On Sep 27, 2005, at 3:06 PM, freesurfer-request@nmr.mgh.harvard.edu wrote:
Message: 2 Date: Tue, 27 Sep 2005 13:42:02 -0400 From: Keith Schneider ks@rcbi.rochester.edu Subject: [Freesurfer] mri_convert doesn't recognize DICOM files To: freesurfer@nmr.mgh.harvard.edu Message-ID: 1F6EBE81-3EC6-41F9-840C-1C2E8B4C05A6@rcbi.rochester.edu 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.