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

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