date:20151209

Re: [Freesurfer] correlations with longitudinal data

2015-12-09 Thread Clara Kühn

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] FreeSurfer 6 recon-all exiting with errors at -cortparc step

2015-12-09 Thread Bruce Fischl


HI Natalia

can you try the dev version? I'm pretty sure I fixed this. You can just 
rerun mris_ca_label. We'll hopefully be cutting a new stable 6 sometime 
soon


cheers
Bruce


On Wed, 9 Dec 2015, Zaretskaya, Natalia wrote:


Dear all,

I am running recon-all with FreeSurfer 6 stable version on launchpad and
have it exiting with errors with all of my 43 brains, always at the same
stage (-cortparc). The same brains used to run through recon-all smoothly
with the dev version just a month or so ago, and I am not doing anything
essentially different than before, except using FreeSurfer 6, so I am
wondering what’s wrong. The output of recon-all before the error looks o.k.

I attached an example recon-all.log file.

Many thanks in advance for your help!
Natalia





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Re: [Freesurfer] Recon-all get stucked without error during processing

2015-12-09 Thread Bruce Fischl

Hi Matthieu

you need to track backwards and see where the problem started. Why is the 
norm warped? Actaully, it shouldn't be warped, although it might be 
truncated if the skull stripping failed.

cheers
Bruce
On Wed, 9 
Dec 2015, Matthieu Vanhoutte wrote:

Hi Bruce,

Indeed norm.mgz isn't empty but doesn't look well (truncated and warped).

Is this bug fixed in the v6 beta release ?

If this is the case :
1) Would you advise me to try on the v6 ?
2) Should I so relaunch all recon-all process on my subjects computed with v5.3 
 and work only with the v6 beta ?

Best regards,
Matthieu

2015-12-09 15:55 GMT+01:00 Bruce Fischl :
  Hi Matthieu

  this might be a bug that is fixed in 6.0. Can you cehck the input to
  mri_cc (norm.mgz) and make sure it is not empty? In older versions if the
  skull stripping failed and generated an empty
  norm.mgz/aseg.auto_noCCseg.mgz the mri_cc code would hang.

  cheers
  Bruce

  On Wed, 9 Dec 2015,
  Matthieu Vanhoutte wrote:

  > Dear FS epxerts,
  >
  > I have launched a recon-all process on a subject. Unfortunately, I 
tried two times but the process get stucked at
  the same step
  > without error.
  >
  > Please found the recon-all.log associated attached to this mail.
  >
  > Thanks in advance for helping !
  >
  > Best regards,
  > Matthieu
  >
  >
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Re: [Freesurfer] ERROR: Talairach QA check failed! and ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm FAILED

2015-12-09 Thread 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 the -notal-check flag follows -all
>> or -autorecon1 in the command string.
>> See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
>> INFO: Attempting MINC mritotal to perform Talairach align
>> #
>> #@# Talairach Fri Dec  4 15:29:39 CET 2015
>> /NAS/tupac/matthieu/FS5.3/M0_2011-02-23/mri
>>
>>  mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale
>> --i orig.mgz --o
>> orig_nu.mgz

Re: [Freesurfer] Recon-all get stucked without error during processing

2015-12-09 Thread Bruce Fischl

Hi Matthieu

this might be a bug that is fixed in 6.0. Can you cehck the input to 
mri_cc (norm.mgz) and make sure it is not empty? In older versions if the 
skull stripping failed and generated an empty 
norm.mgz/aseg.auto_noCCseg.mgz the mri_cc code would hang.

cheers
Bruce

On Wed, 9 Dec 2015, 
Matthieu Vanhoutte wrote:

> Dear FS epxerts,
> 
> I have launched a recon-all process on a subject. Unfortunately, I tried two 
> times but the process get stucked at the same step
> without error.
> 
> Please found the recon-all.log associated attached to this mail.
> 
> Thanks in advance for helping !
> 
> Best regards,
> Matthieu
> 
>
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[Freesurfer] file error

2015-12-09 Thread LIEWALD David

OS Opensuse 13.2

Freesurfer 6 Dev

Logfile Attached


I have had no luck trying to get freesurfer to run. It is failing at the same 
point each time ( Please see log). I have tried with multiple datasets in 
multiple locations both on the local machine and across the network. I have 
also verified that the permissions of the dir are correct and I can manually 
read and write to the. I'm at a loss?



Dave Liewald


Wed Dec  9 11:37:57 GMT 2015
/UK_Biobank_MRI/FS_Output/1006924_20216_2_0
/UK_Biobank_MRI/freesurfer/bin/recon-all
-i 
/UK_Biobank_MRI/WorkDir/1006924_20216_2_0/1.3.12.2.1107.5.2.19.45594.201507130826307583602667.dcm
 -s 1006924_20216_2_0 -sd /UK_Biobank_MRI/FS_Output -no-isrunning -all
subjid 1006924_20216_2_0
setenv SUBJECTS_DIR /UK_Biobank_MRI/FS_Output
FREESURFER_HOME /UK_Biobank_MRI/freesurfer
Actual FREESURFER_HOME /UK_Biobank_MRI/freesurfer
build-stamp.txt: freesurfer-Linux-centos6_x86_64-dev-20151207
Linux CCACE-PROC01 3.16.7-24-desktop #1 SMP PREEMPT Mon Aug 3 14:37:06 UTC 2015 
(ec183cc) x86_64 x86_64 x86_64 GNU/Linux
cputime  unlimited
filesize unlimited
datasize unlimited
stacksize8192 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
vmemoryuse   unlimited
descriptors  1024 
memorylocked 64 kbytes
maxproc  193285 
maxlocks unlimited
maxsignal193285 
maxmessage   819200 
maxnice  0 
maxrtprio0 
maxrttimeunlimited

 total   used   free sharedbuffers cached
Mem:  49495560   435314525964108 119680 242188   41644952
-/+ buffers/cache:1644312   47851248
Swap:314567668   1376  314566292


program versions used
$Id: recon-all,v 1.555 2015/11/17 14:18:41 mreuter Exp $
$Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: -all-info  ProgramVersion: $Name:  
$  TimeStamp: 2015/12/09-11:37:57-GMT  BuildTimeStamp: Dec  7 2015 21:02:52  
CVS: $Id: mri_convert.c,v 1.225 2015/10/19 18:48:26 fischl Exp $  User: root  
Machine: CCACE-PROC01  Platform: Linux  PlatformVersion: 3.16.7-24-desktop  
CompilerName: GCC  CompilerVersion: 40400 
FLIRT version 6.0
$Id: talairach_avi,v 1.11 2015/01/13 20:22:51 nicks Exp $
mri_convert --version 
dev build (use --all-info flag for full version info)
ProgramName: tkregister2_cmdl  ProgramArguments: --all-info  ProgramVersion: 
$Name:  $  TimeStamp: 2015/12/09-11:37:58-GMT  BuildTimeStamp: Dec  7 2015 
21:02:52  CVS: $Id: tkregister2.c,v 1.129 2014/02/26 21:31:58 greve Exp $  
User: root  Machine: CCACE-PROC01  Platform: Linux  PlatformVersion: 
3.16.7-24-desktop  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_make_uchar  ProgramArguments: -all-info  ProgramVersion: 
$Name:  $  TimeStamp: 2015/12/09-11:37:58-GMT  BuildTimeStamp: Dec  7 2015 
21:02:52  CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $  
User: root  Machine: CCACE-PROC01  Platform: Linux  PlatformVersion: 
3.16.7-24-desktop  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name: 
 $  TimeStamp: 2015/12/09-11:37:58-GMT  BuildTimeStamp: Dec  7 2015 21:02:52  
CVS: $Id: mri_normalize.c,v 1.85 2015/08/05 19:24:14 fischl Exp $  User: root  
Machine: CCACE-PROC01  Platform: Linux  PlatformVersion: 3.16.7-24-desktop  
CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: $Name: 
 $  TimeStamp: 2015/12/09-11:37:58-GMT  BuildTimeStamp: Dec  7 2015 21:02:52  
CVS: $Id: mri_watershed.cpp,v 1.101 2015/07/10 18:57:33 greve Exp $  User: root 
 Machine: CCACE-PROC01  Platform: Linux  PlatformVersion: 3.16.7-24-desktop  
CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion: $Name:  $  
TimeStamp: 2015/12/09-11:37:58-GMT  BuildTimeStamp: Dec  7 2015 21:02:52  CVS: 
$Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $  User: root  Machine: 
CCACE-PROC01  Platform: Linux  PlatformVersion: 3.16.7-24-desktop  
CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segment  ProgramArguments: -all-info  ProgramVersion: $Name:  
$  TimeStamp: 2015/12/09-11:37:58-GMT  BuildTimeStamp: Dec  7 2015 21:02:52  
CVS: $Id: mri_segment.c,v 1.43 2015/02/05 23:34:40 zkaufman Exp $  User: root  
Machine: CCACE-PROC01  Platform: Linux  PlatformVersion: 3.16.7-24-desktop  
CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_label2label  ProgramArguments: -all-info  ProgramVersion: 
$Name:  $  TimeStamp: 2015/12/09-11:37:58-GMT  BuildTimeStamp: Dec  7 2015 
21:02:52  CVS: $Id: mri_label2label.c,v 1.47 2014/12/22 19:59:18 greve Exp $  
User: root  Machine: CCACE-PROC01  Platform: Linux  PlatformVersion: 
3.16.7-24-desktop  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_em_register  ProgramArguments: -all-info  ProgramVersion: 
$Name:  $  TimeStamp: 2015/12/09-11:37:58-GMT

[Freesurfer] Qdec - cluster labels

2015-12-09 Thread sabin khadka

Hi all - When you get a significant cluster after doing monte-carlo simulation, 
we get peak vertex/Talairach coordinates and also saved in *summary files. Is 
there a way to find all the parcellated regions (Desikan, or, Destriuex) in the 
significant clusters?
Thanks,Sabin
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Re: [Freesurfer] Recon-all get stucked without error during processing

2015-12-09 Thread Matthieu Vanhoutte

Hi Bruce,

Indeed norm.mgz isn't empty but doesn't look well (truncated and warped).

Is this bug fixed in the v6 beta release ?

If this is the case :
1) Would you advise me to try on the v6 ?
2) Should I so relaunch all recon-all process on my subjects computed with
v5.3  and work only with the v6 beta ?

Best regards,
Matthieu

2015-12-09 15:55 GMT+01:00 Bruce Fischl :

> Hi Matthieu
>
> this might be a bug that is fixed in 6.0. Can you cehck the input to
> mri_cc (norm.mgz) and make sure it is not empty? In older versions if the
> skull stripping failed and generated an empty
> norm.mgz/aseg.auto_noCCseg.mgz the mri_cc code would hang.
>
> cheers
> Bruce
>
> On Wed, 9 Dec 2015,
> Matthieu Vanhoutte wrote:
>
> > Dear FS epxerts,
> >
> > I have launched a recon-all process on a subject. Unfortunately, I tried
> two times but the process get stucked at the same step
> > without error.
> >
> > Please found the recon-all.log associated attached to this mail.
> >
> > Thanks in advance for helping !
> >
> > Best regards,
> > Matthieu
> >
> >
> ___
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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] Recon-all get stucked without error during processing

2015-12-09 Thread Matthieu Vanhoutte

Hi Bruce,

In fact T1.mgz is ok, but the skull stripping failed and seemed to have
taken only the jawbone and the neck.

Best regards,
Matthieu

2015-12-09 16:16 GMT+01:00 Bruce Fischl :

> Hi Matthieu
>
> you need to track backwards and see where the problem started. Why is the
> norm warped? Actaully, it shouldn't be warped, although it might be
> truncated if the skull stripping failed.
>
>
> cheers
> Bruce
> On Wed, 9 Dec 2015, Matthieu Vanhoutte wrote:
>
> Hi Bruce,
>>
>> Indeed norm.mgz isn't empty but doesn't look well (truncated and warped).
>>
>> Is this bug fixed in the v6 beta release ?
>>
>> If this is the case :
>> 1) Would you advise me to try on the v6 ?
>> 2) Should I so relaunch all recon-all process on my subjects computed
>> with v5.3  and work only with the v6 beta ?
>>
>> Best regards,
>> Matthieu
>>
>> 2015-12-09 15:55 GMT+01:00 Bruce Fischl :
>>   Hi Matthieu
>>
>>   this might be a bug that is fixed in 6.0. Can you cehck the input to
>>   mri_cc (norm.mgz) and make sure it is not empty? In older versions
>> if the
>>   skull stripping failed and generated an empty
>>   norm.mgz/aseg.auto_noCCseg.mgz the mri_cc code would hang.
>>
>>   cheers
>>   Bruce
>>
>>   On Wed, 9 Dec 2015,
>>   Matthieu Vanhoutte wrote:
>>
>>   > Dear FS epxerts,
>>   >
>>   > I have launched a recon-all process on a subject. Unfortunately,
>> I tried two times but the process get stucked at
>>   the same step
>>   > without error.
>>   >
>>   > Please found the recon-all.log associated attached to this mail.
>>   >
>>   > Thanks in advance for helping !
>>   >
>>   > Best regards,
>>   > Matthieu
>>   >
>>   >
>> ___
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>> is
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Re: [Freesurfer] Edit the number of segments in the segmentation of the corpus callosum

2015-12-09 Thread UQAM

Hi Doug, Hi Bruce,

Just an update.

I tried this command (see below) to specify each input file since I don't
want to freesurfer to choose the stats/aseg.stats that it uses by default.

but I get this "ERROR: The stats file e0042/stats/e0042_CC12_new.aseg.stats
is not found or is too small to be a valid statsfile".

The files are indeed in the stats folder of subject e0042, but the default
aseg.stats files are 8,5K and my CC_new.aseg.stats files are 4,5K.

Hope it can help to solve the problem ; )

Genevieve

* *
*

asegstats2table -i e0042/stats/e0042_CC12_new.aseg.stats
e0041/stats/e0041_CC12_new.aseg.stats e0035/stats/e0035_CC12_new.aseg.stats
e0048/stats/e0048_CC12_new.aseg.stats e0058/stats/e0058_CC12_new.aseg.stats
e0059/stats/e0059_CC12_new.aseg.stats e0053/stats/e0053_CC12_new.aseg.stats
e0032/stats/e0032_CC12_new.aseg.stats e0047/stats/e0047_CC12_new.aseg.stats
e0036/stats/e0036_CC12_new.aseg.stats e0039/stats/e0039_CC12_new.aseg.stats
e0049/stats/e0049_CC12_new.aseg.stats e0051/stats/e0051_CC12_new.aseg.stats
e0050/stats/e0050_CC12_new.aseg.stats e0045/stats/e0045_CC12_new.aseg.stats
e0061/stats/e0061_CC12_new.aseg.stats e0062/stats/e0062_CC12_new.aseg.stats
e0063/stats/e0063_CC12_new.aseg.stats e0064/stats/e0064_CC12_new.aseg.stats
e0065/stats/e0065_CC12_new.aseg.stats e0066/stats/e0066_CC12_new.aseg.stats
e0067/stats/e0067_CC12_new.aseg.stats e0068/stats/e0068_CC12_new.aseg.stats
e0070/stats/e0070_CC12_new.aseg.stats e0071/stats/e0071_CC12_new.aseg.stats
e0072/stats/e0072_CC12_new.aseg.stats e0073/stats/e0073_CC12_new.aseg.stats
e0074/stats/e0074_CC12_new.aseg.stats e0075/stats/e0075_CC12_new.aseg.stats
e0076/stats/e0076_CC12_new.aseg.stats e0077/stats/e0077_CC12_new.aseg.stats
e0021/stats/e0021_CC12_new.aseg.stats e0004/stats/e0004_CC12_new.aseg.stats
e0078/stats/e0078_CC12_new.aseg.stats e0079/stats/e0079_CC12_new.aseg.stats
e0080/stats/e0080_CC12_new.aseg.stats e0013/stats/e0013_CC12_new.aseg.stats
e0081/stats/e0081_CC12_new.aseg.stats e0082/stats/e0082_CC12_new.aseg.stats
e0083/stats/e0083_CC12_new.aseg.stats a0001/stats/a0001_CC12_new.aseg.stats
a0002/stats/a0002_CC12_new.aseg.stats a0003/stats/a0003_CC12_new.aseg.stats
a0004/stats/a0004_CC12_new.aseg.stats a0005/stats/a0005_CC12_new.aseg.stats
a0006/stats/a0006_CC12_new.aseg.stats a0007/stats/a0007_CC12_new.aseg.stats
a0008/stats/a0008_CC12_new.aseg.stats a0009/stats/a0009_CC12_new.aseg.stats
a0010/stats/a0010_CC12_new.aseg.stats a0011/stats/a0011_CC12_new.aseg.stats
a0012/stats/a0012_CC12_new.aseg.stats a0013/stats/a0013_CC12_new.aseg.stats
a0014/stats/a0014_CC12_new.aseg.stats a0015/stats/a0015_CC12_new.aseg.stats
a0016/stats/a0016_CC12_new.aseg.stats a0017/stats/a0017_CC12_new.aseg.stats
a0018/stats/a0018_CC12_new.aseg.stats a0019/stats/a0019_CC12_new.aseg.stats
a0020/stats/a0020_CC12_new.aseg.stats a0021/stats/a0021_CC12_new.aseg.stats
a0022/stats/a0022_CC12_new.aseg.stats a0023/stats/a0023_CC12_new.aseg.stats
a0024/stats/a0024_CC12_new.aseg.stats a0025/stats/a0025_CC12_new.aseg.stats
a0026/stats/a0026_CC12_new.aseg.stats a0027/stats/a0027_CC12_new.aseg.stats
a0028/stats/a0028_CC12_new.aseg.stats a0029/stats/a0029_CC12_new.aseg.stats
a0030/stats/a0030_CC12_new.aseg.stats a0031/stats/a0031_CC12_new.aseg.stats
a0032/stats/a0032_CC12_new.aseg.stats a0033/stats/a0033_CC12_new.aseg.stats
a0034/stats/a0034_CC12_new.aseg.stats a0035/stats/a0035_CC12_new.aseg.stats
a0036/stats/a0036_CC12_new.aseg.stats a0037/stats/a0037_CC12_new.aseg.stats
a0038/stats/a0038_CC12_new.aseg.stats a0039/stats/a0039_CC12_new.aseg.stats
a0040/stats/a0040_CC12_new.aseg.stats --meas volume --tablefile
aseg_stats_12CC_new.txt




On Tue, Dec 8, 2015 at 6:40 AM, UQAM 
wrote:

> Hi Doug,
>
> See attached an example of an aseg.stats file for subject e0070 (
> e0070_CC12_new.aseg.stats)
>
> Regards,
> Genevieve
>
>
>
>
> On Mon, Dec 7, 2015 at 7:48 PM, Douglas N Greve  > wrote:
>
>> Can you send me one of the e0070_CC12_new.aseg.stats files?
>>
>> On 12/06/2015 08:12 AM, UQAM wrote:
>> > Hi Bruce,
>> >
>> > We used these:
>> >
>> > mri_cc_new -aseg aseg.auto_noCCseg.mgz -o aseg.12segmentsCC_new.mgz -d
>> > 12 e0070
>> > ... (for all the subjects from e0042 to a0040)
>> >
>> > mri_segstats --seg $SUBJECTS_DIR/e0070/mri/aseg.12segmentsCC_new.mgz
>> > --ctab $SUBJECTS_DIR/CColorLUT.txt --nonempty --excludeid 0 --sum
>> > $SUBJECTS_DIR/e0070/stats/e0070_CC12_new.aseg.stats
>> >  (for all the subjects from e0042 to a0040)
>> >
>> > asegstats2table --subjects e0042 e0041 e0035 e0048 e0058 e0059 e0053
>> > e0032 e0047 e0036 e0039 e0049 e0051 e0050 e0045 e0061 e0062 e0063
>> > e0064 e0065 e0066 e0067 e0068 e0070 e0071 e0072 e0073 e0074 e0075
>> > e0076 e0077 e0021 e0004 e0078 e0079 e0080 e0013 e0081 e0082 e0083
>> > a0001 a0002 a0003 a0004 a0005 a0006 a0007 a0008 a0009 a0010 a0011
>> > a0012 a0013 a0014 a0015 a0016 a0017 a0018 a0019 a0020 a0021 a0022
>> > a0023 a0024 a0025 a0026 a0027 a0028 a0029 a0030 a0031

Re: [Freesurfer] Question about Qdec

2015-12-09 Thread levi solomyak

Hi Doug,

Thank you for letting me know.

1) machine being used: Linux localhost.localdomain
3.10.0-229.4.2.el7.x86_64 #1 SMP Wed May 13 10:06:09 UTC 2015 x86_64 x86_64
x86_64 GNU/Linux
2) Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-HCP
3) Current working directory: /projects/IndivRITL/data/leviDiff/Subjects
4) which qdec :  /usr/local/freesurfer/bin/qdec
5) After loading the gui, I attempted to generate a qdec stats table. This
is the error that was returned:

---
asegstats2table --common-segs --meas volume --tablefile
/mnt/engram/projects/IndivRITL/data/leviDiff/Subjects/qdec/stats_tables/aseg.volume.stats.dat
--statsfile=aseg.stats --subjects 100307 101006 104820 105115 110411 111312
111413 111716 112819 113215 113619 113922 114419 115320 116524 117122
117324 118528 135225 135932 150625 150726 151223 151526 170934 171633
172130 172332 172534 172938 173334 175439 177645 177746 178142 200109
200614 20 201414 201818 203418 204016 204521 304020 307127 308331
310621 316633 329440 365343 366042 377451 380036 385450 386250 412528
433839 436239 480141 486759 497865 499566 500222 510326 530635 531536
540436 561242 562446 565452 566454 567052 567961 568963 571548 580044
580347 581349 583858 586460 594156 598568 599671
SUBJECTS_DIR : /mnt/engram/projects/IndivRITL/data/leviDiff/Subjects
Parsing the .stats files
Traceback (most recent call last):
  File "/usr/local/freesurfer/bin/asegstats2table", line 538, in 
id_name_map, measurelist = parsed.parse(options.meas)
  File "/home/usr/local/freesurfer/bin/fsutils.py", line 115, in parse
self.id_name_map[seg] = strlst[4] # Col 4 is Seg Name
IndexError: list index out of range
ERROR: In
/usr/pubsw/packages/KWWidgets/CVS-vtk560/KWWidgets/vtkKWTkUtilities.cxx,
line 230
vtkKWQdecApp (0x278d8060):
Script:
vtkTemp2 GenerateStatsDataTables
Returned Error on line 1:
Uncaught exception: command failed: asegstats2table --common-segs --meas
volume --tablefile
/mnt/engram/projects/IndivRITL/data/leviDiff/Subjects/qdec/stats_tables/aseg.volume.stats.dat
--statsfile=aseg.stats --subjects 100307 101006 104820 105115 110411 111312
111413 111716 112819 113215 113619 113922 114419 115320 116524 117122
117324 118528 135225 135932 150625 150726 151223 151526 170934 171633
172130 172332 172534 172938 173334 175439 177645 177746 178142 200109
200614 20 201414 201818 203418 204016 204521 304020 307127 308331
310621 316633 329440 365343 366042 377451 380036 385450 386250 412528
433839 436239 480141 486759 497865 499566 500222 510326 530635 531536
540436 561242 562446 565452 566454 567052 567961 568963 571548 580044
580347 581349 583858 586460 594156 598568 599671

Stack trace:
Uncaught exception: command failed: asegstats2table --common-segs --meas
volume --tablefile
/mnt/engram/projects/IndivRITL/data/leviDiff/Subjects/qdec/stats_tables/aseg.volume.stats.dat
--statsfile=aseg.stats --subjects 100307 101006 104820 105115 110411 111312
111413 111716 112819 113215 113619 113922 114419 115320 116524 117122
117324 118528 135225 135932 150625 150726 151223 151526 170934 171633
172130 172332 172534 172938 173334 175439 177645 177746 178142 200109
200614 20 201414 201818 203418 204016 204521 304020 307127 308331
310621 316633 329440 365343 366042 377451 380036 385450 386250 412528
433839 436239 480141 486759 497865 499566 500222 510326 530635 531536
540436 561242 562446 565452 566454 567052 567961 568963 571548 580044
580347 581349 583858 586460 594156 598568 599671

while executing
"vtkTemp2 GenerateStatsDataTables"
---


 I've made sure that the files all line up exactly with the qdec table and
that SUBJECTS_DIR  is properly sourced so I'm not sure how to fix this
problem. Any help would be greatly appreciated!

Thanks,
LS



On Tue, Dec 1, 2015 at 4:48 PM, Douglas N Greve 
wrote:

> We need more info. Please see
>
> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
>
> On 12/01/2015 04:43 PM, levi solomyak wrote:
> > Dear experts,
> >
> > I've been attempting to generate a stats data table in qdec, but each
> > time I get a "Index Error: list index is out of range" error. This is
> > occurring when it is trying to parse the .stats file.
> >
> >  I've made sure that the files all line up exactly with the qdec table
> > and that SUBJECTS_DIR  is properly sourced so I'm not sure how to fix
> > this problem. Any help would be greatly appreciated!
> >
> > Thank you,
> > L S
> > --
> >
> >
> >
> > ___
> > 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:

Re: [Freesurfer] selxavg3-sess ERROR

2015-12-09 Thread Christina Pressl

hi doug,

thank you so much for your quick reply.

yes - I saw this error after I sent you the error log.
I checked the paradigm file, corrected it and rerun everything.

now this error is gone but I still get the following:

Error using svd
Input to SVD must not contain NaN or Inf.

Error in cond (line 36)
 s = svd(A);

Error in fast_selxavg3 (line254)
 XCond  = cond(XtX);

>> - - - - - — - - — - - — - — -

EROOR: fast_selxavg3() failed\n

Your help is much appreciated

On Dec 9, 2015, at 1:57 PM, Douglas N Greve 
> wrote:

Did you see the error description:

ERROR:
/space/mdeh5/1/halgdev/projects/christina/FSFAST/Project/NC211_fmri_060515/Sess01/bold/004/oddeven.par
is not correctly formatted. Line 19 only has 0 items

did you check this file?

On 12/09/2015 12:38 PM, Christina Pressl wrote:
Dear Freesurfer Experts,

I am having trouble with selxavg3-sess and was wondering if you could
maybe help me resolving the issue (error log attached)

I ran

#preproc-sess –s Sess01 –surface fsaverage lhrh –mni305 –fwhm 5 –per-run

and the following commands for lh, rh and mni305

#mkanalysis-sess –fsd bold –stc up -surface fsaverage lh -fwhm 5
-event-related  -paradigm oddeven.par -nconditions 3  -spmhrf 0 -TR 2
-refeventdur 10.750 -nskip 4 –mcextreg -polyfit 2  -analysis
oddeven.sm5.lh

#mkcontrast-sess –analysis oddeven.sm5.lh –contrast face-vs-object –a
1 –c 2 –c 3

#mkcontrast-sess –analysis oddeven.sm5.lh –contrast face-vs-fix  –a 1 –c 0

Thank you very much.

Christina

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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
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] selxavg3-sess ERROR

2015-12-09 Thread Douglas N Greve

That means that your design matrix is ill-conditioned.

This error means one of two things is wrong with your .par file (located 
in each run of each subjects bold directory): 1) there are not two or 
more occurrences of one of your conditions; or 2) there is a pattern to 
your conditions (for example condition 3 always follows condition 4). 
You can avoid this error message for the sake of analysis by 1) 
replacing other conditions with occurrences of your missing condition, 
so that each condition is represented at least twice; or 2) by changing 
your conditions so that they break the pattern at least twice. Even 
though the effect of this change is quite small, you should distribute 
the added conditions evenly across the other conditions. Ideally, 
however, you would alter your stimuli so that you do not get this error 
in the first place.


On 12/09/2015 02:19 PM, Christina Pressl wrote:
> hi doug,
>
> thank you so much for your quick reply.
> yes - I saw this error after I sent you the error log.
> I checked the paradigm file, corrected it and rerun everything.
>
> now this error is gone but I still get the following:
>
> Error using svd
> Input to SVD must not contain NaN or Inf.
> Error in cond (line 36)
>  s = svd(A);
>
> Error in fast_selxavg3 (line254)
>  XCond  = cond(XtX);
>
> >> - - - - - — - - — - - — - — -
>
> EROOR: fast_selxavg3() failed\n
>
>
>
> Your help is much appreciated
>
>
>
>> On Dec 9, 2015, at 1:57 PM, Douglas N Greve 
>> > wrote:
>>
>>
>> Did you see the error description:
>>
>> ERROR:
>> /space/mdeh5/1/halgdev/projects/christina/FSFAST/Project/NC211_fmri_060515/Sess01/bold/004/oddeven.par
>> is not correctly formatted. Line 19 only has 0 items
>>
>> did you check this file?
>>
>>
>> On 12/09/2015 12:38 PM, Christina Pressl wrote:
>>> Dear Freesurfer Experts,
>>>
>>> I am having trouble with selxavg3-sess and was wondering if you could
>>> maybe help me resolving the issue (error log attached)
>>>
>>>
>>> I ran
>>>
>>> #preproc-sess –s Sess01 –surface fsaverage lhrh –mni305 –fwhm 5 –per-run
>>>
>>> and the following commands for lh, rh and mni305
>>>
>>> #mkanalysis-sess –fsd bold –stc up -surface fsaverage lh -fwhm 5
>>> -event-related  -paradigm oddeven.par -nconditions 3  -spmhrf 0 -TR 2
>>> -refeventdur 10.750 -nskip 4 –mcextreg -polyfit 2  -analysis
>>> oddeven.sm5.lh
>>>
>>> #mkcontrast-sess –analysis oddeven.sm5.lh –contrast face-vs-object –a
>>> 1 –c 2 –c 3
>>>
>>> #mkcontrast-sess –analysis oddeven.sm5.lh –contrast face-vs-fix  –a 
>>> 1 –c 0
>>>
>>>
>>>
>>> Thank you very much.
>>>
>>> Christina
>>>
>>>
>>>
>>>
>>>
>>>
>>> ___
>>> 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.
>
>
>
> ___
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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
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Re: [Freesurfer] selxavg3-sess ERROR

2015-12-09 Thread Douglas N Greve


Did you see the error description:

ERROR: 
/space/mdeh5/1/halgdev/projects/christina/FSFAST/Project/NC211_fmri_060515/Sess01/bold/004/oddeven.par
 
is not correctly formatted. Line 19 only has 0 items

did you check this file?


On 12/09/2015 12:38 PM, Christina Pressl wrote:
> Dear Freesurfer Experts,
>
> I am having trouble with selxavg3-sess and was wondering if you could 
> maybe help me resolving the issue (error log attached)
>
>
> I ran
>
> #preproc-sess –s Sess01 –surface fsaverage lhrh –mni305 –fwhm 5 –per-run
>
> and the following commands for lh, rh and mni305
>
> #mkanalysis-sess –fsd bold –stc up -surface fsaverage lh -fwhm 5 
> -event-related  -paradigm oddeven.par -nconditions 3  -spmhrf 0 -TR 2 
> -refeventdur 10.750 -nskip 4 –mcextreg -polyfit 2  -analysis 
> oddeven.sm5.lh
>
> #mkcontrast-sess –analysis oddeven.sm5.lh –contrast face-vs-object –a 
> 1 –c 2 –c 3
>
> #mkcontrast-sess –analysis oddeven.sm5.lh –contrast face-vs-fix  –a 1 –c 0
>
>
>
> Thank you very much.
>
> Christina
>
>
>
>
>
>
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[Freesurfer] Qdec questions

2015-12-09 Thread sabin khadka

Hi all - When you get a significant cluster after doing monte-carlo simulation, 
we get peak vertex/Talairach coordinates and also saved in *summary files. Is 
there a way to find all the parcellated regions (Desikan, or, Destriuex) in the 
significant clusters?

Thanks
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Re: [Freesurfer] May you help me with 'recon-all' errors

2015-12-09 Thread Bruce Fischl

Hi Peng

nifti should be fine as input, but definitely don't use analyze. It 
doesn't preserve the direction cosines so once you convert to it you will 
never be sure which side of the image is the left hemim and which is the 
right.

I can't help with the  'can't locate MNI/Startup.pm ' error. Hopefully 
someone else can.

You will need some T1-weighted image with reasonably high res as input 
htough.

cheers
Bruce

On Wed, 9 Dec 2015, Peng Zan wrote:

Hi Bruce,
Thank you for your email! These dicom files are transferred from nifti
files, '.nii.gz' by xmedcon, and I think for this subject(R2261_S0283), they
are not mprage or flash scans and so far I do not have mprage or flash scans
for this subject. 

However, I do have mprage dicom files for other subjects in .img format,
which freesurfer cannot read(I attached two screenshots of my folder in case
you know by their names which files can work). Since I have most of my MRI
data in nifti and .img formats, it is worth the efforts to make these files
work in freesurfer. Do the input files have to be distributed into many
dicom slices or they can be in one file in .nii or .dcm? 

On the other hand, I also tested the my dicom files of subject R2105 (in
flash scans), and here comes the errors 'can't locate MNI/Startup.pm in
@INC...', and the 'log' file warns the input volume axes are not orthogonal.
(see 'recon-all.log' file attached). I think the input dicoms should not
have coordinates themselves, they are aligned and then assigned coordinates
by freesurfer, am I right? 

I am sorry for my verbose problems at this very beginning of using
freesurfer. 

Thank you very much! 

Sincerely,
Peng

On Wed, Dec 9, 2015 at 3:08 PM, Bruce Fischl 
wrote:
  Hi Peng

  it looks like we can't read your input dicom. For example, the
  log says:
  reading from
/Users/Peng/Documents/MNE/MNE_analysis/MRI/R2261_S0283/m000-gm_A0136_N12518
  _S0283_20120817_P5716_averageCBF_normalized.dcm...
  Starting DICOMRead2()
  dcmfile =
/Users/Peng/Documents/MNE/MNE_analysis/MRI/R2261_S0283/m000-gm_A0136_N12518
  _S0283_20120817_P5716_averageCBF_normalized.dcm
  dcmdir = /Users/Peng/Documents/MNE/MNE_analysis/MRI/R2261_S0283
  WARNING: tag ImageNumber not found in
/Users/Peng/Documents/MNE/MNE_analysis/MRI/R2261_S0283/m000-gm_A0136_N12518
  _S0283_20120817_P5716_averageCBF_normalized.dcm
  WARNING: tag SeriesNumber not found in
/Users/Peng/Documents/MNE/MNE_analysis/MRI/R2261_S0283/m000-gm_A0136_N12518
  _S0283_20120817_P5716_averageCBF_normalized.dcm
  WARNING: tag image orientation not found in
/Users/Peng/Documents/MNE/MNE_analysis/MRI/R2261_S0283/m000-gm_A0136_N12518
  _S0283_20120817_P5716_averageCBF_normalized.dcm
  Ref Series No = 0
  Found 5 files, checking for dicoms
  WARNING: tag ImageNumber not found in
/Users/Peng/Documents/MNE/MNE_analysis/MRI/R2261_S0283/m000-gm_A0136_N12518
  _S0283_20120817_P5716_averageCBF_normalized.dcm

  where did that dicom file come from? And is it supposed to be a
  T1-weighted volume like an mprage or FLASH scan?

  cheers
  Bruce

  On Wed, 9 Dec 2015, Peng Zan
  wrote:

  > Dear freesurfer expert,
  > I am a student from University of Maryland, learning
  freesurfer for MNE
  > analysis recently. I have a perhaps silly problem and could
  not solve by
  > myself. The problem occurred as 'recon-all -s R2261_S0283
  exited with
  > errors...' when I was running 'recon-all -autorecon-all
  -subjid
  > R2261_S0283'. I tried several subjects and got the same error.
  I am
  > wondering whether you can look at the 'recon-all.log' file and
  > 'recon-all.error' file and help me figure out what the problem
  is and how to
  > solve it?
  >
  > Thank you very much! Looking forward to your reply!
  >
  > Sincerely,
  > Peng
  >
  >
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[Freesurfer] Processing macaque data

2015-12-09 Thread Mahmoud

Dear Experts,

I am trying to modify the HCP pipeline scripts to work with macaque data (in
vivo, 0.5mm isotropic). The Pipeline uses FSL and a FreeSurfer.

In FreeSurferPipeline.sh there are some steps I'm not sure how to modify
them to work correctly with macaque data instead of the human data:

1-
recon-all -i "$T1wImageFile"_1mm.nii.gz -subjid $SubjectID -sd $SubjectDIR
-motioncor -talairach -nuintensitycor -normalization

>From what I've learned so far the option -talairach works with MNI305
template. Do I need to provide a macaque equivalent template instead of the
MINI305? if yes, what would be the best way to convert my macaque template
to MNI305?


2-
mri_em_register -mask "$SubjectDIR"/"$SubjectID"/mri/brainmask.mgz
"$SubjectDIR"/"$SubjectID"/mri/nu.mgz
$FREESURFER_HOME/average/RB_all_2008-03-26.gca
"$SubjectDIR"/"$SubjectID"/mri/transforms/talairach_with_skull.lta

mri_watershed -T1 -brain_atlas
$FREESURFER_HOME/average/RB_all_withskull_2008-03-26.gca
"$SubjectDIR"/"$SubjectID"/mri/transforms/talairach_with_skull.lta
"$SubjectDIR"/"$SubjectID"/mri/T1.mgz
"$SubjectDIR"/"$SubjectID"/mri/brainmask.auto.mgz

The two commands above use "RB_all_2008-03-26.gca" and
"RB_all_withskull_2008-03-26.gca" which are freesurfer atlases for human
brain. Here I have no clue how to create .gca files from my macaque images.

I appreciate any help or insight.

Thank you!
Mahmoud
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Re: [Freesurfer] May you help me with 'recon-all' errors

2015-12-09 Thread Peng Zan

Thank you! Hopefully, I can either figure it out myself or be helped by
someone.

Thanks!

Best,
Peng

On Wednesday, December 9, 2015, Bruce Fischl 
wrote:

> Hi Peng
>
> nifti should be fine as input, but definitely don't use analyze. It
> doesn't preserve the direction cosines so once you convert to it you will
> never be sure which side of the image is the left hemim and which is the
> right.
>
> I can't help with the  'can't locate MNI/Startup.pm ' error. Hopefully
> someone else can.
>
> You will need some T1-weighted image with reasonably high res as input
> htough.
>
> cheers
> Bruce
>
> On Wed, 9 Dec 2015, Peng Zan wrote:
>
> Hi Bruce,
>> Thank you for your email! These dicom files are transferred from nifti
>> files, '.nii.gz' by xmedcon, and I think for this subject(R2261_S0283),
>> they
>> are not mprage or flash scans and so far I do not have mprage or flash
>> scans
>> for this subject.
>>
>> However, I do have mprage dicom files for other subjects in .img format,
>> which freesurfer cannot read(I attached two screenshots of my folder in
>> case
>> you know by their names which files can work). Since I have most of my MRI
>> data in nifti and .img formats, it is worth the efforts to make these
>> files
>> work in freesurfer. Do the input files have to be distributed into many
>> dicom slices or they can be in one file in .nii or .dcm?
>>
>> On the other hand, I also tested the my dicom files of subject R2105 (in
>> flash scans), and here comes the errors 'can't locate MNI/Startup.pm in
>> @INC...', and the 'log' file warns the input volume axes are not
>> orthogonal.
>> (see 'recon-all.log' file attached). I think the input dicoms should not
>> have coordinates themselves, they are aligned and then assigned
>> coordinates
>> by freesurfer, am I right?
>>
>> I am sorry for my verbose problems at this very beginning of using
>> freesurfer.
>>
>> Thank you very much!
>>
>> Sincerely,
>> Peng
>>
>>
>>
>>
>>
>> On Wed, Dec 9, 2015 at 3:08 PM, Bruce Fischl 
>> wrote:
>>   Hi Peng
>>
>>   it looks like we can't read your input dicom. For example, the
>>   log says:
>>   reading from
>>
>> /Users/Peng/Documents/MNE/MNE_analysis/MRI/R2261_S0283/m000-gm_A0136_N12518
>>   _S0283_20120817_P5716_averageCBF_normalized.dcm...
>>   Starting DICOMRead2()
>>   dcmfile =
>>
>> /Users/Peng/Documents/MNE/MNE_analysis/MRI/R2261_S0283/m000-gm_A0136_N12518
>>   _S0283_20120817_P5716_averageCBF_normalized.dcm
>>   dcmdir = /Users/Peng/Documents/MNE/MNE_analysis/MRI/R2261_S0283
>>   WARNING: tag ImageNumber not found in
>>
>> /Users/Peng/Documents/MNE/MNE_analysis/MRI/R2261_S0283/m000-gm_A0136_N12518
>>   _S0283_20120817_P5716_averageCBF_normalized.dcm
>>   WARNING: tag SeriesNumber not found in
>>
>> /Users/Peng/Documents/MNE/MNE_analysis/MRI/R2261_S0283/m000-gm_A0136_N12518
>>   _S0283_20120817_P5716_averageCBF_normalized.dcm
>>   WARNING: tag image orientation not found in
>>
>> /Users/Peng/Documents/MNE/MNE_analysis/MRI/R2261_S0283/m000-gm_A0136_N12518
>>   _S0283_20120817_P5716_averageCBF_normalized.dcm
>>   Ref Series No = 0
>>   Found 5 files, checking for dicoms
>>   WARNING: tag ImageNumber not found in
>>
>> /Users/Peng/Documents/MNE/MNE_analysis/MRI/R2261_S0283/m000-gm_A0136_N12518
>>   _S0283_20120817_P5716_averageCBF_normalized.dcm
>>
>>   where did that dicom file come from? And is it supposed to be a
>>   T1-weighted volume like an mprage or FLASH scan?
>>
>>   cheers
>>   Bruce
>>
>>
>>
>>   On Wed, 9 Dec 2015, Peng Zan
>>   wrote:
>>
>>   > Dear freesurfer expert,
>>   > I am a student from University of Maryland, learning
>>   freesurfer for MNE
>>   > analysis recently. I have a perhaps silly problem and could
>>   not solve by
>>   > myself. The problem occurred as 'recon-all -s R2261_S0283
>>   exited with
>>   > errors...' when I was running 'recon-all -autorecon-all
>>   -subjid
>>   > R2261_S0283'. I tried several subjects and got the same error.
>>   I am
>>   > wondering whether you can look at the 'recon-all.log' file and
>>   > 'recon-all.error' file and help me figure out what the problem
>>   is and how to
>>   > solve it?
>>   >
>>   > Thank you very much! Looking forward to your reply!
>>   >
>>   > Sincerely,
>>   > Peng
>>   >
>>   >
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>> 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

Re: [Freesurfer] May you help me with 'recon-all' errors

2015-12-09 Thread Bruce Fischl

Hi Peng

it looks like we can't read your input dicom. For example, the log says:
reading from 
/Users/Peng/Documents/MNE/MNE_analysis/MRI/R2261_S0283/m000-gm_A0136_N12518_S0283_20120817_P5716_averageCBF_normalized.dcm...
Starting DICOMRead2()
dcmfile = 
/Users/Peng/Documents/MNE/MNE_analysis/MRI/R2261_S0283/m000-gm_A0136_N12518_S0283_20120817_P5716_averageCBF_normalized.dcm
dcmdir = /Users/Peng/Documents/MNE/MNE_analysis/MRI/R2261_S0283
WARNING: tag ImageNumber not found in 
/Users/Peng/Documents/MNE/MNE_analysis/MRI/R2261_S0283/m000-gm_A0136_N12518_S0283_20120817_P5716_averageCBF_normalized.dcm
WARNING: tag SeriesNumber not found in 
/Users/Peng/Documents/MNE/MNE_analysis/MRI/R2261_S0283/m000-gm_A0136_N12518_S0283_20120817_P5716_averageCBF_normalized.dcm
WARNING: tag image orientation not found in 
/Users/Peng/Documents/MNE/MNE_analysis/MRI/R2261_S0283/m000-gm_A0136_N12518_S0283_20120817_P5716_averageCBF_normalized.dcm
Ref Series No = 0
Found 5 files, checking for dicoms
WARNING: tag ImageNumber not found in 
/Users/Peng/Documents/MNE/MNE_analysis/MRI/R2261_S0283/m000-gm_A0136_N12518_S0283_20120817_P5716_averageCBF_normalized.dcm

where did that dicom file come from? And is it supposed to be a 
T1-weighted volume like an mprage or FLASH scan?

cheers
Bruce

On Wed, 9 Dec 2015, Peng Zan 
wrote:

> Dear freesurfer expert,
> I am a student from University of Maryland, learning freesurfer for MNE
> analysis recently. I have a perhaps silly problem and could not solve by
> myself. The problem occurred as 'recon-all -s R2261_S0283 exited with
> errors...' when I was running 'recon-all -autorecon-all -subjid
> R2261_S0283'. I tried several subjects and got the same error. I am
> wondering whether you can look at the 'recon-all.log' file and
> 'recon-all.error' file and help me figure out what the problem is and how to
> solve it?
> 
> Thank you very much! Looking forward to your reply!
> 
> Sincerely,
> Peng
> 
>
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[Freesurfer] Brainstem Substructures in Freesurfer 6.0 - how to calculate left/right volumes

2015-12-09 Thread Chris Steward

Hello,

I've installed Freesurfer 6.0 beta, and run the -brainstem-structures option to 
recon-all.

The results look ok, but I'd like the left/right volumes for the superior 
cerebellar peduncle (SCP), rather than the total volume.  Is there any easy way 
to do this?

Thanks,
Chris
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[Freesurfer] May you help me with 'recon-all' errors

2015-12-09 Thread Peng Zan

Dear freesurfer expert,

I am a student from University of Maryland, learning freesurfer for MNE
analysis recently. I have a perhaps silly problem and could not solve by
myself. The problem occurred as 'recon-all -s R2261_S0283 exited with
errors...' when I was running 'recon-all -autorecon-all -subjid
R2261_S0283'. I tried several subjects and got the same error. I am
wondering whether you can look at the 'recon-all.log' file and
'recon-all.error' file and help me figure out what the problem is and how
to solve it?

Thank you very much! Looking forward to your reply!

Sincerely,
Peng


recon-all.error
Description: Binary data


recon-all.log
Description: Binary data
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Re: [Freesurfer] selxavg3-sess ERROR

2015-12-09 Thread Christina Pressl

I see, here is a copy of my paradigm

0. 2
11.100 0
21.100 3
32.200 0
42.200 2
53.300 0
63.300 2
74.400 0
84.400  1
95.500  0
105.500 1
116.600 0
126.600 3
137.700 0
147.700 3
158.800 0
168.800 1
179.900 0

I don’t see how this setup reflects one of the two potential errors you 
outlined.

.par files are located separately in each run directory which are located in 
the bold directory.

thank you.

On Dec 9, 2015, at 2:22 PM, Douglas N Greve 
> wrote:

That means that your design matrix is ill-conditioned.

This error means one of two things is wrong with your .par file (located
in each run of each subject’s bold directory): 1) there are not two or
more occurrences of one of your conditions; or 2) there is a pattern to
your conditions (for example condition 3 always follows condition 4).
You can avoid this error message for the sake of analysis by 1)
replacing other conditions with occurrences of your missing condition,
so that each condition is represented at least twice; or 2) by changing
your conditions so that they break the pattern at least twice. Even
though the effect of this change is quite small, you should distribute
the added conditions evenly across the other conditions. Ideally,
however, you would alter your stimuli so that you do not get this error
in the first place.

On 12/09/2015 02:19 PM, Christina Pressl wrote:
hi doug,

thank you so much for your quick reply.
yes - I saw this error after I sent you the error log.
I checked the paradigm file, corrected it and rerun everything.

now this error is gone but I still get the following:

   Error using svd
   Input to SVD must not contain NaN or Inf.
   Error in cond (line 36)
s = svd(A);

   Error in fast_selxavg3 (line254)
XCond  = cond(XtX);

- - - - - — - - — - - — - — -

   EROOR: fast_selxavg3() failed\n

Your help is much appreciated

On Dec 9, 2015, at 1:57 PM, Douglas N Greve

> wrote:

Did you see the error description:

ERROR:
/space/mdeh5/1/halgdev/projects/christina/FSFAST/Project/NC211_fmri_060515/Sess01/bold/004/oddeven.par
is not correctly formatted. Line 19 only has 0 items

did you check this file?

On 12/09/2015 12:38 PM, Christina Pressl wrote:
Dear Freesurfer Experts,

I am having trouble with selxavg3-sess and was wondering if you could
maybe help me resolving the issue (error log attached)

I ran

#preproc-sess –s Sess01 –surface fsaverage lhrh –mni305 –fwhm 5 –per-run

and the following commands for lh, rh and mni305

#mkanalysis-sess –fsd bold –stc up -surface fsaverage lh -fwhm 5
-event-related  -paradigm oddeven.par -nconditions 3  -spmhrf 0 -TR 2
-refeventdur 10.750 -nskip 4 –mcextreg -polyfit 2  -analysis
oddeven.sm5.lh

#mkcontrast-sess –analysis oddeven.sm5.lh –contrast face-vs-object –a
1 –c 2 –c 3

#mkcontrast-sess –analysis oddeven.sm5.lh –contrast face-vs-fix  –a
1 –c 0

Thank you very much.

Christina

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

[Freesurfer] Minc File Error

2015-12-09 Thread MCLAREN, Donald

Zeke and others,

I recently installed Freesurfer v6 (
freesurfer-Darwin-OSX-stable-v6-beta-20151015.dmg
,
MacOS
10.9.5, XQuartz 2.7.8), and Freeview always closes whenever I try to open a
mnc file. Below is the output from the terminal after Freeview closes.

Please let me know what I need to resolve the issue. The file is in fact a
valid minc file as it can be opened by register and display.

Please let me know if additional details are needed.

Best,

Donald


Output begins here:
=

ncopen: filename "XXX.mnc": Not a netCDF file

miopen: MINC package entry point

Error opening XXX.mnc

mincRead(): error reading volume from file .mnc

dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address

  Referenced from:
/Applications/freesurfer/Freeview.app/Contents/MacOS/../Frameworks/libstdc++.6.dylib

  Expected in: /usr/lib/libSystem.B.dylib


dyld: Symbol not found: ___emutls_get_address

  Referenced from:
/Applications/freesurfer/Freeview.app/Contents/MacOS/../Frameworks/libstdc++.6.dylib

  Expected in: /usr/lib/libSystem.B.dylib


[0]PETSC ERROR:


[0]PETSC ERROR: Caught signal number 5 TRAP

[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 darwin12. named Belhavens-Best.local by
mclaren Wed Dec  9 14:42:45 2015

[0]PETSC ERROR: Libraries linked from
/usr/pubsw/packages/petsc/2.3.3-p13-64b/src/petsc-2.3.3-p13/lib/darwin12.2.0-c-opt

[0]PETSC ERROR: Configure run at Mon Dec 17 15:29:35 2012

[0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc
--with-fc=0 --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

[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 darwin12. named Belhavens-Best.local by
mclaren Wed Dec  9 14:42:45 2015

[0]PETSC ERROR: Libraries linked from
/usr/pubsw/packages/petsc/2.3.3-p13-64b/src/petsc-2.3.3-p13/lib/darwin12.2.0-c-opt

[0]PETSC ERROR: Configure run at Mon Dec 17 15:29:35 2012

[0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc
--with-fc=0 --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:

[Freesurfer] selxavg3-sess ERROR

2015-12-09 Thread Christina Pressl

Dear Freesurfer Experts,

I am having trouble with selxavg3-sess and was wondering if you could maybe 
help me resolving the issue (error log attached)


I ran

#preproc-sess –s Sess01 –surface fsaverage lhrh –mni305 –fwhm 5 –per-run

and the following commands for lh, rh and mni305

#mkanalysis-sess –fsd bold –stc up -surface fsaverage lh -fwhm 5 -event-related 
 -paradigm oddeven.par -nconditions 3   -spmhrf 0 -TR 2 -refeventdur 10.750 
-nskip 4 –mcextreg -polyfit 2  -analysis oddeven.sm5.lh

#mkcontrast-sess –analysis oddeven.sm5.lh –contrast face-vs-object –a 1 –c 2 –c 
3

#mkcontrast-sess –analysis oddeven.sm5.lh –contrast face-vs-fix  –a 1 –c 0



Thank you very much.

Christina





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