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...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Martin Reuter
[mreu...@nmr.mgh.harvard.edu]
*Sent:* 18 November 2014 17:04
*To:* Freesurfer support list
*Subject:* Re: [Freesurfer] Longitudinal analysis and hippocampal
subfields
Hi Erik,
yes, you would do the subfields only
. Martin Reuter
Instructor in Neurology
Harvard Medical School
Assistant in Neuroscience
Dept. of Radiology, Massachusetts General Hospital
Dept. of Neurology, Massachusetts General Hospital
Research Affiliate
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Dept. of Electrical Engineering
mardi 21 octobre 2014 16h40, Martin Reuter
mreu...@nmr.mgh.harvard.edu mailto:mreu...@nmr.mgh.harvard.edu a
écrit :
Hi Alex,
you have to duplicate the parameter (it is basically fixed across
time). If you put 0 for tp2, it will average the two values, which is
not what you want. Otherwise I
,
Lars M. Rimol, PhD
Norwegian University of Science and Technology (NTNU)
Trondheim,
Norway
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is
incorrect?
Best regards,
Christian K Tamnes
From: freesurfer-boun...@nmr.mgh.harvard.edu
freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Martin Reuter
mreu...@nmr.mgh.harvard.edu
Sent: 14 October 2014 17:23
To: Freesurfer support list
Hi Janosch,
You could do that, but no further processing will be possible. The long runs
take the asegs from the cross sectional runs and many other results from the
base. Without base and long they can probably be used for statistical analysis
(the roi stuff should work , for surfaces the
One possible solution:
Rename the time point in cross, in the base txt file (directly under the base
directory, something with tps in it), in the base/mri/transforms/* files and in
the long directory names and long/mri/transform files. I think these are all
the places where subject names are
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,
Janosch
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Effects Models*. J.L.Bernal-Rusiel, D.N.Greve, M.Reuter et al.
/NeuroImage 66:249-260, 2012/.
Best, Martin
On 10/23/2014 12:17 AM, Martin Reuter wrote:
Hi Tracy,
When you call recon-all -base simply pass only the single time point -tp.
Best Martin
Sent via my smartphone, please excuse brevity
and parameter 'A' be performed
in this case ?
Additionally, after performing the mri_glmfit described in the
2-stage-model page, in the tksurfer how can I see the plot ? The
y.fsgd file wasn't created. Is there another method ?
Thanks,
Alex
Le mardi 21 octobre 2014 16h40, Martin Reuter
Hi Tracy,
When you call recon-all -base simply pass only the single time point -tp.
Best Martin
Sent via my smartphone, please excuse brevity.
div Original message /divdivFrom: Tracy Melzer
tracy.mel...@otago.ac.nz /divdivDate:10/22/2014 10:59 PM (GMT-05:00)
/divdivTo:
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to
create the cross file. I put a zero at time 2. In qdec design we
analyzed parameter 'A' with -pc1 and -spc. I'm not sure that this is
the correct approach.
I'll continue with LME and mri_glmfit.
Sincerely,
Alex
Le mardi 21 octobre 2014 9h19, Martin Reuter
mreu...@nmr.mgh.harvard.edu a écrit
data. I was
wondering if you had any suggested literature for the number of time
points needed for stability of a template.
Thanks
Koushik Govindarajan
*From:*Martin Reuter [mailto:mreu...@nmr.mgh.harvard.edu]
*Sent:* Friday, March 14, 2014 9:31 AM
*To:* Govindarajan, Koushik Athreya
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was wondering if there also is anyway to get a visual
picture of the percent volume changes like the first spc command provided?
Also is there any command that can give you the percent change in
global brain volume?
Thanks for the help!
Cheers,
Taylor North
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Research
for your help!
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Hi,
many of you are aware of (yes, even excited about) our social media
presence at
Facebook: http://facebook.com/FreeSurferMRI
Twitter: http://www.twitter.com/FreeSurferMRI
and so we have just added a group on
LinkedIn: https://www.linkedin.com/groups/FreeSurfer-8173404
(it's hard to believe,
SUBJECTS_DIR).
How could I come around that problem?
Thanks in advance!
Markus
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for the help!
Taylor
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Instructor in Neurology - Harvard Medical School
MGH / HMS / MIT
A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129
Hi Cedric,
the base image looks bad. The reason could be a mis-registration. More
likely though you have two time points that come from different subjects?
Best, Martin
On 09/02/2014 04:09 AM, Koolschijn, Cédric wrote:
Dear experts,
I'm performing a longitudinal analysis, and have done so
Hi Janosch,
yes, that works if longitudinal changes are really small. You should be
careful with copying edits from base to the long as even with small
atrophy there can be local deformations of the brain, and rigid
alignment and copying may not make sense.
Yet, I believe that even without
Hi Bastian,
yes, I have some code to do what you want. You would duplicate and flip
the good hemisphere in the image and then run FS on the symmetric heads.
This can be done via robust_register and (mis)-using the mid space.
You can find some description of this procedure here:
*Robust and
(right originally healthy) hemispheres, as you may introduce a bias.
Freesurfer atlases are hemisphere specific.
Best, Martin
On 08/19/2014 01:51 PM, Martin Reuter wrote:
Hi Bastian,
yes, I have some code to do what you want. You would duplicate and
flip the good hemisphere in the image
-
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
not have to
specify a flag for the baseid or for each subject, eg -s?
What I did (according to your suggestion)
recon-all -long XXX_1.long XXX_2.long -localGI
This did not work? Do you know why potentially?
On Wed, Mar 26, 2014 at 3:28 PM, Martin Reuter mreu...@nmr.mgh.harvard.edu
wrote
folder
of the base image but am not sure how to apply them (maybe
tkregister2?)
best regards,
Bastian
On 18 July 2014 23:00, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote:
Hi Bastian,
use the longitudinal base for it. Also, once your ROI is in that space
you can simply apply it in each long
can simply see if there are any
thickness differences without using any covariates (so look at any
areas of significant difference in thickness-rate) while correcting
for multiple comparisons using fdr?
Thank you all your help.
Best wishes,
Sal
On Wed, Jul 9, 2014 at 6:13 AM, Martin Reuter
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Dept. of Neurology, Massachusetts General Hospital
Research Affiliate
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long.qdec.table.dat file as described the tutorial, and have the measures of
long.thickness-avg, long.thickness-rate, long.thickness-pc1 and
long.thickness-spc avaialble (again from the tutorial).
Any advice would be greatly appreciated.
Sal
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the
images and all segmentations were accurate.
Thanks,
Mike Kranz
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the inherent segmentation
parcellation differences between MRIs taken on these two machines?
Thank you, Alfred Ochs
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Hi xuan,
You can try freesurfer 5.3 for the base creation and see if that fixes it.
If not, send me the two norm.mgz of the cross time points and I take a look.
Thanks, martin
Sent via my smartphone, please excuse brevity.
Original message
From: XUAN AMELIA TRAN
would be great.
Thanks!
On Jul 2, 2014, at 5:31 PM, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote:
Hi Brianna,
Yes, that is the best option in my opinion. You should include field strength
as a covariate, and maybe other acquisition parameters.
Best Martin
Sent via my
Hi Brianna,
Yes, that is the best option in my opinion. You should include field strength
as a covariate, and maybe other acquisition parameters.
Best Martin
Sent via my smartphone, please excuse brevity.
Original message
From: Brianna Damadian bdama...@buffalo.edu
Hi
I don't know what you mean. The word 'generate' does not appear on that web
page.
Best Martin
Sent via my smartphone, please excuse brevity.
Original message
From: Salil Soman salso...@stanford.edu
Date:07/01/2014 9:50 PM (GMT+01:00)
To: free surfer
Hi salil, the command for that are on the wiki. You'd do a one sample group
mean (-osgm) . This asks if the variable of interest is significantly different
from zero. Since you ran long mris slopes, that variable would be for example
the rate of change or the percent change (one measure per
Hi Bryan,
I can answer the longitudinal question (2), the rest is about cross sectional
editing and can probably better be answered by someone else.
So yes, I would run the base and check brainmask and surfaces there before
going too deep into editing the cross.
Best Martin
Sent via my
only the cross and
fsid's are specified in the qdec table? Is this correct? Kind regards, Anna
On Tue, Jun 24, 2014 at 7:11 PM, Martin Reuter mreu...@nmr.mgh.harvard.edu
wrote:
Hi Anna,
the matlab tools don't know. They only look at the other co-variates that you
might want to include
through the time variable.
Best Martin
Best Martin
Sent via my smartphone, please excuse brevity.
Original message
From: Anna Jonsson ajonsso...@gmail.com
Date:06/24/2014 11:52 AM (GMT+01:00)
To: Martin Reuter mreu...@nmr.mgh.harvard.edu
Cc: Freesurfer support list freesurfer
.
Thanks for help,.
Regards Anna
On Tue, Jun 24, 2014 at 11:26 AM, Martin Reuter mreu...@nmr.mgh.harvard.edu
wrote:
Hi Anna
I am not a statistician, but I would not control for duration separately, but
rather use the time variable for that.
It does not need to be in years (can be days out
Hi Tudor,
You'd add the lgi only to the third step (the -long runs). And you could do a
two stage model with it.
Martin
Sent via my smartphone, please excuse brevity.
Original message
From: Tudor Popescu tud...@gmail.com
Date:06/10/2014 11:51 PM (GMT+01:00)
To: free surfer
, 2014 at 5:01 PM, Martin Reuter mreu...@nmr.mgh.harvard.edu
wrote:
Hi Anna,
Fsid is the cross sectionall name without the .long.
Best martin
Sent via my smartphone, please excuse brevity.
Original message
From: Anna Jonsson
Date:06/04/2014 7:22 AM (GMT-05:00)
To: Freesurfer
processing stream from scratch?
Thanks for all your help!
Doug
Doug Merkitch
Neurological Sciences
Rush University Medical Center
Phone: (312) 563-3853
Fax: (312) 563-4660
Email: douglas_merki...@rush.edu
On May 19, 2014, at 3:52 PM, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote:
Hi Doug
gesendet (www.nitrodesk.com)
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The one that comes with Freesurfer. It's always the same.
Best Martin
Sent via my smartphone, please excuse brevity.
Original message
From: Elijah Mak fk...@medschl.cam.ac.uk
Date:06/04/2014 10:54 AM (GMT-05:00)
To: Martin Reuter mreu...@nmr.mgh.harvard.edu
Cc
Hi Anna,
Fsid is the cross sectionall name without the .long.
Best martin
Sent via my smartphone, please excuse brevity.
Original message
From: Anna Jonsson ajonsso...@gmail.com
Date:06/04/2014 7:22 AM (GMT-05:00)
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Hi Alex,
The time distance does not matter. It's best to use a longitudinal method (both
for the image processing, to reduce noise, and for the statistics, to gain
power).
Your design seems to be missing a control group (unless one off your groups is
placebo). In your design you can compare
to an
erroneous
averaging between timepoints, you see blurs/ghosts in your base
template?
Many thanks!
Tudor
On 9 May 2014 21:33, Martin Reuter mreu...@nmr.mgh.harvard.edu
mailto:mreu...@nmr.mgh.harvard.edu wrote:
Hi Tudor
Hi Mike,
Yes, take the results from the longitudinal stream, they are less noisy.
Best Martin
Sent via my smartphone, please excuse brevity.
Original message
From: Michael Kranz mbkr...@gmail.com
Date:05/31/2014 10:09 AM (GMT-05:00)
To: freesurfer@nmr.mgh.harvard.edu
*| *Department of Psychiatry
Trinity College, Cambridge, CB2 1TQ
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, you see blurs/ghosts in your base
template?
Many thanks!
Tudor
On 9 May 2014 21:33, Martin Reuter mreu...@nmr.mgh.harvard.edu
mailto:mreu...@nmr.mgh.harvard.edu wrote:
Hi Tudor,
the longitudinal pipeline in FS is actually one of the best on
the planet
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/rh.pial_lgi.fwhm10.fsaverage.mgh
but not in the following directories
100674_base/surf
100712_base/surf
100724_base/surf
100733_base/surf
How can I fix this?
Jon
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but not in the following directories
100674_base/surf
100712_base/surf
100724_base/surf
100733_base/surf
How can I fix this?
Jon
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: douglas_merki...@rush.edu mailto:douglas_merki...@rush.edu
Begin forwarded message:
*From: *Martin Reuter mreu...@nmr.mgh.harvard.edu
mailto:mreu...@nmr.mgh.harvard.edu
*Subject: **Re: [Freesurfer] brain.finalsurfs.manedit.mgz file
edits longitudinal processing*
*Date: *May 2, 2014 4:20:17 PM CDT
-CED01_lh_thickness_34xA_9'
Any suggestions?
Sincerely,
Jennifer
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:52:25 -0400
From: Martin Reuter mreu...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] nonlinear models in longitudinal analysis
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: 536d4009.7030...@nmr.mgh.harvard.edu
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hi Jodie,
'years
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Could anyone please shed some light on this? What would be the best
strategy to follow?
Thank you,
Sankalpa
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error.
Corinna
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, Apr 28, 2014 at 9:18 AM, Martin Reuter
mreu...@nmr.mgh.harvard.edu mailto:mreu...@nmr.mgh.harvard.edu wrote:
Hi Corinna,
try to open
/home/Documents/longitudinal_morph/meta/test_subject_2ndpostop/mri/orig/001.mgz
in freeview to see if maybe the file is corrupted.
Best
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Assistant in Neuroscience
Dept
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Martin Reuter, Ph.D.
Instructor in Neurology
Harvard Medical School
Assistant in Neuroscience
Dept. of Radiology, Massachusetts General Hospital
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Martin Reuter, Ph.D.
Instructor in Neurology
Harvard Medical School
Assistant in Neuroscience
Dept. of Radiology, Massachusetts
put the lgi flag on as normal but just replace the subject name with
the long subject name eg ?
recon-all -s _long -localGI
Thank you
On Sat, Mar 15, 2014 at 2:07 PM, Martin Reuter
mreu...@nmr.mgh.harvard.edu mailto:mreu...@nmr.mgh.harvard.edu wrote:
Hi Anna,
for the image
with the same error:
recon-all --long 23061_ip cr096_base --addtp --all
ERROR: 23061_ip is not in
/home/koushikg/data/longitudinal/cr096_base/base-tps
Thanks
Koushik
*From:*freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *Martin
Reuter
*Sent
this method of --addtp to add a new time point but
recon-all failed with the message saying my new timepoint was not in
the 'base-tps' file of the base template. Should I be doing something
else before I run this step?
Thanks
Koushik
*From:*Martin Reuter [mailto:mreu...@nmr.mgh.harvard.edu]
*Sent
@nmr.mgh.harvard.edu
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Dr. Martin Reuter
Assistant in Neuroscience - Massachusetts General Hospital
Instructor in Neurology - Harvard Medical School
MGH / HMS / MIT
A.A.Martinos Center for Biomedical
@nmr.mgh.harvard.edu
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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
freesurfer command to convert surface files
to vtk files ?
Thanks
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Martin Reuter, Ph.D.
Assistant in Neuroscience - Massachusetts
!
Best wishes,
Sasa
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Martin Reuter, Ph.D.
Assistant in Neuroscience - Massachusetts General Hospital
Instructor in Neurology
Date:03/02/2014 5:27 AM (GMT-05:00)
To: Martin Reuter mreu...@nmr.mgh.harvard.edu
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] longitudinal process
Hi thank you for reply. May I ask other question; after editing the base it
says to reocnstruct with recon-all -base -tp1 -tp2
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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
is to leave them out and only do those with 2+ times?
Thank you
Kind Regards,
Anna
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Martin Reuter, Ph.D.
Assistant
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Martin Reuter, Ph.D.
Assistant in Neuroscience - Massachusetts General
the SurferOutput folder in and recreate what's missing?
Thanks,
Mia
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Martin Reuter, Ph.D.
Assistant in Neuroscience
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Instructor in Neurology - Harvard Medical School
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