Can you run it with --debug as the first option and send me the terminal output? It will be a lot, so capture it like this:

mris_preproc ... |& tee proroc.log

doug

On 09/12/2012 04:43 PM, spaeth@nmr.mgh.harvard.edu wrote:

Hi,

I am trying to run mris_preproc on a set of 22 subjects (specified in my fsgd file), but the command only runs on the first subject listed in my fsgd file, and none of the subsequent subjects.

I run the command: mris_preproc --fsgd oa_txeffect_verum.fsgd --target fsaverage --hemi lh --meas thickness --out lh.oa_txeffect_verum.thickness.00.mgh

And only the first subject listed in the fsgd file runs through mris_surf2surf

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#@# 1/1 FSrecon_oaeaa005 Wed Sep 12 16:02:41 EDT 2012 --------------

mri_surf2surf --srcsubject FSrecon_oaeaa005 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.3029/FSrecon_oaeaa005.1.mgh --sval FSrecon_oaeaa005/surf/lh.thickness --sfmt curv --noreshape --no-cortex

I am able to run mris_preproc on each individual subject, specified with the flag --s FSrecon_oaeaa010 by running the following command:

mris_preproc --s FSrecon_oaeaa010 --target fsaverage --hemi rh --meas thickness --out rh.oa_txeffect_verum.thickness.00.mgh

My fsgd file is:

GroupDescriptorFile 1 Title Treatment Effect MeasurementName thickness Class groupVerum Variables tx_effect Input FSrecon_oaeaa005 groupVerum 1.58 Input FSrecon_oaeaa006 groupVerum 9.58 Input FSrecon_oaeaa007 groupVerum 2.08 Input FSrecon_oaeaa008 groupVerum -0.17 Input FSrecon_oaeaa010 groupVerum 1.08 Input FSrecon_oaeaa011 groupVerum 3.5 Input FSrecon_oaeaa013 groupVerum 1.58 Input FSrecon_oaeaa015 groupVerum 4 Input FSrecon_oaeaa016 groupVerum -0.17 Input FSrecon_oaeaa017 groupVerum 1 Input FSrecon_oaeaa021 groupVerum -1.83 Input FSrecon_oaeaa023 groupVerum 4.67 Input FSrecon_oaeaa026 groupVerum 1.83 Input FSrecon_oaeaa028 groupVerum 1.17 Input FSrecon_oaeaa029 groupVerum 0.5 Input FSrecon_oaeaa034 groupVerum -1 Input FSrecon_oaeaa037 groupVerum 1.25 Input FSrecon_oaeaa039 groupVerum -2.08 Input FSrecon_oaeaa040 groupVerum 2.67 Input FSrecon_oaeaa041 groupVerum 2 Input FSrecon_oaeaa043 groupVerum 4.5 Input FSrecon_oaeaa045 groupVerum -0.67

Based on other data sets I have worked with using mris_preproc, it seems that the mri_surf2surf should be run on each subject listed in the fsgd file. Is the format of my fsgd file incorrect? If my fsgd file is not the issue, is there a work around so that I don't have to run each subject through mris_preproc and mri_surf2surf individually?

Thanks,

Rosa

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