[Freesurfer] Re: Freesurfer Digest, Vol 19, Issue 49

[Blaise Frederick]

On Sep 27, 2005, at 3:06 PM, [EMAIL PROTECTED] wrote: Message: 2 Date: Tue, 27 Sep 2005 13:42:02 -0400 From: Keith Schneider <[EMAIL PROTECTED]> Subject: [Freesurfer] mri_convert doesn't recognize DICOM files To: freesurfer@nmr.mgh.harvard.edu Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed I installed Freesurfer on a G5 Tiger Mac, but mri_convert and   mri_parse_sdcmdir don't recognize my Siemens DICOM files (from a   Siemens Trio 3T) as DICOM files.  Has anyone else encountered this? Other programs can read the DICOM files just fine. keith ------------------------------ I have found exactly the same thing.  The thing is, it _used_ to work... Using a G5 with 10.4.2, in a directory with DICOM files pulled off a Siemens Trio using Osirix, I execute the following: /usr/local/freesurfer/bin/Darwin/mri_convert -it dicom -ot analyze IM-0242-0001.dcm hoot I get the following error (many, many times) mri_convert(1841) malloc: ***  Deallocation of a pointer not malloced: 0xd10ea0; This could be a double free(), or free() called with the middle of an allocated block; Try setting environment variable MallocHelp to see tools to help debug However, when all is said and done, I get a correct analyze file.  The binary in question is: -rwxr-xr-x   1 frederic  frederic  2034036 Feb 18  2004 /usr/local/freesurfer/bin/Darwin/mri_convert However, if I execute: /Users/Shared/freesurfer/bin/mri_convert -it dicom -ot analyze IM-0242-0001.dcm hoot2 it returns with: no DICOM files found. Exit This binary is from the newest distribution that I have: -rwxr-xr-x   1 frederic  wheel  6236540 Jul  7 21:23 /Users/Shared/freesurfer/bin/mri_convert So it looks like something broke.  Unfortunately, I don't want to just use the old binary, because it is missing many output formats (particularly nii) Blaise Any information, including protected health information (PHI), transmitted in this email is intended only for the person or entity to which it is addressed and may contain information that is privileged, confidential and/or exempt from disclosure under applicable Federal or State law. Any review, retransmission, dissemination or other use of or taking of any action in reliance upon, PHI by persons or entities other than the intended recipient is prohibited. If you received this email in error, please contact the sender and delete the material from any computer.

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