Re: [Freesurfer] problems of testing freesurfer

[Danny Deng]

Hi Andrew,

I have followed your suggestion and the error pop up like this:

Xues-MacBook-Air:~ DannyDeng$ mkdir test_subjects
mkdir: test_subjects: File exists
Xues-MacBook-Air:~ DannyDeng$ export SUBJECTS_DIR=/path/to/test_subjects
Xues-MacBook-Air:~ DannyDeng$ cd${FREESURFER_HOME}/subjects/sample-001.nii.gz
-bash: cd/Applications/freesurfer/subjects/sample-001.nii.gz: Not a directory
Xues-MacBook-Air:~ DannyDeng$ cd${FREESURFER_HOME}/subjects
-bash: cd/Applications/freesurfer/subjects: Not a directory
Xues-MacBook-Air:~ DannyDeng$ cd ${FREESURFER_HOME}/subjects
Xues-MacBook-Air:subjects DannyDeng$ recon-all -i sample-001.nii.gz -s bert -all
ERROR: cannot find sample-001.nii.gz
Darwin Xues-MacBook-Air.local 16.7.0 Darwin Kernel Version 16.7.0: Thu Jun 15 
17:36:27 PDT 2017; root:xnu-3789.70.16~2/RELEASE_X86_64 x86_64

recon-all -s  exited with ERRORS at Wed Nov  8 16:50:37 HKT 2017

For more details, see the log file 
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Xues-MacBook-Air:subjects DannyDeng$ 

Sorry I am a beginner.

Best Regards,
Danny Deng

> On Nov 8, 2017, at 10:48 AM, Hoopes, Andrew  wrote:
> 
> recon-all -i sample-001.nii.gz -s bert -all
> 

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Re: [Freesurfer] Registration

[N Saf]

Hi Bruce

as you explain I did the registration somewhere else and now I have the
labels_gca in my subject space.
1. is it possible to somehow import this file in freesurfer and run the
rest of the analysis ?
2.my question in general is that : can I in anyway  do any correction for
aseg outputs during the analysis(similar to troubleshooting for
surface-base analysis) e.g. do some step with different method and then
import the result and use the rest steps in freesurfer??
3.Is there any difference between the subcortical segmentation results in
v.6  vs v5.3 (except the hippopotamus subfields segmentation which is
available in v.6 . Is the hole hippocampus volume result  different between
2 versions?)

I'm really appreciated for the help.

Best Regards,
Nazanin



On Mon, Oct 30, 2017 at 5:36 PM, Bruce Fischl 
wrote:

> Hi Nazanin
>
> the nonlinear registration is actually to our segmentation atlas (*.gca).
> I guess you could try using something else, but you should extract a mean
> intensity image from the gca as a target, not the MNI305. You can do this
> with:
>
> mri_convert -nth 0 .gca mean_gca.mgz
>
> FYI, this:
>
> mri_convert -nth 1 .gca labels_gca.mgz
>
> would give you the highest prior label at each spot (and 2 would give you
> the prior)
>
> cheers
> Bruce
>
>
>
>
> On Mon, 30 Oct 2017, N Saf wrote:
>
> Dear Experts,
>> In the volume-based stream, if I'm right the FreeSurfer does two
>> registration with MNI305 ,one affine and one
>> nonlinear , is it possible to perform the nonlinear registration
>> somewhere else and then use the result in
>> FreeSurfer and run the rest of the analysis ?
>>
>> thank's alot for your great support.
>>
>> BRG,
>> Nazanin
>>
>>
>>
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>
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> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
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> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
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[Freesurfer] freesurfer@nmr.mgh.harvard.edu

[aurelie ponz]

Dear Freesurfer users,

I have big issues performing recon-all into the freesurfer VirtualBox.
I dont get any error but no files are created except the 0001.mgz.
Here is what I get.

WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!

Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0
Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0
INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
Actual FREESURFER_HOME /usr/local/freesurfer
Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10
20:41:14 UTC 2012 i686 i686 i386 GNU/Linux
/usr/local/freesurfer/subjects/Groove_009

 mri_convert /media/sf_T1_Groove/Groove_009/Sujet_24_20161214_001_024_T1w.nii
/usr/local/freesurfer/subjects/Groove_009/mri/orig/001.mgz

mri_convert /media/sf_T1_Groove/Groove_009/Sujet_24_20161214_001_024_T1w.nii
/usr/local/freesurfer/subjects/Groove_009/mri/orig/001.mgz
INFO: using NIfTI-1 qform
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /media/sf_T1_Groove/Groove_009/Sujet_24_20161214_001_024_T1w
.nii...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0.0603182, -0.982945, 0.173726)
j_ras = (-0.125291, 0.16521, 0.978268)
k_ras = (0.990285, 0.0807736, 0.113189)
writing to /usr/local/freesurfer/subjects/Groove_009/mri/orig/001.mgz...

Could you please help me I read ;ost threads and tried ;any solutions but I
didnt found a solution,

Many thanks in advance,

Aurelie




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Re: [Freesurfer] QDEC

[Douglas Greve]

Do you have permission to read it? How was it created?


On 11/8/17 1:18 AM, Kinzel, Phillipp wrote:


Hi, I have problems loading project  files in QDEC.

I get the following error:

Loading data table /tmp/qdec_project_archive/qdec.table.dat...

ERROR: could not open /tmp/qdec_project_archive/qdec.table.dat

Error loading the project file.

I would be greatful for any advice.

Best, Philipp



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Re: [Freesurfer] freesurfer@nmr.mgh.harvard.edu

[Douglas Greve]

what is your command line? Please send the recon-all.log file


On 11/8/17 5:24 AM, aurelie ponz wrote:

Dear Freesurfer users,

I have big issues performing recon-all into the freesurfer VirtualBox.
I dont get any error but no files are created except the 0001.mgz.
Here is what I get.

WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!

Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0
Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0
INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
Actual FREESURFER_HOME /usr/local/freesurfer
Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 
20:41:14 UTC 2012 i686 i686 i386 GNU/Linux

/usr/local/freesurfer/subjects/Groove_009

 mri_convert 
/media/sf_T1_Groove/Groove_009/Sujet_24_20161214_001_024_T1w.nii 
/usr/local/freesurfer/subjects/Groove_009/mri/orig/001.mgz


mri_convert 
/media/sf_T1_Groove/Groove_009/Sujet_24_20161214_001_024_T1w.nii 
/usr/local/freesurfer/subjects/Groove_009/mri/orig/001.mgz

INFO: using NIfTI-1 qform
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from 
/media/sf_T1_Groove/Groove_009/Sujet_24_20161214_001_024_T1w.nii...

TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0.0603182, -0.982945, 0.173726)
j_ras = (-0.125291, 0.16521, 0.978268)
k_ras = (0.990285, 0.0807736, 0.113189)
writing to /usr/local/freesurfer/subjects/Groove_009/mri/orig/001.mgz...

Could you please help me I read ;ost threads and tried ;any solutions 
but I didnt found a solution,


Many thanks in advance,

Aurelie






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Re: [Freesurfer] Registration

[Bruce Fischl]

Hi Nazanin

1. The registration is only one step in how we do segmentation, so I 
wouldn't suggest just using it. If you can convert your registration to 
.m3z format and put it in the subjects transforms/talairach.m3z you could 
try running from there forward.


2. Yes, you can edit the aseg in freeview.

3. Yes, the segmentations have improved in V6

cheers
Bruce
On Wed, 8 Nov 2017, N Saf 
wrote:



Hi Bruce
as you explain I did the registration somewhere else and now I have the 
labels_gca in my subject
space.
1. is it possible to somehow import this file in freesurfer and run the rest of 
the analysis ? 
2.my question in general is that : can I in anyway  do any correction for aseg 
outputs during the
analysis(similar to troubleshooting for surface-base analysis) e.g. do some 
step with different
method and then import the result and use the rest steps in freesurfer??
3.Is there any difference between the subcortical segmentation results in v.6  
vs v5.3 (except the
hippopotamus subfields segmentation which is available in v.6 . Is the hole 
hippocampus volume
result  different between 2 versions?) 

I'm really appreciated for the help.

Best Regards,
Nazanin



On Mon, Oct 30, 2017 at 5:36 PM, Bruce Fischl  
wrote:
  Hi Nazanin

  the nonlinear registration is actually to our segmentation atlas (*.gca). 
I guess you
  could try using something else, but you should extract a mean intensity 
image from the
  gca as a target, not the MNI305. You can do this with:

  mri_convert -nth 0 .gca mean_gca.mgz

  FYI, this:

  mri_convert -nth 1 .gca labels_gca.mgz

  would give you the highest prior label at each spot (and 2 would give you 
the prior)

  cheers
  Bruce



  On Mon, 30 Oct 2017, N Saf wrote:

Dear Experts,
In the volume-based stream, if I'm right the FreeSurfer does two
registration with MNI305 ,one affine and one
nonlinear , is it possible to perform the nonlinear registration 
somewhere
else and then use the result in
FreeSurfer and run the rest of the analysis ? 

thank's alot for your great support.

BRG,
Nazanin



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Re: [Freesurfer] freesurfer@nmr.mgh.harvard.edu

[aurelie ponz]

Thank you Douglas for your quick response !
I used the *recon-all -i ' -subjid *

Since it wasnt working I tried *recon-all -autorecon1 -i '
-subjid * and it worked for *SOME* files (including the T1) but I
don't get the hl/rl.pial files.
Then I tried the *autorecon2* on the sa;e data and it does'nt work.
Here is the bug I got.

fsuser@xubuntu-VirtualBox:/media/sf_T1_Groove/Groove_010$ recon-all
-autorecon2 -i leo2014_19_anat01.nii -subjid Groove_010_2

WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!

Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0
Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0
INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
Actual FREESURFER_HOME /usr/local/freesurfer
Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10
20:41:14 UTC 2012 i686 i686 i386 GNU/Linux
/usr/local/freesurfer/subjects/Groove_010_2

 mri_convert /media/sf_T1_Groove/Groove_010/leo2014_19_anat01.nii
/usr/local/freesurfer/subjects/Groove_010_2/mri/orig/001.mgz

mri_convert /media/sf_T1_Groove/Groove_010/leo2014_19_anat01.nii
/usr/local/freesurfer/subjects/Groove_010_2/mri/orig/001.mgz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /media/sf_T1_Groove/Groove_010/leo2014_19_anat01.nii...
TR=945000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0, -1, 0)
j_ras = (0, -0, -1)
k_ras = (1, 0, 0)
writing to /usr/local/freesurfer/subjects/Groove_010_2/mri/orig/001.mgz...
#-
#@# EM Registration Wed Nov  8 11:42:54 EST 2017
/usr/local/freesurfer/subjects/Groove_010_2/mri

 mri_em_register -uns 3 -mask brainmask.mgz nu.mgz
/usr/local/freesurfer/average/RB_all_2008-03-26.gca
transforms/talairach.lta

aligning to atlas containing skull, setting unknown_nbr_spacing = 3
using MR volume brainmask.mgz to mask input volume...
reading 1 input volumes...
logging results to talairach.log
reading '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'...
average std = 6.9   using min determinant for regularization = 4.7
0 singular and 1812 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
mghRead(/usr/local/freesurfer/subjects/Groove_010_2/mri/nu.mgz, -1): could
not open file
mri_em_register: could not open input volume nu.mgz.

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 Groove_010_2 exited with ERRORS at Wed Nov  8 11:42:56 EST 2017

For more details, see the log file /usr/local/freesurfer/
subjects/Groove_010_2/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.
edu/fswiki/BugReporting


THANK YOU very much in advance
Aurelie





On Wed, Nov 8, 2017 at 9:52 AM, Douglas Greve 
wrote:

> what is your command line? Please send the recon-all.log file
>
> On 11/8/17 5:24 AM, aurelie ponz wrote:
>
> Dear Freesurfer users,
>
> I have big issues performing recon-all into the freesurfer VirtualBox.
> I dont get any error but no files are created except the 0001.mgz.
> Here is what I get.
>
> WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!
>
> Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0
> Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0
> INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
> Actual FREESURFER_HOME /usr/local/freesurfer
> Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10
> 20:41:14 UTC 2012 i686 i686 i386 GNU/Linux
> /usr/local/freesurfer/subjects/Groove_009
>
>  mri_convert /media/sf_T1_Groove/Groove_009/Sujet_24_20161214_001_024_T1w.nii
> /usr/local/freesurfer/subjects/Groove_009/mri/orig/001.mgz
>
> mri_convert /media/sf_T1_Groove/Groove_009/Sujet_24_20161214_001_024_T1w.nii
> /usr/local/freesurfer/subjects/Groove_009/mri/orig/001.mgz
> INFO: using NIfTI-1 qform
> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> reading from /media/sf_T1_Groove/Groove_009/Sujet_24_20161214_001_024_T1w
> .nii...
> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (0.0603182, -0.982945, 0.173726)
> j_ras = (-0.125291, 0.16521, 0.978268)
> k_ras = (0.990285, 0.0807736, 0.113189)
> writing to /usr/local/freesurfer/subjects/Groove_009/mri/orig/001.mgz...
>
> Could you please help me I read ;ost threads and tried ;any solutions but
> I didnt found a solution,
>
> Many thanks in advance,
>
> Aurelie
>
>
>
> 
>
>
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> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Com

[Freesurfer] preproc-sess with symbolic links

[Tuominen, Lauri Johannes]

Hi all, 
I’m trying to run preproc-sess using symbolic links in my SUBJECTS_DIR but the 
program exists with error message: could not find session . 

Symbolic links work fine when I run recon-all for instance. 

Suggestion for a fix would be greatly appreaciated. 

Cheers!
Laurio
 

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Re: [Freesurfer] freesurfer@nmr.mgh.harvard.edu

[Douglas Greve]

On the first one, you have to add -all, otherwise it won't do anything


On 11/8/17 11:51 AM, aurelie ponz wrote:

Thank you Douglas for your quick response !
I used the *recon-all -i ' -subjid *

Since it wasnt working I tried *recon-all -autorecon1 -i ' 
-subjid * and it worked for _SOME_ files (including the T1) 
but I don't get the hl/rl.pial files.

Then I tried the *autorecon2* on the sa;e data and it does'nt work.
Here is the bug I got.

fsuser@xubuntu-VirtualBox:/media/sf_T1_Groove/Groove_010$ recon-all 
-autorecon2 -i leo2014_19_anat01.nii -subjid Groove_010_2


WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!

Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0
Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0
INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
Actual FREESURFER_HOME /usr/local/freesurfer
Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 
20:41:14 UTC 2012 i686 i686 i386 GNU/Linux

/usr/local/freesurfer/subjects/Groove_010_2

 mri_convert /media/sf_T1_Groove/Groove_010/leo2014_19_anat01.nii 
/usr/local/freesurfer/subjects/Groove_010_2/mri/orig/001.mgz


mri_convert /media/sf_T1_Groove/Groove_010/leo2014_19_anat01.nii 
/usr/local/freesurfer/subjects/Groove_010_2/mri/orig/001.mgz

$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /media/sf_T1_Groove/Groove_010/leo2014_19_anat01.nii...
TR=945000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0, -1, 0)
j_ras = (0, -0, -1)
k_ras = (1, 0, 0)
writing to /usr/local/freesurfer/subjects/Groove_010_2/mri/orig/001.mgz...
#-
#@# EM Registration Wed Nov  8 11:42:54 EST 2017
/usr/local/freesurfer/subjects/Groove_010_2/mri

 mri_em_register -uns 3 -mask brainmask.mgz nu.mgz 
/usr/local/freesurfer/average/RB_all_2008-03-26.gca 
transforms/talairach.lta


aligning to atlas containing skull, setting unknown_nbr_spacing = 3
using MR volume brainmask.mgz to mask input volume...
reading 1 input volumes...
logging results to talairach.log
reading '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'...
average std = 6.9   using min determinant for regularization = 4.7
0 singular and 1812 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
mghRead(/usr/local/freesurfer/subjects/Groove_010_2/mri/nu.mgz, -1): 
could not open file

mri_em_register: could not open input volume nu.mgz.

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 Groove_010_2 exited with ERRORS at Wed Nov  8 11:42:56 
EST 2017


For more details, see the log file 
/usr/local/freesurfer/subjects/Groove_010_2/scripts/recon-all.log
To report a problem, see 
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting 




THANK YOU very much in advance
Aurelie





On Wed, Nov 8, 2017 at 9:52 AM, Douglas Greve 
mailto:gr...@nmr.mgh.harvard.edu>> wrote:


what is your command line? Please send the recon-all.log file


On 11/8/17 5:24 AM, aurelie ponz wrote:

Dear Freesurfer users,

I have big issues performing recon-all into the freesurfer
VirtualBox.
I dont get any error but no files are created except the 0001.mgz.
Here is what I get.

WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!

Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0
Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0
INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
Actual FREESURFER_HOME /usr/local/freesurfer
Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr
10 20:41:14 UTC 2012 i686 i686 i386 GNU/Linux
/usr/local/freesurfer/subjects/Groove_009

 mri_convert
/media/sf_T1_Groove/Groove_009/Sujet_24_20161214_001_024_T1w.nii
/usr/local/freesurfer/subjects/Groove_009/mri/orig/001.mgz

mri_convert
/media/sf_T1_Groove/Groove_009/Sujet_24_20161214_001_024_T1w.nii
/usr/local/freesurfer/subjects/Groove_009/mri/orig/001.mgz
INFO: using NIfTI-1 qform
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from
/media/sf_T1_Groove/Groove_009/Sujet_24_20161214_001_024_T1w.nii...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0.0603182, -0.982945, 0.173726)
j_ras = (-0.125291, 0.16521, 0.978268)
k_ras = (0.990285, 0.0807736, 0.113189)
writing to
/usr/local/freesurfer/subjects/Groove_009/mri/orig/001.mgz...

Could you please help me I read ;ost threads and tried ;any
solutions but I didnt found a solution,

Many thanks in advance,

Aurelie






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Re: [Freesurfer] problems of testing freesurfer

[Hoopes, Andrew]

When setting SUBJECTS_DIR, you have to specify the actual path to the 
“test_subjects” directory that you created. "/path/to/test_subjects" isn’t a 
real path on your computer. In your case, the path might be something like 
"/Users/DannyDeng/test_subjects”

In recon-all, the -i flag is used to designate the path to an input volume. In 
example 1, sample-001.mgz is converted to sample-001.nii.gz . My guess is you 
haven’t done this step, because freesurfer “cannot find sample-001.nii.gz”. Try 
using “-i  sample-001.mgz” instead, as this file is included in the freesurfer 
distribution under $FREESURFER_HOME/subjects

Andrew

On Nov 8, 2017, at 3:51 AM, Danny Deng 
mailto:dannytang...@gmail.com>> wrote:

Hi Andrew,

I have followed your suggestion and the error pop up like this:

Xues-MacBook-Air:~ DannyDeng$ mkdir test_subjects
mkdir: test_subjects: File exists
Xues-MacBook-Air:~ DannyDeng$ export SUBJECTS_DIR=/path/to/test_subjects
Xues-MacBook-Air:~ DannyDeng$ cd${FREESURFER_HOME}/subjects/sample-001.nii.gz
-bash: cd/Applications/freesurfer/subjects/sample-001.nii.gz: Not a directory
Xues-MacBook-Air:~ DannyDeng$ cd${FREESURFER_HOME}/subjects
-bash: cd/Applications/freesurfer/subjects: Not a directory
Xues-MacBook-Air:~ DannyDeng$ cd ${FREESURFER_HOME}/subjects
Xues-MacBook-Air:subjects DannyDeng$ recon-all -i sample-001.nii.gz -s bert -all
ERROR: cannot find sample-001.nii.gz
Darwin Xues-MacBook-Air.local 16.7.0 Darwin Kernel Version 16.7.0: Thu Jun 15 
17:36:27 PDT 2017; root:xnu-3789.70.16~2/RELEASE_X86_64 x86_64

recon-all -s  exited with ERRORS at Wed Nov  8 16:50:37 HKT 2017

For more details, see the log file
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Xues-MacBook-Air:subjects DannyDeng$

Sorry I am a beginner.

Best Regards,
Danny Deng

On Nov 8, 2017, at 10:48 AM, Hoopes, Andrew 
mailto:ahoo...@mgh.harvard.edu>> wrote:

recon-all -i sample-001.nii.gz -s bert -all


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[Freesurfer] Merge Images

[Cleudiana Lima]

Could you please help me with my problem? I have a Nifti image with
segmented white matter hyperintensity and a wparc image made at freesurfer.
I want to know how I can know the names of the Nifti image areas, using a
wparc as a location map.

So, the problem is:  identify all areas.

I wanted an automatic process that would carry out this evaluation
generating volumetric data and the names of the regions of intersection
between these two images.

-- 


Cleudiana Lima
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[Freesurfer] longitudinal base error. (not a netCDF file)

[miracle ozzoude]

Hello FreeSurfer,

While running base step of the longitudinal pipeline, i got the following
error (please see the rec-all.log file for more details). How do i solve
this problem? Thank you

Best,
Paul


recon-all.log
Description: Binary data
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[Freesurfer] Creating cached versions of Xhemi registrations

[Mehta, Chintan]

Dear FreeSurfer Users,

I'm using FreeSurfer version 6.0. I've processing subjects with recon-all and 
performed surface-based interhemispheric registration (via Xhemi at 
https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi).

I want to run a GLM on the subjects Area and Thickness from the differences 
(Left minus Right). When stacking subjects asymmetry maps, I wanted to use a 
"--cache-only".

The post at 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg27657.html seems 
to imply this requires running
> recon-all -qcache -measure area -target  fsaverage_sym -fwhm 10 -no-isrunning 
> -s subjid -hemi lh
for area at FWHM = 10.

This would create files with the left hemisphere area registered to 
fsaverage_sym at smoothing FWHM = 10:
$subjid/surf/lh.area.fwhm10.fsaverage_sym.mgh

However, how do I do this also for the xhemi registration? I.e. create a file 
like $subjid/xhemi/surf/lh.area.fwhm10.fsaverage_sym.mgh


Then, if I do this, can I stack the subjects using something like:
> mris_preproc --target fsaverage_sym --hemi lh
  --xhemi --paired-diff \
  --srcsurfreg fsaverage_sym.sphere.reg \
  --cache-in area.fwhm10.fsaverage_sym \
  --out lh.lh-rh.area.sm10.mgh \
  --s subj1 --s subj2 ...

Thank you.

Best,
Chintan




mris_preproc --target fsaverage_sym --hemi lh
  --xhemi --paired-diff \

  --srcsurfreg fsaverage_sym.sphere.reg \
  --meas thickness \
  --out lh.lh-rh.thickness.sm00.mgh \
  --s subj1 --s subj2 ...



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Re: [Freesurfer] QDEC

[Kinzel, Phillipp]

Hi Douglas, thank you for your quick response. Yes, I have permission to read 
and write for the file. I modified the permission to be able to execute the 
file as well, but that didn´t change anything. I created the file through the 
qdec- GUI and didn´t have any problems while running the GLM.

Von:  im Auftrag von Douglas Greve 

Antworten an: Freesurfer support list 
Datum: Mittwoch, 8. November 2017 um 09:51
An: "freesurfer@nmr.mgh.harvard.edu" 
Betreff: Re: [Freesurfer] QDEC


Do you have permission to read it? How was it created?

On 11/8/17 1:18 AM, Kinzel, Phillipp wrote:
Hi, I have problems loading project  files in QDEC.

I get the following error:

Loading data table /tmp/qdec_project_archive/qdec.table.dat...
ERROR: could not open /tmp/qdec_project_archive/qdec.table.dat
Error loading the project file.

I would be greatful for any advice.

Best, Philipp






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Re: [Freesurfer] Merge Images

[Bruce Fischl]

HI Cleudiana

the value of the voxels in the nifti image should be indices that you can 
use to lookup names in


$FREESURFER_HOME/FreeSurferColorLUT.txt

is that what you want?

cheers
Bruce
On Wed, 8 Nov 2017, Cleudiana Lima 
wrote:




Could you please help me with my problem? I have a Nifti image with segmented 
white matter
hyperintensity and a wparc image made at freesurfer. I want to know how I can 
know the names of the
Nifti image areas, using a wparc as a location map. 

So, the problem is:  identify all areas.

I wanted an automatic process that would carry out this evaluation generating 
volumetric data and
the names of the regions of intersection between these two images.

--
 
 
Cleudiana Lima

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[Freesurfer] Repeated amygdala dev7-segmentation volumes do not correspond

[Reetta-Liina Armio]

Hi!

I have done twice the analysis of amygdala segmentation (dev 7 version) with 
exactly same way. The volumes do not correspond each other and there is 
approximately 2mm3 difference in volumes randomly in either direction.

Is this normal or is it something to do with the dev 7 version? Should I be 
worried?

Thank you!

Best, Reetta-Liina Armio



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Re: [Freesurfer] mris_preproc srcsurfreg Freesurfer 6.0

[Mehta, Chintan]

Dear Doug,
Are there reasons why registering to my_subject_average (template defined from, 
say, average in a cross-sectional sample) can be better than registering to 
fsaverage?
Thank you.
Best,
Chintan
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[Freesurfer] functional to anatomical registration

[David Beeler]

Hi freesurfer people,

I'm trying to understand preprocessing a little better, especially registration 
of functional data to anatomical space. I am currently running everything in 
the volume, doing motion correction per-run and then pooling all the runs in 
the session together for the first level analysis.

As far as I can tell, running preproc-sess with -per-run takes the raw 
functional data (f.nii.gz), pulls out the middle timepoint and calls it 
template.nii.gz, bbregisters func to anat and creates a register.dof6.lta file 
in each of the functional run folders, transforms the aparc+aseg from the 
subject's mri folder and binarizes it into a brainmask (brain.nii.gz), and runs 
mc-afni using f.nii.gz as the input vol and template.nii.gz as the template vol 
to create the motion corrected volume (fmcpr.nii.gz). Is this correct?

Then when I run selxavg3-sess it somehow mri_converts an intermediary motion 
corrected volume from the mc-afni command above (eg 
/tmp.mc-afni2.20097/outvol.nii.gz) into an fmc.nii.gz file in each run 
folder. Are these fmc.nii.gz's supposed to be coregistered between runs? (i.e. 
if the subject moved a bunch between two of the runs, would those two volumes 
be aligned at all?). How do these files work?

At the end I have an analysis directory with my betas, sigmaps, etc. What 
functional volume is everything registered to? Is the transform between this 
functional volume and anatomical space the register.dof6.lta file located in 
the session directory?

Thanks for bearing with me!
-David


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Re: [Freesurfer] functional to anatomical registration

[Douglas Greve]

On 11/8/17 5:57 PM, David Beeler wrote:

Hi freesurfer people,

I'm trying to understand preprocessing a little better, especially 
registration of functional data to anatomical space. I am currently 
running everything in the volume, doing motion correction per-run and 
then pooling all the runs in the session together for the first level 
analysis.


As far as I can tell, running preproc-sess with -per-run takes the raw 
functional data (f.nii.gz), pulls out the middle timepoint and calls 
it template.nii.gz, bbregisters func to anat and creates a 
register.dof6.lta file in each of the functional run folders, 
transforms the aparc+aseg from the subject's mri folder and binarizes 
it into a brainmask (brain.nii.gz), and runs mc-afni using f.nii.gz as 
the input vol and template.nii.gz as the template vol to create the 
motion corrected volume (fmcpr.nii.gz). Is this correct?

yes


Then when I run selxavg3-sess it somehow mri_converts an intermediary 
motion corrected volume from the mc-afni command above (eg 
/tmp.mc-afni2.20097/outvol.nii.gz) into an fmc.nii.gz file in 
each run folder. Are these fmc.nii.gz's supposed to be coregistered 
between runs? (i.e. if the subject moved a bunch between two of the 
runs, would those two volumes be aligned at all?). How do these files 
work?
Not with -per-run. per-run was designed with the idea that you would be 
resampling to some common space (eg, surface or mni305 or cvs), and then 
running sexlavg3-sess on that data. If you want all the fmc.nii.gz to be 
in the same space, then use -per-session.


At the end I have an analysis directory with my betas, sigmaps, etc. 
What functional volume is everything registered to? Is the transform 
between this functional volume and anatomical space the 
register.dof6.lta file located in the session directory?


Thanks for bearing with me!
-David




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[Freesurfer] Postdoctoral Research Associate in neuroimaging/data science

[Dayan, Eran]

A Postdoctoral Research Associate position is immediately open to work with the 
Network Neuroscience lab 
(dayanlab.web.unc.edu)
 at the Biomedical Research Imaging Center, University of North Carolina at 
Chapel Hill. The position is open to accomplished and highly motivated 
candidates, with an interest in neuroimaging and clinical neuroscience. The lab 
focuses on fundamental questions relating to brain network organization in 
health and disease, while aiming to develop methods and tools that could 
eventually be used in the clinic. The Postdoctoral Research Associate will 
develop and test a dimensional analysis framework for neurological dysfunction, 
using rich existing multimodal neuroimaging datasets obtained from patients and 
age-matched controls. Ample training and career development opportunities will 
be provided, as well as opportunities to collaborate with other groups at UNC.

Ph.D. or an MD/Ph.D. in Neuroscience, Computer Science, Biomedical Engineering, 
Physics, Psychology or other related fields is required. Excellent quantitative 
background, relevant programming experience (MATLAB, Python or R), experience 
analyzing functional and/or structural MRI data and a track record of 
first-author publications in peer-reviewed journals are required. Experience in 
machine learning (particularly deep learning) would be advantageous.
To apply, please visit https://unc.peopleadmin.com/postings/107413 and click 
the Apply for this Job link/button. For informal inquiries about the position, 
please email Dr. Eran Dayan at: eran_da...@med.unc.edu

The University of North Carolina at Chapel Hill is an equal opportunity and 
affirmative action employer. All qualified applicants will receive 
consideration for employment without regard to age, color, disability, gender, 
gender expression, gender identity, genetic information, race, national origin


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Re: [Freesurfer] mris_pmake

[Hyungjun Kim]

Dear Surfer & Rudolph,

Hi,

I tried to run mris_pmake, but only got this message:

I'm sorry, but an error condition has occurred.
While I was checking on the options file,
I couldn't access the options file. Does it exist?

How can I use mris_pmake?

I'm working with Vitaly Napadow, and I would like to measure the
distance between peak activated voxels on somatotopic stimulation.

(I'm running Freesurfer 5.3 stable version on CentOS 6.7 (64 bit machine))

Thanks in advance!

Hyungjun Kim

Senior Researcher

Korea Institute of Oriental Medicine
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Re: [Freesurfer] Local gyrification index - vertex-wise analysis values

[Buse Merve Ürgen]

Thank you so much! Can I also learn whether running vertex-wise analysis 
without GLM analysis in Qdec is possible or not? As I said, I will compare a 
single patient with a group of healthy controls, so GLM would not work. What 
would you suggest for this? Is it possible to extract lGI values from surface 
data?

Thank you for your help,
Buse

—

Douglas N Greve  şunları yazdı (7 Kas 2017 21:12):

> Intensity Mean will be the mean value of the input (lGI) averaged over 
> the ROI.
> 
> STD, Max, Min, and Range are the intensity stddev maximimum mininum 
> andrange=max-min over the ROI
> 
> 
>> On 11/07/2017 12:57 PM, Buse Merve Ürgen wrote:
>> Dear Freesurfers,
>> 
>> I have two questions:
>> 
>> 1) In the last stage of the recon-all -s  -localGI analysis, 
>> local gyrification index values are calculated at each pial vertices. 
>> Is there any way (command?) to extract /vertex-wise local gyrification 
>> index values/ (of individual subjects) /before running GLM analysis in 
>> Qdec/? GLM analysis is not suitable for my study (single-case), so I 
>> need to extract values for each subject and use them for my own 
>> statistical analysis.
>> 
>> 2) As far as I know we can extract /parcel-wise lGI/ values using the 
>> following command:
>> 
>> mri_segstats --annot /subjID/ lh aparc \
>> 
>>   --i $SUBJECTS_DIR//subjID//surf/lh.pial_lgi \
>> 
>>   --sum lh.aparc.pial_lgi.stats
>> 
>> 
>> Running this command provides "Intensity Mean, Intensity STD, 
>> Intensity Max, Intensity Min, Intensity Range" values for each 
>> parcellated area. Can you explain these values and what they mean?
>> 
>> 
>> Thanks,
>> 
>> -Buse
>> 
>> 
>> 
>> 
>> On 5 November 2017 at 19:54, Buse Merve Ürgen > > wrote:
>> 
>>Dear Freesurfer developers,
>> 
>>I would like to run Local Gyrification Index analysis for a group
>>of healthy controls and a single patient. After running recon-all
>>-s  -localGI command, we get lh.pial_lgi and rh.pial_lgi
>>surf files. In the last stage of this analysis, local gyrification
>>index values are calculated at each pial vertices.
>> 
>>In the wiki, it is said that the next process should be done in
>>qdec, but since I have only one patient, GLM analysis would not be
>>suitable. Thus, I would like to get the LGI values of each subject
>>as e.g. text files (like stats files for curvature, thickness, gm
>>volume), and use them for my own analysis (not in qdec). I know
>>that we can get parcel-wise anaysis values using this command:
>>mri_segstats --annot CASE lh aparc \
>> 
>>  --i $SUBJECTS_DIR/CASE/surf/lh.pial_lgi \
>> 
>>  --sum lh.aparc.pial_lgi.stats
>> 
>>But I would like to use vertex-wise analysis values for my won
>>analysis. Is it possible? Can I learn the command I need to use to
>>get these values for each subject?
>> 
>>Thank you,
>>Buse
>> 
>>-- 
>> 
>>Buse
>> 
>>​ Urgen
>> 
>> 
>> 
>> 
>> -- 
>> 
>> Buse M. Ürgen
>> 
>> Ph.D. Candidate Neuroscience Graduate Program National Magnetic 
>> Resonance Research Center (UMRAM) & Aysel Sabuncu Brain Research 
>> Center Bilkent University Ankara, 06800 Turkey
>> 
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> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
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