FreeSurfer Folks,
I am attempting to look at some data with tkmedit-sess
tkmedit-sess -analysis LowTraumaSPMHRF -contrast all_v_fix -d . -s FPPREW09 -map sig -fsd bold
but I am getting the following error.
corRead(): can't open file /exp/REfMRI/fMRI_FPPREW/structural//FPPREW09/mri/orig/COR-.info
Error: Loading volume orig
Couldn't read the anatomical volume.
Tkmedit couldn't read the volume you specified. This could be because the image format wasn't recognized, or it couldn't find the proper header, or the file(s) were unreadable, or it was the wrong size.
I can look at the data with tkmedit (without the sess) loading all the files manually. I have tried the tkmedit-sess several different ways but I always get an error. Does anyone have an idea about how I get this to work?
Thanks, Avram
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Avram Holmes Department of Psychology Harvard University 1210 William James Hall Phone:(617) 495-0790 33 Kirkland Street Fax:(617) 495-3728 Cambridge, MA 02138, USA Email: holmes@fas.harvard.edu ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Can you run it with -debug and send me the result?
Avram Holmes wrote:
FreeSurfer Folks,
I am attempting to look at some data with tkmedit-sess
tkmedit-sess -analysis LowTraumaSPMHRF -contrast all_v_fix -d . -s FPPREW09 -map sig -fsd bold
but I am getting the following error.
corRead(): can't open file /exp/REfMRI/fMRI_FPPREW/structural//FPPREW09/mri/orig/COR-.info
Error: Loading volume orig
Couldn't read the anatomical volume.
Tkmedit couldn't read the volume you specified. This could be because the image format wasn't recognized, or it couldn't find the proper header, or the file(s) were unreadable, or it was the wrong size.
I can look at the data with tkmedit (without the sess) loading all the files manually. I have tried the tkmedit-sess several different ways but I always get an error. Does anyone have an idea about how I get this to work?
Thanks, Avram
Avram Holmes Department of Psychology Harvard University 1210 William James Hall Phone:(617) 495-0790 33 Kirkland Street Fax:(617) 495-3728 Cambridge, MA 02138, USA Email: holmes@fas.harvard.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Doug,
Thanks for the response. It turns out that I was leaving off the -mgz flag (as another helpful user pointed out). Everything seems to be working now.
Thanks again, Avram
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Avram Holmes Department of Psychology Harvard University 1210 William James Hall Phone:(617) 495-0790 33 Kirkland Street Fax:(617) 495-3728 Cambridge, MA 02138, USA Email: holmes@fas.harvard.edu ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
On Fri, 1 Jun 2007, Doug Greve wrote:
Can you run it with -debug and send me the result?
Avram Holmes wrote:
FreeSurfer Folks,
I am attempting to look at some data with tkmedit-sess
tkmedit-sess -analysis LowTraumaSPMHRF -contrast all_v_fix -d . -s FPPREW09 -map sig -fsd bold
but I am getting the following error.
corRead(): can't open file /exp/REfMRI/fMRI_FPPREW/structural//FPPREW09/mri/orig/COR-.info
Error: Loading volume orig
Couldn't read the anatomical volume.
Tkmedit couldn't read the volume you specified. This could be because the image format wasn't recognized, or it couldn't find the proper header, or the file(s) were unreadable, or it was the wrong size.
I can look at the data with tkmedit (without the sess) loading all the files manually. I have tried the tkmedit-sess several different ways but I always get an error. Does anyone have an idea about how I get this to work?
Thanks, Avram
Avram Holmes Department of Psychology Harvard University 1210 William James Hall Phone:(617) 495-0790 33 Kirkland Street Fax:(617) 495-3728 Cambridge, MA 02138, USA Email: holmes@fas.harvard.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
The newer versions to figure that out automatically.
Avram Holmes wrote:
Doug,
Thanks for the response. It turns out that I was leaving off the -mgz flag (as another helpful user pointed out). Everything seems to be working now.
Thanks again, Avram
Avram Holmes Department of Psychology Harvard University 1210 William James Hall Phone:(617) 495-0790 33 Kirkland Street Fax:(617) 495-3728 Cambridge, MA 02138, USA Email: holmes@fas.harvard.eduOn Fri, 1 Jun 2007, Doug Greve wrote:
Can you run it with -debug and send me the result?
Avram Holmes wrote:
FreeSurfer Folks,
I am attempting to look at some data with tkmedit-sess
tkmedit-sess -analysis LowTraumaSPMHRF -contrast all_v_fix -d . -s FPPREW09 -map sig -fsd bold
but I am getting the following error.
corRead(): can't open file /exp/REfMRI/fMRI_FPPREW/structural//FPPREW09/mri/orig/COR-.info
Error: Loading volume orig
Couldn't read the anatomical volume.
Tkmedit couldn't read the volume you specified. This could be because the image format wasn't recognized, or it couldn't find the proper header, or the file(s) were unreadable, or it was the wrong size.
I can look at the data with tkmedit (without the sess) loading all the files manually. I have tried the tkmedit-sess several different ways but I always get an error. Does anyone have an idea about how I get this to work?
Thanks, Avram
Avram Holmes Department of Psychology Harvard University 1210 William James Hall Phone:(617) 495-0790 33 Kirkland Street Fax:(617) 495-3728 Cambridge, MA 02138, USA Email: holmes@fas.harvard.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
All,
This is a repeat question for a problem I am still encountering (see http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg05104.html on the wiki). I am still having trouble getting the intergroupavg-sess to generate all the files that it should. Right now I can generate the 'h-offset' and 'register.dat' files and within each contrast I can get the script to create the 'minsig' and 'sig' files but I don't get a 'sig.bhdr' file so I am unable to check the results.
The command I am using is as follows...
intergroupavg-sess -analysis ${analysis} -contrast ${c} -group1 ${groupA} -group2 ${groupB} -intergroup ${groupA}_v_${groupB} -space tal
The output log file is included below.
Thanks for any help you can offer, Avram
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Avram Holmes Department of Psychology Harvard University 1210 William James Hall Phone:(617) 495-0790 33 Kirkland Street Fax:(617) 495-3728 Cambridge, MA 02138, USA Email: holmes@fas.harvard.edu ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:::::::::::::: intergroupavg-sess.log :::::::::::::: intergroup-sess log file $Id: intergroupavg-sess,v 1.2 2005/08/30 17:05:21 greve Exp $ uid=506(aholmes) gid=500(lab) groups=500(lab),10(wheel),440(REWARD),435(REfMRI),310(ANTCON),325(CONCON),350(DEPFED),358(EMOGNG),380( FPPALL),445(REWPUN),472(ATTLRN),613(phonescreen),506(aholmes),440(REWARD),435(REfMRI),506(aholmes),325(CONCON),358(EMOGNG),310(ANTCO N),445(REWPUN),613(phonescreen),350(DEPFED),380(FPPALL) /net/tucson/Raid/shared/exp/REfMRI/fMRI_FPPREW/functional /apps/freesurfer/freesurfer//fsfast/bin/intergroupavg-sess -analysis taumax30_stc_smooth6 -contrast all_v_fix -group1 LowTrauma -group2 HighTrauma -intergroup LowTrauma_v_HighTrauma -space ta l Linux daplab1.fas.harvard.edu 2.4.18-27.8.0smp #1 SMP Fri Mar 14 07:13:13 EST 2003 i686 athlon i386 GNU/Linux Tue Jun 5 11:11:57 EDT 2007 %%% --------------------------------- %% % temporary matlab script for intergroupavg-sess % /tmp/LowTrauma_v_HighTrauma3582_iga.m global QuitOnError; QuitOnError = 1; if(exist('fast_intergroupavg')==0) qoe('ERROR: matlab path incorrect');end; cd /net/tucson/Raid/shared/exp/REfMRI/fMRI_FPPREW/functional; fast_intergroupavg(... '-avg1', 'LowTrauma/bold/taumax30_stc_smooth6/tal-rfx/all_v_fix/avg', ... '-std1', 'LowTrauma/bold/taumax30_stc_smooth6/tal-rfx/all_v_fix/std', ... /exp/REfMRI/fMRI_FPPREW/functional/log> ls *inter* intergroupavg-sess.log intergroupavg-sess.log.old /exp/REfMRI/fMRI_FPPREW/functional/log> ll intergroupavg-sess.log -rw-rw-r-- 1 aholmes REfMRI 3372 Jun 5 10:59 intergroupavg-sess.log /exp/REfMRI/fMRI_FPPREW/functional/log> more intergroupavg-sess.log intergroup-sess log file $Id: intergroupavg-sess,v 1.2 2005/08/30 17:05:21 greve Exp $ uid=506(aholmes) gid=500(lab) groups=500(lab),10(wheel),440(REWARD),435(REfMRI),310(ANTCON),325(CONCON),350(DEPFED),358(EMOGNG),380( FPPALL),445(REWPUN),472(ATTLRN),613(phonescreen),506(aholmes),440(REWARD),435(REfMRI),506(aholmes),325(CONCON),358(EMOGNG),310(ANTCO N),445(REWPUN),613(phonescreen),350(DEPFED),380(FPPALL) /net/tucson/Raid/shared/exp/REfMRI/fMRI_FPPREW/functional /apps/freesurfer/freesurfer//fsfast/bin/intergroupavg-sess -analysis taumax30_stc_smooth6 -contrast all_v_fix -group1 LowTrauma -group2 HighTrauma -intergroup LowTrauma_v_HighTrauma -space ta l Linux daplab1.fas.harvard.edu 2.4.18-27.8.0smp #1 SMP Fri Mar 14 07:13:13 EST 2003 i686 athlon i386 GNU/Linux Tue Jun 5 11:11:57 EDT 2007 %%% --------------------------------- %% % temporary matlab script for intergroupavg-sess % /tmp/LowTrauma_v_HighTrauma3582_iga.m global QuitOnError; QuitOnError = 1; if(exist('fast_intergroupavg')==0) qoe('ERROR: matlab path incorrect');end; cd /net/tucson/Raid/shared/exp/REfMRI/fMRI_FPPREW/functional; fast_intergroupavg(... '-avg1', 'LowTrauma/bold/taumax30_stc_smooth6/tal-rfx/all_v_fix/avg', ... '-std1', 'LowTrauma/bold/taumax30_stc_smooth6/tal-rfx/all_v_fix/std', ... '-avg2', 'HighTrauma/bold/taumax30_stc_smooth6/tal-rfx/all_v_fix/avg', ... '-std2', 'HighTrauma/bold/taumax30_stc_smooth6/tal-rfx/all_v_fix/std', ... '-tsig', 'LowTrauma_v_HighTrauma/bold/taumax30_stc_smooth6/tal-rfx/all_v_fix/sig', ... '-tminsig', 'LowTrauma_v_HighTrauma/bold/taumax30_stc_smooth6/tal-rfx/all_v_fix/minsig', ... '-polarity', '0', ... '-polarity2', '0' ... );
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>> >> >> >> >> Parsing Arguments
Checking Parameters SynthSeed = 0 _______________________________________________ Intergroup Averaging Parameters avg1id LowTrauma/bold/taumax30_stc_smooth6/tal-rfx/all_v_fix/avg std1id LowTrauma/bold/taumax30_stc_smooth6/tal-rfx/all_v_fix/std dof1 4 avg2id HighTrauma/bold/taumax30_stc_smooth6/tal-rfx/all_v_fix/avg std2id HighTrauma/bold/taumax30_stc_smooth6/tal-rfx/all_v_fix/std dof2 17 tid tsigid LowTrauma_v_HighTrauma/bold/taumax30_stc_smooth6/tal-rfx/all_v_fix/sig tminsigid LowTrauma_v_HighTrauma/bold/taumax30_stc_smooth6/tal-rfx/all_v_fix/minsig synth _______________________________________________ 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 fast_intergroupavg Completed
Tue Jun 5 11:13:17 EDT 2007 intergroup-sess completed SUCCESSFULLY
freesurfer@nmr.mgh.harvard.edu
-
Avram Holmes -
Doug Greve