I doubt any of them will work as they don't have enough slices/files, meaning either the resolution is way too low or the FOV is not whole brain. You typically need at least 128 slices in some T1-weighted volume to get high enough resolution (e.g. <1.5mm or so)

cheers Bruce On Fri, 14 Nov 2014, Douglas N Greve wrote:

That list gives you each acquisition and the protocol used to collect it. You chose one (or more) and pass a single file to recon-all with -i; recon-all will find the rest of the files in that series. As to which series you need, it is hard to say since I did not collect the data :). I'm guessing the 2nd one. doug

On 11/14/2014 02:46 PM, Mattevada, Sravan wrote:

...

Hello Freesurfers,

I am a beginner and have a question about the dicom file I need to select to do the recon-all process.

I ran dcmunpack on the DICOM files I have with the following result

Institution RADIOLOGY ASSOCIATES-CDI

1 LOCALIZER3PLANE 5 20 40 0.546875 ROW 180 /home/freesurfer/Desktop/9160/DICOM/PA000000/ST000000/SE000000/IM000003

2 T1SESAG 8 345 90 0.8984375 ROW 140 /home/freesurfer/Desktop/9160/DICOM/PA000000/ST000000/SE000001/IM000011

3 T2TSEAX 85 4170 180 0.8984375 ROW 110 /home/freesurfer/Desktop/9160/DICOM/PA000000/ST000000/SE000002/IM000011

4 T1SEAX 8 410 90 0.8984375 ROW 140 /home/freesurfer/Desktop/9160/DICOM/PA000000/ST000000/SE000003/IM000011

5 T2FLAIRAX 117 9000 180 0.8984375 ROW 130 /home/freesurfer/Desktop/9160/DICOM/PA000000/ST000000/SE000004/IM000011

6 T2FL2DAXHEMO 27 855 20 0.8984375 ROW 80 /home/freesurfer/Desktop/9160/DICOM/PA000000/ST000000/SE000005/IM000011

7 AXep2d_diff_2scan_trace 98 4100 90 1.796875\1.796875 COL 1260 /home/freesurfer/Desktop/9160/DICOM/PA000000/ST000000/SE000006/IM000011

8 AXep2d_diff_2scan_trace_ADC 98 4100 90 1.796875\1.796875 COL 1260 /home/freesurfer/Desktop/9160/DICOM/PA000000/ST000000/SE000007/IM000011

9 T2TSECOROBL 87 4260 180 0.4296875 ROW 110 /home/freesurfer/Desktop/9160/DICOM/PA000000/ST000000/SE000008/IM000011

I don’t have one specific .dcm file to run the recon-all command

The directory structure on the CD that I have has the

9 Folders (SE00000, SE000001 …)

Each folder has 6 – 25 files (IM00000, IM00000 …)

There are a total of 225 files

When I use the software that came with the CD to see the images, I

can see that each folder has series of images in different angles of the skull (different resolutions)

Does recon-all use all the 225 images in all the folders?

If yes how do I know which of the above dcmunpack results is the best option to start the recon-all process?

I appreciate your help.

Thanks

Sravan

Sravan Mattevada, MSCS

Computer Prog. Analyst III

*UNT Health*

Ph . 817 735 0499

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