mon Apr 17 15:07:23 EDT 2017 Detected input format at nii.gz 170329_xu_binding01_sub02 Update not needed Run: 014 ---------------- Mon Apr 17 15:07:23 EDT 2017 170329_xu_binding01_sub02 014 Update not needed Run: 016 ---------------- Mon Apr 17 15:07:23 EDT 2017 170329_xu_binding01_sub02 016 Update not needed Run: 018 ---------------- Mon Apr 17 15:07:23 EDT 2017 170329_xu_binding01_sub02 018 Update not needed Run: 026 ---------------- Mon Apr 17 15:07:23 EDT 2017 170329_xu_binding01_sub02 026 Update not needed Run: 028 ---------------- Mon Apr 17 15:07:23 EDT 2017 170329_xu_binding01_sub02 028 Update not needed Run: 030 ---------------- Mon Apr 17 15:07:24 EDT 2017 170329_xu_binding01_sub02 030 Update not needed Run: 040 ---------------- Mon Apr 17 15:07:24 EDT 2017 170329_xu_binding01_sub02 040 Update not needed Run: 042 ---------------- Mon Apr 17 15:07:24 EDT 2017 170329_xu_binding01_sub02 042 Update not needed Run: 044 ---------------- Mon Apr 17 15:07:24 EDT 2017 170329_xu_binding01_sub02 044 Update not needed Run: 052 ---------------- Mon Apr 17 15:07:24 EDT 2017 170329_xu_binding01_sub02 052 Update not needed Run: 054 ---------------- Mon Apr 17 15:07:24 EDT 2017 170329_xu_binding01_sub02 054 Update not needed Run: 056 ---------------- Mon Apr 17 15:07:24 EDT 2017 170329_xu_binding01_sub02 056 Update not needed Mon Apr 17 15:07:24 EDT 2017 mktemplate-sess completed 170329_xu_binding01_sub02 Mask ------------------------ mkbrainmask-sess -maskstem brain -fsd bold -s 170329_xu_binding01_sub02 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -rlf runlist_double.txt -nolog -update ------------------------------------------------ /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170329_xu_binding01_sub02 Mon Apr 17 15:07:24 EDT 2017 170329_xu_binding01_sub02 Update not needed for session-level mask 170329_xu_binding01_sub02 Update not needed for run 014 mask 170329_xu_binding01_sub02 Update not needed for run 014 meanval 170329_xu_binding01_sub02 Update not needed for run 016 mask 170329_xu_binding01_sub02 Update not needed for run 016 meanval 170329_xu_binding01_sub02 Update not needed for run 018 mask 170329_xu_binding01_sub02 Update not needed for run 018 meanval 170329_xu_binding01_sub02 Update not needed for run 026 mask 170329_xu_binding01_sub02 Update not needed for run 026 meanval 170329_xu_binding01_sub02 Update not needed for run 028 mask 170329_xu_binding01_sub02 Update not needed for run 028 meanval 170329_xu_binding01_sub02 Update not needed for run 030 mask 170329_xu_binding01_sub02 Update not needed for run 030 meanval 170329_xu_binding01_sub02 Update not needed for run 040 mask 170329_xu_binding01_sub02 Update not needed for run 040 meanval 170329_xu_binding01_sub02 Update not needed for run 042 mask 170329_xu_binding01_sub02 Update not needed for run 042 meanval 170329_xu_binding01_sub02 Update not needed for run 044 mask 170329_xu_binding01_sub02 Update not needed for run 044 meanval 170329_xu_binding01_sub02 Update not needed for run 052 mask 170329_xu_binding01_sub02 Update not needed for run 052 meanval 170329_xu_binding01_sub02 Update not needed for run 054 mask 170329_xu_binding01_sub02 Update not needed for run 054 meanval 170329_xu_binding01_sub02 Update not needed for run 056 mask 170329_xu_binding01_sub02 Update not needed for run 056 meanval Mon Apr 17 15:07:27 EDT 2017 mkbrainmask-sess done 170329_xu_binding01_sub02 Registration ----------------------------- register-sess -s 170329_xu_binding01_sub02 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -fsd bold -dof 6 -rlf runlist_double.txt -per-session -nolog -update -------------------------------------------------------------- register-sess logfile is /dev/null -------------------------------------------------------------- Mon Apr 17 15:07:27 EDT 2017 setenv SUBJECTS_DIR /ncf/vcn/jtaylor/mri-space/subjects cd /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/scripts/glm /ncf/nrg/sw/apps/freesurfer/5.3.0/fsfast/bin/register-sess -s 170329_xu_binding01_sub02 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -fsd bold -dof 6 -rlf runlist_double.txt -per-session -nolog -update freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux ncf2705.rc.fas.harvard.edu 2.6.32-642.6.2.el6.x86_64 #1 SMP Wed Oct 26 06:52:09 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux Session: /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170329_xu_binding01_sub02 ---------------- Mon Apr 17 15:07:27 EDT 2017 /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170329_xu_binding01_sub02 Mon Apr 17 15:07:27 EDT 2017 register-sess completed 170329_xu_binding01_sub02 MC ----------------------------- mc-sess -fstem f -fmcstem fmc -s 170329_xu_binding01_sub02 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -fsd bold -rlf runlist_double.txt -per-session -nolog -update Logfile is /dev/null ------------------------------------------- /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170329_xu_binding01_sub02 RunList: 014 016 018 026 028 030 040 042 044 052 054 056 170329_xu_binding01_sub02 014 Update not needed 170329_xu_binding01_sub02 016 Update not needed 170329_xu_binding01_sub02 018 Update not needed 170329_xu_binding01_sub02 026 Update not needed 170329_xu_binding01_sub02 028 Update not needed 170329_xu_binding01_sub02 030 Update not needed 170329_xu_binding01_sub02 040 Update not needed 170329_xu_binding01_sub02 042 Update not needed 170329_xu_binding01_sub02 044 Update not needed 170329_xu_binding01_sub02 052 Update not needed 170329_xu_binding01_sub02 054 Update not needed 170329_xu_binding01_sub02 056 Update not needed Mon Apr 17 15:07:28 EDT 2017 mc-sess completed SUCCESSFULLY ---------------------------------------- Started at Mon Apr 17 15:07:23 EDT 2017 Ended at Mon Apr 17 15:07:28 EDT 2017 preproc-sess done preproc-sess -s 170402_xu_binding01_sub03 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -a glm_double_all_ps_0 -nolog -------------------------------------------------------------- preproc-sess logfile is /dev/null -------------------------------------------------------------- $Id: preproc-sess,v 1.45.2.3 2013/01/22 22:09:10 greve Exp $ jtaylor setenv FREESURFER_HOME /ncf/nrg/sw/apps/freesurfer/5.3.0 setenv SUBJECTS_DIR /ncf/vcn/jtaylor/mri-space/subjects Linux ncf2705.rc.fas.harvard.edu 2.6.32-642.6.2.el6.x86_64 #1 SMP Wed Oct 26 06:52:09 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/scripts/glm /ncf/vcn/jtaylor/programs/batch_edits/preproc-sess -s 170402_xu_binding01_sub03 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -a glm_double_all_ps_0 -nolog Mon Apr 17 15:07:28 EDT 2017 instem f mc 1 f fmc stc 0 fmc sm 0 fmc mask 1 brain 170402_xu_binding01_sub03 Template ----------------------------- mktemplate-sess -s 170402_xu_binding01_sub03 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -fsd bold -rlf runlist_double.txt -nolog -update Session: /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170402_xu_binding01_sub03 ---------------- Mon Apr 17 15:07:29 EDT 2017 Detected input format at nii.gz 170402_xu_binding01_sub03 Update not needed Run: 008 ---------------- Mon Apr 17 15:07:29 EDT 2017 170402_xu_binding01_sub03 008 Update not needed Run: 010 ---------------- Mon Apr 17 15:07:29 EDT 2017 170402_xu_binding01_sub03 010 Update not needed Run: 012 ---------------- Mon Apr 17 15:07:29 EDT 2017 170402_xu_binding01_sub03 012 Update not needed Run: 020 ---------------- Mon Apr 17 15:07:29 EDT 2017 170402_xu_binding01_sub03 020 Update not needed Run: 022 ---------------- Mon Apr 17 15:07:29 EDT 2017 170402_xu_binding01_sub03 022 Update not needed Run: 024 ---------------- Mon Apr 17 15:07:29 EDT 2017 170402_xu_binding01_sub03 024 Update not needed Run: 034 ---------------- Mon Apr 17 15:07:29 EDT 2017 170402_xu_binding01_sub03 034 Update not needed Run: 036 ---------------- Mon Apr 17 15:07:29 EDT 2017 170402_xu_binding01_sub03 036 Update not needed Run: 038 ---------------- Mon Apr 17 15:07:29 EDT 2017 170402_xu_binding01_sub03 038 Update not needed Run: 046 ---------------- Mon Apr 17 15:07:29 EDT 2017 170402_xu_binding01_sub03 046 Update not needed Run: 048 ---------------- Mon Apr 17 15:07:29 EDT 2017 170402_xu_binding01_sub03 048 Update not needed Run: 050 ---------------- Mon Apr 17 15:07:29 EDT 2017 170402_xu_binding01_sub03 050 Update not needed Mon Apr 17 15:07:29 EDT 2017 mktemplate-sess completed 170402_xu_binding01_sub03 Mask ------------------------ mkbrainmask-sess -maskstem brain -fsd bold -s 170402_xu_binding01_sub03 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -rlf runlist_double.txt -nolog -update ------------------------------------------------ /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170402_xu_binding01_sub03 Mon Apr 17 15:07:29 EDT 2017 170402_xu_binding01_sub03 Update not needed for session-level mask 170402_xu_binding01_sub03 Update not needed for run 008 mask 170402_xu_binding01_sub03 Update not needed for run 008 meanval 170402_xu_binding01_sub03 Update not needed for run 010 mask 170402_xu_binding01_sub03 Update not needed for run 010 meanval 170402_xu_binding01_sub03 Update not needed for run 012 mask 170402_xu_binding01_sub03 Update not needed for run 012 meanval 170402_xu_binding01_sub03 Update not needed for run 020 mask 170402_xu_binding01_sub03 Update not needed for run 020 meanval 170402_xu_binding01_sub03 Update not needed for run 022 mask 170402_xu_binding01_sub03 Update not needed for run 022 meanval 170402_xu_binding01_sub03 Update not needed for run 024 mask 170402_xu_binding01_sub03 Update not needed for run 024 meanval 170402_xu_binding01_sub03 Update not needed for run 034 mask 170402_xu_binding01_sub03 Update not needed for run 034 meanval 170402_xu_binding01_sub03 Update not needed for run 036 mask 170402_xu_binding01_sub03 Update not needed for run 036 meanval 170402_xu_binding01_sub03 Update not needed for run 038 mask 170402_xu_binding01_sub03 Update not needed for run 038 meanval 170402_xu_binding01_sub03 Update not needed for run 046 mask 170402_xu_binding01_sub03 Update not needed for run 046 meanval 170402_xu_binding01_sub03 Update not needed for run 048 mask 170402_xu_binding01_sub03 Update not needed for run 048 meanval 170402_xu_binding01_sub03 Update not needed for run 050 mask 170402_xu_binding01_sub03 Update not needed for run 050 meanval Mon Apr 17 15:07:32 EDT 2017 mkbrainmask-sess done 170402_xu_binding01_sub03 Registration ----------------------------- register-sess -s 170402_xu_binding01_sub03 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -fsd bold -dof 6 -rlf runlist_double.txt -per-session -nolog -update -------------------------------------------------------------- register-sess logfile is /dev/null -------------------------------------------------------------- Mon Apr 17 15:07:32 EDT 2017 setenv SUBJECTS_DIR /ncf/vcn/jtaylor/mri-space/subjects cd /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/scripts/glm /ncf/nrg/sw/apps/freesurfer/5.3.0/fsfast/bin/register-sess -s 170402_xu_binding01_sub03 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -fsd bold -dof 6 -rlf runlist_double.txt -per-session -nolog -update freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux ncf2705.rc.fas.harvard.edu 2.6.32-642.6.2.el6.x86_64 #1 SMP Wed Oct 26 06:52:09 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux Session: /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170402_xu_binding01_sub03 ---------------- Mon Apr 17 15:07:32 EDT 2017 /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170402_xu_binding01_sub03 Mon Apr 17 15:07:32 EDT 2017 register-sess completed 170402_xu_binding01_sub03 MC ----------------------------- mc-sess -fstem f -fmcstem fmc -s 170402_xu_binding01_sub03 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -fsd bold -rlf runlist_double.txt -per-session -nolog -update Logfile is /dev/null ------------------------------------------- /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170402_xu_binding01_sub03 RunList: 008 010 012 020 022 024 034 036 038 046 048 050 170402_xu_binding01_sub03 008 Update not needed 170402_xu_binding01_sub03 010 Update not needed 170402_xu_binding01_sub03 012 Update not needed 170402_xu_binding01_sub03 020 Update not needed 170402_xu_binding01_sub03 022 Update not needed 170402_xu_binding01_sub03 024 Update not needed 170402_xu_binding01_sub03 034 Update not needed 170402_xu_binding01_sub03 036 Update not needed 170402_xu_binding01_sub03 038 Update not needed 170402_xu_binding01_sub03 046 Update not needed 170402_xu_binding01_sub03 048 Update not needed 170402_xu_binding01_sub03 050 Update not needed Mon Apr 17 15:07:33 EDT 2017 mc-sess completed SUCCESSFULLY ---------------------------------------- Started at Mon Apr 17 15:07:28 EDT 2017 Ended at Mon Apr 17 15:07:33 EDT 2017 preproc-sess done preproc-sess -s 170402_xu_binding01_sub04 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -a glm_double_all_ps_0 -nolog -------------------------------------------------------------- preproc-sess logfile is /dev/null -------------------------------------------------------------- $Id: preproc-sess,v 1.45.2.3 2013/01/22 22:09:10 greve Exp $ jtaylor setenv FREESURFER_HOME /ncf/nrg/sw/apps/freesurfer/5.3.0 setenv SUBJECTS_DIR /ncf/vcn/jtaylor/mri-space/subjects Linux ncf2705.rc.fas.harvard.edu 2.6.32-642.6.2.el6.x86_64 #1 SMP Wed Oct 26 06:52:09 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/scripts/glm /ncf/vcn/jtaylor/programs/batch_edits/preproc-sess -s 170402_xu_binding01_sub04 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -a glm_double_all_ps_0 -nolog Mon Apr 17 15:07:33 EDT 2017 instem f mc 1 f fmc stc 0 fmc sm 0 fmc mask 1 brain 170402_xu_binding01_sub04 Template ----------------------------- mktemplate-sess -s 170402_xu_binding01_sub04 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -fsd bold -rlf runlist_double.txt -nolog -update Session: /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170402_xu_binding01_sub04 ---------------- Mon Apr 17 15:07:33 EDT 2017 Detected input format at nii.gz 170402_xu_binding01_sub04 Update not needed Run: 014 ---------------- Mon Apr 17 15:07:34 EDT 2017 170402_xu_binding01_sub04 014 Update not needed Run: 016 ---------------- Mon Apr 17 15:07:34 EDT 2017 170402_xu_binding01_sub04 016 Update not needed Run: 018 ---------------- Mon Apr 17 15:07:34 EDT 2017 170402_xu_binding01_sub04 018 Update not needed Run: 026 ---------------- Mon Apr 17 15:07:34 EDT 2017 170402_xu_binding01_sub04 026 Update not needed Run: 028 ---------------- Mon Apr 17 15:07:34 EDT 2017 170402_xu_binding01_sub04 028 Update not needed Run: 030 ---------------- Mon Apr 17 15:07:34 EDT 2017 170402_xu_binding01_sub04 030 Update not needed Run: 040 ---------------- Mon Apr 17 15:07:34 EDT 2017 170402_xu_binding01_sub04 040 Update not needed Run: 042 ---------------- Mon Apr 17 15:07:34 EDT 2017 170402_xu_binding01_sub04 042 Update not needed Run: 044 ---------------- Mon Apr 17 15:07:34 EDT 2017 170402_xu_binding01_sub04 044 Update not needed Run: 052 ---------------- Mon Apr 17 15:07:34 EDT 2017 170402_xu_binding01_sub04 052 Update not needed Run: 054 ---------------- Mon Apr 17 15:07:34 EDT 2017 170402_xu_binding01_sub04 054 Update not needed Run: 056 ---------------- Mon Apr 17 15:07:34 EDT 2017 170402_xu_binding01_sub04 056 Update not needed Mon Apr 17 15:07:34 EDT 2017 mktemplate-sess completed 170402_xu_binding01_sub04 Mask ------------------------ mkbrainmask-sess -maskstem brain -fsd bold -s 170402_xu_binding01_sub04 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -rlf runlist_double.txt -nolog -update ------------------------------------------------ /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170402_xu_binding01_sub04 Mon Apr 17 15:07:34 EDT 2017 170402_xu_binding01_sub04 Update not needed for session-level mask 170402_xu_binding01_sub04 Update not needed for run 014 mask 170402_xu_binding01_sub04 Update not needed for run 014 meanval 170402_xu_binding01_sub04 Update not needed for run 016 mask 170402_xu_binding01_sub04 Update not needed for run 016 meanval 170402_xu_binding01_sub04 Update not needed for run 018 mask 170402_xu_binding01_sub04 Update not needed for run 018 meanval 170402_xu_binding01_sub04 Update not needed for run 026 mask 170402_xu_binding01_sub04 Update not needed for run 026 meanval 170402_xu_binding01_sub04 Update not needed for run 028 mask 170402_xu_binding01_sub04 Update not needed for run 028 meanval 170402_xu_binding01_sub04 Update not needed for run 030 mask 170402_xu_binding01_sub04 Update not needed for run 030 meanval 170402_xu_binding01_sub04 Update not needed for run 040 mask 170402_xu_binding01_sub04 Update not needed for run 040 meanval 170402_xu_binding01_sub04 Update not needed for run 042 mask 170402_xu_binding01_sub04 Update not needed for run 042 meanval 170402_xu_binding01_sub04 Update not needed for run 044 mask 170402_xu_binding01_sub04 Update not needed for run 044 meanval 170402_xu_binding01_sub04 Update not needed for run 052 mask 170402_xu_binding01_sub04 Update not needed for run 052 meanval 170402_xu_binding01_sub04 Update not needed for run 054 mask 170402_xu_binding01_sub04 Update not needed for run 054 meanval 170402_xu_binding01_sub04 Update not needed for run 056 mask 170402_xu_binding01_sub04 Update not needed for run 056 meanval Mon Apr 17 15:07:36 EDT 2017 mkbrainmask-sess done 170402_xu_binding01_sub04 Registration ----------------------------- register-sess -s 170402_xu_binding01_sub04 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -fsd bold -dof 6 -rlf runlist_double.txt -per-session -nolog -update -------------------------------------------------------------- register-sess logfile is /dev/null -------------------------------------------------------------- Mon Apr 17 15:07:37 EDT 2017 setenv SUBJECTS_DIR /ncf/vcn/jtaylor/mri-space/subjects cd /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/scripts/glm /ncf/nrg/sw/apps/freesurfer/5.3.0/fsfast/bin/register-sess -s 170402_xu_binding01_sub04 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -fsd bold -dof 6 -rlf runlist_double.txt -per-session -nolog -update freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux ncf2705.rc.fas.harvard.edu 2.6.32-642.6.2.el6.x86_64 #1 SMP Wed Oct 26 06:52:09 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux Session: /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170402_xu_binding01_sub04 ---------------- Mon Apr 17 15:07:37 EDT 2017 /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170402_xu_binding01_sub04 Mon Apr 17 15:07:37 EDT 2017 register-sess completed 170402_xu_binding01_sub04 MC ----------------------------- mc-sess -fstem f -fmcstem fmc -s 170402_xu_binding01_sub04 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -fsd bold -rlf runlist_double.txt -per-session -nolog -update Logfile is /dev/null ------------------------------------------- /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170402_xu_binding01_sub04 RunList: 014 016 018 026 028 030 040 042 044 052 054 056 170402_xu_binding01_sub04 014 Update not needed 170402_xu_binding01_sub04 016 Update not needed 170402_xu_binding01_sub04 018 Update not needed 170402_xu_binding01_sub04 026 Update not needed 170402_xu_binding01_sub04 028 Update not needed 170402_xu_binding01_sub04 030 Update not needed 170402_xu_binding01_sub04 040 Update not needed 170402_xu_binding01_sub04 042 Update not needed 170402_xu_binding01_sub04 044 Update not needed 170402_xu_binding01_sub04 052 Update not needed 170402_xu_binding01_sub04 054 Update not needed 170402_xu_binding01_sub04 056 Update not needed Mon Apr 17 15:07:37 EDT 2017 mc-sess completed SUCCESSFULLY ---------------------------------------- Started at Mon Apr 17 15:07:33 EDT 2017 Ended at Mon Apr 17 15:07:37 EDT 2017 preproc-sess done preproc-sess -s 170412_xu_binding01_sub05 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -a glm_double_all_ps_0 -nolog -------------------------------------------------------------- preproc-sess logfile is /dev/null -------------------------------------------------------------- $Id: preproc-sess,v 1.45.2.3 2013/01/22 22:09:10 greve Exp $ jtaylor setenv FREESURFER_HOME /ncf/nrg/sw/apps/freesurfer/5.3.0 setenv SUBJECTS_DIR /ncf/vcn/jtaylor/mri-space/subjects Linux ncf2705.rc.fas.harvard.edu 2.6.32-642.6.2.el6.x86_64 #1 SMP Wed Oct 26 06:52:09 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/scripts/glm /ncf/vcn/jtaylor/programs/batch_edits/preproc-sess -s 170412_xu_binding01_sub05 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -a glm_double_all_ps_0 -nolog Mon Apr 17 15:07:38 EDT 2017 instem f mc 1 f fmc stc 0 fmc sm 0 fmc mask 1 brain 170412_xu_binding01_sub05 Template ----------------------------- mktemplate-sess -s 170412_xu_binding01_sub05 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -fsd bold -rlf runlist_double.txt -nolog -update Session: /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170412_xu_binding01_sub05 ---------------- Mon Apr 17 15:07:38 EDT 2017 Detected input format at nii.gz 170412_xu_binding01_sub05 Update not needed Run: 008 ---------------- Mon Apr 17 15:07:38 EDT 2017 170412_xu_binding01_sub05 008 Update not needed Run: 010 ---------------- Mon Apr 17 15:07:38 EDT 2017 170412_xu_binding01_sub05 010 Update not needed Run: 012 ---------------- Mon Apr 17 15:07:38 EDT 2017 170412_xu_binding01_sub05 012 Update not needed Run: 020 ---------------- Mon Apr 17 15:07:38 EDT 2017 170412_xu_binding01_sub05 020 Update not needed Run: 022 ---------------- Mon Apr 17 15:07:38 EDT 2017 170412_xu_binding01_sub05 022 Update not needed Run: 024 ---------------- Mon Apr 17 15:07:38 EDT 2017 170412_xu_binding01_sub05 024 Update not needed Run: 034 ---------------- Mon Apr 17 15:07:38 EDT 2017 170412_xu_binding01_sub05 034 Update not needed Run: 036 ---------------- Mon Apr 17 15:07:39 EDT 2017 170412_xu_binding01_sub05 036 Update not needed Run: 038 ---------------- Mon Apr 17 15:07:39 EDT 2017 170412_xu_binding01_sub05 038 Update not needed Run: 046 ---------------- Mon Apr 17 15:07:39 EDT 2017 170412_xu_binding01_sub05 046 Update not needed Run: 048 ---------------- Mon Apr 17 15:07:39 EDT 2017 170412_xu_binding01_sub05 048 Update not needed Run: 050 ---------------- Mon Apr 17 15:07:39 EDT 2017 170412_xu_binding01_sub05 050 Update not needed Mon Apr 17 15:07:39 EDT 2017 mktemplate-sess completed 170412_xu_binding01_sub05 Mask ------------------------ mkbrainmask-sess -maskstem brain -fsd bold -s 170412_xu_binding01_sub05 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -rlf runlist_double.txt -nolog -update ------------------------------------------------ /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170412_xu_binding01_sub05 Mon Apr 17 15:07:39 EDT 2017 170412_xu_binding01_sub05 Update not needed for session-level mask 170412_xu_binding01_sub05 Update not needed for run 008 mask 170412_xu_binding01_sub05 Update not needed for run 008 meanval 170412_xu_binding01_sub05 Update not needed for run 010 mask 170412_xu_binding01_sub05 Update not needed for run 010 meanval 170412_xu_binding01_sub05 Update not needed for run 012 mask 170412_xu_binding01_sub05 Update not needed for run 012 meanval 170412_xu_binding01_sub05 Update not needed for run 020 mask 170412_xu_binding01_sub05 Update not needed for run 020 meanval 170412_xu_binding01_sub05 Update not needed for run 022 mask 170412_xu_binding01_sub05 Update not needed for run 022 meanval 170412_xu_binding01_sub05 Update not needed for run 024 mask 170412_xu_binding01_sub05 Update not needed for run 024 meanval 170412_xu_binding01_sub05 Update not needed for run 034 mask 170412_xu_binding01_sub05 Update not needed for run 034 meanval 170412_xu_binding01_sub05 Update not needed for run 036 mask 170412_xu_binding01_sub05 Update not needed for run 036 meanval 170412_xu_binding01_sub05 Update not needed for run 038 mask 170412_xu_binding01_sub05 Update not needed for run 038 meanval 170412_xu_binding01_sub05 Update not needed for run 046 mask 170412_xu_binding01_sub05 Update not needed for run 046 meanval 170412_xu_binding01_sub05 Update not needed for run 048 mask 170412_xu_binding01_sub05 Update not needed for run 048 meanval 170412_xu_binding01_sub05 Update not needed for run 050 mask 170412_xu_binding01_sub05 Update not needed for run 050 meanval Mon Apr 17 15:07:41 EDT 2017 mkbrainmask-sess done 170412_xu_binding01_sub05 Registration ----------------------------- register-sess -s 170412_xu_binding01_sub05 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -fsd bold -dof 6 -rlf runlist_double.txt -per-session -nolog -update -------------------------------------------------------------- register-sess logfile is /dev/null -------------------------------------------------------------- Mon Apr 17 15:07:41 EDT 2017 setenv SUBJECTS_DIR /ncf/vcn/jtaylor/mri-space/subjects cd /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/scripts/glm /ncf/nrg/sw/apps/freesurfer/5.3.0/fsfast/bin/register-sess -s 170412_xu_binding01_sub05 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -fsd bold -dof 6 -rlf runlist_double.txt -per-session -nolog -update freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux ncf2705.rc.fas.harvard.edu 2.6.32-642.6.2.el6.x86_64 #1 SMP Wed Oct 26 06:52:09 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux Session: /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170412_xu_binding01_sub05 ---------------- Mon Apr 17 15:07:41 EDT 2017 /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170412_xu_binding01_sub05 Mon Apr 17 15:07:42 EDT 2017 register-sess completed 170412_xu_binding01_sub05 MC ----------------------------- mc-sess -fstem f -fmcstem fmc -s 170412_xu_binding01_sub05 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -fsd bold -rlf runlist_double.txt -per-session -nolog -update Logfile is /dev/null ------------------------------------------- /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170412_xu_binding01_sub05 RunList: 008 010 012 020 022 024 034 036 038 046 048 050 170412_xu_binding01_sub05 008 Update not needed 170412_xu_binding01_sub05 010 Update not needed 170412_xu_binding01_sub05 012 Update not needed 170412_xu_binding01_sub05 020 Update not needed 170412_xu_binding01_sub05 022 Update not needed 170412_xu_binding01_sub05 024 Update not needed 170412_xu_binding01_sub05 034 Update not needed 170412_xu_binding01_sub05 036 Update not needed 170412_xu_binding01_sub05 038 Update not needed 170412_xu_binding01_sub05 046 Update not needed 170412_xu_binding01_sub05 048 Update not needed 170412_xu_binding01_sub05 050 Update not needed Mon Apr 17 15:07:42 EDT 2017 mc-sess completed SUCCESSFULLY ---------------------------------------- Started at Mon Apr 17 15:07:38 EDT 2017 Ended at Mon Apr 17 15:07:42 EDT 2017 preproc-sess done preproc-sess -s 170416_xu_binding01_sub06 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -a glm_double_all_ps_0 -nolog -------------------------------------------------------------- preproc-sess logfile is /dev/null -------------------------------------------------------------- $Id: preproc-sess,v 1.45.2.3 2013/01/22 22:09:10 greve Exp $ jtaylor setenv FREESURFER_HOME /ncf/nrg/sw/apps/freesurfer/5.3.0 setenv SUBJECTS_DIR /ncf/vcn/jtaylor/mri-space/subjects Linux ncf2705.rc.fas.harvard.edu 2.6.32-642.6.2.el6.x86_64 #1 SMP Wed Oct 26 06:52:09 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/scripts/glm /ncf/vcn/jtaylor/programs/batch_edits/preproc-sess -s 170416_xu_binding01_sub06 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -a glm_double_all_ps_0 -nolog Mon Apr 17 15:07:43 EDT 2017 instem f mc 1 f fmc stc 0 fmc sm 0 fmc mask 1 brain 170416_xu_binding01_sub06 Template ----------------------------- mktemplate-sess -s 170416_xu_binding01_sub06 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -fsd bold -rlf runlist_double.txt -nolog -update Session: /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170416_xu_binding01_sub06 ---------------- Mon Apr 17 15:07:43 EDT 2017 Detected input format at nii.gz 170416_xu_binding01_sub06 Update not needed Run: 014 ---------------- Mon Apr 17 15:07:43 EDT 2017 170416_xu_binding01_sub06 014 Update not needed Run: 016 ---------------- Mon Apr 17 15:07:43 EDT 2017 170416_xu_binding01_sub06 016 Update not needed Run: 018 ---------------- Mon Apr 17 15:07:43 EDT 2017 170416_xu_binding01_sub06 018 Update not needed Run: 026 ---------------- Mon Apr 17 15:07:43 EDT 2017 170416_xu_binding01_sub06 026 Update not needed Run: 028 ---------------- Mon Apr 17 15:07:43 EDT 2017 170416_xu_binding01_sub06 028 Update not needed Run: 030 ---------------- Mon Apr 17 15:07:43 EDT 2017 170416_xu_binding01_sub06 030 Update not needed Run: 040 ---------------- Mon Apr 17 15:07:44 EDT 2017 170416_xu_binding01_sub06 040 Update not needed Run: 042 ---------------- Mon Apr 17 15:07:44 EDT 2017 170416_xu_binding01_sub06 042 Update not needed Run: 044 ---------------- Mon Apr 17 15:07:44 EDT 2017 170416_xu_binding01_sub06 044 Update not needed Run: 052 ---------------- Mon Apr 17 15:07:44 EDT 2017 170416_xu_binding01_sub06 052 Update not needed Run: 054 ---------------- Mon Apr 17 15:07:44 EDT 2017 170416_xu_binding01_sub06 054 Update not needed Run: 056 ---------------- Mon Apr 17 15:07:44 EDT 2017 170416_xu_binding01_sub06 056 Update not needed Mon Apr 17 15:07:44 EDT 2017 mktemplate-sess completed 170416_xu_binding01_sub06 Mask ------------------------ mkbrainmask-sess -maskstem brain -fsd bold -s 170416_xu_binding01_sub06 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -rlf runlist_double.txt -nolog -update ------------------------------------------------ /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170416_xu_binding01_sub06 Mon Apr 17 15:07:44 EDT 2017 170416_xu_binding01_sub06 Update not needed for session-level mask 170416_xu_binding01_sub06 Update not needed for run 014 mask 170416_xu_binding01_sub06 Update not needed for run 014 meanval 170416_xu_binding01_sub06 Update not needed for run 016 mask 170416_xu_binding01_sub06 Update not needed for run 016 meanval 170416_xu_binding01_sub06 Update not needed for run 018 mask 170416_xu_binding01_sub06 Update not needed for run 018 meanval 170416_xu_binding01_sub06 Update not needed for run 026 mask 170416_xu_binding01_sub06 Update not needed for run 026 meanval 170416_xu_binding01_sub06 Update not needed for run 028 mask 170416_xu_binding01_sub06 Update not needed for run 028 meanval 170416_xu_binding01_sub06 Update not needed for run 030 mask 170416_xu_binding01_sub06 Update not needed for run 030 meanval 170416_xu_binding01_sub06 Update not needed for run 040 mask 170416_xu_binding01_sub06 Update not needed for run 040 meanval 170416_xu_binding01_sub06 Update not needed for run 042 mask 170416_xu_binding01_sub06 Update not needed for run 042 meanval 170416_xu_binding01_sub06 Update not needed for run 044 mask 170416_xu_binding01_sub06 Update not needed for run 044 meanval 170416_xu_binding01_sub06 Update not needed for run 052 mask 170416_xu_binding01_sub06 Update not needed for run 052 meanval 170416_xu_binding01_sub06 Update not needed for run 054 mask 170416_xu_binding01_sub06 Update not needed for run 054 meanval 170416_xu_binding01_sub06 Update not needed for run 056 mask 170416_xu_binding01_sub06 Update not needed for run 056 meanval Mon Apr 17 15:07:47 EDT 2017 mkbrainmask-sess done 170416_xu_binding01_sub06 Registration ----------------------------- register-sess -s 170416_xu_binding01_sub06 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -fsd bold -dof 6 -rlf runlist_double.txt -per-session -nolog -update -------------------------------------------------------------- register-sess logfile is /dev/null -------------------------------------------------------------- Mon Apr 17 15:07:47 EDT 2017 setenv SUBJECTS_DIR /ncf/vcn/jtaylor/mri-space/subjects cd /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/scripts/glm /ncf/nrg/sw/apps/freesurfer/5.3.0/fsfast/bin/register-sess -s 170416_xu_binding01_sub06 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -fsd bold -dof 6 -rlf runlist_double.txt -per-session -nolog -update freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux ncf2705.rc.fas.harvard.edu 2.6.32-642.6.2.el6.x86_64 #1 SMP Wed Oct 26 06:52:09 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux Session: /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170416_xu_binding01_sub06 ---------------- Mon Apr 17 15:07:47 EDT 2017 /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170416_xu_binding01_sub06 Mon Apr 17 15:07:47 EDT 2017 register-sess completed 170416_xu_binding01_sub06 MC ----------------------------- mc-sess -fstem f -fmcstem fmc -s 170416_xu_binding01_sub06 -d /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata -fsd bold -rlf runlist_double.txt -per-session -nolog -update Logfile is /dev/null ------------------------------------------- /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170416_xu_binding01_sub06 RunList: 014 016 018 026 028 030 040 042 044 052 054 056 170416_xu_binding01_sub06 014 Update not needed 170416_xu_binding01_sub06 016 Update not needed 170416_xu_binding01_sub06 018 Update not needed 170416_xu_binding01_sub06 026 Update not needed 170416_xu_binding01_sub06 028 Update not needed 170416_xu_binding01_sub06 030 Update not needed 170416_xu_binding01_sub06 040 Update not needed 170416_xu_binding01_sub06 042 Update not needed 170416_xu_binding01_sub06 044 Update not needed 170416_xu_binding01_sub06 052 Update not needed 170416_xu_binding01_sub06 054 Update not needed 170416_xu_binding01_sub06 056 Update not needed Mon Apr 17 15:07:47 EDT 2017 mc-sess completed SUCCESSFULLY ---------------------------------------- Started at Mon Apr 17 15:07:43 EDT 2017 Ended at Mon Apr 17 15:07:47 EDT 2017 preproc-sess done ------------------------------------------- /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170322_xu_binding01_sub01 Mon Apr 17 15:07:48 EDT 2017 anadir = /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170322_xu_binding01_sub01/bold/glm_double_all_ps_0 *ERROR: cannot find /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170322_xu_binding01_sub01/bold/008/fmc.sm0* On Fri, Apr 7, 2017 at 12:00 PM, <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. postdoctoral Research Fellow position at Mayo Clinic > (Senjem, Matthew L., M.S.) > 2. First-level GLM on externally-preprocessed functionals > (Christopher Markiewicz) > 3. Re: Custom color maps (Senften, Peter) > 4. Re: MRIread (load_nifti)- Out of memory (Bruce Fischl) > 5. Re: long mri_ca_register error (Bruce Fischl) > 6. Re: help (Bruce Fischl) > 7. Re: MRIread (load_nifti)- Out of memory (Ilaria Sani) > 8. Re: MRIread (load_nifti)- Out of memory (Douglas N Greve) > 9. Re: QDEC-volume, thickness and area (Douglas N Greve) > 10. Re: Help on "mris_anatomical_stats" (Douglas N Greve) > 11. Re: First-level GLM on externally-preprocessed functionals > (Douglas N Greve) > 12. Re: Custom color maps (Douglas N Greve) > 13. Re: Custom registration template (Douglas N Greve) > 14. Re: Selxavg3-sess Looking for (and can't find) "fmc.sm0" > (Douglas N Greve) > 15. Re: Ventricle-to-Brain Ratio (Douglas N Greve) > 16. Re: ROI seed size (Douglas N Greve) > 17. Re: correlation coefficient R (Douglas N Greve) > 18. Re: Custom color maps (Senften, Peter) > 19. Re: General QDEC clarification queastions (Douglas N Greve) > 20. QDEC and ROI drawing (Arnaud Bor?) > 21. Re: QDEC and ROI drawing (Douglas N Greve) > 22. Re: QDEC-volume, thickness and area (Lim, Lena) > 23. Re: QDEC-volume, thickness and area (Douglas N Greve) > 24. R: Re: R: R: Re: R: Re: Whole preprocessing with FAST without > to perform a seed based analysis (stdp82(a)virgilio.it) > 25. Re: R: Re: R: R: Re: R: Re: Whole preprocessing with FAST > without to perform a seed based analysis (Douglas N Greve) > 26. QDEC-Cortical Thickness (Limachia, Gaurang (NIH/NINDS) [F]) > 27. Re: Custom registration template (Linda Zhang) > 28. Re: Ventricle-to-Brain Ratio (Gullickson, James) > 29. Re: MRIread (load_nifti)- Out of memory (Ilaria Sani) > 30. Re: long mri_ca_register error (Chris Adamson) > 31. Re: help (Dilip Puri) > 32. How to segment subnuclei of thalamus? (Shane S) > 33. withdrawing from the mailing list. (kjunji(a)med.kanazawa-u.ac.jp) > 34. Re: QA Tools v1.2 and future release (Yong Li) > 35. Hippocampal subfield segmentation, file content (Nina Jacobsen) > 36. Re: Multiple Comparisons Correction thresh error (teodora petrova) > 37. Longitudinal Pipeline (Arman Eshaghi) > 38. Re: Hippocampal subfield segmentation, file content > (Iglesias Gonzalez, Eugenio) > 39. Re: How to segment subnuclei of thalamus? (Bruce Fischl) > 40. Analyzing xhemi results (Marissa Pifer) > 41. Re: QDEC and ROI drawing (Arnaud Bor?) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 06 Apr 2017 16:17:30 +0000 > From: "Senjem, Matthew L., M.S." <Senjem.Matthew1(a)mayo.edu> > Subject: [Freesurfer] postdoctoral Research Fellow position at Mayo > Clinic > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <47cabe$66564f(a)ironport10.mayo.edu> > Content-Type: text/plain; charset="windows-1252" > > The Mayo Clinic Departments of Neurology and Diagnostic Radiology in > Rochester, Minnesota are seeking applications for a fully-funded, two-year > postdoctoral Research Fellow position to begin in July of 2017. The > Research Fellow position will primarily work on developing advanced > multi-modal molecular and high-field (3T and 7T) neuroimaging to study > connectomics in pre-clinical and clinical Alzheimer?s disease. The > resulting data will be acquired and analyzed as part of a unique > collaboration between investigators at Mayo Clinic Alzheimer?s Disease > Research Center and the Center for Magnetic Resonance Research at the > University of Minnesota. Basic programing skills and familiarity with > widely used neuroimaging software platforms are required for successful > applicants. Familiarity with the Human Connectome Project imaging and > analyses protocols is preferred but not required. No clinical or > Alzheimer?s specific background is required. Salary will be commensurate > with postdoctoral experience. The position will remain open until filled by > a successful candidate. > > Please send CV, three letters of recommendation, and any inquiries to: > > David T. Jones, M.D. > Mayo Clinic > Department of Neurology > Email: Jones.David(a)mayo.edu<mailto:Jones.David@mayo.edu> > > A Research Fellow at Mayo Clinic is a temporary position intended to > provide training and education in research. Individuals will train in the > research program of a Mayo Clinic principal investigator. Qualified > individuals will demonstrate the potential for research as evidenced by > their training and peer-reviewed publications and should become competitive > for national research grants. Proof of English proficiency is required for > J-1 Short-Term Scholars, Research Scholars, Professors, Specialists, and > Student Interns sponsored by Mayo Clinic. > > Why Mayo Clinic? Learn and grow among the best in your field at the > nation?s top hospital (U.S. News & World Report, 2016-2017), ranked No. 1 > in more specialties than any other care provider. Mayo Clinic is committed > to sustaining and growing research, believes in research-driven care and > establishes a well-defined integration between the clinical practice and > research. At Mayo Clinic, you?ll use the power of collaboration to achieve > the highest standards for medical care and health improvement, working in > the largest integrated, not-for-profit medical group practice in the world > with over 60,000 employees. You?re invited to contribute to a unique > environment that brings together the best in patient care, groundbreaking > research and innovative medical education. We offer exceptional benefits, > and have been recognized by FORTUNE magazine as one of the top 100 ?Best > Companies to Work For?. > > Mayo Clinic is an equal opportunity educator and employer (including > veterans and persons with disabilities). > ------------------------------------------------------------ > ------------------------------------------------------------ > ------------------------------------------------- >

2 1

Inconsistency in SI axis coordinate between FreeSurfer recon-all seg image and BrainVoyager
by Jerry Jeyachandra 18 Apr '17

18 Apr '17

Hi Freesurfer support team, I'm attempting to register coordinates between BrainVoyager anatomical images and freesurfer segmented images with both in native space, however I'm running into inconsistencies specifically along the inferior/superior dimension that I hope you can help me with BrainVoyager reports coordinates as voxel indices which I'm trying to match with FreeView's T1fs_nu_conform coordinates which I assume are in voxel indices as well. Both the AP and RL dimensions match in both programs across all our participants, however the SI axis does not, with offsets varying across participants. Does the recon-all function crop the image such that the Z dimension is no longer matched with native space? I've noticed that the images are cropped specifically from the bottom segment below the neck and was wondering if that was affecting the coordinate report in the SI axis. If this is the case, is this stored in freesurfer such that I can get coordinates relative to the uncropped image or just the offset value for the Z coordinate to compensate for it? Thanks, Jerry Jeyachandra

2 1

Any advices for hires surface reconstruction?
by Damien MARIE 18 Apr '17

18 Apr '17

Hi, I have a project on 7T data. I processed 26 subjects with FreeSurfer6 recon-all with or without the hires flag. The input is MP2RAGE, 0.6 mm^3, bias corrected, skull strip was done despite a slight piece of dura is still present. For the data processed at native resolution, with the hires flag, I mainly used this: recon-all -subject -i -parallel -expert -hires The expert file indicating only mris_inflate -n 50 As a result, skull strip had to be fixed for 5 subjects (missing brain pieces). Bilateral temporal pole is missing in the reconstructed surfaces in 19 subjects. For the downsampled data, without the hires flag : recon-all -subject -i -parallel Bilateral temporal pole is missing in the reconstructed surfaces in only 1 subject. Surfaces are way smoother. I guess such differences between the classic pipeline and the pipeline tuned for hires data are expected. I was just wondering if I was missing something somewhere, some additional options that I would need to tweak, to get better surfaces with the hires data especially in the temporal pole. For now the only things I see that I could do are adding checkpoints or play with this command line: mris_make_surfaces -max_gray_at_csf_border X -max_csf Y Thank you and best, Damien

2 1

Fixing a left/right flip
by Dan Grupe 17 Apr '17

17 Apr '17

Hi all, After running a bunch of subjects through FreeSurfer and making extensive manual edits to the white matter masks, we discovered that the data were left/right flipped during the dicom-to-nifti conversion process. I hope to maintain these manual edits while processing data in the proper orientation and running them through the rest of the pipeline. Is this possible to do? An old thread from 10 years ago directed me to this page: https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal that offered some tips on how to go about this. However, after confirming that the volume was reversed running recon-all -autorecon1 in a new directory, I encountered an error message: > ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) This problem does not arise when running the same command on a copy of this subject’s non-flipped data. Are there different steps that I should be following to rectify the problem? Or can you help me troubleshoot this error? Best, Dan ------ Dan Grupe, Ph.D. Assistant Scientist Waisman Laboratory for Brain Imaging and Behavior and Center for Healthy Minds University of Wisconsin-Madison ------ grupe(a)wisc.edu<mailto:grupe@wisc.edu> 608-263-7572 http://brainimaging.waisman.wisc.edu/~dgrupe

2 1

Matlab packages
by Iman Aganj 17 Apr '17

17 Apr '17

Dear FreeSurfer users, I have recently developed two Matlab packages and made them publicly available, which I'd like to share with you. They include source codes and compiled binaries, and are GPU-compatible. The first one is for deformable registration of same-contrast images, using the mid-space-independent <https://authors.elsevier.com/a/1UgxH3lc~q-QUS> approach. www.nitrc.org/projects/msi-register <http://www.nitrc.org/projects/msi-register> The second one is for diffusion-weighted MRI processing. It includes a pipeline for computation of the q-ball Orientation Distribution Function in Constant Solid Angle (CSA-ODF <http://www.ncbi.nlm.nih.gov/pubmed/20535807> ), in addition to Hough-transform <http://www.ncbi.nlm.nih.gov/pubmed/21376655> based tractography. www.nitrc.org/projects/csaodf-hough <http://www.nitrc.org/projects/csaodf-hough> These are first releases. I highly appreciate any feedback. Best regards, Iman Aganj Assistant Professor of Radiology Harvard Medical School Assistant in Neuroscience Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital

1 0

Re: [Freesurfer] Control point in WM regions
by Antonin Skoch 17 Apr '17

17 Apr '17

Dear Shane, could you please post screenshots of ?h.orig.nofix and ?h.orig in the problematic regions? Antonin Skoch Hello Freesurfer Team, I am trying to recover thin WM strands in the temporal lobe by using control points but to no avail (screenshot) Any suggestions please? These regions also appear to be classified as WM (wm.mgz) but why are the surfaces inaccurate? Thanks for your help. Best Wishes,Shane

1 0

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