External Email - Use Caution        

Hi Bruce,

 

Yes, the brains were registered in fsaverage space. The issue I am facing is my sig.mgh output from GLM will not convert into a .nii file using mri_convert.

 

I am trying to load them both as overlays not view them directly. The sig.mgh file loads fine, it is the .nii file that sees the problem.

 

Similarly, if I do GLM directly with a .nii output, I see the same issues.

 

You asked me to run mri_info on both the .mgh and .nii.gz files, which I gave in my previous email.

 

Please let me know how to proceed from here! 

 

Best wishes,

 

Bruce Fischl Mon, 04 Feb 2019 06:31:00 -0800

Hi Emma
 

the dimensions (163842 x 1 x 1) mean that these are overlays on the fsaverage surface. Can you remind me what issue you are trying to solve? 

 
cheers
Bruce
 
 
        External Email - Use Caution        
 
Hi Bruce,
 
 
I ran the mri_info command on the sig.mgh and the sig.lh.nii.gz files for 
participant 124 and got these outputs...
 
 
For sig.mgh:
 
 
Volume information for sig.mgh
          type: MGH
    dimensions: 163842 x 1 x 1
   voxel sizes: 1.000000, 1.000000, 1.000000
          type: FLOAT (3)
           fov: 163842.000
           dof: 0
        xstart: -81921.0, xend: 81921.0
        ystart: -0.5, yend: 0.5
        zstart: -0.5, zend: 0.5
            TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 
degrees
       nframes: 1
       PhEncDir: UNKNOWN
       FieldStrength: 0.000000
ras xform present
    xform info: x_r =  -1.0000, y_r =   0.0000, z_r =   0.0000, c_r =     0.0000
              : x_a =   0.0000, y_a =   0.0000, z_a =   1.0000, c_a =     0.0000
              : x_s =   0.0000, y_s =  -1.0000, z_s =   0.0000, c_s =     0.0000
 
talairach xfm :
Orientation   : LIA
Primary Slice Direction: coronal
 
voxel to ras transform:
               -1.0000   0.0000   0.0000 81921.0000
                0.0000   0.0000   1.0000    -0.5000
                0.0000  -1.0000   0.0000     0.5000
                0.0000   0.0000   0.0000     1.0000
 
voxel-to-ras determinant -1
 
ras to voxel transform:
               -1.0000  -0.0000  -0.0000 81921.0000
               -0.0000  -0.0000  -1.0000     0.5000
               -0.0000   1.0000  -0.0000     0.5000
               -0.0000  -0.0000  -0.0000     1.0000
 
 
For sig.lh.nii.gz:
 
Volume information for sig.lh.nii.gz
          type: nii
    dimensions: 163842 x 1 x 1
   voxel sizes: 1.000000, 1.000000, 1.000000
          type: FLOAT (3)
           fov: 163842.000
           dof: 0
        xstart: -81921.0, xend: 81921.0
        ystart: -0.5, yend: 0.5
        zstart: -0.5, zend: 0.5
            TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 
degrees
       nframes: 1
       PhEncDir: UNKNOWN
       FieldStrength: 0.000000
ras xform present
    xform info: x_r =  -1.0000, y_r =   0.0000, z_r =   0.0000, c_r = 
-68267.5000
              : x_a =   0.0000, y_a =   0.0000, z_a =   1.0000, c_a =    -2.5000
              : x_s =   0.0000, y_s =  -1.0000, z_s =   0.0000, c_s =     0.0000
Orientation   : LIA
Primary Slice Direction: coronal
 
voxel to ras transform:
               -1.0000   0.0000   0.0000 13653.5000
                0.0000   0.0000   1.0000    -3.0000
                0.0000  -1.0000   0.0000     0.5000
                0.0000   0.0000   0.0000     1.0000
 
voxel-to-ras determinant -1
 
ras to voxel transform:
               -1.0000  -0.0000  -0.0000 13653.5000
               -0.0000  -0.0000  -1.0000     0.5000
               -0.0000   1.0000  -0.0000     3.0000
               -0.0000  -0.0000  -0.0000     1.0000
 
Please let me know if you need any other information in order to help with our 
problem,
 
Best wishes,
 
Emma
 

 

Sent from Mail for Windows 10

 

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of freesurfer-request@nmr.mgh.harvard.edu <freesurfer-request@nmr.mgh.harvard.edu>
Sent: Monday, February 4, 2019 5:00:09 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Freesurfer Digest, Vol 180, Issue 5
 
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
        freesurfer-request@nmr.mgh.harvard.edu

You can reach the person managing the list at
        freesurfer-owner@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. gray matter volume of the entorhinal cortex
      (Laboratorio de Neurociencia Funcional)
   2. Re: problem using recon-all (Shachar Gal)
   3. Re: problem using recon-all (Glasser, Matthew)
   4. Re: Surface to Volume conversion (Bunting, Emma)
   5. Re: gray matter volume of the entorhinal cortex (Bruce Fischl)
   6. Re: Surface to Volume conversion (Bruce Fischl)
   7. Re: gray matter volume of the entorhinal cortex
      (Laboratorio de Neurociencia Funcional)
   8. free surfer install issues (Jordan Fowler)
   9. Re: free surfer install issues (Greve, Douglas N.,Ph.D.)
  10. (no subject) (Jordan Fowler)


----------------------------------------------------------------------

Message: 1
Date: Mon, 4 Feb 2019 10:08:06 +0100
From: Laboratorio de Neurociencia Funcional <neuroaginglnf@gmail.com>
Subject: [Freesurfer] gray matter volume of the entorhinal cortex
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <CABUYonO85t9vP8NBw9HtWuET2n4i-9s-Q_LevCxZ_rK3U4YAew@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

        External Email - Use Caution       

Dear Freesurfers,

gray matter volume of the entorhinal cortex (EC) can be obtained either in
the ?h.aparc.stats or ?h.BA_exvivo.stats/?h.BA_exvivo.thresh.stats files.
Considering that all our T1 images were manually edited on a slice-by-slice
basis to correct pial surface misplacements and erroneous white matter
segmentation, which volume measure of the EC would be more precise?

I assume that gray matter volume contained in ?h.BA_exvivo.thresh.stats
were thresholded at a specific probability value (% of case overlapping).
Which probability value was used? Is there a reference paper explaining how
probabilistic maps of EC were built based on ex vivo MRI contrast?

Thank you in advance.

Best,
Jose L. Cantero
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Message: 2
Date: Mon, 4 Feb 2019 11:32:22 +0200
From: Shachar Gal <gal.shachar@gmail.com>
Subject: Re: [Freesurfer] problem using recon-all
To: "Glasser, Matthew" <glasserm@wustl.edu>
Cc: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>,   Ido
        Tavor <idotavor@gmail.com>
Message-ID:
        <CAPdEuW45LivewtxNzGWFs=tuArcyafXjRK8yC0Bi30jVXqsLJQ@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

        External Email - Use Caution       

hey,
is there any update regarding the release of the FreeSurfer 6
HCP-compatible version?

cheers,
Shachar

On Mon, 14 Jan 2019 at 14:58 Shachar Gal <gal.shachar@gmail.com> wrote:

> thanks,
> hope it'll work
> anyway, looking forward for the version 6 release
>
> cheers,
> Shachar
>
> On Mon, 14 Jan 2019 at 14:08 Glasser, Matthew <glasserm@wustl.edu> wrote:
>
>> Ubuntu 14.04 should still work.
>>
>> Matt.
>>
>> From: Shachar Gal <gal.shachar@gmail.com>
>> Date: Monday, January 14, 2019 at 5:43 AM
>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>, Matt
>> Glasser <glasserm@wustl.edu>, Ido Tavor <idotavor@gmail.com>
>> Subject: Re: problem using recon-all
>>
>> if the problem is with the versions, maybe downgrading my OS for now will
>> do the trick? do you happen know what is the latest ubuntu that is
>> compatible with the 5.3-HCP version?
>> does this also occur in centOS?
>>
>> thanks
>>
>> On Sun, 13 Jan 2019 at 17:46 Shachar Gal <gal.shachar@gmail.com> wrote:
>>
>>> hello,
>>> I using the HCP FreeSurfer Pipeline (using FreeSurfer 5.3-HCP version)
>>> on ubuntu, and I encounter this error (copying from the recon-all.log)
>>> _______________________________________
>>> #@# Talairach Sun Jan 13 17:35:07 IST 2019
>>> /home/shachar/piano_hcp/102/102/mri
>>>
>>>  mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale
>>> --i orig.mgz --o orig_nu.mgz
>>>
>>> Linux maestro 4.15.0-43-generic #46-Ubuntu SMP Thu Dec 6 14:45:28 UTC
>>> 2018 x86_64 x86_64 x86_64 GNU/Linux
>>>
>>> recon-all -s 102 exited with ERRORS at Sun Jan 13 17:35:08 IST 2019
>>> _______________________________________
>>>
>>> i'm a bit confused by the lack of error descriptions, and would
>>> appreciate any leads for solving it :)
>>>
>>> Shachar
>>>
>>
>> ------------------------------
>>
>> The materials in this message are private and may contain Protected
>> Healthcare Information or other information of a sensitive nature. If you
>> are not the intended recipient, be advised that any unauthorized use,
>> disclosure, copying or the taking of any action in reliance on the contents
>> of this information is strictly prohibited. If you have received this email
>> in error, please immediately notify the sender via telephone or return mail.
>>
>
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Message: 3
Date: Mon, 4 Feb 2019 11:09:37 +0000
From: "Glasser, Matthew" <glasserm@wustl.edu>
Subject: Re: [Freesurfer] problem using recon-all
To: Shachar Gal <gal.shachar@gmail.com>
Cc: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>,   Ido
        Tavor <idotavor@gmail.com>
Message-ID: <D87D797D.18A86A%glasserm@wustl.edu>
Content-Type: text/plain; charset="us-ascii"

        External Email - Use Caution       

There is a little more testing we are doing.

Matt.

From: Shachar Gal <gal.shachar@gmail.com<mailto:gal.shachar@gmail.com>>
Date: Monday, February 4, 2019 at 3:32 AM
To: Matt Glasser <glasserm@wustl.edu<mailto:glasserm@wustl.edu>>
Cc: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>, Ido Tavor <idotavor@gmail.com<mailto:idotavor@gmail.com>>
Subject: Re: problem using recon-all

hey,
is there any update regarding the release of the FreeSurfer 6 HCP-compatible version?

cheers,
Shachar

On Mon, 14 Jan 2019 at 14:58 Shachar Gal <gal.shachar@gmail.com<mailto:gal.shachar@gmail.com>> wrote:
thanks,
hope it'll work
anyway, looking forward for the version 6 release

cheers,
Shachar

On Mon, 14 Jan 2019 at 14:08 Glasser, Matthew <glasserm@wustl.edu<mailto:glasserm@wustl.edu>> wrote:
Ubuntu 14.04 should still work.

Matt.

From: Shachar Gal <gal.shachar@gmail.com<mailto:gal.shachar@gmail.com>>
Date: Monday, January 14, 2019 at 5:43 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>, Matt Glasser <glasserm@wustl.edu<mailto:glasserm@wustl.edu>>, Ido Tavor <idotavor@gmail.com<mailto:idotavor@gmail.com>>
Subject: Re: problem using recon-all

if the problem is with the versions, maybe downgrading my OS for now will do the trick? do you happen know what is the latest ubuntu that is compatible with the 5.3-HCP version?
does this also occur in centOS?

thanks

On Sun, 13 Jan 2019 at 17:46 Shachar Gal <gal.shachar@gmail.com<mailto:gal.shachar@gmail.com>> wrote:
hello,
I using the HCP FreeSurfer Pipeline (using FreeSurfer 5.3-HCP version) on ubuntu, and I encounter this error (copying from the recon-all.log)
_______________________________________
#@# Talairach Sun Jan 13 17:35:07 IST 2019
/home/shachar/piano_hcp/102/102/mri

 mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz

Linux maestro 4.15.0-43-generic #46-Ubuntu SMP Thu Dec 6 14:45:28 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s 102 exited with ERRORS at Sun Jan 13 17:35:08 IST 2019 _______________________________________

i'm a bit confused by the lack of error descriptions, and would appreciate any leads for solving it :)

Shachar

________________________________
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

________________________________
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
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Message: 4
Date: Mon, 4 Feb 2019 11:53:19 +0000
From: "Bunting, Emma" <e.bunting.18@ucl.ac.uk>
Subject: Re: [Freesurfer] Surface to Volume conversion
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <DB6PR01MB37659256420A53FA64FD61239D6D0@DB6PR01MB3765.eurprd01.prod.exchangelabs.com>
       
Content-Type: text/plain; charset="iso-8859-1"

        External Email - Use Caution       

Hi Bruce,

I ran the mri_info command on the sig.mgh and the sig.lh.nii.gz files for participant 124 and got these outputs...


For sig.mgh:


Volume information for sig.mgh
          type: MGH
    dimensions: 163842 x 1 x 1
   voxel sizes: 1.000000, 1.000000, 1.000000
          type: FLOAT (3)
           fov: 163842.000
           dof: 0
        xstart: -81921.0, xend: 81921.0
        ystart: -0.5, yend: 0.5
        zstart: -0.5, zend: 0.5
            TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees
       nframes: 1
       PhEncDir: UNKNOWN
       FieldStrength: 0.000000
ras xform present
    xform info: x_r =  -1.0000, y_r =   0.0000, z_r =   0.0000, c_r =     0.0000
              : x_a =   0.0000, y_a =   0.0000, z_a =   1.0000, c_a =     0.0000
              : x_s =   0.0000, y_s =  -1.0000, z_s =   0.0000, c_s =     0.0000

talairach xfm :
Orientation   : LIA
Primary Slice Direction: coronal

voxel to ras transform:
               -1.0000   0.0000   0.0000 81921.0000
                0.0000   0.0000   1.0000    -0.5000
                0.0000  -1.0000   0.0000     0.5000
                0.0000   0.0000   0.0000     1.0000

voxel-to-ras determinant -1

ras to voxel transform:
               -1.0000  -0.0000  -0.0000 81921.0000
               -0.0000  -0.0000  -1.0000     0.5000
               -0.0000   1.0000  -0.0000     0.5000
               -0.0000  -0.0000  -0.0000     1.0000


For sig.lh.nii.gz:

Volume information for sig.lh.nii.gz
          type: nii
    dimensions: 163842 x 1 x 1
   voxel sizes: 1.000000, 1.000000, 1.000000
          type: FLOAT (3)
           fov: 163842.000
           dof: 0
        xstart: -81921.0, xend: 81921.0
        ystart: -0.5, yend: 0.5
        zstart: -0.5, zend: 0.5
            TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees
       nframes: 1
       PhEncDir: UNKNOWN
       FieldStrength: 0.000000
ras xform present
    xform info: x_r =  -1.0000, y_r =   0.0000, z_r =   0.0000, c_r = -68267.5000
              : x_a =   0.0000, y_a =   0.0000, z_a =   1.0000, c_a =    -2.5000
              : x_s =   0.0000, y_s =  -1.0000, z_s =   0.0000, c_s =     0.0000
Orientation   : LIA
Primary Slice Direction: coronal

voxel to ras transform:
               -1.0000   0.0000   0.0000 13653.5000
                0.0000   0.0000   1.0000    -3.0000
                0.0000  -1.0000   0.0000     0.5000
                0.0000   0.0000   0.0000     1.0000

voxel-to-ras determinant -1

ras to voxel transform:
               -1.0000  -0.0000  -0.0000 13653.5000
               -0.0000  -0.0000  -1.0000     0.5000
               -0.0000   1.0000  -0.0000     3.0000
               -0.0000  -0.0000  -0.0000     1.0000

Please let me know if you need any other information in order to help with our problem,

Best wishes,

Emma
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of freesurfer-request@nmr.mgh.harvard.edu <freesurfer-request@nmr.mgh.harvard.edu>
Sent: 25 January 2019 17:00
To: freesurfer@nmr.mgh.harvard.edu
Subject: Freesurfer Digest, Vol 179, Issue 41

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
        freesurfer-request@nmr.mgh.harvard.edu

You can reach the person managing the list at
        freesurfer-owner@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. Re: Longitudinal processing with windows subsystem for linux
      (WSL) using ubuntu 18.04.1 LTS (Hoopes, Andrew)
   2. Re: FSFAST poor registration (Greve, Douglas N.,Ph.D.)
   3. Re: Surface to volume conversion (Bruce Fischl)
   4. Re: Functional connectivty walkthrough step 8 error
      (Greve, Douglas N.,Ph.D.)
   5. Re: cortical thickness calculation based on hammersmith
      segmentation (Greve, Douglas N.,Ph.D.)
   6. Re: FSFAST poor registration (Keri Woods)
   7. Re: Functional connectivty walkthrough step 8 error (Amrita Bedi)
   8. Re: Orientation by direction cosines (Greve, Douglas N.,Ph.D.)
   9. Re: Functional connectivty walkthrough step 8 error (Amrita Bedi)
  10. Re: Functional connectivty walkthrough step 8 error (Amrita Bedi)
  11. Re: Functional connectivty walkthrough step 8 error
      (Greve, Douglas N.,Ph.D.)


----------------------------------------------------------------------

Message: 1
Date: Fri, 25 Jan 2019 16:24:14 +0000
From: "Hoopes, Andrew" <AHOOPES@mgh.harvard.edu>
Subject: Re: [Freesurfer] Longitudinal processing with windows
        subsystem for linux (WSL) using ubuntu 18.04.1 LTS
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <2A2251F1-6E66-4125-9A96-76700348245B@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

I believe this python2 issue has been fixed in the dev version found here https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/long_mris_slopes

best,
Andrew


?On 1/25/19, 10:08 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:

    Hi Falk

    thanks for catching the typo. I fixed it - nice to have an easy thing to
    fix for a change :)

    Bruce


    On Fri, 25 Jan 2019, falk.luesebrink@med.ovgu.de wrote:

    >
    >         External Email - Use Caution
    >
    > Dear Juergen,
    >
    >
    >
    > Thanks for your quick reply! Actually the spelling error is in the error message. Taken from
    > http://martinos.org/~mreuter/long/long_mris_slopes
    >
    >
    >
    > # extensive error checks
    >
    > #    if options.fsgd is None and
    >
    >     if options.qdec is None:
    >
    > #        print 'ERROR: Specify --fsgd or --qedc'
    >
    >         parser.print_help()
    >
    >         print '\nERROR: Specify --qedc (and other required arguments)\n'
    >
    >         sys.exit(1)
    >
    >
    >
    > #    if options.fsgd is not None and options.qdec is not None:
    >
    > #        print 'ERROR: Specify either --fsgd or --qedc, not both'
    >
    > #        sys.exit(1)
    >
    >
    >
    > At least Martin is consistent with his typo. :D
    >
    >
    >
    > Best,
    >
    > Falk
    >
    >
    >
    > Von: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> Im Auftrag von Juergen Haenggi
    > Gesendet: Freitag, 25. Januar 2019 10:35
    > An: Freesurfer Mailinglist <freesurfer@nmr.mgh.harvard.edu>
    > Betreff: Re: [Freesurfer] Longitudinal processing with windows subsystem for linux (WSL) using ubuntu 18.04.1 LTS
    >
    >
    >
    >         External Email - Use Caution
    >
    > Dear Falk
    >
    >
    >
    > I have no idea, but recognised that the error refers to --qedc and not to --qdec.
    >
    > maybe there is a spelling error somewhere that is related to your problem.
    >
    >
    >
    > HTH
    >
    > Cheers
    >
    > J?rgen
    >
    > -----------------------------------------------------------------------------------------------------
    >
    > University of Zurich
    >
    > Dr. J?rgen H?nggi, Ph.D.
    >
    > Department of Psychology
    >
    > Division Neuropsychology
    >
    > Binzmuehlestrasse 14, PO Box 25
    >
    > 8050 Zurich, Switzerland
    >
    >
    >
    > 0041 44 635 73 97 (phone office)
    >
    > 0041 76 445 86 84 (phone mobile)
    >
    > 0041 44 635 74 09 (fax office)
    >
    > BIN 4.D.04 (office room number)
    >
    >
    >
    > j.haenggi@psychologie.uzh.ch (email)
    >
    > http://www.psychologie.uzh.ch/neuropsy/ (website)
    >
    > http://www.juergenhaenggi.ch (private website)
    >
    >
    >
    > This email (and any attachment/s) contains confidential and/or privileged
    >
    > information. If you are not the intended recipient (or have received this
    >
    > email in error) please notify the sender immediately and destroy this
    >
    > email. Any unauthorised copying, disclosure or distribution of the
    >
    > material in this email is strictly forbidden.
    >
    > -----------------------------------------------------------------------------------------------------
    >
    >
    >
    >
    >
    >
    >
    >       On 25 Jan 2019, at 10:26, falk.luesebrink@med.ovgu.de wrote:
    >
    >
    >
    >         External Email - Use Caution
    >
    >
    >
    > Dear all,
    >
    >
    >
    > Has anyone run the longitudinal pipeline successfully using the WSL? I?m running it with Ubuntu 18.04.1 LTS
    > and freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c.
    >
    >
    >
    > I?m trying to process my first longitudinal data set following the instructions of the tutorial as close as
    > possible. The data has been processed without issues and now I want to do the statistical analysis. When I
    > run:
    >
    > long_mris_slopes --qdec ./long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc
    > --do-stack --do-label --time years --qcache fsaverage --sd $SUBJECTS_DIR
    >
    >
    >
    > I get the following error:
    >
    > File "/home/luesebri/Software/FreeSurfer/bin/long_mris_slopes", line 448
    >
    >     print '\nERROR: Specify --qedc (and other required arguments)\n'
    >
    >                                                                    ^
    >
    > SyntaxError: invalid syntax
    >
    >
    >
    > I get comparable errors for any other long_* command I try to run, e.g. long_qdec_table with or without any
    > arguments gives:
    >
    > File "/home/luesebri/Software/FreeSurfer/bin/long_qdec_table", line 119
    >
    >    print '\nERROR: Specify --qedc'
    >
    >                                   ^
    >
    > SyntaxError: Missing parentheses in call to 'print'. Did you mean print('\nERROR: Specify --qedc')?
    >
    >
    >
    > Does anyone have a clue where this error originates from using either WSL or Ubuntu 18.04?
    >
    >
    >
    > Best,
    >
    > Falk
    >
    > ...............................................
    >
    >
    >
    > <image001.gif>
    >
    > Universit?tsklinik f?r Neurologie
    >
    >
    >
    > Otto-von-Guericke-Universit?t Magdeburg
    > Medizinische Fakult?t
    > Leipziger Str. 44
    > 39120 Magdeburg
    >
    >
    >
    > Telefon: +49-391-6117-512
    >
    > falk.luesebrink@med.ovgu.de
    > http://www.kneu.ovgu.de/kneu.html
    >
    >
    >
    > _______________________________________________
    > Freesurfer mailing list
    > Freesurfer@nmr.mgh.harvard.edu
    > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
    >
    >
    >
    >
    >




------------------------------

Message: 2
Date: Fri, 25 Jan 2019 16:34:14 +0000
From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
Subject: Re: [Freesurfer] FSFAST poor registration
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <367a8e86-05d2-f02b-d19b-94401864c91d@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

Yes, that file is the only thing linking the functional to the anatomical. It's too bad you messed up the files, but I'm relieved it was not my software:).

On 1/25/19 5:09 AM, Keri Woods wrote:

        External Email - Use Caution

Hi Douglas

Thanks very much for getting back to me. I created new separate directories and re-processed one of the problem subjects individually, and the registration worked well. So the problem is that the anatomical and functional images come from different subjects. But I've checked and the subjectname files are correct. That's the only thing linking the anatomical and functional images? Thanks very much, you've helped me a lot. Now I just have to go and see where I mixed up the files!

Thanks again,
Keri

On Thu, Jan 24, 2019 at 10:32 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>> wrote:
Can you tar up the anatomical and functional analyses and send them to
me through our filedrop?

https://gate.nmr.mgh.harvard.edu/filedrop2/

when it asks for an email of the recipient, use greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu>


On 1/23/19 5:57 AM, Keri Woods wrote:
>
>         External Email - Use Caution
>
> I meant some are nearly perfect.
>
> On Wed, Jan 23, 2019 at 11:49 AM Keri Woods <keri.woods@gmail.com<mailto:keri.woods@gmail.com>
> <mailto:keri.woods@gmail.com<mailto:keri.woods@gmail.com>>> wrote:
>
>     Hi Douglas
>
>     Thanks for the response.
>
>     No, some of the registrations are fine. Some are close, but not
>     perfect, while others are very bad.
>
>     I've checked the subjectname file for some subjects with poor
>     registration (eg 20_101), and they are correct.
>
>     Thanks,
>     Keri
>
>     On Tue, Jan 22, 2019 at 8:57 PM Greve, Douglas N.,Ph.D.
>     <DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>>> wrote:
>
>         Are you saying that all of them have bad registrations? Some
>         of them
>         (eg, 20_1, 20_10) look like they should be good. Others (eg,
>         20_101)
>         look like they could be bad. For the bad ones, are you totally
>         sure that
>         the subjetname file has the correct name of the subject?
>
>         On 1/21/19 3:19 AM, Keri Woods wrote:
>         >
>         >         External Email - Use Caution
>         >
>         > Hi Douglas
>         >
>         > Thank you for your reply.
>         >
>         > I'm using
>         freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
>         >
>         > I am using whole brain data. The functional and structural
>         images were
>         > acquired in different sessions on the same day, I don't know
>         if that
>         > complicated things? Each subject has 2 runs of the same task.
>         >
>         > This is what I get after running the command in the format of
>         > tkregister-sess -s sess01 -s sess02 -s sess03 -fsd bold
>         -per-run -bbr-sum
>         >
>         > 20_1       013 0.5155
>         > 20_1       014 0.5090
>         > 20_10      013 0.5247
>         > 20_10      014 0.5229
>         > 20_100     038 0.8420
>         > 20_100     040 0.8443
>         > 20_101     008 0.9052
>         > 20_101     010 0.9289
>         > 20_102     058 0.6924
>         > 20_102     059 0.6902
>         > 20_103     045 0.9778
>         > 20_103     046 0.9931
>         > 20_104     010 0.9324
>         > 20_104     012 0.9413
>         > 20_105     013 0.8754
>         > 20_105     014 0.8937
>         > 20_106     047 0.4433
>         > 20_106     048 0.4377
>         > 20_107     008 0.9178
>         > 20_107     010 0.9238
>         > 20_11      013 0.7631
>         > 20_11      014 0.7615
>         > 20_110     048 0.7687
>         > 20_110     049 0.7549
>         > 20_112     013 0.8821
>         > 20_112     014 0.9161
>         > 20_113     052 0.7689
>         > 20_113     053 0.7757
>         > 20_116     046 1.0072
>         > 20_116     047 1.0256
>         > 20_117     008 0.7742
>         > 20_117     010 0.7826
>         > 20_119     013 0.7929
>         > 20_119     014 0.7854
>         > 20_120     048 0.5090
>         > 20_120     049 0.4973
>         > 20_126     047 0.8285
>         > 20_126     048 0.8281
>         > 20_128     046 0.9580
>         > 20_128     047 0.9314
>         > 20_130     047 0.9439
>         > 20_130     048 0.9425
>         > 20_132     047 0.8550
>         > 20_132     048 0.8558
>         > 20_134_1   013 0.5716
>         > 20_134_1   015 0.5744
>         > 20_135     011 0.8357
>         > 20_135     012 0.8401
>         > 20_136     044 0.9995
>         > 20_136     045 0.9604
>         > 20_137     047 0.7922
>         > 20_137     048 0.7990
>         > 20_142     047 0.5282
>         > 20_142     048 0.5278
>         > 20_144     013 0.8755
>         > 20_144     014 0.8838
>         > 20_146     047 0.7997
>         > 20_146     048 0.7895
>         > 20_149     049 0.9251
>         > 20_149     050 0.9408
>         > 20_151     048 0.5905
>         > 20_151     049 0.5519
>         > 20_152     048 0.9024
>         > 20_152     049 0.9021
>         > 20_155     048 0.5285
>         > 20_155     049 0.5324
>         > 20_156     048 0.8883
>         > 20_156     049 0.9267
>         > 20_158     048 0.5404
>         > 20_158     049 0.5297
>         > 20_159     048 0.8021
>         > 20_160     013 0.5002
>         > 20_160     014 0.4942
>         > 20_162     047 0.5401
>         > 20_162     048 0.5401
>         > 20_164     047 0.8944
>         > 20_164     048 0.8940
>         > 20_165     047 0.9163
>         > 20_165     048 0.9077
>         > 20_166     045 0.8787
>         > 20_166     046 0.8848
>         > 20_167     050 0.8428
>         > 20_167     051 0.8442
>         > 20_169     049 0.9407
>         > 20_169     050 0.9462
>         > 20_170     047 0.8921
>         > 20_170     048 0.9113
>         > 20_171     013 0.9060
>         > 20_171     014 0.9060
>         > 20_173     048 0.9193
>         > 20_173     049 0.9141
>         > 20_177     048 0.8695
>         > 20_177     049 0.8600
>         > 20_178     048 1.0327
>         > 20_178     049 0.8979
>         > 20_180     045 0.7999
>         > 20_180     046 0.8002
>         > 20_182     047 0.9135
>         > 20_182     048 0.9130
>         > 20_184     048 0.9842
>         > 20_184     049 0.9960
>         > 20_185     046 0.9640
>         > 20_185     047 0.9514
>         > 20_187     048 0.8134
>         > 20_187     049 0.8082
>         > 20_189     047 1.0063
>         > 20_189     048 0.9701
>         > 20_19      013 0.8485
>         > 20_19      014 0.8534
>         > 20_190     047 0.9279
>         > 20_190     048 0.9169
>         > 20_191     046 0.9586
>         > 20_191     047 0.9751
>         > 20_192     049 0.8544
>         > 20_193     013 0.9084
>         > 20_193     014 0.9110
>         > 20_194     047 0.9220
>         > 20_194     048 0.9166
>         > 20_195     048 0.9552
>         > 20_195     049 0.9508
>         > 20_196     047 0.9098
>         > 20_196     048 0.9011
>         > 20_199     048 0.8569
>         > 20_199     049 0.8567
>         > 20_20      013 0.8750
>         > 20_20      014 0.8749
>         > 20_201     048 0.8864
>         > 20_201     049 1.0040
>         > 20_202     048 0.8542
>         > 20_202     049 0.8516
>         > 20_203     048 1.0267
>         > 20_203     049 1.0060
>         > 20_204     048 0.8513
>         > 20_204     049 0.8588
>         > 20_208     014 0.9130
>         > 20_208     015 0.9329
>         > 20_209     047 1.0020
>         > 20_209     048 1.0120
>         > 20_21      027 0.9747
>         > 20_21      028 1.0081
>         > 20_210     048 0.8607
>         > 20_210     049 0.8564
>         > 20_220     047 0.8888
>         > 20_220     048 0.8903
>         > 20_222     047 0.9998
>         > 20_222     048 0.8597
>         > 20_224     013 0.8122
>         > 20_224     014 0.8107
>         > 20_226     013 0.7855
>         > 20_226     014 0.7845
>         > 20_227     013 0.9372
>         > 20_227     014 0.9818
>         > 20_231     047 0.8355
>         > 20_231     048 0.8506
>         > 20_232     048 0.9730
>         > 20_232     049 0.9591
>         > 20_234     048 0.9357
>         > 20_234     049 0.9429
>         > 20_235     048 0.7528
>         > 20_235     049 0.7483
>         > 20_236     047 0.8997
>         > 20_236     048 0.8922
>         > 20_239     049 0.8920
>         > 20_239     050 0.8817
>         > 20_24      013 0.8197
>         > 20_24      014 0.8280
>         > 20_240     047 0.9109
>         > 20_240     048 0.9231
>         > 20_243     013 0.8227
>         > 20_243     014 0.8333
>         > 20_245     045 0.8620
>         > 20_245     046 0.8635
>         > 20_246     047 0.8236
>         > 20_246     048 0.8269
>         > 20_248     053 0.6015
>         > 20_248     054 0.6091
>         > 20_25      013 0.8676
>         > 20_25      014 0.8658
>         > 20_250     048 0.9124
>         > 20_250     050 0.9090
>         > 20_251     048 0.9061
>         > 20_251     049 0.9078
>         > 20_277     008 0.7923
>         > 20_277     010 0.7970
>         > 20_278     048 0.4834
>         > 20_278     049 0.4845
>         > 20_279     008 0.4363
>         > 20_279     010 0.4370
>         > 20_281     013 0.8672
>         > 20_281     014 0.8647
>         > 20_282     043 0.8884
>         > 20_282     044 0.8886
>         > 20_284     052 0.9152
>         > 20_284     053 0.9118
>         > 20_285     047 0.9546
>         > 20_285     048 0.9517
>         > 20_286     008 0.9607
>         > 20_286     010 0.9596
>         > 20_287     055 0.8976
>         > 20_287     056 0.8756
>         > 20_288     047 1.0127
>         > 20_288     048 1.0307
>         > 20_290     048 1.0089
>         > 20_290     049 1.0391
>         > 20_293     052 0.7792
>         > 20_293     053 0.7772
>         > 20_3       017 0.8530
>         > 20_3       018 0.8501
>         > 20_40      013 0.9392
>         > 20_40      014 0.9787
>         > 20_41      013 0.9562
>         > 20_41      014 0.9547
>         > 20_44      013 0.8725
>         > 20_44      014 0.8872
>         > 20_51      013 0.9420
>         > 20_51      014 0.9417
>         > 20_55      013 0.9796
>         > 20_55      014 0.9837
>         > 20_58      013 0.9677
>         > 20_58      014 0.9506
>         > 20_59      013 0.9180
>         > 20_59      014 0.9157
>         > 20_69      013 0.9265
>         > 20_69      014 0.9283
>         > 20_74      014 0.9476
>         > 20_74      015 0.9201
>         > 20_78      012 0.9822
>         > 20_78      013 0.9501
>         > 20_81      013 0.8664
>         > 20_81      014 0.8693
>         > 20_84      013 0.8827
>         > 20_84      014 0.9196
>         > 20_86      016 0.9138
>         > 20_86      017 0.9152
>         > 20_88      039 0.9905
>         > 20_88      041 1.0168
>         > 20_90      049 0.8263
>         > 20_90      050 1.0208
>         > 20_95      008 0.8892
>         > 20_95      010 0.9359
>         > 20_96      013 0.9191
>         > 20_96      014 0.9326
>         > 20_97      008 0.9569
>         > 20_97      010 0.9731
>         > 20_98      008 0.9317
>         > 20_98      012 0.9409
>         > 20_PHRU    047 0.7797
>         > 20_PHRU    048 0.7894
>         >
>         > So the registration is really poor. I've visually checked the
>         > registration for many of the subjects, and the functional
>         data isn't
>         > left-right reversed, I've also checked some of the
>         subjectname files
>         > (which I created by running a script) and they are correct.
>         >
>         > I'm new to Freesurfer, so maybe I've made a mistake
>         somewhere? I'm
>         > been following these instructions:
>         >
>         > https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorial
>         >
>         > Thanks,
>         > Keri
>         >
>         >
>         > On Fri, Jan 18, 2019 at 6:44 PM Greve, Douglas N.,Ph.D.
>         > <DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>>
>         <mailto:DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>
>         <mailto:DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>>>> wrote:
>         >
>         >     What version of FS are you using? version 6 initializes with
>         >     mri_coreg (the FS equivalent of spm_coreg). On
>         whole-brain data,
>         >     I've found this to be very robust. Is your data whole-brain?
>         >
>         >     On 1/18/19 5:10 AM, Keri Woods wrote:
>         >>
>         >>             External Email - Use Caution
>         >>
>         >>     Hi
>         >>
>         >>     I have a problem very similar to this one:
>         >>
>         >>
>         https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23206.html
>         >>
>         >>     I've tried the suggestions given there, but it didn't
>         fix my problem.
>         >>
>         >>     I'm running the FSFAST preproc-sess stream and the
>         quality of the
>         >>     registration is very poor for most of the subjects.
>         >>
>         >>     I've tried initializing the registration differently, using
>         >>     bbregister with --init-fsl, --init-spm and init-header,
>         which
>         >>     didn't improve the results at all.
>         >>
>         >>     I've also tried register-sess with --init-fsl,
>         --init-spm and
>         >>     init-header, as well as spmregister-sess and
>         fslregister-sess.
>         >>
>         >>     Is there anything else I could try?
>         >>
>         >>     Using the SPM GUI, the registration was fine, so I
>         thought that
>         >>     spmregister-sess would have been an improvement, but it
>         wasn't.
>         >>     Is there anyway I can import the registration obtained
>         using the
>         >>     SPM GUI?
>         >>
>         >>     Thanks for your help.
>         >>
>         >>     Thanks,
>         >>     Keri
>         >>
>         >>
>         >>
>         >>
>         >>
>         >>  _______________________________________________
>         >>     Freesurfer mailing list
>         >> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
>         <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>>
>         <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
>         <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>>>
>         >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>         >
>         >     _______________________________________________
>         >     Freesurfer mailing list
>         > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
>         <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>>
>         <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
>         <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>>>
>         > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>         >
>         >
>         > _______________________________________________
>         > Freesurfer mailing list
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>
>
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------------------------------

Message: 3
Date: Fri, 25 Jan 2019 11:34:38 -0500 (EST)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Surface to volume conversion
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <alpine.LRH.2.20.1901251133510.26643@gate.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

Hi Emma

can you run mri_info on the .mgh and .nii.gz volumes and send us the
output? Is the sig.mgh a surface overlay? If so, you can't visualize it
directly, you have to overlay it on a surface (in either .mgh or .nii.gz
foramt)

cheers
Bruce


On Fri, 25 Jan 2019, Bunting, Emma wrote:

>        External Email - Use Caution
>
> Hi!
>
> I?m trying to convert my sig.mgh output from GLM into a .nii file using mri_convert, and when I load the resulting volume in freeview this is what I see.
>
> The command I?m using is:
> mri_convert ?in-type mgh ?out_type nii.gz ?out_orientation RAS /(root to sig.mgh file)/sig.mgh /(root to output file)/sig.nii.gz,
>
> Is there something I should be doing differently?
>
> Many thanks,
>
> Emma
>
>

------------------------------

Message: 4
Date: Fri, 25 Jan 2019 16:44:25 +0000
From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
Subject: Re: [Freesurfer] Functional connectivty walkthrough step 8
        error
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <f526e7d2-f63e-35c7-9de6-bf8fda8ed9e2@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

Hi Amrita, can you just paste the text into the email?
thanks
doug

On 1/25/19 10:51 AM, Amrita Bedi wrote:

        External Email - Use Caution

Hi Dr Greve,

Ran mris_fwhm and got the attached.

On Thursday, January 24, 2019, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>> wrote:
Based on the output below, it looks like there are problems with running
one of the freesurfer binaries. Can you run mris_fwhm ? Just type the
command and return and see what happens.



/home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm --mask
/share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_recon/Bold1/fc.lpccseed.surf.lh/mask.nii.gz
--i
/share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_recon/Bold1/fc.lpccseed.surf.lh/rho1mn.nii.gz
--o
/share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_recon/Bold1/fc.lpccseed.surf.lh/rho1mn.sm.nii.gz
--fwhm 20.000000 --smooth-only --s fsaverage --hemi lh --sd
/share/VA_Imaging/Projects/salat/2389_TRT/abedi
/home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm:
/home/apps/matlab/MATLAB/R2011b/sys/os/glnxa64/libstdc++.so.6: version
`GLIBCXX_3.4.11' not found (required by
/home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm)



On 1/23/19 10:11 AM, Amrita Bedi wrote:
>
>         External Email - Use Caution
>
> Hi Dr Greve,
>
> Attached is the log file.
>
> On Tuesday, January 22, 2019, Greve, Douglas N.,Ph.D.
> <DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>>> wrote:
>
>     Can you send the full terminal output and/or the log file?
>
>     On 1/22/19 2:53 PM, Amrita Bedi wrote:
>     >
>     >         External Email - Use Caution
>     >
>     > Hello Freesurfer developers,
>     >
>     > I was following the functional connectivity walkthrough for resting
>     > stage BOLD data and I got the attached error when I ran step 8
>     > (selxavg3-sess). Does anyone have any thoughts on how to trouble
>     shoot
>     > this?
>     > Not sure if it?s of any use but I ran this using Freesurfer 6.0 on
>     > Centos 7.4
>     >
>     > Thank You.
>     >
>     > Best
>     > Amrita
>     >
>     > _______________________________________________
>     > Freesurfer mailing list
>     > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
>     <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>>
>     > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>     <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>
>
>     _______________________________________________
>     Freesurfer mailing list
>     Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>>
>     https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>     <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Message: 5
Date: Fri, 25 Jan 2019 16:45:24 +0000
From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
Subject: Re: [Freesurfer] cortical thickness calculation based on
        hammersmith segmentation
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <0fa6801f-f424-863f-8373-2c217f70cf78@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

Those are the commands. Can you send the command lines you used and a fuller description of exactly how it is not working?

On 1/25/19 10:56 AM, Boris Rauchmann wrote:

        External Email - Use Caution
Dear FreeSurfer Developers,

I?m trying to extract the cortical thickness of individuals from a study cohort based on an hammersmith n30r83 atlas segmentation. I have this atlas only in as a volumetric file. I already run recon-all on all subjects. I tried mri_vol2surf and then mris_seg2annot but without success so far. What commands would you recommend me to run?

Thanks,
Boris



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Message: 6
Date: Fri, 25 Jan 2019 18:50:40 +0200
From: Keri Woods <keri.woods@gmail.com>
Subject: Re: [Freesurfer] FSFAST poor registration
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <CAOFXy0n2U4V+QYxXwKzE-eWaiz5960W2aVbCrmmbvopsmXQDOQ@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

        External Email - Use Caution

Good thing it's not the software :) Also makes it easier for me to fix. In
my script there was one tiny mistake - the anatomical image for one subject
was repeated each time instead of using the files for different subjects. I
ran recon-all 100+ times on the same subject!! Checking the registration
was definitely worthwhile. Thanks again for the help, it made me look at
the problem in a different.

On Fri, Jan 25, 2019 at 6:34 PM Greve, Douglas N.,Ph.D. <
DGREVE@mgh.harvard.edu> wrote:

> Yes, that file is the only thing linking the functional to the anatomical.
> It's too bad you messed up the files, but I'm relieved it was not my
> software:).
>
> On 1/25/19 5:09 AM, Keri Woods wrote:
>
>         External Email - Use Caution
> Hi Douglas
>
> Thanks very much for getting back to me. I created new separate
> directories and re-processed one of the problem subjects individually, and
> the registration worked well. So the problem is that the anatomical and
> functional images come from different subjects. But I've checked and the
> subjectname files are correct. That's the only thing linking the anatomical
> and functional images? Thanks very much, you've helped me a lot. Now I just
> have to go and see where I mixed up the files!
>
> Thanks again,
> Keri
>
> On Thu, Jan 24, 2019 at 10:32 PM Greve, Douglas N.,Ph.D. <
> DGREVE@mgh.harvard.edu> wrote:
>
>> Can you tar up the anatomical and functional analyses and send them to
>> me through our filedrop?
>>
>> https://gate.nmr.mgh.harvard.edu/filedrop2/
>>
>> when it asks for an email of the recipient, use greve@nmr.mgh.harvard.edu
>>
>>
>> On 1/23/19 5:57 AM, Keri Woods wrote:
>> >
>> >         External Email - Use Caution
>> >
>> > I meant some are nearly perfect.
>> >
>> > On Wed, Jan 23, 2019 at 11:49 AM Keri Woods <keri.woods@gmail.com
>> > <mailto:keri.woods@gmail.com>> wrote:
>> >
>> >     Hi Douglas
>> >
>> >     Thanks for the response.
>> >
>> >     No, some of the registrations are fine. Some are close, but not
>> >     perfect, while others are very bad.
>> >
>> >     I've checked the subjectname file for some subjects with poor
>> >     registration (eg 20_101), and they are correct.
>> >
>> >     Thanks,
>> >     Keri
>> >
>> >     On Tue, Jan 22, 2019 at 8:57 PM Greve, Douglas N.,Ph.D.
>> >     <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> wrote:
>> >
>> >         Are you saying that all of them have bad registrations? Some
>> >         of them
>> >         (eg, 20_1, 20_10) look like they should be good. Others (eg,
>> >         20_101)
>> >         look like they could be bad. For the bad ones, are you totally
>> >         sure that
>> >         the subjetname file has the correct name of the subject?
>> >
>> >         On 1/21/19 3:19 AM, Keri Woods wrote:
>> >         >
>> >         >         External Email - Use Caution
>> >         >
>> >         > Hi Douglas
>> >         >
>> >         > Thank you for your reply.
>> >         >
>> >         > I'm using
>> >         freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
>> >         >
>> >         > I am using whole brain data. The functional and structural
>> >         images were
>> >         > acquired in different sessions on the same day, I don't know
>> >         if that
>> >         > complicated things? Each subject has 2 runs of the same task.
>> >         >
>> >         > This is what I get after running the command in the format of
>> >         > tkregister-sess -s sess01 -s sess02 -s sess03 -fsd bold
>> >         -per-run -bbr-sum
>> >         >
>> >         > 20_1       013 0.5155
>> >         > 20_1       014 0.5090
>> >         > 20_10      013 0.5247
>> >         > 20_10      014 0.5229
>> >         > 20_100     038 0.8420
>> >         > 20_100     040 0.8443
>> >         > 20_101     008 0.9052
>> >         > 20_101     010 0.9289
>> >         > 20_102     058 0.6924
>> >         > 20_102     059 0.6902
>> >         > 20_103     045 0.9778
>> >         > 20_103     046 0.9931
>> >         > 20_104     010 0.9324
>> >         > 20_104     012 0.9413
>> >         > 20_105     013 0.8754
>> >         > 20_105     014 0.8937
>> >         > 20_106     047 0.4433
>> >         > 20_106     048 0.4377
>> >         > 20_107     008 0.9178
>> >         > 20_107     010 0.9238
>> >         > 20_11      013 0.7631
>> >         > 20_11      014 0.7615
>> >         > 20_110     048 0.7687
>> >         > 20_110     049 0.7549
>> >         > 20_112     013 0.8821
>> >         > 20_112     014 0.9161
>> >         > 20_113     052 0.7689
>> >         > 20_113     053 0.7757
>> >         > 20_116     046 1.0072
>> >         > 20_116     047 1.0256
>> >         > 20_117     008 0.7742
>> >         > 20_117     010 0.7826
>> >         > 20_119     013 0.7929
>> >         > 20_119     014 0.7854
>> >         > 20_120     048 0.5090
>> >         > 20_120     049 0.4973
>> >         > 20_126     047 0.8285
>> >         > 20_126     048 0.8281
>> >         > 20_128     046 0.9580
>> >         > 20_128     047 0.9314
>> >         > 20_130     047 0.9439
>> >         > 20_130     048 0.9425
>> >         > 20_132     047 0.8550
>> >         > 20_132     048 0.8558
>> >         > 20_134_1   013 0.5716
>> >         > 20_134_1   015 0.5744
>> >         > 20_135     011 0.8357
>> >         > 20_135     012 0.8401
>> >         > 20_136     044 0.9995
>> >         > 20_136     045 0.9604
>> >         > 20_137     047 0.7922
>> >         > 20_137     048 0.7990
>> >         > 20_142     047 0.5282
>> >         > 20_142     048 0.5278
>> >         > 20_144     013 0.8755
>> >         > 20_144     014 0.8838
>> >         > 20_146     047 0.7997
>> >         > 20_146     048 0.7895
>> >         > 20_149     049 0.9251
>> >         > 20_149     050 0.9408
>> >         > 20_151     048 0.5905
>> >         > 20_151     049 0.5519
>> >         > 20_152     048 0.9024
>> >         > 20_152     049 0.9021
>> >         > 20_155     048 0.5285
>> >         > 20_155     049 0.5324
>> >         > 20_156     048 0.8883
>> >         > 20_156     049 0.9267
>> >         > 20_158     048 0.5404
>> >         > 20_158     049 0.5297
>> >         > 20_159     048 0.8021
>> >         > 20_160     013 0.5002
>> >         > 20_160     014 0.4942
>> >         > 20_162     047 0.5401
>> >         > 20_162     048 0.5401
>> >         > 20_164     047 0.8944
>> >         > 20_164     048 0.8940
>> >         > 20_165     047 0.9163
>> >         > 20_165     048 0.9077
>> >         > 20_166     045 0.8787
>> >         > 20_166     046 0.8848
>> >         > 20_167     050 0.8428
>> >         > 20_167     051 0.8442
>> >         > 20_169     049 0.9407
>> >         > 20_169     050 0.9462
>> >         > 20_170     047 0.8921
>> >         > 20_170     048 0.9113
>> >         > 20_171     013 0.9060
>> >         > 20_171     014 0.9060
>> >         > 20_173     048 0.9193
>> >         > 20_173     049 0.9141
>> >         > 20_177     048 0.8695
>> >         > 20_177     049 0.8600
>> >         > 20_178     048 1.0327
>> >         > 20_178     049 0.8979
>> >         > 20_180     045 0.7999
>> >         > 20_180     046 0.8002
>> >         > 20_182     047 0.9135
>> >         > 20_182     048 0.9130
>> >         > 20_184     048 0.9842
>> >         > 20_184     049 0.9960
>> >         > 20_185     046 0.9640
>> >         > 20_185     047 0.9514
>> >         > 20_187     048 0.8134
>> >         > 20_187     049 0.8082
>> >         > 20_189     047 1.0063
>> >         > 20_189     048 0.9701
>> >         > 20_19      013 0.8485
>> >         > 20_19      014 0.8534
>> >         > 20_190     047 0.9279
>> >         > 20_190     048 0.9169
>> >         > 20_191     046 0.9586
>> >         > 20_191     047 0.9751
>> >         > 20_192     049 0.8544
>> >         > 20_193     013 0.9084
>> >         > 20_193     014 0.9110
>> >         > 20_194     047 0.9220
>> >         > 20_194     048 0.9166
>> >         > 20_195     048 0.9552
>> >         > 20_195     049 0.9508
>> >         > 20_196     047 0.9098
>> >         > 20_196     048 0.9011
>> >         > 20_199     048 0.8569
>> >         > 20_199     049 0.8567
>> >         > 20_20      013 0.8750
>> >         > 20_20      014 0.8749
>> >         > 20_201     048 0.8864
>> >         > 20_201     049 1.0040
>> >         > 20_202     048 0.8542
>> >         > 20_202     049 0.8516
>> >         > 20_203     048 1.0267
>> >         > 20_203     049 1.0060
>> >         > 20_204     048 0.8513
>> >         > 20_204     049 0.8588
>> >         > 20_208     014 0.9130
>> >         > 20_208     015 0.9329
>> >         > 20_209     047 1.0020
>> >         > 20_209     048 1.0120
>> >         > 20_21      027 0.9747
>> >         > 20_21      028 1.0081
>> >         > 20_210     048 0.8607
>> >         > 20_210     049 0.8564
>> >         > 20_220     047 0.8888
>> >         > 20_220     048 0.8903
>> >         > 20_222     047 0.9998
>> >         > 20_222     048 0.8597
>> >         > 20_224     013 0.8122
>> >         > 20_224     014 0.8107
>> >         > 20_226     013 0.7855
>> >         > 20_226     014 0.7845
>> >         > 20_227     013 0.9372
>> >         > 20_227     014 0.9818
>> >         > 20_231     047 0.8355
>> >         > 20_231     048 0.8506
>> >         > 20_232     048 0.9730
>> >         > 20_232     049 0.9591
>> >         > 20_234     048 0.9357
>> >         > 20_234     049 0.9429
>> >         > 20_235     048 0.7528
>> >         > 20_235     049 0.7483
>> >         > 20_236     047 0.8997
>> >         > 20_236     048 0.8922
>> >         > 20_239     049 0.8920
>> >         > 20_239     050 0.8817
>> >         > 20_24      013 0.8197
>> >         > 20_24      014 0.8280
>> >         > 20_240     047 0.9109
>> >         > 20_240     048 0.9231
>> >         > 20_243     013 0.8227
>> >         > 20_243     014 0.8333
>> >         > 20_245     045 0.8620
>> >         > 20_245     046 0.8635
>> >         > 20_246     047 0.8236
>> >         > 20_246     048 0.8269
>> >         > 20_248     053 0.6015
>> >         > 20_248     054 0.6091
>> >         > 20_25      013 0.8676
>> >         > 20_25      014 0.8658
>> >         > 20_250     048 0.9124
>> >         > 20_250     050 0.9090
>> >         > 20_251     048 0.9061
>> >         > 20_251     049 0.9078
>> >         > 20_277     008 0.7923
>> >         > 20_277     010 0.7970
>> >         > 20_278     048 0.4834
>> >         > 20_278     049 0.4845
>> >         > 20_279     008 0.4363
>> >         > 20_279     010 0.4370
>> >         > 20_281     013 0.8672
>> >         > 20_281     014 0.8647
>> >         > 20_282     043 0.8884
>> >         > 20_282     044 0.8886
>> >         > 20_284     052 0.9152
>> >         > 20_284     053 0.9118
>> >         > 20_285     047 0.9546
>> >         > 20_285     048 0.9517
>> >         > 20_286     008 0.9607
>> >         > 20_286     010 0.9596
>> >         > 20_287     055 0.8976
>> >         > 20_287     056 0.8756
>> >         > 20_288     047 1.0127
>> >         > 20_288     048 1.0307
>> >         > 20_290     048 1.0089
>> >         > 20_290     049 1.0391
>> >         > 20_293     052 0.7792
>> >         > 20_293     053 0.7772
>> >         > 20_3       017 0.8530
>> >         > 20_3       018 0.8501
>> >         > 20_40      013 0.9392
>> >         > 20_40      014 0.9787
>> >         > 20_41      013 0.9562
>> >         > 20_41      014 0.9547
>> >         > 20_44      013 0.8725
>> >         > 20_44      014 0.8872
>> >         > 20_51      013 0.9420
>> >         > 20_51      014 0.9417
>> >         > 20_55      013 0.9796
>> >         > 20_55      014 0.9837
>> >         > 20_58      013 0.9677
>> >         > 20_58      014 0.9506
>> >         > 20_59      013 0.9180
>> >         > 20_59      014 0.9157
>> >         > 20_69      013 0.9265
>> >         > 20_69      014 0.9283
>> >         > 20_74      014 0.9476
>> >         > 20_74      015 0.9201
>> >         > 20_78      012 0.9822
>> >         > 20_78      013 0.9501
>> >         > 20_81      013 0.8664
>> >         > 20_81      014 0.8693
>> >         > 20_84      013 0.8827
>> >         > 20_84      014 0.9196
>> >         > 20_86      016 0.9138
>> >         > 20_86      017 0.9152
>> >         > 20_88      039 0.9905
>> >         > 20_88      041 1.0168
>> >         > 20_90      049 0.8263
>> >         > 20_90      050 1.0208
>> >         > 20_95      008 0.8892
>> >         > 20_95      010 0.9359
>> >         > 20_96      013 0.9191
>> >         > 20_96      014 0.9326
>> >         > 20_97      008 0.9569
>> >         > 20_97      010 0.9731
>> >         > 20_98      008 0.9317
>> >         > 20_98      012 0.9409
>> >         > 20_PHRU    047 0.7797
>> >         > 20_PHRU    048 0.7894
>> >         >
>> >         > So the registration is really poor. I've visually checked the
>> >         > registration for many of the subjects, and the functional
>> >         data isn't
>> >         > left-right reversed, I've also checked some of the
>> >         subjectname files
>> >         > (which I created by running a script) and they are correct.
>> >         >
>> >         > I'm new to Freesurfer, so maybe I've made a mistake
>> >         somewhere? I'm
>> >         > been following these instructions:
>> >         >
>> >         > https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorial
>> >         >
>> >         > Thanks,
>> >         > Keri
>> >         >
>> >         >
>> >         > On Fri, Jan 18, 2019 at 6:44 PM Greve, Douglas N.,Ph.D.
>> >         > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>
>> >         <mailto:DGREVE@mgh.harvard.edu
>> >         <mailto:DGREVE@mgh.harvard.edu>>> wrote:
>> >         >
>> >         >     What version of FS are you using? version 6 initializes
>> with
>> >         >     mri_coreg (the FS equivalent of spm_coreg). On
>> >         whole-brain data,
>> >         >     I've found this to be very robust. Is your data
>> whole-brain?
>> >         >
>> >         >     On 1/18/19 5:10 AM, Keri Woods wrote:
>> >         >>
>> >         >>             External Email - Use Caution
>> >         >>
>> >         >>     Hi
>> >         >>
>> >         >>     I have a problem very similar to this one:
>> >         >>
>> >         >>
>> >
>> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23206.html
>> >         >>
>> >         >>     I've tried the suggestions given there, but it didn't
>> >         fix my problem.
>> >         >>
>> >         >>     I'm running the FSFAST preproc-sess stream and the
>> >         quality of the
>> >         >>     registration is very poor for most of the subjects.
>> >         >>
>> >         >>     I've tried initializing the registration differently,
>> using
>> >         >>     bbregister with --init-fsl, --init-spm and init-header,
>> >         which
>> >         >>     didn't improve the results at all.
>> >         >>
>> >         >>     I've also tried register-sess with --init-fsl,
>> >         --init-spm and
>> >         >>     init-header, as well as spmregister-sess and
>> >         fslregister-sess.
>> >         >>
>> >         >>     Is there anything else I could try?
>> >         >>
>> >         >>     Using the SPM GUI, the registration was fine, so I
>> >         thought that
>> >         >>     spmregister-sess would have been an improvement, but it
>> >         wasn't.
>> >         >>     Is there anyway I can import the registration obtained
>> >         using the
>> >         >>     SPM GUI?
>> >         >>
>> >         >>     Thanks for your help.
>> >         >>
>> >         >>     Thanks,
>> >         >>     Keri
>> >         >>
>> >         >>
>> >         >>
>> >         >>
>> >         >>
>> >         >>  _______________________________________________
>> >         >>     Freesurfer mailing list
>> >         >> Freesurfer@nmr.mgh.harvard.edu
>> >         <mailto:Freesurfer@nmr.mgh.harvard.edu>
>> >         <mailto:Freesurfer@nmr.mgh.harvard.edu
>> >         <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>> >         >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >         >
>> >         >     _______________________________________________
>> >         >     Freesurfer mailing list
>> >         > Freesurfer@nmr.mgh.harvard.edu
>> >         <mailto:Freesurfer@nmr.mgh.harvard.edu>
>> >         <mailto:Freesurfer@nmr.mgh.harvard.edu
>> >         <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>> >         > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >         >
>> >         >
>> >         > _______________________________________________
>> >         > Freesurfer mailing list
>> >         > Freesurfer@nmr.mgh.harvard.edu
>> >         <mailto:Freesurfer@nmr.mgh.harvard.edu>
>> >         > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >
>> >
>> >         _______________________________________________
>> >         Freesurfer mailing list
>> >         Freesurfer@nmr.mgh.harvard.edu
>> >         <mailto:Freesurfer@nmr.mgh.harvard.edu>
>> >         https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >
>> >
>> > _______________________________________________
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> _______________________________________________
> Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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------------------------------

Message: 7
Date: Fri, 25 Jan 2019 11:56:29 -0500
From: Amrita Bedi <amibedi273@gmail.com>
Subject: Re: [Freesurfer] Functional connectivty walkthrough step 8
        error
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <CAPCzK2E+MPzYh2H3Zyd0kNL+jTo_5YmESRA9AT4Sg-qbh4P7rQ@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

        External Email - Use Caution

Here you go.
On Friday, January 25, 2019, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu>
wrote:

> Hi Amrita, can you just paste the text into the email?
> thanks
> doug
>
> On 1/25/19 10:51 AM, Amrita Bedi wrote:
>
>         External Email - Use Caution
> Hi Dr Greve,
>
> Ran mris_fwhm and got the attached.
>
> On Thursday, January 24, 2019, Greve, Douglas N.,Ph.D. <
> DGREVE@mgh.harvard.edu> wrote:
>
>> Based on the output below, it looks like there are problems with running
>> one of the freesurfer binaries. Can you run mris_fwhm ? Just type the
>> command and return and see what happens.
>>
>>
>>
>> /home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm --mask
>> /share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_rec
>> on/Bold1/fc.lpccseed.surf.lh/mask.nii.gz
>> --i
>> /share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_rec
>> on/Bold1/fc.lpccseed.surf.lh/rho1mn.nii.gz
>> --o
>> /share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_rec
>> on/Bold1/fc.lpccseed.surf.lh/rho1mn.sm.nii.gz
>> --fwhm 20.000000 --smooth-only --s fsaverage --hemi lh --sd
>> /share/VA_Imaging/Projects/salat/2389_TRT/abedi
>> /home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm:
>> /home/apps/matlab/MATLAB/R2011b/sys/os/glnxa64/libstdc++.so.6: version
>> `GLIBCXX_3.4.11' not found (required by
>> /home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm)
>>
>>
>>
>> On 1/23/19 10:11 AM, Amrita Bedi wrote:
>> >
>> >         External Email - Use Caution
>> >
>> > Hi Dr Greve,
>> >
>> > Attached is the log file.
>> >
>> > On Tuesday, January 22, 2019, Greve, Douglas N.,Ph.D.
>> > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> wrote:
>> >
>> >     Can you send the full terminal output and/or the log file?
>> >
>> >     On 1/22/19 2:53 PM, Amrita Bedi wrote:
>> >     >
>> >     >         External Email - Use Caution
>> >     >
>> >     > Hello Freesurfer developers,
>> >     >
>> >     > I was following the functional connectivity walkthrough for
>> resting
>> >     > stage BOLD data and I got the attached error when I ran step 8
>> >     > (selxavg3-sess). Does anyone have any thoughts on how to trouble
>> >     shoot
>> >     > this?
>> >     > Not sure if it?s of any use but I ran this using Freesurfer 6.0 on
>> >     > Centos 7.4
>> >     >
>> >     > Thank You.
>> >     >
>> >     > Best
>> >     > Amrita
>> >     >
>> >     > _______________________________________________
>> >     > Freesurfer mailing list
>> >     > Freesurfer@nmr.mgh.harvard.edu
>> >     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>> >     > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >     <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>> >
>> >
>> >     _______________________________________________
>> >     Freesurfer mailing list
>> >     Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.har
>> vard.edu>
>> >     https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >     <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>> >
>> >
>> > _______________________________________________
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> _______________________________________________
> Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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------------------------------

Message: 8
Date: Fri, 25 Jan 2019 16:56:47 +0000
From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
Subject: Re: [Freesurfer] Orientation by direction cosines
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <e7a7e0e7-4fa5-c8f7-e066-c5cea7a060d9@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

mri_info will do it. If you just want the orientation string, you can
add? --orientation. Or do you still want the interpretation of the matrix?

On 1/25/19 10:10 AM, Bruce Fischl wrote:
> Hi Ritesh
>
> I think that mri_info will try to figure this out and tell you (in the
> "Orientation" output).
>
> cheers
> Bruce
>
>
> On Fri, 25 Jan 2019, Ritesh Mahajan wrote:
>
>>         External Email - Use Caution
>>
>> Hello Team,
>>
>> Can any one please explain how we come to know whether it is RAI or RAS or any other orientation through direction cosines:
>>
>> Below is the direction cosine: I saw some non zero and negative values in non diagonal values of matrix. What does this signify ?
>>
>> 0.999377        0        -0.0352819
>> -0.00916448  0.965676    -0.259588
>> 0.0340709      0.25975   0.965075
>>
>> Suppose it is Head First Supine. Any help will be really appreciated.
>>
>> Thanks,
>> Ritesh Mahajan
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer




------------------------------

Message: 9
Date: Fri, 25 Jan 2019 11:57:06 -0500
From: Amrita Bedi <amibedi273@gmail.com>
Subject: Re: [Freesurfer] Functional connectivty walkthrough step 8
        error
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <CAPCzK2EyR1_1HdaVEHmi86tT9_BxeNG9HasRvjMrKUCYU+cGDw@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

        External Email - Use Caution

On Friday, January 25, 2019, Amrita Bedi <amibedi273@gmail.com> wrote:

>
>
> Here you go.
> On Friday, January 25, 2019, Greve, Douglas N.,Ph.D. <
> DGREVE@mgh.harvard.edu> wrote:
>
>> Hi Amrita, can you just paste the text into the email?
>> thanks
>> doug
>>
>> On 1/25/19 10:51 AM, Amrita Bedi wrote:
>>
>>         External Email - Use Caution
>> Hi Dr Greve,
>>
>> Ran mris_fwhm and got the attached.
>>
>> On Thursday, January 24, 2019, Greve, Douglas N.,Ph.D. <
>> DGREVE@mgh.harvard.edu> wrote:
>>
>>> Based on the output below, it looks like there are problems with running
>>> one of the freesurfer binaries. Can you run mris_fwhm ? Just type the
>>> command and return and see what happens.
>>>
>>>
>>>
>>> /home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm --mask
>>> /share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_rec
>>> on/Bold1/fc.lpccseed.surf.lh/mask.nii.gz
>>> --i
>>> /share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_rec
>>> on/Bold1/fc.lpccseed.surf.lh/rho1mn.nii.gz
>>> --o
>>> /share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_rec
>>> on/Bold1/fc.lpccseed.surf.lh/rho1mn.sm.nii.gz
>>> --fwhm 20.000000 --smooth-only --s fsaverage --hemi lh --sd
>>> /share/VA_Imaging/Projects/salat/2389_TRT/abedi
>>> /home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm:
>>> /home/apps/matlab/MATLAB/R2011b/sys/os/glnxa64/libstdc++.so.6: version
>>> `GLIBCXX_3.4.11' not found (required by
>>> /home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm)
>>>
>>>
>>>
>>> On 1/23/19 10:11 AM, Amrita Bedi wrote:
>>> >
>>> >         External Email - Use Caution
>>> >
>>> > Hi Dr Greve,
>>> >
>>> > Attached is the log file.
>>> >
>>> > On Tuesday, January 22, 2019, Greve, Douglas N.,Ph.D.
>>> > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> wrote:
>>> >
>>> >     Can you send the full terminal output and/or the log file?
>>> >
>>> >     On 1/22/19 2:53 PM, Amrita Bedi wrote:
>>> >     >
>>> >     >         External Email - Use Caution
>>> >     >
>>> >     > Hello Freesurfer developers,
>>> >     >
>>> >     > I was following the functional connectivity walkthrough for
>>> resting
>>> >     > stage BOLD data and I got the attached error when I ran step 8
>>> >     > (selxavg3-sess). Does anyone have any thoughts on how to trouble
>>> >     shoot
>>> >     > this?
>>> >     > Not sure if it?s of any use but I ran this using Freesurfer 6.0
>>> on
>>> >     > Centos 7.4
>>> >     >
>>> >     > Thank You.
>>> >     >
>>> >     > Best
>>> >     > Amrita
>>> >     >
>>> >     > _______________________________________________
>>> >     > Freesurfer mailing list
>>> >     > Freesurfer@nmr.mgh.harvard.edu
>>> >     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>> >     > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> >     <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>>> >
>>> >
>>> >     _______________________________________________
>>> >     Freesurfer mailing list
>>> >     Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.har
>>> vard.edu>
>>> >     https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> >     <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>>> >
>>> >
>>> > _______________________________________________
>>> > Freesurfer mailing list
>>> > Freesurfer@nmr.mgh.harvard.edu
>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> _______________________________________________
>> Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
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------------------------------

Message: 10
Date: Fri, 25 Jan 2019 11:58:25 -0500
From: Amrita Bedi <amibedi273@gmail.com>
Subject: Re: [Freesurfer] Functional connectivty walkthrough step 8
        error
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <CAPCzK2GZ4advVMs_oiooNhF_x7-yrygUaNpicksn=jYrW1sFHQ@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

        External Email - Use Caution

Pasted the text in the email but not sure if you can view it

On Friday, January 25, 2019, Amrita Bedi <amibedi273@gmail.com> wrote:

>
>
> On Friday, January 25, 2019, Amrita Bedi <amibedi273@gmail.com> wrote:
>
>>
>>
>> Here you go.
>> On Friday, January 25, 2019, Greve, Douglas N.,Ph.D. <
>> DGREVE@mgh.harvard.edu> wrote:
>>
>>> Hi Amrita, can you just paste the text into the email?
>>> thanks
>>> doug
>>>
>>> On 1/25/19 10:51 AM, Amrita Bedi wrote:
>>>
>>>         External Email - Use Caution
>>> Hi Dr Greve,
>>>
>>> Ran mris_fwhm and got the attached.
>>>
>>> On Thursday, January 24, 2019, Greve, Douglas N.,Ph.D. <
>>> DGREVE@mgh.harvard.edu> wrote:
>>>
>>>> Based on the output below, it looks like there are problems with
>>>> running
>>>> one of the freesurfer binaries. Can you run mris_fwhm ? Just type the
>>>> command and return and see what happens.
>>>>
>>>>
>>>>
>>>> /home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm --mask
>>>> /share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_rec
>>>> on/Bold1/fc.lpccseed.surf.lh/mask.nii.gz
>>>> --i
>>>> /share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_rec
>>>> on/Bold1/fc.lpccseed.surf.lh/rho1mn.nii.gz
>>>> --o
>>>> /share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_rec
>>>> on/Bold1/fc.lpccseed.surf.lh/rho1mn.sm.nii.gz
>>>> --fwhm 20.000000 --smooth-only --s fsaverage --hemi lh --sd
>>>> /share/VA_Imaging/Projects/salat/2389_TRT/abedi
>>>> /home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm:
>>>> /home/apps/matlab/MATLAB/R2011b/sys/os/glnxa64/libstdc++.so.6: version
>>>> `GLIBCXX_3.4.11' not found (required by
>>>> /home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm)
>>>>
>>>>
>>>>
>>>> On 1/23/19 10:11 AM, Amrita Bedi wrote:
>>>> >
>>>> >         External Email - Use Caution
>>>> >
>>>> > Hi Dr Greve,
>>>> >
>>>> > Attached is the log file.
>>>> >
>>>> > On Tuesday, January 22, 2019, Greve, Douglas N.,Ph.D.
>>>> > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> wrote:
>>>> >
>>>> >     Can you send the full terminal output and/or the log file?
>>>> >
>>>> >     On 1/22/19 2:53 PM, Amrita Bedi wrote:
>>>> >     >
>>>> >     >         External Email - Use Caution
>>>> >     >
>>>> >     > Hello Freesurfer developers,
>>>> >     >
>>>> >     > I was following the functional connectivity walkthrough for
>>>> resting
>>>> >     > stage BOLD data and I got the attached error when I ran step 8
>>>> >     > (selxavg3-sess). Does anyone have any thoughts on how to trouble
>>>> >     shoot
>>>> >     > this?
>>>> >     > Not sure if it?s of any use but I ran this using Freesurfer 6.0
>>>> on
>>>> >     > Centos 7.4
>>>> >     >
>>>> >     > Thank You.
>>>> >     >
>>>> >     > Best
>>>> >     > Amrita
>>>> >     >
>>>> >     > _______________________________________________
>>>> >     > Freesurfer mailing list
>>>> >     > Freesurfer@nmr.mgh.harvard.edu
>>>> >     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>> >     > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>> >     <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>>>> >
>>>> >
>>>> >     _______________________________________________
>>>> >     Freesurfer mailing list
>>>> >     Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.har
>>>> vard.edu>
>>>> >     https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>> >     <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>>>> >
>>>> >
>>>> > _______________________________________________
>>>> > Freesurfer mailing list
>>>> > Freesurfer@nmr.mgh.harvard.edu
>>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>
>>>>
>>>> _______________________________________________
>>>> Freesurfer mailing list
>>>> Freesurfer@nmr.mgh.harvard.edu
>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>> _______________________________________________
>>> Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>>
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------------------------------

Message: 11
Date: Fri, 25 Jan 2019 16:58:48 +0000
From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
Subject: Re: [Freesurfer] Functional connectivty walkthrough step 8
        error
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <4886d813-eba9-d277-dc43-bb3c614ae716@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

I don't see anything.

On 1/25/19 11:56 AM, Amrita Bedi wrote:

        External Email - Use Caution

[X]

Here you go.
On Friday, January 25, 2019, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>> wrote:
Hi Amrita, can you just paste the text into the email?
thanks
doug

On 1/25/19 10:51 AM, Amrita Bedi wrote:

        External Email - Use Caution

Hi Dr Greve,

Ran mris_fwhm and got the attached.

On Thursday, January 24, 2019, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>> wrote:
Based on the output below, it looks like there are problems with running
one of the freesurfer binaries. Can you run mris_fwhm ? Just type the
command and return and see what happens.



/home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm --mask
/share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_recon/Bold1/fc.lpccseed.surf.lh/mask.nii.gz
--i
/share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_recon/Bold1/fc.lpccseed.surf.lh/rho1mn.nii.gz
--o
/share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_recon/Bold1/fc.lpccseed.surf.lh/rho1mn.sm.nii.gz
--fwhm 20.000000 --smooth-only --s fsaverage --hemi lh --sd
/share/VA_Imaging/Projects/salat/2389_TRT/abedi
/home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm:
/home/apps/matlab/MATLAB/R2011b/sys/os/glnxa64/libstdc++.so.6: version
`GLIBCXX_3.4.11' not found (required by
/home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm)



On 1/23/19 10:11 AM, Amrita Bedi wrote:
>
>         External Email - Use Caution
>
> Hi Dr Greve,
>
> Attached is the log file.
>
> On Tuesday, January 22, 2019, Greve, Douglas N.,Ph.D.
> <DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>>> wrote:
>
>     Can you send the full terminal output and/or the log file?
>
>     On 1/22/19 2:53 PM, Amrita Bedi wrote:
>     >
>     >         External Email - Use Caution
>     >
>     > Hello Freesurfer developers,
>     >
>     > I was following the functional connectivity walkthrough for resting
>     > stage BOLD data and I got the attached error when I ran step 8
>     > (selxavg3-sess). Does anyone have any thoughts on how to trouble
>     shoot
>     > this?
>     > Not sure if it?s of any use but I ran this using Freesurfer 6.0 on
>     > Centos 7.4
>     >
>     > Thank You.
>     >
>     > Best
>     > Amrita
>     >
>     > _______________________________________________
>     > Freesurfer mailing list
>     > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
>     <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>>
>     > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>     <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>
>
>     _______________________________________________
>     Freesurfer mailing list
>     Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>>
>     https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>     <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>
>
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Message: 5
Date: Mon, 4 Feb 2019 09:28:24 -0500 (EST)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] gray matter volume of the entorhinal cortex
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <alpine.LRH.2.20.1902040927300.26643@gate.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

Hi Jose

the threshold is set so that the EC label has the average surface area of
the labels that went into the average. It is probably more accurate than
the aparc as it is based on actual cytoarchitectural landmarks that are
visible in ex vivo mri.

cheers
Bruce


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

>
> ????????External Email - Use Caution????????
>
> Dear Freesurfers,
>
> gray matter volume of the entorhinal cortex (EC) can be obtained either in the ?h.aparc.stats or
> ?h.BA_exvivo.stats/?h.BA_exvivo.thresh.stats files. Considering that all our T1 images were manually edited on a
> slice-by-slice basis to correct pial surface misplacements and erroneous white matter segmentation, which volume
> measure of the EC would be more precise?
>
> I assume that gray matter volume contained in ?h.BA_exvivo.thresh.stats were thresholded at a specific probability
> value (% of case overlapping). Which probability value was used? Is there a reference paper explaining how
> probabilistic maps of EC were built based on ex vivo MRI contrast?
>
> Thank you in advance.
>
> Best,
> Jose L. Cantero
>
>
>

------------------------------

Message: 6
Date: Mon, 4 Feb 2019 09:30:13 -0500 (EST)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Surface to Volume conversion
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <alpine.LRH.2.20.1902040929340.26643@gate.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="iso-8859-1"

Hi Emma

the dimensions (163842 x 1 x 1) mean that these are overlays on the
fsaverage surface. Can you remind me what issue you are trying to solve?

cheers
Bruce
On
Mon, 4 Feb 2019, Bunting, Emma wrote:

>
> ????????External Email - Use Caution????????
>
> Hi Bruce,
>
>
> I ran the mri_info command on the sig.mgh and the sig.lh.nii.gz files for participant 124 and got these outputs...
>
>
> For sig.mgh:
>
>
> Volume information for sig.mgh
> ????????? type: MGH
> ??? dimensions: 163842 x 1 x 1
> ?? voxel sizes: 1.000000, 1.000000, 1.000000
> ????????? type: FLOAT (3)
> ?????????? fov: 163842.000
> ?????????? dof: 0
> ??????? xstart: -81921.0, xend: 81921.0
> ??????? ystart: -0.5, yend: 0.5
> ??????? zstart: -0.5, zend: 0.5
> ??????????? TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees
> ?????? nframes: 1
> ?????? PhEncDir: UNKNOWN
> ?????? FieldStrength: 0.000000
> ras xform present
> ??? xform info: x_r =? -1.0000, y_r =?? 0.0000, z_r =?? 0.0000, c_r =???? 0.0000
> ????????????? : x_a =?? 0.0000, y_a =?? 0.0000, z_a =?? 1.0000, c_a =???? 0.0000
> ????????????? : x_s =?? 0.0000, y_s =? -1.0000, z_s =?? 0.0000, c_s =???? 0.0000
>
> talairach xfm :
> Orientation?? : LIA
> Primary Slice Direction: coronal
>
> voxel to ras transform:
> ?????????????? -1.0000?? 0.0000?? 0.0000 81921.0000
> ??????????????? 0.0000?? 0.0000?? 1.0000??? -0.5000
> ??????????????? 0.0000? -1.0000?? 0.0000???? 0.5000
> ??????????????? 0.0000?? 0.0000?? 0.0000???? 1.0000
>
> voxel-to-ras determinant -1
>
> ras to voxel transform:
> ?????????????? -1.0000? -0.0000? -0.0000 81921.0000
> ?????????????? -0.0000? -0.0000? -1.0000???? 0.5000
> ?????????????? -0.0000?? 1.0000? -0.0000???? 0.5000
> ?????????????? -0.0000? -0.0000? -0.0000???? 1.0000
>
>
> For sig.lh.nii.gz:
>
> Volume information for sig.lh.nii.gz
> ????????? type: nii
> ??? dimensions: 163842 x 1 x 1
> ?? voxel sizes: 1.000000, 1.000000, 1.000000
> ????????? type: FLOAT (3)
> ?????????? fov: 163842.000
> ?????????? dof: 0
> ??????? xstart: -81921.0, xend: 81921.0
> ??????? ystart: -0.5, yend: 0.5
> ??????? zstart: -0.5, zend: 0.5
> ??????????? TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees
> ?????? nframes: 1
> ?????? PhEncDir: UNKNOWN
> ?????? FieldStrength: 0.000000
> ras xform present
> ??? xform info: x_r =? -1.0000, y_r =?? 0.0000, z_r =?? 0.0000, c_r = -68267.5000
> ????????????? : x_a =?? 0.0000, y_a =?? 0.0000, z_a =?? 1.0000, c_a =??? -2.5000
> ????????????? : x_s =?? 0.0000, y_s =? -1.0000, z_s =?? 0.0000, c_s =???? 0.0000
> Orientation?? : LIA
> Primary Slice Direction: coronal
>
> voxel to ras transform:
> ?????????????? -1.0000?? 0.0000?? 0.0000 13653.5000
> ??????????????? 0.0000?? 0.0000?? 1.0000??? -3.0000
> ??????????????? 0.0000? -1.0000?? 0.0000???? 0.5000
> ??????????????? 0.0000?? 0.0000?? 0.0000???? 1.0000
>
> voxel-to-ras determinant -1
>
> ras to voxel transform:
> ?????????????? -1.0000? -0.0000? -0.0000 13653.5000
> ?????????????? -0.0000? -0.0000? -1.0000???? 0.5000
> ?????????????? -0.0000?? 1.0000? -0.0000???? 3.0000
> ?????????????? -0.0000? -0.0000? -0.0000???? 1.0000
>
> Please let me know if you need any other information in order to help with our problem,
>
> Best wishes,
>
> Emma
>
> ___________________________________________________________________________________________________________________
> From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of
> freesurfer-request@nmr.mgh.harvard.edu <freesurfer-request@nmr.mgh.harvard.edu>
> Sent: 25 January 2019 17:00
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Freesurfer Digest, Vol 179, Issue 41 ?
> 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
> ??????? freesurfer-request@nmr.mgh.harvard.edu
>
> You can reach the person managing the list at
> ??????? freesurfer-owner@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. Re: Longitudinal processing with windows subsystem for linux
> ????? (WSL) using ubuntu 18.04.1 LTS (Hoopes, Andrew)
> ?? 2. Re: FSFAST poor registration (Greve, Douglas N.,Ph.D.)
> ?? 3. Re: Surface to volume conversion (Bruce Fischl)
> ?? 4. Re: Functional connectivty walkthrough step 8 error
> ????? (Greve, Douglas N.,Ph.D.)
> ?? 5. Re: cortical thickness calculation based on hammersmith
> ????? segmentation (Greve, Douglas N.,Ph.D.)
> ?? 6. Re: FSFAST poor registration (Keri Woods)
> ?? 7. Re: Functional connectivty walkthrough step 8 error (Amrita Bedi)
> ?? 8. Re: Orientation by direction cosines (Greve, Douglas N.,Ph.D.)
> ?? 9. Re: Functional connectivty walkthrough step 8 error (Amrita Bedi)
> ? 10. Re: Functional connectivty walkthrough step 8 error (Amrita Bedi)
> ? 11. Re: Functional connectivty walkthrough step 8 error
> ????? (Greve, Douglas N.,Ph.D.)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 25 Jan 2019 16:24:14 +0000
> From: "Hoopes, Andrew" <AHOOPES@mgh.harvard.edu>
> Subject: Re: [Freesurfer] Longitudinal processing with windows
> ??????? subsystem for linux (WSL) using ubuntu 18.04.1 LTS
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Message-ID: <2A2251F1-6E66-4125-9A96-76700348245B@mgh.harvard.edu>
> Content-Type: text/plain; charset="utf-8"
>
> I believe this python2 issue has been fixed in the dev version found here
> https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/long_mris_slopes
>
> best,
> Andrew
>
>
> ?On 1/25/19, 10:08 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl"
> <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:
>
> ??? Hi Falk
> ???
> ??? thanks for catching the typo. I fixed it - nice to have an easy thing to
> ??? fix for a change :)
> ???
> ??? Bruce
> ???
> ???
> ??? On Fri, 25 Jan 2019, falk.luesebrink@med.ovgu.de wrote:
> ???
> ??? >
> ??? >???????? External Email - Use Caution???????
> ??? >
> ??? > Dear Juergen,
> ??? >
> ??? >?
> ??? >
> ??? > Thanks for your quick reply! Actually the spelling error is in the error message. Taken from
> ??? > http://martinos.org/~mreuter/long/long_mris_slopes
> ??? >
> ??? >?
> ??? >
> ??? > # extensive error checks
> ??? >
> ??? > #??? if options.fsgd is None and
> ??? >
> ??? >???? if options.qdec is None:
> ??? >
> ??? > #??????? print 'ERROR: Specify --fsgd or --qedc'
> ??? >
> ??? >???????? parser.print_help()
> ??? >
> ??? >???????? print '\nERROR: Specify --qedc (and other required arguments)\n'
> ??? >
> ??? >???????? sys.exit(1)
> ??? >
> ??? >?
> ??? >
> ??? > #??? if options.fsgd is not None and options.qdec is not None:
> ??? >
> ??? > #??????? print 'ERROR: Specify either --fsgd or --qedc, not both'
> ??? >
> ??? > #??????? sys.exit(1)
> ??? >
> ??? >?
> ??? >
> ??? > At least Martin is consistent with his typo. :D
> ??? >
> ??? >?
> ??? >
> ??? > Best,
> ??? >
> ??? > Falk
> ??? >
> ??? >?
> ??? >
> ??? > Von: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> Im Auftrag von Juergen
> Haenggi
> ??? > Gesendet: Freitag, 25. Januar 2019 10:35
> ??? > An: Freesurfer Mailinglist <freesurfer@nmr.mgh.harvard.edu>
> ??? > Betreff: Re: [Freesurfer] Longitudinal processing with windows subsystem for linux (WSL) using ubuntu 18.04.1
> LTS
> ??? >
> ??? >?
> ??? >
> ??? >???????? External Email - Use Caution???????
> ??? >
> ??? > Dear Falk
> ??? >
> ??? >?
> ??? >
> ??? > I have no idea, but recognised that the error refers to --qedc and not to --qdec.
> ??? >
> ??? > maybe there is a spelling error somewhere that is related to your problem.
> ??? >
> ??? >?
> ??? >
> ??? > HTH
> ??? >
> ??? > Cheers
> ??? >
> ??? > J?rgen
> ??? >
> ??? > -----------------------------------------------------------------------------------------------------
> ??? >
> ??? > University of Zurich
> ??? >
> ??? > Dr. J?rgen H?nggi, Ph.D.
> ??? >
> ??? > Department of Psychology
> ??? >
> ??? > Division Neuropsychology
> ??? >
> ??? > Binzmuehlestrasse 14, PO Box 25
> ??? >
> ??? > 8050 Zurich, Switzerland
> ??? >
> ??? >?
> ??? >
> ??? > 0041 44 635 73 97 (phone office)
> ??? >
> ??? > 0041 76 445 86 84 (phone mobile)??????
> ??? >
> ??? > 0041 44 635 74 09 (fax office)
> ??? >
> ??? > BIN 4.D.04 (office room number)????????????????????
> ??? >
> ??? >?
> ??? >
> ??? > j.haenggi@psychologie.uzh.ch (email)
> ??? >
> ??? > http://www.psychologie.uzh.ch/neuropsy/ (website)
> ??? >
> ??? > http://www.juergenhaenggi.ch (private website)??
> ??? >
> ??? >?
> ??? >
> ??? > This email (and any attachment/s) contains confidential and/or privileged
> ??? >
> ??? > information. If you are not the intended recipient (or have received this
> ??? >
> ??? > email in error) please notify the sender immediately and destroy this
> ??? >
> ??? > email. Any unauthorised copying, disclosure or distribution of the
> ??? >
> ??? > material in this email is strictly forbidden.
> ??? >
> ??? > -----------------------------------------------------------------------------------------------------
> ??? >
> ??? >?
> ??? >
> ??? >?
> ??? >
> ??? >
> ??? >
> ??? >?????? On 25 Jan 2019, at 10:26, falk.luesebrink@med.ovgu.de wrote:
> ??? >
> ??? >?
> ??? >
> ??? >???????? External Email - Use Caution???????
> ??? >
> ??? >?
> ??? >
> ??? > Dear all,
> ??? >
> ??? >?
> ??? >
> ??? > Has anyone run the longitudinal pipeline successfully using the WSL? I?m running it with Ubuntu 18.04.1 LTS
> ??? > and freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c.
> ??? >
> ??? >?
> ??? >
> ??? > I?m trying to process my first longitudinal data set following the instructions of the tutorial as close as
> ??? > possible. The data has been processed without issues and now I want to do the statistical analysis. When I
> ??? > run:
> ??? >
> ??? > long_mris_slopes --qdec ./long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc
> ??? > --do-stack --do-label --time years --qcache fsaverage --sd $SUBJECTS_DIR
> ??? >
> ??? >?
> ??? >
> ??? > I get the following error:
> ??? >
> ??? > File "/home/luesebri/Software/FreeSurfer/bin/long_mris_slopes", line 448
> ??? >
> ??? >???? print '\nERROR: Specify --qedc (and other required arguments)\n'
> ??? >
> ??? >??????????????????????????????????????????????????????????????????? ^
> ??? >
> ??? > SyntaxError: invalid syntax
> ??? >
> ??? >?
> ??? >
> ??? > I get comparable errors for any other long_* command I try to run, e.g. long_qdec_table with or without any
> ??? > arguments gives:
> ??? >
> ??? > File "/home/luesebri/Software/FreeSurfer/bin/long_qdec_table", line 119
> ??? >
> ??? >??? print '\nERROR: Specify --qedc'
> ??? >
> ??? >?????????????????????????????????? ^
> ??? >
> ??? > SyntaxError: Missing parentheses in call to 'print'. Did you mean print('\nERROR: Specify --qedc')?
> ??? >
> ??? >?
> ??? >
> ??? > Does anyone have a clue where this error originates from using either WSL or Ubuntu 18.04??
> ??? >
> ??? >?
> ??? >
> ??? > Best,
> ??? >
> ??? > Falk
> ??? >
> ??? > ...............................................
> ??? >
> ??? >?
> ??? >
> ??? > <image001.gif>
> ??? >
> ??? > Universit?tsklinik f?r Neurologie
> ??? >
> ??? >
> ??? >
> ??? > Otto-von-Guericke-Universit?t Magdeburg
> ??? > Medizinische Fakult?t
> ??? > Leipziger Str. 44
> ??? > 39120 Magdeburg
> ??? >
> ??? >?
> ??? >
> ??? > Telefon: +49-391-6117-512
> ??? >
> ??? > falk.luesebrink@med.ovgu.de
> ??? > http://www.kneu.ovgu.de/kneu.html
> ??? >
> ??? >?
> ??? >
> ??? > _______________________________________________
> ??? > Freesurfer mailing list
> ??? > Freesurfer@nmr.mgh.harvard.edu
> ??? > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> ??? >
> ??? >?
> ??? >
> ??? >
> ??? >
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Fri, 25 Jan 2019 16:34:14 +0000
> From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
> Subject: Re: [Freesurfer] FSFAST poor registration
> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
> Message-ID: <367a8e86-05d2-f02b-d19b-94401864c91d@mgh.harvard.edu>
> Content-Type: text/plain; charset="utf-8"
>
> Yes, that file is the only thing linking the functional to the anatomical. It's too bad you messed up the files,
> but I'm relieved it was not my software:).
>
> On 1/25/19 5:09 AM, Keri Woods wrote:
>
> ??????? External Email - Use Caution
>
> Hi Douglas
>
> Thanks very much for getting back to me. I created new separate directories and re-processed one of the problem
> subjects individually, and the registration worked well. So the problem is that the anatomical and functional
> images come from different subjects. But I've checked and the subjectname files are correct. That's the only thing
> linking the anatomical and functional images? Thanks very much, you've helped me a lot. Now I just have to go and
> see where I mixed up the files!
>
> Thanks again,
> Keri
>
> On Thu, Jan 24, 2019 at 10:32 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>>
> wrote:
> Can you tar up the anatomical and functional analyses and send them to
> me through our filedrop?
>
> https://gate.nmr.mgh.harvard.edu/filedrop2/
>
> when it asks for an email of the recipient, use greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu>
>
>
> On 1/23/19 5:57 AM, Keri Woods wrote:
> >
> >???????? External Email - Use Caution
> >
> > I meant some are nearly perfect.
> >
> > On Wed, Jan 23, 2019 at 11:49 AM Keri Woods <keri.woods@gmail.com<mailto:keri.woods@gmail.com>
> > <mailto:keri.woods@gmail.com<mailto:keri.woods@gmail.com>>> wrote:
> >
> >???? Hi Douglas
> >
> >???? Thanks for the response.
> >
> >???? No, some of the registrations are fine. Some are close, but not
> >???? perfect, while others are very bad.
> >
> >???? I've checked the subjectname file for some subjects with poor
> >???? registration (eg 20_101), and they are correct.
> >
> >???? Thanks,
> >???? Keri
> >
> >???? On Tue, Jan 22, 2019 at 8:57 PM Greve, Douglas N.,Ph.D.
> >???? <DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>
> <mailto:DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>>> wrote:
> >
> >???????? Are you saying that all of them have bad registrations? Some
> >???????? of them
> >???????? (eg, 20_1, 20_10) look like they should be good. Others (eg,
> >???????? 20_101)
> >???????? look like they could be bad. For the bad ones, are you totally
> >???????? sure that
> >???????? the subjetname file has the correct name of the subject?
> >
> >???????? On 1/21/19 3:19 AM, Keri Woods wrote:
> >???????? >
> >???????? >???????? External Email - Use Caution
> >???????? >
> >???????? > Hi Douglas
> >???????? >
> >???????? > Thank you for your reply.
> >???????? >
> >???????? > I'm using
> >???????? freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
> >???????? >
> >???????? > I am using whole brain data. The functional and structural
> >???????? images were
> >???????? > acquired in different sessions on the same day, I don't know
> >???????? if that
> >???????? > complicated things? Each subject has 2 runs of the same task.
> >???????? >
> >???????? > This is what I get after running the command in the format of
> >???????? > tkregister-sess -s sess01 -s sess02 -s sess03 -fsd bold
> >???????? -per-run -bbr-sum
> >???????? >
> >???????? > 20_1?????? 013 0.5155
> >???????? > 20_1?????? 014 0.5090
> >???????? > 20_10????? 013 0.5247
> >???????? > 20_10????? 014 0.5229
> >???????? > 20_100???? 038 0.8420
> >???????? > 20_100???? 040 0.8443
> >???????? > 20_101???? 008 0.9052
> >???????? > 20_101???? 010 0.9289
> >???????? > 20_102???? 058 0.6924
> >???????? > 20_102???? 059 0.6902
> >???????? > 20_103???? 045 0.9778
> >???????? > 20_103???? 046 0.9931
> >???????? > 20_104???? 010 0.9324
> >???????? > 20_104???? 012 0.9413
> >???????? > 20_105???? 013 0.8754
> >???????? > 20_105???? 014 0.8937
> >???????? > 20_106???? 047 0.4433
> >???????? > 20_106???? 048 0.4377
> >???????? > 20_107???? 008 0.9178
> >???????? > 20_107???? 010 0.9238
> >???????? > 20_11????? 013 0.7631
> >???????? > 20_11????? 014 0.7615
> >???????? > 20_110???? 048 0.7687
> >???????? > 20_110???? 049 0.7549
> >???????? > 20_112???? 013 0.8821
> >???????? > 20_112???? 014 0.9161
> >???????? > 20_113???? 052 0.7689
> >???????? > 20_113???? 053 0.7757
> >???????? > 20_116???? 046 1.0072
> >???????? > 20_116???? 047 1.0256
> >???????? > 20_117???? 008 0.7742
> >???????? > 20_117???? 010 0.7826
> >???????? > 20_119???? 013 0.7929
> >???????? > 20_119???? 014 0.7854
> >???????? > 20_120???? 048 0.5090
> >???????? > 20_120???? 049 0.4973
> >???????? > 20_126???? 047 0.8285
> >???????? > 20_126???? 048 0.8281
> >???????? > 20_128???? 046 0.9580
> >???????? > 20_128???? 047 0.9314
> >???????? > 20_130???? 047 0.9439
> >???????? > 20_130???? 048 0.9425
> >???????? > 20_132???? 047 0.8550
> >???????? > 20_132???? 048 0.8558
> >???????? > 20_134_1?? 013 0.5716
> >???????? > 20_134_1?? 015 0.5744
> >???????? > 20_135???? 011 0.8357
> >???????? > 20_135???? 012 0.8401
> >???????? > 20_136???? 044 0.9995
> >???????? > 20_136???? 045 0.9604
> >???????? > 20_137???? 047 0.7922
> >???????? > 20_137???? 048 0.7990
> >???????? > 20_142???? 047 0.5282
> >???????? > 20_142???? 048 0.5278
> >???????? > 20_144???? 013 0.8755
> >???????? > 20_144???? 014 0.8838
> >???????? > 20_146???? 047 0.7997
> >???????? > 20_146???? 048 0.7895
> >???????? > 20_149???? 049 0.9251
> >???????? > 20_149???? 050 0.9408
> >???????? > 20_151???? 048 0.5905
> >???????? > 20_151???? 049 0.5519
> >???????? > 20_152???? 048 0.9024
> >???????? > 20_152???? 049 0.9021
> >???????? > 20_155???? 048 0.5285
> >???????? > 20_155???? 049 0.5324
> >???????? > 20_156???? 048 0.8883
> >???????? > 20_156???? 049 0.9267
> >???????? > 20_158???? 048 0.5404
> >???????? > 20_158???? 049 0.5297
> >???????? > 20_159???? 048 0.8021
> >???????? > 20_160???? 013 0.5002
> >???????? > 20_160???? 014 0.4942
> >???????? > 20_162???? 047 0.5401
> >???????? > 20_162???? 048 0.5401
> >???????? > 20_164???? 047 0.8944
> >???????? > 20_164???? 048 0.8940
> >???????? > 20_165???? 047 0.9163
> >???????? > 20_165???? 048 0.9077
> >???????? > 20_166???? 045 0.8787
> >???????? > 20_166???? 046 0.8848
> >???????? > 20_167???? 050 0.8428
> >???????? > 20_167???? 051 0.8442
> >???????? > 20_169???? 049 0.9407
> >???????? > 20_169???? 050 0.9462
> >???????? > 20_170???? 047 0.8921
> >???????? > 20_170???? 048 0.9113
> >???????? > 20_171???? 013 0.9060
> >???????? > 20_171???? 014 0.9060
> >???????? > 20_173???? 048 0.9193
> >???????? > 20_173???? 049 0.9141
> >???????? > 20_177???? 048 0.8695
> >???????? > 20_177???? 049 0.8600
> >???????? > 20_178???? 048 1.0327
> >???????? > 20_178???? 049 0.8979
> >???????? > 20_180???? 045 0.7999
> >???????? > 20_180???? 046 0.8002
> >???????? > 20_182???? 047 0.9135
> >???????? > 20_182???? 048 0.9130
> >???????? > 20_184???? 048 0.9842
> >???????? > 20_184???? 049 0.9960
> >???????? > 20_185???? 046 0.9640
> >???????? > 20_185???? 047 0.9514
> >???????? > 20_187???? 048 0.8134
> >???????? > 20_187???? 049 0.8082
> >???????? > 20_189???? 047 1.0063
> >???????? > 20_189???? 048 0.9701
> >???????? > 20_19????? 013 0.8485
> >???????? > 20_19????? 014 0.8534
> >???????? > 20_190???? 047 0.9279
> >???????? > 20_190???? 048 0.9169
> >???????? > 20_191???? 046 0.9586
> >???????? > 20_191???? 047 0.9751
> >???????? > 20_192???? 049 0.8544
> >???????? > 20_193???? 013 0.9084
> >???????? > 20_193???? 014 0.9110
> >???????? > 20_194???? 047 0.9220
> >???????? > 20_194???? 048 0.9166
> >???????? > 20_195???? 048 0.9552
> >???????? > 20_195???? 049 0.9508
> >???????? > 20_196???? 047 0.9098
> >???????? > 20_196???? 048 0.9011
> >???????? > 20_199???? 048 0.8569
> >???????? > 20_199???? 049 0.8567
> >???????? > 20_20????? 013 0.8750
> >???????? > 20_20????? 014 0.8749
> >???????? > 20_201???? 048 0.8864
> >???????? > 20_201???? 049 1.0040
> >???????? > 20_202???? 048 0.8542
> >???????? > 20_202???? 049 0.8516
> >???????? > 20_203???? 048 1.0267
> >???????? > 20_203???? 049 1.0060
> >???????? > 20_204???? 048 0.8513
> >???????? > 20_204???? 049 0.8588
> >???????? > 20_208???? 014 0.9130
> >???????? > 20_208???? 015 0.9329
> >???????? > 20_209???? 047 1.0020
> >???????? > 20_209???? 048 1.0120
> >???????? > 20_21????? 027 0.9747
> >???????? > 20_21????? 028 1.0081
> >???????? > 20_210???? 048 0.8607
> >???????? > 20_210???? 049 0.8564
> >???????? > 20_220???? 047 0.8888
> >???????? > 20_220???? 048 0.8903
> >???????? > 20_222???? 047 0.9998
> >???????? > 20_222???? 048 0.8597
> >???????? > 20_224???? 013 0.8122
> >???????? > 20_224???? 014 0.8107
> >???????? > 20_226???? 013 0.7855
> >???????? > 20_226???? 014 0.7845
> >???????? > 20_227???? 013 0.9372
> >???????? > 20_227???? 014 0.9818
> >???????? > 20_231???? 047 0.8355
> >???????? > 20_231???? 048 0.8506
> >???????? > 20_232???? 048 0.9730
> >???????? > 20_232???? 049 0.9591
> >???????? > 20_234???? 048 0.9357
> >???????? > 20_234???? 049 0.9429
> >???????? > 20_235???? 048 0.7528
> >???????? > 20_235???? 049 0.7483
> >???????? > 20_236???? 047 0.8997
> >???????? > 20_236???? 048 0.8922
> >???????? > 20_239???? 049 0.8920
> >???????? > 20_239???? 050 0.8817
> >???????? > 20_24????? 013 0.8197
> >???????? > 20_24????? 014 0.8280
> >???????? > 20_240???? 047 0.9109
> >???????? > 20_240???? 048 0.9231
> >???????? > 20_243???? 013 0.8227
> >???????? > 20_243???? 014 0.8333
> >???????? > 20_245???? 045 0.8620
> >???????? > 20_245???? 046 0.8635
> >???????? > 20_246???? 047 0.8236
> >???????? > 20_246???? 048 0.8269
> >???????? > 20_248???? 053 0.6015
> >???????? > 20_248???? 054 0.6091
> >???????? > 20_25????? 013 0.8676
> >???????? > 20_25????? 014 0.8658
> >???????? > 20_250???? 048 0.9124
> >???????? > 20_250???? 050 0.9090
> >???????? > 20_251???? 048 0.9061
> >???????? > 20_251???? 049 0.9078
> >???????? > 20_277???? 008 0.7923
> >???????? > 20_277???? 010 0.7970
> >???????? > 20_278???? 048 0.4834
> >???????? > 20_278???? 049 0.4845
> >???????? > 20_279???? 008 0.4363
> >???????? > 20_279???? 010 0.4370
> >???????? > 20_281???? 013 0.8672
> >???????? > 20_281???? 014 0.8647
> >???????? > 20_282???? 043 0.8884
> >???????? > 20_282???? 044 0.8886
> >???????? > 20_284???? 052 0.9152
> >???????? > 20_284???? 053 0.9118
> >???????? > 20_285???? 047 0.9546
> >???????? > 20_285???? 048 0.9517
> >???????? > 20_286???? 008 0.9607
> >???????? > 20_286???? 010 0.9596
> >???????? > 20_287???? 055 0.8976
> >???????? > 20_287???? 056 0.8756
> >???????? > 20_288???? 047 1.0127
> >???????? > 20_288???? 048 1.0307
> >???????? > 20_290???? 048 1.0089
> >???????? > 20_290???? 049 1.0391
> >???????? > 20_293???? 052 0.7792
> >???????? > 20_293???? 053 0.7772
> >???????? > 20_3?????? 017 0.8530
> >???????? > 20_3?????? 018 0.8501
> >???????? > 20_40????? 013 0.9392
> >???????? > 20_40????? 014 0.9787
> >???????? > 20_41????? 013 0.9562
> >???????? > 20_41????? 014 0.9547
> >???????? > 20_44????? 013 0.8725
> >???????? > 20_44????? 014 0.8872
> >???????? > 20_51????? 013 0.9420
> >???????? > 20_51????? 014 0.9417
> >???????? > 20_55????? 013 0.9796
> >???????? > 20_55????? 014 0.9837
> >???????? > 20_58????? 013 0.9677
> >???????? > 20_58????? 014 0.9506
> >???????? > 20_59????? 013 0.9180
> >???????? > 20_59????? 014 0.9157
> >???????? > 20_69????? 013 0.9265
> >???????? > 20_69????? 014 0.9283
> >???????? > 20_74????? 014 0.9476
> >???????? > 20_74????? 015 0.9201
> >???????? > 20_78????? 012 0.9822
> >???????? > 20_78????? 013 0.9501
> >???????? > 20_81????? 013 0.8664
> >???????? > 20_81????? 014 0.8693
> >???????? > 20_84????? 013 0.8827
> >???????? > 20_84????? 014 0.9196
> >???????? > 20_86????? 016 0.9138
> >???????? > 20_86????? 017 0.9152
> >???????? > 20_88????? 039 0.9905
> >???????? > 20_88????? 041 1.0168
> >???????? > 20_90????? 049 0.8263
> >???????? > 20_90????? 050 1.0208
> >???????? > 20_95????? 008 0.8892
> >???????? > 20_95????? 010 0.9359
> >???????? > 20_96????? 013 0.9191
> >???????? > 20_96????? 014 0.9326
> >???????? > 20_97????? 008 0.9569
> >???????? > 20_97????? 010 0.9731
> >???????? > 20_98????? 008 0.9317
> >???????? > 20_98????? 012 0.9409
> >???????? > 20_PHRU??? 047 0.7797
> >???????? > 20_PHRU??? 048 0.7894
> >???????? >
> >???????? > So the registration is really poor. I've visually checked the
> >???????? > registration for many of the subjects, and the functional
> >???????? data isn't
> >???????? > left-right reversed, I've also checked some of the
> >???????? subjectname files
> >???????? > (which I created by running a script) and they are correct.
> >???????? >
> >???????? > I'm new to Freesurfer, so maybe I've made a mistake
> >???????? somewhere? I'm
> >???????? > been following these instructions:
> >???????? >
> >???????? > https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorial
> >???????? >
> >???????? > Thanks,
> >???????? > Keri
> >???????? >
> >???????? >
> >???????? > On Fri, Jan 18, 2019 at 6:44 PM Greve, Douglas N.,Ph.D.
> >???????? > <DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>
> <mailto:DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>>
> >???????? <mailto:DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>
> >???????? <mailto:DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>>>> wrote:
> >???????? >
> >???????? >???? What version of FS are you using? version 6 initializes with
> >???????? >???? mri_coreg (the FS equivalent of spm_coreg). On
> >???????? whole-brain data,
> >???????? >???? I've found this to be very robust. Is your data whole-brain?
> >???????? >
> >???????? >???? On 1/18/19 5:10 AM, Keri Woods wrote:
> >???????? >>
> >???????? >>???????????? External Email - Use Caution
> >???????? >>
> >???????? >>???? Hi
> >???????? >>
> >???????? >>???? I have a problem very similar to this one:
> >???????? >>
> >???????? >>
> >???????? https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23206.html
> >???????? >>
> >???????? >>???? I've tried the suggestions given there, but it didn't
> >???????? fix my problem.
> >???????? >>
> >???????? >>???? I'm running the FSFAST preproc-sess stream and the
> >???????? quality of the
> >???????? >>???? registration is very poor for most of the subjects.
> >???????? >>
> >???????? >>???? I've tried initializing the registration differently, using
> >???????? >>???? bbregister with --init-fsl, --init-spm and init-header,
> >???????? which
> >???????? >>???? didn't improve the results at all.
> >???????? >>
> >???????? >>???? I've also tried register-sess with --init-fsl,
> >???????? --init-spm and
> >???????? >>???? init-header, as well as spmregister-sess and
> >???????? fslregister-sess.
> >???????? >>
> >???????? >>???? Is there anything else I could try?
> >???????? >>
> >???????? >>???? Using the SPM GUI, the registration was fine, so I
> >???????? thought that
> >???????? >>???? spmregister-sess would have been an improvement, but it
> >???????? wasn't.
> >???????? >>???? Is there anyway I can import the registration obtained
> >???????? using the
> >???????? >>???? SPM GUI?
> >???????? >>
> >???????? >>???? Thanks for your help.
> >???????? >>
> >???????? >>???? Thanks,
> >???????? >>???? Keri
> >???????? >>
> >???????? >>
> >???????? >>
> >???????? >>
> >???????? >>
> >???????? >>? _______________________________________________
> >???????? >>???? Freesurfer mailing list
> >???????? >> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
> >???????? <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>>
> >???????? <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
> >???????? <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>>>
> >???????? >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >???????? >
> >???????? >???? _______________________________________________
> >???????? >???? Freesurfer mailing list
> >???????? > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
> >???????? <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>>
> >???????? <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
> >???????? <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>>>
> >???????? > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >???????? >
> >???????? >
> >???????? > _______________________________________________
> >???????? > Freesurfer mailing list
> >???????? > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
> >???????? <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>>
> >???????? > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >???????? _______________________________________________
> >???????? Freesurfer mailing list
> >???????? Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
> >???????? <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>>
> >???????? https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> _______________________________________________
> Freesurfer mailing list
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>
> -------------- next part --------------
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> URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20190125/11134a37/attachment-0001.html
>
> ------------------------------
>
> Message: 3
> Date: Fri, 25 Jan 2019 11:34:38 -0500 (EST)
> From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] Surface to volume conversion
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Message-ID:
> ??????? <alpine.LRH.2.20.1901251133510.26643@gate.nmr.mgh.harvard.edu>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Emma
>
> can you run mri_info on the .mgh and .nii.gz volumes and send us the
> output? Is the sig.mgh a surface overlay? If so, you can't visualize it
> directly, you have to overlay it on a surface (in either .mgh or .nii.gz
> foramt)
>
> cheers
> Bruce
>
>
> On Fri, 25 Jan 2019, Bunting, Emma wrote:
>
> >??????? External Email - Use Caution
> >
> > Hi!
> >
> > I?m trying to convert my sig.mgh output from GLM into a .nii file using mri_convert, and when I load the
> resulting volume in freeview this is what I see.
> >
> > The command I?m using is:
> > mri_convert ?in-type mgh ?out_type nii.gz ?out_orientation RAS /(root to sig.mgh file)/sig.mgh /(root to output
> file)/sig.nii.gz,
> >
> > Is there something I should be doing differently?
> >
> > Many thanks,
> >
> > Emma
> >
> >
>
> ------------------------------
>
> Message: 4
> Date: Fri, 25 Jan 2019 16:44:25 +0000
> From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
> Subject: Re: [Freesurfer] Functional connectivty walkthrough step 8
> ??????? error
> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
> Message-ID: <f526e7d2-f63e-35c7-9de6-bf8fda8ed9e2@mgh.harvard.edu>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Amrita, can you just paste the text into the email?
> thanks
> doug
>
> On 1/25/19 10:51 AM, Amrita Bedi wrote:
>
> ??????? External Email - Use Caution
>
> Hi Dr Greve,
>
> Ran mris_fwhm and got the attached.
>
> On Thursday, January 24, 2019, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>>
> wrote:
> Based on the output below, it looks like there are problems with running
> one of the freesurfer binaries. Can you run mris_fwhm ? Just type the
> command and return and see what happens.
>
>
>
> /home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm --mask
> /share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_recon/Bold1/fc.lpccseed.surf.lh/mask.nii.gz
> --i
> /share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_recon/Bold1/fc.lpccseed.surf.lh/rho1mn.nii.gz
> --o
> /share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_recon/Bold1/fc.lpccseed.surf.lh/rho1mn.sm.nii.gz
> --fwhm 20.000000 --smooth-only --s fsaverage --hemi lh --sd
> /share/VA_Imaging/Projects/salat/2389_TRT/abedi
> /home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm:
> /home/apps/matlab/MATLAB/R2011b/sys/os/glnxa64/libstdc++.so.6: version
> `GLIBCXX_3.4.11' not found (required by
> /home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm)
>
>
>
> On 1/23/19 10:11 AM, Amrita Bedi wrote:
> >
> >???????? External Email - Use Caution
> >
> > Hi Dr Greve,
> >
> > Attached is the log file.
> >
> > On Tuesday, January 22, 2019, Greve, Douglas N.,Ph.D.
> > <DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>
> <mailto:DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>>> wrote:
> >
> >???? Can you send the full terminal output and/or the log file?
> >
> >???? On 1/22/19 2:53 PM, Amrita Bedi wrote:
> >???? >
> >???? >???????? External Email - Use Caution
> >???? >
> >???? > Hello Freesurfer developers,
> >???? >
> >???? > I was following the functional connectivity walkthrough for resting
> >???? > stage BOLD data and I got the attached error when I ran step 8
> >???? > (selxavg3-sess). Does anyone have any thoughts on how to trouble
> >???? shoot
> >???? > this?
> >???? > Not sure if it?s of any use but I ran this using Freesurfer 6.0 on
> >???? > Centos 7.4
> >???? >
> >???? > Thank You.
> >???? >
> >???? > Best
> >???? > Amrita
> >???? >
> >???? > _______________________________________________
> >???? > Freesurfer mailing list
> >???? > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
> >???? <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>>
> >???? > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >???? <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> >
> >???? _______________________________________________
> >???? Freesurfer mailing list
> >???? Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
> <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>>
> >???? https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >???? <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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>
>
>
> _______________________________________________
> Freesurfer mailing list
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> ------------------------------
>
> Message: 5
> Date: Fri, 25 Jan 2019 16:45:24 +0000
> From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
> Subject: Re: [Freesurfer] cortical thickness calculation based on
> ??????? hammersmith segmentation
> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
> Message-ID: <0fa6801f-f424-863f-8373-2c217f70cf78@mgh.harvard.edu>
> Content-Type: text/plain; charset="utf-8"
>
> Those are the commands. Can you send the command lines you used and a fuller description of exactly how it is not
> working?
>
> On 1/25/19 10:56 AM, Boris Rauchmann wrote:
>
> ??????? External Email - Use Caution
> Dear FreeSurfer Developers,
>
> I?m trying to extract the cortical thickness of individuals from a study cohort based on an hammersmith n30r83
> atlas segmentation. I have this atlas only in as a volumetric file. I already run recon-all on all subjects. I
> tried mri_vol2surf and then mris_seg2annot but without success so far. What commands would you recommend me to run?
>
> Thanks,
> Boris
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
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> ------------------------------
>
> Message: 6
> Date: Fri, 25 Jan 2019 18:50:40 +0200
> From: Keri Woods <keri.woods@gmail.com>
> Subject: Re: [Freesurfer] FSFAST poor registration
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Message-ID:
> ??????? <CAOFXy0n2U4V+QYxXwKzE-eWaiz5960W2aVbCrmmbvopsmXQDOQ@mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> ??????? External Email - Use Caution???????
>
> Good thing it's not the software :) Also makes it easier for me to fix. In
> my script there was one tiny mistake - the anatomical image for one subject
> was repeated each time instead of using the files for different subjects. I
> ran recon-all 100+ times on the same subject!! Checking the registration
> was definitely worthwhile. Thanks again for the help, it made me look at
> the problem in a different.
>
> On Fri, Jan 25, 2019 at 6:34 PM Greve, Douglas N.,Ph.D. <
> DGREVE@mgh.harvard.edu> wrote:
>
> > Yes, that file is the only thing linking the functional to the anatomical.
> > It's too bad you messed up the files, but I'm relieved it was not my
> > software:).
> >
> > On 1/25/19 5:09 AM, Keri Woods wrote:
> >
> >???????? External Email - Use Caution
> > Hi Douglas
> >
> > Thanks very much for getting back to me. I created new separate
> > directories and re-processed one of the problem subjects individually, and
> > the registration worked well. So the problem is that the anatomical and
> > functional images come from different subjects. But I've checked and the
> > subjectname files are correct. That's the only thing linking the anatomical
> > and functional images? Thanks very much, you've helped me a lot. Now I just
> > have to go and see where I mixed up the files!
> >
> > Thanks again,
> > Keri
> >
> > On Thu, Jan 24, 2019 at 10:32 PM Greve, Douglas N.,Ph.D. <
> > DGREVE@mgh.harvard.edu> wrote:
> >
> >> Can you tar up the anatomical and functional analyses and send them to
> >> me through our filedrop?
> >>
> >> https://gate.nmr.mgh.harvard.edu/filedrop2/
> >>
> >> when it asks for an email of the recipient, use greve@nmr.mgh.harvard.edu
> >>
> >>
> >> On 1/23/19 5:57 AM, Keri Woods wrote:
> >> >
> >> >???????? External Email - Use Caution
> >> >
> >> > I meant some are nearly perfect.
> >> >
> >> > On Wed, Jan 23, 2019 at 11:49 AM Keri Woods <keri.woods@gmail.com
> >> > <mailto:keri.woods@gmail.com>> wrote:
> >> >
> >> >???? Hi Douglas
> >> >
> >> >???? Thanks for the response.
> >> >
> >> >???? No, some of the registrations are fine. Some are close, but not
> >> >???? perfect, while others are very bad.
> >> >
> >> >???? I've checked the subjectname file for some subjects with poor
> >> >???? registration (eg 20_101), and they are correct.
> >> >
> >> >???? Thanks,
> >> >???? Keri
> >> >
> >> >???? On Tue, Jan 22, 2019 at 8:57 PM Greve, Douglas N.,Ph.D.
> >> >???? <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> wrote:
> >> >
> >> >???????? Are you saying that all of them have bad registrations? Some
> >> >???????? of them
> >> >???????? (eg, 20_1, 20_10) look like they should be good. Others (eg,
> >> >???????? 20_101)
> >> >???????? look like they could be bad. For the bad ones, are you totally
> >> >???????? sure that
> >> >???????? the subjetname file has the correct name of the subject?
> >> >
> >> >???????? On 1/21/19 3:19 AM, Keri Woods wrote:
> >> >???????? >
> >> >???????? >???????? External Email - Use Caution
> >> >???????? >
> >> >???????? > Hi Douglas
> >> >???????? >
> >> >???????? > Thank you for your reply.
> >> >???????? >
> >> >???????? > I'm using
> >> >???????? freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
> >> >???????? >
> >> >???????? > I am using whole brain data. The functional and structural
> >> >???????? images were
> >> >???????? > acquired in different sessions on the same day, I don't know
> >> >???????? if that
> >> >???????? > complicated things? Each subject has 2 runs of the same task.
> >> >???????? >
> >> >???????? > This is what I get after running the command in the format of
> >> >???????? > tkregister-sess -s sess01 -s sess02 -s sess03 -fsd bold
> >> >???????? -per-run -bbr-sum
> >> >???????? >
> >> >???????? > 20_1?????? 013 0.5155
> >> >???????? > 20_1?????? 014 0.5090
> >> >???????? > 20_10????? 013 0.5247
> >> >???????? > 20_10????? 014 0.5229
> >> >???????? > 20_100???? 038 0.8420
> >> >???????? > 20_100???? 040 0.8443
> >> >???????? > 20_101???? 008 0.9052
> >> >???????? > 20_101???? 010 0.9289
> >> >???????? > 20_102???? 058 0.6924
> >> >???????? > 20_102???? 059 0.6902
> >> >???????? > 20_103???? 045 0.9778
> >> >???????? > 20_103???? 046 0.9931
> >> >???????? > 20_104???? 010 0.9324
> >> >???????? > 20_104???? 012 0.9413
> >> >???????? > 20_105???? 013 0.8754
> >> >???????? > 20_105???? 014 0.8937
> >> >???????? > 20_106???? 047 0.4433
> >> >???????? > 20_106???? 048 0.4377
> >> >???????? > 20_107???? 008 0.9178
> >> >???????? > 20_107???? 010 0.9238
> >> >???????? > 20_11????? 013 0.7631
> >> >???????? > 20_11????? 014 0.7615
> >> >???????? > 20_110???? 048 0.7687
> >> >???????? > 20_110???? 049 0.7549
> >> >???????? > 20_112???? 013 0.8821
> >> >???????? > 20_112???? 014 0.9161
> >> >???????? > 20_113???? 052 0.7689
> >> >???????? > 20_113???? 053 0.7757
> >> >???????? > 20_116???? 046 1.0072
> >> >???????? > 20_116???? 047 1.0256
> >> >???????? > 20_117???? 008 0.7742
> >> >???????? > 20_117???? 010 0.7826
> >> >???????? > 20_119???? 013 0.7929
> >> >???????? > 20_119???? 014 0.7854
> >> >???????? > 20_120???? 048 0.5090
> >> >???????? > 20_120???? 049 0.4973
> >> >???????? > 20_126???? 047 0.8285
> >> >???????? > 20_126???? 048 0.8281
> >> >???????? > 20_128???? 046 0.9580
> >> >???????? > 20_128???? 047 0.9314
> >> >???????? > 20_130???? 047 0.9439
> >> >???????? > 20_130???? 048 0.9425
> >> >???????? > 20_132???? 047 0.8550
> >> >???????? > 20_132???? 048 0.8558
> >> >???????? > 20_134_1?? 013 0.5716
> >> >???????? > 20_134_1?? 015 0.5744
> >> >???????? > 20_135???? 011 0.8357
> >> >???????? > 20_135???? 012 0.8401
> >> >???????? > 20_136???? 044 0.9995
> >> >???????? > 20_136???? 045 0.9604
> >> >???????? > 20_137???? 047 0.7922
> >> >???????? > 20_137???? 048 0.7990
> >> >???????? > 20_142???? 047 0.5282
> >> >???????? > 20_142???? 048 0.5278
> >> >???????? > 20_144???? 013 0.8755
> >> >???????? > 20_144???? 014 0.8838
> >> >???????? > 20_146???? 047 0.7997
> >> >???????? > 20_146???? 048 0.7895
> >> >???????? > 20_149???? 049 0.9251
> >> >???????? > 20_149???? 050 0.9408
> >> >???????? > 20_151???? 048 0.5905
> >> >???????? > 20_151???? 049 0.5519
> >> >???????? > 20_152???? 048 0.9024
> >> >???????? > 20_152???? 049 0.9021
> >> >???????? > 20_155???? 048 0.5285
> >> >???????? > 20_155???? 049 0.5324
> >> >???????? > 20_156???? 048 0.8883
> >> >???????? > 20_156???? 049 0.9267
> >> >???????? > 20_158???? 048 0.5404
> >> >???????? > 20_158???? 049 0.5297
> >> >???????? > 20_159???? 048 0.8021
> >> >???????? > 20_160???? 013 0.5002
> >> >???????? > 20_160???? 014 0.4942
> >> >???????? > 20_162???? 047 0.5401
> >> >???????? > 20_162???? 048 0.5401
> >> >???????? > 20_164???? 047 0.8944
> >> >???????? > 20_164???? 048 0.8940
> >> >???????? > 20_165???? 047 0.9163
> >> >???????? > 20_165???? 048 0.9077
> >> >???????? > 20_166???? 045 0.8787
> >> >???????? > 20_166???? 046 0.8848
> >> >???????? > 20_167???? 050 0.8428
> >> >???????? > 20_167???? 051 0.8442
> >> >???????? > 20_169???? 049 0.9407
> >> >???????? > 20_169???? 050 0.9462
> >> >???????? > 20_170???? 047 0.8921
> >> >???????? > 20_170???? 048 0.9113
> >> >???????? > 20_171???? 013 0.9060
> >> >???????? > 20_171???? 014 0.9060
> >> >???????? > 20_173???? 048 0.9193
> >> >???????? > 20_173???? 049 0.9141
> >> >???????? > 20_177???? 048 0.8695
> >> >???????? > 20_177???? 049 0.8600
> >> >???????? > 20_178???? 048 1.0327
> >> >???????? > 20_178???? 049 0.8979
> >> >???????? > 20_180???? 045 0.7999
> >> >???????? > 20_180???? 046 0.8002
> >> >???????? > 20_182???? 047 0.9135
> >> >???????? > 20_182???? 048 0.9130
> >> >???????? > 20_184???? 048 0.9842
> >> >???????? > 20_184???? 049 0.9960
> >> >???????? > 20_185???? 046 0.9640
> >> >???????? > 20_185???? 047 0.9514
> >> >???????? > 20_187???? 048 0.8134
> >> >???????? > 20_187???? 049 0.8082
> >> >???????? > 20_189???? 047 1.0063
> >> >???????? > 20_189???? 048 0.9701
> >> >???????? > 20_19????? 013 0.8485
> >> >???????? > 20_19????? 014 0.8534
> >> >???????? > 20_190???? 047 0.9279
> >> >???????? > 20_190???? 048 0.9169
> >> >???????? > 20_191???? 046 0.9586
> >> >???????? > 20_191???? 047 0.9751
> >> >???????? > 20_192???? 049 0.8544
> >> >???????? > 20_193???? 013 0.9084
> >> >???????? > 20_193???? 014 0.9110
> >> >???????? > 20_194???? 047 0.9220
> >> >???????? > 20_194???? 048 0.9166
> >> >???????? > 20_195???? 048 0.9552
> >> >???????? > 20_195???? 049 0.9508
> >> >???????? > 20_196???? 047 0.9098
> >> >???????? > 20_196???? 048 0.9011
> >> >???????? > 20_199???? 048 0.8569
> >> >???????? > 20_199???? 049 0.8567
> >> >???????? > 20_20????? 013 0.8750
> >> >???????? > 20_20????? 014 0.8749
> >> >???????? > 20_201???? 048 0.8864
> >> >???????? > 20_201???? 049 1.0040
> >> >???????? > 20_202???? 048 0.8542
> >> >???????? > 20_202???? 049 0.8516
> >> >???????? > 20_203???? 048 1.0267
> >> >???????? > 20_203???? 049 1.0060
> >> >???????? > 20_204???? 048 0.8513
> >> >???????? > 20_204???? 049 0.8588
> >> >???????? > 20_208???? 014 0.9130
> >> >???????? > 20_208???? 015 0.9329
> >> >???????? > 20_209???? 047 1.0020
> >> >???????? > 20_209???? 048 1.0120
> >> >???????? > 20_21????? 027 0.9747
> >> >???????? > 20_21????? 028 1.0081
> >> >???????? > 20_210???? 048 0.8607
> >> >???????? > 20_210???? 049 0.8564
> >> >???????? > 20_220???? 047 0.8888
> >> >???????? > 20_220???? 048 0.8903
> >> >???????? > 20_222???? 047 0.9998
> >> >???????? > 20_222???? 048 0.8597
> >> >???????? > 20_224???? 013 0.8122
> >> >???????? > 20_224???? 014 0.8107
> >> >???????? > 20_226???? 013 0.7855
> >> >???????? > 20_226???? 014 0.7845
> >> >???????? > 20_227???? 013 0.9372
> >> >???????? > 20_227???? 014 0.9818
> >> >???????? > 20_231???? 047 0.8355
> >> >???????? > 20_231???? 048 0.8506
> >> >???????? > 20_232???? 048 0.9730
> >> >???????? > 20_232???? 049 0.9591
> >> >???????? > 20_234???? 048 0.9357
> >> >???????? > 20_234???? 049 0.9429
> >> >???????? > 20_235???? 048 0.7528
> >> >???????? > 20_235???? 049 0.7483
> >> >???????? > 20_236???? 047 0.8997
> >> >???????? > 20_236???? 048 0.8922
> >> >???????? > 20_239???? 049 0.8920
> >> >???????? > 20_239???? 050 0.8817
> >> >???????? > 20_24????? 013 0.8197
> >> >???????? > 20_24????? 014 0.8280
> >> >???????? > 20_240???? 047 0.9109
> >> >???????? > 20_240???? 048 0.9231
> >> >???????? > 20_243???? 013 0.8227
> >> >???????? > 20_243???? 014 0.8333
> >> >???????? > 20_245???? 045 0.8620
> >> >???????? > 20_245???? 046 0.8635
> >> >???????? > 20_246???? 047 0.8236
> >> >???????? > 20_246???? 048 0.8269
> >> >???????? > 20_248???? 053 0.6015
> >> >???????? > 20_248???? 054 0.6091
> >> >???????? > 20_25????? 013 0.8676
> >> >???????? > 20_25????? 014 0.8658
> >> >???????? > 20_250???? 048 0.9124
> >> >???????? > 20_250???? 050 0.9090
> >> >???????? > 20_251???? 048 0.9061
> >> >???????? > 20_251???? 049 0.9078
> >> >???????? > 20_277???? 008 0.7923
> >> >???????? > 20_277???? 010 0.7970
> >> >???????? > 20_278???? 048 0.4834
> >> >???????? > 20_278???? 049 0.4845
> >> >???????? > 20_279???? 008 0.4363
> >> >???????? > 20_279???? 010 0.4370
> >> >???????? > 20_281???? 013 0.8672
> >> >???????? > 20_281???? 014 0.8647
> >> >???????? > 20_282???? 043 0.8884
> >> >???????? > 20_282???? 044 0.8886
> >> >???????? > 20_284???? 052 0.9152
> >> >???????? > 20_284???? 053 0.9118
> >> >???????? > 20_285???? 047 0.9546
> >> >???????? > 20_285???? 048 0.9517
> >> >???????? > 20_286???? 008 0.9607
> >> >???????? > 20_286???? 010 0.9596
> >> >???????? > 20_287???? 055 0.8976
> >> >???????? > 20_287???? 056 0.8756
> >> >???????? > 20_288???? 047 1.0127
> >> >???????? > 20_288???? 048 1.0307
> >> >???????? > 20_290???? 048 1.0089
> >> >???????? > 20_290???? 049 1.0391
> >> >???????? > 20_293???? 052 0.7792
> >> >???????? > 20_293???? 053 0.7772
> >> >???????? > 20_3?????? 017 0.8530
> >> >???????? > 20_3?????? 018 0.8501
> >> >???????? > 20_40????? 013 0.9392
> >> >???????? > 20_40????? 014 0.9787
> >> >???????? > 20_41????? 013 0.9562
> >> >???????? > 20_41????? 014 0.9547
> >> >???????? > 20_44????? 013 0.8725
> >> >???????? > 20_44????? 014 0.8872
> >> >???????? > 20_51????? 013 0.9420
> >> >???????? > 20_51????? 014 0.9417
> >> >???????? > 20_55????? 013 0.9796
> >> >???????? > 20_55????? 014 0.9837
> >> >???????? > 20_58????? 013 0.9677
> >> >???????? > 20_58????? 014 0.9506
> >> >???????? > 20_59????? 013 0.9180
> >> >???????? > 20_59????? 014 0.9157
> >> >???????? > 20_69????? 013 0.9265
> >> >???????? > 20_69????? 014 0.9283
> >> >???????? > 20_74????? 014 0.9476
> >> >???????? > 20_74????? 015 0.9201
> >> >???????? > 20_78????? 012 0.9822
> >> >???????? > 20_78????? 013 0.9501
> >> >???????? > 20_81????? 013 0.8664
> >> >???????? > 20_81????? 014 0.8693
> >> >???????? > 20_84????? 013 0.8827
> >> >???????? > 20_84????? 014 0.9196
> >> >???????? > 20_86????? 016 0.9138
> >> >???????? > 20_86????? 017 0.9152
> >> >???????? > 20_88????? 039 0.9905
> >> >???????? > 20_88????? 041 1.0168
> >> >???????? > 20_90????? 049 0.8263
> >> >???????? > 20_90????? 050 1.0208
> >> >???????? > 20_95????? 008 0.8892
> >> >???????? > 20_95????? 010 0.9359
> >> >???????? > 20_96????? 013 0.9191
> >> >???????? > 20_96????? 014 0.9326
> >> >???????? > 20_97????? 008 0.9569
> >> >???????? > 20_97????? 010 0.9731
> >> >???????? > 20_98????? 008 0.9317
> >> >???????? > 20_98????? 012 0.9409
> >> >???????? > 20_PHRU??? 047 0.7797
> >> >???????? > 20_PHRU??? 048 0.7894
> >> >???????? >
> >> >???????? > So the registration is really poor. I've visually checked the
> >> >???????? > registration for many of the subjects, and the functional
> >> >???????? data isn't
> >> >???????? > left-right reversed, I've also checked some of the
> >> >???????? subjectname files
> >> >???????? > (which I created by running a script) and they are correct.
> >> >???????? >
> >> >???????? > I'm new to Freesurfer, so maybe I've made a mistake
> >> >???????? somewhere? I'm
> >> >???????? > been following these instructions:
> >> >???????? >
> >> >???????? > https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorial
> >> >???????? >
> >> >???????? > Thanks,
> >> >???????? > Keri
> >> >???????? >
> >> >???????? >
> >> >???????? > On Fri, Jan 18, 2019 at 6:44 PM Greve, Douglas N.,Ph.D.
> >> >???????? > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>
> >> >???????? <mailto:DGREVE@mgh.harvard.edu
> >> >???????? <mailto:DGREVE@mgh.harvard.edu>>> wrote:
> >> >???????? >
> >> >???????? >???? What version of FS are you using? version 6 initializes
> >> with
> >> >???????? >???? mri_coreg (the FS equivalent of spm_coreg). On
> >> >???????? whole-brain data,
> >> >???????? >???? I've found this to be very robust. Is your data
> >> whole-brain?
> >> >???????? >
> >> >???????? >???? On 1/18/19 5:10 AM, Keri Woods wrote:
> >> >???????? >>
> >> >???????? >>???????????? External Email - Use Caution
> >> >???????? >>
> >> >???????? >>???? Hi
> >> >???????? >>
> >> >???????? >>???? I have a problem very similar to this one:
> >> >???????? >>
> >> >???????? >>
> >> >
> >> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23206.html
> >> >???????? >>
> >> >???????? >>???? I've tried the suggestions given there, but it didn't
> >> >???????? fix my problem.
> >> >???????? >>
> >> >???????? >>???? I'm running the FSFAST preproc-sess stream and the
> >> >???????? quality of the
> >> >???????? >>???? registration is very poor for most of the subjects.
> >> >???????? >>
> >> >???????? >>???? I've tried initializing the registration differently,
> >> using
> >> >???????? >>???? bbregister with --init-fsl, --init-spm and init-header,
> >> >???????? which
> >> >???????? >>???? didn't improve the results at all.
> >> >???????? >>
> >> >???????? >>???? I've also tried register-sess with --init-fsl,
> >> >???????? --init-spm and
> >> >???????? >>???? init-header, as well as spmregister-sess and
> >> >???????? fslregister-sess.
> >> >???????? >>
> >> >???????? >>???? Is there anything else I could try?
> >> >???????? >>
> >> >???????? >>???? Using the SPM GUI, the registration was fine, so I
> >> >???????? thought that
> >> >???????? >>???? spmregister-sess would have been an improvement, but it
> >> >???????? wasn't.
> >> >???????? >>???? Is there anyway I can import the registration obtained
> >> >???????? using the
> >> >???????? >>???? SPM GUI?
> >> >???????? >>
> >> >???????? >>???? Thanks for your help.
> >> >???????? >>
> >> >???????? >>???? Thanks,
> >> >???????? >>???? Keri
> >> >???????? >>
> >> >???????? >>
> >> >???????? >>
> >> >???????? >>
> >> >???????? >>
> >> >???????? >>? _______________________________________________
> >> >???????? >>???? Freesurfer mailing list
> >> >???????? >> Freesurfer@nmr.mgh.harvard.edu
> >> >???????? <mailto:Freesurfer@nmr.mgh.harvard.edu>
> >> >???????? <mailto:Freesurfer@nmr.mgh.harvard.edu
> >> >???????? <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> >> >???????? >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >> >???????? >
> >> >???????? >???? _______________________________________________
> >> >???????? >???? Freesurfer mailing list
> >> >???????? > Freesurfer@nmr.mgh.harvard.edu
> >> >???????? <mailto:Freesurfer@nmr.mgh.harvard.edu>
> >> >???????? <mailto:Freesurfer@nmr.mgh.harvard.edu
> >> >???????? <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> >> >???????? > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >> >???????? >
> >> >???????? >
> >> >???????? > _______________________________________________
> >> >???????? > Freesurfer mailing list
> >> >???????? > Freesurfer@nmr.mgh.harvard.edu
> >> >???????? <mailto:Freesurfer@nmr.mgh.harvard.edu>
> >> >???????? > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >> >
> >> >
> >> >???????? _______________________________________________
> >> >???????? Freesurfer mailing list
> >> >???????? Freesurfer@nmr.mgh.harvard.edu
> >> >???????? <mailto:Freesurfer@nmr.mgh.harvard.edu>
> >> >???????? https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >> >
> >> >
> >> > _______________________________________________
> >> > Freesurfer mailing list
> >> > Freesurfer@nmr.mgh.harvard.edu
> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>
> >>
> >> _______________________________________________
> >> Freesurfer mailing list
> >> Freesurfer@nmr.mgh.harvard.edu
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > _______________________________________________
> > Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> -------------- next part --------------
> An HTML attachment was scrubbed...
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>
> ------------------------------
>
> Message: 7
> Date: Fri, 25 Jan 2019 11:56:29 -0500
> From: Amrita Bedi <amibedi273@gmail.com>
> Subject: Re: [Freesurfer] Functional connectivty walkthrough step 8
> ??????? error
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Message-ID:
> ??????? <CAPCzK2E+MPzYh2H3Zyd0kNL+jTo_5YmESRA9AT4Sg-qbh4P7rQ@mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> ??????? External Email - Use Caution???????
>
> Here you go.
> On Friday, January 25, 2019, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu>
> wrote:
>
> > Hi Amrita, can you just paste the text into the email?
> > thanks
> > doug
> >
> > On 1/25/19 10:51 AM, Amrita Bedi wrote:
> >
> >???????? External Email - Use Caution
> > Hi Dr Greve,
> >
> > Ran mris_fwhm and got the attached.
> >
> > On Thursday, January 24, 2019, Greve, Douglas N.,Ph.D. <
> > DGREVE@mgh.harvard.edu> wrote:
> >
> >> Based on the output below, it looks like there are problems with running
> >> one of the freesurfer binaries. Can you run mris_fwhm ? Just type the
> >> command and return and see what happens.
> >>
> >>
> >>
> >> /home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm --mask
> >> /share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_rec
> >> on/Bold1/fc.lpccseed.surf.lh/mask.nii.gz
> >> --i
> >> /share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_rec
> >> on/Bold1/fc.lpccseed.surf.lh/rho1mn.nii.gz
> >> --o
> >> /share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_rec
> >> on/Bold1/fc.lpccseed.surf.lh/rho1mn.sm.nii.gz
> >> --fwhm 20.000000 --smooth-only --s fsaverage --hemi lh --sd
> >> /share/VA_Imaging/Projects/salat/2389_TRT/abedi
> >> /home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm:
> >> /home/apps/matlab/MATLAB/R2011b/sys/os/glnxa64/libstdc++.so.6: version
> >> `GLIBCXX_3.4.11' not found (required by
> >> /home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm)
> >>
> >>
> >>
> >> On 1/23/19 10:11 AM, Amrita Bedi wrote:
> >> >
> >> >???????? External Email - Use Caution
> >> >
> >> > Hi Dr Greve,
> >> >
> >> > Attached is the log file.
> >> >
> >> > On Tuesday, January 22, 2019, Greve, Douglas N.,Ph.D.
> >> > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> wrote:
> >> >
> >> >???? Can you send the full terminal output and/or the log file?
> >> >
> >> >???? On 1/22/19 2:53 PM, Amrita Bedi wrote:
> >> >???? >
> >> >???? >???????? External Email - Use Caution
> >> >???? >
> >> >???? > Hello Freesurfer developers,
> >> >???? >
> >> >???? > I was following the functional connectivity walkthrough for
> >> resting
> >> >???? > stage BOLD data and I got the attached error when I ran step 8
> >> >???? > (selxavg3-sess). Does anyone have any thoughts on how to trouble
> >> >???? shoot
> >> >???? > this?
> >> >???? > Not sure if it?s of any use but I ran this using Freesurfer 6.0 on
> >> >???? > Centos 7.4
> >> >???? >
> >> >???? > Thank You.
> >> >???? >
> >> >???? > Best
> >> >???? > Amrita
> >> >???? >
> >> >???? > _______________________________________________
> >> >???? > Freesurfer mailing list
> >> >???? > Freesurfer@nmr.mgh.harvard.edu
> >> >???? <mailto:Freesurfer@nmr.mgh.harvard.edu>
> >> >???? > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >> >???? <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >> >
> >> >
> >> >???? _______________________________________________
> >> >???? Freesurfer mailing list
> >> >???? Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.har
> >> vard.edu>
> >> >???? https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >> >???? <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >> >
> >> >
> >> > _______________________________________________
> >> > Freesurfer mailing list
> >> > Freesurfer@nmr.mgh.harvard.edu
> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>
> >>
> >> _______________________________________________
> >> Freesurfer mailing list
> >> Freesurfer@nmr.mgh.harvard.edu
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > _______________________________________________
> > Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >
> -------------- next part --------------
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>
> ------------------------------
>
> Message: 8
> Date: Fri, 25 Jan 2019 16:56:47 +0000
> From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
> Subject: Re: [Freesurfer] Orientation by direction cosines
> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
> Message-ID: <e7a7e0e7-4fa5-c8f7-e066-c5cea7a060d9@mgh.harvard.edu>
> Content-Type: text/plain; charset="utf-8"
>
> mri_info will do it. If you just want the orientation string, you can
> add? --orientation. Or do you still want the interpretation of the matrix?
>
> On 1/25/19 10:10 AM, Bruce Fischl wrote:
> > Hi Ritesh
> >
> > I think that mri_info will try to figure this out and tell you (in the
> > "Orientation" output).
> >
> > cheers
> > Bruce
> >
> >
> > On Fri, 25 Jan 2019, Ritesh Mahajan wrote:
> >
> >>???????? External Email - Use Caution
> >>
> >> Hello Team,
> >>
> >> Can any one please explain how we come to know whether it is RAI or RAS or any other orientation through
> direction cosines:
> >>
> >> Below is the direction cosine: I saw some non zero and negative values in non diagonal values of matrix. What
> does this signify ?
> >>
> >> 0.999377??????? 0??????? -0.0352819
> >> -0.00916448? 0.965676??? -0.259588
> >> 0.0340709????? 0.25975?? 0.965075
> >>
> >> Suppose it is Head First Supine. Any help will be really appreciated.
> >>
> >> Thanks,
> >> Ritesh Mahajan
> >>
> >> _______________________________________________
> >> Freesurfer mailing list
> >> Freesurfer@nmr.mgh.harvard.edu
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>
> >>
> >>
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
>
> ------------------------------
>
> Message: 9
> Date: Fri, 25 Jan 2019 11:57:06 -0500
> From: Amrita Bedi <amibedi273@gmail.com>
> Subject: Re: [Freesurfer] Functional connectivty walkthrough step 8
> ??????? error
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Message-ID:
> ??????? <CAPCzK2EyR1_1HdaVEHmi86tT9_BxeNG9HasRvjMrKUCYU+cGDw@mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> ??????? External Email - Use Caution???????
>
> On Friday, January 25, 2019, Amrita Bedi <amibedi273@gmail.com> wrote:
>
> >
> >
> > Here you go.
> > On Friday, January 25, 2019, Greve, Douglas N.,Ph.D. <
> > DGREVE@mgh.harvard.edu> wrote:
> >
> >> Hi Amrita, can you just paste the text into the email?
> >> thanks
> >> doug
> >>
> >> On 1/25/19 10:51 AM, Amrita Bedi wrote:
> >>
> >>???????? External Email - Use Caution
> >> Hi Dr Greve,
> >>
> >> Ran mris_fwhm and got the attached.
> >>
> >> On Thursday, January 24, 2019, Greve, Douglas N.,Ph.D. <
> >> DGREVE@mgh.harvard.edu> wrote:
> >>
> >>> Based on the output below, it looks like there are problems with running
> >>> one of the freesurfer binaries. Can you run mris_fwhm ? Just type the
> >>> command and return and see what happens.
> >>>
> >>>
> >>>
> >>> /home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm --mask
> >>> /share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_rec
> >>> on/Bold1/fc.lpccseed.surf.lh/mask.nii.gz
> >>> --i
> >>> /share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_rec
> >>> on/Bold1/fc.lpccseed.surf.lh/rho1mn.nii.gz
> >>> --o
> >>> /share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_rec
> >>> on/Bold1/fc.lpccseed.surf.lh/rho1mn.sm.nii.gz
> >>> --fwhm 20.000000 --smooth-only --s fsaverage --hemi lh --sd
> >>> /share/VA_Imaging/Projects/salat/2389_TRT/abedi
> >>> /home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm:
> >>> /home/apps/matlab/MATLAB/R2011b/sys/os/glnxa64/libstdc++.so.6: version
> >>> `GLIBCXX_3.4.11' not found (required by
> >>> /home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm)
> >>>
> >>>
> >>>
> >>> On 1/23/19 10:11 AM, Amrita Bedi wrote:
> >>> >
> >>> >???????? External Email - Use Caution
> >>> >
> >>> > Hi Dr Greve,
> >>> >
> >>> > Attached is the log file.
> >>> >
> >>> > On Tuesday, January 22, 2019, Greve, Douglas N.,Ph.D.
> >>> > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> wrote:
> >>> >
> >>> >???? Can you send the full terminal output and/or the log file?
> >>> >
> >>> >???? On 1/22/19 2:53 PM, Amrita Bedi wrote:
> >>> >???? >
> >>> >???? >???????? External Email - Use Caution
> >>> >???? >
> >>> >???? > Hello Freesurfer developers,
> >>> >???? >
> >>> >???? > I was following the functional connectivity walkthrough for
> >>> resting
> >>> >???? > stage BOLD data and I got the attached error when I ran step 8
> >>> >???? > (selxavg3-sess). Does anyone have any thoughts on how to trouble
> >>> >???? shoot
> >>> >???? > this?
> >>> >???? > Not sure if it?s of any use but I ran this using Freesurfer 6.0
> >>> on
> >>> >???? > Centos 7.4
> >>> >???? >
> >>> >???? > Thank You.
> >>> >???? >
> >>> >???? > Best
> >>> >???? > Amrita
> >>> >???? >
> >>> >???? > _______________________________________________
> >>> >???? > Freesurfer mailing list
> >>> >???? > Freesurfer@nmr.mgh.harvard.edu
> >>> >???? <mailto:Freesurfer@nmr.mgh.harvard.edu>
> >>> >???? > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>> >???? <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >>> >
> >>> >
> >>> >???? _______________________________________________
> >>> >???? Freesurfer mailing list
> >>> >???? Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.har
> >>> vard.edu>
> >>> >???? https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>> >???? <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >>> >
> >>> >
> >>> > _______________________________________________
> >>> > Freesurfer mailing list
> >>> > Freesurfer@nmr.mgh.harvard.edu
> >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>>
> >>>
> >>> _______________________________________________
> >>> Freesurfer mailing list
> >>> Freesurfer@nmr.mgh.harvard.edu
> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>
> >>
> >> _______________________________________________
> >> Freesurfer mailing
> listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>
> >>
> >>
> -------------- next part --------------
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>
> ------------------------------
>
> Message: 10
> Date: Fri, 25 Jan 2019 11:58:25 -0500
> From: Amrita Bedi <amibedi273@gmail.com>
> Subject: Re: [Freesurfer] Functional connectivty walkthrough step 8
> ??????? error
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Message-ID:
> ??????? <CAPCzK2GZ4advVMs_oiooNhF_x7-yrygUaNpicksn=jYrW1sFHQ@mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> ??????? External Email - Use Caution???????
>
> Pasted the text in the email but not sure if you can view it
>
> On Friday, January 25, 2019, Amrita Bedi <amibedi273@gmail.com> wrote:
>
> >
> >
> > On Friday, January 25, 2019, Amrita Bedi <amibedi273@gmail.com> wrote:
> >
> >>
> >>
> >> Here you go.
> >> On Friday, January 25, 2019, Greve, Douglas N.,Ph.D. <
> >> DGREVE@mgh.harvard.edu> wrote:
> >>
> >>> Hi Amrita, can you just paste the text into the email?
> >>> thanks
> >>> doug
> >>>
> >>> On 1/25/19 10:51 AM, Amrita Bedi wrote:
> >>>
> >>>???????? External Email - Use Caution
> >>> Hi Dr Greve,
> >>>
> >>> Ran mris_fwhm and got the attached.
> >>>
> >>> On Thursday, January 24, 2019, Greve, Douglas N.,Ph.D. <
> >>> DGREVE@mgh.harvard.edu> wrote:
> >>>
> >>>> Based on the output below, it looks like there are problems with
> >>>> running
> >>>> one of the freesurfer binaries. Can you run mris_fwhm ? Just type the
> >>>> command and return and see what happens.
> >>>>
> >>>>
> >>>>
> >>>> /home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm --mask
> >>>> /share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_rec
> >>>> on/Bold1/fc.lpccseed.surf.lh/mask.nii.gz
> >>>> --i
> >>>> /share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_rec
> >>>> on/Bold1/fc.lpccseed.surf.lh/rho1mn.nii.gz
> >>>> --o
> >>>> /share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_rec
> >>>> on/Bold1/fc.lpccseed.surf.lh/rho1mn.sm.nii.gz
> >>>> --fwhm 20.000000 --smooth-only --s fsaverage --hemi lh --sd
> >>>> /share/VA_Imaging/Projects/salat/2389_TRT/abedi
> >>>> /home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm:
> >>>> /home/apps/matlab/MATLAB/R2011b/sys/os/glnxa64/libstdc++.so.6: version
> >>>> `GLIBCXX_3.4.11' not found (required by
> >>>> /home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm)
> >>>>
> >>>>
> >>>>
> >>>> On 1/23/19 10:11 AM, Amrita Bedi wrote:
> >>>> >
> >>>> >???????? External Email - Use Caution
> >>>> >
> >>>> > Hi Dr Greve,
> >>>> >
> >>>> > Attached is the log file.
> >>>> >
> >>>> > On Tuesday, January 22, 2019, Greve, Douglas N.,Ph.D.
> >>>> > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> wrote:
> >>>> >
> >>>> >???? Can you send the full terminal output and/or the log file?
> >>>> >
> >>>> >???? On 1/22/19 2:53 PM, Amrita Bedi wrote:
> >>>> >???? >
> >>>> >???? >???????? External Email - Use Caution
> >>>> >???? >
> >>>> >???? > Hello Freesurfer developers,
> >>>> >???? >
> >>>> >???? > I was following the functional connectivity walkthrough for
> >>>> resting
> >>>> >???? > stage BOLD data and I got the attached error when I ran step 8
> >>>> >???? > (selxavg3-sess). Does anyone have any thoughts on how to trouble
> >>>> >???? shoot
> >>>> >???? > this?
> >>>> >???? > Not sure if it?s of any use but I ran this using Freesurfer 6.0
> >>>> on
> >>>> >???? > Centos 7.4
> >>>> >???? >
> >>>> >???? > Thank You.
> >>>> >???? >
> >>>> >???? > Best
> >>>> >???? > Amrita
> >>>> >???? >
> >>>> >???? > _______________________________________________
> >>>> >???? > Freesurfer mailing list
> >>>> >???? > Freesurfer@nmr.mgh.harvard.edu
> >>>> >???? <mailto:Freesurfer@nmr.mgh.harvard.edu>
> >>>> >???? > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>>> >???? <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >>>> >
> >>>> >
> >>>> >???? _______________________________________________
> >>>> >???? Freesurfer mailing list
> >>>> >???? Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.har
> >>>> vard.edu>
> >>>> >???? https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>>> >???? <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >>>> >
> >>>> >
> >>>> > _______________________________________________
> >>>> > Freesurfer mailing list
> >>>> > Freesurfer@nmr.mgh.harvard.edu
> >>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> Freesurfer mailing list
> >>>> Freesurfer@nmr.mgh.harvard.edu
> >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>>
> >>>
> >>> _______________________________________________
> >>> Freesurfer mailing
> listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>>
> >>>
> >>>
> -------------- next part --------------
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>
> ------------------------------
>
> Message: 11
> Date: Fri, 25 Jan 2019 16:58:48 +0000
> From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
> Subject: Re: [Freesurfer] Functional connectivty walkthrough step 8
> ??????? error
> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
> Message-ID: <4886d813-eba9-d277-dc43-bb3c614ae716@mgh.harvard.edu>
> Content-Type: text/plain; charset="utf-8"
>
> I don't see anything.
>
> On 1/25/19 11:56 AM, Amrita Bedi wrote:
>
> ??????? External Email - Use Caution
>
> [X]
>
> Here you go.
> On Friday, January 25, 2019, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>> wrote:
> Hi Amrita, can you just paste the text into the email?
> thanks
> doug
>
> On 1/25/19 10:51 AM, Amrita Bedi wrote:
>
> ??????? External Email - Use Caution
>
> Hi Dr Greve,
>
> Ran mris_fwhm and got the attached.
>
> On Thursday, January 24, 2019, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>>
> wrote:
> Based on the output below, it looks like there are problems with running
> one of the freesurfer binaries. Can you run mris_fwhm ? Just type the
> command and return and see what happens.
>
>
>
> /home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm --mask
> /share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_recon/Bold1/fc.lpccseed.surf.lh/mask.nii.gz
> --i
> /share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_recon/Bold1/fc.lpccseed.surf.lh/rho1mn.nii.gz
> --o
> /share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_recon/Bold1/fc.lpccseed.surf.lh/rho1mn.sm.nii.gz
> --fwhm 20.000000 --smooth-only --s fsaverage --hemi lh --sd
> /share/VA_Imaging/Projects/salat/2389_TRT/abedi
> /home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm:
> /home/apps/matlab/MATLAB/R2011b/sys/os/glnxa64/libstdc++.so.6: version
> `GLIBCXX_3.4.11' not found (required by
> /home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm)
>
>
>
> On 1/23/19 10:11 AM, Amrita Bedi wrote:
> >
> >???????? External Email - Use Caution
> >
> > Hi Dr Greve,
> >
> > Attached is the log file.
> >
> > On Tuesday, January 22, 2019, Greve, Douglas N.,Ph.D.
> > <DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>
> <mailto:DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>>> wrote:
> >
> >???? Can you send the full terminal output and/or the log file?
> >
> >???? On 1/22/19 2:53 PM, Amrita Bedi wrote:
> >???? >
> >???? >???????? External Email - Use Caution
> >???? >
> >???? > Hello Freesurfer developers,
> >???? >
> >???? > I was following the functional connectivity walkthrough for resting
> >???? > stage BOLD data and I got the attached error when I ran step 8
> >???? > (selxavg3-sess). Does anyone have any thoughts on how to trouble
> >???? shoot
> >???? > this?
> >???? > Not sure if it?s of any use but I ran this using Freesurfer 6.0 on
> >???? > Centos 7.4
> >???? >
> >???? > Thank You.
> >???? >
> >???? > Best
> >???? > Amrita
> >???? >
> >???? > _______________________________________________
> >???? > Freesurfer mailing list
> >???? > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
> >???? <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>>
> >???? > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >???? <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> >
> >???? _______________________________________________
> >???? Freesurfer mailing list
> >???? Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
> <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>>
> >???? https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >???? <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
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>
> ------------------------------
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> End of Freesurfer Digest, Vol 179, Issue 41
> *******************************************
>
>

------------------------------

Message: 7
Date: Mon, 4 Feb 2019 15:56:17 +0100
From: Laboratorio de Neurociencia Funcional <neuroaginglnf@gmail.com>
Subject: Re: [Freesurfer] gray matter volume of the entorhinal cortex
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <CABUYonOkHTikjsZSp3uWyD+D1gQ6XgPcMR8sxkkugLzx+G0rMQ@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

        External Email - Use Caution       

Thank you!

El lun., 4 feb. 2019 a las 15:29, Bruce Fischl (<fischl@nmr.mgh.harvard.edu>)
escribi?:

> Hi Jose
>
> the threshold is set so that the EC label has the average surface area of
> the labels that went into the average. It is probably more accurate than
> the aparc as it is based on actual cytoarchitectural landmarks that are
> visible in ex vivo mri.
>
> cheers
> Bruce
>
>
> On Mon,
> 4 Feb 2019, Laboratorio de Neurociencia Funcional wrote:
>
> >
> >         External Email - Use Caution
> >
> > Dear Freesurfers,
> >
> > gray matter volume of the entorhinal cortex (EC) can be obtained either
> in the ?h.aparc.stats or
> > ?h.BA_exvivo.stats/?h.BA_exvivo.thresh.stats files. Considering that all
> our T1 images were manually edited on a
> > slice-by-slice basis to correct pial surface misplacements and erroneous
> white matter segmentation, which volume
> > measure of the EC would be more precise?
> >
> > I assume that gray matter volume contained in ?h.BA_exvivo.thresh.stats
> were thresholded at a specific probability
> > value (% of case overlapping). Which probability value was used? Is
> there a reference paper explaining how
> > probabilistic maps of EC were built based on ex vivo MRI contrast?
> >
> > Thank you in advance.
> >
> > Best,
> > Jose L. Cantero
> >
> >
> >_______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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------------------------------

Message: 8
Date: Mon, 4 Feb 2019 16:33:47 +0000
From: Jordan Fowler <jf17b@my.fsu.edu>
Subject: [Freesurfer] free surfer install issues
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <BN7PR05MB59399478ECCFD08098419583926D0@BN7PR05MB5939.namprd05.prod.outlook.com>
       
Content-Type: text/plain; charset="iso-8859-1"

        External Email - Use Caution       

I have recently installed the free surfer software and when testing that it is installed correctly using the examples listed on the website I get a permission denied message.


How can I go about fixing this?


Attached is the terminal output from trying to run the first example.


Thank you,


Jordan Fowler
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------------------------------

Message: 9
Date: Mon, 4 Feb 2019 16:44:00 +0000
From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
Subject: Re: [Freesurfer] free surfer install issues
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <b8e911d3-0d9e-9586-b3df-092448d2e5c4@mgh.harvard.edu>
Content-Type: text/plain; charset="Windows-1252"

Can you just paste the message rather than attaching an image?

On 2/4/19 11:33 AM, Jordan Fowler wrote:
>
> ????????External Email - Use Caution
>
> I have recently installed the free surfer software and when testing
> that it is installed correctly using the examples listed on the
> website I get a permission denied message.
>
>
> How can I go about fixing this?
>
>
> Attached is the terminal output from trying to run the first example.
>
>
> Thank you,
>
>
> Jordan Fowler
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer




------------------------------

Message: 10
Date: Mon, 4 Feb 2019 16:47:21 +0000
From: Jordan Fowler <jf17b@my.fsu.edu>
Subject: [Freesurfer] (no subject)
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <BN7PR05MB5939EACD45A5909D659D7513926D0@BN7PR05MB5939.namprd05.prod.outlook.com>
       
Content-Type: text/plain; charset="iso-8859-1"

        External Email - Use Caution       

Here is the message displayed:


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
Jordans-MacBook-Air-2:~ jordanfowler$ > cp $FREESURFER_HOME/subjects/sample-001.mgz .
-bash: /Applications/freesurfer/subjects/sample-001.mgz: Permission denied


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------------------------------

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End of Freesurfer Digest, Vol 180, Issue 5
******************************************