Re: [Freesurfer] Longitudinal Process

2018-07-04 Thread Martin Reuter 
Hi Samir, 

you can first conform all inputs to 1mm isotropic using mri_convert --conform 
input output

It may make sense to add a covariate in the statistics for the different 
acquisition to control for a linear effect. 

Best, Martin


> On 25. May 2018, at 08:29, Samir Rekic  wrote:
> 
> 
> 
> 
> Dear FreeSurfers,
> I am trying to run the longitudinal process including (recon-all -base and 
> -long) for 5 different timepoints.
> But in my original data one the of five differs in the acquisition 
> orientation and in the size of the field of view, so the results and 
> especially the statistic is distorted.
> Four of my data sets have RPI as acquisition Parameter and a FOV of 230,
> the last data set has LPI and a FOV of 257.
> Does it even make sense to include this last dataset – is it even possible 
> (due to different Parameters)?
> Do I have to pre-process this different data set?
>  
> Thank you in advance!
> Sam
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> 
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[Freesurfer] Longitudinal Process

2018-05-25 Thread Samir Rekic 
External Email - Use Caution

Dear FreeSurfers,
I am trying to run the longitudinal process including (recon-all -base and 
-long) for 5 different timepoints.
But in my original data one the of five differs in the acquisition orientation 
and in the size of the field of view, so the results and especially the 
statistic is distorted.
Four of my data sets have RPI as acquisition Parameter and a FOV of 230,
the last data set has LPI and a FOV of 257.
Does it even make sense to include this last dataset – is it even possible (due 
to different Parameters)?
Do I have to pre-process this different data set?

Thank you in advance!
Sam
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Re: [Freesurfer] longitudinal process

2014-03-02 Thread Martin Reuter 
Hi Anna,
No, you can still use links. When rerunning the base, the cross are not 
changed. Once the base loiks good, you also have to rerun the longs of course.

Best Martin


Sent via my smartphone, please excuse brevity.

 Original message 
From: Anna Jonsson ajonsso...@gmail.com 
Date:03/02/2014  5:27 AM  (GMT-05:00) 
To: Martin Reuter mreu...@nmr.mgh.harvard.edu 
Cc: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] longitudinal process 

Hi thank you for reply. May I ask other question; after editing the base it 
says to reocnstruct with recon-all -base -tp1 -tp2 etc. Does this require that 
all scans are located in the same directory? (Before i used symbolic links as 
scans are in different directories) but i am unsure whether after editing the 
abse anything further is actually done to the cross runs?

Thank you for your help,

Anna


On Tue, Feb 18, 2014 at 7:58 PM, Martin Reuter mreu...@nmr.mgh.harvard.edu 
wrote:
Hi Anna,

the linear mixed effects models can include subjects with a single time point 
and it would be a shame to drop that information. That is why we modified the 
longitudinal pipeline (use 5.3) to allow processing of subjects with a single 
time point. However, it is necessary that these images undergo the same 
processing steps as the rest of the data (to avoid bias). So you run it exactly 
as other subjects, with a cross sectional, -base and a -long step:

recon-all -all -s tp1id -i path_to_tp1_dcm
recon-all -base templateid -tp tp1id -all
recon-all -long tp1id templateid -all

Best, Martin


On 02/18/2014 04:58 AM, Anna Jonsson wrote:
Dear Freesurfer experts,

I want to know if possible when doing longitudinal stream to put subjects with 
only one time-point through the processing (eg base and long runs) in order to 
subsequently use with the Matlab lme tools? Or better is to leave them out and 
only do those with 2+ times?

Thank you 

Kind Regards,

Anna


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-- 
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: 
   mreu...@nmr.mgh.harvard.edu
   reu...@mit.edu
Web  : http://reuter.mit.edu 

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[Freesurfer] longitudinal process

2014-02-18 Thread Anna Jonsson 
Dear Freesurfer experts,

I want to know if possible when doing longitudinal stream to put subjects
with only one time-point through the processing (eg base and long runs) in
order to subsequently use with the Matlab lme tools? Or better is to leave
them out and only do those with 2+ times?

Thank you

Kind Regards,

Anna
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addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] longitudinal process

2014-02-18 Thread Martin Reuter 

Hi Anna,

the linear mixed effects models can include subjects with a single time 
point and it would be a shame to drop that information. That is why we 
modified the longitudinal pipeline (use 5.3) to allow processing of 
subjects with a single time point. However, it is necessary that these 
images undergo the same processing steps as the rest of the data (to 
avoid bias). So you run it exactly as other subjects, with a cross 
sectional, -base and a -long step:


recon-all -all -s tp1id -i path_to_tp1_dcm

recon-all -base templateid -tp tp1id -all

recon-all -long tp1id templateid -all


Best, Martin

On 02/18/2014 04:58 AM, Anna Jonsson wrote:

Dear Freesurfer experts,

I want to know if possible when doing longitudinal stream to put 
subjects with only one time-point through the processing (eg base and 
long runs) in order to subsequently use with the Matlab lme tools? Or 
better is to leave them out and only do those with 2+ times?


Thank you

Kind Regards,

Anna


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--
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:
   mreu...@nmr.mgh.harvard.edu
   reu...@mit.edu
Web  : http://reuter.mit.edu

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