Hi, all<div>Bruce has suggested that we can&nbsp;directly give recon-all&nbsp;dcm file as input. However, I have done recon-all with mgz file as input. Is that input file OK?</div><div>For example, sub1 has 128 dcm files, 001~128, I just ran a syntax:</div>
<div>mri_convert 001 sub1.mgz</div><div>then the computer read 128 dcm files and convert them into sub1.mgz, then I ran recon-all with &quot;sub1.mgz&quot; as input file</div><div>The version I used was&nbsp;freesurfer-Linux-centos4-stable-pub-v4.5.0</div>
<div>Besides, I have checked the aseg.stats and lh/rh.aparc.stats generated from different input files(dcm or mgz) in one subject, and find that they are completely the same.</div><div>It must be a very stupid question, however, I need some confirmation. Too much Thanks!</div>
<div>Jin<br><br><div class="gmail_quote">2010/5/4 Bruce Fischl <span dir="ltr">&lt;<a href="mailto:fischl@nmr.mgh.harvard.edu">fischl@nmr.mgh.harvard.edu</a>&gt;</span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
if the directions are labeled properly then you aer probably ok. In general you are better off just giving recon-all the dicom files as input and not doing any conversions beforehand.<br>
<br>
cheers<br><font color="#888888">
Bruce</font><div><div></div><div class="h5"><br>
On Tue, 4 May 2010, chenchunhuichina wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hello FreeSurfer users,<br>
<br>
I may be asking a stupid question but it really troubled me a while.<br>
<br>
I converted dicom files to nift using dcm2niigui (MRIcron). In fslview, it displayed in RAS coordinates, but template of FSL are in LAS coordinates. Should I filp L-R before doing any further analysis?<br>
Besides, my structrual imagews were scanned in sagittal view, and after &nbsp;dcm2niigui transforation, it&#39;s in PIL coordinates in fslview. Should I reorient the image to LAS coordinates too?<br>
But the letters L R I S A P are labled correctly (at least A-P and I£­S are correct), which means FSL can read in orientation information correctly. So I am confused whether I should reorient my data or not.<br>
I then processed strucutre images with Freesurfer, and the results from reoriented and not-reoriented images are different, so which one is correct?<br>
<br>
Any help is appreciated,<br>
Thanks!<br>
--<br>
<br>
Chunhui Chen<br>
<br>
<br>
2010-05-04<br>
<br>
<br>
<br>
Chunhui Chen<br>
_________________<br>
<br>
Institute of Cognitive Neuroscience and Learning<br>
Beijing Normal University<br>
Beijing, China 100875<br>
</blockquote>
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