date:20130124

Re: [Freesurfer] Downsampling/decimating overlays (not surfaces)

2013-01-24 Thread Nicola Toschi

Hi Alex and Bruce,

thanks a lot for your help. Will play around with MNE - looks like it 
does what I am looking for.

Nicola

On 01/24/2013 07:54 AM, Alexandre Gramfort wrote:
> hi,
>
> what we do with MEG in the MNE package is indeed store downsampled
> overlays (that actually have a temporal dimension). More specifically we
> store the values e.g. only at the vertices of the ico5 subdivision and
> store the ico 5 vertex indices and overlay values. Then to display them
> on the high resolution freesurfer surface we basically use a 
> smoothing/diffusion
> process to fill the missing values. For this downsampling to be valid
> you'll need to make sure the data are smooth enough in order to avoid 
> aliasing.
>
> let me know if you need more details
>
> hope this helps,
>
> Alex
>
> On Thu, Jan 24, 2013 at 3:47 AM, Bruce Fischl
>  wrote:
>> Hi Nicola
>>
>> I think this gets done in the MEG analysis stream, but perhaps Matti
>> (ccd) can comment.
>> cheers
>> BruceOn Thu, 24 Jan 2013, Nicola Toschi wrote:
>>
>>> Hello list,
>>>
>>> is there a quick way to decimate an overlay /while respecting surface
>>> geomery)? I am looking to downsample by about a factor 100.
>>>
>>> Alternatively, I know I can use mris_decimate to downsample a surface, but I
>>> would have to project my highres overlays onto the downsampled surface
>>> (which may not be straightforward).
>>>
>>> Thanks a lot in advance,
>>>
>>> Nicola
>>>
>>> PS apologies for the repost - my subject line was incorrect the first time
>>> around.
>>>
>>>
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[Freesurfer] ERROR: /52/freesurfer/average/3T18yoSchwartzReactN32_as_orig.4dfp.img does not exist!

2013-01-24 Thread Garikoitz Lerma-Usabiaga

Hi FS experts,
I read that the current dev version for recon-all is going to be the same
to the 5.2 version, so I started a new project with the dev version (in
CentOS 4).

I have this very strange error that I am unable to interpret, when running
mpr2mni305 in one case the target is specified as
711-2C_as_mni_average_305, but in the dev version the target is
3T18yoSchwartzReactN32_as_orig, this file does not exist...


What should I try now?

(just in case, this is the command I launch: recon-all --i x -s xxx
-qcache -hippo-subfields -all


(This is the talairach_avi.log)
ERROR WITH DEV VERSION

/home/glerma/FS/52/freesurfer/subjects/TNT/S_08/mri
/home/glerma/FS/52/freesurfer/bin/talairach_avi
--i orig_nu.mgz --xfm transforms/talairach.auto.xfm
$Id: talairach_avi,v 1.10 2012/07/16 15:54:03 nicks Exp $
Linux cajal 2.6.18-164.15.1.el5 #1 SMP Wed Mar 17 11:30:06 EDT 2010 x86_64
x86_64 x86_64 GNU/Linux
Thu Jan 24 00:26:09 CET 2013
mri_convert orig_nu.mgz talsrcimg.img
$Id: mri_convert.c,v 1.202 2012/10/17 19:23:56 greve Exp $
reading from orig_nu.mgz...
TR=2300.00, TE=2.97, TI=1100.00, flip angle=9.00
i_ras = (-1, -3.03407e-09, 2.32831e-10)
j_ras = (1.16415e-10, 0, -1)
k_ras = (3.03407e-09, 1, 3.72529e-09)
writing to talsrcimg.img...
Analyze Output Matrix
-1.000   0.000   0.000   132.933;
-0.000   0.000   1.000  -105.037;
 0.000  -1.000   0.000   161.057;
 0.000   0.000   0.000   1.000;

INFO: set hdr.hist.orient to -1
mpr2mni305 talsrcimg
Thu Jan 24 00:26:10 CET 2013
/home/glerma/FS/52/freesurfer/bin/mpr2mni305 talsrcimg
$Id: mpr2mni305,v 1.4 2009/06/03 16:01:38 nicks Exp $
target=3T18yoSchwartzReactN32_as_orig
ERROR:
/home/glerma/FS/52/freesurfer/average/3T18yoSchwartzReactN32_as_orig.4dfp.img
does not exist!




SAME SUBJECT, SAME HARD and OS, 5.0 VERSION
-
/home/BCBL/glerma/freesurfer/subjects/TNT/S_08/mri
/usr/local/freesurfer/bin/talairach_avi
--i nu.mgz --xfm transforms/talairach.auto.xfm
$Id: talairach_avi,v 1.7 2010/02/07 22:50:52 nicks Exp $
Linux cajal 2.6.18-164.15.1.el5 #1 SMP Wed Mar 17 11:30:06 EDT 2010 x86_64
x86_64 x86_64 GNU/Linux
Sat Aug 25 06:44:15 CEST 2012
mri_convert nu.mgz talsrcimg.img
$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $
reading from nu.mgz...
TR=2300.00, TE=2.97, TI=1100.00, flip angle=9.00
i_ras = (-1, 0, 5.55112e-17)
j_ras = (5.55112e-17, 3.72529e-09, -1)
k_ras = (4.44089e-16, 1, -1.05964e-18)
writing to talsrcimg.img...
Analyze Output Matrix
-1.000   0.000   0.000   132.933;
 0.000   0.000   1.000  -105.037;
 0.000  -1.000  -0.000   161.057;
 0.000   0.000   0.000   1.000;

INFO: set hdr.hist.orient to -1
mpr2mni305 talsrcimg
Sat Aug 25 06:44:16 CEST 2012
/usr/local/freesurfer/bin/mpr2mni305 talsrcimg
$Id: mpr2mni305,v 1.4 2009/06/03 16:01:38 nicks Exp $
target=711-2C_as_mni_average_305

 continues--





and this is the setup output:
 freesurfer-Linux-centos4_x86_64-dev-20121127 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /home/glerma/FS/52/freesurfer
FSFAST_HOME   /home/glerma/glerma/software/freesurfer/fsfast  >> older
version location
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /home/glerma/FS/52/freesurfer/subjects/TNT
MNI_DIR   /home/glerma/FS/52/freesurfer/mni
FSL_DIR   /usr/local/fsl



many thanks!
Gari
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Re: [Freesurfer] Downsampling/decimating overlays (not surfaces)

2013-01-24 Thread Rudolph Pienaar

If you specifically want to project overlays onto 'mris_decimate'd 
surfaces, you won't be able to do that. You could, however, generate new 
overlays using the decimated surface, if that's helpful, using 
'mris_curvature_stats' and feeding it the newly downsampled/demicated 
surface as input.

FWIW.

Best
-=R

On 1/23/13 18:07 , Nicola Toschi wrote:
> Hello list,
>
> is there a quick way to decimate an overlay /while respecting surface 
> geomery)? I am looking to downsample by about a factor 100.
>
> Alternatively, I know I can use mris_decimate to downsample a surface, 
> but I would have to project my highres overlays onto the downsampled 
> surface (which may not be straightforward).
>
> Thanks a lot in advance,
>
> Nicola
>
> PS apologies for the repost - my subject line was incorrect the first 
> time around.
>
>
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-- 
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MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging
149 (2301) 13th Street, Charlestown, MA 02129 USA

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Re: [Freesurfer] mni152reg error (file permission denied)

2013-01-24 Thread Chris McNorgan

Hi Tommi,
The mkdir error suggests to me that there is some system-level permissions
thing going on. If it can't make the directory, then there is no directory into
which fsl can write the refvol.fslregister.nii files, hence the final 2 errors.

From the command line, are you able to navigate to directory:
/usr/pubsw/packages/fsl/current/data/standard/
And within that directory, execute:
mkdir

My guess is that you will get a permission denied error. You can try using
chmod to make the directory writable:
chmod ugo+w /usr/pubsw/packages/fsl/current/data/standard/
and see if you can now do a mkdir in that directory (you might have to be a
superuser to do this)

Dear Surfers,

mni152reg --$SUBJECT exits with the error:

mkdir: cannot create directory
`/usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.18402':
Permission denied

Thereafter, a couple consequential errors follow
...
niiWrite(): error opening file

/usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.18402/refvol.fslregister.nii
...
ERROR: failure writing

/usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.18402/refvol.fslregister.nii

This is on FS 5.1.0 stable. The error seems linux box independent. Please
let me know if you need further info. Thanks!

Bests,

Tommi

--
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Postdoctoral Researcher
Developmental Cognitive Neuroscience Laboratory
Northwestern University, Evanston, IL
DCNL Lab: http://tinyurl.com/9q35abd
Frontiers Profile: http://tinyurl.com/aut488k

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Re: [Freesurfer] Downsampling/decimating overlays (not surfaces)

2013-01-24 Thread Nicola Toschi

Thank you Rudolph,

what I would like to have as an end product is a list of overlay values 
at each vertex of the decimated surface (i.e. I don't want to synthesize 
anything into ROIs).

The overlays are all freesurfer-specific (curvature, thickness, LGI, 
etc). I cannot recompute these on the new (decimated) surface, as they 
will be significantly different and less accurate (they are specific to 
the geometry of the original surface). Rather, I was looking to 
downsample highres overlays after smoothing.

So i am not sure your suggestion would work - please let me know if I 
misunderstood something.

Thanks again for your reprly,

Nicola

On 01/24/2013 04:01 PM, Rudolph Pienaar wrote:
> If you specifically want to project overlays onto 'mris_decimate'd 
> surfaces, you won't be able to do that. You could, however, generate 
> new overlays using the decimated surface, if that's helpful, using 
> 'mris_curvature_stats' and feeding it the newly downsampled/demicated 
> surface as input.
>
> FWIW.
>
> Best
> -=R
>
> On 1/23/13 18:07 , Nicola Toschi wrote:
>> Hello list,
>>
>> is there a quick way to decimate an overlay /while respecting surface 
>> geomery)? I am looking to downsample by about a factor 100.
>>
>> Alternatively, I know I can use mris_decimate to downsample a 
>> surface, but I would have to project my highres overlays onto the 
>> downsampled surface (which may not be straightforward).
>>
>> Thanks a lot in advance,
>>
>> Nicola
>>
>> PS apologies for the repost - my subject line was incorrect the first 
>> time around.
>>
>>
>> ___
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>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

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Re: [Freesurfer] mni152reg error (file permission denied)

2013-01-24 Thread Douglas N Greve

Hi Tommi and Chris, this is a known bug that has been fixed in dev (and 
upcoming 5.2). Can you use the dev version just for this cmd?
doug


On 01/24/2013 12:14 PM, Chris McNorgan wrote:
> Hi Tommi,
> The mkdir error suggests to me that there is some system-level permissions 
> thing going on. If it can't make the directory, then there is no directory 
> into which fsl can write the refvol.fslregister.nii files, hence the final 2 
> errors.
>
> >From the command line, are you able to navigate to directory:
> /usr/pubsw/packages/fsl/current/data/standard/
> And within that directory, execute:
> mkdir 
>
> My guess is that you will get a permission denied error. You can try using 
> chmod to make the directory writable:
> chmod ugo+w /usr/pubsw/packages/fsl/current/data/standard/
> and see if you can now do a mkdir in that directory (you might have to be a 
> superuser to do this)
>
> Dear Surfers,
>
> mni152reg --$SUBJECT exits with the error:
>
> mkdir: cannot create directory
> `/usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.18402':
> Permission denied
>
> Thereafter, a couple consequential errors follow
> ...
> niiWrite(): error opening file
> 
> /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.18402/refvol.fslregister.nii
> ...
> ERROR: failure writing
> 
> /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.18402/refvol.fslregister.nii
>
> This is on FS 5.1.0 stable. The error seems linux box independent. Please
> let me know if you need further info. Thanks!
>
> Bests,
>
> Tommi
>
> -- 
> Chris McNorgan
> Postdoctoral Researcher
> Developmental Cognitive Neuroscience Laboratory
> Northwestern University, Evanston, IL
> DCNL Lab:http://tinyurl.com/9q35abd
> Frontiers Profile:http://tinyurl.com/aut488k
>
>
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Fax: 617-726-7422

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Re: [Freesurfer] Problem with glmfit: matrix is ill-conditioned

2013-01-24 Thread Douglas N Greve

Hi Ed, the problem is that your covariates are highly correlated. Eg, 
column 1 is nearly identical to column 17.
doug


On 01/24/2013 06:36 AM, Ed Gronenschild wrote:
> Hi,
>
> Running mri_glmfit ( v5.0.0, Mac OSX10.6) I got he following
> error message:
>
> ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08
> Possible problem with experimental design:
> Check for duplicate entries and/or lack of range of
> continuous variables within a class.
> If you seek help with this problem, make sure to send:
>   1. Your command line:
> mri_glmfit --y lh.sib_con_cann_aangepast3.thickness.sm0.mgh --fsgd 
> ../../STATS/FSGD/age_gender_scan_educ_hand_cannabis/fsgd_sib_con_cann_aangepast3.fsgd
>  
> dods --glmdir lh.sib_con_cann_aangepast3.dods.sm0.glmdir --surf 
> fsaverage lh --C 
> ../../STATS/FSGD/age_gender_scan_educ_hand_cannabis/group_thickness_gender_scan_age_educ_hand_cann.mtx
>  
>
>   2. The FSGD file (if using one)
>   3. And the design matrix above
>
> Please find attached the requested files.
>
> I noticed that rows 68 and 147 of the matrix Xg.dat are identical,
> and most probably caused the error.
> In the fsgd file I see that the correspondig cases indeed have
> identical values, although they are referring to different data.
> How to proceed?
>
> Cheers,
> Ed
>
> =
>
>
>
>
>
>
>
>
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gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] How to generate Cohen´s d Maps in Freesurfer

2013-01-24 Thread Douglas N Greve

Hi Javier, you don't want to use the gammarvar for Cohen's D. Gammavar 
is like the standard error (square of the std error). Instead, use 
rstd.mgh located in the main glmfit folder. Otherwise, I think your 
equation is right. I don't think you can do this with one call to 
fscalc. I think you'd need at least two.

doug

ps. Please post questions to the list and not directly to me. Thanks!

On 01/24/2013 07:55 AM, Javier Navas wrote:
> Hi Doug,
>
> I´m very new in Freesurfer and I cannot obtain a Cohen´s d Map as a 
> Effect Size measure. Is it possible to generate surface maps for the 
> Cohen´s d in cortical thickness between 2 groups within with Freesurfer.
> I have the mean thickness for each group; after obtained these 
> gamma.mgh I tried with fscalc but I do not know how to do it: | 
> MeanGroup1 sub MeanGroup2 | /sqrt((Std12add Std22)/2) ... it is right???
>
> Is the gammavar.mgh the Standard Deviation (Std) ???
>
> Thank you in advance
>
> -- 
> /**\
> Francisco Javier Navas Sánchez
>  Laboratorio de Imagen Médica U.M.C.E.
>  Hospital General Universitario Gregorio Marañón
>  Dr Esquerdo 46, 28007 Madrid, Spain
>  Phone : (+34) 91 426 50 67   Fax: (+34) 91 426 5108
> e-mail:jna...@hggm.es  
> http://image.hggm.es

-- 
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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] Memory problem

2013-01-24 Thread Nick Schmansky

Mia,

this time it looks like there was plenty of memory, but it exited on a
defect.  make sure the wm.mgz looks good (doesnt have stuff outside the
white matter).  see the 'topological defects' section of our tutorial for
info on what to look for and how to fix it.

Nick

> Hi freesurfers,
>
> So i reran recon-all -make all overnight, and it ended with errors still.
> It looks like the same error (I attached the log). There was another
> process running while I ran the recon the first time, but I made sure that
> wasn't the case this time around. Is the solution running the recon in a
> whole new place with more space?
>
> Thanks so much,
> m
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Nick Schmansky
> [ni...@nmr.mgh.harvard.edu]
> Sent: Wednesday, January 23, 2013 1:45 PM
> To: Douglas N Greve
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Memory problem
>
> Mia,
>
> also i noticed this at the top of the log:
>
>  total   used   free
> Mem:  37010736   19490372   17520364
> -/+ buffers/cache:   10784236   26226500
> Swap:  8393952 1505288243424
>
>
> it shows that just 1.7GB is available for the recon to run, which is
> below what we recommend.  recon-all usually needs at least 2GB.
>
> after inspecting for defects like doug suggests, you could try stopping
> other apps that are consuming mem (or just reboot which will ensure
> maximal free memory) and then run recon-all -make all
>
> Nick
>
>
>
>
> On Wed, 2013-01-23 at 13:23 -0500, Douglas N Greve wrote:
>> Hi Mia, try looking at the lh.orig.nofix surface. There may be a huge
>> defect (like the entire cerebellum is attached). You can run
>>
>> tkmedit MG58_SurferOutput_postop orig.mgz lh.orig.nofix
>>
>> Note that you will get a few error messages when loading the orig.nofix
>> surface. These can be ignored
>>
>> doug
>>
>> On 01/23/2013 12:19 PM, Borzello, Mia wrote:
>> > Hey Freesurfers,
>> >
>> > I received a "Cannot allocate memory" error while running a recon
>> overnight. I think there should be enough space on the machine to
>> store the data so I'm suspicious that it's a different memory problem.
>> > I attached the recon-all.log file.
>> >
>> > Thanks for your help!
>> > m
>> >
>> >
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Re: [Freesurfer] ERROR: /52/freesurfer/average/3T18yoSchwartzReactN32_as_orig.4dfp.img does not exist!

2013-01-24 Thread Nick Schmansky

the best option is to download the beta of v5.2 which linked from here:
https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes  (look for 'Get a
BETA here').  i've confirmed that that atlas is contained in that release.

Nick



> Hi FS experts,
> I read that the current dev version for recon-all is going to be the same
> to the 5.2 version, so I started a new project with the dev version (in
> CentOS 4).
>
> I have this very strange error that I am unable to interpret, when running
> mpr2mni305 in one case the target is specified as
> 711-2C_as_mni_average_305, but in the dev version the target is
> 3T18yoSchwartzReactN32_as_orig, this file does not exist...
>
>
> What should I try now?
>
> (just in case, this is the command I launch: recon-all --i x -s
> xxx
> -qcache -hippo-subfields -all
>
>
> (This is the talairach_avi.log)
> ERROR WITH DEV VERSION
> 
> /home/glerma/FS/52/freesurfer/subjects/TNT/S_08/mri
> /home/glerma/FS/52/freesurfer/bin/talairach_avi
> --i orig_nu.mgz --xfm transforms/talairach.auto.xfm
> $Id: talairach_avi,v 1.10 2012/07/16 15:54:03 nicks Exp $
> Linux cajal 2.6.18-164.15.1.el5 #1 SMP Wed Mar 17 11:30:06 EDT 2010 x86_64
> x86_64 x86_64 GNU/Linux
> Thu Jan 24 00:26:09 CET 2013
> mri_convert orig_nu.mgz talsrcimg.img
> $Id: mri_convert.c,v 1.202 2012/10/17 19:23:56 greve Exp $
> reading from orig_nu.mgz...
> TR=2300.00, TE=2.97, TI=1100.00, flip angle=9.00
> i_ras = (-1, -3.03407e-09, 2.32831e-10)
> j_ras = (1.16415e-10, 0, -1)
> k_ras = (3.03407e-09, 1, 3.72529e-09)
> writing to talsrcimg.img...
> Analyze Output Matrix
> -1.000   0.000   0.000   132.933;
> -0.000   0.000   1.000  -105.037;
>  0.000  -1.000   0.000   161.057;
>  0.000   0.000   0.000   1.000;
> 
> INFO: set hdr.hist.orient to -1
> mpr2mni305 talsrcimg
> Thu Jan 24 00:26:10 CET 2013
> /home/glerma/FS/52/freesurfer/bin/mpr2mni305 talsrcimg
> $Id: mpr2mni305,v 1.4 2009/06/03 16:01:38 nicks Exp $
> target=3T18yoSchwartzReactN32_as_orig
> ERROR:
> /home/glerma/FS/52/freesurfer/average/3T18yoSchwartzReactN32_as_orig.4dfp.img
> does not exist!
>
>
>
>
> SAME SUBJECT, SAME HARD and OS, 5.0 VERSION
> -
> /home/BCBL/glerma/freesurfer/subjects/TNT/S_08/mri
> /usr/local/freesurfer/bin/talairach_avi
> --i nu.mgz --xfm transforms/talairach.auto.xfm
> $Id: talairach_avi,v 1.7 2010/02/07 22:50:52 nicks Exp $
> Linux cajal 2.6.18-164.15.1.el5 #1 SMP Wed Mar 17 11:30:06 EDT 2010 x86_64
> x86_64 x86_64 GNU/Linux
> Sat Aug 25 06:44:15 CEST 2012
> mri_convert nu.mgz talsrcimg.img
> $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $
> reading from nu.mgz...
> TR=2300.00, TE=2.97, TI=1100.00, flip angle=9.00
> i_ras = (-1, 0, 5.55112e-17)
> j_ras = (5.55112e-17, 3.72529e-09, -1)
> k_ras = (4.44089e-16, 1, -1.05964e-18)
> writing to talsrcimg.img...
> Analyze Output Matrix
> -1.000   0.000   0.000   132.933;
>  0.000   0.000   1.000  -105.037;
>  0.000  -1.000  -0.000   161.057;
>  0.000   0.000   0.000   1.000;
> 
> INFO: set hdr.hist.orient to -1
> mpr2mni305 talsrcimg
> Sat Aug 25 06:44:16 CEST 2012
> /usr/local/freesurfer/bin/mpr2mni305 talsrcimg
> $Id: mpr2mni305,v 1.4 2009/06/03 16:01:38 nicks Exp $
> target=711-2C_as_mni_average_305
>
>  continues--
>
>
>
>
>
> and this is the setup output:
>  freesurfer-Linux-centos4_x86_64-dev-20121127 
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> FREESURFER_HOME   /home/glerma/FS/52/freesurfer
> FSFAST_HOME   /home/glerma/glerma/software/freesurfer/fsfast  >> older
> version location
> FSF_OUTPUT_FORMAT nii.gz
> SUBJECTS_DIR  /home/glerma/FS/52/freesurfer/subjects/TNT
> MNI_DIR   /home/glerma/FS/52/freesurfer/mni
> FSL_DIR   /usr/local/fsl
>
>
>
> many thanks!
> Gari
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Re: [Freesurfer] Results Vary

2013-01-24 Thread Nick Schmansky

Derin,

the results vary only a tiny bit because of differences in the
talairach_with_skull.lta file, which was created twice, the second time
with aseg info, which would cause the brainmask to vary slightly if run a
second time.  the result differences are well below what you would find
with randomness enabled.

Nick

> Hi Nick,
>
> Could you clarify this? So if we re-run a subject in 5.1 (say after doing
> some edits), we would then need to run it again a third time in order to
> maintain consistency? Thanks.
>
> -Derin
>
>
> On Jan 22, 2013, at 2:17 PM, Nick Schmansky 
> wrote:
>
>> also there is an issue in v5.1 where the second run of recon-all on a
>> given platform will produce different results from the first (but
>> subsequent runs should produce identical results).  this issue has been
>> fixed in the upcoming v5.2 release.
>>
>> nick
>>
>>
>> On Tue, 2013-01-22 at 10:18 -0500, Douglas N Greve wrote:
>>> Hi Chikku, while we try to resolve these differences, you are not
>>> guaranteed to get identical results when you use different platforms.
>>> This is an issue with using different computes and applies to all
>>> software, not just FS.It is caused by the use of different math
>>> libraries and different binary operations. The difference you show is
>>> only 0.3% which should not be enough to cause false results.
>>> doug
>>>
>>>
>>>
>>> On 01/22/2013 08:13 AM, Varghese Chikku wrote:

 Dear FS team,
 I processed two set of MRI  data for a  single  patient,Thats BL scan
 and TP1.I ran both scans on a Mcbook Pro and  a PC with Virtual
 machine installed.
 Though I was expecting the  same segstats,the  results vary from
 Macpro to VM.For eg , for BL in Mac  SubCortGrayVol is 178038 but  for
 the  same  images in VM  the  results are 177432.Does it happened to
 any one beforeWhats the  reson its  happening and how  can  I
 remedy,validate the  results.
 Much appreciate  your  advice,...
 In Thanks
 Chikku.




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>>
>>
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>> it is
>> addressed. If you believe this e-mail was sent to you in error and the
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>> HelpLine at
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>> but does not contain patient information, please contact the sender and
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>> dispose of the e-mail.
>>
>
>
>
>

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[Freesurfer] thickness=0, what that means?

2013-01-24 Thread jm

Dears Freesurfer:

We are looking into *lh.thickness.fwhm15.fsaverage**.mgh* file and we
can see some vertexes with thickness value equal to 0 (thickness=0 mm).
Could you tell me when that value is reported by Freesurfer? what do
(thickness=0) means?

Thanks in advance !!!
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Re: [Freesurfer] thickness=0, what that means?

2013-01-24 Thread Douglas N Greve

It usually means that it is part of the medial wall where there is no 
cortex. For technical reasons we need to have the surface be a closed 
surface (like a sphere). That means that there have to be places that 
don't have cortex but we still need to represent. In these places 
thickness is set to 0.
doug
On 01/24/2013 02:21 PM, jm wrote:
> Dears Freesurfer:
>
> We are looking into *lh.thickness.fwhm15.fsaverage**.mgh* file and we
> can see some vertexes with thickness value equal to 0 (thickness=0 mm).
> Could you tell me when that value is reported by Freesurfer? what do
> (thickness=0) means?
>
> Thanks in advance !!!
>
>
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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: 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] thickness=0, what that means?

2013-01-24 Thread Bruce Fischl

those are probably in non-cortical regions like the midline

cheers
Bruce
On Thu, 24 Jan 
2013, jm wrote:

> Dears Freesurfer:
>
> We are looking into *lh.thickness.fwhm15.fsaverage**.mgh* file and we
> can see some vertexes with thickness value equal to 0 (thickness=0 mm).
> Could you tell me when that value is reported by Freesurfer? what do
> (thickness=0) means?
>
> Thanks in advance !!!
>
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[Freesurfer] mean cluster surface area in mri_glmfit

2013-01-24 Thread xiangbo_2010

Dear Freesurfer Experts,
I would like the mean surface area measures of each cluster i found using 
command line (mri_glmfit). I used mri_glmfit for a group comparison in surface 
area between a patient group and a healthy control group. I found 4 different 
significant clusters (using FDR corrected, is not Clusterwise Correction for 
Multiple Comparisons). I would like to extract the mean surface area  of each 
significant cluster in the patient group and in the healthy control group.  
Where can i found the file with this information? thanks!

 
Bo Xiang



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[Freesurfer] Testing new beta v5.2.0: Error in mri_segstats --euler

2013-01-24 Thread Johnson, Hans J

In mri_segstats command line generated from autorecon, I get an error that the 
option "--euler" is unknown.


== /nfsscratch/PREDICT/opt/freesurfer-5.2-beta/freesurfer/bin/recon-all
3667   if( ( -e surf/lh.orig.nofix ) && ( -e surf/rh.orig.nofix ) ) then
3668   set cmd = ($cmd --euler)
3669   endif




Cut-and-paste the following info into your FreeSurfer problem report:
-

FREESURFER_HOME: /nfsscratch/PREDICT/opt/freesurfer-5.2-beta/freesurfer

Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0

RedHat release: CentOS release 5.8 (Final)

Kernel info: Linux 2.6.18-308.16.1.el5 x86_64

-
Please include the following additional information in your report:

  1) subject name
  2) the entire command-line executed
  3) the error message generated
  4) optionally include the subject's /script/recon-all.log

See also: http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

1)Subject Name = 12126_12126_20091110_30

2) We are running on a shared cluster of computers, so we wanted to break it 
into 3 sections to make it more robust to failing jobs.

#!/bin/bash
export FREESURFER_HOME=/nfsscratch/PREDICT/opt/freesurfer-5.2-beta/freesurfer
export 
SUBJECTS_DIR=/nfsscratch/PREDICT/hjohnson/TrackOn/Experiments/20130109_TrackOn_CACHE/12126/BAWFS_SUBJECTS
source /nfsscratch/PREDICT/opt/freesurfer-5.2-beta/freesurfer/FreeSurferEnv.sh
/nfsscratch/PREDICT/opt/freesurfer-5.2-beta/freesurfer/bin/recon-all -debug 
-subjid 12126_12126_20091110_30 -make autorecon1
status=$?
exit $status

#!/bin/bash
export FREESURFER_HOME=/nfsscratch/PREDICT/opt/freesurfer-5.2-beta/freesurfer
export 
SUBJECTS_DIR=/nfsscratch/PREDICT/hjohnson/TrackOn/Experiments/20130109_TrackOn_CACHE/12126/BAWFS_SUBJECTS
source /nfsscratch/PREDICT/opt/freesurfer-5.2-beta/freesurfer/FreeSurferEnv.sh
/nfsscratch/PREDICT/opt/freesurfer-5.2-beta/freesurfer/bin/recon-all -debug 
-subjid 12126_12126_20091110_30 -make autorecon2
status=$?
exit $status

#!/bin/bash
export FREESURFER_HOME=/nfsscratch/PREDICT/opt/freesurfer-5.2-beta/freesurfer
export 
SUBJECTS_DIR=/nfsscratch/PREDICT/hjohnson/TrackOn/Experiments/20130109_TrackOn_CACHE/12126/BAWFS_SUBJECTS
source /nfsscratch/PREDICT/opt/freesurfer-5.2-beta/freesurfer/FreeSurferEnv.sh
/nfsscratch/PREDICT/opt/freesurfer-5.2-beta/freesurfer/bin/recon-all -debug 
-subjid 12126_12126_20091110_30 -make autorecon3
status=$?
exit $status

3)
#
#@# ASeg Stats Thu Jan 24 20:57:29 CST 2013
/nfsscratch/PREDICT/hjohnson/TrackOn/Experiments/20130109_TrackOn_CACHE/12126/BAWFS_SUBJECTS/12126_12126_20091110_30

 mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz 
--empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 
--excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name 
norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray 
--euler --ctab 
/nfsscratch/PREDICT/opt/freesurfer-5.2-beta/freesurfer/ASegStatsLUT.txt 
--subject 12126_12126_20091110_30

ERROR: Option --euler unknown
Linux helium-login-0-0.local 2.6.18-308.16.1.el5 #1 SMP Tue Oct 2 22:01:43 EDT 
2012 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s 12126_12126_20091110_30 exited with ERRORS at Thu Jan 24 20:57:30 
CST 2013






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may be legally privileged.  If you are not the intended recipient, you are 
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Re: [Freesurfer] Testing new beta v5.2.0: Error in mri_segstats --euler

2013-01-24 Thread Douglas Greve

I think the version of 5.2 that Nick cut was a little out of synch with 
some changes I made. Try using this version of mri_segstats


ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.centos4

doug

On 1/24/13 10:14 PM, Johnson, Hans J wrote:
In mri_segstats command line generated from autorecon, I get an error 
that the option "--euler" is unknown.



== /nfsscratch/PREDICT/opt/freesurfer-5.2-beta/freesurfer/bin/recon-all
3667   if( ( -e surf/lh.orig.nofix ) && ( -e surf/rh.orig.nofix ) ) then
3668   set cmd = ($cmd --euler)
3669   endif




Cut-and-paste the following info into your FreeSurfer problem report:
-

FREESURFER_HOME: /nfsscratch/PREDICT/opt/freesurfer-5.2-beta/freesurfer

Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0

RedHat release: CentOS release 5.8 (Final)

Kernel info: Linux 2.6.18-308.16.1.el5 x86_64

-
Please include the following additional information in your report:

  1) subject name
  2) the entire command-line executed
  3) the error message generated
  4) optionally include the subject's /script/recon-all.log

See also: http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

1)Subject Name = 12126_12126_20091110_30

2) We are running on a shared cluster of computers, so we wanted to 
break it into 3 sections to make it more robust to failing jobs.


#!/bin/bash
export 
FREESURFER_HOME=/nfsscratch/PREDICT/opt/freesurfer-5.2-beta/freesurfer
export 
SUBJECTS_DIR=/nfsscratch/PREDICT/hjohnson/TrackOn/Experiments/20130109_TrackOn_CACHE/12126/BAWFS_SUBJECTS
source 
/nfsscratch/PREDICT/opt/freesurfer-5.2-beta/freesurfer/FreeSurferEnv.sh
/nfsscratch/PREDICT/opt/freesurfer-5.2-beta/freesurfer/bin/recon-all 
-debug -subjid 12126_12126_20091110_30 -make autorecon1

status=$?
exit $status

#!/bin/bash
export 
FREESURFER_HOME=/nfsscratch/PREDICT/opt/freesurfer-5.2-beta/freesurfer
export 
SUBJECTS_DIR=/nfsscratch/PREDICT/hjohnson/TrackOn/Experiments/20130109_TrackOn_CACHE/12126/BAWFS_SUBJECTS
source 
/nfsscratch/PREDICT/opt/freesurfer-5.2-beta/freesurfer/FreeSurferEnv.sh
/nfsscratch/PREDICT/opt/freesurfer-5.2-beta/freesurfer/bin/recon-all 
-debug -subjid 12126_12126_20091110_30 -make autorecon2

status=$?
exit $status

#!/bin/bash
export 
FREESURFER_HOME=/nfsscratch/PREDICT/opt/freesurfer-5.2-beta/freesurfer
export 
SUBJECTS_DIR=/nfsscratch/PREDICT/hjohnson/TrackOn/Experiments/20130109_TrackOn_CACHE/12126/BAWFS_SUBJECTS
source 
/nfsscratch/PREDICT/opt/freesurfer-5.2-beta/freesurfer/FreeSurferEnv.sh
/nfsscratch/PREDICT/opt/freesurfer-5.2-beta/freesurfer/bin/recon-all 
-debug -subjid 12126_12126_20091110_30 -make autorecon3

status=$?
exit $status

3)
#
#@# ASeg Stats Thu Jan 24 20:57:29 CST 2013
/nfsscratch/PREDICT/hjohnson/TrackOn/Experiments/20130109_TrackOn_CACHE/12126/BAWFS_SUBJECTS/12126_12126_20091110_30

 mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv 
mri/norm.mgz --empty --brainmask mri/brainmask.mgz 
--brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent 
--subcortgray --in mri/norm.mgz --in-intensity-name norm 
--in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol 
--totalgray --euler --ctab 
/nfsscratch/PREDICT/opt/freesurfer-5.2-beta/freesurfer/ASegStatsLUT.txt --subject 12126_12126_20091110_30 



ERROR: Option --euler unknown
Linux helium-login-0-0.local 2.6.18-308.16.1.el5 #1 SMP Tue Oct 2 
22:01:43 EDT 2012 x86_64 x86_64 x86_64 GNU/Linux


recon-all -s 12126_12126_20091110_30 exited with ERRORS at Thu Jan 24 
20:57:30 CST 2013







Notice: This UI Health Care e-mail (including attachments) is covered 
by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is 
confidential and may be legally privileged.  If you are not the 
intended recipient, you are hereby notified that any retention, 
dissemination, distribution, or copying of this communication is 
strictly prohibited.  Please reply to the sender that you have 
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Re: [Freesurfer] Downsampling/decimating overlays (not surfaces)

[Freesurfer] ERROR: /52/freesurfer/average/3T18yoSchwartzReactN32_as_orig.4dfp.img does not exist!

Re: [Freesurfer] Downsampling/decimating overlays (not surfaces)

Re: [Freesurfer] mni152reg error (file permission denied)

Re: [Freesurfer] Downsampling/decimating overlays (not surfaces)

Re: [Freesurfer] mni152reg error (file permission denied)

Re: [Freesurfer] Problem with glmfit: matrix is ill-conditioned

Re: [Freesurfer] How to generate Cohen´s d Maps in Freesurfer

Re: [Freesurfer] Memory problem

Re: [Freesurfer] ERROR: /52/freesurfer/average/3T18yoSchwartzReactN32_as_orig.4dfp.img does not exist!

Re: [Freesurfer] Results Vary

[Freesurfer] thickness=0, what that means?

Re: [Freesurfer] thickness=0, what that means?

Re: [Freesurfer] thickness=0, what that means?

[Freesurfer] mean cluster surface area in mri_glmfit

[Freesurfer] Testing new beta v5.2.0: Error in mri_segstats --euler

Re: [Freesurfer] Testing new beta v5.2.0: Error in mri_segstats --euler

17 matches

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