[Freesurfer] Longitudinal processing

[Linn Mittlestein]

Dear Freesurfer group.

I am having some concerns about Freesurfer and the different steps. I have
used version 5.0 for the cross-sectional timepoints, and I am now using
version 5.3 for the longitudinal processing. I am doing therefore the
several different steps involved in longitudinal processing, for example
-base, -long runs and now for the lme analysis with matlab also the
smoothing steps etc. I am very concerned however because looking at the
brain masks after these steps have been done (ie the cross-sectional runs),
they look much worse than they did before the longitudinal editing began;
large chunks of surfaces are missing. Has anybody else reported this
problem? Could it be because the longitudinal steps are now being done with
version 5.3 as opposed to 5? Surely this should not have such a large
effect on the brainmasks, as to completely "deform" them?

Kind Regards,

Linn
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[Freesurfer] Longitudinal processing

[Jonathan Holt]

As I'm having trouble importing nifti files into the first step of the 
longitudinal work flow, I'm wondering if I can use volumes generated from 
recon-all -s  for the second and third steps of the workflow.

jon
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[Freesurfer] Longitudinal processing

[Allison Gruber]

Hello,

I am using the longitudinal processing stream to analyze a data set. I  
have two questions:

1: We are expecting there to be significant changes in the volume of  
certain structures and gray matter between time point 1 and 2. We  
wanted to make sure the longitudinal stream is still appropriate.

2: If some subjects do not have both time points, should we process  
them as individual time points or should we use a template brain in  
order to use the longitudinal stream?

Thank you very much,
Allison

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[Freesurfer] longitudinal processing

[Catherine Bois]

Hi, just to clarify,

When beginning longitudinal analysis, the first step is the same as  
cross-sectional processing, eg just the "normal" recon-all command,  
for each subject, and each individual time point? Then the norm.mgz  
files are used?

Thanks

-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.


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[Freesurfer] longitudinal processing

[Catherine Bois]

Sorry, another question about longitudinal processing; just realized  
that my institution has been using version 5.0, so all the cross  
sectional processing has been done with this version, is it ok to go  
ahead and do base and long with version 5.1 once I have managed to get  
this installed?

Thanks,

- Forwarded message from c.b...@sms.ed.ac.uk -
 Date: Wed, 09 Jan 2013 13:35:12 +
 From: Catherine Bois 
  Subject: longitudinal processing
   To: freesurfer@nmr.mgh.harvard.edu

Hi, just to clarify,

When beginning longitudinal analysis, the first step is the same as  
cross-sectional processing, eg just the "normal" recon-all command,  
for each subject, and each individual time point? Then the norm.mgz  
files are used?

Thanks

-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.



- End forwarded message -


-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.


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[Freesurfer] longitudinal processing

[Linn Mittlestein]

Dear Freesurfer experts,

 I just tried creating the -base for longitudinal processing on two time
points using

recon-all -base  -tp  -tp  ... -all

After doing this, I received no error messages and a third folder
named after the template name I had given
 it it was present in the subjects directory, however all of these
files were empty. What have I done
 wrong?

Regards
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[Freesurfer] longitudinal processing

[ccongle]

Hello,

I'm trying to run the longitudinal processing pipeline, but can't figure
out a command that works.   Below is what I've tried and what has happened
(MC-07M_prereconEDIT is the 'pre' timepoint, and MC-07M_post is the
'post').  Can you help?

In dev env:
jizo:ccongle[103] recon-all-long -long -tp1 MC-07M_prereconEDIT -s
MC-07M_post
recon-all-long: Command not found.

jizo:ccongle[104] recon-all -long -tp1 MC-07M_prereconEDIT -s MC-07M_post
INFO: SUBJECTS_DIR is /autofs/space/jizo_001/users/STRUCTURALS/MBSR
Actual FREESURFER_HOME /autofs/space/freesurfer/centos4.0_x86_64/dev
ERROR: nothing to do

In stable env:
jizo:ccongle[85] recon-all -long -tp1 MC-07M_prereconEDIT -s MC-07M_post
ERROR: Flag -long unrecognized.
-long -tp1 MC-07M_prereconEDIT -s MC-07M_post

jizo:ccongle[87] recon-all-long -tp1 MC-07M_prereconEDIT -s MC-07M_post
recon-all-long: Command not found.

Thanks,
Christina
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[Freesurfer] longitudinal processing

[ccongle]

Hi,

I'm working with the recon-all -long processing stream.  It went all the
way through on one of my brains yesterday, but today it's stopping around
here:


invert the first LTA before applying it
Talairach xfrm src file is
/space/jizo/1/users/STRUCTURALS/MBSR/MS2-09M_prereconEDIT/mri/orig.mgz
Talairach xfrm dst file is
/usr/local/freesurfer/stable/mni/bin/../share/mni_autoreg/average_305.mnc
INFO: dst volume info differs from the one stored in lta.  gets modified now.
volume geometry:
extent  : (172, 220, 156)
voxel   : ( 1.,  1.,  1.)
x_(ras) : ( 1.,  0.,  0.)
y_(ras) : ( 0.,  1.,  0.)
z_(ras) : ( 0.,  0.,  1.)
c_(ras) : (-0.0950, -16.5100,  9.7500)
file:
/usr/local/freesurfer/stable/mni/bin/../share/mni_autoreg/average_305.mnc
volume geometry:
extent  : (86, 110, 68)
voxel   : ( 2.,  2.,  2.)
x_(ras) : ( 1.,  0.,  0.)
y_(ras) : ( 0.,  1.,  0.)
z_(ras) : ( 0.,  0.,  1.)
c_(ras) : (-0.0950, -16.5100,  9.7500)
file:
/usr/local/freesurfer/stable/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc
volume geometry:
extent  : (256, 256, 256)
voxel   : ( 1.,  1.,  1.)
x_(ras) : (-1.,  0.,  0.)
y_(ras) : ( 0.,  0., -1.)
z_(ras) : ( 0.,  1.,  0.)
c_(ras) : ( 7.4766,  9.4936, -0.2721)
file:
/space/jizo/1/users/STRUCTURALS/MBSR/MS2-09M_prereconEDIT/mri/orig.mgzvolume
geometry:
extent  : (256, 256, 256)
voxel   : ( 1.,  1.,  1.)
x_(ras) : (-1.,  0.,  0.)
y_(ras) : ( 0.,  0., -1.)
z_(ras) : ( 0.,  1.,  0.)
c_(ras) : ( 7.4766,  9.4936, -0.2721)
file:
/space/jizo/1/users/STRUCTURALS/MBSR/MS2-09M_prereconEDIT/mri/orig.mgzRead
individual LTAs
Warning: dst volume of lta1 doesn't match src volume of lta2
Volume geometry for lta1-dst:
Volume geometry for lta2-src:
Combine the two LTAs to get a RAS-to-RAS from src of LTA1 to dst of LTA2
xfma: Undefined variable.
jizo:ccongle[116]
_

I'm not sure what the 'xfma' is.  Do you know what the problem might be?

Thanks,
Christina

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[Freesurfer] longitudinal processing

[Marie Schaer]

Hi,

I am planing to process a longitudinal dataset with 3 timepoints. Is  
it worthy to begin already the cross-sectional processing with version  
5.0 and then wait version 5.1 to continue from the template part. Or  
would you advice me to wait the release of version 5.1 for the entire  
processing?

Thank you for your help,

Marie
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[Freesurfer] longitudinal processing

[Nicola Hobbs]

Hi there,

We would like to do some longitudinal processing.  Our baseline scans 
have been run through v4.0.3, and we spent a long time manually editing 
the cortical segmentations.  Ideally we would like to use these 
segmentations as the reference for our longitudinal processing (v4.1.0), 
but we are worried that using different versions for the same study 
could introduce errors.  Could you advise us on whether we need to 
re-run our baseline data through v4.1.0 before we attempt any 
longitudinal processing?


Many thanks for your help,
Nicola
--


Nicola Hobbs

Dementia Research Centre
National Hospital for Neurology and Neurosurgery
Queen Square
London WC1N 3BG

+44 (0)845 155 5000 ext. 723839

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[Freesurfer] longitudinal processing

[Jared Price]

Hi everybody,
2 quick questions about longitudinal processing.
   1) does the longitudinal processing even call the default gca atlas 
or does it use something else?
   2) when processing say 7 time points should all longitudinal scans 
be processed from baseline or should time 3 be processed from time 2 etc.


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[Freesurfer] longitudinal processing

[Dana W. Moore]

FreeSurfers,

I am using the longitudinal processing stream to look at change in 
the lateral ventricles at several timepoints.  As a control measure, 
we are running two consecutive baseline images in the scanner. These 
images were done back-to-back, exactly the same, and the subject did 
not get out of the scanner nor reposition.  Motion was not a 
problem.  I have processed this first subject, and the longitudinal 
stream gives me a 2% change in lateral ventricular volume, comparing 
the two baseline scans.  This is bigger than I'd like to see, as we 
are interested in changes over time as small as 2%.  Is this kind of 
variability expected, or am I doing something wrong?  I just used the 
first baseline as tp1, processed it cross-sectionally, and then 
longitudinally, and then I used the second baseline as tp2.


Thanks,
Dana


Dana W. Moore, Ph.D.
Neuropsychology Fellow
Cornell Neuropsychology Service
Weill Medical College of Cornell University
New York Presbyterian Hospital
Department of Neurology & Neuroscience
428 East 72nd Street, Suite 500
New York, NY 10021
Phone: 212-746-2441
Fax: 212-746-5584
Email: dwm2...@med.cornell.edu

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[Freesurfer] Longitudinal processing

[falk.luesebr...@med.ovgu.de]

External Email - Use Caution

Dear all,

I'm a beginner in using the longitudinal processing pipeline (as well as 
statistical analysis) and it would be great to get some insights or hints to 
analyze my data.

I have a dataset consisting of 11 subjects each acquired at 7 different time 
points with an isotropic resolution of 1 and 0.8 mm at 3T using a 64-channel 
head coil. Using that dataset I want to investigate short term differences in 
e.g. cortical thickness with the goal to assess the degree of biological 
variance during that time period.

I have plotted the mean cortical thickness of each time point of every subject 
(using lme_timePlot and lme_lowessPlot) showing a somewhat random distribution 
across time and from my perspective fairly high standard deviation. I wanted to 
have a look at the individual percent change by overlaying the symmetric 
percent change on fsaverage, but wasn't quite sure of the scale. Is it in 
percent? So in case I set the scale bar between 1 and 5, the color relates to 1 
to 5 percent?

What other ways would make sense to have a look at? I definitely cannot compare 
groups, as there is just one. The days and time of acquistion are rather 
randomly choosen, so I potentially cannot use either as a covariate.

Best,
Falk

...

[klinikum_logo_schmal_e-mail_blau]
University Clinic for Neurology

Otto-von-Guericke-university Magdeburg
Medical faculty
Leipziger Str. 44
39120 Magdeburg

Phone +49-391-6117-512

falk.luesebr...@med.ovgu.de
http://www.kneu.ovgu.de/kneu.html

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[Freesurfer] Longitudinal processing

[AJ]

External Email - Use Caution

Hi,

After running longitudinal processing and creating base and long runs, When
looking at volumes of various structures over time of the same subject, are
the volumes not need to be corrected by eTIV since head size does not vary
overtime?

Many thanks for your input.
Sincerely,

AJ
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Re: [Freesurfer] Longitudinal processing

[Martin Reuter]

Hi Linn,

do you mean the brain mask in the cross sectional runs gets worse after you run 
the longitudinal steps (base and long)? That is not really possible, as these 
steps don't touch the cross data (only read from it).

If you mean that the brain mask in the long looks worse than in the cross (of 
same subject time point), then you need to check the brain mask in the base. 
That one is copied to all the longitudinal runs, so it needs to be accurate in 
the base. If it is accurate there, but still not in a specific longitudinal run 
then that indicates a mis-alignment to the base. If that is the case, the first 
thing I'd try is rename base and all longitudinals and re-run those from scatch 
to make sure it's not a hick-up (e.g. io problem).

Best, Martin


On Jun 18, 2013, at 5:16 AM, Linn Mittlestein  wrote:

> Dear Freesurfer group.
> 
> I am having some concerns about Freesurfer and the different steps. I have 
> used version 5.0 for the cross-sectional timepoints, and I am now using 
> version 5.3 for the longitudinal processing. I am doing therefore the several 
> different steps involved in longitudinal processing, for example -base, -long 
> runs and now for the lme analysis with matlab also the smoothing steps etc. I 
> am very concerned however because looking at the brain masks after these 
> steps have been done (ie the cross-sectional runs), they look much worse than 
> they did before the longitudinal editing began; large chunks of surfaces are 
> missing. Has anybody else reported this problem? Could it be because the 
> longitudinal steps are now being done with version 5.3 as opposed to 5? 
> Surely this should not have such a large effect on the brainmasks, as to 
> completely "deform" them?
> 
> Kind Regards,
> 
> Linn
> 
> 
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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: 
   mreu...@nmr.mgh.harvard.edu
   reu...@mit.edu
Web  : http://reuter.mit.edu 

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[Freesurfer] Longitudinal Processing Error

[Jonathan Holt]

Log file indicates manual talairach alignment may be necessary.

ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
***FAILED*** (p=0.0079, pval=0. < threshold=0.0050)
Manual Talairach alignment may be necessary

Can anyone provide direction. Alternatively, the error indicates talairach
alignment can be skipped with -notal-check flag. Is this step completely
necessary?

jon
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Re: [Freesurfer] Longitudinal processing

[Allison Stevens Player]

In short, the answer is yes. The 2nd and 3rd steps will take the subject 
ID and find the relevant files. But I would expect the first step to take 
nifti just fine. Can you send the command you are running?

On Mon, 8 Jul 2013, Jonathan Holt wrote:

> As I'm having trouble importing nifti files into the first step of the 
> longitudinal work flow, I'm wondering if I can use volumes generated from 
> recon-all -s  for the second and third steps of the workflow.
>
> jon
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>
>
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Re: [Freesurfer] Longitudinal processing

[Jonathan Holt]

Allison I'm running the followingrecon-all -all -s  -i path/to/nifti attatched is the error recon log I've already gone over this with bruce, martin. It seems as if the 001.mgz, orig.mgz, and orig_nu.mgz all have incorrect orientations. This is coming straight out of the nifti files I've passed and these mgz's are generated before the recon-all process exits with errors.

recon-all.log
Description: Binary data
On Jul 8, 2013, at 1:37 PM, Allison Stevens Player wrote:In short, the answer is yes. The 2nd and 3rd steps will take the subject ID and find the relevant files. But I would expect the first step to take nifti just fine. Can you send the command you are running?On Mon, 8 Jul 2013, Jonathan Holt wrote:As I'm having trouble importing nifti files into the first step of the longitudinal work flow, I'm wondering if I can use volumes generated from recon-all -s  for the second and third steps of the workflow.jon___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThe information in this e-mail is intended only for the person to whom it isaddressed. If you believe this e-mail was sent to you in error and the e-mailcontains patient information, please contact the Partners Compliance HelpLine athttp://www.partners.org/complianceline . If the e-mail was sent to you in errorbut does not contain patient information, please contact the sender and properlydispose of the e-mail.___
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Re: [Freesurfer] Longitudinal processing

[Allison Stevens Player]

I see now. If the orientation information is incorrect, this will continue 
to be a problem. It sounds like you have access to the dicoms? If so, it's 
better to wait and use those.

Allison

On Mon, 8 Jul 2013, Jonathan Holt wrote:


Allison I'm running the following

recon-all -all -s  -i path/to/nifti

attatched is the error recon log

I've already gone over this with bruce, martin. It seems as if the 001.mgz, 
orig.mgz, and orig_nu.mgz all have incorrect orientations. This is coming 
straight out of the nifti files I've passed and these mgz's are generated 
before the recon-all process exits with errors.




On Jul 8, 2013, at 1:37 PM, Allison Stevens Player wrote:


In short, the answer is yes. The 2nd and 3rd steps will take the subject ID and 
find the relevant files. But I would expect the first step to take nifti just 
fine. Can you send the command you are running?

On Mon, 8 Jul 2013, Jonathan Holt wrote:


As I'm having trouble importing nifti files into the first step of the longitudinal 
work flow, I'm wondering if I can use volumes generated from recon-all -s 
 for the second and third steps of the workflow.

jon
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[Freesurfer] longitudinal processing versioning

[Harms, Michael]

Hi guys,
We have some longitudinal scans in which the time1 (T1) scans were processed with FS 5.1, and the T2/T3 scans haven't been processed yet.


I'm trying to assess whether the differences between FS 5.1 and 5.3 warrant us re-running the T1 scans under FS 5.3.  
I see two possible options:
1) Process all "cross-sectional" runs under FS 5.1.  i.e., we already have T1 under FS 5.1, so do the cross-runs of T2/T3 under 5.1 as well.  (I'm assuming that it wouldn't be desirable to have a mix of versions at the cross-sectional stage).  Then switch
 to using FS 5.3 for creating the template (-base) and longitudinal (-long) data.


2) Re-process the cross-sectional scans for T1 using FS 5.3, and do everything with FS 5.3.


Do you have any reason to expect relevant differences in the final -long output between these two approaches?
And, if approach (2) is necessary, do we need to re-run the T1 through FS 5.3 with the "-clean" flag?  i.e,. if we were to re-run the cross-sectional version of the T1 scan using FS 5.3, but keeping previous edits, would that potentially bias the T1 scan
 in some fashion, since the T2/T3 scans will be run fresh in FS 5.3 without any prior manual edits?


thanks,
-MH




-- 
Michael Harms, Ph.D.

---
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Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu






 



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Re: [Freesurfer] Longitudinal processing

[Martin Reuter]

Hi Jon,

I am also confused about this whole discussion. It seems from what you said 
earlier that at some point you have been able to run freesurfer on your images. 
You did not use the -i flag back then, but somehow managed to get from the 
original dicom (via nifti, via some mri_convert command) to some image that 
free surfer was able to use.

Just do the same thing here and then once that is done, run the base and long 
stream on top of it.

Best, Martin

On Jul 8, 2013, at 2:45 PM, Jonathan Holt  wrote:

> I potentially have access to dicoms. My PI was confused as we're using GE 2D 
> dcm images with 126 images per timepoint, he wasn't sure how to have them 
> organized for a test run.
> 
> 
> On Jul 8, 2013, at 2:20 PM, Allison Stevens Player wrote:
> 
>> I see now. If the orientation information is incorrect, this will continue 
>> to be a problem. It sounds like you have access to the dicoms? If so, it's 
>> better to wait and use those.
>> Allison
>> 
>> On Mon, 8 Jul 2013, Jonathan Holt wrote:
>> 
>>> Allison I'm running the following
>>> 
>>> recon-all -all -s  -i path/to/nifti
>>> 
>>> attatched is the error recon log
>>> 
>>> I've already gone over this with bruce, martin. It seems as if the 001.mgz, 
>>> orig.mgz, and orig_nu.mgz all have incorrect orientations. This is coming 
>>> straight out of the nifti files I've passed and these mgz's are generated 
>>> before the recon-all process exits with errors.
>>> 
>>> 
>>> 
>>> 
>>> On Jul 8, 2013, at 1:37 PM, Allison Stevens Player wrote:
>>> 
 In short, the answer is yes. The 2nd and 3rd steps will take the subject 
 ID and find the relevant files. But I would expect the first step to take 
 nifti just fine. Can you send the command you are running?
 
 On Mon, 8 Jul 2013, Jonathan Holt wrote:
 
> As I'm having trouble importing nifti files into the first step of the 
> longitudinal work flow, I'm wondering if I can use volumes generated from 
> recon-all -s  for the second and third steps of the workflow.
> 
> jon
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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: 
   mreu...@nmr.mgh.harvard.edu
   reu...@mit.edu
Web  : http://reuter.mit.edu 

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[Freesurfer] Longitudinal Processing Pipeline

[David Tate]

Question regarding longitudinal processing pipeline.

Is there a way to force the -long procedure to use an individual base template 
for a time point not used to create the base in the first place?  

David F. Tate, Ph.D.

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Re: [Freesurfer] Longitudinal processing

[Martin Reuter]

Hi Allison,

with very large changes across time, the longitudinal stream can fail or
may need more manual intervention (edits). We have run it successfully
on Huntington's Disease patients with large changes and many time
points. The only way to find out if it works on your data is to run it.

I have recently made changes to the longitudinal stream (to be available
in FS 5.2) that will allow inclusion of subject with a single time
point. Currently we recommend to exclude them instead of running them as
individual time points. The reason is that results in those cross
sectional runs will be different from longitudinal runs and this may
introduce a bias (especially if single time points subjects are more
likely from one group than the other). 

Best, Martin


On Thu, 2012-09-27 at 10:51 -0400, Allison Gruber wrote:
> Hello,
> 
> I am using the longitudinal processing stream to analyze a data set. I  
> have two questions:
> 
> 1: We are expecting there to be significant changes in the volume of  
> certain structures and gray matter between time point 1 and 2. We  
> wanted to make sure the longitudinal stream is still appropriate.
> 
> 2: If some subjects do not have both time points, should we process  
> them as individual time points or should we use a template brain in  
> order to use the longitudinal stream?
> 
> Thank you very much,
> Allison
> 
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Re: [Freesurfer] longitudinal processing

[Martin Reuter]

Hi Catherine, 

yes, the first step is independent (cross sectional) processing of all
time points (normal recon-all).

We usually do not recommend to mix versions. But the 5.1 longitudinal
stream has been designed in a way that it can take the cross sectional
data from 5.0. So it is possible. Just make sure that if you add time
points and subjects you still use 5.0 for the cross sectional recons and
5.1 for base and long to be consistent.

Alternatively wait a little longer and re-run everything from scratch
with the new 5.2 version that will come out hopefully this month.

Best, Martin

On Wed, 2013-01-09 at 14:22 +, Catherine Bois wrote:
> Sorry, another question about longitudinal processing; just realized  
> that my institution has been using version 5.0, so all the cross  
> sectional processing has been done with this version, is it ok to go  
> ahead and do base and long with version 5.1 once I have managed to get  
> this installed?
> 
> Thanks,
> 
> - Forwarded message from c.b...@sms.ed.ac.uk -
>  Date: Wed, 09 Jan 2013 13:35:12 +
>  From: Catherine Bois 
>   Subject: longitudinal processing
>To: freesurfer@nmr.mgh.harvard.edu
> 
> Hi, just to clarify,
> 
> When beginning longitudinal analysis, the first step is the same as  
> cross-sectional processing, eg just the "normal" recon-all command,  
> for each subject, and each individual time point? Then the norm.mgz  
> files are used?
> 
> Thanks
> 
> -- 
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
> 
> 
> 
> - End forwarded message -
> 
> 


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Re: [Freesurfer] longitudinal processing

[Martin Reuter]

Hi Catherine,

with edits I think it is best to re-use the 5.0 cross data for the
longitudinal processing.

Also conceptually there is a difference between longitudinal processing
and longitudinal statistical analysis. 
The image processing will reduce variability of your measures and even
if you are interested in cross sectional differences between groups
(e.g. thickness differences at baseline), it would be a good idea to run
everything through the longitudinal stream. If there is longitudinal
image data, I think it will always be advantageous to process it with
the longitudinal stream as opposed to the cross sectional. 

Different scanners are usually not problematic if each subject stays on
their scanner and scanners are randomly assigned across groups. If
scanners get switched in a longitudinal study, many bad things can
happen:
- one group switches on average earlier than the other -> bias
- only a single or very few time points are on one side of the switch ->
cannot model the scanner effect well, as there is no reliable slope on
that side of the switch.
Anyway it may be a good idea to model the scanner as a covariate and
test for a scanner effect. We have seen effects even in software updates
on the scanner (e.g. growing brains) and certainly a hardware switch
will drastically change the images.

Linear mixed effects models are the right mechanism to analyze
longitudinal data.

Best, Martin



On Wed, 2013-01-09 at 19:22 +, Catherine Bois wrote:
> Thank you for your reply. I am currently trying to decide which method  
> would be the best to analyze the data we have...We have ca 500 scans  
> of individuals with differing number of time points for different  
> individuals and certain clinical measures we wish to relate to  
> particularly cortical thickness and different cortical regions.  
> However, the problem is that the scans were not all collected with the  
> same scanner; would longitudinal still prove to be advantageous over  
> cross-sectional analysis. As all the manual edits have been conducted  
> in version 5.0 it would be preferable to keep these and use version  
> 5.1 for -base -long (unless of course this could be done with better  
> consistency if using version 5.1?). I was also planning to analyze the  
> data with linear mixed effect models, does this sound reasonable?
> 
> Thanks very much for your help
> 
> 
> 
> 
> Quoting Martin Reuter  on Wed, 09 Jan  
> 2013 13:46:35 -0500:
> 
> > Hi Catherine,
> >
> > yes, the first step is independent (cross sectional) processing of all
> > time points (normal recon-all).
> >
> > We usually do not recommend to mix versions. But the 5.1 longitudinal
> > stream has been designed in a way that it can take the cross sectional
> > data from 5.0. So it is possible. Just make sure that if you add time
> > points and subjects you still use 5.0 for the cross sectional recons and
> > 5.1 for base and long to be consistent.
> >
> > Alternatively wait a little longer and re-run everything from scratch
> > with the new 5.2 version that will come out hopefully this month.
> >
> > Best, Martin
> >
> > On Wed, 2013-01-09 at 14:22 +, Catherine Bois wrote:
> >> Sorry, another question about longitudinal processing; just realized
> >> that my institution has been using version 5.0, so all the cross
> >> sectional processing has been done with this version, is it ok to go
> >> ahead and do base and long with version 5.1 once I have managed to get
> >> this installed?
> >>
> >> Thanks,
> >>
> >> - Forwarded message from c.b...@sms.ed.ac.uk -
> >> Date: Wed, 09 Jan 2013 13:35:12 +
> >> From: Catherine Bois 
> >>  Subject: longitudinal processing
> >>   To: freesurfer@nmr.mgh.harvard.edu
> >>
> >> Hi, just to clarify,
> >>
> >> When beginning longitudinal analysis, the first step is the same as
> >> cross-sectional processing, eg just the "normal" recon-all command,
> >> for each subject, and each individual time point? Then the norm.mgz
> >> files are used?
> >>
> >> Thanks
> >>
> >> --
> >> The University of Edinburgh is a charitable body, registered in
> >> Scotland, with registration number SC005336.
> >>
> >>
> >>
> >> - End forwarded message -
> >>
> >>
> >
> >
> >
> >
> > The information in this e-mail is intended only for the person to whom it is
> > 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
> > http://www.partners.org/complianceline . If the e-mail was sent to  
> > you in error
> > but does not contain patient information, please contact the sender  
> > and properly
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> 
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Re: [Freesurfer] longitudinal processing

[Martin Reuter]

Hi Linn,

did you ever solve this?

you need to specify a name for the base and the tp1id and tp2id are 
placeholders for the id's of the corresponding 2 cross sectional time 
points. Don't typ;e the '...'


So for example:

recon-all -base linn-base -tp linn1 -tp linn2 -all

linn1 and linn2 should be there already and contain the results from the 
first step, the independent processing. After this you should see also 
the directory linn-base.


Best, Martin

On 02/01/2013 09:02 AM, Linn Mittlestein wrote:

Dear Freesurfer experts,

 I just tried creating the -base for longitudinal processing on two 
time points using

recon-all -base  -tp  -tp  ... -all


After doing this, I received no error messages and a third folder named after 
the template name I had given
  it it was present  in the subjects directory, however all of these files were 
empty. What have I done

  wrong?

Regards


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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 processing error

[Rashmi Singh]

Hello,
 I am running longitudinal stream processing on mprage scans of some subjects 
who have been scanned multiple times using the same sequence with 32 NOVA 
channels on GE scanner.
For most subjects the base run exited without error, however for few error was 
reported in the runs.
The error was with Tailarach failure. When I looked at the recon-all runs of 
the individual tps for those subjects, there was no error and recon-all had 
completed the runs without error on these timepoints.
Why am I getting the error on base run when there was no error in the recon 
–all run ? And and how do I correct it?
Please advise.
Thanks,
Rashmi.



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Re: [Freesurfer] longitudinal processing

[Nick Schmansky]

Christina,

You need an additional flag specifying a stage, like -all, or -
autorecon1.  I'll update the help text, as this is not obvious, sorry.

Nick

On Thu, 2007-03-01 at 15:51 -0500, [EMAIL PROTECTED] wrote:
> Hello,
> 
> I'm trying to run the longitudinal processing pipeline, but can't figure
> out a command that works.   Below is what I've tried and what has happened
> (MC-07M_prereconEDIT is the 'pre' timepoint, and MC-07M_post is the
> 'post').  Can you help?
> 
> In dev env:
> jizo:ccongle[103] recon-all-long -long -tp1 MC-07M_prereconEDIT -s
> MC-07M_post
> recon-all-long: Command not found.
> 
> jizo:ccongle[104] recon-all -long -tp1 MC-07M_prereconEDIT -s MC-07M_post
> INFO: SUBJECTS_DIR is /autofs/space/jizo_001/users/STRUCTURALS/MBSR
> Actual FREESURFER_HOME /autofs/space/freesurfer/centos4.0_x86_64/dev
> ERROR: nothing to do
> 
> In stable env:
> jizo:ccongle[85] recon-all -long -tp1 MC-07M_prereconEDIT -s MC-07M_post
> ERROR: Flag -long unrecognized.
> -long -tp1 MC-07M_prereconEDIT -s MC-07M_post
> 
> jizo:ccongle[87] recon-all-long -tp1 MC-07M_prereconEDIT -s MC-07M_post
> recon-all-long: Command not found.
> 
> Thanks,
> Christina
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[Freesurfer] Longitudinal processing edits

[Pierson, Ronald K]

I apologize if this has been covered before, but I wanted to make sure I
understand the best way to edit at the appropriate times during the
longitudinal stream.  

 

1)  Run recon-all -all on each scan

2)  If needed, control points are chosen on the individual scans,
and recon-all using the -cp option

3)  Run the -base processing for the subject

4)  WM and brain (pial) edits are done on the base, rerun as needed

5)  Final longitudinal processing of each scan

 

I assume the final processing of the individual scans should need very
little manual intervention, since the control points and edits will be
carried through to that stage.  

 

Is this correct, or have I oversimplified or missed something?

 

Ronald Pierson

Administrative Chair of Imaging, PREDICT-HD
Manager, Research and Development
Department of Psychiatry, Carver College of Medicine
W-278 GH, 200 Hawkins Dr
Iowa City, IA 52242 

  

 

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Re: [Freesurfer] Longitudinal processing

[Martin Reuter]

Hi Sandra,
(and the list, I think this might be interesting for others)

1. 
the longitudinal ?h.thickness files are in registration (within subject)
so in order to compute the difference or the rate you can simply use:
mris_calc -o lh.outdiff sdir2/surf/lh.thickness sdir1/surf/lh.thickness
and for the rate, you can divide by time 1 thickness or by the average
thickness. If the time points are not equally spaced across subjects,
you can also divide by difference in time.
It is best to smooth the thickness files before you do all this (i.e.
within time point smooth the ?h.thickness files with mri_surf2surf).

2. 
then map everything to your template (e.g. fsaverage) with mri_surf2surf

3. there you can stack the thick-differences or thick-rates with
mri_concat

4. do the glm

Beste Gruesse, Martin


On Tue, 2010-06-29 at 21:50 +0200, Sandra Duezel wrote:
> Hi Martin
> 
> I just have got your answer to the longitudinal processing question  
> from Michele and have some other questions regarding the output data  
> from the longitudinal stream.
> Our study contains MRI scans of 45 elderly subjects from 2 timepoints.  
> I have done all steps from the longitudinal stream and it worked  
> without any problems.
> 
> Now I would like calculate the thickness difference maps between the  
> prae and post scans, which are already longitudinally processed.
> 
> I have tried the thickdiffmap-script using the .long and  
> .long data. It creates a .mgz file in each subject but also a new  
> folder "groupstudy"
> with the prae/post data resampled to  fsaverage (its an .mgh file)
> 
> Is this the right way to calculate the difference for longitudinal data?
> 
> Do I also need to proceed with GLM analysis as suggestet in 
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis 
>   or do I need to handle the longitudial data in a different way?
> 
> Thank you very much for your help and answers!
> 
> Best regards
> 
> Sandra
> 
> 
> 
> 
> 
> 
> 
> 
> Am 29.06.2010 um 17:24 schrieb Martin Reuter:
> 
> > There is a step by step description on the longitudinal stream.
> > It basically means:
> > 1. to process your two time points individually through freesurfer
> > (standard processing).
> > 2. to create a template for each subjects from these processed time
> > points
> > 3. to run the two time points again (passing it the template) to  
> > compute
> > better longitudinal results (less variability, more accuracy).
> 
> 

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Re: [Freesurfer] Longitudinal processing

[Douglas N Greve]

Alternatively, you can run mris_preproc for both time point 1 and 2 to 
create separate files with all your subjects in them, then use mris_calc 
like below to create a difference file, then follow the standard 
command-line stream as is described on the wiki.

doug

Martin Reuter wrote:
> Hi Sandra,
> (and the list, I think this might be interesting for others)
>
> 1. 
> the longitudinal ?h.thickness files are in registration (within subject)
> so in order to compute the difference or the rate you can simply use:
> mris_calc -o lh.outdiff sdir2/surf/lh.thickness sdir1/surf/lh.thickness
> and for the rate, you can divide by time 1 thickness or by the average
> thickness. If the time points are not equally spaced across subjects,
> you can also divide by difference in time.
> It is best to smooth the thickness files before you do all this (i.e.
> within time point smooth the ?h.thickness files with mri_surf2surf).
>
> 2. 
> then map everything to your template (e.g. fsaverage) with mri_surf2surf
>
> 3. there you can stack the thick-differences or thick-rates with
> mri_concat
>
> 4. do the glm
>
> Beste Gruesse, Martin
>
>
> On Tue, 2010-06-29 at 21:50 +0200, Sandra Duezel wrote:
>   
>> Hi Martin
>>
>> I just have got your answer to the longitudinal processing question  
>> from Michele and have some other questions regarding the output data  
>> from the longitudinal stream.
>> Our study contains MRI scans of 45 elderly subjects from 2 timepoints.  
>> I have done all steps from the longitudinal stream and it worked  
>> without any problems.
>>
>> Now I would like calculate the thickness difference maps between the  
>> prae and post scans, which are already longitudinally processed.
>>
>> I have tried the thickdiffmap-script using the .long and  
>> .long data. It creates a .mgz file in each subject but also a new  
>> folder "groupstudy"
>> with the prae/post data resampled to  fsaverage (its an .mgh file)
>>
>> Is this the right way to calculate the difference for longitudinal data?
>>
>> Do I also need to proceed with GLM analysis as suggestet in 
>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis 
>>   or do I need to handle the longitudial data in a different way?
>>
>> Thank you very much for your help and answers!
>>
>> Best regards
>>
>> Sandra
>>
>>
>>
>>
>>
>>
>>
>>
>> Am 29.06.2010 um 17:24 schrieb Martin Reuter:
>>
>> 
>>> There is a step by step description on the longitudinal stream.
>>> It basically means:
>>> 1. to process your two time points individually through freesurfer
>>> (standard processing).
>>> 2. to create a template for each subjects from these processed time
>>> points
>>> 3. to run the two time points again (passing it the template) to  
>>> compute
>>> better longitudinal results (less variability, more accuracy).
>>>   
>> 
>
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>
>   

-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] longitudinal processing

[Bruce Fischl]

Hi Marie,

wait for 5.1. Martin has made some significant improvements.

cheers
Bruce
On Mon, 18 Oct 
2010, Marie Schaer wrote:

> Hi,
>
> I am planing to process a longitudinal dataset with 3 timepoints. Is
> it worthy to begin already the cross-sectional processing with version
> 5.0 and then wait version 5.1 to continue from the template part. Or
> would you advice me to wait the release of version 5.1 for the entire
> processing?
>
> Thank you for your help,
>
> Marie
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>
>
>
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Re: [Freesurfer] longitudinal processing

[Pedro Paulo de Magalhães Oliveira Junior]

Hi Bruce,

What's the ETA for 5.1?

thanks
-
Pedro Paulo de Magalhães Oliveira Junior
Diretor de Operações
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://www.netfilter.com.br/mobile




On Mon, Oct 18, 2010 at 10:39, Bruce Fischl wrote:

> Hi Marie,
>
> wait for 5.1. Martin has made some significant improvements.
>
> cheers
> Bruce
> On Mon, 18 Oct
> 2010, Marie Schaer wrote:
>
> > Hi,
> >
> > I am planing to process a longitudinal dataset with 3 timepoints. Is
> > it worthy to begin already the cross-sectional processing with version
> > 5.0 and then wait version 5.1 to continue from the template part. Or
> > would you advice me to wait the release of version 5.1 for the entire
> > processing?
> >
> > Thank you for your help,
> >
> > Marie
> > ___
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> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >
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>
>
> The information in this e-mail is intended only for the person to whom it
> is
> 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
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Re: [Freesurfer] longitudinal processing

[Bruce Fischl]

I'll leave that for Martin

Bruce
On Mon, 18 Oct 2010, Pedro Paulo de Magalhães 
Oliveira Junior wrote:



Hi Bruce,

What's the ETA for 5.1?

thanks
-
Pedro Paulo de Magalhães Oliveira Junior
Diretor de Operações
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://www.netfilter.com.br/mobile




On Mon, Oct 18, 2010 at 10:39, Bruce Fischl wrote:


Hi Marie,

wait for 5.1. Martin has made some significant improvements.

cheers
Bruce
On Mon, 18 Oct
2010, Marie Schaer wrote:


Hi,

I am planing to process a longitudinal dataset with 3 timepoints. Is
it worthy to begin already the cross-sectional processing with version
5.0 and then wait version 5.1 to continue from the template part. Or
would you advice me to wait the release of version 5.1 for the entire
processing?

Thank you for your help,

Marie
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Re: [Freesurfer] longitudinal processing

[Derin Cobia]

So if I understand correctly, you would not recommend getting a jump start on 
cross-sectional processing and editing under 5.0, rerunning everything under 
5.1 once it comes out, then run (for the first time) longitudinal under 5.1?  
Are there going to be some incompatibilities with 5.1, where it cannot be run 
on top of 5.0 data?  Thanks.

-Derin


On Oct 18, 2010, at 7:54 AM, Bruce Fischl wrote:

> I'll leave that for Martin
> 
> Bruce
> On Mon, 18 Oct 2010, Pedro Paulo de Magalhães Oliveira Junior wrote:
> 
>> Hi Bruce,
>> 
>> What's the ETA for 5.1?
>> 
>> thanks
>> -
>> Pedro Paulo de Magalhães Oliveira Junior
>> Diretor de Operações
>> Netfilter & SpeedComm Telecom
>> -- www.netfilter.com.br
>> -- For mobile: http://www.netfilter.com.br/mobile
>> 
>> 
>> 
>> 
>> On Mon, Oct 18, 2010 at 10:39, Bruce Fischl 
>> wrote:
>> 
>>> Hi Marie,
>>> 
>>> wait for 5.1. Martin has made some significant improvements.
>>> 
>>> cheers
>>> Bruce
>>> On Mon, 18 Oct
>>> 2010, Marie Schaer wrote:
>>> 
 Hi,
 
 I am planing to process a longitudinal dataset with 3 timepoints. Is
 it worthy to begin already the cross-sectional processing with version
 5.0 and then wait version 5.1 to continue from the template part. Or
 would you advice me to wait the release of version 5.1 for the entire
 processing?
 
 Thank you for your help,
 
 Marie
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 
 
 
>>> ___
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>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> 
>>> 
>>> The information in this e-mail is intended only for the person to whom it
>>> is
>>> 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
>>> http://www.partners.org/complianceline . If the e-mail was sent to you in
>>> error
>>> but does not contain patient information, please contact the sender and
>>> properly
>>> dispose of the e-mail.
>>> 
>>> 
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> 
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> at
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Re: [Freesurfer] longitudinal processing

[Bruce Fischl]

I'll leave that for Martin also
On Mon, 18 Oct 2010, Derin Cobia wrote:


So if I understand correctly, you would not recommend getting a jump start on 
cross-sectional processing and editing under 5.0, rerunning everything under 
5.1 once it comes out, then run (for the first time) longitudinal under 5.1?  
Are there going to be some incompatibilities with 5.1, where it cannot be run 
on top of 5.0 data?  Thanks.

-Derin


On Oct 18, 2010, at 7:54 AM, Bruce Fischl wrote:


I'll leave that for Martin

Bruce
On Mon, 18 Oct 2010, Pedro Paulo de Magalhães Oliveira Junior wrote:


Hi Bruce,

What's the ETA for 5.1?

thanks
-
Pedro Paulo de Magalhães Oliveira Junior
Diretor de Operações
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://www.netfilter.com.br/mobile




On Mon, Oct 18, 2010 at 10:39, Bruce Fischl wrote:


Hi Marie,

wait for 5.1. Martin has made some significant improvements.

cheers
Bruce
On Mon, 18 Oct
2010, Marie Schaer wrote:


Hi,

I am planing to process a longitudinal dataset with 3 timepoints. Is
it worthy to begin already the cross-sectional processing with version
5.0 and then wait version 5.1 to continue from the template part. Or
would you advice me to wait the release of version 5.1 for the entire
processing?

Thank you for your help,

Marie
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Re: [Freesurfer] longitudinal processing

[Martin Reuter]

Hi everyone,

it is ok to run 5.0 cross sectionally and use that data for 5.1 base and
long. We will try hard to make this work, even if new cross sectional
files are needed (they will then be created in the base or long
stream). 
However, these are reasons, why it might make sense to wait with the
cross sectionals also:
- there might be changes that result in slightly different cross
sectional results when processing it with 5.1, and in more stable motion
correction. Especially if you have cases where motion correction fails
in 5.0 (and works with the fixed mri_robust_template), you should wait.
- when reporting results in a paper, you will have to explain the more
complicated setup
- the whole concept of edits will be looked at and changed, so it is
unclear at the moment, how/if cross sectional edits will be propagated
into the base and long stream.

Release date target is end of November. (This is concerning the parts
that I am involved with, not sure if there are significant other
improvements that cannot wait for a later release, eg. in the cross
sectional stream and that take more time to include). But we really want
to get 5.1 out soon, so I guess in the case of doubt, other stuff would
have to wait for 5.2.

We have a meeting Wednesday. If the release target changes based on the
discussion, we'll let you know Wed. afternoon, but that is unlikely.

Best, Martin


On Mon, 2010-10-18 at 09:20 -0500, Derin Cobia wrote:
> So if I understand correctly, you would not recommend getting a jump
> start on cross-sectional processing and editing under 5.0, rerunning
> everything under 5.1 once it comes out, then run (for the first time)
> longitudinal under 5.1?  Are there going to be some incompatibilities
> with 5.1, where it cannot be run on top of 5.0 data?  Thanks.
> 
> 
> -Derin
> 
> 
> 
> On Oct 18, 2010, at 7:54 AM, Bruce Fischl wrote:
> 
> > I'll leave that for Martin
> > 
> > Bruce
> > On Mon, 18 Oct 2010, Pedro Paulo de Magalhães Oliveira Junior wrote:
> > 
> > > Hi Bruce,
> > > 
> > > What's the ETA for 5.1?
> > > 
> > > thanks
> > > -
> > > Pedro Paulo de Magalhães Oliveira Junior
> > > Diretor de Operações
> > > Netfilter & SpeedComm Telecom
> > > -- www.netfilter.com.br
> > > -- For mobile: http://www.netfilter.com.br/mobile
> > > 
> > > 
> > > 
> > > 
> > > On Mon, Oct 18, 2010 at 10:39, Bruce Fischl
> > > wrote:
> > > 
> > > > Hi Marie,
> > > > 
> > > > wait for 5.1. Martin has made some significant improvements.
> > > > 
> > > > cheers
> > > > Bruce
> > > > On Mon, 18 Oct
> > > > 2010, Marie Schaer wrote:
> > > > 
> > > > > Hi,
> > > > > 
> > > > > I am planing to process a longitudinal dataset with 3
> > > > > timepoints. Is
> > > > > it worthy to begin already the cross-sectional processing with
> > > > > version
> > > > > 5.0 and then wait version 5.1 to continue from the template
> > > > > part. Or
> > > > > would you advice me to wait the release of version 5.1 for the
> > > > > entire
> > > > > processing?
> > > > > 
> > > > > Thank you for your help,
> > > > > 
> > > > > Marie
> > > > > ___
> > > > > Freesurfer mailing list
> > > > > Freesurfer@nmr.mgh.harvard.edu
> > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > > > > 
> > > > > 
> > > > > 
> > > > ___
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> > > > 
> > > > 
> > > > The information in this e-mail is intended only for the person
> > > > to whom it
> > > > is
> > > > 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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> > > > to you in
> > > > error
> > > > but does not contain patient information, please contact the
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> > > > properly
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> > > > 
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Re: [Freesurfer] longitudinal processing

[Marie Schaer]

Great, thank you for your rapid response,

Marie

On 18 oct. 10, at 17:19, Martin Reuter wrote:

> Hi everyone,
>
> it is ok to run 5.0 cross sectionally and use that data for 5.1 base  
> and
> long. We will try hard to make this work, even if new cross sectional
> files are needed (they will then be created in the base or long
> stream).
> However, these are reasons, why it might make sense to wait with the
> cross sectionals also:
> - there might be changes that result in slightly different cross
> sectional results when processing it with 5.1, and in more stable  
> motion
> correction. Especially if you have cases where motion correction fails
> in 5.0 (and works with the fixed mri_robust_template), you should  
> wait.
> - when reporting results in a paper, you will have to explain the more
> complicated setup
> - the whole concept of edits will be looked at and changed, so it is
> unclear at the moment, how/if cross sectional edits will be propagated
> into the base and long stream.
>
> Release date target is end of November. (This is concerning the parts
> that I am involved with, not sure if there are significant other
> improvements that cannot wait for a later release, eg. in the cross
> sectional stream and that take more time to include). But we really  
> want
> to get 5.1 out soon, so I guess in the case of doubt, other stuff  
> would
> have to wait for 5.2.
>
> We have a meeting Wednesday. If the release target changes based on  
> the
> discussion, we'll let you know Wed. afternoon, but that is unlikely.
>
> Best, Martin
>
>
> On Mon, 2010-10-18 at 09:20 -0500, Derin Cobia wrote:
>> So if I understand correctly, you would not recommend getting a jump
>> start on cross-sectional processing and editing under 5.0, rerunning
>> everything under 5.1 once it comes out, then run (for the first time)
>> longitudinal under 5.1?  Are there going to be some incompatibilities
>> with 5.1, where it cannot be run on top of 5.0 data?  Thanks.
>>
>>
>> -Derin
>>
>>
>>
>> On Oct 18, 2010, at 7:54 AM, Bruce Fischl wrote:
>>
>>> I'll leave that for Martin
>>>
>>> Bruce
>>> On Mon, 18 Oct 2010, Pedro Paulo de Magalhães Oliveira Junior wrote:
>>>
 Hi Bruce,

 What's the ETA for 5.1?

 thanks
 -
 Pedro Paulo de Magalhães Oliveira Junior
 Diretor de Operações
 Netfilter & SpeedComm Telecom
 -- www.netfilter.com.br
 -- For mobile: http://www.netfilter.com.br/mobile




 On Mon, Oct 18, 2010 at 10:39, Bruce Fischl
 wrote:

> Hi Marie,
>
> wait for 5.1. Martin has made some significant improvements.
>
> cheers
> Bruce
> On Mon, 18 Oct
> 2010, Marie Schaer wrote:
>
>> Hi,
>>
>> I am planing to process a longitudinal dataset with 3
>> timepoints. Is
>> it worthy to begin already the cross-sectional processing with
>> version
>> 5.0 and then wait version 5.1 to continue from the template
>> part. Or
>> would you advice me to wait the release of version 5.1 for the
>> entire
>> processing?
>>
>> Thank you for your help,
>>
>> Marie
>> ___
>> 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
>
>
> The information in this e-mail is intended only for the person
> to whom it
> is
> 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
> http://www.partners.org/complianceline . If the e-mail was sent
> to you in
> error
> but does not contain patient information, please contact the
> sender and
> properly
> dispose of the e-mail.
>
>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>> The information in this e-mail is intended only for the person to
>>> whom it is
>>> 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
>>> http://www.partners.org/complianceline . If the e-mail was sent to
>>> you in error
>>> but does not contain patient information, please contact the sender
>>> and properly
>>> dispose of the e-mail.
>>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> __

Re: [Freesurfer] longitudinal processing

[Muhammad Ayaz]

Hi Martin,

We have processed groups of controls(40) and patients(15)for two time
points using longitudinal processing. In few controls and even patients we
saw increase in cortical volume. Ideally there should be no change in
cortical volume or we might expect cortical loss specially in the
patients, when compare two time points. Has any body else seen this effect
in their cohort? Would this be solved in the newer version.

Does this problem arise from the initial starting point failure when 2nd
step of longitudinal processing is run where each time point is processed
using the template.

Thanks
Ayaz


On Mon, October 18, 2010 11:19 am, Martin Reuter wrote:
> Hi everyone,
>
> it is ok to run 5.0 cross sectionally and use that data for 5.1 base and
> long. We will try hard to make this work, even if new cross sectional
> files are needed (they will then be created in the base or long
> stream).
> However, these are reasons, why it might make sense to wait with the
> cross sectionals also:
> - there might be changes that result in slightly different cross
> sectional results when processing it with 5.1, and in more stable motion
> correction. Especially if you have cases where motion correction fails
> in 5.0 (and works with the fixed mri_robust_template), you should wait.
> - when reporting results in a paper, you will have to explain the more
> complicated setup
> - the whole concept of edits will be looked at and changed, so it is
> unclear at the moment, how/if cross sectional edits will be propagated
> into the base and long stream.
>
> Release date target is end of November. (This is concerning the parts
> that I am involved with, not sure if there are significant other
> improvements that cannot wait for a later release, eg. in the cross
> sectional stream and that take more time to include). But we really want
> to get 5.1 out soon, so I guess in the case of doubt, other stuff would
> have to wait for 5.2.
>
> We have a meeting Wednesday. If the release target changes based on the
> discussion, we'll let you know Wed. afternoon, but that is unlikely.
>
> Best, Martin
>
>
> On Mon, 2010-10-18 at 09:20 -0500, Derin Cobia wrote:
>> So if I understand correctly, you would not recommend getting a jump
>> start on cross-sectional processing and editing under 5.0, rerunning
>> everything under 5.1 once it comes out, then run (for the first time)
>> longitudinal under 5.1?  Are there going to be some incompatibilities
>> with 5.1, where it cannot be run on top of 5.0 data?  Thanks.
>>
>>
>> -Derin
>>
>>
>>
>> On Oct 18, 2010, at 7:54 AM, Bruce Fischl wrote:
>>
>> > I'll leave that for Martin
>> >
>> > Bruce
>> > On Mon, 18 Oct 2010, Pedro Paulo de Magalhães Oliveira Junior wrote:
>> >
>> > > Hi Bruce,
>> > >
>> > > What's the ETA for 5.1?
>> > >
>> > > thanks
>> > > -
>> > > Pedro Paulo de Magalhães Oliveira Junior
>> > > Diretor de Operações
>> > > Netfilter & SpeedComm Telecom
>> > > -- www.netfilter.com.br
>> > > -- For mobile: http://www.netfilter.com.br/mobile
>> > >
>> > >
>> > >
>> > >
>> > > On Mon, Oct 18, 2010 at 10:39, Bruce Fischl
>> > > wrote:
>> > >
>> > > > Hi Marie,
>> > > >
>> > > > wait for 5.1. Martin has made some significant improvements.
>> > > >
>> > > > cheers
>> > > > Bruce
>> > > > On Mon, 18 Oct
>> > > > 2010, Marie Schaer wrote:
>> > > >
>> > > > > Hi,
>> > > > >
>> > > > > I am planing to process a longitudinal dataset with 3
>> > > > > timepoints. Is
>> > > > > it worthy to begin already the cross-sectional processing with
>> > > > > version
>> > > > > 5.0 and then wait version 5.1 to continue from the template
>> > > > > part. Or
>> > > > > would you advice me to wait the release of version 5.1 for the
>> > > > > entire
>> > > > > processing?
>> > > > >
>> > > > > Thank you for your help,
>> > > > >
>> > > > > Marie
>> > > > > ___
>> > > > > 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
>> > > >
>> > > >
>> > > > The information in this e-mail is intended only for the person
>> > > > to whom it
>> > > > is
>> > > > 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
>> > > > http://www.partners.org/complianceline . If the e-mail was sent
>> > > > to you in
>> > > > error
>> > > > but does not contain patient information, please contact the
>> > > > sender and
>> > > > properly
>> > > > dispose of the e-mail.
>> > > >
>> > > >
>> > ___
>> > Freesurf

Re: [Freesurfer] longitudinal processing

[Martin Reuter]

Hi Ayaz,

A few questions first:
what FS version? How far are the TP apart? Same Scanner and same
software version on the scanner? Is the volume increase significant? How
much percent increase?

Generally: there can always  be individual cases with volume increase,
e.g. due to motion in the scanner and blurry images, due to noise,
gradient non-linearities etc. We have seen cases where it looks to an
expert like there really is thickening. Have you checked the surfaces,
do they look alright?

Another thing you can do is: look at the cross sectional results. Do
they show the same behavior (usually they do, but with larger
variability). And again, you should always look at the whole group.
Individual images can show strange behavior. If individual subjects show
outlier results, check everything and if there is strong motion
artifacts etc. you might want to remove that subject.

Best, Martin


On Mon, 2010-10-18 at 12:06 -0400, Muhammad Ayaz wrote:
> Hi Martin,
> 
> We have processed groups of controls(40) and patients(15)for two time
> points using longitudinal processing. In few controls and even patients we
> saw increase in cortical volume. Ideally there should be no change in
> cortical volume or we might expect cortical loss specially in the
> patients, when compare two time points. Has any body else seen this effect
> in their cohort? Would this be solved in the newer version.
> 
> Does this problem arise from the initial starting point failure when 2nd
> step of longitudinal processing is run where each time point is processed
> using the template.
> 
> Thanks
> Ayaz
> 
> 
> On Mon, October 18, 2010 11:19 am, Martin Reuter wrote:
> > Hi everyone,
> >
> > it is ok to run 5.0 cross sectionally and use that data for 5.1 base and
> > long. We will try hard to make this work, even if new cross sectional
> > files are needed (they will then be created in the base or long
> > stream).
> > However, these are reasons, why it might make sense to wait with the
> > cross sectionals also:
> > - there might be changes that result in slightly different cross
> > sectional results when processing it with 5.1, and in more stable motion
> > correction. Especially if you have cases where motion correction fails
> > in 5.0 (and works with the fixed mri_robust_template), you should wait.
> > - when reporting results in a paper, you will have to explain the more
> > complicated setup
> > - the whole concept of edits will be looked at and changed, so it is
> > unclear at the moment, how/if cross sectional edits will be propagated
> > into the base and long stream.
> >
> > Release date target is end of November. (This is concerning the parts
> > that I am involved with, not sure if there are significant other
> > improvements that cannot wait for a later release, eg. in the cross
> > sectional stream and that take more time to include). But we really want
> > to get 5.1 out soon, so I guess in the case of doubt, other stuff would
> > have to wait for 5.2.
> >
> > We have a meeting Wednesday. If the release target changes based on the
> > discussion, we'll let you know Wed. afternoon, but that is unlikely.
> >
> > Best, Martin
> >
> >
> > On Mon, 2010-10-18 at 09:20 -0500, Derin Cobia wrote:
> >> So if I understand correctly, you would not recommend getting a jump
> >> start on cross-sectional processing and editing under 5.0, rerunning
> >> everything under 5.1 once it comes out, then run (for the first time)
> >> longitudinal under 5.1?  Are there going to be some incompatibilities
> >> with 5.1, where it cannot be run on top of 5.0 data?  Thanks.
> >>
> >>
> >> -Derin
> >>
> >>
> >>
> >> On Oct 18, 2010, at 7:54 AM, Bruce Fischl wrote:
> >>
> >> > I'll leave that for Martin
> >> >
> >> > Bruce
> >> > On Mon, 18 Oct 2010, Pedro Paulo de Magalhães Oliveira Junior wrote:
> >> >
> >> > > Hi Bruce,
> >> > >
> >> > > What's the ETA for 5.1?
> >> > >
> >> > > thanks
> >> > > -
> >> > > Pedro Paulo de Magalhães Oliveira Junior
> >> > > Diretor de Operações
> >> > > Netfilter & SpeedComm Telecom
> >> > > -- www.netfilter.com.br
> >> > > -- For mobile: http://www.netfilter.com.br/mobile
> >> > >
> >> > >
> >> > >
> >> > >
> >> > > On Mon, Oct 18, 2010 at 10:39, Bruce Fischl
> >> > > wrote:
> >> > >
> >> > > > Hi Marie,
> >> > > >
> >> > > > wait for 5.1. Martin has made some significant improvements.
> >> > > >
> >> > > > cheers
> >> > > > Bruce
> >> > > > On Mon, 18 Oct
> >> > > > 2010, Marie Schaer wrote:
> >> > > >
> >> > > > > Hi,
> >> > > > >
> >> > > > > I am planing to process a longitudinal dataset with 3
> >> > > > > timepoints. Is
> >> > > > > it worthy to begin already the cross-sectional processing with
> >> > > > > version
> >> > > > > 5.0 and then wait version 5.1 to continue from the template
> >> > > > > part. Or
> >> > > > > would you advice me to wait the release of version 5.1 for the
> >> > > > > entire
> >> > > > > processing?
> >> > > > 

Re: [Freesurfer] Longitudinal processing

[sima chalavi]

Dear Martin and Douglas,

I had the same question as Sandra and searching the mailing list I found
your answers. However, it is not still clear for me which data I need to use
for the mris_calc (reply from Martin) or mris_preproc (reply from Douglas),
i.e. ( & ) or (.long. &
.long.). Could you please clarify it for me?

Thanks in advance,

Sima.

On Tue, Jun 29, 2010 at 9:34 PM, Douglas N Greve
wrote:

> Alternatively, you can run mris_preproc for both time point 1 and 2 to
> create separate files with all your subjects in them, then use mris_calc
> like below to create a difference file, then follow the standard
> command-line stream as is described on the wiki.
>
> doug
>
> Martin Reuter wrote:
> > Hi Sandra,
> > (and the list, I think this might be interesting for others)
> >
> > 1.
> > the longitudinal ?h.thickness files are in registration (within subject)
> > so in order to compute the difference or the rate you can simply use:
> > mris_calc -o lh.outdiff sdir2/surf/lh.thickness sdir1/surf/lh.thickness
> > and for the rate, you can divide by time 1 thickness or by the average
> > thickness. If the time points are not equally spaced across subjects,
> > you can also divide by difference in time.
> > It is best to smooth the thickness files before you do all this (i.e.
> > within time point smooth the ?h.thickness files with mri_surf2surf).
> >
> > 2.
> > then map everything to your template (e.g. fsaverage) with mri_surf2surf
> >
> > 3. there you can stack the thick-differences or thick-rates with
> > mri_concat
> >
> > 4. do the glm
> >
> > Beste Gruesse, Martin
> >
> >
> > On Tue, 2010-06-29 at 21:50 +0200, Sandra Duezel wrote:
> >
> >> Hi Martin
> >>
> >> I just have got your answer to the longitudinal processing question
> >> from Michele and have some other questions regarding the output data
> >> from the longitudinal stream.
> >> Our study contains MRI scans of 45 elderly subjects from 2 timepoints.
> >> I have done all steps from the longitudinal stream and it worked
> >> without any problems.
> >>
> >> Now I would like calculate the thickness difference maps between the
> >> prae and post scans, which are already longitudinally processed.
> >>
> >> I have tried the thickdiffmap-script using the .long and
> >> .long data. It creates a .mgz file in each subject but also a new
> >> folder "groupstudy"
> >> with the prae/post data resampled to  fsaverage (its an .mgh file)
> >>
> >> Is this the right way to calculate the difference for longitudinal data?
> >>
> >> Do I also need to proceed with GLM analysis as suggestet in
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
> >>   or do I need to handle the longitudial data in a different way?
> >>
> >> Thank you very much for your help and answers!
> >>
> >> Best regards
> >>
> >> Sandra
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> Am 29.06.2010 um 17:24 schrieb Martin Reuter:
> >>
> >>
> >>> There is a step by step description on the longitudinal stream.
> >>> It basically means:
> >>> 1. to process your two time points individually through freesurfer
> >>> (standard processing).
> >>> 2. to create a template for each subjects from these processed time
> >>> points
> >>> 3. to run the two time points again (passing it the template) to
> >>> compute
> >>> better longitudinal results (less variability, more accuracy).
> >>>
> >>
> >
> > ___
> > 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
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> 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
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
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d

Re: [Freesurfer] Longitudinal processing

[Martin Reutet]

Hi always use the data from tp.long.base , they are less variable and more 
accurate than the cross sectional results. (that is why you tun the long stream 
at all).

Best Martin

On 27.10.2010, at 09:13, sima chalavi  wrote:

> Dear Martin and Douglas,
> I had the same question as Sandra and searching the mailing list I found your 
> answers. However, it is not still clear for me which data I need to use for 
> the mris_calc (reply from Martin) or mris_preproc (reply from Douglas), i.e. 
> ( & ) or (.long. & .long.). 
> Could you please clarify it for me?
> Thanks in advance,
> Sima.
> 
> On Tue, Jun 29, 2010 at 9:34 PM, Douglas N Greve  
> wrote:
> Alternatively, you can run mris_preproc for both time point 1 and 2 to
> create separate files with all your subjects in them, then use mris_calc
> like below to create a difference file, then follow the standard
> command-line stream as is described on the wiki.
> 
> doug
> 
> Martin Reuter wrote:
> > Hi Sandra,
> > (and the list, I think this might be interesting for others)
> >
> > 1.
> > the longitudinal ?h.thickness files are in registration (within subject)
> > so in order to compute the difference or the rate you can simply use:
> > mris_calc -o lh.outdiff sdir2/surf/lh.thickness sdir1/surf/lh.thickness
> > and for the rate, you can divide by time 1 thickness or by the average
> > thickness. If the time points are not equally spaced across subjects,
> > you can also divide by difference in time.
> > It is best to smooth the thickness files before you do all this (i.e.
> > within time point smooth the ?h.thickness files with mri_surf2surf).
> >
> > 2.
> > then map everything to your template (e.g. fsaverage) with mri_surf2surf
> >
> > 3. there you can stack the thick-differences or thick-rates with
> > mri_concat
> >
> > 4. do the glm
> >
> > Beste Gruesse, Martin
> >
> >
> > On Tue, 2010-06-29 at 21:50 +0200, Sandra Duezel wrote:
> >
> >> Hi Martin
> >>
> >> I just have got your answer to the longitudinal processing question
> >> from Michele and have some other questions regarding the output data
> >> from the longitudinal stream.
> >> Our study contains MRI scans of 45 elderly subjects from 2 timepoints.
> >> I have done all steps from the longitudinal stream and it worked
> >> without any problems.
> >>
> >> Now I would like calculate the thickness difference maps between the
> >> prae and post scans, which are already longitudinally processed.
> >>
> >> I have tried the thickdiffmap-script using the .long and
> >> .long data. It creates a .mgz file in each subject but also a new
> >> folder "groupstudy"
> >> with the prae/post data resampled to  fsaverage (its an .mgh file)
> >>
> >> Is this the right way to calculate the difference for longitudinal data?
> >>
> >> Do I also need to proceed with GLM analysis as suggestet in 
> >> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
> >>   or do I need to handle the longitudial data in a different way?
> >>
> >> Thank you very much for your help and answers!
> >>
> >> Best regards
> >>
> >> Sandra
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> Am 29.06.2010 um 17:24 schrieb Martin Reuter:
> >>
> >>
> >>> There is a step by step description on the longitudinal stream.
> >>> It basically means:
> >>> 1. to process your two time points individually through freesurfer
> >>> (standard processing).
> >>> 2. to create a template for each subjects from these processed time
> >>> points
> >>> 3. to run the two time points again (passing it the template) to
> >>> compute
> >>> better longitudinal results (less variability, more accuracy).
> >>>
> >>
> >
> > ___
> > 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
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
> 
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> 
> The information in this e-mail is intended only for the person to whom it is
> 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
> http://www.partners.org/complianceline . If the e-mail was sent to you in 
> error
> but does not contain patient information, please contact the sender and 
> properly
> dispose of the e-mail.
> 
> 
> 
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Re: [Freesurfer] longitudinal processing

[Nick Schmansky]

Nicola,

You should not need to re-run your existing baseline 'cross-sectional'
subjects (that is, the subjects already processed by the default recon-
all stream in v4.0.3).  That data will be used to initialize the
subcortical and cortical data used for the necessary 'longitudinal'
baseline subject.

For the new longitudinal analysis scheme, you will first need to create
a new baseline (timepoint 1) 'longitudinal' subject (following the
instructions in the longitudinal processing section of recon-all --
help), this way:

recon-all -all -long tp1subj tp1subj -i path/to/tp1subj/inputs

for example, lets say your existing processed baseline subject is named
nick10, and has two input files (which were already converted to mgz)
the command would be:

recon-all -all -long nick10 nick10 \
  -i $SUBJECTS_DIR/nick10/mri/orig/001.mgz \
  -i $SUBJECTS_DIR/nick10/mri/orig/002.mgz


this will create a new baseline longitudinal subject named:

  nick10.long.nick10

which will be the subject data considered 'timepoint 1' against which
you will compare future timepoints.  This recon-all command will take
the aseg file, and white and pial surfaces from your existing 'nick10'
data, and create nick10.long.nick10 subject data, processed through the
same longitudinal stream as your future timepoint data will be
processed.  By doing this (by having this baseline longitudinal
subject), it reduces the small variability that would otherwise be
introduced by the difference in processing of the longitudinal stream
versus the default cross-sectional stream.

Then, your timepoint 2 data would be processed this way:

recon-all -all -long nick10 nick10_tp2 \
  -i path/to/nick10_tp2/dicom1 \
  -i path/to/nick10_tp2/dicom2

which will create the subject:

nick10_tp2.long.nick10

and you would compare the aseg or aparc stats of nick_tp2.long.nick10
with nick10.long.nick10.  Note that you do not need to process
timepoints beyond timepoint 1 (the baseline) using the default (cross-
sectional) recon-all stream, only the longitudinal stream is necessary.
That is why, in the timepoint 2 command shown above, it is pointing
directly at the source structural dicoms for 'subject' nick10_tp2 (which
doesnt exist, and is only a placeholder name in this case).  This
timepoint 2 longitudinal command will also take the aseg and surface
data from the baseline cross-sectional 'nick10' subject, and use it as
initialization data (which will get 'warped' toward whatever change
happened between time 1 and time2).

Hope this is clear.  Probably not, so feel free to send along further
questions.

Nick


On Thu, 2008-10-16 at 18:21 +0100, Nicola Hobbs wrote:
> Hi there,
> 
> We would like to do some longitudinal processing.  Our baseline scans
> have been run through v4.0.3, and we spent a long time manually
> editing the cortical segmentations.  Ideally we would like to use
> these segmentations as the reference for our longitudinal processing
> (v4.1.0), but we are worried that using different versions for the
> same study could introduce errors.  Could you advise us on whether we
> need to re-run our baseline data through v4.1.0 before we attempt any
> longitudinal processing?
> 
> Many thanks for your help,
> Nicola
> -- 
> 
> 
> 
> Nicola Hobbs 
>  
> Dementia Research Centre 
> National Hospital for Neurology and Neurosurgery 
> Queen Square 
> London WC1N 3BG 
> 
> +44 (0)845 155 5000 ext. 723839
> 
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] longitudinal processing

[Bruce Fischl]

Hi Jared,

1) it uses the same atlas.
2) this is a tough question, and we don't have much experience with 
processing multiple time points (yet). I would say you want the analysis 
of every one to be the same to prevent the introduction of methodological 
artifacts, so for now I would do them all to the first.


cheers,
Bruce
On Fri, 14 Nov 2008, 
Jared Price wrote:



Hi everybody,
2 quick questions about longitudinal processing.
  1) does the longitudinal processing even call the default gca atlas or 
does it use something else?
  2) when processing say 7 time points should all longitudinal scans be 
processed from baseline or should time 3 be processed from time 2 etc.


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Re: [Freesurfer] longitudinal processing

[Bruce Fischl]

Hi Dana,

we have uncovered a problem with the longitudinal stream that may account 
for this. We're hoping to have a fix in the near term.


cheers,
Bruce



On Wed, 29 Apr 2009, Dana W. Moore wrote:


FreeSurfers,

I am using the longitudinal processing stream to look at change in the 
lateral ventricles at several timepoints.  As a control measure, we are 
running two consecutive baseline images in the scanner. These images were 
done back-to-back, exactly the same, and the subject did not get out of the 
scanner nor reposition.  Motion was not a problem.  I have processed this 
first subject, and the longitudinal stream gives me a 2% change in lateral 
ventricular volume, comparing the two baseline scans.  This is bigger than 
I'd like to see, as we are interested in changes over time as small as 2%. 
Is this kind of variability expected, or am I doing something wrong?  I just 
used the first baseline as tp1, processed it cross-sectionally, and then 
longitudinally, and then I used the second baseline as tp2.


Thanks,
Dana


Dana W. Moore, Ph.D.
Neuropsychology Fellow
Cornell Neuropsychology Service
Weill Medical College of Cornell University
New York Presbyterian Hospital
Department of Neurology & Neuroscience
428 East 72nd Street, Suite 500
New York, NY 10021
Phone: 212-746-2441
Fax: 212-746-5584
Email: dwm2...@med.cornell.edu

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[Freesurfer] longitudinal processing stream

[Dana W. Moore]

Hi freesurfer team,

I noticed in the new version release notes that the longitudinal 
stream is still a work in progress.  Any idea of what the time-frame 
is for this fix?


Also, I was wondering if there is a way after longitudinal processing 
to look at change maps in tkmedit or tksurfer (e.g. a color-coded 
segmentation that shows atrophy)?


Thanks,
Dana


Dana W. Moore, Ph.D.
Neuropsychology Fellow
Cornell Neuropsychology Service
Weill Medical College of Cornell University
New York Presbyterian Hospital
Department of Neurology & Neuroscience
428 East 72nd Street, Suite 500
New York, NY 10021
Phone: 212-746-2441
Fax: 212-746-5584
Email: dwm2...@med.cornell.edu

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[Freesurfer] Longitudinal processing clarification

[Derin Cobia]

(Questions for all, but maybe more directed towards Martin)

I have some questions about manual edits in regard to the longitudinal stream.  
Based on the current info on the wiki page, it appears that no edits are pushed 
forward from the cross-sectional (initial) runs of the subject data, as any 
information on the *.long.* runs come from the template.  However, I've noticed 
that WM edits and surfs from the template are used in for the *.long.* 
processing.  In essence, my question is when/where should manual edits (i.e., 
control points, WM, pial edits) occur when conducting longitudinal processing 
in 4.5?  It seems I remember that in 4.3 edits in the cross-sectional work 
would be pushed forward to the *.long.* images, but such is not the case 
anymore (?).  Are edits to occur in the template (i.e., 'base') now, or in the 
*.long.* runs?  Thanks.

-Derin


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[Freesurfer] Longitudinal processing clarification

[Derin Cobia]

Bumping this back up to the list.  Could someone please address?  

To be more concise, during longitudinal processing, where are wm/gm edits made? 
 On the cross-sectional runs, to the base, or on the .long. runs themselves?  
Thanks.

-Derin

Begin forwarded message:

> From: Derin Cobia 
> Date: February 1, 2010 3:54:46 PM CST
> To: "freesurfer@nmr.mgh.harvard.edu Help" 
> Subject: Longitudinal processing clarification
> 
> (Questions for all, but maybe more directed towards Martin)
> 
> I have some questions about manual edits in regard to the longitudinal 
> stream.  Based on the current info on the wiki page, it appears that no edits 
> are pushed forward from the cross-sectional (initial) runs of the subject 
> data, as any information on the *.long.* runs come from the template.  
> However, I've noticed that WM edits and surfs from the template are used for 
> the *.long.* processing.  In essence, my question is when/where should manual 
> edits (i.e., control points, WM, pial edits) occur when conducting 
> longitudinal processing in 4.5?  It seems I remember that in 4.3 edits in the 
> cross-sectional work would be pushed forward to the *.long.* images, but such 
> is not the case anymore (?).  Are edits to occur in the template (i.e., 
> 'base') now, or in the *.long.* runs?  Thanks.
> 
> -Derin
> 
> 

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[Freesurfer] Longitudinal Processing question

[Nillo, Ryan Michael R]

External Email - Use Caution

Hello FreeSurfer experts,

I have a few questions on the longitudinal processing stream. I am interested 
in studying longitudinal morphometry changes in a pediatric population. The age 
range of this population is between 4-20 years with age deltas between a few 
months to < 2 years. I want to know what are appropriate/acceptable age deltas 
used for longitudinal processing. I looked through the archives and one 
researcher asked about age deltas. One of the answers was that “if the time 
delta is relatively small, this has good chances to work”. What does 
“relatively small” mean? If the time points exit the longitudinal pipeline 
without errors and the surfaces look correct, does this mean the data is 
relevant?? When I correct for head size, should I use the eTIV values from the 
cross-sectional directories or the longitudinal directories?

Thanks in advance,

Ryan Michael Nillo
Staff Research Associate I
University of California San Francisco
Department of Radiology and Biomedical Imaging


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Re: [Freesurfer] Longitudinal processing

[Martin Reuter]

Hi Falk, 

yes, the output of long_mris_slopes and long_stats_slopes is in percent
(100 * rate / value_of_fit_at_mid_time). 

Also running 1mm data is different (as you know :-) from .8 so maybe
you would analyze both separately, e.g. creating one base on 1mm time
points and another on the .8mm ? 

If you re-scan in short time interals (and if these are young and
healthy, then even for mid to long intervals), you would not expect
anatomical aging effects. Then the variance is probably mainly
acquisition noise (e.g. induced by motion etc, see eg 
https://www.ncbi.nlm.nih.gov/pubmed/25498430) plus some processing
noise (different surface placement etc). Maybe there are also hydration
effects (see https://www.ncbi.nlm.nih.gov/pubmed/26381562 ). 

Best, Martin


On Thu, 2019-05-09 at 09:51 +, falk.luesebr...@med.ovgu.de wrote:
> External Email - Use Caution
> Dear all,
>  
> I’m a beginner in using the longitudinal processing pipeline (as well
> as statistical analysis) and it would be great to get some insights
> or hints to analyze my data.
>  
> I have a dataset consisting of 11 subjects each acquired at 7
> different time points with an isotropic resolution of 1 and 0.8 mm at
> 3T using a 64-channel head coil. Using that dataset I want to
> investigate short term differences in e.g. cortical thickness with
> the goal to assess the degree of biological variance during that time
> period.
>  
> I have plotted the mean cortical thickness of each time point of
> every subject (using lme_timePlot and lme_lowessPlot) showing a
> somewhat random distribution across time and from my perspective
> fairly high standard deviation. I wanted to have a look at the
> individual percent change by overlaying the symmetric percent change
> on fsaverage, but wasn’t quite sure of the scale. Is it in percent?
> So in case I set the scale bar between 1 and 5, the color relates to
> 1 to 5 percent?
>  
> What other ways would make sense to have a look at? I definitely
> cannot compare groups, as there is just one. The days and time of
> acquistion are rather randomly choosen, so I potentially cannot use
> either as a covariate.  
>  
> Best,
> Falk
>  
> ...
>  
> 
> University Clinic for Neurology
>  
> Otto-von-Guericke-university Magdeburg
> Medical faculty
> Leipziger Str. 44
> 39120 Magdeburg
>  
> Phone +49-391-6117-512
> 
> falk.luesebr...@med.ovgu.de
> http://www.kneu.ovgu.de/kneu.html
>  
> ___
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Re: [Freesurfer] Longitudinal processing

[falk.luesebr...@med.ovgu.de]

External Email - Use Caution

Hi Martin,

thanks for your quick reply and the clarification regarding the output.

I have processed the 1 and 0.8 mm separately, so one base for each subject and 
resolution - no mixing has been conducted! :)

Actually, I want to look into changes due to hydration and other biological 
effects, e.g. due to hormone status. However, this is just a preliminary 
assessment of the variance in general (and getting to know the processing 
pipeline) as no meta data was acquired to correlate the measures against. 

Best,
Falk

-Ursprüngliche Nachricht-
Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 Im Auftrag von Martin Reuter
Gesendet: Montag, 13. Mai 2019 12:56
An: Freesurfer support list 
Betreff: Re: [Freesurfer] Longitudinal processing

Hi Falk, 

yes, the output of long_mris_slopes and long_stats_slopes is in percent
(100 * rate / value_of_fit_at_mid_time). 

Also running 1mm data is different (as you know :-) from .8 so maybe you would 
analyze both separately, e.g. creating one base on 1mm time points and another 
on the .8mm ? 

If you re-scan in short time interals (and if these are young and healthy, then 
even for mid to long intervals), you would not expect anatomical aging effects. 
Then the variance is probably mainly acquisition noise (e.g. induced by motion 
etc, see eg
https://www.ncbi.nlm.nih.gov/pubmed/25498430) plus some processing noise 
(different surface placement etc). Maybe there are also hydration effects (see 
https://www.ncbi.nlm.nih.gov/pubmed/26381562 ). 

Best, Martin


On Thu, 2019-05-09 at 09:51 +, falk.luesebr...@med.ovgu.de wrote:
> External Email - Use Caution
> Dear all,
>  
> I’m a beginner in using the longitudinal processing pipeline (as well 
> as statistical analysis) and it would be great to get some insights or 
> hints to analyze my data.
>  
> I have a dataset consisting of 11 subjects each acquired at 7 
> different time points with an isotropic resolution of 1 and 0.8 mm at 
> 3T using a 64-channel head coil. Using that dataset I want to 
> investigate short term differences in e.g. cortical thickness with the 
> goal to assess the degree of biological variance during that time 
> period.
>  
> I have plotted the mean cortical thickness of each time point of every 
> subject (using lme_timePlot and lme_lowessPlot) showing a somewhat 
> random distribution across time and from my perspective fairly high 
> standard deviation. I wanted to have a look at the individual percent 
> change by overlaying the symmetric percent change on fsaverage, but 
> wasn’t quite sure of the scale. Is it in percent?
> So in case I set the scale bar between 1 and 5, the color relates to
> 1 to 5 percent?
>  
> What other ways would make sense to have a look at? I definitely 
> cannot compare groups, as there is just one. The days and time of 
> acquistion are rather randomly choosen, so I potentially cannot use 
> either as a covariate.
>  
> Best,
> Falk
>  
> ...
>  
> 
> University Clinic for Neurology
>  
> Otto-von-Guericke-university Magdeburg Medical faculty Leipziger Str. 
> 44
> 39120 Magdeburg
>  
> Phone +49-391-6117-512
> 
> falk.luesebr...@med.ovgu.de
> http://www.kneu.ovgu.de/kneu.html
>  
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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[Freesurfer] Longitudinal processing: QA

[Malo Gaubert]

External Email - Use Caution

Hello FreeSurfer developers,

I am trying to apply longitudinal processing on T1w MRI data for two
timepoints (~8 months between the two TP) in adolescents in order to
perform vertex-based analyses.
I am following the online tutorial here for the preprocessing:
https://secure-web.cisco.com/1AR-A4eBY63Zb7ogV-L0wed0Mf63cN1cf9Evvcu56pwG2mEf9LvTFus4zaos9QqygGOWZ8BgmmC4RMvMfE5zNf2Je5rgm9IW1XaeE_6_sNjrQE6WaXOp8FjjSRWAeVoQb0zZO71FPNvgk4c5WKgfyUzFo8iDaY_zJQY2mNwych8RK3rXx9rO7ngQd7gFN8Y6Hhnis_4AWfiEYpqcMmZQjJRenE6tG2KBjizNvXV8dATp-qKPtLhP2L3LzWCYbC3IMtyoRl1PEHVEuOaXOXoVFxQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FLongitudinalTutorial
Thus I launched the creation of BASE followed by the LONGITUDINAL.
Everything went well for recon-all for these 3 steps.
Now, I want to do the QA on the data and I have two questions regarding
this QA:

1/ For one subject, for the two timepoints, the white and pial surface are
entering in the left lateral ventricle as displayed in figure 1 below
(session 1 of the subject; cross-sectional), while the aseg is fine (this
area is considered as Lateral ventricle, see figure 2, see below).
What correction could I apply for this case ?

2/ For some subjects, there is a small shift between the pial of the two
sessions (or the white; see figure 3 (see below)=display of the norm of my
norm and pial/white for the two timepoints (long)) and/or some weird/non
straight/zigzag lines for pial or white (see figure 3, especially between
temporal pole and the rest of the brain). What could be the problem in this
case? Could it be related to some bad quality of T1w images?

1) FreeSurfer version: freesurfer-linux-centos7_x86_64-7.1.0.tar.gz
2) Platform: Ubuntu 18 (Virtual Machine on remote server)
3) uname -a: Linux ubuntu18-cbrain-042020 4.15.0-135-generic #139-Ubuntu
SMP Mon Jan 18 17:38:24 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux

Any help would be appreciated.

Best regards,
Malo

Link to figure 1:
https://secure-web.cisco.com/1Z0OIVNfAyd0P4dX5TvUfticgFxyac5XLFP9qZ15LY2KoHskWdAzJX_gGdfCw5X82CUm4tqdSGHzSj0WbrGTnkeLY5G_mVLf68DjbgDSC-xRbRT5QaeW2mMYp5QJdiYpfNHDdMmcGg4cgk_aC-nwYOrT-o-uRfUSbMQceX06rRep2G7uq339vdTeZEmEvgfcbF-avVOyM9yDOP7BnkmQoy-sGjhnzLbmeBhubK66u2wNAzlNPc8enWUMiPnNjqLMdxOR0sTnbRsRtU2mD05NxnA/https%3A%2F%2Fsyncandshare.lrz.de%2Fgetlink%2FfirX4m94zEkMQG17AR9vpEm%2Ffigure_1_cross_pial-white.PNG
Link to figure2:
https://secure-web.cisco.com/1dkQLGxh5x41ISY3MzCyMUowvQmrn9m-TXAqgZfq29hFI5LjInJXCxyxE2LyE7-XrsfmD8UMI_DG-4fR9lptGcPfVMft9c5rW6Xa2Q3WMPtXLHSwZpksyQu57ualrN7htcbizk4gKW7XM_S46uEdUzF7SFByOwLN8kI6if9nQi6ybWaAmOLZmJUIHXO2WUSyPrCqFYwHPxD0M8arXXhSg7lgznju4KnIrOghRYoNv2mrVMZzjlqaMdAs6Vf4-tdpvioEx8j41Kxbvok2uaLiecg/https%3A%2F%2Fsyncandshare.lrz.de%2Fgetlink%2FfiFdfAfGsWA3Mtk7eHPiLiPE%2Ffigure_2_cross_aseg.PNG

Link to figure3:
https://secure-web.cisco.com/1Nqbq7hapdkZjMI0hXAMBIcoKgeG0dkh3UzuuOGbjE_sUP9tB41ThsdkSchjSXtOqfP7Cu0da1aZz6o5TR1L-WZb87eB6G7U7Hm4FwYFXbtAYqN28-OCfZH_TgHyTlO0ByyCmtAzwkCrH_BR6ZRtqfVhtUtDNvDMkoM86oG4L0OKKjyrqEHE43a0PfJc3CBPVIPpxw1M-fadT5YDPPH-Xa7jEmutbAEvGLI8ZfGCna__4JiRXXh27NFoNj9iyIYk2Fp6p_Ef-tYkjf5vixj9Z9Q/https%3A%2F%2Fsyncandshare.lrz.de%2Fgetlink%2FfiQ3nGkLbtSdBEZLLsvmmgqg%2Ffigure_3_longitudinal.PNG
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Re: [Freesurfer] Longitudinal processing

[Douglas N. Greve]

If you are going to compare the volume across subject, then it does need 
to be corrected with eTIV


On 6/15/2021 8:06 AM, AJ wrote:


External Email - Use Caution

Hi,

After running longitudinal processing and creating base and long runs, 
When looking at volumes of various structures over time of the same 
subject, are the volumes not need to be corrected by eTIV since head 
size does not vary overtime?


Many thanks for your input.
Sincerely,

AJ

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Re: [Freesurfer] Longitudinal processing

[AJ]

External Email - Use Caution

Many thanks.
Best regards

On Thu, Jun 24, 2021, 10:07 Douglas N. Greve  wrote:

> If you are going to compare the volume across subject, then it does need
> to be corrected with eTIV
>
> On 6/15/2021 8:06 AM, AJ wrote:
>
> External Email - Use Caution
> Hi,
>
> After running longitudinal processing and creating base and long runs,
> When looking at volumes of various structures over time of the same
> subject, are the volumes not need to be corrected by eTIV since head size
> does not vary overtime?
>
> Many thanks for your input.
> Sincerely,
>
> AJ
>
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Re: [Freesurfer] Longitudinal Processing Error

[Bruce Fischl]

Hi Jon

have you visually inspected the results of the tal xform?
Bruce
On Mon, 1 Jul 
2013, Jonathan Holt wrote:



Log file indicates manual talairach alignment may be necessary. 
ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm 
***FAILED*** (p=0.0079,
pval=0. < threshold=0.0050)
Manual Talairach alignment may be necessary

Can anyone provide direction. Alternatively, the error indicates talairach 
alignment can be skipped
with -notal-check flag. Is this step completely necessary?

jon

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Re: [Freesurfer] Longitudinal Processing Error

[Jonathan Holt]

I have tried to inspect the tal xfms that were created in the brief time
this string was running

  recon-all -all -s  -i path_to_tpN_dcm


while viewing orig.mgz in tkmedit. they were talairach.xfm and
talairach.auto.xfm, both were empty and the tkmedit window was empty.

upon further inspection the log file is complaining about my nifty.

WARNING: neither NIfTI-1 qform or sform are valid
WARNING: your volume will probably be incorrectly oriented
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from
/net/data4/ALSSCI/FreeSurfer201211/Subjects/DT/100922dt/anatomy/ht1spgr.nii...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
WARNING: it does not appear that there was sufficient information





On Mon, Jul 1, 2013 at 1:46 PM, Bruce Fischl wrote:

> can you cc the list so that others can answer?
>
> On Mon, 1 Jul 2013, Jonathan Holt wrote:
>
>  I have not and I am not certain how to do so
>>
>>
>>
>> On Jul 1, 2013, at 1:03 PM, Bruce Fischl wrote:
>>
>>  Hi Jon
>>>
>>> have you visually inspected the results of the tal xform?
>>> Bruce
>>> On Mon, 1 Jul 2013, Jonathan Holt wrote:
>>>
>>>  Log file indicates manual talairach alignment may be necessary.
 ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
 ***FAILED*** (p=0.0079,
 pval=0. < threshold=0.0050)
 Manual Talairach alignment may be necessary
 Can anyone provide direction. Alternatively, the error indicates
 talairach alignment can be skipped
 with -notal-check flag. Is this step completely necessary?
 jon


>>>
>>> The information in this e-mail is intended only for the person to whom
>>> it is
>>> 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
>>> http://www.partners.org/**complianceline.
>>>  If the e-mail was sent to you in error
>>> but does not contain patient information, please contact the sender and
>>> properly
>>> dispose of the e-mail.
>>>
>>
>>
>>
>>
>>
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Re: [Freesurfer] Longitudinal Processing Error

[Jonathan Holt]

Martin,

I did find that info and tried to follow the instructions, but you'll see
based on my last message the talairach files didn't seem to contain
anything?




On Mon, Jul 1, 2013 at 2:29 PM, Jonathan Holt  wrote:

> I have tried to inspect the tal xfms that were created in the brief time
> this string was running
>
>   recon-all -all -s  -i path_to_tpN_dcm
>
>
> while viewing orig.mgz in tkmedit. they were talairach.xfm and
> talairach.auto.xfm, both were empty and the tkmedit window was empty.
>
> upon further inspection the log file is complaining about my nifty.
>
> WARNING: neither NIfTI-1 qform or sform are valid
> WARNING: your volume will probably be incorrectly oriented
> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> reading from
> /net/data4/ALSSCI/FreeSurfer201211/Subjects/DT/100922dt/anatomy/ht1spgr.nii...
> TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
> WARNING: it does not appear that there was sufficient information
>
>
>
>
>
> On Mon, Jul 1, 2013 at 1:46 PM, Bruce Fischl 
> wrote:
>
>> can you cc the list so that others can answer?
>>
>> On Mon, 1 Jul 2013, Jonathan Holt wrote:
>>
>>  I have not and I am not certain how to do so
>>>
>>>
>>>
>>> On Jul 1, 2013, at 1:03 PM, Bruce Fischl wrote:
>>>
>>>  Hi Jon

 have you visually inspected the results of the tal xform?
 Bruce
 On Mon, 1 Jul 2013, Jonathan Holt wrote:

  Log file indicates manual talairach alignment may be necessary.
> ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
> ***FAILED*** (p=0.0079,
> pval=0. < threshold=0.0050)
> Manual Talairach alignment may be necessary
> Can anyone provide direction. Alternatively, the error indicates
> talairach alignment can be skipped
> with -notal-check flag. Is this step completely necessary?
> jon
>
>

 The information in this e-mail is intended only for the person to whom
 it is
 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
 http://www.partners.org/**complianceline.
  If the e-mail was sent to you in error
 but does not contain patient information, please contact the sender and
 properly
 dispose of the e-mail.

>>>
>>>
>>>
>>>
>>>
>
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Re: [Freesurfer] Longitudinal Processing Error

[Martin Reuter]

Hi Jon,

are you passing your images?
 is a placeholder for the id of your subject+time point, for 
example it could be jon_01 the "path_to_tpN_dcm" needs to specify the 
path to the dicom files, point it to the first file in the MPRAGE series 
(or multi echo mprage or what you are using). This is the full path on 
your file system to that file.


Best, Martin

On 07/01/2013 02:29 PM, Jonathan Holt wrote:
I have tried to inspect the tal xfms that were created in the brief 
time this string was running


   recon-all -all -s  -i path_to_tpN_dcm

while viewing orig.mgz in tkmedit. they were talairach.xfm and 
talairach.auto.xfm, both were empty and the tkmedit window was empty.


upon further inspection the log file is complaining about my nifty.

WARNING: neither NIfTI-1 qform or sform are valid
WARNING: your volume will probably be incorrectly oriented
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from 
/net/data4/ALSSCI/FreeSurfer201211/Subjects/DT/100922dt/anatomy/ht1spgr.nii...

TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
WARNING: it does not appear that there was sufficient information





On Mon, Jul 1, 2013 at 1:46 PM, Bruce Fischl 
mailto:fis...@nmr.mgh.harvard.edu>> wrote:


can you cc the list so that others can answer?

On Mon, 1 Jul 2013, Jonathan Holt wrote:

I have not and I am not certain how to do so



On Jul 1, 2013, at 1:03 PM, Bruce Fischl wrote:

Hi Jon

have you visually inspected the results of the tal xform?
Bruce
On Mon, 1 Jul 2013, Jonathan Holt wrote:

Log file indicates manual talairach alignment may be
necessary.
ERROR: talairach_afd: Talairach Transform:
transforms/talairach.xfm ***FAILED*** (p=0.0079,
pval=0. < threshold=0.0050)
Manual Talairach alignment may be necessary
Can anyone provide direction. Alternatively, the error
indicates talairach alignment can be skipped
with -notal-check flag. Is this step completely necessary?
jon



The information in this e-mail is intended only for the
person to whom it is
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
http://www.partners.org/complianceline . If the e-mail was
sent to you in error
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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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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
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Re: [Freesurfer] Longitudinal Processing Error

[Martin Reuter]

Hi Jon,

this is not really a longitudinal problem. You can look at this tutorial 
on how to check/fix bad talairach:

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview

Best, Martin

On 07/01/2013 01:03 PM, Bruce Fischl wrote:

Hi Jon

have you visually inspected the results of the tal xform?
Bruce
On Mon, 1 Jul 2013, Jonathan Holt wrote:


Log file indicates manual talairach alignment may be necessary.
ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm 
***FAILED*** (p=0.0079,

pval=0. < threshold=0.0050)
Manual Talairach alignment may be necessary

Can anyone provide direction. Alternatively, the error indicates 
talairach alignment can be skipped

with -notal-check flag. Is this step completely necessary?

jon





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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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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
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Re: [Freesurfer] Longitudinal Processing Error

[Jonathan Holt]

Martin,

definitely passing my images and naming time points appropriately. I have been 
passing nifti as opposed to dicom and it's entirely possible that may be the 
issue?

jon
On Jul 1, 2013, at 2:32 PM, Martin Reuter wrote:

> Hi Jon,
> 
> are you passing your images?
>  is a placeholder for the id of your subject+time point, for example 
> it could be jon_01 the "path_to_tpN_dcm" needs to specify the path to the 
> dicom files, point it to the first file in the MPRAGE series (or multi echo 
> mprage or what you are using). This is the full path on your file system to 
> that file.
> 
> Best, Martin
> 
> On 07/01/2013 02:29 PM, Jonathan Holt wrote:
>> I have tried to inspect the tal xfms that were created in the brief time 
>> this string was running 
>> 
>>   recon-all -all -s  -i path_to_tpN_dcm
>> 
>> while viewing orig.mgz in tkmedit. they were talairach.xfm and 
>> talairach.auto.xfm, both were empty and the tkmedit window was empty. 
>> 
>> upon further inspection the log file is complaining about my nifty. 
>> 
>> WARNING: neither NIfTI-1 qform or sform are valid
>> WARNING: your volume will probably be incorrectly oriented
>> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
>> reading from 
>> /net/data4/ALSSCI/FreeSurfer201211/Subjects/DT/100922dt/anatomy/ht1spgr.nii...
>> TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
>> WARNING: it does not appear that there was sufficient information
>> 
>> 
>> 
>> 
>> 
>> On Mon, Jul 1, 2013 at 1:46 PM, Bruce Fischl  
>> wrote:
>> can you cc the list so that others can answer?
>> 
>> On Mon, 1 Jul 2013, Jonathan Holt wrote:
>> 
>> I have not and I am not certain how to do so
>> 
>> 
>> 
>> On Jul 1, 2013, at 1:03 PM, Bruce Fischl wrote:
>> 
>> Hi Jon
>> 
>> have you visually inspected the results of the tal xform?
>> Bruce
>> On Mon, 1 Jul 2013, Jonathan Holt wrote:
>> 
>> Log file indicates manual talairach alignment may be necessary.
>> ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm 
>> ***FAILED*** (p=0.0079,
>> pval=0. < threshold=0.0050)
>> Manual Talairach alignment may be necessary
>> Can anyone provide direction. Alternatively, the error indicates talairach 
>> alignment can be skipped
>> with -notal-check flag. Is this step completely necessary?
>> jon
>> 
>> 
>> 
>> The information in this e-mail is intended only for the person to whom it is
>> 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
>> http://www.partners.org/complianceline . If the e-mail was sent to you in 
>> error
>> but does not contain patient information, please contact the sender and 
>> properly
>> dispose of the e-mail.
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> -- 
> 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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Re: [Freesurfer] Longitudinal Processing Error

[Martin Reuter]

No, it's not nifti, that should work.

Can you send me your log file and the command you issued.

Thanks, Martin

On 07/01/2013 03:13 PM, Jonathan Holt wrote:

Martin,

definitely passing my images and naming time points appropriately. I 
have been passing nifti as opposed to dicom and it's entirely possible 
that may be the issue?


jon
On Jul 1, 2013, at 2:32 PM, Martin Reuter wrote:


Hi Jon,

are you passing your images?
 is a placeholder for the id of your subject+time point, for 
example it could be jon_01 the "path_to_tpN_dcm" needs to specify the 
path to the dicom files, point it to the first file in the MPRAGE 
series (or multi echo mprage or what you are using). This is the full 
path on your file system to that file.


Best, Martin

On 07/01/2013 02:29 PM, Jonathan Holt wrote:
I have tried to inspect the tal xfms that were created in the brief 
time this string was running


   recon-all -all -s  -i path_to_tpN_dcm

while viewing orig.mgz in tkmedit. they were talairach.xfm and 
talairach.auto.xfm, both were empty and the tkmedit window was empty.


upon further inspection the log file is complaining about my nifty.

WARNING: neither NIfTI-1 qform or sform are valid
WARNING: your volume will probably be incorrectly oriented
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from 
/net/data4/ALSSCI/FreeSurfer201211/Subjects/DT/100922dt/anatomy/ht1spgr.nii...

TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
WARNING: it does not appear that there was sufficient information





On Mon, Jul 1, 2013 at 1:46 PM, Bruce Fischl 
mailto:fis...@nmr.mgh.harvard.edu>> wrote:


can you cc the list so that others can answer?

On Mon, 1 Jul 2013, Jonathan Holt wrote:

I have not and I am not certain how to do so



On Jul 1, 2013, at 1:03 PM, Bruce Fischl wrote:

Hi Jon

have you visually inspected the results of the tal xform?
Bruce
On Mon, 1 Jul 2013, Jonathan Holt wrote:

Log file indicates manual talairach alignment may be
necessary.
ERROR: talairach_afd: Talairach Transform:
transforms/talairach.xfm ***FAILED*** (p=0.0079,
pval=0. < threshold=0.0050)
Manual Talairach alignment may be necessary
Can anyone provide direction. Alternatively, the
error indicates talairach alignment can be skipped
with -notal-check flag. Is this step completely
necessary?
jon



The information in this e-mail is intended only for the
person to whom it is
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
http://www.partners.org/complianceline . If the e-mail
was sent to you in error
but does not contain patient information, please contact
the sender and properly
dispose of the e-mail.








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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  




--
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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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 Processing Error

[Jonathan Holt]

Here ya go (to list)


On Tue, Jul 2, 2013 at 12:38 PM, Jonathan Holt  wrote:

> Here ya go.
>
>
> On Mon, Jul 1, 2013 at 3:31 PM, Martin Reuter  > wrote:
>
>>  No, it's not nifti, that should work.
>>
>> Can you send me your log file and the command you issued.
>>
>> Thanks, Martin
>>
>>
>> On 07/01/2013 03:13 PM, Jonathan Holt wrote:
>>
>> Martin,
>>
>>  definitely passing my images and naming time points appropriately. I
>> have been passing nifti as opposed to dicom and it's entirely possible that
>> may be the issue?
>>
>>  jon
>>  On Jul 1, 2013, at 2:32 PM, Martin Reuter wrote:
>>
>>  Hi Jon,
>>
>> are you passing your images?
>>  is a placeholder for the id of your subject+time point, for
>> example it could be jon_01 the "path_to_tpN_dcm" needs to specify the path
>> to the dicom files, point it to the first file in the MPRAGE series (or
>> multi echo mprage or what you are using). This is the full path on your
>> file system to that file.
>>
>> Best, Martin
>>
>> On 07/01/2013 02:29 PM, Jonathan Holt wrote:
>>
>> I have tried to inspect the tal xfms that were created in the brief time
>> this string was running
>>
>>recon-all -all -s  -i path_to_tpN_dcm
>>
>>
>>  while viewing orig.mgz in tkmedit. they were talairach.xfm and
>> talairach.auto.xfm, both were empty and the tkmedit window was empty.
>>
>>  upon further inspection the log file is complaining about my nifty.
>>
>>  WARNING: neither NIfTI-1 qform or sform are valid
>> WARNING: your volume will probably be incorrectly oriented
>> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
>> reading from
>> /net/data4/ALSSCI/FreeSurfer201211/Subjects/DT/100922dt/anatomy/ht1spgr.nii...
>> TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
>> WARNING: it does not appear that there was sufficient information
>>
>>
>>
>>
>>
>> On Mon, Jul 1, 2013 at 1:46 PM, Bruce Fischl 
>> wrote:
>>
>>> can you cc the list so that others can answer?
>>>
>>> On Mon, 1 Jul 2013, Jonathan Holt wrote:
>>>
>>>  I have not and I am not certain how to do so



 On Jul 1, 2013, at 1:03 PM, Bruce Fischl wrote:

  Hi Jon
>
> have you visually inspected the results of the tal xform?
> Bruce
> On Mon, 1 Jul 2013, Jonathan Holt wrote:
>
>  Log file indicates manual talairach alignment may be necessary.
>> ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
>> ***FAILED*** (p=0.0079,
>> pval=0. < threshold=0.0050)
>> Manual Talairach alignment may be necessary
>> Can anyone provide direction. Alternatively, the error indicates
>> talairach alignment can be skipped
>> with -notal-check flag. Is this step completely necessary?
>> jon
>>
>>
>
> The information in this e-mail is intended only for the person to whom
> it is
> 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
> http://www.partners.org/complianceline . If the e-mail was sent to
> you in error
> but does not contain patient information, please contact the sender
> and properly
> dispose of the e-mail.
>





>>
>>
>> ___
>> Freesurfer mailing 
>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> --
>> 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
>>
>>
>>
>> --
>> 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
>>
>>
>


nohup.out
Description: Binary data
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] Longitudinal Processing Error

[Jonathan Holt]

and the command

nohup recon-all -s 100922dt_01 -i 100922dt_nifti_revised.nii



On Tue, Jul 2, 2013 at 12:40 PM, Jonathan Holt  wrote:

> Here ya go (to list)
>
>
> On Tue, Jul 2, 2013 at 12:38 PM, Jonathan Holt  wrote:
>
>> Here ya go.
>>
>>
>> On Mon, Jul 1, 2013 at 3:31 PM, Martin Reuter <
>> mreu...@nmr.mgh.harvard.edu> wrote:
>>
>>>  No, it's not nifti, that should work.
>>>
>>> Can you send me your log file and the command you issued.
>>>
>>> Thanks, Martin
>>>
>>>
>>> On 07/01/2013 03:13 PM, Jonathan Holt wrote:
>>>
>>> Martin,
>>>
>>>  definitely passing my images and naming time points appropriately. I
>>> have been passing nifti as opposed to dicom and it's entirely possible that
>>> may be the issue?
>>>
>>>  jon
>>>  On Jul 1, 2013, at 2:32 PM, Martin Reuter wrote:
>>>
>>>  Hi Jon,
>>>
>>> are you passing your images?
>>>  is a placeholder for the id of your subject+time point, for
>>> example it could be jon_01 the "path_to_tpN_dcm" needs to specify the path
>>> to the dicom files, point it to the first file in the MPRAGE series (or
>>> multi echo mprage or what you are using). This is the full path on your
>>> file system to that file.
>>>
>>> Best, Martin
>>>
>>> On 07/01/2013 02:29 PM, Jonathan Holt wrote:
>>>
>>> I have tried to inspect the tal xfms that were created in the brief time
>>> this string was running
>>>
>>>recon-all -all -s  -i path_to_tpN_dcm
>>>
>>>
>>>  while viewing orig.mgz in tkmedit. they were talairach.xfm and
>>> talairach.auto.xfm, both were empty and the tkmedit window was empty.
>>>
>>>  upon further inspection the log file is complaining about my nifty.
>>>
>>>  WARNING: neither NIfTI-1 qform or sform are valid
>>> WARNING: your volume will probably be incorrectly oriented
>>> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
>>> reading from
>>> /net/data4/ALSSCI/FreeSurfer201211/Subjects/DT/100922dt/anatomy/ht1spgr.nii...
>>> TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
>>> WARNING: it does not appear that there was sufficient information
>>>
>>>
>>>
>>>
>>>
>>> On Mon, Jul 1, 2013 at 1:46 PM, Bruce Fischl >> > wrote:
>>>
 can you cc the list so that others can answer?

 On Mon, 1 Jul 2013, Jonathan Holt wrote:

  I have not and I am not certain how to do so
>
>
>
> On Jul 1, 2013, at 1:03 PM, Bruce Fischl wrote:
>
>  Hi Jon
>>
>> have you visually inspected the results of the tal xform?
>> Bruce
>> On Mon, 1 Jul 2013, Jonathan Holt wrote:
>>
>>  Log file indicates manual talairach alignment may be necessary.
>>> ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
>>> ***FAILED*** (p=0.0079,
>>> pval=0. < threshold=0.0050)
>>> Manual Talairach alignment may be necessary
>>> Can anyone provide direction. Alternatively, the error indicates
>>> talairach alignment can be skipped
>>> with -notal-check flag. Is this step completely necessary?
>>> jon
>>>
>>>
>>
>> The information in this e-mail is intended only for the person to
>> whom it is
>> 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
>> http://www.partners.org/complianceline . If the e-mail was sent to
>> you in error
>> but does not contain patient information, please contact the sender
>> and properly
>> dispose of the e-mail.
>>
>
>
>
>
>
>>>
>>>
>>> ___
>>> Freesurfer mailing 
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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
>>>
>>>
>>>
>>> --
>>> 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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Re: [Freesurfer] longitudinal processing versioning

[Martin Reuter]

Hi Michael,

I think you should be fine with option 1. Just make sure that all cross are run 
with the same version (5.1). It is a little more complicated to keep track of 
things, but there should be no bias. That way you don't have to worry about 
edits. 

If you only have very few edits, I would do the clean thing an re-run all data 
from scratch with 5.3 manually transferring edits only where needed.

Best, Martin

On Jul 9, 2013, at 3:01 PM, "Harms, Michael"  wrote:

> 
> Hi guys,
> We have some longitudinal scans in which the time1 (T1) scans were processed 
> with FS 5.1, and the T2/T3 scans haven't been processed yet.
> 
> I'm trying to assess whether the differences between FS 5.1 and 5.3 warrant 
> us re-running the T1 scans under FS 5.3.  
> I see two possible options:
> 1) Process all "cross-sectional" runs under FS 5.1.  i.e., we already have T1 
> under FS 5.1, so do the cross-runs of T2/T3 under 5.1 as well.  (I'm assuming 
> that it wouldn't be desirable to have a mix of versions at the 
> cross-sectional stage).  Then switch to using FS 5.3 for creating the 
> template (-base) and longitudinal (-long) data.
> 
> 2) Re-process the cross-sectional scans for T1 using FS 5.3, and do 
> everything with FS 5.3.
> 
> Do you have any reason to expect relevant differences in the final -long 
> output between these two approaches?
> And, if approach (2) is necessary, do we need to re-run the T1 through FS 5.3 
> with the "-clean" flag?  i.e,. if we were to re-run the cross-sectional 
> version of the T1 scan using FS 5.3, but keeping previous edits, would that 
> potentially bias the T1 scan in some fashion, since the T2/T3 scans will be 
> run fresh in FS 5.3 without any prior manual edits?
> 
> thanks,
> -MH
> 
> -- 
> Michael Harms, Ph.D.
> ---
> Conte Center for the Neuroscience of Mental Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave.  Tel: 314-747-6173
> St. Louis, MO  63110  Email: mha...@wustl.edu
> 
>  
> The materials in this message are private and may contain Protected 
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> information is strictly prohibited. If you have received this email in error, 
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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: 
   mreu...@nmr.mgh.harvard.edu
   reu...@mit.edu
Web  : http://reuter.mit.edu 

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[Freesurfer] Longitudinal processing - Surface area

[Chung, Yoonho]

Dear all,

I am interested in looking at developmental changes in the brain during 
adolescence period in normal subjects and also comparing our controls to our 
clinical patients. Examples in the longitudinal processing stream tutorial have 
only mentioned volume and thickness, so I was wondering if area is also 
something we could look at and analyze. I successfully generated rate of 
change, spc, pc2 etc  .mgz files in the post processing stage using 
'long_mris_slopes' using '--meas area', but I just wanted to make sure if rate 
of change in surface area using freesurfer longitudinal stream is something we 
can report in our ms. I haven't found any papers reporting changes in the 
surface area using fs long stream so I was wondering if this measure is good to 
go or if it is something that is still work in progress

Cheers,
Yoon

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Re: [Freesurfer] Longitudinal Processing Pipeline

[Martin Reuter]

Hi David,

in newer versions (not sure exactly when I added this) you can pass 
-addtp to the -long run. That will add the time point to the study 
without re-running the base. However this will probably introduce a 
processing bias as this time point will be treated differently from the 
other time points and therefore is not recommended. You may get away 
with it if you have sufficiently many tps in the base and this one is 
not expected to be too different from the others.


Best, Martin

On 08/28/2013 10:51 AM, David Tate wrote:

Question regarding longitudinal processing pipeline.

Is there a way to force the -long procedure to use an individual base 
template for a time point not used to create the base in the first place?


David F. Tate, Ph.D.



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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 processing with -FLAIRpial

[Charles Malpas]

Dear Freesurfer Ninjas,

I have been playing around with the new beta version, and am very
interested in the -FLAIRpial option. I have been using this successfully on
cross-sectional runs, but would like to extend it to cross sectional runs.

I have played around with trying to get this to work, including copying
FLAIRconf.mgz to the longitudinal run directions (subjid.long.template) and
the recon-alll -long command with -FLAIRpial. Although this runs, it
produces cortical thickness estimates that appear underestimated on visual
inspection.

Is there a better way to incorporate -FLAIRpial on longitudinal runs? Is it
even possible at this stage?

Many thanks for your time,

- Charles



-- 
*Charles Malpas *
Master of Psychology (Clinical Neuropsychology) / PhD Candidate
Melbourne School of Psychological Sciences & Department of Medicine (RMH)
The University of Melbourne 3010

*Melbourne Brain Centre @ RMH*
Neuropsychiatry Research Group* *
Level 4, Main Building, Royal Melbourne Hospital
Phone: 0451 116 434
Email: c.mal...@student.unimelb.edu.au
Skype: charles.malpas
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Re: [Freesurfer] Longitudinal processing error

[Martin Reuter]

Hi Sabin,

what was the recon-all command you used for this?

Thanks, Martin

On 02/05/2013 09:51 AM, Sabin Khadka wrote:

Hi all,

I am running longitudinal processing and it keeps on crashing with no 
error message whatsoever in middle of one or the other processing 
steps. I am not sure if this is an memory issue. Any 
thoughts/suggestions would be helpful.


I have attached error log as well.

-Sabin


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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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Re: [Freesurfer] Longitudinal processing clarification

[Nick Schmansky]

You can edit just the base if you will only be working with the
longitudinal stream.  Currently, running the cross-sectional stream is
necessary only to get the 'norm.mgz' file, for input to the base
subject.

n.

On Sun, 2010-02-14 at 14:06 -0800, Mehul Sampat wrote:
> Hi  Nick (and Martin)
> 
> Could you please clarify if the edits come only from the base or if
> they are copied from the cross-sectionals ? 
> 
> It would be great if I only had to make edit in  the base .
> We have 5 timepoints for each subject (each a year apart) and i want
> to use the results from the longitudinal pipeline only.
> If I did not need to edit the cross-sectional timepoints and if
> editing only the base was okay this would be very helpful.
> 
> Martin, do you normally only make edits to base when using the
> longitudinal pipeline ? 
> Thanks
> Mehul
> 
> 
> On Fri, Feb 12, 2010 at 6:01 PM, Martin Reuter
>  wrote:
> Hi Derin,
> 
> this is how I see it:
> 
> The base might need edits and if it does, they should be made.
> As you
> say, the surfaces of the longitudinal runs are initialized
> with the
> surface of the base, so, if it is not correct, this will
> pollute all
> time points.
> 
> Another reason to edit the base is that wm edits (255) and
> deletes (1)
> are copied from the base to all time points, as you mentioned.
> 
> Usually this should be sufficient, but maybe you need further
> edits in a
> specific longitudinal run, never happened to me.
> 
> The old longitudinal processing stream really did not have any
> cross
> sectional runs. Instead of the base they processed TP1
> (introducing a
> bias) and copied the edits from there to the longitudinals. We
> now copy
> it from the base.
> 
> Hope that helps.
> 
> Nick mentioned that edits are copied from the cross
> sectionals, but I
> think they only come from the base. At least that is what I
> think was
> done and therefore put it on the wiki. Maybe Nick can verify
> what really
> goes on in recon-all as he programmed that part?
> 
> It might make sense to edit the cross sectionals anyway
> because:
> - you then get more reliable cross sectional results (to
> compare to
> etc).
> - the cross sectional asegs are 'fused' (probabilistic
> voting), to
> initialize the labeling in the longitudinal runs, so more
> accuracy in
> the cross sectionals cannot hurt. However I never really found
> this to
> be necessary, but my data was usually high quality.
> 
> Best, Martin
> 
> 
> On Fri, 2010-02-12 at 13:51 -0600, Derin Cobia wrote:
> 
> 
> > Bumping this back up to the list.  Could someone please
> address?
> >
> >
> > To be more concise, during longitudinal processing, where
> are wm/gm
> > edits made?  On the cross-sectional runs, to the base, or on
> > the .long. runs themselves?  Thanks.
> >
> >
> > -Derin
> >
> > Begin forwarded message:
> >
> > > From: Derin Cobia 
> > >
> > > Date: February 1, 2010 3:54:46 PM CST
> > >
> > > To: "freesurfer@nmr.mgh.harvard.edu Help"
> > > 
> > >
> > > Subject: Longitudinal processing clarification
> > >
> > >
> > > (Questions for all, but maybe more directed towards
> Martin)
> > >
> > >
> > > I have some questions about manual edits in regard to the
> > > longitudinal stream.  Based on the current info on the
> wiki page, it
> > > appears that no edits are pushed forward from the
> cross-sectional
> > > (initial) runs of the subject data, as any information on
> > > the *.long.* runs come from the template.  However, I've
> noticed
> > > that WM edits and surfs from the template are used for the
> *.long.*
> > > processing.  In essence, my question is when/where should
> manual
> > > edits (i.e., control points, WM, pial edits) occur when
> conducting
> > > longitudinal processing in 4.5?  It seems I remember that
> in 4.3
> > > edits in the cross-sectional work would be pushed forward
> to the
> > > *.long.* images, but such is not the case anymore (?).
>  Are edits to
> > > occur in the template (i.e., 'base') now, or in the
> *.long.* runs?
> > >  Thanks.
> > >
> > >
> > > -Derin
> > >
> > >
> > >
> > >
> >
>  

Re: [Freesurfer] Longitudinal processing edits

[Allison Stevens]

Ronald,
This looks correct for now. I believe Martin is working on a way to make 
this easier for the future.
Allison

-- 

On Tue, 23 Mar 2010, Pierson, Ronald K wrote:

> I apologize if this has been covered before, but I wanted to make sure I
> understand the best way to edit at the appropriate times during the
> longitudinal stream.
>
>
>
> 1)  Run recon-all -all on each scan
>
> 2)  If needed, control points are chosen on the individual scans,
> and recon-all using the -cp option
>
> 3)  Run the -base processing for the subject
>
> 4)  WM and brain (pial) edits are done on the base, rerun as needed
>
> 5)  Final longitudinal processing of each scan
>
>
>
> I assume the final processing of the individual scans should need very
> little manual intervention, since the control points and edits will be
> carried through to that stage.
>
>
>
> Is this correct, or have I oversimplified or missed something?
>
>
>
> Ronald Pierson
>
> Administrative Chair of Imaging, PREDICT-HD
> Manager, Research and Development
> Department of Psychiatry, Carver College of Medicine
> W-278 GH, 200 Hawkins Dr
> Iowa City, IA 52242
>
>
>
>
>
>
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[Freesurfer] Longitudinal processing , possible bias_shift ?

[Anthony]

Hi all,

Recently I tried out longitudinal processing on my 1st time point subjects ( 
directly generated by recon-all, no post processing or manual editing involved) 
. Then I ran asegstat2table for both 1st and 2nd time point subjects to compare 
cortical WM and cortical cortex volumes. From what I observed , there was 
possibly  a bias_shift in WM between those time points as most of the 
differences ( WM at tp2 -WM at tp1 ) were positive , I was expecting the mean 
difference would be close to 0 . It would be great if anyone could share 
her/his insights about this .Is it normal and what might cause this behavior ?

Thanks alot



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Re: [Freesurfer] longitudinal processing stream

[Bruce Fischl]

Hi Dana,

we're probably a couple of weeks off. We do have some tools for 
visualizing change maps, and can release that as well when get things 
together.


cheers,
Bruce


On Fri, 22 May 2009, Dana W. Moore wrote:


Hi freesurfer team,

I noticed in the new version release notes that the longitudinal stream is 
still a work in progress.  Any idea of what the time-frame is for this fix?


Also, I was wondering if there is a way after longitudinal processing to look 
at change maps in tkmedit or tksurfer (e.g. a color-coded segmentation that 
shows atrophy)?


Thanks,
Dana


Dana W. Moore, Ph.D.
Neuropsychology Fellow
Cornell Neuropsychology Service
Weill Medical College of Cornell University
New York Presbyterian Hospital
Department of Neurology & Neuroscience
428 East 72nd Street, Suite 500
New York, NY 10021
Phone: 212-746-2441
Fax: 212-746-5584
Email: dwm2...@med.cornell.edu

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Re: [Freesurfer] Longitudinal processing clarification

[Nick Schmansky]

edits should be made to the cross-sectional subjects and the base
subjects.  edits do not need to be made to the longitudinal runs, as
they will be transferred from the cross-sectional subject run.  the base
subject does not get edits transferred from the composing set of
cross-sectional subjects because each of those runs will be slightly
different, and edits to one time-point may not apply to another
time-point.

n.

On Fri, 2010-02-12 at 13:51 -0600, Derin Cobia wrote:
> Bumping this back up to the list.  Could someone please address?  
> 
> 
> To be more concise, during longitudinal processing, where are wm/gm
> edits made?  On the cross-sectional runs, to the base, or on
> the .long. runs themselves?  Thanks.
> 
> 
> -Derin
> 
> Begin forwarded message:
> 
> > From: Derin Cobia 
> > 
> > Date: February 1, 2010 3:54:46 PM CST
> > 
> > To: "freesurfer@nmr.mgh.harvard.edu Help"
> > 
> > 
> > Subject: Longitudinal processing clarification
> > 
> > 
> > (Questions for all, but maybe more directed towards Martin)
> > 
> > 
> > I have some questions about manual edits in regard to the
> > longitudinal stream.  Based on the current info on the wiki page, it
> > appears that no edits are pushed forward from the cross-sectional
> > (initial) runs of the subject data, as any information on
> > the *.long.* runs come from the template.  However, I've noticed
> > that WM edits and surfs from the template are used for the *.long.*
> > processing.  In essence, my question is when/where should manual
> > edits (i.e., control points, WM, pial edits) occur when conducting
> > longitudinal processing in 4.5?  It seems I remember that in 4.3
> > edits in the cross-sectional work would be pushed forward to the
> > *.long.* images, but such is not the case anymore (?).  Are edits to
> > occur in the template (i.e., 'base') now, or in the *.long.* runs?
> >  Thanks.
> > 
> > 
> > -Derin
> > 
> > 
> > 
> > 
> 
> 
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Re: [Freesurfer] Longitudinal processing clarification

[Martin Reuter]

Hi Derin,

this is how I see it:

The base might need edits and if it does, they should be made. As you
say, the surfaces of the longitudinal runs are initialized with the
surface of the base, so, if it is not correct, this will pollute all
time points.

Another reason to edit the base is that wm edits (255) and deletes (1)
are copied from the base to all time points, as you mentioned. 

Usually this should be sufficient, but maybe you need further edits in a
specific longitudinal run, never happened to me.

The old longitudinal processing stream really did not have any cross
sectional runs. Instead of the base they processed TP1 (introducing a
bias) and copied the edits from there to the longitudinals. We now copy
it from the base.

Hope that helps. 

Nick mentioned that edits are copied from the cross sectionals, but I
think they only come from the base. At least that is what I think was
done and therefore put it on the wiki. Maybe Nick can verify what really
goes on in recon-all as he programmed that part?

It might make sense to edit the cross sectionals anyway because:
- you then get more reliable cross sectional results (to compare to
etc).
- the cross sectional asegs are 'fused' (probabilistic voting), to
initialize the labeling in the longitudinal runs, so more accuracy in
the cross sectionals cannot hurt. However I never really found this to
be necessary, but my data was usually high quality. 

Best, Martin


On Fri, 2010-02-12 at 13:51 -0600, Derin Cobia wrote:
> Bumping this back up to the list.  Could someone please address?  
> 
> 
> To be more concise, during longitudinal processing, where are wm/gm
> edits made?  On the cross-sectional runs, to the base, or on
> the .long. runs themselves?  Thanks.
> 
> 
> -Derin
> 
> Begin forwarded message:
> 
> > From: Derin Cobia 
> > 
> > Date: February 1, 2010 3:54:46 PM CST
> > 
> > To: "freesurfer@nmr.mgh.harvard.edu Help"
> > 
> > 
> > Subject: Longitudinal processing clarification
> > 
> > 
> > (Questions for all, but maybe more directed towards Martin)
> > 
> > 
> > I have some questions about manual edits in regard to the
> > longitudinal stream.  Based on the current info on the wiki page, it
> > appears that no edits are pushed forward from the cross-sectional
> > (initial) runs of the subject data, as any information on
> > the *.long.* runs come from the template.  However, I've noticed
> > that WM edits and surfs from the template are used for the *.long.*
> > processing.  In essence, my question is when/where should manual
> > edits (i.e., control points, WM, pial edits) occur when conducting
> > longitudinal processing in 4.5?  It seems I remember that in 4.3
> > edits in the cross-sectional work would be pushed forward to the
> > *.long.* images, but such is not the case anymore (?).  Are edits to
> > occur in the template (i.e., 'base') now, or in the *.long.* runs?
> >  Thanks.
> > 
> > 
> > -Derin
> > 
> > 
> > 
> > 
> 
> 
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Re: [Freesurfer] Longitudinal processing clarification

[Mehul Sampat]

Hi  Nick (and Martin)

Could you please clarify if the edits come only from the base or if they are
copied from the cross-sectionals ?

It would be great if I only had to make edit in  the base .
We have 5 timepoints for each subject (each a year apart) and i want to use
the results from the longitudinal pipeline only.
If I did not need to edit the cross-sectional timepoints and if editing only
the base was okay this would be very helpful.

Martin, do you normally only make edits to base when using the longitudinal
pipeline ?
Thanks
Mehul


On Fri, Feb 12, 2010 at 6:01 PM, Martin Reuter
wrote:

> Hi Derin,
>
> this is how I see it:
>
> The base might need edits and if it does, they should be made. As you
> say, the surfaces of the longitudinal runs are initialized with the
> surface of the base, so, if it is not correct, this will pollute all
> time points.
>
> Another reason to edit the base is that wm edits (255) and deletes (1)
> are copied from the base to all time points, as you mentioned.
>
> Usually this should be sufficient, but maybe you need further edits in a
> specific longitudinal run, never happened to me.
>
> The old longitudinal processing stream really did not have any cross
> sectional runs. Instead of the base they processed TP1 (introducing a
> bias) and copied the edits from there to the longitudinals. We now copy
> it from the base.
>
> Hope that helps.
>
> Nick mentioned that edits are copied from the cross sectionals, but I
> think they only come from the base. At least that is what I think was
> done and therefore put it on the wiki. Maybe Nick can verify what really
> goes on in recon-all as he programmed that part?
>
> It might make sense to edit the cross sectionals anyway because:
> - you then get more reliable cross sectional results (to compare to
> etc).
> - the cross sectional asegs are 'fused' (probabilistic voting), to
> initialize the labeling in the longitudinal runs, so more accuracy in
> the cross sectionals cannot hurt. However I never really found this to
> be necessary, but my data was usually high quality.
>
> Best, Martin
>
>
> On Fri, 2010-02-12 at 13:51 -0600, Derin Cobia wrote:
> > Bumping this back up to the list.  Could someone please address?
> >
> >
> > To be more concise, during longitudinal processing, where are wm/gm
> > edits made?  On the cross-sectional runs, to the base, or on
> > the .long. runs themselves?  Thanks.
> >
> >
> > -Derin
> >
> > Begin forwarded message:
> >
> > > From: Derin Cobia 
> > >
> > > Date: February 1, 2010 3:54:46 PM CST
> > >
> > > To: "freesurfer@nmr.mgh.harvard.edu Help"
> > > 
> > >
> > > Subject: Longitudinal processing clarification
> > >
> > >
> > > (Questions for all, but maybe more directed towards Martin)
> > >
> > >
> > > I have some questions about manual edits in regard to the
> > > longitudinal stream.  Based on the current info on the wiki page, it
> > > appears that no edits are pushed forward from the cross-sectional
> > > (initial) runs of the subject data, as any information on
> > > the *.long.* runs come from the template.  However, I've noticed
> > > that WM edits and surfs from the template are used for the *.long.*
> > > processing.  In essence, my question is when/where should manual
> > > edits (i.e., control points, WM, pial edits) occur when conducting
> > > longitudinal processing in 4.5?  It seems I remember that in 4.3
> > > edits in the cross-sectional work would be pushed forward to the
> > > *.long.* images, but such is not the case anymore (?).  Are edits to
> > > occur in the template (i.e., 'base') now, or in the *.long.* runs?
> > >  Thanks.
> > >
> > >
> > > -Derin
> > >
> > >
> > >
> > >
> >
> >
> > ___
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[Freesurfer] Longitudinal processing -qcache ERROR

[Lisa Delalande]

Hi everyone,

During my PhD, I'm using some longitudinal data and at the setp called
"BASE" but when i want to make a qcache processing with the last version of
FreeSurfer (i.e. 6.0)(command used : "*recon-all -base template_1-02
-qcache*") it doesn't work. I have a error message :
"Error : cannot find /.../template_1-02/surf/*lh.w-g.pct.mgh*"
I would like to kown if you know where the problem comes ? And what can I
do to fix it ?

Thank you,
Best regards,

Lisa
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Re: [Freesurfer] Longitudinal Processing question

[Martin Reuter]

Hi Ryan, 

 FreeSurfers Longitudinal pipeline assumes head size is relatively fixed. The 
problem with growing heads is that the surfaces from the subject-template will 
not fit well to later (or earlier) time points and that the algorithm can 
potentially not recover. If surfaces look OK it means it worked. I have no idea 
how large the time delta is for it to fail but I guess if you scan a 4 year old 
and then again when they are 12 that could be problematic. 

You should use eTIV from the cross stream. In the long stream eTiv is fixed 
across time.


Best, Martin

> On 9. Jul 2018, at 20:51, Nillo, Ryan Michael R  
> wrote:
> 
>External Email - Use Caution
> 
> Hello FreeSurfer experts,
> 
> I have a few questions on the longitudinal processing stream. I am interested 
> in studying longitudinal morphometry changes in a pediatric population. The 
> age range of this population is between 4-20 years with age deltas between a 
> few months to < 2 years. I want to know what are appropriate/acceptable age 
> deltas used for longitudinal processing. I looked through the archives and 
> one researcher asked about age deltas. One of the answers was that “if the 
> time delta is relatively small, this has good chances to work”. What does 
> “relatively small” mean? If the time points exit the longitudinal pipeline 
> without errors and the surfaces look correct, does this mean the data is 
> relevant?? When I correct for head size, should I use the eTIV values from 
> the cross-sectional directories or the longitudinal directories?
> 
> Thanks in advance,
> 
> Ryan Michael Nillo
> Staff Research Associate I
> University of California San Francisco
> Department of Radiology and Biomedical Imaging
> 
> 
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> 


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[Freesurfer] Longitudinal Processing Stream Version

[Sunavsky's Stocks]

External Email - Use Caution

Hello,

I have a question about longitudinal stream processing. On the wiki page (
https://secure-web.cisco.com/1ak_FVO1o5iVON2RkYI_Y4g9zeL4DobzwWVTa4pFlVvLOZsX_otgrcR9pl8LiCuUek5_DaMIuShxR8HZw9Z308Nn-Oea8XuRbsYfnymCNabPqzCdzt84rgttn8r-TZoxD9u2drr8KzKAdNuvBM-L08S4UNGMblPO3019c6bsKoeDbcR7oy4pJgv3BmhzYuzbclV9-2V6Japcx9Bgzd7W8tcqooQdNWHI8XLCcrGN5-C8irviXzXMCE9m_kfxt9m0Z_QAdcWVGatwSnsQm7YVtElYmByyAnsebe2nBNR-YqzV_DAxO3SVj_eDsyF5AXS3vq0rIUtUiUMfuUe5wca3_4A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FLongitudinalProcessing)
 it states
that you can do longitudinal processing up to version 6.0 of FS. I was
wondering if later versions of FS (7.4.x) can also be used to do
longitudinal processing.

Thank you for your help,
Adam.
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Re: [Freesurfer] longitudinal processing with -FLAIRpial

[Martin Reuter]

Hi Charles,

the FLAIRpial is a recent addition and has only been added to the cross 
sectional stream so far. I can take a look at porting this to the longitudinal 
stream but probably not for 5.2.

Best, Martin

On Feb 7, 2013, at 7:23 AM, Charles Malpas  
wrote:

> Dear Freesurfer Ninjas,
> 
> I have been playing around with the new beta version, and am very interested 
> in the -FLAIRpial option. I have been using this successfully on 
> cross-sectional runs, but would like to extend it to cross sectional runs. 
> 
> I have played around with trying to get this to work, including copying 
> FLAIRconf.mgz to the longitudinal run directions (subjid.long.template) and 
> the recon-alll -long command with -FLAIRpial. Although this runs, it produces 
> cortical thickness estimates that appear underestimated on visual inspection.
> 
> Is there a better way to incorporate -FLAIRpial on longitudinal runs? Is it 
> even possible at this stage?
> 
> Many thanks for your time,
> 
> - Charles
> 
> 
> 
> -- 
> Charles Malpas 
> Master of Psychology (Clinical Neuropsychology) / PhD Candidate
> Melbourne School of Psychological Sciences & Department of Medicine (RMH)
> The University of Melbourne 3010
> 
> Melbourne Brain Centre @ RMH
> Neuropsychiatry Research Group 
> Level 4, Main Building, Royal Melbourne Hospital
> Phone: 0451 116 434
> Email: c.mal...@student.unimelb.edu.au
> Skype: charles.malpas
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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: 
   mreu...@nmr.mgh.harvard.edu
   reu...@mit.edu
Web  : http://reuter.mit.edu 

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[Freesurfer] longitudinal processing of one timepoint

[Luigi Angelo Maglanoc]

Dear FreeSurfer experts,

I know that it is possible to submit data with only one timepoint into 
the longitudinal stream with FreeSurfer 5.2. My question is, what is the exact 
command?
is it:
1) recon-all -base  -tp  -all
or
2) recon-all -base  -tp  -tp  -allI have accidently 
run them with the second command, and I am also wondering
whether this will have a negative impact?

Thank you for your time and consideration!

Sincerely
Luigi

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[Freesurfer] longitudinal processing (base-tps error)

[Sabin Khadka]

HI all,
I ran longitudinal processing with
reco-all -base  -tp  -tp  -all

but in base-tps file of template ID I found the subject ID of MRI_T1 twice
instead of MRI_T1 and MRI_T2. I want to run recon-all -long which I am able
to do for MRI_T1 but could not do the same for MRI_T2.
ANy help would be appreciated.
Thanks
SK
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[Freesurfer] longitudinal processing for lgi comparison

[Sabin Khadka]

Hi all,
Is there a longitudinal processing stream to compare local gyrification
index (lgi) across two time points.
-Sabin
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[Freesurfer] manually run freesurfer longitudinal processing

[Xie, Hong]

Hello, group,
 
I am running longitudinal process step by step following the wiki page of 
12 differences between longitudinal and recon-all process. But some needed 
files are not generated by these 12 steps, for example, brain.mgz, wm.seg.mgz, 
wm.asegedit.mgz, aseg.auto_noCCseg.mgz, wm.mgz, fill.mgz, 
brain.finalsurfers.mgz, ?h.smoothwm, ?h.inflated, ?h.sulc, and ?h.aparc.annot.
Should I use recon-all commands to create these files or just copy ( or 
transform) them from tp1 to tp2?
Thank you for help.
 
Hong

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[Freesurfer] longitudinal processing - OS re-installation

[Mihaela Stefan]

Dear FreeSurfers,

I use FS v5.3 on Ubuntu 12.04.3 LTS. I am working on a longitudinal study
and now I have problems with my machine. It started to work very slowly and
it's losing the Internet connection frequently without apparent reason. I
believe there's a bug that affects its performance quite seriously.

I wonder if I can re-install Ubuntu 12.04.3 LTS without affecting my
longitudinal processing.

Thanks!
Mihaela
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Re: [Freesurfer] Longitudinal processing -qcache ERROR

[Martin Reuter]

Hi Lisa,

not sure where the problem comes from. But generally one would not do 
the qcache on the base. Qcache maps results to fsaverage and nobody 
should ever look at the base results except for debugging purposes. The 
base is the within-subject template and it is used to initialize the 
longitudinal processing. It is not the baseline (=first time point).


Best, Martin



Am 15.09.2017 um 16:00 schrieb Lisa Delalande:

Hi everyone,

During my PhD, I'm using some longitudinal data and at the setp called 
"BASE" but when i want to make a qcache processing with the last 
version of FreeSurfer (i.e. 6.0)(command used : "*recon-all -base 
template_1-02 -qcache*") it doesn't work. I have a error message :

"Error : cannot find /.../template_1-02/surf/_*lh.w-g.pct.mgh*_"_*
*_
I would like to kown if you know where the problem comes ? And what 
can I do to fix it ?


Thank you,
Best regards,

Lisa


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[Freesurfer] longitudinal processing, template and flags

[Daniel Ferreira]

Dear experts,

I have two questions regarding the longitudinal stream:

- I am including Baseline and 12 months follow-up in my study. However, I
also have 6 months follow-up. I wonder if it is conceptually right to
include these 6 months scans in template creation with the idea of
increasing registration.

- I am applying the -mprage flag in the crossectional first step. Should I
use it in the -base and -longs steps too?

Thanks very much

Daniel Ferreira
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[Freesurfer] Longitudinal processing with freesurfer 7.1.0

[Angela Favaro]

External Email - Use Caution

Dear Freesurfer experts, 
I am trying to process a dataset with a longitudinal design.
However, after building the template, at the “recon-all -long” command I got 
this error:

longmc Done
/Users/angelafavaro/Desktop/Aachen/subj201.long.template4/mri
\n cp -f --preserve=timestamps 
/Users/angelafavaro/Desktop/Aachen/template4/mri/brainmask.mgz 
./brainmask_template4.mgz \n
cp: illegal option -- -
usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file target_file
   cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file ... 
target_directory
ERROR:
Darwin iMac-di-Angela.local 19.0.0 Darwin Kernel Version 19.0.0: Thu Oct 17 
16:17:15 PDT 2019; root:xnu-6153.41.3~29/RELEASE_X86_64 x86_64

recon-all -s subj201.long.template4 exited with ERRORS at Sat May 23 03:47:31 
CEST 2020

For more details, see the log file 
/Users/angelafavaro/Desktop/Aachen/subj201.long.template4/scripts/recon-all.log


Thank you for any help!

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[Freesurfer] Longitudinal Processing - Retaining Manual Edits

[KALEY E ELLIS]

External Email - Use Caution

Dear FreeSurfer Developers,

We are using your longitudinal processing pipeline (version 6.0) for our study 
(n=140, 3 timepoints). Our scanner was upgraded a year ago and the  a filter 
was used on the raw images to adjust for hyperintensities in the images due to 
using a multi-channel coil.

At this point, our bases have already been processed and consist of three 
timepoints with a mix of filters: T1 no filter, T2 no filter, T3 with filter. 
Since we have invested many resources into the manual editing process, we want 
to try to retain all the manual edits that have been done to the base. We still 
have the original scan and the filtered scan for each subject. We have some 
ideas on how we might be able to retain the edits, but would you be able to 
provide  input regarding whether this seems reasonable? Your feedback is 
greatly appreciated!

Plan A:
1) Create a new T3 cross-sectional with the correct nifti
2) Run recon-all on the existing base
Q: Will this retain the previous manual edits AND incorporate the new 
cross-sectional image?

Plan B:
1) Create a new T3 cross-sectional with the correct nifti
2) Create a new base
Q: Is it possible to transfer data from old manual edits to a new base? If so, 
how?

Thank you!
Kaley


Associate Research Specialist
Center for Healthy Minds
Waisman Center for Brain Imaging and Behavior
University of Wisconsin-Madison
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[Freesurfer] Longitudinal processing and paralllel flag

[Erik O'Hanlon]

External Email - Use Caution

Hi FS experts,


I'm running a longitudinal process with three time points per subject and was 
wondering if you can advise on the typical time to process? Can the -parallel 
flag be added to the base and long steps? I'm running this on a cluster that 
has 16 core nodes with 32gigs of ram so it might give me a good tme saving if 
these steps can be parallelized.


Thanks and regards


Erik


Postdoctoral Research Fellow
Dept. Of Psychiatry
Royal College of Surgeons in Ireland
ERC Building
Beaumont Hospital
Dublin
&
Dept. Of Psychiatry
Trinity College Institute of Neuroscience
The Llyod Institute
Trinity College Dublin
D2

Erik O'Hanlon
Postdoctoral researcher

[cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png]

RCSI Psychiatry
Royal College of Surgeons in Ireland
Beaumont Road, Beaumont D9 Ireland
T: 8093740
E: erikohan...@rcsi.ie W: www.rcsi.com


Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 
2018-2022


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Re: [Freesurfer] Longitudinal Processing Stream Version

[Huang, Yujing]

External Email - Use Caution

Hi Adam,

Yes, the longitudinal pipeline is also available in FS 6.0 and up.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Sunavsky's Stocks
Sent: Wednesday, August 16, 2023 6:33 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Longitudinal Processing Stream Version


External Email - Use Caution
Hello,

I have a question about longitudinal stream processing. On the wiki page 
(MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
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 it states that you can do longitudinal processing up to version 6.0 of FS. I 
was wondering if later versions of FS (7.4.x) can also be used to do 
longitudinal processing.

Thank you for your help,
Adam.
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[Freesurfer] Longitudinal processing 3 time point error

[Kawadler, Jamie]

Hello,

I have a dataset of patients with 3 time points each. While 2-time point 
processing works just fine in the longitudinal stream, when I run a base with 3 
time points, the process fails and exits with errors.

Please see the output below:

Resolution: 0  S( 256 256 256 )  T( 256 256 256 )
 Iteration(f): 1 -- diff. to prev. transform: 0.160049
 Iteration(f): 2mri_robust_template(778) malloc: *** mmap(size=262144) failed 
(error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
MRIalloc(256, 256, 256): could not allocate 262144 bytes for 129th slice

Cannot allocate memory
Darwin Jamies-iMac.local 11.4.0 Darwin Kernel Version 11.4.0: Mon Apr  9 
19:32:15 PDT 2012; root:xnu-1699.26.8~1/RELEASE_X86_64 x86_64

recon-all -s EB1312_61-66-77_base exited with ERRORS at Wed Sep 26 12:19:11 BST 
2012

This is similar to a message on the mailing list from Liz Bowman (30 Jul 2012), 
in which the response was to get more memory. My command was done on a Mac with 
16GB of RAM and ample disk space.

I'd appreciate any help!

Thanks,
Jamie Kawadler
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Re: [Freesurfer] longitudinal processing of one timepoint

[Martin Reuter]

Hi Luigi,

1 is the right way of calling it. 2 will have a negative effect in the 
sense that it takes the same image twice and then creates the mid-space 
at the same location, so 2 could be biased.
1 is creating an artifical mid-space and makes sure the image gets 
mapped there.


Best, Martin

On 02/13/2013 08:39 AM, Luigi Angelo Maglanoc wrote:

Dear FreeSurfer experts,

I know that it is possible to submit data with only one timepoint into
the longitudinal stream with FreeSurfer 5.2. My question is, what is 
the exact command?

is it:
1) recon-all -base  -tp  -all
or
2) recon-all -base  -tp  -tp  -all
I have accidently run them with the second command, and I am also 
wondering

whether this will have a negative impact?

Thank you for your time and consideration!

Sincerely
Luigi


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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
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Re: [Freesurfer] longitudinal processing (base-tps error)

[Martin Reuter]

Hi Sabin,
If the base-tps file contains a time point twice, that indicates that it has 
been created by passing the same time point twice, probably a typo.
You need to remove the base and tp1.long and run again with the correct 
parameters.

Best Martin

On Apr 11, 2012, at 9:31, Sabin Khadka  wrote:

> HI all,
> I ran longitudinal processing with 
> reco-all -base  -tp  -tp  -all
> 
> but in base-tps file of template ID I found the subject ID of MRI_T1 twice 
> instead of MRI_T1 and MRI_T2. I want to run recon-all -long which I am able 
> to do for MRI_T1 but could not do the same for MRI_T2.
> ANy help would be appreciated.
> Thanks
> SK
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Re: [Freesurfer] longitudinal processing for lgi comparison

[Martin Reuter]

No,
should be very similar across time, or not?

But the surfaces will be more reliable after longitudinal processing,
can't you just run the lgi analysis on the tp?.long.base directories?

Best, Martin

On Wed, 2012-04-11 at 15:49 -0400, Sabin Khadka wrote:
> Hi all,
> Is there a longitudinal processing stream to compare local
> gyrification index (lgi) across two time points.
> -Sabin
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Re: [Freesurfer] manually run freesurfer longitudinal processing

[Nick Schmansky]

Hong,

If you add -help to recon-all, it has a section on longitudinal
processing.  longitudinal processing assumes your timepoint 1 subject
has already been processed by the normal stream (ie, recon-all -all -s
).  That will produce the files you mention.

However, we have recently made significant improvements in the
longitudinal stream, which will appear in the next stable release.  If
you want to work with those updates, you can get them for centos4 here:

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/dev/centos4

copy them to your $FREESURFER_HOME/bin.

You will still need to process your tp1 subject by the normal-stream
(and also the longitudinal stream).

Nick


On Mon, 2008-09-08 at 09:02 -0400, Xie, Hong wrote:
> Hello, group,
>  
> I am running longitudinal process step by step following the wiki
> page of 12 differences between longitudinal and recon-all process. But
> some needed files are not generated by these 12 steps, for example,
> brain.mgz, wm.seg.mgz, wm.asegedit.mgz, aseg.auto_noCCseg.mgz, wm.mgz,
> fill.mgz, brain.finalsurfers.mgz, ?h.smoothwm, ?h.inflated, ?h.sulc,
> and ?h.aparc.annot.
> Should I use recon-all commands to create these files or just copy
> ( or transform) them from tp1 to tp2?
> Thank you for help.
>  
> Hong
> 
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[Freesurfer] Longitudinal processing with variable time points?

[Dankner, Nathan (NIH/NIMH) [F]]

Hello all,

I am hoping to do some longitudinal processing on a dataset.  However, the 
intervals between time points for each subject are not uniform.  Can 
freesurfer's longitudinal processing stream handle this, or do all of the time 
points need to be equal?

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Re: [Freesurfer] longitudinal processing - OS re-installation

[Bruce Fischl]

that should be fine
Bruce
On Wed, 8 Apr 2015, Mihaela Stefan wrote:

> Dear FreeSurfers,
> I use FS v5.3 on Ubuntu 12.04.3 LTS. I am working on a longitudinal study
> and now I have problems with my machine. It started to work very slowly and
> it's losing the Internet connection frequently without apparent reason. I
> believe there's a bug that affects its performance quite seriously.
> 
> I wonder if I can re-install Ubuntu 12.04.3 LTS without affecting my
> longitudinal processing.
> 
> Thanks!
> Mihaela
> 
>
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Re: [Freesurfer] longitudinal processing - OS re-installation

[Mihaela Stefan]

Thanks!
Mihaela

On Wed, Apr 8, 2015 at 12:19 PM, Bruce Fischl 
wrote:

> that should be fine
> Bruce
> On Wed, 8 Apr 2015, Mihaela Stefan wrote:
>
> > Dear FreeSurfers,
> > I use FS v5.3 on Ubuntu 12.04.3 LTS. I am working on a longitudinal study
> > and now I have problems with my machine. It started to work very slowly
> and
> > it's losing the Internet connection frequently without apparent reason. I
> > believe there's a bug that affects its performance quite seriously.
> >
> > I wonder if I can re-install Ubuntu 12.04.3 LTS without affecting my
> > longitudinal processing.
> >
> > Thanks!
> > Mihaela
> >
> >
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[Freesurfer] Longitudinal processing with different FS versions

[Susanna Carmona Cañabate]

Dear Freesurfers,

We are running a longitudinal study with 4 time points. The first two time
points were processed and edited with the 5.3 version of Freesurfer and the
other two time points with FS6. I assume we have to re-run the first two
time points with the new versión, but is there a way to preserve the
editings?

In the same line, on a transversal study, would it be a lot of bias if most
of the subjects of one group are processed with version 5.3 and most of the
subjects of the other group with FS6?

Thanks a lot for your time
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Re: [Freesurfer] longitudinal processing, template and flags

[Martin Reuter]

Hi Daniel,

1. yes. But why not include 6 month in your study if you have those 
scans??? You will get much more reliable slope estimates with 3 time 
points compared to 2, so including that time point will not only help 
for the image processing part, but also in your statistics (you gain power).


2. I am not familiar with the mprage flag and think it mainly affects 
the normalization. If you are sure you need it, then also add it to the 
-base and -long runs, just to be safe.


best, Martin

On 01/29/2014 09:08 AM, Daniel Ferreira wrote:

Dear experts,

I have two questions regarding the longitudinal stream:

- I am including Baseline and 12 months follow-up in my study. 
However, I also have 6 months follow-up. I wonder if it is 
conceptually right to include these 6 months scans in template 
creation with the idea of increasing registration.


- I am applying the -mprage flag in the crossectional first step. 
Should I use it in the -base and -longs steps too?


Thanks very much

Daniel Ferreira


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Instructor in Neurology   - Harvard Medical School
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149 Thirteenth Street, Suite 2301
Charlestown, MA 02129

Phone: +1-617-724-5652
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   reu...@mit.edu
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