Hi Nick, I tried running the script you attached to this thread, and the error was similar, albeit slightly different (see below). Any ideas? Thanks, Alex

make_average_surface --subjects 1000186 1000187 1000188 --out test_avg --echo if ( 0 ) then breaksw end while ( 0 != 0 ) goto parse_args_return goto check_params if ( ! 1 ) then if ( ! 1 ) then if ( ! -e /data/flanders/work/alex/freesurfer/subjects ) then if ( ! 1 ) then if ( ! -e /usr/local/freesurfer ) then goto check_params_return echo ==================== ==================== echo make_average_surface make_average_surface echo ==================== ==================== echo input subjects: 1000186 1000187 1000188 input subjects: 1000186 1000187 1000188 echo output subject: test_avg output subject: test_avg mkdir -p /data/flanders/work/alex/freesurfer/subjects/test_avg /data/flanders/work/alex/freesurfer/subjects/test_avg/surf /data/flanders/work/alex/freesurfer/subjects/test_avg/mri /data/flanders/work/alex/freesurfer/subjects/test_avg/mri/transforms /data/flanders/work/alex/freesurfer/subjects/test_avg/mri/T1 /data/flanders/work/alex/freesurfer/subjects/test_avg/mri/orig /data/flanders/work/alex/freesurfer/subjects/test_avg/mri/label if ( -e /data/flanders/work/alex/freesurfer/subjects/test_avg == 0 ) then mkdir -p /data/flanders/work/alex/freesurfer/subjects/test_avg/surf endif set tmp_subjects = ( 1000186 1000187 1000188 ) cp /data/flanders/work/alex/freesurfer/subjects/1000186/mri/T1/COR-.info /data/flanders/work/alex/freesurfer/subjects/test_avg/mri/T1 cp /data/flanders/work/alex/freesurfer/subjects/1000186/mri/orig/COR-.info /data/flanders/work/alex/freesurfer/subjects/test_avg/mri/orig foreach hemi ( lh rh ) foreach c ( sulc curv ) echo mris_average_curvature... mris_average_curvature... mris_average_curvature sulc lh sphere.reg 1000186 1000187 1000188 ../test_avg/surf/lh.avg_sulc processing subject 1000186... processing subject 1000187... processing subject 1000188... MRISwriteCurvature: could not open ../test_avg/surf/lh.avg_sulc No such file or directory end echo mris_average_curvature... mris_average_curvature... mris_average_curvature sulc lh sphere.reg 1000186 1000187 1000188 ../test_avg/surf/lh.avg_curv processing subject 1000186... processing subject 1000187... processing subject 1000188... MRISwriteCurvature: could not open ../test_avg/surf/lh.avg_curv No such file or directory end foreach s ( orig white pial inflated ) echo mris_make_average_surface... mris_make_average_surface... mris_make_average_surface -i 7 -o orig lh orig_avg sphere.reg test_avg 1000186 1000187 1000188 reading vertex positions from orig... processing subject 1000186... The following must be revisited********************************** Segmentation fault

-----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Wed 7/27/2005 5:33 AM To: Goldman, Aaron (NIH/NIMH) Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] mris_glm analysis Aaron,

Hi, can you tell me the version of make_average_surface you are running? Type:

make_average_surface --version

Just in case yours in out-of-date, I've attached the latest make_average_surface script, which should not have the SUBJECTS bug that you describe.

The file is gzipped, so do the following:

- copy the file to $FREESURFER_HOME/bin - change directory to $FREESURFER_HOME/bin - type: gunzip make_average_surface.gz

Then you should be able rerun the make_average_surface utility.

Nick

On Tue, 2005-07-26 at 15:11 -0400, Goldman, Aaron (NIH/NIMH) wrote:

Hi, I’m trying to do a thickness analysis with mris_glm, and I had a couple of questions:

1. I made an average surface using mris_make_average_surface, but I

won’t load it with tksurfer because it “could not find anatomical header information.” Do you know how I can fix this? I also tried “make_average_surface -subjects subject1… subject111,” but it said SUBJECTS wasn’t defined, and wouldn’t run.

2. I’ve been able to successfully run a test mris_glm command using a

design file like:

subject1 0 1

subject2 1 0

etc

and the following commands:

foreach h ( lh rh )

mris_glm    --design $SUBJECTS_DIR/results/test_design.txt \

                    --surfmeas thickness \

                    --hemi $h \

                    --trgsubj Colin \

                    --nsmooth 300 \

                    --beta ${h}_test_beta bfloat \

                    --var ${h}_test_var bfloat

mris_glm    --design $SUBJECTS_DIR/results/test_design.txt \

                    --hemi $h \

                    --trgsubj Colin \

                    --beta_in ${h}_test_beta bfloat \

                    --var_in ${h}_test_var bfloat \

                    --gcv 1 -1 \

                    --sigt $SUBJECTS_DIR/Colin/surf/${h}_test_sigt

paint \

                    --t $SUBJECTS_DIR/$trgsubj/surf/${h}_test_t

paint

end

where a 1 in column 2 indicates one allele of the gene we’re studying, whereas a 1 in column 3 indicates the other. However, I’d like to also covary for age and gender, and I was wondering how I would need to edit my design file and mris_glm commands to do that.

Thanks,

-Aaron-

Aaron L. Goldman

Post-Bacc IRTA

Genes, Cognition and Psychosis Program, NIMH

Building 10, Room 3C108

Phone: (301) 435-0944

Email: aarong@mail.nih.gov

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