External Email - Use Caution        

After running the permutation and finding significant clusters, I am trying to calculate the value for each participant for these significant clusters.

The perm.th30.abs.y.ocn.dat contain the raw values, and I am trying to get the adjusted values accounting for age, sex, and ICV (this is a three group design). 

The X matrix was 240x12 (see attached file)
  • Column 1: 1s for Group 1 and 0s for Group 2 and 0s for Group 3
  • Column 2: 0s for Group 1 and 1s for Group 2 and 0s for Group 3
  • Column 3: 0s for Group 1 and 0s for Group 2 and 1s for Group 3
  • Column 4: Age for Group 1 and 0s for Group 2 and 0s for Group 3
  • Column 5: 0s for Group 1 and Age for Group 2 and 0s for Group 3
  • Column 6: 0s for Group 1 and 0s for Group 2 and Age for Group 3
  • Column 7: Sex for Group 1 and 0s for Group 2 and 0s for Group 3
  • Column 8: 0s for Group 1 and Sex for Group 2 and 0s for Group 3
  • Column 9: 0s for Group 1 and 0s for Group 2 and Sex for Group 3
  • Column 10: zICV for Group 1 and 0s for Group 2 and 0s for Group 3
  • Column 11: 0s for Group 1 and zICV for Group 2 and 0s for Group 3
  • Column 12: 0s for Group 1 and 0s for Group 2 and zICV for Group 3

I was not sure how to modify the last line in your code in order to calculate adjusted values accounting for age, sex, and ICV for each participant.  

Your code: 

There is not an easy way to do it, but you can do it in matlab
cd glmdir
X = load('Xg.dat');
y = load('perm.th30.abs.y.ocn.dat');
beta = inv(X'*X)*X'*y;
yhat = X(:,[i j k ...]*beta([i j k ...])

where i j k ... indicate the factors you want keep in your data. Each
factor gets a column in the design matrix (and a beta). If you need help
figuring this out, send the fsgd file.



---

Jessica Hua, M.A.
Cognitive and Emotional Control Lab
Doctoral Candidate Clinical Psychology 
University of Missouri
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: Tuesday, May 19, 2020 10:18 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Freesurfer Digest, Vol 195, Issue 47
 
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Today's Topics:

   1. Re: vol2subfield single time course from multiple regions
      (stdp82@virgilio.it)
   2. Re: Longitudinal edits on norm.mgz instead of brainmask
      (Douglas N. Greve)
   3. Re: Volume timeseries to native and fsaverage (Douglas N. Greve)
   4. Re: Group Analysis Covariates (Hua, Jessica)
   5. Re: Group Analysis Covariates (Hua, Jessica)
   6. Re: qdec and mris_anatomical_stats help
      (Lab of Autism and Developmental Neuroscience,    Lab of Autism and Developmental Neuroscience)
   7. Re: Robust Regression with Univariate LME (Hua, Jessica)
   8. Re: Longitudinal edits on norm.mgz instead of brainmask
      (Elena Pozzi)
   9. Freesurfer hippocampal segmentation in patient with       temporal
      lesion (Linda Zhang)
  10. Unable to visualize last Topics (Ferraro, Pilar)
  11. freesurfer subcortical segmentation (ZhangBo)
  12. FREESURFER-7.1: recon-all exited with error "ERROR: cannot
      find or read transforms/talairach.m3z" (Safi Ullah .)


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

Message: 1
Date: Mon, 18 May 2020 18:46:35 +0200 (CEST)
From: stdp82@virgilio.it
Subject: Re: [Freesurfer] vol2subfield single time course from
        multiple regions
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>,   Bruce
        Fischl <fischl@nmr.mgh.harvard.edu>
Cc: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Message-ID: <163566753.837213.1589820395908@mail1.virgilio.it>
Content-Type: text/plain; charset="utf-8"

        External Email - Use Caution       

thanks!

>     Il 18 maggio 2020 alle 16.23 Bruce Fischl < fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu > ha scritto:
>
>
>     --replaceonly <label 1 to remove> <label 1 to replace with> \
>     --replaceonly <label 2 to remove> <label 2 to replace with> \
>     .
>     .
>     .
>
>     On Mon, 18 May 2020, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote:
>
>
>         > >                 External Email - Use Caution       
> >
> >         As reported in previous mails I have do it but with some problems.
> >
> >         Moreover, how can I do with multiple arguments (more than 2)?
> >
> >     >
>         > >         Il 17 maggio 2020 alle 21.30 Bruce Fischl <
> >         fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu > ha scritto:
> >
> >
> >         Hi Stefano
> >
> >         --replaceonly takes two arguments - the label you want to replace and
> >         the
> >         one you want to replace it with
> >
> >         cheers
> >         Bruce
> >
> >
> >         On Sun, 17 May 2020, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote:
> >
> >     >
>         > >                 External Email - Use Caution       
> >
> >         just a kind reminder
> >
> >         many thanks
> >
> >     >
>         > >         Il 15 maggio 2020 alle 1.05 stdp82@virgilio.it mailto:stdp82@virgilio.it ha scritto:
> >
> >     >
>         > >         mri_binarize --i
> >         $SUBJECTS_DIR/mri/ThalamicNuclei.v10.T1.mgz
> >         --replaceonly 8204 --replaceonly 8205 --replaceonly 8206
> >         --replaceonly 8217 --replaceonly 8218 --o
> >         $SUBJECTS_DIR/R-Intralaminar.mgz
> >
> >         ERROR: Option 8205 unknown
> >
> >
> >         mri_binarize --i $SUBJECTS_DIR/mri/ThalamicNuclei.v10.T1.mgz
> >         --replaceonly 8204 --replaceonly 8205 --replaceonly 8217
> >         --replaceonly
> >         8218 --o $SUBJECTS_DIR/R-Intralaminar.mgz
> >
> >         ERROR: Option 8217 unknown
> >         Il 14 maggio 2020 alle 17.39 "Douglas N. Greve"
> >         < dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu > ha scritto:
> >
> >     >
>         > >         Just add more --replaceonly args
> >
> >     >
>         > >         On 5/14/2020 10:38 AM, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote:
> >
> >     >
>         > >                 External Email - Use Caution       
> >
> >     >
>         > >         Moreover, how can I merge, with mri_binarize, more
> >         thalamic regions?
> >
> >     >
>         > >         e.g. 8204 8205 8206 8217 8218
> >
> >     >
>         > >         Il 13 maggio 2020 alle 23.03 "Douglas N.
> >         Greve" < dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu > ha
> >         scritto:
> >
> >     >
>         > >         It problably means that seg 8130 does
> >         not exist in the input mgz. Can you
> >         confirm that it does?
> >
> >     >
>         > >         On 5/13/2020 12:51 PM,
> >         stdp82@virgilio.it mailto:stdp82@virgilio.it wrote:
> >
> >     >
>         > >                 External Email - Use
> >         Caution       
> >
> >     >
>         > >         indeed. I would like to merge two
> >         regions and extract the fMRI time serie.
> >         if no difference is there, somewhat is
> >         wrong. the L-VP file contains the same
> >         information of ThalamicNuclei.v10.T1.
> >
> >     >
>         > >         thanks
> >
> >     >
>         > >         Il 13 maggio 2020 alle 17.02
> >         "Douglas N. Greve"
> >         < dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu > ha
> >         scritto:
> >
> >     >
>         > >         That means there is no
> >         difference
> >
> >     >
>         > >         On 5/13/2020 10:47 AM,
> >         stdp82@virgilio.it mailto:stdp82@virgilio.it wrote:
> >
> >     >
>         > >                 External Email - Use
> >         Caution       
> >
> >     >
>         > >         is the command line ok?
> >
> >     >
>         > >         by running
> >
> >     >
>         > >         mri_binarize --i
> >         ThalamicNuclei.v10.T1.mgz
> >         --replace-only 8130 8133 --o
> >         L-VP.mgz
> >
> >     >
>         > >         mri_diff --po
> >         mri/ThalamicNuclei.v10.T1.mgz
> >         L-VP.mgz 
> >
> >     >
>         > >         I obtain
> >         diffcount 0
> >
> >     >
>         > >         Il 12 maggio 2020 alle
> >         0.53
> >         stdp82@virgilio.it mailto:stdp82@virgilio.it ha
> >         scritto:
> >
> >     >
>         > >         by running
> >         mri_diff --po
> >         mri/ThalamicNuclei.v10.T1.mgz
> >         L-VP.mgz 
> >         I obtain
> >         diffcount 0
> >
> >     >
>         > >         Il 11 maggio
> >         2020 alle 19.18
> >         "Douglas N.
> >         Greve"
> >         < dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu >
> >         ha scritto:
> >
> >     >
>         > >         Try running this
> >         to see if there
> >         is a difference
> >         mri_diff --po
> >         ThalamicNuclei.v10.T1.mgz
> >         Left-Ventroposterior.mgz
> >         Sometimes it is
> >         not easy to see
> >         a difference
> >         that is just a
> >         few voxels
> >
> >     >
>         > >         On 5/11/2020
> >         3:02 AM,
> >         stdp82@virgilio.it mailto:stdp82@virgilio.it
> >         wrote:
> >
> >     >
>         > >                 External
> >         Email -
> >         Use
> >         Caution       
> >
> >     >
>         > >         By
> >         visualizing
> >         the output
> >         by
> >         freeview,
> >         I found
> >         that it
> >         was the
> >         same
> >         of ThalamicNuclei.v10.T1.mgz.
> >
> >     >
>         > >         Thanks
> >
> >     >
>         > >         Il
> >         11
> >         maggio
> >         2020
> >         alle
> >         2.19
> >         Bruce
> >         Fischl
> >         <
> >         fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >
> >         ha
> >         scritto:
> >
> >
> >         Hi Stefano
> >
> >         can you
> >         elaborate?
> >         Why do you
> >         suspect
> >         there is
> >         an error?
> >
> >         cheers
> >         Bruce
> >         On Mon, 11
> >         May
> >         2020,
> >         stdp82@virgilio.it mailto:stdp82@virgilio.it
> >         wrote:
> >
> >     >
>         > >                 External
> >         Email
> >         -
> >         Use
> >         Caution       
> >
> >         Please,
> >         could
> >         you
> >         check
> >         the
> >         command
> >         line.
> >         I
> >         suspect
> >         that
> >         an
> >         error
> >         is
> >         there.
> >         Thanks.
> >         Stefano
> >
> >         mri_binarize
> >         --i
> >         ThalamicNuclei.v10.T1.mgz
> >         --replace-only
> >         8130
> >
> >         8133
> >         --o
> >         Left-Ventroposterior.mgz
> >
> >     >
>         > >         Il
> >         30
> >         aprile
> >         2020
> >         alle
> >         18.51
> >         "Douglas
> >         N.
> >         Greve"
> >         <
> >         dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu >
> >         ha
> >         scritto:
> >
> >     >
>         > >         You
> >         can
> >         use
> >         mri_binarize
> >         --i
> >         ThalamicNuclei.v10.T1.mgz
> >         --replace-only
> >         segid
> >         segidreplace
> >         ...
> >         --o
> >         newseg.mgz
> >         to
> >         create
> >         a
> >         new
> >         segmentation
> >         with
> >         merged
> >         segments,
> >         then
> >         using
> >         vol2subfield
> >         with
> >         the
> >         newseg
> >         seg
> >         as
> >         --sf
> >
> >     >
>         > >         On
> >         4/29/2020
> >         7:57
> >         PM,
> >         stdp82@virgilio.it mailto:stdp82@virgilio.it
> >         wrote:
> >
> >     >
>         > >                 External
> >         Email
> >         -
> >         Use
> >         Caution       
> >
> >     >
>         > >         Hi
> >         list,
> >
> >     >
>         > >         vol2subfield
> >         --i
> >         fmcpr.nii.gz
> >         --reg
> >         register.dof6.lta
> >         --sf
> >         ThalamicNuclei.v10.T1.mgz
> >         --stats
> >         stats.dat
> >         --avgwf
> >         avgwf.dat
> >         --avgwfvol
> >         avgwfvol.mgz
> >         --o
> >         f2subf.nii.gz
> >
> >     >
>         > >         extracts
> >         the
> >         time
> >         course
> >         from
> >         each
> >         thalamic
> >         subregions.
> >
> >     >
>         > >         If
> >         I
> >         would
> >         like
> >         to
> >         merge
> >         multiple
> >         regions
> >         (e.g. --id
> >         8115
> >         --id
> >         8116)
> >         and
> >         extract
> >         a
> >         single
> >         time
> >         course
> >         from
> >         them,
> >         which
> >         is
> >         the
> >         way?
> >
> >     >
>         > >         Thanks
> >
> >     >
>         > >         Stefano
> >
> >
> >
> >         _______________________________________________
> >         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
> >
> >
> >
> >         The information in
> >         this e-mail is
> >         intended only for the
> >         person to whom it is
> >         addressed. If you
> >         believe this e-mail
> >         was sent to you in
> >         error and the e-mail
> >         contains patient
> >         information, please
> >         contact the Partners
> >         Compliance HelpLine at
> >         http://www.partners.org/complianceline
> >         . If the e-mail was
> >         sent to you in error
> >         but does not contain
> >         patient information,
> >         please contact the
> >         sender and properly
> >         dispose of the e-mail.
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >         _______________________________________________
> >         Freesurfer mailing list
> >         Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu
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> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >         _______________________________________________
> >         Freesurfer mailing list
> >         Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu
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> >
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> >
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Message: 2
Date: Mon, 18 May 2020 16:34:57 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] Longitudinal edits on norm.mgz instead of
        brainmask
To: <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <9867db37-54e1-2142-2d6f-78ee313a03f6@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"; format=flowed

If all you did was to remove voxels from the mask, then you should be
able to run
mri_mask brainmask.mgz norm.mgz?? brainmask.mgz

(make backups of brainmask.mgz before you run that as it will be
overwritten).



On 5/17/2020 7:55 PM, Elena Pozzi wrote:
>          External Email - Use Caution
>
> Hi Douglas,
>
> I added some control points, but also and mostly made edits meant to fix the mask (e.g., deleted some voxels).
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



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

Message: 3
Date: Mon, 18 May 2020 16:37:10 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] Volume timeseries to native and fsaverage
To: <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <715c0f22-3412-cd92-b7a2-c6dc45937c0e@mgh.harvard.edu>
Content-Type: text/plain; charset="iso-8859-3"

oh, if you want them in conformed space, they are already there

On 5/18/2020 11:34 AM, ?zen? ta?k?n wrote:
>
> ????????External Email - Use Caution
>
> Awesome, thanks Doug. That's pretty helpful. I should also use the
> orig.mgz with tkregister2 instead of rawavg.mgz if the aim is to get
> surface maps in native space, am I right ? And by native space I mean
> the subjects' native brain structure and not necessarily the native
> xyz coordinates (I guess conformed space is the right term for this,
> but I am not sure).
>
> Best,
> Ozzy
>
> ------------------------------------------------------------------------
> *From:* freesurfer-bounces@nmr.mgh.harvard.edu
> <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
> <dgreve@mgh.harvard.edu>
> *Sent:* Wednesday, May 13, 2020 3:07 PM
> *To:* freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
> *Subject:* Re: [Freesurfer] Volume timeseries to native and fsaverage
>
>
> On 5/11/2020 5:53 PM, ?zen? taskin wrote:
>>
>> ????????External Email - Use Caution
>>
>> Hello Freesurfer developers,
>>
>> I am trying to map a 4D?volumetric EPI image between different
>> surfaces and I'd like a little bit of guidance as I am slightly
>> confused about some of the outputs of freesurfer.
>>
>> I have a preprocessed nifti EPI image in subject's anatomical space.
>> First, I'd like to map this timeseries image to subject's native
>> surface. Here is how I am currently doing this operation:
>>
>> 1 - Create a register.dat by using fsl identity matrix since I am
>> already in the native space:
>>
>>     tkregister2_cmdl --mov <epi> --fsl <ident.mat> --targ
>>     <rawavg.nii> --noedit --reg <register.dat>
>>
> This is ok, but unnecessary. You can use --regheader subject in
> mri_vol2surf below instead of --reg
>>
>> 2 - Then, using this register.dat to make surfaces from the 4D
>> timeseries with:
>>
>>     mri_vol2surf --mov <epi> --ref <anat> --reg <register.dat> --hemi
>>     lh --o <output_surface.mgz>
>>
> Add --projfrac 0.5 to sample in the middle of the ribbon.
>>
>> I used these functions in the past to map statistical images to
>> surface, but it might not be the right thing to do for timeseries in
>> which case please let me know. Assuming this is correct though, next
>> I want to move this native surface timeseries to fsaverage surface. I
>> am pretty sure the calculations are in there, but I am not really
>> sure which ones I need to use and with which freesurfer commands I
>> can do this.
> Time series are no different than a single frame. You can actually map
> directly to fsaverage in mri_vol2surf with --trgsubject fsaverage (or
> you can take the vol2surf output and run mri_surf2surf on it)
>>
>> Lastly, I came across this freesurfer page
>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat which
>> talks about fsaverage to native surface conversion and the examples
>> there made me a bit confused. Aren't the surface files in the surf
>> directory (e.g lh.pial, lh.inflated) already in the native space ? Do
>> I need to create a lh.pial.native using these commands to overlay my
>> timeseries image ?
> No, you do not. That page just talks about if you want an actual
> surface file with xyz in the native coordinates. You do not need to
> have this file.
>>
>> Best,
>> Ozzy
>>
>>
>>
>>
>> _______________________________________________
>> 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

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

Message: 4
Date: Tue, 19 May 2020 01:52:02 +0000
From: "Hua, Jessica" <jphc55@mail.missouri.edu>
Subject: Re: [Freesurfer] Group Analysis Covariates
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <CH2PR01MB5654207AE415A97388AC320B93B90@CH2PR01MB5654.prod.exchangelabs.com>
       
Content-Type: text/plain; charset="iso-8859-1"

        External Email - Use Caution       

I was not sure how to modify the last line in your code in order to calculate adjusted values accounting for age, sex, and ICV for each participant (this is a three group design).

Your code:

There is not an easy way to do it, but you can do it in matlab
cd glmdir
X = load('Xg.dat');
y = load('perm.th30.abs.y.ocn.dat');
beta = inv(X'*X)*X'*y;
yhat = X(:,[i j k ...]*beta([i j k ...])

where i j k ... indicate the factors you want keep in your data. Each
factor gets a column in the design matrix (and a beta). If you need help
figuring this out, send the fsgd file.



---

Jessica Hua, M.A.
Cognitive and Emotional Control Lab
Doctoral Candidate Clinical Psychology
University of Missouri
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Message: 5
Date: Tue, 19 May 2020 01:57:34 +0000
From: "Hua, Jessica" <jphc55@mail.missouri.edu>
Subject: Re: [Freesurfer] Group Analysis Covariates
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <CH2PR01MB565426A10AF50F1409E3FE7D93B90@CH2PR01MB5654.prod.exchangelabs.com>
       
Content-Type: text/plain; charset="iso-8859-1"

        External Email - Use Caution       

Attached are the fsgd and Xg.dat files.

---

Jessica Hua, M.A.
Cognitive and Emotional Control Lab
Doctoral Candidate Clinical Psychology
University of Missouri
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------------------------------

Message: 6
Date: Mon, 18 May 2020 22:10:32 -0400
From: "Lab of Autism and Developmental Neuroscience,    Lab of Autism and
        Developmental Neuroscience" <ladn@email.gwu.edu>
Subject: Re: [Freesurfer] qdec and mris_anatomical_stats help
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <CACE7MBKmP=n+LbJ68XnnEy7fiOuJ96=Fkx82kKp1LOkWcPcvBQ@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

        External Email - Use Caution       

Hello Freesurfer experts,
Just wanted to follow-up from my last email. If any clarification is needed
regarding what I'm trying to understand from mris_anatomical_stats, please
let me know!

Kind regards,
Alex

On Fri, May 15, 2020 at 8:17 PM Lab of Autism and Developmental
Neuroscience, Lab of Autism and Developmental Neuroscience <
ladn@email.gwu.edu> wrote:

> Dear Freesurfer experts,
>
> Hope everyone is doing well! Could someone please clarify some things
> about mris_anatomical_stats, done after running qdec + mapping label to all
> subjects?
> From what I can  understand, the following code should be used:
>
> mris_anatomical_stats -l lh.supramarg.label \
>   -t lh.thickness -b -f 004/stats/lh.supramarg.stats 004 lh
>
> But if I created the ".label" file directly on qdec, by "mapping label to
> all subjects", and didn't use the mri_label2label code for "target
> subjects", how should I work around this to perform mris_anatomical_stat
> correctly?
> Also, I'm confused on when + where this "lh.thickness" file is created and
> stored.
> Please let me know if you need any other information about my code or my
> qdec output.
>
> Thank you,
> Alex Job Said
>
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------------------------------

Message: 7
Date: Tue, 19 May 2020 02:47:40 +0000
From: "Hua, Jessica" <jphc55@mail.missouri.edu>
Subject: Re: [Freesurfer] Robust Regression with Univariate LME
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <CH2PR01MB565484600AFB80C16173DCE793B90@CH2PR01MB5654.prod.exchangelabs.com>
       
Content-Type: text/plain; charset="iso-8859-1"

        External Email - Use Caution       

Hi FreeSurfer Experts,

Just bumping this item up.

There are a couple of outliers in my data.  I had winsorized the variable, but now I am trying to use robust regression to weight these outliers in my longitudinal analyses.  In Matlab there is a robustfit function. Is there a way to modify the lme_fit_FS code to incorporate robust regression?

Best,

Jessica

---

Jessica Hua, M.A.
Cognitive and Emotional Control Lab
Doctoral Candidate Clinical Psychology
University of Missouri
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------------------------------

Message: 8
Date: Tue, 19 May 2020 14:55:28 +1000
From: Elena Pozzi <elena1pozzi@gmail.com>
Subject: Re: [Freesurfer] Longitudinal edits on norm.mgz instead of
        brainmask
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
        <CAAmdNWjEBdJ3Xoj_ge6Ko=frUGR-dFw-KwGXkB+AW+QBLgDxBg@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

        External Email - Use Caution       

Hi Douglas,

Thank you very much for your answer. I tried the command you suggested and
it did not seem to transfer the edits, so I added the flag
-keep_mask_deletion_edits and that seems to work. Would you mind confirming
that the final command mri_mask -keep_mask_deletion_edits brainmask.mgz
norm.mgz brainmask.mgz is safe to run to transfer the edits (i.e., voxel
deleted) from the norm.mgz to the brainmask.mgz? Thanks again!

Elena
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------------------------------

Message: 9
Date: Tue, 19 May 2020 10:49:40 +0200
From: Linda Zhang <lzhang87@gmail.com>
Subject: [Freesurfer] Freesurfer hippocampal segmentation in patient
        with    temporal lesion
To: Freesurfer <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <CABCBU0V=5dTD67uonziGVzWYd2aDKmg8U9nNy5w6uMH7Qry_-w@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

        External Email - Use Caution       

Dear all,

I have a subject for whom I need to segment the right hippocampal and
amygdalar subfields.  However, they have a significant white matter
lesion and large ventricles in the right temporal lobe, such that
skull-stripping consistently cuts away the cortex in that region, and
subsequent aseg and surface reconstruction is inaccurate.

My question is, does the hippocampal subfield module (I'm using the
old segmentHA_T1.sh for consistency with our other subjects) use the
aseg froom recon-all as a basis for its segmentation?  If I just
manually correct the
hippocampus in the aseg and try running the subfields again, would it
work?  I've tried adjusting the skull-strip and no combination of
wsthresh and no-wgcsaatlas has helped.  I'm running FS6.0 on Ubuntu
18.

Thank you!

Regards,
Linda



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

Message: 10
Date: Tue, 19 May 2020 09:57:32 +0000
From: "Ferraro, Pilar" <FerraroP@pennmedicine.upenn.edu>
Subject: [Freesurfer] Unable to visualize last Topics
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <1D716143-2F30-473C-9073-EB66BAA876BB@pennmedicine.upenn.edu>
Content-Type: text/plain; charset="utf-8"

        External Email - Use Caution       

Hi Freesurfer experts,

I?ve sent few days ago the Topic number 4 below (New PETSurfer Questions). I see from the summary that Topic number 5 contains the reply from Douglas, but I?m unable to visualize any topics after the number 4 (as you can see below).

Would you able to resend the reply (Topic number 5), please?

Sorry for the inconvenience and many thanks,

Best,

Pilar


> Il giorno 7 mag 2020, alle ore 10:24 PM, freesurfer-request@nmr.mgh.harvard.edu ha scritto:
>
> 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: HCPMMP1 parcellation to aseg (.mgz) (pooja prabhu)
>   2. Re: HCPMMP1 parcellation to aseg (.mgz) (Douglas N. Greve)
>   3. Re: HCPMMP1 parcellation to aseg (.mgz) (Glasser, Matthew)
>   4. New PETSurfer Questions (Ferraro, Pilar)
>   5. Re: New PETSurfer Questions (Douglas N. Greve)
>   6. Re: HCPMMP1 parcellation to aseg (.mgz) (Douglas N. Greve)
>   7. Re: Get Atlas surfaces in subject space (Douglas N. Greve)
>   8. Compare individual to a group (Xiaojiang Yang)
>   9. Re: Compare individual to a group (Douglas N. Greve)
>  10. Re: Get Atlas surfaces in subject space (Ian Hardingham)
>  11. FW:  HCPMMP1 parcellation to aseg (.mgz) (Glasser, Matthew)
>  12. Re: FreeSurfer 7 stable (Mina Rizkallah)
>  13. Re: FreeSurfer 7 stable (Douglas N. Greve)
>  14. Re: freesurfer 7.0.0 in a virtual machine... (fsbuild)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 7 May 2020 21:47:46 +0530
> From: pooja prabhu <prabhuppooja@gmail.com>
> Subject: Re: [Freesurfer] HCPMMP1 parcellation to aseg (.mgz)
> To: freesurfer@nmr.mgh.harvard.edu
> Message-ID:
>        <CANeOyK=NpztkVy3_N1wWPoHQuAFeDJ8rDFSLbf4HrAv-AJuFHA@mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
>        External Email - Use Caution       
>
>> HCPMMP1 parcellation is multi modal parcellation
>> We need the file something like we have for 'aparc' parcellation.
>> The file format should be in .mgz (aparc.HCPMMP1+aseg.mgz)
>> How can i do it? (i have lh.HCPMMP1.annot and rh.HCPMMP1.annot)
>
>
> Date: Thu, May 7, 2020 at 2:16 PM
> Subject: HCPMMP1 parcellation to aseg (.mgz)
> To: <freesurfer@nmr.mgh.harvard.edu>
>
>
> Hai list,
>>> Can I get some insight on how to convert HCPMMP1 to aseg(provided we have annotation
> files) for fsaverage brain?
>>> For example: for aparc parcellation we use aparc2aseg and get
> aparc+aseg.mgz.
>>> Similarly I need for HCPMMP1.
>>> Can someone help me with this?
>>> Thank you
>
> From: "Glasser, Matthew" <glasserm@wustl.edu>
> Subject: Re: [Freesurfer] HCPMMP1 parcellation to aseg (.mgz)
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Cc: Timothy Coalson <tsc5yc@mst.edu>
> Message-ID: <29142489-F691-4E6E-A069-F7377D9C7A63@wustl.edu>
> Content-Type: text/plain; charset="utf-8"
>
>        External Email - Use Caution
>
> That is our multi-modal parcellation.  Tim has some instructions to get
> data from the fs_LR mesh to fsaverage in GIFTI format.  Doug perhaps you
> can say how to convert from GIFTI to annot?
>
> Matt.
>
>
>
> --
> Thank You
> Pooja Prabhu
> -------------- next part --------------
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>
> ------------------------------
>
> Message: 2
> Date: Thu, 7 May 2020 13:21:29 -0400
> From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
> Subject: Re: [Freesurfer] HCPMMP1 parcellation to aseg (.mgz)
> To: <freesurfer@nmr.mgh.harvard.edu>
> Message-ID: <092c0f9b-3d1b-0212-d5a2-6d0226e58ef2@mgh.harvard.edu>
> Content-Type: text/plain; charset="utf-8"
>
> If you have the annot files in your individual subject's space, then you
> can create a volume in the same way that aparc+aseg.mgz is created. In
> v6 and before, run mri_aparc2aseg. In v7, run mri_surf2volseg. Look in
> recon-all.log to see how it was run to craeate aparc+aseg.mgz and change
> the command line to indicate a different annot and a different output
>
> On 5/7/2020 12:17 PM, pooja prabhu wrote:
>>
>> ????????External Email - Use Caution
>>
>>> HCPMMP1 parcellation is multi modal parcellation
>>> We need the file something like we have for 'aparc' parcellation.
>>> The file format should be in .mgz (aparc.HCPMMP1+aseg.mgz)
>>> How can i do it? (i have lh.HCPMMP1.annot and rh.HCPMMP1.annot)
>>
>>
>> Date: Thu, May 7, 2020 at 2:16 PM
>> Subject: HCPMMP1 parcellation to aseg (.mgz)
>> To: <freesurfer@nmr.mgh.harvard.edu
>> <mailto:freesurfer@nmr.mgh.harvard.edu>>
>>
>>
>> Hai list,
>>>> Can I get some insight on how to convert HCPMMP1 to aseg(provided we
>> have annotation files) for fsaverage brain?
>>>> For example: for aparc parcellation we use aparc2aseg and get
>> aparc+aseg.mgz.
>>>> Similarly I need for HCPMMP1.
>>>> Can someone help me with this?
>>>> Thank you
>>
>> From: "Glasser, Matthew" <glasserm@wustl.edu <mailto:glasserm@wustl.edu>>
>> Subject: Re: [Freesurfer] HCPMMP1 parcellation to aseg (.mgz)
>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu
>> <mailto:freesurfer@nmr.mgh.harvard.edu>>
>> Cc: Timothy Coalson <tsc5yc@mst.edu <mailto:tsc5yc@mst.edu>>
>> Message-ID: <29142489-F691-4E6E-A069-F7377D9C7A63@wustl.edu
>> <mailto:29142489-F691-4E6E-A069-F7377D9C7A63@wustl.edu>>
>> Content-Type: text/plain; charset="utf-8"
>>
>> ? ? ? External Email - Use Caution
>>
>> That is our multi-modal parcellation.? Tim has some instructions to
>> get data from the fs_LR mesh to fsaverage in GIFTI format.? Doug
>> perhaps you can say how to convert from GIFTI to annot?
>>
>> Matt.
>>
>>
>>
>> --
>> Thank You
>> Pooja Prabhu
>>
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> -------------- next part --------------
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>
> ------------------------------
>
> Message: 3
> Date: Thu, 7 May 2020 17:23:39 +0000
> From: "Glasser, Matthew" <glasserm@wustl.edu>
> Subject: Re: [Freesurfer] HCPMMP1 parcellation to aseg (.mgz)
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Message-ID: <555A273D-0C15-4F0A-BBA7-5275413A5E6E@wustl.edu>
> Content-Type: text/plain; charset="utf-8"
>
>        External Email - Use Caution       
>
> Hi  Doug,
>
> Is there a way to convert from GIFTI label to annot?
>
> Matt.
>
> From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Douglas N. Greve" <dgreve@mgh.harvard.edu>
> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Date: Thursday, May 7, 2020 at 12:21 PM
> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] HCPMMP1 parcellation to aseg (.mgz)
>
> * External Email - Caution *
> If you have the annot files in your individual subject's space, then you can create a volume in the same way that aparc+aseg.mgz is created. In v6 and before, run mri_aparc2aseg. In v7, run mri_surf2volseg. Look in recon-all.log to see how it was run to craeate aparc+aseg.mgz and change the command line to indicate a different annot and a different output
> On 5/7/2020 12:17 PM, pooja prabhu wrote:
>
>        External Email - Use Caution
>> HCPMMP1 parcellation is multi modal parcellation
>> We need the file something like we have for 'aparc' parcellation.
>> The file format should be in .mgz (aparc.HCPMMP1+aseg.mgz)
>> How can i do it? (i have lh.HCPMMP1.annot and rh.HCPMMP1.annot)
>
>
> Date: Thu, May 7, 2020 at 2:16 PM
> Subject: HCPMMP1 parcellation to aseg (.mgz)
> To: <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
>
> Hai list,
>>> Can I get some insight on how to convert HCPMMP1 to aseg(provided we have annotation files) for fsaverage brain?
>>> For example: for aparc parcellation we use aparc2aseg and get aparc+aseg.mgz.
>>> Similarly I need for HCPMMP1.
>>> Can someone help me with this?
>>> Thank you
>
> From: "Glasser, Matthew" <glasserm@wustl.edu<mailto:glasserm@wustl.edu>>
> Subject: Re: [Freesurfer] HCPMMP1 parcellation to aseg (.mgz)
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
> Cc: Timothy Coalson <tsc5yc@mst.edu<mailto:tsc5yc@mst.edu>>
> Message-ID: <29142489-F691-4E6E-A069-F7377D9C7A63@wustl.edu<mailto:29142489-F691-4E6E-A069-F7377D9C7A63@wustl.edu>>
> Content-Type: text/plain; charset="utf-8"
>
>        External Email - Use Caution
>
> That is our multi-modal parcellation.  Tim has some instructions to get data from the fs_LR mesh to fsaverage in GIFTI format.  Doug perhaps you can say how to convert from GIFTI to annot?
> Matt.
>
>
>
> --
> Thank You
> Pooja Prabhu
>
>
>
>
> _______________________________________________
>
> Freesurfer mailing list
>
> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ________________________________
> 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.
> -------------- next part --------------
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>
> ------------------------------
>
> Message: 4
> Date: Thu, 7 May 2020 17:31:14 +0000
> From: "Ferraro, Pilar" <FerraroP@pennmedicine.upenn.edu>
> Subject: [Freesurfer] New PETSurfer Questions
> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
> Message-ID:
>        <CBB1901D-D742-4443-AE34-52E047ACC332@pennmedicine.upenn.edu>
> Content-Type: text/plain; charset="us-ascii"
>
>        External Email - Use Caution       
>
> Dear Freesurfer experts,
>
> As previously mentioned, we are currently trying to test the effects of different PVC corrections on metabolism estimation in a group of patients.
>
> We would like to also include MZ and MG methods in the analyses, comparing them to SGTM and no PVC.
> However, while both MG and MZ provide voxel-wise results, we would like to use them in ROI analyses in order to be able to compare their outputs with the ones obtained with SGTM and no PVC.
> Are there any procedures that you would recommend to do this?
>
> Many thanks in advance for any help,
>
> Best,
>
> Pilar
>
>
>
>> Il giorno 7 mag 2020, alle ore 6:00 PM, freesurfer-request@nmr.mgh.harvard.edu ha scritto:
>>
>> 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: HCPMMP1 parcellation to aseg (.mgz) (pooja prabhu)
>>  2. Re: HCPMMP1 parcellation to aseg (.mgz) (Douglas N. Greve)
>>  3. Re: Recon-all exited WITH errors {Disarmed} (Mason Wells)
>>  4. Re: freesurfer 7.0.0 in a virtual machine... (Gonzalo Rojas Costa)
>>  5. Re: Recon-all exited WITH errors {Disarmed} (Douglas N. Greve)
>>  6. Re: flirt.fsl error (NEWMAT::SingularException) when running
>>     bbregister in Freesurfer 7.0.0 (Hoopes, Andrew)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Thu, 7 May 2020 20:55:21 +0530
>> From: pooja prabhu <prabhuppooja@gmail.com>
>> Subject: Re: [Freesurfer] HCPMMP1 parcellation to aseg (.mgz)
>> To: freesurfer@nmr.mgh.harvard.edu
>> Message-ID:
>>       <CANeOyKnobqGKPPSdX+Pr1CmvHRYE2d+ziRvEMfz9BQJ4-RsGbA@mail.gmail.com>
>> Content-Type: text/plain; charset="utf-8"
>>
>>       External Email - Use Caution       
>>
>> HCPMMP1 parcellation is multi modal parcellation
>> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4990127/
>>
>> We need the file something like we have for 'aparc' parcellation.
>> The file format should be in .mgz (aparc.HCPMMP1+aseg.mgz)
>> How can i do it? (i have lh.HCPMMP1.annot and rh.HCPMMP1.annot)
>>
>> --
>> Thank You
>> Pooja Prabhu
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>> URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200507/a041a4a6/attachment-0001.html
>>
>> ------------------------------
>>
>> Message: 2
>> Date: Thu, 7 May 2020 11:26:14 -0400
>> From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
>> Subject: Re: [Freesurfer] HCPMMP1 parcellation to aseg (.mgz)
>> To: <freesurfer@nmr.mgh.harvard.edu>
>> Message-ID: <01355b15-25bd-9a44-2d75-e2eefe70ae33@mgh.harvard.edu>
>> Content-Type: text/plain; charset="utf-8"
>>
>> sorry, can you include the previous emails?
>>
>> On 5/7/2020 11:25 AM, pooja prabhu wrote:
>>>
>>> ????????External Email - Use Caution
>>>
>>> HCPMMP1 parcellation is multi modal parcellation
>>> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4990127/
>>>
>>> We need the file something like we have for 'aparc' parcellation.
>>> The file format should be in .mgz (aparc.HCPMMP1+aseg.mgz)
>>> How can i do it? (i have lh.HCPMMP1.annot and rh.HCPMMP1.annot)
>>>
>>> --
>>> Thank You
>>> Pooja Prabhu
>>>
>>>
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>> URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200507/86de4fd9/attachment-0001.html
>>
>> ------------------------------
>>
>> Message: 3
>> Date: Thu, 7 May 2020 15:33:26 +0000
>> From: Mason Wells <WellsMT1@cardiff.ac.uk>
>> Subject: Re: [Freesurfer] Recon-all exited WITH errors {Disarmed}
>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>> Message-ID: <D4803927-B60A-40D9-840E-B0201A6FBFDF@cardiff.ac.uk>
>> Content-Type: text/plain; charset="utf-8"
>>
>>       External Email - Use Caution       
>>
>> Terminal output is below:
>>
>>
>> export SUBJECTS_DIR=/home/c1749990/Documents/Analysis/Data/freesurfer/subjects
>>
>> c1749990@l029:~/Documents/Analysis/Data/PMA_retinoScans/PPT_004$ recon-all -i pre_processed_anatomy/T1.nii.gz -s PPT_004 -parcstats3 -label_v1
>> recon-all -i pre_processed_anatomy/T1.nii.gz -s PPT_004 -parcstats3 -label_v1
>>
>> Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
>> Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
>> INFO: SUBJECTS_DIR is /home/c1749990/Documents/Analysis/Data/freesurfer/subjects
>> Actual FREESURFER_HOME /cubric/software/freesurfer.versions/5.3.0
>> Linux l029.cubric.cf.ac.uk 3.10.0-957.12.1.el7.x86_64 #1 SMP Mon Apr 29 14:59:59 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
>> /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_004
>>
>> mri_convert /home/c1749990/Documents/Analysis/Data/PMA_retinoScans/PPT_004/pre_processed_anatomy/T1.nii.gz /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_004/mri/orig/001.mgz
>>
>> mri_convert /home/c1749990/Documents/Analysis/Data/PMA_retinoScans/PPT_004/pre_processed_anatomy/T1.nii.gz /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_004/mri/orig/001.mgz
>> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
>> reading from /home/c1749990/Documents/Analysis/Data/PMA_retinoScans/PPT_004/pre_processed_anatomy/T1.nii.gz...
>> TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
>> i_ras = (-1, 0, 0)
>> j_ras = (0, 1, 0)
>> k_ras = (0, 0, 1)
>> writing to /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_004/mri/orig/001.mgz...
>> #-----------------------------------------
>> #@# Parcellation Stats 3 lh Thu May  7 16:32:30 BST 2020
>> /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_004/scripts
>>
>> mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas40.stats -b -a ../label/lh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab PPT_004 lh white
>>
>> No such file or directory
>> mris_anatomical_stats: could not open label file ../label/lh.cortex.label
>> INFO: assuming MGZ format for volumes.
>> Invalid argument
>>
>> Invalid argument
>> Linux l029.cubric.cf.ac.uk 3.10.0-957.12.1.el7.x86_64 #1 SMP Mon Apr 29 14:59:59 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
>>
>> recon-all -s PPT_004 exited with ERRORS at Thu May  7 16:32:30 BST 2020
>>
>> For more details, see the log file /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_004/scripts/recon-all.log
>> To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>
>>
>> Mason T Wells, MSc
>> PhD student
>> School of Optometry and Vision Sciences
>> & Cardiff University Brain Research
>> Imaging Centre (CUBRIC), School of Psychology
>> Cardiff University
>> Cardiff
>> CF24 4HQ
>> UK
>>
>> Email: WellsMT1@cardiff.ac.uk<mailto:WellsMT1@cardiff.ac.uk>
>> Tel: 02920 879628
>> Web: Cardiff University webpage<https://www.cardiff.ac.uk/people/research-students/view/974214->
>> Mason T Wells, MSc
>> Myfyriwr PhD
>> Yr Ysgol Optometreg a Gwyddorau?r Golwg
>> & Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg
>> Prifysgol Caerdydd
>> Heol Maindy
>> Caerdydd
>> CF24 4HQ
>> DU
>>
>> E-bost: WellsMT1@caerdydd.ac.uk<mailto:WellsMT1@caerdydd.ac.uk>
>> Ff?n: 02920 879628
>>
>>
>> From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Douglas N. Greve" <dgreve@mgh.harvard.edu>
>> Reply to: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>> Date: Thursday, 7 May 2020 at 15:59
>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>> Subject: Re: [Freesurfer] Recon-all exited WITH errors {Disarmed}
>>
>> No all, just one. And try running it with just the -parcstats3 flag (ie, don't use -all or -autreconX). You should have an answer in seconds
>> On 5/7/2020 7:50 AM, Mason Wells wrote:
>>
>>       External Email - Use Caution
>> Hi Doug,
>>
>> Sorry I am a bit confused. I ran recon-all as a bash for 30 participants. None of which had the right hemisphere completed and recon-all log says exited with errors (as the log in the original email shows). Are you suggesting I go back and re-run recon-all via the bash and see if I get the same issue?
>>
>> Thanks for all your help.
>> Mason
>>
>> Mason T Wells, MSc
>> PhD student
>> School of Optometry and Vision Sciences
>> & Cardiff University Brain Research
>> Imaging Centre (CUBRIC), School of Psychology
>> Cardiff University
>> Cardiff
>> CF24 4HQ
>> UK
>>
>> Email: WellsMT1@cardiff.ac.uk<mailto:WellsMT1@cardiff.ac.uk>
>> Tel: 02920 879628
>> Web: Cardiff University webpage<https://www.cardiff.ac.uk/people/research-students/view/974214->
>> Mason T Wells, MSc
>> Myfyriwr PhD
>> Yr Ysgol Optometreg a Gwyddorau?r Golwg
>> & Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg
>> Prifysgol Caerdydd
>> Heol Maindy
>> Caerdydd
>> CF24 4HQ
>> DU
>>
>> E-bost: WellsMT1@caerdydd.ac.uk<mailto:WellsMT1@caerdydd.ac.uk>
>> Ff?n: 02920 879628
>>
>>
>> From: <freesurfer-bounces@nmr.mgh.harvard.edu><mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Douglas N. Greve" <dgreve@mgh.harvard.edu><mailto:dgreve@mgh.harvard.edu>
>> Reply to: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
>> Date: Wednesday, 6 May 2020 at 23:11
>> To: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
>> Subject: Re: [Freesurfer] Recon-all exited WITH errors
>>
>> It looks like that command finished without error. Have you tried running it in recon-all again to see if it fails again? You can just run that command with -parcstats3
>>
>>
>> On 5/6/2020 6:41 AM, Mason Wells wrote:
>>
>>       External Email - Use Caution
>> Hi Doug,
>>
>> Not sure if my email below got to you? I sent the terminal outputs of the command you told me to run. Any idea what?s going on or how to fix it?
>>
>> Cheers,
>> Mason
>>
>> Mason T Wells, MSc
>> PhD student
>> School of Optometry and Vision Sciences
>> & Cardiff University Brain Research
>> Imaging Centre (CUBRIC), School of Psychology
>> Cardiff University
>> Cardiff
>> CF24 4HQ
>> UK
>>
>> Email: WellsMT1@cardiff.ac.uk<mailto:WellsMT1@cardiff.ac.uk>
>> Tel: 02920 879628
>> Web: Cardiff University webpage<https://www.cardiff.ac.uk/people/research-students/view/974214->
>> Mason T Wells, MSc
>> Myfyriwr PhD
>> Yr Ysgol Optometreg a Gwyddorau?r Golwg
>> & Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg
>> Prifysgol Caerdydd
>> Heol Maindy
>> Caerdydd
>> CF24 4HQ
>> DU
>>
>> E-bost: WellsMT1@caerdydd.ac.uk<mailto:WellsMT1@caerdydd.ac.uk>
>> Ff?n: 02920 879628
>>
>>
>> From: <freesurfer-bounces@nmr.mgh.harvard.edu><mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Mason Wells <WellsMT1@cardiff.ac.uk><mailto:WellsMT1@cardiff.ac.uk>
>> Reply to: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
>> Date: Monday, 4 May 2020 at 20:01
>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
>> Subject: Re: [Freesurfer] Recon-all exited WITH errors {Disarmed}
>>
>>
>>       External Email - Use Caution
>> Ah yes. I just set the SUBJECTS_DIR correctly, Terminal out below:
>>
>> mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas40.stats -b -a ../label/lh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab PPT_001 lh white
>> INFO: assuming MGZ format for volumes.
>> INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
>> computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot.
>> reading volume /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/mri/wm.mgz...
>> reading input surface /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/surf/lh.white...
>> reading input pial surface /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/surf/lh.pial...
>> reading input white surface /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/surf/lh.white...
>> reading colortable from annotation file...
>> colortable with 36 entries read (originally /Applications/freesurfer/average/colortable_desikan_killiany.txt)
>> Saving annotation colortable ../label/aparc.annot.DKTatlas40.ctab
>>
>> table columns are:
>>   number of vertices
>>   total surface area (mm^2)
>>   total gray matter volume (mm^3)
>>   average cortical thickness +- standard deviation (mm)
>>   integrated rectified mean curvature
>>   integrated rectified Gaussian curvature
>>   folding index
>>   intrinsic curvature index
>>   structure name
>>
>> 1698   1132   3274  2.730 0.526     0.130     0.032       26     2.4  caudalanteriorcingulate
>> 4375   2908   8369  2.594 0.599     0.127     0.040       46     7.0  caudalmiddlefrontal
>> 3883   2464   5378  2.087 0.498     0.149     0.082       74     9.4  cuneus
>> 546    373   1423  2.817 0.999     0.154     0.087       11     1.9  entorhinal
>> 5411   3506  10979  2.768 0.567     0.137     0.059      101    14.8  fusiform
>> 6159   4159  11629  2.543 0.520     0.133     0.045       86    11.0  inferiorparietal
>> 5973   3945  13736  2.965 0.705     0.138     0.060      130    13.4  inferiortemporal
>> 1536    934   2788  2.725 0.838     0.164     0.090       50     5.1  isthmuscingulate
>> 6953   4476  11030  2.320 0.542     0.147     0.055      110    15.3  lateraloccipital
>> 3897   2512   7780  2.641 0.630     0.147     0.077       99    13.1  lateralorbitofrontal
>> 5273   3237   7567  2.161 0.603     0.151     0.956      191    20.8  lingual
>> 2015   1290   4210  2.576 0.773     0.157     0.084       64     6.5  medialorbitofrontal
>> 6073   4091  14456  3.026 0.553     0.130     0.043       80    11.0  middletemporal
>> 1012    711   2254  2.886 0.735     0.133     0.112       16     6.3  parahippocampal
>> 2182   1401   4296  2.690 0.669     0.128     0.044       26     4.5  paracentral
>> 3247   2175   6722  2.682 0.501     0.121     0.038       34     5.1  parsopercularis
>> 1195    793   2520  2.549 0.514     0.138     0.045       21     2.1  parsorbitalis
>> 2780   1882   5377  2.457 0.608     0.131     0.043       37     5.0  parstriangularis
>> 2229   1444   2359  1.685 0.476     0.155     0.067       41     6.1  pericalcarine
>> 7692   4818  11728  2.218 0.657     0.130     0.053      114    16.0  postcentral
>> 1983   1360   4109  2.902 0.617     0.167     0.079       44     6.1  posteriorcingulate
>> 7681   4765  13220  2.521 0.549     0.123     0.056      119    15.1  precentral
>> 6240   4189  11573  2.532 0.576     0.145     0.052      104    13.3  precuneus
>> 1613    992   3166  2.820 0.661     0.136     0.055       54     3.6  rostralanteriorcingulate
>> 6644   4495  12118  2.347 0.579     0.144     0.052      117    13.9  rostralmiddlefrontal
>> 12967   8768  28469  2.839 0.612     0.132     0.047      170    25.1  superiorfrontal
>> 7963   5213  12201  2.095 0.481     0.125     0.053      125    16.2  superiorparietal
>> 9021   6069  20753  3.059 0.612     0.130     0.050      183    19.9  superiortemporal
>> 7970   5269  15543  2.684 0.502     0.149     0.074      910    17.4  supramarginal
>> 702    454   1432  2.844 0.618     0.133     0.046        8     1.3  transversetemporal
>> 2953   1947   6539  3.228 0.801     0.124     0.056       33     6.4  insula
>>
>> Mason T Wells, MSc
>> PhD student
>> School of Optometry and Vision Sciences
>> & Cardiff University Brain Research
>> Imaging Centre (CUBRIC), School of Psychology
>> Cardiff University
>> Cardiff
>> CF24 4HQ
>> UK
>>
>> Email: WellsMT1@cardiff.ac.uk<mailto:WellsMT1@cardiff.ac.uk>
>> Tel: 02920 879628
>> Web: Cardiff University webpage<https://www.cardiff.ac.uk/people/research-students/view/974214->
>> Mason T Wells, MSc
>> Myfyriwr PhD
>> Yr Ysgol Optometreg a Gwyddorau?r Golwg
>> & Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg
>> Prifysgol Caerdydd
>> Heol Maindy
>> Caerdydd
>> CF24 4HQ
>> DU
>>
>> E-bost: WellsMT1@caerdydd.ac.uk<mailto:WellsMT1@caerdydd.ac.uk>
>> Ff?n: 02920 879628
>>
>>
>> From: <freesurfer-bounces@nmr.mgh.harvard.edu><mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Douglas N. Greve" <dgreve@mgh.harvard.edu><mailto:dgreve@mgh.harvard.edu>
>> Reply to: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
>> Date: Monday, 4 May 2020 at 19:56
>> To: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
>> Subject: Re: [Freesurfer] Recon-all exited WITH errors {Disarmed}
>>
>> Something else has gone wrong. wm.mgz should have been there in order to get as far as it did. Is your SUBJECTS_DIR set properly?
>> On 5/4/2020 2:49 PM, Mason Wells wrote:
>>
>>       External Email - Use Caution
>> Hi,
>>
>> Terminal output is below:
>>
>> /Documents/Analysis/Data/freesurfer/subjects/PPT_001/scripts$ mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas40.stats -b -a ../label/lh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab PPT_001 lh white
>> INFO: assuming MGZ format for volumes.
>> INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
>> computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot.
>> reading volume /cubric/data/c1749990/freesurfer/subjects/PPT_001/mri/wm.mgz...
>> mghRead(/cubric/data/c1749990/freesurfer/subjects/PPT_001/mri/wm.mgz, -1): could not open file
>> mris_anatomical_stats: could not read input volume /cubric/data/c1749990/freesurfer/subjects/PPT_001/mri/wm.mgz
>>
>> Cheers,
>> Mason
>>
>> Mason T Wells, MSc
>> PhD student
>> School of Optometry and Vision Sciences
>> & Cardiff University Brain Research
>> Imaging Centre (CUBRIC), School of Psychology
>> Cardiff University
>> Cardiff
>> CF24 4HQ
>> UK
>>
>> Email: WellsMT1@cardiff.ac.uk<mailto:WellsMT1@cardiff.ac.uk>
>> Tel: 02920 879628
>> Web: Cardiff University webpage<https://www.cardiff.ac.uk/people/research-students/view/974214->
>> Mason T Wells, MSc
>> Myfyriwr PhD
>> Yr Ysgol Optometreg a Gwyddorau?r Golwg
>> & Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg
>> Prifysgol Caerdydd
>> Heol Maindy
>> Caerdydd
>> CF24 4HQ
>> DU
>>
>> E-bost: WellsMT1@caerdydd.ac.uk<mailto:WellsMT1@caerdydd.ac.uk>
>> Ff?n: 02920 879628
>>
>>
>> From: <freesurfer-bounces@nmr.mgh.harvard.edu><mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Douglas N. Greve" <dgreve@mgh.harvard.edu><mailto:dgreve@mgh.harvard.edu>
>> Reply to: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
>> Date: Monday, 4 May 2020 at 18:54
>> To: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
>> Subject: Re: [Freesurfer] Recon-all exited WITH errors
>>
>> Unfortunately, the log file does not indicate what went wrong. But it does show that the error happened on the LH (so it is not just RH). Run the command below and send all terminal output
>>
>> cd /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/scripts
>> mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas40.stats -b -a ../label/lh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab PPT_001 lh white
>>
>>
>>
>>
>>
>>
>> On 5/4/2020 1:34 PM, Mason Wells wrote:
>>
>>       External Email - Use Caution
>> Hi Experts,
>>
>> I appear to be having some issues with recon-all. I ran the command from a bash script (see attached), and it appears to work fine for the left hemisphere as the correct files are in the surf folder. However, there are no right hemisphere surf files. I have attached the log and error log for PPT01 and PPT02. Any advice on as to why this has happened would be great.
>>
>> Thanks in advance,
>> Mason
>>
>> Mason T Wells, MSc
>> PhD student
>> School of Optometry and Vision Sciences
>> & Cardiff University Brain Research
>> Imaging Centre (CUBRIC), School of Psychology
>> Cardiff University
>> Cardiff
>> CF24 4HQ
>> UK
>>
>> Email: WellsMT1@cardiff.ac.uk<mailto:WellsMT1@cardiff.ac.uk>
>> Tel: 02920 879628
>> Web: Cardiff University webpage<https://www.cardiff.ac.uk/people/research-students/view/974214->
>> Mason T Wells, MSc
>> Myfyriwr PhD
>> Yr Ysgol Optometreg a Gwyddorau?r Golwg
>> & Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg
>> Prifysgol Caerdydd
>> Heol Maindy
>> Caerdydd
>> CF24 4HQ
>> DU
>>
>> E-bost: WellsMT1@caerdydd.ac.uk<mailto:WellsMT1@caerdydd.ac.uk>
>> Ff?n: 02920 879628
>>
>>
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>>
>> Freesurfer mailing list
>>
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>>
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>>
>>
>>
>>
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>>
>>
>>
>>
>>
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>> _______________________________________________
>>
>> Freesurfer mailing list
>>
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>>
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>>
>> ------------------------------
>>
>> Message: 4
>> Date: Thu, 7 May 2020 15:34:37 -0400
>> From: Gonzalo Rojas Costa <gonzalo.rojas.costa@gmail.com>
>> Subject: Re: [Freesurfer] freesurfer 7.0.0 in a virtual machine...
>> To: ts+ml@rcmd.org
>> Cc: freesurfer@nmr.mgh.harvard.edu
>> Message-ID:
>>       <CAHPHMw7tiFRNOL=qSddTQr-z6b=nuqE7ZMvBV7tq=GbrzmiHtQ@mail.gmail.com>
>> Content-Type: text/plain; charset="utf-8"
>>
>>       External Email - Use Caution       
>>
>> Hi:
>>
>> No... I don't have any specific issue... I have a previous freesurfer
>> version installed that I want to continue using. So I want to install
>> version freesurfer 7.0 on a virtual machine...
>>
>> Sincerely,
>>
>>
>> Gonzalo Rojas Costa
>>
>>
>>> Message: 4
>>> Date: Thu, 7 May 2020 12:43:56 +0200 (CEST)
>>> From: Tim Sch?fer <ts+ml@rcmd.org>
>>> Subject: Re: [Freesurfer] freesurfer 7.0.0 in a virtual machine...
>>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>>> Message-ID: <1445340988.123994.1588848236854@ox.hosteurope.de>
>>> Content-Type: text/plain; charset="utf-8"
>>>
>>>     External Email - Use Caution
>>>
>>> There should be no difference to installation on a physical machine. Are
>> you
>>> running into any specific issues?
>>>
>>> Tim
>>>
>>>> On May 7, 2020 at 3:51 AM Gonzalo Rojas Costa <
>> gonzalo.rojas.costa@gmail.com> wrote:
>>>>
>>>>
>>>>       External Email - Use Caution
>>>>
>>>> Hi:
>>>>
>>>> How can install freesurfer 7.0.0 in a virtual machine ?
>>>>
>>>> Sincerely,
>>>>
>>>>
>>>> Gonzalo Rojas Costa
>>>> _______________________________________________
>>>> Freesurfer mailing list
>>>> Freesurfer@nmr.mgh.harvard.edu
>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>> --
>>> Dr. Tim Sch?fer
>>> Postdoc Computational Neuroimaging
>>> Department of Child and Adolescent Psychiatry, Psychosomatics and
>>> Psychotherapy
>>> University Hospital Frankfurt, Goethe University Frankfurt am Main,
>> Germany
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>> ------------------------------
>>
>> Message: 5
>> Date: Thu, 7 May 2020 11:47:15 -0400
>> From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
>> Subject: Re: [Freesurfer] Recon-all exited WITH errors {Disarmed}
>> To: <freesurfer@nmr.mgh.harvard.edu>
>> Message-ID: <f05dbd88-2bbd-775e-6a11-38c2858344c6@mgh.harvard.edu>
>> Content-Type: text/plain; charset="utf-8"
>>
>> Does
>> /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_004/label/lh.cortex.label
>> exist?
>>
>> On 5/7/2020 11:33 AM, Mason Wells wrote:
>>>
>>> ????????External Email - Use Caution
>>>
>>> Terminal output is below:
>>>
>>> export
>>> SUBJECTS_DIR=/home/c1749990/Documents/Analysis/Data/freesurfer/subjects
>>>
>>> c1749990@l029:~/Documents/Analysis/Data/PMA_retinoScans/PPT_004$
>>> recon-all -i pre_processed_anatomy/T1.nii.gz -s PPT_004 -parcstats3
>>> -label_v1
>>>
>>> recon-all -i pre_processed_anatomy/T1.nii.gz -s PPT_004 -parcstats3
>>> -label_v1
>>>
>>> Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
>>>
>>> Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
>>>
>>> INFO: SUBJECTS_DIR is
>>> /home/c1749990/Documents/Analysis/Data/freesurfer/subjects
>>>
>>> Actual FREESURFER_HOME /cubric/software/freesurfer.versions/5.3.0
>>>
>>> Linux l029.cubric.cf.ac.uk 3.10.0-957.12.1.el7.x86_64 #1 SMP Mon Apr
>>> 29 14:59:59 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
>>>
>>> /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_004
>>>
>>> mri_convert
>>> /home/c1749990/Documents/Analysis/Data/PMA_retinoScans/PPT_004/pre_processed_anatomy/T1.nii.gz
>>> /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_004/mri/orig/001.mgz
>>>
>>>
>>> mri_convert
>>> /home/c1749990/Documents/Analysis/Data/PMA_retinoScans/PPT_004/pre_processed_anatomy/T1.nii.gz
>>> /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_004/mri/orig/001.mgz
>>>
>>>
>>> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
>>>
>>> reading from
>>> /home/c1749990/Documents/Analysis/Data/PMA_retinoScans/PPT_004/pre_processed_anatomy/T1.nii.gz...
>>>
>>> TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
>>>
>>> i_ras = (-1, 0, 0)
>>>
>>> j_ras = (0, 1, 0)
>>>
>>> k_ras = (0, 0, 1)
>>>
>>> writing to
>>> /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_004/mri/orig/001.mgz...
>>>
>>> #-----------------------------------------
>>>
>>> #@# Parcellation Stats 3 lh Thu May? 7 16:32:30 BST 2020
>>>
>>> /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_004/scripts
>>>
>>> mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f
>>> ../stats/lh.aparc.DKTatlas40.stats -b -a
>>> ../label/lh.aparc.DKTatlas40.annot -c
>>> ../label/aparc.annot.DKTatlas40.ctab PPT_004 lh white
>>>
>>> No such file or directory
>>>
>>> mris_anatomical_stats: could not open label file ../label/lh.cortex.label
>>>
>>> INFO: assuming MGZ format for volumes.
>>>
>>> Invalid argument
>>>
>>> Invalid argument
>>>
>>> Linux l029.cubric.cf.ac.uk 3.10.0-957.12.1.el7.x86_64 #1 SMP Mon Apr
>>> 29 14:59:59 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
>>>
>>> recon-all -s PPT_004 exited with ERRORS at Thu May? 7 16:32:30 BST 2020
>>>
>>> For more details, see the log file
>>> /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_004/scripts/recon-all.log
>>>
>>> To report a problem, see
>>> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>>
>>> *Mason T Wells, MSc*
>>>
>>> *PhD student*
>>>
>>> School of Optometry?and Vision Sciences
>>>
>>> & Cardiff University Brain Research
>>>
>>> Imaging?Centre (CUBRIC), School of Psychology
>>>
>>> Cardiff University
>>>
>>> Cardiff
>>>
>>> CF24 4HQ
>>>
>>> UK
>>>
>>> */Email/*: WellsMT1@cardiff.ac.uk <mailto:WellsMT1@cardiff.ac.uk>
>>>
>>> */Tel/*: 02920 879628
>>>
>>> */Web/*: Cardiff University webpage
>>> <https://www.cardiff.ac.uk/people/research-students/view/974214->
>>>
>>>     
>>>
>>> *Mason T Wells, MSc*
>>>
>>> *Myfyriwr PhD*
>>>
>>> Yr Ysgol Optometreg?a Gwyddorau?r?Golwg
>>>
>>> & Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr
>>> Ysgol Seicoleg
>>>
>>> Prifysgol Caerdydd
>>>
>>> Heol Maindy
>>>
>>> Caerdydd
>>>
>>> CF24 4HQ
>>>
>>> DU
>>>
>>> */E-bost/*: WellsMT1@caerdydd.ac.uk <mailto:WellsMT1@caerdydd.ac.uk>
>>>
>>> */Ff?n/*: 02920 879628
>>>
>>> *From: *<freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Douglas
>>> N. Greve" <dgreve@mgh.harvard.edu>
>>> *Reply to: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>>> *Date: *Thursday, 7 May 2020 at 15:59
>>> *To: *"freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>>> *Subject: *Re: [Freesurfer] Recon-all exited WITH errors {Disarmed}
>>>
>>> No all, just one. And try running it with just the -parcstats3 flag
>>> (ie, don't use -all or -autreconX). You should have an answer in seconds
>>>
>>> On 5/7/2020 7:50 AM, Mason Wells wrote:
>>>
>>>   *????????External Email - Use Caution *
>>>
>>>   Hi Doug,
>>>
>>>   Sorry I am a bit confused. I ran recon-all as a bash for 30
>>>   participants. None of which had the right hemisphere completed and
>>>   recon-all log says exited with errors (as the log in the original
>>>   email shows). Are you suggesting I go back and re-run recon-all
>>>   via the bash and see if I get the same issue?
>>>
>>>   Thanks for all your help.
>>>
>>>   Mason
>>>
>>>   *Mason T Wells, MSc*
>>>
>>>   *PhD student*
>>>
>>>   School of Optometry?and Vision Sciences
>>>
>>>   & Cardiff University Brain Research
>>>
>>>   Imaging?Centre (CUBRIC), School of Psychology
>>>
>>>   Cardiff University
>>>
>>>   Cardiff
>>>
>>>   CF24 4HQ
>>>
>>>   UK
>>>
>>>   */Email/*: WellsMT1@cardiff.ac.uk <mailto:WellsMT1@cardiff.ac.uk>
>>>
>>>   */Tel/*: 02920 879628
>>>
>>>   */Web/*: Cardiff University webpage
>>>   <https://www.cardiff.ac.uk/people/research-students/view/974214->
>>>
>>>     
>>>
>>>   *Mason T Wells, MSc*
>>>
>>>   *Myfyriwr PhD*
>>>
>>>   Yr Ysgol Optometreg?a Gwyddorau?r?Golwg
>>>
>>>   & Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd
>>>   (CUBRIC), Yr Ysgol Seicoleg
>>>
>>>   Prifysgol Caerdydd
>>>
>>>   Heol Maindy
>>>
>>>   Caerdydd
>>>
>>>   CF24 4HQ
>>>
>>>   DU
>>>
>>>   */E-bost/*: WellsMT1@caerdydd.ac.uk <mailto:WellsMT1@caerdydd.ac.uk>
>>>
>>>   */Ff?n/*: 02920 879628
>>>
>>>   *From: *<freesurfer-bounces@nmr.mgh.harvard.edu>
>>>   <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of
>>>   "Douglas N. Greve" <dgreve@mgh.harvard.edu>
>>>   <mailto:dgreve@mgh.harvard.edu>
>>>   *Reply to: *Freesurfer support list
>>>   <freesurfer@nmr.mgh.harvard.edu>
>>>   <mailto:freesurfer@nmr.mgh.harvard.edu>
>>>   *Date: *Wednesday, 6 May 2020 at 23:11
>>>   *To: *"freesurfer@nmr.mgh.harvard.edu"
>>>   <mailto:freesurfer@nmr.mgh.harvard.edu>
>>>   <freesurfer@nmr.mgh.harvard.edu>
>>>   <mailto:freesurfer@nmr.mgh.harvard.edu>
>>>   *Subject: *Re: [Freesurfer] Recon-all exited WITH errors
>>>
>>>   It looks like that command finished without error. Have you tried
>>>   running it in recon-all again to see if it fails again? You can
>>>   just run that command with -parcstats3
>>>
>>>
>>>   On 5/6/2020 6:41 AM, Mason Wells wrote:
>>>
>>>       *????????External Email - Use Caution *
>>>
>>>       Hi Doug,
>>>
>>>       Not sure if my email below got to you? I sent the terminal
>>>       outputs of the command you told me to run. Any idea what?s
>>>       going on or how to fix it?
>>>
>>>       Cheers,
>>>
>>>       Mason
>>>
>>>       *Mason T Wells, MSc*
>>>
>>>       *PhD student*
>>>
>>>       School of Optometry?and Vision Sciences
>>>
>>>       & Cardiff University Brain Research
>>>
>>>       Imaging?Centre (CUBRIC), School of Psychology
>>>
>>>       Cardiff University
>>>
>>>       Cardiff
>>>
>>>       CF24 4HQ
>>>
>>>       UK
>>>
>>>       */Email/*: WellsMT1@cardiff.ac.uk <mailto:WellsMT1@cardiff.ac.uk>
>>>
>>>       */Tel/*: 02920 879628
>>>
>>>       */Web/*: Cardiff University webpage
>>>       <https://www.cardiff.ac.uk/people/research-students/view/974214->
>>>
>>>             
>>>
>>>       *Mason T Wells, MSc*
>>>
>>>       *Myfyriwr PhD*
>>>
>>>       Yr Ysgol Optometreg?a Gwyddorau?r?Golwg
>>>
>>>       & Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd
>>>       (CUBRIC), Yr Ysgol Seicoleg
>>>
>>>       Prifysgol Caerdydd
>>>
>>>       Heol Maindy
>>>
>>>       Caerdydd
>>>
>>>       CF24 4HQ
>>>
>>>       DU
>>>
>>>       */E-bost/*: WellsMT1@caerdydd.ac.uk
>>>       <mailto:WellsMT1@caerdydd.ac.uk>
>>>
>>>       */Ff?n/*: 02920 879628
>>>
>>>       *From: *<freesurfer-bounces@nmr.mgh.harvard.edu>
>>>       <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of
>>>       Mason Wells <WellsMT1@cardiff.ac.uk>
>>>       <mailto:WellsMT1@cardiff.ac.uk>
>>>       *Reply to: *Freesurfer support list
>>>       <freesurfer@nmr.mgh.harvard.edu>
>>>       <mailto:freesurfer@nmr.mgh.harvard.edu>
>>>       *Date: *Monday, 4 May 2020 at 20:01
>>>       *To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>>>       <mailto:freesurfer@nmr.mgh.harvard.edu>
>>>       *Subject: *Re: [Freesurfer] Recon-all exited WITH errors
>>>       {Disarmed}
>>>
>>>       *????????External Email - Use Caution *
>>>
>>>       Ah yes. I just set the SUBJECTS_DIR correctly, Terminal out below:
>>>
>>>       mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f
>>>       ../stats/lh.aparc.DKTatlas40.stats -b -a
>>>       ../label/lh.aparc.DKTatlas40.annot -c
>>>       ../label/aparc.annot.DKTatlas40.ctab PPT_001 lh white
>>>
>>>       INFO: assuming MGZ format for volumes.
>>>
>>>       INFO: using ../label/lh.cortex.label as mask to calc cortex
>>>       NumVert, SurfArea and MeanThickness.
>>>
>>>       computing statistics for each annotation in
>>>       ../label/lh.aparc.DKTatlas40.annot.
>>>
>>>       reading volume
>>>       /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/mri/wm.mgz...
>>>
>>>       reading input surface
>>>       /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/surf/lh.white...
>>>
>>>       reading input pial surface
>>>       /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/surf/lh.pial...
>>>
>>>       reading input white surface
>>>       /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/surf/lh.white...
>>>
>>>       reading colortable from annotation file...
>>>
>>>       colortable with 36 entries read (originally
>>>       /Applications/freesurfer/average/colortable_desikan_killiany.txt)
>>>
>>>       Saving annotation colortable ../label/aparc.annot.DKTatlas40.ctab
>>>
>>>       table columns are:
>>>
>>>       number of vertices
>>>
>>>       total surface area (mm^2)
>>>
>>>       total gray matter volume (mm^3)
>>>
>>>       average cortical thickness +- standard deviation (mm)
>>>
>>>       integrated rectified mean curvature
>>>
>>>       integrated rectified Gaussian curvature
>>>
>>>       folding index
>>>
>>>       intrinsic curvature index
>>>
>>>       structure name
>>>
>>>       1698 1132?? 3274? 2.730 0.526???? 0.130???? 0.032 26???? 2.4?
>>>       caudalanteriorcingulate
>>>
>>>       4375 2908?? 8369? 2.594 0.599???? 0.127???? 0.040 46???? 7.0?
>>>       caudalmiddlefrontal
>>>
>>>       3883 2464?? 5378? 2.087 0.498???? 0.149???? 0.082 74???? 9.4
>>>       ?cuneus
>>>
>>>       546??? 373?? 1423? 2.817 0.999???? 0.154???? 0.087 11???? 1.9?
>>>       entorhinal
>>>
>>>       5411 3506? 10979? 2.768 0.567???? 0.137???? 0.059????? 101
>>>       14.8? fusiform
>>>
>>>       6159 4159? 11629? 2.543 0.520???? 0.133???? 0.045?????? 86
>>>       11.0? inferiorparietal
>>>
>>>       5973 3945? 13736? 2.965 0.705???? 0.138???? 0.060????? 130
>>>       13.4? inferiortemporal
>>>
>>>       1536 934?? 2788? 2.725 0.838???? 0.164???? 0.090?????? 50 5.1?
>>>       isthmuscingulate
>>>
>>>       6953 4476? 11030? 2.320 0.542???? 0.147???? 0.055????? 110
>>>       15.3? lateraloccipital
>>>
>>>       3897 2512?? 7780? 2.641 0.630???? 0.147???? 0.077?????? 99
>>>       13.1? lateralorbitofrontal
>>>
>>>       5273 3237?? 7567? 2.161 0.603???? 0.151???? 0.956????? 191
>>>       20.8? lingual
>>>
>>>       2015 1290?? 4210? 2.576 0.773???? 0.157???? 0.084 64???? 6.5?
>>>       medialorbitofrontal
>>>
>>>       6073 4091? 14456? 3.026 0.553???? 0.130???? 0.043?????? 80
>>>       11.0? middletemporal
>>>
>>>       1012 711?? 2254? 2.886 0.735???? 0.133???? 0.112?????? 16 6.3?
>>>       parahippocampal
>>>
>>>       2182 1401?? 4296? 2.690 0.669???? 0.128???? 0.044 26???? 4.5?
>>>       paracentral
>>>
>>>       3247 2175?? 6722? 2.682 0.501???? 0.121???? 0.038 34???? 5.1?
>>>       parsopercularis
>>>
>>>       1195 793?? 2520? 2.549 0.514???? 0.138???? 0.045?????? 21 2.1?
>>>       parsorbitalis
>>>
>>>       2780 1882?? 5377? 2.457 0.608???? 0.131???? 0.043 37???? 5.0?
>>>       parstriangularis
>>>
>>>       2229 1444?? 2359? 1.685 0.476???? 0.155???? 0.067 41???? 6.1?
>>>       pericalcarine
>>>
>>>       7692 4818? 11728? 2.218 0.657???? 0.130???? 0.053????? 114
>>>       16.0? postcentral
>>>
>>>       1983 1360?? 4109? 2.902 0.617???? 0.167???? 0.079 44???? 6.1?
>>>       posteriorcingulate
>>>
>>>       7681 4765? 13220? 2.521 0.549???? 0.123???? 0.056????? 119
>>>       15.1? precentral
>>>
>>>       6240 4189? 11573? 2.532 0.576???? 0.145???? 0.052????? 104
>>>       13.3? precuneus
>>>
>>>       1613 992?? 3166? 2.820 0.661???? 0.136???? 0.055?????? 54 3.6?
>>>       rostralanteriorcingulate
>>>
>>>       6644 4495? 12118? 2.347 0.579???? 0.144???? 0.052????? 117
>>>       13.9? rostralmiddlefrontal
>>>
>>>       12967 8768? 28469? 2.839 0.612???? 0.132???? 0.047????? 170
>>>       25.1? superiorfrontal
>>>
>>>       7963 5213? 12201? 2.095 0.481???? 0.125???? 0.053????? 125
>>>       16.2? superiorparietal
>>>
>>>       9021 6069? 20753? 3.059 0.612???? 0.130???? 0.050????? 183
>>>       19.9? superiortemporal
>>>
>>>       7970 5269? 15543? 2.684 0.502???? 0.149???? 0.074????? 910
>>>       17.4? supramarginal
>>>
>>>       702??? 454?? 1432? 2.844 0.618???? 0.133 0.046??????? 8????
>>>       1.3? transversetemporal
>>>
>>>       2953 1947?? 6539? 3.228 0.801???? 0.124???? 0.056 33???? 6.4?
>>>       insula
>>>
>>>       *Mason T Wells, MSc*
>>>
>>>       *PhD student*
>>>
>>>       School of Optometry?and Vision Sciences
>>>
>>>       & Cardiff University Brain Research
>>>
>>>       Imaging?Centre (CUBRIC), School of Psychology
>>>
>>>       Cardiff University
>>>
>>>       Cardiff
>>>
>>>       CF24 4HQ
>>>
>>>       UK
>>>
>>>       */Email/*: WellsMT1@cardiff.ac.uk <mailto:WellsMT1@cardiff.ac.uk>
>>>
>>>       */Tel/*: 02920 879628
>>>
>>>       */Web/*: Cardiff University webpage
>>>       <https://www.cardiff.ac.uk/people/research-students/view/974214->
>>>
>>>             
>>>
>>>       *Mason T Wells, MSc*
>>>
>>>       *Myfyriwr PhD*
>>>
>>>       Yr Ysgol Optometreg?a Gwyddorau?r?Golwg
>>>
>>>       & Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd
>>>       (CUBRIC), Yr Ysgol Seicoleg
>>>
>>>       Prifysgol Caerdydd
>>>
>>>       Heol Maindy
>>>
>>>       Caerdydd
>>>
>>>       CF24 4HQ
>>>
>>>       DU
>>>
>>>       */E-bost/*: WellsMT1@caerdydd.ac.uk
>>>       <mailto:WellsMT1@caerdydd.ac.uk>
>>>
>>>       */Ff?n/*: 02920 879628
>>>
>>>       *From: *<freesurfer-bounces@nmr.mgh.harvard.edu>
>>>       <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of
>>>       "Douglas N. Greve" <dgreve@mgh.harvard.edu>
>>>       <mailto:dgreve@mgh.harvard.edu>
>>>       *Reply to: *Freesurfer support list
>>>       <freesurfer@nmr.mgh.harvard.edu>
>>>       <mailto:freesurfer@nmr.mgh.harvard.edu>
>>>       *Date: *Monday, 4 May 2020 at 19:56
>>>       *To: *"freesurfer@nmr.mgh.harvard.edu"
>>>       <mailto:freesurfer@nmr.mgh.harvard.edu>
>>>       <freesurfer@nmr.mgh.harvard.edu>
>>>       <mailto:freesurfer@nmr.mgh.harvard.edu>
>>>       *Subject: *Re: [Freesurfer] Recon-all exited WITH errors
>>>       {Disarmed}
>>>
>>>       Something else has gone wrong. wm.mgz should have been there
>>>       in order to get as far as it did. Is your SUBJECTS_DIR set
>>>       properly?
>>>
>>>       On 5/4/2020 2:49 PM, Mason Wells wrote:
>>>
>>>           *????????External Email - Use Caution *
>>>
>>>           Hi,
>>>
>>>           Terminal output is below:
>>>
>>>           /Documents/Analysis/Data/freesurfer/subjects/PPT_001/scripts$
>>>           mris_anatomical_stats -mgz -cortex
>>>           ../label/lh.cortex.label -f
>>>           ../stats/lh.aparc.DKTatlas40.stats -b -a
>>>           ../label/lh.aparc.DKTatlas40.annot -c
>>>           ../label/aparc.annot.DKTatlas40.ctab PPT_001 lh white
>>>
>>>           INFO: assuming MGZ format for volumes.
>>>
>>>           INFO: using ../label/lh.cortex.label as mask to calc
>>>           cortex NumVert, SurfArea and MeanThickness.
>>>
>>>           computing statistics for each annotation in
>>>           ../label/lh.aparc.DKTatlas40.annot.
>>>
>>>           reading volume
>>>           /cubric/data/c1749990/freesurfer/subjects/PPT_001/mri/wm.mgz...
>>>
>>>           mghRead(/cubric/data/c1749990/freesurfer/subjects/PPT_001/mri/wm.mgz,
>>>           -1): could not open file
>>>
>>>           mris_anatomical_stats: could not read input volume
>>>           /cubric/data/c1749990/freesurfer/subjects/PPT_001/mri/wm.mgz
>>>
>>>           Cheers,
>>>
>>>           Mason
>>>
>>>           *Mason T Wells, MSc*
>>>
>>>           *PhD student*
>>>
>>>           School of Optometry?and Vision Sciences
>>>
>>>           & Cardiff University Brain Research
>>>
>>>           Imaging?Centre (CUBRIC), School of Psychology
>>>
>>>           Cardiff University
>>>
>>>           Cardiff
>>>
>>>           CF24 4HQ
>>>
>>>           UK
>>>
>>>           */Email/*: WellsMT1@cardiff.ac.uk
>>>           <mailto:WellsMT1@cardiff.ac.uk>
>>>
>>>           */Tel/*: 02920 879628
>>>
>>>           */Web/*: Cardiff University webpage
>>>           <https://www.cardiff.ac.uk/people/research-students/view/974214->
>>>
>>>             
>>>
>>>           *Mason T Wells, MSc*
>>>
>>>           *Myfyriwr PhD*
>>>
>>>           Yr Ysgol Optometreg?a Gwyddorau?r?Golwg
>>>
>>>           & Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd
>>>           (CUBRIC), Yr Ysgol Seicoleg
>>>
>>>           Prifysgol Caerdydd
>>>
>>>           Heol Maindy
>>>
>>>           Caerdydd
>>>
>>>           CF24 4HQ
>>>
>>>           DU
>>>
>>>           */E-bost/*: WellsMT1@caerdydd.ac.uk
>>>           <mailto:WellsMT1@caerdydd.ac.uk>
>>>
>>>           */Ff?n/*: 02920 879628
>>>
>>>           *From: *<freesurfer-bounces@nmr.mgh.harvard.edu>
>>>           <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf
>>>           of "Douglas N. Greve" <dgreve@mgh.harvard.edu>
>>>           <mailto:dgreve@mgh.harvard.edu>
>>>           *Reply to: *Freesurfer support list
>>>           <freesurfer@nmr.mgh.harvard.edu>
>>>           <mailto:freesurfer@nmr.mgh.harvard.edu>
>>>           *Date: *Monday, 4 May 2020 at 18:54
>>>           *To: *"freesurfer@nmr.mgh.harvard.edu"
>>>           <mailto:freesurfer@nmr.mgh.harvard.edu>
>>>           <freesurfer@nmr.mgh.harvard.edu>
>>>           <mailto:freesurfer@nmr.mgh.harvard.edu>
>>>           *Subject: *Re: [Freesurfer] Recon-all exited WITH errors
>>>
>>>           Unfortunately, the log file does not indicate what went
>>>           wrong. But it does show that the error happened on the LH
>>>           (so it is not just RH). Run the command below and send all
>>>           terminal output
>>>
>>>           cd
>>>           /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/scripts
>>>           ?mris_anatomical_stats -mgz -cortex
>>>           ../label/lh.cortex.label -f
>>>           ../stats/lh.aparc.DKTatlas40.stats -b -a
>>>           ../label/lh.aparc.DKTatlas40.annot -c
>>>           ../label/aparc.annot.DKTatlas40.ctab PPT_001 lh white
>>>
>>>
>>>
>>>
>>>
>>>
>>>           On 5/4/2020 1:34 PM, Mason Wells wrote:
>>>
>>>               *????????External Email - Use Caution *
>>>
>>>               Hi Experts,
>>>
>>>               I appear to be having some issues with recon-all. I
>>>               ran the command from a bash script (see attached), and
>>>               it appears to work fine for the left hemisphere as the
>>>               correct files are in the surf folder. However, there
>>>               are no right hemisphere surf files. I have attached
>>>               the log and error log for PPT01 and PPT02. Any advice
>>>               on as to why this has happened would be great.
>>>
>>>               Thanks in advance,
>>>
>>>               Mason
>>>
>>>               *Mason T Wells, MSc*
>>>
>>>               *PhD student*
>>>
>>>               School of Optometry?and Vision Sciences
>>>
>>>               & Cardiff University Brain Research
>>>
>>>               Imaging?Centre (CUBRIC), School of Psychology
>>>
>>>               Cardiff University
>>>
>>>               Cardiff
>>>
>>>               CF24 4HQ
>>>
>>>               UK
>>>
>>>               */Email/*: WellsMT1@cardiff.ac.uk
>>>               <mailto:WellsMT1@cardiff.ac.uk>
>>>
>>>               */Tel/*: 02920 879628
>>>
>>>               */Web/*: Cardiff University webpage
>>>               <https://www.cardiff.ac.uk/people/research-students/view/974214->
>>>
>>>                     
>>>
>>>               *Mason T Wells, MSc*
>>>
>>>               *Myfyriwr PhD*
>>>
>>>               Yr Ysgol Optometreg?a Gwyddorau?r?Golwg
>>>
>>>               & Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol
>>>               Caerdydd (CUBRIC), Yr Ysgol Seicoleg
>>>
>>>               Prifysgol Caerdydd
>>>
>>>               Heol Maindy
>>>
>>>               Caerdydd
>>>
>>>               CF24 4HQ
>>>
>>>               DU
>>>
>>>               */E-bost/*: WellsMT1@caerdydd.ac.uk
>>>               <mailto:WellsMT1@caerdydd.ac.uk>
>>>
>>>               */Ff?n/*: 02920 879628
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>               _______________________________________________
>>>
>>>               Freesurfer mailing list
>>>
>>>               Freesurfer@nmr.mgh.harvard.edu  <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>
>>>               *MailScanner has detected a possible fraud attempt
>>>               from "eur03.safelinks.protection.outlook.com" claiming
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>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>           _______________________________________________
>>>
>>>           Freesurfer mailing list
>>>
>>>           Freesurfer@nmr.mgh.harvard.edu  <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>
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>>>           https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer  <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=02%7C01%7CWellsMT1%40cardiff.ac.uk%7Cdf9eb81b587e4f34ab0908d7f2972ca0%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C637244603426581476&sdata=9FzX4UxRBUrO5onyn1ZwE7pjqrUEv5WMHV1MB1u1%2FG8%3D&reserved=0>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>       _______________________________________________
>>>
>>>       Freesurfer mailing list
>>>
>>>       Freesurfer@nmr.mgh.harvard.edu  <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>
>>>       *MailScanner has detected a possible fraud attempt from
>>>       "eur03.safelinks.protection.outlook.com" claiming to be*
>>>       https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer  <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=02%7C01%7CWellsMT1%40cardiff.ac.uk%7Cdf9eb81b587e4f34ab0908d7f2972ca0%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C637244603426591477&sdata=KRIOcP2dXJl7bJbUCXXRpgTBoji0jSteH5S5oT7YZcc%3D&reserved=0>
>>>
>>>
>>>
>>>
>>>
>>>
>>>   _______________________________________________
>>>
>>>   Freesurfer mailing list
>>>
>>>   Freesurfer@nmr.mgh.harvard.edu  <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>
>>>   *MailScanner has detected a possible fraud attempt from
>>>   "eur03.safelinks.protection.outlook.com" claiming to be*
>>>   https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer  <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=02%7C01%7CWellsMT1%40cardiff.ac.uk%7Cdf9eb81b587e4f34ab0908d7f2972ca0%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C637244603426601472&sdata=fXDymBlzoXir0xwsk4dREaQs1r7YWliUKBnK2sV%2B49c%3D&reserved=0>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>> URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200507/b7629997/attachment-0001.html
>>
>> ------------------------------
>>
>> Message: 6
>> Date: Thu, 7 May 2020 15:50:26 +0000
>> From: "Hoopes, Andrew" <AHOOPES@mgh.harvard.edu>
>> Subject: Re: [Freesurfer] flirt.fsl error (NEWMAT::SingularException)
>>       when running bbregister in Freesurfer 7.0.0
>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>> Message-ID: <EBCA186E-5FD0-47BA-95C3-3D80252ACC59@mgh.harvard.edu>
>> Content-Type: text/plain; charset="utf-8"
>>
>> Hi Julien,
>>
>> Just to test something out, can you try running this again after replacing the flirt.fsl binary in your new 7.0 install with the flirt.fsl binary from 6.0? i.e.
>>
>> cp /path/to/freesurfer/6.0.0/bin/flirst.fsl /path/to/freesurfer/7.0.0/bin/flirst.fsl
>>
>> Let me know how that works.
>>
>> Best
>> Andrew
>>
>>
>> ?On 5/7/20, 8:04 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of julienbesle" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of julienbesle@gmail.com> wrote:
>>
>>           External Email - Use Caution       
>>
>>   Hi,
>>
>>   I just installed freesurfer v7 and I'm getting an error in a script that
>>   calls bbregister with the --fslmat and --init-fsl options. This error
>>   does not occur in freesurfer v6 even when using exactly the same data,
>>   but it does also occur with a development version of freesurfer I
>>   downloaded in Sept 2019 (exact same error).
>>
>>   The call is:
>>
>>   DEBUG    : 2020-05-06 12:07:12,816 : runCmd     : Running: bbregister
>>   --s HLOSS_p5 --mov
>>   /home/julien/data/HLOSS/pilot05_B/DWI/B0_corrected_mean_resampled_MPRAGE.nii
>>   --reg
>>   /home/julien/data/HLOSS/pilot05_B/DWI/easy_lausanne_test/b0-TO-orig.dat
>>   --fslmat
>>   /home/julien/data/HLOSS/pilot05_B/DWI/easy_lausanne_test/b0-TO-orig.mat
>>   --init-fsl --dti
>>
>>   The error occurs when bbregister calls fsl.flirt:
>>
>>   INFO     : 2020-05-06 12:08:24,560 : main       : flirt.fsl -ref
>>   /home/julien/data/HLOSS/pilot05_B/DWI/easy_lausanne_test/tmp.bbregister.8331/fslregister/refvol.fslregister.nii
>>   -in
>>   /home/julien/data/HLOSS/pilot05_B/DWI/easy_lausanne_test/tmp.bbregister.8331/fslregister/movvol.fslregister.nii
>>   -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90
>>   -searchrz -90 90 -verbose 0 -omat
>>   /home/julien/data/HLOSS/pilot05_B/DWI/easy_lausanne_test/tmp.bbregister.8331/fslregister/fslmat0.trans.mat
>>   -schedule /usr/local/freesurfer/bin/fsl.5.0.2.xyztrans.sch -init
>>   /home/julien/data/HLOSS/pilot05_B/DWI/easy_lausanne_test/tmp.bbregister.8331/reg.init.dat.fsl.mat0
>>   INFO     : 2020-05-06 12:08:55,102 : main       : Wed May  6 12:08:54
>>   EEST 2020
>>   INFO     : 2020-05-06 12:08:55,603 : main       : /mnt/f/data/HLOSS
>>   INFO     : 2020-05-06 12:08:56,105 : main       : flirt.fsl -ref
>>   /home/julien/data/HLOSS/pilot05_B/DWI/easy_lausanne_test/tmp.bbregister.8331/fslregister/refvol.fslregister.nii
>>   -in
>>   /home/julien/data/HLOSS/pilot05_B/DWI/easy_lausanne_test/tmp.bbregister.8331/fslregister/movvol.fslregister.nii
>>   -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90
>>   -searchrz -90 90 -verbose 0 -omat
>>   /home/julien/data/HLOSS/pilot05_B/DWI/easy_lausanne_test/tmp.bbregister.8331/reg.init.dat.fsl.mat
>>   -init
>>   /home/julien/data/HLOSS/pilot05_B/DWI/easy_lausanne_test/tmp.bbregister.8331/fslregister/fslmat0.trans.mat
>>   -schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch
>>   INFO     : 2020-05-06 12:09:15,632 : main       : terminate called after
>>   throwing an instance of 'NEWMAT::SingularException'
>>   INFO     : 2020-05-06 12:09:15,633 : main       : Abort (core dumped)
>>   INFO     : 2020-05-06 12:09:15,634 : main       : ERROR: flirt
>>   CRITICAL : 2020-05-06 12:09:15,634 : runCmd     : Return Value: 1
>>
>>   It looks like the first time flirt.fsl is called everything goes fine,
>>   but the second time, the error occurs. Unfortunately this is not a
>>   script I wrote myself, so I'm not sure what this particular call to
>>   bbregister is supposed to achieve. I'm not sure the call to fsl.flirt
>>   depends on which version of FSL I have installed, but just in case, I
>>   used the FSL v6 and didn't change anything to the FSL installation
>>   between trying Freesurfer v6, dev or v7. I run everything on Ubuntu
>>   16.04 running on WSL on Windows 10.
>>
>>   Any idea what could be going wrong?
>>
>>   Thanks
>>
>>   Julien
>>
>>   --
>>   -------------------------------------
>>   Julien Besle
>>   Lagos Center, Apt 9A
>>   Sadat Street
>>   Beirut
>>   Lebanon
>>
>>   tel: +961 78 980 317
>>   -------------------------------------
>>
>>
>>   _______________________________________________
>>   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
>>
>> End of Freesurfer Digest, Vol 195, Issue 24
>> *******************************************
>
>
>
>
>
> ------------------------------
>
> Message: 5
> Date: Thu, 7 May 2020 13:55:37 -0400
> From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
> Subject: Re: [Freesurfer] New PETSurfer Questions
> To: <freesurfer@nmr.mgh.harvard.edu>
> Message-ID: <b2bae494-721a-86d5-ee49-17286c539937@mgh.harvard.edu>
> Content-Type: text/plain; charset="utf-8"; format=flowed
>
> No special procedures come to mind. You can use mri_segstats using the
> PVC'ed PET image as input and aux/seg.nii.gz as the segmentation and
> aux/seg.ctab as the colortable.
>
> On 5/7/2020 1:31 PM, Ferraro, Pilar wrote:
>>         External Email - Use Caution
>>
>> Dear Freesurfer experts,
>>
>> As previously mentioned, we are currently trying to test the effects of different PVC corrections on metabolism estimation in a group of patients.
>>
>> We would like to also include MZ and MG methods in the analyses, comparing them to SGTM and no PVC.
>> However, while both MG and MZ provide voxel-wise results, we would like to use them in ROI analyses in order to be able to compare their outputs with the ones obtained with SGTM and no PVC.
>> Are there any procedures that you would recommend to do this?
>>
>> Many thanks in advance for any help,
>>
>> Best,
>>
>> Pilar
>>
>>
>>
>>> Il giorno 7 mag 2020, alle ore 6:00 PM, freesurfer-request@nmr.mgh.harvard.edu ha scritto:
>>>
>>> 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: HCPMMP1 parcellation to aseg (.mgz) (pooja prabhu)
>>>   2. Re: HCPMMP1 parcellation to aseg (.mgz) (Douglas N. Greve)
>>>   3. Re: Recon-all exited WITH errors {Disarmed} (Mason Wells)
>>>   4. Re: freesurfer 7.0.0 in a virtual machine... (Gonzalo Rojas Costa)
>>>   5. Re: Recon-all exited WITH errors {Disarmed} (Douglas N. Greve)
>>>   6. Re: flirt.fsl error (NEWMAT::SingularException) when running
>>>      bbregister in Freesurfer 7.0.0 (Hoopes, Andrew)
>>>
>>>
>>> ----------------------------------------------------------------------
>>>
>>> Message: 1
>>> Date: Thu, 7 May 2020 20:55:21 +0530
>>> From: pooja prabhu <prabhuppooja@gmail.com>
>>> Subject: Re: [Freesurfer] HCPMMP1 parcellation to aseg (.mgz)
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Message-ID:
>>>      <CANeOyKnobqGKPPSdX+Pr1CmvHRYE2d+ziRvEMfz9BQJ4-RsGbA@mail.gmail.com>
>>> Content-Type: text/plain; charset="utf-8"
>>>
>>>        External Email - Use Caution
>>>
>>> HCPMMP1 parcellation is multi modal parcellation
>>> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4990127/
>>>
>>> We need the file something like we have for 'aparc' parcellation.
>>> The file format should be in .mgz (aparc.HCPMMP1+aseg.mgz)
>>> How can i do it? (i have lh.HCPMMP1.annot and rh.HCPMMP1.annot)
>>>
>>> --
>>> Thank You
>>> Pooja Prabhu
>>> -------------- next part --------------
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>>>
>>> ------------------------------
>>>
>>> Message: 2
>>> Date: Thu, 7 May 2020 11:26:14 -0400
>>> From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
>>> Subject: Re: [Freesurfer] HCPMMP1 parcellation to aseg (.mgz)
>>> To: <freesurfer@nmr.mgh.harvard.edu>
>>> Message-ID: <01355b15-25bd-9a44-2d75-e2eefe70ae33@mgh.harvard.edu>
>>> Content-Type: text/plain; charset="utf-8"
>>>
>>> sorry, can you include the previous emails?
>>>
>>> On 5/7/2020 11:25 AM, pooja prabhu wrote:
>>>> ????????External Email - Use Caution
>>>>
>>>> HCPMMP1 parcellation is multi modal parcellation
>>>> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4990127/
>>>>
>>>> We need the file something like we have for 'aparc' parcellation.
>>>> The file format should be in .mgz (aparc.HCPMMP1+aseg.mgz)
>>>> How can i do it? (i have lh.HCPMMP1.annot and rh.HCPMMP1.annot)
>>>>
>>>> --
>>>> Thank You
>>>> Pooja Prabhu
>>>>
>>>>
>>>> _______________________________________________
>>>> Freesurfer mailing list
>>>> Freesurfer@nmr.mgh.harvard.edu
>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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>>>
>>> ------------------------------
>>>
>>> Message: 3
>>> Date: Thu, 7 May 2020 15:33:26 +0000
>>> From: Mason Wells <WellsMT1@cardiff.ac.uk>
>>> Subject: Re: [Freesurfer] Recon-all exited WITH errors {Disarmed}
>>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>>> Message-ID: <D4803927-B60A-40D9-840E-B0201A6FBFDF@cardiff.ac.uk>
>>> Content-Type: text/plain; charset="utf-8"
>>>
>>>        External Email - Use Caution
>>>
>>> Terminal output is below:
>>>
>>>
>>> export SUBJECTS_DIR=/home/c1749990/Documents/Analysis/Data/freesurfer/subjects
>>>
>>> c1749990@l029:~/Documents/Analysis/Data/PMA_retinoScans/PPT_004$ recon-all -i pre_processed_anatomy/T1.nii.gz -s PPT_004 -parcstats3 -label_v1
>>> recon-all -i pre_processed_anatomy/T1.nii.gz -s PPT_004 -parcstats3 -label_v1
>>>
>>> Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
>>> Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
>>> INFO: SUBJECTS_DIR is /home/c1749990/Documents/Analysis/Data/freesurfer/subjects
>>> Actual FREESURFER_HOME /cubric/software/freesurfer.versions/5.3.0
>>> Linux l029.cubric.cf.ac.uk 3.10.0-957.12.1.el7.x86_64 #1 SMP Mon Apr 29 14:59:59 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
>>> /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_004
>>>
>>> mri_convert /home/c1749990/Documents/Analysis/Data/PMA_retinoScans/PPT_004/pre_processed_anatomy/T1.nii.gz /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_004/mri/orig/001.mgz
>>>
>>> mri_convert /home/c1749990/Documents/Analysis/Data/PMA_retinoScans/PPT_004/pre_processed_anatomy/T1.nii.gz /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_004/mri/orig/001.mgz
>>> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
>>> reading from /home/c1749990/Documents/Analysis/Data/PMA_retinoScans/PPT_004/pre_processed_anatomy/T1.nii.gz...
>>> TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
>>> i_ras = (-1, 0, 0)
>>> j_ras = (0, 1, 0)
>>> k_ras = (0, 0, 1)
>>> writing to /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_004/mri/orig/001.mgz...
>>> #-----------------------------------------
>>> #@# Parcellation Stats 3 lh Thu May  7 16:32:30 BST 2020
>>> /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_004/scripts
>>>
>>> mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas40.stats -b -a ../label/lh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab PPT_004 lh white
>>>
>>> No such file or directory
>>> mris_anatomical_stats: could not open label file ../label/lh.cortex.label
>>> INFO: assuming MGZ format for volumes.
>>> Invalid argument
>>>
>>> Invalid argument
>>> Linux l029.cubric.cf.ac.uk 3.10.0-957.12.1.el7.x86_64 #1 SMP Mon Apr 29 14:59:59 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
>>>
>>> recon-all -s PPT_004 exited with ERRORS at Thu May  7 16:32:30 BST 2020
>>>
>>> For more details, see the log file /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_004/scripts/recon-all.log
>>> To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>>
>>>
>>> Mason T Wells, MSc
>>> PhD student
>>> School of Optometry and Vision Sciences
>>> & Cardiff University Brain Research
>>> Imaging Centre (CUBRIC), School of Psychology
>>> Cardiff University
>>> Cardiff
>>> CF24 4HQ
>>> UK
>>>
>>> Email: WellsMT1@cardiff.ac.uk<mailto:WellsMT1@cardiff.ac.uk>
>>> Tel: 02920 879628
>>> Web: Cardiff University webpage<https://www.cardiff.ac.uk/people/research-students/view/974214->
>>> Mason T Wells, MSc
>>> Myfyriwr PhD
>>> Yr Ysgol Optometreg a Gwyddorau?r Golwg
>>> & Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg
>>> Prifysgol Caerdydd
>>> Heol Maindy
>>> Caerdydd
>>> CF24 4HQ
>>> DU
>>>
>>> E-bost: WellsMT1@caerdydd.ac.uk<mailto:WellsMT1@caerdydd.ac.uk>
>>> Ff?n: 02920 879628
>>>
>>>
>>> From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Douglas N. Greve" <dgreve@mgh.harvard.edu>
>>> Reply to: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>>> Date: Thursday, 7 May 2020 at 15:59
>>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>>> Subject: Re: [Freesurfer] Recon-all exited WITH errors {Disarmed}
>>>
>>> No all, just one. And try running it with just the -parcstats3 flag (ie, don't use -all or -autreconX). You should have an answer in seconds
>>> On 5/7/2020 7:50 AM, Mason Wells wrote:
>>>
>>>        External Email - Use Caution
>>> Hi Doug,
>>>
>>> Sorry I am a bit confused. I ran recon-all as a bash for 30 participants. None of which had the right hemisphere completed and recon-all log says exited with errors (as the log in the original email shows). Are you suggesting I go back and re-run recon-all via the bash and see if I get the same issue?
>>>
>>> Thanks for all your help.
>>> Mason
>>>
>>> Mason T Wells, MSc
>>> PhD student
>>> School of Optometry and Vision Sciences
>>> & Cardiff University Brain Research
>>> Imaging Centre (CUBRIC), School of Psychology
>>> Cardiff University
>>> Cardiff
>>> CF24 4HQ
>>> UK
>>>
>>> Email: WellsMT1@cardiff.ac.uk<mailto:WellsMT1@cardiff.ac.uk>
>>> Tel: 02920 879628
>>> Web: Cardiff University webpage<https://www.cardiff.ac.uk/people/research-students/view/974214->
>>> Mason T Wells, MSc
>>> Myfyriwr PhD
>>> Yr Ysgol Optometreg a Gwyddorau?r Golwg
>>> & Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg
>>> Prifysgol Caerdydd
>>> Heol Maindy
>>> Caerdydd
>>> CF24 4HQ
>>> DU
>>>
>>> E-bost: WellsMT1@caerdydd.ac.uk<mailto:WellsMT1@caerdydd.ac.uk>
>>> Ff?n: 02920 879628
>>>
>>>
>>> From: <freesurfer-bounces@nmr.mgh.harvard.edu><mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Douglas N. Greve" <dgreve@mgh.harvard.edu><mailto:dgreve@mgh.harvard.edu>
>>> Reply to: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
>>> Date: Wednesday, 6 May 2020 at 23:11
>>> To: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
>>> Subject: Re: [Freesurfer] Recon-all exited WITH errors
>>>
>>> It looks like that command finished without error. Have you tried running it in recon-all again to see if it fails again? You can just run that command with -parcstats3
>>>
>>>
>>> On 5/6/2020 6:41 AM, Mason Wells wrote:
>>>
>>>        External Email - Use Caution
>>> Hi Doug,
>>>
>>> Not sure if my email below got to you? I sent the terminal outputs of the command you told me to run. Any idea what?s going on or how to fix it?
>>>
>>> Cheers,
>>> Mason
>>>
>>> Mason T Wells, MSc
>>> PhD student
>>> School of Optometry and Vision Sciences
>>> & Cardiff University Brain Research
>>> Imaging Centre (CUBRIC), School of Psychology
>>> Cardiff University
>>> Cardiff
>>> CF24 4HQ
>>> UK
>>>
>>> Email: WellsMT1@cardiff.ac.uk<mailto:WellsMT1@cardiff.ac.uk>
>>> Tel: 02920 879628
>>> Web: Cardiff University webpage<https://www.cardiff.ac.uk/people/research-students/view/974214->
>>> Mason T Wells, MSc
>>> Myfyriwr PhD
>>> Yr Ysgol Optometreg a Gwyddorau?r Golwg
>>> & Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg
>>> Prifysgol Caerdydd
>>> Heol Maindy
>>> Caerdydd
>>> CF24 4HQ
>>> DU
>>>
>>> E-bost: WellsMT1@caerdydd.ac.uk<mailto:WellsMT1@caerdydd.ac.uk>
>>> Ff?n: 02920 879628
>>>
>>>
>>> From: <freesurfer-bounces@nmr.mgh.harvard.edu><mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Mason Wells <WellsMT1@cardiff.ac.uk><mailto:WellsMT1@cardiff.ac.uk>
>>> Reply to: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
>>> Date: Monday, 4 May 2020 at 20:01
>>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
>>> Subject: Re: [Freesurfer] Recon-all exited WITH errors {Disarmed}
>>>
>>>
>>>        External Email - Use Caution
>>> Ah yes. I just set the SUBJECTS_DIR correctly, Terminal out below:
>>>
>>> mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas40.stats -b -a ../label/lh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab PPT_001 lh white
>>> INFO: assuming MGZ format for volumes.
>>> INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
>>> computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot.
>>> reading volume /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/mri/wm.mgz...
>>> reading input surface /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/surf/lh.white...
>>> reading input pial surface /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/surf/lh.pial...
>>> reading input white surface /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/surf/lh.white...
>>> reading colortable from annotation file...
>>> colortable with 36 entries read (originally /Applications/freesurfer/average/colortable_desikan_killiany.txt)
>>> Saving annotation colortable ../label/aparc.annot.DKTatlas40.ctab
>>>
>>> table columns are:
>>>    number of vertices
>>>    total surface area (mm^2)
>>>    total gray matter volume (mm^3)
>>>    average cortical thickness +- standard deviation (mm)
>>>    integrated rectified mean curvature
>>>    integrated rectified Gaussian curvature
>>>    folding index
>>>    intrinsic curvature index
>>>    structure name
>>>
>>> 1698   1132   3274  2.730 0.526     0.130     0.032       26     2.4  caudalanteriorcingulate
>>> 4375   2908   8369  2.594 0.599     0.127     0.040       46     7.0  caudalmiddlefrontal
>>> 3883   2464   5378  2.087 0.498     0.149     0.082       74     9.4  cuneus
>>>  546    373   1423  2.817 0.999     0.154     0.087       11     1.9  entorhinal
>>> 5411   3506  10979  2.768 0.567     0.137     0.059      101    14.8  fusiform
>>> 6159   4159  11629  2.543 0.520     0.133     0.045       86    11.0  inferiorparietal
>>> 5973   3945  13736  2.965 0.705     0.138     0.060      130    13.4  inferiortemporal
>>> 1536    934   2788  2.725 0.838     0.164     0.090       50     5.1  isthmuscingulate
>>> 6953   4476  11030  2.320 0.542     0.147     0.055      110    15.3  lateraloccipital
>>> 3897   2512   7780  2.641 0.630     0.147     0.077       99    13.1  lateralorbitofrontal
>>> 5273   3237   7567  2.161 0.603     0.151     0.956      191    20.8  lingual
>>> 2015   1290   4210  2.576 0.773     0.157     0.084       64     6.5  medialorbitofrontal
>>> 6073   4091  14456  3.026 0.553     0.130     0.043       80    11.0  middletemporal
>>> 1012    711   2254  2.886 0.735     0.133     0.112       16     6.3  parahippocampal
>>> 2182   1401   4296  2.690 0.669     0.128     0.044       26     4.5  paracentral
>>> 3247   2175   6722  2.682 0.501     0.121     0.038       34     5.1  parsopercularis
>>> 1195    793   2520  2.549 0.514     0.138     0.045       21     2.1  parsorbitalis
>>> 2780   1882   5377  2.457 0.608     0.131     0.043       37     5.0  parstriangularis
>>> 2229   1444   2359  1.685 0.476     0.155     0.067       41     6.1  pericalcarine
>>> 7692   4818  11728  2.218 0.657     0.130     0.053      114    16.0  postcentral
>>> 1983   1360   4109  2.902 0.617     0.167     0.079       44     6.1  posteriorcingulate
>>> 7681   4765  13220  2.521 0.549     0.123     0.056      119    15.1  precentral
>>> 6240   4189  11573  2.532 0.576     0.145     0.052      104    13.3  precuneus
>>> 1613    992   3166  2.820 0.661     0.136     0.055       54     3.6  rostralanteriorcingulate
>>> 6644   4495  12118  2.347 0.579     0.144     0.052      117    13.9  rostralmiddlefrontal
>>> 12967   8768  28469  2.839 0.612     0.132     0.047      170    25.1  superiorfrontal
>>> 7963   5213  12201  2.095 0.481     0.125     0.053      125    16.2  superiorparietal
>>> 9021   6069  20753  3.059 0.612     0.130     0.050      183    19.9  superiortemporal
>>> 7970   5269  15543  2.684 0.502     0.149     0.074      910    17.4  supramarginal
>>>  702    454   1432  2.844 0.618     0.133     0.046        8     1.3  transversetemporal
>>> 2953   1947   6539  3.228 0.801     0.124     0.056       33     6.4  insula
>>>
>>> Mason T Wells, MSc
>>> PhD student
>>> School of Optometry and Vision Sciences
>>> & Cardiff University Brain Research
>>> Imaging Centre (CUBRIC), School of Psychology
>>> Cardiff University
>>> Cardiff
>>> CF24 4HQ
>>> UK
>>>
>>> Email: WellsMT1@cardiff.ac.uk<mailto:WellsMT1@cardiff.ac.uk>
>>> Tel: 02920 879628
>>> Web: Cardiff University webpage<https://www.cardiff.ac.uk/people/research-students/view/974214->
>>> Mason T Wells, MSc
>>> Myfyriwr PhD
>>> Yr Ysgol Optometreg a Gwyddorau?r Golwg
>>> & Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg
>>> Prifysgol Caerdydd
>>> Heol Maindy
>>> Caerdydd
>>> CF24 4HQ
>>> DU
>>>
>>> E-bost: WellsMT1@caerdydd.ac.uk<mailto:WellsMT1@caerdydd.ac.uk>
>>> Ff?n: 02920 879628
>>>
>>>
>>> From: <freesurfer-bounces@nmr.mgh.harvard.edu><mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Douglas N. Greve" <dgreve@mgh.harvard.edu><mailto:dgreve@mgh.harvard.edu>
>>> Reply to: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
>>> Date: Monday, 4 May 2020 at 19:56
>>> To: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
>>> Subject: Re: [Freesurfer] Recon-all exited WITH errors {Disarmed}
>>>
>>> Something else has gone wrong. wm.mgz should have been there in order to get as far as it did. Is your SUBJECTS_DIR set properly?
>>> On 5/4/2020 2:49 PM, Mason Wells wrote:
>>>
>>>        External Email - Use Caution
>>> Hi,
>>>
>>> Terminal output is below:
>>>
>>> /Documents/Analysis/Data/freesurfer/subjects/PPT_001/scripts$ mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas40.stats -b -a ../label/lh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab PPT_001 lh white
>>> INFO: assuming MGZ format for volumes.
>>> INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
>>> computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot.
>>> reading volume /cubric/data/c1749990/freesurfer/subjects/PPT_001/mri/wm.mgz...
>>> mghRead(/cubric/data/c1749990/freesurfer/subjects/PPT_001/mri/wm.mgz, -1): could not open file
>>> mris_anatomical_stats: could not read input volume /cubric/data/c1749990/freesurfer/subjects/PPT_001/mri/wm.mgz
>>>
>>> Cheers,
>>> Mason
>>>
>>> Mason T Wells, MSc
>>> PhD student
>>> School of Optometry and Vision Sciences
>>> & Cardiff University Brain Research
>>> Imaging Centre (CUBRIC), School of Psychology
>>> Cardiff University
>>> Cardiff
>>> CF24 4HQ
>>> UK
>>>
>>> Email: WellsMT1@cardiff.ac.uk<mailto:WellsMT1@cardiff.ac.uk>
>>> Tel: 02920 879628
>>> Web: Cardiff University webpage<https://www.cardiff.ac.uk/people/research-students/view/974214->
>>> Mason T Wells, MSc
>>> Myfyriwr PhD
>>> Yr Ysgol Optometreg a Gwyddorau?r Golwg
>>> & Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg
>>> Prifysgol Caerdydd
>>> Heol Maindy
>>> Caerdydd
>>> CF24 4HQ
>>> DU
>>>
>>> E-bost: WellsMT1@caerdydd.ac.uk<mailto:WellsMT1@caerdydd.ac.uk>
>>> Ff?n: 02920 879628
>>>
>>>
>>> From: <freesurfer-bounces@nmr.mgh.harvard.edu><mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Douglas N. Greve" <dgreve@mgh.harvard.edu><mailto:dgreve@mgh.harvard.edu>
>>> Reply to: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
>>> Date: Monday, 4 May 2020 at 18:54
>>> To: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
>>> Subject: Re: [Freesurfer] Recon-all exited WITH errors
>>>
>>> Unfortunately, the log file does not indicate what went wrong. But it does show that the error happened on the LH (so it is not just RH). Run the command below and send all terminal output
>>>
>>> cd /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/scripts
>>> mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas40.stats -b -a ../label/lh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab PPT_001 lh white
>>>
>>>
>>>
>>>
>>>
>>>
>>> On 5/4/2020 1:34 PM, Mason Wells wrote:
>>>
>>>        External Email - Use Caution
>>> Hi Experts,
>>>
>>> I appear to be having some issues with recon-all. I ran the command from a bash script (see attached), and it appears to work fine for the left hemisphere as the correct files are in the surf folder. However, there are no right hemisphere surf files. I have attached the log and error log for PPT01 and PPT02. Any advice on as to why this has happened would be great.
>>>
>>> Thanks in advance,
>>> Mason
>>>
>>> Mason T Wells, MSc
>>> PhD student
>>> School of Optometry and Vision Sciences
>>> & Cardiff University Brain Research
>>> Imaging Centre (CUBRIC), School of Psychology
>>> Cardiff University
>>> Cardiff
>>> CF24 4HQ
>>> UK
>>>
>>> Email: WellsMT1@cardiff.ac.uk<mailto:WellsMT1@cardiff.ac.uk>
>>> Tel: 02920 879628
>>> Web: Cardiff University webpage<https://www.cardiff.ac.uk/people/research-students/view/974214->
>>> Mason T Wells, MSc
>>> Myfyriwr PhD
>>> Yr Ysgol Optometreg a Gwyddorau?r Golwg
>>> & Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg
>>> Prifysgol Caerdydd
>>> Heol Maindy
>>> Caerdydd
>>> CF24 4HQ
>>> DU
>>>
>>> E-bost: WellsMT1@caerdydd.ac.uk<mailto:WellsMT1@caerdydd.ac.uk>
>>> Ff?n: 02920 879628
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>>
>>> Freesurfer mailing list
>>>
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>>>
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>>>
>>>
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>>>
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>>
>>> Freesurfer mailing list
>>>
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>>>
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>>> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>
>>> MailScanner has detected a possible fraud attempt from "eur03.safelinks.protection.outlook.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=02%7C01%7CWellsMT1%40cardiff.ac.uk%7Cdf9eb81b587e4f34ab0908d7f2972ca0%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C637244603426591477&sdata=KRIOcP2dXJl7bJbUCXXRpgTBoji0jSteH5S5oT7YZcc%3D&reserved=0>
>>>
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>>
>>> Freesurfer mailing list
>>>
>>> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=02%7C01%7CWellsMT1%40cardiff.ac.uk%7Cdf9eb81b587e4f34ab0908d7f2972ca0%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C637244603426601472&sdata=fXDymBlzoXir0xwsk4dREaQs1r7YWliUKBnK2sV%2B49c%3D&reserved=0>
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>>>
>>> ------------------------------
>>>
>>> Message: 4
>>> Date: Thu, 7 May 2020 15:34:37 -0400
>>> From: Gonzalo Rojas Costa <gonzalo.rojas.costa@gmail.com>
>>> Subject: Re: [Freesurfer] freesurfer 7.0.0 in a virtual machine...
>>> To: ts+ml@rcmd.org
>>> Cc: freesurfer@nmr.mgh.harvard.edu
>>> Message-ID:
>>>      <CAHPHMw7tiFRNOL=qSddTQr-z6b=nuqE7ZMvBV7tq=GbrzmiHtQ@mail.gmail.com>
>>> Content-Type: text/plain; charset="utf-8"
>>>
>>>        External Email - Use Caution
>>>
>>> Hi:
>>>
>>>  No... I don't have any specific issue... I have a previous freesurfer
>>> version installed that I want to continue using. So I want to install
>>> version freesurfer 7.0 on a virtual machine...
>>>
>>>  Sincerely,
>>>
>>>
>>> Gonzalo Rojas Costa
>>>
>>>
>>>> Message: 4
>>>> Date: Thu, 7 May 2020 12:43:56 +0200 (CEST)
>>>> From: Tim Sch?fer <ts+ml@rcmd.org>
>>>> Subject: Re: [Freesurfer] freesurfer 7.0.0 in a virtual machine...
>>>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>>>> Message-ID: <1445340988.123994.1588848236854@ox.hosteurope.de>
>>>> Content-Type: text/plain; charset="utf-8"
>>>>
>>>>      External Email - Use Caution
>>>>
>>>> There should be no difference to installation on a physical machine. Are
>>> you
>>>> running into any specific issues?
>>>>
>>>> Tim
>>>>
>>>>> On May 7, 2020 at 3:51 AM Gonzalo Rojas Costa <
>>> gonzalo.rojas.costa@gmail.com> wrote:
>>>>>
>>>>>        External Email - Use Caution
>>>>>
>>>>> Hi:
>>>>>
>>>>> How can install freesurfer 7.0.0 in a virtual machine ?
>>>>>
>>>>>  Sincerely,
>>>>>
>>>>>
>>>>> Gonzalo Rojas Costa
>>>>> _______________________________________________
>>>>> Freesurfer mailing list
>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>> --
>>>> Dr. Tim Sch?fer
>>>> Postdoc Computational Neuroimaging
>>>> Department of Child and Adolescent Psychiatry, Psychosomatics and
>>>> Psychotherapy
>>>> University Hospital Frankfurt, Goethe University Frankfurt am Main,
>>> Germany
>>> -------------- next part --------------
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>>>
>>> ------------------------------
>>>
>>> Message: 5
>>> Date: Thu, 7 May 2020 11:47:15 -0400
>>> From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
>>> Subject: Re: [Freesurfer] Recon-all exited WITH errors {Disarmed}
>>> To: <freesurfer@nmr.mgh.harvard.edu>
>>> Message-ID: <f05dbd88-2bbd-775e-6a11-38c2858344c6@mgh.harvard.edu>
>>> Content-Type: text/plain; charset="utf-8"
>>>
>>> Does
>>> /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_004/label/lh.cortex.label
>>> exist?
>>>
>>> On 5/7/2020 11:33 AM, Mason Wells wrote:
>>>> ????????External Email - Use Caution
>>>>
>>>> Terminal output is below:
>>>>
>>>> export
>>>> SUBJECTS_DIR=/home/c1749990/Documents/Analysis/Data/freesurfer/subjects
>>>>
>>>> c1749990@l029:~/Documents/Analysis/Data/PMA_retinoScans/PPT_004$
>>>> recon-all -i pre_processed_anatomy/T1.nii.gz -s PPT_004 -parcstats3
>>>> -label_v1
>>>>
>>>> recon-all -i pre_processed_anatomy/T1.nii.gz -s PPT_004 -parcstats3
>>>> -label_v1
>>>>
>>>> Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
>>>>
>>>> Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
>>>>
>>>> INFO: SUBJECTS_DIR is
>>>> /home/c1749990/Documents/Analysis/Data/freesurfer/subjects
>>>>
>>>> Actual FREESURFER_HOME /cubric/software/freesurfer.versions/5.3.0
>>>>
>>>> Linux l029.cubric.cf.ac.uk 3.10.0-957.12.1.el7.x86_64 #1 SMP Mon Apr
>>>> 29 14:59:59 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
>>>>
>>>> /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_004
>>>>
>>>> mri_convert
>>>> /home/c1749990/Documents/Analysis/Data/PMA_retinoScans/PPT_004/pre_processed_anatomy/T1.nii.gz
>>>> /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_004/mri/orig/001.mgz
>>>>
>>>>
>>>> mri_convert
>>>> /home/c1749990/Documents/Analysis/Data/PMA_retinoScans/PPT_004/pre_processed_anatomy/T1.nii.gz
>>>> /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_004/mri/orig/001.mgz
>>>>
>>>>
>>>> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
>>>>
>>>> reading from
>>>> /home/c1749990/Documents/Analysis/Data/PMA_retinoScans/PPT_004/pre_processed_anatomy/T1.nii.gz...
>>>>
>>>> TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
>>>>
>>>> i_ras = (-1, 0, 0)
>>>>
>>>> j_ras = (0, 1, 0)
>>>>
>>>> k_ras = (0, 0, 1)
>>>>
>>>> writing to
>>>> /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_004/mri/orig/001.mgz...
>>>>
>>>> #-----------------------------------------
>>>>
>>>> #@# Parcellation Stats 3 lh Thu May? 7 16:32:30 BST 2020
>>>>
>>>> /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_004/scripts
>>>>
>>>> mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f
>>>> ../stats/lh.aparc.DKTatlas40.stats -b -a
>>>> ../label/lh.aparc.DKTatlas40.annot -c
>>>> ../label/aparc.annot.DKTatlas40.ctab PPT_004 lh white
>>>>
>>>> No such file or directory
>>>>
>>>> mris_anatomical_stats: could not open label file ../label/lh.cortex.label
>>>>
>>>> INFO: assuming MGZ format for volumes.
>>>>
>>>> Invalid argument
>>>>
>>>> Invalid argument
>>>>
>>>> Linux l029.cubric.cf.ac.uk 3.10.0-957.12.1.el7.x86_64 #1 SMP Mon Apr
>>>> 29 14:59:59 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
>>>>
>>>> recon-all -s PPT_004 exited with ERRORS at Thu May? 7 16:32:30 BST 2020
>>>>
>>>> For more details, see the log file
>>>> /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_004/scripts/recon-all.log
>>>>
>>>> To report a problem, see
>>>> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>>>
>>>> *Mason T Wells, MSc*
>>>>
>>>> *PhD student*
>>>>
>>>> School of Optometry?and Vision Sciences
>>>>
>>>> & Cardiff University Brain Research
>>>>
>>>> Imaging?Centre (CUBRIC), School of Psychology
>>>>
>>>> Cardiff University
>>>>
>>>> Cardiff
>>>>
>>>> CF24 4HQ
>>>>
>>>> UK
>>>>
>>>> */Email/*: WellsMT1@cardiff.ac.uk <mailto:WellsMT1@cardiff.ac.uk>
>>>>
>>>> */Tel/*: 02920 879628
>>>>
>>>> */Web/*: Cardiff University webpage
>>>> <https://www.cardiff.ac.uk/people/research-students/view/974214->
>>>>
>>>>    
>>>>
>>>> *Mason T Wells, MSc*
>>>>
>>>> *Myfyriwr PhD*
>>>>
>>>> Yr Ysgol Optometreg?a Gwyddorau?r?Golwg
>>>>
>>>> & Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr
>>>> Ysgol Seicoleg
>>>>
>>>> Prifysgol Caerdydd
>>>>
>>>> Heol Maindy
>>>>
>>>> Caerdydd
>>>>
>>>> CF24 4HQ
>>>>
>>>> DU
>>>>
>>>> */E-bost/*: WellsMT1@caerdydd.ac.uk <mailto:WellsMT1@caerdydd.ac.uk>
>>>>
>>>> */Ff?n/*: 02920 879628
>>>>
>>>> *From: *<freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Douglas
>>>> N. Greve" <dgreve@mgh.harvard.edu>
>>>> *Reply to: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>>>> *Date: *Thursday, 7 May 2020 at 15:59
>>>> *To: *"freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>>>> *Subject: *Re: [Freesurfer] Recon-all exited WITH errors {Disarmed}
>>>>
>>>> No all, just one. And try running it with just the -parcstats3 flag
>>>> (ie, don't use -all or -autreconX). You should have an answer in seconds
>>>>
>>>> On 5/7/2020 7:50 AM, Mason Wells wrote:
>>>>
>>>>    *????????External Email - Use Caution *
>>>>
>>>>    Hi Doug,
>>>>
>>>>    Sorry I am a bit confused. I ran recon-all as a bash for 30
>>>>    participants. None of which had the right hemisphere completed and
>>>>    recon-all log says exited with errors (as the log in the original
>>>>    email shows). Are you suggesting I go back and re-run recon-all
>>>>    via the bash and see if I get the same issue?
>>>>
>>>>    Thanks for all your help.
>>>>
>>>>    Mason
>>>>
>>>>    *Mason T Wells, MSc*
>>>>
>>>>    *PhD student*
>>>>
>>>>    School of Optometry?and Vision Sciences
>>>>
>>>>    & Cardiff University Brain Research
>>>>
>>>>    Imaging?Centre (CUBRIC), School of Psychology
>>>>
>>>>    Cardiff University
>>>>
>>>>    Cardiff
>>>>
>>>>    CF24 4HQ
>>>>
>>>>    UK
>>>>
>>>>    */Email/*: WellsMT1@cardiff.ac.uk <mailto:WellsMT1@cardiff.ac.uk>
>>>>
>>>>    */Tel/*: 02920 879628
>>>>
>>>>    */Web/*: Cardiff University webpage
>>>>    <https://www.cardiff.ac.uk/people/research-students/view/974214->
>>>>
>>>>    
>>>>
>>>>    *Mason T Wells, MSc*
>>>>
>>>>    *Myfyriwr PhD*
>>>>
>>>>    Yr Ysgol Optometreg?a Gwyddorau?r?Golwg
>>>>
>>>>    & Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd
>>>>    (CUBRIC), Yr Ysgol Seicoleg
>>>>
>>>>    Prifysgol Caerdydd
>>>>
>>>>    Heol Maindy
>>>>
>>>>    Caerdydd
>>>>
>>>>    CF24 4HQ
>>>>
>>>>    DU
>>>>
>>>>    */E-bost/*: WellsMT1@caerdydd.ac.uk <mailto:WellsMT1@caerdydd.ac.uk>
>>>>
>>>>    */Ff?n/*: 02920 879628
>>>>
>>>>    *From: *<freesurfer-bounces@nmr.mgh.harvard.edu>
>>>>    <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of
>>>>    "Douglas N. Greve" <dgreve@mgh.harvard.edu>
>>>>    <mailto:dgreve@mgh.harvard.edu>
>>>>    *Reply to: *Freesurfer support list
>>>>    <freesurfer@nmr.mgh.harvard.edu>
>>>>    <mailto:freesurfer@nmr.mgh.harvard.edu>
>>>>    *Date: *Wednesday, 6 May 2020 at 23:11
>>>>    *To: *"freesurfer@nmr.mgh.harvard.edu"
>>>>    <mailto:freesurfer@nmr.mgh.harvard.edu>
>>>>    <freesurfer@nmr.mgh.harvard.edu>
>>>>    <mailto:freesurfer@nmr.mgh.harvard.edu>
>>>>    *Subject: *Re: [Freesurfer] Recon-all exited WITH errors
>>>>
>>>>    It looks like that command finished without error. Have you tried
>>>>    running it in recon-all again to see if it fails again? You can
>>>>    just run that command with -parcstats3
>>>>
>>>>
>>>>    On 5/6/2020 6:41 AM, Mason Wells wrote:
>>>>
>>>>        *????????External Email - Use Caution *
>>>>
>>>>        Hi Doug,
>>>>
>>>>        Not sure if my email below got to you? I sent the terminal
>>>>        outputs of the command you told me to run. Any idea what?s
>>>>        going on or how to fix it?
>>>>
>>>>        Cheers,
>>>>
>>>>        Mason
>>>>
>>>>        *Mason T Wells, MSc*
>>>>
>>>>        *PhD student*
>>>>
>>>>        School of Optometry?and Vision Sciences
>>>>
>>>>        & Cardiff University Brain Research
>>>>
>>>>        Imaging?Centre (CUBRIC), School of Psychology
>>>>
>>>>        Cardiff University
>>>>
>>>>        Cardiff
>>>>
>>>>        CF24 4HQ
>>>>
>>>>        UK
>>>>
>>>>        */Email/*: WellsMT1@cardiff.ac.uk <mailto:WellsMT1@cardiff.ac.uk>
>>>>
>>>>        */Tel/*: 02920 879628
>>>>
>>>>        */Web/*: Cardiff University webpage
>>>>        <https://www.cardiff.ac.uk/people/research-students/view/974214->
>>>>
>>>>            
>>>>
>>>>        *Mason T Wells, MSc*
>>>>
>>>>        *Myfyriwr PhD*
>>>>
>>>>        Yr Ysgol Optometreg?a Gwyddorau?r?Golwg
>>>>
>>>>        & Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd
>>>>        (CUBRIC), Yr Ysgol Seicoleg
>>>>
>>>>        Prifysgol Caerdydd
>>>>
>>>>        Heol Maindy
>>>>
>>>>        Caerdydd
>>>>
>>>>        CF24 4HQ
>>>>
>>>>        DU
>>>>
>>>>        */E-bost/*: WellsMT1@caerdydd.ac.uk
>>>>        <mailto:WellsMT1@caerdydd.ac.uk>
>>>>
>>>>        */Ff?n/*: 02920 879628
>>>>
>>>>        *From: *<freesurfer-bounces@nmr.mgh.harvard.edu>
>>>>        <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of
>>>>        Mason Wells <WellsMT1@cardiff.ac.uk>
>>>>        <mailto:WellsMT1@cardiff.ac.uk>
>>>>        *Reply to: *Freesurfer support list
>>>>        <freesurfer@nmr.mgh.harvard.edu>
>>>>        <mailto:freesurfer@nmr.mgh.harvard.edu>
>>>>        *Date: *Monday, 4 May 2020 at 20:01
>>>>        *To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>>>>        <mailto:freesurfer@nmr.mgh.harvard.edu>
>>>>        *Subject: *Re: [Freesurfer] Recon-all exited WITH errors
>>>>        {Disarmed}
>>>>
>>>>        *????????External Email - Use Caution *
>>>>
>>>>        Ah yes. I just set the SUBJECTS_DIR correctly, Terminal out below:
>>>>
>>>>        mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f
>>>>        ../stats/lh.aparc.DKTatlas40.stats -b -a
>>>>        ../label/lh.aparc.DKTatlas40.annot -c
>>>>        ../label/aparc.annot.DKTatlas40.ctab PPT_001 lh white
>>>>
>>>>        INFO: assuming MGZ format for volumes.
>>>>
>>>>        INFO: using ../label/lh.cortex.label as mask to calc cortex
>>>>        NumVert, SurfArea and MeanThickness.
>>>>
>>>>        computing statistics for each annotation in
>>>>        ../label/lh.aparc.DKTatlas40.annot.
>>>>
>>>>        reading volume
>>>>        /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/mri/wm.mgz...
>>>>
>>>>        reading input surface
>>>>        /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/surf/lh.white...
>>>>
>>>>        reading input pial surface
>>>>        /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/surf/lh.pial...
>>>>
>>>>        reading input white surface
>>>>        /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/surf/lh.white...
>>>>
>>>>        reading colortable from annotation file...
>>>>
>>>>        colortable with 36 entries read (originally
>>>>        /Applications/freesurfer/average/colortable_desikan_killiany.txt)
>>>>
>>>>        Saving annotation colortable ../label/aparc.annot.DKTatlas40.ctab
>>>>
>>>>        table columns are:
>>>>
>>>>        number of vertices
>>>>
>>>>        total surface area (mm^2)
>>>>
>>>>        total gray matter volume (mm^3)
>>>>
>>>>        average cortical thickness +- standard deviation (mm)
>>>>
>>>>        integrated rectified mean curvature
>>>>
>>>>        integrated rectified Gaussian curvature
>>>>
>>>>        folding index
>>>>
>>>>        intrinsic curvature index
>>>>
>>>>        structure name
>>>>
>>>>        1698 1132?? 3274? 2.730 0.526???? 0.130???? 0.032 26???? 2.4?
>>>>        caudalanteriorcingulate
>>>>
>>>>        4375 2908?? 8369? 2.594 0.599???? 0.127???? 0.040 46???? 7.0?
>>>>        caudalmiddlefrontal
>>>>
>>>>        3883 2464?? 5378? 2.087 0.498???? 0.149???? 0.082 74???? 9.4
>>>>        ?cuneus
>>>>
>>>>        546??? 373?? 1423? 2.817 0.999???? 0.154???? 0.087 11???? 1.9?
>>>>        entorhinal
>>>>
>>>>        5411 3506? 10979? 2.768 0.567???? 0.137???? 0.059????? 101
>>>>        14.8? fusiform
>>>>
>>>>        6159 4159? 11629? 2.543 0.520???? 0.133???? 0.045?????? 86
>>>>        11.0? inferiorparietal
>>>>
>>>>        5973 3945? 13736? 2.965 0.705???? 0.138???? 0.060????? 130
>>>>        13.4? inferiortemporal
>>>>
>>>>        1536 934?? 2788? 2.725 0.838???? 0.164???? 0.090?????? 50 5.1?
>>>>        isthmuscingulate
>>>>
>>>>        6953 4476? 11030? 2.320 0.542???? 0.147???? 0.055????? 110
>>>>        15.3? lateraloccipital
>>>>
>>>>        3897 2512?? 7780? 2.641 0.630???? 0.147???? 0.077?????? 99
>>>>        13.1? lateralorbitofrontal
>>>>
>>>>        5273 3237?? 7567? 2.161 0.603???? 0.151???? 0.956????? 191
>>>>        20.8? lingual
>>>>
>>>>        2015 1290?? 4210? 2.576 0.773???? 0.157???? 0.084 64???? 6.5?
>>>>        medialorbitofrontal
>>>>
>>>>        6073 4091? 14456? 3.026 0.553???? 0.130???? 0.043?????? 80
>>>>        11.0? middletemporal
>>>>
>>>>        1012 711?? 2254? 2.886 0.735???? 0.133???? 0.112?????? 16 6.3?
>>>>        parahippocampal
>>>>
>>>>        2182 1401?? 4296? 2.690 0.669???? 0.128???? 0.044 26???? 4.5?
>>>>        paracentral
>>>>
>>>>        3247 2175?? 6722? 2.682 0.501???? 0.121???? 0.038 34???? 5.1?
>>>>        parsopercularis
>>>>
>>>>        1195 793?? 2520? 2.549 0.514???? 0.138???? 0.045?????? 21 2.1?
>>>>        parsorbitalis
>>>>
>>>>        2780 1882?? 5377? 2.457 0.608???? 0.131???? 0.043 37???? 5.0?
>>>>        parstriangularis
>>>>
>>>>        2229 1444?? 2359? 1.685 0.476???? 0.155???? 0.067 41???? 6.1?
>>>>        pericalcarine
>>>>
>>>>        7692 4818? 11728? 2.218 0.657???? 0.130???? 0.053????? 114
>>>>        16.0? postcentral
>>>>
>>>>        1983 1360?? 4109? 2.902 0.617???? 0.167???? 0.079 44???? 6.1?
>>>>        posteriorcingulate
>>>>
>>>>        7681 4765? 13220? 2.521 0.549???? 0.123???? 0.056????? 119
>>>>        15.1? precentral
>>>>
>>>>        6240 4189? 11573? 2.532 0.576???? 0.145???? 0.052????? 104
>>>>        13.3? precuneus
>>>>
>>>>        1613 992?? 3166? 2.820 0.661???? 0.136???? 0.055?????? 54 3.6?
>>>>        rostralanteriorcingulate
>>>>
>>>>        6644 4495? 12118? 2.347 0.579???? 0.144???? 0.052????? 117
>>>>        13.9? rostralmiddlefrontal
>>>>
>>>>        12967 8768? 28469? 2.839 0.612???? 0.132???? 0.047????? 170
>>>>        25.1? superiorfrontal
>>>>
>>>>        7963 5213? 12201? 2.095 0.481???? 0.125???? 0.053????? 125
>>>>        16.2? superiorparietal
>>>>
>>>>        9021 6069? 20753? 3.059 0.612???? 0.130???? 0.050????? 183
>>>>        19.9? superiortemporal
>>>>
>>>>        7970 5269? 15543? 2.684 0.502???? 0.149???? 0.074????? 910
>>>>        17.4? supramarginal
>>>>
>>>>        702??? 454?? 1432? 2.844 0.618???? 0.133 0.046??????? 8????
>>>>        1.3? transversetemporal
>>>>
>>>>        2953 1947?? 6539? 3.228 0.801???? 0.124???? 0.056 33???? 6.4?
>>>>        insula
>>>>
>>>>        *Mason T Wells, MSc*
>>>>
>>>>        *PhD student*
>>>>
>>>>        School of Optometry?and Vision Sciences
>>>>
>>>>        & Cardiff University Brain Research
>>>>
>>>>        Imaging?Centre (CUBRIC), School of Psychology
>>>>
>>>>        Cardiff University
>>>>
>>>>        Cardiff
>>>>
>>>>        CF24 4HQ
>>>>
>>>>        UK
>>>>
>>>>        */Email/*: WellsMT1@cardiff.ac.uk <mailto:WellsMT1@cardiff.ac.uk>
>>>>
>>>>        */Tel/*: 02920 879628
>>>>
>>>>        */Web/*: Cardiff University webpage
>>>>        <https://www.cardiff.ac.uk/people/research-students/view/974214->
>>>>
>>>>            
>>>>
>>>>        *Mason T Wells, MSc*
>>>>
>>>>        *Myfyriwr PhD*
>>>>
>>>>        Yr Ysgol Optometreg?a Gwyddorau?r?Golwg
>>>>
>>>>        & Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd
>>>>        (CUBRIC), Yr Ysgol Seicoleg
>>>>
>>>>        Prifysgol Caerdydd
>>>>
>>>>        Heol Maindy
>>>>
>>>>        Caerdydd
>>>>
>>>>        CF24 4HQ
>>>>
>>>>        DU
>>>>
>>>>        */E-bost/*: WellsMT1@caerdydd.ac.uk
>>>>        <mailto:WellsMT1@caerdydd.ac.uk>
>>>>
>>>>        */Ff?n/*: 02920 879628
>>>>
>>>>        *From: *<freesurfer-bounces@nmr.mgh.harvard.edu>
>>>>        <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of
>>>>        "Douglas N. Greve" <dgreve@mgh.harvard.edu>
>>>>        <mailto:dgreve@mgh.harvard.edu>
>>>>        *Reply to: *Freesurfer support list
>>>>        <freesurfer@nmr.mgh.harvard.edu>
>>>>        <mailto:freesurfer@nmr.mgh.harvard.edu>
>>>>        *Date: *Monday, 4 May 2020 at 19:56
>>>>        *To: *"freesurfer@nmr.mgh.harvard.edu"
>>>>        <mailto:freesurfer@nmr.mgh.harvard.edu>
>>>>        <freesurfer@nmr.mgh.harvard.edu>
>>>>        <mailto:freesurfer@nmr.mgh.harvard.edu>
>>>>        *Subject: *Re: [Freesurfer] Recon-all exited WITH errors
>>>>        {Disarmed}
>>>>
>>>>        Something else has gone wrong. wm.mgz should have been there
>>>>        in order to get as far as it did. Is your SUBJECTS_DIR set
>>>>        properly?
>>>>
>>>>        On 5/4/2020 2:49 PM, Mason Wells wrote:
>>>>
>>>>            *????????External Email - Use Caution *
>>>>
>>>>            Hi,
>>>>
>>>>            Terminal output is below:
>>>>
>>>>            /Documents/Analysis/Data/freesurfer/subjects/PPT_001/scripts$
>>>>            mris_anatomical_stats -mgz -cortex
>>>>            ../label/lh.cortex.label -f
>>>>            ../stats/lh.aparc.DKTatlas40.stats -b -a
>>>>            ../label/lh.aparc.DKTatlas40.annot -c
>>>>            ../label/aparc.annot.DKTatlas40.ctab PPT_001 lh white
>>>>
>>>>            INFO: assuming MGZ format for volumes.
>>>>
>>>>            INFO: using ../label/lh.cortex.label as mask to calc
>>>>            cortex NumVert, SurfArea and MeanThickness.
>>>>
>>>>            computing statistics for each annotation in
>>>>            ../label/lh.aparc.DKTatlas40.annot.
>>>>
>>>>            reading volume
>>>>            /cubric/data/c1749990/freesurfer/subjects/PPT_001/mri/wm.mgz...
>>>>
>>>>            mghRead(/cubric/data/c1749990/freesurfer/subjects/PPT_001/mri/wm.mgz,
>>>>            -1): could not open file
>>>>
>>>>            mris_anatomical_stats: could not read input volume
>>>>            /cubric/data/c1749990/freesurfer/subjects/PPT_001/mri/wm.mgz
>>>>
>>>>            Cheers,
>>>>
>>>>            Mason
>>>>
>>>>            *Mason T Wells, MSc*
>>>>
>>>>            *PhD student*
>>>>
>>>>            School of Optometry?and Vision Sciences
>>>>
>>>>            & Cardiff University Brain Research
>>>>
>>>>            Imaging?Centre (CUBRIC), School of Psychology
>>>>
>>>>            Cardiff University
>>>>
>>>>            Cardiff
>>>>
>>>>            CF24 4HQ
>>>>
>>>>            UK
>>>>
>>>>            */Email/*: WellsMT1@cardiff.ac.uk
>>>>            <mailto:WellsMT1@cardiff.ac.uk>
>>>>
>>>>            */Tel/*: 02920 879628
>>>>
>>>>            */Web/*: Cardiff University webpage
>>>>            <https://www.cardiff.ac.uk/people/research-students/view/974214->
>>>>
>>>>            
>>>>
>>>>            *Mason T Wells, MSc*
>>>>
>>>>            *Myfyriwr PhD*
>>>>
>>>>            Yr Ysgol Optometreg?a Gwyddorau?r?Golwg
>>>>
>>>>            & Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd
>>>>            (CUBRIC), Yr Ysgol Seicoleg
>>>>
>>>>            Prifysgol Caerdydd
>>>>
>>>>            Heol Maindy
>>>>
>>>>            Caerdydd
>>>>
>>>>            CF24 4HQ
>>>>
>>>>            DU
>>>>
>>>>            */E-bost/*: WellsMT1@caerdydd.ac.uk
>>>>            <mailto:WellsMT1@caerdydd.ac.uk>
>>>>
>>>>            */Ff?n/*: 02920 879628
>>>>
>>>>            *From: *<freesurfer-bounces@nmr.mgh.harvard.edu>
>>>>            <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf
>>>>            of "Douglas N. Greve" <dgreve@mgh.harvard.edu>
>>>>            <mailto:dgreve@mgh.harvard.edu>
>>>>            *Reply to: *Freesurfer support list
>>>>            <freesurfer@nmr.mgh.harvard.edu>
>>>>            <mailto:freesurfer@nmr.mgh.harvard.edu>
>>>>            *Date: *Monday, 4 May 2020 at 18:54
>>>>            *To: *"freesurfer@nmr.mgh.harvard.edu"
>>>>            <mailto:freesurfer@nmr.mgh.harvard.edu>
>>>>            <freesurfer@nmr.mgh.harvard.edu>
>>>>            <mailto:freesurfer@nmr.mgh.harvard.edu>
>>>>            *Subject: *Re: [Freesurfer] Recon-all exited WITH errors
>>>>
>>>>            Unfortunately, the log file does not indicate what went
>>>>            wrong. But it does show that the error happened on the LH
>>>>            (so it is not just RH). Run the command below and send all
>>>>            terminal output
>>>>
>>>>            cd
>>>>            /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/scripts
>>>>            ?mris_anatomical_stats -mgz -cortex
>>>>            ../label/lh.cortex.label -f
>>>>            ../stats/lh.aparc.DKTatlas40.stats -b -a
>>>>            ../label/lh.aparc.DKTatlas40.annot -c
>>>>            ../label/aparc.annot.DKTatlas40.ctab PPT_001 lh white
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>            On 5/4/2020 1:34 PM, Mason Wells wrote:
>>>>
>>>>                *????????External Email - Use Caution *
>>>>
>>>>                Hi Experts,
>>>>
>>>>                I appear to be having some issues with recon-all. I
>>>>                ran the command from a bash script (see attached), and
>>>>                it appears to work fine for the left hemisphere as the
>>>>                correct files are in the surf folder. However, there
>>>>                are no right hemisphere surf files. I have attached
>>>>                the log and error log for PPT01 and PPT02. Any advice
>>>>                on as to why this has happened would be great.
>>>>
>>>>                Thanks in advance,
>>>>
>>>>                Mason
>>>>
>>>>                *Mason T Wells, MSc*
>>>>
>>>>                *PhD student*
>>>>
>>>>                School of Optometry?and Vision Sciences
>>>>
>>>>                & Cardiff University Brain Research
>>>>
>>>>                Imaging?Centre (CUBRIC), School of Psychology
>>>>
>>>>                Cardiff University
>>>>
>>>>                Cardiff
>>>>
>>>>                CF24 4HQ
>>>>
>>>>                UK
>>>>
>>>>                */Email/*: WellsMT1@cardiff.ac.uk
>>>>                <mailto:WellsMT1@cardiff.ac.uk>
>>>>
>>>>                */Tel/*: 02920 879628
>>>>
>>>>                */Web/*: Cardiff University webpage
>>>>                <https://www.cardiff.ac.uk/people/research-students/view/974214->
>>>>
>>>>                    
>>>>
>>>>                *Mason T Wells, MSc*
>>>>
>>>>                *Myfyriwr PhD*
>>>>
>>>>                Yr Ysgol Optometreg?a Gwyddorau?r?Golwg
>>>>
>>>>                & Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol
>>>>                Caerdydd (CUBRIC), Yr Ysgol Seicoleg
>>>>
>>>>                Prifysgol Caerdydd
>>>>
>>>>                Heol Maindy
>>>>
>>>>                Caerdydd
>>>>
>>>>                CF24 4HQ
>>>>
>>>>                DU
>>>>
>>>>                */E-bost/*: WellsMT1@caerdydd.ac.uk
>>>>                <mailto:WellsMT1@caerdydd.ac.uk>
>>>>
>>>>                */Ff?n/*: 02920 879628
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>                _______________________________________________
>>>>
>>>>                Freesurfer mailing list
>>>>
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>>>>
>>>>                *MailScanner has detected a possible fraud attempt
>>>>                from "eur03.safelinks.protection.outlook.com" claiming
>>>>                to be*
>>>>                https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer  <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=02%7C01%7CWellsMT1%40cardiff.ac.uk%7Cdf9eb81b587e4f34ab0908d7f2972ca0%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C637244603426581476&sdata=9FzX4UxRBUrO5onyn1ZwE7pjqrUEv5WMHV1MB1u1%2FG8%3D&reserved=0>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>            _______________________________________________
>>>>
>>>>            Freesurfer mailing list
>>>>
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>>>>
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>>>>            https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer  <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=02%7C01%7CWellsMT1%40cardiff.ac.uk%7Cdf9eb81b587e4f34ab0908d7f2972ca0%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C637244603426581476&sdata=9FzX4UxRBUrO5onyn1ZwE7pjqrUEv5WMHV1MB1u1%2FG8%3D&reserved=0>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>        _______________________________________________
>>>>
>>>>        Freesurfer mailing list
>>>>
>>>>        Freesurfer@nmr.mgh.harvard.edu  <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>
>>>>        *MailScanner has detected a possible fraud attempt from
>>>>        "eur03.safelinks.protection.outlook.com" claiming to be*
>>>>        https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer  <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=02%7C01%7CWellsMT1%40cardiff.ac.uk%7Cdf9eb81b587e4f34ab0908d7f2972ca0%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C637244603426591477&sdata=KRIOcP2dXJl7bJbUCXXRpgTBoji0jSteH5S5oT7YZcc%3D&reserved=0>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>    _______________________________________________
>>>>
>>>>    Freesurfer mailing list
>>>>
>>>>    Freesurfer@nmr.mgh.harvard.edu  <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>
>>>>    *MailScanner has detected a possible fraud attempt from
>>>>    "eur03.safelinks.protection.outlook.com" claiming to be*
>>>>    https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer  <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=02%7C01%7CWellsMT1%40cardiff.ac.uk%7Cdf9eb81b587e4f34ab0908d7f2972ca0%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C637244603426601472&sdata=fXDymBlzoXir0xwsk4dREaQs1r7YWliUKBnK2sV%2B49c%3D&reserved=0>
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Freesurfer mailing list
>>>> Freesurfer@nmr.mgh.harvard.edu
>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> -------------- next part --------------
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>>>
>>> ------------------------------
>>>
>>> Message: 6
>>> Date: Thu, 7 May 2020 15:50:26 +0000
>>> From: "Hoopes, Andrew" <AHOOPES@mgh.harvard.edu>
>>> Subject: Re: [Freesurfer] flirt.fsl error (NEWMAT::SingularException)
>>>      when running bbregister in Freesurfer 7.0.0
>>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>>> Message-ID: <EBCA186E-5FD0-47BA-95C3-3D80252ACC59@mgh.harvard.edu>
>>> Content-Type: text/plain; charset="utf-8"
>>>
>>> Hi Julien,
>>>
>>> Just to test something out, can you try running this again after replacing the flirt.fsl binary in your new 7.0 install with the flirt.fsl binary from 6.0? i.e.
>>>
>>> cp /path/to/freesurfer/6.0.0/bin/flirst.fsl /path/to/freesurfer/7.0.0/bin/flirst.fsl
>>>
>>> Let me know how that works.
>>>
>>> Best
>>> Andrew
>>>
>>>
>>> ?On 5/7/20, 8:04 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of julienbesle" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of julienbesle@gmail.com> wrote:
>>>
>>>            External Email - Use Caution
>>>
>>>    Hi,
>>>
>>>    I just installed freesurfer v7 and I'm getting an error in a script that
>>>    calls bbregister with the --fslmat and --init-fsl options. This error
>>>    does not occur in freesurfer v6 even when using exactly the same data,
>>>    but it does also occur with a development version of freesurfer I
>>>    downloaded in Sept 2019 (exact same error).
>>>
>>>    The call is:
>>>
>>>    DEBUG    : 2020-05-06 12:07:12,816 : runCmd     : Running: bbregister
>>>    --s HLOSS_p5 --mov
>>>    /home/julien/data/HLOSS/pilot05_B/DWI/B0_corrected_mean_resampled_MPRAGE.nii
>>>    --reg
>>>    /home/julien/data/HLOSS/pilot05_B/DWI/easy_lausanne_test/b0-TO-orig.dat
>>>    --fslmat
>>>    /home/julien/data/HLOSS/pilot05_B/DWI/easy_lausanne_test/b0-TO-orig.mat
>>>    --init-fsl --dti
>>>
>>>    The error occurs when bbregister calls fsl.flirt:
>>>
>>>    INFO     : 2020-05-06 12:08:24,560 : main       : flirt.fsl -ref
>>>    /home/julien/data/HLOSS/pilot05_B/DWI/easy_lausanne_test/tmp.bbregister.8331/fslregister/refvol.fslregister.nii
>>>    -in
>>>    /home/julien/data/HLOSS/pilot05_B/DWI/easy_lausanne_test/tmp.bbregister.8331/fslregister/movvol.fslregister.nii
>>>    -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90
>>>    -searchrz -90 90 -verbose 0 -omat
>>>    /home/julien/data/HLOSS/pilot05_B/DWI/easy_lausanne_test/tmp.bbregister.8331/fslregister/fslmat0.trans.mat
>>>    -schedule /usr/local/freesurfer/bin/fsl.5.0.2.xyztrans.sch -init
>>>    /home/julien/data/HLOSS/pilot05_B/DWI/easy_lausanne_test/tmp.bbregister.8331/reg.init.dat.fsl.mat0
>>>    INFO     : 2020-05-06 12:08:55,102 : main       : Wed May  6 12:08:54
>>>    EEST 2020
>>>    INFO     : 2020-05-06 12:08:55,603 : main       : /mnt/f/data/HLOSS
>>>    INFO     : 2020-05-06 12:08:56,105 : main       : flirt.fsl -ref
>>>    /home/julien/data/HLOSS/pilot05_B/DWI/easy_lausanne_test/tmp.bbregister.8331/fslregister/refvol.fslregister.nii
>>>    -in
>>>    /home/julien/data/HLOSS/pilot05_B/DWI/easy_lausanne_test/tmp.bbregister.8331/fslregister/movvol.fslregister.nii
>>>    -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90
>>>    -searchrz -90 90 -verbose 0 -omat
>>>    /home/julien/data/HLOSS/pilot05_B/DWI/easy_lausanne_test/tmp.bbregister.8331/reg.init.dat.fsl.mat
>>>    -init
>>>    /home/julien/data/HLOSS/pilot05_B/DWI/easy_lausanne_test/tmp.bbregister.8331/fslregister/fslmat0.trans.mat
>>>    -schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch
>>>    INFO     : 2020-05-06 12:09:15,632 : main       : terminate called after
>>>    throwing an instance of 'NEWMAT::SingularException'
>>>    INFO     : 2020-05-06 12:09:15,633 : main       : Abort (core dumped)
>>>    INFO     : 2020-05-06 12:09:15,634 : main       : ERROR: flirt
>>>    CRITICAL : 2020-05-06 12:09:15,634 : runCmd     : Return Value: 1
>>>
>>>    It looks like the first time flirt.fsl is called everything goes fine,
>>>    but the second time, the error occurs. Unfortunately this is not a
>>>    script I wrote myself, so I'm not sure what this particular call to
>>>    bbregister is supposed to achieve. I'm not sure the call to fsl.flirt
>>>    depends on which version of FSL I have installed, but just in case, I
>>>    used the FSL v6 and didn't change anything to the FSL installation
>>>    between trying Freesurfer v6, dev or v7. I run everything on Ubuntu
>>>    16.04 running on WSL on Windows 10.
>>>
>>>    Any idea what could be going wrong?
>>>
>>>    Thanks
>>>
>>>    Julien
>>>
>>>    --
>>>    -------------------------------------
>>>    Julien Besle
>>>    Lagos Center, Apt 9A
>>>    Sadat Street
>>>    Beirut
>>>    Lebanon
>>>
>>>    tel: +961 78 980 317
>>>    -------------------------------------
>>>
>>>
>>>    _______________________________________________
>>>    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
>>>
>>> End of Freesurfer Digest, Vol 195, Issue 24
>>> *******************************************
>>
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> ------------------------------
>
> Message: 6
> Date: Thu, 7 May 2020 14:00:41 -0400
> From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
> Subject: Re: [Freesurfer] HCPMMP1 parcellation to aseg (.mgz)
> To: <freesurfer@nmr.mgh.harvard.edu>
> Message-ID: <d2badc92-5756-087c-b2af-afbf7cb24562@mgh.harvard.edu>
> Content-Type: text/plain; charset="utf-8"
>
> It looks like mris_convert will do, but I've never tried it.
>
> On 5/7/2020 1:23 PM, Glasser, Matthew wrote:
>>
>> ????????External Email - Use Caution
>>
>> Hi? Doug,
>>
>> Is there a way to convert from GIFTI label to annot?
>>
>> Matt.
>>
>> *From: *<freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Douglas
>> N. Greve" <dgreve@mgh.harvard.edu>
>> *Reply-To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>> *Date: *Thursday, May 7, 2020 at 12:21 PM
>> *To: *"freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>> *Subject: *Re: [Freesurfer] HCPMMP1 parcellation to aseg (.mgz)
>>
>> ** External Email - Caution **
>>
>> If you have the annot files in your individual subject's space, then
>> you can create a volume in the same way that aparc+aseg.mgz is
>> created. In v6 and before, run mri_aparc2aseg. In v7, run
>> mri_surf2volseg. Look in recon-all.log to see how it was run to
>> craeate aparc+aseg.mgz and change the command line to indicate a
>> different annot and a different output
>>
>> On 5/7/2020 12:17 PM, pooja prabhu wrote:
>>
>>    *????????External Email - Use Caution *
>>
>>> HCPMMP1 parcellation is multi modal parcellation
>>
>>> We need the file something like we have for 'aparc' parcellation.
>>
>>> The file format should be in .mgz (aparc.HCPMMP1+aseg.mgz)
>>
>>> How can i do it? (i have lh.HCPMMP1.annot and rh.HCPMMP1.annot)
>>
>>
>>    Date: Thu, May 7, 2020 at 2:16 PM
>>    Subject: HCPMMP1 parcellation to aseg (.mgz)
>>    To: <freesurfer@nmr.mgh.harvard.edu
>>    <mailto:freesurfer@nmr.mgh.harvard.edu>>
>>
>>    Hai list,
>>
>>>> Can I get some insight on how to convert HCPMMP1 to aseg(provided
>>    we have annotation files) for fsaverage brain?
>>
>>>> For example: for aparc parcellation we use aparc2aseg and get
>>    aparc+aseg.mgz.
>>
>>>> Similarly I need for HCPMMP1.
>>
>>>> Can someone help me with this?
>>
>>>> Thank you
>>
>>    From: "Glasser, Matthew" <glasserm@wustl.edu
>>    <mailto:glasserm@wustl.edu>>
>>
>>    Subject: Re: [Freesurfer] HCPMMP1 parcellation to aseg (.mgz)
>>    To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu
>>    <mailto:freesurfer@nmr.mgh.harvard.edu>>
>>    Cc: Timothy Coalson <tsc5yc@mst.edu <mailto:tsc5yc@mst.edu>>
>>    Message-ID: <29142489-F691-4E6E-A069-F7377D9C7A63@wustl.edu
>>    <mailto:29142489-F691-4E6E-A069-F7377D9C7A63@wustl.edu>>
>>    Content-Type: text/plain; charset="utf-8"
>>
>>    ? ? ? ? External Email - Use Caution
>>
>>    That is our multi-modal parcellation.? Tim has some instructions
>>    to get data from the fs_LR mesh to fsaverage in GIFTI format.?
>>    Doug perhaps you can say how to convert from GIFTI to annot?
>>
>>    Matt.
>>
>>
>>    --
>>
>>    Thank You
>>
>>    Pooja Prabhu
>>
>>
>>
>>    _______________________________________________
>>
>>    Freesurfer mailing list
>>
>>    Freesurfer@nmr.mgh.harvard.edu  <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>
>>    https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> ------------------------------------------------------------------------
>>
>> 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
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>> 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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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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> ------------------------------
>
> Message: 7
> Date: Thu, 7 May 2020 14:02:57 -0400
> From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
> Subject: Re: [Freesurfer] Get Atlas surfaces in subject space
> To: <freesurfer@nmr.mgh.harvard.edu>
> Message-ID: <12a03584-c208-0804-32fe-aed33a9f98f8@mgh.harvard.edu>
> Content-Type: text/plain; charset="utf-8"
>
> It comes down to how you want to define "roughly in the same place".
> Does this mean an affine (12dof) transform? And what information do you
> want? An XYZ coordinate?
>
> On 5/7/2020 11:06 AM, Ian Hardingham wrote:
>>
>> ????????External Email - Use Caution
>>
>> I'd like to get a set of points to compare across several brains, so
>> that the nth point in brain A is in roughly the same place as the nth
>> point in brain B - so I'd like to have an agreed upon set of vertices
>> (the source brain's vertices) translated to positions on the target
>> brain (which may well not be vertices in the target geometry.)
>>
>> On 07/05/2020 15:59, Douglas N. Greve wrote:
>>> I don't understand. What is the difference between the target brain
>>> and the target subject's vertices?
>>>
>>> On 5/7/2020 2:17 AM, Ian Hardingham wrote:
>>>>
>>>> ????????External Email - Use Caution
>>>>
>>>> Ok, thanks Doug, but I'm looking to get the positions of the source
>>>> vertexes on the target brain, not the target subject's vertices...
>>>>
>>>> On 06/05/2020 23:07, Douglas N. Greve wrote:
>>>>> That looks like it could be right. It has 102,020 vertices, which
>>>>> should be the number of vertices in the target subject (and is in
>>>>> the typical range for an individual subject)
>>>>>
>>>>> On 5/6/2020 10:21 AM, Ian Hardingham wrote:
>>>>>>
>>>>>> ????????External Email - Use Caution
>>>>>>
>>>>>> FSLInfo attached, thanks Bruce.
>>>>>>
>>>>>> When trying to run freeview I get "freeview.bin: error while
>>>>>> loading shared libraries: libpng12.so.0: cannot open shared object
>>>>>> file: No such file or directory" - do I need to add
>>>>>> /usr/local/freesurfer/lib/* to path or something along those lines?
>>>>>>
>>>>>> SURFACE INFO ========================================
>>>>>> type??????? : MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE
>>>>>> num vertices: 102020
>>>>>> num faces?? : 204036
>>>>>> num strips? : 0
>>>>>> surface area: 65520.5
>>>>>> AvgVtxArea?????? 0.642232
>>>>>> AvgVtxDist?????? 0.940503
>>>>>> StdVtxDist?????? 0.417776
>>>>>> ctr???????? : (-31.9056, -18.8197, 16.3545)
>>>>>> vertex locs : surfaceRAS
>>>>>> Volume Geometry (vg)
>>>>>> volume geometry:
>>>>>> extent? : (176, 224, 256)
>>>>>> voxel?? : ( 1.0000,? 1.0000,? 1.0000)
>>>>>> x_(ras) : (-0.9990, -0.0436,? 0.0000)
>>>>>> y_(ras) : (-0.0436,? 0.9990,? 0.0000)
>>>>>> z_(ras) : ( 0.0000,? 0.0000,? 1.0000)
>>>>>> c_(ras) : (-0.5431,? 8.9290, -17.0723)
>>>>>> file??? : /media/ian/bronson/subject/T1_nifti.nii.gz
>>>>>> Volume Geometry vox2ras
>>>>>> -0.99905? -0.04362?? 0.00000?? 92.25847;
>>>>>> -0.04362?? 0.99905?? 0.00000? -99.12585;
>>>>>> ?0.00000?? 0.00000?? 1.00000? -145.07230;
>>>>>> ?0.00000?? 0.00000?? 0.00000?? 1.00000;
>>>>>> Volume Geometry vox2ras-tkr
>>>>>> -1.00000?? 0.00000?? 0.00000?? 88.00000;
>>>>>> ?0.00000?? 0.00000?? 1.00000? -128.00000;
>>>>>> ?0.00000? -1.00000?? 0.00000?? 112.00000;
>>>>>> ?0.00000?? 0.00000?? 0.00000?? 1.00000;
>>>>>> cmd[0]: mris_remove_intersection ../surf/lh.orig ../surf/lh.orig
>>>>>> ProgramVersion: $Name: stable5 $ TimeStamp:
>>>>>> 2016/05/26-23:14:53-GMT? BuildTimeStamp: May 13 2013 18:53:32?
>>>>>> CVS: $Id: mris_remove_intersection.c,v 1.6 2011/03/02 00:04:32
>>>>>> nicks Exp $? User: fsuser Machine: xubuntu-VirtualBox? Platform:
>>>>>> Linux PlatformVersion: 3.2.0-23-generic? CompilerName: GCC
>>>>>> CompilerVersion: 30400
>>>>>> cmd[1]: mris_make_surfaces -noaparc -whiteonly -mgz -T1
>>>>>> brain.finalsurfs T1_MDEFT_BONANN lh ProgramVersion: $Name: stable5
>>>>>> $? TimeStamp: 2016/05/26-23:14:56-GMT BuildTimeStamp: May 13 2013
>>>>>> 18:53:32? CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12
>>>>>> 22:28:01 nicks Exp $? User: fsuser? Machine: xubuntu-VirtualBox
>>>>>> Platform: Linux? PlatformVersion: 3.2.0-23-generic CompilerName:
>>>>>> GCC? CompilerVersion: 30400
>>>>>> cmd[2]: mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white
>>>>>> ../surf/lh.smoothwm ProgramVersion: $Name: stable5 $ TimeStamp:
>>>>>> 2016/05/26-23:18:33-GMT? BuildTimeStamp: May 13 2013 18:53:32?
>>>>>> CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $?
>>>>>> User: fsuser? Machine: xubuntu-VirtualBox? Platform: Linux?
>>>>>> PlatformVersion: 3.2.0-23-generic? CompilerName: GCC?
>>>>>> CompilerVersion: 30400
>>>>>> cmd[3]: mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated
>>>>>> ProgramVersion: $Name: stable5 $ TimeStamp:
>>>>>> 2016/05/26-23:18:36-GMT? BuildTimeStamp: May 13 2013 18:53:32?
>>>>>> CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $?
>>>>>> User: fsuser? Machine: xubuntu-VirtualBox? Platform: Linux?
>>>>>> PlatformVersion: 3.2.0-23-generic? CompilerName: GCC?
>>>>>> CompilerVersion: 30400
>>>>>> cmd[4]: mris_sphere -seed 1234 ../surf/lh.inflated
>>>>>> ../surf/lh.sphere ProgramVersion: $Name: stable5 $ TimeStamp:
>>>>>> 2016/05/26-23:20:12-GMT? BuildTimeStamp: May 13 2013 18:53:32?
>>>>>> CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $?
>>>>>> User: fsuser? Machine: xubuntu-VirtualBox? Platform: Linux?
>>>>>> PlatformVersion: 3.2.0-23-generic? CompilerName: GCC?
>>>>>> CompilerVersion: 30400
>>>>>> cmd[5]: mris_register -curv ../surf/lh.sphere
>>>>>> /usr/local/freesurfer/average/lh.average.curvature.filled.buckner40.tif
>>>>>> ../surf/lh.sphere.reg ProgramVersion: $Name: stable5 $ TimeStamp:
>>>>>> 2016/05/27-00:03:14-GMT? BuildTimeStamp: May 13 2013 18:53:32?
>>>>>> CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $?
>>>>>> User: fsuser? Machine: xubuntu-VirtualBox? Platform: Linux?
>>>>>> PlatformVersion: 3.2.0-23-generic? CompilerName: GCC?
>>>>>> CompilerVersion: 30400
>>>>>> mris_info
>>>>>> creationtime 2020/05/06-14:18:48-GMT
>>>>>> sysname? Linux
>>>>>> hostname ryzen-cumnor
>>>>>> machine? x86_64
>>>>>> surfacefile /home/ian/cdm_registered_test/registered_lh.white
>>>>>> hemicode??? 1
>>>>>> talairach_flag? 0
>>>>>> rescale???? 0.000000
>>>>>> nvertices?? 102020
>>>>>> nfaces????? 204036
>>>>>> total_area? 65520.492188
>>>>>> group_avg_vtxarea_loaded 0
>>>>>> avgvtxarea? 0.642232
>>>>>> avgvtxdist? 0.940503
>>>>>> stdvtxdist? 0.417776
>>>>>> vtx0xyz?? -8.576451 -101.319672 3.333434
>>>>>>
>>>>>> On 06/05/2020 15:00, Bruce Fischl wrote:
>>>>>>> can you run mris_info on the output surfcae? And maybe send a
>>>>>>> freeview snapshot of it (in 3d rendering mode)
>>>>>>>
>>>>>>> On Wed, 6 May 2020, Ian wrote:
>>>>>>>
>>>>>>>> ?????? External Email - Use Caution
>>>>>>>> Thanks Tim and Doug.
>>>>>>>>
>>>>>>>> I have the files generating and loading properly now, but I'm
>>>>>>>> not convinced it's giving the output I'm looking for.
>>>>>>>>
>>>>>>>> I am trying to convert the "fsaverage" subject's surface
>>>>>>>> coordinates to my own subject's surface space.
>>>>>>>>
>>>>>>>> FSaverage's lh.white file is 5898808 bytes:
>>>>>>>>
>>>>>>>> 5898808 Apr 11? 2013
>>>>>>>> /usr/local/freesurfer/subjects/fsaverage/surf/lh.white
>>>>>>>>
>>>>>>>> After converting with this command:
>>>>>>>>
>>>>>>>> mri_surf2surf --hemi lh --srcsubject fsaverage --sval-xyz white
>>>>>>>> --trgsubject fs_target --tval-xyz {input_dir}/T1_nifti.nii.gz
>>>>>>>> --trgsurfval {output_dir}/registered_lh.white
>>>>>>>>
>>>>>>>> My newly registered lh.white file is half the size:
>>>>>>>>
>>>>>>>> 3316997 May? 6 10:41
>>>>>>>> /home/ian/cdm_registered_test/registered_lh.white
>>>>>>>>
>>>>>>>> (and appears to have half the vertices accordingly.)
>>>>>>>>
>>>>>>>> So this must be incorrect, or at least not my intended purpose.
>>>>>>>>
>>>>>>>> To try and be clear, I'm looking to get the position of every
>>>>>>>> vertex in fsaverage's surfaces "on" the surface of my subject's
>>>>>>>> surfaces.? So if there's a vertex at the peak of a particular
>>>>>>>> sulcii on fsaverage, I'm looking to find where the peak of that
>>>>>>>> sulcii is on my subject.
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>> Ian
>>>>>>>>
>>>>>>>> On 06/05/2020 09:08, Tim Sch?fer wrote:
>>>>>>>>> ????????? External Email - Use Caution
>>>>>>>>>
>>>>>>>>> ?Just a note: there should be no need to convert to gifti,
>>>>>>>>> nibabel can read
>>>>>>>>> ?the FreeSurer binary surface format directly with
>>>>>>>>> ?`nibabel.freesurfer.io.read_geometry()`.
>>>>>>>>>
>>>>>>>>> ?The docs are here:
>>>>>>>>> https://nipy.org/nibabel/reference/nibabel.freesurfer.html#nibabel.freesurfer.io.read_geometry
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> ?Best,
>>>>>>>>>
>>>>>>>>> ?Tim
>>>>>>>>>
>>>>>>>>>> ?On May 5, 2020 at 7:59 PM "Douglas N. Greve"
>>>>>>>>>> <dgreve@mgh.harvard.edu>
>>>>>>>>>> ?wrote:
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> ?You should load the surfaces in FV. If it load in FV ok but
>>>>>>>>>> nibable is
>>>>>>>>>> ?crashing, you should contact them.
>>>>>>>>>>
>>>>>>>>>> ?On 5/5/2020 1:05 PM, Ian Hardingham wrote:
>>>>>>>>>>> ? ????????External Email - Use Caution
>>>>>>>>>>>
>>>>>>>>>>> ?Thank you both.
>>>>>>>>>>>
>>>>>>>>>>> ?I've made edits and these are the current commands:
>>>>>>>>>>>
>>>>>>>>>>> ?mri_surf2surf --hemi lh --srcsubject fsaverage --sval-xyz white
>>>>>>>>>>> ?--trgsubject fs_target --tval-xyz {input_dir}/T1_nifti.nii.gz
>>>>>>>>>>> ?--trgsurfval {output_dir}/registered_lh.white
>>>>>>>>>>> ?mri_surf2surf --hemi rh --srcsubject fsaverage --sval-xyz white
>>>>>>>>>>> ?--trgsubject fs_target --tval-xyz {input_dir}/T1_nifti.nii.gz
>>>>>>>>>>> ?--trgsurfval {output_dir}/registered_rh.white
>>>>>>>>>>> ?mri_surf2surf --hemi lh --srcsubject fsaverage --sval-xyz pial
>>>>>>>>>>> ?--trgsubject fs_target --tval-xyz {input_dir}/T1_nifti.nii.gz
>>>>>>>>>>> ?--trgsurfval {output_dir}/registered_lh.pial
>>>>>>>>>>> ?mri_surf2surf --hemi rh --srcsubject fsaverage --sval-xyz pial
>>>>>>>>>>> ?--trgsubject fs_target --tval-xyz {input_dir}/T1_nifti.nii.gz
>>>>>>>>>>> ?--trgsurfval {output_dir}/registered_rh.pial
>>>>>>>>>>>
>>>>>>>>>>> ?These execute successfully and the file size looks about
>>>>>>>>>>> right, but
>>>>>>>>>>> ?after using mris_convert to convert to Gifti format nibabel
>>>>>>>>>>> crashes on
>>>>>>>>>>> ?trying to load them - is there anything obviously wrong in
>>>>>>>>>>> my commands?
>>>>>>>>>>>
>>>>>>>>>>> ?I'll also take a look at mris_apply_reg.
>>>>>>>>>>>
>>>>>>>>>>> ?On 05/05/2020 18:01, Douglas N. Greve wrote:
>>>>>>>>>>>> ?Don't specify a --trg_type. But add --tval-xyz
>>>>>>>>>>>> ?mris_apply_reg will do the same thing, but the interface
>>>>>>>>>>>> might be a
>>>>>>>>>>>> ?little easier
>>>>>>>>>>>>
>>>>>>>>>>>> ?On 5/5/2020 12:49 PM, Bruce Fischl wrote:
>>>>>>>>>>>>> ?no definitely not "w" format, which we don't use for anything
>>>>>>>>>>>>> ?anymore. YOu should use tval-xyz also I think
>>>>>>>>>>>>> ?On Tue, 5 May 2020, Ian Hardingham wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> ? ????????External Email - Use Caution
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> ?It would appear not, as I'm getting an error on my pial
>>>>>>>>>>>>>> output
>>>>>>>>>>>>>> ?files but not
>>>>>>>>>>>>>> ?my white ones.? Here are my commands:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> ?mri_surf2surf --hemi lh --srcsubject fsaverage --sval-xyz
>>>>>>>>>>>>>> white
>>>>>>>>>>>>>> ?--trgsubject
>>>>>>>>>>>>>> ?fs_target --trgsurfval ./registered_lh.white --trg_type w
>>>>>>>>>>>>>> ?mri_surf2surf --hemi rh --srcsubject fsaverage --sval-xyz
>>>>>>>>>>>>>> white
>>>>>>>>>>>>>> ?--trgsubject
>>>>>>>>>>>>>> ?fs_target --trgsurfval ./registered_rh.white --trg_type w
>>>>>>>>>>>>>> ?mri_surf2surf --hemi lh --srcsubject fsaverage --sval-xyz
>>>>>>>>>>>>>> pial
>>>>>>>>>>>>>> ?--trgsubject
>>>>>>>>>>>>>> ?fs_target --trgsurfval ./registered_lh.pial --trg_type w
>>>>>>>>>>>>>> ?mri_surf2surf --hemi rh --srcsubject fsaverage --sval-xyz
>>>>>>>>>>>>>> pial
>>>>>>>>>>>>>> ?--trgsubject
>>>>>>>>>>>>>> ?fs_target --trgsurfval ./registered_rh.pial --trg_type w
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> ?The white calls output seems to be fine, but the pial
>>>>>>>>>>>>>> ones aren't.? I
>>>>>>>>>>>>>> ?somewhat naively trued trg_type pial but that wasn't
>>>>>>>>>>>>>> correct.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> ?On 05/05/2020 17:33, Ian Hardingham wrote:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> ? ????? Thanks Bruce, extremely helpful.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> ? ????? Can I just check that the "w" format is what is
>>>>>>>>>>>>>> used by both
>>>>>>>>>>>>>> ? the
>>>>>>>>>>>>>> ? ????? lh/rh.pial and the lh/rh.white files?? I only ask
>>>>>>>>>>>>>> because my
>>>>>>>>>>>>>> ? ????? surf2surf command outputs the exact output
>>>>>>>>>>>>>> filename if the end
>>>>>>>>>>>>>> ? ????? is ".white", but if it's ".pial" it outputs
>>>>>>>>>>>>>> ".pial.w", which I
>>>>>>>>>>>>>> ? ????? find a little curious.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> ? ????? Ian
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> ? ????? On 05/05/2020 16:34, Bruce Fischl wrote:
>>>>>>>>>>>>>> ? ????? yes, check out options like:
>>>>>>>>>>>>>> ? ????? --sval-xyz
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> ? ????? if you need further help though I'll have to defer
>>>>>>>>>>>>>> to Doug
>>>>>>>>>>>>>> ? ????? :)
>>>>>>>>>>>>>> ? ????? Bruce
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> ? ????? On Tue, 5 May 2020, Ian Hardingham wrote:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> ? ??????????? ????????External Email - Use Caution
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> ? ??????????? Bruce, I've read the docs on mri_surf2surf - I
>>>>>>>>>>>>>> ? ??????????? wish to get surface files out
>>>>>>>>>>>>>> ? ??????????? (again, lh.pial, rh.pial, lh.white, and
>>>>>>>>>>>>>> ? ??????????? rh.white) rather than values for
>>>>>>>>>>>>>> ? ??????????? something such as thickness - is there an
>>>>>>>>>>>>>> ? ??????????? option for mri_surf2surf to allow
>>>>>>>>>>>>>> ? ??????????? this?
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> ? ??????????? On 05/05/2020 14:43, Bruce Fischl wrote:
>>>>>>>>>>>>>> ? ??????????? ????? Hi Ian
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> ? ??????????? ????? you can use mri_surf2surf to map
>>>>>>>>>>>>>> ? ??????????? surfaces between subjects, but
>>>>>>>>>>>>>> ? ??????????? ????? our atlas isn't really a surface. You
>>>>>>>>>>>>>> ? ??????????? can use the surfaces in
>>>>>>>>>>>>>> ? ??????????? ????? the fsaverage dir, but they are meant
>>>>>>>>>>>>>> ? ??????????? for visualization and are
>>>>>>>>>>>>>> ? ??????????? ????? much smoother than individuals
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> ? ??????????? ????? cheers
>>>>>>>>>>>>>> ? ??????????? ????? Bruce
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> ? ??????????? ????? On Tue, 5 May 2020, Ian wrote:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> ? ??????????? ??????????? ????????External Email - Use
>>>>>>>>>>>>>> ? ??????????? Caution
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> ? ??????????? ??????????? Hi Freesurfers.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> ? ??????????? ??????????? I have a subject S with recon-all
>>>>>>>>>>>>>> ? ??????????? having been run on
>>>>>>>>>>>>>> ? ??????????? ??????????? it.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> ? ??????????? ??????????? I have the subject-specific
>>>>>>>>>>>>>> ? ??????????? surface files
>>>>>>>>>>>>>> ? ??????????? ??????????? /surf/lh.pial, rh.pial, lh.white,
>>>>>>>>>>>>>> ? ??????????? ??????????? and rh.white.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> ? ??????????? ??????????? I would like an Atlas's lh.pial,
>>>>>>>>>>>>>> ? ??????????? rh.pial, lh.white,
>>>>>>>>>>>>>> ? ??????????? ??????????? and rh.white in subject
>>>>>>>>>>>>>> ? ??????????? ??????????? space.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> ? ??????????? ??????????? Any helpers on how to achieve
>>>>>>>>>>>>>> ? ??????????? this?
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> ? ??????????? ??????????? Thanks,
>>>>>>>>>>>>>> ? ??????????? ??????????? Ian
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> ? ??????????? ??????????? --
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> ? ??????????? ??????????? Ian Hardingham
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>> ? ??????????? 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 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 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
>>>>>>>>> ?--
>>>>>>>>> ?Dr. Tim Sch?fer
>>>>>>>>> ?Postdoc Computational Neuroimaging
>>>>>>>>> ?Department of Child and Adolescent Psychiatry, Psychosomatics and
>>>>>>>>> ?Psychotherapy
>>>>>>>>> ?University Hospital Frankfurt, Goethe University Frankfurt am
>>>>>>>>> Main,
>>>>>>>>> ?Germany
>>>>>>>>>
>>>>>>>>> ?_______________________________________________
>>>>>>>>> ?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 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 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 list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
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> ------------------------------
>
> Message: 8
> Date: Thu, 7 May 2020 13:44:13 -0500
> From: "Xiaojiang Yang" <xjyangxj@gmail.com>
> Subject: [Freesurfer] Compare individual to a group
> To: <freesurfer@nmr.mgh.harvard.edu>
> Message-ID: <00c801d6249f$81a4a7a0$84edf6e0$@gmail.com>
> Content-Type: text/plain; charset="us-ascii"
>
>        External Email - Use Caution       
>
> Dear FS experts,
>
> I have a group of healthy subjects. Given a new individual subject, I want
> to compare its cortical thickness to the healthy group so that I can find
> where the thickness is abnormal (thickening or thinning).
>
> I use fsaverage as the template subject to calculate mean and std of the
> healthy group. Since subjects in the healthy group have different ages, I do
> a "normalization" process to all the subjects in the group BEFORE
> calculating the mean and std. Thus the normalized healthy group can be
> regarded as all subjects having the same "standard" age. The normalization
> process is just multiplying some pre-obtained scale (varied by age, but not
> linearly ) to the file ?h.thickness.fwhm0.fsaverage.mgh of each subject that
> are already calculated by "recon-all --qcache" command. So the mean and std
> of the group are actually weighted in the sense of Freesurfer's recon-all
> results.
>
> My questions are:
>
> 1)      If I do vertex-wise t-tests by simply comparing individual subject's
> thickness to the group using mris_calc but WITHOUT using mri_glmfit, can I
> still use mri_glmfit-sim to do multiple comparisons correction? If yes, how?
>
> 2)      If the answer is no for the above question, how should I use
> mris_glmft to implement my above thoughts so that I can use use
> mri_glmfit-sim? Specifically, how can I use the weighted mean for the group?
>
> 3)      Take a step back, if I consider the weight is linearly correlated
> with the age, how to design the fsdg and contrast file?
>
> Thank you very much!
>
> Xiao
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
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> ------------------------------
>
> Message: 9
> Date: Thu, 7 May 2020 14:54:29 -0400
> From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
> Subject: Re: [Freesurfer] Compare individual to a group
> To: <freesurfer@nmr.mgh.harvard.edu>
> Message-ID: <87c5fe41-c186-26c1-d23c-bcb87b9fa4ef@mgh.harvard.edu>
> Content-Type: text/plain; charset="windows-1252"
>
> I think it will work properly if you use the raw data as input and
> create an FSGD file with two classes: (1) the individual subject and (2)
> healthy subjects. Also include age as a covariate. Use DOSS instead of
> DODS. Then set your contrast to be 1 -1 0 and run mri_glmfit. I think
> that should properly account for age.
>
> On 5/7/2020 2:44 PM, Xiaojiang Yang wrote:
>>
>> ????????External Email - Use Caution
>>
>> Dear FS experts,
>>
>> I have a group of healthy subjects. Given a new individual subject, I
>> want to compare its cortical thickness to the healthy group so that I
>> can find where the thickness is abnormal (thickening or thinning).
>>
>> I use fsaverage as the template subject to calculate mean and std of
>> the healthy group. Since subjects in the healthy group have different
>> ages, I do a ?normalization? process to all the subjects in the group
>> BEFORE calculating the mean and std. Thus the normalized healthy group
>> can be regarded as all subjects having the same ?standard? age. The
>> normalization process is just multiplying some pre-obtained scale
>> (varied by age, but not linearly ) to the file
>> *?h.thickness.fwhm0.fsaverage.mgh* of each subject that are already
>> calculated by ?recon-all --qcache? command. So the mean and std of the
>> group are actually weighted in the sense of Freesurfer?s recon-all
>> results.
>>
>> My questions are:
>>
>> 1)If I do vertex-wise t-tests by simply comparing individual subject?s
>> thickness to the group using mris_calc but WITHOUT using mri_glmfit,
>> can I still use mri_glmfit-sim to do multiple comparisons correction?
>> If yes, how?
>>
>> 2)If the answer is no for the above question, how should I use
>> mris_glmft to implement my above thoughts so that I can use use
>> mri_glmfit-sim? Specifically, how can I use the weighted mean for the
>> group?
>>
>> 3)Take a step back, if I consider the weight is linearly correlated
>> with the age, how to design the fsdg and contrast file?
>>
>> Thank you very much!
>>
>> Xiao
>>
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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> Message: 10
> Date: Thu, 7 May 2020 20:08:53 +0100
> From: Ian Hardingham <ian@mode7.games>
> Subject: Re: [Freesurfer] Get Atlas surfaces in subject space
> To: freesurfer@nmr.mgh.harvard.edu
> Message-ID: <bc020f56-9899-3961-affd-a3b61ebc5aff@mode7.games>
> Content-Type: text/plain; charset="utf-8"
>
>        External Email - Use Caution       
>
> Thanks Doug - yes, I'd like the vertex coordinates in the same format as
> the local subject surface files are in.
>
> On 07/05/2020 19:02, Douglas N. Greve wrote:
>> It comes down to how you want to define "roughly in the same place".
>> Does this mean an affine (12dof) transform? And what information do
>> you want? An XYZ coordinate?
>>
>> On 5/7/2020 11:06 AM, Ian Hardingham wrote:
>>>
>>> ????????External Email - Use Caution
>>>
>>> I'd like to get a set of points to compare across several brains, so
>>> that the nth point in brain A is in roughly the same place as the nth
>>> point in brain B - so I'd like to have an agreed upon set of vertices
>>> (the source brain's vertices) translated to positions on the target
>>> brain (which may well not be vertices in the target geometry.)
>>>
>>> On 07/05/2020 15:59, Douglas N. Greve wrote:
>>>> I don't understand. What is the difference between the target brain
>>>> and the target subject's vertices?
>>>>
>>>> On 5/7/2020 2:17 AM, Ian Hardingham wrote:
>>>>>
>>>>> ????????External Email - Use Caution
>>>>>
>>>>> Ok, thanks Doug, but I'm looking to get the positions of the source
>>>>> vertexes on the target brain, not the target subject's vertices...
>>>>>
>>>>> On 06/05/2020 23:07, Douglas N. Greve wrote:
>>>>>> That looks like it could be right. It has 102,020 vertices, which
>>>>>> should be the number of vertices in the target subject (and is in
>>>>>> the typical range for an individual subject)
>>>>>>
>>>>>> On 5/6/2020 10:21 AM, Ian Hardingham wrote:
>>>>>>>
>>>>>>> ????????External Email - Use Caution
>>>>>>>
>>>>>>> FSLInfo attached, thanks Bruce.
>>>>>>>
>>>>>>> When trying to run freeview I get "freeview.bin: error while
>>>>>>> loading shared libraries: libpng12.so.0: cannot open shared
>>>>>>> object file: No such file or directory" - do I need to add
>>>>>>> /usr/local/freesurfer/lib/* to path or something along those lines?
>>>>>>>
>>>>>>> SURFACE INFO ========================================
>>>>>>> type??????? : MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE
>>>>>>> num vertices: 102020
>>>>>>> num faces?? : 204036
>>>>>>> num strips? : 0
>>>>>>> surface area: 65520.5
>>>>>>> AvgVtxArea?????? 0.642232
>>>>>>> AvgVtxDist?????? 0.940503
>>>>>>> StdVtxDist?????? 0.417776
>>>>>>> ctr???????? : (-31.9056, -18.8197, 16.3545)
>>>>>>> vertex locs : surfaceRAS
>>>>>>> Volume Geometry (vg)
>>>>>>> volume geometry:
>>>>>>> extent? : (176, 224, 256)
>>>>>>> voxel?? : ( 1.0000,? 1.0000,? 1.0000)
>>>>>>> x_(ras) : (-0.9990, -0.0436,? 0.0000)
>>>>>>> y_(ras) : (-0.0436,? 0.9990,? 0.0000)
>>>>>>> z_(ras) : ( 0.0000,? 0.0000,? 1.0000)
>>>>>>> c_(ras) : (-0.5431,? 8.9290, -17.0723)
>>>>>>> file??? : /media/ian/bronson/subject/T1_nifti.nii.gz
>>>>>>> Volume Geometry vox2ras
>>>>>>> -0.99905? -0.04362?? 0.00000?? 92.25847;
>>>>>>> -0.04362?? 0.99905?? 0.00000? -99.12585;
>>>>>>> ?0.00000?? 0.00000?? 1.00000? -145.07230;
>>>>>>> ?0.00000?? 0.00000?? 0.00000?? 1.00000;
>>>>>>> Volume Geometry vox2ras-tkr
>>>>>>> -1.00000?? 0.00000?? 0.00000?? 88.00000;
>>>>>>> ?0.00000?? 0.00000?? 1.00000? -128.00000;
>>>>>>> ?0.00000? -1.00000?? 0.00000?? 112.00000;
>>>>>>> ?0.00000?? 0.00000?? 0.00000?? 1.00000;
>>>>>>> cmd[0]: mris_remove_intersection ../surf/lh.orig ../surf/lh.orig
>>>>>>> ProgramVersion: $Name: stable5 $ TimeStamp:
>>>>>>> 2016/05/26-23:14:53-GMT? BuildTimeStamp: May 13 2013 18:53:32?
>>>>>>> CVS: $Id: mris_remove_intersection.c,v 1.6 2011/03/02 00:04:32
>>>>>>> nicks Exp $? User: fsuser? Machine: xubuntu-VirtualBox? Platform:
>>>>>>> Linux? PlatformVersion: 3.2.0-23-generic? CompilerName: GCC?
>>>>>>> CompilerVersion: 30400
>>>>>>> cmd[1]: mris_make_surfaces -noaparc -whiteonly -mgz -T1
>>>>>>> brain.finalsurfs T1_MDEFT_BONANN lh ProgramVersion: $Name:
>>>>>>> stable5 $? TimeStamp: 2016/05/26-23:14:56-GMT? BuildTimeStamp:
>>>>>>> May 13 2013 18:53:32? CVS: $Id: mris_make_surfaces.c,v 1.127.2.6
>>>>>>> 2013/05/12 22:28:01 nicks Exp $? User: fsuser Machine:
>>>>>>> xubuntu-VirtualBox? Platform: Linux PlatformVersion:
>>>>>>> 3.2.0-23-generic? CompilerName: GCC CompilerVersion: 30400
>>>>>>> cmd[2]: mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white
>>>>>>> ../surf/lh.smoothwm ProgramVersion: $Name: stable5 $? TimeStamp:
>>>>>>> 2016/05/26-23:18:33-GMT BuildTimeStamp: May 13 2013 18:53:32?
>>>>>>> CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $
>>>>>>> User: fsuser? Machine: xubuntu-VirtualBox? Platform: Linux?
>>>>>>> PlatformVersion: 3.2.0-23-generic CompilerName: GCC?
>>>>>>> CompilerVersion: 30400
>>>>>>> cmd[3]: mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated
>>>>>>> ProgramVersion: $Name: stable5 $ TimeStamp:
>>>>>>> 2016/05/26-23:18:36-GMT? BuildTimeStamp: May 13 2013 18:53:32?
>>>>>>> CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $?
>>>>>>> User: fsuser Machine: xubuntu-VirtualBox? Platform: Linux
>>>>>>> PlatformVersion: 3.2.0-23-generic? CompilerName: GCC
>>>>>>> CompilerVersion: 30400
>>>>>>> cmd[4]: mris_sphere -seed 1234 ../surf/lh.inflated
>>>>>>> ../surf/lh.sphere ProgramVersion: $Name: stable5 $ TimeStamp:
>>>>>>> 2016/05/26-23:20:12-GMT? BuildTimeStamp: May 13 2013 18:53:32?
>>>>>>> CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $?
>>>>>>> User: fsuser Machine: xubuntu-VirtualBox? Platform: Linux
>>>>>>> PlatformVersion: 3.2.0-23-generic? CompilerName: GCC
>>>>>>> CompilerVersion: 30400
>>>>>>> cmd[5]: mris_register -curv ../surf/lh.sphere
>>>>>>> /usr/local/freesurfer/average/lh.average.curvature.filled.buckner40.tif
>>>>>>> ../surf/lh.sphere.reg ProgramVersion: $Name: stable5 $?
>>>>>>> TimeStamp: 2016/05/27-00:03:14-GMT? BuildTimeStamp: May 13 2013
>>>>>>> 18:53:32? CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33
>>>>>>> nicks Exp $? User: fsuser Machine: xubuntu-VirtualBox? Platform:
>>>>>>> Linux PlatformVersion: 3.2.0-23-generic? CompilerName: GCC
>>>>>>> CompilerVersion: 30400
>>>>>>> mris_info
>>>>>>> creationtime 2020/05/06-14:18:48-GMT
>>>>>>> sysname? Linux
>>>>>>> hostname ryzen-cumnor
>>>>>>> machine? x86_64
>>>>>>> surfacefile /home/ian/cdm_registered_test/registered_lh.white
>>>>>>> hemicode??? 1
>>>>>>> talairach_flag? 0
>>>>>>> rescale???? 0.000000
>>>>>>> nvertices?? 102020
>>>>>>> nfaces????? 204036
>>>>>>> total_area? 65520.492188
>>>>>>> group_avg_vtxarea_loaded 0
>>>>>>> avgvtxarea? 0.642232
>>>>>>> avgvtxdist? 0.940503
>>>>>>> stdvtxdist? 0.417776
>>>>>>> vtx0xyz?? -8.576451 -101.319672 3.333434
>>>>>>>
>>>>>>> On 06/05/2020 15:00, Bruce Fischl wrote:
>>>>>>>> can you run mris_info on the output surfcae? And maybe send a
>>>>>>>> freeview snapshot of it (in 3d rendering mode)
>>>>>>>>
>>>>>>>> On Wed, 6 May 2020, Ian wrote:
>>>>>>>>
>>>>>>>>> ?????? External Email - Use Caution
>>>>>>>>> Thanks Tim and Doug.
>>>>>>>>>
>>>>>>>>> I have the files generating and loading properly now, but I'm
>>>>>>>>> not convinced it's giving the output I'm looking for.
>>>>>>>>>
>>>>>>>>> I am trying to convert the "fsaverage" subject's surface
>>>>>>>>> coordinates to my own subject's surface space.
>>>>>>>>>
>>>>>>>>> FSaverage's lh.white file is 5898808 bytes:
>>>>>>>>>
>>>>>>>>> 5898808 Apr 11? 2013
>>>>>>>>> /usr/local/freesurfer/subjects/fsaverage/surf/lh.white
>>>>>>>>>
>>>>>>>>> After converting with this command:
>>>>>>>>>
>>>>>>>>> mri_surf2surf --hemi lh --srcsubject fsaverage --sval-xyz white
>>>>>>>>> --trgsubject fs_target --tval-xyz {input_dir}/T1_nifti.nii.gz
>>>>>>>>> --trgsurfval {output_dir}/registered_lh.white
>>>>>>>>>
>>>>>>>>> My newly registered lh.white file is half the size:
>>>>>>>>>
>>>>>>>>> 3316997 May? 6 10:41
>>>>>>>>> /home/ian/cdm_registered_test/registered_lh.white
>>>>>>>>>
>>>>>>>>> (and appears to have half the vertices accordingly.)
>>>>>>>>>
>>>>>>>>> So this must be incorrect, or at least not my intended purpose.
>>>>>>>>>
>>>>>>>>> To try and be clear, I'm looking to get the position of every
>>>>>>>>> vertex in fsaverage's surfaces "on" the surface of my subject's
>>>>>>>>> surfaces.? So if there's a vertex at the peak of a particular
>>>>>>>>> sulcii on fsaverage, I'm looking to find where the peak of that
>>>>>>>>> sulcii is on my subject.
>>>>>>>>>
>>>>>>>>> Thanks,
>>>>>>>>> Ian
>>>>>>>>>
>>>>>>>>> On 06/05/2020 09:08, Tim Sch?fer wrote:
>>>>>>>>>> ????????? External Email - Use Caution
>>>>>>>>>>
>>>>>>>>>> ?Just a note: there should be no need to convert to gifti,
>>>>>>>>>> nibabel can read
>>>>>>>>>> ?the FreeSurer binary surface format directly with
>>>>>>>>>> ?`nibabel.freesurfer.io.read_geometry()`.
>>>>>>>>>>
>>>>>>>>>> ?The docs are here:
>>>>>>>>>> https://nipy.org/nibabel/reference/nibabel.freesurfer.html#nibabel.freesurfer.io.read_geometry
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> ?Best,
>>>>>>>>>>
>>>>>>>>>> ?Tim
>>>>>>>>>>
>>>>>>>>>>> ?On May 5, 2020 at 7:59 PM "Douglas N. Greve"
>>>>>>>>>>> <dgreve@mgh.harvard.edu>
>>>>>>>>>>> ?wrote:
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> ?You should load the surfaces in FV. If it load in FV ok but
>>>>>>>>>>> nibable is
>>>>>>>>>>> ?crashing, you should contact them.
>>>>>>>>>>>
>>>>>>>>>>> ?On 5/5/2020 1:05 PM, Ian Hardingham wrote:
>>>>>>>>>>>> ? ????????External Email - Use Caution
>>>>>>>>>>>>
>>>>>>>>>>>> ?Thank you both.
>>>>>>>>>>>>
>>>>>>>>>>>> ?I've made edits and these are the current commands:
>>>>>>>>>>>>
>>>>>>>>>>>> ?mri_surf2surf --hemi lh --srcsubject fsaverage --sval-xyz
>>>>>>>>>>>> white
>>>>>>>>>>>> ?--trgsubject fs_target --tval-xyz {input_dir}/T1_nifti.nii.gz
>>>>>>>>>>>> ?--trgsurfval {output_dir}/registered_lh.white
>>>>>>>>>>>> ?mri_surf2surf --hemi rh --srcsubject fsaverage --sval-xyz
>>>>>>>>>>>> white
>>>>>>>>>>>> ?--trgsubject fs_target --tval-xyz {input_dir}/T1_nifti.nii.gz
>>>>>>>>>>>> ?--trgsurfval {output_dir}/registered_rh.white
>>>>>>>>>>>> ?mri_surf2surf --hemi lh --srcsubject fsaverage --sval-xyz pial
>>>>>>>>>>>> ?--trgsubject fs_target --tval-xyz {input_dir}/T1_nifti.nii.gz
>>>>>>>>>>>> ?--trgsurfval {output_dir}/registered_lh.pial
>>>>>>>>>>>> ?mri_surf2surf --hemi rh --srcsubject fsaverage --sval-xyz pial
>>>>>>>>>>>> ?--trgsubject fs_target --tval-xyz {input_dir}/T1_nifti.nii.gz
>>>>>>>>>>>> ?--trgsurfval {output_dir}/registered_rh.pial
>>>>>>>>>>>>
>>>>>>>>>>>> ?These execute successfully and the file size looks about
>>>>>>>>>>>> right, but
>>>>>>>>>>>> ?after using mris_convert to convert to Gifti format nibabel
>>>>>>>>>>>> crashes on
>>>>>>>>>>>> ?trying to load them - is there anything obviously wrong in
>>>>>>>>>>>> my commands?
>>>>>>>>>>>>
>>>>>>>>>>>> ?I'll also take a look at mris_apply_reg.
>>>>>>>>>>>>
>>>>>>>>>>>> ?On 05/05/2020 18:01, Douglas N. Greve wrote:
>>>>>>>>>>>>> ?Don't specify a --trg_type. But add --tval-xyz
>>>>>>>>>>>>> ?mris_apply_reg will do the same thing, but the interface
>>>>>>>>>>>>> might be a
>>>>>>>>>>>>> ?little easier
>>>>>>>>>>>>>
>>>>>>>>>>>>> ?On 5/5/2020 12:49 PM, Bruce Fischl wrote:
>>>>>>>>>>>>>> ?no definitely not "w" format, which we don't use for
>>>>>>>>>>>>>> anything
>>>>>>>>>>>>>> ?anymore. YOu should use tval-xyz also I think
>>>>>>>>>>>>>> ?On Tue, 5 May 2020, Ian Hardingham wrote:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> ? ????????External Email - Use Caution
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> ?It would appear not, as I'm getting an error on my pial
>>>>>>>>>>>>>>> output
>>>>>>>>>>>>>>> ?files but not
>>>>>>>>>>>>>>> ?my white ones.? Here are my commands:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> ?mri_surf2surf --hemi lh --srcsubject fsaverage
>>>>>>>>>>>>>>> --sval-xyz white
>>>>>>>>>>>>>>> ?--trgsubject
>>>>>>>>>>>>>>> ?fs_target --trgsurfval ./registered_lh.white --trg_type w
>>>>>>>>>>>>>>> ?mri_surf2surf --hemi rh --srcsubject fsaverage
>>>>>>>>>>>>>>> --sval-xyz white
>>>>>>>>>>>>>>> ?--trgsubject
>>>>>>>>>>>>>>> ?fs_target --trgsurfval ./registered_rh.white --trg_type w
>>>>>>>>>>>>>>> ?mri_surf2surf --hemi lh --srcsubject fsaverage
>>>>>>>>>>>>>>> --sval-xyz pial
>>>>>>>>>>>>>>> ?--trgsubject
>>>>>>>>>>>>>>> ?fs_target --trgsurfval ./registered_lh.pial --trg_type w
>>>>>>>>>>>>>>> ?mri_surf2surf --hemi rh --srcsubject fsaverage
>>>>>>>>>>>>>>> --sval-xyz pial
>>>>>>>>>>>>>>> ?--trgsubject
>>>>>>>>>>>>>>> ?fs_target --trgsurfval ./registered_rh.pial --trg_type w
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> ?The white calls output seems to be fine, but the pial
>>>>>>>>>>>>>>> ones aren't.? I
>>>>>>>>>>>>>>> ?somewhat naively trued trg_type pial but that wasn't
>>>>>>>>>>>>>>> correct.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> ?On 05/05/2020 17:33, Ian Hardingham wrote:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> ? ????? Thanks Bruce, extremely helpful.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> ? ????? Can I just check that the "w" format is what is
>>>>>>>>>>>>>>> used by both
>>>>>>>>>>>>>>> ? the
>>>>>>>>>>>>>>> ? ????? lh/rh.pial and the lh/rh.white files?? I only ask
>>>>>>>>>>>>>>> because my
>>>>>>>>>>>>>>> ? ????? surf2surf command outputs the exact output
>>>>>>>>>>>>>>> filename if the end
>>>>>>>>>>>>>>> ? ????? is ".white", but if it's ".pial" it outputs
>>>>>>>>>>>>>>> ".pial.w", which I
>>>>>>>>>>>>>>> ? ????? find a little curious.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> ? ????? Ian
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> ? ????? On 05/05/2020 16:34, Bruce Fischl wrote:
>>>>>>>>>>>>>>> ? ????? yes, check out options like:
>>>>>>>>>>>>>>> ? ????? --sval-xyz
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> ? ????? if you need further help though I'll have to
>>>>>>>>>>>>>>> defer to Doug
>>>>>>>>>>>>>>> ? ????? :)
>>>>>>>>>>>>>>> ? ????? Bruce
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> ? ????? On Tue, 5 May 2020, Ian Hardingham wrote:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> ? ??????????? ????????External Email - Use Caution
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> ? ??????????? Bruce, I've read the docs on mri_surf2surf - I
>>>>>>>>>>>>>>> ? ??????????? wish to get surface files out
>>>>>>>>>>>>>>> ? ??????????? (again, lh.pial, rh.pial, lh.white, and
>>>>>>>>>>>>>>> ? ??????????? rh.white) rather than values for
>>>>>>>>>>>>>>> ? ??????????? something such as thickness - is there an
>>>>>>>>>>>>>>> ? ??????????? option for mri_surf2surf to allow
>>>>>>>>>>>>>>> ? ??????????? this?
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> ? ??????????? On 05/05/2020 14:43, Bruce Fischl wrote:
>>>>>>>>>>>>>>> ? ??????????? ????? Hi Ian
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> ? ??????????? ????? you can use mri_surf2surf to map
>>>>>>>>>>>>>>> ? ??????????? surfaces between subjects, but
>>>>>>>>>>>>>>> ? ??????????? ????? our atlas isn't really a surface. You
>>>>>>>>>>>>>>> ? ??????????? can use the surfaces in
>>>>>>>>>>>>>>> ? ??????????? ????? the fsaverage dir, but they are meant
>>>>>>>>>>>>>>> ? ??????????? for visualization and are
>>>>>>>>>>>>>>> ? ??????????? ????? much smoother than individuals
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> ? ??????????? ????? cheers
>>>>>>>>>>>>>>> ? ??????????? ????? Bruce
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> ? ??????????? ????? On Tue, 5 May 2020, Ian wrote:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> ????????External Email - Use
>>>>>>>>>>>>>>> ? ??????????? Caution
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> ? ??????????? ??????????? Hi Freesurfers.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> ? ??????????? ??????????? I have a subject S with recon-all
>>>>>>>>>>>>>>> ? ??????????? having been run on
>>>>>>>>>>>>>>> ? ??????????? ??????????? it.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> ? ??????????? ??????????? I have the subject-specific
>>>>>>>>>>>>>>> ? ??????????? surface files
>>>>>>>>>>>>>>> ? ??????????? ??????????? /surf/lh.pial, rh.pial, lh.white,
>>>>>>>>>>>>>>> ? ??????????? ??????????? and rh.white.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> ? ??????????? ??????????? I would like an Atlas's lh.pial,
>>>>>>>>>>>>>>> ? ??????????? rh.pial, lh.white,
>>>>>>>>>>>>>>> ? ??????????? ??????????? and rh.white in subject
>>>>>>>>>>>>>>> ? ??????????? ??????????? space.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> ? ??????????? ??????????? Any helpers on how to achieve
>>>>>>>>>>>>>>> ? ??????????? this?
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> ? ??????????? ??????????? Thanks,
>>>>>>>>>>>>>>> ? ??????????? ??????????? Ian
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> ? ??????????? ??????????? --
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> ? ??????????? ??????????? Ian Hardingham
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>> ? ??????????? 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 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 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
>>>>>>>>>> ?--
>>>>>>>>>> ?Dr. Tim Sch?fer
>>>>>>>>>> ?Postdoc Computational Neuroimaging
>>>>>>>>>> ?Department of Child and Adolescent Psychiatry, Psychosomatics
>>>>>>>>>> and
>>>>>>>>>> ?Psychotherapy
>>>>>>>>>> ?University Hospital Frankfurt, Goethe University Frankfurt am
>>>>>>>>>> Main,
>>>>>>>>>> ?Germany
>>>>>>>>>>
>>>>>>>>>> ?_______________________________________________
>>>>>>>>>> ?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 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 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 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
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> ------------------------------
>
> Message: 11
> Date: Thu, 7 May 2020 19:41:07 +0000
> From: "Glasser, Matthew" <glasserm@wustl.edu>
> Subject: [Freesurfer] FW:  HCPMMP1 parcellation to aseg (.mgz)
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Message-ID: <38276C69-655C-4C4F-9074-90A8B07C79A5@wustl.edu>
> Content-Type: text/plain; charset="utf-8"
>
>        External Email - Use Caution       
>
>
>
> From: Timothy Coalson <tsc5yc@mst.edu>
> Reply-To: Timothy Coalson <tsc5yc@mst.edu>
> Date: Thursday, May 7, 2020 at 2:30 PM
> To: "Glasser, Matthew" <glasserm@wustl.edu>
> Cc: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] HCPMMP1 parcellation to aseg (.mgz)
>
> The way to map data between freesurfer and fs_LR is in faq #9:
>
> https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-9.HowdoImapdatabetweenFreeSurferandHCP?
>
> I seem to recall that the colors in the colored version of our MMP atlas ended up unique (at least within the hemisphere), so that should remove one hurdle from converting to freesurfer format.
>
> Tim
>
>
> On Thu, May 7, 2020 at 10:01 AM Glasser, Matthew <glasserm@wustl.edu<mailto:glasserm@wustl.edu>> wrote:
> That is our multi-modal parcellation.  Tim has some instructions to get data from the fs_LR mesh to fsaverage in GIFTI format.  Doug perhaps you can say how to convert from GIFTI to annot?
>
> Matt.
>
> From: <freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of "Douglas N. Greve" <dgreve@mgh.harvard.edu<mailto:dgreve@mgh.harvard.edu>>
> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
> Date: Thursday, May 7, 2020 at 9:59 AM
> To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
> Subject: Re: [Freesurfer] HCPMMP1 parcellation to aseg (.mgz)
>
> * External Email - Caution *
> what's hcpmmp1?
> On 5/7/2020 4:46 AM, pooja prabhu wrote:
>
>        External Email - Use Caution
> Hai list,
> Can I get some insight on how to convert HCPMMP1 to aseg(provided we have annotation files) for fsaverage brain?
> For example: for aparc parcellation we use aparc2aseg and get aparc+aseg.mgz.
> Similarly I need for HCPMMP1.
> Can someone help me with this?
> Thank you
>
>
> _______________________________________________
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>
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>
>
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>
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> 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: 12
> Date: Thu, 7 May 2020 19:58:06 +0000
> From: Mina Rizkallah <dr.minafakhry@live.com>
> Subject: Re: [Freesurfer] FreeSurfer 7 stable
> To: "fsbuild@contbay.com" <fsbuild@contbay.com>, Freesurfer support
>        list    <freesurfer@nmr.mgh.harvard.edu>
> Message-ID:
>        <DB6PR04MB298206A19251FA711DB1FED89FA50@DB6PR04MB2982.eurprd04.prod.outlook.com>
>       
> Content-Type: text/plain; charset="us-ascii"
>
>        External Email - Use Caution       
>
> Hello again,
>
> I successfully installed FreeSurfer 7 on Centos 8 and it works smoothly.
>
> my concern is regarding the CUDA compatibility, in recon-all help I found the (-use-gpu) flag is present but when I tried to use it, I got error for unrecognized flag.
>
> Is there a way to take the part of code concerning CUDA from freesurfer 6 and include it in version 7 as it save a huge amount of time
>
> best regards
> Mina
>
>
> Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10
>
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> ------------------------------
>
> Message: 13
> Date: Thu, 7 May 2020 16:23:29 -0400
> From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
> Subject: Re: [Freesurfer] FreeSurfer 7 stable
> To: <freesurfer@nmr.mgh.harvard.edu>
> Message-ID: <ccb032ac-d813-eaa7-b0b0-69b3ffa48580@mgh.harvard.edu>
> Content-Type: text/plain; charset="windows-1252"
>
> Sorry, we are no longer supporting CUDA. Too much of a moving target.
> That flag should have been deleted (and will be in future updates)
>
>
> On 5/7/2020 3:58 PM, Mina Rizkallah wrote:
>>
>> ????????External Email - Use Caution
>>
>> Hello again,
>>
>> I successfully installed FreeSurfer 7 on Centos 8 and it works smoothly.
>>
>> my concern is regarding the CUDA compatibility, in recon-all help I
>> found the (-use-gpu) flag is present but when I tried to use it, I got
>> error for unrecognized flag.
>>
>> Is there a way to take the part of code concerning CUDA from
>> freesurfer 6 and include it in version 7 as it save a huge amount of time
>>
>> best regards
>>
>> Mina
>>
>> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for
>> Windows 10
>>
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
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> ------------------------------
>
> Message: 14
> Date: Thu, 07 May 2020 22:24:07 +0200
> From: fsbuild <fsbuild@contbay.com>
> Subject: Re: [Freesurfer] freesurfer 7.0.0 in a virtual machine...
> To: freesurfer@nmr.mgh.harvard.edu
> Cc: ts+ml@rcmd.org
> Message-ID: <1588883047.5eb46e67dc2ea@trashmail.com>
> Content-Type: text/plain; charset="utf-8"
>
>        External Email - Use Caution       
>
> Hello Gonzalo,
> If you don?t mind using Ubuntu 18 as the OS in the virtual machine, then we already have a virtual machine you can run with virtualbox that is close to what you want. &nbsp; It has the previous version 7 beta 1 release of freesurfer (and also freesurfer 6). &nbsp;You could start with this VM and update to the 7.0.0 release.
> The Ubuntu VM is here,https://surfer.nmr.mgh.harvard.edu/fswiki/VM_67
> The 7.0.0 release archive is here,freesurfer-linux-centos7_x86_64-7.0.0.tar.gz
> Once you bring up the VM (instructions on the web site for doing it on MacOS and Windows), then you could:1) delete everything under /usr/local/freesurfer/7.0.0.0-1b12) rename that subdir from&nbsp;7.0.0.0-1b1 to 7.0.03) untar the 7.0.0 release archive under the new 7.0.0 archive4) change the bashrc file to use 7.0.0 wherever it says 7.0.0-b1
> You could also run the Ubuntu VM on linux - the instructions would be mostly the same as listed for the Mac or Windows.
> If you want to run some other OS besides Ubuntu and create your own VM from scratch, then you could use&nbsp;osboxes.org&nbsp;to get the base image to create a VM from.
> - R.
> On May 7, 2020, at 15:34, Gonzalo Rojas Costa &lt;gonzalo.rojas.costa@gmail.com&gt; wrote:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Hi:&nbsp; No... I don't have any specific issue... I have a previous freesurfer version installed that I want to continue using.. So I want to install version freesurfer 7.0 on a virtual machine...&nbsp; Sincerely,Gonzalo Rojas Costa&gt; Message: 4&gt; Date: Thu, 7 May 2020 12:43:56 +0200 (CEST)&gt; From: Tim Sch?fer &lt;ts+ml@rcmd.org&gt;&gt; Subject: Re: [Freesurfer] freesurfer 7.0.0 in a virtual machine...&gt; To: Freesurfer support list &lt;freesurfer@nmr.mgh.harvard.edu&gt;&gt; Message-ID: &lt;1445340988.123994.1588848236854@ox.hosteurope.de&gt;&gt; Content-Type: text/plain; charset="utf-8"&gt;&gt; &nbsp; &nbsp; &nbsp; External Email - Use Caution&nbsp; &nbsp; &nbsp; &nbsp;&nbsp;&gt;&gt; There should be no difference to installation on a physical machine. Are you&gt; running into any specific issues?&gt;&gt; Tim&gt;&gt;&gt; On May 7, 2020 at 3:51 AM Gonzalo Rojas Costa &lt;gonzalo.rojas.costa@gmail.com&gt; wrote:&gt;&gt;&nbsp;&gt;&gt;&nbsp;&gt;&gt;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;External Email - Use Caution&nbsp; &nbsp; &nbsp; &nbsp;&nbsp;&gt;&gt;&nbsp;&gt;&gt; Hi:&gt;&gt;&nbsp;&gt;&gt;&nbsp; How can install freesurfer 7.0.0 in a virtual machine ?&gt;&gt;&nbsp;&gt;&gt;&nbsp; &nbsp;Sincerely,&gt;&gt;&nbsp;&gt;&gt;&nbsp;&gt;&gt; Gonzalo Rojas Costa&gt;&gt; _______________________________________________&gt;&gt; Freesurfer mailing list&gt;&gt;&nbsp;Freesurfer@nmr.mgh.harvard.edu&gt;&gt;&nbsp;https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer&gt;&gt;--&gt; Dr.. Tim Sch?fer&gt; Postdoc Computational Neuroimaging&gt; Department of Child and Adolescent Psychiatry, Psychosomatics and&gt; Psychotherapy&gt; University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps:!
 //!
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------------------------------

Message: 11
Date: Tue, 19 May 2020 22:17:04 +0800 (CST)
From: ZhangBo <zhangbo_1008@163.com>
Subject: [Freesurfer] freesurfer subcortical segmentation
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <373dd039.9c1f.1722d4b8a3b.Coremail.zhangbo_1008@163.com>
Content-Type: text/plain; charset="gbk"

        External Email - Use Caution       

Hi teams,
Does freesurfer supports calculate subcortical volumes like globus pallidus internus, globus pallidus externa, subthalamic nucleus , ventral intermedius nucleus, like these areas?


Thanks
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Message: 12
Date: Wed, 20 May 2020 00:17:20 +0900
From: "Safi Ullah ." <safi.ullah@uog.edu.pk>
Subject: [Freesurfer] FREESURFER-7.1: recon-all exited with error
        "ERROR: cannot find or read transforms/talairach.m3z"
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <CACzMhqzNrJcHO1xRUsqEaT4zNJx2c1B3XWx+5CFQhcpVqm4NBg@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

        External Email - Use Caution       

Dear Freesurfer,

Using Freesurfer version 7.1, I was running recon-all on 13 subjects, using
the command below
ls *.nii | parallel -jobs 8 recon-all -s {.} -I {} -all ?qcache
(also checked with this one find . -name '*.nii' | parallel -j 8 recon-all
-s {.} -i {} -all -qcache)
but each time i face the same error as attached with the mail.
I checked the transformation folder, but the said file, talairach.m3z, is
not there.
the error is not same for all cases, some cases showed a different errors,
stating "IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH
ERROR RETURN OF LINE SEARCH:" as attached file recon-all(2nd type).log

Regards
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