date:20140513


Hi Mark

if you upload a subject that failed and the gca I'll take a look
Bruce
On Mon, 12 
May 2014, Mark Plantz wrote:



Yes, I created my own atlas for use with 1-2 year olds. It seems to be 
happening for all of
the subjects. I am wondering if changing the recon-all code to load the manual 
talairach.lta
 file for the EM_registration and CA_normalization would possibly fix the 
problem. It seems
strange that the wm/gm means were OK for skull stripping, but then suddenly 
null for the
other steps.


On Mon, May 12, 2014 at 7:49 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu 
wrote:
  Hi Mark

  did you create your own .gca file? If so, why? Does it happen for all your
  subjects?
  Bruce




  On Mon, 12 May 2014, Mark Plantz wrote:

As a quick update to this problem, it looks like the wm_mean and
gm_mean are reasonable
during the #SkullLTA and #SkullStripping steps. However, wm mean = 0
and gm mean = 0 for the
#CA_normalize and #EM_registration steps. 
Could this have anything to do with using a manual talairach
alignment in previous steps? I
did include the -nogcareg flag with the recon-all command.


On Mon, May 12, 2014 at 4:36 PM, Mark Plantz
markplantz2...@u.northwestern.edu wrote:
      Hi Freesurfers,
   Does anyone know if it is possible to manually set the brain
centroid during the EM
Registration step of the recon-all pipeline. I am using a
non-default atlas, and have
discovered that many of my difficulties have resulted from the brain
centroid being
incorrectly assigned to a region of black space. Thank you for the
help!

Best,

MP 




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Re: [Freesurfer] Measuring cortical thickness at a specific location

I see. Then measure the thickness normally, then see how it changes in 
those directions. You could average the thickness along each A/P coordinate 
- that wouldn't be a problem. You just don't want to measure it that way

cheers
Bruce


On Mon, 12 May 2014, 
pfot...@nmr.mgh.harvard.edu wrote:

 Hi Bruce,

 Thank you for your reply. I was interested in looking how the thickness
 changes from the posterior to the anterior side of the brain and vice
 versa (the thickness gradient).

 Thank you again for your time!
 Panos


 Hi Panos

 it would certainly be possible to make that measurement, but it wouldn't
 tell you anything biologically interesting. Why would you want to do such
 a
 thing? It will reflect the (arbitrary) image slice orientation and not the
 brain.

 cheers
 Bruce


 On Mon, 12 May 2014, pfot...@nmr.mgh.harvard.edu wrote:

 Hi FS experts,

 I was wondering whether it would be possible to measure the average
 cortical thickness at a specific slice (either axial, coronal, or
 sagittal). I read in Bruce's paper: Measuring the thickness of the
 human
 cerebral cortex from magnetic resonance images that Measuring the
 thickness from the coronal slice at the point indicated by the green
 cross
 would result in an estimate in excess of 1 cm. Is that always the case,
 or has there been a way to bypass that issue?

 Thank you for your time,
 Panos
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Re: [Freesurfer] mri_surf2surf


Hi Qiongmin

try making the output format .mgz (or maybe .nii) and see if that fixes the 
problem


cheers
Bruce


On Tue, 13 May 2014, Caka wrote:


Dear Doug and All,

I want to register the individual subject surface into the fsaverage surface. I 
used mdi_surf2surf command. But one error occurred. Could you please help me 
with this. Here are the scripts:

—

[root@localhost sub001]# mri_surf2surf --hemi lh --srcsubject sub001 
--srcsurfval thickness --src_type curv --trgsubject fsaverage --trgsurfval 
./sub001-thickness-lh.img
srcsubject = sub001
srcval = thickness
srctype= curv
trgsubject = fsaverage
trgval = ./sub001-thickness-lh.img
trgtype=
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
srchemi= lh
trghemi= lh
frame  = 0
fwhm-in= 0
fwhm-out   = 0
label-src  = (null)
label-trg  = (null)
OKToRevFaceOrder  = 1
Reading source surface reg 
/disk250/data_analysis/data_female_male_140/sub001/surf/lh.sphere.reg
Loading source data
Reading curvature file 
/disk250/data_analysis/data_female_male_140/sub001/surf/lh.thickness
Reading target surface reg 
/disk250/data_analysis/data_female_male_140/fsaverage/surf/lh.sphere.reg
Done
Mapping Source Volume onto Source Subject Surface
surf2surf_nnfr: building source hash (res=16).
Surf2Surf: Forward Loop (163842)

surf2surf_nnfr: building target hash (res=16).
Surf2Surf: Reverse Loop (132230)
Reverse Loop had 21224 hits
Surf2Surf: Dividing by number of hits (163842)
INFO: nSrcLost = 0
nTrg121 = 146822, nTrgMulti = 17020, MnTrgMultiHits = 2.247
nSrc121 = 93121, nSrcLost = 0, nSrcMulti = 39109, MnSrcMultiHits = 2.35099
Saving target data
Saving to ./sub001-thickness-lh.img
ANALYZE FORMAT ERROR: ncols 163842 in volume exceeds 32768
—

Thank you very much!

Qiongmin





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Re: [Freesurfer] Cannot allocate memory

can you send us the recon-all.log?
On Tue, 13 May 2014, Mayer Kristina 
wrote:

 Dear Bruce,

 I was running:
 recon-all -autorecon2-cp, after adding control points.
 When I then look at the surfaces using tkmedit -surfs or inflated surfaces 
 using tksurfer, everything seems to fit and I can open every output I like.
 Also values for volumes seem reasonable.

 Thanks in advance.

 Best,
 Kristina
 
 Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu]quot; im Auftrag von quot;Bruce 
 Fischl [fis...@nmr.mgh.harvard.edu]
 Gesendet: Montag, 12. Mai 2014 15:44
 An: Freesurfer support list
 Betreff: Re: [Freesurfer] Cannot allocate memory

 Hi Kristina

 you need to give us more context. What command is running when you get
 that error?

 cheers
 Bruce

 On Mon, 12 May 2014, Mayer Kristina wrote:

 Hi there,

 I am using freesurfer on MRI data of children.
 In one dataset I have following error appearing, I did not find described 
 before.

 MRISalloc(41043678, 76): could not allocate faces
 Cannot allocate memory
 Linux cs2.kispi.int 3.13.5-103.fc19.x86_64 #1 SMP Mon Mar 3 18:46:36 UTC 
 2014 x86_64 x86_64 x86_64 GNU/Linux

 Waht do I have to check or edit manually?

 Thanks!

 Best,
 Kristina


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Re: [Freesurfer] problem with pial surface reconstruction using T1 (MPRAGE) and T2 (SPACE) weighted images

Hi Emil

I would need the entire subject dir plus the T2-space volume

cheers
Bruce
On Tue, 13 May
2014, Emil H.J. Nijhuis wrote:

Dear Bruce Matt,
thank you for your help.

@Bruce: I would be happy to send you the data, just let me know by e-mail which
files you wo
uld need.

@Matt: Could you please specify the commands for the flags -nsigma_above and
-nsigma_below a
nd how you would rerun the pipeline? Also what values would be recommended?

I did not find any manual/help files regarding the flags, so it would be
helpful to document
it.

NB. I found another thread in the maillist which probably relates to the issue:
https://mail
.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-September/033550.html . However I could not
verify this, due to expired dropbox files.

Yours,

Emil

Probably Emil¹s current example would be best because it is failing in
your recon-all setup.

Matt.

On 5/9/14, 9:31 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:

Hi Matt

if you can send me an example I'll try to find time to take a look
Bruce
On Fri, 9
May 2014, Matt Glasser wrote:

Hi Bruce,

For whatever reason, sometimes the T2w surface adjustment will be way

off.
Adjusting the -nsigma_above # -nsigma_below # even a little bit up
and
down can get it out of the minimum and make it work, so there might be a
bug.

Peace,

Matt.

From: Emil H.J. Nijhuis emil.nijh...@gmail.com

Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Date: Friday, May 9, 2014 at 4:53 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] problem with pial surface reconstruction
using T1
(MPRAGE) and T2 (SPACE) weighted images

Dear Bruce,

thank you for your help.

attached I have put an fslview, tkmedit screen-shot of the T2 image and

a tk
surfer image of lh.woT2.pial.

It appears that without consideration of the T2 this effect does not

happen.

What would be your recommendation if I would like to keep using the T2

weigh
ted image?

Yours,

Emil

Hi Emil

how do the surfaces look before you apply the T2 deformation? And how do

they look visualized over the T2 instead of the T1?

cheers

Bruce

On Thu, 8 May 2014, Emil H.J. Nijhuis wrote:

Hi,

I have been using Freesurfer v5.3 to perform surface reconstruct for 1mm

isotropic T1 (MPRAGE) and T2 (SPACE) weighted images from a Siemens 3T
Trio
scanner with a 32-channel head coil. Unfortunately for half of my
subjects I
receive an rather odd pial surface artefact, while the 'white' surfaces
do
not suffer from the same issue.

The command line I have used was:

recon-all -all -subjid subjectid -T2 subjectdir/mri/orig/T2.mgz

-T2pial
-3T

Are you familiar with this issue and do you have some advice for me?

Thank you very much for your help.

Yours sincerely,

Emil

--
Emil H.J. Nijhuis, PhD
Researcher - Division of Diagnostic and Interventional Neuroradiology
University Hospital Basel
Petersgraben 4
CH 4031 Basel Switzerland

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Re: [Freesurfer] white matter surface (tkmedit -surfs) vs wm.mgz

Hi Kristina

are you running:

recon-all -autorecon2-cp -autorecon3 ...

after adding control points and editing the wm?

Bruce
On Tue, 13 May 2014, Mayer 
Kristina 
wrote:

 Dear all

 I am segmenting data of 2 year olds and as freesurfer fails on segmneting 
 inferior parts of the temporal lobe, I try to edit this manually using 
 tkmedit (protocol from fswiki: WhiteMatterEdits_tktools, PialEdits_tktools, 
 ControlPoints_tktools).
 I first add control points, with successfull amelioration of brainmask 
 volumes. As this leads to integration of too much tissue in the white matter 
 surface (displayed as tkmedit brainmask.mgz -surfs), i tried to manually edit 
 wm.mgz. When I edit wm.mgz, there is no change in -surfs. When looking at the 
 data in tkmedit (tkmedit subjid wm.mgz -surfs), total WM surface (-surfs), 
 and wm.mgz are not the same.

 Where is the file generated that is shown in tkmedit as -surfs and which 
 volume/file do I have to edit to ameliorate output of -surfs?

 Best, Kristina


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Re: [Freesurfer] LME Matlab toolbox

2014-05-13 Thread jorge luis

Hi Victor 


As explained in the wikifs_read_surf.m  andfs_read_Y.m  depend on Freesurfer's 
scripts so you need to have installed 
Freesurfer software package and included the Freesurfer's matlab 
subdirectory in your Matlab's search path. 


Best
-Jorge

El Martes 13 de Mayo de 2014 4:40, Victor Montal Blancafort 
victor.mon...@gmail.com escribió:
 
Greetings,



 The aim of this mail is about some problems that I am facing using the 
standalone copy (that is becouse I am using v5.1) of the LNE Matlab Tool 
provided on the FreeSurfer Wiki 
(http://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels).



Currently, I am carrying out a longitudinal mass-univariate study. However, I 
get blocked when I try to open the smoothed thickness '.mgh' file obtained 
using the 'mris_preproc' and 'mri_surf2surf' command or also when I try to 
open the fsaverage sphere.


Analyzing the code, I have realized that problems are caused due to that some 
'.m' files such as 'load_mgh.m' or  'read_surf.m' can't be opened because they 
are not provided on the package.  Should I download them from another source 
or maybe there is another problem I am not realizing?


Thank you in advance for you attention and your help!


Bests,
Victor 




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Re: [Freesurfer] Measuring cortical thickness at a specific location

Hi Bruce,

Just to clarify, when you say average the thickness along each A/P
coordinate do you mean by looking up at the average cortical thickness of
each parcellation and then calculating their average from P-A, or is
there another way to find the average thickness of each slice and then see
how that average changes from P-A?
Thanks again for your time,
Panos

 I see. Then measure the thickness normally, then see how it changes in
 those directions. You could average the thickness along each A/P
 coordinate
 - that wouldn't be a problem. You just don't want to measure it that way

 cheers
 Bruce


 On Mon, 12 May 2014,
 pfot...@nmr.mgh.harvard.edu wrote:

 Hi Bruce,

 Thank you for your reply. I was interested in looking how the thickness
 changes from the posterior to the anterior side of the brain and vice
 versa (the thickness gradient).

 Thank you again for your time!
 Panos


 Hi Panos

 it would certainly be possible to make that measurement, but it
 wouldn't
 tell you anything biologically interesting. Why would you want to do
 such
 a
 thing? It will reflect the (arbitrary) image slice orientation and not
 the
 brain.

 cheers
 Bruce


 On Mon, 12 May 2014, pfot...@nmr.mgh.harvard.edu wrote:

 Hi FS experts,

 I was wondering whether it would be possible to measure the average
 cortical thickness at a specific slice (either axial, coronal, or
 sagittal). I read in Bruce's paper: Measuring the thickness of the
 human
 cerebral cortex from magnetic resonance images that Measuring the
 thickness from the coronal slice at the point indicated by the green
 cross
 would result in an estimate in excess of 1 cm. Is that always the
 case,
 or has there been a way to bypass that issue?

 Thank you for your time,
 Panos
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[Freesurfer] R: R: R: R: Filipping issue

2014-05-13 Thread Paola Valsasina

Dear Doug,

I am trying to run mris_preproc as you indicated, but it fails with the
following error:

MRISread($SUBJECTS_DIR/fsaverage/surf/lh.fsaverage_sym.sphere.reg): could
not open file.

Why is target file searched in the fsaverage folder? I was expecting it is
searched in the fsaverage_sym folder?

Thank you in advance
Kind regards
Paola


Paola Valsasina, MSc
Research Fellow
Neuroimaging Research Unit (Director Prof. M. Filippi)
Institute of Experimental Neurology, Division of Neuroscience,
Scientific Institute and University Vita-Salute San Raffaele
Via Olgettina 60, 20132 Milan, Italy
--
IL MIO 5XMILLE VA AL SAN RAFFAELE DI MILANO
PERCHE' QUI LA RICERCA DIVENTA CURA.
CF 07636600962
SE NON QUI, DOVE?
Info: 5xmi...@hsr.it - http://www.5xmille.org/

Disclaimer added by CodeTwo Exchange Rules 2007 
http://www.codetwo.com  

-Messaggio originale-
Da: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] 
Inviato: martedì 29 aprile 2014 18.25
A: Valsasina Paola; Freesurfer@nmr.mgh.harvard.edu
Oggetto: Re: R: R: R: [Freesurfer] Filipping issue


You can't use qdec for this, you will have to use mris_preproc, 
mri_surf2surf, mri_glmfit, and mri_glmfit-sim. The first step is the 
tricky one in that you will have to run mris_preproc twice then merge 
the two data sets.

For the subjects that you want the left hemisphere, run mris_preproc as 
normal

mris_preproc --hemi lh --meas thickness --surfreg 
fsaverage_sym.sphere.reg --s subject1 --s subject2 --o subjects.lh.sm00.mgh

For the right hemi subjects run

mris_preproc --hemi lh --meas thickness --surfreg 
fsaverage_sym.sphere.reg --s subject3/xhemi --s subject4/xhemi --o 
subjects.rh.sm00.mgh

Note above that you still specify --hemi lh but that the subject name 
changes to subject/xhemi

Now concatenate the two files together

mri_concat subjects.lh.sm00.mgh subjects.rh.sm00.mgh --o subjects.sm00.mgh

Then proceed with smoothing, etc. When you do the glm, make sure that 
your FSGD file has the proper order of subjects (above it would be 
subject1, subject2, 3, 4)

doug



On 04/29/2014 12:07 PM, Paola Valsasina wrote:
 Dear Doug,

 I registered with surfreg the hemispheres I would like to analyze. How
 should I proceed now for the final statistical vertex-wise analysis?
 Should I smooth the surfaces and perform between-group comparison with
qdec?
 Thank you in advance
 Paola

 Paola Valsasina, MSc
 Research Fellow
 Neuroimaging Research Unit (Director Prof. M. Filippi)
 Institute of Experimental Neurology, Division of Neuroscience,
 Scientific Institute and University Vita-Salute San Raffaele
 Via Olgettina 60, 20132 Milan, Italy
 --
 IL MIO 5XMILLE VA AL SAN RAFFAELE DI MILANO
 PERCHE' QUI LA RICERCA DIVENTA CURA.
 CF 07636600962
 SE NON QUI, DOVE?
 Info: 5xmi...@hsr.it - http://www.5xmille.org/


 Disclaimer added by CodeTwo Exchange Rules 2007   
 http://www.codetwo.com
   
 -Messaggio originale-
 Da: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
 Inviato: martedì 22 aprile 2014 18.20
 A: Valsasina Paola; Freesurfer@nmr.mgh.harvard.edu
 Oggetto: Re: R: R: [Freesurfer] Filipping issue


 You can register just the hemisphere you want to fsaverage_sym. But if
 you have a subject whose right hemi you want, you would run the surfreg
 with --rh, but later you would specify that you want the lh of
subject/xhemi

 doug

 On 04/22/2014 12:04 PM, Paola Valsasina wrote:
 Sorry, I didn't note I was replying to you only..
 Anyway, thank you for the reply! So I will apply the command I mentioned
 to
 you in my previous e-mail to create flipped RH and LH surfaces for the
 subjects with the right hemisphere affected.
 Should I register to the fsaverage_sym atlas also the subjects I don't
 want
 to flip (i.e., those with the left hemisphere affected), to pool them
 together in the statistic with the flipped subjects?
 Thank you again
 Paola

 Paola Valsasina, MSc
 Research Fellow
 Neuroimaging Research Unit (Director Prof. M. Filippi)
 Institute of Experimental Neurology, Division of Neuroscience,
 Scientific Institute and University Vita-Salute San Raffaele
 Via Olgettina 60, 20132 Milan, Italy


--
 IL MIO 5XMILLE VA AL SAN RAFFAELE DI MILANO
 PERCHE' QUI LA RICERCA DIVENTA CURA.
 CF 07636600962
 SE NON QUI, DOVE?
 Info: 5xmi...@hsr.it - http://www.5xmille.org/


 Disclaimer added by CodeTwo Exchange Rules 2007  
 http://www.codetwo.com   
  
 -Messaggio originale-
 Da: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
 Inviato: martedì 22 aprile 2014 17.56
 A: Valsasina Paola; Freesurfer@nmr.mgh.harvard.edu
 Oggetto: Re: R: [Freesurfer] Filipping issue


 Hi Paola, please remember to post to the list and not to us personally.
 thanks! I would still use the xhemi tools for this. If you have

[Freesurfer] lme and survival (time-to-event) analysis tools on github

2014-05-13 Thread jorge luis

 
Hi everyone

Just wanted to point
out that all the technology required to implement the statistical
methods used in our last paper:

Event time analysis
of longitudinal neuroimage data. Neuroimage. doi:
10.1016/j.neuroimage.2014.04.015.

is available on
github:

https://github.com/NeuroStats

I will try to add
more features when I have some time. There is already a new useful
script included in lme to compute subject-specific random effects for
mass-univariate analyses.

The survival
(time-to-event) statistical analysis toolbox works pretty similar to lme. You 
can
load your neuroimage data from Freesurfer using the scripts in lme:
fs_read_label.m, fs_read_surf.m, fs_read_Y.m  and then perform a
survival analysis alone or a lme-survival joint analysis. 

Hope those tools
help you make new exciting findings!

Cheers
-Jorge___
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Re: [Freesurfer] problem with pial surface reconstruction using T1 (MPRAGE) and T2 (SPACE) weighted images

2014-05-13 Thread Matt Glasser

I don’t know if recon-all will pass those flags in or not.  Probably best
to let Bruce take a look.

Peace,

Matt.

On 5/13/14, 7:36 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:

Hi Emil

I would need the entire subject dir plus the T2-space volume

cheers
Bruce
On Tue, 13 May 
2014, Emil H.J. Nijhuis wrote:

 
 Dear Bruce  Matt,
 thank you for your help.
 
 @Bruce: I would be happy to send you the data, just let me know by
e-mail which files you wo
 uld need.
 
 @Matt: Could you please specify the commands for the flags
-nsigma_above and -nsigma_below a
 nd how you would rerun the pipeline? Also what values would be
recommended?
 
 I did not find any manual/help files regarding the flags, so it would
be helpful to document
  it.
 
 NB. I found another thread in the maillist which probably relates to
the issue: https://mail
 .nmr.mgh.harvard.edu/pipermail//freesurfer/2013-September/033550.html .
However I could not
 verify this, due to expired dropbox files.
 
 Yours,

  Emil
 
 Probably Emil¹s current example would be best because it is failing in
 your recon-all setup.
 
 Matt.
 
 On 5/9/14, 9:31 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:
 
 Hi Matt
 
 if you can send me an example I'll try to find time to take a look
 Bruce
 On Fri, 9 
 May 2014, Matt Glasser wrote:
 
  Hi Bruce,
  
  For whatever reason, sometimes the T2w surface adjustment will be way
 off.
   Adjusting the -nsigma_above # -nsigma_below # even a little bit
up
 and
  down can get it out of the minimum and make it work, so there might
be a
  bug. 
  
  Peace,
  
  Matt.
  
  From: Emil H.J. Nijhuis emil.nijh...@gmail.com
  Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
  Date: Friday, May 9, 2014 at 4:53 AM
  To: freesurfer@nmr.mgh.harvard.edu
  Subject: Re: [Freesurfer] problem with pial surface reconstruction
 using T1
  (MPRAGE) and T2 (SPACE) weighted images
  
  Dear Bruce,
  
  thank you for your help.
  
  attached I have put an fslview, tkmedit screen-shot of the T2 image
and
 a tk
  surfer image of lh.woT2.pial.
  
  It appears that without consideration of the T2 this effect does not
 happen.
  
  What would be your recommendation if I would like to keep using the
T2
 weigh
  ted image?
  
  Yours,
   Emil
  
  Hi Emil
  
  how do the surfaces look before you apply the T2 deformation? And
how do
  they look visualized over the T2 instead of the T1?
  
  cheers
  Bruce
  
  On Thu, 8 May 2014, Emil H.J. Nijhuis wrote:
  
  Hi,
  
  I have been using Freesurfer v5.3 to perform surface reconstruct for
1mm
  isotropic T1 (MPRAGE) and T2 (SPACE) weighted images from a Siemens
3T
 Trio
  scanner with a 32-channel head coil. Unfortunately for half of my
 subjects I
  receive an rather odd pial surface artefact, while the 'white'
surfaces
 do
  not suffer from the same issue.
  
  The command line I have used was:
  
  recon-all -all -subjid subjectid -T2  subjectdir/mri/orig/T2.mgz
 -T2pial
  -3T
  
  Are you familiar with this issue and do you have some advice for me?
  
  Thank you very much for your help.
  
  Yours sincerely,
  
   Emil
  
  --
  --
  Emil H.J. Nijhuis, PhD
  Researcher - Division of Diagnostic and Interventional Neuroradiology
  University Hospital Basel
  Petersgraben 4
  CH 4031 Basel Switzerland
  
  
  
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Re: [Freesurfer] Measuring cortical thickness at a specific location

Hi Panos

I would make an average thickness map in fsaverage space, then in matlab 
divvy up the a-p direction into bins (say 100 of them) and compute the 
average in each bin based on the a/p coordinate

cheers
Bruce
On Tue, 13 May 2014, 
pfot...@nmr.mgh.harvard.edu wrote:

 Hi Bruce,

 Just to clarify, when you say average the thickness along each A/P
 coordinate do you mean by looking up at the average cortical thickness of
 each parcellation and then calculating their average from P-A, or is
 there another way to find the average thickness of each slice and then see
 how that average changes from P-A?
 Thanks again for your time,
 Panos

 I see. Then measure the thickness normally, then see how it changes in
 those directions. You could average the thickness along each A/P
 coordinate
 - that wouldn't be a problem. You just don't want to measure it that way

 cheers
 Bruce


 On Mon, 12 May 2014,
 pfot...@nmr.mgh.harvard.edu wrote:

 Hi Bruce,

 Thank you for your reply. I was interested in looking how the thickness
 changes from the posterior to the anterior side of the brain and vice
 versa (the thickness gradient).

 Thank you again for your time!
 Panos


 Hi Panos

 it would certainly be possible to make that measurement, but it
 wouldn't
 tell you anything biologically interesting. Why would you want to do
 such
 a
 thing? It will reflect the (arbitrary) image slice orientation and not
 the
 brain.

 cheers
 Bruce


 On Mon, 12 May 2014, pfot...@nmr.mgh.harvard.edu wrote:

 Hi FS experts,

 I was wondering whether it would be possible to measure the average
 cortical thickness at a specific slice (either axial, coronal, or
 sagittal). I read in Bruce's paper: Measuring the thickness of the
 human
 cerebral cortex from magnetic resonance images that Measuring the
 thickness from the coronal slice at the point indicated by the green
 cross
 would result in an estimate in excess of 1 cm. Is that always the
 case,
 or has there been a way to bypass that issue?

 Thank you for your time,
 Panos
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[Freesurfer] bbregister surf2vol

2014-05-13 Thread 刘东博

Dear Freesurfer
  I want to use surf2vol to get volume files of gray
thickness.And the --volreg Contains the matrix that maps XYZ in the
reference anatomical to XYZ in the functional volume. So I use
bbregister.Why I need not  invert the BBR registration matrix with
surf2vol?I mean , the BBR registration matrix is  functional to anatomial
volume,the surf2vol need anatomical to XYZ And I use bbregister --s sub1
--mov /sub1/mri/orig.nii --init-fsl --reg/sub1/register.dat --t1;mri_surf2vol
--surfval /sub1/surf/lh.thickness.fwhm0.fsaverage.mgh --hemi lh --surf
pialfs --volreg /sub1/register.dat --outvol ./ --template
/sub1/mri/orig.nii the resluts are 256 volumes.Why this happen?Should the
voulme  be 1 file?
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Re: [Freesurfer] Measuring cortical thickness at a specific location

Hi Bruce,

I see, that's really helpful, thank you!

Best,
Panos


 Hi Panos

 I would make an average thickness map in fsaverage space, then in matlab
 divvy up the a-p direction into bins (say 100 of them) and compute the
 average in each bin based on the a/p coordinate

 cheers
 Bruce
 On Tue, 13 May 2014,
 pfot...@nmr.mgh.harvard.edu wrote:

 Hi Bruce,

 Just to clarify, when you say average the thickness along each A/P
 coordinate do you mean by looking up at the average cortical thickness
 of
 each parcellation and then calculating their average from P-A, or is
 there another way to find the average thickness of each slice and then
 see
 how that average changes from P-A?
 Thanks again for your time,
 Panos

 I see. Then measure the thickness normally, then see how it changes in
 those directions. You could average the thickness along each A/P
 coordinate
 - that wouldn't be a problem. You just don't want to measure it that
 way

 cheers
 Bruce


 On Mon, 12 May 2014,
 pfot...@nmr.mgh.harvard.edu wrote:

 Hi Bruce,

 Thank you for your reply. I was interested in looking how the
 thickness
 changes from the posterior to the anterior side of the brain and vice
 versa (the thickness gradient).

 Thank you again for your time!
 Panos


 Hi Panos

 it would certainly be possible to make that measurement, but it
 wouldn't
 tell you anything biologically interesting. Why would you want to do
 such
 a
 thing? It will reflect the (arbitrary) image slice orientation and
 not
 the
 brain.

 cheers
 Bruce


 On Mon, 12 May 2014, pfot...@nmr.mgh.harvard.edu wrote:

 Hi FS experts,

 I was wondering whether it would be possible to measure the average
 cortical thickness at a specific slice (either axial, coronal, or
 sagittal). I read in Bruce's paper: Measuring the thickness of the
 human
 cerebral cortex from magnetic resonance images that Measuring the
 thickness from the coronal slice at the point indicated by the green
 cross
 would result in an estimate in excess of 1 cm. Is that always the
 case,
 or has there been a way to bypass that issue?

 Thank you for your time,
 Panos
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[Freesurfer] how to save an intensity contour?

2014-05-13 Thread Burke, Sarah

Hello,
I am using the intensity contour tool for defining a white/gray matter border 
of my ROI.
I can adjust my ROI according to this contour and save it. However, the contour 
itself is not saved (to the same layer as the ROI) and will not be loaded when 
opening the ROI layer again later.
Is there a possibility to save the contour (maybe to an extra layer)?

Thank you very much!
Sarah
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Re: [Freesurfer] problems about extracting specific vertex thickness value and getting a average thickness for a specific mask

2014-05-13 Thread charujing123

Hi doug
Thanks doug.
My mask and input mgh file are all fsaverage space.
I try the mri_segstats, and I cannot get what you mean clearly. So I read the 
help of mri_segstats, but neither do I get the information. Then I have to try 
to run this: 
mri_segstats --i ./rh.36sb.10.mgh --mask ./cluster1.mgh --avgwf mytext --seg 
../fsaverage/surf/rh.thickness
But it aborted. I cannot find the problem, although I believe something is 
wrong. Also this command echo this error information:
==
$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
cwd
cmdline mri_segstats --i ./rh.36sb.10.mgh --mask ./cluster1.mgh --avgwf mytext 
--seg ../fsaverage/surf/rh.thickness
sysname  Linux
hostname centos2
machine  x86_64
user psylab16
UseRobust  0
Loading ../fsaverage/surf/rh.thickness
Loading ./rh.36sb.10.mgh
Loading ./cluster1.mgh
NOT INVERTING
There were 83 voxels in the orginal mask
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found   2 segmentations
Computing statistics for each segmentation
  0 0 163759  163759.000
  1 2 83  83.000

Reporting on   2 segmentations
Computing spatial average of each frame
  0  1
Writing to mytext
*** glibc detected *** mri_segstats: malloc(): memory corruption: 0x2e6228f8 ***
=== Backtrace: =
/lib/libc.so.6[0x9e11dd]
/lib/libc.so.6(__libc_malloc+0x67)[0x9e2d97]
/lib/libc.so.6[0x9cf4cf]
/lib/libc.so.6(fopen64+0x2c)[0x9d1a7c]
mri_segstats[0x80536cd]
/lib/libc.so.6(__libc_start_main+0xdc)[0x98ce9c]
mri_segstats(__gxx_personality_v0+0x1c9)[0x804f791]
=== Memory map: 
00958000-00973000 r-xp  fd:00 60785448   
/lib/ld-2.5.so
00973000-00974000 r-xp 0001a000 fd:00 60785448   
/lib/ld-2.5.so
00974000-00975000 rwxp 0001b000 fd:00 60785448   
/lib/ld-2.5.so
00977000-00acb000 r-xp  fd:00 60784655   
/lib/libc-2.5.so
00acb000-00acc000 ---p 00154000 fd:00 60784655   
/lib/libc-2.5.so
00acc000-00ace000 r-xp 00154000 fd:00 60784655   
/lib/libc-2.5.so
00ace000-00acf000 rwxp 00156000 fd:00 60784655   
/lib/libc-2.5.so
00acf000-00ad2000 rwxp 00acf000 00:00 0
00ad4000-00add000 r-xp  fd:00 60784725   
/lib/libcrypt-2.5.so
00add000-00ade000 r-xp 8000 fd:00 60784725   
/lib/libcrypt-2.5.so
00ade000-00adf000 rwxp 9000 fd:00 60784725   
/lib/libcrypt-2.5.so
00adf000-00b06000 rwxp 00adf000 00:00 0
00b22000-00b2d000 r-xp  fd:00 60784686   
/lib/libgcc_s-4.1.2-20080825.so.1
00b2d000-00b2e000 rwxp a000 fd:00 60784686   
/lib/libgcc_s-4.1.2-20080825.so.1
00c68000-00d48000 r-xp  fd:00 56176146   
/usr/lib/libstdc++.so.6.0.8
00d48000-00d4c000 r-xp 000df000 fd:00 56176146   
/usr/lib/libstdc++.so.6.0.8
00d4c000-00d4d000 rwxp 000e3000 fd:00 56176146   
/usr/lib/libstdc++.so.6.0.8
00d4d000-00d53000 rwxp 00d4d000 00:00 0
00d72000-00d84000 r-xp  fd:00 60784662   
/lib/libz.so.1.2.3
00d84000-00d85000 rwxp 00011000 fd:00 60784662   
/lib/libz.so.1.2.3
08048000-08817000 r-xp 08048000 00:00 0
08817000-2e63b000 rwxp 08817000 00:00 0  [heap]
f630-f6321000 rwxp f630 00:00 0
f6321000-f640 ---p f6321000 00:00 0
f6434000-f7cbb000 rwxp f6434000 00:00 0
f7d5c000-f7ea rwxp f7d5c000 00:00 0
f7ea-f7ec7000 r-xp  fd:00 60784705   
/lib/libm-2.5.so
f7ec7000-f7ec8000 r-xp 00026000 fd:00 60784705   
/lib/libm-2.5.so
f7ec8000-f7ec9000 rwxp 00027000 fd:00 60784705   
/lib/libm-2.5.so
f7ec9000-f7ede000 r-xp  fd:00 60784716   
/lib/libpthread-2.5.so
f7ede000-f7edf000 ---p 00015000 fd:00 60784716   
/lib/libpthread-2.5.so
f7edf000-f7ee r-xp 00015000 fd:00 60784716   
/lib/libpthread-2.5.so
f7ee-f7ee1000 rwxp 00016000 fd:00 60784716   
/lib/libpthread-2.5.so
f7ee1000-f7ee3000 rwxp f7ee1000 00:00 0
f7ee3000-f7ee6000 r-xp  fd:00 60784670   
/lib/libdl-2.5.so
f7ee6000-f7ee7000 r-xp 2000 fd:00 60784670   
/lib/libdl-2.5.so
f7ee7000-f7ee8000 rwxp 3000 fd:00 60784670   
/lib/libdl-2.5.so
f7ee8000-f7ee9000 rwxp f7ee8000 00:00 0
f7f0b000-f7f15000 r-xp  fd:00 60784678   
/lib/libnss_files-2.5.so
f7f15000-f7f16000 r-xp 9000 fd:00 60784678   
/lib/libnss_files-2.5.so
f7f16000-f7f17000 rwxp a000 fd:00 60784678

Re: [Freesurfer] how to save an intensity contour?

Hi Sarah

what tool are you using to draw the contour?

Bruce
On Tue, 13 May 2014, Burke, 
Sarah wrote:

 Hello,
 I am using the intensity contour tool for defining a white/gray matter
 border of my ROI.
 I can adjust my ROI according to this contour and save it. However, the
 contour itself is not saved (to the same layer as the ROI) and will not be
 loaded when opening the ROI layer again later.
 Is there a possibility to save the contour (maybe to an extra layer)?
 
 Thank you very much!
 Sarah
 

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Re: [Freesurfer] how to save an intensity contour?

2014-05-13 Thread Burke, Sarah

Hi Bruce, 
in Freeview, I am using the voxel edit tool called Contour. 

Sarah

Van: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] namens Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Verzonden: dinsdag 13 mei 2014 17:29
Aan: Freesurfer support list
Onderwerp: Re: [Freesurfer] how to save an intensity contour?

Hi Sarah

what tool are you using to draw the contour?

Bruce
On Tue, 13 May 2014, Burke,
Sarah wrote:

 Hello,
 I am using the intensity contour tool for defining a white/gray matter
 border of my ROI.
 I can adjust my ROI according to this contour and save it. However, the
 contour itself is not saved (to the same layer as the ROI) and will not be
 loaded when opening the ROI layer again later.
 Is there a possibility to save the contour (maybe to an extra layer)?

 Thank you very much!
 Sarah


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[Freesurfer] question about surf2vol

2014-05-13 Thread gmail


 
 Dear Freesurfer
   I want to use surf2vol to get volume files of gray 
 thickness.And the --volreg Contains the matrix that maps XYZ in the reference 
 anatomical to XYZ in the functional volume. So I use bbregister.Why I need 
 not  invert the BBR registration matrix with surf2vol?I mean , the BBR 
 registration matrix is  functional to anatomial volume,the surf2vol need 
 anatomical to XYZ And I use bbregister --s sub1 --mov /sub1/mri/orig.nii 
 --init-fsl --reg/sub1/register.dat --t1;mri_surf2vol --surfval 
 /sub1/surf/lh.thickness.fwhm0.fsaverage.mgh --hemi lh --surf pialfs --volreg 
 /sub1/register.dat --outvol ./ --template /sub1/mri/orig.nii the resluts are 
 256 volumes.Why this happen?Should the voulme  be 1 file?


Best
   Dongbo Liu___
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Re: [Freesurfer] Measuring cortical thickness at a specific location

Hi Bruce,

Sorry, I had a last follow up question. I just realized that the resulting
bins will be in the fsaverage space, and hence I wouldn't be able to use
mris_anatomical_stats to calculate the average thickness of the bins,
since the fsaverage subject does not have a wm.mgz file. Did you have
another way in mind to calculate the thickness of each bin, or do you
believe that mris_anatomical stats should do the trick with a specific
flag?

Thanks a ton,
Panos

 Hi Bruce,

 I see, that's really helpful, thank you!

 Best,
 Panos


 Hi Panos

 I would make an average thickness map in fsaverage space, then in matlab
 divvy up the a-p direction into bins (say 100 of them) and compute the
 average in each bin based on the a/p coordinate

 cheers
 Bruce
 On Tue, 13 May 2014,
 pfot...@nmr.mgh.harvard.edu wrote:

 Hi Bruce,

 Just to clarify, when you say average the thickness along each A/P
 coordinate do you mean by looking up at the average cortical thickness
 of
 each parcellation and then calculating their average from P-A, or is
 there another way to find the average thickness of each slice and then
 see
 how that average changes from P-A?
 Thanks again for your time,
 Panos

 I see. Then measure the thickness normally, then see how it changes in
 those directions. You could average the thickness along each A/P
 coordinate
 - that wouldn't be a problem. You just don't want to measure it that
 way

 cheers
 Bruce


 On Mon, 12 May 2014,
 pfot...@nmr.mgh.harvard.edu wrote:

 Hi Bruce,

 Thank you for your reply. I was interested in looking how the
 thickness
 changes from the posterior to the anterior side of the brain and vice
 versa (the thickness gradient).

 Thank you again for your time!
 Panos


 Hi Panos

 it would certainly be possible to make that measurement, but it
 wouldn't
 tell you anything biologically interesting. Why would you want to do
 such
 a
 thing? It will reflect the (arbitrary) image slice orientation and
 not
 the
 brain.

 cheers
 Bruce


 On Mon, 12 May 2014, pfot...@nmr.mgh.harvard.edu wrote:

 Hi FS experts,

 I was wondering whether it would be possible to measure the average
 cortical thickness at a specific slice (either axial, coronal, or
 sagittal). I read in Bruce's paper: Measuring the thickness of the
 human
 cerebral cortex from magnetic resonance images that Measuring the
 thickness from the coronal slice at the point indicated by the
 green
 cross
 would result in an estimate in excess of 1 cm. Is that always the
 case,
 or has there been a way to bypass that issue?

 Thank you for your time,
 Panos
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Re: [Freesurfer] Measuring cortical thickness at a specific location

Hi Panos

no, mris_anatomical_stats won't do it. I would map the average thickness 
to fsaverage coords, then load that into matlab and go from there using 
the [xyz] coords of fsaverage for the binning, which is pretty much 
MNI305

cheers
Bruce
On Tue, 13 May 2014, pfot...@nmr.mgh.harvard.edu wrote:

 Hi Bruce,

 Sorry, I had a last follow up question. I just realized that the resulting
 bins will be in the fsaverage space, and hence I wouldn't be able to use
 mris_anatomical_stats to calculate the average thickness of the bins,
 since the fsaverage subject does not have a wm.mgz file. Did you have
 another way in mind to calculate the thickness of each bin, or do you
 believe that mris_anatomical stats should do the trick with a specific
 flag?

 Thanks a ton,
 Panos

 Hi Bruce,

 I see, that's really helpful, thank you!

 Best,
 Panos


 Hi Panos

 I would make an average thickness map in fsaverage space, then in matlab
 divvy up the a-p direction into bins (say 100 of them) and compute the
 average in each bin based on the a/p coordinate

 cheers
 Bruce
 On Tue, 13 May 2014,
 pfot...@nmr.mgh.harvard.edu wrote:

 Hi Bruce,

 Just to clarify, when you say average the thickness along each A/P
 coordinate do you mean by looking up at the average cortical thickness
 of
 each parcellation and then calculating their average from P-A, or is
 there another way to find the average thickness of each slice and then
 see
 how that average changes from P-A?
 Thanks again for your time,
 Panos

 I see. Then measure the thickness normally, then see how it changes in
 those directions. You could average the thickness along each A/P
 coordinate
 - that wouldn't be a problem. You just don't want to measure it that
 way

 cheers
 Bruce


 On Mon, 12 May 2014,
 pfot...@nmr.mgh.harvard.edu wrote:

 Hi Bruce,

 Thank you for your reply. I was interested in looking how the
 thickness
 changes from the posterior to the anterior side of the brain and vice
 versa (the thickness gradient).

 Thank you again for your time!
 Panos


 Hi Panos

 it would certainly be possible to make that measurement, but it
 wouldn't
 tell you anything biologically interesting. Why would you want to do
 such
 a
 thing? It will reflect the (arbitrary) image slice orientation and
 not
 the
 brain.

 cheers
 Bruce


 On Mon, 12 May 2014, pfot...@nmr.mgh.harvard.edu wrote:

 Hi FS experts,

 I was wondering whether it would be possible to measure the average
 cortical thickness at a specific slice (either axial, coronal, or
 sagittal). I read in Bruce's paper: Measuring the thickness of the
 human
 cerebral cortex from magnetic resonance images that Measuring the
 thickness from the coronal slice at the point indicated by the
 green
 cross
 would result in an estimate in excess of 1 cm. Is that always the
 case,
 or has there been a way to bypass that issue?

 Thank you for your time,
 Panos
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Re: [Freesurfer] Measuring cortical thickness at a specific location

Hi Bruce,

I was having issues with the part after that, that is how to calculate the
average thickness of those bins, after I create them. Thanks again
Best,
Panos

 Hi Panos

 no, mris_anatomical_stats won't do it. I would map the average thickness
 to fsaverage coords, then load that into matlab and go from there using
 the [xyz] coords of fsaverage for the binning, which is pretty much
 MNI305

 cheers
 Bruce
 On Tue, 13 May 2014, pfot...@nmr.mgh.harvard.edu wrote:

 Hi Bruce,

 Sorry, I had a last follow up question. I just realized that the
 resulting
 bins will be in the fsaverage space, and hence I wouldn't be able to use
 mris_anatomical_stats to calculate the average thickness of the bins,
 since the fsaverage subject does not have a wm.mgz file. Did you have
 another way in mind to calculate the thickness of each bin, or do you
 believe that mris_anatomical stats should do the trick with a specific
 flag?

 Thanks a ton,
 Panos

 Hi Bruce,

 I see, that's really helpful, thank you!

 Best,
 Panos


 Hi Panos

 I would make an average thickness map in fsaverage space, then in
 matlab
 divvy up the a-p direction into bins (say 100 of them) and compute the
 average in each bin based on the a/p coordinate

 cheers
 Bruce
 On Tue, 13 May 2014,
 pfot...@nmr.mgh.harvard.edu wrote:

 Hi Bruce,

 Just to clarify, when you say average the thickness along each A/P
 coordinate do you mean by looking up at the average cortical
 thickness
 of
 each parcellation and then calculating their average from P-A, or is
 there another way to find the average thickness of each slice and
 then
 see
 how that average changes from P-A?
 Thanks again for your time,
 Panos

 I see. Then measure the thickness normally, then see how it changes
 in
 those directions. You could average the thickness along each A/P
 coordinate
 - that wouldn't be a problem. You just don't want to measure it that
 way

 cheers
 Bruce


 On Mon, 12 May 2014,
 pfot...@nmr.mgh.harvard.edu wrote:

 Hi Bruce,

 Thank you for your reply. I was interested in looking how the
 thickness
 changes from the posterior to the anterior side of the brain and
 vice
 versa (the thickness gradient).

 Thank you again for your time!
 Panos


 Hi Panos

 it would certainly be possible to make that measurement, but it
 wouldn't
 tell you anything biologically interesting. Why would you want to
 do
 such
 a
 thing? It will reflect the (arbitrary) image slice orientation and
 not
 the
 brain.

 cheers
 Bruce


 On Mon, 12 May 2014, pfot...@nmr.mgh.harvard.edu wrote:

 Hi FS experts,

 I was wondering whether it would be possible to measure the
 average
 cortical thickness at a specific slice (either axial, coronal, or
 sagittal). I read in Bruce's paper: Measuring the thickness of
 the
 human
 cerebral cortex from magnetic resonance images that Measuring
 the
 thickness from the coronal slice at the point indicated by the
 green
 cross
 would result in an estimate in excess of 1 cm. Is that always
 the
 case,
 or has there been a way to bypass that issue?

 Thank you for your time,
 Panos
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Re: [Freesurfer] NHP surface reconstruction in FS5.3

2014-05-13 Thread S.V.Shepherd [work]

Just to follow up, it looks like mris_thickness needs to be run, but
mris_curvature is unchanged by changes to the pial surface.  Thanks again
for the help!

stephen

*stephen v. shepherd   phd*
The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA
// 212.327.7620


On Sun, May 11, 2014 at 9:08 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote:

 don't rerun that as it will rerun the surface deformation. Use
 mris_thickness and mris_curvature


 On Sun, 11 May 2014, S.V.Shepherd [work] wrote:

  Looking over our scripts, it appears we normally generates the surfaces
 etc. through
   recon-all -autorecon2-wm ... -noaseg
 despite that ?h.pial isn't explicitly listed as an output in the dev table
 (http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable).

 It looks like a step from autorecon3 might be useful:
   mris_make_surfaces subjID ?h -orig_white ?h.orig orig_pial ?h.pial
 to update the curvature and thickness files without changing the wm and
 pial -- but I'm not
 sure this is how it works.

 stephen

 stephen v. shepherd   phd
 The Rockefeller University / 1230 York Avenue / New York NY 10065-6307
 USA // 212.327.7620


 On Sun, May 11, 2014 at 5:22 PM, S.V.Shepherd [work] 
 stephen.v.sheph...@gmail.com wrote:
   Hi Bruce,

   How would I go about updating the thickness estimates
 (?h.thickness, I presume)
   after manually adjusting the pial surface in FreeView?  Are the
 other surfaces
   (inflated, sphere, etc.) unaffected by this change, or should they
 be
   recalculated as well?

   stephen

 stephen v. shepherd   phd
 The Rockefeller University / 1230 York Avenue / New York NY 10065-6307
 USA //
 212.327.7620


 On Sun, May 11, 2014 at 3:51 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu
 wrote:
   Hi Stephen

   only the thickness estimates should matter, unless you've lost an
 entire
   gyrus or something
   Bruce

   On Sun, 11 May 2014, S.V.Shepherd [work] wrote:

 Hi Bruce,

 This is the manual edit of the pial surface in FreeView,
 correcting locations where the grey
 matter failed to grow out of the white matter. It took place
 after the pipeline had
 completed, but I'm not sure if I need to rerun/regenerate
 steps which are dependent on the
 pial surface. For example, are mris_sphere, mris_curvature,
 and mris_flatten dependent upon
 the pial surface or cortical thickness, or do they work
 directly off the wm/orig surface?
 If the former, I should rerun them; if the latter I don't need
 to do anything but just
 repaint the functional statistics of interest using
 mri_vol2surf and the updated cortical
 bounds (which I presume happens automatically, having
 corrected ?h.pial).

 My comment about morphometry was meant to note that, since I'm
 manually changing the
 distance between the wm and pial surface in places where there
 were medial surface
 artifacts, it would be unwise to try to draw any conclusions
 from comparing
 manually-adjusted and automatically-calculated cortical
 thicknesses.

 stephen




 stephen v. shepherd   phd
 The Rockefeller University / 1230 York Avenue / New York
 NY 10065-6307 USA // 212.327.7620


 On Sun, May 11, 2014 at 9:50 AM, Bruce Fischl
 fis...@nmr.mgh.harvard.edu wrote:
   Hi Stephen

   why do you say it invalidates the morphometry? And we
 need to know what pial
   surface editing you did in order to answer your
 questions (and what recon-all
   steps you rerean)

   cheers
   Bruce


   On Sun, 11 May 2014, S.V.Shepherd [work] wrote:

 Hi Bruce,

 Thanks again for your help at the FreeSurfer
 course. I've corrected
 the pial surface
 manually (knowing that this invalidates the
 morphometry, but that by
 restoring the medial
 surface it does let me process functional data).
 Having done this,
 do I need to remake
 spheres and patches, or are these unchanged?  For
 example, when
 using mri_vol2surf, does
 freesurfer know what elements to sample by
 consulting the ?h.orig
 and ?h.pial, or are there
 downstream files I should update as well?

 Thanks!

 stephen

Re: [Freesurfer] Quesion about lobar volumes

Just use mri_binarize
doug

On 05/07/2014 05:08 PM, pfot...@nmr.mgh.harvard.edu wrote:
 Hi Doug,

 That sounds great! I'll go ahead and do that. I would just be interested
 in coming up with the binary maps of the lobes, not their associated
 stats. Should I still go ahead and use mri_segstats or should I use
 mri_binarize with the --match flag and the new color map instead?
 Thanks for all your help,
 Panos


 you'll need to get the code associated with each lobe. You can do this
 by running
 tkmedit subject nu.mgz -seg lobeseg.mgz -aux lobeseg.mgz

 This will show colors for the seg, but the names will be wrong. Click on
 a seg and see what number it gets in the aux. Then create a new color
 table to match, then run mri_segstats

 doug

 On 05/07/2014 04:51 PM, pfot...@nmr.mgh.harvard.edu wrote:
 Hi Doug,

 Thanks for your help, the mri_aparc2aseg command worked fine. In
 addition,
 is there a way to get a binary volume for each of the lobes based on the
 result of the mri_aparc2aseg command?
 In other parcellation volumes, I would use mri_binarize and the
 FreeSurferColorLUT.txt table but here I coudn't think how this could be
 applicable.

 Thanks again,
 Panos


 Try using mri_aparc2aseg instead of label2vol. See the --help and/or
 look in the recon-all.log file to get the command line used to create
 the aparc+aseg.mgz file
 doug

 On 05/07/2014 11:12 AM, pfot...@nmr.mgh.harvard.edu wrote:
 Hi FS Community,

 I created a lobes annotation file with the --lobesStrict flag of the
 mri_annotation2label and then converted it to a volume with the
 mri_label2vol command and the --annot flag. However, the resulting
 volume
 is just overlapping on top of the white surface, and not on the whole
 cortex. Is there a way to create a volume for the lobes that covers
 the
 whole cerebral cortex? That is a volume that shows you which part of
 the
 cerebral cortex belongs to each of the 6 lobes individually?

 Thank you in advance,
 Panos
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 --
 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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 --
 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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-- 
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] LOOK FOR HELP


surf2vol understands which direction the registration goes and applies 
it appropriately. Use --outvol thicknessvolume.nii to get a single nifti 
file output


On 05/07/2014 10:22 PM, 刘东博 wrote:
 Dear Greve
 Thank you for your reply
 I want to use surf2vol to get volume files of gray thickness.And
 the --volreg Contains the matrix that maps XYZ in the reference anatomical
 to XYZ in the functional volume. So I use bbregister.Why I need not invert
 the BBR registration matrix with surf2vol?I mean , the BBR registration
 matrix is functional to anatomial volume,the surf2vol need anatomical to
 XYZ And I use bbregister --s sub1 --mov /sub1/mri/orig.nii --init-fsl
 --reg/sub1/register.dat
 --t1;mri_surf2vol --surfval /sub1/surf/lh.thickness.fwhm0.fsaverage.mgh
 --hemi lh --surf pialfs --volreg /sub1/register.dat --outvol ./ --template
 /sub1/mri/orig.nii
 the resluts are 256 volumes.Why this happen?Should the voulme be 1 file?


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Re: [Freesurfer] Fwd: extracting rois for connectivity analysis


This is a very vague request. What kind of connectivity analysis? fMRI 
or DTI? What software are you using?


On 05/08/2014 05:43 AM, Jutta Ernst wrote:


 Dear Freesurfer's

 I draw a roi to extract the cortical thickness for my two groups and 
 that worked fine.
 Now I'm trying to export the very same roi to use it for further 
 connectivity analysis.
 Can anyone please help me and tell me how to do it?
 Thanks in advance!! :-)

 Cheers
 Jutta



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Re: [Freesurfer] Fwd: extracting rois for connectivity analysis

Sorry, I was going through old emails and did not see this had already 
been addressed. Please ignore, which I'm sure most of you were doing 
anyway :-)


On 05/13/2014 01:37 PM, Douglas N Greve wrote:
 This is a very vague request. What kind of connectivity analysis? fMRI
 or DTI? What software are you using?


 On 05/08/2014 05:43 AM, Jutta Ernst wrote:

 Dear Freesurfer's

 I draw a roi to extract the cortical thickness for my two groups and
 that worked fine.
 Now I'm trying to export the very same roi to use it for further
 connectivity analysis.
 Can anyone please help me and tell me how to do it?
 Thanks in advance!! :-)

 Cheers
 Jutta



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Re: [Freesurfer] NHP surface reconstruction in FS5.3


the pial curvatures will change, but you probably don't use them anyway

cheers
Bruce


On Tue, 13 May 2014, S.V.Shepherd [work] wrote:


Just to follow up, it looks like mris_thickness needs to be run, but
mris_curvature is unchanged by changes to the pial surface.  Thanks again
for the help!

stephen

stephen v. shepherd   phd
The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA
// 212.327.7620


On Sun, May 11, 2014 at 9:08 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:
  don't rerun that as it will rerun the surface deformation. Use
  mris_thickness and mris_curvature

  On Sun, 11 May 2014, S.V.Shepherd [work] wrote:

Looking over our scripts, it appears we normally
generates the surfaces etc. through
  recon-all -autorecon2-wm ... -noaseg
despite that ?h.pial isn't explicitly listed as an
output in the dev table
(http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable).

It looks like a step from autorecon3 might be
useful:
  mris_make_surfaces subjID ?h -orig_white ?h.orig
orig_pial ?h.pial
to update the curvature and thickness files without
changing the wm and pial -- but I'm not
sure this is how it works.

stephen

stephen v. shepherd   phd
The Rockefeller University / 1230 York Avenue / New
York NY 10065-6307 USA // 212.327.7620


On Sun, May 11, 2014 at 5:22 PM, S.V.Shepherd [work]
stephen.v.sheph...@gmail.com wrote:
      Hi Bruce,

      How would I go about updating the thickness
estimates (?h.thickness, I presume)
      after manually adjusting the pial surface in
FreeView?  Are the other surfaces
      (inflated, sphere, etc.) unaffected by this
change, or should they be
      recalculated as well?

      stephen

stephen v. shepherd   phd
The Rockefeller University / 1230 York Avenue / New
York NY 10065-6307 USA //
212.327.7620


On Sun, May 11, 2014 at 3:51 PM, Bruce Fischl
fis...@nmr.mgh.harvard.edu wrote:
      Hi Stephen

      only the thickness estimates should matter,
unless you've lost an entire
      gyrus or something
      Bruce

      On Sun, 11 May 2014, S.V.Shepherd [work]
wrote:

            Hi Bruce,

            This is the manual edit of the pial
surface in FreeView,
            correcting locations where the grey
            matter failed to grow out of the white
matter. It took place
            after the pipeline had
            completed, but I'm not sure if I need to
rerun/regenerate
            steps which are dependent on the
            pial surface. For example, are
mris_sphere, mris_curvature,
            and mris_flatten dependent upon
            the pial surface or cortical thickness,
or do they work
            directly off the wm/orig surface? 
            If the former, I should rerun them; if
the latter I don't need
            to do anything but just
            repaint the functional statistics of
interest using
            mri_vol2surf and the updated cortical
            bounds (which I presume happens
automatically, having
            corrected ?h.pial).

            My comment about morphometry was meant
to note that, since I'm
            manually changing the
            distance between the wm and pial surface
in places where there
            were medial surface
            artifacts, it would be unwise to try to
draw any conclusions
            from comparing
            manually-adjusted and
automatically-calculated cortical
            thicknesses.

            stephen




            stephen v. shepherd   phd
            The Rockefeller University / 1230 York
Avenue / New York
            NY 10065-6307 USA // 212.327.7620


            On Sun, May 11, 2014 at 9:50 AM, Bruce
Fischl
            fis...@nmr.mgh.harvard.edu wrote:
                  Hi Stephen

                  why do you say it invalidates the
morphometry? And we
            need to know what pial
                  surface editing you did in order
to

Re: [Freesurfer] Subcortical volume calculation from aparc+aseg.mgz?


The partial volume correction is done based on the intensity and label 
of the surrounding voxels. By using aparc+aseg you change the label of 
the surrounding structures and it changes the PV correction. Use 
aseg.mgz and not aparc+aseg
doug

On 05/09/2014 05:27 AM, Schreiber, Stefanie wrote:
 Dear all,

 For the evaluation of the subcortical volumes we executed ‘mri_segstats’ on 
 ‘aseg.mgz’ and for comparison on ‘aparc+aseg.mgz’ in a number of individuals. 
 Apparently the volume of subcortical structures, like the hippocampus, is 
 calculated as the same values if calculated (without partial volume 
 correction) from ‘aseg.mgz’ and ‘aparc+aseg.mgz’.
 However, when partial volume correction is applied, the resulting values for 
 e.g. hippocampal volumes differ between the ‘mri_segstats’ calculation for 
 ‘aseg.mgz’ and ‘aparc+aseg.mgz’. How could those differences resulting from 
 the partial volume correction in these cases be explained?

 The command used to calculate the subcortical volumes with partial volume 
 correction was:
 mri_segstats --seg ./mri/aparc+aseg.mgz --ctab 
 $FREESURFER_HOME/FreeSurferColorLUT.txt --excludeid 0 --sum 
 ./stats/my.test.stats --pv ./mri/norm.mgz

 Previously we have been using the subcortical volumes from ‘aseg.stats’, 
 which, as I understand it, is generated by recon-all from ‘aseg.mgz’ via 
 ‘mri_segstats’ (with partial volume correction).  From your experience, would 
 it be also valid to use subcortical volumes generated by applying 
 ‘mri_segstats’ (with partial volume correction) on ‘aparc+aseg.mgz’, even 
 though the resulting values might differ from the values in aseg.stats?

 Thank you very much in advance,

 Steffi Schreiber


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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] mri_surf2surf

You can't use analyze for this. mgh format will work. nii might work

On 05/13/2014 04:37 AM, Caka wrote:
 Dear Doug and All,

 I want to register the individual subject surface into the fsaverage surface. 
 I used mdi_surf2surf command. But one error occurred. Could you please help 
 me with this. Here are the scripts:

 —

 [root@localhost sub001]# mri_surf2surf --hemi lh --srcsubject sub001 
 --srcsurfval thickness --src_type curv --trgsubject fsaverage --trgsurfval 
 ./sub001-thickness-lh.img
 srcsubject = sub001
 srcval = thickness
 srctype= curv
 trgsubject = fsaverage
 trgval = ./sub001-thickness-lh.img
 trgtype=
 srcsurfreg = sphere.reg
 trgsurfreg = sphere.reg
 srchemi= lh
 trghemi= lh
 frame  = 0
 fwhm-in= 0
 fwhm-out   = 0
 label-src  = (null)
 label-trg  = (null)
 OKToRevFaceOrder  = 1
 Reading source surface reg 
 /disk250/data_analysis/data_female_male_140/sub001/surf/lh.sphere.reg
 Loading source data
 Reading curvature file 
 /disk250/data_analysis/data_female_male_140/sub001/surf/lh.thickness
 Reading target surface reg 
 /disk250/data_analysis/data_female_male_140/fsaverage/surf/lh.sphere.reg
 Done
 Mapping Source Volume onto Source Subject Surface
 surf2surf_nnfr: building source hash (res=16).
 Surf2Surf: Forward Loop (163842)

 surf2surf_nnfr: building target hash (res=16).
 Surf2Surf: Reverse Loop (132230)
 Reverse Loop had 21224 hits
 Surf2Surf: Dividing by number of hits (163842)
 INFO: nSrcLost = 0
 nTrg121 = 146822, nTrgMulti = 17020, MnTrgMultiHits = 2.247
 nSrc121 = 93121, nSrcLost = 0, nSrcMulti = 39109, MnSrcMultiHits = 2.35099
 Saving target data
 Saving to ./sub001-thickness-lh.img
 ANALYZE FORMAT ERROR: ncols 163842 in volume exceeds 32768
 —

 Thank you very much!

 Qiongmin





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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] Viewing functional data on the inflated brain

Sorry, I've totally lost the thread on this one. Can you send the
command line, the terminal output, and the log file again?
doug

On 05/12/2014 04:11 PM, Sherryse Corrow wrote:
Hi Douglas,

I don’t receive any emails from anyone, I only receive the the digest
which is what I “reply” to. So I am not sure what you mean by “try
responding to the email that I sent.” This is why I attempted to email
you directly as I thought that is what you were asking for.

I hope to have straightened things out by finding each part of our
conversation and pasting them below (in reverse order). If you have
further questions, please let me know.

Sincerely,
Sherryse

Message: 9
Date: Fri, 09 May 2014 17:36:36 -0400
From: Douglas N Greve gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Viewing functional data on the inflated
brain
To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu
Message-ID: 536d4a64.5000...@nmr.mgh.harvard.edu
mailto:536d4a64.5000...@nmr.mgh.harvard.edu
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

both of what? Sorry, it looks like the thread was garbled below or
somehow the digest got into it. Try responding to the email that I sent
to keep things in order

On 05/09/2014 05:09 PM, Sherryse Corrow wrote:
Thanks Douglas. Yes, both of those exist.

Douglas N Greve
http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.eduq=from:%22Douglas+N+Greve%22

Wed, 07 May 2014 12:51:02 –0700
http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.eduq=date:20140507

It is looking for subject P143 in /usr/local/freesurfer/subjects

Does it exist? If so, does
/usr/local/freesurfer/subjects/P143/mri/brainmask.mgz
Exist?

Sherryse Corrow
http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.eduq=from:%22Sherryse+Corrow%22

Wed, 07 May 2014 11:00:54 -0700
http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.eduq=date:20140507

Thanks Douglas. We tried that . . . The registration matrix that we need
is not created. Here is the output log file (attached). I am a bit new to
this so I am hoping it has the information you need. After taking a quick
glance at the log file, we noticed there are errors in the log file.
Step by step, this is what we did after we ran recon-all:
Reg-feat2anat ‹feat OurFeatDirectory.feat ‹subject P143

When we open the folder experiment.feat/reg/freesurfer, there is no
anat2exf.register.dat file. However, there is a file called:
anat2exf.register.dat.init.

Thanks,
Sherryse

Douglas Greve
http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.eduq=from:%22Douglas+Greve%22

Mon, 05 May 2014 19:58:31 –0700
http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.eduq=date:20140505

Run reg-feat2anat. If that does not work, then send the command line
and terminal output. Just saying that something does not work will not
get you closer to a solution. We need to know what you did and what
happened

Doug

Sherryse Corrow
http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.eduq=from:%22Sherryse+Corrow%22

Mon, 05 May 2014 16:56:58 –0700
http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.eduq=date:20140505

Hi all,

Earlier today, I posted the message listed below. However, we discovered
part
of our issue. When we run reg-feat2anat, there is no anat2exf.register.dat
file created. Therefore, we have no registration matrix to use. Before, we
were inadvertently using the anat2std file instead. Any suggestions on how to
get the anat2exf.register.dat file created?
Thanks,
Sherryse

Douglas Greve
http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.eduq=from:%22Douglas+Greve%22

Mon, 05 May 2014 19:50:18 –0700
http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.eduq=date:20140505

Can you tell us specifically what you have done? I mean command lines …

doug

Sherryse Corrow
http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.eduq=from:%22Sherryse+Corrow%22

Mon, 05 May 2014 15:58:35 -0700
http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.eduq=date:20140505

Dear FreeSurfer community,

We are having some issues registering our functional data (or masks) from FSL
to an inflated brain in FreeSurfer. Some of our masks, when registered to the
inflated brain and viewed in FreeSurfer, are not showing up on the cortical
surface. We have followed web-tutorials for registration but are still having
the issue. Any suggestions?

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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
FileDrop:

Re: [Freesurfer] nonlinear models in longitudinal analysis

2014-05-13 Thread Martin Reuter

Hi Jodie,

are you familiar with mixed effects models? If not I would recommend you 
include a biostatistician.
What I mean (and you can do this in the matlab code, no need to include 
it in the qdec file) is to use a piecewise linear model.

So for a subject with visits at 0, 0.4 and 0.9 years you would have this 
design matrix:

1  0 0
1  0.4  0
1  0.9  0.5

your model could be like this:
Y_ij = beta0 + b_i + beta1 x_ij + beta2 z_ij +e_ij

(i is subject index, j is time point: 1,2,3)

where you have a random effect b_i for a subject specific intercept, 
x_ij is years and z_ij is the third column in your matrix:
z_i1 = 0
z_i2 = 0
z_i3 = x_i3 - x_i2

for hypothesis testing contrast, see my email below.

Best, Martin

On 05/12/2014 01:14 PM, Jodie Davies-Thompson wrote:
 Hi Martin,

 Thanks for your reply. I'm not entirely sure what you mean (sorry - I'm new 
 to this!). Do you mean something like this?

 For examining an increase between timepoint 1 and 2, but the same between 
 timepoint 2 and 3?

 fsid   fsid-base   years   years-to-years
 Day1   base   0   0.4
 Day2   base   0.4   0.4
 Day3   base   0.8   0

 All the best,
 Jodie



 Message: 6
 Date: Fri, 09 May 2014 16:52:25 -0400
 From: Martin Reuter mreu...@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] nonlinear models in longitudinal analysis
 To: freesurfer@nmr.mgh.harvard.edu
 Message-ID: 536d4009.7030...@nmr.mgh.harvard.edu
 Content-Type: text/plain; charset=ISO-8859-1; format=flowed

 Hi Jodie,

 'years' should contain the real time between time points (usually,
 unless you have test-retest where time is irrelevant, or different task
 that can be ordered as you like). For what you are trying to do you
 should use linear mixed effects models with a piecewise linear setup.
 This will allow you to estimate a slope before and after timepoint 2 and
 compare those slopes.
 Your design matrix would probably have the column of 1, years and a
 column with
 years-years(at tp2 of that subject)   if that value is positive
 0 otherwise

 Testing if the coef of the 3rd column is  0 is asking if the slope
 increases in the second interval. Not exactly what you want, but close
 and of course you can test if the slope in interval 1 is different from
 zero (second column) and if the slope in interval 2 is different from
 zero ( 0 1 1, ie the sum of the last two columns).

 Best, Martin

 On 05/08/2014 03:48 PM, Jodie Davies-Thompson wrote:
 Dear Freesurfer experts,

 I am attempting to do a longitudinal analysis of cortical thickness with 3 
 timepoints. So far, I have successfully completed the analysis for 
 long_mris_slopes comparing timepoint 1 to timepoint 2, timepoint 2 to 
 timepoint 3, and a linear increase for timepoint 1 to 2 to 3.

 However, I am primarily interested in finding regions which show a) an 
 increase between timepoint 1 and 2, but no difference between 2 and 3, and 
 b) no difference between timepoint 1 and 2, but an increase between 2 and 3.

 Would the correct way of 'modelling' these two in the qdec file be:

 a)
 fsid fsid-base years
 day1 base 0
 day2 base 3
 day3 base 3

 and b)
 fsid fsid-base years
 day1 base 0
 day2 base 0
 day3 base 3

 All the best,
 Jodie

 -
 ---
 Jodie Davies-Thompson, Postdoctoral Fellow
 Department of Ophthalmology  Visual Sciences
 UBC/VGH Eye Care Centre
 2550 Willow Street
 Vancouver, BC, V5Z 3N9
 Canada
 Tel: 604-875-4111 ext 69003

 -
 ---
 Jodie Davies-Thompson, Postdoctoral Fellow
 Department of Ophthalmology  Visual Sciences
 UBC/VGH Eye Care Centre
 2550 Willow Street
 Vancouver, BC, V5Z 3N9
 Canada
 Tel: 604-875-4111 ext 69003



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-- 
Martin Reuter, Ph.D.

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

A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129

Phone: +1-617-724-5652
Email:
mreu...@nmr.mgh.harvard.edu
reu...@mit.edu
Web  : http://reuter.mit.edu

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Re: [Freesurfer] Coomand not found

2014-05-13 Thread Z K

Not exactly sure why your getting a permission denied error. Can you 
please try the following and provide us with the relevant output?

1) What is the output of the following:
ls -ld $FREESURFER_HOME/bin

2) After sourcing FreeSurfer, what happens when you type:
tkmedit -f $SUBJECTS_DIR/sample-001.mgz

3) Does freeview open (just type 'freeview' after sourcing FreeSurfer)?

-Zeke

On 05/13/2014 06:51 AM, Francesca Strappini wrote:
 Sure, thanks!

 tcsh
 shalim-ubunut:/media/Shared_Data/freesurfer setenv FREESURFER_HOME
 /media/Shared_Data/freesurfer
 shalim-ubunut:/media/Shared_Data/freesurfer source
 $FREESURFER_HOME/SetUpFreeSurfer.csh

  freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 
 Setting up environment for FreeSurfer/FS-FAST (and FSL)
 FREESURFER_HOME   /media/Shared_Data/freesurfer
 FSFAST_HOME   /media/Shared_Data/freesurfer/fsfast
 FSF_OUTPUT_FORMAT nii.gz
 SUBJECTS_DIR  /media/Shared_Data/freesurfer/subjects
 MNI_DIR   /media/Shared_Data/freesurfer/mni

 shalim-ubunut:/media/Shared_Data/freesurfer pwd
 /media/Shared_Data/freesurfer

 shalim-ubunut:/media/Shared_Data/freesurfer tkmedit bert orig.mgz
 /media/Shared_Data/freesurfer/bin/tkmedit: Permission denied.

 shalim-ubunut:/media/Shared_Data/freesurfer sudo tkmedit bert orig.mgz
 sudo: tkmedit: command not found

 shalim-ubunut:/media/Shared_Data/freesurfer/bin ls -la tkmedit
 -rwxrwxrwx 1 francesca francesca 102 May 14  2013 tkmedit

 2014-05-12 18:52 GMT+03:00 Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu:
 Ok, could you send the entire terminal output?
 Thanks.
 -Louis

 On Mon, 12 May 2014, Francesca Strappini wrote:

 Thanks Louis!

 Yes, I did run tkmedit from the same terminal window I have sourced
 freesurfer...

 Francesca

 2014-05-12 16:57 GMT+03:00 Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu:
 Hi Francesca,
 Are you trying to run the tkmedit command in the same terminal window you
 have sourced freesurfer?  You'll need to source freesurfer in any new
 terminal window you open before being able to run any freesurfer commands.

 It's possible to set it up so that freesurfer is sourced automatically
 when opening a new terminal or setting up an alias to make the process
 quicker.
 -Louis

 On Sat, 10 May 2014, Francesca Strappini wrote:

 Hi, I'm just starting out with freesurfer. I downloaded CentOS6_x86_64
 and I have Ubuntu 12.04 LTS. I have set up the licence file and
 configured freesurfer:

 tcsh
 setenv FREESURFER_HOME /media/Shared_Data/freesurfer
 source $FREESURFER_HOME/SetUpFreeSurfer.csh

  freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 
 Setting up environment for FreeSurfer/FS-FAST (and FSL)
 FREESURFER_HOME   /media/Shared_Data/freesurfer
 FSFAST_HOME   /media/Shared_Data/freesurfer/fsfast
 FSF_OUTPUT_FORMAT nii.gz
 SUBJECTS_DIR  /media/Shared_Data/freesurfer/subjects
 MNI_DIR   /media/Shared_Data/freesurfer/mni

 When I try to run any type of command, like tkmedit bert orig.mgz, I
 get this error:

 command not found.

 Thanks for the help!

 Francesca
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 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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[Freesurfer] Freeview/Freesurfer Version Compatibility

2014-05-13 Thread Sarah Blankenship

During the Spring Freesurfer workshop the newest version of Freeview was
used as the primary viewing tool.  Are there compatibility issues with
using the newest version of Freeview while running analyses in an older
version of Freesurfer (v5.1.0)?  That is, if you run recon-all through
v5.1.0, can you view and make manual edits using the newest release of
Freeview (11 May 2014 build) or should you only use the Freeview build that
is specific to your Freesurfer version (22 May 2011 build for 5.1.0)?

Thank you,
Sarah Blankenship
Graduate Research Assistant
Neuroscience and Cognitive Science Program
University of Maryland, College Park
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Re: [Freesurfer] R: R: R: R: Filipping issue


Sorry, in both of those mris_preproc commands add

--target fsaverage_sym

doug


On 05/13/2014 09:48 AM, Paola Valsasina wrote:
 Dear Doug,

 I am trying to run mris_preproc as you indicated, but it fails with the
 following error:

 MRISread($SUBJECTS_DIR/fsaverage/surf/lh.fsaverage_sym.sphere.reg): could
 not open file.

 Why is target file searched in the fsaverage folder? I was expecting it is
 searched in the fsaverage_sym folder?

 Thank you in advance
 Kind regards
 Paola


 Paola Valsasina, MSc
 Research Fellow
 Neuroimaging Research Unit (Director Prof. M. Filippi)
 Institute of Experimental Neurology, Division of Neuroscience,
 Scientific Institute and University Vita-Salute San Raffaele
 Via Olgettina 60, 20132 Milan, Italy
 --
 IL MIO 5XMILLE VA AL SAN RAFFAELE DI MILANO
 PERCHE' QUI LA RICERCA DIVENTA CURA.
 CF 07636600962
 SE NON QUI, DOVE?
 Info: 5xmi...@hsr.it - http://www.5xmille.org/

 Disclaimer added by CodeTwo Exchange Rules 2007   
 http://www.codetwo.com
   
 -Messaggio originale-
 Da: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
 Inviato: martedì 29 aprile 2014 18.25
 A: Valsasina Paola; Freesurfer@nmr.mgh.harvard.edu
 Oggetto: Re: R: R: R: [Freesurfer] Filipping issue


 You can't use qdec for this, you will have to use mris_preproc,
 mri_surf2surf, mri_glmfit, and mri_glmfit-sim. The first step is the
 tricky one in that you will have to run mris_preproc twice then merge
 the two data sets.

 For the subjects that you want the left hemisphere, run mris_preproc as
 normal

 mris_preproc --hemi lh --meas thickness --surfreg
 fsaverage_sym.sphere.reg --s subject1 --s subject2 --o subjects.lh.sm00.mgh

 For the right hemi subjects run

 mris_preproc --hemi lh --meas thickness --surfreg
 fsaverage_sym.sphere.reg --s subject3/xhemi --s subject4/xhemi --o
 subjects.rh.sm00.mgh

 Note above that you still specify --hemi lh but that the subject name
 changes to subject/xhemi

 Now concatenate the two files together

 mri_concat subjects.lh.sm00.mgh subjects.rh.sm00.mgh --o subjects.sm00.mgh

 Then proceed with smoothing, etc. When you do the glm, make sure that
 your FSGD file has the proper order of subjects (above it would be
 subject1, subject2, 3, 4)

 doug



 On 04/29/2014 12:07 PM, Paola Valsasina wrote:
 Dear Doug,

 I registered with surfreg the hemispheres I would like to analyze. How
 should I proceed now for the final statistical vertex-wise analysis?
 Should I smooth the surfaces and perform between-group comparison with
 qdec?
 Thank you in advance
 Paola

 Paola Valsasina, MSc
 Research Fellow
 Neuroimaging Research Unit (Director Prof. M. Filippi)
 Institute of Experimental Neurology, Division of Neuroscience,
 Scientific Institute and University Vita-Salute San Raffaele
 Via Olgettina 60, 20132 Milan, Italy
 --
 IL MIO 5XMILLE VA AL SAN RAFFAELE DI MILANO
 PERCHE' QUI LA RICERCA DIVENTA CURA.
 CF 07636600962
 SE NON QUI, DOVE?
 Info: 5xmi...@hsr.it - http://www.5xmille.org/


 Disclaimer added by CodeTwo Exchange Rules 2007  
 http://www.codetwo.com   
  
 -Messaggio originale-
 Da: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
 Inviato: martedì 22 aprile 2014 18.20
 A: Valsasina Paola; Freesurfer@nmr.mgh.harvard.edu
 Oggetto: Re: R: R: [Freesurfer] Filipping issue


 You can register just the hemisphere you want to fsaverage_sym. But if
 you have a subject whose right hemi you want, you would run the surfreg
 with --rh, but later you would specify that you want the lh of
 subject/xhemi
 doug

 On 04/22/2014 12:04 PM, Paola Valsasina wrote:
 Sorry, I didn't note I was replying to you only..
 Anyway, thank you for the reply! So I will apply the command I mentioned
 to
 you in my previous e-mail to create flipped RH and LH surfaces for the
 subjects with the right hemisphere affected.
 Should I register to the fsaverage_sym atlas also the subjects I don't
 want
 to flip (i.e., those with the left hemisphere affected), to pool them
 together in the statistic with the flipped subjects?
 Thank you again
 Paola

 Paola Valsasina, MSc
 Research Fellow
 Neuroimaging Research Unit (Director Prof. M. Filippi)
 Institute of Experimental Neurology, Division of Neuroscience,
 Scientific Institute and University Vita-Salute San Raffaele
 Via Olgettina 60, 20132 Milan, Italy


 --
 IL MIO 5XMILLE VA AL SAN RAFFAELE DI MILANO
 PERCHE' QUI LA RICERCA DIVENTA CURA.
 CF 07636600962
 SE NON QUI, DOVE?
 Info: 5xmi...@hsr.it - http://www.5xmille.org/


 Disclaimer added by CodeTwo Exchange Rules 2007 
 http://www.codetwo.com  
 
 -Messaggio originale-
 Da: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
 Inviato: martedì 22 aprile 2014 17.56
 A: Valsasina Paola; Freesurfer@nmr.mgh.harvard.edu
 Oggetto:

Re: [Freesurfer] problems about extracting specific vertex thickness value and getting a average thickness for a specific mask


There are a lot of things that I don't understand about your command 
line. Why are you passing the thickness as the segmentation? The mask 
only limits the computations to be inside the mask. What precisely are 
you trying to do?




On 05/13/2014 11:27 AM, charujing123 wrote:
 Hi doug
 Thanks doug.
 My mask and input mgh file are all fsaverage space.
 I try the mri_segstats, and I cannot get what you mean clearly. So I 
 read the help of mri_segstats, but neither do I get the information. 
 Then I have to try to run this:
 *mri_segstats --i ./rh.36sb.10.mgh --mask ./cluster1.mgh --avgwf 
 mytext --seg ../fsaverage/surf/rh.thickness*
 But it aborted. I cannot find the problem, although I believe 
 something is wrong. Also this command echo this error information:
 ==
 $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
 cwd
 cmdline mri_segstats --i ./rh.36sb.10.mgh --mask ./cluster1.mgh 
 --avgwf mytext --seg ../fsaverage/surf/rh.thickness
 sysname Linux
 hostname centos2
 machine x86_64
 user psylab16
 UseRobust 0
 Loading ../fsaverage/surf/rh.thickness
 Loading ./rh.36sb.10.mgh
 Loading ./cluster1.mgh
 NOT INVERTING
 There were 83 voxels in the orginal mask
 Voxel Volume is 1 mm^3
 Generating list of segmentation ids
 Found 2 segmentations
 Computing statistics for each segmentation
 0 0 163759 163759.000
 1 2 83 83.000
 Reporting on 2 segmentations
 Computing spatial average of each frame
 0 1
 Writing to mytext
 *** glibc detected *** mri_segstats: malloc(): memory corruption: 
 0x2e6228f8 ***
 === Backtrace: =
 /lib/libc.so.6[0x9e11dd]
 /lib/libc.so.6(__libc_malloc+0x67)[0x9e2d97]
 /lib/libc.so.6[0x9cf4cf]
 /lib/libc.so.6(fopen64+0x2c)[0x9d1a7c]
 mri_segstats[0x80536cd]
 /lib/libc.so.6(__libc_start_main+0xdc)[0x98ce9c]
 mri_segstats(__gxx_personality_v0+0x1c9)[0x804f791]
 === Memory map: 
 00958000-00973000 r-xp  fd:00 60785448 /lib/ld-2.5.so
 00973000-00974000 r-xp 0001a000 fd:00 60785448 /lib/ld-2.5.so
 00974000-00975000 rwxp 0001b000 fd:00 60785448 /lib/ld-2.5.so
 00977000-00acb000 r-xp  fd:00 60784655 /lib/libc-2.5.so
 00acb000-00acc000 ---p 00154000 fd:00 60784655 /lib/libc-2.5.so
 00acc000-00ace000 r-xp 00154000 fd:00 60784655 /lib/libc-2.5.so
 00ace000-00acf000 rwxp 00156000 fd:00 60784655 /lib/libc-2.5.so
 00acf000-00ad2000 rwxp 00acf000 00:00 0
 00ad4000-00add000 r-xp  fd:00 60784725 /lib/libcrypt-2.5.so
 00add000-00ade000 r-xp 8000 fd:00 60784725 /lib/libcrypt-2.5.so
 00ade000-00adf000 rwxp 9000 fd:00 60784725 /lib/libcrypt-2.5.so
 00adf000-00b06000 rwxp 00adf000 00:00 0
 00b22000-00b2d000 r-xp  fd:00 60784686 
 /lib/libgcc_s-4.1.2-20080825.so.1
 00b2d000-00b2e000 rwxp a000 fd:00 60784686 
 /lib/libgcc_s-4.1.2-20080825.so.1
 00c68000-00d48000 r-xp  fd:00 56176146 /usr/lib/libstdc++.so.6.0.8
 00d48000-00d4c000 r-xp 000df000 fd:00 56176146 /usr/lib/libstdc++.so.6.0.8
 00d4c000-00d4d000 rwxp 000e3000 fd:00 56176146 /usr/lib/libstdc++.so.6.0.8
 00d4d000-00d53000 rwxp 00d4d000 00:00 0
 00d72000-00d84000 r-xp  fd:00 60784662 /lib/libz.so.1.2.3
 00d84000-00d85000 rwxp 00011000 fd:00 60784662 /lib/libz.so.1.2.3
 08048000-08817000 r-xp 08048000 00:00 0
 08817000-2e63b000 rwxp 08817000 00:00 0 [heap]
 f630-f6321000 rwxp f630 00:00 0
 f6321000-f640 ---p f6321000 00:00 0
 f6434000-f7cbb000 rwxp f6434000 00:00 0
 f7d5c000-f7ea rwxp f7d5c000 00:00 0
 f7ea-f7ec7000 r-xp  fd:00 60784705 /lib/libm-2.5.so
 f7ec7000-f7ec8000 r-xp 00026000 fd:00 60784705 /lib/libm-2.5.so
 f7ec8000-f7ec9000 rwxp 00027000 fd:00 60784705 /lib/libm-2.5.so
 f7ec9000-f7ede000 r-xp  fd:00 60784716 /lib/libpthread-2.5.so
 f7ede000-f7edf000 ---p 00015000 fd:00 60784716 /lib/libpthread-2.5.so
 f7edf000-f7ee r-xp 00015000 fd:00 60784716 /lib/libpthread-2.5.so
 f7ee-f7ee1000 rwxp 00016000 fd:00 60784716 /lib/libpthread-2.5.so
 f7ee1000-f7ee3000 rwxp f7ee1000 00:00 0
 f7ee3000-f7ee6000 r-xp  fd:00 60784670 /lib/libdl-2.5.so
 f7ee6000-f7ee7000 r-xp 2000 fd:00 60784670 /lib/libdl-2.5.so
 f7ee7000-f7ee8000 rwxp 3000 fd:00 60784670 /lib/libdl-2.5.so
 f7ee8000-f7ee9000 rwxp f7ee8000 00:00 0
 f7f0b000-f7f15000 r-xp  fd:00 60784678 /lib/libnss_files-2.5.so
 f7f15000-f7f16000 r-xp 9000 fd:00 60784678 /lib/libnss_files-2.5.so
 f7f16000-f7f17000 rwxp a000 fd:00 60784678 /lib/libnss_files-2.5.so
 f7f17000-f7f18000 rwxp f7f17000 00:00 0
 ffcc-ffcd5000 rwxp 7ffe9000 00:00 0 [stack]
 e000-f000 r-xp e000 00:00 0
 Aborted
 
 All the best
 Rujing Zha
 2014-05-13
 
 charujing123
 
 *发件人：*Douglas N Greve gr...@nmr.mgh.harvard.edu
 *发送时间：*2014-05-12 23:18
 *主题：*Re: [Freesurfer] problems about extracting specific

Re: [Freesurfer] Freeview/Freesurfer Version Compatibility