You&#39;ve already fixed it!  I didn&#39;t realize the computer I was using was a couple of versions behind (fsl 4.1.1) and this is definitely fixed in 4.1.6. <br><br>Thanks,<br>Jeanette<br><br><div class="gmail_quote">On Thu, Aug 19, 2010 at 1:24 AM, Stephen Smith <span dir="ltr">&lt;<a href="mailto:[log in to unmask]"><a href="/cgi-bin/wa-jisc.exe?LOGON=A3%3Dind1008%26L%3DFSL%26E%3Dquoted-printable%26P%3D1848258%26B%3D--001636c9246e407032048e2db4c2%26T%3Dtext%252Fhtml%3B%2520charset%3DISO-8859-1%26pending%3D" target="_parent" >[log in to unmask]</a></a>&gt;</span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div style="word-wrap: break-word;">Urgh - thanks for looking into this Jeanette.  We&#39;ll delve deeper.<div>
Cheers.<div><div></div><div class="h5"><br><div><br></div><div><br><div><div>On 18 Aug 2010, at 22:05, Jeanette Mumford wrote:</div><br><blockquote type="cite">Hi,<br>I don&#39;t know if it would be a computer problem (this error has occurred on two machines), but we used the -B option previously with no error and the problem popped up with fsl 4.1.1.  Here is what happens when I ran bet with  -m -B -d<br>

<br>Here is the error message again:<br><span style="color: rgb(0, 0, 153);">/Applications/fsl/bin/bet: line 383:  8794 Segmentation fault      ${FSLDIR}/bin/fast -oba 100 ${OUT}_tmp_premask 1&gt;&amp;/dev/null</span><br style="color: rgb(0, 0, 153);">

<span style="color: rgb(0, 0, 153);">** ERROR (nifti_image_read): failed to find header file for &#39;mprage_defaced_brain_tmp_premask_abias&#39;</span><br style="color: rgb(0, 0, 153);"><span style="color: rgb(0, 0, 153);">** ERROR: nifti_image_open(mprage_defaced_brain_tmp_premask_abias): bad header info</span><br style="color: rgb(0, 0, 153);">

<span style="color: rgb(0, 0, 153);">Error: failed to open file mprage_defaced_brain_tmp_premask_abias</span><br style="color: rgb(0, 0, 153);"><span style="color: rgb(0, 0, 153);">ERROR: Could not open image mprage_defaced_brain_tmp_premask_abias</span><br style="color: rgb(0, 0, 153);">

<span style="color: rgb(0, 0, 153);">Image Exception : #22 :: Failed to read volume mprage_defaced_brain_tmp_premask_abias</span><br style="color: rgb(0, 0, 153);"><span style="color: rgb(0, 0, 153);">terminate called after throwing an instance of &#39;RBD_COMMON::BaseException&#39;</span><br style="color: rgb(0, 0, 153);">

<span style="color: rgb(0, 0, 153);">/Applications/fsl/bin/bet: line 383:  8802 Abort trap              ${FSLDIR}/bin/fslmaths $IN -mul ${OUT}_tmp_premask_abias ${OUT}_tmp_unbiased</span><br style="color: rgb(0, 0, 153);">

<span style="color: rgb(0, 0, 153);">Input image mprage_defaced_brain_tmp_unbiased not valid</span><br style="color: rgb(0, 0, 153);"><br style="color: rgb(0, 0, 153);"><span style="color: rgb(0, 0, 153);">Error: input image mprage_defaced_brain_tmp_unbiased_premask not valid</span><br style="color: rgb(0, 0, 153);">

<br>and here is the list of files that were created:<br><br><span style="color: rgb(0, 0, 153);">mprage_defaced_brain.nii.gz</span><br style="color: rgb(0, 0, 153);"><span style="color: rgb(0, 0, 153);">mprage_defaced_brain_mask.nii.gz</span><br style="color: rgb(0, 0, 153);">

<span style="color: rgb(0, 0, 153);">mprage_defaced_brain_skull.nii.gz</span><br style="color: rgb(0, 0, 153);"><span style="color: rgb(0, 0, 153);">mprage_defaced_brain_tmp_premask.nii.gz</span><br style="color: rgb(0, 0, 153);">

<span style="color: rgb(0, 0, 153);">mprage_defaced_brain_tmp_premask_tmp_masked.nii.gz</span><br style="color: rgb(0, 0, 153);"><span style="color: rgb(0, 0, 153);">mprage_defaced_brain_tmp_premask_tmp_standard_mask.nii.gz</span><br style="color: rgb(0, 0, 153);">

<span style="color: rgb(0, 0, 153);">mprage_defaced_brain_tmp_premask_tmp_standard_mask_to_in.nii.gz</span><br style="color: rgb(0, 0, 153);"><span style="color: rgb(0, 0, 153);">mprage_defaced_brain_tmp_premask_tmp_to_std.mat</span><br style="color: rgb(0, 0, 153);">

<span style="color: rgb(0, 0, 153);">mprage_defaced_brain_tmp_premask_tmp_to_std.nii.gz</span><br style="color: rgb(0, 0, 153);"><span style="color: rgb(0, 0, 153);">mprage_defaced_brain_tmp_premask_tmp_to_std_inv.mat</span><br style="color: rgb(51, 51, 255);">

<br style="color: rgb(51, 51, 255);"><br>So, I went through the bet script and I think it is hung up when it calls fast, so I ran that line of code (line 371 in our version of bet, but of course I omitted &quot;&gt;&amp; /dev/null&quot;)<br>

<br>fast -oba 100 mprage_defaced_brain_tmp_premask<br><br>Here is the error message<br><span style="color: rgb(0, 0, 153);">Could not open matrix file mprage_defaced_brain_tmp_premask</span><br style="color: rgb(0, 0, 153);">

<span style="color: rgb(0, 0, 153);">Could not open matrix file mprage_defaced_brain_tmp_premask</span><br style="color: rgb(0, 0, 153);"><span style="color: rgb(0, 0, 153);">Could not open matrix file mprage_defaced_brain_tmp_premask</span><br style="color: rgb(0, 0, 153);">

<span style="color: rgb(0, 0, 153);">csf prior image not transformed correctly! priors are not used!</span><br style="color: rgb(0, 0, 153);"><span style="color: rgb(0, 0, 153);">Segmentation fault</span><br style="color: rgb(0, 0, 153);">

<br>Is it looking for a mat file to pair up with the -a flag?  I&#39;m not sure what the 100 does.<br><br>Thanks for the help!<br><br>Jeanette<br><br><br><div class="gmail_quote">On Wed, Aug 18, 2010 at 3:45 AM, Stephen Smith <span dir="ltr">&lt;<a href="mailto:[log in to unmask]" target="_blank"><a href="/cgi-bin/wa-jisc.exe?LOGON=A3%3Dind1008%26L%3DFSL%26E%3Dquoted-printable%26P%3D1848258%26B%3D--001636c9246e407032048e2db4c2%26T%3Dtext%252Fhtml%3B%2520charset%3DISO-8859-1%26pending%3D" target="_parent" >[log in to unmask]</a></a>&gt;</span> wrote:<br>

<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div style="word-wrap: break-word;">Hi - this means that FAST has not run successfully - maybe the image is too large for FAST to run on your computer?<div>

If you use the -d flag it should leave behind as many of the intermediate steps as do complete, which should make it easier to test what&#39;s going on.</div><div>Cheers.</div><div><div><div></div><div><br><div>
<div>On 17 Aug 2010, at 20:29, Jeanette Mumford wrote:</div><br><blockquote type="cite">Hi,<br><br>When I run bet with the -B flag I get the following error message:<br><br>/Applications/fsl/bin/bet: line 383: 18901 Segmentation fault      ${FSLDIR}/bin/fast -oba 100 ${OUT}_tmp_premask 1&gt;&amp;/dev/null<br>



** ERROR (nifti_image_read): failed to find header file for &#39;mprage_defaced_brain3_tmp_premask_abias&#39;<br>** ERROR: nifti_image_open(mprage_defaced_brain3_tmp_premask_abias): bad header info<br>Error: failed to open file mprage_defaced_brain3_tmp_premask_abias<br>



ERROR: Could not open image mprage_defaced_brain3_tmp_premask_abias<br>Image Exception : #22 :: Failed to read volume mprage_defaced_brain3_tmp_premask_abias<br>terminate called after throwing an instance of &#39;RBD_COMMON::BaseException&#39;<br>



/Applications/fsl/bin/bet: line 383: 18909 Abort trap              ${FSLDIR}/bin/fslmaths $IN -mul ${OUT}_tmp_premask_abias ${OUT}_tmp_unbiased<br>Input image mprage_defaced_brain3_tmp_unbiased not valid<br><br>Error: input image mprage_defaced_brain3_tmp_unbiased_premask not valid<br>



<br><br><br>The results I&#39;m getting seem okay (image seems to have had bias field correction and the mask is much better than without the -B flag).  I was just wondering what the error was about and if there would be anything wrong with using the resulting images.<br>



<br>Thanks,<br>Jeanette  <br>
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