Blaise (and Keith),

I was able to recreate the problem that Keith is seeing using a sample dicom file he sent, so I am working to resolve that issue. It seems to be a Mac-centric issue, as the same dicom will convert correctly on Linux.

The odd thing is that the siemens_dicom files output from our scanner at MGH seem to convert correctly on the Mac using mri_convert, so that is one aspect to this problem that we are looking at (differences in formating). We use the Syngo sw on the scanner workstations.

Can you also send me one of the dcm files that is failing for you? Its helpful to have multiple failure cases to test against. Thanks.

Nick

On Tue, 2005-09-27 at 15:34 -0400, Blaise Frederick wrote:

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: ***Â 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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