Brian,
Glad it worked. Clearly that portion of the script needs to be updated
for better compatibility.
The messages you are seeing (about nu_8_dxyz.mnc and COR-.info) can be
ignored, as they are not errors. In the newest dev release, these
messages have been suppressed, because they do not indicate any useful
information and give the impression of errors. You do not need to get
this new dev release though, as your current release produces valid
average surface and volume files.
Nick
On Fri, 2005-10-07 at 16:36 -0700, Brian Schweinsburg, Ph.D. wrote:
> Nick,
> This appears to have done the trick. Make_average_subject ran and created
> the surfaces. It echos the following error message many times, but I assume
> this does not matter as it occurs with recon-all as well: INFO: Volume
> /tmp/mritotal_9750/nu_8_dxyz.mnc cannot be found.
>
> It also specifies the following and created an error log (that later
> disappeared) saying:
> INFO: Volume unknown cannot be found.
> INFO: Volume unknown cannot be found.
> corRead(): can't open file ./../mri/orig/COR-.info
>
> I assume that this is because I am using mgz files rather than COR? The
> appropriate volumes were written out in mgz format.
>
> The volumes and surfaces look okay to me.
>
> I included the make_average log file below in case there was something
> specific that you wanted to see.
>
> Thanks for your help.
>
> Brian
>
> ***********make_average log file*****************
> Fri Oct 7 16:23:33 PDT 2005
> /apps/freesurfer/subjects
> /apps/freesurfer/bin//make_average_volume
> --out test --subjects SC011 SC012 SC013
> setenv SUBJECTS_DIR /apps/freesurfer/subjects
> SC011 SC012 SC013
> mri_convert /apps/freesurfer/subjects/SC011/mri/orig.mgz
> /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/orig-SC011.mgz
> --apply_transform
> /apps/freesurfer/subjects/SC011/mri/transforms/talairach.xfm -oc 0 0 0
> --devolvexfm SC011
> mri_convert /apps/freesurfer/subjects/SC011/mri/orig.mgz
> /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/orig-SC011.mgz
> --apply_transform
> /apps/freesurfer/subjects/SC011/mri/transforms/talairach.xfm -oc 0 0 0
> --devolvexfm SC011
> reading from /apps/freesurfer/subjects/SC011/mri/orig.mgz...
> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (-1, 0, 0)
> j_ras = (0, 0, -1)
> k_ras = (0, 1, 0)
> INFO: Applying transformation from file
> /apps/freesurfer/subjects/SC011/mri/transforms/talairach.xfm...
> Reading transform
> INFO: devolving XFM (SC011)
> -------- before ---------
> 1.078 -0.019 -0.014 0.327;
> 0.020 1.035 0.187 -11.399;
> 0.010 -0.185 1.025 -15.094;
> 0.000 0.000 0.000 1.000;
> Trying /apps/freesurfer/subjects/SC011/mri/orig
> Trying /apps/freesurfer/subjects/SC011/mri/orig.mgz
> -------- after ---------
> 1.078 -0.019 -0.014 0.812;
> 0.020 1.035 0.187 -11.390;
> 0.010 -0.185 1.025 -15.089;
> 0.000 0.000 0.000 1.000;
> -----------------
> ---------------------------------
> INFO: Transform Matrix
> 1.078 -0.019 -0.014 0.812;
> 0.020 1.035 0.187 -11.390;
> 0.010 -0.185 1.025 -15.089;
> 0.000 0.000 0.000 1.000;
> ---------------------------------
> Reslicing using trilinear interpolation
> writing to
> /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/orig-SC011.mgz...
> mri_convert /apps/freesurfer/subjects/SC012/mri/orig.mgz
> /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/orig-SC012.mgz
> --apply_transform
> /apps/freesurfer/subjects/SC012/mri/transforms/talairach.xfm -oc 0 0 0
> --devolvexfm SC012
> mri_convert /apps/freesurfer/subjects/SC012/mri/orig.mgz
> /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/orig-SC012.mgz
> --apply_transform
> /apps/freesurfer/subjects/SC012/mri/transforms/talairach.xfm -oc 0 0 0
> --devolvexfm SC012
> reading from /apps/freesurfer/subjects/SC012/mri/orig.mgz...
> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (-1, 0, 0)
> j_ras = (0, 0, -1)
> k_ras = (0, 1, 0)
> INFO: Applying transformation from file
> /apps/freesurfer/subjects/SC012/mri/transforms/talairach.xfm...
> Reading transform
> INFO: devolving XFM (SC012)
> -------- before ---------
> 1.073 0.022 0.034 0.454;
> -0.028 1.071 0.189 -11.925;
> -0.034 -0.211 1.188 -18.689;
> 0.000 0.000 0.000 1.000;
> Trying /apps/freesurfer/subjects/SC012/mri/orig
> Trying /apps/freesurfer/subjects/SC012/mri/orig.mgz
> -------- after ---------
> 1.073 0.022 0.034 0.401;
> -0.028 1.071 0.189 -11.924;
> -0.034 -0.211 1.188 -18.687;
> 0.000 0.000 0.000 1.000;
> -----------------
> ---------------------------------
> INFO: Transform Matrix
> 1.073 0.022 0.034 0.401;
> -0.028 1.071 0.189 -11.924;
> -0.034 -0.211 1.188 -18.687;
> 0.000 0.000 0.000 1.000;
> ---------------------------------
> Reslicing using trilinear interpolation
> writing to
> /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/orig-SC012.mgz...
> mri_convert /apps/freesurfer/subjects/SC013/mri/orig.mgz
> /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/orig-SC013.mgz
> --apply_transform
> /apps/freesurfer/subjects/SC013/mri/transforms/talairach.xfm -oc 0 0 0
> --devolvexfm SC013
> mri_convert /apps/freesurfer/subjects/SC013/mri/orig.mgz
> /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/orig-SC013.mgz
> --apply_transform
> /apps/freesurfer/subjects/SC013/mri/transforms/talairach.xfm -oc 0 0 0
> --devolvexfm SC013
> reading from /apps/freesurfer/subjects/SC013/mri/orig.mgz...
> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (-1, 0, 0)
> j_ras = (0, 0, -1)
> k_ras = (0, 1, 0)
> INFO: Applying transformation from file
> /apps/freesurfer/subjects/SC013/mri/transforms/talairach.xfm...
> Reading transform
> INFO: devolving XFM (SC013)
> -------- before ---------
> 1.118 -0.032 -0.017 -0.677;
> 0.032 1.031 0.204 -17.741;
> 0.010 -0.214 1.079 -9.616;
> 0.000 0.000 0.000 1.000;
> Trying /apps/freesurfer/subjects/SC013/mri/orig
> Trying /apps/freesurfer/subjects/SC013/mri/orig.mgz
> -------- after ---------
> 1.118 -0.032 -0.017 2.509;
> 0.032 1.031 0.204 -17.650;
> 0.010 -0.214 1.079 -9.587;
> 0.000 0.000 0.000 1.000;
> -----------------
> ---------------------------------
> INFO: Transform Matrix
> 1.118 -0.032 -0.017 2.509;
> 0.032 1.031 0.204 -17.650;
> 0.010 -0.214 1.079 -9.587;
> 0.000 0.000 0.000 1.000;
> ---------------------------------
> Reslicing using trilinear interpolation
> writing to
> /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/orig-SC013.mgz...
> mri_average
> /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/orig-SC011.mgz
> /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/orig-SC012.mgz
> /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/orig-SC013.mgz
> /apps/freesurfer/subjects/test/mri/orig.mgz
> mri_convert /apps/freesurfer/subjects/SC011/mri/T1.mgz
> /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/T1-SC011.mgz
> --apply_transform
> /apps/freesurfer/subjects/SC011/mri/transforms/talairach.xfm -oc 0 0 0
> --devolvexfm SC011
> mri_convert /apps/freesurfer/subjects/SC011/mri/T1.mgz
> /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/T1-SC011.mgz
> --apply_transform
> /apps/freesurfer/subjects/SC011/mri/transforms/talairach.xfm -oc 0 0 0
> --devolvexfm SC011
> reading from /apps/freesurfer/subjects/SC011/mri/T1.mgz...
> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (-1, 0, 0)
> j_ras = (0, 0, -1)
> k_ras = (0, 1, 0)
> INFO: Applying transformation from file
> /apps/freesurfer/subjects/SC011/mri/transforms/talairach.xfm...
> Reading transform
> INFO: devolving XFM (SC011)
> -------- before ---------
> 1.078 -0.019 -0.014 0.327;
> 0.020 1.035 0.187 -11.399;
> 0.010 -0.185 1.025 -15.094;
> 0.000 0.000 0.000 1.000;
> Trying /apps/freesurfer/subjects/SC011/mri/orig
> Trying /apps/freesurfer/subjects/SC011/mri/orig.mgz
> -------- after ---------
> 1.078 -0.019 -0.014 0.812;
> 0.020 1.035 0.187 -11.390;
> 0.010 -0.185 1.025 -15.089;
> 0.000 0.000 0.000 1.000;
> -----------------
> ---------------------------------
> INFO: Transform Matrix
> 1.078 -0.019 -0.014 0.812;
> 0.020 1.035 0.187 -11.390;
> 0.010 -0.185 1.025 -15.089;
> 0.000 0.000 0.000 1.000;
> ---------------------------------
> Reslicing using trilinear interpolation
> writing to
> /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/T1-SC011.mgz...
> mri_convert /apps/freesurfer/subjects/SC012/mri/T1.mgz
> /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/T1-SC012.mgz
> --apply_transform
> /apps/freesurfer/subjects/SC012/mri/transforms/talairach.xfm -oc 0 0 0
> --devolvexfm SC012
> mri_convert /apps/freesurfer/subjects/SC012/mri/T1.mgz
> /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/T1-SC012.mgz
> --apply_transform
> /apps/freesurfer/subjects/SC012/mri/transforms/talairach.xfm -oc 0 0 0
> --devolvexfm SC012
> reading from /apps/freesurfer/subjects/SC012/mri/T1.mgz...
> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (-1, 0, 0)
> j_ras = (0, 0, -1)
> k_ras = (0, 1, 0)
> INFO: Applying transformation from file
> /apps/freesurfer/subjects/SC012/mri/transforms/talairach.xfm...
> Reading transform
> INFO: devolving XFM (SC012)
> -------- before ---------
> 1.073 0.022 0.034 0.454;
> -0.028 1.071 0.189 -11.925;
> -0.034 -0.211 1.188 -18.689;
> 0.000 0.000 0.000 1.000;
> Trying /apps/freesurfer/subjects/SC012/mri/orig
> Trying /apps/freesurfer/subjects/SC012/mri/orig.mgz
> -------- after ---------
> 1.073 0.022 0.034 0.401;
> -0.028 1.071 0.189 -11.924;
> -0.034 -0.211 1.188 -18.687;
> 0.000 0.000 0.000 1.000;
> -----------------
> ---------------------------------
> INFO: Transform Matrix
> 1.073 0.022 0.034 0.401;
> -0.028 1.071 0.189 -11.924;
> -0.034 -0.211 1.188 -18.687;
> 0.000 0.000 0.000 1.000;
> ---------------------------------
> Reslicing using trilinear interpolation
> writing to
> /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/T1-SC012.mgz...
> mri_convert /apps/freesurfer/subjects/SC013/mri/T1.mgz
> /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/T1-SC013.mgz
> --apply_transform
> /apps/freesurfer/subjects/SC013/mri/transforms/talairach.xfm -oc 0 0 0
> --devolvexfm SC013
> mri_convert /apps/freesurfer/subjects/SC013/mri/T1.mgz
> /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/T1-SC013.mgz
> --apply_transform
> /apps/freesurfer/subjects/SC013/mri/transforms/talairach.xfm -oc 0 0 0
> --devolvexfm SC013
> reading from /apps/freesurfer/subjects/SC013/mri/T1.mgz...
> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (-1, 0, 0)
> j_ras = (0, 0, -1)
> k_ras = (0, 1, 0)
> INFO: Applying transformation from file
> /apps/freesurfer/subjects/SC013/mri/transforms/talairach.xfm...
> Reading transform
> INFO: devolving XFM (SC013)
> -------- before ---------
> 1.118 -0.032 -0.017 -0.677;
> 0.032 1.031 0.204 -17.741;
> 0.010 -0.214 1.079 -9.616;
> 0.000 0.000 0.000 1.000;
> Trying /apps/freesurfer/subjects/SC013/mri/orig
> Trying /apps/freesurfer/subjects/SC013/mri/orig.mgz
> -------- after ---------
> 1.118 -0.032 -0.017 2.509;
> 0.032 1.031 0.204 -17.650;
> 0.010 -0.214 1.079 -9.587;
> 0.000 0.000 0.000 1.000;
> -----------------
> ---------------------------------
> INFO: Transform Matrix
> 1.118 -0.032 -0.017 2.509;
> 0.032 1.031 0.204 -17.650;
> 0.010 -0.214 1.079 -9.587;
> 0.000 0.000 0.000 1.000;
> ---------------------------------
> Reslicing using trilinear interpolation
> writing to
> /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/T1-SC013.mgz...
> mri_average
> /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/T1-SC011.mgz
> /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/T1-SC012.mgz
> /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/T1-SC013.mgz
> /apps/freesurfer/subjects/test/mri/T1.mgz
> mri_convert /apps/freesurfer/subjects/SC011/mri/brain.mgz
> /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/brain-SC011.mgz
> --apply_transform
> /apps/freesurfer/subjects/SC011/mri/transforms/talairach.xfm -oc 0 0 0
> --devolvexfm SC011
> mri_convert /apps/freesurfer/subjects/SC011/mri/brain.mgz
> /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/brain-SC011.mgz
> --apply_transform
> /apps/freesurfer/subjects/SC011/mri/transforms/talairach.xfm -oc 0 0 0
> --devolvexfm SC011
> reading from /apps/freesurfer/subjects/SC011/mri/brain.mgz...
> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (-1, 0, 0)
> j_ras = (0, 0, -1)
> k_ras = (0, 1, 0)
> INFO: Applying transformation from file
> /apps/freesurfer/subjects/SC011/mri/transforms/talairach.xfm...
> Reading transform
> INFO: devolving XFM (SC011)
> -------- before ---------
> 1.078 -0.019 -0.014 0.327;
> 0.020 1.035 0.187 -11.399;
> 0.010 -0.185 1.025 -15.094;
> 0.000 0.000 0.000 1.000;
> Trying /apps/freesurfer/subjects/SC011/mri/orig
> Trying /apps/freesurfer/subjects/SC011/mri/orig.mgz
> -------- after ---------
> 1.078 -0.019 -0.014 0.812;
> 0.020 1.035 0.187 -11.390;
> 0.010 -0.185 1.025 -15.089;
> 0.000 0.000 0.000 1.000;
> -----------------
> ---------------------------------
> INFO: Transform Matrix
> 1.078 -0.019 -0.014 0.812;
> 0.020 1.035 0.187 -11.390;
> 0.010 -0.185 1.025 -15.089;
> 0.000 0.000 0.000 1.000;
> ---------------------------------
> Reslicing using trilinear interpolation
> writing to
> /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/brain-SC011.mgz...
> mri_convert /apps/freesurfer/subjects/SC012/mri/brain.mgz
> /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/brain-SC012.mgz
> --apply_transform
> /apps/freesurfer/subjects/SC012/mri/transforms/talairach.xfm -oc 0 0 0
> --devolvexfm SC012
> mri_convert /apps/freesurfer/subjects/SC012/mri/brain.mgz
> /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/brain-SC012.mgz
> --apply_transform
> /apps/freesurfer/subjects/SC012/mri/transforms/talairach.xfm -oc 0 0 0
> --devolvexfm SC012
> reading from /apps/freesurfer/subjects/SC012/mri/brain.mgz...
> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (-1, 0, 0)
> j_ras = (0, 0, -1)
> k_ras = (0, 1, 0)
> INFO: Applying transformation from file
> /apps/freesurfer/subjects/SC012/mri/transforms/talairach.xfm...
> Reading transform
> INFO: devolving XFM (SC012)
> -------- before ---------
> 1.073 0.022 0.034 0.454;
> -0.028 1.071 0.189 -11.925;
> -0.034 -0.211 1.188 -18.689;
> 0.000 0.000 0.000 1.000;
> Trying /apps/freesurfer/subjects/SC012/mri/orig
> Trying /apps/freesurfer/subjects/SC012/mri/orig.mgz
> -------- after ---------
> 1.073 0.022 0.034 0.401;
> -0.028 1.071 0.189 -11.924;
> -0.034 -0.211 1.188 -18.687;
> 0.000 0.000 0.000 1.000;
> -----------------
> ---------------------------------
> INFO: Transform Matrix
> 1.073 0.022 0.034 0.401;
> -0.028 1.071 0.189 -11.924;
> -0.034 -0.211 1.188 -18.687;
> 0.000 0.000 0.000 1.000;
> ---------------------------------
> Reslicing using trilinear interpolation
> writing to
> /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/brain-SC012.mgz...
> mri_convert /apps/freesurfer/subjects/SC013/mri/brain.mgz
> /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/brain-SC013.mgz
> --apply_transform
> /apps/freesurfer/subjects/SC013/mri/transforms/talairach.xfm -oc 0 0 0
> --devolvexfm SC013
> mri_convert /apps/freesurfer/subjects/SC013/mri/brain.mgz
> /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/brain-SC013.mgz
> --apply_transform
> /apps/freesurfer/subjects/SC013/mri/transforms/talairach.xfm -oc 0 0 0
> --devolvexfm SC013
> reading from /apps/freesurfer/subjects/SC013/mri/brain.mgz...
> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (-1, 0, 0)
> j_ras = (0, 0, -1)
> k_ras = (0, 1, 0)
> INFO: Applying transformation from file
> /apps/freesurfer/subjects/SC013/mri/transforms/talairach.xfm...
> Reading transform
> INFO: devolving XFM (SC013)
> -------- before ---------
> 1.118 -0.032 -0.017 -0.677;
> 0.032 1.031 0.204 -17.741;
> 0.010 -0.214 1.079 -9.616;
> 0.000 0.000 0.000 1.000;
> Trying /apps/freesurfer/subjects/SC013/mri/orig
> Trying /apps/freesurfer/subjects/SC013/mri/orig.mgz
> -------- after ---------
> 1.118 -0.032 -0.017 2.509;
> 0.032 1.031 0.204 -17.650;
> 0.010 -0.214 1.079 -9.587;
> 0.000 0.000 0.000 1.000;
> -----------------
> ---------------------------------
> INFO: Transform Matrix
> 1.118 -0.032 -0.017 2.509;
> 0.032 1.031 0.204 -17.650;
> 0.010 -0.214 1.079 -9.587;
> 0.000 0.000 0.000 1.000;
> ---------------------------------
> Reslicing using trilinear interpolation
> writing to
> /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/brain-SC013.mgz...
> mri_average
> /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/brain-SC011.mgz
> /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/brain-SC012.mgz
> /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/brain-SC013.mgz
> /apps/freesurfer/subjects/test/mri/brain.mgz
> Fri Oct 7 16:29:49 PDT 2005
> make_average_volume done
>
>
> --
> Brian C. Schweinsburg, Ph.D.
> Assistant Adjunct Professor of Psychiatry
> University of California, San Diego
> Office: 858-552-8585 x6109
> Cell: 858-354-3756
>
>
> > From: Nick Schmansky <[EMAIL PROTECTED]>
> > Date: Fri, 07 Oct 2005 18:52:12 -0400
> > To: "Brian Schweinsburg, Ph.D." <[EMAIL PROTECTED]>
> > Cc: Freesurfer Mailing List <freesurfer@nmr.mgh.harvard.edu>
> > Subject: Re: [Freesurfer] RE: make_average_surface
> >
> > This is a puzzling problem. Unfortunately I don't have access to a FC4
> > system to try to recreate what you are seeing.
> >
> > However, can you edit your make_average_subject/surface/volume scripts
> > to comment-out these lines (shown here with comment-out chars added):
> >
> > #set n = `echo $argv | grep -e --help | wc -l`
> > #if($n != 0) then
> > # set PrintHelp = 1;
> > # goto usage_exit;
> > #endif
> >
> > #set n = `echo $argv | grep -e --version | wc -l`
> > #if($n != 0) then
> > # echo $VERSION
> > # exit 0;
> > #endif
> >
> > This appears to be where your script is stopping, and I would like to
> > see what it does if it gets beyond this point.
> >
> > Thanks
> >
> > On Fri, 2005-10-07 at 15:24 -0700, Brian Schweinsburg, Ph.D. wrote:
> >> This sounds like a problem I am having, The same script works fine on my
> >> mac, but not on my FC4 machine. Here is the output, and a message I sent to
> >> before.
> >>
> >> I changed the flags to ³efxv² as Doug recommended, and here is the output
> >> for make_average_subject, make_average_volume and make_average_surface. The
> >> script doesn¹t seem to be accepting my command line arguments. I am using
> >> the current dev version on a Fedora Core 4 system, if that helps.
> >>
> >> Thanks,
> >> Brian
> >>
> >> [EMAIL PROTECTED] subjects]$ make_average_subject --out average_bcs
> >> --subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017 SC018 SC019 SC020
> >> SC021
> >> SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031 SC032 SC033 SC034 SC035
> >> SC036
> >>
> >> set VERSION = '$Id: make_average_subject,v 1.2 2005/09/09 14:37:17 nicks
> >> Exp
> >> $'
> >> set VERSION = $Id: make_average_subject,v 1.2 2005/09/09 14:37:17 nicks Exp
> >> $
> >>
> >> set PrintHelp = 0 ;
> >> set PrintHelp = 0
> >>
> >> if ( $?SUBJECTS ) then
> >> if ( 0 ) then
> >> if ( $?SUBJECTS_DIR ) then
> >> if ( 1 ) then
> >> set SUBJECTS_DIR= ( $SUBJECTS_DIR )
> >> set SUBJECTS_DIR= ( /apps/freesurfer/subjects )
> >> endif
> >> endif
> >>
> >> set average_subject=average
> >> set average_subject=average
> >> set ddir = ${SUBJECTS_DIR}/${average_subject}
> >> set ddir = /apps/freesurfer/subjects/average
> >> set transform_fname=""
> >> set transform_fname=
> >> set XFORM_FLAG=""
> >> set XFORM_FLAG=
> >>
> >> if ( $#argv == 0 ) then
> >> if ( 27 == 0 ) then
> >>
> >> set n = `echo $argv | grep -e --help | wc -l`
> >> set n = `echo $argv | grep -e --help | wc -l`
> >> echo --out average_bcs --subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017
> >> SC018 SC019 SC020 SC021 SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031
> >> SC032 SC033 SC034 SC035 SC036
> >> grep -e --help
> >> wc -l
> >>
> >> **
> >> [EMAIL PROTECTED] subjects]$ make_average_volume --out average_bcs
> >> --subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017 SC018 SC019 SC020
> >> SC021
> >> SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031 SC032 SC033 SC034 SC035
> >> SC036
> >>
> >> set VERSION = '$Id: make_average_volume,v 1.2 2005/08/19 21:27:19 greve Exp
> >> $' ;
> >> set VERSION = $Id: make_average_volume,v 1.2 2005/08/19 21:27:19 greve Exp
> >> $
> >>
> >> set PrintHelp = 0 ;
> >> set PrintHelp = 0
> >> set cleanup = 0 ;
> >> set cleanup = 0
> >> set transform_fname = talairach.xfm
> >> set transform_fname = talairach.xfm
> >>
> >> if ( $?SUBJECTS ) then
> >> if ( 0 ) then
> >> if ( $?SUBJECTS_DIR ) then
> >> if ( 1 ) then
> >> set SUBJECTS_DIR= ( $SUBJECTS_DIR )
> >> set SUBJECTS_DIR= ( /apps/freesurfer/subjects )
> >> endif
> >> endif
> >>
> >> set average_subject = average
> >> set average_subject = average
> >>
> >> set cmdargs = ( $argv ) ;
> >> set cmdargs = ( --out average_bcs --subjects SC010 SC011 SC012 SC013 SC015
> >> SC016 SC017 SC018 SC019 SC020 SC021 SC022 SC023 SC024 SC025 SC026 SC027
> >> SC030 SC031 SC032 SC033 SC034 SC035 SC036 )
> >> if ( $#argv == 0 ) then
> >> if ( 27 == 0 ) then
> >>
> >> set n = `echo $argv | grep -e --help | wc -l`
> >> set n = `echo $argv | grep -e --help | wc -l`
> >> echo --out average_bcs --subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017
> >> SC018 SC019 SC020 SC021 SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031
> >> SC032 SC033 SC034 SC035 SC036
> >> grep -e --help
> >> wc -l
> >>
> >> **
> >> [EMAIL PROTECTED] subjects]$ make_average_surface --out average_bcs
> >> --subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017 SC018 SC019 SC020
> >> SC021
> >> SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031 SC032 SC033 SC034 SC035
> >> SC036
> >> set VERSION = '$Id: make_average_surface,v 1.10 2005/08/19 21:36:46 greve
> >> Exp $' ;
> >> set VERSION = $Id: make_average_surface,v 1.10 2005/08/19 21:36:46 greve
> >> Exp
> >> $
> >>
> >> set PrintHelp = 0 ;
> >> set PrintHelp = 0
> >>
> >> if ( $?SUBJECTS ) then
> >> if ( 0 ) then
> >> if ( $?SUBJECTS_DIR ) then
> >> if ( 1 ) then
> >> set SUBJECTS_DIR= ( $SUBJECTS_DIR )
> >> set SUBJECTS_DIR= ( /apps/freesurfer/subjects )
> >> endif
> >> endif
> >>
> >> set average_subject=average
> >> set average_subject=average
> >> set ddir = ${SUBJECTS_DIR}/${average_subject}
> >> set ddir = /apps/freesurfer/subjects/average
> >> set transform_fname=""
> >> set transform_fname=
> >> set XFORM_FLAG=""
> >> set XFORM_FLAG=
> >>
> >> if ( $#argv == 0 ) then
> >> if ( 27 == 0 ) then
> >>
> >> set n = `echo $argv | grep -e --help | wc -l`
> >> set n = `echo $argv | grep -e --help | wc -l`
> >> echo --out average_bcs --subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017
> >> SC018 SC019 SC020 SC021 SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031
> >> SC032 SC033 SC034 SC035 SC036
> >> grep -e --help
> >> wc -l
> >>
> >>
> >>
> >>
> >>
> >>
> >> From: Doug Greve <[EMAIL PROTECTED]>
> >> Date: Tue, 27 Sep 2005 15:04:59 -0400
> >> To: "Brian Schweinsburg, Ph.D." <[EMAIL PROTECTED]>
> >> Cc: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
> >> Subject: Re: [Freesurfer] make_average_subject error?
> >>
> >>
> >> Try editing those scripts so that the first line is:
> >>
> >> #!/bin/tcsh -efxv
> >>
> >> ie, adding "xv"
> >>
> >> This turns on all kinds of debugging
> >>
> >>
> >> Brian Schweinsburg, Ph.D. wrote:
> >>> Re: [Freesurfer] make_average_subject error? Hi Doug,
> >>> The same thing happens when I try to run them separately. It exits to the
> >>> prompt with no messages.
> >>>
> >>> Brian
> >>>
> >>> --
> >>> Brian C. Schweinsburg, Ph.D.
> >>> Assistant Adjunct Professor of Psychiatry
> >>> University of California, San Diego
> >>> Office: 858-552-8585 x6109
> >>> Cell: 858-354-3756
> >>>
> >>>
> >>>
> >>>
> >>> From: Doug Greve <[EMAIL PROTECTED]>
> >>> <mailto:[EMAIL PROTECTED]>
> >>> Date: Tue, 27 Sep 2005 11:16:00 -0400
> >>> To: "Brian Schweinsburg, Ph.D." <[EMAIL PROTECTED]>
> >>> <mailto:[EMAIL PROTECTED]>
> >>> Cc: "freesurfer@nmr.mgh.harvard.edu"
> >>> <mailto:freesurfer@nmr.mgh.harvard.edu>
> >>> <freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu>
> >>> Subject: Re: [Freesurfer] make_average_subject error?
> >>>
> >>>
> >>> Can you run make_average_surface and make_average_volume separately?
> >>>
> >>> Brian Schweinsburg, Ph.D. wrote:
> >>>
> >>>>
> >>>> I ran it with make_average_subject --debug \
> >>>> --subjects SC010 SC012 ...
> >>>>
> >>>> I also tried it with --echo. It provides no output.
> >>>>
> >>>> I checked the script and it is executable. I looked through the code and
> >>>> everything seems reasonable given my system except the part that says:
> >>>> "if person = brian; exit 0"
> >>>>
> >>>> Brian
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>>
> >>>>> From: Doug Greve <[EMAIL PROTECTED]>
> >>>>> <mailto:[EMAIL PROTECTED]> <mailto:[EMAIL PROTECTED]>
> >>>>> Date: Mon, 26 Sep 2005 16:40:48 -0400
> >>>>> To: "Brian Schweinsburg, Ph.D." <[EMAIL PROTECTED]>
> >>>>> <mailto:[EMAIL PROTECTED]> <mailto:[EMAIL PROTECTED]>
> >>>>> Cc: "freesurfer@nmr.mgh.harvard.edu"
> >>>>> <mailto:freesurfer@nmr.mgh.harvard.edu>
> >>>>> <mailto:freesurfer@nmr.mgh.harvard.edu>
> >>>>> <freesurfer@nmr.mgh.harvard.edu>
> >>>>> <mailto:freesurfer@nmr.mgh.harvard.edu>
> >>>>> <mailto:freesurfer@nmr.mgh.harvard.edu>
> >>>>> Subject: Re: [Freesurfer] make_average_subject error?
> >>>>>
> >>>>>
> >>>>> try running it with --debug and send us the output
> >>>>>
> >>>>> Brian Schweinsburg, Ph.D. wrote:
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>>
> >>>>>> Hi Folks,
> >>>>>>
> >>>>>> I tried running the latest make_average_subject script (and the
> >>>>>> make_average_surface/volume scripts) using the expected command line
> >>>>>> syntax
> >>>>>> and after hitting enter it immediately exits to the csh without error,
> >>>>>> but
> >>>>>> does not produce anything.
> >>>>>>
> >>>>>> make_average_subject --subjects SC010 SC011 SC012 ...
> >>>>>>
> >>>>>> I am running the latested dev release with Fedora Core 4.
> >>>>>>
> >>>>>> Any ideas as to the problem?
> >>>>>> Brian
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> _______________________________________________
> >>>>>> 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
> >>>>> [EMAIL PROTECTED]
> >>>>> Phone Number: 617-724-2358
> >>>>> Fax: 617-726-7422
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> 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
> >>> [EMAIL PROTECTED]
> >>> Phone Number: 617-724-2358
> >>> Fax: 617-726-7422
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> _______________________________________________
> >>> 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
> >> [EMAIL PROTECTED]
> >> Phone Number: 617-724-2358
> >> Fax: 617-726-7422
> >>
> >>
> >>
> >> --
> >> Brian C. Schweinsburg, Ph.D.
> >> Assistant Adjunct Professor of Psychiatry
> >> University of California, San Diego
> >> Office: 858-552-8585 x6109
> >> Cell: 858-354-3756
> >>
> >>
> >>> From: Nick Schmansky <[EMAIL PROTECTED]>
> >>> Date: Fri, 07 Oct 2005 18:04:25 -0400
> >>> To: Antao Du <[EMAIL PROTECTED]>
> >>> Cc: Freesurfer Mailing List <freesurfer@nmr.mgh.harvard.edu>
> >>> Subject: Re: [Freesurfer] RE: make_average_surface
> >>>
> >>> Add --echo to the command to print its activity, and then send me the
> >>> output.
> >>>
> >>> On Fri, 2005-10-07 at 15:00 -0700, Antao Du wrote:
> >>>> Hi, When I run make_average_surface --subjects AD1293 AD1297 AD1299 --out
> >>>> average_cn, it finished within 1 second without any output and any error
> >>>> message. I don't know what is wrong. Any helps there?
> >>>>
> >>>> I have not updated my freesurface so I downloaded make_average_surface
> >>>> from
> >>>> a post by Nick in July, 2005.
> >>>>
> >>>> Thanks,
> >>>>
> >>>> Antao
> >>>>
> >>>> _______________________________________________
> >>>> Freesurfer mailing list
> >>>> Freesurfer@nmr.mgh.harvard.edu
> >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>>>
> >>>>
> >>>
> >>> _______________________________________________
> >>> Freesurfer mailing list
> >>> Freesurfer@nmr.mgh.harvard.edu
> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>
> >>
> >>
> >> _______________________________________________
> >> Freesurfer mailing list
> >> Freesurfer@nmr.mgh.harvard.edu
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>
> >>
> >
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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