Hi Mohamad

You could convert the Dicoms in other s/w to .nii and then read them. Maybe Bruce and Doug have more elegant solutions

Hth Shantanu

On Mon, October 20, 2014 10:41 am, Alshikho, Mohamad J. wrote:

Hi , The command <unpacksdcmdir> is only used to unpack Siemens DICOM files, How can I unpack the non Siemens DICOMs?

Thanks, Moahmad _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Hi Doug, But in freeSurfer wiki https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastUnpackData they mentioned the following "The program that does this is unpacksdcmdir (this is only used to unpack Siemens DICOM files)." when I used this command on a my data set it gives me an error for certain subjects!

Thanks ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Monday, October 20, 2014 11:35 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] unpacksdcmdir

dcmunpack will unpack any dicoms

On 10/20/2014 11:21 AM, Shantanu Ghosh wrote:

Hi Mohamad

You could convert the Dicoms in other s/w to .nii and then read them. Maybe Bruce and Doug have more elegant solutions

Hth Shantanu

On Mon, October 20, 2014 10:41 am, Alshikho, Mohamad J. wrote:

...

Hi , The command <unpacksdcmdir> is only used to unpack Siemens DICOM files, How can I unpack the non Siemens DICOMs?

Thanks, Moahmad _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Sorry I did not notice that this is a different command. I will try it now. and I will let you now

Thanks a lot ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Monday, October 20, 2014 3:31 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] unpacksdcmdir

did you try dcmunpack?

On 10/20/2014 03:30 PM, Alshikho, Mohamad J. wrote:

Hi Doug, But in freeSurfer wiki https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastUnpackData they mentioned the following "The program that does this is unpacksdcmdir (this is only used to unpack Siemens DICOM files)." when I used this command on a my data set it gives me an error for certain subjects!

Thanks ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Monday, October 20, 2014 11:35 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] unpacksdcmdir

dcmunpack will unpack any dicoms

On 10/20/2014 11:21 AM, Shantanu Ghosh wrote:

...

Hi Mohamad

You could convert the Dicoms in other s/w to .nii and then read them. Maybe Bruce and Doug have more elegant solutions

Hth Shantanu

On Mon, October 20, 2014 10:41 am, Alshikho, Mohamad J. wrote:

...

Hi , The command <unpacksdcmdir> is only used to unpack Siemens DICOM files, How can I unpack the non Siemens DICOMs?

Thanks, Moahmad _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Run it with -help to get more info

On 10/21/14 12:25 AM, Alshikho, Mohamad J. wrote:

Hi Doug, I ran the following command line dcmunpack -scr <dicoms dir path> in my script and it gives me a list of the run/series. How can I save this list as a log file. I tried to add the flag -targ and the flag -log but it gives me an error and asked me to specify the series run numbe? Any suggestions please?. ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Alshikho, Mohamad J. Sent: Monday, October 20, 2014 3:33 PM To: Freesurfer support list Subject: Re: [Freesurfer] unpacksdcmdir

Sorry I did not notice that this is a different command. I will try it now. and I will let you now

Thanks a lot ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Monday, October 20, 2014 3:31 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] unpacksdcmdir

did you try dcmunpack?

On 10/20/2014 03:30 PM, Alshikho, Mohamad J. wrote:

...

Hi Doug, But in freeSurfer wiki https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastUnpackData they mentioned the following "The program that does this is unpacksdcmdir (this is only used to unpack Siemens DICOM files)." when I used this command on a my data set it gives me an error for certain subjects!

Thanks ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Monday, October 20, 2014 11:35 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] unpacksdcmdir

dcmunpack will unpack any dicoms

On 10/20/2014 11:21 AM, Shantanu Ghosh wrote:

...

Hi Mohamad

You could convert the Dicoms in other s/w to .nii and then read them. Maybe Bruce and Doug have more elegant solutions

Hth Shantanu

On Mon, October 20, 2014 10:41 am, Alshikho, Mohamad J. wrote:

...

Hi , The command <unpacksdcmdir> is only used to unpack Siemens DICOM files, How can I unpack the non Siemens DICOMs?

Thanks, Moahmad _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer