[Freesurfer] using multiple cores

[Lukas . Scheef]

Hi folks!

I try to use -openmp option on an iMAC with 4 cores. Unfortunately, I do
not see any accelartion when processing a single data set with or without
the flag -openmp flag set.

recon-all -s ernie_1 -all

leads to ~6,4h processing time.

Unfortunately
recon-all -s ernie_2 -all -openmp 4

did not change anything. Do I miss anything? Do I have to prepare my system
in a special way? Or run any scripts in advance?

(System: iMac, 32GbRam,Intel i5, 4 cores, Mac Os 10.9, latest FS version)

Best wishes,

Luke

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Re: [Freesurfer] using multiple cores

[Bruce Fischl]

Hi Luke

what version of FS are you running? We see significant speedups. Try 
running top in a unix terminal and seeing if the cpu usage of 
mri_ca_register (during autorecon2, the longest single step) is more than 
100%


cheers
Bruce

On Fri, 2 May 2014, 
lukas.sch...@ukb.uni-bonn.de wrote:




Hi folks!

I try to use -openmp option on an iMAC with 4 cores. Unfortunately, I do not
see any accelartion when processing a single data set with or without the
flag -openmp flag set.

recon-all -s ernie_1 -all

leads to ~6,4h processing time.

Unfortunately
recon-all -s ernie_2 -all -openmp 4

did not change anything. Do I miss anything? Do I have to prepare my system
in a special way? Or run any scripts in advance?

(System: iMac, 32GbRam,Intel i5, 4 cores, Mac Os 10.9, latest FS version)

Best wishes,

Luke



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[Freesurfer] When/What to edit?

[O'Shea,Andrew]

Hello FS experts,
I have had a continuing curiosity regarding when/what to edit in FS cortical 
reconstructions. The wiki does a good job at showing how to deal with large 
scale problems, (i.e. invalid tal transformation, white matter not being 
recognized, large portions of the skull included in the surface) however I have 
yet to come across much that guides edits besides a "trained eye". How do we 
know when a problem is "big enough" that it needs attention?

Are there any tool boxes/ quantitative guidelines that may help someone 
determine which scans need edits? I know QA tools outputs info on SNR/white 
matter intensity and I have looked for outliers here. However, I was wondering 
how else to automate/guide the decision process. Much of the discussion I have 
seen on this topic in manuscripts is either vague or nonexistent.

Does anyone know of any manuscripts that have compared "raw" FS datasets to 
"selectively edited" datasets? What sort of effects do edits make in the grand 
scheme of a study? One could imagine problems with someone editing the data 
when they are knowledgable of the study's hypotheses and groups.

Any additional info or guidance on this topic would be much appreciated.

-Andrew
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Re: [Freesurfer] using multiple cores

[Lukas . Scheef]

Hi Bruce!

Thanks for the fast response. I used the current stable version 5.3.0.1
(freesurfer-Darwin-lion-stable-pub-v5.3.0.1).
So I will try as you have suggested ...

Best wishes,

Lukas

> Bruce Fischl Fri, 02 May 2014 05:47:26 -0700
>
> Hi Luke
>
> what version of FS are you running? We see significant speedups. Try
> running top in a unix terminal and seeing if the cpu usage of
> mri_ca_register (during autorecon2, the longest single step) is morethan
100%
>
> cheers
> Bruce
>
> On Fri, 2 May 2014, lukas.sch...@ukb.uni-bonn.de wrote:
>
>
> > Hi folks!
> >
> > I try to use -openmp option on an iMAC with 4 cores. Unfortunately, I
do not
> > see any accelartion when processing a single data set with or without
the
> > flag -openmp flag set.
> >
> > recon-all -s ernie_1 -all
> >
> > leads to ~6,4h processing time.
> >
> > Unfortunately
> > recon-all -s ernie_2 -all -openmp 4
> >
> > did not change anything. Do I miss anything? Do I have to prepare my
system
> > in a special way? Or run any scripts in advance?
> >
> > (System: iMac, 32GbRam,Intel i5, 4 cores, Mac Os 10.9, latest FS
version)
> >
> > Best wishes,
> >
> > Luke




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[Freesurfer] brain.finalsurfs.manedit.mgz file edits & longitudinal processing

[Douglas Merkitch]

Dear Freesurfer experts,

I have a question regarding longitudinal edits. Specifically the 
brain.finalsurfs.manedit.mgz file and the longitudinal processing stream in 
Freesufer 5.1 on a Mac (freesurfer-i686-apple-darwin9.8.0-stable5-20110525).

The problem that I am having is that the edits saved in the 
brain.finalsurfs.manedit.mgz file do not carry over when processing 
longitudinally.

Previous posts have addressed this topic, but have not (to my knowledge) solved 
the issue. Please see the threads from the Freesurfer archive below for a brief 
context:

1. http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg27695.html

2. http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg33471.html

Please let me know if more information is needed to understand the issue.

Any insight/ideas regarding this issue would be greatly appreciated!

Thanks,

Doug

Doug Merkitch
Neurological Sciences
Rush University Medical Center
Phone: (312) 563-3853
Fax: (312) 563-4660
Email: douglas_merki...@rush.edu



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Re: [Freesurfer] Multi-echo FLASH

[Jon Houck]

Hi Bruce,

Great, that will simplify things considerably.  Thank you for the info.

Jon


On Fri, Apr 25, 2014 at 9:35 PM, Bruce Fischl wrote:

> Hi Jon
>
> yes, that works fine. The mprage gives better CNR/unit time in the cortex,
> but if you are really only interested in MEG that is probably a secondary
> concern (it would be important if you were doing e.g. a thickness study)
>
> cheers
> Bruce
>
> On Fri, 25 Apr 2014, Jon Houck wrote:
>
>  Hi all,
>>
>> I'm building a scan protocol for what is primarily a MEG study, which
>> needs T1 information for
>> co-registration and T1/T2 information to construct an accurate BEM from
>> the inner skull surface.  It
>> seems like the two multi-echo FLASH sequences at 5 and 30 degrees would
>> give me all of the information
>> that I need without an MPRAGE, but I'm not sure how well the two MEFs
>> work in the standard Freesurfer
>> pipeline.
>>
>> Would it be reasonable to acquire no MPRAGE but two MEF sequences at 5
>> and 30 degrees, combine them
>> following the method from https://surfer.nmr.mgh.harvard.edu/fswiki/MEF,
>> and send the resulting T1 to
>> recon-all?  With my scan time constraints, the alternative would be to
>> acquire a multi-echo MPRAGE and
>> a single 5-degree MEF.
>>
>> Thanks for any help on what is probably a naïve question.
>>
>> Jon Houck
>>
>>
>>
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[Freesurfer] effect size for conjunction analyses?

[Caspar M. Schwiedrzik]

Hi!
I am doing some conjunction analyses (Nichols et al.) on my fMRI data, and
I was wondering whether anyone can make a recommendation how to display
effect sizes for this kind of analyses?
Would you show the effect size estimate corresponding to the p-value that
is chosen, an average, or anything else?
Thanks, Caspar
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Re: [Freesurfer] per voxel regressor in LME toolbox?

[jorge luis]

Yes you can do something like this:


XM = [X, pvr(:,i)];

Best
-Jorge

El Jueves 1 de Mayo de 2014 23:39, Marnie Shaw  
escribió:
 
Hi Jorge, 
> 
>Thanks for your reply. Actually I don’t want to have different numbers of 
>columns in the design matrix for different vertices. Instead I want to add an 
>extra column to the design matrix, the value of which varies across vertices. 
> 
>It looks like I can just add an extra column in the design matrix for each 
>vertex within lme_mass_fit i.e. within the loop over vertices (~ line 174)
> 
>X=[X,pvr(:,i)];
> 
>Where pvr is my per-voxel-regressor and i is the vertex no. 
> 
>Do you see any problem with this approach?
> 
>Thanks again, 
> 
>Marnie
> 
> 
> 
> 
> 
> 
> 
> 
> 
>From:jorge luis [mailto:jbernal0...@yahoo.es] 
>Sent: Friday, 2 May 2014 1:51 AM
>To: Freesurfer support list
>Cc: Marnie Shaw; Douglas N Greve
>Subject: Re: [Freesurfer] per voxel regressor in LME toolbox?
> 
> 
>The lme toolbox allows you to have different regression models across 
>locations. If there is a missed data value at some location (vertex/voxel) for 
>a given time-point for a given subject then you can exclude the corresponding 
>row of the full design matrix at that location using the parameter Xrows of :
> 
>[stats,st] = lme_mass_fit_vw(X,Zcols,Y,ni,maskvtx,fname,prs,e,Xrows)
> 
>This allows you to use a different number of rows from your design matrix 
>across locations. Xrows is just a matrix of zeros and ones. Look at the header 
>of lme_mass_fit_vw for more info. 
> 
>If you also want to have a different number of columns from your "maximal 
>model" design matrix (this the design mtrix for the model that contains the 
>maximum number of regressors you are going to use at any location) then you 
>need to work directly with 
> 
>[stats,st] = lme_mass_fit(X,Xcols,Xrows,Zcols,Y,ni)    (this script is call by 
>lme_mass_fit_vw)
> 
>Look at the header of this script for more info. The parameter Xcols is a 
>matrix of zeros and ones that allows you to choose a different subset of 
>columns from your “maximal design matrix” at each location.
> 
> 
>Hope this makes sense.
> 
>Best
>-Jorge
>El Miércoles 30 de abril de 2014 18:47, Marnie Shaw  
>escribió:
>Dear Freesurfers,
>> 
>>Is there a way to include a per voxel regressor in an LME model within the 
>>matlab LME toolbox? Just like you can do with mri_glmfit?
>> 
>>Cheers, 
>>Marnie
>> 
>> 
>>
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>>
>
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[Freesurfer] MICCAI PC workshop -- May 16 (fwd)

[Bruce Fischl]

FYI

-- Forwarded message --
Date: Fri, 2 May 2014 11:28:11 -0400
From: Polina Golland 
To: Bruce Fischl 
Subject: MICCAI PC workshop -- May 16

Hi Bruce,

Can you please forward this around?

Thanks,
Polina.



MICCAI PC Workshop

May 16, 2014, 1-6pm, CSAIL Kiva and Star Conference rooms (32-D463,
32-G449).

MICCAI program committee members will present their work in areas of
Medical Image Computing and Computer Assisted Interventions. This is a
great opportunity to hear about current research of 20 MICCAI groups
from all around the world. Open to public; anyone interested in the
topics of MICCAI is welcome to attend.  Tentative Program can be found
here: http://miccai2014.org/pc_workshop.html.


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[Freesurfer] Fwd: Optseq2: ntp

[Conchy PF]

Dear Douglas,

I would like to use optseq2 to set up my experiment sequence. However it is
not clear for me what “number of time points” means. I guessed that it was
the number a waveform is sampled, but I saw in some mailing lists that it
is the time the event is repeated during the run.

In case it is the first meaning, how can I get the information about the
number a waveform is sampled?

Thanks in advance and kind regards.

Conchy
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Re: [Freesurfer] using multiple cores

[Lukas . Scheef]

 Hi Bruce!I just run: recon-all -s ernie2  -autorecon2 -openmp 4
mri_ca_register  uses 100.9% CPU at most ...
Any idea?  Should I try to recompile FS for the current MacOS release? If so, do I have to take care on special librariwa in order to enable the openmp option?
Best wishes,Lukas>Hi Bruce!
>>Thanks for the fast response. I used the current stable version 5.3.0.1
>(freesurfer-Darwin-lion-stable-pub-v5.3.0.1).
>So I will try as you have suggested ...>
>Best wishes,>>Lukas
>> Bruce Fischl Fri, 02 May 2014 05:47:26 -0700
 Hi Luke>>
>> what version of FS are you running? We see significant speedups. Try
>> running top in a unix terminal and seeing if the cpu usage of
>> mri_ca_register (during autorecon2, the longest single step) is morethan
>>100%
 cheers
>> Bruce>>
>> On Fri, 2 May 2014, lukas.sch...@ukb.uni-bonn.de wrote:

>> > Hi folks!>
> >>> > I try to use -openmp option on an iMAC with 4 cores. Unfortunately, I
>
>>do not>> > see any accelartion when processing a single data set with or without
>
>>the>> > flag -openmp flag set.
>> >>> > recon-all -s ernie_1 -all
>> >>> > leads to ~6,4h processing time.
>> >>> > Unfortunately
>> > recon-all -s ernie_2 -all -openmp 4
>> >>> > did not change anything. Do I miss anything? Do I have to prepare my
>
>>system>> > in a special way? Or run any scripts in advance?
>> >>> > (System: iMac, 32GbRam,Intel i5, 4 cores, Mac Os 10.9, latest FS
>>
>version)
>> >>> > Best wishes,
>> >>> > Luke


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Re: [Freesurfer] using multiple cores

[Bruce Fischl]

Hi Lukas

sorry, I'm out of my depth on the mac. Perhaps Zeke knows what's going on? 
Does OpenMP have to be enabled somehow?


Bruce


On Fri, 2 May 2014, 
lukas.sch...@ukb.uni-bonn.de wrote:



Hi Bruce!

I just run: recon-all -s ernie2  -autorecon2 -openmp 4

mri_ca_register  uses 100.9% CPU at most ...

Any idea?  Should I try to recompile FS for the current MacOS release? If
so, do I have to take care on special librariwa in order to enable the
openmp option?

Best wishes,

Lukas

>Hi Bruce!
>
>Thanks for the fast response. I used the current stable version 5.3.0.1
>(freesurfer-Darwin-lion-stable-pub-v5.3.0.1).
>So I will try as you have suggested ...
>
>Best wishes,
>
>Lukas

>> Bruce Fischl Fri, 02 May 2014 05:47:26 -0700
>>
>> Hi Luke
>>
>> what version of FS are you running? We see significant speedups. Try
>> running top in a unix terminal and seeing if the cpu usage of
>> mri_ca_register (during autorecon2, the longest single step) is morethan
>>100%
>>
>> cheers
>> Bruce
>>
>> On Fri, 2 May 2014, lukas.sch...@ukb.uni-bonn.de wrote:
>>
>>
>> > Hi folks!
> > >
>> > I try to use -openmp option on an iMAC with 4 cores. Unfortunately, I
> >>do not
>> > see any accelartion when processing a single data set with or without
> >>the
>> > flag -openmp flag set.
>> >
>> > recon-all -s ernie_1 -all
>> >
>> > leads to ~6,4h processing time.
>> >
>> > Unfortunately
>> > recon-all -s ernie_2 -all -openmp 4
>> >
>> > did not change anything. Do I miss anything? Do I have to prepare my
> >>system
>> > in a special way? Or run any scripts in advance?
>> >
>> > (System: iMac, 32GbRam,Intel i5, 4 cores, Mac Os 10.9, latest FS
>> >version)
>> >
>> > Best wishes,
>> >
>> > Luke




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Re: [Freesurfer] using multiple cores

[Matt Glasser]

If you are compiling with clang openmp might not work.

Peace,

Matt.

On 5/2/14, 2:13 PM, "Bruce Fischl"  wrote:

>Hi Lukas
>
>sorry, I'm out of my depth on the mac. Perhaps Zeke knows what's going
>on? 
>Does OpenMP have to be enabled somehow?
>
>Bruce
>
>
>On Fri, 2 May 2014,
>lukas.sch...@ukb.uni-bonn.de wrote:
>
>> Hi Bruce!
>> 
>> I just run: recon-all -s ernie2  -autorecon2 -openmp 4
>> 
>> mri_ca_register  uses 100.9% CPU at most ...
>> 
>> Any idea?  Should I try to recompile FS for the current MacOS release?
>>If
>> so, do I have to take care on special librariwa in order to enable the
>> openmp option?
>> 
>> Best wishes,
>> 
>> Lukas
>> 
>> >Hi Bruce!
>> >
>> >Thanks for the fast response. I used the current stable version 5.3.0.1
>> >(freesurfer-Darwin-lion-stable-pub-v5.3.0.1).
>> >So I will try as you have suggested ...
>> >
>> >Best wishes,
>> >
>> >Lukas
>> 
>> >> Bruce Fischl Fri, 02 May 2014 05:47:26 -0700
>> >>
>> >> Hi Luke
>> >>
>> >> what version of FS are you running? We see significant speedups. Try
>> >> running top in a unix terminal and seeing if the cpu usage of
>> >> mri_ca_register (during autorecon2, the longest single step) is
>>morethan
>> >>100%
>> >>
>> >> cheers
>> >> Bruce
>> >>
>> >> On Fri, 2 May 2014, lukas.sch...@ukb.uni-bonn.de wrote:
>> >>
>> >>
>> >> > Hi folks!
>> > > >
>> >> > I try to use -openmp option on an iMAC with 4 cores.
>>Unfortunately, I
>> > >>do not
>> >> > see any accelartion when processing a single data set with or
>>without
>> > >>the
>> >> > flag -openmp flag set.
>> >> >
>> >> > recon-all -s ernie_1 -all
>> >> >
>> >> > leads to ~6,4h processing time.
>> >> >
>> >> > Unfortunately
>> >> > recon-all -s ernie_2 -all -openmp 4
>> >> >
>> >> > did not change anything. Do I miss anything? Do I have to prepare
>>my
>> > >>system
>> >> > in a special way? Or run any scripts in advance?
>> >> >
>> >> > (System: iMac, 32GbRam,Intel i5, 4 cores, Mac Os 10.9, latest FS
>> >> >version)
>> >> >
>> >> > Best wishes,
>> >> >
>> >> > Luke
>> 
>> 
>> 
>> 
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Re: [Freesurfer] Fwd: Optseq2: ntp

[Douglas Greve]

It is the number of samples in the time series. Eg, if you scan for 
10min with a TR=2, then you would have 600/2=300 time points

doug


On 5/2/14 3:07 PM, Conchy PF wrote:


Dear Douglas,

I would like to use optseq2 to set up my experiment sequence. However 
it is not clear for me what "number of time points" means. I guessed 
that it was the number a waveform is sampled, but I saw in some 
mailing lists that it is the time the event is repeated during the run.


In case it is the first meaning, how can I get the information about 
the number a waveform is sampled?


Thanks in advance and kind regards.

Conchy




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Re: [Freesurfer] effect size for conjunction analyses?

[Douglas Greve]

Hmmm, I'm not sure an effect size makes sense. I guess I would use the 
one from the chosen p-value

doug


On 5/2/14 12:52 PM, Caspar M. Schwiedrzik wrote:

Hi!
I am doing some conjunction analyses (Nichols et al.) on my fMRI data, 
and I was wondering whether anyone can make a recommendation how to 
display effect sizes for this kind of analyses?
Would you show the effect size estimate corresponding to the p-value 
that is chosen, an average, or anything else?

Thanks, Caspar



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[Freesurfer] FSGD and contrast files for group analysis

[Kenza Drissi]

Dear Marie,I want to run a group analysis on a set of subjects, correcting for 
gender(Male/Female), diagnois regarding epilepsy (no focus/focus in rh/focus 
inlh/focus in both h), age and IQ. Should my FSGD file look somewhat like 
thisbelow:GroupDescriptorFile 2Class NoFocus_MaleClass NoFocus_FemaleClass 
RhFocus_MaleClass LhFocus_MaleClass BhFocus_MaleClass RhFocus_FemaleClass 
LhFocus_FemaleClass BhFocus_FemaleVariables age IQIf so, considering that I 
want to investigate the effect of epilepsy on corticalgyrification, what should 
my contrast matrix look like?The hypothesis is that the gyrification index is 
diminished for epilepticpatients, probably more when there is bilateral focus.I 
know that we need as many number as regressors, so I expect there to be 
10numbers, is it so?Thank you so very much for clarifying this point,Kenza  
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Re: [Freesurfer] FSGD and contrast files for group analysis

[Douglas Greve]

The FSGD looks right (you have a 2x4 design, so 8 classes, plus 2 
covariates).


[1 1 -1  0 0 -1 0 0   0 0 0 0 0 0 0 0] tests for a difference between 
NoFocus and RhFocus (No-RH)
[0 0 1 -1 0 1 -1 0   0 0 0 0 0 0 0 0] tests for a difference between 
RhFocus and LhFocus (RH-RH)


probably you can figure out the rest from the pattern




On 5/2/14 4:40 PM, Kenza Drissi wrote:

Dear Marie,

I want to run a group analysis on a set of subjects, correcting for gender
(Male/Female), diagnois regarding epilepsy (no focus/focus in rh/focus in
lh/focus in both h), age and IQ. Should my FSGD file look somewhat 
like this

below:

GroupDescriptorFile 2

Class NoFocus_Male
Class NoFocus_Female
Class RhFocus_Male
Class LhFocus_Male
Class BhFocus_Male
Class RhFocus_Female
Class LhFocus_Female
Class BhFocus_Female

Variables age IQ

If so, considering that I want to investigate the effect of epilepsy 
on cortical

gyrification, what should my contrast matrix look like?
The hypothesis is that the gyrification index is diminished for epileptic
patients, probably more when there is bilateral focus.

I know that we need as many number as regressors, so I expect there to 
be 10

numbers, is it so?

Thank you so very much for clarifying this point,
Kenza


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Re: [Freesurfer] brain.finalsurfs.mgz editing

[Martin Reuter]

Hi Khadka,

Although it is an old mail (sorry), because this topic came up in 
another thread, I reply here also.
You need to edit the brain.finalsurfs.manedit.mgz file. Create this file 
by copying :

cp brain.finalsurfs.mgz brain.finalsurfs.manedit.mgz
then edit the manedit file.

Best, Martin


On 01/16/2014 01:07 PM, Khadka, Sankalpa wrote:

Dear freesurfer community,

My question is directed to those who have experience with editing 
brain.finalsurfs.mgz.


According to the tutorials, after making edits on 
brainmask.finalsurfs.mgz (which is normally done when the pial surface 
is not accurate), we can run,

recon-all -autorecon-pial -subjid subj"

However, I found an anomaly when I looked at the steps that 
-autorecon-pial flag goes through. The very first step of 
autorecon-pial flag is "mri_mask" command. This takes brain.mgz and 
brainmask.mgz as inputs and gives brain.finalsurfs.mgz as output.


Now, if we have made edits on brain.finalsurfs.mgz, it will be 
overwritten by the new one and hence our edits won't take an effect.


I ran few experiments too.
First, I made edits on brain.finalsurfs.mgz and ran recon-all with 
autorecon-pial flag. I ended up with a new brain.finalsurfs.mgz and my 
edits did not make any changes.
Second, I made edits on brain.finalsurfs.mgz and ran with white, 
smooth2, inflate2, autorecon3 flag (basically starting from 
mri_make_surfaces command). On doing so, the edits made desirable 
changes and brain.finalsurfs.mgz remained intact.


Third, I made changes on brainmask.mgz and brain.mgz (inputs for 
mri_mask). It also works as expected.


Finally, I also followed the recommended steps from the tutorial by 
creating brainmask.finalsurfs.manedit.mgz, however, the edits from 
"manedit" were not carried on to brainmask.finalsurfs.mgz
Could anyone please shed some light on this? What would be the best 
strategy to follow?


Thank you,
Sankalpa



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--
Martin Reuter, Ph.D.

Instructor in Neurology
  Harvard Medical School
Assistant in Neuroscience
  Dept. of Radiology, Massachusetts General Hospital
  Dept. of Neurology, Massachusetts General Hospital
Research Affiliate
  Computer Science and Artificial Intelligence Lab,
  Dept. of Electrical Engineering and Computer Science,
  Massachusetts Institute of Technology

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] brain.finalsurfs.manedit.mgz file edits & longitudinal processing

[Martin Reuter]

Hi Doug,

so you
1. edited the cross sectionals and surfaces look fine (make sure you 
edit the brain.finalsurfs.manedit.mgz file, which you create as a copy 
of the brain.finalsurfs.mgz)

2. checked/edited the base and surfaces look fine too
3. ran the longitudinal from scratch (w/o any edits)

and then in the long, the surface looks not good?

Edits should automatically be copied from cross->long (if the manedit 
file exist). Surfaces are taken from the base to initialize longitudinal 
processing. That is why both step1 and step2 above are important. Step3 
is a good idea to make sure that the longs are not polluted by some 
earlier edits. For example edits from cross are only copied over if the 
long has no manedit file, else only the edits in the long will be used. 
(I think this also answers some of the questions in the archive mail 1 
you cite below, the archive mail 2 is a question about cross sectional 
processing, but I think there the problem is that 
brainmask.finalsurfs.mgz was edited directly, not the manedit file, so 
edits probably get overwritten).


I also have the feeling that we fixed something about the editing in 
longitudinal processing after 5.1, but cannot find it documented on the 
wiki (so not sure). You may want to try to run this with 5.3 if it does 
not work with 5.1


Best, Martin


On 05/02/2014 10:45 AM, Douglas Merkitch wrote:

Dear Freesurfer experts,

I have a question regarding longitudinal edits. Specifically the 
brain.finalsurfs.manedit.mgz file and the longitudinal processing 
stream in Freesufer 5.1 on a Mac 
(freesurfer-i686-apple-darwin9.8.0-stable5-20110525).


The problem that I am having is that the edits saved in the 
brain.finalsurfs.manedit.mgz file do not carry over when processing 
longitudinally.


Previous posts have addressed this topic, but have not (to my 
knowledge) solved the issue. Please see the threads from the 
Freesurfer archive below for a brief context:


1. 
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg27695.html


2. 
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg33471.html


Please let me know if more information is needed to understand the issue.

Any insight/ideas regarding this issue would be greatly appreciated!

Thanks,

Doug

Doug Merkitch
Neurological Sciences
Rush University Medical Center
Phone: (312) 563-3853 
Fax: (312) 563-4660 
Email: douglas_merki...@rush.edu 





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--
Martin Reuter, Ph.D.

Instructor in Neurology
  Harvard Medical School
Assistant in Neuroscience
  Dept. of Radiology, Massachusetts General Hospital
  Dept. of Neurology, Massachusetts General Hospital
Research Affiliate
  Computer Science and Artificial Intelligence Lab,
  Dept. of Electrical Engineering and Computer Science,
  Massachusetts Institute of Technology

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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