<div dir="ltr"><div>Dear Michael and Philip,</div><div>You were right and I just did it successfully.</div><div>Thank u very much.</div><div>Cheers,</div><div>Maedeh,<br></div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr">On Mon, Dec 3, 2018 at 7:43 PM Cook, Philip <<a href="mailto:cookpa@pennmedicine.upenn.edu">cookpa@pennmedicine.upenn.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word;line-break:after-white-space">
Thanks Michael.
<div><br>
</div>
<div> You also have the option of reading in the DWI data directly as NIFTI, eg</div>
<div><br>
</div>
<div> wdtfit 4Ddwi_b1000.nii.gz dwi.scheme -outputfile dt.Bdouble</div>
<div><br>
</div>
<div>You'll still need to increase the available RAM to do this.</div>
<div>
<div><br>
<blockquote type="cite">
<div>On Dec 3, 2018, at 7:36 AM, Michael Dayan <<a href="mailto:mdayan.research@gmail.com" target="_blank">mdayan.research@gmail.com</a>> wrote:</div>
<br class="m_-8140688311895322315Apple-interchange-newline">
<div>
<div dir="ltr">
<div dir="ltr">Hi Maedeh,
<div><br>
</div>
<div>You are running out of memory. You have to increase it by changing the maximum value with the following command:</div>
<div>
<div><br>
</div>
<div><font face="monospace, monospace">export CAMINO_HEAP_SIZE=2000</font></div>
<div><br>
</div>
<div>where 2000 = 2000 Mb and can be set to whatever maximum amount of RAM you want Camino to use (within the amount of RAM you have obviously).</div>
</div>
<div><br>
</div>
<div>You can do it as a one off by typing this command in your terminal, or set it permanently by writing it in your
<font face="monospace, monospace"><HOME_DIR>/.bashrc</font> file (for the changes to take effect you will need to refresh your current terminal with the new bash settings by typing <font face="monospace, monospace">source ~/.bashrc</font>,
or you can just start a new terminal).</div>
<div><br>
</div>
<div>Best,</div>
<div><br>
</div>
<div>Michael</div>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr">On Sun, Dec 2, 2018 at 5:15 PM maedeh khalilian <<a href="mailto:maedeh.kh73@gmail.com" target="_blank">maedeh.kh73@gmail.com</a>> wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">
<div dir="ltr">
<div dir="ltr">
<div>Dear Camino experts,</div>
<div>I want to reconstruct my DWI image to create dt.Bdouble in order to do a tractography.</div>
<div>But when I run the command below:</div>
<div>image2voxel -4dimage 4Ddwi_b1000.nii.gz -outputfile dwi.Bfloat<br>
</div>
<div>I see the error below and the created dt.Bdouble is empty !!</div>
<div>Exception in thread "main" java.lang.OutOfMemoryError: Java heap space<br>
at data.ScannerOrderDataSource.init(ScannerOrderDataSource.java:169)<br>
at data.ScannerOrderDataSource.<init>(ScannerOrderDataSource.java:134)<br>
at data.ScannerOrderScaledDataSource.<init>(ScannerOrderScaledDataSource.java:52)<br>
at imaging.Nifti1Dataset.getImageDataSource(Nifti1Dataset.java:2312)<br>
at apps.ImageToVoxel.execute(ImageToVoxel.java:104)<br>
at apps.EntryPoint.main(EntryPoint.java:293)<br>
<br>
</div>
<div>I dunno where the problem is from.</div>
<div>let me know if my scheme file and DWI image is necessary for checking.<br>
</div>
<div>I would be grateful if u could help me.</div>
<div>Cheers</div>
<div>Maedeh<br>
</div>
<div><br>
</div>
</div>
</div>
</div>
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