Re: [Freesurfer] freesurfer vs ITK build from sources on ubuntu(LUCID)

[Nedialko I. Krouchev]

To follow up on my previous message:
the FS build is not facilitated by the scarcity and incompleteness of build
instructions.

For example
ITK, PETSC  (and possibly other packages) which are not even mentioned
explicitly as FS prerequisites (!)
need to be installed at a (version-matching!) dev-level
(in ubuntu this can be done through the package-mgmt system),
and the corresponding directories skillfully linked to the FS build
configure options.

This - paired with the scarcity of binaries for the various unix platforms
hardly contributes for expanding the circle of FS users,
unless the users in question are accomplished unix gurus familiar with all
the inner workings of a modern code maintenance.

Please contact me offline for further details and exchange.
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Re: [Freesurfer] recon-all script order

[Lauren Bystrom]

That's what I was thinking.
Thank you !

On Wednesday, November 18, 2015, Douglas N Greve 
wrote:

> There is not an automated way to do this. You might be able to run the
> steps piecemeal by specifying the flags for each step individually
>
> On 11/18/2015 04:29 PM, Lauren Bystrom wrote:
> > Hello all,
> > I am trying to run freesurfer on a set of subjects that have tumors in
> > their brain. To get around the tumor, I only want to run freesurfer on
> > one of the hemispheres. When I use hemi -?h, freesurfer exits once it
> > hits the other hemisphere.
> > This is a problem because it doesn't go back to finish the rest of
> > recon-all for the hemisphere I want.
> > Is there a way to change the order of files created with the recon-all
> > script so all of the volumetric, and all of the wm, and all of
> > broadmann's area, etc. is completed for one hemisphere before being
> > run for the other?
> > Thanks!
> > Lauren Bystrom
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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>
>
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> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
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Re: [Freesurfer] recon-all script order

[Douglas N Greve]

There is not an automated way to do this. You might be able to run the 
steps piecemeal by specifying the flags for each step individually

On 11/18/2015 04:29 PM, Lauren Bystrom wrote:
> Hello all,
> I am trying to run freesurfer on a set of subjects that have tumors in 
> their brain. To get around the tumor, I only want to run freesurfer on 
> one of the hemispheres. When I use hemi -?h, freesurfer exits once it 
> hits the other hemisphere.
> This is a problem because it doesn't go back to finish the rest of 
> recon-all for the hemisphere I want.
> Is there a way to change the order of files created with the recon-all 
> script so all of the volumetric, and all of the wm, and all of 
> broadmann's area, etc. is completed for one hemisphere before being 
> run for the other?
> Thanks!
> Lauren Bystrom
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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

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[Freesurfer] recon-all script order

[Lauren Bystrom]

Hello all,
I am trying to run freesurfer on a set of subjects that have tumors in
their brain. To get around the tumor, I only want to run freesurfer on one
of the hemispheres. When I use hemi -?h, freesurfer exits once it hits the
other hemisphere.
This is a problem because it doesn't go back to finish the rest of
recon-all for the hemisphere I want.
Is there a way to change the order of files created with the recon-all
script so all of the volumetric, and all of the wm, and all of broadmann's
area, etc. is completed for one hemisphere before being run for the other?
Thanks!
Lauren Bystrom
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Re: [Freesurfer] FreeSurfer question

[Bruce Fischl]

glad to hear it
Bruce
On Wed, 18 Nov 2015, Tsapanou, Angeliki wrote:


Hi Bruce,
Thank you for your respond. It was good that it was 'brown' but after 
re-running it, it was staying brown. Thankfully, after days of unsuccessful 
trials, I started everything from the beginning and finally it worked!
Thanks,
Angeliki

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Wednesday, November 18, 2015 2:42 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] FreeSurfer question

Hi Angeliki

not sure if anyone answered, and also I'm not sure that I understand. If the cerebellum 
is "brown" in the aseg.mgz that is good - it should be. Is there a problem with 
the skull stripping that you are trying to fix?

cheers
Bruce
On Thu,
12 Nov 2015, Tsapanou, Angeliki wrote:



Hello,

I am dealing with a problem on FreeSurfer a couple of days now.

I want to fix the scull strip and I run the following commands:

cd /users/Angeliki/studyname

export SUBJECTS_DIR=studyname/subjid/session/T1/

recon-all –skullstrip –wsthresh 20 –clean-bm –no-wsgcaatlas –subjid
FreeSurfer

 

Then, the command works and the part of the cerebellum that I don’t
need turns brown.

I close it and I save the script with:  gedit
~/FreeSurfer/Angeliki/run_reconalls_aut1.sh

And type at the script for echo: recon-all –autorecon2 –autorecon3
–subjid FreeSurfer

Finally, I submit it to the cluster with the command:
~/FreeSurfer/Angeliki/run_reconalls_aut1.sh

 

The problem is that even though it runs properly (and I tried to add
some control points and they work), the brown part of the cerebellum
does not disappear, but remains there.

 

Is there something I have to change?

 

Thank you,

Best,

Angeliki Tsapanou

 

 





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Re: [Freesurfer] FreeSurfer question

[Tsapanou, Angeliki]

Hi Bruce, 
Thank you for your respond. It was good that it was 'brown' but after 
re-running it, it was staying brown. Thankfully, after days of unsuccessful 
trials, I started everything from the beginning and finally it worked! 
Thanks, 
Angeliki 

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Wednesday, November 18, 2015 2:42 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] FreeSurfer question

Hi Angeliki

not sure if anyone answered, and also I'm not sure that I understand. If the 
cerebellum is "brown" in the aseg.mgz that is good - it should be. Is there a 
problem with the skull stripping that you are trying to fix?

cheers
Bruce
On Thu,
12 Nov 2015, Tsapanou, Angeliki wrote:

> 
> Hello,
> 
> I am dealing with a problem on FreeSurfer a couple of days now.
> 
> I want to fix the scull strip and I run the following commands:
> 
> cd /users/Angeliki/studyname
> 
> export SUBJECTS_DIR=studyname/subjid/session/T1/
> 
> recon-all –skullstrip –wsthresh 20 –clean-bm –no-wsgcaatlas –subjid 
> FreeSurfer
> 
>  
> 
> Then, the command works and the part of the cerebellum that I don’t 
> need turns brown.
> 
> I close it and I save the script with:  gedit 
> ~/FreeSurfer/Angeliki/run_reconalls_aut1.sh
> 
> And type at the script for echo: recon-all –autorecon2 –autorecon3 
> –subjid FreeSurfer
> 
> Finally, I submit it to the cluster with the command:
> ~/FreeSurfer/Angeliki/run_reconalls_aut1.sh
> 
>  
> 
> The problem is that even though it runs properly (and I tried to add 
> some control points and they work), the brown part of the cerebellum 
> does not disappear, but remains there.
> 
>  
> 
> Is there something I have to change?
> 
>  
> 
> Thank you,
> 
> Best,
> 
> Angeliki Tsapanou
> 
>  
> 
>  
> 
> 
>

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Re: [Freesurfer] FreeSurfer question

[Bruce Fischl]

Hi Angeliki

not sure if anyone answered, and also I'm not sure that I understand. If 
the cerebellum is "brown" in the aseg.mgz that is good - it should be. Is 
there a problem with the skull stripping that you are trying to fix?


cheers
Bruce
On Thu, 
12 Nov 2015, Tsapanou, Angeliki wrote:




Hello,

I am dealing with a problem on FreeSurfer a couple of days now.

I want to fix the scull strip and I run the following commands:

cd /users/Angeliki/studyname

export SUBJECTS_DIR=studyname/subjid/session/T1/

recon-all –skullstrip –wsthresh 20 –clean-bm –no-wsgcaatlas –subjid
FreeSurfer

 

Then, the command works and the part of the cerebellum that I don’t need
turns brown.

I close it and I save the script with:  gedit
~/FreeSurfer/Angeliki/run_reconalls_aut1.sh 

And type at the script for echo: recon-all –autorecon2 –autorecon3 –subjid
FreeSurfer

Finally, I submit it to the cluster with the command:
~/FreeSurfer/Angeliki/run_reconalls_aut1.sh

 

The problem is that even though it runs properly (and I tried to add some
control points and they work), the brown part of the cerebellum does not
disappear, but remains there.

 

Is there something I have to change?

 

Thank you,

Best,

Angeliki Tsapanou

 

 


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[Freesurfer] malloc error running glm_glmfit-sim

[Lawrence Ryner]

Hi,
I'm a new FS user just trying to run through the tutorials. In the Group 
Analysis tutorial, doing the multiple comparisons correction, when I run 
mri_flmfit-sim I get a malloc() memory corruption error. The output is below. I 
am running the VirtualBox Xubuntu 12.04 Freesurfer 5.3.0 version on a PC with 
64-bit Windows 7 and 3472 MB of RAM (assigning more RAM than that causes the 
VirtualBox to crash). I setup a shared folder on my E: drive to store the 
buckner tutorial data. Had to add fsuser to vboxsf using usermod to be able to 
access the data from xubuntu. Also can't setup symbolic links on a shared 
folder so I had to copy the fsaverage dataset to the E: drive. Not sure if that 
is a good way to set things up but I couldn't find much guidance on the best 
way to do this.  Found lots of mailing list threads related to this error, but 
none of them actually seem to provide a solution. Any help would be appreciated.

*
mri_glmfit-sim \
> --glmdir lh.gender_age.glmdir \
> --cache 4 neg \
> --cwpvalthresh 0.05 \
> --2spaces
cmdline mri_glmfit --y lh.gender_age.thickness.10.mgh --fsgd gender_age.fsgd 
dods --C lh-Avg-thickness-age-Cor.mtx --surf fsaverage lh --cortex --glmdir 
lh.gender_age.glmdir
SURFACE: fsaverage lh
log file is lh.gender_age.glmdir/cache.mri_glmfit-sim.log

cd 
/media/sf_Data/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial/glm
/usr/local/freesurfer/bin/mri_glmfit-sim
--glmdir lh.gender_age.glmdir --cache 4 neg --cwpvalthresh 0.05 --2spaces

$Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $
Wed Nov 18 13:15:50 EST 2015
Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:41:14 
UTC 2012 i686 i686 i386 GNU/Linux
fsuser
setenv SUBJECTS_DIR 
/media/sf_Data/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial
FREESURFER_HOME /usr/local/freesurfer

Original mri_glmfit command line:
cmdline mri_glmfit --y lh.gender_age.thickness.10.mgh --fsgd gender_age.fsgd 
dods --C lh-Avg-thickness-age-Cor.mtx --surf fsaverage lh --cortex --glmdir 
lh.gender_age.glmdir

DoSim = 0
UseCache = 1
DoPoll = 0
DoPBSubmit = 0
DoBackground = 0
DiagCluster = 0
gd2mtx = dods
fwhm = 13.914377
CSD 
/usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm14/neg/th40/mc-z.csd
mri_surfcluster --in lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh 
--csd 
/usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm14/neg/th40/mc-z.csd
 --mask lh.gender_age.glmdir/mask.mgh --cwsig 
lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.cluster.mgh 
--vwsig 
lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.voxel.mgh 
--sum 
lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.cluster.summary
 --ocn lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.ocn.mgh 
--oannot 
lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.ocn.annot 
--annot aparc --csdpdf 
lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.pdf.dat 
--cwpvalthresh 0.05 --o 
lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.masked.mgh 
--no-fixmni --bonferroni 2 --surf white
Creating CDFs from CSD files
csd->threshsign = -1
thsign = neg, id = -1
version $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $
hemi   = lh
srcid  = lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh
srcsubjid  = fsaverage
srcsurf= white
srcframe   = 0
thsign = neg
thmin  = 4
thmax  = -1
fdr= -1
minarea= 0
Bonferroni  = 2
xfmfile= talairach.xfm
nth = -1
outid= 
lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.masked.mgh MGH
ocnid= 
lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.ocn.mgh MGH
sumfile  = 
lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.cluster.summary
subjectsdir= 
/media/sf_Data/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial
FixMNI = 0
Found 149953 vertices in mask
Found 149953 vertices in mask
Found 149953 points in clabel.
- XFM matrix (RAS2RAS) ---
/media/sf_Data/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial/fsaverage/mri/transforms/talairach.xfm
 1.000   0.000   0.000   0.000;
 0.000   1.000   0.000   0.000;
 0.000   0.000   1.000   0.000;
 0.000   0.000   0.000   1.000;

Reading source surface 
/media/sf_Data/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial/fsaverage/surf/lh.white
Done reading source surface
Reading annotation 
/media/sf_Data/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial/fsaverage/label/lh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally 
/autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
Computing metric properties
Loading source values
number of voxels in s

Re: [Freesurfer] gender as nuisance factor

[Douglas N Greve]

Just specify gender as a factor then look at the contrasts where it says 
that gender is accounted for or regressed out. There is really no 
difference between a factor of interest and a nuisance factor, it is 
only a matter of interpretation

On 11/18/2015 02:04 PM, Tesse, Marcello wrote:
> Dear FreeSurfer experts,
> >
> >
> > I a PhD student at King's college London.
> >
> > I am running cortical thickness analysis with QDEC.
> >
> > I would like to investigate some cortical thickness differences
> > between 2 groups,
> >
> > using as nuisance factors 'age' and 'gender'.
> >
> >
> > No problem at all with age. But the gender as dicotomic variable is
> >
> > listed on fixed factor in qdec, in design window.
> >
> > My question is:
> >
> > how can I run the analysis using 'gender' as nuisance factor??
> >
> >
> >
> > thank you very much
> >
> > MARCELLO
>
>
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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] selxavg3-sess error empty conditions in paradigm file

[Douglas N Greve]

There is not a way to model empty conditions. The easiest thing to do is 
to just change another condition to say it is the missing condition. It 
should have little effect on the final results.

On 11/18/2015 02:06 PM, Danielle Miller wrote:
> Hello Freesurfer Experts,
>
> I am reposting this as this has not come up on the mail archive thread.
> I keep running into the following error (see below) when selxavg3-sess gets
> to my third subject. I am assuming this is because this subject does not
> have all of the conditions modeled (that is, this particular subject does
> not have any incorrect responses). Is there a way to model an empty
> condition to get around this? I want a general contrast of Incorrect >
> Correct, but some subjects do not make any errors and therefore would not
> have this condition in their paradigm files.
> Any advice would be greatly appreciated.
>
>
> #@# CC_003_recon ###
> /Volumes/VA_Imaging/Projects/dmiller/COGCON/FSFAST/CC_003_recon
> -
> $Id: fast_selxavg3.m,v 1.100 2011/03/02 16:14:38 greve Exp $
> /Applications/freesurfer/fsfast/toolbox/fast_selxavg3.m
> /Applications/freesurfer/fsfast/toolbox/fast_ldanaflac.m
> /Applications/freesurfer-5.3/matlab/MRIread.m
> -
> outtop = /Volumes/VA_Imaging/Projects/dmiller/COGCON/FSFAST
> Extension format = nii.gz
> INFO: key PerSession unrecognized, line 6, skipping
> INFO: key ApplySubCortMask unrecognized, line 12, skipping
>   1 Correct-v-Incorrect.mat
>   2 Incorrect-v-base.mat
> nruns = 4
> autostimdur =
>
>
> outanadir =
> /Volumes/VA_Imaging/Projects/dmiller/COGCON/FSFAST/CC_003_recon/Bold1/correct.sm15.mni305
> Found 57600/537168 (10.7) voxels in mask
> Creating Design Matrix
>   ... creation time =  0.008 sec
> DoMCFit = 1
> ntptot = 740, nX = 27, DOF = 713
> Saving X matrix to
> /Volumes/VA_Imaging/Projects/dmiller/COGCON/FSFAST/CC_003_recon/Bold1/correct.sm15.mni305/Xtmp.mat
> ??? Error using ==> svd
> Input to SVD must not contain NaN or Inf.
>
> Error in ==> cond at 39
> s = svd(A);
>
> Error in ==> fast_selxavg3 at 254
>XCond = cond(XtX);
>
> >> --
> ERROR: fast_selxavg3() failed\n
>
> Thanks,
> Danielle
>
> -- 
> Ph.D. Program in Behavioral Neuroscience
> Boston University School of Medicine L-815
> 72 E. Concord St
> Boston, MA 02118
>
>
> VA Boston Healthcare System Jamaica Plain
> Memory Disorders Research Center
> 150 South Huntington Ave  D11-103
> Boston, MA 02130
> OFFICE:(857) 364-2130
>
>
>
> ___
> 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
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[Freesurfer] Fw: gender as nuisance factor

[Tesse, Marcello]

Dear Dr, Douglas,
Apology if I have written the email to you, but I am try to ask this question 
on FS list mailsince two days, and nobody answered me.
The email sent to freesurfer@nmr.mgh.harvard.edu is below.
Thank uyou very much, sorry again
MARCELLO



From: Tesse, Marcello
Sent: 18 November 2015 19:04
To: freesurfer@nmr.mgh.harvard.edu
Subject: gender as nuisance factor

Dear FreeSurfer experts,
>
>
> I a PhD student at King's college London.
>
> I am running cortical thickness analysis with QDEC.
>
> I would like to investigate some cortical thickness differences
> between 2 groups,
>
> using as nuisance factors 'age' and 'gender'.
>
>
> No problem at all with age. But the gender as dicotomic variable is
>
> listed on fixed factor in qdec, in design window.
>
> My question is:
>
> how can I run the analysis using 'gender' as nuisance factor??
>
>
>
> thank you very much
>
> MARCELLO
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[Freesurfer] selxavg3-sess error empty conditions in paradigm file

[Danielle Miller]

Hello Freesurfer Experts,

I am reposting this as this has not come up on the mail archive thread.

I keep running into the following error (see below) when selxavg3-sess gets
to my third subject. I am assuming this is because this subject does not
have all of the conditions modeled (that is, this particular subject does
not have any incorrect responses). Is there a way to model an empty
condition to get around this? I want a general contrast of Incorrect >
Correct, but some subjects do not make any errors and therefore would not
have this condition in their paradigm files.

Any advice would be greatly appreciated.


#@# CC_003_recon ###
/Volumes/VA_Imaging/Projects/dmiller/COGCON/FSFAST/CC_003_recon
-
$Id: fast_selxavg3.m,v 1.100 2011/03/02 16:14:38 greve Exp $
/Applications/freesurfer/fsfast/toolbox/fast_selxavg3.m
/Applications/freesurfer/fsfast/toolbox/fast_ldanaflac.m
/Applications/freesurfer-5.3/matlab/MRIread.m
-
outtop = /Volumes/VA_Imaging/Projects/dmiller/COGCON/FSFAST
Extension format = nii.gz
INFO: key PerSession unrecognized, line 6, skipping
INFO: key ApplySubCortMask unrecognized, line 12, skipping
 1 Correct-v-Incorrect.mat
 2 Incorrect-v-base.mat
nruns = 4
autostimdur =


outanadir =
/Volumes/VA_Imaging/Projects/dmiller/COGCON/FSFAST/CC_003_recon/Bold1/correct.sm15.mni305
Found 57600/537168 (10.7) voxels in mask
Creating Design Matrix
 ... creation time =  0.008 sec
DoMCFit = 1
ntptot = 740, nX = 27, DOF = 713
Saving X matrix to
/Volumes/VA_Imaging/Projects/dmiller/COGCON/FSFAST/CC_003_recon/Bold1/correct.sm15.mni305/Xtmp.mat
??? Error using ==> svd
Input to SVD must not contain NaN or Inf.

Error in ==> cond at 39
   s = svd(A);

Error in ==> fast_selxavg3 at 254
  XCond = cond(XtX);

>> --
ERROR: fast_selxavg3() failed\n

Thanks,
Danielle


-- 
Ph.D. Program in Behavioral Neuroscience
Boston University School of Medicine L-815
72 E. Concord St
Boston, MA 02118


VA Boston Healthcare System Jamaica Plain
Memory Disorders Research Center
150 South Huntington Ave  D11-103
Boston, MA 02130
OFFICE:(857) 364-2130
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[Freesurfer] gender as nuisance factor

[Tesse, Marcello]

Dear FreeSurfer experts,
>
>
> I a PhD student at King's college London.
>
> I am running cortical thickness analysis with QDEC.
>
> I would like to investigate some cortical thickness differences
> between 2 groups,
>
> using as nuisance factors 'age' and 'gender'.
>
>
> No problem at all with age. But the gender as dicotomic variable is
>
> listed on fixed factor in qdec, in design window.
>
> My question is:
>
> how can I run the analysis using 'gender' as nuisance factor??
>
>
>
> thank you very much
>
> MARCELLO
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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
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Re: [Freesurfer] FSFAST First-Levels: Fast_selxavg3() ERROR

[Afzal, Afsana]

Hi Doug, 

Just checking up on the error below. 

__
Afsana Afzal
Clinical Research Coordinator
Massachusetts General Hospital
Division of Neurotherapeutics
Department of Psychiatry: Neurosciences
149 13th St, Room 2612
Charlestown, MA 02129
Phone: 617-643-5129
Fax: 617-726-4078


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Afzal, Afsana 
[aaf...@mgh.harvard.edu]
Sent: Monday, November 16, 2015 2:14 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] FSFAST First-Levels: Fast_selxavg3() ERROR

Yeah sorry, I was rerunning the preproc. Should be there now.

__
Afsana Afzal
Clinical Research Coordinator
Massachusetts General Hospital
Division of Neurotherapeutics
Department of Psychiatry: Neurosciences
149 13th St, Room 2612
Charlestown, MA 02129
Phone: 617-643-5129
Fax: 617-726-4078


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Monday, November 16, 2015 12:48 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] FSFAST First-Levels: Fast_selxavg3() ERROR

When I look in  hc016/msit/001/ I only see:

cfg.txt  f.nii  mag.dat  mag.nii  phase.dat  phase.nii

Have you deleted the previous analysis?


On 11/16/2015 11:41 AM, Afzal, Afsana wrote:
> Hi Doug,
>
> Command: selxavg3-sess -s hc016 -analysis
> msit.analysis.sm04.b0dc.mni305 -force
> Folder: /autofs/space/lilli_002/users/DARPA-FAST
> $SUBJECTS_DIR: /autofs/space/lilli_001/users/DARPA-MEG/freesurfs
>
> The problem might actually lie with preprocessing.
>
> Just looking at file sizes, the fmcpr.sm4.mni305.2mm.b0dc.nii.gz file
> size for hc016 is 471kb, but it's ~46mb for other subjects. The lh and
> rh files for hc016 are also pretty small compared to other subjects.
> Not sure what's causing this.
>
> This is the preproc command I used: preproc-sess -s hc016 -surface
> fsaverage lhrh -mni305 -fwhm 4 -per-run -fsd msit -nostc -b0dc -force
>
> Thanks for your help!
>
> - Afsana
> __
> *Afsana Afzal*
> Clinical Research Coordinator
> Massachusetts General Hospital
> Division of Neurotherapeutics
> Department of Psychiatry: Neurosciences
> 149 13th St, Room 2612
> Charlestown, MA 02129
> Phone: 617-643-5129
> Fax: 617-726-4078
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve
> [gr...@nmr.mgh.harvard.edu]
> *Sent:* Friday, November 13, 2015 5:04 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] FSFAST First-Levels: Fast_selxavg3() ERROR
>
> hmmm, not sure. Can you send me your selxavg3-sess command and the
> folder your ran it from and the $SUBJECTS_DIR ?
> doug
>
> On 11/13/15 4:16 PM, Afzal, Afsana wrote:
>> Hi,
>>
>> I'm doing first level analysis in FSFAST and I'm consistently getting
>> the following error when running fast_selxavg3():
>>
>> Saving to
>> /autofs/space/lilli_002/users/DARPA-FAST/hc016/msit/msit.analysis.sm04.b0dc.mni305/rho1mn.sm.nii.gz
>> SmoothOnly requested, so exiting now
>>
>> Found 0 voxels with corrected AR1 > 0.90
>> Whitening
>> Attempted to access indedge(0); index must be a positive integer or
>> logical.
>>
>> Error in fast_histeq (line 53)
>> if(indedge(end) ~= ny) indedge = [indedge ny]; end
>>
>> Error in fast_selxavg3 (line 640)
>> [edge bincenter binmap] = fast_histeq(nrho1mn.vol(indmask),
>> flac0.acfbins);
>>
>> >> --
>> ERROR: fast_selxavg3() failed\n
>>
>>
>> I'm only getting the error for mni305 (lh and rh analyses are
>> completing without a hitch). I have re-preprocessed and attempted to
>> run the analysis several times, but without any success. It's not
>> clear what the error means or what's causing it.
>>
>> Thank you for any help,
>>
>> Afsana
>>
>> __
>> *Afsana Afzal*
>> Clinical Research Coordinator
>> Massachusetts General Hospital
>> Division of Neurotherapeutics
>> Department of Psychiatry: Neurosciences
>> 149 13th St, Room 2612
>> Charlestown, MA 02129
>> Phone: 617-643-5129
>> Fax: 617-726-4078
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> ___
> 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://s

Re: [Freesurfer] PET tools in FS dev v6.0

[Douglas N Greve]

For single frame, you can just run
mri_convert input.nii output.nii --frame F
where F is the 0-based frame number, then run mri_gtmpvc on output.nii

The PVC "image" is a bit tricky. You can get a muller-gartner image 
(--mgx) or region-based voxel-wise (RBV) image with --rbv.



On 11/18/2015 12:36 PM, Pradeep wrote:
> Hello Doug,
>
> I am in the process of testing the FS PVC procedure and I was 
> wondering if there is a way to do this procedure with single frame PET 
> data and get the partial volume corrected SUVR image. I know that this 
> is still new and not all the processes is documented yet, but any 
> inputs on this would be appreciated. I have successfully ran steps 1 
> and 2 from the process you have outlines above.
>
> Thanks,
> Pradeep
>
> On Mon, Sep 28, 2015 at 10:03 PM, Jonathan DuBois 
> mailto:jonathan.m.dub...@gmail.com>> wrote:
>
> Hi Doug,
>
> I uploaded the files you requested. I'm not sure if it matters,
> but one thing I forgot to mention was that in order to get the pet
> file in the right format and orientation, I ended up using
> (ecattominc pet.v pet.mnc) and (itk_convert --inv-y --inv-x
> pet.mnc pet.nii). I couldn't find a good tool to convert directly
> form ECAT to NIFTI, but perhaps this conversion process interferes
> with the pet processing?
>
> Best,
> Jonathan
>
> Message: 7
> Date: Mon, 28 Sep 2015 18:07:18 -0400
> From: Douglas N Greve  >
> Subject: Re: [Freesurfer] PET tools in FS dev v6.0
> To: freesurfer@nmr.mgh.harvard.edu
> Message-ID:
> <5609ba16.2090...@nmr.mgh.harvard.edu
> >
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
> Can you upload the FS subject, pet data, and .lta?
> https://gate.nmr.mgh.harvard.edu/filedrop2
>
>
>
> On 09/28/2015 12:08 PM, Jonathan DuBois wrote:
> > Hi Doug,
> >
> > I was told you were away last week so I'm reposting this message.
> > Thanks for sending me the information on the PET scripts. I
> > ran gtmseg, and bbregister successfully (I inspected both and they
> > look accurate), but I am getting a segfault with mri_gtmpvc at the
> > auto mask step.
> >
> > I copied the command and the error below. I thought that it could 
> be a
> > memory issue due to the size of the matrix (I ran it on a mac with
> > 8gb) but I also tried to run it with the --tt-reduce and got the 
> same
> > error. The data is from an HRRT PET scanner with a PSF of 4mm. For 
> the
> > auto-mask input I used 6 .01, as your instructions were PSF+2. Is 
> this
> > correct?
> >
> > Thanks
> > Jonathan
> >
> > mri_gtmpvc --i pet.nii.gz --psf 4 --auto-mask 6 .01 --seg
> > /Users/jonathandubois/data/fssub/epc_02/mri/gtmseg.mgz --reg
> > pet_avt_reg.lta --default-seg-merge --mgx .01 --o gtmpvc.output
> > --km-hb 11 12 13 50 51 52 --km-ref 8 47 --no-rescale
> > Loading input pet.nii.gz
> >   done loading input 26 frames
> >
> > $Id: mri_gtmpvc.c,v 1.57 2015/05/29 19:51:24 greve Exp $
> > setenv SUBJECTS_DIR /Users/jonathandubois/data/fssub
> > cd /Volumes/my_passport/external/Documents/fssub2/test
> > mri_gtmpvc --i pet.nii.gz --psf 4 --auto-mask 6 .01 --seg
> > /Users/jonathandubois/data/fssub/epc_02/mri/gtmseg.mgz --reg
> > pet_avt_reg.lta --default-seg-merge --mgx .01 --o gtmpvc.output
> > --km-hb 11 12 13 50 51 52 --km-ref 8 47 --no-rescale
> > sysnameDarwin
> > hostname Jons-MacBook-Air.local
> > machinex86_64
> > user jonathandubois
> > vgthresh 0.001000
> > nReplace 18
> > 0. 0. 0. 0. 0. 0.
> > 4 avail.processors, using 1
> > Creating output directory gtmpvc.output
> > Loading seg for gtm
> > /Users/jonathandubois/data/fssub/epc_02/mri/gtmseg.mgz
> > Loading seg ctab
> > /Users/jonathandubois/data/fssub/epc_02/mri/gtmseg.ctab
> > Reading /Users/jonathandubois/data/fssub/epc_02/mri/gtmseg.lta
> > Replacing 18
> > Pruning ctab
> > done with seg vol
> > maxFWHM = 3.28205 (voxels), PadThresh=0.0001, nPad=10
> > Computing auto mask
> > Segmentation fault: 11
> >
> >
> > Message: 13
> > Date: Tue, 08 Sep 2015 14:34:11 -0400
> > From: Douglas N Greve  >
>   >>
> > Subject: Re: [Freesurfer] PET tools in FS dev v6.0
> > To:freesurfer@nmr.mgh.harvard.

Re: [Freesurfer] Multimodality analysis in FreeSurfer

[Douglas N Greve]

If I understand you, you want to do a vertex-wise correlation between 
thickness and myelin. You can do this with a "per vertex regressor", 
--pvr input to mri_glmfit, something like

mri_glmfit --y thickness.mgh --pvr myelin.mgh --surf fsaverage lh --C 
contrats.mtx --o glmdir

with contrast.mtx being 0 1

This will set up a model thickness = offset + beta*myelin and then test 
whether beta=0

doug


On 11/18/2015 02:48 AM, Silas wrote:
> I've mapped cortical thickness and the myelination data onto the fsaverage, 
> and also used general linear modelling to investigate the one sample group 
> mean of myelination data og cortical thickness (not very useful since the 
> mean thickness or myelination should never be 0) data separately.
> I would like to map the correlation between cortical thickness and 
> myelination onto the fsaverage. I've investigated this statistical 
> correlation by a vertex wise correlation study in matlab, and it should be 
> possible to map this onto the fsaverage. Though, I would like to perform this 
> correlation study entirely in FreeSurfer - in this way I would easily be able 
> to correlate for multiple comparisons using the standardized pipeline for 
> FreeSurfer group analysis.
>
> Best, Silas
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Douglas N Greve 
> 
> Sent: Tuesday, November 17, 2015 7:10 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Multimodality analysis in FreeSurfer
>
> I'm not sure what you mean. You say that you have mapped the thickness
> and myelin data into fsaverage space but then need to map the
> correlation into fsaverage. Isn't it already there?
>
> On 11/17/2015 10:33 AM, Silas wrote:
>> Dear Freesurfer team,
>>
>>
>> I've scanned a group of subjects and gained structural and myelination
>> data. Then, I've used mris_preproc to map the data onto the surface of
>> fsaverage (and concatenating the data). I would like to investigate
>> the correlation between cortical thickness and myelination by mapping
>> this correlation onto the fsaverage (an one sample group mean
>> analysis) - is this possible? Do you have an existing guide
>> approaching this problem?
>>
>>
>> Thank you!
>>
>>
>> Best, Silas
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine 
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in 
> error
> but does not contain patient information, please contact the sender and 
> properly
> dispose of the e-mail.
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] PET tools in FS dev v6.0

[Pradeep]

Hello Doug,

I am in the process of testing the FS PVC procedure and I was wondering if
there is a way to do this procedure with single frame PET data and get the
partial volume corrected SUVR image. I know that this is still new and not
all the processes is documented yet, but any inputs on this would be
appreciated. I have successfully ran steps 1 and 2 from the process you
have outlines above.

Thanks,
Pradeep

On Mon, Sep 28, 2015 at 10:03 PM, Jonathan DuBois <
jonathan.m.dub...@gmail.com> wrote:

> Hi Doug,
>
> I uploaded the files you requested. I'm not sure if it matters, but one
> thing I forgot to mention was that in order to get the pet file in the
> right format and orientation, I ended up using (ecattominc pet.v pet.mnc)
> and (itk_convert --inv-y --inv-x pet.mnc pet.nii). I couldn't find a good
> tool to convert directly form ECAT to NIFTI, but perhaps this conversion
> process interferes with the pet processing?
>
> Best,
> Jonathan
>
>
>> Message: 7
>> Date: Mon, 28 Sep 2015 18:07:18 -0400
>> From: Douglas N Greve 
>> Subject: Re: [Freesurfer] PET tools in FS dev v6.0
>> To: freesurfer@nmr.mgh.harvard.edu
>> Message-ID: <5609ba16.2090...@nmr.mgh.harvard.edu>
>> Content-Type: text/plain; charset=windows-1252; format=flowed
>>
>> Can you upload the FS subject, pet data, and .lta?
>> https://gate.nmr.mgh.harvard.edu/filedrop2
>>
>>
>>
>> On 09/28/2015 12:08 PM, Jonathan DuBois wrote:
>> > Hi Doug,
>> >
>> > I was told you were away last week so I'm reposting this message.
>> > Thanks for sending me the information on the PET scripts. I
>> > ran gtmseg, and bbregister successfully (I inspected both and they
>> > look accurate), but I am getting a segfault with mri_gtmpvc at the
>> > auto mask step.
>> >
>> > I copied the command and the error below. I thought that it could be a
>> > memory issue due to the size of the matrix (I ran it on a mac with
>> > 8gb) but I also tried to run it with the --tt-reduce and got the same
>> > error. The data is from an HRRT PET scanner with a PSF of 4mm. For the
>> > auto-mask input I used 6 .01, as your instructions were PSF+2. Is this
>> > correct?
>> >
>> > Thanks
>> > Jonathan
>> >
>> > mri_gtmpvc --i pet.nii.gz --psf 4 --auto-mask 6 .01 --seg
>> > /Users/jonathandubois/data/fssub/epc_02/mri/gtmseg.mgz --reg
>> > pet_avt_reg.lta --default-seg-merge --mgx .01 --o gtmpvc.output
>> > --km-hb 11 12 13 50 51 52 --km-ref 8 47 --no-rescale
>> > Loading input pet.nii.gz
>> >   done loading input 26 frames
>> >
>> > $Id: mri_gtmpvc.c,v 1.57 2015/05/29 19:51:24 greve Exp $
>> > setenv SUBJECTS_DIR /Users/jonathandubois/data/fssub
>> > cd /Volumes/my_passport/external/Documents/fssub2/test
>> > mri_gtmpvc --i pet.nii.gz --psf 4 --auto-mask 6 .01 --seg
>> > /Users/jonathandubois/data/fssub/epc_02/mri/gtmseg.mgz --reg
>> > pet_avt_reg.lta --default-seg-merge --mgx .01 --o gtmpvc.output
>> > --km-hb 11 12 13 50 51 52 --km-ref 8 47 --no-rescale
>> > sysname  Darwin
>> > hostname Jons-MacBook-Air.local
>> > machine  x86_64
>> > user jonathandubois
>> > vgthresh   0.001000
>> > nReplace   18
>> > 0. 0. 0. 0. 0. 0.
>> > 4 avail.processors, using 1
>> > Creating output directory gtmpvc.output
>> > Loading seg for gtm
>> > /Users/jonathandubois/data/fssub/epc_02/mri/gtmseg.mgz
>> > Loading seg ctab
>> > /Users/jonathandubois/data/fssub/epc_02/mri/gtmseg.ctab
>> > Reading /Users/jonathandubois/data/fssub/epc_02/mri/gtmseg.lta
>> > Replacing 18
>> > Pruning ctab
>> > done with seg vol
>> > maxFWHM = 3.28205 (voxels), PadThresh=0.0001, nPad=10
>> > Computing auto mask
>> > Segmentation fault: 11
>> >
>> >
>> > Message: 13
>> > Date: Tue, 08 Sep 2015 14:34:11 -0400
>> > From: Douglas N Greve > > >
>> > Subject: Re: [Freesurfer] PET tools in FS dev v6.0
>> > To: freesurfer@nmr.mgh.harvard.edu
>> > Message-ID:
>> > <55ef2a23.3070...@nmr.mgh.harvard.edu
>> > >
>> > Content-Type: text/plain; charset=windows-1252; format=flowed
>> > Yes there are both. For KM we have MRTM1 and MRTM2 so far. They
>> > are not
>> > well documented yet.
>> > 1. To start, run
>> > gtmseg --s subject
>> > This will take a couple of hours and produces some files needed
>> > for GTM
>> > PVC (which is used for GTM, MG, RBV).
>> > 2. You'd then register the PET to the anatomical with bbregister
>> (with
>> > --t2 weighting). Make sure to save the output as an LTA (--lta). I
>> > usually use the mean TAC as the input. You can do this in parallel
>> > with #1.
>> > 3. You'd then run mri_gtmpvc, something like
>> > mri_gtmpvc --i tac.nii.gz --psf PSF  --auto-mask PSF+2 .01 --seg
>> > gtmseg.mgz --reg reg.lta --default-seg-merge --mgx .01 --o
>> > gtmpvc.output
>> > --km-hb 11 12 13 50 51 52 --km-ref 8 47 --no-rescale
>> > PSF is the point-s

[Freesurfer] Obtaining MNI-305 Coordinates for Destrieux ROIs

[Riley North]

Hello,

I was following the conversation (recreated below) about converting the
Destrieux ROI labels to MNI-305 coordinates and was wondering if all issues
were resolved but not posted to the list. I attempted the same commands as
were recommended in the original conversation:

*mri_annotation2label --subject fsaverage --hemi lh --annotation
aparc.a2009s  *

followed by

*mri_surfcluster --in fsaverage/surf/rh.thickness --clabel my_label.label
--sum sum.my_label --centroid --thmin 0 --hemi lh --subject fsaverage
--nofixmni  *

*(where my_label is a given Destrieux ROI)*
The 'sum' files returned by the second command all show the same MNI x-y-z
coordinates as one another: [-29.4 -22.0 17.4] for lh ROIs and [29.8 -20.7
18.0] for rh ROIs. The original poster also said he observed that the x-y-z
coordinates were the same for all of the ROIs for a given hemisphere. Like
the original poster, I'm trying to get a single x-y-z MNI305-space
coordinate triplet for each Destrieux ROI for use in network display
software. Is there a modification to the above command that will return
what I'm looking for?

The original conversation (italicized) is posted below in chronological
order:

*Post
#1: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg42598.html
*

*Hi Freesurfer Experts,

For the purpose of defining nodes in a graph theory analysis, I would like
to generate a list of X Y Z coordinates in MNI space for all the labels in
the Destrieux atlas. I came across a previous post with the following steps:*

*Step 1:

mri_annotation2label --subject fsaverage --hemi lh --annotation
aparc.a2009s --outdir /Users/ElijahMak

Step 2:

mri_surfcluster --in
/Applications/freesurfer/subjects/fsaverage/surf/lh.thickness --clabel
lh.G_and_S_frontomargin.label --sum sum.lh.G_and_S_frontomargin
--centroid --thmin 0 --hemi lh --subject fsaverage
Everything went smoothly, but I would like to check my steps with you
before I proceed to generate the coordinates individually for each ROI
per hemisphere.



The output from #2 is sum.lh.G_and_S_frontomargin. When I load it, I see


dhcp-172-17-218-173:~ ElijahMak$ cat sum.lh.G_and_S_frontomargin

# Cluster Growing Summary (mri_surfcluster)

# $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $

# $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $

# CreationTime 2015/08/10-12:29:31-GMT

# cmdline mri_surfcluster --in
/Applications/freesurfer/subjects/fsaverage/surf/lh.thickness --clabel
lh.G_and_S_frontomargin.label --sum sum.lh.G_and_S_frontomargin
--centroid --thmin 0 --hemi lh --subject fsaverage

# cwd /Users/ElijahMak

# sysname  Darwin

# hostname dhcp-172-17-218-173.eduroam.wireless.private.cam.ac.uk


# machine  x86_64

# FixVertexAreaFlag 1

# FixSurfClusterArea 1

#

# Input  /Applications/freesurfer/subjects/fsaverage/surf/lh.thickness

# Frame Number  0

# srcsubj fsaverage

# hemi lh

# surface white

# SUBJECTS_DIR /Applications/freesurfer/subjects

# SearchSpace_mm2 65416.6

# SearchSpace_vtx 932

# Bonferroni 0

# Minimum Threshold 0

# Maximum Threshold infinity

# Threshold Signabs

# AdjustThreshWhenOneTail 1

# Area Threshold0 mm^2

# clabelfile lh.G_and_S_frontomargin.label

# clabelinv  0

# Overall max 3.33248 at vertex 83949

# Overall min 0 at vertex 0

# NClusters  1

# Total Cortical Surface Area 65416.6 (mm^2)

# FixMNI = 1

#

# ClusterNo  Max   VtxMax   Size(mm^2)  TalX   TalY   TalZNVtxs

   13.332   83949  82219.39-29.4  -22.0   17.4  163842


 Are those TalX TalY TalZ the values I'm looking for?



Many thanks for your time.



Best Wishes,

Elijah*


*Reply to Post
#1: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg42656.html
*

*Those are more-or-less talairach coords, not MNI. If you add --nofixmni,
the results will be reported in mni305 coords. - Douglas N Greve*


*Post #2: 
**https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg42693.html
*


*Hi Douglas,

Thanks for the help! However, when I tried the --nofixmni flag, all the
ROIs appeared to have identical MNI coordinates. I have pasted the output
from 3 ROIS in the LH.*

*# ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZNVtxs
   13.332   83949  82219.39-29.4  -22.0   17.4  163842
   13.533  117158  82219.39-29.4  -22.0   17.4  163842
   13.170   83424  82219.39-29.4  -22.0   17.4  163842


The same thing happens to the ROIs on the RH (XYZ: 29.8 29.8 18.0).

Best Wishes,
*

*Elijah *


Thanks,

Riley
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The info

Re: [Freesurfer] direction for restart in the middle

[Krieger, Donald N.]

Thanks, Bruce. - Don


> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
> boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
> Sent: Wednesday, November 18, 2015 8:55 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] direction for restart in the middle
> 
> Hi Don
> 
> the defect is too big to fix, and probably means something dramatic is wrong
> (e.g. skull or cerebellum attached to the brain component of the wm.mgz).
> Check out the ?h.inflated.nofix and see what is going on and correct it before
> rerunning
> 
> cheers
> Bruce
> On Wed, 18 Nov 2015, Krieger, Donald N. wrote:
> 
> >
> > I have run freesurfer 6Beta on the scan with very large CSF spaces
> >
> > With flags: -bigventricles and –notal-check .
> >
> > I used the latter flag per suggestions in the log as the first run
> > failed on a talaraich check.
> >
> > This second run appears to be hung as it has not written anything new
> > into the recon-all.log file for 7 hours.
> >
> > I would like to restart this at a reasonable point rather than at the
> > beginning.
> >
> > Can you recognize where it is and what is are suggested restart flags?
> >
> >
> >
> > Here are the files which have appeared in the mri directory.
> >
> > aseg.auto.mgz   aseg.presurf.mgz   brainmask.mgz  error.log
> > mri_nu_correct.mni.log.bak  nu_noneck.mgz  orig_nu.log  segment.dat
> >  talairach.log   transforms   wm.mgz
> >
> > aseg.auto_noCCseg.label_intensities.txt  brain.finalsurfs.mgz
> > brain.mgz  filled.mgz  norm.mgz orig
> > orig_nu.mgz  T1.mgz talairach_with_skull_2.log  v.mgz
> > wm.seg.mgz
> >
> > aseg.auto_noCCseg.mgz    brainmask.auto.mgz
> > ctrl_pts.mgz   mri_nu_correct.mni.log  nu.mgz orig.mgz
> > rawavg.mgz   talairach.label_intensities.txt talairach_with_skull.log
> > wm.asegedit.mgz
> >
> >
> >
> > Here are the last 50 lines or so of the log file:
> >
> > ProgramName: mri_ca_normalize  ProgramArguments: -all-
> info  ProgramVersion:
> > $Name: stable5 $  TimeStamp: 2
> >
> > ion: 3.10.73-1.el6.elrepo.x86_64  CompilerName: GCC  CompilerVersion:
> > 40400
> >
> > ...skipping...
> >
> > mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 201 lh
> >
> >
> >
> > reading spherical homeomorphism from 'qsphere.nofix'
> >
> > using genetic algorithm with optimized parameters
> >
> > setting seed for random number genererator to 1234
> >
> >
> >
> > *
> >
> > Topology Correction Parameters
> >
> > retessellation mode:   genetic search
> >
> > number of patches/generation : 10
> >
> > number of generations :    10
> >
> > surface mri loglikelihood coefficient : 1.0
> >
> > volume mri loglikelihood coefficient :  10.0
> >
> > normal dot loglikelihood coefficient :  1.0
> >
> > quadratic curvature loglikelihood coefficient : 1.0
> >
> > volume resolution : 2
> >
> > eliminate vertices during search :  1
> >
> > initial patch selection :   1
> >
> > select all defect vertices :    0
> >
> > ordering dependant retessellation:  0
> >
> > use precomputed edge table :    0
> >
> > smooth retessellated patch :    2
> >
> > match retessellated patch : 1
> >
> > verbose mode :  0
> >
> >
> >
> > *
> >
> > INFO: assuming .mgz format
> >
> > $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $
> >
> >   $Id: mrisurf.c,v 1.767.2.2 2015/07/06 21:59:21 greve Exp $
> >
> > before topology correction, eno=-510 (nv=99342, nf=199704, ne=299556,
> > g=256)
> >
> > using quasi-homeomorphic spherical map to tessellate cortical surface...
> >
> >
> >
> > Correction of the Topology
> >
> > Finding true center and radius of Spherical Surface...done
> >
> > Surface centered at (0,0,0) with radius 100.0 in 10 iterations
> >
> > marking ambiguous vertices...
> >
> > 111330 ambiguous faces found in tessellation
> >
> > segmenting defects...
> >
> > 38 defects found, arbitrating ambiguous regions...
> >
> > analyzing neighboring defects...
> >
> >   -merging segment 13 into 0
> >
> >   -merging segment 23 into 0
> >
> >   -merging segment 29 into 0
> >
> >   -merging segment 32 into 0
> >
> >   -merging segment 36 into 0
> >
> >   -merging segment 16 into 12
> >
> >   -merging segment 15 into 14
> >
> > 31 defects to be corrected
> >
> > 0 vertices coincident
> >
> > reading input
> > surface/oasis/scratch/comet/donkri/temp_project/subjects/201/surf/lh.q
> > sphere.nofix
> > ...
> >
> > reading brain volume from brain...
> >
> > reading wm segmentation from wm...
> >
> > Computing Initial Surface Statistics
> >
> >   -face   loglikelihood: -9.2710  (-4.6355)
> >
> >   -vertex loglikelihood: -8.2866  (-4.1

Re: [Freesurfer] Hippocampal Subfields 6.0 with 5.3 recons

[Eugenio Iglesias]

Hi Andrew, 
it's perfectly possible. It would just make your results a bit harder to 
reproduce, but that's about it ;-) 
Cheers, 
Eugenio 

Juan Eugenio Iglesias 
Postdoctoral researcher BCBL 
www.jeiglesias.com 
www.bcbl.eu 

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer 


From: "O'Shea,Andrew"  
To: "Freesurfer support list"  
Sent: Wednesday, November 18, 2015 3:07:04 PM 
Subject: [Freesurfer] Hippocampal Subfields 6.0 with 5.3 recons 



Hello all, 
I was wondering if anyone with knowledge of the new hippocampal subfield 
segmentation that is going to be released with version 6.0 could answer a quick 
question. We have previously processed subjects in v5.3 and would like to use 
the new hippocampal seg algorithm. How “standalone” is the new process? Does 
the new process use any inputs from the recon-all stream which have changed in 
the upcoming version? Thanks! 
-Andrew 

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[Freesurfer] Hippocampal Subfields 6.0 with 5.3 recons

[O'Shea,Andrew]

Hello all,
I was wondering if anyone with knowledge of the new hippocampal subfield 
segmentation that is going to be released with version 6.0 could answer a quick 
question. We have previously processed subjects in v5.3 and would like to use 
the new hippocampal seg algorithm. How "standalone" is the new process? Does 
the new process use any inputs from the recon-all stream which have changed in 
the upcoming version? Thanks!
-Andrew
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[Freesurfer] Issue with Talairach - mritotal

[Amlung, Michael]

We are getting an error with recon-all at the stage of Talairach slignment. The 
error is the one described on the known issues: Can't locate shellwords.pl in 
@INC. We are running perl5.18, so I downloaded and installed perl5.12 and 
changed the first line of mritotal as indicated on the ReleaseNotes. We are now 
getting a different error (pasted below). It appears I need to do manual 
Talairach alignment, but not entirely sure how to proceed with that (is there 
documentation available)? Any other suggestions? 

#@# Talairach Failure Detection Mon Nov 16 12:48:42 EST 2015
/Users/PBCAR/neuro/TNE/freesurfer_data/309/mri
\n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n
ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm 
***FAILED*** (p=0., pval=0. < threshold=0.0050)
Manual Talairach alignment may be necessary, or
include the -notal-check flag to skip this test,
making sure the -notal-check flag follows -all
or -autorecon1 in the command string.
See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach


recon-all -s 309 exited with ERRORS at Mon Nov 16 12:48:42 EST 2015




Michael Amlung, Ph.D.
Assistant Professor

Department of Psychiatry and Behavioural Neurosciences
DeGroote School of Medicine
McMaster University

Peter Boris Centre for Addictions Research
100 West 5th Street
Hamilton, Ontario L8N 3K7 
Canada

Telephone: (+1) 905-522-1155, ext. 39014
Email: amlu...@mcmaster.ca
Web: http://fhs.mcmaster.ca/psychiatryneuroscience/AmlungMichael.html
Lab Website: Cognitive Neuroscience of Addictions Laboratory (CNALab)



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Re: [Freesurfer] direction for restart in the middle

[Bruce Fischl]

Hi Don

the defect is too big to fix, and probably means something dramatic is 
wrong (e.g. skull or cerebellum attached to the brain component of the 
wm.mgz). Check out the ?h.inflated.nofix and see what is going on and 
correct it before rerunning


cheers
Bruce
On Wed, 18 Nov 2015, Krieger, Donald N. wrote:



I have run freesurfer 6Beta on the scan with very large CSF spaces

With flags: -bigventricles and –notal-check .

I used the latter flag per suggestions in the log as the first run failed on
a talaraich check.

This second run appears to be hung as it has not written anything new into
the recon-all.log file for 7 hours.

I would like to restart this at a reasonable point rather than at the
beginning.

Can you recognize where it is and what is are suggested restart flags?

 

Here are the files which have appeared in the mri directory.

aseg.auto.mgz   aseg.presurf.mgz   brainmask.mgz  error.log   
mri_nu_correct.mni.log.bak  nu_noneck.mgz  orig_nu.log  segment.dat
 talairach.log   transforms   wm.mgz

aseg.auto_noCCseg.label_intensities.txt  brain.finalsurfs.mgz 
brain.mgz  filled.mgz  norm.mgz   
orig   orig_nu.mgz  T1.mgz  
talairach_with_skull_2.log  v.mgz    wm.seg.mgz

aseg.auto_noCCseg.mgz    brainmask.auto.mgz   
ctrl_pts.mgz   mri_nu_correct.mni.log  nu.mgz 
orig.mgz   rawavg.mgz   talairach.label_intensities.txt 
talairach_with_skull.log    wm.asegedit.mgz

 

Here are the last 50 lines or so of the log file:

ProgramName: mri_ca_normalize  ProgramArguments: -all-info  ProgramVersion:
$Name: stable5 $  TimeStamp: 2

ion: 3.10.73-1.el6.elrepo.x86_64  CompilerName: GCC  CompilerVersion: 40400

...skipping...

mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 201 lh

 

reading spherical homeomorphism from 'qsphere.nofix'

using genetic algorithm with optimized parameters

setting seed for random number genererator to 1234

 

*

Topology Correction Parameters

retessellation mode:   genetic search

number of patches/generation : 10

number of generations :    10

surface mri loglikelihood coefficient : 1.0

volume mri loglikelihood coefficient :  10.0

normal dot loglikelihood coefficient :  1.0

quadratic curvature loglikelihood coefficient : 1.0

volume resolution : 2

eliminate vertices during search :  1

initial patch selection :   1

select all defect vertices :    0

ordering dependant retessellation:  0

use precomputed edge table :    0

smooth retessellated patch :    2

match retessellated patch : 1

verbose mode :  0

 

*

INFO: assuming .mgz format

$Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $

  $Id: mrisurf.c,v 1.767.2.2 2015/07/06 21:59:21 greve Exp $

before topology correction, eno=-510 (nv=99342, nf=199704, ne=299556, g=256)

using quasi-homeomorphic spherical map to tessellate cortical surface...

 

Correction of the Topology

Finding true center and radius of Spherical Surface...done

Surface centered at (0,0,0) with radius 100.0 in 10 iterations

marking ambiguous vertices...

111330 ambiguous faces found in tessellation

segmenting defects...

38 defects found, arbitrating ambiguous regions...

analyzing neighboring defects...

  -merging segment 13 into 0

  -merging segment 23 into 0

  -merging segment 29 into 0

  -merging segment 32 into 0

  -merging segment 36 into 0

  -merging segment 16 into 12

  -merging segment 15 into 14

31 defects to be corrected

0 vertices coincident

reading input 
surface/oasis/scratch/comet/donkri/temp_project/subjects/201/surf/lh.qsphere.nofix
...

reading brain volume from brain...

reading wm segmentation from wm...

Computing Initial Surface Statistics

  -face   loglikelihood: -9.2710  (-4.6355)

  -vertex loglikelihood: -8.2866  (-4.1433)

  -normal dot loglikelihood: -3.4816  (-3.4816)

  -quad curv  loglikelihood: -6.0138  (-3.0069)

  Total Loglikelihood : -27.0531

 

CORRECTING DEFECT 0 (vertices=53053, convex hull=8873)

 

Thanks for your direction on this.  - Don

 


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[Freesurfer] direction for restart in the middle

[Krieger, Donald N.]

I have run freesurfer 6Beta on the scan with very large CSF spaces
With flags: -bigventricles and -notal-check .
I used the latter flag per suggestions in the log as the first run failed on a 
talaraich check.
This second run appears to be hung as it has not written anything new into the 
recon-all.log file for 7 hours.
I would like to restart this at a reasonable point rather than at the beginning.
Can you recognize where it is and what is are suggested restart flags?

Here are the files which have appeared in the mri directory.
aseg.auto.mgz   aseg.presurf.mgz   brainmask.mgz  error.log
mri_nu_correct.mni.log.bak  nu_noneck.mgz  orig_nu.log  segment.dat  
talairach.log   transforms   wm.mgz
aseg.auto_noCCseg.label_intensities.txt  brain.finalsurfs.mgz  brain.mgz  
filled.mgz  norm.mgzorig   orig_nu.mgz  
T1.mgz   talairach_with_skull_2.log  v.mgz
wm.seg.mgz
aseg.auto_noCCseg.mgzbrainmask.auto.mgzctrl_pts.mgz   
mri_nu_correct.mni.log  nu.mgz  orig.mgz   rawavg.mgz   
talairach.label_intensities.txt  talairach_with_skull.logwm.asegedit.mgz

Here are the last 50 lines or so of the log file:
ProgramName: mri_ca_normalize  ProgramArguments: -all-info  ProgramVersion: 
$Name: stable5 $  TimeStamp: 2
ion: 3.10.73-1.el6.elrepo.x86_64  CompilerName: GCC  CompilerVersion: 40400
...skipping...
mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 201 lh

reading spherical homeomorphism from 'qsphere.nofix'
using genetic algorithm with optimized parameters
setting seed for random number genererator to 1234

*
Topology Correction Parameters
retessellation mode:   genetic search
number of patches/generation : 10
number of generations :10
surface mri loglikelihood coefficient : 1.0
volume mri loglikelihood coefficient :  10.0
normal dot loglikelihood coefficient :  1.0
quadratic curvature loglikelihood coefficient : 1.0
volume resolution : 2
eliminate vertices during search :  1
initial patch selection :   1
select all defect vertices :0
ordering dependant retessellation:  0
use precomputed edge table :0
smooth retessellated patch :2
match retessellated patch : 1
verbose mode :  0

*
INFO: assuming .mgz format
$Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $
  $Id: mrisurf.c,v 1.767.2.2 2015/07/06 21:59:21 greve Exp $
before topology correction, eno=-510 (nv=99342, nf=199704, ne=299556, g=256)
using quasi-homeomorphic spherical map to tessellate cortical surface...

Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 10 iterations
marking ambiguous vertices...
111330 ambiguous faces found in tessellation
segmenting defects...
38 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
  -merging segment 13 into 0
  -merging segment 23 into 0
  -merging segment 29 into 0
  -merging segment 32 into 0
  -merging segment 36 into 0
  -merging segment 16 into 12
  -merging segment 15 into 14
31 defects to be corrected
0 vertices coincident
reading input surface 
/oasis/scratch/comet/donkri/temp_project/subjects/201/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
  -face   loglikelihood: -9.2710  (-4.6355)
  -vertex loglikelihood: -8.2866  (-4.1433)
  -normal dot loglikelihood: -3.4816  (-3.4816)
  -quad curv  loglikelihood: -6.0138  (-3.0069)
  Total Loglikelihood : -27.0531

CORRECTING DEFECT 0 (vertices=53053, convex hull=8873)

Thanks for your direction on this.  - Don

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Re: [Freesurfer] How to edit the corpus callosum segmentation

[Bruce Fischl]

Hi Geneviève

did the mri_cc step work? Looking at the code it (inexplicably) limits the 
max # of divisions to 5. I'm surprised it didn't segfault. If that part 
worked I defer to Doug on the rest, but if not we can send you a new mri_cc 
that should fix the problem


cheers
Bruce

On Wed, 18 Nov 2015, UQAM wrote:


Hi,
I would like to segment the corpus callosum into twelve even lenght segments
instead of the five segments that freesurfer identifies by default.

- First I ran a mri_cc on subject e0070: 

mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.12segmentsCC.mgz -d 12 e0070

- Then I edited the ColorLUT.txt file and renamed it CColorLUT.txt (see
attachment, segments 251 to 262).

- Finally I ran a mri_segstats to compute the statistics on segmented
volumes. 

mri_segstats seg $SUBJECTS_DIR/e0070/mri/aseg.12segmentsCC.mgz --ctab
$SUBJECTS_DIR/CColorLUT.txt --nonempty --excludeid 0 sum
--e0070_CC12.aseg.stats

The e0070_CC12.aseg.stats file still displays only five segments of the
corpus callosum.

Any tips or clues on how I could do things differently to get 12 segments?

Thanks in advance,

Geneviève



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Re: [Freesurfer] -hippocampal-subfields-T1

[Eugenio Iglesias]

Hi Daniele, 
do you think you could send us the subject? norm.mgz, wmparc.mgz and aseg.mgz 
should be enough. 
Also, have you experienced this problem with other subjects? 
Cheers, 
Eugenio 


Juan Eugenio Iglesias 
Postdoctoral researcher BCBL 
www.jeiglesias.com 
www.bcbl.eu 

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer 


From: "Daniele Orlandi"  
To: "Freesurfer support list"  
Sent: Wednesday, November 18, 2015 10:20:10 AM 
Subject: [Freesurfer] -hippocampal-subfields-T1 

dear all, 
I'm running analysis with the new FS-v6.0 using the flag 
-hippocampal-subfields-T1 and I get the following error: 

none 
Matrix: 
-3.3 0 0 
0 0 -3.3 
0 3.3 0 
Offset: [-34.0783, 128.423, -71.9905] 
Center: [0, 0, 0] 
Translation: [-34.0783, 128.423, -71.9905] 
Inverse: 
-0.3 0 0 
0 0 0.3 
0 -0.3 0 
Singular: 0 
I am WriteImage and I'm running! 
Wrote image to file asmr2.mgz 
This file does not contain MRI parameters 
Error using zeros 
NaN and Inf not allowed. 

Error in segmentSubjectT1_autoEstimateAlveusML (line 1396) 

MATLAB:nonaninf 


How I can solve it? 

Best, 
Daniele 


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properly 
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[Freesurfer] -hippocampal-subfields-T1

[Daniele Orlandi]

dear all,
I'm running analysis with the new FS-v6.0 using the flag
-hippocampal-subfields-T1 and  I get the following error:

none
  Matrix:
-3.3 0 0
0 0 -3.3
0 3.3 0
  Offset: [-34.0783, 128.423, -71.9905]
  Center: [0, 0, 0]
  Translation: [-34.0783, 128.423, -71.9905]
  Inverse:
-0.3 0 0
0 0 0.3
0 -0.3 0
  Singular: 0
I am WriteImage and I'm running!
Wrote image to file asmr2.mgz
This file does not contain MRI parameters
Error using zeros
NaN and Inf not allowed.

Error in segmentSubjectT1_autoEstimateAlveusML (line 1396)

MATLAB:nonaninf


How I can solve it?

Best,
Daniele
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