date:20190219

Re: [Freesurfer] MRISalloc error during automatic reconstruction

2019-02-19 Thread Julia Ströhlein

External Email - Use Caution

Hi Bruce,

I created a link with the Martinos File Drop System, because ftp upload did
not work.
It's probably the best idea to send the links to your personal mail address?

Best
Julia

-Ursprüngliche Nachricht-
Von: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl
Gesendet: Montag, 18. Februar 2019 15:52
An: Freesurfer support list 
Betreff: Re: [Freesurfer] MRISalloc error during automatic reconstruction

Hi Julia

why don't you tar and gzip the subject directory and put it on our ftp site
so we can take a look

cheers
Bruce
On Mon, 18 Feb 2019, Julia Ströhlein wrote:

>External Email - Use Caution
>
> Hi Bruce,
> thanks for the advice. I ran the subject again with 4.5G, but it ended 
> with the same error. It only happens with this subject, the stream 
> worked fine for all the other subjects.
> However, I tried running the subject with my Macbook, and it also 
> ended with an error (see the recon-all.log attached). I think it has 
> something to do with the MRI of the subject. Do you have any ideas?
> Thanks for any help.
> Best,
> Julia
>
> -Ursprüngliche Nachricht-
> Von: freesurfer-boun...@nmr.mgh.harvard.edu
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Bruce 
> Fischl
> Gesendet: Mittwoch, 13. Februar 2019 15:58
> An: Freesurfer support list 
> Betreff: Re: [Freesurfer] MRISalloc error during automatic 
> reconstruction
>
> Hi Julia
>
> I think you only have about 1.5G free memory at the beinning of 
> running recon-all, which is not enough for this subject. It looks like 
> some other process is using another 2G, which might be enough if you 
> can free it up. In general though you probably want a machine with 
> more ram
>
> cheers
> Bruce
>
>
> On Wed, 13 Feb
> 2019, Julia Ströhlein wrote:
>
>>External Email - Use Caution
>>
>> Hi,
>> of course.
>>
>> Julia
>>
>> -Ursprüngliche Nachricht-
>> Von: freesurfer-boun...@nmr.mgh.harvard.edu
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Bruce 
>> Fischl
>> Gesendet: Dienstag, 12. Februar 2019 16:12
>> An: Freesurfer support list 
>> Betreff: Re: [Freesurfer] MRISalloc error during automatic 
>> reconstruction
>>
>> Hi Julia
>>
>> can you send us the recon-all.log file?
>>
>> cheers
>> Bruce
>> On Tue, 12 Feb 2019,
>> Julia Ströhlein wrote:
>>
>>>
>>> External Email - Use Caution
>>>
>>> Dear experts,
>>>
>>> while running one of my subjects, I got this error:
>>>
>>>  
>>>
>>> MRISalloc(732595, 480): could not allocate vertices
>>>
>>> Cannot allocate memory
>>>
>>> Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10
>>>
>>> 20:41:14 UTC 2012 i686 i686 i386 GNU/Linux
>>>
>>>  
>>>
>>> recon-all -s P_04 exited with ERRORS at Mon Feb  4 16:40:03 EST 2019
>>>
>>>  
>>>
>>> Do you know what went wrong and how I can fix this?
>>>
>>> Best regards,
>>>
>>> Julia
>>>
>>>  
>>>
>>>  
>>>
>>> Unbenannt
>>>
>>>  
>>>
>>>
>>>
>>
>



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[Freesurfer] average MRI scans

2019-02-19 Thread Vivek Sharma

External Email - Use Caution

I'm working on source reconstruction using MEG data. For which segmented T1
images of MRI scans are required. I use recon -all for individual subjects.
Can we have a common average template made from MRI scans of all subjects.
If I have MRI scans from 10 subjects, how can I have average template of
these 10 scans.

-- 
Vivek
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Re: [Freesurfer] Average subject

2019-02-19 Thread Laboratorio de Neurociencia Funcional

External Email - Use Caution

Thank, Bruce. So the final message is that I should use the same average
subject to display results of cortical thickness even when samples to be
compared have highly different brain morphology. Is that correct?

El lun., 18 feb. 2019 a las 23:37, Bruce Fischl ()
escribió:

> Hi Jose
>
> usually we don't need multiple averages (or study specific ones), which
> simplifies things considerably. Is there a reason you think you need one?
> We intentially use the gray/white boundary for this reason, which is
> insensitive to any possible cortical atrophy.
>
> cheers
> Bruce
>
> On Mon, 18 Feb 2019, Laboratorio de
> Neurociencia Funcional wrote:
>
> >
> > External Email - Use Caution
> >
> > Dear all,
> >
> > I am planning to run separate regression analysis with cortical
> thickness in two very different
> > populations (young and elderly subjects). Depending on results, it may
> happen that I am interested
> > in comparing regression slopes between the two groups. My question is:
> should I build one average
> > subject for each within-group regression analysis (one for young and
> another for elderly), and
> > another different average subject merging all subjects of the two
> samples to compare regression
> > slopes? Or I should preferably use only one average subjects with all
> subjects in all within and
> > between regression analysis?
> >
> > Many thanks in in advance.
> >
> > Best regards,
> > Jose
> >
> >___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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[Freesurfer] Information about argument -erode in command mri_extract_label

2019-02-19 Thread Viktor Domazetoski

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Dear FreeSurfer experts,

I would like to enquire about the command mri_extract_label. More specifically 
I am looking for information about the -erode argument. Therefore I have a few 
questions:

  1.  Is a 3D erosion of the entire brain or a 2D slice by slice erosion used?
  2.  What structuring element (regarding the shape and size of the kernel) is 
used for the erosion for a given argument value (e.g. for the command 
mri_extract_label -erode 1)?

Thank you in advance!
Kind regards,
Viktor
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Re: [Freesurfer] Recon-all XL defect detected...

2019-02-19 Thread Matthieu VANHOUTTE

   External Email - Use Caution


Hi Bruce,

I don't see major thing that could be wrong.

I uploaded on the FileDrop the subject directory compressed. Could you 
have a look at it and tell me what you think ?


Best,
Matthieu

On 18/02/2019 15:56, Bruce Fischl wrote:

Hi Matthieu

have you looked at the lh.inflated.nofix to see if anything major is 
wrong? The code doesn't exit when it detects an XL defect - it just 
warns you and doesn't search as thoroughly for solutions (which would 
take forever). It sounds like the 0 faces error is your problem, but 
they are likely related. Take a look at the inflated.nofix and see if 
you can identify the XL defect. It is probably near the back of the 
brain since it is one of the first defects encountered.


cheers
Bruce




 On Mon, 18 Feb 2019, Matthieu VANHOUTTE wrote:



External Email - Use Caution

Dear Freesurfer's experts,

I have run recon-all on one subject and it stopped with a "XL defect 
detected..."  (please see below

the log):

#@# Fix Topology lh Sat Feb 16 08:22:31 CET 2019

 mris_fix_topology -rusage 
/FS6.0.1/awellv3s013/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere

qsphere.nofix -ga -seed 1234 awellv3s013 lh

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

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

*
INFO: assuming .mgz format
$Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
before topology correction, eno=-112 (nv=135382, nf=270988, 
ne=406482, g=57)

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

Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 10 iterations
marking ambiguous vertices...
39303 ambiguous faces found in tessellation
segmenting defects...
22 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
  -merging segment 16 into 2
21 defects to be corrected
0 vertices coincident
reading input surface FS6.0.1/awellv3s013/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
  -face   loglikelihood: -9.1744  (-4.5872)
  -vertex loglikelihood: -6.3047  (-3.1523)
  -normal dot loglikelihood: -3.6091  (-3.6091)
  -quad curv  loglikelihood: -5.8524  (-2.9262)
  Total Loglikelihood : -24.9405

CORRECTING DEFECT 0 (vertices=41, convex hull=76, v0=1825)
After retessellation of defect 0 (v0=1825), euler #=-4 
(114791,342427,227632) : difference with

theory (-18) = -14

CORRECTING DEFECT 1 (vertices=22, convex hull=53, v0=6219)
After retessellation of defect 1 (v0=6219), euler #=-3 
(114805,342485,227677) : difference with

theory (-17) = -14

CORRECTING DEFECT 2 (vertices=19736, convex hull=2755, v0=16117)
normal vector of length zero at vertex 115020 with 0 faces
vertex 115020 has 0 face
XL defect detected...
No such file or directory
Linux hpc1.cyceron.fr 3.10.0-693.11.6.el7.x86_64 #1 SMP Thu Jan 4 
01:06:37 UTC 2018 x86_64 x86_64

x86_64 GNU/Linux

recon-all -s awellv3s013 exited with ERRORS at Sat Feb 16 10:17:17 
CET 2019


I looked at the ?h.orig.nofix but didn't see anything wrong, despite 
the fact that these surfaces

are very not smooth.

What could I do ?

Best,

Matthieu





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Re: [Freesurfer] commends of GLM for volume

2019-02-19 Thread ??

External Email - Use Caution

Hello Greve,
I am glad to tell you that after 3 hours, something did print more on terminal. 
when I was doing the GLM follow the tutorial, it only provided the example of 
the cortical thickness. And I did not know how to transfer it into volume.
Here is my commends
 
mris_preproc --fsgd FSGD/PDDvsHC.fsgd --cache-in volmue.fwhm10.fsaverage 
--target fsaverage --hemi lh --out lh.PDDvsHC.volume.10.mgh
 
 mri_glmfit --y lh.PDDvsHC.volume.10.mgh --fsgd FSGD/PDDvsHC.fsgd --C 
Contras-HC-PDD.mtx --surf fsaverage lh --cortex --glmdir 
lh.volume.PDDvsHC.glimdir --eres-save
 
 mri_glmfit-sim --glmdir rh.PDDvsHC.volume.glmdir --cache 1.3 pos --cwp 999 
--2spaces

We I check the results, it still talked about the cortical thickness , so could 
you tell me how to change this commends to the volume of subcortical. Or do you 
have the example which use GLM for comparing the difference of subcortical 
volume between two groups.

Thanks so much for your help

Yours

Zeng

Here is the results 

 


ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZCWPCWPLow
CWPHi   NVtxsWghtVtx   Annot

 


   16.960   86488   4544.63 15.7  -77.36.7  0.00020  0.0  
0.00040   789115125.67  pericalcarine

 


   23.529  158070   3287.33 55.0  -52.98.2  0.00020  0.0  
0.00040   679611225.54  inferiorparietal

 


   32.630   67804   1909.67 43.3   45.8   -9.3  0.00220  0.00140  
0.00300   2858 4399.15  parsorbitalis

  Here is the terminal output.

  

$Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $

 


cwd /Volumes/NIU20/volumetric_FS/glm

 


cmdline mri_glmfit.bin --glmdir lh.PDDvsHC.volume.glmdir --y 
lh.PDDvsHC.volume.10.mgh --fsgd FSGD/PDDvsHC.fsgd --C 
Contrasts/lh-thickness-HC-PDD.mtx --surface fsaverage lh --eres-save 

 


sysname  Darwin

 


hostname dyn3199-104.wlan.ic.ac.uk

 


machine  x86_64

 


user cengzhou

 


FixVertexAreaFlag = 1

 


UseMaskWithSmoothing 1

 


OneSampleGroupMean 0

 


y/Volumes/NIU20/volumetric_FS/glm/lh.PDDvsHC.volume.10.mgh

 


logyflag 0

 


usedti  0

 


FSGD FSGD/PDDvsHC.fsgd

 


labelmask  /Volumes/NIU20/volumetric_FS/glm/fsaverage/label/lh.cortex.label

 


maskinv 0

 


glmdir lh.PDDvsHC.volume.glmdir

 


IllCondOK 0

 


ReScaleX 1

 


DoFFx 0

 


ResidualFWHM 14.826153

 


SearchSpace 73852.172969

 


anattype surface

 


 

 


 

 


cd /Volumes/NIU20/volumetric_FS/glm

 


/Applications/freesurfer/bin/mri_glmfit-sim

 


--glmdir rh.PDDvsHC.volume.glmdir --cache 1.3 pos --cwp 999 --2spaces

 


 

 


$Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $

 


Mon Feb 18 15:52:07 GMT 2019

 


Darwin dyn3199-104.wlan.ic.ac.uk 14.5.0 Darwin Kernel Version 14.5.0: Wed Jul 
29 02:26:53 PDT 2015; root:xnu-2782.40.9~1/RELEASE_X86_64 x86_64

 


cengzhou

 


setenv SUBJECTS_DIR /Volumes/NIU20/volumetric_FS/glm

 


FREESURFER_HOME /Applications/freesurfer

 


 

 


Original mri_glmfit command line:

 


cmdline mri_glmfit.bin --glmdir rh.PDDvsHC.volume.glmdir --y 
rh.PDDvsHC.volume.10.mgh --fsgd FSGD/PDDvsHC.fsgd --C 
Contrasts/lh-thickness-HC-PDD.mtx --surface fsaverage rh --eres-save

 


 

 


DoSim = 0

 


UseCache = 1

 


DoPoll = 0

 


DoPBSubmit = 0

 


DoBackground = 0

 


DiagCluster = 0

 


gd2mtx = dods

 


fwhm = 14.506572

 


CSD 
/Applications/freesurfer/average/mult-comp-cor/fsaverage/rh/cortex/fwhm15/pos/th13/mc-z.csd

 


mri_surfcluster --in rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/sig.mgh --mask 
rh.PDDvsHC.volume.glmdir/mask.mgh --cwsig 
rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.cluster.mgh --sum 
rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.cluster.summary 
--ocn rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.ocn.mgh 
--annot aparc --cwpvalthresh 999 --o 
rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.masked.mgh 
--no-fixmni --csd 
/Applications/freesurfer/average/mult-comp-cor/fsaverage/rh/cortex/fwhm15/pos/th13/mc-z.csd
 --csdpdf rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.pdf.dat 
--vwsig rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.voxel.mgh 
--vwsigmax 
rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.voxel.max.dat 
--oannot rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.ocn.annot 
--bonferroni 2 --surf white

 


Creating CDFs from CSD files

 


csd->threshsign = 1

 


thsign = pos, id = 1

 


version $Id: mri_surfcluster.c,v 1.57.2.3 2016/11/17 18:19:42 zkaufman Exp $

 


hemi   = rh

 


srcid  = rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/sig.mgh 

 


srcsubjid  = fsaverage

 


srcsurf= white

 


srcframe   = 0

 


thsign = pos

 


thmin  = 1.3

 


thmax  = -1

 


fdr= -1

 


minarea= 0

 


Bonferroni  = 2

 


xfmfile= talairach.xfm

 


nth = -1

[Freesurfer] Choroid plexus analysis

2019-02-19 Thread Benjamin Luerweg

External Email - Use Caution

Dear community,

anyone out there who can give me some information regarding how valid a volume 
detection of the choroid plexus is? 
I used fs 6.0. 

Kind regards,
Ben



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[Freesurfer] anat2dti error after dt_recon

2019-02-19 Thread Daniel Davidson Callow

External Email - Use Caution

Hello,

I ran a successful dt_recon and then wanted to use

mri_vol2vol --mov $subj_dir/dtrecons/${subj}.${cond}/lowb.nii.gz --targ
$subj_dir/diffusion_recons/${subj}.${cond}/mri/aparc+aseg.mgz --inv
--interp nearest --o
$subj_dir/dtrecons/${subj}.${cond}/aparc+aseg2diff.nii.gz --reg
$subj_dir/dtrecon/${subj}.${cond}/register.dat --no-save-reg


to get the anatomical segmentations into diffusion space. However, when
running the above code I get the following error message?


echo subj =  AES139 , cond =  Rest

subj =  AES139 , cond =  Rest

set echo

cd /Volumes/DANIEL/dti_freesurf

mri_vol2vol --mov
/Volumes/DANIEL/dti_freesurf/dtrecons/AES139.Rest/lowb.nii.gz --targ
/Volumes/DANIEL/dti_freesurf/diffusion_recons/AES139.Rest/mri/aparc+aseg.mgz
--inv --interp nearest --o
/Volumes/DANIEL/dti_freesurf/dtrecons/AES139.Rest/aparc+aseg2diff.nii.gz
--reg /Volumes/DANIEL/dti_freesurf/dtrecon/AES139.Rest/register.dat
--no-save-reg

regio_read_register(): No such file or directory

Could not open /Volumes/DANIEL/dti_freesurf/dtrecon/AES139.Rest/register.dat


Matrix from regfile:

MatrixPrint: mat = NULL!

No such file or directory


I have attached an example register.dat file in case that is the issue.


also the output for ls -l register.dat

-rwxrwxrwx  1 administrator  staff  323 Feb 18 13:59 register.dat


Any advice with troubleshooting is greatly appreciated!


Best,
*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
dcal...@umd.edu 
443-254-6298


register.dat
Description: Binary data
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Re: [Freesurfer] MRISalloc error during automatic reconstruction

2019-02-19 Thread Bruce Fischl


Hi Julia

did you upload the entire subject dir (gzipped and tarred)? And what 
happened with ftp? We can help you get that working. I would think the 
whole subject dir would be too big for the filedrop, but feel free to 
send me the link


cheers
Bruce
On Tue, 19 Feb 2019, Julia Ströhlein wrote:


   External Email - Use Caution

Hi Bruce,

I created a link with the Martinos File Drop System, because ftp upload did
not work.
It's probably the best idea to send the links to your personal mail address?

Best
Julia

-Ursprüngliche Nachricht-
Von: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl
Gesendet: Montag, 18. Februar 2019 15:52
An: Freesurfer support list 
Betreff: Re: [Freesurfer] MRISalloc error during automatic reconstruction

Hi Julia

why don't you tar and gzip the subject directory and put it on our ftp site
so we can take a look

cheers
Bruce
On Mon, 18 Feb 2019, Julia Ströhlein wrote:


   External Email - Use Caution

Hi Bruce,
thanks for the advice. I ran the subject again with 4.5G, but it ended
with the same error. It only happens with this subject, the stream
worked fine for all the other subjects.
However, I tried running the subject with my Macbook, and it also
ended with an error (see the recon-all.log attached). I think it has
something to do with the MRI of the subject. Do you have any ideas?
Thanks for any help.
Best,
Julia

-Ursprüngliche Nachricht-
Von: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Bruce
Fischl
Gesendet: Mittwoch, 13. Februar 2019 15:58
An: Freesurfer support list 
Betreff: Re: [Freesurfer] MRISalloc error during automatic
reconstruction

Hi Julia

I think you only have about 1.5G free memory at the beinning of
running recon-all, which is not enough for this subject. It looks like
some other process is using another 2G, which might be enough if you
can free it up. In general though you probably want a machine with
more ram

cheers
Bruce


On Wed, 13 Feb
2019, Julia Ströhlein wrote:


   External Email - Use Caution

Hi,
of course.

Julia

-Ursprüngliche Nachricht-
Von: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Bruce
Fischl
Gesendet: Dienstag, 12. Februar 2019 16:12
An: Freesurfer support list 
Betreff: Re: [Freesurfer] MRISalloc error during automatic
reconstruction

Hi Julia

can you send us the recon-all.log file?

cheers
Bruce
On Tue, 12 Feb 2019,
Julia Ströhlein wrote:



External Email - Use Caution

Dear experts,

while running one of my subjects, I got this error:

 

MRISalloc(732595, 480): could not allocate vertices

Cannot allocate memory

Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10

20:41:14 UTC 2012 i686 i686 i386 GNU/Linux

 

recon-all -s P_04 exited with ERRORS at Mon Feb  4 16:40:03 EST 2019

 

Do you know what went wrong and how I can fix this?

Best regards,

Julia

 

 

Unbenannt

 











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Re: [Freesurfer] Average subject

2019-02-19 Thread Bruce Fischl

yes, because the differences in their morphology don't change the average 
very much. You can try it both ways to verify this is true for your 
subjects.

cheers
Bruce

On Tue, 19 Feb 2019, 
Laboratorio de Neurociencia Funcional wrote:

External Email - Use Caution

Thank, Bruce. So the final message is that I should use the same average 
subject to display results
of cortical thickness even when samples to be compared have highly different 
brain morphology. Is
that correct?

El lun., 18 feb. 2019 a las 23:37, Bruce Fischl () 
escribió:
  Hi Jose

  usually we don't need multiple averages (or study specific ones), which
  simplifies things considerably. Is there a reason you think you need one?
  We intentially use the gray/white boundary for this reason, which is
  insensitive to any possible cortical atrophy.

  cheers
  Bruce

  On Mon, 18 Feb 2019, Laboratorio de
  Neurociencia Funcional wrote:

  >
  > External Email - Use Caution
  >
  > Dear all,
  >
  > I am planning to run separate regression analysis with cortical 
thickness in two very
  different
  > populations (young and elderly subjects). Depending on results, it may 
happen that I
  am interested
  > in comparing regression slopes between the two groups. My question is: 
should I build
  one average
  > subject for each within-group regression analysis (one for young and 
another for
  elderly), and
  > another different average subject merging all subjects of the two 
samples to compare
  regression
  > slopes? Or I should preferably use only one average subjects with all 
subjects in all
  within and
  > between regression analysis?
  >
  > Many thanks in in advance.
  >
  > Best regards,
  > Jose
  >
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Re: [Freesurfer] Information about argument -erode in command mri_extract_label

2019-02-19 Thread Bruce Fischl


Hi Viktor

it is a 3D erosion, and a cubic 3x3x3 structuring element.

cheers
Bruce
On Tue, 19 Feb 
2019, Viktor Domazetoski wrote:




External Email - Use Caution

Dear FreeSurfer experts,

I would like to enquire about the command mri_extract_label. More specifically 
I am looking for
information about the -erode argument. Therefore I have a few questions: 
 1. Is a 3D erosion of the entire brain or a 2D slice by slice erosion used?
 2. What structuring element (regarding the shape and size of the kernel) is 
used for the erosion
for a given argument value (e.g. for the command mri_extract_label -erode 
1)?
Thank you in advance!
Kind regards,
Viktor 

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Re: [Freesurfer] Recon-all XL defect detected...

2019-02-19 Thread Bruce Fischl


will do
On Tue, 19 Feb 2019, Matthieu VANHOUTTE wrote:



External Email - Use Caution

Hi Bruce,

I don't see major thing that could be wrong.

I uploaded on the FileDrop the subject directory compressed. Could you have a 
look at it and tell me
what you think ?

Best,
Matthieu

On 18/02/2019 15:56, Bruce Fischl wrote:
  Hi Matthieu

  have you looked at the lh.inflated.nofix to see if anything major is 
wrong? The code
  doesn't exit when it detects an XL defect - it just warns you and doesn't 
search as
  thoroughly for solutions (which would take forever). It sounds like the 0 
faces error is
  your problem, but they are likely related. Take a look at the 
inflated.nofix and see if
  you can identify the XL defect. It is probably near the back of the brain 
since it is
  one of the first defects encountered.

  cheers
  Bruce




   On Mon, 18 Feb 2019, Matthieu VANHOUTTE wrote:


External Email - Use Caution

Dear Freesurfer's experts,

I have run recon-all on one subject and it stopped with a "XL defect
detected..."  (please see below
the log):

#@# Fix Topology lh Sat Feb 16 08:22:31 CET 2019

 mris_fix_topology -rusage
/FS6.0.1/awellv3s013/touch/rusage.mris_fix_topology.lh.dat -mgz 
-sphere
qsphere.nofix -ga -seed 1234 awellv3s013 lh

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

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

*
INFO: assuming .mgz format
$Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman 
Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
before topology correction, eno=-112 (nv=135382, nf=270988, 
ne=406482, g=57)
using quasi-homeomorphic spherical map to tessellate cortical 
surface...

Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 10 iterations
marking ambiguous vertices...
39303 ambiguous faces found in tessellation
segmenting defects...
22 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
  -merging segment 16 into 2
21 defects to be corrected
0 vertices coincident
reading input surface FS6.0.1/awellv3s013/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
  -face   loglikelihood: -9.1744  (-4.5872)
  -vertex loglikelihood: -6.3047  (-3.1523)
  -normal dot loglikelihood: -3.6091  (-3.6091)
  -quad curv  loglikelihood: -5.8524  (-2.9262)
  Total Loglikelihood : -24.9405

CORRECTING DEFECT 0 (vertices=41, convex hull=76, v0=1825)
After retessellation of defect 0 (v0=1825), euler #=-4
(114791,342427,227632) : difference with
theory (-18) = -14

CORRECTING DEFECT 1 (vertices=22, convex hull=53, v0=6219)
After retessellation of defect 1 (v0=6219), euler #=-3
(114805,342485,227677) : difference with
theory (-17) = -14

CORRECTING DEFECT 2 (vertices=19736, convex hull=2755, v0=16117)
normal vector of length zero at vertex 115020 with 0 faces
vertex 115020 has 0 face
XL defect detected...
No such file or directory
Linux hpc1.cyceron.fr 3.10.0-693.11.6.el7.x86

[Freesurfer] recon-all tries to call mri_relabel_hypointensities -all-info

2019-02-19 Thread Drucker, Daniel


freesurfer-6.0.1/bin/recon-all line 630 calls:


mri_relabel_hypointensities -all-info


However, -all-info is not a valid option:


$ mri_relabel_hypointensities
usage: mri_relabel_hypointensities [options]   


This program measures a variety of anatomical properties

valid options are:

-l   - limit calculations to specified label
-a  - compute properties for each label
   in the annotation file separately

$ mri_relabel_hypointensities -all-info
unknown option -all-info




--

Daniel M. Drucker, Ph.D.

Director of IT, McLean Imaging Center
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Re: [Freesurfer] recon-all tries to call mri_relabel_hypointensities -all-info

2019-02-19 Thread Bruce Fischl


Hi Daniel

do you have a mixed version of binaries? This works fine for me:
/usr/local/freesurfer/stable6_0_0/bin/mri_relabel_hypointensities -all-info
ProgramName: mri_relabel_hypointensities  ProgramArguments: -all-info 
ProgramVersion: $Name: stable6 $  TimeStamp: 2019/02/19-16:01:28-GMT 
BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: 
mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $  User: 
fischl  Machine: tiamat.nmr.mgh.harvard.edu  Platform: Linux 
PlatformVersion: 3.10.0-957.1.3.el7.x86_64  CompilerName: GCC 
CompilerVersion: 40400



maybe you need a new version of mri_relabel_hypointensities?

cheers
Bruce
 On Tue, 19 Feb 
2019, Drucker, Daniel wrote:





freesurfer-6.0.1/bin/recon-all line 630 calls:


mri_relabel_hypointensities -all-info


However, -all-info is not a valid option:


$ mri_relabel_hypointensities
usage: mri_relabel_hypointensities [options]   


This program measures a variety of anatomical properties

valid options are:

-l               - limit calculations to specified label
-a          - compute properties for each label
                               in the annotation file separately

$ mri_relabel_hypointensities -all-info
unknown option -all-info



--

Daniel M. Drucker, Ph.D.

Director of IT, McLean Imaging Center


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Re: [Freesurfer] [EXTERNAL] Re: mri_surf2surf QC

2019-02-19 Thread Winkelbeiner, Stephanie A

External Email - Use Caution

Hi Bruce, 

Thank you for your quick and helpful reply. 
Unfortunately, I wasn't able to figure out what comes between -f and -ss...
Would you mind explaining what you meant with ... ?

Thanks a lot, 
Stephanie

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Friday, February 15, 2019 11:03 AM
To: Freesurfer support list 
Subject: [EXTERNAL] Re: [Freesurfer] mri_surf2surf QC

 External Email. Use Caution.

Hi Stephanie

I guess visually. You can write a script to run freeview and save a snapshot 
using something like:

foreach s ($SUBJECTS)
   freeview -f ... -ss  
> External Email - Use Caution
> 
> Hi Freesurfers,
> 
>  
> 
> I ran mri_surf2surf and registered self-created parcels from fsaverage 
> to all my subjects. What is the best way to do QC and check if everything 
> went right?
> 
>  
> 
> Thanks for your help!
> 
> Stephanie
> 
>  
> 
> 
> The information contained in this electronic e-mail transmission and 
> any attachments are intended only for the use of the individual or 
> entity to whom or to which it is addressed, and may contain 
> information that is privileged, confidential and exempt from 
> disclosure under applicable law. If the reader of this communication 
> is not the intended recipient, or the employee or agent responsible 
> for delivering this communication to the intended recipient, you are 
> hereby notified that any dissemination, distribution, copying or 
> disclosure of this communication and any attachment is strictly 
> prohibited. If you have received this transmission in error, please notify 
> the sender immediately by telephone and electronic mail, and delete the 
> original communication and any attachment from any computer, server or other 
> electronic recording or storage device or medium. Receipt by anyone other 
> than the intended recipient is not a waiver of any attorney-client, 
> physician-patient or other privilege.
>


The information contained in this electronic e-mail transmission and any 
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Re: [Freesurfer] [EXTERNAL] Re: mri_surf2surf QC

2019-02-19 Thread Bruce Fischl


Hi Stephanie

if you have an annot named lh.myannot.annot you could use:

freeview -f lh.inflated:annot=lh.myannot.annot -ss filename.tif

where of course you will need paths to the various files and will want to 
change the filename for each subject


cheers
Bruce

On Tue, 19 Feb 2019, Winkelbeiner, Stephanie A wrote:


   External Email - Use Caution

Hi Bruce,

Thank you for your quick and helpful reply.
Unfortunately, I wasn't able to figure out what comes between -f and -ss...
Would you mind explaining what you meant with ... ?

Thanks a lot,
Stephanie

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Friday, February 15, 2019 11:03 AM
To: Freesurfer support list 
Subject: [EXTERNAL] Re: [Freesurfer] mri_surf2surf QC

External Email. Use Caution.

Hi Stephanie

I guess visually. You can write a script to run freeview and save a snapshot 
using something like:

foreach s ($SUBJECTS)
  freeview -f ... -ss 

External Email - Use Caution

Hi Freesurfers,

 

I ran mri_surf2surf and registered self-created parcels from fsaverage
to all my subjects. What is the best way to do QC and check if everything went 
right?

 

Thanks for your help!

Stephanie

 


The information contained in this electronic e-mail transmission and
any attachments are intended only for the use of the individual or
entity to whom or to which it is addressed, and may contain
information that is privileged, confidential and exempt from
disclosure under applicable law. If the reader of this communication
is not the intended recipient, or the employee or agent responsible
for delivering this communication to the intended recipient, you are
hereby notified that any dissemination, distribution, copying or
disclosure of this communication and any attachment is strictly
prohibited. If you have received this transmission in error, please notify the 
sender immediately by telephone and electronic mail, and delete the original 
communication and any attachment from any computer, server or other electronic 
recording or storage device or medium. Receipt by anyone other than the 
intended recipient is not a waiver of any attorney-client, physician-patient or 
other privilege.




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Re: [Freesurfer] [EXTERNAL] Re: mri_surf2surf QC

2019-02-19 Thread Winkelbeiner, Stephanie A

External Email - Use Caution

Dear Bruce

Thanks a lot for this very helpful explanation! This is much appreciated and it 
is now much clearer to me what I have to do.

Thank you,
Stephanie


> On Feb 19, 2019, at 11:09 AM, Bruce Fischl  wrote:
> 
> External Email. Use Caution.
> 
> Hi Stephanie
> 
> if you have an annot named lh.myannot.annot you could use:
> 
> freeview -f lh.inflated:annot=lh.myannot.annot -ss filename.tif
> 
> where of course you will need paths to the various files and will want to 
> change the filename for each subject
> 
> cheers
> Bruce
> 
>> On Tue, 19 Feb 2019, Winkelbeiner, Stephanie A wrote:
>> 
>>   External Email - Use Caution
>> 
>> Hi Bruce,
>> 
>> Thank you for your quick and helpful reply.
>> Unfortunately, I wasn't able to figure out what comes between -f and -ss...
>> Would you mind explaining what you meant with ... ?
>> 
>> Thanks a lot,
>> Stephanie
>> 
>> -Original Message-
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
>> Sent: Friday, February 15, 2019 11:03 AM
>> To: Freesurfer support list 
>> Subject: [EXTERNAL] Re: [Freesurfer] mri_surf2surf QC
>> 
>> External Email. Use Caution.
>> 
>> Hi Stephanie
>> 
>> I guess visually. You can write a script to run freeview and save a snapshot 
>> using something like:
>> 
>> foreach s ($SUBJECTS)
>>  freeview -f ... -ss > 
>> then you can zip through them in nmovie (or nmovie_qt, which I guess is what 
>> we support now)
>> 
>> cheers
>> Bruce
>> 
>> 
>>> On Fri, 15 Feb 2019, Winkelbeiner, Stephanie A wrote:
>>> 
>>> 
>>> External Email - Use Caution
>>> 
>>> Hi Freesurfers,
>>> 
>>>  
>>> 
>>> I ran mri_surf2surf and registered self-created parcels from fsaverage
>>> to all my subjects. What is the best way to do QC and check if everything 
>>> went right?
>>> 
>>>  
>>> 
>>> Thanks for your help!
>>> 
>>> Stephanie
>>> 
>>>  
>>> 
>>> 
>>> The information contained in this electronic e-mail transmission and
>>> any attachments are intended only for the use of the individual or
>>> entity to whom or to which it is addressed, and may contain
>>> information that is privileged, confidential and exempt from
>>> disclosure under applicable law. If the reader of this communication
>>> is not the intended recipient, or the employee or agent responsible
>>> for delivering this communication to the intended recipient, you are
>>> hereby notified that any dissemination, distribution, copying or
>>> disclosure of this communication and any attachment is strictly
>>> prohibited. If you have received this transmission in error, please notify 
>>> the sender immediately by telephone and electronic mail, and delete the 
>>> original communication and any attachment from any computer, server or 
>>> other electronic recording or storage device or medium. Receipt by anyone 
>>> other than the intended recipient is not a waiver of any attorney-client, 
>>> physician-patient or other privilege.
>>> 
>> 
>> 
>> The information contained in this electronic e-mail transmission and any 
>> attachments are intended only for the use of the individual or entity to 
>> whom or to which it is addressed, and may contain information that is 
>> privileged, confidential and exempt from disclosure under applicable law. If 
>> the reader of this communication is not the intended recipient, or the 
>> employee or agent responsible for delivering this communication to the 
>> intended recipient, you are hereby notified that any dissemination, 
>> distribution, copying or disclosure of this communication and any attachment 
>> is strictly prohibited. If you have received this transmission in error, 
>> please notify the sender immediately by telephone and electronic mail, and 
>> delete the original communication and any attachment from any computer, 
>> server or other electronic recording or storage device or medium. Receipt by 
>> anyone other than the intended recipient is not a waiver of any 
>> attorney-client, physician-patient or other privilege.
>> 
>> 
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[Freesurfer] Qdec tutorial video

2019-02-19 Thread Korom, Marta

External Email - Use Caution

Hello Freesurfers,

I was wondering if anyone has access to a Qdec tutorial, other than the one
on the Freesurfer website. The one on the website only covers the basics
and it does not have a video component. In case you have a better tutorial
available or a video that goes into detail, please send it to me.

Thank you,
Marta
-- 
*Marta Korom  |  *PhD Candidate
University of Delaware, Clinical Science
e-mail: mko...@udel.edu
phone: 646 861 8461
http://www.abcintervention.org/
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[Freesurfer] overlay cortical thickness estimates

2019-02-19 Thread forsteca

External Email - Use Caution

Hello Freesurfer Community,

I want to view my cortical thickness estimates (I calculated standard 
deviations for different subjects) on a 3D file.
I thought I could replace the lh.thickness part in the following code by 
my own estimations:

freeview -f  \
/Datasets/sSUBJ_DAY_01_01/surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0
 
\
/Datasets/sSUBJ_DAY_01_01/surf/lh.pial:annot=aparc.a2009s.annot:name=pial_aparc_des:visible=0
 
\
/Datasets/SUBJ_DAY_01_01/surf/lh.inflated:overlay=lh.thickness.asc:overlay_threshold=0.1,3::name=inflated_thickness:visible=0
 
\
/Datasets/sSUBJ_DAY_01_01/surf/lh.inflated:visible=0 \
/Datasets/sSUBJ_DAY_01_01/surf/lh.white:visible=0 \
/Datasets/sSUBJ_DAY_01_01/surf/lh.pial \
--viewport 3d


I tried loading a binary mat, as lh.thickness is a binary file as well.
I got the following error:

couldn't determine type of file

Can you clarify what file structure the thickness overlay file should 
be, so that Freesurfer is able to read the thickness information ?

Thank you so much.

(addional info: mat file 163842x1 double)



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[Freesurfer] hippocampal subfield segmentation input mask?

2019-02-19 Thread Malone, Ian

External Email - Use Caution

Dear FreeSurfer list,


I'm wondering if there is any way to input different starting 
segmentations for the hippocampus into the hippocampal subfield 
segmentation? We've got a hippocampus specific segmentation algorithm 
which we'd like to try as input to see if it provides a better starting 
point than whole brain labels. Are there any other inputs we'd need?


Best wishes,

Ian Malone

-- 

Research Associate
Dementia Research Centre
Queen Square Institute of Neurology
UCL
London WC1N 3BG


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[Freesurfer] fixing errors with pial boundary

2019-02-19 Thread Morgan Botdorf

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Dear Freesurfer Experts,

We have come across several subjects where the pial boundary line does not
extend far enough outward and misses some gray matter. We know that control
points can be used to fix a similar issue with white matter boundaries. Are
there any tools that can be used to fix this type of gray matter error?

Thank you,
Morgan Botdorf
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Re: [Freesurfer] overlay cortical thickness estimates

2019-02-19 Thread Bruce Fischl

what format did you save your estimates in? If you want to overlay it on 
the surface, it has to be a "volume" where the first dimension is the 
number of vertices in the surface, and the others are all 1. Unless it is 
nifti in which case you have to split up the first dimension since it is 
too big for the nifti format


cheers
Bruce

  On Tue, 19 Feb 2019, 
forst...@hu-berlin.de wrote:

>External Email - Use Caution
>
> Hello Freesurfer Community,
>
> I want to view my cortical thickness estimates (I calculated standard
> deviations for different subjects) on a 3D file.
> I thought I could replace the lh.thickness part in the following code by
> my own estimations:
>
> freeview -f  \
> /Datasets/sSUBJ_DAY_01_01/surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0
> \
> /Datasets/sSUBJ_DAY_01_01/surf/lh.pial:annot=aparc.a2009s.annot:name=pial_aparc_des:visible=0
> \
> /Datasets/SUBJ_DAY_01_01/surf/lh.inflated:overlay=lh.thickness.asc:overlay_threshold=0.1,3::name=inflated_thickness:visible=0
> \
> /Datasets/sSUBJ_DAY_01_01/surf/lh.inflated:visible=0 \
> /Datasets/sSUBJ_DAY_01_01/surf/lh.white:visible=0 \
> /Datasets/sSUBJ_DAY_01_01/surf/lh.pial \
> --viewport 3d
>
>
> I tried loading a binary mat, as lh.thickness is a binary file as well.
> I got the following error:
>
> couldn't determine type of file
>
> Can you clarify what file structure the thickness overlay file should
> be, so that Freesurfer is able to read the thickness information ?
>
> Thank you so much.
>
> (addional info: mat file 163842x1 double)
>
>
>
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>
>
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Re: [Freesurfer] fixing errors with pial boundary

2019-02-19 Thread Bruce Fischl


Hi Morgan

can you send us some pictures? Control points can sometimes help the pial 
also, but it depends on what the cause of your inaccuracy is.



cheers
Bruce
On Tue, 19 Feb 2019, Morgan Botdorf wrote:



External Email - Use Caution

Dear Freesurfer Experts,
We have come across several subjects where the pial boundary line does not 
extend far enough outward
and misses some gray matter. We know that control points can be used to fix a 
similar issue with
white matter boundaries. Are there any tools that can be used to fix this type 
of gray matter error?

Thank you,
Morgan Botdorf




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[Freesurfer] commends of GLM for volume

2019-02-19 Thread ??

External Email - Use Caution

---Original---
From: "??"<646102...@qq.com>
Date: Tue, Feb 19, 2019 11:00 AM
To: "Greve, Douglas N.,Ph.D.";
Subject: Re:  commends of  GLM for volume


Hello developer,
I am glad to tell you that after 3 hours, something did print more on terminal. 
when I was doing the GLM follow the tutorial, it only provided the example of 
the cortical thickness. And I did not know how to transfer it into volume.
Thanks so much for your help 
Here is my commends
 
mris_preproc --fsgd FSGD/PDDvsHC.fsgd --cache-in volmue.fwhm10.fsaverage 
--target fsaverage --hemi lh --out lh.PDDvsHC.volume.10.mgh
 
 mri_glmfit --y lh.PDDvsHC.volume.10.mgh --fsgd FSGD/PDDvsHC.fsgd --C 
Contras-HC-PDD.mtx --surf fsaverage lh --cortex --glmdir 
lh.volume.PDDvsHC.glimdir --eres-save
 
 mri_glmfit-sim --glmdir rh.PDDvsHC.volume.glmdir --cache 1.3 pos --cwp 999 
--2spaces

We I check the results, it still talked about the cortical thickness , so could 
you tell me how to change this commends to the volume of subcortical. Or do you 
have the example which use GLM for comparing the difference of subcortical 
volume between two groups.

Thanks so much for your help

Yours

Zeng

Here is the results 

 


ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZCWPCWPLow
CWPHi   NVtxsWghtVtx   Annot

 


   16.960   86488   4544.63 15.7  -77.36.7  0.00020  0.0  
0.00040   789115125.67  pericalcarine

 


   23.529  158070   3287.33 55.0  -52.98.2  0.00020  0.0  
0.00040   679611225.54  inferiorparietal

 


   32.630   67804   1909.67 43.3   45.8   -9.3  0.00220  0.00140  
0.00300   2858 4399.15  parsorbitalis

  Here is the terminal output.

  

$Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $

 


cwd /Volumes/NIU20/volumetric_FS/glm

 


cmdline mri_glmfit.bin --glmdir lh.PDDvsHC.volume.glmdir --y 
lh.PDDvsHC.volume.10.mgh --fsgd FSGD/PDDvsHC.fsgd --C 
Contrasts/lh-thickness-HC-PDD.mtx --surface fsaverage lh --eres-save 

 


sysname  Darwin

 


hostname dyn3199-104.wlan.ic.ac.uk

 


machine  x86_64

 


user cengzhou

 


FixVertexAreaFlag = 1

 


UseMaskWithSmoothing 1

 


OneSampleGroupMean 0

 


y/Volumes/NIU20/volumetric_FS/glm/lh.PDDvsHC.volume.10.mgh

 


logyflag 0

 


usedti  0

 


FSGD FSGD/PDDvsHC.fsgd

 


labelmask  /Volumes/NIU20/volumetric_FS/glm/fsaverage/label/lh.cortex.label

 


maskinv 0

 


glmdir lh.PDDvsHC.volume.glmdir

 


IllCondOK 0

 


ReScaleX 1

 


DoFFx 0

 


ResidualFWHM 14.826153

 


SearchSpace 73852.172969

 


anattype surface

 


 

 


 

 


cd /Volumes/NIU20/volumetric_FS/glm

 


/Applications/freesurfer/bin/mri_glmfit-sim

 


--glmdir rh.PDDvsHC.volume.glmdir --cache 1.3 pos --cwp 999 --2spaces

 


 

 


$Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $

 


Mon Feb 18 15:52:07 GMT 2019

 


Darwin dyn3199-104.wlan.ic.ac.uk 14.5.0 Darwin Kernel Version 14.5.0: Wed Jul 
29 02:26:53 PDT 2015; root:xnu-2782.40.9~1/RELEASE_X86_64 x86_64

 


cengzhou

 


setenv SUBJECTS_DIR /Volumes/NIU20/volumetric_FS/glm

 


FREESURFER_HOME /Applications/freesurfer

 


 

 


Original mri_glmfit command line:

 


cmdline mri_glmfit.bin --glmdir rh.PDDvsHC.volume.glmdir --y 
rh.PDDvsHC.volume.10.mgh --fsgd FSGD/PDDvsHC.fsgd --C 
Contrasts/lh-thickness-HC-PDD.mtx --surface fsaverage rh --eres-save

 


 

 


DoSim = 0

 


UseCache = 1

 


DoPoll = 0

 


DoPBSubmit = 0

 


DoBackground = 0

 


DiagCluster = 0

 


gd2mtx = dods

 


fwhm = 14.506572

 


CSD 
/Applications/freesurfer/average/mult-comp-cor/fsaverage/rh/cortex/fwhm15/pos/th13/mc-z.csd

 


mri_surfcluster --in rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/sig.mgh --mask 
rh.PDDvsHC.volume.glmdir/mask.mgh --cwsig 
rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.cluster.mgh --sum 
rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.cluster.summary 
--ocn rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.ocn.mgh 
--annot aparc --cwpvalthresh 999 --o 
rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.masked.mgh 
--no-fixmni --csd 
/Applications/freesurfer/average/mult-comp-cor/fsaverage/rh/cortex/fwhm15/pos/th13/mc-z.csd
 --csdpdf rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.pdf.dat 
--vwsig rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.voxel.mgh 
--vwsigmax 
rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.voxel.max.dat 
--oannot rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.ocn.annot 
--bonferroni 2 --surf white

 


Creating CDFs from CSD files

 


csd->threshsign = 1

 


thsign = pos, id = 1

 


version $Id: mri_surfcluster.c,v 1.57.2.3 2016/11/17 18:19:42 zkaufman Exp $

 


hemi   = rh

 


srcid  = rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/sig.mgh 

 


srcsubjid  = fsaverage

 


srcsurf= white

 


srcframe   = 0

 


thsign = po

Re: [Freesurfer] Second order (square) link function for GLM

2019-02-19 Thread Greve, Douglas N.,Ph.D.

It sounds like you will just need to create your own design matrix and 
then feed it into mri_glmfit with --X (and not include --fsgd)


On 2/12/19 12:03 AM, Abhinav Yadav wrote:
>
> External Email - Use Caution
>
> Hello,
>
> I am trying to do GLM analysis for cortical thickness with a 
> behavioral score. I wanted to explore square fit in the GLM. Basically 
> wanted to see weather the behaviour is related in a quadratic function 
> instead of linear one.
>
> Couldn't find any option for this is GLM fit.
>
>  I was thinking of feeding a squareroot values of the behavioural 
> parameter in the GLM as an alternative. But not sure weather that will 
> work. Please any one can help me with this.
>
> Thanks,
> Abhinav
>
> ___
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[Freesurfer] clusters annotation file in surface

2019-02-19 Thread Barletta, Valeria

Dear Freesurfers,

I have a 3D volume mask of cortical lesions with 8 different clusters (8 
cortical lesions).

I projected this mask to the cortex and obtained a .mgh file with the command 
vol2surf:

mri_vol2surf --src $path_to_lesion/$subj/combined-$lesion.nii.gz --out 
$path_to_output/$subj/surf/$hemi".surf_combined-"$lesion".mgh" --projfrac-avg 
-0.1 1 0.05 --hemi $hemi --regheader $subj


Now I need to extract label files from this surface file, one label for each 
cluster, and then an annotation file summarizing all the label files.

How can I do this?

Thanks,

Vale





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Re: [Freesurfer] mris_preproc calling on incorrect target surface

2019-02-19 Thread Greve, Douglas N.,Ph.D.

If you want to use a target other than fsaverage, then you need to 
register each subject to that target (eg, with surfreg). If you have 
found a problem with mris_make_subject, please document it in a separate 
post.


On 2/12/19 6:38 AM, Bunting, Emma wrote:
>
> External Email - Use Caution
>
> Hi Freesurfer Pros,
>
> I'm trying to perform mris_preproc with an average subject that I 
> created called 'avgsubject.Patients_EB', as my target.
>
> Although it appears to take avgsubject.Patients_EB as the target 
> subject, and VIPD_010 (the first subject in my fsgd file) as the 
> source subject, it then somehow swaps the target and source surfaces 
> (sphere.reg's) it is trying to call upon. I am therefore getting an 
> error because there is no avgsubject.Patients_EB.sphere.reg file 
> within the VIPD_010 subject folder.
>
> The commands I use for the mri_preproc are below, with the sections I 
> am referring to highlighted in bold.
>
> ebunting@img-140:.../MRI_data/freesurfer$ mris_preproc --fsgd 
> PDonly_Liu_EB.fsgd \
>
> *> --target avgsubject.Patients_EB \*
>
> > --hemi lh \
>
> > --meas thickness \
>
> > --out lh.PDonly_Liu_AvgSubjectPatients_EB.thickness.00.mgh \
>
> >
>
> nsubjects = 97
>
> tmpdir is ./tmp.mris_preproc.12493
>
> /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer
>
> Log file is 
> lh.PDonly_Liu_AvgSubjectPatients_EB.thickness.00.mris_preproc.log
>
> Tue Feb 12 11:20:49 GMT 2019
>
> setenv SUBJECTS_DIR 
> /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer
>
> cd /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer
>
> /var/drc/software/64bit/freesurfer-6.0.0//bin/mris_preproc --fsgd 
> PDonly_Liu_EB.fsgd --target avgsubject.Patients_EB --hemi lh --meas 
> thickness --out lh.PDonly_Liu_AvgSubjectPatients_EB.thickness.00.mgh
>
> Linux img-140.drc.ion.ucl.ac.uk 2.6.32-279.el6.x86_64 #1 SMP Wed Jun 
> 13 18:24:36 EDT 2012 x86_64 x86_64 x86_64 GNU/Linux
>
> $Id: mris_preproc,v 1.76.2.1 2016/08/12 17:55:45 zkaufman Exp $
>
> freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
>
> tmpdir is ./tmp.mris_preproc.12493
>
> Src lh avgsubject.Patients_EB.sphere.reg
>
> Trg lh sphere.reg
>
> ---
>
> #@# 1/97 VIPD_010 Tue Feb 12 11:20:49 GMT 2019 --
>
> ---
>
> mri_surf2surf *--srcsubject VIPD_010* --srchemi lh -*-srcsurfreg 
> avgsubject.Patients_EB.sphere.reg* -*-trgsubject 
> avgsubject.Patients_EB* --trghemi lh *--trgsurfreg sphere.reg *--tval 
> ./tmp.mris_preproc.12493/VIPD_010.1.mgh --sval 
> /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer/VIPD_010/surf/lh.thickness
>  
> --sfmt curv --noreshape --cortex
>
> MRISread(/var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer/VIPD_010/surf/lh.avgsubject.Patients_EB.sphere.reg):
>  
> could not open file
>
> *Source registration surface changed to avgsubject.Patients_EB.sphere.reg*
>
> *Target registration surface changed to sphere.reg*
>
> $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $
>
> setenv SUBJECTS_DIR 
> /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer
>
> cd /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer
>
> mri_surf2surf -*-srcsubject VIPD_010 -*-srchemi lh *--srcsurfreg 
> avgsubject.Patients_EB.sphere.reg* *--trgsubject 
> avgsubject.Patients_EB* --trghemi lh *--trgsurfreg sphere.reg* --tval 
> ./tmp.mris_preproc.12493/VIPD_010.1.mgh --sval 
> /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer/VIPD_010/surf/lh.thickness
>  
> --sfmt curv --noreshape --cortex
>
> sysnameLinux
>
> hostname img-140.drc.ion.ucl.ac.uk
>
> machinex86_64
>
> userebunting
>
> srcsubject = VIPD_010
>
> srcval= 
> /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer/VIPD_010/surf/lh.thickness
>
> srctype= curv
>
> *trgsubject = avgsubject.Patients_EB*
>
> trgval= ./tmp.mris_preproc.12493/VIPD_010.1.mgh
>
> trgtype=
>
> *srcsurfreg = avgsubject.Patients_EB.sphere.reg*
>
> trgsurfreg = sphere.reg
>
> srchemi= lh
>
> trghemi= lh
>
> frame= 0
>
> fwhm-in= 0
>
> fwhm-out= 0
>
> label-src= lh.cortex.label
>
> label-trg= lh.cortex.label
>
> OKToRevFaceOrder= 1
>
> UseDualHemi = 0
>
> *Reading source surface reg 
> /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer/VIPD_010/surf/lh.avgsubject.Patients_EB.sphere.reg*
>
> *No such file or directory*
>
> *mri_surf2surf: could not read surface 
> /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer/VIPD_010/surf/lh.avgsubject.Patients_EB.sphere.reg*
>
> *No such file or directory*
>
> n.b. that the lh.avgsubject.Patients_EB.sphere.reg file can be found 
> within the avgsubject.Patients_EB/surf folder, so I believe this is an 
> issue of simply mixing the target and source surfaces.
>
> It is also worth noting that I have found your bug fix for the 
> make_average_*surface *script, which now completes without err

Re: [Freesurfer] partial FoV - registration failure

2019-02-19 Thread Greve, Douglas N.,Ph.D.

yes

On 2/12/19 11:28 AM, Francesca Strappini wrote:
>
> External Email - Use Caution
>
> Thank you! Unfortunately, I don't have any whole brain scan.
> I registered the template and all the runs with tkregisterfv and the I 
> run bbregsiter.
> Now, should I just re-run selxavg3-sess?
>
> Thanks
> Best
>
> Il giorno lun 26 nov 2018 alle ore 22:31 Greve, Douglas N.,Ph.D. 
> mailto:dgr...@mgh.harvard.edu>> ha scritto:
>
> And you only have partial field of view fmri data on that day? No
> whole
> brain localizer? Really, any whole-brain volume will do. If you do
> not,
> then you'll have to initialize the bbr registration by hand, which
> is a
> bit of a pain. You'd run something like
> tkregisterfv --mov template.nii.gz --init-header --reg manual.reg.lta
> --surfs
> Then adjust the registration to be within 5mm of being right. Then
> run
> bbregister using that registration as the --init-reg
> If you have other scans where you have both the partial FoV and a
> whole
> brain, you might be able to get an init reg by registering the
> partial
> FoVs from different days.
> good luck
>
>
>
> On 11/26/2018 03:19 PM, Francesca Strappini wrote:
> >
> > External Email - Use Caution
> >
> > Thanks for the fast reply!
> >
> > Unfortunately, I have only 3 mprage scans that were collected in
> > another day but no whole-head functional data.
> >
> > Il giorno lun 26 nov 2018 alle ore 22:07 Greve, Douglas N.,Ph.D.
> > mailto:dgr...@mgh.harvard.edu>
> >>
> ha scritto:
> >
> >     Do you have any scan that was acquired at the same time that
> is whole
> >     head? Any scan will do. If so, you can run register-sess
> using the
> >     -bbr-int option (or bbregister directly). Eg, if the
> anatomical was
> >     acquired at the same time, then, to use register-sess, create a
> >     folder
> >     in the session folder called anatomical/001 and put the
> anatomical in
> >     there (eg, anat.nii.gz), then use -bbr-int anatomical anat
> >
> >
> >     On 11/26/2018 02:58 PM, Francesca Strappini wrote:
> >     >
> >     > External Email - Use Caution
> >     >
> >     > Dear freesurfer experts,
> >     >
> >     > I am using freesurfer to analyze some fMRI data collected
> on two
> >     > monkeys. My runs have a partial field of view, since just the
> >     > posterior part of the brain was scanned. Unfortunately, no
> >     full-head
> >     > EPI was collected. The registration between the processed
> >     functional
> >     > data and the T1 is bad. All the values in the
> register.dof6.mincost
> >     > file are above 0.8 and also visually I can see some
> mismatch. I
> >     though
> >     > to run bbregister, could you suggest me which is the best
> procedure
> >     > and which steps of the preprocessing I should re-run after?
> >     >
> >     > Thanks
> >     >
> >     > --
> >     > Francesca Strappini, Ph.D.
> >     > Neurobiology Department
> >     > Weizmann Institute of Science
> >     > 234 Herzl Street, Rehovot 7610001 Israel
> >     > Tel.: +972 58 444 2584
> >     > E-mail: francesca.strapp...@weizmann.ac.il
> 
> >      >
> >     >  
> >      >>
> >     >
> >     >
> >     > ___
> >     > 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
> >
> >
> >
> > --
> > Francesca Strappini, Ph.D.
> > Neurobiology Department
> > Weizmann Institute of Science
> > 234 Herzl Street, Rehovot 7610001 Israel
> > Tel.: +972 58 444 2584
> > E-mail: francesca.strapp...@weizmann.ac.il
> 
> >  >
>

Re: [Freesurfer] fcseedcor_multiple runs

2019-02-19 Thread Greve, Douglas N.,Ph.D.

I would average the R values across run

On 2/15/19 11:34 AM, Nasiriavanaki, Zahra wrote:
>
> Dear Freesurfer experts
>
>
> I have asked this question before and I really do appreciate if you 
> could please reply whenever you had a chance.
>
> I have been doing seed to seed connectivity analysis using fcseedcor.
> I have _multiple runs for each subject,_ and based on the fcseedcor 
> help, I am supposed to average runs before comparing across subjects.
> So, does it mean I should average timeseries across runs?or Should I 
> average the acquired r values? (because after running fcseedcor, 
> separate r and p values are made for each run).
>
> Thanks so much
> Mona
>
>
>
>
> 
> *From:* Nasiriavanaki, Zahra
> *Sent:* Thursday, February 7, 2019 5:39:39 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] fcseedcor_multiple runs
>
> Thank you so much for your reply.
>
> Yes, It does make a separate r and p for each run.
>
> But, I would like to have one correlation coefficient for each 
> subject, so I can compare them to each other.
>
> Based on help, I should average runs before comparing across subjects. 
> My question is how should I average runs? Should average the .dat 
> files? the r values?
>
>
> Thanks
>
> Mona
>
>
>
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Greve, Douglas 
> N.,Ph.D. 
> *Sent:* Thursday, February 7, 2019 5:33:09 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] fcseedcor_multiple runs
> Looking at the help, it looks like it will produce a separate file for
> each run for each session. Is that what you want?
>
> On 2/1/19 9:41 AM, Nasiriavanaki, Zahra wrote:
> >
> > Dear Freesurfers
> >
> >
> > Hi
> >
> >
> > I have been doing seed to seed connectivity analysis using fcseedcor.
> >
> > I have multiple runs for each subject, and based on the fcseedcor
> > help, I am supposed to average runs before comparing across subjects.
> >
> > So, does it mean I should average all seed.dat files and the
> > regressors (including vscf,wm,global waveform, mcprextreg) across runs?
> >
> > I appreciate your time and consideration.
> >
> >
> > Thanks
> >
> > Mona
> >
> >
> >
> > *Zahra (Mona) Nasiriavanaki*
> >
> > Postdoctoral Research Fellow
> >
> > Martinos Center for Biomedical Imaging
> >
> > Massachusetts General Hospital
> >
> > 149 13th Street, 149-2615
> >
> > Charlestown, MA, USA, 02129
> >
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
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>
> ___
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Re: [Freesurfer] recon-all -all

2019-02-19 Thread Greve, Douglas N.,Ph.D.

When you say it stopped running, do you mean that it exited or that it 
kept running but nothing printed out and it did not proceed to further 
steps?

On 2/15/19 12:42 PM, ?? wrote:
>
> ?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2External Email - Use Caution
>
> Hello FreeSurfer Developers,
>
> when i was run the recon-all -all,?0?2sometimes the terminal would show 
> randomSeed 1234, and stop running the?0?2process
>
> here is my
>
> #@# Curvature Stats rh Fri Feb 15 17:31:38 GMT 2019
>
> /Users/cengzhou/Desktop/volumetric_FS/subject1/subject/surf
>
> \n mris_curvature_stats -m --writeCurvatureFiles -G -o 
> ../stats/rh.curv.stats -F smoothwm subject rh curv sulc \n
>
> ?0?2?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 Toggling save flag on curvature files ?0?2 
> ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 
> ?0?2 [ ok ]
>
> ?0?2?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 Outputting results using filestem 
> ?0?2 [ 
> ../stats/rh.curv.stats ]
>
> ?0?2?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 Toggling save flag on curvature files ?0?2 
> ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 
> ?0?2 [ ok ]
>
> Setting surface?0?2 ?0?2 ?0?2 [ subject/rh.smoothwm ]
>
> ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 
> ?0?2 Reading surface... ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 
> ?0?2 [ ok ]
>
> Setting texture ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 [ curv ]
>
> ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 
> ?0?2 Reading texture... ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 
> ?0?2 [ ok ]
>
> Setting texture ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 [ sulc ]
>
> ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 
> ?0?2 Reading texture...Gb_filter = 0
>
> ?0?2?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 [ ok ]
>
> ?0?2 ?0?2 ?0?2 Calculating Discrete Principal Curvatures...
>
> ?0?2?0?2 Determining geometric order for vertex faces... 
> [] [ ok ]
>
> ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 Determining KH 
> curvatures... 
> [] [ ok ]
>
> ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 Determining k1k2 
> curvatures... 
> [] [ ok ]
>
> deltaViolations?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 [ 257 ]
>
> Gb_filter = 0
>
>
> WARN:?0?2 ?0?2 S lookup ?0?2 min: ?0?2 ?0?2 ?0?2 ?0?2 -0.254695
>
> WARN:?0?2 ?0?2 S explicit min: ?0?2 ?0?2 ?0?2 ?0?2 0.00vertex = 112
>
> #
>
> #@# Sphere lh Fri Feb 15 17:31:44 GMT 2019
>
> /Users/cengzhou/Desktop/volumetric_FS/subject1/subject/scripts
>
> \n mris_sphere -rusage 
> /Users/cengzhou/Desktop/volumetric_FS/subject1/subject/touch/rusage.mris_sphere.lh.dat
>  
> -seed 1234 ../surf/lh.inflated ../surf/lh.sphere \n
>
> setting seed for random number genererator to 1234
>
> $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $
>
> ?0?2 $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
>
> reading original vertex positions...
>
> unfolding cortex into spherical form...
>
> surface projected - minimizing metric distortion...
>
>
> == Number of threads available to mris_sphere for OpenMP = 1 ==
>
> scaling brain by 0.321...
>
> MRISunfold() max_passes = 1 ---
>
> tol=5.0e-01, sigma=0.0, host=cengz, nav=1024, nbrs=2, l_area=1.000, 
> l_dist=1.000
>
> using quadratic fit line minimization
>
> complete_dist_mat 0
>
> rms 0
>
> smooth_averages 0
>
> remove_neg 0
>
> ico_order 0
>
> which_surface 0
>
> target_radius 0.00
>
> nfields 0
>
> scale 1.00
>
> desired_rms_height -1.00
>
> momentum 0.90
>
> nbhd_size 7
>
> max_nbrs 8
>
> niterations 25
>
> nsurfaces 0
>
> SURFACES 3
>
> flags 0 (0)
>
> use curv 0
>
> no sulc 0
>
> no rigid align 0
>
> mris->nsize 2
>
> mris->hemisphere 0
>
> randomSeed 1234>
>
> i have attached the recon-all log
>
> cheers
>
> Zeng
>
>
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[Freesurfer] Problem with freeview in linux subsystem for windows

2019-02-19 Thread Williamson, Brady

External Email - Use Caution

Hi,

I am trying to run freeview in the linux subsystem (Ubuntu 18.04) for windows 
10 but keep getting the following error:

failed to get the current screen resources
QXcbConnection: XCB error: 170 (Unknown), sequence: 170, resource id: 90, major 
code: 146 (Unknown), minor code: 20
QXcbConnection: XCB error: 170 (Unknown), sequence: 170, resource id: 90, major 
code: 146 (Unknown), minor code: 20


Freeview opens but there is no image. Is there a fix for this issue?

Thanks,
Brady
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Re: [Freesurfer] anat2dti error after dt_recon

2019-02-19 Thread Greve, Douglas N.,Ph.D.

what do you get when you run
ls -l /Volumes/DANIEL/dti_freesurf/dtrecon/AES139.Rest/register.dat

On 2/19/19 8:44 AM, Daniel Davidson Callow wrote:
>
> External Email - Use Caution
>
> Hello,
>
> I ran a successful dt_recon and then wanted to use
>
> mri_vol2vol --mov $subj_dir/dtrecons/${subj}.${cond}/lowb.nii.gz 
> --targ $subj_dir/diffusion_recons/${subj}.${cond}/mri/aparc+aseg.mgz 
> --inv --interp nearest --o 
> $subj_dir/dtrecons/${subj}.${cond}/aparc+aseg2diff.nii.gz --reg 
> $subj_dir/dtrecon/${subj}.${cond}/register.dat --no-save-reg
>
>
> to get the anatomical segmentations into diffusion space. However, 
> when running the above code I get the following error message?
>
>
> echo subj =AES139 , cond =Rest
>
> subj =AES139 , cond =Rest
>
> set echo
>
> cd /Volumes/DANIEL/dti_freesurf
>
> mri_vol2vol --mov 
> /Volumes/DANIEL/dti_freesurf/dtrecons/AES139.Rest/lowb.nii.gz --targ 
> /Volumes/DANIEL/dti_freesurf/diffusion_recons/AES139.Rest/mri/aparc+aseg.mgz 
> --inv --interp nearest --o 
> /Volumes/DANIEL/dti_freesurf/dtrecons/AES139.Rest/aparc+aseg2diff.nii.gz 
> --reg /Volumes/DANIEL/dti_freesurf/dtrecon/AES139.Rest/register.dat 
> --no-save-reg
>
> regio_read_register(): No such file or directory
>
> Could not open 
> /Volumes/DANIEL/dti_freesurf/dtrecon/AES139.Rest/register.dat
>
>
> Matrix from regfile:
>
> MatrixPrint: mat = NULL!
>
> No such file or directory
>
>
> I have attached an example register.dat file in case that is the issue.
>
>
> also the output for ls -l register.dat
>
> -rwxrwxrwx1 administratorstaff323 Feb 18 13:59 register.dat
>
>
> Any advice with troubleshooting is greatly appreciated!
>
>
> Best,
>
> *Daniel Callow*
> /PhD Student, Neuroscience and Cognitive Science/
> Exercise for Brain Health Lab
> University of Maryland, College Park
> dcal...@umd.edu 
> 443-254-6298
>
>
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Re: [Freesurfer] zero values when run recon-all with T2pial flag (V6.0)

2019-02-19 Thread Greve, Douglas N.,Ph.D.

did  you analyze them with different versions of FS?


On 2/15/19 3:28 PM, Morgan Botdorf wrote:
>
> External Email - Use Caution
>
> Thanks for taking a look at the file I sent! I think I have figured 
> out the issue for the most part. While it shows that there is data in 
> the recon-all log for the various cortical regions and eTIV, the data 
> I extracted using aparcstats2table gives me zeros. Part of the problem 
> seems to be that in the table aparcstats2table produces using the 
> Destrieux atlas, some variables are listed twice, but in a different 
> format. For example, frontomarginal thickness is listed as both 
> rh_G_and_S_frontomargin_thickness and as 
> rh_G_&_S_frontomargin_thickness. Some subjects have data for one 
> variable and some for the other variable. This happened for 13 
> variables. I've attached an excel file with data from 2 subjects that 
> shows the variables that are listed twice and how some subjects have 
> data for some variables and others have data for other variables. 
> Please let me if you have any ideas of why this may have happened.
>
> Thanks!
> Morgan
>
> -- 
>
> Morgan Botdorf, M.S.
>
> Graduate Student
>
> Neurocognitive Development Lab
>
> University of Maryland, College Park
>
> mbotd...@terpmail.umd.edu 
>
> Office: 301.405.5922 
>
>
>
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Re: [Freesurfer] lh.PDDvsHC.thinckness.00.mris_preproc

2019-02-19 Thread Greve, Douglas N.,Ph.D.

Check the lh.orig and lh.inflated surfaces

On 2/15/19 3:34 PM, ?? wrote:
>
> ?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2External Email - Use Caution
>
> For more than 3 hours
>
> ---Original---
> *From:* "Greve, Douglas N.,Ph.D."
> *Date:* Fri, Feb 15, 2019 20:03 PM
> *To:* "freesurfer@nmr.mgh.harvard.edu";
> *Subject:* Re: [Freesurfer] lh.PDDvsHC.thinckness.00.mris_preproc
>
> how long?
>
> On 2/15/19 2:49 PM, ?? wrote:
>>
>> ?0?2?0?2?0?2?0?2?0?2?0?2?0?2 External Email - Use Caution
>>
>> Hi
>> Thanks for your quickly reply, yes continue to run but not print more 
>> on terminal anymore.
>>
>> ---Original---
>> *From:* "Greve, Douglas N.,Ph.D."
>> *Date:* Fri, Feb 15, 2019 19:01 PM
>> *To:* "freesurfer@nmr.mgh.harvard.edu";
>> *Subject:* Re: [Freesurfer] lh.PDDvsHC.thinckness.00.mris_preproc
>>
>> Do you mean that it continues to run but does not do anything (eg, 
>> print more to the terminal) or that it has crashed? If it is hanging, 
>> how long? Nothing looks suspicious in the output.
>>
>> On 2/15/19 12:59 PM, ?? wrote:
>>>
>>> ?0?2?0?2?0?2?0?2?0?2 ?0?2 External Email - Use Caution
>>>
>>> Hi Greve,
>>> i solved this problem, but had a new one with recon-all, when i run 
>>> the recon-all data, sometimes it hang in the very last step of the 
>>> recon-all. here is the related part of output in terminal. i have 
>>> attached the recon-all log and status log. Have a nice weekend!
>>> cheers
>>>
>>> #@# Curv .H and .K rh Fri Feb 15 17:30:27 GMT 2019
>>>
>>> /Users/cengzhou/Desktop/volumetric_FS/subject1/subject/surf
>>>
>>> \n mris_curvature -w rh.white.preaparc \n
>>>
>>> total integrated curvature = 11.983*4pi (150.582) --> -11 handles
>>>
>>> ICI = 180.5, FI = 1886.9, variation=29597.577
>>>
>>> writing Gaussian curvature to 
>>> /Users/cengzhou/Desktop/volumetric_FS/subject1/subject/surf/rh.white.preaparc.K...done.
>>>
>>> writing mean curvature to 
>>> /Users/cengzhou/Desktop/volumetric_FS/subject1/subject/surf/rh.white.preaparc.H...done.
>>>
>>> rm -f rh.white.H
>>>
>>> ln -s rh.white.preaparc.H rh.white.H
>>>
>>> rm -f rh.white.K
>>>
>>> ln -s rh.white.preaparc.K rh.white.K
>>>
>>> \n mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 
>>> rh.inflated \n
>>>
>>> normalizing curvature values.
>>>
>>> averaging curvature patterns 5 times.
>>>
>>> sampling 10 neighbors out to a distance of 10 mm
>>>
>>> 148 vertices thresholded to be in k1 ~ [-1.38 0.32], k2 ~ [-0.18 0.09]
>>>
>>> total integrated curvature = 0.554*4pi (6.968) --> 0 handles
>>>
>>> ICI = 1.3, FI = 8.1, variation=139.341
>>>
>>> 115 vertices thresholded to be in [-0.05 0.02]
>>>
>>> writing Gaussian curvature to 
>>> /Users/cengzhou/Desktop/volumetric_FS/subject1/subject/surf/rh.inflated.K...thresholding
>>>  
>>> curvature at 99.90% level
>>>
>>> curvature mean = 0.000, std = 0.001
>>>
>>> 77 vertices thresholded to be in [-0.20 0.15]
>>>
>>> done.
>>>
>>> writing mean curvature to 
>>> /Users/cengzhou/Desktop/volumetric_FS/subject1/subject/surf/rh.inflated.H...curvature
>>>  
>>> mean = -0.018, std = 0.022
>>>
>>> done.
>>>
>>> \n#-
>>>
>>> #@# Curvature Stats lh Fri Feb 15 17:31:32 GMT 2019
>>>
>>> /Users/cengzhou/Desktop/volumetric_FS/subject1/subject/surf
>>>
>>> \n mris_curvature_stats -m --writeCurvatureFiles -G -o 
>>> ../stats/lh.curv.stats -F smoothwm subject lh curv sulc \n
>>>
>>> ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 Toggling save flag on curvature files ?0?2 
>>> ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 
>>> ?0?2 ?0?2 [ ok ]
>>>
>>> Outputting results using filestem ?0?2 [ ../stats/lh.curv.stats ]
>>>
>>> ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 Toggling save flag on curvature files ?0?2 
>>> ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 
>>> ?0?2 ?0?2 [ ok ]
>>>
>>> ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 Setting surface?0?2 ?0?2 ?0?2 [ 
>>> subject/lh.smoothwm ]
>>>
>>> ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 
>>> ?0?2 Reading surface... ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 
>>> [ ok ]
>>>
>>> ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 Setting texture ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 
>>> ?0?2 ?0?2 ?0?2 [ curv ]
>>>
>>> ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 
>>> ?0?2 Reading texture... ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 
>>> [ ok ]
>>>
>>> ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 Setting texture ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 
>>> ?0?2 ?0?2 ?0?2 [ sulc ]
>>>
>>> ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 
>>> ?0?2 Reading texture...Gb_filter = 0
>>>
>>> ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 [ ok ]
>>>
>>> ?0?2 ?0?2 ?0?2 Calculating Discrete Principal Curvatures...
>>>
>>> ?0?2 Determining geometric order for vertex faces... 
>>> [] [ ok ]
>>>
>>> ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 Determining KH 
>>> curvatures... 
>>> [] [ ok ]
>>>
>>> ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 Determining k1k2 
>>> curvatures... 
>>> [] [ ok ]

[Freesurfer] Glm for volume

2019-02-19 Thread ??

External Email - Use Caution

Hello developer,
I am glad to tell you that after 3 hours, something did print more on terminal. 
when I was doing the GLM follow the tutorial, it only provided the example of 
the cortical thickness. And I did not know how to transfer it into volume.
Thanks so much for your help
Here is my commends

mris_preproc --fsgd FSGD/PDDvsHC.fsgd --cache-in volmue.fwhm10.fsaverage 
--target fsaverage --hemi lh --out lh.PDDvsHC.volume.10.mgh

 mri_glmfit --y lh.PDDvsHC.volume.10.mgh --fsgd FSGD/PDDvsHC.fsgd --C 
Contras-HC-PDD.mtx --surf fsaverage lh --cortex --glmdir 
lh.volume.PDDvsHC.glimdir --eres-save

 mri_glmfit-sim --glmdir rh.PDDvsHC.volume.glmdir --cache 1.3pos --cwp 999 
--2spaces

We I check the results, it still talked about the cortical thickness , so could 
you tell me how to change this commends to the volume of subcortical. Or do you 
have the example which use GLM for comparing the difference of subcortical 
volume between two groups.

Thanks so much for your help

Yours

Zeng

Here is the results




ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY  MNIZCWPCWPLow
CWPHi   NVtxsWghtVtx  Annot




   16.960   86488   4544.63 15.7  -77.36.7 0.00020  0.0  
0.00040   789115125.67 pericalcarine




   23.529  158070   3287.33 55.0  -52.98.2 0.00020  0.0  
0.00040   679611225.54 inferiorparietal




   32.630   67804   1909.67 43.3   45.8   -9.3 0.00220  0.00140  
0.00300   2858 4399.15 parsorbitalis

Here is the terminal output.

 

$Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $




cwd /Volumes/NIU20/volumetric_FS/glm




cmdline mri_glmfit.bin --glmdir lh.PDDvsHC.volume.glmdir --y 
lh.PDDvsHC.volume.10.mgh --fsgd FSGD/PDDvsHC.fsgd --C 
Contrasts/lh-thickness-HC-PDD.mtx --surface fsaverage lh --eres-save




sysname  Darwin




hostname dyn3199-104.wlan.ic.ac.uk




machine  x86_64




user cengzhou




FixVertexAreaFlag = 1




UseMaskWithSmoothing 1




OneSampleGroupMean 0




y   /Volumes/NIU20/volumetric_FS/glm/lh.PDDvsHC.volume.10.mgh




logyflag 0




usedti  0




FSGD FSGD/PDDvsHC.fsgd




labelmask /Volumes/NIU20/volumetric_FS/glm/fsaverage/label/lh.cortex.label




maskinv 0




glmdir lh.PDDvsHC.volume.glmdir




IllCondOK 0




ReScaleX 1




DoFFx 0




ResidualFWHM 14.826153




SearchSpace 73852.172969




anattype surface




 




 




cd /Volumes/NIU20/volumetric_FS/glm




/Applications/freesurfer/bin/mri_glmfit-sim




--glmdir rh.PDDvsHC.volume.glmdir --cache 1.3 pos --cwp 999 --2spaces




 




$Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $




Mon Feb 18 15:52:07 GMT 2019




Darwin dyn3199-104.wlan.ic.ac.uk 14.5.0 Darwin Kernel Version 14.5.0: Wed Jul 
2902:26:53 PDT 2015; root:xnu-2782.40.9~1/RELEASE_X86_64 x86_64




cengzhou




setenv SUBJECTS_DIR /Volumes/NIU20/volumetric_FS/glm




FREESURFER_HOME /Applications/freesurfer




 




Original mri_glmfit command line:




cmdline mri_glmfit.bin --glmdir rh.PDDvsHC.volume.glmdir --y 
rh.PDDvsHC.volume.10.mgh --fsgd FSGD/PDDvsHC.fsgd --C 
Contrasts/lh-thickness-HC-PDD.mtx --surface fsaverage rh --eres-save




 




DoSim = 0




UseCache = 1




DoPoll = 0




DoPBSubmit = 0




DoBackground = 0




DiagCluster = 0




gd2mtx = dods




fwhm = 14.506572




CSD 
/Applications/freesurfer/average/mult-comp-cor/fsaverage/rh/cortex/fwhm15/pos/th13/mc-z.csd




mri_surfcluster --in rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/sig.mgh --mask 
rh.PDDvsHC.volume.glmdir/mask.mgh --cwsig 
rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.cluster.mgh --sum 
rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.cluster.summary 
--ocn rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.ocn.mgh 
--annot aparc --cwpvalthresh 999 --o 
rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.masked.mgh 
--no-fixmni --csd 
/Applications/freesurfer/average/mult-comp-cor/fsaverage/rh/cortex/fwhm15/pos/th13/mc-z.csd
 --csdpdf rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.pdf.dat 
--vwsig rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.voxel.mgh 
--vwsigmax 
rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.voxel.max.dat 
--oannot rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.ocn.annot 
--bonferroni 2 --surf white




Creating CDFs from CSD files




csd->threshsign = 1




thsign = pos, id = 1




version $Id: mri_surfcluster.c,v 1.57.2.32016/11/17 18:19:42 zkaufman Exp $




hemi   = rh




srcid  = rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/sig.mgh




srcsubjid  = fsaverage




srcsurf= white




srcframe   = 0




thsign = pos




thmin  = 1.3




thmax  = -1




fdr= -1




minarea= 0




Bonferroni  = 2




xfmfile= talairach.xfm




nth = -1




outid= 
rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/c

Re: [Freesurfer] Group level T map

2019-02-19 Thread Greve, Douglas N.,Ph.D.

A tmap is not produced. You can get one with
fscalc gamma.nii.gz sign -o gamma.sign.nii.gz
fscalc F.nii.gz sqrt mul gamma.sign.nii.gz
doug

On 2/15/19 4:12 PM, Lauri Tuominen wrote:
>  External Email - Use Caution
>
> Dear freesurfers,
> I am trying to find a t-map for my group level test. In a one sample group 
> mean test folder I have:
>
> gamma.nii.gz
> gammavar.nii.gz
> cnr.nii.gz
> sig.nii.gz
> F.nii.gz
>
> The gamma.nii.gz corresponds to the beta.nii.gz from the folder above, which 
> I take means that it is the beta coefficient map.
>
> Which one would be the t-value map or should I calculate this separately?
>
> Thank you so much!!
> Lauri Tuominen
>
>
>
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Re: [Freesurfer] Difference between target surface and target of registration file in mri_surf2surf

2019-02-19 Thread Greve, Douglas N.,Ph.D.


I'm not sure what you are trying to do here. Ico7 is just a 7th order 
icosahedron and does not "belong" to any subject. What belongs to 
fsaverage or fsaverage_sym is the atlas of curvatures and registrations 
derived from them (eg, lh.sphere.reg). It might be easier to use 
mris_apply_reg rather than mri_surf2surf. One of the reasons I wrote 
mris_apply_reg was to apply the xhemi registrations because the 
structure of mri_surf2surf makes it really hard to get the specification 
right.


On 2/15/19 7:41 PM, Alon Baram wrote:
>
> External Email - Use Caution
>
> Hello,
>
> I am trying to understand some code I came across and am having 
> trouble understanding the difference between the target surface in 
> mri_surf2surf and the surface used as target for the registration. The 
> code first uses freesurfer_registerXhem register the subject's right 
> hemisphere to the left and register both hemispheres to fsaverage_sym, 
> producing the registration file fsaverage_sym.sphere.reg.
>
> I then use the following command:
>
> mri_surf2surf --srcsubject $subj  --hemi lh --trgsubject 
> ico--trgicoorder 7 --surfreg fsaverage_sym.sphere.reg --srcsurfval 
> temp.curv --src_type curv --trgsurfval tempN.curv --trg_type curv 
> --mapmethod nnf --nsmooth-out 1
>
>
> to resample the registered subject surface to ico7. To my 
> understanding, ico7 is exactly the same as fsaverage, but fsaverage is 
> not exactly the same as fsaverage_sym. So I find it strange that the 
> code is using a registration file which is registered to one surface 
> (fsaverage_sym) with a different target surface (fsaverage).
>
>
> I'm not sure which space the result will actually be in - fsaverage or 
> fsaverage_sym?
>
> I'm obviously missing something basic here.
>
>
> Thanks very much for the help!
>
>
> Alon
>
>
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Re: [Freesurfer] PETSurfer: Problem with "mri_gtmpvc --no-reduce-fov" + time consuming when using "--psf 0 --no-tfe"

2019-02-19 Thread Greve, Douglas N.,Ph.D.



On 2/16/19 2:54 PM, Matthieu Vanhoutte wrote:
>
> External Email - Use Caution
>
> Dear Douglas,
>
> I wanted just to compute rescaled PET image without any PVC but 
> following the same process as if I would have applied PVC. Moreover, I 
> didn’t want to reduce FOV with auto mask generated (to still be in the 
> gtmseg space). So I ran the following command:
>
> mri_gtmpvc --i PET.lps.nii.gz --reg Pet2T1.register.dof6.lta --psf 0 
> --no-tfe --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 
> --no-reduce-fov --rbv --o nopvc_nGMcerebpons --threads 4 --rescale 8 
> 47 174
>
> 1) However, in the output directory rbv.nii.gz file still had a 
> reduced fov:
>           type: nii
>     dimensions: 297 x 381 x 363
>    voxel sizes: 0.50, 0.50, 0.50
>           type: FLOAT (3)
>            fov: 148.500
Try adding --no-mask_rbv_to_brain
>
> Compared to the gtmseg.mgz:
>          type: MGH
>     dimensions: 334 x 452 x 424
>    voxel sizes: 0.50, 0.50, 0.50
>           type: INT (1)
>            fov: 226.000
>
> I tried also to remove the —auto-mask option without success. Did I 
> miss something?
>
> 2) I wonder why the process took so much time while there is just a 
> rescaling to apply when using --psf 0 --no-tfe?
It does not know that it is only applying a scaling. It is going through 
the entire process
>
> Best,
> Matthieu
>
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Re: [Freesurfer] Extracting stats from palm results (.mgz)

2019-02-19 Thread Greve, Douglas N.,Ph.D.

see this page
https://surfer.nmr.mgh.harvard.edu/fswiki/FsPalm

On 2/16/19 6:48 PM, Daniel Leopold wrote:
>
> External Email - Use Caution
>
> Hi all,
>
> Do you have any suggestions on how I could extract stats (e.g., 
> thickness, area, LGI, etc.) from a cluster(s) identified via palm? 
> I've tried mri_label2label in order to turn the palm output .mgz into 
> a paint .label file, but mri_label2label cannot seem to read the .mgz, 
> .mgz.nii (i.e., .mgz mri_converted to .nii), or .mgz.nii.gz files. My 
> inputs to palm are 4D .mgh files, hence the .mgz results, which are in 
> a data-per-vertex format. Here are the errors I get when trying 
> convert/input .mgz and .mgz.nii files:
>
> G??M{?Kӭ7?xK/i?Mb4Ե??(???.!?t:6>|???ѧ???+F??c\Ϟ??U}??m?/8q?~ي???\???C??n?h+???~?}?w*jo???ʵS_??_??w?>ԏ??N?no+?8w
> mri_label2label: could not scan # of lines from label file
> ERROR reading 
> wordadhd_lgi_cft3.1/wordadhd_lgi_cft3.1_lh_tfce_tstat_cfwep_c4.mgz
>
> / mri_label2label: could not scan # of lines from label file
> ERROR reading 
> wordadhd_lgi_cft3.1/wordadhd_lgi_cft3.1_lh_tfce_tstat_cfwep_c4.mgz.nii
>
>
> As a follow-up to this question, is it possible to threshold the input 
> label/cluster map during the mri_label2label process? Given that my 
> palm .mgz results were saved as logp files, I'd like to threshold the 
> maps at 1.301. My assumption is that I'd instead have to do the following:
>
> 1) mri_binarize --i ${map} --o ${map}_bin --min 1.301
> 2) mri_label2label --s fsaverage --srclabel ${map}_bin --trglabel 
> $subjects/${map}_bin.label --regmethod surface --hemi ${hemi}
> 3) mri_anatomical_stats -l ${map}_bin.label -f label_stats $subjects $hemi
> 4) aparcstats2table etc.
>
> Thank you for your attention and help!
>
>
> With gratitude,
> Dan
>
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Re: [Freesurfer] surf2vol ERROR

2019-02-19 Thread Greve, Douglas N.,Ph.D.

yes, run it twice. The second time specify the output of the first run 
with --merge

On 2/17/19 3:29 PM, Bruce Fischl wrote:
> sorry, I'm not sure what your question is. You probably have to run it 
> twice - once for each hemi
> cheers
> Bruce
> On Sun, 17 Feb 2019, Barletta, Valeria wrote:
>
>>
>> It is actually registering only 1 hemi (screenshot), the last I type 
>> in the command:
>>
>>
>> panarea:/autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3
>>  
>> $ mri_surf2vol
>> --subject MS089_R01_29 --hemi rh 
>> --surfval/autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/surf2vol/M
>> S089_R01_29/rh.MS089_R01_29.subjspace.mgh --merge
>> /autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3/MS089_R01_29/mri/T1.mgz
>>  
>>
>> --identity MS089_R01_29 --hemi lh 
>> --surfval/autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/surf2vol/M
>> S089_R01_29/lh.MS089_R01_29.subjspace.mgh --merge
>> /autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3/MS089_R01_29/mri/T1.mgz
>>  
>>
>> --identity MS089_R01_29 
>> --o/autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/surf2vol/M
>> S089_R01_29/CME_MS089_R01_29.nii.gz
>> gdiagno = -1
>> Using merge volume as template
>> Using identity matrix for registration
>> Overriding reg subject MS089_R01_29 with MS089_R01_29
>> Qa2v: SurfXYZ to VolCRS: --
>> -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;
>> --
>> subjects dir 
>>  /autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3
>> surface value 
>> path 
>> /autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/surf2vol/M
>> S089_R01_29/lh.MS089_R01_29.subjspace.mgh
>> hemi           lh
>> mksurfmask     0
>> projfrac       0
>> outvol 
>>  path 
>> /autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/surf2vol/M
>> S089_R01_29/CME_MS089_R01_29.nii.gz
>> template path
>> /autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3/MS089_R01_29/mri/T1.mgz
>>  
>>
>> --- Anat2Vol Registration (TkReg)
>>  1.000   0.000   0.000   0.000;
>>  0.000   1.000   0.000   0.000;
>>  0.000   0.000   1.000   0.000;
>>  0.000   0.000   0.000   1.000;
>> -
>> height = 256
>>  width = 256
>>  depth = 256
>>  xsize = 1.00
>>  ysize = 1.00
>>  zsize = 1.00
>>   cdc  = -1.00 0.00 -0.00
>>   rdc  = 0.00 -0.00 -1.00
>>   sdc  = 0.00 1.00 -0.00
>>   xyz0 = 3.587784 22.749557 -8.968880
>> Gdiag_no  -1
>> Reading surface
>> /autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3/MS089_R01_29/surf/lh.white
>>  
>>
>> Done reading source surface
>> INFO: 
>> reading 
>> /autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/surf2vol/M
>> S089_R01_29/lh.MS089_R01_29.subjspace.mgh as MGH
>> Done loading source values (nvtxs = 137036)
>> INFO: mapping vertices to closest voxel
>> INFO: resampling surface to volume
>> INFO: sampled 85686 voxels in the volume
>> INFO: writing output volume 
>> to/autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/surf2vol/M
>> S089_R01_29/CME_MS089_R01_29.nii.gz
>>
>> 
>>  
>>
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>  on behalf of
>> Bruce Fischl 
>> Sent: Sunday, February 17, 2019 2:05:58 PM
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] surf2vol ERROR
>> you have a typo. It's not "-identify" it is "--identity"
>>
>> On Sun, 17 Feb
>> 2019, Barletta, Valeria wrote:
>>
>> >
>> > Sure... There is also a screenshot attached
>> >
>> >
>> > 
>> panarea:/autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3
>>  
>> $
>> > 
>> panarea:/autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3
>>  
>> $ mri_surf2vol
>> > --subject MS089_R01_29 --hemi 
>> rh--surfval/autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/s
>> urf2vol/M
>> > S089_R01_29/rh.MS089_R01_29.subjspace.mgh --hemi 
>> lh--surfval/autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/s
>> urf2vol/M
>> > 
>> S089_R01_29/lh.MS089_R01_29.subjspace.mgh--o/autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/surf2vo
>> l/M
>> > S089_R01_29/CME_MS089_R01_29.nii.gz --merge
>> > 
>> /autofs/space/alicudi_002/users/mscat/users/celine/lesion_mask/MS089_R01_29/combined-CL.nii.gz
>> > --regheader MS089_R01_29
>> > ERROR: Option --regheader unknown
>> >
>> > 
>> panarea:/autofs/space/alicudi_002/users/mscat/users/caterin

Re: [Freesurfer] Qdecrc File

2019-02-19 Thread Greve, Douglas N.,Ph.D.

Sorry, qdec is not really being supported anymore. You'll have to use 
the "command line" stream (ie, creating an FSGD file, running 
mris_preproc, mri_surf2surf, mri_glmfit). See the group analysis tutorial

On 2/18/19 2:21 AM, Hua, Jessica wrote:
>
> External Email - Use Caution
>
> Hi FreeSurfer Experts,
>
>
> Also, I looked in the Home folder of my computer and I cannot find the 
> .Qdecrc file. I am not sure why I cannot find it. Is it possible to 
> send me a new one that I can drop into my Home folder? Thank you!
>
>
> Best,
>
>
> Jessica
>
>
> ---
>
> Jessica Hua, M.A.
>
> 
> *From:* Hua, Jessica
> *Sent:* Sunday, February 17, 2019 5:39:38 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Qdecrc File
>
> Hi FreeSurfer Experts,
>
>
> I am trying to modify my .Qdecrc file in order to run lGI analyses.  
> However, I cannot seem to find it. Do you know where I can find this file?
>
>
> Best,
>
>
> Jessica
>
>
> ---
>
> Jessica Hua, M.A.
>
>
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Re: [Freesurfer] Artefacts from simultaneous MRI and EEG measurement

2019-02-19 Thread Greve, Douglas N.,Ph.D.

what are the artefacts exactly? It looks like the back of the brain was 
not segmented. Is there something in the raw data? Otherwise, look 
though the trouble shooting tutorial.

On 2/18/19 12:19 PM, Backhausen, Lea wrote:
>
> External Email - Use Caution
>
> Dear FreeSurer experts,
>
> we recently did a simultaneous measurement of MRI and EEG in 
> adolescent patients with obsessive-compulsive-disorder. Due to the 
> electrode gel we see image artifacts mostly in parietal and frontal 
> regions (please see attached images).
>
> Has anyone experience with these kinds of measurements? Is there a way 
> to fix the artifacts?
>
> We are worried that the calculation of eTIV will also be corrupted and 
> we cannot use it to correct for head size in the subcortical 
> structures (which are our ROIs, mostly striatum).
>
> Thanks a lot for any advice!
>
> Lea
>
> --
>
> Lea Backhausen
>
> Ph.D. Student (M.Sc. Psychology/Neuroscience)
>
> Department of Child and Adolescent Psychiatry, Faculty of Medicine of 
> the TU Dresden, Germany
> http://www.uniklinikum-dresden.de 
>
>
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Re: [Freesurfer] average MRI scans

2019-02-19 Thread Greve, Douglas N.,Ph.D.

Not sure exactly what you mean by a template or what you would want to 
do with such a thing. You can run make_average_subject to create a 
folding atlas.

On 2/19/19 3:24 AM, Vivek Sharma wrote:
>
> External Email - Use Caution
>
> I'm working on source reconstruction using MEG data. For which 
> segmented T1 images of MRI scans are required. I use recon -all for 
> individual subjects.
> Can we have a common average template made from MRI scans of all 
> subjects. If I have MRI scans from 10 subjects, how can I have average 
> template of these 10 scans.
>
> -- 
> Vivek
>
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Re: [Freesurfer] commends of GLM for volume

2019-02-19 Thread Greve, Douglas N.,Ph.D.

IIs this an fMRI analysis? If so, you should use permutation for both 
surface and subcort. See 
http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV6.0/FsFastGroupLevelPerm

On 2/19/19 6:00 AM, ?? wrote:
>
> ?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2External Email - Use Caution
>
> Hello Greve,
> I am glad to tell you that after 3 hours, something did print more on 
> terminal. when I was doing the GLM follow the tutorial, it only 
> provided the example of the cortical thickness. And I did not know how 
> to transfer it into volume.
> Here is my commends
>
> mris_preproc --fsgd FSGD/PDDvsHC.fsgd --cache-in 
> volmue.fwhm10.fsaverage --target fsaverage --hemi lh --out 
> lh.PDDvsHC.volume.10.mgh
>
> mri_glmfit --y lh.PDDvsHC.volume.10.mgh --fsgd FSGD/PDDvsHC.fsgd --C 
> Contras-HC-PDD.mtx --surf fsaverage lh --cortex --glmdir 
> lh.volume.PDDvsHC.glimdir --eres-save
>
> mri_glmfit-sim --glmdir rh.PDDvsHC.volume.glmdir --cache 1.3 pos --cwp 
> 999 --2spaces
>
> We I check the results, it still talked about the cortical thickness , 
> so could you tell me how to change this commends to the volume of 
> subcortical. Or do you have the example which?0?2use GLM for comparing 
> the difference of subcortical?0?2volume?0?2between two groups.
>
> Thanks so much for your help
>
> Yours
>
> Zeng
>
> Here is the results
>
>
> ClusterNoMax VtxMax Size(mm^2)MNIX MNIY MNIZCWPCWPLowCWPHi 
> NVtxsWghtVtx Annot
>
>
> 16.960 86488 4544.63 15.7-77.36.70.000200.00.00040 
> 789115125.67pericalcarine
>
>
> 23.529158070 3287.33 55.0-52.98.20.000200.00.00040 
> 679611225.54inferiorparietal
>
>
> 32.630 67804 1909.67 43.3 45.8 -9.30.002200.001400.00300 2858 
> 4399.15parsorbitalis
>
> Here is the terminal output.
>
> $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $
>
>
> cwd /Volumes/NIU20/volumetric_FS/glm
>
>
> cmdline mri_glmfit.bin --glmdir lh.PDDvsHC.volume.glmdir --y 
> lh.PDDvsHC.volume.10.mgh --fsgd FSGD/PDDvsHC.fsgd --C 
> Contrasts/lh-thickness-HC-PDD.mtx --surface fsaverage lh --eres-save
>
>
> sysnameDarwin
>
>
> hostname dyn3199-104.wlan.ic.ac.uk
>
>
> machinex86_64
>
>
> usercengzhou
>
>
> FixVertexAreaFlag = 1
>
>
> UseMaskWithSmoothing1
>
>
> OneSampleGroupMean 0
>
>
> y/Volumes/NIU20/volumetric_FS/glm/lh.PDDvsHC.volume.10.mgh
>
>
> logyflag 0
>
>
> usedti0
>
>
> FSGD FSGD/PDDvsHC.fsgd
>
>
> labelmask/Volumes/NIU20/volumetric_FS/glm/fsaverage/label/lh.cortex.label
>
>
> maskinv 0
>
>
> glmdir lh.PDDvsHC.volume.glmdir
>
>
> IllCondOK 0
>
>
> ReScaleX 1
>
>
> DoFFx 0
>
>
> ResidualFWHM 14.826153
>
>
> SearchSpace 73852.172969
>
>
> anattype surface
>
>
>
>
> cd /Volumes/NIU20/volumetric_FS/glm
>
>
> /Applications/freesurfer/bin/mri_glmfit-sim
>
>
> --glmdir rh.PDDvsHC.volume.glmdir --cache 1.3 pos --cwp 999 --2spaces
>
>
>
> $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $
>
>
> Mon Feb 18 15:52:07 GMT 2019
>
>
> Darwin dyn3199-104.wlan.ic.ac.uk 14.5.0 Darwin Kernel Version 14.5.0: 
> Wed Jul 29 02:26:53 PDT 2015; root:xnu-2782.40.9~1/RELEASE_X86_64 x86_64
>
>
> cengzhou
>
>
> setenv SUBJECTS_DIR /Volumes/NIU20/volumetric_FS/glm
>
>
> FREESURFER_HOME /Applications/freesurfer
>
>
>
> Original mri_glmfit command line:
>
>
> cmdline mri_glmfit.bin --glmdir rh.PDDvsHC.volume.glmdir --y 
> rh.PDDvsHC.volume.10.mgh --fsgd FSGD/PDDvsHC.fsgd --C 
> Contrasts/lh-thickness-HC-PDD.mtx --surface fsaverage rh --eres-save
>
>
>
> DoSim = 0
>
>
> UseCache = 1
>
>
> DoPoll = 0
>
>
> DoPBSubmit = 0
>
>
> DoBackground = 0
>
>
> DiagCluster = 0
>
>
> gd2mtx = dods
>
>
> fwhm = 14.506572
>
>
> CSD 
> /Applications/freesurfer/average/mult-comp-cor/fsaverage/rh/cortex/fwhm15/pos/th13/mc-z.csd
>
>
> mri_surfcluster --in rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/sig.mgh 
> --mask rh.PDDvsHC.volume.glmdir/mask.mgh --cwsig 
> rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.cluster.mgh 
> --sum 
> rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.cluster.summary 
> --ocn 
> rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.ocn.mgh 
> --annot aparc --cwpvalthresh 999 --o 
> rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.masked.mgh 
> --no-fixmni --csd 
> /Applications/freesurfer/average/mult-comp-cor/fsaverage/rh/cortex/fwhm15/pos/th13/mc-z.csd--csdpdf
>  
> rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.pdf.dat 
> --vwsig 
> rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.voxel.mgh 
> --vwsigmax 
> rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.voxel.max.dat--oannot
>  
> rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.ocn.annot 
> --bonferroni 2 --surf white
>
>
> Creating CDFs from CSD files
>
>
> csd->threshsign = 1
>
>
> thsign = pos, id = 1
>
>
> version $Id: mri_surfcluster.c,v 1.57.2.3 2016/11/17 18:19:42 zkaufman 
> Exp $
>
>
> hemi= rh
>
>
> srcid= rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/sig.mgh
>
>
> srcsubjid= fsaverage
>
>
> srcsurf= white
>
>
> srcframe= 0
>
>
> thsign= pos
>
>
> thmin= 1.3
>
>
>

Re: [Freesurfer] clusters annotation file in surface

2019-02-19 Thread Greve, Douglas N.,Ph.D.

You can create an annotation with mris_seg2annot (you basically have a 
surface-based segmentation). Run it with --help to get more info 
including examples. You will need to create your own color table

On 2/19/19 3:21 PM, Barletta, Valeria wrote:
>
> Dear Freesurfers,
>
> I have a 3D volume mask of cortical lesions with 8 different clusters 
> (8 cortical lesions).
>
> I projected this mask to the cortex and obtained a .mgh file with the 
> command vol2surf:
>
> mri_vol2surf --src $path_to_lesion/$subj/combined-$lesion.nii.gz --out 
> $path_to_output/$subj/surf/$hemi".surf_combined-"$lesion".mgh" 
> --projfrac-avg -0.1 1 0.05 --hemi $hemi --regheader $subj
>
>
> Now I need to extract label files from this surface file, one 
> label for each cluster, and then an annotation file summarizing all 
> the label files.
>
> How can I do this?
>
> Thanks,
>
> Vale
>
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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[Freesurfer] Moving Between Fsaverage Vertexwise Parcellations Without Recon-all?

2019-02-19 Thread Alexander Samir Hatoum

External Email - Use Caution

Hello,

I am currently working with the fsaverage7 parcellation and would like to
move to a lower resolution brain parcelltation (fsaverage4, 5, or 6 for
example).  I was wondering if there is a simple way to translate my data
without rerunning recon-all? So essentially, is there a way to turn
fsaverage7 parcellation into 6 or lower?

Best,

Alex

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Re: [Freesurfer] Moving Between Fsaverage Vertexwise Parcellations Without Recon-all?

2019-02-19 Thread Bruce Fischl


Hi Alex

yes, the vertices of the lower res fsaverage representations come first in 
the ordering. So the first 12 are ico0, then the first 42 are ico 0 and ico 
1, etc


cheers
Bruce


On Tue, 19 Feb 2019, Alexander 
Samir Hatoum wrote:




External Email - Use Caution

Hello,
I am currently working with the fsaverage7 parcellation and would like to move 
to a lower resolution
brain parcelltation (fsaverage4, 5, or 6 for example).  I was wondering if 
there is a simple way to
translate my data without rerunning recon-all? So essentially, is there a way 
to turn  fsaverage7
parcellation into 6 or lower? 

Best,

Alex

--


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Re: [Freesurfer] Extracting stats from palm results (.mgz)

2019-02-19 Thread Daniel Leopold

External Email - Use Caution

Thank you, Doug. I'm aware of fspalm, but stayed with palm in order to take
advantage of NPC and exchangeability blocks because I've got twins and
singletons in the sample. Does --pargs allow for all palm functionality,
including things like TFCE, eb's, and npc? Per another thread, I looked
through the fspalm code and my next approach is to try mri_surfcluster or
mri_volcluster with the .mgz palm results I've already got.


Thanks,
Dan
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Re: [Freesurfer] commends of GLM for volume

2019-02-19 Thread ??

External Email - Use Caution

Hi,
Thanks for your reply. it is a just a normal mri analysis, but I want to 
compare the subcortical volume and Cortical thinkness  between PD dementia 
patient and healthy control group. I only got the t1image. 


 
---Original---
From: "Greve, Douglas N.,Ph.D."
Date: Tue, Feb 19, 2019 21:29 PM
To: "freesurfer@nmr.mgh.harvard.edu";
Subject: Re: [Freesurfer] commends of GLM for volume


IIs this an fMRI analysis? If so, you should use permutation for both 
surface and subcort. See 
http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV6.0/FsFastGroupLevelPerm

On 2/19/19 6:00 AM, ?? wrote:
>
> External Email - Use Caution
>
> Hello Greve,
> I am glad to tell you that after 3 hours, something did print more on 
> terminal. when I was doing the GLM follow the tutorial, it only 
> provided the example of the cortical thickness. And I did not know how 
> to transfer it into volume.
> Here is my commends
>
> mris_preproc --fsgd FSGD/PDDvsHC.fsgd --cache-in 
> volmue.fwhm10.fsaverage --target fsaverage --hemi lh --out 
> lh.PDDvsHC.volume.10.mgh
>
> mri_glmfit --y lh.PDDvsHC.volume.10.mgh --fsgd FSGD/PDDvsHC.fsgd --C 
> Contras-HC-PDD.mtx --surf fsaverage lh --cortex --glmdir 
> lh.volume.PDDvsHC.glimdir --eres-save
>
> mri_glmfit-sim --glmdir rh.PDDvsHC.volume.glmdir --cache 1.3 pos --cwp 
> 999 --2spaces
>
> We I check the results, it still talked about the cortical thickness , 
> so could you tell me how to change this commends to the volume of 
> subcortical. Or do you have the example which use GLM for comparing 
> the difference of subcortical volume between two groups.
>
> Thanks so much for your help
>
> Yours
>
> Zeng
>
> Here is the results
>
>
> ClusterNoMax VtxMax Size(mm^2)MNIX MNIY MNIZCWPCWPLowCWPHi 
> NVtxsWghtVtx Annot
>
>
> 16.960 86488 4544.63 15.7-77.36.70.000200.00.00040 
> 789115125.67pericalcarine
>
>
> 23.529158070 3287.33 55.0-52.98.20.000200.00.00040 
> 679611225.54inferiorparietal
>
>
> 32.630 67804 1909.67 43.3 45.8 -9.30.002200.001400.00300 2858 
> 4399.15parsorbitalis
>
> Here is the terminal output.
>
> $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $
>
>
> cwd /Volumes/NIU20/volumetric_FS/glm
>
>
> cmdline mri_glmfit.bin --glmdir lh.PDDvsHC.volume.glmdir --y 
> lh.PDDvsHC.volume.10.mgh --fsgd FSGD/PDDvsHC.fsgd --C 
> Contrasts/lh-thickness-HC-PDD.mtx --surface fsaverage lh --eres-save
>
>
> sysnameDarwin
>
>
> hostname dyn3199-104.wlan.ic.ac.uk
>
>
> machinex86_64
>
>
> usercengzhou
>
>
> FixVertexAreaFlag = 1
>
>
> UseMaskWithSmoothing1
>
>
> OneSampleGroupMean 0
>
>
> y/Volumes/NIU20/volumetric_FS/glm/lh.PDDvsHC.volume.10.mgh
>
>
> logyflag 0
>
>
> usedti0
>
>
> FSGD FSGD/PDDvsHC.fsgd
>
>
> labelmask/Volumes/NIU20/volumetric_FS/glm/fsaverage/label/lh.cortex.label
>
>
> maskinv 0
>
>
> glmdir lh.PDDvsHC.volume.glmdir
>
>
> IllCondOK 0
>
>
> ReScaleX 1
>
>
> DoFFx 0
>
>
> ResidualFWHM 14.826153
>
>
> SearchSpace 73852.172969
>
>
> anattype surface
>
>
>
>
> cd /Volumes/NIU20/volumetric_FS/glm
>
>
> /Applications/freesurfer/bin/mri_glmfit-sim
>
>
> --glmdir rh.PDDvsHC.volume.glmdir --cache 1.3 pos --cwp 999 --2spaces
>
>
>
> $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $
>
>
> Mon Feb 18 15:52:07 GMT 2019
>
>
> Darwin dyn3199-104.wlan.ic.ac.uk 14.5.0 Darwin Kernel Version 14.5.0: 
> Wed Jul 29 02:26:53 PDT 2015; root:xnu-2782.40.9~1/RELEASE_X86_64 x86_64
>
>
> cengzhou
>
>
> setenv SUBJECTS_DIR /Volumes/NIU20/volumetric_FS/glm
>
>
> FREESURFER_HOME /Applications/freesurfer
>
>
>
> Original mri_glmfit command line:
>
>
> cmdline mri_glmfit.bin --glmdir rh.PDDvsHC.volume.glmdir --y 
> rh.PDDvsHC.volume.10.mgh --fsgd FSGD/PDDvsHC.fsgd --C 
> Contrasts/lh-thickness-HC-PDD.mtx --surface fsaverage rh --eres-save
>
>
>
> DoSim = 0
>
>
> UseCache = 1
>
>
> DoPoll = 0
>
>
> DoPBSubmit = 0
>
>
> DoBackground = 0
>
>
> DiagCluster = 0
>
>
> gd2mtx = dods
>
>
> fwhm = 14.506572
>
>
> CSD 
> /Applications/freesurfer/average/mult-comp-cor/fsaverage/rh/cortex/fwhm15/pos/th13/mc-z.csd
>
>
> mri_surfcluster --in rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/sig.mgh 
> --mask rh.PDDvsHC.volume.glmdir/mask.mgh --cwsig 
> rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.cluster.mgh 
> --sum 
> rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.cluster.summary 
> --ocn 
> rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.ocn.mgh 
> --annot aparc --cwpvalthresh 999 --o 
> rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.masked.mgh 
> --no-fixmni --csd 
> /Applications/freesurfer/average/mult-comp-cor/fsaverage/rh/cortex/fwhm15/pos/th13/mc-z.csd--csdpdf
>  
> rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.pdf.dat 
> --vwsig 
> rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.voxel.mgh 
> --vwsigmax 
> rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.voxel.max.dat--oannot
>  
> rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.

Re: [Freesurfer] commends of GLM for volume

2019-02-19 Thread ??

External Email - Use Caution

Or I can not use mri to do the Glm for subcortical volume analysis ?


 
---Original---
From: "Greve, Douglas N.,Ph.D."
Date: Tue, Feb 19, 2019 21:29 PM
To: "freesurfer@nmr.mgh.harvard.edu";
Subject: Re: [Freesurfer] commends of GLM for volume


IIs this an fMRI analysis? If so, you should use permutation for both 
surface and subcort. See 
http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV6.0/FsFastGroupLevelPerm

On 2/19/19 6:00 AM, ?? wrote:
>
> External Email - Use Caution
>
> Hello Greve,
> I am glad to tell you that after 3 hours, something did print more on 
> terminal. when I was doing the GLM follow the tutorial, it only 
> provided the example of the cortical thickness. And I did not know how 
> to transfer it into volume.
> Here is my commends
>
> mris_preproc --fsgd FSGD/PDDvsHC.fsgd --cache-in 
> volmue.fwhm10.fsaverage --target fsaverage --hemi lh --out 
> lh.PDDvsHC.volume.10.mgh
>
> mri_glmfit --y lh.PDDvsHC.volume.10.mgh --fsgd FSGD/PDDvsHC.fsgd --C 
> Contras-HC-PDD.mtx --surf fsaverage lh --cortex --glmdir 
> lh.volume.PDDvsHC.glimdir --eres-save
>
> mri_glmfit-sim --glmdir rh.PDDvsHC.volume.glmdir --cache 1.3 pos --cwp 
> 999 --2spaces
>
> We I check the results, it still talked about the cortical thickness , 
> so could you tell me how to change this commends to the volume of 
> subcortical. Or do you have the example which use GLM for comparing 
> the difference of subcortical volume between two groups.
>
> Thanks so much for your help
>
> Yours
>
> Zeng
>
> Here is the results
>
>
> ClusterNoMax VtxMax Size(mm^2)MNIX MNIY MNIZCWPCWPLowCWPHi 
> NVtxsWghtVtx Annot
>
>
> 16.960 86488 4544.63 15.7-77.36.70.000200.00.00040 
> 789115125.67pericalcarine
>
>
> 23.529158070 3287.33 55.0-52.98.20.000200.00.00040 
> 679611225.54inferiorparietal
>
>
> 32.630 67804 1909.67 43.3 45.8 -9.30.002200.001400.00300 2858 
> 4399.15parsorbitalis
>
> Here is the terminal output.
>
> $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $
>
>
> cwd /Volumes/NIU20/volumetric_FS/glm
>
>
> cmdline mri_glmfit.bin --glmdir lh.PDDvsHC.volume.glmdir --y 
> lh.PDDvsHC.volume.10.mgh --fsgd FSGD/PDDvsHC.fsgd --C 
> Contrasts/lh-thickness-HC-PDD.mtx --surface fsaverage lh --eres-save
>
>
> sysnameDarwin
>
>
> hostname dyn3199-104.wlan.ic.ac.uk
>
>
> machinex86_64
>
>
> usercengzhou
>
>
> FixVertexAreaFlag = 1
>
>
> UseMaskWithSmoothing1
>
>
> OneSampleGroupMean 0
>
>
> y/Volumes/NIU20/volumetric_FS/glm/lh.PDDvsHC.volume.10.mgh
>
>
> logyflag 0
>
>
> usedti0
>
>
> FSGD FSGD/PDDvsHC.fsgd
>
>
> labelmask/Volumes/NIU20/volumetric_FS/glm/fsaverage/label/lh.cortex.label
>
>
> maskinv 0
>
>
> glmdir lh.PDDvsHC.volume.glmdir
>
>
> IllCondOK 0
>
>
> ReScaleX 1
>
>
> DoFFx 0
>
>
> ResidualFWHM 14.826153
>
>
> SearchSpace 73852.172969
>
>
> anattype surface
>
>
>
>
> cd /Volumes/NIU20/volumetric_FS/glm
>
>
> /Applications/freesurfer/bin/mri_glmfit-sim
>
>
> --glmdir rh.PDDvsHC.volume.glmdir --cache 1.3 pos --cwp 999 --2spaces
>
>
>
> $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $
>
>
> Mon Feb 18 15:52:07 GMT 2019
>
>
> Darwin dyn3199-104.wlan.ic.ac.uk 14.5.0 Darwin Kernel Version 14.5.0: 
> Wed Jul 29 02:26:53 PDT 2015; root:xnu-2782.40.9~1/RELEASE_X86_64 x86_64
>
>
> cengzhou
>
>
> setenv SUBJECTS_DIR /Volumes/NIU20/volumetric_FS/glm
>
>
> FREESURFER_HOME /Applications/freesurfer
>
>
>
> Original mri_glmfit command line:
>
>
> cmdline mri_glmfit.bin --glmdir rh.PDDvsHC.volume.glmdir --y 
> rh.PDDvsHC.volume.10.mgh --fsgd FSGD/PDDvsHC.fsgd --C 
> Contrasts/lh-thickness-HC-PDD.mtx --surface fsaverage rh --eres-save
>
>
>
> DoSim = 0
>
>
> UseCache = 1
>
>
> DoPoll = 0
>
>
> DoPBSubmit = 0
>
>
> DoBackground = 0
>
>
> DiagCluster = 0
>
>
> gd2mtx = dods
>
>
> fwhm = 14.506572
>
>
> CSD 
> /Applications/freesurfer/average/mult-comp-cor/fsaverage/rh/cortex/fwhm15/pos/th13/mc-z.csd
>
>
> mri_surfcluster --in rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/sig.mgh 
> --mask rh.PDDvsHC.volume.glmdir/mask.mgh --cwsig 
> rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.cluster.mgh 
> --sum 
> rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.cluster.summary 
> --ocn 
> rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.ocn.mgh 
> --annot aparc --cwpvalthresh 999 --o 
> rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.masked.mgh 
> --no-fixmni --csd 
> /Applications/freesurfer/average/mult-comp-cor/fsaverage/rh/cortex/fwhm15/pos/th13/mc-z.csd--csdpdf
>  
> rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.pdf.dat 
> --vwsig 
> rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.voxel.mgh 
> --vwsigmax 
> rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.voxel.max.dat--oannot
>  
> rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.ocn.annot 
> --bonferroni 2 --surf white
>
>
> Creating CDFs from CSD files
>
>
> csd->threshsign = 1
>
>
> thsign = pos, id = 1
>
>
> versio

Re: [Freesurfer] Moving Between Fsaverage Vertexwise Parcellations Without Recon-all?

2019-02-19 Thread Greve, Douglas N.,Ph.D.

You can use mri_surf2surf or mris_apply_reg to do the transferring

On 2/19/19 4:51 PM, Bruce Fischl wrote:
> Hi Alex
>
> yes, the vertices of the lower res fsaverage representations come 
> first in the ordering. So the first 12 are ico0, then the first 42 are 
> ico 0 and ico 1, etc
>
> cheers
> Bruce
>
>
> On Tue, 19 Feb 2019, Alexander Samir Hatoum wrote:
>
>>
>> External Email - Use Caution
>>
>> Hello,
>> I am currently working with the fsaverage7 parcellation and would 
>> like to move to a lower resolution
>> brain parcelltation (fsaverage4, 5, or 6 for example).  I was 
>> wondering if there is a simple way to
>> translate my data without rerunning recon-all? So essentially, is 
>> there a way to turn  fsaverage7
>> parcellation into 6 or lower?
>>
>> Best,
>>
>> Alex
>>
>> -- 
>>
>>
>> [icon-envelope-tick-round-orange-animated-no-repeat-v1.gif]
>> Virus-free. www.avast.com
>>
>>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Re: [Freesurfer] Extracting stats from palm results (.mgz)

2019-02-19 Thread Greve, Douglas N.,Ph.D.

I have not really stressed the code with --pargs (it is a relatively new 
program), but if it produces the same output, then it should work

On 2/19/19 5:01 PM, Daniel Leopold wrote:
>
> External Email - Use Caution
>
> Thank you, Doug. I'm aware of fspalm, but stayed with palm in order to 
> take advantage of NPC and exchangeability blocks because I've got 
> twins and singletons in the sample. Does --pargs allow for all palm 
> functionality, including things like TFCE, eb's, and npc? Per another 
> thread, I looked through the fspalm code and my next approach is to 
> try mri_surfcluster or mri_volcluster with the .mgz palm results I've 
> already got.
>
>
> Thanks,
> Dan
>
> ___
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Re: [Freesurfer] commends of GLM for volume

2019-02-19 Thread Greve, Douglas N.,Ph.D.

You can get the volumes of structures, eg, hipocampal volume, for each 
structure and subject using asegstats2table, then mri_glmfit can read in 
that table. But it is an ROI analysis, not a voxel-wise analysis. Is 
that what you want to do?

On 2/19/19 5:20 PM, ?? wrote:
>
> ?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2External Email - Use Caution
>
> Or I can not use mri to do the Glm for subcortical volume analysis ?
>
> ---Original---
> *From:* "Greve, Douglas N.,Ph.D."
> *Date:* Tue, Feb 19, 2019 21:29 PM
> *To:* "freesurfer@nmr.mgh.harvard.edu";
> *Subject:* Re: [Freesurfer] commends of GLM for volume
>
> IIs this an fMRI analysis? If so, you should use permutation for both
> surface and subcort. See
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV6.0/FsFastGroupLevelPerm
>
> On 2/19/19 6:00 AM, ?? wrote:
> >
> > ?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2External Email - Use Caution
> >
> > Hello Greve,
> > I am glad to tell you that after 3 hours, something did print more on
> > terminal. when I was doing the GLM follow the tutorial, it only
> > provided the example of the cortical thickness. And I did not know how
> > to transfer it into volume.
> > Here is my commends
> >
> > mris_preproc --fsgd FSGD/PDDvsHC.fsgd --cache-in
> > volmue.fwhm10.fsaverage --target fsaverage --hemi lh --out
> > lh.PDDvsHC.volume.10.mgh
> >
> > mri_glmfit --y lh.PDDvsHC.volume.10.mgh --fsgd FSGD/PDDvsHC.fsgd --C
> > Contras-HC-PDD.mtx --surf fsaverage lh --cortex --glmdir
> > lh.volume.PDDvsHC.glimdir --eres-save
> >
> > mri_glmfit-sim --glmdir rh.PDDvsHC.volume.glmdir --cache 1.3 pos --cwp
> > 999 --2spaces
> >
> > We I check the results, it still talked about the cortical thickness ,
> > so could you tell me how to change this commends to the volume of
> > subcortical. Or do you have the example which?0?2use GLM for comparing
> > the difference of subcortical?0?2volume?0?2between two groups.
> >
> > Thanks so much for your help
> >
> > Yours
> >
> > Zeng
> >
> > Here is the results
> >
> >
> > ClusterNoMax VtxMax Size(mm^2)MNIX MNIY MNIZCWPCWPLowCWPHi
> > NVtxsWghtVtx Annot
> >
> >
> > 16.960 86488 4544.63 15.7-77.36.70.000200.00.00040
> > 789115125.67pericalcarine
> >
> >
> > 23.529158070 3287.33 55.0-52.98.20.000200.00.00040
> > 679611225.54inferiorparietal
> >
> >
> > 32.630 67804 1909.67 43.3 45.8 -9.30.002200.001400.00300 2858
> > 4399.15parsorbitalis
> >
> > Here is the terminal output.
> >
> > $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $
> >
> >
> > cwd /Volumes/NIU20/volumetric_FS/glm
> >
> >
> > cmdline mri_glmfit.bin --glmdir lh.PDDvsHC.volume.glmdir --y
> > lh.PDDvsHC.volume.10.mgh --fsgd FSGD/PDDvsHC.fsgd --C
> > Contrasts/lh-thickness-HC-PDD.mtx --surface fsaverage lh --eres-save
> >
> >
> > sysnameDarwin
> >
> >
> > hostname dyn3199-104.wlan.ic.ac.uk
> >
> >
> > machinex86_64
> >
> >
> > usercengzhou
> >
> >
> > FixVertexAreaFlag = 1
> >
> >
> > UseMaskWithSmoothing1
> >
> >
> > OneSampleGroupMean 0
> >
> >
> > y/Volumes/NIU20/volumetric_FS/glm/lh.PDDvsHC.volume.10.mgh
> >
> >
> > logyflag 0
> >
> >
> > usedti0
> >
> >
> > FSGD FSGD/PDDvsHC.fsgd
> >
> >
> > 
> labelmask/Volumes/NIU20/volumetric_FS/glm/fsaverage/label/lh.cortex.label
> >
> >
> > maskinv 0
> >
> >
> > glmdir lh.PDDvsHC.volume.glmdir
> >
> >
> > IllCondOK 0
> >
> >
> > ReScaleX 1
> >
> >
> > DoFFx 0
> >
> >
> > ResidualFWHM 14.826153
> >
> >
> > SearchSpace 73852.172969
> >
> >
> > anattype surface
> >
> >
> >
> >
> > cd /Volumes/NIU20/volumetric_FS/glm
> >
> >
> > /Applications/freesurfer/bin/mri_glmfit-sim
> >
> >
> > --glmdir rh.PDDvsHC.volume.glmdir --cache 1.3 pos --cwp 999 --2spaces
> >
> >
> >
> > $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $
> >
> >
> > Mon Feb 18 15:52:07 GMT 2019
> >
> >
> > Darwin dyn3199-104.wlan.ic.ac.uk 14.5.0 Darwin Kernel Version 14.5.0:
> > Wed Jul 29 02:26:53 PDT 2015; root:xnu-2782.40.9~1/RELEASE_X86_64 x86_64
> >
> >
> > cengzhou
> >
> >
> > setenv SUBJECTS_DIR /Volumes/NIU20/volumetric_FS/glm
> >
> >
> > FREESURFER_HOME /Applications/freesurfer
> >
> >
> >
> > Original mri_glmfit command line:
> >
> >
> > cmdline mri_glmfit.bin --glmdir rh.PDDvsHC.volume.glmdir --y
> > rh.PDDvsHC.volume.10.mgh --fsgd FSGD/PDDvsHC.fsgd --C
> > Contrasts/lh-thickness-HC-PDD.mtx --surface fsaverage rh --eres-save
> >
> >
> >
> > DoSim = 0
> >
> >
> > UseCache = 1
> >
> >
> > DoPoll = 0
> >
> >
> > DoPBSubmit = 0
> >
> >
> > DoBackground = 0
> >
> >
> > DiagCluster = 0
> >
> >
> > gd2mtx = dods
> >
> >
> > fwhm = 14.506572
> >
> >
> > CSD
> > 
> /Applications/freesurfer/average/mult-comp-cor/fsaverage/rh/cortex/fwhm15/pos/th13/mc-z.csd
> >
> >
> > mri_surfcluster --in rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/sig.mgh
> > --mask rh.PDDvsHC.volume.glmdir/mask.mgh --cwsig
> > 
> rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.cluster.mgh
> > --sum
> > 
> rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.cluster.summary 
>
> > --ocn
> > rh.PDDvsHC.volume.glmdir/rh-volume

Re: [Freesurfer] commends of GLM for volume

2019-02-19 Thread ??

External Email - Use Caution

Yes, one more question where can I get the example of mri glimfit  for ROI 
analysis 


 
---Original---
From: "Greve, Douglas N.,Ph.D."
Date: Tue, Feb 19, 2019 22:47 PM
To: "freesurfer@nmr.mgh.harvard.edu";
Subject: Re: [Freesurfer] commends of GLM for volume


You can get the volumes of structures, eg, hipocampal volume, for each 
structure and subject using asegstats2table, then mri_glmfit can read in 
that table. But it is an ROI analysis, not a voxel-wise analysis. Is 
that what you want to do?

On 2/19/19 5:20 PM, ?? wrote:
>
> External Email - Use Caution
>
> Or I can not use mri to do the Glm for subcortical volume analysis ?
>
> ---Original---
> *From:* "Greve, Douglas N.,Ph.D."
> *Date:* Tue, Feb 19, 2019 21:29 PM
> *To:* "freesurfer@nmr.mgh.harvard.edu";
> *Subject:* Re: [Freesurfer] commends of GLM for volume
>
> IIs this an fMRI analysis? If so, you should use permutation for both
> surface and subcort. See
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV6.0/FsFastGroupLevelPerm
>
> On 2/19/19 6:00 AM, ?? wrote:
> >
> > External Email - Use Caution
> >
> > Hello Greve,
> > I am glad to tell you that after 3 hours, something did print more on
> > terminal. when I was doing the GLM follow the tutorial, it only
> > provided the example of the cortical thickness. And I did not know how
> > to transfer it into volume.
> > Here is my commends
> >
> > mris_preproc --fsgd FSGD/PDDvsHC.fsgd --cache-in
> > volmue.fwhm10.fsaverage --target fsaverage --hemi lh --out
> > lh.PDDvsHC.volume.10.mgh
> >
> > mri_glmfit --y lh.PDDvsHC.volume.10.mgh --fsgd FSGD/PDDvsHC.fsgd --C
> > Contras-HC-PDD.mtx --surf fsaverage lh --cortex --glmdir
> > lh.volume.PDDvsHC.glimdir --eres-save
> >
> > mri_glmfit-sim --glmdir rh.PDDvsHC.volume.glmdir --cache 1.3 pos --cwp
> > 999 --2spaces
> >
> > We I check the results, it still talked about the cortical thickness ,
> > so could you tell me how to change this commends to the volume of
> > subcortical. Or do you have the example which use GLM for comparing
> > the difference of subcortical volume between two groups.
> >
> > Thanks so much for your help
> >
> > Yours
> >
> > Zeng
> >
> > Here is the results
> >
> >
> > ClusterNoMax VtxMax Size(mm^2)MNIX MNIY MNIZCWPCWPLowCWPHi
> > NVtxsWghtVtx Annot
> >
> >
> > 16.960 86488 4544.63 15.7-77.36.70.000200.00.00040
> > 789115125.67pericalcarine
> >
> >
> > 23.529158070 3287.33 55.0-52.98.20.000200.00.00040
> > 679611225.54inferiorparietal
> >
> >
> > 32.630 67804 1909.67 43.3 45.8 -9.30.002200.001400.00300 2858
> > 4399.15parsorbitalis
> >
> > Here is the terminal output.
> >
> > $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $
> >
> >
> > cwd /Volumes/NIU20/volumetric_FS/glm
> >
> >
> > cmdline mri_glmfit.bin --glmdir lh.PDDvsHC.volume.glmdir --y
> > lh.PDDvsHC.volume.10.mgh --fsgd FSGD/PDDvsHC.fsgd --C
> > Contrasts/lh-thickness-HC-PDD.mtx --surface fsaverage lh --eres-save
> >
> >
> > sysnameDarwin
> >
> >
> > hostname dyn3199-104.wlan.ic.ac.uk
> >
> >
> > machinex86_64
> >
> >
> > usercengzhou
> >
> >
> > FixVertexAreaFlag = 1
> >
> >
> > UseMaskWithSmoothing1
> >
> >
> > OneSampleGroupMean 0
> >
> >
> > y/Volumes/NIU20/volumetric_FS/glm/lh.PDDvsHC.volume.10.mgh
> >
> >
> > logyflag 0
> >
> >
> > usedti0
> >
> >
> > FSGD FSGD/PDDvsHC.fsgd
> >
> >
> > 
> labelmask/Volumes/NIU20/volumetric_FS/glm/fsaverage/label/lh.cortex.label
> >
> >
> > maskinv 0
> >
> >
> > glmdir lh.PDDvsHC.volume.glmdir
> >
> >
> > IllCondOK 0
> >
> >
> > ReScaleX 1
> >
> >
> > DoFFx 0
> >
> >
> > ResidualFWHM 14.826153
> >
> >
> > SearchSpace 73852.172969
> >
> >
> > anattype surface
> >
> >
> >
> >
> > cd /Volumes/NIU20/volumetric_FS/glm
> >
> >
> > /Applications/freesurfer/bin/mri_glmfit-sim
> >
> >
> > --glmdir rh.PDDvsHC.volume.glmdir --cache 1.3 pos --cwp 999 --2spaces
> >
> >
> >
> > $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $
> >
> >
> > Mon Feb 18 15:52:07 GMT 2019
> >
> >
> > Darwin dyn3199-104.wlan.ic.ac.uk 14.5.0 Darwin Kernel Version 14.5.0:
> > Wed Jul 29 02:26:53 PDT 2015; root:xnu-2782.40.9~1/RELEASE_X86_64 x86_64
> >
> >
> > cengzhou
> >
> >
> > setenv SUBJECTS_DIR /Volumes/NIU20/volumetric_FS/glm
> >
> >
> > FREESURFER_HOME /Applications/freesurfer
> >
> >
> >
> > Original mri_glmfit command line:
> >
> >
> > cmdline mri_glmfit.bin --glmdir rh.PDDvsHC.volume.glmdir --y
> > rh.PDDvsHC.volume.10.mgh --fsgd FSGD/PDDvsHC.fsgd --C
> > Contrasts/lh-thickness-HC-PDD.mtx --surface fsaverage rh --eres-save
> >
> >
> >
> > DoSim = 0
> >
> >
> > UseCache = 1
> >
> >
> > DoPoll = 0
> >
> >
> > DoPBSubmit = 0
> >
> >
> > DoBackground = 0
> >
> >
> > DiagCluster = 0
> >
> >
> > gd2mtx = dods
> >
> >
> > fwhm = 14.506572
> >
> >
> > CSD
> > 
> /Applications/freesurfer/average/mult-comp-cor/fsaverage/rh/cortex/fwhm15/pos/th13/mc-z.csd
> >
> >
> > mri_surfcluster --in rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/sig.mgh
> > --mask rh.PDDvsHC.volu

Re: [Freesurfer] Fwd: segmentation error

2019-02-19 Thread Bruce Fischl

wow, that looks pretty bad. Can you send us the recon-all.log (or upload 
the entire subject and we will investigate)?
On Tue, 19 Feb 2019, mara alves 
wrote:




External Email - Use Caution

Hi there,

I ran the recon -all command in two samples, one of young participants and 
another of older
subjects.

The segmentation worked well for young participants, however it seems that for 
older participants
the white.pial segmentation it is being done incorrectly. I believe it is 
segmenting the gray matter
instead (please see the pics attached).

Best,
Mara

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Re: [Freesurfer] anat2dti error after dt_recon

2019-02-19 Thread Daniel Callow

External Email - Use Caution

Hi Douglas!

Thank you for the response. I figured out it was simply an issue with the
pathing to the register.dat file!

Thanks,
*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
*ddcc2...@gmail.com *
443-254-6298


On Tue, Feb 19, 2019 at 3:52 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> what do you get when you run
> ls -l /Volumes/DANIEL/dti_freesurf/dtrecon/AES139.Rest/register.dat
>
> On 2/19/19 8:44 AM, Daniel Davidson Callow wrote:
> >
> > External Email - Use Caution
> >
> > Hello,
> >
> > I ran a successful dt_recon and then wanted to use
> >
> > mri_vol2vol --mov $subj_dir/dtrecons/${subj}.${cond}/lowb.nii.gz
> > --targ $subj_dir/diffusion_recons/${subj}.${cond}/mri/aparc+aseg.mgz
> > --inv --interp nearest --o
> > $subj_dir/dtrecons/${subj}.${cond}/aparc+aseg2diff.nii.gz --reg
> > $subj_dir/dtrecon/${subj}.${cond}/register.dat --no-save-reg
> >
> >
> > to get the anatomical segmentations into diffusion space. However,
> > when running the above code I get the following error message?
> >
> >
> > echo subj =AES139 , cond =Rest
> >
> > subj =AES139 , cond =Rest
> >
> > set echo
> >
> > cd /Volumes/DANIEL/dti_freesurf
> >
> > mri_vol2vol --mov
> > /Volumes/DANIEL/dti_freesurf/dtrecons/AES139.Rest/lowb.nii.gz --targ
> >
> /Volumes/DANIEL/dti_freesurf/diffusion_recons/AES139.Rest/mri/aparc+aseg.mgz
>
> > --inv --interp nearest --o
> > /Volumes/DANIEL/dti_freesurf/dtrecons/AES139.Rest/aparc+aseg2diff.nii.gz
> > --reg /Volumes/DANIEL/dti_freesurf/dtrecon/AES139.Rest/register.dat
> > --no-save-reg
> >
> > regio_read_register(): No such file or directory
> >
> > Could not open
> > /Volumes/DANIEL/dti_freesurf/dtrecon/AES139.Rest/register.dat
> >
> >
> > Matrix from regfile:
> >
> > MatrixPrint: mat = NULL!
> >
> > No such file or directory
> >
> >
> > I have attached an example register.dat file in case that is the issue.
> >
> >
> > also the output for ls -l register.dat
> >
> > -rwxrwxrwx1 administratorstaff323 Feb 18 13:59 register.dat
> >
> >
> > Any advice with troubleshooting is greatly appreciated!
> >
> >
> > Best,
> >
> > *Daniel Callow*
> > /PhD Student, Neuroscience and Cognitive Science/
> > Exercise for Brain Health Lab
> > University of Maryland, College Park
> > dcal...@umd.edu 
> > 443-254-6298
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
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[Freesurfer] Issue posting to the listserve

2019-02-19 Thread Daniel Callow

External Email - Use Caution

Hello,

When trying to post to the freesurfer listserv with this account my emails
don't seem to go through. When using my university email dcal...@umd.edu it
works. Unfortunately, I don't get and can't respond to responses to emails
I submit from that email so I would like to fix the issue I am having with
posting to the listserv with my ddcc2...@gmail.com email address.

Thank you,
*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
*ddcc2...@gmail.com *
443-254-6298
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