Diff for "SpmBatch2" - MRC CBU Imaging Wiki
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This is a tiny page introducing a set of batch scripts to do a full analysis with SPM2, including undistortion. It is specifically tailored to the CBU/Cambridge processing stream, but may be useful to others as examples for things like coregistration, normalization, etc.The scripts are available from the [http://imaging.mrc-cbu.cam.ac.uk/downloads/SPM2_batch CBU Imagers SPM2 batch directory]. This is a tiny page introducing a set of batch scripts to do a full analysis with SPM2, including undistortion. It is specifically tailored to the CBU/Cambridge processing stream, but may be useful to others as examples for things like coregistration, normalization, etc.The scripts are available from the [[http://imaging.mrc-cbu.cam.ac.uk/downloads/SPM2_batch|CBU Imagers SPM2 batch directory]].
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For users of the Rhodri Cusack's [wiki:FmBackground undistortion toolbox], there's an edited version of fieldmap_mireg.m which works with SPM2. For the undistortion, you'll need SPM99 on the path after SPM2, so matlab finds the SPM2 functions first. For users of the Rhodri Cusack's [[FmBackground|undistortion toolbox]], there's an edited version of fieldmap_mireg.m which works with SPM2. For the undistortion, you'll need SPM99 on the path after SPM2, so matlab finds the SPM2 functions first.
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The scripts also uses custom routines, which combine the realignment, undistortion, normalization and smoothing in one resampling step. If you want to replicate this, you will need to download these [http://imaging.mrc-cbu.cam.ac.uk/downloads/Undistort_reslice undistort_reslice routines]. If you don't want to use undistort_reslice, it should be easy to see from the scripts how to use standard SPM2 reslicing instead. The scripts also uses custom routines, which combine the realignment, undistortion, normalization and smoothing in one resampling step. If you want to replicate this, you will need to download these [[http://imaging.mrc-cbu.cam.ac.uk/downloads/Undistort_reslice|undistort_reslice routines]]. If you don't want to use undistort_reslice, it should be easy to see from the scripts how to use standard SPM2 reslicing instead.
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Another overall batch script for SPM2 (with some differences from our processing stream) is available at the FIL website:http://www.fil.ion.ucl.ac.uk/~wpenny/datasets/face-rep/SPM2.html. Here are some relevant emails from the SPM list:Some suggestions from John Ashburner on [http://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind0303&L=spm&T=0&F=&S=&P=45776 batching preprocessing]. Another overall batch script for SPM2 (with some differences from our processing stream) is available at the FIL website:http://www.fil.ion.ucl.ac.uk/~wpenny/datasets/face-rep/SPM2.html. Here are some relevant emails from the SPM list:Some suggestions from John Ashburner on [[http://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind0303&L=spm&T=0&F=&S=&P=45776|batching preprocessing]].
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Edited [http://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind0307&L=spm&P=R32114&I=-1&T=0 batch scripts from Ron Peeters]. Edited [[http://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind0307&L=spm&P=R32114&I=-1&T=0|batch scripts from Ron Peeters]].
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SPM2 batch [http://www.md.ucl.ac.be/rdgn/autospm2.html scripts from the University Catholique de Louvain]. SPM2 batch [[http://www.md.ucl.ac.be/rdgn/autospm2.html|scripts from the University Catholique de Louvain]].

SPM2 batch scripts

This is a tiny page introducing a set of batch scripts to do a full analysis with SPM2, including undistortion. It is specifically tailored to the CBU/Cambridge processing stream, but may be useful to others as examples for things like coregistration, normalization, etc.The scripts are available from the CBU Imagers SPM2 batch directory.

To get an idea how the scripts can be customized to your own situation, mave a look at the myv.m file, and the do_ana_spm2.m file, which runs all the steps. The README file explains the data directory structure on which the scripts are based.

For users of the Rhodri Cusack's undistortion toolbox, there's an edited version of fieldmap_mireg.m which works with SPM2. For the undistortion, you'll need SPM99 on the path after SPM2, so matlab finds the SPM2 functions first.

The scripts also uses custom routines, which combine the realignment, undistortion, normalization and smoothing in one resampling step. If you want to replicate this, you will need to download these undistort_reslice routines. If you don't want to use undistort_reslice, it should be easy to see from the scripts how to use standard SPM2 reslicing instead.

Other sources of SPM2 batch information

Another overall batch script for SPM2 (with some differences from our processing stream) is available at the FIL website:http://www.fil.ion.ucl.ac.uk/~wpenny/datasets/face-rep/SPM2.html. Here are some relevant emails from the SPM list:Some suggestions from John Ashburner on batching preprocessing.

Edited batch scripts from Ron Peeters.

SPM2 batch scripts from the University Catholique de Louvain.

As usual, in the wierd world of batch,

Good luck.

Matthew Brett

CbuImaging: SpmBatch2 (last edited 2013-03-07 21:24:01 by localhost)