Hi Sam,

you can try like this below,

umount cdrecorder cd dicom;ls cd ######; ls output will be 2 strings of numbers

unpacksdcmdir –src /mnt/cdrom/dicom/INITIAL#/1STof2#’s -targ ./ –scanonly unpacklog

Repeat command line with second number

Make a cfg.file

Save as cfg.file in SUBJECT’s folder

then again rpeat above commands with the cfg flag,

unpacksdcmdir –src /mnt/cdrom/dicom/INITIAL#/1STof2#’s -targ ./ –cfg /path to cfg.file

Hello,

My name is Sam Enumah and I am an undergraduate working in the A.A. Martinos Imaging Center at MGH Navy Yard. I have become familiar with Freesurfer's tkmedit function and I am able to analyze my data once I am given a set of 144 MR dicom files. While the mri_convert tool works for the dicom files that are on the local machine, I cannot seem to get it to work for the files I have tried to retrieve from a CD. The files on my local host machine all display the extension ".dcm" while the files from the CD do not display a file extension and are files with names that consist of 8 unique numbers (e.g 48480095)

As you may know, when running mri_convert, the user need only input one of the files in a series and it recognizes all the other files and creates the desired output (in this case the ".nii" file type to be read by tkmedit). However, when I tried to input these 8 digit file names into mri_convert, I received the following error:

[gordo:12250000] (nmr-std-env) mri_convert 48480995.dcm adc.nii mri_convert 48480995.dcm adc.nii $Id: mri_convert.c,v 1.146.2.3 2008/08/11 22:18:58 nicks Exp $ reading from 48480995.dcm... Starting DICOMRead2() dcmfile = /autofs/homes/014/xmlentz/Desktop/dicom/08110217/12250000/48480995.dcmdcmdir = /autofs/homes/014/xmlentz/Desktop/dicom/08110217/12250000 Ref Series No = 805 ERROR: bits = 8 not supported. Send email to freesurfer@nmr.mgh.harvard.edu

I tried "mri_convert <filename> --in_type ge adc.nii" but kept getting the error: genesisRead(): can't determine file name format

Essentially, my problem is that I have roughly 1000 dicom files (as evidenced by command "file" in terminal) without an identifiable extension and I need to find a way to change these into one of any of the set MR001.dcm - MR144.dcm to be read by mri_convert.

As it stands now, I don't know what series (average DC, isotropic, FA, etc.) these 8 digit numbers correspond to so I'm unsure of how to proceed. Suggestions?

Thanks for your time.

-Sam

-- Sam Enumah Harvard College Class of 2010 Concentrator in Neurobiology senumah@fas.harvard.edu _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Dear Sam,

you might want to try other tools that can read and convert DICOMs, like (x)medcon, mricron, SPM5/SPM8 (if you have MATLAB available).

Volkmar

Quoting Sam Enumah senumah@fas.harvard.edu:

Hello,

My name is Sam Enumah and I am an undergraduate working in the A.A. Martinos Imaging Center at MGH Navy Yard. I have become familiar with Freesurfer's tkmedit function and I am able to analyze my data once I am given a set of 144 MR dicom files. While the mri_convert tool works for the dicom files that are on the local machine, I cannot seem to get it to work for the files I have tried to retrieve from a CD. The files on my local host machine all display the extension ".dcm" while the files from the CD do not display a file extension and are files with names that consist of 8 unique numbers (e.g 48480095)

As you may know, when running mri_convert, the user need only input one of the files in a series and it recognizes all the other files and creates the desired output (in this case the ".nii" file type to be read by tkmedit). However, when I tried to input these 8 digit file names into mri_convert, I received the following error:

[gordo:12250000] (nmr-std-env) mri_convert 48480995.dcm adc.nii mri_convert 48480995.dcm adc.nii $Id: mri_convert.c,v 1.146.2.3 2008/08/11 22:18:58 nicks Exp $ reading from 48480995.dcm... Starting DICOMRead2() dcmfile = /autofs/homes/014/xmlentz/Desktop/dicom/08110217/12250000/48480995.dcmdcmdir = /autofs/homes/014/xmlentz/Desktop/dicom/08110217/12250000 Ref Series No = 805 ERROR: bits = 8 not supported. Send email to freesurfer@nmr.mgh.harvard.edu

I tried "mri_convert <filename> --in_type ge adc.nii" but kept getting the error: genesisRead(): can't determine file name format

Essentially, my problem is that I have roughly 1000 dicom files (as evidenced by command "file" in terminal) without an identifiable extension and I need to find a way to change these into one of any of the set MR001.dcm - MR144.dcm to be read by mri_convert.

As it stands now, I don't know what series (average DC, isotropic, FA, etc.) these 8 digit numbers correspond to so I'm unsure of how to proceed. Suggestions?

Thanks for your time.

-Sam

-- Sam Enumah Harvard College Class of 2010 Concentrator in Neurobiology senumah@fas.harvard.edu