Re: [Freesurfer] Make_average_subject
Alex,
The make_average_ scripts are such that they will exit on any
error encountered (via the -e arg to tcsh at the top of the script).
It appears make_average_surface is exiting after executing the command:
id | tee -
a
/data/kang/work/struct/alex/freesurfer/subjects_cann/testavg/scripts/make_average_surface.log
Can you run the above command (after fixing where it was cut-off in this
email) and then run:
echo $status
after that. It will probably not display 0. Is the disk full where
that log file is being written to? I am trying to think of reasons why
'id' would exit with a non-zero status.
Nick
On Fri, 2007-10-26 at 12:21 +1000, Alexander Fornito wrote:
> Sorry, I ran the --debug flag after running the first command. It is not
> the cause of the error. Here is the output after testavg has been deleted.
>
>
> make_average_surface --subjects cann01 cann02 cann04 cann05 cann06 cann07
> cann08 cann09 cann10 cann13 cann14 cann15 cann16 cann17 cann18 cann19
> cann20 cann21 cann22 cann23 cann24 cann25 cann27 cann28 cann29 cann30
> cann31 cann32 cann33 cann34 cann35 cann36 cann37 cann38 cann39 cann40
> cann41 cann43 cann44 cann46 cann47 cann48 cann49 cann50 cann51 cann52
> cann53 cann54 cann55 cann56 --out testavg --debug
> set verbose = 1
> if ( $getting_subjects ) then
> if ( 0 ) then
> breaksw
> breaksw
>
> end
> end
> while ( $#argv != 0 )
> while ( 0 != 0 )
>
> goto parse_args_return ;
> goto parse_args_return
>
> goto check_params ;
> goto check_params
> if ( ! $?SUBJECTS ) then
> if ( ! 1 ) then
> if ( ! $?SUBJECTS_DIR ) then
> if ( ! 1 ) then
> if ( ! -e $SUBJECTS_DIR ) then
> if ( ! -e /data/kang/work/struct/alex/freesurfer/subjects_cann ) then
> if ( ! $?FREESURFER_HOME ) then
> if ( ! 1 ) then
> if ( ! -e $FREESURFER_HOME ) then
> if ( ! -e /usr/local/freesurfer_4.0 ) then
> if ( $#sdout == 0 ) set sdout = $SUBJECTS_DIR ;
> if ( 0 == 0 ) set sdout =
> /data/kang/work/struct/alex/freesurfer/subjects_cann
> set sdout = /data/kang/work/struct/alex/freesurfer/subjects_cann
> goto check_params_return ;
> goto check_params_return
>
>
>
> set ddir = ${sdout}/${average_subject}
> set ddir = /data/kang/work/struct/alex/freesurfer/subjects_cann/testavg
>
> mkdir -p ${ddir} ${ddir}/surf ${ddir}/mri ${ddir}/mri/transforms
> ${ddir}/scripts ${ddir}/label ${ddir}/stats
> mkdir -p /data/kang/work/struct/alex/freesurfer/subjects_cann/testavg
> /data/kang/work/struct/alex/freesurfer/subjects_cann/testavg/surf
> /data/kang/work/struct/alex/freesurfer/subjects_cann/testavg/mri
> /data/kang/work/struct/alex/freesurfer/subjects_cann/testavg/mri/transforms
> /data/kang/work/struct/alex/freesurfer/subjects_cann/testavg/scripts
> /data/kang/work/struct/alex/freesurfer/subjects_cann/testavg/label
> /data/kang/work/struct/alex/freesurfer/subjects_cann/testavg/stats
>
> set LF = ${ddir}/scripts/make_average_surface.log
> set LF =
> /data/kang/work/struct/alex/freesurfer/subjects_cann/testavg/scripts/make_average_surface.log
> if ( -e $LF ) mv $LF $LF.bak
> if ( -e
> /data/kang/work/struct/alex/freesurfer/subjects_cann/testavg/scripts/make_average_surface.log
> ) mv
> /data/kang/work/struct/alex/freesurfer/subjects_cann/testavg/scripts/make_average_surface.log
> /data/kang/work/struct/alex/freesurfer/subjects_cann/testavg/scripts/make_average_surface.log.bak
>
> echo $VERSION | tee -a $LF
> echo $Id: make_average_surface,v 1.39 2007/08/13 20:54:29 greve Exp $
> tee -a
> /data/kang/work/struct/alex/freesurfer/subjects_cann/testavg/scripts/make_average_surface.log
> $Id: make_average_surface,v 1.39 2007/08/13 20:54:29 greve Exp $
> date | tee -a $LF
> date
> tee -a
> /data/kang/work/struct/alex/freesurfer/subjects_cann/testavg/scripts/make_average_surface.log
> Fri Oct 26 12:30:42 EST 2007
> pwd | tee -a $LF
> pwd
> tee -a
> /data/kang/work/struct/alex/freesurfer/subjects_cann/testavg/scripts/make_average_surface.log
> /data/kang/work/struct/alex/freesurfer/subjects_cann
> echo "setenv SUBJECTS_DIR $SUBJECTS_DIR" | tee -a $LF
> echo setenv SUBJECTS_DIR /data/kang/work/struct/alex/freesurfer/subjects_cann
> tee -a
> /data/kang/work/struct/alex/freesurfer/subjects_cann/testavg/scripts/make_average_surface.log
> setenv SUBJECTS_DIR /data/kang/work/struct/alex/freesurfer/subjects_cann
> echo "output ddir is $sdout" | tee -a $LF
> echo output ddir is /data/kang/work/struct/alex/freesurfer/subjects_cann
> tee -a
> /data/kang/work/struct/alex/freesurfer/subjects_cann/testavg/scripts/make_average_surface.log
> output ddir is /data/kang/work/struct/alex/freesurfer/subjects_cann
> id | tee -a $LF
> id
> tee -a
> /data/kang/work/struct/alex/freesurfer/subjects_cann/testavg/scripts/make_average_surface.log
> uid=1003(alex) gid=1003 groups=200(mnc),201(fmri),1003
>
>
>
>
> > Alex,
> >
> > It looks like the subject 'testavg' already exists. To overwrite it,
> > add --force to the make_average_subject, or choose a different name for
> > the --out arg (or delete the 'testavg' subject).
> >
> > Nick
> >
> >
> > On
Re: [Freesurfer] Make_average_subject
Sorry, I ran the --debug flag after running the first command. It is not
the cause of the error. Here is the output after testavg has been deleted.
make_average_surface --subjects cann01 cann02 cann04 cann05 cann06 cann07
cann08 cann09 cann10 cann13 cann14 cann15 cann16 cann17 cann18 cann19
cann20 cann21 cann22 cann23 cann24 cann25 cann27 cann28 cann29 cann30
cann31 cann32 cann33 cann34 cann35 cann36 cann37 cann38 cann39 cann40
cann41 cann43 cann44 cann46 cann47 cann48 cann49 cann50 cann51 cann52
cann53 cann54 cann55 cann56 --out testavg --debug
set verbose = 1
if ( $getting_subjects ) then
if ( 0 ) then
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 0 != 0 )
goto parse_args_return ;
goto parse_args_return
goto check_params ;
goto check_params
if ( ! $?SUBJECTS ) then
if ( ! 1 ) then
if ( ! $?SUBJECTS_DIR ) then
if ( ! 1 ) then
if ( ! -e $SUBJECTS_DIR ) then
if ( ! -e /data/kang/work/struct/alex/freesurfer/subjects_cann ) then
if ( ! $?FREESURFER_HOME ) then
if ( ! 1 ) then
if ( ! -e $FREESURFER_HOME ) then
if ( ! -e /usr/local/freesurfer_4.0 ) then
if ( $#sdout == 0 ) set sdout = $SUBJECTS_DIR ;
if ( 0 == 0 ) set sdout =
/data/kang/work/struct/alex/freesurfer/subjects_cann
set sdout = /data/kang/work/struct/alex/freesurfer/subjects_cann
goto check_params_return ;
goto check_params_return
set ddir = ${sdout}/${average_subject}
set ddir = /data/kang/work/struct/alex/freesurfer/subjects_cann/testavg
mkdir -p ${ddir} ${ddir}/surf ${ddir}/mri ${ddir}/mri/transforms
${ddir}/scripts ${ddir}/label ${ddir}/stats
mkdir -p /data/kang/work/struct/alex/freesurfer/subjects_cann/testavg
/data/kang/work/struct/alex/freesurfer/subjects_cann/testavg/surf
/data/kang/work/struct/alex/freesurfer/subjects_cann/testavg/mri
/data/kang/work/struct/alex/freesurfer/subjects_cann/testavg/mri/transforms
/data/kang/work/struct/alex/freesurfer/subjects_cann/testavg/scripts
/data/kang/work/struct/alex/freesurfer/subjects_cann/testavg/label
/data/kang/work/struct/alex/freesurfer/subjects_cann/testavg/stats
set LF = ${ddir}/scripts/make_average_surface.log
set LF =
/data/kang/work/struct/alex/freesurfer/subjects_cann/testavg/scripts/make_average_surface.log
if ( -e $LF ) mv $LF $LF.bak
if ( -e
/data/kang/work/struct/alex/freesurfer/subjects_cann/testavg/scripts/make_average_surface.log
) mv
/data/kang/work/struct/alex/freesurfer/subjects_cann/testavg/scripts/make_average_surface.log
/data/kang/work/struct/alex/freesurfer/subjects_cann/testavg/scripts/make_average_surface.log.bak
echo $VERSION | tee -a $LF
echo $Id: make_average_surface,v 1.39 2007/08/13 20:54:29 greve Exp $
tee -a
/data/kang/work/struct/alex/freesurfer/subjects_cann/testavg/scripts/make_average_surface.log
$Id: make_average_surface,v 1.39 2007/08/13 20:54:29 greve Exp $
date | tee -a $LF
date
tee -a
/data/kang/work/struct/alex/freesurfer/subjects_cann/testavg/scripts/make_average_surface.log
Fri Oct 26 12:30:42 EST 2007
pwd | tee -a $LF
pwd
tee -a
/data/kang/work/struct/alex/freesurfer/subjects_cann/testavg/scripts/make_average_surface.log
/data/kang/work/struct/alex/freesurfer/subjects_cann
echo "setenv SUBJECTS_DIR $SUBJECTS_DIR" | tee -a $LF
echo setenv SUBJECTS_DIR /data/kang/work/struct/alex/freesurfer/subjects_cann
tee -a
/data/kang/work/struct/alex/freesurfer/subjects_cann/testavg/scripts/make_average_surface.log
setenv SUBJECTS_DIR /data/kang/work/struct/alex/freesurfer/subjects_cann
echo "output ddir is $sdout" | tee -a $LF
echo output ddir is /data/kang/work/struct/alex/freesurfer/subjects_cann
tee -a
/data/kang/work/struct/alex/freesurfer/subjects_cann/testavg/scripts/make_average_surface.log
output ddir is /data/kang/work/struct/alex/freesurfer/subjects_cann
id | tee -a $LF
id
tee -a
/data/kang/work/struct/alex/freesurfer/subjects_cann/testavg/scripts/make_average_surface.log
uid=1003(alex) gid=1003 groups=200(mnc),201(fmri),1003
> Alex,
>
> It looks like the subject 'testavg' already exists. To overwrite it,
> add --force to the make_average_subject, or choose a different name for
> the --out arg (or delete the 'testavg' subject).
>
> Nick
>
>
> On Fri, 2007-10-26 at 11:03 +1000, Alexander Fornito wrote:
>> Hi all,
>> I've been having problems with make_average_subject. The command and
>> error
>> are below. Below this is the same command with the output generated by
>> the
>> --debug flag.
>>
>> I am running version 4.0 (redhat) on Linux Debian.
>>
>> I'd appreciate any help on this.
>> Thanks,
>> Alex
>>
>>
>>
>> make_average_surface --subjects cann01 cann02 cann04 cann05 cann06
>> cann07
>> cann08 cann09 cann10 cann13 cann14 cann15 cann16 cann17 cann18 cann19
>> cann20 cann21 cann22 cann23 cann24 cann25 cann27 cann28 cann29 cann30
>> cann31 cann32 cann33 cann34 cann35 cann36 cann37 cann38 cann39 cann40
>> cann41 cann43 cann44 cann46 cann47 cann48 cann49 cann50 cann51 cann52
>> cann53 cann54 cann55 cann56 --out testavg
>> $Id: make_average_surface,v 1.39 2007/08/13 20:54:29 greve Exp $
>> Fri Oct 26 11:03:31 EST 2007
>> /data/kang/wor
Re: [Freesurfer] Make_average_subject
Alex, It looks like the subject 'testavg' already exists. To overwrite it, add --force to the make_average_subject, or choose a different name for the --out arg (or delete the 'testavg' subject). Nick On Fri, 2007-10-26 at 11:03 +1000, Alexander Fornito wrote: > Hi all, > I've been having problems with make_average_subject. The command and error > are below. Below this is the same command with the output generated by the > --debug flag. > > I am running version 4.0 (redhat) on Linux Debian. > > I'd appreciate any help on this. > Thanks, > Alex > > > > make_average_surface --subjects cann01 cann02 cann04 cann05 cann06 cann07 > cann08 cann09 cann10 cann13 cann14 cann15 cann16 cann17 cann18 cann19 > cann20 cann21 cann22 cann23 cann24 cann25 cann27 cann28 cann29 cann30 > cann31 cann32 cann33 cann34 cann35 cann36 cann37 cann38 cann39 cann40 > cann41 cann43 cann44 cann46 cann47 cann48 cann49 cann50 cann51 cann52 > cann53 cann54 cann55 cann56 --out testavg > $Id: make_average_surface,v 1.39 2007/08/13 20:54:29 greve Exp $ > Fri Oct 26 11:03:31 EST 2007 > /data/kang/work/struct/alex/freesurfer/subjects_cann > setenv SUBJECTS_DIR /data/kang/work/struct/alex/freesurfer/subjects_cann > output ddir is /data/kang/work/struct/alex/freesurfer/subjects_cann > uid=1003(alex) gid=1003 groups=200(mnc),201(fmri),1003 > > > > > make_average_subject --subjects cann01 cann02 cann04 cann05 cann06 cann07 > cann08 cann09 cann10 cann13 cann14 cann15 cann16 cann17 cann18 cann19 > cann20 cann21 cann22 cann23 cann24 cann25 cann27 cann28 cann29 cann30 > cann31 cann32 cann33 cann34 cann35 cann36 cann37 cann38 cann39 cann40 > cann41 cann43 cann44 cann46 cann47 cann48 cann49 cann50 cann51 cann52 > cann53 cann54 cann55 cann56 --out testavg --debug > set verbose = 1 > breaksw > breaksw > > end > end > while ( $#argv != 0 ) > while ( 0 != 0 ) > goto parse_args_return ; > goto parse_args_return > > goto check_params ; > goto check_params > if ( ! $?SUBJECTS_DIR ) then > if ( ! 1 ) then > if ( ! -e $SUBJECTS_DIR ) then > if ( ! -e /data/kang/work/struct/alex/freesurfer/subjects_cann ) then > if ( ! $?FREESURFER_HOME ) then > if ( ! 1 ) then > if ( ! -e $FREESURFER_HOME ) then > if ( ! -e /usr/local/freesurfer_4.0 ) then > if ( $#sdout == 0 ) set sdout = $SUBJECTS_DIR > if ( 0 == 0 ) set sdout = > /data/kang/work/struct/alex/freesurfer/subjects_cann > set sdout = /data/kang/work/struct/alex/freesurfer/subjects_cann > set outdir = $sdout/$average_subject > set outdir = /data/kang/work/struct/alex/freesurfer/subjects_cann/testavg > if ( -e $outdir && ! $Force ) then > if ( -e /data/kang/work/struct/alex/freesurfer/subjects_cann/testavg && ! > 0 ) then > echo "ERROR: $outdir already exists, select a new average subject name" > echo ERROR: /data/kang/work/struct/alex/freesurfer/subjects_cann/testavg > already exists, select a new average subject name > ERROR: /data/kang/work/struct/alex/freesurfer/subjects_cann/testavg > already exists, select a new average subject name > echo " or delete and rerun" > echoor delete and rerun >or delete and rerun > exit 1 ; > exit 1 > > > > ___ > 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] Make_average_subject
Hi all, I've been having problems with make_average_subject. The command and error are below. Below this is the same command with the output generated by the --debug flag. I am running version 4.0 (redhat) on Linux Debian. I'd appreciate any help on this. Thanks, Alex make_average_surface --subjects cann01 cann02 cann04 cann05 cann06 cann07 cann08 cann09 cann10 cann13 cann14 cann15 cann16 cann17 cann18 cann19 cann20 cann21 cann22 cann23 cann24 cann25 cann27 cann28 cann29 cann30 cann31 cann32 cann33 cann34 cann35 cann36 cann37 cann38 cann39 cann40 cann41 cann43 cann44 cann46 cann47 cann48 cann49 cann50 cann51 cann52 cann53 cann54 cann55 cann56 --out testavg $Id: make_average_surface,v 1.39 2007/08/13 20:54:29 greve Exp $ Fri Oct 26 11:03:31 EST 2007 /data/kang/work/struct/alex/freesurfer/subjects_cann setenv SUBJECTS_DIR /data/kang/work/struct/alex/freesurfer/subjects_cann output ddir is /data/kang/work/struct/alex/freesurfer/subjects_cann uid=1003(alex) gid=1003 groups=200(mnc),201(fmri),1003 make_average_subject --subjects cann01 cann02 cann04 cann05 cann06 cann07 cann08 cann09 cann10 cann13 cann14 cann15 cann16 cann17 cann18 cann19 cann20 cann21 cann22 cann23 cann24 cann25 cann27 cann28 cann29 cann30 cann31 cann32 cann33 cann34 cann35 cann36 cann37 cann38 cann39 cann40 cann41 cann43 cann44 cann46 cann47 cann48 cann49 cann50 cann51 cann52 cann53 cann54 cann55 cann56 --out testavg --debug set verbose = 1 breaksw breaksw end end while ( $#argv != 0 ) while ( 0 != 0 ) goto parse_args_return ; goto parse_args_return goto check_params ; goto check_params if ( ! $?SUBJECTS_DIR ) then if ( ! 1 ) then if ( ! -e $SUBJECTS_DIR ) then if ( ! -e /data/kang/work/struct/alex/freesurfer/subjects_cann ) then if ( ! $?FREESURFER_HOME ) then if ( ! 1 ) then if ( ! -e $FREESURFER_HOME ) then if ( ! -e /usr/local/freesurfer_4.0 ) then if ( $#sdout == 0 ) set sdout = $SUBJECTS_DIR if ( 0 == 0 ) set sdout = /data/kang/work/struct/alex/freesurfer/subjects_cann set sdout = /data/kang/work/struct/alex/freesurfer/subjects_cann set outdir = $sdout/$average_subject set outdir = /data/kang/work/struct/alex/freesurfer/subjects_cann/testavg if ( -e $outdir && ! $Force ) then if ( -e /data/kang/work/struct/alex/freesurfer/subjects_cann/testavg && ! 0 ) then echo "ERROR: $outdir already exists, select a new average subject name" echo ERROR: /data/kang/work/struct/alex/freesurfer/subjects_cann/testavg already exists, select a new average subject name ERROR: /data/kang/work/struct/alex/freesurfer/subjects_cann/testavg already exists, select a new average subject name echo " or delete and rerun" echoor delete and rerun or delete and rerun exit 1 ; exit 1 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] WM volume & CSF & BPF
On Thu, 25 Oct 2007, Gallo, Antonio (NIH/NINDS) [F] wrote: Dear All, We are dealing with MPRAGE data acquired at a 3.0T MRI scanner and analyzed with FS 3.0.5. Images belong to a group of Multiple Sclerosis patients. We would like to ask some questions and we apologize for the fact that we have quite a number of them :-) First, regarding measurements coming from mris_anatomical_stats: 1) What is exactly included in total WM volume? in mris_anatomical_stats this is the total volume occupied by voxels in the wm.mgz volume that are "on". We now use mris_wm_volume to compute the volume using the surfaces, which we believe is more accurate. 2) Is total WM volume the sum of left and right WM hemisphere or just the WM volume from the side we specify (but if this is case, why we got the same values after running mris_anatomical_stats for lh and rh hemisphere) ? there is no lateralization in this calculation, but you could use the aseg.mgz to get lh and rh volumes (in the aseg.stats file) 3) Since there are many WM lesions (with many juxta-cortical lesions that need manual editing), we were wondering if total WM volume does include the WM hypointensities as well or those are just treated separately. it depends whether they were classified as wm in the wm.mgz. If you use the mris_wm_volume method, then the hypointensities *will* be included in the volume. 4) Does the total GM volume include the volume of the subcortical structures and cerebellum or just refer to the cortical GM volume? just cortical GM. Second, some other questions on the aseg.stat file: 1) What is exactly included in CSF label? Does it comprehend the CSF in the ventricles + the sulcal CSF, or just the the sulcal CSF? CSF is sulcal CSF and we don't label very much of it, as you can't really see it well on a T1-weighted MRI. The ventricles have their volumes given individually. > 2) Does the volume of the WM hypointensities manually edited (which happens very often with MS lesions close to the cortex) end up in the WM hypointensities volume? if they are labeled as hypointensities in the aseg.mgz. Are you manually editing them there or in the wm.mgz? Last, as we are interested in measuring subjects' BPF, we were wondering which would be the best way to compute it? Thanks a lot in advance, Antonio Antonio Gallo, MD NIB-NINDS-NIH 10 Center Drive Building 10, Room 5B16 Bethesda, MD, 20892 - USA ph #: 001-301-402.6391 fax #: 001-301-402.0373 *** ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] WM volume & CSF & BPF
Dear All, We are dealing with MPRAGE data acquired at a 3.0T MRI scanner and analyzed with FS 3.0.5. Images belong to a group of Multiple Sclerosis patients. We would like to ask some questions and we apologize for the fact that we have quite a number of them :-) First, regarding measurements coming from mris_anatomical_stats: 1) What is exactly included in total WM volume? 2) Is total WM volume the sum of left and right WM hemisphere or just the WM volume from the side we specify (but if this is case, why we got the same values after running mris_anatomical_stats for lh and rh hemisphere) ? 3) Since there are many WM lesions (with many juxta-cortical lesions that need manual editing), we were wondering if total WM volume does include the WM hypointensities as well or those are just treated separately. 4) Does the total GM volume include the volume of the subcortical structures and cerebellum or just refer to the cortical GM volume? Second, some other questions on the aseg.stat file: 1) What is exactly included in CSF label? Does it comprehend the CSF in the ventricles + the sulcal CSF, or just the the sulcal CSF? 2) Does the volume of the WM hypointensities manually edited (which happens very often with MS lesions close to the cortex) end up in the WM hypointensities volume? Last, as we are interested in measuring subjects' BPF, we were wondering which would be the best way to compute it? Thanks a lot in advance, Antonio Antonio Gallo, MD NIB-NINDS-NIH 10 Center Drive Building 10, Room 5B16 Bethesda, MD, 20892 - USA ph #: 001-301-402.6391 fax #: 001-301-402.0373 *** ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] talairach failure detection
Mike, Can you send me the input files for that subject? That is, the files found in this directory of yours: /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/010502_61774/mri/orig If so, you can upload them to me via the filedrop: https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Nick On Thu, 2007-10-25 at 12:41 -0500, Michael Harms wrote: > Hello, > Thought that this might be of interest: > We've found a case for which the talairach.xfm is grossly wrong (checked > using tkregister2) but the automatic-failure detection of version 4.0.1 > indicated no problems. > > # > [EMAIL PROTECTED] Talairach Failure Detection Thu Oct 25 12:29:08 CDT 2007 > /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/010502_61774/mri > > talairach_afd -T 0.005 -xfm transforms/talairach.xfm > > talairach_afd: Talairach Transform: transforms/talairach.xfm OK > (p=0.2262, pval=0.0169 >= threshold=0.0050) > > #-- > > > Is this something that anyone else has noticed so far? > > thanks, > Mike H. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] talairach failure detection
Hello, Thought that this might be of interest: We've found a case for which the talairach.xfm is grossly wrong (checked using tkregister2) but the automatic-failure detection of version 4.0.1 indicated no problems. # [EMAIL PROTECTED] Talairach Failure Detection Thu Oct 25 12:29:08 CDT 2007 /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/010502_61774/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.2262, pval=0.0169 >= threshold=0.0050) #-- Is this something that anyone else has noticed so far? thanks, Mike H. -- Michael Harms, Ph.D. Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6615 Tel: 314-747-6173 660 South Euclid Ave.Fax: 314-747-2182 St. Louis, MO 63110 Email: [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer]thickness difference map
Xin,
It sounds like you will need to get the newer mri_surf2surf to create
the thickness difference maps you want. You can either install the
v4.0.1 of freesurfer, or I have posted just mri_surf2surf for you to
copy to your existing install. That file is located here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/dev/linux
Copy mri_surf2surf to your $FREESURFER_HOME/bin, and then type:
cd $FREESURFER_HOME/bin
chmod a+x mri_surf2surf
You may want to save the old mri_surf2surf somewhere.
Nick
On Thu, 2007-10-25 at 12:25 -0400, Doug Greve wrote:
> Actually, I think it still needs the --tfmt because it cannot
> determine that it is a curv file from the name of the file.
>
> doug
>
> Nick Schmansky wrote:
> > Support for the curv format as a target was added to mri_surf2surf in
> > freesurfer v4.0. For your version, you can just exclude the -tfmt curv
> > parameter.
> >
> >
> > On Wed, 2007-10-24 at 21:19 -0400, Wang, Xin wrote:
> >
> > > ERROR: Cannot select curv as target format.
> > >
> > > Thank you, Nick.
> > >
> > > Xin Wang
> > >
> > >
> > > __
> > > From: Nick Schmansky [mailto:[EMAIL PROTECTED]
> > > Sent: 2007-10-24 (星期三) 21:16
> > > To: Wang, Xin
> > > Cc: Doug Greve; Freesurfer Mailing List
> > > Subject: Re: {Spam?} 答复: [Freesurfer]thickness difference map
> > >
> > >
> > >
> > > Can you send along the output text that shows the error?
> > >
> > > On Wed, 2007-10-24 at 21:10 -0400, Wang, Xin wrote:
> > >
> > > > Thank you for your response, Doug. I attached all the commends I
> > > > modified from Han's note. I worked through step1 & 2. But the step3
> > > >
> > > is
> > >
> > > > the problem now. step4 hasn't been tried. I look forward to hearing
> > > > your suggestions.
> > > >
> > > > Thank you again,
> > > >
> > > > Xin
> > > >
> > > >
> > > >
> > > >
> > > __
> > >
> > > > From: Doug Greve [mailto:[EMAIL PROTECTED]
> > > > Sent: 2007-10-24 (星期三) 19:12
> > > > To: Wang, Xin
> > > > Cc: Nick Schmansky; Freesurfer Mailing List
> > > > Subject: RE: [Freesurfer] thickness difference map
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > What is your cmd line and what is the terminal output?
> > > >
> > > >
> > > >
> > > > On Wed, 24 Oct 2007, Wang, Xin wrote:
> > > >
> > > >
> > > > > Thank you very much, Nick. I ran into a problem when I ran the
> > > > >
> > > step
> > >
> > > > 3 of Han's note of thickness repeatability. The --tfmt of
> > > > mri_surf2surf is curv. The step can not be completed.
> > > >
> > > > > Please help me.
> > > > >
> > > > > Thank you again,
> > > > >
> > > > > Xin
> > > > >
> > > > >
> > > > >
> > > > > From: Nick Schmansky [mailto:[EMAIL PROTECTED]
> > > > > Sent: Sat 10/20/2007 5:34 PM
> > > > > To: Wang, Xin
> > > > > Cc: Freesurfer Mailing List
> > > > > Subject: Re: [Freesurfer] thickness difference map
> > > > >
> > > > >
> > > > >
> > > > > Xin,
> > > > >
> > > > > Have a look at this wiki page written by Xiao (the author of the
> > > > >
> > > > paper):
> > > >
> > > > > http://surfer.nmr.mgh.harvard.edu/fswiki/ThicknessRepeatibility
> > > > >
> > > > > It describes the procedure for how Figure 2 was created.
> > > > >
> > > > > Nick
> > > > >
> > > > > On Fri, 2007-10-19 at 15:42 -0400, Wang, Xin wrote:
> > > > >
> > > > > > Hello, Group,
> > > > > >
> > > > > > We want to make a figure as Fig2 in Han X et al. 2006 reliability
> > > > > > paper. Does anyone kindly share his/her way to make a map of
> > > > > > difference in average thickness between two groups?
> > > > > >
> > > > > > Thank you in advance,
> > > > > >
> > > > > > Xin Wang
> > > > > > ___
> > > > > > 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
> > > >
> > > > In order to help us help you, please follow the steps in:
> > > > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > > >
> > > >
> > > >
> > > >
> > > >
> > >
> > >
> > >
> >
> >
> >
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> [EMAIL PROTECTED]
> 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
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer]thickness difference map
Actually, I think it still needs the --tfmt because it cannot determine
that it is a curv file from the name of the file.
doug
Nick Schmansky wrote:
Support for the curv format as a target was added to mri_surf2surf in
freesurfer v4.0. For your version, you can just exclude the -tfmt curv
parameter.
On Wed, 2007-10-24 at 21:19 -0400, Wang, Xin wrote:
ERROR: Cannot select curv as target format.
Thank you, Nick.
Xin Wang
__
From: Nick Schmansky [mailto:[EMAIL PROTECTED]
Sent: 2007-10-24 (星期三) 21:16
To: Wang, Xin
Cc: Doug Greve; Freesurfer Mailing List
Subject: Re: {Spam?} 答复: [Freesurfer]thickness difference map
Can you send along the output text that shows the error?
On Wed, 2007-10-24 at 21:10 -0400, Wang, Xin wrote:
Thank you for your response, Doug. I attached all the commends I
modified from Han's note. I worked through step1 & 2. But the step3
is
the problem now. step4 hasn't been tried. I look forward to hearing
your suggestions.
Thank you again,
Xin
__
From: Doug Greve [mailto:[EMAIL PROTECTED]
Sent: 2007-10-24 (星期三) 19:12
To: Wang, Xin
Cc: Nick Schmansky; Freesurfer Mailing List
Subject: RE: [Freesurfer] thickness difference map
What is your cmd line and what is the terminal output?
On Wed, 24 Oct 2007, Wang, Xin wrote:
Thank you very much, Nick. I ran into a problem when I ran the
step
3 of Han's note of thickness repeatability. The --tfmt of
mri_surf2surf is curv. The step can not be completed.
Please help me.
Thank you again,
Xin
From: Nick Schmansky [mailto:[EMAIL PROTECTED]
Sent: Sat 10/20/2007 5:34 PM
To: Wang, Xin
Cc: Freesurfer Mailing List
Subject: Re: [Freesurfer] thickness difference map
Xin,
Have a look at this wiki page written by Xiao (the author of the
paper):
http://surfer.nmr.mgh.harvard.edu/fswiki/ThicknessRepeatibility
It describes the procedure for how Figure 2 was created.
Nick
On Fri, 2007-10-19 at 15:42 -0400, Wang, Xin wrote:
Hello, Group,
We want to make a figure as Fig2 in Han X et al. 2006 reliability
paper. Does anyone kindly share his/her way to make a map of
difference in average thickness between two groups?
Thank you in advance,
Xin Wang
___
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
In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
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
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] stats for average subject...
Cameron, mris_info will show number of vertices and surface area, and other basic stats, for a surface file. Nick On Thu, 2007-10-25 at 11:06 -0400, Cameron Ellis wrote: > Hi, > Does anyone know if it is possible to generate an aparc.stats file for an > average subject? mris_anatomical stats does not seem like it will work > because it requires wm.mgz which is not generated in the > make_average_subject process. I would like to find the number of vertices > and the surface area of each hemisphere. I think the average surface area > can be found in the make_average_subject log file but I cannot find the > number of vertices there. Any suggestions? > Thanks, > Cameron > > ___ > 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] stats for average subject...
Hi, Does anyone know if it is possible to generate an aparc.stats file for an average subject? mris_anatomical stats does not seem like it will work because it requires wm.mgz which is not generated in the make_average_subject process. I would like to find the number of vertices and the surface area of each hemisphere. I think the average surface area can be found in the make_average_subject log file but I cannot find the number of vertices there. Any suggestions? Thanks, Cameron ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Incorrect results after re-run.
hmm, not sure what happened on the 2nd run, but you should be able to corect those problems by putting some control points in superior regions (in the white matter at the base of the strands that are lost). Make sure they are completely in the wm and not in partial-volumed voxels. Bruce On Thu, 25 Oct 2007 [EMAIL PROTECTED] wrote: Hi, I did some editing, add in control points and edit pial surface on one set of our data on the left hand side of the screenshot attached, and re-run recon-all -autorecon2 -autorecon3 -s subjID The result turned out to be wrong as shown in the right hand side of the screenshot. The algorithm worked well at the temporal lobe where control points were added, but it failed at the superior part. Can you suggest why it is so? Thanks Zheng Hui ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
