date:20151211

Re: [Freesurfer] ERROR: Talairach QA check failed! and ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm FAILED

2015-12-11 Thread Matthieu Vanhoutte

Hi Bruce,

Do you have an idea of what to do concerning this problem (below) ? I have
re-run with -notal-check and it worked not for all cases

Best regards,
Matthieu

2015-12-09 15:15 GMT+01:00 Matthieu Vanhoutte :

> Hi Bruce,
>
> I tried to follow the tutorial :
> http://freesurfer.net/fswiki/FsTutorial/Talairach_freeview
>
> But nothing appeared in the image window of tkregister2 command... Below
> you'll find the log of the command :
>
> tkregister2 --mgz --s M0_2010-03-25 --fstal
> tkregister_tcl /home/global//freesurfer5.3//tktools/tkregister2.tcl
> INFO: no target volume specified, assuming FreeSurfer orig volume.
> target  volume orig
> movable volume (null)
> reg file   (null)
> LoadVol1
> ZeroCRAS   1
> $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $
> Diagnostic Level -1
>
> %Fri Dec  4 15:13:39 2015>>>
> /home/global//freesurfer5.3//mni/bin/minctracc -clobber -debug
> /tmp/1504527.1.M32_q/mritotal_31071/src_8_dxyz.mnc
> /home/global//freesurfer5.3//mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc
> transforms/talairach.auto.xfm -transformation
> /tmp/1504527.1.M32_q/mritotal_31071/src_8tmp2c.xfm -lsq9 -xcorr -model_mask
> /home/global//freesurfer5.3//mni/bin/../share/mni_autoreg/average_305_8_mask.mnc
> -center 5.23 17.591406 -32.821045 -step 4 4 4 -tol 0.004 -simplex 2
>
> talairach.xfm -
>  0.708   0.183  -0.254  -31.077;
> -0.311   0.477  -0.525  -62.791;
>  0.033   0.582   0.509   156.288;
>  0.000   0.000   0.000   1.000;
> INFO: loading target /NAS/tupac/matthieu/FS5.3/M0_2010-03-25/mri/orig.mgz
> Zeroing CRAS of target
> new xfm -
>  0.708   0.183  -0.254  -25.242;
> -0.311   0.477  -0.525  -57.556;
>  0.033   0.582   0.509   165.535;
>  0.000   0.000   0.000   1.000;
> -
> INFO: changing target type to float
> Ttarg: 
> -1.000  -0.000   0.000   128.000;
> -0.000  -0.000   1.000  -128.000;
>  0.000  -1.000   0.000   128.000;
>  0.000   0.000   0.000   1.000;
> INFO: loading movable /home/global//freesurfer5.3//average/mni305.cor.mgz
> INFO: changing move type to float
> Tmov: 
> -1.000   0.000   0.000   128.000;
>  0.000   0.000   1.000  -128.000;
>  0.000  -1.000   0.000   128.000;
>  0.000   0.000   0.000   1.000;
> mkheaderreg = 0, float2int = 0
>  Input registration matrix 
>  0.708   0.183  -0.254  -25.242;
> -0.311   0.477  -0.525  -57.556;
>  0.033   0.582   0.509   165.535;
>  0.000   0.000   0.000   1.000;
> Determinant 0.464133
> subject = M0_2010-03-25
> Zoom Factor = 2, SQR() = 4
> FOV = 256
> Opening window M0_2010-03-25
> Opening M0_2010-03-25, xnum = 256, xdim = 512
> Setting scale
> tkregister2: interface:
> /home/global//freesurfer5.3//tktools/tkregister2.tcl
> tkregister.tcl: startup done
> tkregister.tcl: default macro interface (to change: macro,mini,micro)
> tkregister.tcl: or: setenv tkregisterinterface {macro,mini,micro}
>
> T1.mgz, brainmask.mgz and subject's surfaces haven't been created yet. I
> have checked that my input volume has the correct direction cosines.
>
> Could you explain me what's wrong ?
>
> Thanks !
>
> Best regards,
> Matthieu
>
> 2015-12-08 22:08 GMT+01:00 Bruce Fischl :
>
>> Hi Matthieu
>>
>> did you check the talairach registration as suggested? ALso, make sure
>> that your input volume has the correct direction cosines (that is, that
>> what freeview thinks is anterior is actually anterior, etc...)
>> cheers
>> Bruce
>>
>>
>>
>> On Tue, 8 Dec 2015, Matthieu Vanhoutte wrote:
>>
>> Dear FS experts,
>>>
>>> I got no answer to my question. Could anyone explain me what is the
>>> problem and how to solve it ?
>>>
>>> Best regards,
>>> Matthieu
>>>
>>> 2015-12-04 16:11 GMT+01:00 Matthieu Vanhoutte <
>>> matthieuvanhou...@gmail.com>:
>>>   Dear experts,
>>>
>>> I am confronted with some problem in the "recon-all" of a few subjects
>>> concerning Talairach
>>> space, but don't know how to manage these.
>>>
>>> Please find below the recon-all log with errors :
>>>
>>> #
>>> #@# Talairach Failure Detection Fri Dec  4 15:29:38 CET 2015
>>> /NAS/tupac/matthieu/FS5.3/M0_2011-02-23/mri
>>>
>>>  talairach_afd -T 0.005 -xfm transforms/talairach.xfm
>>>
>>> talairach_afd: Talairach Transform: transforms/talairach.xfm OK
>>> (p=0.6911, pval=0.4932 >=
>>> threshold=0.0050)
>>>
>>>  awk -f /home/global//freesurfer5.3//bin/extract_talairach_avi_QA.awk
>>> /NAS/tupac/matthieu/FS5.3/M0_2011-02-23/mri/transforms/talairach_avi.log
>>>
>>>
>>>  tal_QC_AZS
>>> /NAS/tupac/matthieu/FS5.3/M0_2011-02-23/mri/transforms/talairach_avi.log
>>>
>>> TalAviQA: 0.93027
>>> z-score: -10
>>> ERROR: Talairach QA check failed!
>>>z-score = -10 <= -9 = threshold
>>>atlas xform error = 0 < -60 | > 24
>>> Manual Talairach alignment may be necessary, or
>>> include the -notal-check flag to skip this test,
>>> making sure

Re: [Freesurfer] ERROR: Talairach QA check failed! and ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm FAILED

2015-12-11 Thread Bruce Fischl

did it have the correct orientation? Can you explain what the initial 
images were? Usually if you start from dicoms right from the scanner with a 
reasonable scan this isn't a problem so if it's happening frequently then 
it may be that something else is wrong.


cheers
Bruce

On Fri, 11 Dec 2015, Matthieu 
Vanhoutte wrote:



Hi Bruce,

Do you have an idea of what to do concerning this problem (below) ? I have
re-run with -notal-check and it worked not for all cases

Best regards,
Matthieu

2015-12-09 15:15 GMT+01:00 Matthieu Vanhoutte :
  Hi Bruce,

I tried to follow the tutorial :
http://freesurfer.net/fswiki/FsTutorial/Talairach_freeview

But nothing appeared in the image window of tkregister2 command...
Below you'll find the log of the command :

tkregister2 --mgz --s M0_2010-03-25 --fstal
tkregister_tcl /home/global//freesurfer5.3//tktools/tkregister2.tcl
INFO: no target volume specified, assuming FreeSurfer orig volume.
target  volume orig
movable volume (null)
reg file   (null)
LoadVol    1
ZeroCRAS   1
$Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $
Diagnostic Level -1

%Fri Dec  4 15:13:39 2015>>>
/home/global//freesurfer5.3//mni/bin/minctracc -clobber -debug
/tmp/1504527.1.M32_q/mritotal_31071/src_8_dxyz.mnc/home/global//freesurfer5.3//mni/bin/../share/mni_autoreg/average_305_8_dxy
z.mnc transforms/talairach.auto.xfm -transformation
/tmp/1504527.1.M32_q/mritotal_31071/src_8tmp2c.xfm -lsq9 -xcorr
-model_mask/home/global//freesurfer5.3//mni/bin/../share/mni_autoreg/average_305_8_mas
k.mnc -center 5.23 17.591406 -32.821045 -step 4 4 4 -tol 0.004
-simplex 2

talairach.xfm -
 0.708   0.183  -0.254  -31.077;
-0.311   0.477  -0.525  -62.791;
 0.033   0.582   0.509   156.288;
 0.000   0.000   0.000   1.000;
INFO: loading target
/NAS/tupac/matthieu/FS5.3/M0_2010-03-25/mri/orig.mgz
Zeroing CRAS of target
new xfm -
 0.708   0.183  -0.254  -25.242;
-0.311   0.477  -0.525  -57.556;
 0.033   0.582   0.509   165.535;
 0.000   0.000   0.000   1.000;
-
INFO: changing target type to float
Ttarg: 
-1.000  -0.000   0.000   128.000;
-0.000  -0.000   1.000  -128.000;
 0.000  -1.000   0.000   128.000;
 0.000   0.000   0.000   1.000;
INFO: loading movable
/home/global//freesurfer5.3//average/mni305.cor.mgz
INFO: changing move type to float
Tmov: 
-1.000   0.000   0.000   128.000;
 0.000   0.000   1.000  -128.000;
 0.000  -1.000   0.000   128.000;
 0.000   0.000   0.000   1.000;
mkheaderreg = 0, float2int = 0
 Input registration matrix 
 0.708   0.183  -0.254  -25.242;
-0.311   0.477  -0.525  -57.556;
 0.033   0.582   0.509   165.535;
 0.000   0.000   0.000   1.000;
Determinant 0.464133
subject = M0_2010-03-25
Zoom Factor = 2, SQR() = 4
FOV = 256
Opening window M0_2010-03-25
Opening M0_2010-03-25, xnum = 256, xdim = 512
Setting scale
tkregister2: interface:
/home/global//freesurfer5.3//tktools/tkregister2.tcl
tkregister.tcl: startup done
tkregister.tcl: default macro interface (to change: macro,mini,micro)
tkregister.tcl: or: setenv tkregisterinterface {macro,mini,micro}

T1.mgz, brainmask.mgz and subject's surfaces haven't been created yet.
I have checked that my input volume has the correct direction cosines.

Could you explain me what's wrong ?

Thanks !

Best regards,
Matthieu

2015-12-08 22:08 GMT+01:00 Bruce Fischl :
  Hi Matthieu

  did you check the talairach registration as suggested?
  ALso, make sure that your input volume has the correct
  direction cosines (that is, that what freeview thinks is
  anterior is actually anterior, etc...)
  cheers
  Bruce


  On Tue, 8 Dec 2015, Matthieu Vanhoutte wrote:

Dear FS experts,

I got no answer to my question. Could anyone
explain me what is the problem and how to
solve it ?

Best regards,
Matthieu

2015-12-04 16:11 GMT+01:00 Matthieu Vanhoutte
:
      Dear experts,

I am confronted with some problem in the
"recon-all" of a few subjects concerning
Talairach
space, but don't know how to manage these.

Please find below the recon-all log with
errors :

#
#@# Talairach Failure Detection Fri Dec  4
15:29:38 CET 2015
/NAS/tupac/matthieu/FS5.3/M0_2011-02-23/mri

 talairach_afd -T 0.005 -xfm
transforms/talairach.xfm

talairach_afd: Talairach Transform:
transforms/talairach.xfm OK (p=0.6911,
pval=0.4932 >=
threshold=0.0050)

 awk -f
/home/global//freesurfer5.3//bin/extract_talairach_avi_QA.awk

Re: [Freesurfer] Convert TAL coordinates to surface RAS coordinates

2015-12-11 Thread Inês Violante

Using the previous equation I tried to calculate [tkrR tkrA tkrS] for
MNI = [43 -69 47]. Which are ~ MNI coordinates for P4 (electrode 10-20
system)

[43 -69 47 1]/(TalXFM*Norig*inv(Torig))

This resulted in [46.0541   -7.9735   -4.1630]. However, this
coordinates in RAS surface space are not even near the place where
they were supposed to be, taking into account the projection of P4 to
the cortex.

Any ideas about what could be wrong?

Thank you very much,

ines

On Fri, Dec 11, 2015 at 4:20 PM, Inês Violante  wrote:
> Dear Douglas,
>
> I've been looking a that page for a while now and I am very confused...
>
> Are you referring to this example?
>
> 2. I have an RAS point on the surface (tkrR tkrA tkrS) ("Vertex RAS"
> from tksurfer) and want to compute the MNI305 RAS that corresponds to
> this point:
>
> MNI305RAS = TalXFM*Norig*inv(Torig)*[tkrR tkrA tkrS 1]'
>
> TalXFM: subject/orig/transforms/talairach.xfm Norig: mri_info
> --vox2ras orig.mgz Torig: mri_info --vox2ras-tkr orig.mgz
>
> So, is it the case that I just do the equation like this:
>
> [tkrR tkrA tkrS 1]' = [X Y Z (in MNIspace)] / TalXFM*Norig*inv(Torig)
>
>
> Thank you,
>
> ines
>
> On Fri, Dec 11, 2015 at 4:12 PM, Douglas Greve
>  wrote:
>>
>> See if this helps
>>
>> https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
>>
>>
>> On 12/11/15 10:23 AM, Inês Violante wrote:
>>> Dear experts,
>>>
>>> I have a set of Talairach coordinates that I want to convert to the
>>> individual subject surf RAS coordinates.
>>> How can I do this?
>>>
>>> Thank you very much.
>>>
>>> Ines
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>
>> ___
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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
>> http://www.partners.org/complianceline . If the e-mail was sent to you in 
>> error
>> but does not contain patient information, please contact the sender and 
>> properly
>> dispose of the e-mail.
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Re: [Freesurfer] correlations with longitudinal data

2015-12-11 Thread Clara Kühn

Hi Freesurfer experts,

I eventually used the recon-all -s subjectname -qcache -target my_template to 
get the smoothed surfaces to use in qdec and therefore do cross-sectional 
analyses on the single tps of my longitudinal data.
I did the analyses on the left hemisphere so far. Now that I tried using the 
right hemisphere I get the error message "multiple surfaces must have the same 
number of vertices". What does that mean? As far as I understood, the recon-all 
-qcache created smoothed surfaces for the right and left hemisphere. At least 
everything is in the respective folders...

Cheers and thanks in advance!
Clara

- Ursprüngliche Mail -
Von: "ckuehn" 
An: "Freesurfer support list" 
Gesendet: Mittwoch, 9. Dezember 2015 10:27:40
Betreff: Re: [Freesurfer] correlations with longitudinal data

Hi Martin, 

thanks for your reply.
I have created a qdec file with the fsidtp1.long.fsid.base as first column and 
specified the long directories with /path_to_data/*.long.*. And each subject 
has a ?h.thickness file from the recon-process. However, Qdec is asking for a 
very specific file ?h.thickness.fwhm10.nameoftemplate.mgz or .mgh (even when I 
pick 0 smoothing).

If I understand correctly, that is the file that I get when running the 
mris_slope command. But you said I wouldn't need that. Is there a way to get 
these files for a cross-sectional analysis of the *.long.*.base timepoints? 

My qdec file currently looks like this:

fsid group sex age (in months) ... (behavioral measures)
_1.long..base 1 0 52 ... 
_1.long..base 2 1 48 ...
...

Thank you,
Clara

- Ursprüngliche Mail -
Von: "mreuter" 
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Dienstag, 8. Dezember 2015 18:14:40
Betreff: Re: [Freesurfer] correlations with longitudinal data

Hi Clara,

you would do the analysis of a single time point the same way you'd run 
a regular glm or qdec analysis on cross sectional data. You cannot use 
LME as that is for longitudinal data (more than 1 time point per 
subject, at least for most subjects). Also the two stage model, first 
reduces to multiple measures in each subject to a single measure (slope 
of the linear fit). It would not be the right tool for selecting a 
single time point.

You could for example create a qdec table with the first row  fsid
timepoint1.long.base
for each subject and then use qdec.

If you want to make use of the improved data from the longitudinal image 
processing, you need to specify the *.long.base directories, so that 
data is taken from there.

Good luck, Martin

On 12/08/2015 04:24 AM, Clara Kühn wrote:
> Dear FreeSurfer experts,
>
> I have a subsample of my longitudinal data with 3 scans per subjects fully 
> preprocessed and would like to start with some simple correlations of 
> thickness at time 1 with behavioral measures and other factors like age.
>
> Is there a way to do that with LME (since I was planning on using that as a 
> method of choice) or is it possible to do that with QDEC? I've prepared my 
> data for both methods (LME and linear two stage model) but if I use the 
> cross.qdec.table derived from the longitudinal data, it uses the registered 
> and smoothed (with mris_slopes) surfaces from the Base, right?
> So, I would like to know how I can analyzse a single time point within my 
> longitudinal design.
>
> Cheers,
> Clara
>
>

-- 
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web  : http://reuter.mit.edu

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Re: [Freesurfer] Freeview PETSC Error

2015-12-11 Thread Z K

Hello,

I think that link pointed you to the centos6 version of freeview.bin, 
but you would want the centos4 version. You can download the correct 
version using the following link:

 
ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/freeview/linux_centos4_x86_64/freeview.bin

Hope this help.

-Zeke

On 12/10/2015 06:25 PM, Udunna Anazodo wrote:
> Hi,
>
> I downloaded and installed Freesurfer stable release 5.3 distribution
> linux_centos4_x86_64 on an Ubuntu 12.04 system. However freeview crashes
> with a PETSC error. I read the freesurfer archives and followed the
> instructions found on
> https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-November/041243.html.
> I downloaded the most recent version of freeview.bin using wget as
> suggested but I still get the same error message. Any ideas how to work
> around this. Thanks
>
> [0]PETSC ERROR:
> 
> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
> probably memory access out of range
> [0]PETSC ERROR: Try option -start_in_debugger or
> -on_error_attach_debugger
> [0]PETSC ERROR: or see
> http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
> ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to
> find memory corruption errors
> [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link,
> and run
> [0]PETSC ERROR: to get more information on the crash.
> [0]PETSC ERROR: - Error Message
> 
> [0]PETSC ERROR: Signal received!
> [0]PETSC ERROR:
> 
> [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15
> 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> [0]PETSC ERROR: See docs/index.html for manual pages.
> [0]PETSC ERROR:
> 
> [0]PETSC ERROR: Unknown Name on a linux-gnu named udunna-work by udunna
> Thu Dec 10 17:42:30 2015
> [0]PETSC ERROR: Libraries linked from
> /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt
> [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010
> [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc
> --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1
> --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3
> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
> [0]PETSC ERROR:
> 
> [0]PETSC ERROR: User provided function() line 0 in unknown directory
> unknown file
> [unset]: aborting job:
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
>
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Re: [Freesurfer] Convert TAL coordinates to surface RAS coordinates

2015-12-11 Thread Inês Violante

Dear Douglas,

I've been looking a that page for a while now and I am very confused...

Are you referring to this example?

2. I have an RAS point on the surface (tkrR tkrA tkrS) ("Vertex RAS"
from tksurfer) and want to compute the MNI305 RAS that corresponds to
this point:

MNI305RAS = TalXFM*Norig*inv(Torig)*[tkrR tkrA tkrS 1]'

TalXFM: subject/orig/transforms/talairach.xfm Norig: mri_info
--vox2ras orig.mgz Torig: mri_info --vox2ras-tkr orig.mgz

So, is it the case that I just do the equation like this:

[tkrR tkrA tkrS 1]' = [X Y Z (in MNIspace)] / TalXFM*Norig*inv(Torig)


Thank you,

ines

On Fri, Dec 11, 2015 at 4:12 PM, Douglas Greve
 wrote:
>
> See if this helps
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
>
>
> On 12/11/15 10:23 AM, Inês Violante wrote:
>> Dear experts,
>>
>> I have a set of Talairach coordinates that I want to convert to the
>> individual subject surf RAS coordinates.
>> How can I do this?
>>
>> Thank you very much.
>>
>> Ines
>> ___
>> 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
>
>
> 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 
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[Freesurfer] Convert TAL coordinates to surface RAS coordinates

2015-12-11 Thread Inês Violante

Dear experts,

I have a set of Talairach coordinates that I want to convert to the
individual subject surf RAS coordinates.
How can I do this?

Thank you very much.

Ines
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Re: [Freesurfer] Convert TAL coordinates to surface RAS coordinates

2015-12-11 Thread Douglas Greve

See if this helps

https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems

On 12/11/15 10:23 AM, Inês Violante wrote:
> Dear experts,
>
> I have a set of Talairach coordinates that I want to convert to the
> individual subject surf RAS coordinates.
> How can I do this?
>
> Thank you very much.
>
> Ines
> ___
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Re: [Freesurfer] HSF in 5.3

2015-12-11 Thread Eugenio Iglesias

Hi Alan, 
the subfield module is not present in 5.3; you'll need to download the 
development version (or wait until 6.0 is released, which should be pretty 
soon=. 
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: "Alan Francis"  
To: "Freesurfer support list" , "eiglesias" 
 
Sent: Friday, December 11, 2015 6:36:42 PM 
Subject: HSF in 5.3 

Hi Eugenio: 
I am trying to run the HSF method on 42 subjects. The FS version on our cluster 
is 5.3. However when I use the following command I get an error message. 



[alanf@micc alanf]$ recon-all -s Smoke_d004 -hippocampal-subfields 

ERROR: Flag -hippocampal-subfields unrecognized. 

-s Smoke_d004 -hippocampal-subfields 

Linux micc 2.6.32-358.el6.x86_64 #1 SMP Tue Jan 29 11:47:41 EST 2013 x86_64 
x86_64 x86_64 GNU/Linux 




recon-all -s Smoke_d004 exited with ERRORS at Thu Dec 10 16:54:44 EST 2015 




For more details, see the log file 

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting 





I tried adding the -hippocampal-subfields-T1 but that did not work too. 




thanks, 




Alan 
-- 
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| 

Alan N . Francis PhD 
NIDA T32 Fellow in Computational Neuroscience 
Brain Imaging Center 
McLean Hospital 
Harvard Medical School 
115 Mill Street, Belmont, MA 02478 
al...@bwh.harvard.edu 
afran...@mclean.harvard.edu 

|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| 

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Re: [Freesurfer] HSF in 5.3

2015-12-11 Thread Alan Francis

Thanks for the very quick reply Eugenio. Will download the 6.0 beta.

Alan

On Fri, Dec 11, 2015 at 12:51 PM, Eugenio Iglesias 
wrote:

> Hi Alan,
> the subfield module is not present in 5.3; you'll need to download the
> development version (or wait until 6.0 is released, which should be pretty
> soon=.
> 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: *"Alan Francis" 
> *To: *"Freesurfer support list" ,
> "eiglesias" 
> *Sent: *Friday, December 11, 2015 6:36:42 PM
> *Subject: *HSF in 5.3
>
> Hi Eugenio:
> I am trying to run the HSF method on 42 subjects. The FS version on our
> cluster is 5.3. However when I use the following command I get an error
> message.
>
> [alanf@micc alanf]$ recon-all -s Smoke_d004 -hippocampal-subfields
>
> ERROR: Flag -hippocampal-subfields unrecognized.
>
> -s Smoke_d004 -hippocampal-subfields
>
> Linux micc 2.6.32-358.el6.x86_64 #1 SMP Tue Jan 29 11:47:41 EST 2013
> x86_64 x86_64 x86_64 GNU/Linux
>
>
> recon-all -s Smoke_d004 exited with ERRORS at Thu Dec 10 16:54:44 EST 2015
>
>
> For more details, see the log file
>
> To report a problem, see
> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
>
> I tried adding the  -hippocampal-subfields-T1 but that did not work too.
>
>
> thanks,
>
>
> Alan
>
> --
> |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
>
> *Alan N. Francis PhD*
> NIDA T32  Fellow in Computational Neuroscience
> Brain Imaging Center
> McLean Hospital
> Harvard Medical School
> 115 Mill Street, Belmont, MA 02478
> al...@bwh.harvard.edu 
> afran...@mclean.harvard.edu
>
>
> |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
>
>


-- 
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

*Alan N. Francis PhD*
NIDA T32  Fellow in Computational Neuroscience
Brain Imaging Center
McLean Hospital
Harvard Medical School
115 Mill Street, Belmont, MA 02478
al...@bwh.harvard.edu 
afran...@mclean.harvard.edu


|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
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[Freesurfer] R: Re: FDR in FS-FAST

2015-12-11 Thread stdp82

Thanks, in which folder I should put this file?

Stefano


>Messaggio originale
>Da: gr...@nmr.mgh.harvard.edu
>Data: 7-dic-2015 19.23
>A: 
>Ogg: Re: [Freesurfer] FDR in FS-FAST
>
>
>
>On 12/07/2015 08:35 AM, std...@virgilio.it wrote:
>> Hi list,
>> I have two concerns, please:
>> 1) It is possible to apply FDR correction on rs-fMRI seed based 
>> analysis by FS-FAST? If yes, I can I do it?
>try this binary
>ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_fdr
>> 2) I have apply the FS guidelines and I have used Montecarlo 
>> correction with threshold at 1.3 but in the within group analysis 
the 
>> clusters are very large. In the guide I read examples with a 
threshold 
>> at 3. Is there a specific reason?
>There is not a hard-and-fast criteria for the voxel-wise threshold. 3 
is 
>fine as is 1.3
>> Thanks
>>
>> Stefano
>>
>>
>> ___
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>
>-- 
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>MGH-NMR Center
>gr...@nmr.mgh.harvard.edu
>Phone Number: 617-724-2358
>Fax: 617-726-7422
>
>Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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>www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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edu/transfer/outgoing/flat/greve/
>
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HelpLine at
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Re: [Freesurfer] R: Re: FDR in FS-FAST

2015-12-11 Thread Douglas Greve

$FREESURFER_HOME/bin

On 12/11/15 2:08 PM, std...@virgilio.it wrote:
> Thanks, in which folder I should put this file?
>
> Stefano
>
>
>> Messaggio originale
>> Da: gr...@nmr.mgh.harvard.edu
>> Data: 7-dic-2015 19.23
>> A: 
>> Ogg: Re: [Freesurfer] FDR in FS-FAST
>>
>>
>>
>> On 12/07/2015 08:35 AM, std...@virgilio.it wrote:
>>> Hi list,
>>> I have two concerns, please:
>>> 1) It is possible to apply FDR correction on rs-fMRI seed based
>>> analysis by FS-FAST? If yes, I can I do it?
>> try this binary
>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_fdr
>>> 2) I have apply the FS guidelines and I have used Montecarlo
>>> correction with threshold at 1.3 but in the within group analysis
> the
>>> clusters are very large. In the guide I read examples with a
> threshold
>>> at 3. Is there a specific reason?
>> There is not a hard-and-fast criteria for the voxel-wise threshold. 3
> is
>> fine as is 1.3
>>> Thanks
>>>
>>> Stefano
>>>
>>>
>>> ___
>>> 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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>>
>>
>> The information in this e-mail is intended only for the person to
> whom it is
>> addressed. If you believe this e-mail was sent to you in error and
> the e-mail
>> contains patient information, please contact the Partners Compliance
> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to
> you in error
>> but does not contain patient information, please contact the sender
> and properly
>> dispose of the e-mail.
>>
>>
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[Freesurfer] questions about summary of Monte Carlo simulation‏

2015-12-11 Thread Karl Liu

Dear Freesurfer experts,


I repost my question from
yesterday since it is not answered. Thanks in advance for any help. 


After running  Monte Carlo simulation from the command line,
I noticed two cluster summary files are produced for each contrast:  
cache.th20.neg.sig.cluster.summary and
mc-z.neg.th20.sig.cluster.summary. They are quite similar, with different
number of surviving clusters in some cases. I am wondering which is the one to
report final results. Will you explain a bit more about the differences between
them?


Also, after reading the summary
file, we still have to visualize the results. If the MC simulation is done in
QDEC GUI, then the QDEC automatically presents the outcome from
mc-z.neg.th20.sig.cluster.mgh, but I am not sure if this is the right file. I
am using FS version 5.3 without tksurferfv. I found the tksurfer is running
quite slow and unresponsive. Any other suggestions?


Thank you very much!


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Re: [Freesurfer] questions about summary of Monte Carlo simulation‏

2015-12-11 Thread Douglas N Greve


How did you do the MC simulation? Does your mri_glmfit include a mask? I 
need command-lines ...


On 12/11/2015 03:18 PM, Karl Liu wrote:
>
> Dear Freesurfer experts,
>
>
> I repost my question from yesterday since it is not answered. Thanks 
> in advance for any help.
>
>
> After running  Monte Carlo simulation from the command line, I noticed 
> two cluster summary files are produced for each contrast:  
> cache.th20.neg.sig.cluster.summary and 
> mc-z.neg.th20.sig.cluster.summary. They are quite similar, with 
> different number of surviving clusters in some cases. I am wondering 
> which is the one to report final results. Will you explain a bit more 
> about the differences between them?
>
>
> Also, after reading the summary file, we still have to visualize the 
> results. If the MC simulation is done in QDEC GUI, then the QDEC 
> automatically presents the outcome from mc-z.neg.th20.sig.cluster.mgh, 
> but I am not sure if this is the right file. I am using FS version 5.3 
> without tksurferfv. I found the tksurfer is running quite slow and 
> unresponsive. Any other suggestions?
>
>
> Thank you very much!
>
>
> Karl
>
>
> ___
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
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Re: [Freesurfer] HSF in 5.3

2015-12-11 Thread Ritobrato Datta

Hello All,

I have run my data through free surfer 5.1. If I run recon-all distributed with 
free surfer 6 as follows

/Applications/freesurfer6/bin/recon-all -s bert -brainstem-structures 

where bert was created using freesurfer 5.1, will it work ?

Best

Ri

- Original Message -
From: Eugenio Iglesias 
To: Alan Francis 
Cc: Freesurfer support list 
Sent: Fri, 11 Dec 2015 12:51:24 -0500 (EST)
Subject: Re: [Freesurfer] HSF in 5.3

Hi Alan, 
the subfield module is not present in 5.3; you'll need to download the 
development version (or wait until 6.0 is released, which should be pretty 
soon=. 
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: "Alan Francis"  
To: "Freesurfer support list" , "eiglesias" 
 
Sent: Friday, December 11, 2015 6:36:42 PM 
Subject: HSF in 5.3 

Hi Eugenio: 
I am trying to run the HSF method on 42 subjects. The FS version on our cluster 
is 5.3. However when I use the following command I get an error message. 



[alanf@micc alanf]$ recon-all -s Smoke_d004 -hippocampal-subfields 

ERROR: Flag -hippocampal-subfields unrecognized. 

-s Smoke_d004 -hippocampal-subfields 

Linux micc 2.6.32-358.el6.x86_64 #1 SMP Tue Jan 29 11:47:41 EST 2013 x86_64 
x86_64 x86_64 GNU/Linux 




recon-all -s Smoke_d004 exited with ERRORS at Thu Dec 10 16:54:44 EST 2015 




For more details, see the log file 

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting 





I tried adding the -hippocampal-subfields-T1 but that did not work too. 




thanks, 




Alan 
-- 
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| 

Alan N . Francis PhD 
NIDA T32 Fellow in Computational Neuroscience 
Brain Imaging Center 
McLean Hospital 
Harvard Medical School 
115 Mill Street, Belmont, MA 02478 
al...@bwh.harvard.edu 
afran...@mclean.harvard.edu 

|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| 
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[Freesurfer] average cortical thickness measure?

2015-12-11 Thread Maria Kharitonova

I know that the aseg atlas provides a number of voume measures (e.g. 
EstimatedTotalIntraCranialVol, TotalGrayVol), but is there a variable for an 
average cortical thickness? I'd like to see if thickness in some of the regions 
is associated with a variable of interest over and above an overall main 
effect, so would like to control for the average thickness, but can't figure 
out a good way to do that.

Thanks!
Maria

-
Maria Kharitonova, PhD
Research Assistant Professor
Department of Medical Social Sciences
Northwestern University Feinberg School of Medicine
625 N. Michigan Ave, Suite 2700
Chicago, IL 60611
Phone: (312) 503-6503
Email: 
maria.khariton...@northwestern.edu

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Re: [Freesurfer] average cortical thickness measure?

2015-12-11 Thread Douglas N Greve

In ?h.aparc.stats, you'll find a line like

# Measure Cortex, MeanThickness, Mean Thickness, 2.40617, mm

You'll have to get the value for each hemi and compute the mean


On 12/11/2015 01:38 PM, Maria Kharitonova wrote:
> I know that the aseg atlas provides a number of voume measures 
> (e.g. EstimatedTotalIntraCranialVol, TotalGrayVol), but is there a 
> variable for an average cortical thickness? I’d like to see if 
> thickness in some of the regions is associated with a variable of 
> interest over and above an overall main effect, so would like to 
> control for the average thickness, but can’t figure out a good way to 
> do that.
>
> Thanks!
> Maria
>
> —
> Maria Kharitonova, PhD
> Research Assistant Professor
> Department of Medical Social Sciences
> Northwestern University Feinberg School of Medicine
> 625 N. Michigan Ave, Suite 2700
> Chicago, IL 60611
> Phone: (312) 503-6503
> Email: maria.khariton...@northwestern.edu 
> 
>
>
>
> ___
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gr...@nmr.mgh.harvard.edu
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Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] ERROR: Talairach QA check failed! and ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm FAILED

Re: [Freesurfer] ERROR: Talairach QA check failed! and ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm FAILED

Re: [Freesurfer] Convert TAL coordinates to surface RAS coordinates

Re: [Freesurfer] correlations with longitudinal data

Re: [Freesurfer] Freeview PETSC Error

Re: [Freesurfer] Convert TAL coordinates to surface RAS coordinates

[Freesurfer] Convert TAL coordinates to surface RAS coordinates

Re: [Freesurfer] Convert TAL coordinates to surface RAS coordinates

Re: [Freesurfer] HSF in 5.3

Re: [Freesurfer] HSF in 5.3

[Freesurfer] R: Re: FDR in FS-FAST

Re: [Freesurfer] R: Re: FDR in FS-FAST

[Freesurfer] questions about summary of Monte Carlo simulation‏

Re: [Freesurfer] questions about summary of Monte Carlo simulation‏

Re: [Freesurfer] HSF in 5.3

[Freesurfer] average cortical thickness measure?

Re: [Freesurfer] average cortical thickness measure?

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