Re: [Freesurfer] FS V6.0 GTM PVC ROI definition

[Pradeep]

Thank you! I will.

On Mon, Jun 20, 2016, 7:00 PM Bruce Fischl 
wrote:

> Hi Pradeep
>
> Doug is on vacation and is the best one to answer your question. If you
> don't get a response in a week or 10 days can you repost?
>
> thanks
> Bruce
> On Tue, 21 Jun
> 2016, Pradeep wrote:
>
> > Hello Freesrufer Team,
> >
> > I am trying to use the Partial volume correction procedure implemented in
> > the freesurfer 6 beta version and have a few questions.
> >
> > In your recent Neuroimaging paper, the left and right hemispheres were
> > combined by taking the average of the two as they did not show any
> > age-by-hemisphere interaction.
> >
> > I might have interpreted the Supplementary figure 1 incorrectly, but the
> > Geometric transfer matrix seem to show around 52 ROI's, So were the L
> and R
> > ROIs combined for the PVC results you reported in  that paper? Or were
> the
> > same 52 used for the general PVC in the FS pipeline?
> >
> > Do you have any concrete results to examine the effects of the size
> > variation over the ROIs used for PVC? Should a threshold be set for the
> > sizes of these ROIs?
> >
> > How were the white matter hypo-intensities dealt with while generating
> the
> > ROI masks?
> >
> >
> > Thanks,
> > Pradeep
> >
> >
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[Freesurfer] cortical surface pattern matching

[GREGORY R KIRK]

Hi,


has anyone created functionality to compare the spatial correlation/similarity

of two patterns in the form of cortical surface overlays. What I am looking at 
is a have

scalar at every point on the cortical surface. obviously this is just a list of 
vertices with

a scalar value associated with each. obviously I can map these both onto an 
average cortical surface and then simply compute the correlation of both of 
these.


but of course pattern similarity is an inherently spatial problem and for 
cortical

surfaces a 2 dimensional spatial correlation or other similarity metric would be

what you want. Here the order of vertices in a vertex list maps somewhat like a

string around the cortex and so the next wrap around you have vertices which are

adjacent on the surface but distant by the metric of vertex count.


is there any implementation of a similarity metric which takes this coordinate 
problem into account. In my measure every vertex across both hemi has a value 
and so i am not interested in something for a small localized patch.


any thoughts appreciated


Greg
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Re: [Freesurfer] FSFAST- Cerebellum

[Thomas Yeo]

Hi Sabin,

The structures 601-628 FreeSurferCololLUT.txt correspond to anatomical
substructures of the cerebellum (e.g., Crus I, etc). Is that what you
want? Or are you looking to use the functional parcels defined in
Buckner 2011?

In addition, I do not know how mri_segstats works, so I cannot verify
how you call the command is correct. Maybe others can provide feedback
here.

However, the Buckner cerebellar parcellations in
$FREESURFER_HOME/average/Buckner_JNeurophysiol11_MNI152/ is in MNI152
space. From your command, I assume your data is in MNI305 space. So
you might need to transform the parcellation from MNI152 to MNI305.

Thanks,
Thomas

On Sat, Jun 18, 2016 at 8:49 AM, Sabin Khadka  wrote:
> Hi all,
>
> I am trying to extract mean time series BOLD data using FSFAST from Cortical
> ROIs + sub cortical ROIs and cerebellum.
>
> preproc-sess -s rest210 -fsd bold -surface fsaverage lhrh -mni305 -fwhm 6
> -per-run -stc oddmri_segstats --annot fsaverage lh aparc --i
> rest210/bold/001/fmcpr.odd.sm6.fsaverage.lh.nii.gz --excludeid 1000
> --excludeid 1004 --avgwf CorticalTimeSeries_lh.txt
> mri_segstats --annot fsaverage rh aparc --i
> rest210/bold/001/fmcpr.odd.sm6.fsaverage.rh.nii.gz --excludeid 2000
> --excludeid 2004 --avgwf CorticalTimeSeries_rh.txt
>
> and for cortical time series
>
> mri_segstats --seg fsaverage/mri.2mm/aseg.mgz --ctab
> /opt/freesurfer/FreeSurferColorLUT.txt --id 10 --id 11 --id 12 --id 13 --id
> 17 --id 18 --id 26 --id 49 --id 50 --id 51 --id 52 --id 53 --id 54 --id 58
> --i rest210/bold/001/fmcpr.odd.sm6.mni305.2mm.nii.gz --avgwf
> subCorticalTimeSeries.txt
>
> But I am not sure on how exactly to extract time series from cerebellar
> regions. So if I want to extract time series from regions as described in
> Buckner et.al 2011. Could I just use mri_segstats for the labels 601-628 in
> FreeSurferCololLUT.txt? If not could you please direct me to processes that
> I can use.
>
> Cheers,
> Sabin Khadka
>
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Re: [Freesurfer] FS V6.0 GTM PVC ROI definition

[Bruce Fischl]

Hi Pradeep

Doug is on vacation and is the best one to answer your question. If you 
don't get a response in a week or 10 days can you repost?


thanks
Bruce
On Tue, 21 Jun 
2016, Pradeep wrote:



Hello Freesrufer Team, 

I am trying to use the Partial volume correction procedure implemented in
the freesurfer 6 beta version and have a few questions. 

In your recent Neuroimaging paper, the left and right hemispheres were
combined by taking the average of the two as they did not show any
age-by-hemisphere interaction.

I might have interpreted the Supplementary figure 1 incorrectly, but the
Geometric transfer matrix seem to show around 52 ROI's, So were the L and R
ROIs combined for the PVC results you reported in  that paper? Or were the
same 52 used for the general PVC in the FS pipeline?

Do you have any concrete results to examine the effects of the size
variation over the ROIs used for PVC? Should a threshold be set for the
sizes of these ROIs?

How were the white matter hypo-intensities dealt with while generating the
ROI masks? 


Thanks,
Pradeep 


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[Freesurfer] XQuartz 2.7.9 update results in errors

[Kate Mills]

Hi All,

My lab is having difficulty loading the freeview gui after updating to the
latest version of XQuartz (2.7.9). We were wondering if others have
experienced this issue? We have reverted by to XQuartz 2.7.8 on our
machines for now. In case relevant, this errors seems to span Mac OS
versions.

Thank you!

Kate
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[Freesurfer] FS V6.0 GTM PVC ROI definition

[Pradeep]

Hello Freesrufer Team,

I am trying to use the Partial volume correction procedure implemented in
the freesurfer 6 beta version and have a few questions.

In your recent Neuroimaging paper, the left and right hemispheres were
combined by taking the average of the two as they did not show any
age-by-hemisphere interaction.

I might have interpreted the Supplementary figure 1 incorrectly, but the
Geometric transfer matrix seem to show around 52 ROI's, So were the L and R
ROIs combined for the PVC results you reported in  that paper? Or were the
same 52 used for the general PVC in the FS pipeline?

Do you have any concrete results to examine the effects of the size
variation over the ROIs used for PVC? Should a threshold be set for the
sizes of these ROIs?

How were the white matter hypo-intensities dealt with while generating the
ROI masks?


Thanks,
Pradeep
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Re: [Freesurfer] matlab crashes on selxavg

[S.V.Shepherd [work]]

A follow up, in case anyone else encounters thread-related bugs:  It
*appears* that this error was resolved by adding the line

maxNumCompThreads(4);

to *startup.m*

stephen

*stephen v. shepherd   phd*
The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA
// 212.327.7699

On Thu, May 19, 2016 at 11:41 AM, Douglas N Greve  wrote:

> sorry, I have no idea
>
> On 05/19/2016 11:35 AM, S.V.Shepherd [work] wrote:
> > It happens when I run more than 3-4 analyses at once. It appears to be
> > sensitive to other instances of Matlab being open. however, I don't
> > see clear evidence I'm memory limited. for example, I'm currently
> > running four selxavg in parallel, along with a separate melodic
> > analysis. One more would cause a crash.
> >
> > free -g returns, in the "free" column:
> >   mem: 4
> >   buffers/cache 480
> >   swap 127
> >
> > i think this means I have 480gb free, no?
> >
> > stephen
> >
> >
> >
> >
> > _stephen v. shepherd   phd_
> > The Rockefeller University / 1230 York Avenue / New York NY 10065-6307
> > USA // 212.327.7699
> >
> > On Thu, May 19, 2016 at 11:03 AM, Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >
> > Does it always die like that? It may be out of memory.
> >
> > On 05/18/2016 01:50 PM, S.V.Shepherd [work] wrote:
> > > Hello,
> > >
> > > When running more than 3 analyses in parallel in FreeSurfer 5.3,
> > I am
> > > getting matlab crashes. Mathworks has politely declined to provide
> > > support unless I can replicate outside FsFAST.
> > >
> > > The errors are variants of
> > >
> > > """
> > >
> > > OMP: Error #34: System unable to allocate necessary resources
> > for OMP
> > > thread:
> > > OMP: System error #11: Resource temporarily unavailable
> > >  [...]
> > > MATLAB is exiting because of fatal error
> > > Killed
> > > --
> > > ERROR: fast_selxavg3() failed\n
> > >
> > > """
> > >
> > > thread_monitor Resource temporarily unavailable in pthread_create
> > > *** glibc detected *** /usr/local/MATLAB/R2015b/bin/glnxa64/MATLAB:
> > > double free or corruption (!prev): 0x7f585308c390 ***
> > > Segmentation fault (core dumped)
> > >
> > > """
> > >
> > > I have copied Matlab version info below. Any tips on how to
> > troubleshoot?
> > >
> > >
> >
>  
> 
> > > MATLAB Version: 8.6.0.267246 (R2015b)
> > > MATLAB License Number: 1098672
> > > Operating System: Linux 2.6.32-573.18.1.el6.x86_64 #1 SMP Wed Jan 6
> > > 11:20:49 EST 2016 x86_64
> > > Java Version: Java 1.7.0_60-b19 with Oracle Corporation Java
> > > HotSpot(TM) 64-Bit Server VM mixed mode
> > >
> >
>  
> 
> > > MATLAB Version 8.6 (R2015b)
> > > Computer Vision System Toolbox Version 7.0  (R2015b)
> > > Image Processing Toolbox Version 9.3  (R2015b)
> > > Optimization Toolbox Version 7.3 (R2015b)
> > > Signal Processing Toolbox Version 7.1  (R2015b)
> > > Statistics and Machine Learning Toolbox Version 10.1
> (R2015b)
> > >
> > >
> > >
> > >
> > >
> > > _stephen v. shepherd   phd_
> > > The Rockefeller University / 1230 York Avenue / New York NY
> 10065-6307
> > > USA // 212.327.7699 
> > >
> > >
> > > ___
> > > 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/complia

Re: [Freesurfer] Error loading a constructed annotation file

[Bruce Fischl]

Hi Nora

sorry for the long response time. Doug is on vacation and that slows 
everything down! Can you send the full command line and full terminal 
output? I think the "1 -1 NOT_FOUND ..." error refers to not being able to 
find an annotation/parcellation NOT to the orig surface.


cheers
Bruce

On Fri, 17 Jun 2016, 
Bittner, Nora wrote:



Dear Bruce,

thank you for your quick reply.
Attached I send you the command line, the color table I used, the terminal 
output from mris_label2annot and the error message that appears when loading my 
annotation file into freeview.
In the terminal output of mris_label2annot I recognized an error message in 
line 21. It seems that the rh.orig surface can´t be found, although it actual 
is in the subject´s folder ( I controlled this twice). I don´t understand this. 
I will put the first lines here, but the complete terminal output of 
mris_label2annot is attached.

Terminal Output:
"Reading ctab 
/data/Team_Caspers/1000Brains-Projects/Freesurfer/rh.fronparnetwork.txt
Number of ctab entries 5

$Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $
cwd /data/Team_Caspers/Bittner/Skripte_Freesurfer
cmdline mris_label2annot --h rh --subject 995005 --ctab 
/data/Team_Caspers/1000Brains-Projects/Freesurfer/rh.fronparnetwork.txt --a 
fronparnetwork --l /data/Team_Caspers/1000Brains-   
Projects/Freesurfer/995005/label/rh.cortex.label --l 
/data/Team_Caspers/1000Brains-Projects/Freesurfer/995005/label/mask_Blob1_nonlinear.label
 --l /data/Team_Caspers/1000Brains-   
Projects/Freesurfer/995005/label/mask_Blob3_nonlinear.label --l 
/data/Team_Caspers/1000Brains-Projects/Freesurfer/995005/label/mask_Blob5_nonlinear.label
 --nhits nhits.mgh
sysname  Linux
hostname imecas08
machine  x86_64
user cjockwitz

subject 995005
hemirh
SUBJECTS_DIR /data/Team_Caspers/1000Brains-Projects/Freesurfer
ColorTable 
/data/Team_Caspers/1000Brains-Projects/Freesurfer/rh.fronparnetwork.txt
AnnotName  fronparnetwork
NHitsFile nhits.mgh
nlables 4
LabelThresh 0 0.00
Loading 
/data/Team_Caspers/1000Brains-Projects/Freesurfer/995005/surf/rh.orig
 1 -1 NOT_FOUND ..."

Might this be the problem?

Thank you in advance,

Nora


Arbeitsgruppe Konnektivität
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   Forschungszentrum Jülich GmbH
   52425 Jülich
   Tel.: 02461-612412
   Email: n.bitt...@fz-juelich.de

und

Arbeitsgruppe Konnektivität im menschlichen Gehirn
   C. und O. Vogt Institut für Hirnforschung
   Heinrich-Heine-Universität Düsseldorf
   Universitätsklinikum Düsseldorf
   40225 Düsseldorf
  Tel.: 0211-8106109
   Email: n.bitt...@fz-juelich.de

-Ursprüngliche Nachricht-
Von: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl
Gesendet: Donnerstag, 16. Juni 2016 16:54
An: Freesurfer support list
Betreff: Re: [Freesurfer] Error loading a constructed annotation file

Hi Nora

you need to send us the complete command line you ran and also the error 
message and the complete terminal outpu

cheers
Bruce
On Thu, 16 Jun 2016, Bittner, Nora wrote:



Dear freesurfer experts,

 

I constructed an annotation file using mris_label2annot. I did this
several times and every time it worked very well. I was able to use a
ctab to define several colors, load my annotation file into freeview, and look 
at it.

Now I tried to construct another annotation file in the same manner,
but  if I try to load it into freeview, freeview just crashes. When I
constructed the annotation file I received no error from the terminal output.

 

I can´t understand the error message the terminal gives in the moment
freeview crashes. Since I was always successful in constructing my
annotation files, I wonder why this happens now.

 

I hope you can tell me, what the attached error message means.

Thanking you in advance,

 

Nora Bittner

 

 

 

Arbeitsgruppe Konnektivität

   Institut für Neurowissenschaften und Medizin (INM-1)

   Forschungszentrum Jülich GmbH

   52425 Jülich

   Tel.: 02461-612412

   Email: n.bitt...@fz-juelich.de

 

und

 

Arbeitsgruppe Konnektivität im menschlichen Gehirn

   C. und O. Vogt Institut für Hirnforschung

   Heinrich-Heine-Universität Düsseldorf

   Universitätsklinikum Düsseldorf

   40225 Düsseldorf

   Tel.: 0211-8106109

   Email: n.bitt...@fz-juelich.de

 



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Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
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Karsten Bene

Re: [Freesurfer] registering to fsaverage

[Bruce Fischl]

Hi Trisanna

the binaries that take mandatory command-line arguments (i.e. without a -- 
or - in front of them) require all options to be given before the mandatory 
arguments


cheers
Bruce

On Mon, 20 Jun 2016, Trisanna Sprung-Much 
wrote:



thanks, Bruce. Yes in the end through trial and error I tried "mri_average 
-noconform input output" and it worked. I was
surprised that I had to put the -noconform first as normally one can put the 
argument anywhere in the command.

Best

Trisanna

--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology


On Mon, Jun 20, 2016 at 9:27 AM, Bruce Fischl  
wrote:
  yes, your last file on the command line should be the output file (the 
average)

  cheers
  Bruce

  On Mon, 20 Jun 2016, Trisanna Sprung-Much wrote:

  As a follow-up, here is the mri_info for one of my overlays in the folder
  and the output file that mri_average seems to create (if I don't specify 
an
  output and it re-writes my last file). The dimensions are off:
  Any ideas?

  Trisanna


  
Tgtrisanna@kaplan:/data-01/trisanna/freesurfer/fsaverage/DISPLAY_overlays_fsa
  vee_left/aalf_lh$ mri_info fsaverage_overlay_aalf_icbm-102_left.mgz 
  Volume information for fsaverage_overlay_aalf_icbm-102_left.mgz
            type: MGH
      dimensions: 163842 x 1 x 1
     voxel sizes: 1., 1., 1.
            type: FLOAT (3)
             fov: 163842.000
             dof: 0
          xstart: -81921.0, xend: 81921.0
          ystart: -0.5, yend: 0.5
          zstart: -0.5, zend: 0.5
              TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
  degrees
         nframes: 1
         PhEncDir: UNKNOWN
  ras xform present
      xform info: x_r =   1., y_r =   0., z_r =   0., c_r =    
  0.5000
                : x_a =   0., y_a =   1., z_a =   0., c_a =  
  -17.5000
                : x_s =   0., y_s =   0., z_s =   1., c_s =  
   18.5000

  talairach xfm : 
  Orientation   : RAS
  Primary Slice Direction: axial

  voxel to ras transform:
                  1.   0.   0. -81920.5000
                  0.   1.   0.   -18.
                  0.   0.   1.    18.
                  0.   0.   0.     1.

  voxel-to-ras determinant 1

  ras to voxel transform:
                  1.  -0.  -0. 81920.5000
                 -0.   1.  -0.    18.
                 -0.  -0.   1.   -18.
                  0.   0.   0.     1.


  
trisanna@kaplan:/data-01/trisanna/freesurfer/fsaverage/DISPLAY_overlays_fsa
  verage_left/aalf_lh$ mri_info fsaverage_overlay_aalf_icbm-350_left.mgz 
  Volume information for fsaverage_overlay_aalf_icbm-350_left.mgz
            type: MGH
      dimensions: 256 x 256 x 256
     voxel sizes: 1., 1., 1.
            type: FLOAT (3)
             fov: 256.000
             dof: 0
          xstart: -128.0, xend: 128.0
          ystart: -128.0, yend: 128.0
          zstart: -128.0, zend: 128.0
              TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
  degrees
         nframes: 1
         PhEncDir: UNKNOWN
  ras xform present
      xform info: x_r =  -1., y_r =   0., z_r =   0., c_r =    
  0.5000
                : x_a =   0., y_a =   0., z_a =   1., c_a =  
  -17.5000
                : x_s =   0., y_s =  -1., z_s =   0., c_s =  
   18.5000

  talairach xfm : 
  Orientation   : LIA
  Primary Slice Direction: coronal

  --
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology


On Mon, Jun 20, 2016 at 12:32 AM, Trisanna Sprung-Much
 wrote:
      Hi Dr. Fischl
I ran the following mri_average and consistently get this message. It
seems to be trying to read my output as one of the input volumes. If I
don't specify an output it re-writes my last file in the input folder
and when I try to open this it doesn't work at all.

What exactly does MRIchangeType mean?



(navigated to folder with all .mgz volumes want to average)
mri_average *.mgz test.mgz --noconform

1 of 51: reading fsaverage_overlay_aalf_icbm-102_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
2 of 51: reading fsaverage_overlay_aalf_icbm-103_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
3 of 51: reading fsaverage_overlay_aalf_icbm-104_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
4 of 51: reading fsaverage_overlay_aalf_icbm-105_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
5 of 51: reading fsaverage_overlay_aalf_icbm-106_left.mgz...
embedding and inte

Re: [Freesurfer] registering to fsaverage

[Trisanna Sprung-Much]

thanks, Bruce. Yes in the end through trial and error I tried "mri_average
-noconform input output" and it worked. I was surprised that I had to put
the -noconform first as normally one can put the argument anywhere in the
command.

Best

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Mon, Jun 20, 2016 at 9:27 AM, Bruce Fischl 
wrote:

> yes, your last file on the command line should be the output file (the
> average)
>
> cheers
> Bruce
>
>
> On Mon, 20 Jun 2016, Trisanna Sprung-Much wrote:
>
> As a follow-up, here is the mri_info for one of my overlays in the folder
>> and the output file that mri_average seems to create (if I don't specify
>> an
>> output and it re-writes my last file). The dimensions are off:
>> Any ideas?
>>
>> Trisanna
>>
>>
>> Tgtrisanna@kaplan
>> :/data-01/trisanna/freesurfer/fsaverage/DISPLAY_overlays_fsa
>> vee_left/aalf_lh$ mri_info fsaverage_overlay_aalf_icbm-102_left.mgz
>> Volume information for fsaverage_overlay_aalf_icbm-102_left.mgz
>>   type: MGH
>> dimensions: 163842 x 1 x 1
>>voxel sizes: 1., 1., 1.
>>   type: FLOAT (3)
>>fov: 163842.000
>>dof: 0
>> xstart: -81921.0, xend: 81921.0
>> ystart: -0.5, yend: 0.5
>> zstart: -0.5, zend: 0.5
>> TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
>> degrees
>>nframes: 1
>>PhEncDir: UNKNOWN
>> ras xform present
>> xform info: x_r =   1., y_r =   0., z_r =   0., c_r =
>> 0.5000
>>   : x_a =   0., y_a =   1., z_a =   0., c_a =
>> -17.5000
>>   : x_s =   0., y_s =   0., z_s =   1., c_s =
>>  18.5000
>>
>> talairach xfm :
>> Orientation   : RAS
>> Primary Slice Direction: axial
>>
>> voxel to ras transform:
>> 1.   0.   0. -81920.5000
>> 0.   1.   0.   -18.
>> 0.   0.   1.18.
>> 0.   0.   0. 1.
>>
>> voxel-to-ras determinant 1
>>
>> ras to voxel transform:
>> 1.  -0.  -0. 81920.5000
>>-0.   1.  -0.18.
>>-0.  -0.   1.   -18.
>> 0.   0.   0. 1.
>>
>>
>> trisanna@kaplan
>> :/data-01/trisanna/freesurfer/fsaverage/DISPLAY_overlays_fsa
>> verage_left/aalf_lh$ mri_info fsaverage_overlay_aalf_icbm-350_left.mgz
>> Volume information for fsaverage_overlay_aalf_icbm-350_left.mgz
>>   type: MGH
>> dimensions: 256 x 256 x 256
>>voxel sizes: 1., 1., 1.
>>   type: FLOAT (3)
>>fov: 256.000
>>dof: 0
>> xstart: -128.0, xend: 128.0
>> ystart: -128.0, yend: 128.0
>> zstart: -128.0, zend: 128.0
>> TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
>> degrees
>>nframes: 1
>>PhEncDir: UNKNOWN
>> ras xform present
>> xform info: x_r =  -1., y_r =   0., z_r =   0., c_r =
>> 0.5000
>>   : x_a =   0., y_a =   0., z_a =   1., c_a =
>> -17.5000
>>   : x_s =   0., y_s =  -1., z_s =   0., c_s =
>>  18.5000
>>
>> talairach xfm :
>> Orientation   : LIA
>> Primary Slice Direction: coronal
>>
>> --
>> Ph.D. CandidateMcGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Mon, Jun 20, 2016 at 12:32 AM, Trisanna Sprung-Much
>>  wrote:
>>   Hi Dr. Fischl
>> I ran the following mri_average and consistently get this message. It
>> seems to be trying to read my output as one of the input volumes. If I
>> don't specify an output it re-writes my last file in the input folder
>> and when I try to open this it doesn't work at all.
>>
>> What exactly does MRIchangeType mean?
>>
>>
>>
>> (navigated to folder with all .mgz volumes want to average)
>> mri_average *.mgz test.mgz --noconform
>>
>> 1 of 51: reading fsaverage_overlay_aalf_icbm-102_left.mgz...
>> embedding and interpolating volume
>> MRIchangeType: Building histogram
>> 2 of 51: reading fsaverage_overlay_aalf_icbm-103_left.mgz...
>> embedding and interpolating volume
>> MRIchangeType: Building histogram
>> 3 of 51: reading fsaverage_overlay_aalf_icbm-104_left.mgz...
>> embedding and interpolating volume
>> MRIchangeType: Building histogram
>> 4 of 51: reading fsaverage_overlay_aalf_icbm-105_left.mgz...
>> embedding and interpolating volume
>> MRIchangeType: Building histogram
>> 5 of 51: reading fsaverage_overlay_aalf_icbm-106_left.mgz...
>> embedding and interpolating volume
>> MRIchangeType: Building histogram
>> 6 of 51: reading fsaverage_overlay_aalf_icbm-107_left.mgz...
>> embedding and interpolating volume
>> MRIchangeType: Building histogram
>> 7 of 51: reading fsaverage_overlay_aalf_icbm-108_left.mgz...
>> embedding and interpolating volume
>> MRIchangeType: Building histogram
>> 8 of 51: reading fsaverage_ov

Re: [Freesurfer] Hippocampal subfields error

[June Kang]

I am also experiencing same problem.

I tried to change ct., but when I change the extension to ctf,It also give 
errors as below.
Error:CTF file 
'/usr/local/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.ctf' failed to 
open for 'Read' access. Error message: 'Open a zip file for read/modify failed.'
Ubuntu 14.04, nightly dev. version of freesurfer.I also use several mac on 
10.9~10.10.5, but they all works well with new hippocampal subfields 
segmentation function in latest dev. version.
June.


On Jun 17, 2016, at 2:01 AM, Greenberg, Jonathan  
wrote:Thanks.
Has anyone else encountered this error message or knows how it can be solved?
Thank you
Jonathan

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Hibert, Matthew Louis 
[mhib...@mgh.harvard.edu]
Sent: Thursday, June 16, 2016 12:44 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal subfields error

No, I just wanted to mention that in case it helps with troubleshooting what 
went wrong with the new dev version build.

Matt

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Greenberg, Jonathan 
[jgreenbe...@mgh.harvard.edu]
Sent: Thursday, June 16, 2016 11:24 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal subfields error

Thanks Matt. Did you somehow get it to work or recognize the file without the 
ctf extension?
Thanks
Jonathan

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Hibert, Matthew Louis 
[mhib...@mgh.harvard.edu]
Sent: Thursday, June 16, 2016 11:10 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal subfields error

I've also gotten this error recently, with T1, T2, and combined T1+T2 
hippocampal segmentations.  It looks like the  files exist at 
/autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf
 exist, they just don't have the ".ctf" file extension.

Matt

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Greenberg, Jonathan 
[jgreenbe...@mgh.harvard.edu]
Sent: Thursday, June 16, 2016 10:29 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Hippocampal subfields error

Hi all
I ran recon-all on data from about 60 participants pre and post an 
intervention, with the hippocampal subfields flag
(e.g. "recon-all -all -subjid SPS01-1910_pre_lazar -hippocampal-subfields-T1"). 
The recon-all.log file states that the process finished without errors. 
However, the hippocampal-subfieldsT1.log indicated the following:
"Error:Cannot find CTF archive 
/autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf"
 (see below for the full content of hippocampal-subfieldsT1.log).
I tried to run only the hippocampal subfield recon-all again (e.g. "recon-all 
-s recon-all -all -subjid SPS01-1910_pre_lazar hippocampal-subfields-T1") and 
received the same error message.
I tried to look in the indicated folder 
("/autofs/cluster/freesurfer/centos6_x86_64/dev/bin") and found a file named 
segmentSubjectT1_autoEstimateAlveusML (without the ctf extension). I do not 
know if this is the source of the problem.

My FREESURFER_HOME directory is 
/autofs/cluster/freesurfer/centos6_x86_64/stable6/. My SUBJECTS_DIR is 
/autofs/cluster/lazar/Projects/jonathan-miracle/unpacking-dicoms/SUBJECTS_DIR/.

Any suggestions? (full hippocampal-subfieldsT1.log below)
Thank you!
Jonathan

hippocampal-subfieldsT1.log content:

#
#@# Hippocampal Subfields processing (T1 only) left Thu Jun 16 09:58:23 EDT 2016
--
Setting up environment variables
---
LD_LIBRARY_PATH is 
.:/usr/local/freesurfer/stable6/MCRv80/runtime/glnxa64:/usr/local/freesurfer/stable6/MCRv80/bin/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:
Error:Cannot find CTF archive 
/autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf
#
#@# Hippocampal Subfields processing (T1 only) right Thu Jun 16 09:58:26 EDT 
2016
--
Setting up environment variables
---
LD_LIBRARY_PATH is 
.:/usr/local/freesurfer/stable6/MCRv80/runtime/glnxa64:/usr/local/freesurfer/stable6/MCRv80/bin/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd

Re: [Freesurfer] mri_defacing: a faulty stripping of cortex

[Bruce Fischl]

YOu could try increasing the density of the search (which will slow it 
down considerably). Maybe -s 7? It's hard to diagnose without looking at 
your data, so feel free to upload it if this fails and also send us the 
exact command line you ran


On Mon, 20 Jun 2016, HONG Sujin wrote:



Hello,


I'm having a problem to use MRI_defacing (default radius 7), which stripped
off some  frontal areas  as well.  Does anyone have any similar
problems/solutions?


I've increased the radius up to 14, which seems reducing the stripping
areas, but still remained this stripping problem within the cortex.


Best wishes,

Sujin






Research fellow, 
Sujin Hong
NRlabs Neuropolitics Research
School of Social and Political Science
The University of Edinburgh
Room 2.03
18 Buccleuch Place
Edinburgh
EH8 9LN
 
Tel: +44 131 650 6632
sujin.h...@ed.ac.uk

&

Edinburgh Imaging
The University of Edinburgh
Room GU426D Chancellor's Building
49 Little France Crescnet
Edinburgh 
EH16 4SB 





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Re: [Freesurfer] registering to fsaverage

[Bruce Fischl]

yes, your last file on the command line should be the output file (the 
average)


cheers
Bruce

On Mon, 20 Jun 2016, Trisanna Sprung-Much wrote:


As a follow-up, here is the mri_info for one of my overlays in the folder
and the output file that mri_average seems to create (if I don't specify an
output and it re-writes my last file). The dimensions are off:
Any ideas?

Trisanna


Tgtrisanna@kaplan:/data-01/trisanna/freesurfer/fsaverage/DISPLAY_overlays_fsa
vee_left/aalf_lh$ mri_info fsaverage_overlay_aalf_icbm-102_left.mgz 
Volume information for fsaverage_overlay_aalf_icbm-102_left.mgz
          type: MGH
    dimensions: 163842 x 1 x 1
   voxel sizes: 1., 1., 1.
          type: FLOAT (3)
           fov: 163842.000
           dof: 0
        xstart: -81921.0, xend: 81921.0
        ystart: -0.5, yend: 0.5
        zstart: -0.5, zend: 0.5
            TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
degrees
       nframes: 1
       PhEncDir: UNKNOWN
ras xform present
    xform info: x_r =   1., y_r =   0., z_r =   0., c_r =    
0.5000
              : x_a =   0., y_a =   1., z_a =   0., c_a =  
-17.5000
              : x_s =   0., y_s =   0., z_s =   1., c_s =  
 18.5000

talairach xfm : 
Orientation   : RAS
Primary Slice Direction: axial

voxel to ras transform:
                1.   0.   0. -81920.5000
                0.   1.   0.   -18.
                0.   0.   1.    18.
                0.   0.   0.     1.

voxel-to-ras determinant 1

ras to voxel transform:
                1.  -0.  -0. 81920.5000
               -0.   1.  -0.    18.
               -0.  -0.   1.   -18.
                0.   0.   0.     1.


trisanna@kaplan:/data-01/trisanna/freesurfer/fsaverage/DISPLAY_overlays_fsa
verage_left/aalf_lh$ mri_info fsaverage_overlay_aalf_icbm-350_left.mgz 
Volume information for fsaverage_overlay_aalf_icbm-350_left.mgz
          type: MGH
    dimensions: 256 x 256 x 256
   voxel sizes: 1., 1., 1.
          type: FLOAT (3)
           fov: 256.000
           dof: 0
        xstart: -128.0, xend: 128.0
        ystart: -128.0, yend: 128.0
        zstart: -128.0, zend: 128.0
            TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
degrees
       nframes: 1
       PhEncDir: UNKNOWN
ras xform present
    xform info: x_r =  -1., y_r =   0., z_r =   0., c_r =    
0.5000
              : x_a =   0., y_a =   0., z_a =   1., c_a =  
-17.5000
              : x_s =   0., y_s =  -1., z_s =   0., c_s =  
 18.5000

talairach xfm : 
Orientation   : LIA
Primary Slice Direction: coronal

--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology


On Mon, Jun 20, 2016 at 12:32 AM, Trisanna Sprung-Much
 wrote:
  Hi Dr. Fischl
I ran the following mri_average and consistently get this message. It
seems to be trying to read my output as one of the input volumes. If I
don't specify an output it re-writes my last file in the input folder
and when I try to open this it doesn't work at all.

What exactly does MRIchangeType mean?



(navigated to folder with all .mgz volumes want to average)
mri_average *.mgz test.mgz --noconform

1 of 51: reading fsaverage_overlay_aalf_icbm-102_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
2 of 51: reading fsaverage_overlay_aalf_icbm-103_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
3 of 51: reading fsaverage_overlay_aalf_icbm-104_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
4 of 51: reading fsaverage_overlay_aalf_icbm-105_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
5 of 51: reading fsaverage_overlay_aalf_icbm-106_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
6 of 51: reading fsaverage_overlay_aalf_icbm-107_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
7 of 51: reading fsaverage_overlay_aalf_icbm-108_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
8 of 51: reading fsaverage_overlay_aalf_icbm-109_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
9 of 51: reading fsaverage_overlay_aalf_icbm-110_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
10 of 51: reading fsaverage_overlay_aalf_icbm-111_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
11 of 51: reading fsaverage_overlay_aalf_icbm-112_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
12 of 51: reading fsaverage_overlay_aalf_icbm-113_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
13 of 51: reading fsaverage_overlay_aalf_icbm-114_left.mgz...
embedding and interpolating volume
MRIcha

Re: [Freesurfer] registering to fsaverage

[Bruce Fischl]

try it with the noconform as the first argument. I think it will ignore it 
at the end






Hi Dr. Fischl
I ran the following mri_average and consistently get this message. It seems
to be trying to read my output as one of the input volumes. If I don't
specify an output it re-writes my last file in the input folder and when I
try to open this it doesn't work at all.

What exactly does MRIchangeType mean?



(navigated to folder with all .mgz volumes want to average)
mri_average *.mgz test.mgz --noconform

1 of 51: reading fsaverage_overlay_aalf_icbm-102_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
2 of 51: reading fsaverage_overlay_aalf_icbm-103_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
3 of 51: reading fsaverage_overlay_aalf_icbm-104_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
4 of 51: reading fsaverage_overlay_aalf_icbm-105_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
5 of 51: reading fsaverage_overlay_aalf_icbm-106_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
6 of 51: reading fsaverage_overlay_aalf_icbm-107_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
7 of 51: reading fsaverage_overlay_aalf_icbm-108_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
8 of 51: reading fsaverage_overlay_aalf_icbm-109_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
9 of 51: reading fsaverage_overlay_aalf_icbm-110_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
10 of 51: reading fsaverage_overlay_aalf_icbm-111_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
11 of 51: reading fsaverage_overlay_aalf_icbm-112_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
12 of 51: reading fsaverage_overlay_aalf_icbm-113_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
13 of 51: reading fsaverage_overlay_aalf_icbm-114_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
14 of 51: reading fsaverage_overlay_aalf_icbm-115_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
15 of 51: reading fsaverage_overlay_aalf_icbm-116_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
16 of 51: reading fsaverage_overlay_aalf_icbm-117_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
17 of 51: reading fsaverage_overlay_aalf_icbm-118_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
18 of 51: reading fsaverage_overlay_aalf_icbm-119_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
19 of 51: reading fsaverage_overlay_aalf_icbm-120_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
20 of 51: reading fsaverage_overlay_aalf_icbm-121_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
21 of 51: reading fsaverage_overlay_aalf_icbm-122_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
22 of 51: reading fsaverage_overlay_aalf_icbm-123_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
23 of 51: reading fsaverage_overlay_aalf_icbm-124_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
24 of 51: reading fsaverage_overlay_aalf_icbm-125_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
25 of 51: reading fsaverage_overlay_aalf_icbm-126_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
26 of 51: reading fsaverage_overlay_aalf_icbm-127_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
27 of 51: reading fsaverage_overlay_aalf_icbm-131_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
28 of 51: reading fsaverage_overlay_aalf_icbm-133_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
29 of 51: reading fsaverage_overlay_aalf_icbm-134_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
30 of 51: reading fsaverage_overlay_aalf_icbm-135_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
31 of 51: reading fsaverage_overlay_aalf_icbm-137_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
32 of 51: reading fsaverage_overlay_aalf_icbm-139_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
33 of 51: reading fsaverage_overlay_aalf_icbm-140_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
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MRIchangeType: Building histogram 
35 of 51

Re: [Freesurfer] Freesurfer Digest, Vol 148, Issue 28

[Bruce Fischl]

Hi Arkadiy

Doug is on vacation and his response time is likely to be slow. Can you 
tell us exactly what script you mean?


cheers
Bruce


On Sun, 19 Jun 2016, Arkadiy 
Maksimovskiy wrote:



Hi Doug,
Still no luck getting the script- the site does not load for some reason.
Any chance you might be able to paste it into the message body?

Thanks,
- Arkadiy

On Sun, Jun 19, 2016 at 12:00 PM, 
wrote:
  Send Freesurfer mailing list submissions to
          freesurfer@nmr.mgh.harvard.edu

  To subscribe or unsubscribe via the World Wide Web, visit
         
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
  or, via email, send a message with subject or body 'help' to
          freesurfer-requ...@nmr.mgh.harvard.edu

  You can reach the person managing the list at
          freesurfer-ow...@nmr.mgh.harvard.edu

  When replying, please edit your Subject line so it is more
  specific
  than "Re: Contents of Freesurfer digest..."


  Today's Topics:

     1. Re: GLM_Fit Question (Douglas Greve)
     2. Using Freesurfer commands in matlab (HARI GURAGAIN)
     3. change the algorithm (N Saf)
     4. Re: change the algorithm (Bruce Fischl)
     5. Re: registering to fsaverage (Trisanna Sprung-Much)
     6. Re: registering to fsaverage (Bruce Fischl)


  --

  Message: 1
  Date: Sat, 18 Jun 2016 23:54:18 +0200
  From: Douglas Greve 
  Subject: Re: [Freesurfer] GLM_Fit Question
  To: freesurfer@nmr.mgh.harvard.edu
  Message-ID: <5765c30a.5080...@nmr.mgh.harvard.edu>
  Content-Type: text/plain; charset="windows-1252"

  try now

  On 6/16/16 11:50 PM, Arkadiy Maksimovskiy wrote:
  > Hi Freesurfers,
  >
  > I am having a similar problem with the FSGD file as the user
  indicated
  > at this thread:
  >
  >
  https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg40599.html
  >
  > I am trying to access the script that Doug wrote in order to
  fix it,
  > however, the link to download the script does not seem to be
  working.
  > I was wondering if someone might be able to upload it again.
  >
  > Thank you in advance for your help,
  >
  > Arkadiy
  >
  >
  > ___
  > Freesurfer mailing list
  > Freesurfer@nmr.mgh.harvard.edu
  > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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  Message: 2
  Date: Sat, 18 Jun 2016 18:02:26 -0500
  From: HARI GURAGAIN 
  Subject: [Freesurfer] Using Freesurfer commands in matlab
  To: Freesurfer support list 
  Message-ID:
         
  
  Content-Type: text/plain; charset="utf-8"

  Dear Freesurfer,

  I am using the new development version of freesurfer (
  ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev).
  I am trying to call some of the freesurfer commands like:
  mri_coreg or some
  other. When I use the something like the following in Matlab:
  command='/Applications/freesurfer/bin/mri_coreg'
  and the below:
  [status,cmdout]=system(command)
  It is showing a weird error message like below:
  ###
  dyld: lazy symbol binding failed: Symbol not found:
  ___emutls_get_address
    Referenced from:
  /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
    Expected in: /usr/lib/libSystem.B.dylib

  dyld: Symbol not found: ___emutls_get_address
    Referenced from:
  /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
    Expected in: /usr/lib/libSystem.B.dylib
  ###
  I really don't understand why this error is coming. I have seen
  people have
  used the mri_*** commands a lot of times in matlab but
  unfortunately, it
  shows the above error in my case.
  Is it the error from Matlab, freesurfer, mac or something else?

  Any help in solving this issue will be greatly appreciated.

  Thank you.
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  Message: 3
  Date: Sun, 19 Jun 2016 12:06:56 +0430
  From: N Saf 
  Subject: [Freesurfer] change the algorithm
  To: freesurfer@nmr.mgh.harvard.edu
  Message-ID:
         
  
  Content-Type: text/plain; charset="utf-8"

  Dear Freesurfer,

  I wonder if it is po

[Freesurfer] mri_defacing: a faulty stripping of cortex

[HONG Sujin]

Hello,


I'm having a problem to use MRI_defacing (default radius 7), which stripped off 
some  frontal areas  as well.  Does anyone have any similar problems/solutions?


I've increased the radius up to 14, which seems reducing the stripping areas, 
but still remained this stripping problem within the cortex.


Best wishes,

Sujin





Research fellow,
Sujin Hong
NRlabs Neuropolitics Research
School of Social and Political Science
The University of Edinburgh
Room 2.03
18 Buccleuch Place
Edinburgh
EH8 9LN

Tel: +44 131 650 6632
sujin.h...@ed.ac.uk

&

Edinburgh Imaging
The University of Edinburgh
Room GU426D Chancellor's Building
49 Little France Crescnet
Edinburgh
EH16 4SB



The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
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Re: [Freesurfer] change the algorithm

[N Saf]

Dear Bruce,

thank you for your fast and helpful response.

I have read in some papers (e.g. paper1

,paper2
)
that FreeSurfer overestimates hippocampus volume a little  compared to the
manual segmentation. I know this is to be expected, but I wanted to see if
there are some parameters that I can work with to reduce this problem as
much as possible.can I access to probabilities which computed for
subcortical segmentation  from training data  in FreeSurfer ?

Sincerely,
Nazanin

On Sun, Jun 19, 2016 at 7:21 PM, Bruce Fischl 
wrote:

> Hi Nazanin
>
> no, sorry, that isn't possible. Our accuracy is improved by the fact that
> we model all subcortical structures simultaneously.
>
> As for your second question you need to be more specific. Are you finding
> some inaccuracies that you want to correct?
>
> cheers
> Bruce
>
>
>
> On Sun, 19 Jun 2016, N Saf wrote:
>
> Dear Freesurfer,
>>
>> I wonder if it is possible to segment just one sub-cortical structures
>> like
>> hippocampus by changing the algorithm (e.g. according to spatial prior
>> knowledge divided the image to some sub-images and do analysis just on
>> that
>> sub-image which we sure the hippocampus located)and by that reducing the
>> processing time ? and another general question I have is that in
>> sub-cortical segmentation commands 1to12 commands of -all flag  which
>> parameters can I change to affect the outputs?
>>
>> Sincerely,
>> Nazanin
>>
>>
>>
>>
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> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
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