Re: [Freesurfer] Error using selexavg3-sess

[Morenikeji Adebayo]

Just following up on this - thanks!

> On Sep 29, 2015, at 1:29 PM, Morenikeji Adebayo  
> wrote:
> 
> Hi there,
> 
> I’m running into difficulty executing the “selexavg3-sess” command for a few 
> participants. For example, when I run the command:
> 
> foreach c(lh rh mni305)
> selxavg3-sess -analysis analysis_encoding_stimXmem.$c -s nmasa_045_130621 -d 
> . -no-preproc
> end
> 
> 
> I get the following error:
> 
> 
> Error using svd
> Input to SVD must not contain NaN or Inf.
> 
> Error in cond (line 36)
> s = svd(A);
> 
> Error in fast_selxavg3 (line 279)
>   XCond = cond(XtX);
> 
> Any help on this error would be much appreciated!
> 
> Thanks,
> Keji
> 
> ---
> Morenikeji Adebayo
> Clinical Research Coordinator
> Department of Psychiatric Neuroscience
> Massachusetts General Hospital
> (p) 617.643.6347
> k...@nmr.mgh.harvard.edu 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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---
Morenikeji Adebayo
Clinical Research Coordinator
Department of Psychiatric Neuroscience
Massachusetts General Hospital
(p) 617.643.6347
k...@nmr.mgh.harvard.edu

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[Freesurfer] Fwd: Re: PVE correction tool within the V 6 beta

[Mohamed Ali Bahri]

 Forwarded Message 
Subject:Re: [Freesurfer] PVE correction tool within the V 6 beta
Date:   Thu, 1 Oct 2015 17:08:07 +0200 (CEST)
From:   m.ba...@ulg.ac.be
To: Freesurfer support list 



Dear Greve,

Thank you for your answer. Steps 1 and 2 are ok but in step 3 there are some 
unclear options (e.g. --mgx .01)
Could you please explain which method is used for the pve correction and how 
can I obtain the 4D-pve-corrected images? Is it possible to extract the TACS of 
all regions?

Many thanks for your help,

Best,

Mohamed

- Mail original -
De: "Douglas Greve" 
À: freesurfer@nmr.mgh.harvard.edu
Envoyé: Lundi 28 Septembre 2015 17:49:49
Objet: Re: [Freesurfer] PVE correction tool within the V 6 beta

I'm still putting all the documentation together, but you can start with the 
instructions below. They are assuming you will use kinetic modeling. If you 
have a static scan, #1 and #2 are still the same, but #3 changes and #4 and #5 
not needed. Let me know and I can give you further instructions.
doug


1. To start, run

gtmseg --s subject

This will take a couple of hours and produces some files needed for GTM PVC 
(which is used for GTM, MG, RBV).

2. You'd then register the PET to the anatomical with bbregister (with --t2 
weighting). Make sure to save the output as an LTA (--lta). I usually use the 
mean TAC as the input. You can do this in parallel with #1.

3. You'd then run mri_gtmpvc, something like

mri_gtmpvc --i tac.nii.gz --psf PSF  --auto-mask PSF+2 .01 --seg gtmseg.mgz 
--reg reg.lta --default-seg-merge --mgx .01 --o gtmpvc.output --km-hb 11 12 13 
50 51 52 --km-ref 8 47 --no-rescale

PSF is the point-spread FWHM of the scanner; reg.lta is the registration from 
#2.  --km-hb specifies the highbinding region for MRTM2. --km-ref specifies the 
reference region.  --mgx specifies to output a muller-gartner map (not 
necessary for GTM ROI analysis).

4. For the GTM (ROI) MRTM1 KM analysis, you would then run

  mri_glmfit --y km.hb.tac.nii.gz --mrtm1 km.ref.tac.dat time.dat --o mrtm1 
--no-est-fwhm --nii.gz

where time.dat is a text file withe acquisition time of each time point in the 
tac.

5. For the MRTM2 analysis

set k2p = `cat mrtm1/k2prime.dat`
mri_glmfit --y km.hb.tac.nii.gz --mrtm2 km.ref.tac.dat time.dat $k2p --o mrtm1 
--no-est-fwhm --nii.gz

If you want to run a voxel-wise analysis, then you can use the mgx
volume as input (--y). Probably you'll want to sample this to the
surface using mri_vol2surf and the registration file aux/anat2pet.lta,
then smooth on the surface



On 9/28/15 11:38 AM, Mohamed Ali Bahri wrote:

Dear Expert,

Are there any explanation (steps to follow) about the use of FreeSurfer
(version 6 beta) to correct for the partial volume effect (PET dynamic
data)?

Many thanks in advance,

Best,

Mohamed



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Re: [Freesurfer] warping surface label to volume space

[Jacobs H (NP)]

Hi Doug,

Thanks for checking the data!
I just removed the output volume, ran the command again and got the same
weird output.
Since it worked for you, I tried it again… no change.
However, then I noticed that the mri_vol2label uses the SUBJECTS_DIR path
and this was not set to this folder (I was trying some things out in a
temporary folder). So, probably, it was using data from the subject in the
original SUBJECTS_DIR folder? I changed that and the output looks
beautiful now! It is kind of weird, as the original SUBJECTS_DIR was done
in the same version.

But it is working beautifully now!!! Thank you so much for your help!
Best
Heidi



On 02/10/15 20:57, "Douglas N Greve"  wrote:

>I'm at a loss here. I run the exact same command with the same version.
>I get the same terminal output, but my output volume looks ok. The only
>thing I can think of is that there is an old version that output volume
>that is not getting overwritten. Can you name the output file
>differently and make sure that it does not exist prior to running the
>command?
>
>On 09/30/2015 04:37 PM, Jacobs H (NP) wrote:
>> Hi Doug,
>>
>> Just as a reminder: I uploaded the data yesterday.
>>
>> Best
>> Heidi
>>
>> From: Douglas Greve > >
>> Reply-To: Freesurfer support list > >
>> Date: Tuesday 29 September 2015 17:01
>> To: "freesurfer@nmr.mgh.harvard.edu
>> "
>> mailto:freesurfer@nmr.mgh.harvard.edu>>
>> Subject: Re: [Freesurfer] warping surface label to volume space
>>
>> filedrop2 url at the end of this email
>>
>> On 9/29/15 10:34 AM, Jacobs H (NP) wrote:
>>> Sure, where should I upload it to?
>>> Thanks!
>>> Heidi
>>>
>>> From: Douglas Greve >> >
>>> Reply-To: Freesurfer support list >> >
>>> Date: Tuesday 29 September 2015 16:28
>>> To: "freesurfer@nmr.mgh.harvard.edu
>>> "
>>> >>>
>>> Subject: Re: [Freesurfer] warping surface label to volume space
>>>
>>> Can you upload the subject so I can look at it?
>>>
>>> On 9/29/15 9:05 AM, Jacobs H (NP) wrote:
 Hi Doug,

 The label looks actually ok and the surface as well. I attached the
images to this email, Not sure where it went wrong?

 Best
 Heidi

 
 Van:freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] namens Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
 Verzonden: maandag 28 september 2015 23:58
 Aan:freesurfer@nmr.mgh.harvard.edu
 Onderwerp: Re: [Freesurfer] warping surface label to volume space

 Something is definitely going wrong. Can you load the label as well
and
 verify that the label itself looks ok?

 On 09/28/2015 05:32 PM, Jacobs H (NP) wrote:
> Yes, here it is!
> Thanks! Heidi
>
>
>
> Yes, here it is!
> Thanks! Heidi
>
>
> image1.png
>
>
>
> ATT1.txt
>
>
>
>> Op 28 sep. 2015 om 17:26 heeft Douglas N
>>Greve   het volgende geschreven:
>>
>> Can you send a picture?
>>
>>> On 09/28/2015 05:08 PM, Jacobs H (NP) wrote:
>>> Dear Doug,
>>>
>>> By looking at it in Freeview. Anatomically, I would expect that
>>>the entorhinal cortex would not be localized so laterally? And some
>>>voxels are not in the temporal lobe.
>>>
>>> Best
>>> Heidi
>>>
>>> 
>>> Van:freesurfer-boun...@nmr.mgh.harvard.edu
>>>[freesurfer-boun...@nmr.mgh.harvard.edu] namens Douglas N Greve
>>>[gr...@nmr.mgh.harvard.edu]
>>> Verzonden: maandag 28 september 2015 23:00
>>> Aan:freesurfer@nmr.mgh.harvard.edu
>>> Onderwerp: Re: [Freesurfer] warping surface label to volume space
>>>
>>> how are you determining that it is not in the right place? When I
>>>run
>>> this it works.
>>>
 On 09/28/2015 04:54 PM, Jacobs H (NP) wrote:
 Hi,

 Bringing this to the FS list:
 I am trying to warp the entorhinal cortex label (ex vivo) to
volume
 space, so that I can see and use the full ROI. Using the command
 stated below doesn’t seem to work, as it is not in the right
location
 of the subject’s brain. Any thoughts?

 I used this command:
 mri_label2vol --label S_3RSPPP/label/lh.entorhinal_exvivo.label
 --regheader $SUBJECTS_DIR/S_3RSPPP/mri/orig.mgz --o
 lh.entorhinal_exvivo_vol.mgz --fill-ribbon --subject S_3RSPPP
--hemi l

 This was the output on the terminal:
 subject S_3RSPPP --hemi lh
 INFO: subject not needed, igorning.
 Number of labels: 1
 S_3RSPPP/label/lh.entorhinal_exvivo.label
 Annot File:  (null)
>>>

Re: [Freesurfer] mris_surf2vol

[Bruce Fischl]

not really - that's the price you pay for voxelizing. I guess you could 
thicken it a bit or fill the ribbon and do some type of morphological 
erosion

On Fri, 2 Oct 2015, Kevin Aquino wrote:


Ah sorry for not being clear,
Basically I would like the output from mris_surf2vol with the mask option to
be less speckled. 

For example, in the image attached:
http://www.physics.usyd.edu.au/~aquino/example_mri_surf2vol.png

there are some voxels missing. Is there an option to fill these voxels?


Cheers,


Dr Kevin Aquino
Research fellow,
Sir Peter Mansfield Magnetic Resonance Center, The University of
Nottingham. 

Honorary Research Fellow
School of Physics, Faculty of Science, University of Sydney

E kevin.aqu...@nottingham.ac.uk, aqu...@physics.usyd.edu.au | W
www.physics.usyd.edu.au/~aquino/

--

The brain is a wonderful organ. It starts working the moment you get up and
does not stop until you get into the office.
-
Robert Frost

CRICOS 00026A
This email plus any attachments to it are confidential. Any unauthorised use
is strictly prohibited. If you receive this email in error, please delete it
and any attachments.

Please think of our environment and only print this e-mail if necessary.


On Fri, Oct 2, 2015 at 1:42 PM, Bruce Fischl 
wrote:
  Hi Kevin

  I'm not clear on what you need. Would mri_surf2vol --fillribbon
  do what you want? I don't really know what else "voxelize" means

  cheers
  Bruce

  On Fri, 2 Oct 2015, Kevin Aquino wrote:

Hi all,
I am trying to "voxelize" the cortical surfaces
generated in freesurfer and
I am a little stuck.

I have been using mris_surf2vol with the --mask
option however this
generates a very speckled representation of the
cortical surface on the
voxels. What I would prefer would be the level sets
of the cortical surface
interpolated onto voxels, even if they are at a
different resolution that
could be enough. Is this possible with any of the
available commands?

I also went down the route of mris_volmask however,
this generates the
cortical ribbon, which is something that I don't
need.

Cheers,


Dr Kevin Aquino
Research fellow,
Sir Peter Mansfield Magnetic Imaging Center,
School of Physics & astronomy, The University of
Nottingham. 

Honorary Research Fellow
School of Physics, Faculty of Science, University of
Sydney.

E
kevin.aqu...@nottingham.ac.uk, aqu...@physics.usyd.edu.au
| W
www.physics.usyd.edu.au/~aquino/

--

The brain is a wonderful organ. It starts working
the moment you get up and
does not stop until you get into the office.
-
Robert Frost

CRICOS 00026A
This email plus any attachments to it are
confidential. Any unauthorised use
is strictly prohibited. If you receive this email in
error, please delete it
and any attachments.

Please think of our environment and only print this
e-mail if necessary.



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Re: [Freesurfer] fsaverage error with recon-all

[Douglas Greve]

Try removing -ba_labels (it will do that with -all anyway)

On 9/29/15 9:02 PM, 葉丁瑞 wrote:

Dear All,

I ran the following script:
recon-all -i /Volumes/yang/S002_AD1118_20090116/NCKU-0003--1.dcm -s 
S002_ba -sd /Volumes/yang/S002_AD1118_20090116/ -all -ba_labels
and got the error below at the end. Could anybody please let me know how to fix 
it.
---

SUBJECTS_DIR/Volumes/yang/S002_AD1118_20090116

FREESURFER_HOME /Applications/freesurfer

Loading source label.

No such file or directory

ERROR reading 
/Volumes/yang/S002_AD1118_20090116/fsaverage/label/lh.BA1.label


Darwin MRI2deiMac.local 13.4.0 Darwin Kernel Version 13.4.0: Wed Mar 
18 16:20:14 PDT 2015; root:xnu-2422.115.14~1/RELEASE_X86_64 x86_64


recon-all -s S002 exited with ERRORS at Sat Sep 26 21:57:00 CST 2015

For more details, see the log file 
/Volumes/yang/S002_AD1118_20090116/S002/scripts/recon-all.log


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


---

I follow the below step at freesurfer message board
cd  /Volume/yang

ln -s /Applications/freesurfer/subjects/fsaverage

recon-all -i /Volumes/yang/S002_AD1118_20090116/NCKU-0003--1.dcm -s 
S002_ba -sd /Volumes/yang/S002_AD1118_20090116/ -all -ba_labels
but the error is not resoled.please see attached file below
my environment for Freesurfer/FS-FAST

 freesurfer-Darwin-lion-stable-pub-v5.3.0 


Setting up environment for FreeSurfer/FS-FAST (and FSL)


FREESURFER_HOME   /Applications/freesurfer


FSFAST_HOME   /Applications/freesurfer/fsfast


FSF_OUTPUT_FORMAT nii.gz


SUBJECTS_DIR  /Applications/freesurfer/subjects


MNI_DIR   /Applications/freesurfer/mni


FSL_DIR   /usr/local/fsl

Thank you,

TING-JUI YEH


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Re: [Freesurfer] warping surface label to volume space

[Douglas N Greve]

I'm at a loss here. I run the exact same command with the same version. 
I get the same terminal output, but my output volume looks ok. The only 
thing I can think of is that there is an old version that output volume 
that is not getting overwritten. Can you name the output file 
differently and make sure that it does not exist prior to running the 
command?

On 09/30/2015 04:37 PM, Jacobs H (NP) wrote:
> Hi Doug,
>
> Just as a reminder: I uploaded the data yesterday.
>
> Best
> Heidi
>
> From: Douglas Greve  >
> Reply-To: Freesurfer support list  >
> Date: Tuesday 29 September 2015 17:01
> To: "freesurfer@nmr.mgh.harvard.edu 
> " 
> mailto:freesurfer@nmr.mgh.harvard.edu>>
> Subject: Re: [Freesurfer] warping surface label to volume space
>
> filedrop2 url at the end of this email
>
> On 9/29/15 10:34 AM, Jacobs H (NP) wrote:
>> Sure, where should I upload it to?
>> Thanks!
>> Heidi
>>
>> From: Douglas Greve > >
>> Reply-To: Freesurfer support list > >
>> Date: Tuesday 29 September 2015 16:28
>> To: "freesurfer@nmr.mgh.harvard.edu 
>> " 
>> mailto:freesurfer@nmr.mgh.harvard.edu>>
>> Subject: Re: [Freesurfer] warping surface label to volume space
>>
>> Can you upload the subject so I can look at it?
>>
>> On 9/29/15 9:05 AM, Jacobs H (NP) wrote:
>>> Hi Doug,
>>>
>>> The label looks actually ok and the surface as well. I attached the images 
>>> to this email, Not sure where it went wrong?
>>>
>>> Best
>>> Heidi
>>>
>>> 
>>> Van:freesurfer-boun...@nmr.mgh.harvard.edu  
>>> [freesurfer-boun...@nmr.mgh.harvard.edu] namens Douglas N Greve 
>>> [gr...@nmr.mgh.harvard.edu]
>>> Verzonden: maandag 28 september 2015 23:58
>>> Aan:freesurfer@nmr.mgh.harvard.edu
>>> Onderwerp: Re: [Freesurfer] warping surface label to volume space
>>>
>>> Something is definitely going wrong. Can you load the label as well and
>>> verify that the label itself looks ok?
>>>
>>> On 09/28/2015 05:32 PM, Jacobs H (NP) wrote:
 Yes, here it is!
 Thanks! Heidi



 Yes, here it is!
 Thanks! Heidi


 image1.png



 ATT1.txt



> Op 28 sep. 2015 om 17:26 heeft Douglas N Greve 
>   het volgende geschreven:
>
> Can you send a picture?
>
>> On 09/28/2015 05:08 PM, Jacobs H (NP) wrote:
>> Dear Doug,
>>
>> By looking at it in Freeview. Anatomically, I would expect that the 
>> entorhinal cortex would not be localized so laterally? And some voxels 
>> are not in the temporal lobe.
>>
>> Best
>> Heidi
>>
>> 
>> Van:freesurfer-boun...@nmr.mgh.harvard.edu   
>> [freesurfer-boun...@nmr.mgh.harvard.edu] namens Douglas N Greve 
>> [gr...@nmr.mgh.harvard.edu]
>> Verzonden: maandag 28 september 2015 23:00
>> Aan:freesurfer@nmr.mgh.harvard.edu
>> Onderwerp: Re: [Freesurfer] warping surface label to volume space
>>
>> how are you determining that it is not in the right place? When I run
>> this it works.
>>
>>> On 09/28/2015 04:54 PM, Jacobs H (NP) wrote:
>>> Hi,
>>>
>>> Bringing this to the FS list:
>>> I am trying to warp the entorhinal cortex label (ex vivo) to volume
>>> space, so that I can see and use the full ROI. Using the command
>>> stated below doesn’t seem to work, as it is not in the right location
>>> of the subject’s brain. Any thoughts?
>>>
>>> I used this command:
>>> mri_label2vol --label S_3RSPPP/label/lh.entorhinal_exvivo.label
>>> --regheader $SUBJECTS_DIR/S_3RSPPP/mri/orig.mgz --o
>>> lh.entorhinal_exvivo_vol.mgz --fill-ribbon --subject S_3RSPPP --hemi l
>>>
>>> This was the output on the terminal:
>>> subject S_3RSPPP --hemi lh
>>> INFO: subject not needed, igorning.
>>> Number of labels: 1
>>> S_3RSPPP/label/lh.entorhinal_exvivo.label
>>> Annot File:  (null)
>>> Template Volume: (null)
>>> Outut Volume: lh.entorhinal_exvivo_vol.mgz
>>> Registration File: (null)
>>> Fill Threshold: 0
>>> Label Vox Vol:  1
>>> ProjType: (null)
>>> ProjTypeId: 0
>>> ProjStart:  0
>>> ProjStop: 0
>>> ProjDelta:  0.1
>>> Subject:  S_3RSPPP
>>> Hemi: lh
>>> UseNewASeg2Vol:  0
>>> DoLabelStatVol  0
>>> LabelCodeOffset  0
>>> setenv SUBJECTS_DIR 
>>> /autofs/space/schopenhauer_003/users/hjacobs/SUBJECTS
>>> $Id: mri_label2vol.c,v 1.46 2014/12/08 21:11:54 greve Exp $
>>>INFO: loading
>>> surface  
>>> /autofs/space/schopenhauer_003/users/hjacobs/SUBJECTS/S_3RSPPP/surf/lh.white
>>>
>>> nvertices = 120130
>>> Reading thickness
>>> /autofs/space/schopenhauer_003/users/hjacobs/SUBJECTS/S_3RSPPP/surf/

Re: [Freesurfer] Error Messages for Accessing Bin

[Timothy Quang-Tin Le]

Hi,
Thank you very much for your response. The output of that command was:

tle7@sni-vcs-gotlib:~$ ls -l /home/tle7/freesurfer/bin/mri_convert
-rwxrwx--x 1 tle7 stanford 1672136 Aug 15  2010
/home/tle7/freesurfer/bin/mri_convert
tle7@sni-vcs-gotlib:~$


On Fri, Oct 2, 2015 at 10:39 AM, dgw  wrote:

> Timothy,
>
> What is the output of this command:
>
> ls -l /home/tle7/freesurfer/bin/mri_convert
>
> ?
>
> hth
> d
>
> On Fri, Oct 2, 2015 at 1:36 PM, Timothy Quang-Tin Le 
> wrote:
> > Hi,
> > I tried the chmod command, but it did not work. How I check that I've
> > downloaded the correct version?
> > Thank you very much
> > Timothy
> >
> > On Thu, Oct 1, 2015 at 8:10 AM, Bruce Fischl  >
> > wrote:
> >>
> >> can you try chmod a+x on one of them and see if it can then be executed?
> >> e.g.:
> >>
> >> chmod a+x  /home/tle7/freesurfer/bin/mri_convert
> >>  /home/tle7/freesurfer/bin/mri_convert
> >>
> >> and see if you get an error. If not, you probably downloaded the wrong
> >> hardware version
> >> cheers
> >> Bruce
> >>
> >>
> >>
> >> On Tue, 29 Sep 2015, Timothy Quang-Tin Le wrote:
> >>
> >>>
> >>>   Hello,
> >>> When I run the command "sFSstart" on version 5.0.0, I am receiving the
> >>> messages below. Would you please explain to me what the problem is? It
> >>> seems like there is trouble accessing the bin.
> >>> Thank you
> >>>
> >>>  freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0 
> >>> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> >>> FREESURFER_HOME   /home/tle7/freesurfer
> >>> FSFAST_HOME   /home/tle7/freesurfer/fsfast
> >>> FSF_OUTPUT_FORMAT nii
> >>> SUBJECTS_DIR  /home/tle7/freesurfer/subjects
> >>> MNI_DIR   /home/tle7/freesurfer/mni
> >>> tle7@sni-vcs-gotlib:~$ sFSstart practicemotherdaughter 00152-DT2
> >>> studyPath /home/tle7/freesurfer/subjects/practicemotherdaughter
> >>> H 0
> >>> checking sid number 00152-DT2
> >>> 1
> >>> 00152-DT2/MR.1.2.840.113619.2.283.4120.7575399.15360.1319907833.100.dcm
> >>> Subject Stamp: freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0
> >>> Current Stamp: freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0
> >>> INFO: SUBJECTS_DIR is /home/tle7/freesurfer/subjects
> >>> Actual FREESURFER_HOME /home/tle7/freesurfer
> >>> Linux sni-vcs-gotlib.stanford.edu 3.13.0-61-generic #100-Ubuntu SMP
> >>> Wed Jul 29 11:21:34 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
> >>> /home/tle7/freesurfer/bin/mri_convert: Exec format error. Binary file
> >>> not executable.
> >>> /home/tle7/freesurfer/bin/flirt.fsl: Exec format error. Binary file
> >>> not executable.
> >>> /home/tle7/freesurfer/bin/mri_convert: Exec format error. Binary file
> >>> not executable.
> >>> /home/tle7/freesurfer/bin/tkregister2_cmdl: Exec format error. Binary
> >>> file not executable.
> >>> /home/tle7/freesurfer/bin/mri_normalize: Exec format error. Binary
> >>> file not executable.
> >>> /home/tle7/freesurfer/bin/mri_watershed: Exec format error. Binary
> >>> file not executable.
> >>> /home/tle7/freesurfer/bin/mri_gcut: Exec format error. Binary file not
> >>> executable.
> >>> /home/tle7/freesurfer/bin/mri_segment: Exec format error. Binary file
> >>> not executable.
> >>> /home/tle7/freesurfer/bin/mri_label2label: Exec format error. Binary
> >>> file not executable.
> >>> /home/tle7/freesurfer/bin/mri_em_register: Exec format error. Binary
> >>> file not executable.
> >>> /home/tle7/freesurfer/bin/mri_ca_normalize: Exec format error. Binary
> >>> file not executable.
> >>> /home/tle7/freesurfer/bin/mri_ca_register: Exec format error. Binary
> >>> file not executable.
> >>> /home/tle7/freesurfer/bin/mri_ca_label: Exec format error. Binary file
> >>> not executable.
> >>> /home/tle7/freesurfer/bin/mri_pretess: Exec format error. Binary file
> >>> not executable.
> >>> /home/tle7/freesurfer/bin/mri_fill: Exec format error. Binary file not
> >>> executable.
> >>> /home/tle7/freesurfer/bin/mri_tessellate: Exec format error. Binary
> >>> file not executable.
> >>> /home/tle7/freesurfer/bin/mri_concatenate_lta: Exec format error.
> >>> Binary file not executable.
> >>> /home/tle7/freesurfer/bin/mri_normalize_tp2: Exec format error. Binary
> >>> file not executable.
> >>> /home/tle7/freesurfer/bin/mris_smooth: Exec format error. Binary file
> >>> not executable.
> >>> /home/tle7/freesurfer/bin/mris_inflate: Exec format error. Binary file
> >>> not executable.
> >>> /home/tle7/freesurfer/bin/mris_curvature: Exec format error. Binary
> >>> file not executable.
> >>> /home/tle7/freesurfer/bin/mris_sphere: Exec format error. Binary file
> >>> not executable.
> >>> /home/tle7/freesurfer/bin/mris_fix_topology: Exec format error. Binary
> >>> file not executable.
> >>> /home/tle7/freesurfer/bin/mris_topo_fixer: Exec format error. Binary
> >>> file not executable.
> >>> /home/tle7/freesurfer/bin/mris_ca_label: Exec format error. Binary
> >>> file not executable.
> >>> /home/tle7/freesurfer/bin/mris_euler_number: Exec format error. Binary
> >>> file not executable.
> >>

Re: [Freesurfer] mri_convert doubles file size when changing TR header information

[Douglas Greve]

It is probably changing the data type from short to float. Try adding 
-odt short --no_scale 1

You can also look at the data type with

mri_info --type file.nii



On 10/1/15 10:52 AM, Shaun Patel wrote:
> I noticed after running slice-time correction with SPM, the resulting Nifti 
> files do not have TR information in the header. This breaks the Freesurfer 
> pipeline. To get around this, I attempted to use the mir_convert function 
> with the “tr” flag to set the TR. However, in doing so, I noticed that the 
> resulting nifti file doubles in size. I used the following command: 
> mri_convert f.nii f.nii -tr 2000, to set the TR to 2s. Any suggestions as to 
> what is happening to the file size and how to prevent it?
>
> Many Thanks,
>
> Shaun
>
> --
> Shaun Patel, Ph.D.
> Research Fellow
> Department of Neurosurgery
> Massachusetts General Hospital
> Harvard Medical School
> e. shaun.pa...@me.com
> w. http://shaunpatel.com
> c. 317.340.7260
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] ] dt_recon

[Douglas Greve]

I don't think I would use "DTI Morphometry" to describe it. I'm not sure 
what term I would use. It is basically a FA ROI analysis


On 10/2/15 1:28 PM, Alshikho, Mohamad J. wrote:

Hi Doug,
Thank you very much for your answers!

Kindly I have one more question:
At the end of DTI analysis using the tool “dt_recon” we will have  “ stats” 
file including the FA value for every segment and parcellate in the brain. 
Depending on this output can we use the term “ DTI morphometry” to describe the 
analysis?


Thanks
Mohamad

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve
Sent: Monday, September 28, 2015 11:26 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] dt_recon


On 9/25/15 9:28 AM, Alshikho, Mohamad J. wrote:
Hi Doug and Bruce,
After running the command :
dt_recon --i 6-1025.dcm --s M87102113 --o dti dt_recon --i f.nii --b f.bvals f.bvecs --s 
M87102113 --o dti  <<< source:   Freesurfer wiki>>>

I need to generate the final statistics ( FA for every parcellate and segment 
in aseg and wmparc atlases) using the command “mri_segstats”

In order to do so I need to move “fa.nii” to anatomical space using the command:

mri_vol2vol –mov fa.nii –lta register.lta –fstarg –o fa.anat.mgh  <<< 
source:   Freesurfer wiki>>>


My questions are about the file “register.lta” :

1.   What is the difference between this file and the file “register.dat” ( 
which I can see it as an output of  the command ” bbregister” in the final 
analysis using the command “dt_recon”)
They hold the same basic registration information just in different formats. We 
are trying to move to the LTA as it is a much better format for these things.


2.   How can I generate the file “ register.lta”?
Use lta_convert, something like
lta_convert --inreg register.dat --outlta register.lta --src lowb.nii.gz 
--trg $SUBJECTS_DIR/$subject/mri/orig.mgz


3.   Can I feed the file “ register.dat” instead of the file “ 
register.lta” into the command “mri_vol2vol “  (in order to move the ‘’fa.nii” 
to anatomical space). If so which flag I should use instead of the flag “--lta” 
in the command mri_vol2vol?
Yes, pass it with --reg flag.



Many thanks
Mohamad




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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Group Analysis

[Douglas Greve]

What you use depends on what you are trying to do. Starting with the 
sig.mgh is good because it has not been corrected for multiple 
comparisons. You have a pretty high threshold (4, which means p<.0001). 
Try lowering it to 2 or even 1.3 to see if any activation pops out. At 
some point you'll need to correct for multiple comparisons.


On 10/2/15 1:51 PM, Ali Radaideh wrote:
Sorry, as I am quite new to this type of analysis, does the sig.mgh 
show any significance? if so how can I report it? I mean are they 
saved somewhere in SUBJECTS_DIR?


Also, it seems the corrected one does not show anything, am I true?

The last thing about this, shall I use sig.mgh or F.mgh?

Many thanks for your great help.
Ali

On Fri, Oct 2, 2015 at 8:25 PM, Douglas Greve 
mailto:gr...@nmr.mgh.harvard.edu>> wrote:


what about them?

On 10/2/15 1:20 PM, Ali Radaideh wrote:

Thanks Douglas,

The second line worked fine, but can I show you the results
attached to this email?



Thanks,
Ali

On Fri, Oct 2, 2015 at 7:22 PM, Douglas Greve
mailto:gr...@nmr.mgh.harvard.edu>> wrote:

I notice from the image that the overlay is turned off. Try
turning it on. Also, you can try

tksurferfv fsaverage lh inflated -aparc -ov sig.mgh

If that does not work, then

tksurfer fsaverage lh inflated -aparc -ov sig.mgh


On 10/2/15 12:08 PM, Ali Radaideh wrote:

Hi,

I am running a group analysis (patients versus controls). I
am following the tutorial and managed to create the FSGD
file with four classes
MSMale
MSFemale
HealthyMale
HealthyFemale

and one variable: Age


So the number of NregressorsDODS is equal to 8

[ MSMale MSFemale HealthyMale HealthyFemale  Age_ MSMale
 Age_ MSFemale  Age_ HealthyMale  Age_ HealthyFemale ]

I have created my own contrast files as follows:

lh-female_MS_vs_Healthy
​ .mtx /
to
//
compare between Female MS and Female Healthy regardless of age
/:
*[ 0 1 0 -1 0 0 0 0 ]​*

/
/
/lh-female_MS_vs_Healthy_Age
​ .mtx
//
​​
/
​
/
to
//
compare between Female MS and Female Healthy_with age effect
/:
*
​[​
0 0 0 0 0 1 0 -1
​]
*

/lh-male_MS_vs_Healthy
​ .mtx
/
​
/
to
//
compare between Male MS and Male Healthy regardless of age
/:
/*
​[ ​
1 0 -1 0 0 0 0 0
​] ​
*
/
/
/
/lh-male_MS_vs_Healthy_Age
​ .mtx​  to
//
compare between Male MS and Male Healthy_with age effect
//
/:
*/
[
//0 0 0 0 1 0 -1 0
​ ]​
/*
/

/
/
​
//
​
//lh-MS_vs_Healthy
​ .mtx​   to compare between MS and Healthy regardless of
Age and Gender
/:
*/
​ [
//0.5 0.5 -0.5 -0.5 0 0 0 0 //
] ​
/*
/

/
/

/
/
I ran the glm_fit using the following command line:
/
/
mri_glmfit --y lh.disease_Healthy_Age.thickness.10.mgh
--fsgd disease_Healthy_Age.fsgd dods --C
lh-MS_vs_Healthy.mtx --C lh-male_MS_vs_Healthy_Age.mtx --C
lh-male_MS_vs_Healthy.mtx --C
lh-female_MS_vs_Healthy_Age.mtx --C
lh-female_MS_vs_Healthy.mtx --surf fsaverage lh --cortex
--glmdir lh.disease_Healthy_Age.glmdir
/
/

/

/
Everything went OK except when loading the sig.mgh in
freeview using the following command:
/
/

/
/
freeview -f

$SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=lh.disease_Healthy_Age.glmdir/lh-MS_vs_Healthy/sig.mgh:overlay_threshold=4,5
-viewport 3d

1- It complained that the flag /
annot_outline=1 is not recognized
/
/
2- after removing this flag from the command line, t
//
he overlay only was two colors (green and red) (I have
attached a copy of it)
/
/
/
/
/
​ Then I did
/ a cluster-wise correction for multiple comparisons
​ by​
run
​ n​
ing​
a simulation/
​ as follows:
/
/
mri_glmfit-sim --glmdir lh.disease_Healthy_Age.glmdir
--cache 4 neg --cwp  0.05 --2spaces
/
/

/
/
Nothing has changed. i_n free view the same overlay._
/
/

/
/
I opened the   "
/cache.th40.neg.sig.cluster.summary
​ " file​
​ and got the foll

Re: [Freesurfer] Group Analysis

[Ali Radaideh]

Sorry, as I am quite new to this type of analysis, does the sig.mgh show
any significance? if so how can I report it? I mean are they saved
somewhere in SUBJECTS_DIR?

Also, it seems the corrected one does not show anything, am I true?

The last thing about this, shall I use sig.mgh or F.mgh?

Many thanks for your great help.
Ali

On Fri, Oct 2, 2015 at 8:25 PM, Douglas Greve 
wrote:

> what about them?
>
> On 10/2/15 1:20 PM, Ali Radaideh wrote:
>
> Thanks Douglas,
>
> The second line worked fine, but can I show you the results attached to
> this email?
>
>
>
> Thanks,
> Ali
>
> On Fri, Oct 2, 2015 at 7:22 PM, Douglas Greve 
> wrote:
>
>> I notice from the image that the overlay is turned off. Try turning it
>> on. Also, you can try
>>
>> tksurferfv fsaverage lh inflated -aparc -ov sig.mgh
>>
>> If that does not work, then
>>
>> tksurfer fsaverage lh inflated -aparc -ov sig.mgh
>>
>>
>> On 10/2/15 12:08 PM, Ali Radaideh wrote:
>>
>> Hi,
>>
>> I am running a group analysis (patients versus controls). I am following
>> the tutorial and managed to create the FSGD file with four classes
>> MSMale
>> MSFemale
>> HealthyMale
>> HealthyFemale
>>
>> and one variable: Age
>>
>>
>> So the number of NregressorsDODS is equal to 8
>>
>> [ MSMale MSFemale HealthyMale HealthyFemale  Age_ MSMale  Age_ MSFemale
>>  Age_ HealthyMale  Age_ HealthyFemale ]
>>
>> I have created my own contrast files as follows:
>>
>> lh-female_MS_vs_Healthy
>> ​ .mtx
>> * to  *
>> * compare between Female MS and Female Healthy regardless of age *:
>> *[ 0 1 0 -1 0 0 0 0 ]​*
>>
>>
>> *lh-female_MS_vs_Healthy_Age ​ .mtx *
>> * ​​   *
>> ​
>> * to  *
>> * compare between Female MS and Female Healthy_with age effect *:
>> * ​[​ 0 0 0 0 0 1 0 -1 ​] *
>>
>> *lh-male_MS_vs_Healthy ​ .mtx*
>> ​
>> * to  *
>> * compare between Male MS and Male Healthy regardless of age *:
>>
>> * ​[ ​ 1 0 -1 0 0 0 0 0 ​] ​ *
>>
>> *lh-male_MS_vs_Healthy_Age ​ .mtx​  to  *
>> * compare between Male MS and Male Healthy_with age effect *
>>   :
>> * [ 0 0 0 0 1 0 -1 0  ​ ]​ *
>>
>> * ​ *
>> * ​ *
>> *lh-MS_vs_Healthy ​ .mtx​   to compare between MS and Healthy regardless
>> of Age and Gender *:
>> * ​ [  0.5 0.5 -0.5 -0.5 0 0 0 0  ] ​ *
>>
>>
>> * I ran the glm_fit using the following command line: *
>>
>> * mri_glmfit --y lh.disease_Healthy_Age.thickness.10.mgh --fsgd
>> disease_Healthy_Age.fsgd dods --C lh-MS_vs_Healthy.mtx --C
>> lh-male_MS_vs_Healthy_Age.mtx --C lh-male_MS_vs_Healthy.mtx --C
>> lh-female_MS_vs_Healthy_Age.mtx --C lh-female_MS_vs_Healthy.mtx --surf
>> fsaverage lh --cortex --glmdir lh.disease_Healthy_Age.glmdir *
>>
>>
>> * Everything went OK except when loading the sig.mgh in freeview using
>> the following command: *
>>
>>
>> * freeview -f
>> $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=lh.disease_Healthy_Age.glmdir/lh-MS_vs_Healthy/sig.mgh:overlay_threshold=4,5
>> -viewport 3d 1- It complained that the flag  annot_outline=1 is not
>> recognized 2- after removing this flag from the command line, t he overlay
>> only was two colors (green and red) (I have attached a copy of it)  *
>>
>> * ​ Then I did * a cluster-wise correction for multiple comparisons
>> ​ by​
>> run
>> ​ n​
>> ing​
>> a simulation
>> * ​ as follows: *
>>
>> * mri_glmfit-sim --glmdir lh.disease_Healthy_Age.glmdir --cache 4 neg
>> --cwp  0.05 --2spaces *
>>
>> * Nothing has changed. in free view the same overlay. *
>>
>> * I opened the   " *cache.th40.neg.sig.cluster.summary
>> ​" file​
>> ​ and got the following:
>>
>> # Cluster Growing Summary (mri_surfcluster)
>> # $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $
>> # $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
>> # CreationTime 2015/10/02-15:06:07-GMT
>> # cmdline mri_surfcluster --in
>> lh.disease_Healthy_Age.glmdir/lh-MS_vs_Healthy/sig.mgh --csd
>> /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm15/neg/th40/mc-z.csd
>> --mask lh.disease_Healthy_Age.glmdir/mask.mgh --cwsig
>> lh.disease_Healthy_Age.glmdir/lh-MS_vs_Healthy/cache.th40.neg.sig.cluster.mgh
>> --vwsig
>> lh.disease_Healthy_Age.glmdir/lh-MS_vs_Healthy/cache.th40.neg.sig.voxel.mgh
>> --sum
>> lh.disease_Healthy_Age.glmdir/lh-MS_vs_Healthy/cache.th40.neg.sig.cluster.summary
>> --ocn
>> lh.disease_Healthy_Age.glmdir/lh-MS_vs_Healthy/cache.th40.neg.sig.ocn.mgh
>> --oannot
>> lh.disease_Healthy_Age.glmdir/lh-MS_vs_Healthy/cache.th40.neg.sig.ocn.annot
>> --annot aparc --csdpdf
>> lh.disease_Healthy_Age.glmdir/lh-MS_vs_Healthy/cache.th40.neg.pdf.dat
>> --cwpvalthresh 0.05 --o
>> lh.disease_Healthy_Age.glmdir/lh-MS_vs_Healthy/cache.th40.neg.sig.masked.mgh
>> --no-fixmni --bonferroni 2 --surf white
>> # cwd
>> /media/ali/HU_Research/HU_Research/HU/MS_Project/MS_analysis/freesurfer_HU
>> # sysname  Linux
>> # hostname ali-XPS-L501X
>> # machine  x86_64
>> # FixVertexAreaFlag 1
>> # FixSurfClusterArea 1
>> #
>> # Input  lh.disease_Healthy_Age.glmdir/lh-MS_vs_Healthy/sig.mgh
>> # Fr

Re: [Freesurfer] Error Messages for Accessing Bin

[dgw]

Timothy,

What is the output of this command:

ls -l /home/tle7/freesurfer/bin/mri_convert

?

hth
d

On Fri, Oct 2, 2015 at 1:36 PM, Timothy Quang-Tin Le  wrote:
> Hi,
> I tried the chmod command, but it did not work. How I check that I've
> downloaded the correct version?
> Thank you very much
> Timothy
>
> On Thu, Oct 1, 2015 at 8:10 AM, Bruce Fischl 
> wrote:
>>
>> can you try chmod a+x on one of them and see if it can then be executed?
>> e.g.:
>>
>> chmod a+x  /home/tle7/freesurfer/bin/mri_convert
>>  /home/tle7/freesurfer/bin/mri_convert
>>
>> and see if you get an error. If not, you probably downloaded the wrong
>> hardware version
>> cheers
>> Bruce
>>
>>
>>
>> On Tue, 29 Sep 2015, Timothy Quang-Tin Le wrote:
>>
>>>
>>>   Hello,
>>> When I run the command "sFSstart" on version 5.0.0, I am receiving the
>>> messages below. Would you please explain to me what the problem is? It
>>> seems like there is trouble accessing the bin.
>>> Thank you
>>>
>>>  freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0 
>>> Setting up environment for FreeSurfer/FS-FAST (and FSL)
>>> FREESURFER_HOME   /home/tle7/freesurfer
>>> FSFAST_HOME   /home/tle7/freesurfer/fsfast
>>> FSF_OUTPUT_FORMAT nii
>>> SUBJECTS_DIR  /home/tle7/freesurfer/subjects
>>> MNI_DIR   /home/tle7/freesurfer/mni
>>> tle7@sni-vcs-gotlib:~$ sFSstart practicemotherdaughter 00152-DT2
>>> studyPath /home/tle7/freesurfer/subjects/practicemotherdaughter
>>> H 0
>>> checking sid number 00152-DT2
>>> 1
>>> 00152-DT2/MR.1.2.840.113619.2.283.4120.7575399.15360.1319907833.100.dcm
>>> Subject Stamp: freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0
>>> Current Stamp: freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0
>>> INFO: SUBJECTS_DIR is /home/tle7/freesurfer/subjects
>>> Actual FREESURFER_HOME /home/tle7/freesurfer
>>> Linux sni-vcs-gotlib.stanford.edu 3.13.0-61-generic #100-Ubuntu SMP
>>> Wed Jul 29 11:21:34 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
>>> /home/tle7/freesurfer/bin/mri_convert: Exec format error. Binary file
>>> not executable.
>>> /home/tle7/freesurfer/bin/flirt.fsl: Exec format error. Binary file
>>> not executable.
>>> /home/tle7/freesurfer/bin/mri_convert: Exec format error. Binary file
>>> not executable.
>>> /home/tle7/freesurfer/bin/tkregister2_cmdl: Exec format error. Binary
>>> file not executable.
>>> /home/tle7/freesurfer/bin/mri_normalize: Exec format error. Binary
>>> file not executable.
>>> /home/tle7/freesurfer/bin/mri_watershed: Exec format error. Binary
>>> file not executable.
>>> /home/tle7/freesurfer/bin/mri_gcut: Exec format error. Binary file not
>>> executable.
>>> /home/tle7/freesurfer/bin/mri_segment: Exec format error. Binary file
>>> not executable.
>>> /home/tle7/freesurfer/bin/mri_label2label: Exec format error. Binary
>>> file not executable.
>>> /home/tle7/freesurfer/bin/mri_em_register: Exec format error. Binary
>>> file not executable.
>>> /home/tle7/freesurfer/bin/mri_ca_normalize: Exec format error. Binary
>>> file not executable.
>>> /home/tle7/freesurfer/bin/mri_ca_register: Exec format error. Binary
>>> file not executable.
>>> /home/tle7/freesurfer/bin/mri_ca_label: Exec format error. Binary file
>>> not executable.
>>> /home/tle7/freesurfer/bin/mri_pretess: Exec format error. Binary file
>>> not executable.
>>> /home/tle7/freesurfer/bin/mri_fill: Exec format error. Binary file not
>>> executable.
>>> /home/tle7/freesurfer/bin/mri_tessellate: Exec format error. Binary
>>> file not executable.
>>> /home/tle7/freesurfer/bin/mri_concatenate_lta: Exec format error.
>>> Binary file not executable.
>>> /home/tle7/freesurfer/bin/mri_normalize_tp2: Exec format error. Binary
>>> file not executable.
>>> /home/tle7/freesurfer/bin/mris_smooth: Exec format error. Binary file
>>> not executable.
>>> /home/tle7/freesurfer/bin/mris_inflate: Exec format error. Binary file
>>> not executable.
>>> /home/tle7/freesurfer/bin/mris_curvature: Exec format error. Binary
>>> file not executable.
>>> /home/tle7/freesurfer/bin/mris_sphere: Exec format error. Binary file
>>> not executable.
>>> /home/tle7/freesurfer/bin/mris_fix_topology: Exec format error. Binary
>>> file not executable.
>>> /home/tle7/freesurfer/bin/mris_topo_fixer: Exec format error. Binary
>>> file not executable.
>>> /home/tle7/freesurfer/bin/mris_ca_label: Exec format error. Binary
>>> file not executable.
>>> /home/tle7/freesurfer/bin/mris_euler_number: Exec format error. Binary
>>> file not executable.
>>> /home/tle7/freesurfer/bin/mris_make_surfaces: Exec format error.
>>> Binary file not executable.
>>> /home/tle7/freesurfer/bin/mris_register: Exec format error. Binary
>>> file not executable.
>>> /home/tle7/freesurfer/bin/mris_volmask: Exec format error. Binary file
>>> not executable.
>>> /home/tle7/freesurfer/bin/mris_anatomical_stats: Exec format error.
>>> Binary file not executable.
>>> /home/tle7/freesurfer/bin/mrisp_paint: Exec format error. Binary file
>>> not executable.
>>> /home/tle7/freesurfer/bin/mris_curvat

[Freesurfer] Error Messages for Accessing Bin

[Timothy Quang-Tin Le]

Hi,
I tried the chmod command, but it did not work. How I check that I've
downloaded the correct version?
Thank you very much
Timothy

On Thu, Oct 1, 2015 at 8:10 AM, Bruce Fischl 
wrote:

> can you try chmod a+x on one of them and see if it can then be executed?
> e.g.:
>
> chmod a+x  /home/tle7/freesurfer/bin/mri_convert
>  /home/tle7/freesurfer/bin/mri_convert
>
> and see if you get an error. If not, you probably downloaded the wrong
> hardware version
> cheers
> Bruce
>
>
>
> On Tue, 29 Sep 2015, Timothy Quang-Tin Le wrote:
>
>
>>   Hello,
>> When I run the command "sFSstart" on version 5.0.0, I am receiving the
>> messages below. Would you please explain to me what the problem is? It
>> seems like there is trouble accessing the bin.
>> Thank you
>>
>>  freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0 
>> Setting up environment for FreeSurfer/FS-FAST (and FSL)
>> FREESURFER_HOME   /home/tle7/freesurfer
>> FSFAST_HOME   /home/tle7/freesurfer/fsfast
>> FSF_OUTPUT_FORMAT nii
>> SUBJECTS_DIR  /home/tle7/freesurfer/subjects
>> MNI_DIR   /home/tle7/freesurfer/mni
>> tle7@sni-vcs-gotlib:~$ sFSstart practicemotherdaughter 00152-DT2
>> studyPath /home/tle7/freesurfer/subjects/practicemotherdaughter
>> H 0
>> checking sid number 00152-DT2
>> 1
>> 00152-DT2/MR.1.2.840.113619.2.283.4120.7575399.15360.1319907833.100.dcm
>> Subject Stamp: freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0
>> Current Stamp: freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0
>> INFO: SUBJECTS_DIR is /home/tle7/freesurfer/subjects
>> Actual FREESURFER_HOME /home/tle7/freesurfer
>> Linux sni-vcs-gotlib.stanford.edu 3.13.0-61-generic #100-Ubuntu SMP
>> Wed Jul 29 11:21:34 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
>> /home/tle7/freesurfer/bin/mri_convert: Exec format error. Binary file
>> not executable.
>> /home/tle7/freesurfer/bin/flirt.fsl: Exec format error. Binary file
>> not executable.
>> /home/tle7/freesurfer/bin/mri_convert: Exec format error. Binary file
>> not executable.
>> /home/tle7/freesurfer/bin/tkregister2_cmdl: Exec format error. Binary
>> file not executable.
>> /home/tle7/freesurfer/bin/mri_normalize: Exec format error. Binary
>> file not executable.
>> /home/tle7/freesurfer/bin/mri_watershed: Exec format error. Binary
>> file not executable.
>> /home/tle7/freesurfer/bin/mri_gcut: Exec format error. Binary file not
>> executable.
>> /home/tle7/freesurfer/bin/mri_segment: Exec format error. Binary file
>> not executable.
>> /home/tle7/freesurfer/bin/mri_label2label: Exec format error. Binary
>> file not executable.
>> /home/tle7/freesurfer/bin/mri_em_register: Exec format error. Binary
>> file not executable.
>> /home/tle7/freesurfer/bin/mri_ca_normalize: Exec format error. Binary
>> file not executable.
>> /home/tle7/freesurfer/bin/mri_ca_register: Exec format error. Binary
>> file not executable.
>> /home/tle7/freesurfer/bin/mri_ca_label: Exec format error. Binary file
>> not executable.
>> /home/tle7/freesurfer/bin/mri_pretess: Exec format error. Binary file
>> not executable.
>> /home/tle7/freesurfer/bin/mri_fill: Exec format error. Binary file not
>> executable.
>> /home/tle7/freesurfer/bin/mri_tessellate: Exec format error. Binary
>> file not executable.
>> /home/tle7/freesurfer/bin/mri_concatenate_lta: Exec format error.
>> Binary file not executable.
>> /home/tle7/freesurfer/bin/mri_normalize_tp2: Exec format error. Binary
>> file not executable.
>> /home/tle7/freesurfer/bin/mris_smooth: Exec format error. Binary file
>> not executable.
>> /home/tle7/freesurfer/bin/mris_inflate: Exec format error. Binary file
>> not executable.
>> /home/tle7/freesurfer/bin/mris_curvature: Exec format error. Binary
>> file not executable.
>> /home/tle7/freesurfer/bin/mris_sphere: Exec format error. Binary file
>> not executable.
>> /home/tle7/freesurfer/bin/mris_fix_topology: Exec format error. Binary
>> file not executable.
>> /home/tle7/freesurfer/bin/mris_topo_fixer: Exec format error. Binary
>> file not executable.
>> /home/tle7/freesurfer/bin/mris_ca_label: Exec format error. Binary
>> file not executable.
>> /home/tle7/freesurfer/bin/mris_euler_number: Exec format error. Binary
>> file not executable.
>> /home/tle7/freesurfer/bin/mris_make_surfaces: Exec format error.
>> Binary file not executable.
>> /home/tle7/freesurfer/bin/mris_register: Exec format error. Binary
>> file not executable.
>> /home/tle7/freesurfer/bin/mris_volmask: Exec format error. Binary file
>> not executable.
>> /home/tle7/freesurfer/bin/mris_anatomical_stats: Exec format error.
>> Binary file not executable.
>> /home/tle7/freesurfer/bin/mrisp_paint: Exec format error. Binary file
>> not executable.
>> /home/tle7/freesurfer/bin/mris_curvature_stats: Exec format error.
>> Binary file not executable.
>> /home/tle7/freesurfer/bin/mris_calc: Exec format error. Binary file
>> not executable.
>> /home/tle7/freesurfer/bin/mri_robust_register: Exec format error.
>> Binary file not executable.
>> /home/tle7/freesurfer/bin/mri_r

[Freesurfer] ] dt_recon

[Alshikho, Mohamad J.]

Hi Doug,
Thank you very much for your answers!

Kindly I have one more question:
At the end of DTI analysis using the tool “dt_recon” we will have  “ stats” 
file including the FA value for every segment and parcellate in the brain. 
Depending on this output can we use the term “ DTI morphometry” to describe the 
analysis?


Thanks
Mohamad

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve
Sent: Monday, September 28, 2015 11:26 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] dt_recon


On 9/25/15 9:28 AM, Alshikho, Mohamad J. wrote:
Hi Doug and Bruce,
After running the command :
dt_recon --i 6-1025.dcm --s M87102113 --o dti dt_recon --i f.nii --b f.bvals 
f.bvecs --s M87102113 --o dti  <<< source:   Freesurfer wiki>>>

I need to generate the final statistics ( FA for every parcellate and segment 
in aseg and wmparc atlases) using the command “mri_segstats”

In order to do so I need to move “fa.nii” to anatomical space using the command:

mri_vol2vol –mov fa.nii –lta register.lta –fstarg –o fa.anat.mgh
  <<< source:   Freesurfer wiki>>>


My questions are about the file “register.lta” :

1.   What is the difference between this file and the file “register.dat” ( 
which I can see it as an output of  the command ” bbregister” in the final 
analysis using the command “dt_recon”)
They hold the same basic registration information just in different formats. We 
are trying to move to the LTA as it is a much better format for these things.


2.   How can I generate the file “ register.lta”?
Use lta_convert, something like
   lta_convert --inreg register.dat --outlta register.lta --src lowb.nii.gz 
--trg $SUBJECTS_DIR/$subject/mri/orig.mgz


3.   Can I feed the file “ register.dat” instead of the file “ 
register.lta” into the command “mri_vol2vol “  (in order to move the ‘’fa.nii” 
to anatomical space). If so which flag I should use instead of the flag “--lta” 
in the command mri_vol2vol?
Yes, pass it with --reg flag.



Many thanks
Mohamad




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Re: [Freesurfer] mris_surf2vol

[Douglas Greve]

Try using Method 1 from this version of mri_surf2vol

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_surf2vol

On 10/2/15 11:38 AM, Kevin Aquino wrote:

Ah sorry for not being clear,

Basically I would like the output from mris_surf2vol with the mask 
option to be less speckled.


For example, in the image attached:
http://www.physics.usyd.edu.au/~aquino/example_mri_surf2vol.png 



there are some voxels missing. Is there an option to fill these voxels?


Cheers,


*Dr Kevin Aquino*
Research fellow,
Sir Peter Mansfield Magnetic Resonance Center, The University of 
Nottingham.


Honorary Research Fellow
School of Physics, Faculty of Science, University of Sydney

*E* kevin.aqu...@nottingham.ac.uk 
, aqu...@physics.usyd.edu.au 
 | *W* 
www.physics.usyd.edu.au/~aquino/ 



--

The brain is a wonderful organ. It starts working the moment you get 
up and does not stop until you get into the office.

-
Robert Frost

CRICOS 00026A
This email plus any attachments to it are confidential. Any 
unauthorised use is strictly prohibited. If you receive this email in 
error, please delete it and any attachments.


Please think of our environment and only print this e-mail if necessary.


On Fri, Oct 2, 2015 at 1:42 PM, Bruce Fischl 
mailto:fis...@nmr.mgh.harvard.edu>> wrote:


Hi Kevin

I'm not clear on what you need. Would mri_surf2vol --fillribbon do
what you want? I don't really know what else "voxelize" means

cheers
Bruce


On Fri, 2 Oct 2015, Kevin Aquino wrote:

Hi all,
I am trying to "voxelize" the cortical surfaces generated in
freesurfer and
I am a little stuck.

I have been using mris_surf2vol with the --mask option however
this
generates a very speckled representation of the cortical
surface on the
voxels. What I would prefer would be the level sets of the
cortical surface
interpolated onto voxels, even if they are at a different
resolution that
could be enough. Is this possible with any of the available
commands?

I also went down the route of mris_volmask however, this
generates the
cortical ribbon, which is something that I don't need.

Cheers,


Dr Kevin Aquino
Research fellow,
Sir Peter Mansfield Magnetic Imaging Center,
School of Physics & astronomy, The University of Nottingham.

Honorary Research Fellow
School of Physics, Faculty of Science, University of Sydney.

E kevin.aqu...@nottingham.ac.uk
,
aqu...@physics.usyd.edu.au  | W
www.physics.usyd.edu.au/~aquino/


--

The brain is a wonderful organ. It starts working the moment
you get up and
does not stop until you get into the office.
-
Robert Frost

CRICOS 00026A
This email plus any attachments to it are confidential. Any
unauthorised use
is strictly prohibited. If you receive this email in error,
please delete it
and any attachments.

Please think of our environment and only print this e-mail if
necessary.



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Re: [Freesurfer] Group Analysis

[Douglas Greve]

what about them?

On 10/2/15 1:20 PM, Ali Radaideh wrote:

Thanks Douglas,

The second line worked fine, but can I show you the results attached 
to this email?




Thanks,
Ali

On Fri, Oct 2, 2015 at 7:22 PM, Douglas Greve 
mailto:gr...@nmr.mgh.harvard.edu>> wrote:


I notice from the image that the overlay is turned off. Try
turning it on. Also, you can try

tksurferfv fsaverage lh inflated -aparc -ov sig.mgh

If that does not work, then

tksurfer fsaverage lh inflated -aparc -ov sig.mgh


On 10/2/15 12:08 PM, Ali Radaideh wrote:

Hi,

I am running a group analysis (patients versus controls). I am
following the tutorial and managed to create the FSGD file with
four classes
MSMale
MSFemale
HealthyMale
HealthyFemale

and one variable: Age


So the number of NregressorsDODS is equal to 8

[ MSMale MSFemale HealthyMale HealthyFemale  Age_ MSMale
 Age_ MSFemale  Age_ HealthyMale  Age_ HealthyFemale ]

I have created my own contrast files as follows:

lh-female_MS_vs_Healthy
​ .mtx /
to
//
compare between Female MS and Female Healthy regardless of age
/:
*[ 0 1 0 -1 0 0 0 0 ]​*

/
/
/lh-female_MS_vs_Healthy_Age
​ .mtx
//
​​
/
​
/
to
//
compare between Female MS and Female Healthy_with age effect
/:
*
​[​
0 0 0 0 0 1 0 -1
​]
*

/lh-male_MS_vs_Healthy
​ .mtx
/
​
/
to
//
compare between Male MS and Male Healthy regardless of age
/:
/*
​[ ​
1 0 -1 0 0 0 0 0
​] ​
*
/
/
/
/lh-male_MS_vs_Healthy_Age
​ .mtx​  to
//
compare between Male MS and Male Healthy_with age effect
//
/:
*/
[
//0 0 0 0 1 0 -1 0
​ ]​
/*
/

/
/
​
//
​
//lh-MS_vs_Healthy
​ .mtx​   to compare between MS and Healthy regardless of Age and
Gender
/:
*/
​ [
//0.5 0.5 -0.5 -0.5 0 0 0 0 //
] ​
/*
/

/
/

/
/
I ran the glm_fit using the following command line:
/
/
mri_glmfit --y lh.disease_Healthy_Age.thickness.10.mgh --fsgd
disease_Healthy_Age.fsgd dods --C lh-MS_vs_Healthy.mtx --C
lh-male_MS_vs_Healthy_Age.mtx --C lh-male_MS_vs_Healthy.mtx --C
lh-female_MS_vs_Healthy_Age.mtx --C lh-female_MS_vs_Healthy.mtx
--surf fsaverage lh --cortex --glmdir lh.disease_Healthy_Age.glmdir
/
/

/

/
Everything went OK except when loading the sig.mgh in freeview
using the following command:
/
/

/
/
freeview -f

$SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=lh.disease_Healthy_Age.glmdir/lh-MS_vs_Healthy/sig.mgh:overlay_threshold=4,5
-viewport 3d

1- It complained that the flag /
annot_outline=1 is not recognized
/
/
2- after removing this flag from the command line, t
//
he overlay only was two colors (green and red) (I have attached a
copy of it)
/
/
/
/
/
​ Then I did
/ a cluster-wise correction for multiple comparisons
​ by​
run
​ n​
ing​
a simulation/
​ as follows:
/
/
mri_glmfit-sim --glmdir lh.disease_Healthy_Age.glmdir --cache 4
neg --cwp  0.05 --2spaces
/
/

/
/
Nothing has changed. i_n free view the same overlay._
/
/

/
/
I opened the   "
/cache.th40.neg.sig.cluster.summary
​" file​
​ and got the following:

# Cluster Growing Summary (mri_surfcluster)
# $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $
# $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
# CreationTime 2015/10/02-15:06:07-GMT
# cmdline mri_surfcluster --in
lh.disease_Healthy_Age.glmdir/lh-MS_vs_Healthy/sig.mgh --csd

/usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm15/neg/th40/mc-z.csd
--mask lh.disease_Healthy_Age.glmdir/mask.mgh --cwsig

lh.disease_Healthy_Age.glmdir/lh-MS_vs_Healthy/cache.th40.neg.sig.cluster.mgh
--vwsig
lh.disease_Healthy_Age.glmdir/lh-MS_vs_Healthy/cache.th40.neg.sig.voxel.mgh
--sum

lh.disease_Healthy_Age.glmdir/lh-MS_vs_Healthy/cache.th40.neg.sig.cluster.summary
--ocn
lh.disease_Healthy_Age.glmdir/lh-MS_vs_Healthy/cache.th40.neg.sig.ocn.mgh
--oannot
lh.disease_Healthy_Age.glmdir/lh-MS_vs_Healthy/cache.th40.neg.sig.ocn.annot
--annot aparc --csdpdf
lh.disease_Healthy_Age.glmdir/lh-MS_vs_Healthy/cache.th40.neg.pdf.dat
--cwpvalthresh 0.05 --o
lh.disease_Healthy_Age.glmdir/lh-MS_vs_Healthy/cache.th40.neg.sig.masked.mgh
--no-fixmni --bonferroni 2 --surf white
# cwd
/media/ali/HU_Research/HU_Research/HU/MS_Project/MS_analysis/freesurfer_HU
# sysname  Linux
# hostname ali-XPS-L501X
# machine  x86_64
# FixVertexAreaFlag 1
# FixSurfClusterArea 1
#
# Input  lh.disease_Healthy_Age.glmdir/lh

Re: [Freesurfer] Parcellation stats

[Douglas Greve]

Try

cd $SUBJECTS_DIR/subject/scripts
 mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f 
../stats/lh.yeo.stats -b -a ../label/lh.yeo2011_17Networks_N1000.annot 
-c ../label/aparc.annot.ctab subject lh white




On 10/2/15 12:19 PM, Ali Radaideh wrote:
I am trying to extract the cortical volume, thickness, and area based 
on these 17Networks cortical parcellation.


Thanks,
Ali

On Fri, Oct 2, 2015 at 6:23 PM, Douglas Greve 
mailto:gr...@nmr.mgh.harvard.edu>> wrote:


You should not use both --seg and --annot. What are you trying to
accomplish?

On 10/2/15 3:34 AM, Ali Radaideh wrote:

Hi Bruce,

I have used the following command line:

mri_segstats --seg scz01/mri/aseg.mgz --annot scz01 lh
lh.yeo2011_17Networks_N1000.annot --sum scz01.aseg.sum

and got the following:

# ColHeaders  Index SegId NVoxels Volume_mm3 StructName
  1   0  15766121 15766121.0  Seg
  2   2182848 182848.0  Seg0002
  3   3215011 215011.0  Seg0003
  4   4  6547 6547.0  Seg0004
  5   5   572  572.0  Seg0005
  6   7 14053  14053.0  Seg0007
  7   8 47779  47779.0  Seg0008
  8  10  7151 7151.0  Seg0010
  9  11  4464 4464.0  Seg0011
 10  12  5264 5264.0  Seg0012
 11  13  1680 1680.0  Seg0013
 12  14   889  889.0  Seg0014
 13  15  1731 1731.0  Seg0015
 14  16 17307  17307.0  Seg0016
 15  17  3842 3842.0  Seg0017
 16  18  1106 1106.0  Seg0018
 17  24  1228 1228.0  Seg0024
 18  26   656  656.0  Seg0026
 19  28  3941 3941.0  Seg0028
 20  3026 26.0  Seg0030
 21  31  1222 1222.0  Seg0031
 22  41191593 191593.0  Seg0041
 23  42200955 200955.0  Seg0042
 24  43  6321 6321.0  Seg0043
 25  44   295  295.0  Seg0044
 26  46 16106  16106.0  Seg0046
 27  47 46472  46472.0  Seg0047
 28  49  6684 6684.0  Seg0049
 29  50  4308 4308.0  Seg0050
 30  51  5099 5099.0  Seg0051
 31  52  1459 1459.0  Seg0052
 32  53  4005 4005.0  Seg0053
 33  54   988  988.0  Seg0054
 34  58   633  633.0  Seg0058
 35  60  3554 3554.0  Seg0060
 36  6236 36.0  Seg0062
 37  63  1518 1518.0  Seg0063
 38  7218 18.0  Seg0072
 39  77  1040 1040.0  Seg0077
 40  8022 22.0  Seg0080
 41  85   124  124.0  Seg0085
 42 251   721  721.0  Seg0251
 43 252   403  403.0  Seg0252
 44 253   322  322.0  Seg0253
 45 254   360  360.0  Seg0254
 46 255   742  742.0  Seg0255


However,
I don't see the segmentation names (cortical parts). is my
command true/ complete or not?
These are 46 segmentations although I am using 17 networks
cortical parcellation, is this true?
Can I add anything to make the output more informative?. Also can
I get any surface area etc?



Many thanks in advance.
Ali

On Thu, Oct 1, 2015 at 10:43 PM, Bruce Fischl
mailto:fis...@nmr.mgh.harvard.edu>>
wrote:

sure, you can use mri_segstats to get stats from it
Bruce
On Thu, 1 Oct 2015, Ali Radaideh wrote:

Can we get any stats from this type of parcellation? I
only can see two
annotation files after running the mri_surf2surf command
and these can be
loaded tksurfer as an overlay.


Thanks,
Ali

On Tue, Sep 29, 2015 at 7:31 PM, Bruce Fischl
mailto:fis...@nmr.mgh.harvard.edu>>
wrote:
  that will generate a parcellation on the individual
subject
  surface of Thomas Yeo's 17-network clustering. It
won't do
  anything with the thickness though. What are you
trying to do?

  On Tue, 29 Sep 2015, Ali Radaideh wrote:

mri_surf2surf --srcsubject fsaverage --trgsubject
scz10 --hemi rh

--sval-annot$FREESURFER_HOME/subjects/fsaverage/label/rh.Yeo2011_17Networks
_N1000.annot
--tval
$SUBJECTS_DIR/scz10/label/rh.Yeo2011_17Networks_N1000.annot

scz10 is my subject name

On Tue, Sep 29, 2015 at 2:46 AM, Douglas Greve
mailto:gr...@nmr.mgh.harvard.edu>>
wrote:
  what is your surf2surf command?

  On 9/28/15 5:11 PM, Ali Radaideh wrote:
  Dear Douglas,

Thanks for your email. I meant to say that after
running the
recon-all, i ran the sur2surf command to get the
cortical
parcellation using Thomas Yeo Atlas.

  

Re: [Freesurfer] Group Analysis

[Douglas Greve]

I notice from the image that the overlay is turned off. Try turning it 
on. Also, you can try


tksurferfv fsaverage lh inflated -aparc -ov sig.mgh

If that does not work, then

tksurfer fsaverage lh inflated -aparc -ov sig.mgh


On 10/2/15 12:08 PM, Ali Radaideh wrote:

Hi,

I am running a group analysis (patients versus controls). I am 
following the tutorial and managed to create the FSGD file with four 
classes

MSMale
MSFemale
HealthyMale
HealthyFemale

and one variable: Age


So the number of NregressorsDODS is equal to 8

[ MSMale MSFemale HealthyMale HealthyFemale  Age_ MSMale 
 Age_ MSFemale  Age_ HealthyMale  Age_ HealthyFemale ]


I have created my own contrast files as follows:

lh-female_MS_vs_Healthy
​.mtx /
to
//
compare between Female MS and Female Healthy regardless of age
/:
*[ 0 1 0 -1 0 0 0 0 ]​*

/
/
/lh-female_MS_vs_Healthy_Age
​ .mtx
//
​​
/
​
/
to
//
compare between Female MS and Female Healthy_with age effect
/:
*
​[​
0 0 0 0 0 1 0 -1
​]
*

/lh-male_MS_vs_Healthy
​ .mtx
/
​
/
to
//
compare between Male MS and Male Healthy regardless of age
/:
/*
​[ ​
1 0 -1 0 0 0 0 0
​] ​
*
/
/
/
/lh-male_MS_vs_Healthy_Age
​ .mtx​  to
//
compare between Male MS and Male Healthy_with age effect
//
/:
*/
[
//0 0 0 0 1 0 -1 0
​ ]​
/*
/

/
/
​
//
​
//lh-MS_vs_Healthy
​ .mtx​   to compare between MS and Healthy regardless of Age and Gender
/:
*/
​ [
//0.5 0.5 -0.5 -0.5 0 0 0 0 //
] ​
/*
/

/
/

/
/
I ran the glm_fit using the following command line:
/
/
mri_glmfit --y lh.disease_Healthy_Age.thickness.10.mgh --fsgd 
disease_Healthy_Age.fsgd dods --C lh-MS_vs_Healthy.mtx --C 
lh-male_MS_vs_Healthy_Age.mtx --C lh-male_MS_vs_Healthy.mtx --C 
lh-female_MS_vs_Healthy_Age.mtx --C lh-female_MS_vs_Healthy.mtx --surf 
fsaverage lh --cortex --glmdir lh.disease_Healthy_Age.glmdir

/
/

/

/
Everything went OK except when loading the sig.mgh in freeview using 
the following command:

/
/

/
/
freeview -f 
$SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=lh.disease_Healthy_Age.glmdir/lh-MS_vs_Healthy/sig.mgh:overlay_threshold=4,5 
-viewport 3d


1- It complained that the flag /
annot_outline=1 is not recognized
/
/
2- after removing this flag from the command line, t
//
he overlay only was two colors (green and red) (I have attached a copy 
of it)

/
/
/
/
/
​ Then I did
/ a cluster-wise correction for multiple comparisons
​ by​
run
​n​
ing​
a simulation/
​ as follows:
/
/
mri_glmfit-sim --glmdir lh.disease_Healthy_Age.glmdir --cache 4 neg 
--cwp  0.05 --2spaces

/
/

/
/
Nothing has changed. i_n free view the same overlay._
/
/

/
/
I opened the   "
/cache.th40.neg.sig.cluster.summary
​" file​
​ and got the following:

# Cluster Growing Summary (mri_surfcluster)
# $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $
# $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
# CreationTime 2015/10/02-15:06:07-GMT
# cmdline mri_surfcluster --in 
lh.disease_Healthy_Age.glmdir/lh-MS_vs_Healthy/sig.mgh --csd 
/usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm15/neg/th40/mc-z.csd 
--mask lh.disease_Healthy_Age.glmdir/mask.mgh --cwsig 
lh.disease_Healthy_Age.glmdir/lh-MS_vs_Healthy/cache.th40.neg.sig.cluster.mgh 
--vwsig 
lh.disease_Healthy_Age.glmdir/lh-MS_vs_Healthy/cache.th40.neg.sig.voxel.mgh 
--sum 
lh.disease_Healthy_Age.glmdir/lh-MS_vs_Healthy/cache.th40.neg.sig.cluster.summary 
--ocn 
lh.disease_Healthy_Age.glmdir/lh-MS_vs_Healthy/cache.th40.neg.sig.ocn.mgh 
--oannot 
lh.disease_Healthy_Age.glmdir/lh-MS_vs_Healthy/cache.th40.neg.sig.ocn.annot 
--annot aparc --csdpdf 
lh.disease_Healthy_Age.glmdir/lh-MS_vs_Healthy/cache.th40.neg.pdf.dat 
--cwpvalthresh 0.05 --o 
lh.disease_Healthy_Age.glmdir/lh-MS_vs_Healthy/cache.th40.neg.sig.masked.mgh 
--no-fixmni --bonferroni 2 --surf white
# cwd 
/media/ali/HU_Research/HU_Research/HU/MS_Project/MS_analysis/freesurfer_HU

# sysname  Linux
# hostname ali-XPS-L501X
# machine  x86_64
# FixVertexAreaFlag 1
# FixSurfClusterArea 1
#
# Input  lh.disease_Healthy_Age.glmdir/lh-MS_vs_Healthy/sig.mgh
# Frame Number  0
# srcsubj fsaverage
# hemi lh
# surface white
# annot aparc
# SUBJECTS_DIR 
/media/ali/HU_Research/HU_Research/HU/MS_Project/MS_analysis/freesurfer_HU

# SearchSpace_mm2 65416.6
# SearchSpace_vtx 149955
# Bonferroni 2
# Minimum Threshold 4
# Maximum Threshold infinity
# Threshold Signneg
# AdjustThreshWhenOneTail 1
# CW PValue Threshold: 0.05
# Area Threshold0 mm^2
# CSD thresh  4.00
# CSD nreps1
# CSD simtype  null-z
# CSD contrast NA
# CSD confint  90.00
# Overall max 2.82441 at vertex 65720
# Overall min -3.14816 at vertex 26640
# NClusters  0
# Total Cortical Surface Area 65416.6 (mm^2)
# FixMNI = 0
#
# ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZCWP   
 CWPLowCWPHi NVtxs   Annot



​As you can see, the columns are empty!!!


Any ideas please? was there any mistake in my processing?

Many thanks for your help.

Ali​


/Ali M. Al-Radaideh. PhD/
/Head o

Re: [Freesurfer] Parcellation stats

[Ali Radaideh]

I am trying to extract the cortical volume, thickness, and area based on
these 17Networks cortical parcellation.

Thanks,
Ali

On Fri, Oct 2, 2015 at 6:23 PM, Douglas Greve 
wrote:

> You should not use both --seg and --annot. What are you trying to
> accomplish?
>
> On 10/2/15 3:34 AM, Ali Radaideh wrote:
>
> Hi Bruce,
>
> I have used the following command line:
>
> mri_segstats --seg scz01/mri/aseg.mgz --annot scz01 lh
> lh.yeo2011_17Networks_N1000.annot --sum scz01.aseg.sum
>
> and got the following:
>
> # ColHeaders  Index SegId NVoxels Volume_mm3 StructName
>   1   0  15766121 15766121.0  Seg
>   2   2182848   182848.0  Seg0002
>   3   3215011   215011.0  Seg0003
>   4   4  6547 6547.0  Seg0004
>   5   5   572  572.0  Seg0005
>   6   7 1405314053.0  Seg0007
>   7   8 4777947779.0  Seg0008
>   8  10  7151 7151.0  Seg0010
>   9  11  4464 4464.0  Seg0011
>  10  12  5264 5264.0  Seg0012
>  11  13  1680 1680.0  Seg0013
>  12  14   889  889.0  Seg0014
>  13  15  1731 1731.0  Seg0015
>  14  16 1730717307.0  Seg0016
>  15  17  3842 3842.0  Seg0017
>  16  18  1106 1106.0  Seg0018
>  17  24  1228 1228.0  Seg0024
>  18  26   656  656.0  Seg0026
>  19  28  3941 3941.0  Seg0028
>  20  3026   26.0  Seg0030
>  21  31  1222 1222.0  Seg0031
>  22  41191593   191593.0  Seg0041
>  23  42200955   200955.0  Seg0042
>  24  43  6321 6321.0  Seg0043
>  25  44   295  295.0  Seg0044
>  26  46 1610616106.0  Seg0046
>  27  47 4647246472.0  Seg0047
>  28  49  6684 6684.0  Seg0049
>  29  50  4308 4308.0  Seg0050
>  30  51  5099 5099.0  Seg0051
>  31  52  1459 1459.0  Seg0052
>  32  53  4005 4005.0  Seg0053
>  33  54   988  988.0  Seg0054
>  34  58   633  633.0  Seg0058
>  35  60  3554 3554.0  Seg0060
>  36  6236   36.0  Seg0062
>  37  63  1518 1518.0  Seg0063
>  38  7218   18.0  Seg0072
>  39  77  1040 1040.0  Seg0077
>  40  8022   22.0  Seg0080
>  41  85   124  124.0  Seg0085
>  42 251   721  721.0  Seg0251
>  43 252   403  403.0  Seg0252
>  44 253   322  322.0  Seg0253
>  45 254   360  360.0  Seg0254
>  46 255   742  742.0  Seg0255
>
>
> However,
> I don't see the segmentation names (cortical parts). is my command true/
> complete or not?
> These are 46 segmentations although I am using 17 networks cortical
> parcellation, is this true?
> Can I add anything to make the output more informative?. Also can I get
> any surface area etc?
>
>
>
> Many thanks in advance.
> Ali
>
> On Thu, Oct 1, 2015 at 10:43 PM, Bruce Fischl 
> wrote:
>
>> sure, you can use mri_segstats to get stats from it
>> Bruce
>> On Thu, 1 Oct 2015, Ali Radaideh wrote:
>>
>> Can we get any stats from this type of parcellation? I only can see two
>>> annotation files after running the mri_surf2surf command and these can be
>>> loaded tksurfer as an overlay.
>>>
>>>
>>> Thanks,
>>> Ali
>>>
>>> On Tue, Sep 29, 2015 at 7:31 PM, Bruce Fischl <
>>> fis...@nmr.mgh.harvard.edu>
>>> wrote:
>>>   that will generate a parcellation on the individual subject
>>>   surface of Thomas Yeo's 17-network clustering. It won't do
>>>   anything with the thickness though. What are you trying to do?
>>>
>>>   On Tue, 29 Sep 2015, Ali Radaideh wrote:
>>>
>>> mri_surf2surf --srcsubject fsaverage --trgsubject
>>> scz10 --hemi rh
>>>
>>> --sval-annot$FREESURFER_HOME/subjects/fsaverage/label/rh.Yeo2011_17Networks
>>> _N1000.annot
>>> --tval
>>> $SUBJECTS_DIR/scz10/label/rh.Yeo2011_17Networks_N1000.annot
>>>
>>> scz10 is my subject name
>>>
>>> On Tue, Sep 29, 2015 at 2:46 AM, Douglas Greve
>>> 
>>> wrote:
>>>   what is your surf2surf command?
>>>
>>>   On 9/28/15 5:11 PM, Ali Radaideh wrote:
>>>   Dear Douglas,
>>>
>>> Thanks for your email. I meant to say that after
>>> running the
>>> recon-all, i ran the sur2surf command to get the
>>> cortical
>>> parcellation using Thomas Yeo Atlas.
>>>
>>> I thought that the extracted cortical thickness
>>> after running
>>> the surf2surf command will be different from the one
>>> extracted
>>> before running the command. But, Bruce kindly
>>> replied to my
>>> email saying that it is the same if it is calculated
>>> on
>>> vertex-wise basis.
>>>
>>> Thanks,
>>> Ali
>>>
>>> On Mon, Sep 28, 2015 at 11:01 PM, Douglas N Greve
>>>  wrote:
>>>   I can't understand what you are asking. Can
>>>  

Re: [Freesurfer] mris_surf2vol

[Kevin Aquino]

Ah sorry for not being clear,

Basically I would like the output from mris_surf2vol with the mask option
to be less speckled.

For example, in the image attached:
http://www.physics.usyd.edu.au/~aquino/example_mri_surf2vol.png

there are some voxels missing. Is there an option to fill these voxels?


Cheers,


*Dr Kevin Aquino*
Research fellow,
Sir Peter Mansfield Magnetic Resonance Center, The University of
Nottingham.

Honorary Research Fellow
School of Physics, Faculty of Science, University of Sydney

*E* kevin.aqu...@nottingham.ac.uk, aqu...@physics.usyd.edu.au | *W*
www.physics.usyd.edu.au/~aquino/

--

The brain is a wonderful organ. It starts working the moment you get up and
does not stop until you get into the office.
-
Robert Frost

CRICOS 00026A
This email plus any attachments to it are confidential. Any unauthorised
use is strictly prohibited. If you receive this email in error, please
delete it and any attachments.

Please think of our environment and only print this e-mail if necessary.


On Fri, Oct 2, 2015 at 1:42 PM, Bruce Fischl 
wrote:

> Hi Kevin
>
> I'm not clear on what you need. Would mri_surf2vol --fillribbon do what
> you want? I don't really know what else "voxelize" means
>
> cheers
> Bruce
>
>
> On Fri, 2 Oct 2015, Kevin Aquino wrote:
>
> Hi all,
>> I am trying to "voxelize" the cortical surfaces generated in freesurfer
>> and
>> I am a little stuck.
>>
>> I have been using mris_surf2vol with the --mask option however this
>> generates a very speckled representation of the cortical surface on the
>> voxels. What I would prefer would be the level sets of the cortical
>> surface
>> interpolated onto voxels, even if they are at a different resolution that
>> could be enough. Is this possible with any of the available commands?
>>
>> I also went down the route of mris_volmask however, this generates the
>> cortical ribbon, which is something that I don't need.
>>
>> Cheers,
>>
>>
>> Dr Kevin Aquino
>> Research fellow,
>> Sir Peter Mansfield Magnetic Imaging Center,
>> School of Physics & astronomy, The University of Nottingham.
>>
>> Honorary Research Fellow
>> School of Physics, Faculty of Science, University of Sydney.
>>
>> E kevin.aqu...@nottingham.ac.uk, aqu...@physics.usyd.edu.au | W
>> www.physics.usyd.edu.au/~aquino/
>>
>> --
>>
>> The brain is a wonderful organ. It starts working the moment you get up
>> and
>> does not stop until you get into the office.
>> -
>> Robert Frost
>>
>> CRICOS 00026A
>> This email plus any attachments to it are confidential. Any unauthorised
>> use
>> is strictly prohibited. If you receive this email in error, please delete
>> it
>> and any attachments.
>>
>> Please think of our environment and only print this e-mail if necessary.
>>
>>
>>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
___
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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] FreeSurfer Ubuntu Server

[Rudolph Pienaar]

Your best bet I fear might be to try and build FreeSurfer yourself on 
your specific distro of Ubuntu.


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

While not impossible (we have done this), it does require some detailed 
knowledge of Linux in general and Ubuntu in particular as you will have 
to resolve all the required dependencies and adapt the build commands 
accordingly. Still compiling your own FreeSurfer  will mean that there 
will be no library version conflicts which is what most likely will 
happen in the case of running the CentOS version on Ubuntu. And once you 
compile your own version from source, it will run on all your cluster 
nodes w/o issues.


If you use a binary version (like the CentOS build), you would have to 
execute the instructions I presented (i.e. the synlinks) on *every* 
cluster node.


CentOS, like Ubuntu, is a distribution of Linux. That means that they 
are all Linux, but differ in the type and versions of various 
applications and libraries. CentOS is typically more conservative and 
generally has older versions of libraries than Ubuntu. Since the 
distributed FreeSurfer is dynamically compiled against the installation 
of CentOS at the NMR, it expects very specific version numbers on 
various system libraries. Usually these versions are no longer bundled 
on other more agile distributions like Ubuntu. Thankfully, it is usually 
sufficient to "trick" the various CentOS FreeSurfer apps on Ubuntu by 
simply making a symbolic from an existing system library to the 
name/version the FreeSurfer app expects. This is a "hack" and not 
guaranteed to always work. Having said that, the CentOS build of 
FreeSurfer works fine on Ubuntu 14.04+ using the link commands I listed 
earlier.


All you need to do is Just download the CentOS version and try those 
link command. Although, I'm not 100% sure about Ubuntu 12.04. As I said, 
those link instructions are valid for Ubuntu 14.04 and above, so your 
mileage might vary. Also, you will need to have root access on each 
machine that you want to run those commands on. In the case of a 
cluster, this would mean running those command (as sudo) on *all* 
cluster nodes.  Unless you are the cluster administrator, this might be 
difficult (or impossible) to do.


It might be that the best option for you is to roll your own FreeSurfer 
by compiling it from source in your environment.


HTH
-=R

On 10/02/2015 10:53 AM, Bruno LAD wrote:

Thanks for you reply, Rudolph.

We have a cluster environment in our university, and the best Ubuntu 
version to us for now is Ubuntu 12.04 (in a closest future we will 
update to a newer version, but not now...).


In the download page there is only FreeSurfer for CentOS, Mac and a 
Virtual Machine of Xubuntu, but not to Ubuntu. ( 
https://surfer.nmr.mgh.harvard.edu/fswiki/Download )


I couldn't find the binaries to compile, too. I've looked at ( 
http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/ ).


To me the best choice is the binaries or the compiled source (not apt, 
yum, etc..) , because we put all applications in "/usr/local".



Could you help me to find one of these options to download?


Thanks again

--
Att,
Bruno Bragança Mendes
Laboratório de Alto Desempenho LAD/PUCRS
Av. Ipiranga, 6681 - Prédio 32 Térreo - Sala 120
+55 51 33538001 

2015-10-01 18:40 GMT-03:00 Rudolph Pienaar >:


Yes, FreeSurfer can be installed on Ubuntu without any issues.
There is
also no functional difference between Ubuntu server and Ubuntu
Desktop.

Do you have a compelling reason for wanting to use Ubuntu 12.04?
It was
released in 2012 and is rather ancient in Ubuntu terms. The current
version of Ubuntu is 15.04 and in fact 15.10 is about to released in
three weeks.

I'd strongly recommend you update to a modern Ubuntu.

Having said that, certainly on Ubuntu 14.04 and above, once installed
you need to simply symlink some libraries since the versions
FreeSurfer
has been compiled against are depreciated on Ubuntu 14.04 and later.

In a terminal, simply type (make sure that each command is on a single
line -- the email formatting might have split it in two):

For Trackvis and dtk

sudo ln -s /usr/lib/x86_64-linux-gnu/libtiff.so.5
/usr/lib/x86_64-linux-gnu/libtiff.so.3

sudo ln -s /usr/lib/x86_64-linux-gnu/libmng.so.2.0.2
/usr/lib/x86_64-linux-gnu/libmng.so.1

For FreeSurfer:

sudo ln -s /usr/lib/x86_64-linux-gnu/libvnl_algo.so
/usr/lib/x86_64-linux-gnu/libvnl_algo.so.1.14

sudo ln -s /usr/lib/x86_64-linux-gnu/libvnl.so
/usr/lib/x86_64-linux-gnu/libvnl.so.1.14

sudo ln -s /usr/lib/x86_64-linux-gnu/libv3p_netlib.so
/usr/lib/x86_64-linux-gnu/libv3p_netlib.so.1.14

HTH
-=R

On 10/1/15 15:58 , Bruno LAD wrote:
> Hi, could you help me please, because a couldn't find the answer
for my
> question in the wiki.
>
> Can FreeSurfer be installed on ub

Re: [Freesurfer] Parcellation stats

[Douglas Greve]

You should not use both --seg and --annot. What are you trying to 
accomplish?


On 10/2/15 3:34 AM, Ali Radaideh wrote:

Hi Bruce,

I have used the following command line:

mri_segstats --seg scz01/mri/aseg.mgz --annot scz01 lh 
lh.yeo2011_17Networks_N1000.annot --sum scz01.aseg.sum


and got the following:

# ColHeaders  Index SegId NVoxels Volume_mm3 StructName
  1   0  15766121 15766121.0  Seg
  2   2182848   182848.0  Seg0002
  3   3215011   215011.0  Seg0003
  4   4  6547 6547.0  Seg0004
  5   5   572  572.0  Seg0005
  6   7 1405314053.0  Seg0007
  7   8 4777947779.0  Seg0008
  8  10  7151 7151.0  Seg0010
  9  11  4464 4464.0  Seg0011
 10  12  5264 5264.0  Seg0012
 11  13  1680 1680.0  Seg0013
 12  14   889  889.0  Seg0014
 13  15  1731 1731.0  Seg0015
 14  16 1730717307.0  Seg0016
 15  17  3842 3842.0  Seg0017
 16  18  1106 1106.0  Seg0018
 17  24  1228 1228.0  Seg0024
 18  26   656  656.0  Seg0026
 19  28  3941 3941.0  Seg0028
 20  3026   26.0  Seg0030
 21  31  1222 1222.0  Seg0031
 22  41191593   191593.0  Seg0041
 23  42200955   200955.0  Seg0042
 24  43  6321 6321.0  Seg0043
 25  44   295  295.0  Seg0044
 26  46 1610616106.0  Seg0046
 27  47 4647246472.0  Seg0047
 28  49  6684 6684.0  Seg0049
 29  50  4308 4308.0  Seg0050
 30  51  5099 5099.0  Seg0051
 31  52  1459 1459.0  Seg0052
 32  53  4005 4005.0  Seg0053
 33  54   988  988.0  Seg0054
 34  58   633  633.0  Seg0058
 35  60  3554 3554.0  Seg0060
 36  6236   36.0  Seg0062
 37  63  1518 1518.0  Seg0063
 38  7218   18.0  Seg0072
 39  77  1040 1040.0  Seg0077
 40  8022   22.0  Seg0080
 41  85   124  124.0  Seg0085
 42 251   721  721.0  Seg0251
 43 252   403  403.0  Seg0252
 44 253   322  322.0  Seg0253
 45 254   360  360.0  Seg0254
 46 255   742  742.0  Seg0255


However,
I don't see the segmentation names (cortical parts). is my command 
true/ complete or not?
These are 46 segmentations although I am using 17 networks cortical 
parcellation, is this true?
Can I add anything to make the output more informative?. Also can I 
get any surface area etc?




Many thanks in advance.
Ali

On Thu, Oct 1, 2015 at 10:43 PM, Bruce Fischl 
mailto:fis...@nmr.mgh.harvard.edu>> wrote:


sure, you can use mri_segstats to get stats from it
Bruce
On Thu, 1 Oct 2015, Ali Radaideh wrote:

Can we get any stats from this type of parcellation? I only
can see two
annotation files after running the mri_surf2surf command and
these can be
loaded tksurfer as an overlay.


Thanks,
Ali

On Tue, Sep 29, 2015 at 7:31 PM, Bruce Fischl
mailto:fis...@nmr.mgh.harvard.edu>>
wrote:
  that will generate a parcellation on the individual subject
  surface of Thomas Yeo's 17-network clustering. It won't do
  anything with the thickness though. What are you trying
to do?

  On Tue, 29 Sep 2015, Ali Radaideh wrote:

mri_surf2surf --srcsubject fsaverage --trgsubject
scz10 --hemi rh

--sval-annot$FREESURFER_HOME/subjects/fsaverage/label/rh.Yeo2011_17Networks
_N1000.annot
--tval
$SUBJECTS_DIR/scz10/label/rh.Yeo2011_17Networks_N1000.annot

scz10 is my subject name

On Tue, Sep 29, 2015 at 2:46 AM, Douglas Greve
mailto:gr...@nmr.mgh.harvard.edu>>
wrote:
  what is your surf2surf command?

  On 9/28/15 5:11 PM, Ali Radaideh wrote:
  Dear Douglas,

Thanks for your email. I meant to say that after
running the
recon-all, i ran the sur2surf command to get the
cortical
parcellation using Thomas Yeo Atlas.

I thought that the extracted cortical thickness
after running
the surf2surf command will be different from the one
extracted
before running the command. But, Bruce kindly
replied to my
email saying that it is the same if it is calculated
on
vertex-wise basis.

Thanks,
Ali

On Mon, Sep 28, 2015 at 11:01 PM, Douglas N Greve
mailto:gr...@nmr.mgh.harvard.edu>> wrote:
  I can't understand what you are asking. Can
you
  elaborate?

Re: [Freesurfer] FreeSurfer Ubuntu Server

[Bruno LAD]

Thanks for you reply, Rudolph.

We have a cluster environment in our university, and the best Ubuntu
version to us for now is Ubuntu 12.04 (in a closest future we will update
to a newer version, but not now...).

In the download page there is only FreeSurfer for CentOS, Mac and a Virtual
Machine of Xubuntu, but not to Ubuntu. (
https://surfer.nmr.mgh.harvard.edu/fswiki/Download )

I couldn't find the binaries to compile, too. I've looked at (
http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/ ).

To me the best choice is the binaries or the compiled source (not apt, yum,
etc..) , because we put all applications in "/usr/local".


Could you help me to find one of these options to download?


Thanks again

-- 
Att,
Bruno Bragança Mendes
Laboratório de Alto Desempenho LAD/PUCRS
Av. Ipiranga, 6681 - Prédio 32 Térreo - Sala 120
+55 51 33538001

2015-10-01 18:40 GMT-03:00 Rudolph Pienaar :

> Yes, FreeSurfer can be installed on Ubuntu without any issues. There is
> also no functional difference between Ubuntu server and Ubuntu Desktop.
>
> Do you have a compelling reason for wanting to use Ubuntu 12.04? It was
> released in 2012 and is rather ancient in Ubuntu terms. The current
> version of Ubuntu is 15.04 and in fact 15.10 is about to released in
> three weeks.
>
> I'd strongly recommend you update to a modern Ubuntu.
>
> Having said that, certainly on Ubuntu 14.04 and above, once installed
> you need to simply symlink some libraries since the versions FreeSurfer
> has been compiled against are depreciated on Ubuntu 14.04 and later.
>
> In a terminal, simply type (make sure that each command is on a single
> line -- the email formatting might have split it in two):
>
> For Trackvis and dtk
>
> sudo ln -s /usr/lib/x86_64-linux-gnu/libtiff.so.5
> /usr/lib/x86_64-linux-gnu/libtiff.so.3
>
> sudo ln -s /usr/lib/x86_64-linux-gnu/libmng.so.2.0.2
> /usr/lib/x86_64-linux-gnu/libmng.so.1
>
> For FreeSurfer:
>
> sudo ln -s /usr/lib/x86_64-linux-gnu/libvnl_algo.so
> /usr/lib/x86_64-linux-gnu/libvnl_algo.so.1.14
>
> sudo ln -s /usr/lib/x86_64-linux-gnu/libvnl.so
> /usr/lib/x86_64-linux-gnu/libvnl.so.1.14
>
> sudo ln -s /usr/lib/x86_64-linux-gnu/libv3p_netlib.so
> /usr/lib/x86_64-linux-gnu/libv3p_netlib.so.1.14
>
> HTH
> -=R
>
> On 10/1/15 15:58 , Bruno LAD wrote:
> > Hi, could you help me please, because a couldn't find the answer for my
> > question in the wiki.
> >
> > Can FreeSurfer be installed on ubuntu server 12.04? How can I do it, if
> > it's possible?
> >
> >
> > Thank you.
> >
> > --
> > Best Regards
> > Bruno Bragança Mendes
> > Laboratório de Alto Desempenho LAD/PUCRS
> > Av. Ipiranga, 6681 - Prédio 32 Térreo - Sala 120
> > +55 51 33538001 
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > The information in this e-mail is intended only for the person to whom
> it is
> > addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> > contains patient information, please contact the Partners Compliance
> HelpLine at
> > http://www.partners.org/complianceline . If the e-mail was sent to you
> in error
> > but does not contain patient information, please contact the sender and
> properly
> > dispose of the e-mail.
> >
>
>
> --
> Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu
> MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging
> 149 (2301) 13th Street, Charlestown, MA 02129 USA
> ___
> Freesurfer mailing list
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Re: [Freesurfer] mris_surf2vol

[Bruce Fischl]

Hi Kevin

I'm not clear on what you need. Would mri_surf2vol --fillribbon do what 
you want? I don't really know what else "voxelize" means


cheers
Bruce

On Fri, 2 Oct 2015, Kevin Aquino wrote:


Hi all,
I am trying to "voxelize" the cortical surfaces generated in freesurfer and
I am a little stuck.

I have been using mris_surf2vol with the --mask option however this
generates a very speckled representation of the cortical surface on the
voxels. What I would prefer would be the level sets of the cortical surface
interpolated onto voxels, even if they are at a different resolution that
could be enough. Is this possible with any of the available commands?

I also went down the route of mris_volmask however, this generates the
cortical ribbon, which is something that I don't need.

Cheers,


Dr Kevin Aquino
Research fellow,
Sir Peter Mansfield Magnetic Imaging Center,
School of Physics & astronomy, The University of Nottingham. 

Honorary Research Fellow
School of Physics, Faculty of Science, University of Sydney.

E kevin.aqu...@nottingham.ac.uk, aqu...@physics.usyd.edu.au | W
www.physics.usyd.edu.au/~aquino/

--

The brain is a wonderful organ. It starts working the moment you get up and
does not stop until you get into the office.
-
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CRICOS 00026A
This email plus any attachments to it are confidential. Any unauthorised use
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Please think of our environment and only print this e-mail if necessary.


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Re: [Freesurfer] White Matter Edits vs. Control Points, & third party software

[Bruce Fischl]

Hi Alberto

1. No, this is not the same. The control points are used to estimate the 
bias field, which can affect an entire regions. Replacing a voxel in the 
brainmask with a 110 will only affect that voxel.


2. You can do this if you want but you have to be careful how you edit. 
When we turn something "off" we set it to 1, not 0 so we can track and 
preserve it, and similarly when we turn it "on" we set it to 255.


cheers
Bruce

On Fri, 2 Oct 2015, Julio 
Alberto González Torre wrote:



I have some questions about how to manually correct the white matter
regions.

It's the same manually edit the volume "brainmask.mgz" and use control
points? Would I get the same result? My intention is not to use control
points, but directly replace the voxels that have not been classified as
white matter with the value 110. Is it right to do this?

My second question is: Is it possible to edit the volumes with a third party
program? My intention here is to turn the volume "brainmask.mgz" to
"brainmask.nii" using "mri_convert" command. Then edit the values of the
voxels manually with a third party software or painting tool, and finally,
turn the volume back to "brainmask.mgz", replace the file in their
respective directory, and finally execute "-autorecon2- wm". Is it right to
do this? Or this may compromise my data?

Thanks in advance,
Alberto.

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Re: [Freesurfer] White matter Error

[Bruce Fischl]

Hi Trinh

can you just attach the images? Your link didn't work for me. You can check 
the topology of the surface computationally using mris_euler_number. You 
might also try moving backwards/forwards a few slices to try to understand 
what is going on.


cheers
Bruce

On Fri, 2 Oct 
2015, Thục Trinh wrote:





​[icon_10_generic_list.png]  NCP140539_2_recon.rar
​Hi Freesurfer Experts,

We are on the process of troubleshooting our subjects's recon and we came
across with this error that we can not determine what kind of problem this
is: 
It seems there is no white matter and pial errors on all slices as we check
on three different views (sagital,coronal and axial);however, when we load
rh.inflated.nofix surface on both freeview and tksurfer, there is a big
difference that at the frontal cortex (area near the medial wall), it
appears a handle error and also some hole errors on freeview while it does
not on tksurfer.
Would you explain how it is visualized that makes us so confused to
troubleshoot since we can not find anything wrong on white matter volume to
be fixed?
Here is our data,

Have a nice day,

Trinh


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[Freesurfer] Statistical tests on Tracula's path spline

[Yuwen Hung]

Hi, 
Thanks for the great FreeSurfer Course this past week.
After running through Tracula and extracted the path stats (by voxel) across 
all subjects, can I apply mri_glmfit to test the group differences using the 
generated txt file that has all subject's diffusion meassure (e.g., FA) along 
particular spline voxels (the pathstats.byvoxel.txt, for example)?

Thanks!

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of 
freesurfer-requ...@nmr.mgh.harvard.edu [freesurfer-requ...@nmr.mgh.harvard.edu]
Sent: 01 October 2015 12:00
To: freesurfer@nmr.mgh.harvard.edu
Subject: Freesurfer Digest, Vol 140, Issue 3

Send Freesurfer mailing list submissions to
freesurfer@nmr.mgh.harvard.edu

To subscribe or unsubscribe via the World Wide Web, visit
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
or, via email, send a message with subject or body 'help' to
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You can reach the person managing the list at
freesurfer-ow...@nmr.mgh.harvard.edu

When replying, please edit your Subject line so it is more specific
than "Re: Contents of Freesurfer digest..."


Today's Topics:

   1. WM segmentation error longitudinal stream (Adam, Ruth)
   2. Test incoming emails - (pablo najt)
   3. Re: dt_recon (Alshikho, Mohamad J.)
   4. mri_convert doubles file size when changing TR header
  information (Shaun Patel)
   5. Re: PVE correction tool within the V 6 beta (m.ba...@ulg.ac.be)
   6. Re: Error Messages for Accessing Bin (Bruce Fischl)
   7. Re: Calculate the cortical thickness in patients with brain
  tumor (Bruce Fischl)
   8. Re: Calculating local gyrification using CIVET's surface file
  ('.obj') (Bruce Fischl)


--

Message: 1
Date: Thu, 1 Oct 2015 14:35:30 +0200
From: "Adam, Ruth" 
Subject: [Freesurfer] WM segmentation error longitudinal stream
To: Freesurfer support list 
Message-ID: 
Content-Type: text/plain; charset="us-ascii"

Hi all,

We have run longitudinal analysis on two time points.
The resulting longitudinal WM surface for both time points excludes large parts 
of the cortex.
The cross sectional surfaces and the wm.mgz are correct.
The base wm.mgz also seems to be fine, however, the base white and pial 
surfaces do not follow the wm volume properly.

We have rerun the longitudinal anlaysis (recon-all -long) according to the 
cheat sheet:
1. marking the base wm.mgz border with 255 voxel value (instead of 110)
2. adding control points to the base wm.mgz
but it did not change the original result.

Any idea how this can be fixed?
Thank you very much in advance!

Best,
ruthi


--

Message: 2
Date: Thu, 1 Oct 2015 13:27:37 +
From: pablo najt 
Subject: [Freesurfer] Test incoming emails -
To: "freesurfer@nmr.mgh.harvard.edu" 
Message-ID: 
Content-Type: text/plain; charset="iso-8859-1"

I am sending this message as a test since my income emails from FS stopped 
working on the 29 of September.Regards

-- next part --
An HTML attachment was scrubbed...
URL: 
http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20151001/a068fe7f/attachment.html

--

Message: 3
Date: Thu, 1 Oct 2015 14:03:27 +
From: "Alshikho, Mohamad J." 
Subject: Re: [Freesurfer] dt_recon
To: Freesurfer support list 
Message-ID:

Content-Type: text/plain; charset="us-ascii"

Hi Doug,
Thank you very much for your answers!

Kindly I have one more question:
At the end of DTI analysis using the tool "dt_recon" we will have  " stats" 
file including the FA value for every segment and parcellate in the brain. 
Depending on this output can we use the term " DTI morphometry" to describe the 
analysis?


Thanks
Mohamad

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve
Sent: Monday, September 28, 2015 11:26 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] dt_recon


On 9/25/15 9:28 AM, Alshikho, Mohamad J. wrote:
Hi Doug and Bruce,
After running the command :
dt_recon --i 6-1025.dcm --s M87102113 --o dti dt_recon --i f.nii --b f.bvals 
f.bvecs --s M87102113 --o dti  <<< source:   Freesurfer wiki>>>

I need to generate the final statistics ( FA for every parcellate and segment 
in aseg and wmparc atlases) using the command "mri_segstats"

In order to do so I need to move "fa.nii" to anatomical space using the command:

mri_vol2vol -mov fa.nii -lta register.lta -fstarg -o fa.anat.mgh
  <<< source:   Freesurfer wiki>>>


My questions are about the file "register.lta" :

1.   What is the difference between this file and the file "register.dat" ( 
which I can see it as an output of  the command " bbregister" in the final 
analysis using the command "dt_recon")
They hold the same basic

[Freesurfer] mris_surf2vol

[Kevin Aquino]

Hi all,

I am trying to "voxelize" the cortical surfaces generated in freesurfer and
I am a little stuck.

I have been using mris_surf2vol with the --mask option however this
generates a very speckled representation of the cortical surface on the
voxels. What I would prefer would be the level sets of the cortical surface
interpolated onto voxels, even if they are at a different resolution that
could be enough. Is this possible with any of the available commands?

I also went down the route of mris_volmask however, this generates the
cortical ribbon, which is something that I don't need.

Cheers,


*Dr Kevin Aquino*
Research fellow,
Sir Peter Mansfield Magnetic Imaging Center,
School of Physics & astronomy, The University of Nottingham.

Honorary Research Fellow
School of Physics, Faculty of Science, University of Sydney.

*E* kevin.aqu...@nottingham.ac.uk, aqu...@physics.usyd.edu.au | *W*
www.physics.usyd.edu.au/~aquino/

--

The brain is a wonderful organ. It starts working the moment you get up and
does not stop until you get into the office.
-
Robert Frost

CRICOS 00026A
This email plus any attachments to it are confidential. Any unauthorised
use is strictly prohibited. If you receive this email in error, please
delete it and any attachments.

Please think of our environment and only print this e-mail if necessary.
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Re: [Freesurfer] White Matter Edits vs. Control Points, & third party software

[dgw]

Alberto,

I included detailed replies below, but I have a question before you get 
to those. Why don't you want to follow the FreeSurfer techniques for 
reconstruction? You suggested several other ways, but I don't understand 
your motivation for not wanting to follow the instructions for FreeSurfer.

On 10/2/15 5:49 AM, Julio Alberto González Torre wrote:
> I have some questions about how to manually correct the white matter
> regions.
>
> It's the same manually edit the volume "brainmask.mgz" and use control
> points?Would I get the same result? My intention is not to use control
> points, but directly replace the voxels that have not been classified as
> white matter with the value 110. Is it right to do this?

Why don't you want to use control points? They do more than replace the 
value with 110. They let FreeSurfer know that that voxel is definitely 
white matter even though the intensity is different. It can then tweak 
what it sees as white matter locally in that space and get you a good 
measure of the border. Remember the border is likely to occur in the 
middle of voxels with partial voluming effects, where the intensity is 
not 110, and also where you should not make the volume 110.

>
> My second question is: Is it possible to edit the volumes with a third
> party program? My intention here is to turn the volume "brainmask.mgz"
> to "brainmask.nii" using "mri_convert" command. Then edit the values of
> the voxels manually with a third party software or painting tool, and
> finally, turn the volume back to "brainmask.mgz", replace the file in
> their respective directory, and finally execute "-autorecon2- wm". Is it
> right to do this? Or this may compromise my data?

While I am not a FreeSurfer dev, I would strongly discourage you from 
doing this. First, it will be easier to get help, troubleshoot and do 
things properly, if follow the FreeSurfer techniques, plus you will need 
their tools to do any corrections to the Talairach etc. Second, the 
NIFTI format is pretty bad and lacks a lot of data which the mgz format 
preserves.

>
> Thanks in advance,
> Alberto.
>
>
> ___
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> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in 
> error
> but does not contain patient information, please contact the sender and 
> properly
> dispose of the e-mail.
>
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[Freesurfer] Cannot change min threshold in Configure Overlay Display TKSurfer

[Oana Georgiana Rus]

Dear developers/users?

When I load a *mgh.sig* file in *TkSurfer* and I go on *Configure 
Overlay Display* and want to change the *min Threshold on 1.3* or 
wathever number I can't edit or do that?


did somebody encounter the same problem?
How can you solve it?

Thank You.

--
Oana Georgiana Rus
PhD Student
Neuroimaging Center TUM-NIC
Klinikum rechts der Isar
Technische Universität München
Einsteinstr.1
81675 München
Raum 5.8

Tel. 089 4140 7971

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Re: [Freesurfer] Hippocampus visualisation

[Erik O'Hanlon]

That's super Eugenio,


Thanks so much. Exactly what I needed.


Cheers


Erik


From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Eugenio Iglesias [e.igles...@bcbl.eu]
Sent: 02 October 2015 10:57
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampus visualisation





Hi Erik,

one possible way of doing this:

1. For a single subfield: set the color map to Lookup Table. Tick "show as isosurface in 3d view". Tick "label volume". Then, set both values of the range to the numeric code of the subfield you want to display (e.g., for CA1, it would be 206).

2. For all subfields simultaneously: same as before, but setting the range to 200-226. This will color each subfield differently.

3. For showing the whole hippocampus in the same color: an easy, quick way is to switch the color map to grayscale, tick "show as isosurface in 3d view", untick "label volume", and set the lower and upper thresholds to 200 and 226, respectively.

Cheers,

Eugenio





Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer




From: "Erik O'Hanlon" 
To: "Freesurfer support list" 
Sent: Friday, October 2, 2015 10:31:17 AM
Subject: [Freesurfer] Hippocampus visualisation




Hi Freesurfer experts,


I've run the subfield analysis with Dev v6 and am just wondering if it is possible to display only certain subfields (say the CA1 and Subiculum rendered in 3D using freeview? Can I also render the entire hippocampus that is basically the addition of all
 the subfields given in the table output? Sorry for the basic question, just trying to put together some images.


Thanks in advance 


erik


Erik O'Hanlon 

Postdoctoral researcher



RCSI Psychiatry
Royal College of Surgeons in Ireland
Beaumont Road, Beaumont, D9, Ireland
T: 8093740

E: erikohan...@rcsi.ie W: www.rcsi.ie


RCSI DEVELOPING HEALTHCARE LEADERS
WHO MAKE A DIFFERENCE WORLDWIDE 

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Re: [Freesurfer] Hippocampus visualisation

[Eugenio Iglesias]

Hi Erik, 
one possible way of doing this: 
1. For a single subfield: set the color map to Lookup Table. Tick "show as 
isosurface in 3d view". Tick "label volume". Then, set both values of the range 
to the numeric code of the subfield you want to display (e.g., for CA1, it 
would be 206). 
2. For all subfields simultaneously: same as before, but setting the range to 
200-226. This will color each subfield differently. 
3. For showing the whole hippocampus in the same color: an easy, quick way is 
to switch the color map to grayscale, tick "show as isosurface in 3d view", 
untick "label volume", and set the lower and upper thresholds to 200 and 226, 
respectively. 
Cheers, 
Eugenio 


Juan Eugenio Iglesias 
Postdoctoral researcher BCBL 
www.jeiglesias.com 
www.bcbl.eu 

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer 


From: "Erik O'Hanlon"  
To: "Freesurfer support list"  
Sent: Friday, October 2, 2015 10:31:17 AM 
Subject: [Freesurfer] Hippocampus visualisation 

Hi Freesurfer experts, 

I've run the subfield analysis with Dev v6 and am just wondering if it is 
possible to display only certain subfields (say the CA1 and Subiculum rendered 
in 3D using freeview? Can I also render the entire hippocampus that is 
basically the addition of all the subfields given in the table output? Sorry 
for the basic question, just trying to put together some images. 

Thanks in advance 

erik 


Erik O'Hanlon 
Postdoctoral researcher 




RCSI Psychiatry 
Royal College of Surgeons in Ireland 
Beaumont Road, Beaumont, D9, Ireland 
T: 8093740 
E: erikohan...@rcsi.ie W: www.rcsi.ie 


RCSI DEVELOPING HEALTHCARE LEADERS 
WHO MAKE A DIFFERENCE WORLDWIDE 
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[Freesurfer] White Matter Edits vs. Control Points, & third party software

[Julio Alberto González Torre]

I have some questions about how to manually correct the white matter regions
.

It's the same manually edit the volume "brainmask.mgz" and use control
points? Would I get the same result? My intention is not to use control
points, but directly replace the voxels that have not been classified as white
matter with the value 110. Is it right to do this?

My second question is: Is it possible to edit the volumes with a third
party program? My intention here is to turn the volume "brainmask.mgz" to "
brainmask.nii" using "mri_convert" command. Then edit the values of the
voxels manually with a third party software or painting tool, and finally, turn
the volume back to "brainmask.mgz", replace the file in their respective
directory, and finally execute "-autorecon2- wm". Is it right to do
this? Or this
may compromise my data?

Thanks in advance,
Alberto.
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[Freesurfer] Hippocampus visualisation

[Erik O'Hanlon]

Hi Freesurfer experts,


I've run the subfield analysis with Dev v6 and am just wondering if it is possible to display only certain subfields (say the CA1 and Subiculum rendered in 3D using freeview? Can I also render the entire hippocampus that is basically the addition of all
 the subfields given in the table output? Sorry for the basic question, just trying to put together some images.


Thanks in advance 


erik


Erik O'Hanlon 

Postdoctoral researcher



RCSI Psychiatry
Royal College of Surgeons in Ireland
Beaumont Road, Beaumont, D9, Ireland
T: 8093740

E: erikohan...@rcsi.ie W: www.rcsi.ie

RCSI DEVELOPING HEALTHCARE LEADERS
WHO MAKE A DIFFERENCE WORLDWIDE 


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Re: [Freesurfer] Parcellation stats

[Ali Radaideh]

Hi Bruce,

I have used the following command line:

mri_segstats --seg scz01/mri/aseg.mgz --annot scz01 lh
lh.yeo2011_17Networks_N1000.annot --sum scz01.aseg.sum

and got the following:

# ColHeaders  Index SegId NVoxels Volume_mm3 StructName
  1   0  15766121 15766121.0  Seg
  2   2182848   182848.0  Seg0002
  3   3215011   215011.0  Seg0003
  4   4  6547 6547.0  Seg0004
  5   5   572  572.0  Seg0005
  6   7 1405314053.0  Seg0007
  7   8 4777947779.0  Seg0008
  8  10  7151 7151.0  Seg0010
  9  11  4464 4464.0  Seg0011
 10  12  5264 5264.0  Seg0012
 11  13  1680 1680.0  Seg0013
 12  14   889  889.0  Seg0014
 13  15  1731 1731.0  Seg0015
 14  16 1730717307.0  Seg0016
 15  17  3842 3842.0  Seg0017
 16  18  1106 1106.0  Seg0018
 17  24  1228 1228.0  Seg0024
 18  26   656  656.0  Seg0026
 19  28  3941 3941.0  Seg0028
 20  3026   26.0  Seg0030
 21  31  1222 1222.0  Seg0031
 22  41191593   191593.0  Seg0041
 23  42200955   200955.0  Seg0042
 24  43  6321 6321.0  Seg0043
 25  44   295  295.0  Seg0044
 26  46 1610616106.0  Seg0046
 27  47 4647246472.0  Seg0047
 28  49  6684 6684.0  Seg0049
 29  50  4308 4308.0  Seg0050
 30  51  5099 5099.0  Seg0051
 31  52  1459 1459.0  Seg0052
 32  53  4005 4005.0  Seg0053
 33  54   988  988.0  Seg0054
 34  58   633  633.0  Seg0058
 35  60  3554 3554.0  Seg0060
 36  6236   36.0  Seg0062
 37  63  1518 1518.0  Seg0063
 38  7218   18.0  Seg0072
 39  77  1040 1040.0  Seg0077
 40  8022   22.0  Seg0080
 41  85   124  124.0  Seg0085
 42 251   721  721.0  Seg0251
 43 252   403  403.0  Seg0252
 44 253   322  322.0  Seg0253
 45 254   360  360.0  Seg0254
 46 255   742  742.0  Seg0255


However,
I don't see the segmentation names (cortical parts). is my command true/
complete or not?
These are 46 segmentations although I am using 17 networks cortical
parcellation, is this true?
Can I add anything to make the output more informative?. Also can I get any
surface area etc?



Many thanks in advance.
Ali

On Thu, Oct 1, 2015 at 10:43 PM, Bruce Fischl 
wrote:

> sure, you can use mri_segstats to get stats from it
> Bruce
> On Thu, 1 Oct 2015, Ali Radaideh wrote:
>
> Can we get any stats from this type of parcellation? I only can see two
>> annotation files after running the mri_surf2surf command and these can be
>> loaded tksurfer as an overlay.
>>
>>
>> Thanks,
>> Ali
>>
>> On Tue, Sep 29, 2015 at 7:31 PM, Bruce Fischl > >
>> wrote:
>>   that will generate a parcellation on the individual subject
>>   surface of Thomas Yeo's 17-network clustering. It won't do
>>   anything with the thickness though. What are you trying to do?
>>
>>   On Tue, 29 Sep 2015, Ali Radaideh wrote:
>>
>> mri_surf2surf --srcsubject fsaverage --trgsubject
>> scz10 --hemi rh
>>
>> --sval-annot$FREESURFER_HOME/subjects/fsaverage/label/rh.Yeo2011_17Networks
>> _N1000.annot
>> --tval
>> $SUBJECTS_DIR/scz10/label/rh.Yeo2011_17Networks_N1000.annot
>>
>> scz10 is my subject name
>>
>> On Tue, Sep 29, 2015 at 2:46 AM, Douglas Greve
>> 
>> wrote:
>>   what is your surf2surf command?
>>
>>   On 9/28/15 5:11 PM, Ali Radaideh wrote:
>>   Dear Douglas,
>>
>> Thanks for your email. I meant to say that after
>> running the
>> recon-all, i ran the sur2surf command to get the
>> cortical
>> parcellation using Thomas Yeo Atlas.
>>
>> I thought that the extracted cortical thickness
>> after running
>> the surf2surf command will be different from the one
>> extracted
>> before running the command. But, Bruce kindly
>> replied to my
>> email saying that it is the same if it is calculated
>> on
>> vertex-wise basis.
>>
>> Thanks,
>> Ali
>>
>> On Mon, Sep 28, 2015 at 11:01 PM, Douglas N Greve
>>  wrote:
>>   I can't understand what you are asking. Can
>> you
>>   elaborate?
>>
>>   On 09/28/2015 01:51 PM, Ali Radaideh wrote:
>>   > Thanks alot Douglas,
>>   >
>>   > Yes it is there but after checking it many
>> time I
>>   found it corrupted
>>   > for some subjects due to copying them many
>> times
>>   between machines.
>>   >
>>   > But May I ask you some thing related. I have
>>