[Freesurfer] Area after fsaverage resample

[Lachlan Strike]

Dear FreeSurfer Developers

I have a question regarding the area measures for subjects following 
registration to fsaverage (produced through the qcache flag – 
lh/rh.area.fsaverage.mgh).

What do the values for each vertex represent? Is it correct to state that these 
measures are in mm2, or are these measures now somehow relative to the 
corresponding vertex values within fsaverage?

Best regards

Lachlan

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[Freesurfer] aparcstats2table

[Martin Juneja]

Hi everyone,

I am trying to use following command to save stats from a set of subjects
in a table format:

aparcstats2table --qdec qdec.dat --hemi lh --meas thickness -t zzz.txt

But after I run this, I get following error:

Traceback (most recent call last):

  File "/usr/local/freesurfer/bin/aparcstats2table", line 353, in 

subj_listoftuples = assemble_inputs(options)

  File "/usr/local/freesurfer/bin/aparcstats2table", line 228, in
assemble_inputs

fsid=row['fsid'].strip()

KeyError: 'fsid'

My qdec.dat file looks like below:

fsid
HC003_1
HC004_1
HC006_1
HC015_1

This command works fine if I use subject IDs individually here e.g.
aparcstats2table --subjects HC_Example HC003_1 HC004_1 HC006_1 HC015_1
--hemi lh --meas thickness -t zzz.txt

Another question I have here is: How can I average these thickness stats
and display it on standard fsaverage?

Any help would be really appreciated.
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Re: [Freesurfer] GM ROI list?

[P Taylor]

OK, thanks for that list of complementary ROIs.

I've always wondered what is the maximal set of regions that can be
returned by the standard recon-all with no other options for aparc+aseg and
aparc+aseg2009?  Looking at the FreeSurferColorLUT.txt, I guess there is a
batch from lines 1-231 (spanning integer range 0-255), then some groupings
of regions get skipped, picking up again at ~line 415 with the comment
about mri_aparc2aseg (integer range 1000-2035, the max of which seems to be
the largest int in the aparc+aseg), and then is there a jump again to line
1079, starting with the comment about the --a2009s flag (integer range
11100-12175, the last of which seems to be the largest int in the
aparc+aseg2009)?

Is that a correct set of regions that are returned?  And out of that
combined set, we can deselect any of the "MatchValues" of
WM/CSF/background/etc. to be left with GM?

Thanks,
pt


On Tue, Nov 8, 2016 at 1:32 PM, Douglas Greve 
wrote:

> Actually, what it does is to binarize all the labels that it thinks are
> not GM, and then invert the mask to give GM. for what it is worth, there
> are the non-GM numbers
> MatchValues[nMatch++] =  2;
>   MatchValues[nMatch++] = 41;
>   MatchValues[nMatch++] = 77;
>   MatchValues[nMatch++] = 251;
>   MatchValues[nMatch++] = 252;
>   MatchValues[nMatch++] = 253;
>   MatchValues[nMatch++] = 254;
>   MatchValues[nMatch++] = 255;
>   MatchValues[nMatch++] =  7; // Cerebellar WM
>   MatchValues[nMatch++] = 46; // Cerebellar WM
>   MatchValues[nMatch++] =  4; // Left-Lateral-Ventricle
>   MatchValues[nMatch++] =  5; // Left-Inf-Lat-Vent
>   MatchValues[nMatch++] = 14; // 3rd-Ventricle
>   MatchValues[nMatch++] = 43; // Right-Lateral-Ventricle
>   MatchValues[nMatch++] = 44; // Right-Inf-Lat-Vent
>   MatchValues[nMatch++] = 15; // 4th-Ventricle
>   MatchValues[nMatch++] = 72; // 5th-Ventricle
>   MatchValues[nMatch++] = 31; // Left-choroid-plexus
>   MatchValues[nMatch++] = 63; // Right-choroid-plexus
>   MatchValues[nMatch++] =  0; // Background
>   MatchValues[nMatch++] = 24; // CSF
>
>
> On 11/8/16 1:06 PM, P Taylor wrote:
>
> OK.  But going back to my question that kicked this thread off, actually
> what I was looking for was just such a rule.
>
> I could make a fairly solid list of GM from using this new "mri_binarize
> --gm " on several recon-all outputs.  Would it be possible to have the
> rule (presumably a list of numbers corresponding to GM ROIs?) so I can have
> as secure a set of GM labels as possible?
>
> Thanks,
> pt
>
>
> On Tue, Nov 8, 2016 at 12:29 PM, Douglas Greve 
> wrote:
>
>> Yes. It  just uses a rule on the numbers that it expects to be GM. At
>> some point, I'll add both tissue type and laterality info to the ROIs, but
>> not for version 6
>>
>> On 11/8/16 12:03 PM, P Taylor wrote:
>>
>> And a final question, which might be a silly one--
>> This GM map applies to both the aparc.a2009s+aseg.mgz and aparc+aseg.mgz
>> files, right?
>>
>> Running "mri_binarize --gm ..." on each of those files separately gave
>> the same mask-- I believe this should be a general property?
>>
>> Thanks,
>> pt
>>
>>
>> On Tue, Nov 8, 2016 at 11:57 AM, Douglas Greve > > wrote:
>>
>>> yes
>>>
>>> On 11/8/16 11:51 AM, P Taylor wrote:
>>>
>>> Ah, cool, that looks like it does the trick-- thanks much.
>>>
>>> Will that version of mri_binarize be in the next release of FS?
>>>
>>> Thanks,
>>> pt
>>>
>>>
>>>
>>> On Tue, Nov 8, 2016 at 11:35 AM, Douglas Greve <
>>> gr...@nmr.mgh.harvard.edu> wrote:
>>>
 Try this one https://gate.nmr.mgh.harvard.e
 du/safelinks/greve/mri_binarize

 On 11/8/16 11:26 AM, P Taylor wrote:

 Thanks, I'd like to try that.  However, my mri_binarize doesn't show
 that option, and when I try running it, that option isn't recognized:

 $ mri_binarize --gm --o map_gm.nii --i aparc+aseg.mgz
 ERROR: Option --gm unknown

 Looking at the mri_binarize help, I see '--wm' exists, and that does,
 indeed, produce a WM-looking volume.  I also see an option "--wm+vcsf";
 would subtracting that resulting map leave only GM?

 My version of FS is:
 --
 You are running this version of FreeSurfer:

   freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
 --

 In the online description of mri_binarize:
 https://surfer.nmr.mgh.harvard.edu/fswiki/mri_binarize
 I see a "--subcort-gm" option that doesn't appear to work for me, but I
 guess that isn't full WM.

 So, am I somehow behind the times?  From the download page:
 https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
 it looks like my v5.3 is the most currently available?

 ... and, in 

[Freesurfer] Longitudinal Stream on HCP Data

[Timothy Hendrickson]

Aww thank you for clarifying Michael. I definitely misread Matthew's post.

-Tim

Timothy Hendrickson
Department of Psychiatry
University of Minnesota
Mobile: 507-259-3434 (texts okay)
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[Freesurfer] Fwd: [HCP-Users] HCP to FreeSurfer Resampling

[Timothy Hendrickson]

FreeSurfer experts,

I am attempting to resample HCP data into FreeSurfer space with the
following how to document: https://wiki.humanconnectome.
org/display/PublicData/HCP+Users+FAQ.

I believe I have resampled the GIFTI file into fs_average space, however I
am running to problems visualizing it in freeview or tksurfer. Please see
the error message in the forwarded message below?

-Tim

Timothy Hendrickson
Department of Psychiatry
University of Minnesota
Mobile: 507-259-3434 (texts okay)

-- Forwarded message --
From: Timothy Hendrickson 
Date: Tue, Nov 8, 2016 at 8:51 AM
Subject: Re: [HCP-Users] HCP to FreeSurfer Resampling
To: Timothy Coalson 
Cc: "hcp-us...@humanconnectome.org" 


Hi Tim,

Thank you for taking a look at my script, I really appreciate it. I am now
running into another problem. After re-sampling into fs_average space I am
attempting to visualize that file as an overlay in tksurfer or freeview
(freesurfer visualization tools) however I receive the following
error: *mriseadGIFTIfile:
mris is NULL! found when parsing file rh.43242.32k_TJH_fsavg.func.gii*. I
know that freesurfer can handle GIFTI file so that is not the problem. I
wonder if the GIFTI file was created incorrectly...

Any advice?

-Tim


Timothy Hendrickson
Department of Psychiatry
University of Minnesota
Mobile: 507-259-3434 (texts okay)
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Re: [Freesurfer] mapping ROI to surface space

[Bruce Fischl]

hou could do it easily enough in matlab with read_label.m and 
write_wfile.m, but as Doug says, w files are a goofy format that we never 
use anymore.


 On Tue, 8 Nov 2016, Douglas Greve wrote:


Not sure. We are trying to get away from .w files for this reason. Can
you use something other than a w file?


On 11/8/16 12:35 PM, Andrews, Derek wrote:

Thank you Doug that worked perfectly.

Is it possible then to go back to a .w from a label?



Derek Sayre Andrews, MSc
PhD Candidate

The Sackler Institute for Translational Neurodevelopment
Department of Forensic and Neurodevelopmental Sciences
Institute of Psychiatry, Psychology & Neuroscience, King's College London

Telephone: +44 (0)20 7848 5701
Email: derek.andr...@kcl.ac.uk





On 08/11/2016 16:10, "Douglas Greve"  wrote:


Use mri_surf2surf to convert it to an mgh or mgz file, then use
mri_cor2label with the --surf option to convert it to a label


On 11/8/16 9:41 AM, Andrews, Derek wrote:

Hi Bruce and Freesurfer developers,

Thank you. Any suggestions on converting a binary .w file to a label
would
be very helpful.

Best, Derek



Derek Sayre Andrews, MSc
PhD Candidate

The Sackler Institute for Translational Neurodevelopment
Department of Forensic and Neurodevelopmental Sciences
Institute of Psychiatry, Psychology & Neuroscience, King's College
London

Telephone: +44 (0)20 7848 5701
Email: derek.andr...@kcl.ac.uk





On 08/11/2016 14:04, "Bruce Fischl"  wrote:


Hi Derek

I'll cc the FS list so others can answer. It depends on the reason the
holes exist.  It also depends on the size of the holes. The dev version
of
mri_label2labels supports morphological close operations. It takes an
integer parameter which should be about the radius of the holes you
would
like to fill in. Note that this will also fill in some concavities in
the
boundary of the label.

cheers
Bruce


On Tue, 8 Nov 2016, Andrews, Derek wrote:


Hi Bruce,

Apologies for contacting you directly but I’m not sure if my message
is
getting through to the list.

I have gotten ahold of the dev version of mri_label2label.

Currently I have a .w file that I need to “fill in the holes” on.
Could
you please specify the steps I will need to take to make my .w file an
acceptable input for mri_label2label, and any recommendations you may
have
for the value of N for the —close flag.

Any help you could provide would be appreciated.

Best, Derek





Derek Sayre Andrews, MSc
PhD Candidate

The Sackler Institute for Translational Neurodevelopment
Department of Forensic and Neurodevelopmental Sciences
Institute of Psychiatry, Psychology & Neuroscience, King's College
London

Telephone: +44 (0)20 7848 5701
Email: derek.andr...@kcl.ac.uk





On 28/10/2016 15:53, "Bruce Fischl" 
wrote:


Hi Derek

I think the dev version of mri_label2label supports
open/close/dilate/erode
operations:

mri_label2label --help
USAGE: mri_label2label.bin

 --srclabel input label file

 --erode  N erode the label N times before writing
 --open   N open the label N times before writing
 --close  N close the label N times before writing
 --dilate  Ndilate the label N times before writing
   .
.
.

if your version doesn't have these operations let us know and we can
get
you an updated one

cheers
Bruce



On Fri, 28 Oct 2016,
Andrews, Derek wrote:


Hi Bruce,

As always thank you for your prompt reply.

For the morphological close operation, would you suggest using
mris_fill
on the surface ROI I created and then running mri_vol2surf again on
the
volume output by mris_fill?

Best, Derek



Derek Sayre Andrews, MSc
PhD Candidate

The Sackler Institute for Translational Neurodevelopment
Department of Forensic and Neurodevelopmental Sciences
Institute of Psychiatry, Psychology & Neuroscience, King's College
London

Telephone: +44 (0)20 7848 5701
Email: derek.andr...@kcl.ac.uk





On 28/10/2016 14:54, "Bruce Fischl" 
wrote:


p.s. you could remove many/most of these holes using a
morphological
close operation
On Fri, 28 Oct 2016, Andrews, Derek wrote:


Hello Freesurfer Developers and Community,

I am looking to map a ROI.nii based on the MNI152 template to the
fsaverage
pial surface.

I have used the following commands

Bbregister ‹s fsaverage ‹mov MNI152.nii ‹reg register.dat
‹init-fsl
‹12
‹t1

Then

mri_vol2surf ‹src ROI.nii ‹out ROI.mgh ‹srcreg register.dat ‹hemi
lh

The ROI appears to be in the right place however is very blotchy.
Have I
missed a step? Or is this correct?

See bellow a picture of the ROI highlighted in FSL and in tksurfer
after
mapped using the above.

Thank you for your support,

Best, Derek

[IMAGE]







___
__
__
__
___

Derek Sayre 

Re: [Freesurfer] mapping ROI to surface space

[Douglas Greve]

Not sure. We are trying to get away from .w files for this reason. Can 
you use something other than a w file?


On 11/8/16 12:35 PM, Andrews, Derek wrote:
> Thank you Doug that worked perfectly.
>
> Is it possible then to go back to a .w from a label?
>
>
> 
> Derek Sayre Andrews, MSc
> PhD Candidate
>
> The Sackler Institute for Translational Neurodevelopment
> Department of Forensic and Neurodevelopmental Sciences
> Institute of Psychiatry, Psychology & Neuroscience, King's College London
>
> Telephone: +44 (0)20 7848 5701
> Email: derek.andr...@kcl.ac.uk
>
>
>
>
>
> On 08/11/2016 16:10, "Douglas Greve"  wrote:
>
>> Use mri_surf2surf to convert it to an mgh or mgz file, then use
>> mri_cor2label with the --surf option to convert it to a label
>>
>>
>> On 11/8/16 9:41 AM, Andrews, Derek wrote:
>>> Hi Bruce and Freesurfer developers,
>>>
>>> Thank you. Any suggestions on converting a binary .w file to a label
>>> would
>>> be very helpful.
>>>
>>> Best, Derek
>>>
>>>
>>> 
>>> Derek Sayre Andrews, MSc
>>> PhD Candidate
>>>
>>> The Sackler Institute for Translational Neurodevelopment
>>> Department of Forensic and Neurodevelopmental Sciences
>>> Institute of Psychiatry, Psychology & Neuroscience, King's College
>>> London
>>>
>>> Telephone: +44 (0)20 7848 5701
>>> Email: derek.andr...@kcl.ac.uk
>>>
>>>
>>>
>>>
>>>
>>> On 08/11/2016 14:04, "Bruce Fischl"  wrote:
>>>
 Hi Derek

 I'll cc the FS list so others can answer. It depends on the reason the
 holes exist.  It also depends on the size of the holes. The dev version
 of
 mri_label2labels supports morphological close operations. It takes an
 integer parameter which should be about the radius of the holes you
 would
 like to fill in. Note that this will also fill in some concavities in
 the
 boundary of the label.

 cheers
 Bruce


 On Tue, 8 Nov 2016, Andrews, Derek wrote:

> Hi Bruce,
>
> Apologies for contacting you directly but I’m not sure if my message
> is
> getting through to the list.
>
> I have gotten ahold of the dev version of mri_label2label.
>
> Currently I have a .w file that I need to “fill in the holes” on.
> Could
> you please specify the steps I will need to take to make my .w file an
> acceptable input for mri_label2label, and any recommendations you may
> have
> for the value of N for the —close flag.
>
> Any help you could provide would be appreciated.
>
> Best, Derek
>
>
>
>
> 
> Derek Sayre Andrews, MSc
> PhD Candidate
>
> The Sackler Institute for Translational Neurodevelopment
> Department of Forensic and Neurodevelopmental Sciences
> Institute of Psychiatry, Psychology & Neuroscience, King's College
> London
>
> Telephone: +44 (0)20 7848 5701
> Email: derek.andr...@kcl.ac.uk
>
>
>
>
>
> On 28/10/2016 15:53, "Bruce Fischl" 
> wrote:
>
>> Hi Derek
>>
>> I think the dev version of mri_label2label supports
>> open/close/dilate/erode
>> operations:
>>
>> mri_label2label --help
>> USAGE: mri_label2label.bin
>>
>>  --srclabel input label file
>>
>>  --erode  N erode the label N times before writing
>>  --open   N open the label N times before writing
>>  --close  N close the label N times before writing
>>  --dilate  Ndilate the label N times before writing
>>.
>> .
>> .
>>
>> if your version doesn't have these operations let us know and we can
>> get
>> you an updated one
>>
>> cheers
>> Bruce
>>
>>
>>
>> On Fri, 28 Oct 2016,
>> Andrews, Derek wrote:
>>
>>> Hi Bruce,
>>>
>>> As always thank you for your prompt reply.
>>>
>>> For the morphological close operation, would you suggest using
>>> mris_fill
>>> on the surface ROI I created and then running mri_vol2surf again on
>>> the
>>> volume output by mris_fill?
>>>
>>> Best, Derek
>>>
>>>
>>> 
>>> Derek Sayre Andrews, MSc
>>> PhD Candidate
>>>
>>> The Sackler Institute for Translational Neurodevelopment
>>> Department of Forensic and Neurodevelopmental Sciences
>>> Institute of Psychiatry, Psychology & Neuroscience, King's College
>>> London
>>>
>>> Telephone: +44 (0)20 7848 5701
>>> Email: derek.andr...@kcl.ac.uk
>>>
>>>
>>>
>>>
>>>
>>> On 28/10/2016 14:54, "Bruce Fischl" 
>>> wrote:
>>>
 p.s. you could remove many/most of these holes using a
 morphological
 close operation

Re: [Freesurfer] GM ROI list?

[Douglas Greve]

Actually, what it does is to binarize all the labels that it thinks are 
not GM, and then invert the mask to give GM. for what it is worth, there 
are the non-GM numbers


MatchValues[nMatch++] =  2;
  MatchValues[nMatch++] = 41;
  MatchValues[nMatch++] = 77;
  MatchValues[nMatch++] = 251;
  MatchValues[nMatch++] = 252;
  MatchValues[nMatch++] = 253;
  MatchValues[nMatch++] = 254;
  MatchValues[nMatch++] = 255;
  MatchValues[nMatch++] =  7; // Cerebellar WM
  MatchValues[nMatch++] = 46; // Cerebellar WM
  MatchValues[nMatch++] =  4; // Left-Lateral-Ventricle
  MatchValues[nMatch++] =  5; // Left-Inf-Lat-Vent
  MatchValues[nMatch++] = 14; // 3rd-Ventricle
  MatchValues[nMatch++] = 43; // Right-Lateral-Ventricle
  MatchValues[nMatch++] = 44; // Right-Inf-Lat-Vent
  MatchValues[nMatch++] = 15; // 4th-Ventricle
  MatchValues[nMatch++] = 72; // 5th-Ventricle
  MatchValues[nMatch++] = 31; // Left-choroid-plexus
  MatchValues[nMatch++] = 63; // Right-choroid-plexus
  MatchValues[nMatch++] =  0; // Background
  MatchValues[nMatch++] = 24; // CSF

On 11/8/16 1:06 PM, P Taylor wrote:
OK.  But going back to my question that kicked this thread off, 
actually what I was looking for was just such a rule.


I could make a fairly solid list of GM from using this new 
"mri_binarize --gm " on several recon-all outputs. Would it be 
possible to have the rule (presumably a list of numbers corresponding 
to GM ROIs?) so I can have as secure a set of GM labels as possible?


Thanks,
pt


On Tue, Nov 8, 2016 at 12:29 PM, Douglas Greve 
> wrote:


Yes. It  just uses a rule on the numbers that it expects to be GM.
At some point, I'll add both tissue type and laterality info to
the ROIs, but not for version 6


On 11/8/16 12:03 PM, P Taylor wrote:

And a final question, which might be a silly one--
This GM map applies to both the aparc.a2009s+aseg.mgz and
aparc+aseg.mgz files, right?

Running "mri_binarize --gm ..." on each of those files separately
gave the same mask-- I believe this should be a general property?

Thanks,
pt


On Tue, Nov 8, 2016 at 11:57 AM, Douglas Greve
> wrote:

yes


On 11/8/16 11:51 AM, P Taylor wrote:

Ah, cool, that looks like it does the trick-- thanks much.

Will that version of mri_binarize be in the next release of FS?

Thanks,
pt



On Tue, Nov 8, 2016 at 11:35 AM, Douglas Greve
> wrote:

Try this one
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_binarize



On 11/8/16 11:26 AM, P Taylor wrote:

Thanks, I'd like to try that. However, my mri_binarize
doesn't show that option, and when I try running it,
that option isn't recognized:

$ mri_binarize --gm --o map_gm.nii --i aparc+aseg.mgz
ERROR: Option --gm unknown

Looking at the mri_binarize help, I see '--wm' exists,
and that does, indeed, produce a WM-looking volume.  I
also see an option "--wm+vcsf"; would subtracting that
resulting map leave only GM?

My version of FS is:

--
You are running this version of FreeSurfer:

freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

--

In the online description of mri_binarize:
https://surfer.nmr.mgh.harvard.edu/fswiki/mri_binarize

I see a "--subcort-gm" option that doesn't appear to
work for me, but I guess that isn't full WM.

So, am I somehow behind the times?  From the download page:
https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall

it looks like my v5.3 is the most currently available?

... and, in case it's useful, the explicit version of
my mri_binarize (bottom line of the help) is:
$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50
greve Exp $

Thanks,
pt




On Tue, Nov 8, 2016 at 11:08 AM, Douglas Greve
> wrote:


We don't currently have that information (ie,
tissue type) stored with the ROI. One thing you can
do is to run mri_binarize with the --gm 

Re: [Freesurfer] GM ROI list?

[P Taylor]

OK.  But going back to my question that kicked this thread off, actually
what I was looking for was just such a rule.

I could make a fairly solid list of GM from using this new "mri_binarize
--gm " on several recon-all outputs.  Would it be possible to have the
rule (presumably a list of numbers corresponding to GM ROIs?) so I can have
as secure a set of GM labels as possible?

Thanks,
pt


On Tue, Nov 8, 2016 at 12:29 PM, Douglas Greve 
wrote:

> Yes. It  just uses a rule on the numbers that it expects to be GM. At some
> point, I'll add both tissue type and laterality info to the ROIs, but not
> for version 6
>
> On 11/8/16 12:03 PM, P Taylor wrote:
>
> And a final question, which might be a silly one--
> This GM map applies to both the aparc.a2009s+aseg.mgz and aparc+aseg.mgz
> files, right?
>
> Running "mri_binarize --gm ..." on each of those files separately gave the
> same mask-- I believe this should be a general property?
>
> Thanks,
> pt
>
>
> On Tue, Nov 8, 2016 at 11:57 AM, Douglas Greve 
> wrote:
>
>> yes
>>
>> On 11/8/16 11:51 AM, P Taylor wrote:
>>
>> Ah, cool, that looks like it does the trick-- thanks much.
>>
>> Will that version of mri_binarize be in the next release of FS?
>>
>> Thanks,
>> pt
>>
>>
>>
>> On Tue, Nov 8, 2016 at 11:35 AM, Douglas Greve > > wrote:
>>
>>> Try this one https://gate.nmr.mgh.harvard.e
>>> du/safelinks/greve/mri_binarize
>>>
>>> On 11/8/16 11:26 AM, P Taylor wrote:
>>>
>>> Thanks, I'd like to try that.  However, my mri_binarize doesn't show
>>> that option, and when I try running it, that option isn't recognized:
>>>
>>> $ mri_binarize --gm --o map_gm.nii --i aparc+aseg.mgz
>>> ERROR: Option --gm unknown
>>>
>>> Looking at the mri_binarize help, I see '--wm' exists, and that does,
>>> indeed, produce a WM-looking volume.  I also see an option "--wm+vcsf";
>>> would subtracting that resulting map leave only GM?
>>>
>>> My version of FS is:
>>> --
>>> You are running this version of FreeSurfer:
>>>
>>>   freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
>>> --
>>>
>>> In the online description of mri_binarize:
>>> https://surfer.nmr.mgh.harvard.edu/fswiki/mri_binarize
>>> I see a "--subcort-gm" option that doesn't appear to work for me, but I
>>> guess that isn't full WM.
>>>
>>> So, am I somehow behind the times?  From the download page:
>>> https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
>>> it looks like my v5.3 is the most currently available?
>>>
>>> ... and, in case it's useful, the explicit version of my mri_binarize
>>> (bottom line of the help) is:
>>> $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
>>>
>>> Thanks,
>>> pt
>>>
>>>
>>>
>>>
>>> On Tue, Nov 8, 2016 at 11:08 AM, Douglas Greve <
>>> gr...@nmr.mgh.harvard.edu> wrote:
>>>

 We don't currently have that information (ie, tissue type) stored with
 the ROI. One thing you can do is to run mri_binarize with the --gm option
 on aparc+aseg.mgz This uses some rules to determine what is GM and creates
 a mask of GM. You can then feed this into mri_segstats with --mask, and it
 should only return ROIs that are in the GM mask.

 On 11/7/16 8:10 PM, P Taylor wrote:

 Thanks, that's useful for getting the ROI volumes and a list of all
 that's been found for a particular data set.

 I would still like to have a way to identify a listed region as gray
 matter or not so that I can parse the file for only GM regions that have
 been returned, particularly as different numbers of ROIs are typically
 returned in an aparc+aseg file.

 I see in the aseg.stats file that there are volumetric summations for
 GM quantities, such as:
 # Measure lhCortex, lhCortexVol, Left hemisphere cortical gray matter
 volume, 238183.759207, mm^3
 # Measure rhCortex, rhCortexVol, Right hemisphere cortical gray matter
 volume, 240824.502797, mm^3
 # Measure Cortex, CortexVol, Total cortical gray matter volume,
 479008.262004, mm^3
 
 # Measure SubCortGray, SubCortGrayVol, Subcortical gray matter volume,
 57815.00, mm^3
 # Measure TotalGray, TotalGrayVol, Total gray matter volume,
 643956.262004, mm^3

 Are these calculated by summing individual ROI volumes, so that a list
 of all possible GM volumes does already exist somewhere?

 Thanks,
 pt





 On Mon, Nov 7, 2016 at 3:39 PM, Douglas N Greve <
 gr...@nmr.mgh.harvard.edu> wrote:

> I don't know that we have a complete list in one place of just the
> aparc+aseg ROIs, but you can get one by running
>
> mri_segstats --seg aparc+aseg.mgz --ctab-default --sum sum.dat
>
> then look in the sum.dat file
>
>
> On 11/03/2016 04:32 

Re: [Freesurfer] mapping ROI to surface space

[Douglas Greve]

use mri_label2label with the --outmask option


On 11/8/16 12:37 PM, Andrews, Derek wrote:
> Apologies I meant from a label to a .mgh
>
> Best, Derek
>
>
> 
> Derek Sayre Andrews, MSc
> PhD Candidate
>
> The Sackler Institute for Translational Neurodevelopment
> Department of Forensic and Neurodevelopmental Sciences
> Institute of Psychiatry, Psychology & Neuroscience, King's College London
>
> Telephone: +44 (0)20 7848 5701
> Email: derek.andr...@kcl.ac.uk
>
>
>
>
>
> On 08/11/2016 17:35, "Andrews, Derek"  wrote:
>
>> This sender failed our fraud detection checks and may not be who they
>> appear to be. Learn about spoofing at http://aka.ms/LearnAboutSpoofing
>>
>> Thank you Doug that worked perfectly.
>>
>> Is it possible then to go back to a .w from a label?
>>
>>
>> 
>> Derek Sayre Andrews, MSc
>> PhD Candidate
>>
>> The Sackler Institute for Translational Neurodevelopment
>> Department of Forensic and Neurodevelopmental Sciences
>> Institute of Psychiatry, Psychology & Neuroscience, King's College London
>>
>> Telephone: +44 (0)20 7848 5701
>> Email: derek.andr...@kcl.ac.uk
>>
>>
>>
>>
>>
>> On 08/11/2016 16:10, "Douglas Greve"  wrote:
>>
>>> Use mri_surf2surf to convert it to an mgh or mgz file, then use
>>> mri_cor2label with the --surf option to convert it to a label
>>>
>>>
>>> On 11/8/16 9:41 AM, Andrews, Derek wrote:
 Hi Bruce and Freesurfer developers,

 Thank you. Any suggestions on converting a binary .w file to a label
 would
 be very helpful.

 Best, Derek


 
 Derek Sayre Andrews, MSc
 PhD Candidate

 The Sackler Institute for Translational Neurodevelopment
 Department of Forensic and Neurodevelopmental Sciences
 Institute of Psychiatry, Psychology & Neuroscience, King's College
 London

 Telephone: +44 (0)20 7848 5701
 Email: derek.andr...@kcl.ac.uk





 On 08/11/2016 14:04, "Bruce Fischl"  wrote:

> Hi Derek
>
> I'll cc the FS list so others can answer. It depends on the reason the
> holes exist.  It also depends on the size of the holes. The dev
> version
> of
> mri_label2labels supports morphological close operations. It takes an
> integer parameter which should be about the radius of the holes you
> would
> like to fill in. Note that this will also fill in some concavities in
> the
> boundary of the label.
>
> cheers
> Bruce
>
>
> On Tue, 8 Nov 2016, Andrews, Derek wrote:
>
>> Hi Bruce,
>>
>> Apologies for contacting you directly but I’m not sure if my message
>> is
>> getting through to the list.
>>
>> I have gotten ahold of the dev version of mri_label2label.
>>
>> Currently I have a .w file that I need to “fill in the holes” on.
>> Could
>> you please specify the steps I will need to take to make my .w file
>> an
>> acceptable input for mri_label2label, and any recommendations you may
>> have
>> for the value of N for the —close flag.
>>
>> Any help you could provide would be appreciated.
>>
>> Best, Derek
>>
>>
>>
>>
>> 
>> Derek Sayre Andrews, MSc
>> PhD Candidate
>>
>> The Sackler Institute for Translational Neurodevelopment
>> Department of Forensic and Neurodevelopmental Sciences
>> Institute of Psychiatry, Psychology & Neuroscience, King's College
>> London
>>
>> Telephone: +44 (0)20 7848 5701
>> Email: derek.andr...@kcl.ac.uk
>>
>>
>>
>>
>>
>> On 28/10/2016 15:53, "Bruce Fischl" 
>> wrote:
>>
>>> Hi Derek
>>>
>>> I think the dev version of mri_label2label supports
>>> open/close/dilate/erode
>>> operations:
>>>
>>> mri_label2label --help
>>> USAGE: mri_label2label.bin
>>>
>>>  --srclabel input label file
>>>
>>>  --erode  N erode the label N times before writing
>>>  --open   N open the label N times before writing
>>>  --close  N close the label N times before writing
>>>  --dilate  Ndilate the label N times before writing
>>>.
>>> .
>>> .
>>>
>>> if your version doesn't have these operations let us know and we can
>>> get
>>> you an updated one
>>>
>>> cheers
>>> Bruce
>>>
>>>
>>>
>>> On Fri, 28 Oct 2016,
>>> Andrews, Derek wrote:
>>>
 Hi Bruce,

 As always thank you for your prompt reply.

 For the morphological close operation, would you suggest using
 mris_fill
 on the surface ROI I created and then running mri_vol2surf again on
 

Re: [Freesurfer] mapping ROI to surface space

[Andrews, Derek]

Apologies I meant from a label to a .mgh

Best, Derek 



Derek Sayre Andrews, MSc
PhD Candidate

The Sackler Institute for Translational Neurodevelopment
Department of Forensic and Neurodevelopmental Sciences
Institute of Psychiatry, Psychology & Neuroscience, King's College London

Telephone: +44 (0)20 7848 5701
Email: derek.andr...@kcl.ac.uk





On 08/11/2016 17:35, "Andrews, Derek"  wrote:

>This sender failed our fraud detection checks and may not be who they
>appear to be. Learn about spoofing at http://aka.ms/LearnAboutSpoofing
>
>Thank you Doug that worked perfectly.
>
>Is it possible then to go back to a .w from a label?
>
>
>
>Derek Sayre Andrews, MSc
>PhD Candidate
>
>The Sackler Institute for Translational Neurodevelopment
>Department of Forensic and Neurodevelopmental Sciences
>Institute of Psychiatry, Psychology & Neuroscience, King's College London
>
>Telephone: +44 (0)20 7848 5701
>Email: derek.andr...@kcl.ac.uk
>
>
>
>
>
>On 08/11/2016 16:10, "Douglas Greve"  wrote:
>
>>Use mri_surf2surf to convert it to an mgh or mgz file, then use
>>mri_cor2label with the --surf option to convert it to a label
>>
>>
>>On 11/8/16 9:41 AM, Andrews, Derek wrote:
>>> Hi Bruce and Freesurfer developers,
>>>
>>> Thank you. Any suggestions on converting a binary .w file to a label
>>>would
>>> be very helpful.
>>>
>>> Best, Derek
>>>
>>>
>>> 
>>> Derek Sayre Andrews, MSc
>>> PhD Candidate
>>>
>>> The Sackler Institute for Translational Neurodevelopment
>>> Department of Forensic and Neurodevelopmental Sciences
>>> Institute of Psychiatry, Psychology & Neuroscience, King's College
>>>London
>>>
>>> Telephone: +44 (0)20 7848 5701
>>> Email: derek.andr...@kcl.ac.uk
>>>
>>>
>>>
>>>
>>>
>>> On 08/11/2016 14:04, "Bruce Fischl"  wrote:
>>>
 Hi Derek

 I'll cc the FS list so others can answer. It depends on the reason the
 holes exist.  It also depends on the size of the holes. The dev
version
 of
 mri_label2labels supports morphological close operations. It takes an
 integer parameter which should be about the radius of the holes you
would
 like to fill in. Note that this will also fill in some concavities in
the
 boundary of the label.

 cheers
 Bruce


 On Tue, 8 Nov 2016, Andrews, Derek wrote:

> Hi Bruce,
>
> Apologies for contacting you directly but I’m not sure if my message
>is
> getting through to the list.
>
> I have gotten ahold of the dev version of mri_label2label.
>
> Currently I have a .w file that I need to “fill in the holes” on.
>Could
> you please specify the steps I will need to take to make my .w file
>an
> acceptable input for mri_label2label, and any recommendations you may
> have
> for the value of N for the —close flag.
>
> Any help you could provide would be appreciated.
>
> Best, Derek
>
>
>
>
> 
> Derek Sayre Andrews, MSc
> PhD Candidate
>
> The Sackler Institute for Translational Neurodevelopment
> Department of Forensic and Neurodevelopmental Sciences
> Institute of Psychiatry, Psychology & Neuroscience, King's College
> London
>
> Telephone: +44 (0)20 7848 5701
> Email: derek.andr...@kcl.ac.uk
>
>
>
>
>
> On 28/10/2016 15:53, "Bruce Fischl" 
>wrote:
>
>> Hi Derek
>>
>> I think the dev version of mri_label2label supports
>> open/close/dilate/erode
>> operations:
>>
>> mri_label2label --help
>> USAGE: mri_label2label.bin
>>
>> --srclabel input label file
>>
>> --erode  N erode the label N times before writing
>> --open   N open the label N times before writing
>> --close  N close the label N times before writing
>> --dilate  Ndilate the label N times before writing
>>   .
>> .
>> .
>>
>> if your version doesn't have these operations let us know and we can
>> get
>> you an updated one
>>
>> cheers
>> Bruce
>>
>>
>>
>> On Fri, 28 Oct 2016,
>> Andrews, Derek wrote:
>>
>>> Hi Bruce,
>>>
>>> As always thank you for your prompt reply.
>>>
>>> For the morphological close operation, would you suggest using
>>> mris_fill
>>> on the surface ROI I created and then running mri_vol2surf again on
>>> the
>>> volume output by mris_fill?
>>>
>>> Best, Derek
>>>
>>>
>>> 
>>> Derek Sayre Andrews, MSc
>>> PhD Candidate
>>>
>>> The Sackler Institute for Translational Neurodevelopment
>>> Department of Forensic and 

Re: [Freesurfer] mapping ROI to surface space

[Andrews, Derek]

Thank you Doug that worked perfectly.

Is it possible then to go back to a .w from a label?



Derek Sayre Andrews, MSc
PhD Candidate

The Sackler Institute for Translational Neurodevelopment
Department of Forensic and Neurodevelopmental Sciences
Institute of Psychiatry, Psychology & Neuroscience, King's College London

Telephone: +44 (0)20 7848 5701
Email: derek.andr...@kcl.ac.uk





On 08/11/2016 16:10, "Douglas Greve"  wrote:

>Use mri_surf2surf to convert it to an mgh or mgz file, then use
>mri_cor2label with the --surf option to convert it to a label
>
>
>On 11/8/16 9:41 AM, Andrews, Derek wrote:
>> Hi Bruce and Freesurfer developers,
>>
>> Thank you. Any suggestions on converting a binary .w file to a label
>>would
>> be very helpful.
>>
>> Best, Derek
>>
>>
>> 
>> Derek Sayre Andrews, MSc
>> PhD Candidate
>>
>> The Sackler Institute for Translational Neurodevelopment
>> Department of Forensic and Neurodevelopmental Sciences
>> Institute of Psychiatry, Psychology & Neuroscience, King's College
>>London
>>
>> Telephone: +44 (0)20 7848 5701
>> Email: derek.andr...@kcl.ac.uk
>>
>>
>>
>>
>>
>> On 08/11/2016 14:04, "Bruce Fischl"  wrote:
>>
>>> Hi Derek
>>>
>>> I'll cc the FS list so others can answer. It depends on the reason the
>>> holes exist.  It also depends on the size of the holes. The dev version
>>> of
>>> mri_label2labels supports morphological close operations. It takes an
>>> integer parameter which should be about the radius of the holes you
>>>would
>>> like to fill in. Note that this will also fill in some concavities in
>>>the
>>> boundary of the label.
>>>
>>> cheers
>>> Bruce
>>>
>>>
>>> On Tue, 8 Nov 2016, Andrews, Derek wrote:
>>>
 Hi Bruce,

 Apologies for contacting you directly but I’m not sure if my message
is
 getting through to the list.

 I have gotten ahold of the dev version of mri_label2label.

 Currently I have a .w file that I need to “fill in the holes” on.
Could
 you please specify the steps I will need to take to make my .w file an
 acceptable input for mri_label2label, and any recommendations you may
 have
 for the value of N for the —close flag.

 Any help you could provide would be appreciated.

 Best, Derek




 
 Derek Sayre Andrews, MSc
 PhD Candidate

 The Sackler Institute for Translational Neurodevelopment
 Department of Forensic and Neurodevelopmental Sciences
 Institute of Psychiatry, Psychology & Neuroscience, King's College
 London

 Telephone: +44 (0)20 7848 5701
 Email: derek.andr...@kcl.ac.uk





 On 28/10/2016 15:53, "Bruce Fischl" 
wrote:

> Hi Derek
>
> I think the dev version of mri_label2label supports
> open/close/dilate/erode
> operations:
>
> mri_label2label --help
> USAGE: mri_label2label.bin
>
> --srclabel input label file
>
> --erode  N erode the label N times before writing
> --open   N open the label N times before writing
> --close  N close the label N times before writing
> --dilate  Ndilate the label N times before writing
>   .
> .
> .
>
> if your version doesn't have these operations let us know and we can
> get
> you an updated one
>
> cheers
> Bruce
>
>
>
> On Fri, 28 Oct 2016,
> Andrews, Derek wrote:
>
>> Hi Bruce,
>>
>> As always thank you for your prompt reply.
>>
>> For the morphological close operation, would you suggest using
>> mris_fill
>> on the surface ROI I created and then running mri_vol2surf again on
>> the
>> volume output by mris_fill?
>>
>> Best, Derek
>>
>>
>> 
>> Derek Sayre Andrews, MSc
>> PhD Candidate
>>
>> The Sackler Institute for Translational Neurodevelopment
>> Department of Forensic and Neurodevelopmental Sciences
>> Institute of Psychiatry, Psychology & Neuroscience, King's College
>> London
>>
>> Telephone: +44 (0)20 7848 5701
>> Email: derek.andr...@kcl.ac.uk
>>
>>
>>
>>
>>
>> On 28/10/2016 14:54, "Bruce Fischl" 
>> wrote:
>>
>>> p.s. you could remove many/most of these holes using a
>>>morphological
>>> close operation
>>> On Fri, 28 Oct 2016, Andrews, Derek wrote:
>>>
 Hello Freesurfer Developers and Community,

 I am looking to map a ROI.nii based on the MNI152 template to the
 fsaverage
 pial surface.

 I have used the following commands

 Bbregister ‹s fsaverage ‹mov MNI152.nii ‹reg 

Re: [Freesurfer] GM ROI list?

[Douglas Greve]

Yes. It  just uses a rule on the numbers that it expects to be GM. At 
some point, I'll add both tissue type and laterality info to the ROIs, 
but not for version 6



On 11/8/16 12:03 PM, P Taylor wrote:

And a final question, which might be a silly one--
This GM map applies to both the aparc.a2009s+aseg.mgz and 
aparc+aseg.mgz files, right?


Running "mri_binarize --gm ..." on each of those files separately gave 
the same mask-- I believe this should be a general property?


Thanks,
pt


On Tue, Nov 8, 2016 at 11:57 AM, Douglas Greve 
> wrote:


yes


On 11/8/16 11:51 AM, P Taylor wrote:

Ah, cool, that looks like it does the trick-- thanks much.

Will that version of mri_binarize be in the next release of FS?

Thanks,
pt



On Tue, Nov 8, 2016 at 11:35 AM, Douglas Greve
> wrote:

Try this one
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_binarize



On 11/8/16 11:26 AM, P Taylor wrote:

Thanks, I'd like to try that. However, my mri_binarize
doesn't show that option, and when I try running it, that
option isn't recognized:

$ mri_binarize --gm --o map_gm.nii --i aparc+aseg.mgz
ERROR: Option --gm unknown

Looking at the mri_binarize help, I see '--wm' exists, and
that does, indeed, produce a WM-looking volume.  I also see
an option "--wm+vcsf";  would subtracting that resulting map
leave only GM?

My version of FS is:
--
You are running this version of FreeSurfer:

  freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
--

In the online description of mri_binarize:
https://surfer.nmr.mgh.harvard.edu/fswiki/mri_binarize

I see a "--subcort-gm" option that doesn't appear to work
for me, but I guess that isn't full WM.

So, am I somehow behind the times?  From the download page:
https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall

it looks like my v5.3 is the most currently available?

... and, in case it's useful, the explicit version of my
mri_binarize (bottom line of the help) is:
$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $

Thanks,
pt




On Tue, Nov 8, 2016 at 11:08 AM, Douglas Greve
> wrote:


We don't currently have that information (ie, tissue
type) stored with the ROI. One thing you can do is to
run mri_binarize with the --gm option on aparc+aseg.mgz
This uses some rules to determine what is GM and creates
a mask of GM. You can then feed this into mri_segstats
with --mask, and it should only return ROIs that are in
the GM mask.


On 11/7/16 8:10 PM, P Taylor wrote:

Thanks, that's useful for getting the ROI volumes and a
list of all that's been found for a particular data set.

I would still like to have a way to identify a listed
region as gray matter or not so that I can parse the
file for only GM regions that have been returned,
particularly as different numbers of ROIs are typically
returned in an aparc+aseg file.

I see in the aseg.stats file that there are volumetric
summations for GM quantities, such as:
# Measure lhCortex, lhCortexVol, Left hemisphere
cortical gray matter volume, 238183.759207, mm^3
# Measure rhCortex, rhCortexVol, Right hemisphere
cortical gray matter volume, 240824.502797, mm^3
# Measure Cortex, CortexVol, Total cortical gray matter
volume, 479008.262004, mm^3

# Measure SubCortGray, SubCortGrayVol, Subcortical gray
matter volume, 57815.00, mm^3
# Measure TotalGray, TotalGrayVol, Total gray matter
volume, 643956.262004, mm^3

Are these calculated by summing individual ROI volumes,
so that a list of all possible GM volumes does already
exist somewhere?

Thanks,
pt





On Mon, Nov 7, 2016 at 3:39 PM, Douglas N Greve
> wrote:

I don't know that we have a complete list in one
place of just the
aparc+aseg 

[Freesurfer] MP2RAGEs

[Torrisi, Sam (NIH/NIMH) [E]]

hi there,

will FS 6.0 have any special options for MP2RAGE sequences? specifically i'm 
trying to decide whether to collect MPRAGE or MP2RAGE T1s; either would be at 
0.7mm iso (7T data). i've heard skull-stripping is the main issue with the 
MP2RAGE and so i'm curious if FS 6.0 will have any adaptations for that. 
improved subcortical gm/wm contrast is what's drawing me towards MP2RAGE. 
thanks!

-Sam


Section on Neurobiology of Fear and Anxiety

National Institute of Mental Health
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Re: [Freesurfer] GM ROI list?

[P Taylor]

And a final question, which might be a silly one--
This GM map applies to both the aparc.a2009s+aseg.mgz and aparc+aseg.mgz
files, right?

Running "mri_binarize --gm ..." on each of those files separately gave the
same mask-- I believe this should be a general property?

Thanks,
pt


On Tue, Nov 8, 2016 at 11:57 AM, Douglas Greve 
wrote:

> yes
>
> On 11/8/16 11:51 AM, P Taylor wrote:
>
> Ah, cool, that looks like it does the trick-- thanks much.
>
> Will that version of mri_binarize be in the next release of FS?
>
> Thanks,
> pt
>
>
>
> On Tue, Nov 8, 2016 at 11:35 AM, Douglas Greve 
> wrote:
>
>> Try this one https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_binariz
>> e
>>
>> On 11/8/16 11:26 AM, P Taylor wrote:
>>
>> Thanks, I'd like to try that.  However, my mri_binarize doesn't show that
>> option, and when I try running it, that option isn't recognized:
>>
>> $ mri_binarize --gm --o map_gm.nii --i aparc+aseg.mgz
>> ERROR: Option --gm unknown
>>
>> Looking at the mri_binarize help, I see '--wm' exists, and that does,
>> indeed, produce a WM-looking volume.  I also see an option "--wm+vcsf";
>> would subtracting that resulting map leave only GM?
>>
>> My version of FS is:
>> --
>> You are running this version of FreeSurfer:
>>
>>   freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
>> --
>>
>> In the online description of mri_binarize:
>> https://surfer.nmr.mgh.harvard.edu/fswiki/mri_binarize
>> I see a "--subcort-gm" option that doesn't appear to work for me, but I
>> guess that isn't full WM.
>>
>> So, am I somehow behind the times?  From the download page:
>> https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
>> it looks like my v5.3 is the most currently available?
>>
>> ... and, in case it's useful, the explicit version of my mri_binarize
>> (bottom line of the help) is:
>> $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
>>
>> Thanks,
>> pt
>>
>>
>>
>>
>> On Tue, Nov 8, 2016 at 11:08 AM, Douglas Greve > > wrote:
>>
>>>
>>> We don't currently have that information (ie, tissue type) stored with
>>> the ROI. One thing you can do is to run mri_binarize with the --gm option
>>> on aparc+aseg.mgz This uses some rules to determine what is GM and creates
>>> a mask of GM. You can then feed this into mri_segstats with --mask, and it
>>> should only return ROIs that are in the GM mask.
>>>
>>> On 11/7/16 8:10 PM, P Taylor wrote:
>>>
>>> Thanks, that's useful for getting the ROI volumes and a list of all
>>> that's been found for a particular data set.
>>>
>>> I would still like to have a way to identify a listed region as gray
>>> matter or not so that I can parse the file for only GM regions that have
>>> been returned, particularly as different numbers of ROIs are typically
>>> returned in an aparc+aseg file.
>>>
>>> I see in the aseg.stats file that there are volumetric summations for GM
>>> quantities, such as:
>>> # Measure lhCortex, lhCortexVol, Left hemisphere cortical gray matter
>>> volume, 238183.759207, mm^3
>>> # Measure rhCortex, rhCortexVol, Right hemisphere cortical gray matter
>>> volume, 240824.502797, mm^3
>>> # Measure Cortex, CortexVol, Total cortical gray matter volume,
>>> 479008.262004, mm^3
>>> 
>>> # Measure SubCortGray, SubCortGrayVol, Subcortical gray matter volume,
>>> 57815.00, mm^3
>>> # Measure TotalGray, TotalGrayVol, Total gray matter volume,
>>> 643956.262004, mm^3
>>>
>>> Are these calculated by summing individual ROI volumes, so that a list
>>> of all possible GM volumes does already exist somewhere?
>>>
>>> Thanks,
>>> pt
>>>
>>>
>>>
>>>
>>>
>>> On Mon, Nov 7, 2016 at 3:39 PM, Douglas N Greve <
>>> gr...@nmr.mgh.harvard.edu> wrote:
>>>
 I don't know that we have a complete list in one place of just the
 aparc+aseg ROIs, but you can get one by running

 mri_segstats --seg aparc+aseg.mgz --ctab-default --sum sum.dat

 then look in the sum.dat file


 On 11/03/2016 04:32 PM, P Taylor wrote:
 > Is there an available list of GM regions within the list of regions in
 > the FreeSurferColorLUT.txt?
 >
 > (In particular, I am interested in a list of GM regions output in a
 > default run of recon-all, which seems to have a maximum regionnumber
 > of 2035.  But a full list is great, too-- I'm not sure which might be
 > already available or easier to generate.)
 >
 > I had thought of using the segmentation volumes to help me
 > differentiate ROIs. For example, I could get rid of regions that
 > overlap with the WM volume, but I think that the segmentation might
 > come from a slightly different bit of information than the sum of
 > segmented regions.  As shown in the attached slice image, if I
 > underlay the WM segmentation volume (color = 

Re: [Freesurfer] GM ROI list?

[Douglas Greve]

yes


On 11/8/16 11:51 AM, P Taylor wrote:

Ah, cool, that looks like it does the trick-- thanks much.

Will that version of mri_binarize be in the next release of FS?

Thanks,
pt



On Tue, Nov 8, 2016 at 11:35 AM, Douglas Greve 
> wrote:


Try this one
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_binarize



On 11/8/16 11:26 AM, P Taylor wrote:

Thanks, I'd like to try that.  However, my mri_binarize doesn't
show that option, and when I try running it, that option isn't
recognized:

$ mri_binarize --gm --o map_gm.nii --i aparc+aseg.mgz
ERROR: Option --gm unknown

Looking at the mri_binarize help, I see '--wm' exists, and that
does, indeed, produce a WM-looking volume.  I also see an option
"--wm+vcsf";  would subtracting that resulting map leave only GM?

My version of FS is:
--
You are running this version of FreeSurfer:

  freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
--

In the online description of mri_binarize:
https://surfer.nmr.mgh.harvard.edu/fswiki/mri_binarize

I see a "--subcort-gm" option that doesn't appear to work for me,
but I guess that isn't full WM.

So, am I somehow behind the times?  From the download page:
https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall

it looks like my v5.3 is the most currently available?

... and, in case it's useful, the explicit version of my
mri_binarize (bottom line of the help) is:
$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $

Thanks,
pt




On Tue, Nov 8, 2016 at 11:08 AM, Douglas Greve
> wrote:


We don't currently have that information (ie, tissue type)
stored with the ROI. One thing you can do is to run
mri_binarize with the --gm option on aparc+aseg.mgz This uses
some rules to determine what is GM and creates a mask of GM.
You can then feed this into mri_segstats with --mask, and it
should only return ROIs that are in the GM mask.


On 11/7/16 8:10 PM, P Taylor wrote:

Thanks, that's useful for getting the ROI volumes and a list
of all that's been found for a particular data set.

I would still like to have a way to identify a listed region
as gray matter or not so that I can parse the file for only
GM regions that have been returned, particularly as
different numbers of ROIs are typically returned in an
aparc+aseg file.

I see in the aseg.stats file that there are volumetric
summations for GM quantities, such as:
# Measure lhCortex, lhCortexVol, Left hemisphere cortical
gray matter volume, 238183.759207, mm^3
# Measure rhCortex, rhCortexVol, Right hemisphere cortical
gray matter volume, 240824.502797, mm^3
# Measure Cortex, CortexVol, Total cortical gray matter
volume, 479008.262004, mm^3

# Measure SubCortGray, SubCortGrayVol, Subcortical gray
matter volume, 57815.00, mm^3
# Measure TotalGray, TotalGrayVol, Total gray matter volume,
643956.262004, mm^3

Are these calculated by summing individual ROI volumes, so
that a list of all possible GM volumes does already exist
somewhere?

Thanks,
pt





On Mon, Nov 7, 2016 at 3:39 PM, Douglas N Greve
> wrote:

I don't know that we have a complete list in one place
of just the
aparc+aseg ROIs, but you can get one by running

mri_segstats --seg aparc+aseg.mgz --ctab-default --sum
sum.dat

then look in the sum.dat file


On 11/03/2016 04:32 PM, P Taylor wrote:
> Is there an available list of GM regions within the
list of regions in
> the FreeSurferColorLUT.txt?
>
> (In particular, I am interested in a list of GM
regions output in a
> default run of recon-all, which seems to have a
maximum regionnumber
> of 2035.  But a full list is great, too-- I'm not sure
which might be
> already available or easier to generate.)
>
> I had thought of using the segmentation volumes to help me
> differentiate ROIs. For example, I could get rid of
regions that
> overlap with the WM volume, but I think that the
   

Re: [Freesurfer] GM ROI list?

[P Taylor]

Ah, cool, that looks like it does the trick-- thanks much.

Will that version of mri_binarize be in the next release of FS?

Thanks,
pt



On Tue, Nov 8, 2016 at 11:35 AM, Douglas Greve 
wrote:

> Try this one https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_binarize
>
> On 11/8/16 11:26 AM, P Taylor wrote:
>
> Thanks, I'd like to try that.  However, my mri_binarize doesn't show that
> option, and when I try running it, that option isn't recognized:
>
> $ mri_binarize --gm --o map_gm.nii --i aparc+aseg.mgz
> ERROR: Option --gm unknown
>
> Looking at the mri_binarize help, I see '--wm' exists, and that does,
> indeed, produce a WM-looking volume.  I also see an option "--wm+vcsf";
> would subtracting that resulting map leave only GM?
>
> My version of FS is:
> --
> You are running this version of FreeSurfer:
>
>   freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
> --
>
> In the online description of mri_binarize:
> https://surfer.nmr.mgh.harvard.edu/fswiki/mri_binarize
> I see a "--subcort-gm" option that doesn't appear to work for me, but I
> guess that isn't full WM.
>
> So, am I somehow behind the times?  From the download page:
> https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
> it looks like my v5.3 is the most currently available?
>
> ... and, in case it's useful, the explicit version of my mri_binarize
> (bottom line of the help) is:
> $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
>
> Thanks,
> pt
>
>
>
>
> On Tue, Nov 8, 2016 at 11:08 AM, Douglas Greve 
> wrote:
>
>>
>> We don't currently have that information (ie, tissue type) stored with
>> the ROI. One thing you can do is to run mri_binarize with the --gm option
>> on aparc+aseg.mgz This uses some rules to determine what is GM and creates
>> a mask of GM. You can then feed this into mri_segstats with --mask, and it
>> should only return ROIs that are in the GM mask.
>>
>> On 11/7/16 8:10 PM, P Taylor wrote:
>>
>> Thanks, that's useful for getting the ROI volumes and a list of all
>> that's been found for a particular data set.
>>
>> I would still like to have a way to identify a listed region as gray
>> matter or not so that I can parse the file for only GM regions that have
>> been returned, particularly as different numbers of ROIs are typically
>> returned in an aparc+aseg file.
>>
>> I see in the aseg.stats file that there are volumetric summations for GM
>> quantities, such as:
>> # Measure lhCortex, lhCortexVol, Left hemisphere cortical gray matter
>> volume, 238183.759207, mm^3
>> # Measure rhCortex, rhCortexVol, Right hemisphere cortical gray matter
>> volume, 240824.502797, mm^3
>> # Measure Cortex, CortexVol, Total cortical gray matter volume,
>> 479008.262004, mm^3
>> 
>> # Measure SubCortGray, SubCortGrayVol, Subcortical gray matter volume,
>> 57815.00, mm^3
>> # Measure TotalGray, TotalGrayVol, Total gray matter volume,
>> 643956.262004, mm^3
>>
>> Are these calculated by summing individual ROI volumes, so that a list of
>> all possible GM volumes does already exist somewhere?
>>
>> Thanks,
>> pt
>>
>>
>>
>>
>>
>> On Mon, Nov 7, 2016 at 3:39 PM, Douglas N Greve <
>> gr...@nmr.mgh.harvard.edu> wrote:
>>
>>> I don't know that we have a complete list in one place of just the
>>> aparc+aseg ROIs, but you can get one by running
>>>
>>> mri_segstats --seg aparc+aseg.mgz --ctab-default --sum sum.dat
>>>
>>> then look in the sum.dat file
>>>
>>>
>>> On 11/03/2016 04:32 PM, P Taylor wrote:
>>> > Is there an available list of GM regions within the list of regions in
>>> > the FreeSurferColorLUT.txt?
>>> >
>>> > (In particular, I am interested in a list of GM regions output in a
>>> > default run of recon-all, which seems to have a maximum regionnumber
>>> > of 2035.  But a full list is great, too-- I'm not sure which might be
>>> > already available or easier to generate.)
>>> >
>>> > I had thought of using the segmentation volumes to help me
>>> > differentiate ROIs. For example, I could get rid of regions that
>>> > overlap with the WM volume, but I think that the segmentation might
>>> > come from a slightly different bit of information than the sum of
>>> > segmented regions.  As shown in the attached slice image, if I
>>> > underlay the WM segmentation volume (color = white), and overlay a
>>> > "recon-all" parcellation+segmentation map (color = red for GM on
>>> > right, yellow for GM on left, and green for non-GM) to look for
>>> > overlap, I see that some of the WM seg volume overlaps with GM ROIs
>>> > (overlaps are isolated pink-ish voxels and light yellow voxels; one
>>> > highlighted in cross hairs).  I guess this difference occurs because
>>> > the segmentation volume comes from the surfaces themselves?
>>> >
>>> > Anyways, this makes me think that I can't automate finding the GM, and
>>> > I would 

Re: [Freesurfer] GM ROI list?

[Douglas Greve]

Try this one https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_binarize


On 11/8/16 11:26 AM, P Taylor wrote:
Thanks, I'd like to try that.  However, my mri_binarize doesn't show 
that option, and when I try running it, that option isn't recognized:


$ mri_binarize --gm --o map_gm.nii --i aparc+aseg.mgz
ERROR: Option --gm unknown

Looking at the mri_binarize help, I see '--wm' exists, and that does, 
indeed, produce a WM-looking volume.  I also see an option 
"--wm+vcsf";  would subtracting that resulting map leave only GM?


My version of FS is:
--
You are running this version of FreeSurfer:

  freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
--

In the online description of mri_binarize:
https://surfer.nmr.mgh.harvard.edu/fswiki/mri_binarize
I see a "--subcort-gm" option that doesn't appear to work for me, but 
I guess that isn't full WM.


So, am I somehow behind the times?  From the download page:
https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
it looks like my v5.3 is the most currently available?

... and, in case it's useful, the explicit version of my mri_binarize 
(bottom line of the help) is:

$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $

Thanks,
pt




On Tue, Nov 8, 2016 at 11:08 AM, Douglas Greve 
> wrote:



We don't currently have that information (ie, tissue type) stored
with the ROI. One thing you can do is to run mri_binarize with the
--gm option on aparc+aseg.mgz This uses some rules to determine
what is GM and creates a mask of GM. You can then feed this into
mri_segstats with --mask, and it should only return ROIs that are
in the GM mask.


On 11/7/16 8:10 PM, P Taylor wrote:

Thanks, that's useful for getting the ROI volumes and a list of
all that's been found for a particular data set.

I would still like to have a way to identify a listed region as
gray matter or not so that I can parse the file for only GM
regions that have been returned, particularly as different
numbers of ROIs are typically returned in an aparc+aseg file.

I see in the aseg.stats file that there are volumetric summations
for GM quantities, such as:
# Measure lhCortex, lhCortexVol, Left hemisphere cortical gray
matter volume, 238183.759207, mm^3
# Measure rhCortex, rhCortexVol, Right hemisphere cortical gray
matter volume, 240824.502797, mm^3
# Measure Cortex, CortexVol, Total cortical gray matter volume,
479008.262004, mm^3

# Measure SubCortGray, SubCortGrayVol, Subcortical gray matter
volume, 57815.00, mm^3
# Measure TotalGray, TotalGrayVol, Total gray matter volume,
643956.262004, mm^3

Are these calculated by summing individual ROI volumes, so that a
list of all possible GM volumes does already exist somewhere?

Thanks,
pt





On Mon, Nov 7, 2016 at 3:39 PM, Douglas N Greve
> wrote:

I don't know that we have a complete list in one place of
just the
aparc+aseg ROIs, but you can get one by running

mri_segstats --seg aparc+aseg.mgz --ctab-default --sum sum.dat

then look in the sum.dat file


On 11/03/2016 04:32 PM, P Taylor wrote:
> Is there an available list of GM regions within the list of
regions in
> the FreeSurferColorLUT.txt?
>
> (In particular, I am interested in a list of GM regions
output in a
> default run of recon-all, which seems to have a maximum
regionnumber
> of 2035.  But a full list is great, too-- I'm not sure
which might be
> already available or easier to generate.)
>
> I had thought of using the segmentation volumes to help me
> differentiate ROIs. For example, I could get rid of regions
that
> overlap with the WM volume, but I think that the
segmentation might
> come from a slightly different bit of information than the
sum of
> segmented regions.  As shown in the attached slice image, if I
> underlay the WM segmentation volume (color = white), and
overlay a
> "recon-all" parcellation+segmentation map (color = red for
GM on
> right, yellow for GM on left, and green for non-GM) to look for
> overlap, I see that some of the WM seg volume overlaps with
GM ROIs
> (overlaps are isolated pink-ish voxels and light yellow
voxels; one
> highlighted in cross hairs).  I guess this difference
occurs because
> the segmentation volume comes from the surfaces themselves?
>
> Anyways, this makes me think that I can't automate finding
the GM, and
> 

Re: [Freesurfer] GM ROI list?

[P Taylor]

Thanks, I'd like to try that.  However, my mri_binarize doesn't show that
option, and when I try running it, that option isn't recognized:

$ mri_binarize --gm --o map_gm.nii --i aparc+aseg.mgz
ERROR: Option --gm unknown

Looking at the mri_binarize help, I see '--wm' exists, and that does,
indeed, produce a WM-looking volume.  I also see an option "--wm+vcsf";
would subtracting that resulting map leave only GM?

My version of FS is:
--
You are running this version of FreeSurfer:

  freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
--

In the online description of mri_binarize:
https://surfer.nmr.mgh.harvard.edu/fswiki/mri_binarize
I see a "--subcort-gm" option that doesn't appear to work for me, but I
guess that isn't full WM.

So, am I somehow behind the times?  From the download page:
https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
it looks like my v5.3 is the most currently available?

... and, in case it's useful, the explicit version of my mri_binarize
(bottom line of the help) is:
$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $

Thanks,
pt




On Tue, Nov 8, 2016 at 11:08 AM, Douglas Greve 
wrote:

>
> We don't currently have that information (ie, tissue type) stored with the
> ROI. One thing you can do is to run mri_binarize with the --gm option on
> aparc+aseg.mgz This uses some rules to determine what is GM and creates a
> mask of GM. You can then feed this into mri_segstats with --mask, and it
> should only return ROIs that are in the GM mask.
>
> On 11/7/16 8:10 PM, P Taylor wrote:
>
> Thanks, that's useful for getting the ROI volumes and a list of all that's
> been found for a particular data set.
>
> I would still like to have a way to identify a listed region as gray
> matter or not so that I can parse the file for only GM regions that have
> been returned, particularly as different numbers of ROIs are typically
> returned in an aparc+aseg file.
>
> I see in the aseg.stats file that there are volumetric summations for GM
> quantities, such as:
> # Measure lhCortex, lhCortexVol, Left hemisphere cortical gray matter
> volume, 238183.759207, mm^3
> # Measure rhCortex, rhCortexVol, Right hemisphere cortical gray matter
> volume, 240824.502797, mm^3
> # Measure Cortex, CortexVol, Total cortical gray matter volume,
> 479008.262004, mm^3
> 
> # Measure SubCortGray, SubCortGrayVol, Subcortical gray matter volume,
> 57815.00, mm^3
> # Measure TotalGray, TotalGrayVol, Total gray matter volume,
> 643956.262004, mm^3
>
> Are these calculated by summing individual ROI volumes, so that a list of
> all possible GM volumes does already exist somewhere?
>
> Thanks,
> pt
>
>
>
>
>
> On Mon, Nov 7, 2016 at 3:39 PM, Douglas N Greve  > wrote:
>
>> I don't know that we have a complete list in one place of just the
>> aparc+aseg ROIs, but you can get one by running
>>
>> mri_segstats --seg aparc+aseg.mgz --ctab-default --sum sum.dat
>>
>> then look in the sum.dat file
>>
>>
>> On 11/03/2016 04:32 PM, P Taylor wrote:
>> > Is there an available list of GM regions within the list of regions in
>> > the FreeSurferColorLUT.txt?
>> >
>> > (In particular, I am interested in a list of GM regions output in a
>> > default run of recon-all, which seems to have a maximum regionnumber
>> > of 2035.  But a full list is great, too-- I'm not sure which might be
>> > already available or easier to generate.)
>> >
>> > I had thought of using the segmentation volumes to help me
>> > differentiate ROIs. For example, I could get rid of regions that
>> > overlap with the WM volume, but I think that the segmentation might
>> > come from a slightly different bit of information than the sum of
>> > segmented regions.  As shown in the attached slice image, if I
>> > underlay the WM segmentation volume (color = white), and overlay a
>> > "recon-all" parcellation+segmentation map (color = red for GM on
>> > right, yellow for GM on left, and green for non-GM) to look for
>> > overlap, I see that some of the WM seg volume overlaps with GM ROIs
>> > (overlaps are isolated pink-ish voxels and light yellow voxels; one
>> > highlighted in cross hairs).  I guess this difference occurs because
>> > the segmentation volume comes from the surfaces themselves?
>> >
>> > Anyways, this makes me think that I can't automate finding the GM, and
>> > I would rather go from LUT numbers, and hence the above question.
>> >
>> > Thanks,
>> > pt
>> >
>> >
>> >
>> > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> 

Re: [Freesurfer] Longitudinal Stream on HCP Data

[Bruce Fischl]

yes, thanks Mike, that is true as well. The new V6 works very nicely on 
data that is higher res than 1mm

On Tue, 8 Nov 2016, Harms, Michael wrote:



To clarify, in that post, Matt wasn’t saying that FS was going to
incorporate myelin maps.  Rather, the new (v6) version of FS, with its
support of data acquired with < 1 mm resolution, may eliminate the need for
some of the steps that are currently the HCP Pipelines that are there to
take full advantage of higher resolution structural acquisitions.

cheers,
-MH

-- 
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO  63110 Email: mha...@wustl.edu

From:  on behalf of Timothy
Hendrickson 
Reply-To: Freesurfer support list 
Date: Tuesday, November 8, 2016 at 9:15 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Longitudinal Stream on HCP Data

Hi Freesurfer/HCP experts,

I am curious if there is a way to incorporate HCP data (i.e. myelin maps)
into the FreeSurfer processing stream.
Matthew Glasser mentioned in a post on the HCP mailing list about a month
back that this is being actively worked on by FreeSurfer:
http://www.mail-archive.com/hcp-users@humanconnectome.org/msg03477.html.
Are there any workflows or development versions that I can download in order
to perform something like this.

Respectfully,

-Tim

Timothy Hendrickson
Department of Psychiatry
University of Minnesota
Mobile: 507-259-3434 (texts okay)

 





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Re: [Freesurfer] Fw: recon-all steps question

[Bruce Fischl]

The brainmask.auto.mgz will be our stripping, but the brain,ask.mgz will be 
yours

Cheers
Bruce

> On Nov 8, 2016, at 10:21 AM, miracoo...@gmail.com wrote:
> 
> Thank you very much Bruce. Last questions. When I replace FS generated 
> brainmask.mgz with mine, does the original also remain in the mri folder( 
> that's having 2 brainmask.mgz)  or  is the original permanently replaced with 
> my own brainmask.mgz ( that's only 1 brainmask.mgz which is mine)? Second, 
> any reasons why you suggested I avoid " - no" flags? This is because I 
> searched through the forum and it seem the " -no flag" was  encouraged 
> whenever someone wanted to replace FS generated volume with their own, 
> especially in the case of skull stripping. Third, should my last recon step 
> be "recon-all -autorecon2-wm -autorecon3 " once I have replaced the FS 
> generated wm.seg.mgz with mine in order to complete the recon-all processing? 
> Lastly, how do I check if my replaced volumes are correctly aligned with FS 
> volumes from recon-all -all ? 
> Best, 
> Paul
> 
> Sent from my BlackBerry 10 smartphone.
>   Original Message  
> From: Bruce Fischl
> Sent: Sunday, November 6, 2016 7:08 PM
> To: Freesurfer support list
> Reply To: Freesurfer support list
> Subject: Re: [Freesurfer] Fw: recon-all steps question
> 
> Yes, I think so
> Bruce 
> 
>> On Nov 6, 2016, at 6:34 PM, miracoo...@gmail.com wrote:
>> 
>> Hence, you are saying I should run recon-all -autorecon1 -i -s subjid then 
>> replace the FS generated brainmask.mgz with my own stripped volume. Also, 
>> should I run recon-all -autorecon2 with wm segmentation ( after replacing 
>> the stripped volume ) and replace FS generated wm.seg.mgz with my wm 
>> segmentation volume? Thank you. 
>> Best, 
>> Paul ‎
>> Sent from my BlackBerry 10 smartphone.‎
>> Original Message 
>> From: Bruce Fischl
>> Sent: Sunday, November 6, 2016 6:15 PM
>> To: Freesurfer support list
>> Reply To: Freesurfer support list
>> Subject: Re: [Freesurfer] Fw: recon-all steps question
>> 
>> I would run autorecon1 witth skull stripping, then replace it with your 
>> own stripped volume (the brainmask.mgz). It will treat that as a "manual 
>> edit" since brainmask.mgz will be different than brainmask.auto.mgz, and 
>> hence it won't override it
>> 
>> cheers
>> Bruce
>> 
>> 
>> On Sun, 6 Nov 2016, 
>> miracoo...@gmail.com wrote:
>> 
>>> Thank very much Bruce. Does it mean I have to run recon-all -autorecon1 
>>> -noskullstrip, then recon-all -autorecon2 -nosegmentation ( with the skull 
>>> stripped volume) . Finally, recon-all -autorecon2-wm -autorecon3 -s subjid( 
>>> with the wm and lesion stuff)?
>>> Thanks >
>>> Sent from my BlackBerry 10 smartphone.
>>> Original Message 
>>> From: Bruce Fischl
>>> Sent: Sunday, November 6, 2016 12:14 PM
>>> To: Freesurfer support list
>>> Reply To: Freesurfer support list
>>> Subject: Re: [Freesurfer] Fw: recon-all steps question
>>> 
>>> Hi Paul
>>> 
>>> hmm, you have to be a bit careful with the -no* flags as you want to avoid
>>> running those steps, but you want make sure FS knows that the typical
>>> output of the steps you skipped exists and should be used. Others can help
>>> you with the logic of recon-all better than I can, but I think you are
>>> probably best off replacing the relevant volumes and running from there
>>> forward. You might need to run autorecon1, then insert your skull-stripped
>>> volume, then autorecon2, insert your wm and lesion stuff, then run
>>> autorecon2-wm, but I'm not totally sure since what you are doing is so
>>> non-standard.
>>> 
>>> cheers
>>> Bruce
>>> 
>>> 
>>> On Fri, 4 Nov 2016,
>>> miracoo...@gmail.com wrote:
>>> 
 We have already skull stripped and white matter segmented volume ( used 
 lesion explorer) . Hence, I want to replace freesurfer 's generated 
 outputs for this steps ( brainmask.mgz for skull strip and wm.seg.mgz (not 
 wm.mgz ) for white matter) with ours. I know recon-all -all performs all 
 31 steps and inserting " -nostep " flag tells freesurfer to skip that 
 step. Covering and Creating a symbolic link to our files and then, running 
 the remaining steps of recon-all might help achieve this ( I believe) . 
 Replacing this freesurfer outputs with ours will reduce time spent on pial 
 and white matter edits. 
 Best,
 Paul
 
 Sent from my BlackBerry 10 smartphone.
 Original Message 
 From: Bruce Fischl
 Sent: Friday, November 4, 2016 3:37 PM
 To: Freesurfer support list
 Reply To: Freesurfer support list
 Subject: Re: [Freesurfer] Fw: recon-all steps question
 
 
 Hi Paul
 
 can we take a step back. What are you trying to achieve by avoiding these
 steps?
 
 cheers
 Bruce
 
 
> On Fri, 4 Nov 2016, miracoo...@gmail.com wrote:
> 
> Thanks Bruce. Another question, since " -no segmentation " flag skips the
> white matter segmentation step of recon-all. Can I also use the same

Re: [Freesurfer] Longitudinal Stream on HCP Data

[Bruce Fischl]

Hi Tim

for a long time we have had a post-processing routine that uses T2 or 
FLAIR images for post-hoc surface deformation. This existed long before the 
HCP, although I did tweak it for the Wash U HCP acquisition to make it 
perform better. The upcoming v6 has the overall best performance with the 
T2s I believe


cheers
Bruce

On Tue, 8 Nov 2016, Timothy Hendrickson wrote:

> Hi Freesurfer/HCP experts,
> 
> I am curious if there is a way to incorporate HCP data (i.e. myelin maps)
> into the FreeSurfer processing stream.
> Matthew Glasser mentioned in a post on the HCP mailing list about a month
> back that this is being actively worked on by FreeSurfer:
> http://www.mail-archive.com/hcp-users@humanconnectome.org/msg03477.html.
> Are there any workflows or development versions that I can download in order
> to perform something like this.
> 
> Respectfully,
> 
> -Tim
> 
> Timothy Hendrickson
> Department of Psychiatry
> University of Minnesota
> Mobile: 507-259-3434 (texts okay)
> 
>
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Re: [Freesurfer] mapping ROI to surface space

[Douglas Greve]

Use mri_surf2surf to convert it to an mgh or mgz file, then use 
mri_cor2label with the --surf option to convert it to a label


On 11/8/16 9:41 AM, Andrews, Derek wrote:
> Hi Bruce and Freesurfer developers,
>
> Thank you. Any suggestions on converting a binary .w file to a label would
> be very helpful.
>
> Best, Derek
>
>
> 
> Derek Sayre Andrews, MSc
> PhD Candidate
>
> The Sackler Institute for Translational Neurodevelopment
> Department of Forensic and Neurodevelopmental Sciences
> Institute of Psychiatry, Psychology & Neuroscience, King's College London
>
> Telephone: +44 (0)20 7848 5701
> Email: derek.andr...@kcl.ac.uk
>
>
>
>
>
> On 08/11/2016 14:04, "Bruce Fischl"  wrote:
>
>> Hi Derek
>>
>> I'll cc the FS list so others can answer. It depends on the reason the
>> holes exist.  It also depends on the size of the holes. The dev version
>> of
>> mri_label2labels supports morphological close operations. It takes an
>> integer parameter which should be about the radius of the holes you would
>> like to fill in. Note that this will also fill in some concavities in the
>> boundary of the label.
>>
>> cheers
>> Bruce
>>
>>
>> On Tue, 8 Nov 2016, Andrews, Derek wrote:
>>
>>> Hi Bruce,
>>>
>>> Apologies for contacting you directly but I’m not sure if my message is
>>> getting through to the list.
>>>
>>> I have gotten ahold of the dev version of mri_label2label.
>>>
>>> Currently I have a .w file that I need to “fill in the holes” on. Could
>>> you please specify the steps I will need to take to make my .w file an
>>> acceptable input for mri_label2label, and any recommendations you may
>>> have
>>> for the value of N for the —close flag.
>>>
>>> Any help you could provide would be appreciated.
>>>
>>> Best, Derek
>>>
>>>
>>>
>>>
>>> 
>>> Derek Sayre Andrews, MSc
>>> PhD Candidate
>>>
>>> The Sackler Institute for Translational Neurodevelopment
>>> Department of Forensic and Neurodevelopmental Sciences
>>> Institute of Psychiatry, Psychology & Neuroscience, King's College
>>> London
>>>
>>> Telephone: +44 (0)20 7848 5701
>>> Email: derek.andr...@kcl.ac.uk
>>>
>>>
>>>
>>>
>>>
>>> On 28/10/2016 15:53, "Bruce Fischl"  wrote:
>>>
 Hi Derek

 I think the dev version of mri_label2label supports
 open/close/dilate/erode
 operations:

 mri_label2label --help
 USAGE: mri_label2label.bin

 --srclabel input label file

 --erode  N erode the label N times before writing
 --open   N open the label N times before writing
 --close  N close the label N times before writing
 --dilate  Ndilate the label N times before writing
   .
 .
 .

 if your version doesn't have these operations let us know and we can
 get
 you an updated one

 cheers
 Bruce



 On Fri, 28 Oct 2016,
 Andrews, Derek wrote:

> Hi Bruce,
>
> As always thank you for your prompt reply.
>
> For the morphological close operation, would you suggest using
> mris_fill
> on the surface ROI I created and then running mri_vol2surf again on
> the
> volume output by mris_fill?
>
> Best, Derek
>
>
> 
> Derek Sayre Andrews, MSc
> PhD Candidate
>
> The Sackler Institute for Translational Neurodevelopment
> Department of Forensic and Neurodevelopmental Sciences
> Institute of Psychiatry, Psychology & Neuroscience, King's College
> London
>
> Telephone: +44 (0)20 7848 5701
> Email: derek.andr...@kcl.ac.uk
>
>
>
>
>
> On 28/10/2016 14:54, "Bruce Fischl" 
> wrote:
>
>> p.s. you could remove many/most of these holes using a morphological
>> close operation
>> On Fri, 28 Oct 2016, Andrews, Derek wrote:
>>
>>> Hello Freesurfer Developers and Community,
>>>
>>> I am looking to map a ROI.nii based on the MNI152 template to the
>>> fsaverage
>>> pial surface.
>>>
>>> I have used the following commands
>>>
>>> Bbregister ‹s fsaverage ‹mov MNI152.nii ‹reg register.dat ‹init-fsl
>>> ‹12
>>> ‹t1
>>>
>>> Then
>>>
>>> mri_vol2surf ‹src ROI.nii ‹out ROI.mgh ‹srcreg register.dat ‹hemi lh
>>>
>>> The ROI appears to be in the right place however is very blotchy.
>>> Have I
>>> missed a step? Or is this correct?
>>>
>>> See bellow a picture of the ROI highlighted in FSL and in tksurfer
>>> after
>>> mapped using the above.
>>>
>>> Thank you for your support,
>>>
>>> Best, Derek
>>>
>>> [IMAGE]
>>>
>>>
>>>
>>>
>>>
>>>
>>> _
>>> __
>>> __
>>> ___
>>>
>>> Derek 

Re: [Freesurfer] GM ROI list?

[Douglas Greve]

We don't currently have that information (ie, tissue type) stored with 
the ROI. One thing you can do is to run mri_binarize with the --gm 
option on aparc+aseg.mgz This uses some rules to determine what is GM 
and creates a mask of GM. You can then feed this into mri_segstats with 
--mask, and it should only return ROIs that are in the GM mask.



On 11/7/16 8:10 PM, P Taylor wrote:
Thanks, that's useful for getting the ROI volumes and a list of all 
that's been found for a particular data set.


I would still like to have a way to identify a listed region as gray 
matter or not so that I can parse the file for only GM regions that 
have been returned, particularly as different numbers of ROIs are 
typically returned in an aparc+aseg file.


I see in the aseg.stats file that there are volumetric summations for 
GM quantities, such as:
# Measure lhCortex, lhCortexVol, Left hemisphere cortical gray matter 
volume, 238183.759207, mm^3
# Measure rhCortex, rhCortexVol, Right hemisphere cortical gray matter 
volume, 240824.502797, mm^3
# Measure Cortex, CortexVol, Total cortical gray matter volume, 
479008.262004, mm^3


# Measure SubCortGray, SubCortGrayVol, Subcortical gray matter volume, 
57815.00, mm^3
# Measure TotalGray, TotalGrayVol, Total gray matter volume, 
643956.262004, mm^3


Are these calculated by summing individual ROI volumes, so that a list 
of all possible GM volumes does already exist somewhere?


Thanks,
pt





On Mon, Nov 7, 2016 at 3:39 PM, Douglas N Greve 
> wrote:


I don't know that we have a complete list in one place of just the
aparc+aseg ROIs, but you can get one by running

mri_segstats --seg aparc+aseg.mgz --ctab-default --sum sum.dat

then look in the sum.dat file


On 11/03/2016 04:32 PM, P Taylor wrote:
> Is there an available list of GM regions within the list of
regions in
> the FreeSurferColorLUT.txt?
>
> (In particular, I am interested in a list of GM regions output in a
> default run of recon-all, which seems to have a maximum regionnumber
> of 2035.  But a full list is great, too-- I'm not sure which
might be
> already available or easier to generate.)
>
> I had thought of using the segmentation volumes to help me
> differentiate ROIs. For example, I could get rid of regions that
> overlap with the WM volume, but I think that the segmentation might
> come from a slightly different bit of information than the sum of
> segmented regions.  As shown in the attached slice image, if I
> underlay the WM segmentation volume (color = white), and overlay a
> "recon-all" parcellation+segmentation map (color = red for GM on
> right, yellow for GM on left, and green for non-GM) to look for
> overlap, I see that some of the WM seg volume overlaps with GM ROIs
> (overlaps are isolated pink-ish voxels and light yellow voxels; one
> highlighted in cross hairs).  I guess this difference occurs because
> the segmentation volume comes from the surfaces themselves?
>
> Anyways, this makes me think that I can't automate finding the
GM, and
> I would rather go from LUT numbers, and hence the above question.
>
> Thanks,
> pt
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu

> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu 
Phone Number: 617-724-2358 
Fax: 617-726-7422 

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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

www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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


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Re: [Freesurfer] perl & bbregister conflicts

[Douglas Greve]

fyi: the new version of bbregister will use the FS-native mri_coreg, so 
this problem will disappear


On 11/8/16 10:17 AM, Z K wrote:
> Thank you for this information. I believe we test against the same
> version of fsl (5.0.7). I'll look into it.
>
> On 11/08/2016 06:32 AM, GREGORY R KIRK wrote:
>> Hi folks,
>>
>>
>> somebody stuck me with Ubuntu 16 for a month
>>
>> and I found the perl problem and so switched to
>>
>> the dev version which solved that problem.
>>
>>
>> discovered that with the dev version bbregister
>>
>> throws an error having to do with fsl
>>
>>
>> flirt throws an error `terminate after throwing an instance of
>> NEWMAT::SingularException
>>
>>
>> the version of fsl i have installed is 5.0
>>
>>
>> of course so i use dev for recon and 5.3 for bbregister
>>
>> so just to let you know the bbregister/fsl problem is there in the
>> latest dev
>>
>>
>> cheers
>>
>>
>> Greg
>>
>>
>>
>> ___
>> 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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Re: [Freesurfer] Longitudinal Stream on HCP Data

[Harms, Michael]

To clarify, in that post, Matt wasn’t saying that FS was going to incorporate 
myelin maps.  Rather, the new (v6) version of FS, with its support of data 
acquired with < 1 mm resolution, may eliminate the need for some of the steps 
that are currently the HCP Pipelines that are there to take full advantage of 
higher resolution structural acquisitions.

cheers,
-MH

--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO  63110 Email: mha...@wustl.edu

From: 
>
 on behalf of Timothy Hendrickson >
Reply-To: Freesurfer support list 
>
Date: Tuesday, November 8, 2016 at 9:15 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
>
Subject: [Freesurfer] Longitudinal Stream on HCP Data

Hi Freesurfer/HCP experts,

I am curious if there is a way to incorporate HCP data (i.e. myelin maps) into 
the FreeSurfer processing stream.
Matthew Glasser mentioned in a post on the HCP mailing list about a month back 
that this is being actively worked on by FreeSurfer: 
http://www.mail-archive.com/hcp-users@humanconnectome.org/msg03477.html.
Are there any workflows or development versions that I can download in order to 
perform something like this.

Respectfully,

-Tim

Timothy Hendrickson
Department of Psychiatry
University of Minnesota
Mobile: 507-259-3434 (texts okay)


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Re: [Freesurfer] Fw: recon-all steps question

[miracooloz]

Thank you very much Bruce. Last questions. When I replace FS generated 
brainmask.mgz with mine, does the original also remain in the mri folder( 
that's having 2 brainmask.mgz)  or  is the original permanently replaced with 
my own brainmask.mgz ( that's only 1 brainmask.mgz which is mine)? Second, any 
reasons why you suggested I avoid " - no" flags? This is because I searched 
through the forum and it seem the " -no flag" was  encouraged whenever someone 
wanted to replace FS generated volume with their own, especially in the case of 
skull stripping. Third, should my last recon step be "recon-all -autorecon2-wm 
-autorecon3 " once I have replaced the FS generated wm.seg.mgz with mine in 
order to complete the recon-all processing? Lastly, how do I check if my 
replaced volumes are correctly aligned with FS volumes from recon-all -all ? 
Best, 
Paul

Sent from my BlackBerry 10 smartphone.
  Original Message  
From: Bruce Fischl
Sent: Sunday, November 6, 2016 7:08 PM
To: Freesurfer support list
Reply To: Freesurfer support list
Subject: Re: [Freesurfer] Fw: recon-all steps question

Yes, I think so
Bruce 

> On Nov 6, 2016, at 6:34 PM, miracoo...@gmail.com wrote:
> 
> Hence, you are saying I should run recon-all -autorecon1 -i -s subjid then 
> replace the FS generated brainmask.mgz with my own stripped volume. Also, 
> should I run recon-all -autorecon2 with wm segmentation ( after replacing the 
> stripped volume ) and replace FS generated wm.seg.mgz with my wm segmentation 
> volume? Thank you. 
> Best, 
> Paul ‎
> Sent from my BlackBerry 10 smartphone.‎
> Original Message 
> From: Bruce Fischl
> Sent: Sunday, November 6, 2016 6:15 PM
> To: Freesurfer support list
> Reply To: Freesurfer support list
> Subject: Re: [Freesurfer] Fw: recon-all steps question
> 
> I would run autorecon1 witth skull stripping, then replace it with your 
> own stripped volume (the brainmask.mgz). It will treat that as a "manual 
> edit" since brainmask.mgz will be different than brainmask.auto.mgz, and 
> hence it won't override it
> 
> cheers
> Bruce
> 
> 
> On Sun, 6 Nov 2016, 
> miracoo...@gmail.com wrote:
> 
>> Thank very much Bruce. Does it mean I have to run recon-all -autorecon1 
>> -noskullstrip, then recon-all -autorecon2 -nosegmentation ( with the skull 
>> stripped volume) . Finally, recon-all -autorecon2-wm -autorecon3 -s subjid( 
>> with the wm and lesion stuff)?
>> Thanks >
>> Sent from my BlackBerry 10 smartphone.
>> Original Message 
>> From: Bruce Fischl
>> Sent: Sunday, November 6, 2016 12:14 PM
>> To: Freesurfer support list
>> Reply To: Freesurfer support list
>> Subject: Re: [Freesurfer] Fw: recon-all steps question
>> 
>> Hi Paul
>> 
>> hmm, you have to be a bit careful with the -no* flags as you want to avoid
>> running those steps, but you want make sure FS knows that the typical
>> output of the steps you skipped exists and should be used. Others can help
>> you with the logic of recon-all better than I can, but I think you are
>> probably best off replacing the relevant volumes and running from there
>> forward. You might need to run autorecon1, then insert your skull-stripped
>> volume, then autorecon2, insert your wm and lesion stuff, then run
>> autorecon2-wm, but I'm not totally sure since what you are doing is so
>> non-standard.
>> 
>> cheers
>> Bruce
>> 
>> 
>> On Fri, 4 Nov 2016,
>> miracoo...@gmail.com wrote:
>> 
>>> We have already skull stripped and white matter segmented volume ( used 
>>> lesion explorer) . Hence, I want to replace freesurfer 's generated outputs 
>>> for this steps ( brainmask.mgz for skull strip and wm.seg.mgz (not wm.mgz ) 
>>> for white matter) with ours. I know recon-all -all performs all 31 steps 
>>> and inserting " -nostep " flag tells freesurfer to skip that step. Covering 
>>> and Creating a symbolic link to our files and then, running the remaining 
>>> steps of recon-all might help achieve this ( I believe) . Replacing this 
>>> freesurfer outputs with ours will reduce time spent on pial and white 
>>> matter edits. 
>>> Best,
>>> Paul
>>> 
>>> Sent from my BlackBerry 10 smartphone.
>>> Original Message 
>>> From: Bruce Fischl
>>> Sent: Friday, November 4, 2016 3:37 PM
>>> To: Freesurfer support list
>>> Reply To: Freesurfer support list
>>> Subject: Re: [Freesurfer] Fw: recon-all steps question
>>> 
>>> 
>>> Hi Paul
>>> 
>>> can we take a step back. What are you trying to achieve by avoiding these
>>> steps?
>>> 
>>> cheers
>>> Bruce
>>> 
>>> 
 On Fri, 4 Nov 2016, miracoo...@gmail.com wrote:
 
 Thanks Bruce. Another question, since " -no segmentation " flag skips the
 white matter segmentation step of recon-all. Can I also use the same
 logic as the "-noskullstrip" flag to replace the wm.seg.mgz file? That's,
 run " recon-all -autorecon1 -autorecon2 -nosegmentation -s subjid ". Then
 copy/convert my already segmented brain and name it wm.seg.mgz. After
 that, treat it as if I had freesurfer's wm.seg.mgz and finally, run "

Re: [Freesurfer] perl & bbregister conflicts

[Z K]

Thank you for this information. I believe we test against the same 
version of fsl (5.0.7). I'll look into it.

On 11/08/2016 06:32 AM, GREGORY R KIRK wrote:
> Hi folks,
>
>
> somebody stuck me with Ubuntu 16 for a month
>
> and I found the perl problem and so switched to
>
> the dev version which solved that problem.
>
>
> discovered that with the dev version bbregister
>
> throws an error having to do with fsl
>
>
> flirt throws an error `terminate after throwing an instance of
> NEWMAT::SingularException
>
>
> the version of fsl i have installed is 5.0
>
>
> of course so i use dev for recon and 5.3 for bbregister
>
> so just to let you know the bbregister/fsl problem is there in the
> latest dev
>
>
> cheers
>
>
> Greg
>
>
>
> ___
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>
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[Freesurfer] Longitudinal Stream on HCP Data

[Timothy Hendrickson]

Hi Freesurfer/HCP experts,

I am curious if there is a way to incorporate HCP data (i.e. myelin maps)
into the FreeSurfer processing stream.
Matthew Glasser mentioned in a post on the HCP mailing list about a month
back that this is being actively worked on by FreeSurfer:
http://www.mail-archive.com/hcp-users@humanconnectome.org/msg03477.html.

Are there any workflows or development versions that I can download in
order to perform something like this.

Respectfully,

-Tim

Timothy Hendrickson
Department of Psychiatry
University of Minnesota
Mobile: 507-259-3434 (texts okay)
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Re: [Freesurfer] FreeSurfer Dev Releases

[Z K]

On 11/07/2016 05:39 AM, Elia S. wrote:
> Dear FreeSurfer Developers,
>
>
> We have been trying out, for the past few months, the freesurfer dev
> releases, and in particular this one:
>
>
> freesurfer-X86_64-unknown-linux-gnu-dev5-20150924
>
>
> My question is, does the above version classify as a nightly version of
> FreeSurfer 5, or as an early beta of the 6?
>
> Or..do the dev versions fall in some kind of grey area that are
> neither 5 or 6?

This. dev versions are nightly builds that include latest features and 
bug fixes, but are not adequately tested, and do not undergo the same 
rigorous testing that a released version would get. We anticipate a v6 
beta version before the end of this month.

-Zeke



>
>
> Thank you in advance,
>
> Elia.
>
>
>
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Re: [Freesurfer] mapping ROI to surface space

[Andrews, Derek]

Hi Bruce and Freesurfer developers,

Thank you. Any suggestions on converting a binary .w file to a label would
be very helpful.

Best, Derek 



Derek Sayre Andrews, MSc
PhD Candidate

The Sackler Institute for Translational Neurodevelopment
Department of Forensic and Neurodevelopmental Sciences
Institute of Psychiatry, Psychology & Neuroscience, King's College London

Telephone: +44 (0)20 7848 5701
Email: derek.andr...@kcl.ac.uk





On 08/11/2016 14:04, "Bruce Fischl"  wrote:

>Hi Derek
>
>I'll cc the FS list so others can answer. It depends on the reason the
>holes exist.  It also depends on the size of the holes. The dev version
>of 
>mri_label2labels supports morphological close operations. It takes an
>integer parameter which should be about the radius of the holes you would
>like to fill in. Note that this will also fill in some concavities in the
>boundary of the label.
>
>cheers
>Bruce
>
>
>On Tue, 8 Nov 2016, Andrews, Derek wrote:
>
>> Hi Bruce,
>>
>> Apologies for contacting you directly but I’m not sure if my message is
>> getting through to the list.
>>
>> I have gotten ahold of the dev version of mri_label2label.
>>
>> Currently I have a .w file that I need to “fill in the holes” on. Could
>> you please specify the steps I will need to take to make my .w file an
>> acceptable input for mri_label2label, and any recommendations you may
>>have
>> for the value of N for the —close flag.
>>
>> Any help you could provide would be appreciated.
>>
>> Best, Derek
>>
>>
>>
>>
>> 
>> Derek Sayre Andrews, MSc
>> PhD Candidate
>>
>> The Sackler Institute for Translational Neurodevelopment
>> Department of Forensic and Neurodevelopmental Sciences
>> Institute of Psychiatry, Psychology & Neuroscience, King's College
>>London
>>
>> Telephone: +44 (0)20 7848 5701
>> Email: derek.andr...@kcl.ac.uk
>>
>>
>>
>>
>>
>> On 28/10/2016 15:53, "Bruce Fischl"  wrote:
>>
>>> Hi Derek
>>>
>>> I think the dev version of mri_label2label supports
>>> open/close/dilate/erode
>>> operations:
>>>
>>> mri_label2label --help
>>> USAGE: mri_label2label.bin
>>>
>>>--srclabel input label file
>>>
>>>--erode  N erode the label N times before writing
>>>--open   N open the label N times before writing
>>>--close  N close the label N times before writing
>>>--dilate  Ndilate the label N times before writing
>>>  .
>>> .
>>> .
>>>
>>> if your version doesn't have these operations let us know and we can
>>>get
>>> you an updated one
>>>
>>> cheers
>>> Bruce
>>>
>>>
>>>
>>> On Fri, 28 Oct 2016,
>>> Andrews, Derek wrote:
>>>
 Hi Bruce,

 As always thank you for your prompt reply.

 For the morphological close operation, would you suggest using
mris_fill
 on the surface ROI I created and then running mri_vol2surf again on
the
 volume output by mris_fill?

 Best, Derek


 
 Derek Sayre Andrews, MSc
 PhD Candidate

 The Sackler Institute for Translational Neurodevelopment
 Department of Forensic and Neurodevelopmental Sciences
 Institute of Psychiatry, Psychology & Neuroscience, King's College
 London

 Telephone: +44 (0)20 7848 5701
 Email: derek.andr...@kcl.ac.uk





 On 28/10/2016 14:54, "Bruce Fischl" 
wrote:

> p.s. you could remove many/most of these holes using a morphological
> close operation
> On Fri, 28 Oct 2016, Andrews, Derek wrote:
>
>> Hello Freesurfer Developers and Community,
>>
>> I am looking to map a ROI.nii based on the MNI152 template to the
>> fsaverage
>> pial surface.
>>
>> I have used the following commands
>>
>> Bbregister ‹s fsaverage ‹mov MNI152.nii ‹reg register.dat ‹init-fsl
>> ‹12
>> ‹t1
>>
>> Then
>>
>> mri_vol2surf ‹src ROI.nii ‹out ROI.mgh ‹srcreg register.dat ‹hemi lh
>>
>> The ROI appears to be in the right place however is very blotchy.
>> Have I
>> missed a step? Or is this correct?
>>
>> See bellow a picture of the ROI highlighted in FSL and in tksurfer
>> after
>> mapped using the above.
>>
>> Thank you for your support,
>>
>> Best, Derek
>>
>> [IMAGE]
>>
>>
>>
>>
>>
>> 
>>_
>>__
>> __
>> ___
>>
>> Derek Sayre Andrews, MSc
>> PhD Candidate
>>
>> The Sackler Institute for Translational Neurodevelopment
>>
>> Department of Forensic and Neurodevelopmental Sciences
>>
>> Institute of Psychiatry, Psychology & Neuroscience, King's College
>> London
>>
>> Telephone: +44 (0)20 7848 5701
>> Email: derek.andr...@kcl.ac.uk
>>
>>
>>
>> 

Re: [Freesurfer] FW: Manual pial and white matter corrections cause irregularities

[Bruce Fischl]

Hi Cleo

to check I need the actual subject directories. Can you tar, gzip and 
upload the before and after ones?


cheers
Bruce


On Tue, 8 Nov 2016, Cleo 
Vandervost wrote:




Hi Bruce; 


Sorry to send this email once again but I didn't get an answer to my previous one. 
As you asked, I uploaded the recon-all log-file for that subject, edited and 
unedited.  We're using version 5.3. How can you check for sure that the WM 
significantly gets  >110?

I also uploaded the pictures once again.

Thanks,

Cleo

Van: freesurfer-boun...@nmr.mgh.harvard.edu  
namens Bruce Fischl 
Verzonden: vrijdag 21 oktober 2016 02:14
Aan: Freesurfer support list
Onderwerp: Re: [Freesurfer] Manual pial and white matter corrections cause 
irregularities

Hi Cleo

can you upload a subject before and after editing so we can replicate what
you are seeing? And what version of FreeSurfer are you using? Does the WM
after editing get signifcantly >110? If so, you may have accidentally
placed a control point in a gray matter voxel

cheers
Bruce


On Thu, 20 Oct 2016, Cleo Vandervost wrote:



​Hello Freesurfer team,


For my thesis I'm researching the differences in grey and white matter and 
cortical thickness between
children with and without dyslexia. My supervisor advised me to manually edit 
the Freesurfer-generated
data. I've been editing my data as follows:

- adding control points to (larger) WM-areas that FS did not include

- manually editing (smaller) WM-areas through recon-editing

- correcting the pial surface through recon-editing


After finishing and saving my edits I reran recon-all with this command: 
recon-all -autorecon2-cp
-autorecon -subjid (subject number). When I opened my data again in Freesurfer 
to check my edits, I saw
that there were two big problems:

- 'distortions' in the pial surface

- sometimes large areas of WM suddenly were excluded, even when I didn't make 
any edits in that area

​It makes the edited data look much worse than the original data, which is 
weird I suppose.


I've included some pictures so you can see what I mean.

- Picture (a) is the original unedited version.

- Picture (b) is the edited version: control points and WM edits. You can see 
that there's a large area
in the left hemisfere excluded from the original WM area

- Picture (c) is the re-edited version of (b), control points added in that 
large area. This time it's
included but the pial surface shows a lot of irregularities.


Me and my supervisor tried a couple of times with other data, but we still had 
the same results. We also
tried by only adding control points and editing manually, without the 
pial-corrections.


Do you have any idea of what's going wrong in the editing proces?


Thank you very much,


Kind regards


Cleo Vandervost

1st master speech and language therapy

Katholieke Universiteit Leuven




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Re: [Freesurfer] mapping ROI to surface space

[Bruce Fischl]

Hi Derek

I'll cc the FS list so others can answer. It depends on the reason the 
holes exist.  It also depends on the size of the holes. The dev version of 
mri_label2labels supports morphological close operations. It takes an 
integer parameter which should be about the radius of the holes you would 
like to fill in. Note that this will also fill in some concavities in the 
boundary of the label.


cheers
Bruce


On Tue, 8 Nov 2016, Andrews, Derek wrote:


Hi Bruce,

Apologies for contacting you directly but I’m not sure if my message is
getting through to the list.

I have gotten ahold of the dev version of mri_label2label.

Currently I have a .w file that I need to “fill in the holes” on. Could
you please specify the steps I will need to take to make my .w file an
acceptable input for mri_label2label, and any recommendations you may have
for the value of N for the —close flag.

Any help you could provide would be appreciated.

Best, Derek





Derek Sayre Andrews, MSc
PhD Candidate

The Sackler Institute for Translational Neurodevelopment
Department of Forensic and Neurodevelopmental Sciences
Institute of Psychiatry, Psychology & Neuroscience, King's College London

Telephone: +44 (0)20 7848 5701
Email: derek.andr...@kcl.ac.uk





On 28/10/2016 15:53, "Bruce Fischl"  wrote:


Hi Derek

I think the dev version of mri_label2label supports
open/close/dilate/erode
operations:

mri_label2label --help
USAGE: mri_label2label.bin

   --srclabel input label file

   --erode  N erode the label N times before writing
   --open   N open the label N times before writing
   --close  N close the label N times before writing
   --dilate  Ndilate the label N times before writing
 .
.
.

if your version doesn't have these operations let us know and we can get
you an updated one

cheers
Bruce



On Fri, 28 Oct 2016,
Andrews, Derek wrote:


Hi Bruce,

As always thank you for your prompt reply.

For the morphological close operation, would you suggest using mris_fill
on the surface ROI I created and then running mri_vol2surf again on the
volume output by mris_fill?

Best, Derek



Derek Sayre Andrews, MSc
PhD Candidate

The Sackler Institute for Translational Neurodevelopment
Department of Forensic and Neurodevelopmental Sciences
Institute of Psychiatry, Psychology & Neuroscience, King's College
London

Telephone: +44 (0)20 7848 5701
Email: derek.andr...@kcl.ac.uk





On 28/10/2016 14:54, "Bruce Fischl"  wrote:


p.s. you could remove many/most of these holes using a morphological
close operation
On Fri, 28 Oct 2016, Andrews, Derek wrote:


Hello Freesurfer Developers and Community,

I am looking to map a ROI.nii based on the MNI152 template to the
fsaverage
pial surface.

I have used the following commands

Bbregister ‹s fsaverage ‹mov MNI152.nii ‹reg register.dat ‹init-fsl
‹12
‹t1

Then

mri_vol2surf ‹src ROI.nii ‹out ROI.mgh ‹srcreg register.dat ‹hemi lh

The ROI appears to be in the right place however is very blotchy.
Have I
missed a step? Or is this correct?

See bellow a picture of the ROI highlighted in FSL and in tksurfer
after
mapped using the above.

Thank you for your support,

Best, Derek

[IMAGE]





___
__
___

Derek Sayre Andrews, MSc
PhD Candidate

The Sackler Institute for Translational Neurodevelopment

Department of Forensic and Neurodevelopmental Sciences

Institute of Psychiatry, Psychology & Neuroscience, King's College
London

Telephone: +44 (0)20 7848 5701
Email: derek.andr...@kcl.ac.uk



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[Freesurfer] perl & bbregister conflicts

[GREGORY R KIRK]

Hi folks,


somebody stuck me with Ubuntu 16 for a month

and I found the perl problem and so switched to

the dev version which solved that problem.


discovered that with the dev version bbregister

throws an error having to do with fsl


flirt throws an error `terminate after throwing an instance of 
NEWMAT::SingularException


the version of fsl i have installed is 5.0


of course so i use dev for recon and 5.3 for bbregister

so just to let you know the bbregister/fsl problem is there in the latest dev


cheers


Greg
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