Re: [Freesurfer] free-surfer longitudinal Qdec table

[Anna Jonsson]

Ok, so even though in the qdec table you only specify the cross names as
your fsid's, when you actually do the analysis the longs need to be in the
same directory as the cross and bases (ie everything in the same directory)
and matlab automatically uses the .long files, even though 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 
wrote:

> Hi Anna,
>
> the matlab tools don't know. They only look at the other co-variates that
> you might want to include into your study (the fsid-base for grouping, the
> time variable and others from the table). The stack of thickness maps needs
> to be in the same order as the rows in the qdec table. That is why it is a
> good idea to use the same table to assemble the stack (and for that you'd
> use the -long-qdec flag and it uses the .long.base file names).
>
> Best, Martin
>
>
> On Jun 24, 2014, at 5:23 PM, Anna Jonsson  wrote:
>
> Thank you. I just another question about the fsid groupings for the qdec
> table for lme. If in the qdec I specify only the fisid (eg nt the
> longitudinally processed subject with XX.long), and the XX.longs are in a
> different folder, than how when I do the matlab lme tools does freesurfer
> know to use the XXX.long scans? This is confusing me.
>
> 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 months).
>> Measures closer in time are more correlated than measures further apart.
>> Lme makes use of that information through the time variable.
>> Best Martin
>> Best Martin
>>
>> Sent via my smartphone, please excuse brevity.
>>
>>  Original message 
>> From: Anna Jonsson
>> Date:06/24/2014 11:52 AM (GMT+01:00)
>> To: Martin Reuter
>> Cc: Freesurfer support list
>> Subject: Re: [Freesurfer] free-surfer longitudinal Qdec table
>>
>> thank you. and one other question; rather than putting years as the time
>> variable, can i do time 1 (for baseline) and 2 (for follow-up), and jsut
>> control for time between scans instead?
>>
>>
>> On Fri, Jun 13, 2014 at 5:42 PM, Martin Reuter <
>> mreu...@nmr.mgh.harvard.edu> wrote:
>>
>>> Hi Anna, whenever it says qdec-long the table is in qdec format (with a
>>> fsid-base as second column. It would then use the longitudinally processed
>>> results, which is what you want , both for lme and 2 stage model.
>>> Best Martin
>>>
>>>
>>> Sent via my smartphone, please excuse brevity.
>>>
>>>  Original message 
>>> From: Anna Jonsson
>>> Date:06/09/2014 3:47 PM (GMT+01:00)
>>> To: Freesurfer support list
>>> Subject: Re: [Freesurfer] free-surfer longitudinal Qdec table
>>>
>>> Hi, sorry for more questions, but i have a few. When running the first
>>> step of the lme implemented tools, doing the command *mris_preproc*
>>> --qdec-long qdec.table.dat --target study_average --hemi lh --meas
>>> thickness --out lh.thickness.mgh (assembles your thickness data into a
>>> single lh.thickness.mgh file), am I correct that this just needs to be a
>>> "normal" cross-sectional qdec table that free surfer subsequently makes
>>> into long format by --qdec-long option? so the lnogitudinal qdec table is
>>> only used in the two stage modell? This too just uses the cross-sectionally
>>> derived scans?  Im confused where the .long runs become used?
>>>
>>> thank you and kind wishes
>>>
>>>
>>> On Wed, Jun 4, 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 support list
 Subject: [Freesurfer] free-surfer longitudinal Qdec table

 Hi,

 I would like to make my freesurfer longitudinal qdec table for the to
 use in the lme matlab tools. However, does the fsid need to refer to the
 longitidunally derived subject; eg XXX.long, or the cross-sectionally
 derived subject, eg XXX. Im not sure based on the specification online.
  Kind Regards

 Anna

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Re: [Freesurfer] visualize group analysis results of qdec

[Anna Jonsson]

I also have this problem now. did this query ever resolve?


On Wed, Jun 4, 2014 at 10:55 PM, Qijing Yu  wrote:

> Hello FreeSufers,
>
> I ran several analyses in qdec, and now have problem visualize previous
> analyses results...which sounds dumb... Please let me know if you have any
> ideas.
>
> I used fsaverage. I found this page
> http://freesurfer.net/fswiki/FsTutorial/Visualization using tksurfer, but
> it needs to do the "make_average". And it mentioned some "pre-computed
> results", I thought which would be the results of analyses via command
> line. Does this apply to the results by qdec?
>
> I also found the following command using Freeview:
> freeview -f
> SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5
> -viewport 3d
>
> But I don't know which part of the command should I change. I tried the
> command as it is above anyway and the error is: Unrecognized sub-option
> flag 'annot_outline'
>
> Many thanks! All the best,
> Qijing
>
>
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>
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> properly
> dispose of the e-mail.
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>
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Re: [Freesurfer] free-surfer longitudinal Qdec table

[Martin Reuter]

Almost true.
The stacking (smoothing and mapping to eg fsaverage) is done outside of matlab, 
using mris_preproc and that uses the .long.base names.

Matlab only opens that single file (stack) and reads additional info from the 
qdec table. Matlab does not need access to the .long.base directories directly.

Best martin


Sent via my smartphone, please excuse brevity.

 Original message 
From: Anna Jonsson  
Date:06/25/2014  10:00 AM  (GMT+01:00) 
To: Freesurfer support list  
Subject: Re: [Freesurfer] free-surfer longitudinal Qdec table 

Ok, so even though in the qdec table you only specify the cross names as your 
fsid's, when you actually do the analysis the longs need to be in the same 
directory as the cross and bases (ie everything in the same directory) and 
matlab automatically uses the .long files, even though 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  
wrote:
Hi Anna, 

the matlab tools don't know. They only look at the other co-variates that you 
might want to include into your study (the fsid-base for grouping, the time 
variable and others from the table). The stack of thickness maps needs to be in 
the same order as the rows in the qdec table. That is why it is a good idea to 
use the same table to assemble the stack (and for that you'd use the -long-qdec 
flag and it uses the .long.base file names).

Best, Martin


On Jun 24, 2014, at 5:23 PM, Anna Jonsson  wrote:

Thank you. I just another question about the fsid groupings for the qdec table 
for lme. If in the qdec I specify only the fisid (eg nt the longitudinally 
processed subject with XX.long), and the XX.longs are in a different folder, 
than how when I do the matlab lme tools does freesurfer know to use the 
XXX.long scans? This is confusing me.

Thanks for help,.

Regards Anna


On Tue, Jun 24, 2014 at 11:26 AM, Martin Reuter  
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 months).
Measures closer in time are more correlated than measures further apart. Lme 
makes use of that information through the time variable.
Best Martin
Best Martin

Sent via my smartphone, please excuse brevity.

 Original message 
From: Anna Jonsson 
Date:06/24/2014 11:52 AM (GMT+01:00) 
To: Martin Reuter 
Cc: Freesurfer support list 
Subject: Re: [Freesurfer] free-surfer longitudinal Qdec table 

thank you. and one other question; rather than putting years as the time 
variable, can i do time 1 (for baseline) and 2 (for follow-up), and jsut 
control for time between scans instead? 


On Fri, Jun 13, 2014 at 5:42 PM, Martin Reuter  
wrote:
Hi Anna, whenever it says qdec-long the table is in qdec format (with a 
fsid-base as second column. It would then use the longitudinally processed 
results, which is what you want , both for lme and 2 stage model.
Best Martin


Sent via my smartphone, please excuse brevity.

 Original message 
From: Anna Jonsson 
Date:06/09/2014  3:47 PM (GMT+01:00) 
To: Freesurfer support list 
Subject: Re: [Freesurfer] free-surfer longitudinal Qdec table 

Hi, sorry for more questions, but i have a few. When running the first step of 
the lme implemented tools, doing the command mris_preproc --qdec-long 
qdec.table.dat --target study_average --hemi lh --meas thickness --out 
lh.thickness.mgh (assembles your thickness data into a single lh.thickness.mgh 
file), am I correct that this just needs to be a "normal" cross-sectional qdec 
table that free surfer subsequently makes into long format by --qdec-long 
option? so the lnogitudinal qdec table is only used in the two stage modell? 
This too just uses the cross-sectionally derived scans?  Im confused where the 
.long runs become used?

thank you and kind wishes


On Wed, Jun 4, 2014 at 5:01 PM, Martin Reuter  
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 support list 
Subject: [Freesurfer] free-surfer longitudinal Qdec table 

Hi,

I would like to make my freesurfer longitudinal qdec table for the to use in 
the lme matlab tools. However, does the fsid need to refer to the 
longitidunally derived subject; eg XXX.long, or the cross-sectionally derived 
subject, eg XXX. Im not sure based on the specification online.
 Kind Regards

Anna

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[Freesurfer] group comparison issue

[melinda dora]

Dear list,

I have a question re group comparisons. I have one group factor with three 
levels. I have done group-wise comparisons with these groups using qdec (ie 
doing pairwise comparisons, as it only allows group comparisons between two 
groups as far as I am aware?) as well as using mri glm fit, specifying the 
contrast as 1 0 -1 to compare two groups without the effect of the other third 
group being included. I have found that I get different results for these two 
methods; using mriglmfit I get no vertices surviving multiple comparisons, 
whilst I get several using qdec. Could this be because of the differences in 
using FDR/monte carlo simulation or does it point towards a bigger problem, for 
example me doing something wrong at some stage? Or is there another explanation?

Very grateful for prompt response and help,

Cheers,

Melinda


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Re: [Freesurfer] group comparison issue

[Douglas N Greve]

So the mri_glmfit results are less significant than the QDEC results? 
That is a little surprising because the glmfit results will have a 
higher DOF. The contrast (gamma.mgh) should be the same. It may be that 
your FWHM increased (compare the fwhm.dat files). You can also run the 
two group analysis in glmfit to make sure you get identical results to qdec
doug

On 06/25/2014 10:15 AM, melinda dora wrote:
> Dear list,
>
> I have a question re group comparisons. I have one group factor with 
> three levels. I have done group-wise comparisons with these groups 
> using qdec (ie doing pairwise comparisons, as it only allows group 
> comparisons between two groups as far as I am aware?) as well as using 
> mri glm fit, specifying the contrast as 1 0 -1 to compare two groups 
> without the effect of the other third group being included. I have 
> found that I get different results for these two methods; using 
> mriglmfit I get no vertices surviving multiple comparisons, whilst I 
> get several using qdec. Could this be because of the differences in 
> using FDR/monte carlo simulation or does it point towards a bigger 
> problem, for example me doing something wrong at some stage? Or is 
> there another explanation?
>
> Very grateful for prompt response and help,
>
> Cheers,
>
> Melinda
>
>
>
>
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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] interpreting qdec results

[Douglas N Greve]

Your interpretation is right (ie, controls > patients for 
red/yellow/orange). When you compared the two groups in your separate 
analysis, did you control for age?
doug


On 06/24/2014 02:19 PM, Emma Thompson wrote:
> Hi Freesurfers,
> I am reposting this as my last email bounced.
>
> I have conducted a DODS analysis in qdec with group (controls vs 
> patients) set as my fixed factor and age as a nuisance variable to 
> determine if my groups differ in cortical thickness. Controls were 
> added first in the .levels file followed by patients. When I view the 
> results in the display window for "do controls differ from patients in 
> cortical thickness" I see a significant cluster for the caudal 
> anterior cingulate, denoted by a red-orange blob and a positive 
> t-value. I'm wondering if this simply means that controls had greater 
> cortical thickness compared to patients after controlling for age? The 
> reason I ask is that I'm a little confused since when I created an ROI 
> for this cluster using tksurfer and then extracted the means and sd, I 
> see that the patients actually have larger means than the controls, 
> the opposite of my interpretation of the results presented by the qdec 
> display. Furthermore, if I extract the means and sds for the entire 
> caudal anterior cingulate using the aparc file, I get means that are 
> larger in controls, compared to patients, which seems consistent with 
> qdec. Any ideas? Thanks for all the help.
>
>
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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] Extracting the individual or average cortical thickness value of significant cluster after multiple compression correction by FDR.

[Douglas N Greve]

This is not an easy thing to do in QDEC. An alternative is to run 
mri_glmfit-sim on the QDEC output folder, setting the thresholds to the 
same that you used in QDEC. mri_glmfit-sim will compute means foreach 
subject and cluster.

doug



On 06/24/2014 06:40 PM, Santosh Yadav wrote:
>
> Dear FreeSurfer Experts:
>
> I have question regarding extracting the individual or average 
> cortical thickness value of significant cluster after multiple 
> compression correction by FDR. For example I have 100s of subjects in 
> an analysis and several blobs showing significant difference between 
> groups after FDR, how do I export mean or individual subjects cortical 
> thickness values for significant blob? I can click on each data point 
> and copy the terminal readout or create an ROI, map label to subjects 
> and export it out but both approaches are time consuming and prone to 
> human error. Is there a way of using existing QDEC setup files to 
> export all this data out more cleanly?
>
> With best Regards,
>
> Santosh
>
>
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Re: [Freesurfer] problem with qdec stats tables

[Douglas N Greve]

There is no "right" one. aparc has fewer but larger ROIs. aparc.a2005s 
has more but smaller ROIs. The smaller are going to be more specific but 
probably noisier too
doug


On 06/23/2014 04:26 PM, Kristina Kuhlmann wrote:
> Dear mailing-list,
> I’ve got a question concerning the file types of stats tables in qdec. 
> After generating the stats tables there are two files e.g. 
> lh.aparc.a2005s.area.stats and lh.aparc.area.stats. Which one is the 
> right one to work with ( statistical analysis)? How do they differ in 
> characteristics and values?
> Thanks,
> best regards, Kristina
>
>
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Fax: 617-726-7422

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Re: [Freesurfer] recon-all ERROR, no idea why

[Douglas N Greve]

This is dying somewhere in the MNI nu_correct code. Look at the orig.mgz 
to see if that looks ok


On 06/23/2014 03:58 PM, Remy Wahnoun wrote:
>
> Thanks Douglas,
>
> I definitely appreciate your help.
>
> Here is what it Spit out,
>
> *Rémy Wahnoun, PhD*
>
> Biomedical Research Group Manager
>
> Barrow Neurological Institute at Phoenix Children's Hospital
>
> Adjunct Faculty, Arizona State University
>
> /www.NeuralControl.net /
>
> set echo = 1 ;
>
> set debug = 1 ;
>
> set debug = 1
>
> breaksw
>
> breaksw
>
> end
>
> end
>
> while ( $#argv != 0 )
>
> while ( 11 != 0 )
>
> set flag = $argv[1] ; shift ;
>
> set flag = --n
>
> shift
>
> switch ( $flag )
>
> switch ( --n )
>
> if ( $#argv == 0 ) goto arg1err ;
>
> if ( 10 == 0 ) goto arg1err
>
> set nIters = $argv[1] ; shift ;
>
> set nIters = 1
>
> shift
>
> breaksw
>
> breaksw
>
> end
>
> end
>
> while ( $#argv != 0 )
>
> while ( 9 != 0 )
>
> set flag = $argv[1] ; shift ;
>
> set flag = --proto-iters
>
> shift
>
> switch ( $flag )
>
> switch ( --proto-iters )
>
> if ( $#argv == 0 ) goto arg1err ;
>
> if ( 8 == 0 ) goto arg1err
>
> set nProtoIters = $argv[1] ; shift ;
>
> set nProtoIters = 1000
>
> shift
>
> breaksw
>
> breaksw
>
> end
>
> end
>
> while ( $#argv != 0 )
>
> while ( 7 != 0 )
>
> set flag = $argv[1] ; shift ;
>
> set flag = --distance
>
> shift
>
> switch ( $flag )
>
> switch ( --distance )
>
> if ( $#argv == 0 ) goto arg1err ;
>
> if ( 6 == 0 ) goto arg1err
>
> set Distance = $argv[1] ; shift ;
>
> set Distance = 50
>
> shift
>
> breaksw
>
> breaksw
>
> end
>
> end
>
> while ( $#argv != 0 )
>
> while ( 5 != 0 )
>
> set flag = $argv[1] ; shift ;
>
> set flag = --no-rescale
>
> shift
>
> switch ( $flag )
>
> switch ( --no-rescale )
>
> set DoRescale = 0 ;
>
> set DoRescale = 0
>
> breaksw
>
> breaksw
>
> end
>
> end
>
> while ( $#argv != 0 )
>
> while ( 4 != 0 )
>
> set flag = $argv[1] ; shift ;
>
> set flag = --i
>
> shift
>
> switch ( $flag )
>
> switch ( --i )
>
> if ( $#argv == 0 ) goto arg1err ;
>
> if ( 3 == 0 ) goto arg1err
>
> set InVol = $argv[1] ; shift ;
>
> set InVol = orig.mgz
>
> shift
>
> breaksw
>
> breaksw
>
> end
>
> end
>
> while ( $#argv != 0 )
>
> while ( 2 != 0 )
>
> set flag = $argv[1] ; shift ;
>
> set flag = --o
>
> shift
>
> switch ( $flag )
>
> switch ( --o )
>
> if ( $#argv == 0 ) goto arg1err ;
>
> if ( 1 == 0 ) goto arg1err
>
> set OutVol = $argv[1] ; shift ;
>
> set OutVol = orig_nu.mgz
>
> shift
>
> breaksw
>
> breaksw
>
> end
>
> end
>
> while ( $#argv != 0 )
>
> while ( 0 != 0 )
>
> goto parse_args_return ;
>
> goto parse_args_return
>
> goto check_params ;
>
> goto check_params
>
> if ( $#InVol == 0 ) then
>
> if ( 1 == 0 ) then
>
> if ( ! -e $InVol ) then
>
> if ( ! -e orig.mgz ) then
>
> if ( $#OutVol == 0 ) then
>
> if ( 1 == 0 ) then
>
> goto check_params_return ;
>
> goto check_params_return
>
> set OutDir = `dirname $OutVol` ;
>
> set OutDir = `dirname $OutVol`
>
> dirname orig_nu.mgz
>
> mkdir -p $OutDir ;
>
> mkdir -p .
>
> if ( $#LF == 0 ) set LF = $OutDir/mri_nu_correct.mni.log
>
> if ( 0 == 0 ) set LF = ./mri_nu_correct.mni.log
>
> set LF = ./mri_nu_correct.mni.log
>
> if ( -e $LF ) mv $LF $LF.bak
>
> if ( -e ./mri_nu_correct.mni.log ) mv ./mri_nu_correct.mni.log 
> ./mri_nu_correct.mni.log.bak
>
> mv ./mri_nu_correct.mni.log ./mri_nu_correct.mni.log.bak
>
> pwd | tee -a $LF
>
> pwd
>
> tee -a ./mri_nu_correct.mni.log
>
> /media/sf_Imagery/FreeSurfer/xx/mri
>
> which mri_nu_correct.mni | tee -a $LF
>
> which mri_nu_correct.mni
>
> tee -a ./mri_nu_correct.mni.log
>
> /usr/local/freesurfer/bin/mri_nu_correct.mni
>
> echo $cmdargs | tee -a $LF
>
> echo --debug --n 1 --proto-iters 1000 --distance 50 --no-rescale --i 
> orig.mgz --o orig_nu.mgz
>
> tee -a ./mri_nu_correct.mni.log
>
> --debug --n 1 --proto-iters 1000 --distance 50 --no-rescale --i 
> orig.mgz --o orig_nu.mgz
>
> echo "nIters $nIters" | tee -a $LF
>
> echo nIters 1
>
> tee -a ./mri_nu_correct.mni.log
>
> nIters 1
>
> echo $VERSION | tee -a $LF
>
> tee -a ./mri_nu_correct.mni.log
>
> echo $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $
>
> $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $
>
> uname -a | tee -a $LF
>
> uname -a
>
> tee -a ./mri_nu_correct.mni.log
>
> Linux xubuntu-VirtualBox 3.2.0-64-generic #97-Ubuntu SMP Wed Jun 4 
> 22:03:48 UTC 2014 i686 i686 i386 GNU/Linux
>
> date | tee -a $LF
>
> date
>
> tee -a ./mri_nu_correct.mni.log
>
> Mon Jun 23 15:32:45 EDT 2014
>
> nu_correct -version | tee -a $LF
>
> nu_correct -version
>
> tee -a ./mri_nu_correct.mni.log
>
> Program nu_correct, built from:
>
> Package MNI N3, version 1.10, compiled by nicks@fishie 
> (i686-pc-linux-gnu) on 2010-02-20 at 20:19:13
>
> if ( ! $#tmpdir ) set tmpdir = $OutDir/tmp.mri_nu_correct.mni.$$
>
> if ( ! 0 ) set tmpdir = ./tmp.mri_nu_correct.mni.1745
>
> set tmpdir = ./tmp.mri_nu_correct.mni.1745
>
> mkdir -p $tmpdir
>
> mkdir -p ./tmp.mri_nu_correct.mni.1745
>
> echo "tmpdir is $tmpdi

Re: [Freesurfer] interpreting qdec results

[Emma Thompson]

Thanks Doug, yes I did control for age in both instances.


On Wed, Jun 25, 2014 at 10:14 AM, Douglas N Greve  wrote:

>
> Your interpretation is right (ie, controls > patients for
> red/yellow/orange). When you compared the two groups in your separate
> analysis, did you control for age?
> doug
>
>
> On 06/24/2014 02:19 PM, Emma Thompson wrote:
> > Hi Freesurfers,
> > I am reposting this as my last email bounced.
> >
> > I have conducted a DODS analysis in qdec with group (controls vs
> > patients) set as my fixed factor and age as a nuisance variable to
> > determine if my groups differ in cortical thickness. Controls were
> > added first in the .levels file followed by patients. When I view the
> > results in the display window for "do controls differ from patients in
> > cortical thickness" I see a significant cluster for the caudal
> > anterior cingulate, denoted by a red-orange blob and a positive
> > t-value. I'm wondering if this simply means that controls had greater
> > cortical thickness compared to patients after controlling for age? The
> > reason I ask is that I'm a little confused since when I created an ROI
> > for this cluster using tksurfer and then extracted the means and sd, I
> > see that the patients actually have larger means than the controls,
> > the opposite of my interpretation of the results presented by the qdec
> > display. Furthermore, if I extract the means and sds for the entire
> > caudal anterior cingulate using the aparc file, I get means that are
> > larger in controls, compared to patients, which seems consistent with
> > qdec. Any ideas? Thanks for all the help.
> >
> >
> > ___
> > 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: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> 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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addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] interpreting qdec results

[Douglas N Greve]

what software did you use? Are you sure you are using the same model as 
qdec uses?


On 06/25/2014 11:03 AM, Emma Thompson wrote:
> Thanks Doug, yes I did control for age in both instances.
>
>
> On Wed, Jun 25, 2014 at 10:14 AM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>
> Your interpretation is right (ie, controls > patients for
> red/yellow/orange). When you compared the two groups in your separate
> analysis, did you control for age?
> doug
>
>
> On 06/24/2014 02:19 PM, Emma Thompson wrote:
> > Hi Freesurfers,
> > I am reposting this as my last email bounced.
> >
> > I have conducted a DODS analysis in qdec with group (controls vs
> > patients) set as my fixed factor and age as a nuisance variable to
> > determine if my groups differ in cortical thickness. Controls were
> > added first in the .levels file followed by patients. When I
> view the
> > results in the display window for "do controls differ from
> patients in
> > cortical thickness" I see a significant cluster for the caudal
> > anterior cingulate, denoted by a red-orange blob and a positive
> > t-value. I'm wondering if this simply means that controls had
> greater
> > cortical thickness compared to patients after controlling for
> age? The
> > reason I ask is that I'm a little confused since when I created
> an ROI
> > for this cluster using tksurfer and then extracted the means and
> sd, I
> > see that the patients actually have larger means than the controls,
> > the opposite of my interpretation of the results presented by
> the qdec
> > display. Furthermore, if I extract the means and sds for the entire
> > caudal anterior cingulate using the aparc file, I get means that are
> > larger in controls, compared to patients, which seems consistent
> with
> > qdec. Any ideas? Thanks for all the help.
> >
> >
> > ___
> > 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: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
> Outgoing:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> 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

-- 
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: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] hippocampal subfields in young subjects

[Koen Van Leemput]

Hi Joana,

Sorry for the delayed response. I'm a bit puzzled because it really
looks like a visualization issue in freeview. Could you please send me
the original *.mgz files, so I can try the visualization myself?

Thanks,

Koen


On Mon, Jun 23, 2014 at 9:38 PM, Joana Braga Pereira
 wrote:
> Dear Koen and Freesurfers,
>
> I haven't receive any further replies regarding the black lines surrounding
> the subfields I found in the sample of subjects I am analyzing.
>
> As I said the subjects are quite young (9-14 years of age) and I visualized
> the subfields with Freeview.
>
> Do you have any idea why this is happening? This does mean the GEMS tool
> should not be applied in such young subjects?
>
> Any help would be greatly appreciated!
>
> Many thanks,
>
> joana
>
>
>
>
> 2014-06-13 15:40 GMT+02:00 Joana Braga Pereira :
>
>> Hi Koen,
>>
>> Thanks for such a prompt reply.
>>
>> I visualized it in freeview with:
>>
>> freeview nu.mgz -p-labels posterior_left_* posterior_Left-Hippocampus.mgz
>> -p-labels posterior_right* posterior_Right-Hippocampus.mgz -p-prefix
>> posterior_ -p-lut $FREESURFER_HOME/FreeSurferColorLUT.txt
>>
>> Thanks,
>>
>> Joana
>>
>>
>> 2014-06-13 15:23 GMT+02:00 Koen Van Leemput :
>>
>>> Hi Joana,
>>>
>>> This looks like a visualization issue rather than a segmentation error to
>>> me. How did you visualize this?
>>>
>>> Koen
>>>
>>> On Jun 13, 2014 2:59 PM, "Joana Braga Pereira" 
>>> wrote:

 Dear all,

 I'm running the GEMS tool in Freesurfer 5.3 to measure the volumes of
 hippocampal subfields in subjects between 9 and 14 years of age with 3T
 T1-weighted MRI scans.

 I noticed that a blackline is consistently drawn around the surface of
 the subfields (see attached figure) and was wondering whether this is
 normal.

 Since the tool has not been validated in young subjects I would like to
 know if the black line observed in the figure shows that the segmentation
 has not been carried out correctly.

 Any help will be greatly appreciated.

 Many thanks,

 Joana

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 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
>
>
> 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] editing aseg

[Bruce Fischl]

Hi Andrea

if the surfaces are ok you probably don't need to worry about it, as we 
recommend using the surface-based stats not the voxel-based ones for 
cortex and cerebral white matter. It does look like the pial surface is 
grabbing a bit of the tentorium, which  you could fix if you care about 
that area


cheers
Bruce
 On Wed, 25 Jun 2014, Andrea Horváth wrote:


Dear All,

After running recon-all and checked all the required steps, some part of the
right cerebral white matter was still segmented as right cerebral cortex in
the aseg.mgz as seen in the attached pictures (red cross). I would like to
edit these two labels in aseg which is OK, but how can I get the correct
values in the aseg.stats file?

Thank you for your help!

Andrea

Szövegközi kép 4 Szövegközi kép 3

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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] editing aseg

[Louis Nicholas Vinke]

Hi Andrea,
To regenerate the aseg.stats file after aseg edits you can run:

recon-all -segstats -s 

-Louis

On Wed, 25 Jun 2014, Andrea Horváth wrote:


Dear All,

After running recon-all and checked all the required steps, some part of the 
right cerebral white matter was
still segmented as right cerebral cortex in the aseg.mgz as seen in the 
attached pictures (red cross). I would
like to edit these two labels in aseg which is OK, but how can I get the 
correct values in the aseg.stats file?

Thank you for your help!

Andrea

Szövegközi kép 4 Szövegközi kép 3

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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] trac-all error (segmentation fault?)

[Anastasia Yendiki]

Hi Durai - You cannot run all 3 steps of trac-all at the same time. The 3 
steps need to be run separately. Please check the tutorial on the wiki for 
more details.


a.y

On Tue, 24 Jun 2014, Durai Arasan wrote:


Hi Freesurfer experts,
I tried running trac-all with my config file and received the following
error :

Segmentation fault 
Linux 129-x-xx-xxx 3.4.33-2.24-desktop #1 SMP PREEMPT Tue Feb 26 03:34:33
UTC 2013 (5f00a32) x86_64 x86_64 x86_64 GNU/Linux

trac-paths exited with ERRORS at Tue Jun 24 11:15:12 EDT 2014

Any help would be greatly appreciated! I am attaching the config file, log
and error files.

Thank you!
Durai


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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] control points - voxels in wm mask being ignored

[Bruce Fischl]

Hi Elissa

the control point can still have an effect if the brainmask.mgz intensity 
is not 110. Please make sure that you aren't adding control points to gray 
matter though - that will mess everything up!

Bruce


On Wed, 25 Jun 2014, Elissa McIntosh wrote:

> Hello freesurfer experts,
> 
> I have a question. I think some of the gray matter is being underestimated
> and some white matter isn't being classified in particular areas. I went to
> add control points and I noticed that sometimes the places I want to put
> control points in have voxels there in the wm.mgz mask. What does it mean
> when this happens? Should I still add control points or leave it alone? I've
> attached an example.
> 
> Thank you!
> 
>
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Re: [Freesurfer] interpreting qdec results

[Emma Thompson]

I'm using SPSS. I'm not sure if my analysis reflects exactly what qdec is
doing, do you know which analysis in SPSS would be most appropriate? I'm
doing a simple ANCOVA.


On Wed, Jun 25, 2014 at 11:07 AM, Douglas N Greve  wrote:

>
> what software did you use? Are you sure you are using the same model as
> qdec uses?
>
>
> On 06/25/2014 11:03 AM, Emma Thompson wrote:
> > Thanks Doug, yes I did control for age in both instances.
> >
> >
> > On Wed, Jun 25, 2014 at 10:14 AM, Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >
> >
> > Your interpretation is right (ie, controls > patients for
> > red/yellow/orange). When you compared the two groups in your separate
> > analysis, did you control for age?
> > doug
> >
> >
> > On 06/24/2014 02:19 PM, Emma Thompson wrote:
> > > Hi Freesurfers,
> > > I am reposting this as my last email bounced.
> > >
> > > I have conducted a DODS analysis in qdec with group (controls vs
> > > patients) set as my fixed factor and age as a nuisance variable to
> > > determine if my groups differ in cortical thickness. Controls were
> > > added first in the .levels file followed by patients. When I
> > view the
> > > results in the display window for "do controls differ from
> > patients in
> > > cortical thickness" I see a significant cluster for the caudal
> > > anterior cingulate, denoted by a red-orange blob and a positive
> > > t-value. I'm wondering if this simply means that controls had
> > greater
> > > cortical thickness compared to patients after controlling for
> > age? The
> > > reason I ask is that I'm a little confused since when I created
> > an ROI
> > > for this cluster using tksurfer and then extracted the means and
> > sd, I
> > > see that the patients actually have larger means than the controls,
> > > the opposite of my interpretation of the results presented by
> > the qdec
> > > display. Furthermore, if I extract the means and sds for the entire
> > > caudal anterior cingulate using the aparc file, I get means that
> are
> > > larger in controls, compared to patients, which seems consistent
> > with
> > > qdec. Any ideas? Thanks for all the help.
> > >
> > >
> > > ___
> > > 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: https://gate.nmr.mgh.harvard.edu/filedrop2
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > 
> > Outgoing:
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu  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
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
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Re: [Freesurfer] interpreting qdec results

[Douglas N Greve]

No, I've never used SPSS. If you know matlab, I can step you through how 
to do it there

On 06/25/2014 04:13 PM, Emma Thompson wrote:
> I'm using SPSS. I'm not sure if my analysis reflects exactly what qdec 
> is doing, do you know which analysis in SPSS would be most 
> appropriate? I'm doing a simple ANCOVA.
>
>
> On Wed, Jun 25, 2014 at 11:07 AM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>
> what software did you use? Are you sure you are using the same
> model as
> qdec uses?
>
>
> On 06/25/2014 11:03 AM, Emma Thompson wrote:
> > Thanks Doug, yes I did control for age in both instances.
> >
> >
> > On Wed, Jun 25, 2014 at 10:14 AM, Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>
>  >> wrote:
> >
> >
> > Your interpretation is right (ie, controls > patients for
> > red/yellow/orange). When you compared the two groups in your
> separate
> > analysis, did you control for age?
> > doug
> >
> >
> > On 06/24/2014 02:19 PM, Emma Thompson wrote:
> > > Hi Freesurfers,
> > > I am reposting this as my last email bounced.
> > >
> > > I have conducted a DODS analysis in qdec with group
> (controls vs
> > > patients) set as my fixed factor and age as a nuisance
> variable to
> > > determine if my groups differ in cortical thickness.
> Controls were
> > > added first in the .levels file followed by patients. When I
> > view the
> > > results in the display window for "do controls differ from
> > patients in
> > > cortical thickness" I see a significant cluster for the caudal
> > > anterior cingulate, denoted by a red-orange blob and a
> positive
> > > t-value. I'm wondering if this simply means that controls had
> > greater
> > > cortical thickness compared to patients after controlling for
> > age? The
> > > reason I ask is that I'm a little confused since when I
> created
> > an ROI
> > > for this cluster using tksurfer and then extracted the
> means and
> > sd, I
> > > see that the patients actually have larger means than the
> controls,
> > > the opposite of my interpretation of the results presented by
> > the qdec
> > > display. Furthermore, if I extract the means and sds for
> the entire
> > > caudal anterior cingulate using the aparc file, I get
> means that are
> > > larger in controls, compared to patients, which seems
> consistent
> > with
> > > qdec. Any ideas? Thanks for all the help.
> > >
> > >
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> >  >
> > > 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
> 
> > 
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> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
> > 
> > Outgoing:
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> >
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> >
> > The information in this e-mail is intended only for the
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> > whom it is
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> > the e-mail
> > contains patient information, please contact the Partners
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> 

[Freesurfer] mri_segstats question

[Martins, Brad]

Hi everyone,

I’m new to Freesurfer and I have a question about the output of mri_segstats. I 
have created an ROI in which I am measuring cortical thickness. When I run 
mri_segstats I get a table with 2 rows of segmentation values. What are the 2 
rows? The SegId of the two rows are 0 and 1 but I don’t know what segmentations 
that corresponds to or where to find out. Any help would be greatly appreciated!

Thanks,

Brad
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[Freesurfer] Post-Doctoral fellowship available at University of California San Francisco Memory & Aging Center

[Rabinovici, Gil]

Seeking a highly motivated and energetic post-doctoral fellow interested in 
applying multi-modal neuroimaging to improve diagnostic accuracy and study 
mechanisms that drive clinical and anatomic heterogeneity in Alzheimer's 
disease, frontotemporal dementia and related disorders. Imaging techniques 
acquired include structural MRI, functional connectivity ("resting-state") MRI, 
DTI, amyloid PET and Tau PET.

Candidates must have an MD and/or PhD in Neuroscience related field. Strong 
quantitative skills and statistical knowledge are a pre-requisite. Previous 
neuroimaging research experience and programming knowledge are preferred but 
not required.

Interested candidates should send a CV and cover letter to the PI:

Gil Rabinovici, MD
Associate Professor of Neurology
UCSF Memory & Aging Center
Email: grabinov...@memory.ucsf.edu
http://memory.ucsf.edu/ourcenter/staff/grabinovici



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Re: [Freesurfer] free surfer

[Sam Raby]

Hi, Would someone kindly let me know that, in order to segment a tumor in
brain, how/whether I can segment only one slice so it propagates through
the adjacent slices and cover up the tumor?
thanks,
-S


On Tue, Jun 24, 2014 at 8:31 PM, Sam Raby  wrote:

> Thanks.
> I would like to start learning and using freesurfer.
> I have a DICOM MRI of the brain which has a tumor in it. I would like to
> segment this tumor as automatically as possible. Can I segment only one
> slice so it propagates through the adjacent slices? Which tool in
> freesurfer do I need to use to achieve this?
>
> Thanks,
> -S
>
>
> On Tue, Jun 17, 2014 at 5:51 PM, Markus Gschwind <
> markus.gschw...@gmail.com> wrote:
>
>> Hi,
>>
>> You can see here what to do:
>> https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
>>  no 4., 5 and 6 especailly.
>>
>> Cheers,
>> M
>>
>>
>> 2014-06-18 0:45 GMT+02:00 Sam Raby :
>>
>>> I have downloaded the following file
>>>
>>> freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz
>>>
>>> and have extracted the contained files, and I was wondering where the
>>> binary file is so that I can open the freesurfer with?
>>> 
>>>
>>> thanks
>>> -S
>>>
>>>
>>>
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>>> it is
>>> addressed. If you believe this e-mail was sent to you in error and the
>>> e-mail
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>>> HelpLine at
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>>> properly
>>> dispose of the e-mail.
>>>
>>>
>>
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>> dispose of the e-mail.
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>>
>
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Re: [Freesurfer] free surfer

[Bruce Fischl]

Hi Sam

no, I don't think there is anything we have that will do tumor 
segmentation. I think there are some tools for manually segmenting 
structures and propagating segmentations from one slice to the next. 
Perhaps Ruopeng or some other power freeview user can comment?


cheers
Bruce
On Wed, 25 Jun 2014, Sam Raby wrote:


Hi, Would someone kindly let me know that, in order to segment a tumor in
brain, how/whether I can segment only one slice so it propagates through the
adjacent slices and cover up the tumor? thanks,
-S


On Tue, Jun 24, 2014 at 8:31 PM, Sam Raby  wrote:
  Thanks. I would like to start learning and using freesurfer. 
I have a DICOM MRI of the brain which has a tumor in it. I would like
to segment this tumor as automatically as possible. Can I segment only
one slice so it propagates through the adjacent slices? Which tool in
freesurfer do I need to use to achieve this? 

Thanks,
-S 


On Tue, Jun 17, 2014 at 5:51 PM, Markus Gschwind
 wrote:
  Hi, 
You can see here what to do:
https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
no 4., 5 and 6 especailly.

Cheers,
M


2014-06-18 0:45 GMT+02:00 Sam Raby :
  I have downloaded the following file
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz

and have extracted the contained files, and I was
wondering where the binary file is so that I can open the
freesurfer with?

thanks
-S

 

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[Freesurfer] meaning of foldind

[kangchengwang0...@gmail.com]

Dear experts,
   In the Group stats files, there is a file of lh.a2009s.foldind (or 
rh.a2009s.foldind). What's the meaning of foldind?
Thank you


Wang Kangcheng

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