On Jul 1, 2013, at 11:35 AM, Martin Reuter wrote:

Hi Jon

That is one way of calling the regular recon-all stream. You point it to any input file with the -i flag. Here dcm could be a dicom image, but can be nifti or another format.

Best, Martin

On 07/01/2013 10:17 AM, Jonathan Holt wrote:
Martin,

I'm going to experiment with data with better image quality using the longitudinal stream. In the first step of the workflow I'm confused to what 'dcm' stands for in the following command
  recon-all -all -s <tpNid> -i path_to_tpN_dcm
could you elaborate?

jon
On Sat, Jun 29, 2013 at 12:29 AM, Martin Reuter <mreuter@nmr.mgh.harvard.edu> wrote:

Hi Jon,

The longitudinal stream in freesurfer is designed to reduce variability in situations where you have several scans from the same subject. The information, that it is the same subject, is valuable and by initializing many steps in recon-all with common data we can increase reliability of measures. The stream has three steps
1. process your data independently (called cross)

2. create a within-subject template and process that (called base)

3. initialize each time point with information from the template (called long).

you can find some more info here:

https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing

and here:

Within-Subject Template Estimation for Unbiased Longitudinal Image Analysis
M. Reuter, N.J. Schmansky, H.D. Rosas, B. Fischl.
NeuroImage 61(4), pp. 1402-1418, 2012.

http://reuter.mit.edu/papers/reuter-long12.pdf

Not sure if this will fix things for you. If the image quality is bad and if the cross sectional stream (first step) has severe problems already, it is unlikely that everything will recover without any edits. But if, for example, one time point has motion artifiacts and the others not, then the template will be fine and there is a good chance that results on all time points will be good after the 3rd step.

Best, Martin

On Jun 28, 2013, at 9:14 PM, Jonathan Holt <whatsdac@umich.edu> wrote:

Martin,

I hate to be noobish, but can you elaborate on the longitudinal stream? It may be that I'm doing entirely too much work.

jon

On Jun 28, 2013, at 11:38 AM, Martin Reuter wrote:

So you are not processing this with the longitudinal stream? You are just running each image independently through freesurfer and look at the results?
Is there motion in all the 4 time points in this subject or only in the one image that you send? With motion artifacts, surfaces are not very reliable.

Best, martin

On Jun 28, 2013, at 11:36 AM, Jonathan Holt <whatsdac@umich.edu> wrote:

We have 4 time points for that subject and it's an issue in all 4, to a lesser degree in one of them, but still an issue. Same area, same hemisphere, every time. Perhaps it is pathology based, I am not entirely sure.

On Jun 28, 2013, at 11:19 AM, Martin Reuter wrote:

Hi Jonathan,

is this in cross sectional processing or in longitudinal?

One thing I notice is significant motion artifacts (ringing), which seem to lead to underestimation of WM, also you could fine tune the skull strip.

Best, Martin

On Jun 28, 2013, at 10:19 AM, Jonathan Holt <whatsdac@umich.edu> wrote:

Hi all,

I'm having a bit of trouble with one particular subject for which we brains for 4-5 different time points. The pial surface is consistently misplaced in the same area, see attached main/aux volume images. I'm hesitant to manually replace the white matter myself as I fear it wouldn't be as accurate. Suggestions on other methods to fix this?

The problem is always in the LH temporal right around the lateral inferior ventricle and the fusiform and other subcortical structures.

<Screen Shot 2013-06-28 at 10.18.59 AM.png><Screen Shot 2013-06-28 at 10.14.50 AM.png>_______________________________________________
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---------------------------------

Dr. Martin Reuter

Assistant in Neuroscience - Massachusetts General Hospital
Instructor in Neurology   - Harvard Medical School
MGH / HMS / MIT

A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129

Phone: +1-617-724-5652
Email:

mreuter@nmr.mgh.harvard.edu

reuter@mit.edu

Web : http://reuter.mit.edu

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---------------------------------

Dr. Martin Reuter

Assistant in Neuroscience - Massachusetts General Hospital
Instructor in Neurology   - Harvard Medical School
MGH / HMS / MIT

A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129

Phone: +1-617-724-5652
Email:

mreuter@nmr.mgh.harvard.edu

reuter@mit.edu

Web : http://reuter.mit.edu

---------------------------------

Dr. Martin Reuter

Assistant in Neuroscience - Massachusetts General Hospital
Instructor in Neurology   - Harvard Medical School
MGH / HMS / MIT

A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129

Phone: +1-617-724-5652
Email:

mreuter@nmr.mgh.harvard.edu

reuter@mit.edu

Web : http://reuter.mit.edu
-- 
Martin Reuter, Ph.D.
Assistant in Neuroscience - Massachusetts General Hospital
Instructor in Neurology   - Harvard Medical School
MGH / HMS / MIT

A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129

Phone: +1-617-724-5652
Email: 
   mreuter@nmr.mgh.harvard.edu
   reuter@mit.edu
Web  : http://reuter.mit.edu 