<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Dear Sophie,<div><br></div><div>What happens if you don't specify <a href="http://cfg.name">cfg.name</a>? It seems that you don't need the output to be written to a file anyway (since you also specify cfg.write = 'no');</div><div><br></div><div>Best,</div><div><br></div><div>Jan-Mathijs</div><div><br></div><div><br></div><div><br></div><div><br></div><div><div><div>On Feb 12, 2013, at 11:46 AM, sophie chen wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Dear Fieldtripers<br><br>I am having some errors when running recent fieldtrip releases while calling ft_volumesegment that I don't have with former fieldtrip version, following what I get: <br><b>with fieldtrip fieldtrip-20111024 </b><br>
<br> cfg = [];<br><a href="http://cfg.name/">cfg.name</a> = 'ctf';<br>cfg.output= { 'tpm' }; <br>segmentedmri = ft_volumesegment(cfg, mri);<br><br>Warning: adding D:\SOPHIE\Software\fieldtrip-20111024\external\spm8 toolbox to your Matlab path <br>
<br>the input is volume data with dimensions [256 256 256]<br>Converting the coordinate system from ctf to spm<br>performing the segmentation on the specified volume<br>segmentedmri = <br> dim: [256 256 256]<br> transform: [4x4 double]<br>
coordsys: 'ctf'<br> unit: 'mm'<br> gray: [256x256x256 double]<br> white: [256x256x256 double]<br> csf: [256x256x256 double]<br> cfg: [1x1 struct]<br><br><b>with fieldtrip 'fieldtrip-20121203' <br>
</b><br>>> cfg = [];<br><a href="http://cfg.name/">cfg.name</a> = 'ctf';<br>cfg.write = 'no';<br>cfg.output= { 'tpm' }; <br>segmentedmri = ft_volumesegment(cfg, mri);<br><br>Warning: FieldTrip is not yet on your MATLAB path, adding D:<a href="smb://SOPHIE//Software//fieldtrip-20121203(1)//fieldtrip-20121203">\\SOPHIE\\Software\\fieldtrip-20121203(1)\\fieldtrip-20121203</a> <br>
> In ft_defaults at 60<br> In ft_volumesegment at 130 <br>the input is volume data with dimensions [256 256 256]<br>Converting the coordinate system from ctf to spm<br>Rescaling NIFTI: slope = 0.00342945, intercept = 0<br>
Smoothing by 0 & 8mm..<br>Coarse Affine Registration..<br>Fine Affine Registration..<br>Error using ft_write_mri (line 128)<br>unsupported data format<br>Error in ft_volumesegment (line 274)<br> Va = ft_write_mri([<a href="http://cfg.name/">cfg.name</a>,'.img'], mri.anatomy, 'transform', mri.transform, 'spmversion', cfg.spmversion); <b><br>
<br><br>and 'fieldtrip-20130210</b>'<br><br>cfg = [];<br><a href="http://cfg.name/">cfg.name</a> = 'ctf';<br>cfg.write = 'no';<br>cfg.output= { 'tpm' }; <br>segmentedmri = ft_volumesegment(cfg, mri);<br>
<br>the input is volume data with dimensions [256 256 256]<br><br>Warning: adding D:\SOPHIE\Software\fieldtrip-20130210\fieldtrip-20130210\external\spm8 toolbox to your Matlab path <br><br>Converting the coordinate system from ctf to spm<br>
<br>Warning: adding D:\SOPHIE\Software\fieldtrip-20130210\fieldtrip-20130210\external\freesurfer toolbox to your Matlab path <br><br>Rescaling NIFTI: slope = 0.00342945, intercept = 0<br>Smoothing by 0 & 8mm..<br>Coarse Affine Registration..<br>
Fine Affine Registration..<br>Warning: could not open ctf.img <br>> In fileio\private\warning_once at 116<br> In fileio\private\filetype_check_header at 54<br> In ft_filetype at 338<br> In ft_write_mri at 54<br> In ft_volumesegment at 282 <br>
Error using ft_write_mri (line 128)<br>unsupported data format<br>Error in ft_volumesegment (line 282)<br> Va = ft_write_mri([<a href="http://cfg.name/">cfg.name</a>,'.img'], mri.anatomy, 'transform', mri.transform, 'spmversion', cfg.spmversion); <br>
<br>Please help... :-) it's not convenient to switch fieldtrip version while running scripts...<br>Thanks a lot!<br><br>cheers<br>Sophie<br>
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<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Jan-Mathijs Schoffelen, MD PhD </div><div><br></div><div>Donders Institute for Brain, Cognition and Behaviour, <br>Centre for Cognitive Neuroimaging,<br>Radboud University Nijmegen, The Netherlands</div><div><br></div><div>Max Planck Institute for Psycholinguistics,</div><div>Nijmegen, The Netherlands</div><div><br></div><div><a href="mailto:J.Schoffelen@donders.ru.nl">J.Schoffelen@donders.ru.nl</a></div><div>Telephone: +31-24-3614793</div></div></span></div></span></div></span></div></span></div></span></span>
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