[Freesurfer] error for input volume

2020-07-01 Thread N Saf 
External Email - Use Caution

Dear Freesurfer experts,

I've tried to perform an autorecon1 for a patient's brain MRI(T1). There
are some dark regions in white matter areas. an error has occurred which
I've attached the corresponding log file here as well as the raw nii data.
I wonder if there is any approach to let me do the recon-all analysis for
this case. Any help would be very appreciated and thank you for your time.
All best wishes,
Nazanin
 khameh1.nii

‫چهارشنبه ۰۱ ژوئیه ۲۰، ساعت ۱۳:۴۶:۰۲ (+0430)‬
/home/nazanin/freesurfer/subjects/khameh
/home/nazanin/freesurfer/bin/recon-all
-i khameh1.nii -s khameh -autorecon1
subjid khameh
setenv SUBJECTS_DIR /home/nazanin/freesurfer/subjects
FREESURFER_HOME /home/nazanin/freesurfer
Actual FREESURFER_HOME /home/nazanin/freesurfer
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Linux nazanin-Aspire-V3-571G 4.15.0-76-generic #86-Ubuntu SMP Fri Jan 17 17:24:28 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
cputime  unlimited
filesize unlimited
datasize unlimited
stacksize8192 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
vmemoryuse   unlimited
descriptors  1024 
memorylocked 16384 kbytes
maxproc  23236 
maxlocks unlimited
maxsignal23236 
maxmessage   819200 
maxnice  0 
maxrtprio0 
maxrttimeunlimited

  totalusedfree  shared  buff/cache   available
Mem:5993296 1051208 2255352  317668 2686736 4325436
Swap:   4999164   0 4999164


program versions used
$Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $
$Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $
mri_convert.bin -all-info 
ProgramName: mri_convert.bin  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2020/07/01-09:16:02-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $  User: nazanin  Machine: nazanin-Aspire-V3-571G  Platform: Linux  PlatformVersion: 4.15.0-76-generic  CompilerName: GCC  CompilerVersion: 40400 
FLIRT version 5.5
$Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $
mri_convert.bin --version 
stable6
ProgramName: tkregister2_cmdl  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2020/07/01-09:16:02-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $  User: nazanin  Machine: nazanin-Aspire-V3-571G  Platform: Linux  PlatformVersion: 4.15.0-76-generic  CompilerName: GCC  CompilerVersion: 40400 
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
ProgramName: mri_make_uchar  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2020/07/01-09:16:02-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $  User: nazanin  Machine: nazanin-Aspire-V3-571G  Platform: Linux  PlatformVersion: 4.15.0-76-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2020/07/01-09:16:02-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $  User: nazanin  Machine: nazanin-Aspire-V3-571G  Platform: Linux  PlatformVersion: 4.15.0-76-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2020/07/01-09:16:02-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $  User: nazanin  Machine: nazanin-Aspire-V3-571G  Platform: Linux  PlatformVersion: 4.15.0-76-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2020/07/01-09:16:02-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $  User: nazanin  Machine: nazanin-Aspire-V3-571G  Platform: Linux  PlatformVersion: 4.15.0-76-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segment  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2020/07/01-09:16:02-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $  User: nazanin  Machine: nazanin-Aspire-V3-571G  Platform: Linux  PlatformVersion: 4.15.0-76-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_label2label.bin  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2020/07/01-09:16:02-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $  User: nazanin

[Freesurfer] mri_convert

2019-01-25 Thread N Saf 
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Dear Bruce,
I had a problem with bringing aseg.mgz into my subject space and you
recommend this command before:

mri_convert -rl rawavg.mgz -rt nearest aseg.mgz aseg.resliced.mgz

which perfectly worked for me but now when I want to try it in
 new version6 it does not work and the aseg.resliced file contains just
corpus callosum!, I don't know which I do wrong because it worked
before and still
work with the analysis which I done with last version. would you please

help me to figure it out?thank you very much for your help.

best regards,

Nazain

PS:the link of previous
mail:https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50794.html
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Re: [Freesurfer] masking cortical thickness

2018-10-11 Thread N Saf 
External Email - Use Caution

Hi,

Thank you so much , it works.

BRG,
Nazanin

On Wed, Oct 10, 2018 at 9:41 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> if you want to mask the thickness, then use mri_mask
>
> On 10/10/2018 10:30 AM, N Saf wrote:
> >
> > External Email - Use Caution
> >
> > Dear Douglos,
> >
> > as you recommended, I used the --outmask and create the binary mask of
> > a label in mgh format. as I use the mri_binarize command with this
> > mask and ?h.thickness; the output is binary too or if I use --match
> > flag or --min --max flag the out put is 1 for those range, but I want
> > the thickness values on my mask, not 1 all over it , how should I do
> that?
> >
> > any detail information will be appreciated.
> >
> > BRG,
> > Nazanin
> >
> >
> > On Tue, Oct 9, 2018 at 7:27 PM Greve, Douglas N.,Ph.D.
> > mailto:dgr...@mgh.harvard.edu>> wrote:
> >
> > Use the --outmask option
> >
> > On 10/07/2018 08:59 AM, N Saf wrote:
> > >
> > > External Email - Use Caution
> > >
> > > Dear Douglos,
> > >
> > > I did not understand how to use mri_label2label with the mask
> > > option(there is srcmask options not mask alone !). I extract my
> > labels
> > > and as you explained I wanted to create i.e. binary mask of
> > > rh.fusiform.label  with mri_label2label :
> > >   mri_label2label  --srcsubject case1 --srclabel rh.fusiform.label
> > > --trgsubject case1 --trglabel outputlabel.mgh --regmethod surface
> > > --hemi rh
> > >
> > > but it creats another label file not binary with mgh format I
> > did not
> > > get how can I create mybinary.mgh mask in order to use in third
> > > command "mri_binarize --i lh.thickness --mask youmask.mgh --o
> > > lh.thickness.masked.mgh"
> > >
> > > would you please help me with this, it would be a great favor.
> > >
> > > Best regards,
> > > Nazanin
> > >
> > > On Mon, Jul 30, 2018 at 10:59 PM Douglas N. Greve
> > > mailto:dgr...@mgh.harvard.edu>
> > <mailto:dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>>>
> > wrote:
> > >
> > > Yes, that should work. You can create a mask by breaking the
> > > annotation
> > > into labels (mri_annotation2label), then converting the
> > label into a
> > > binary mask (mri_label2label with --mask option), then
> > > mri_binarize --i
> > > lh.thickness --mask youmask.mgh --o lh.thickness.masked.mgh
> > >
> > >
> > > On 07/30/2018 01:47 AM, N Saf wrote:
> > > >
> > > > External Email - Use Caution
> > > >
> > > > Dear Freesurfer Experts,
> > > >
> > > > I wonder how can I show the cortical thickness surface on
> > just one
> > > > region of my interest in Freeview.  assume that I want to
> > see the
> > > > thickness surface of one of the regions in DKTatlas. does it
> > > work if I
> > > > make a binary mask of that specific region on
> > > aparcDKTatlas.annot and
> > > > then multiply it to the ?h.thickness surface ?? any help
> > will be
> > > > appreciated.
> > > >
> > > > Best Regards,
> > > > Nazanin
> > > >
> > > >
> > > > ___
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> > > > Freesurfer@nmr.mgh.harvard.edu
> > <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > > <mailto:Freesurfer@nmr.mgh.harvard.edu
> > <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > >
> > > ___
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> > > Freesurfer@nmr.mgh.harvard.edu
> > <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> > <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > > https://mail.nmr.

Re: [Freesurfer] masking cortical thickness

2018-10-10 Thread N Saf 
External Email - Use Caution

Dear Douglos,

as you recommended, I used the --outmask and create the binary mask of a
label in mgh format. as I use the mri_binarize command with this mask and
?h.thickness; the output is binary too or if I use --match flag or --min
--max flag the out put is 1 for those range, but I want the thickness
values on my mask, not 1 all over it , how should I do that?

any detail information will be appreciated.

BRG,
Nazanin


On Tue, Oct 9, 2018 at 7:27 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> Use the --outmask option
>
> On 10/07/2018 08:59 AM, N Saf wrote:
> >
> > External Email - Use Caution
> >
> > Dear Douglos,
> >
> > I did not understand how to use mri_label2label with the mask
> > option(there is srcmask options not mask alone !). I extract my labels
> > and as you explained I wanted to create i.e. binary mask of
> > rh.fusiform.label  with mri_label2label :
> >   mri_label2label  --srcsubject case1 --srclabel rh.fusiform.label
> > --trgsubject case1 --trglabel outputlabel.mgh --regmethod surface
> > --hemi rh
> >
> > but it creats another label file not binary with mgh format I did not
> > get how can I create mybinary.mgh mask in order to use in third
> > command "mri_binarize --i lh.thickness --mask youmask.mgh --o
> > lh.thickness.masked.mgh"
> >
> > would you please help me with this, it would be a great favor.
> >
> > Best regards,
> > Nazanin
> >
> > On Mon, Jul 30, 2018 at 10:59 PM Douglas N. Greve
> > mailto:dgr...@mgh.harvard.edu>> wrote:
> >
> > Yes, that should work. You can create a mask by breaking the
> > annotation
> > into labels (mri_annotation2label), then converting the label into a
> > binary mask (mri_label2label with --mask option), then
> > mri_binarize --i
> > lh.thickness --mask youmask.mgh --o lh.thickness.masked.mgh
> >
> >
> > On 07/30/2018 01:47 AM, N Saf wrote:
> > >
> > > External Email - Use Caution
> > >
> > > Dear Freesurfer Experts,
> > >
> > > I wonder how can I show the cortical thickness surface on just one
> > > region of my interest in Freeview.  assume that I want to see the
> > > thickness surface of one of the regions in DKTatlas. does it
> > work if I
> > > make a binary mask of that specific region on
> > aparcDKTatlas.annot and
> > > then multiply it to the ?h.thickness surface ?? any help will be
> > > appreciated.
> > >
> > > Best Regards,
> > > Nazanin
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> > ___
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> > Freesurfer@nmr.mgh.harvard.edu  Freesurfer@nmr.mgh.harvard.edu>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > The information in this e-mail is intended only for the person to
> > whom it is
> > addressed. If you believe this e-mail was sent to you in error and
> > the e-mail
> > contains patient information, please contact the Partners
> > Compliance HelpLine at
> > http://www.partners.org/complianceline . If the e-mail was sent to
> > you in error
> > but does not contain patient information, please contact the
> > sender and properly
> > dispose of the e-mail.
> >
> >
> >
> > ___
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Re: [Freesurfer] masking cortical thickness

2018-10-07 Thread N Saf 
External Email - Use Caution

Dear Douglos,

I did not understand how to use mri_label2label with the mask option(there
is srcmask options not mask alone !). I extract my labels and as you
explained I wanted to create i.e. binary mask of rh.fusiform.label  with
mri_label2label :
  mri_label2label  --srcsubject case1 --srclabel rh.fusiform.label
--trgsubject case1 --trglabel outputlabel.mgh --regmethod surface --hemi rh

but it creats another label file not binary with mgh format I did not get
how can I create mybinary.mgh mask in order to use in third command
"mri_binarize --i lh.thickness --mask youmask.mgh --o
lh.thickness.masked.mgh"

would you please help me with this, it would be a great favor.

Best regards,
Nazanin

On Mon, Jul 30, 2018 at 10:59 PM Douglas N. Greve 
wrote:

> Yes, that should work. You can create a mask by breaking the annotation
> into labels (mri_annotation2label), then converting the label into a
> binary mask (mri_label2label with --mask option), then mri_binarize --i
> lh.thickness --mask youmask.mgh --o lh.thickness.masked.mgh
>
>
> On 07/30/2018 01:47 AM, N Saf wrote:
> >
> > External Email - Use Caution
> >
> > Dear Freesurfer Experts,
> >
> > I wonder how can I show the cortical thickness surface on just one
> > region of my interest in Freeview.  assume that I want to see the
> > thickness surface of one of the regions in DKTatlas. does it work if I
> > make a binary mask of that specific region on aparcDKTatlas.annot and
> > then multiply it to the ?h.thickness surface ?? any help will be
> > appreciated.
> >
> > Best Regards,
> > Nazanin
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
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>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
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[Freesurfer] masking cortical thickness

2018-07-29 Thread N Saf 
External Email - Use Caution

Dear Freesurfer Experts,

I wonder how can I show the cortical thickness surface on just one region
of my interest in Freeview.  assume that I want to see the thickness
surface of one of the regions in DKTatlas. does it work if I make a binary
mask of that specific region on aparcDKTatlas.annot and then multiply it to
the ?h.thickness surface ?? any help will be appreciated.

Best Regards,
Nazanin
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[Freesurfer] viewing the flatten sheet

2018-01-08 Thread N Saf 
Dear experts,

I cut the inflated surface in tksurfer and obtain the flatten sheet by
mris_flatten but I can not load the $h.flaten.patch.3d not in freeview nor
in tksurfer it somehow collapse! my laptop is RAM:6G , core i5 , would you
please help me how can I see the 2D flatten sheet ??

many thanks to any help you can provide me.

BRG,
Nazanin
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Re: [Freesurfer] Feat

2017-12-31 Thread N Saf 
thank you indeed.

On Mon, Jan 1, 2018 at 1:50 AM, Douglas Greve <gr...@nmr.mgh.harvard.edu>
wrote:

> Use tkmeditfv and tksurferfv and it will bring up freeview instead.
>
> On 12/26/17 4:17 AM, N Saf wrote:
>
> Dear FreeSurfer experts,
>
> I am trying to view the Feat on volume and surface by following commands:
>
>
> tkmedit bert orig.mgz -aux brain.mgz
>   -overlay ./fbert1.feat/stats/zstat1.nii.gz
>   -overlay-reg ./fbert1.feat/reg/freesurfer/anat2exf.register.dat
>   -fthresh 2.3 –fmax 4.3  -seg aparc+aseg.mgz
>
> and
>
> tksurfer bert rh inflated
>   -overlay ./fbert1.feat/stats/zstat1.nii.gz
>   -overlay-reg ./fbert1.feat/reg/freesurfer/anat2exf.register.dat
>   -fthresh 2.3 -fmid 3.3 -fslope 1
>
> it works but thats my question:
>
> Is it possible to do the same thing with freeview ? I can not convert
> above  commands in a way which be meaningful for freeview.
>
> many thanks to any help you can provide me.
>
> BRG,
> Nazanin
>
>
>
> ___
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>
>
>
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>
>
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> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
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> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
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[Freesurfer] Feat

2017-12-26 Thread N Saf 
Dear FreeSurfer experts,

I am trying to view the Feat on volume and surface by following commands:


tkmedit bert orig.mgz -aux brain.mgz
  -overlay ./fbert1.feat/stats/zstat1.nii.gz
  -overlay-reg ./fbert1.feat/reg/freesurfer/anat2exf.register.dat
  -fthresh 2.3 –fmax 4.3  -seg aparc+aseg.mgz

and

tksurfer bert rh inflated
  -overlay ./fbert1.feat/stats/zstat1.nii.gz
  -overlay-reg ./fbert1.feat/reg/freesurfer/anat2exf.register.dat
  -fthresh 2.3 -fmid 3.3 -fslope 1

it works but thats my question:

Is it possible to do the same thing with freeview ? I can not convert
above  commands in a way which be meaningful for freeview.

many thanks to any help you can provide me.

BRG,
Nazanin
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Re: [Freesurfer] Registration

2017-11-08 Thread N Saf 
Hi Bruce

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

I'm really appreciated for the help.

Best Regards,
Nazanin



On Mon, Oct 30, 2017 at 5:36 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:

> Hi Nazanin
>
> the nonlinear registration is actually to our segmentation atlas (*.gca).
> I guess you could try using something else, but you should extract a mean
> intensity image from the gca as a target, not the MNI305. You can do this
> with:
>
> mri_convert -nth 0 .gca mean_gca.mgz
>
> FYI, this:
>
> mri_convert -nth 1 .gca labels_gca.mgz
>
> would give you the highest prior label at each spot (and 2 would give you
> the prior)
>
> cheers
> Bruce
>
>
>
>
> On Mon, 30 Oct 2017, N Saf wrote:
>
> Dear Experts,
>> In the volume-based stream, if I'm right the FreeSurfer does two
>> registration with MNI305 ,one affine and one
>> nonlinear , is it possible to perform the nonlinear registration
>> somewhere else and then use the result in
>> FreeSurfer and run the rest of the analysis ?
>>
>> thank's alot for your great support.
>>
>> BRG,
>> Nazanin
>>
>>
>>
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[Freesurfer] Registration

2017-10-30 Thread N Saf 
Dear Experts,

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

thank's alot for your great support.

BRG,
Nazanin
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Re: [Freesurfer] cortical marker

2017-09-30 Thread N Saf 
Dear Bruce,

Thank you very much for the help. as you recommended I read the lh.sulc and
lh.jacobian_white in Matlab and I have two vectors for each one of them.
the vector is for whole left hemisphere ,unfortunately I still did not
understand how can I have the values of each vector correspond to
parcellation roi's. for example which number sires in each vector related
to middle temporal lob or other roi's.

I really appreciated if you make me realize that.

BRG,
Nazanin

On Thu, Sep 28, 2017 at 6:03 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:

> Hi Nazanin
>
> 1. We don't put maps into stats files as they would be way too big. You
> can load the sulc into matlab with the read_curv command.
>
> 2. This should also be straightforward in matlab. mris_info will give you
> the total surface area of any surface. Or I think mris_jacobian will do
> this entire calculation for you
>
> cheers
> Bruce
>
>
>
> On Thu, 28 Sep 2017, N Saf wrote:
>
> Dear FreeSurfer experts,
>> I have 2 questions:
>> 1- I try to measure average convexity for temporal lobe by FreeSurfer, I
>> can see the values for each
>> vertex when I overlay the e.g. lh.sulc in lh.inflated, but I wonder if I
>> can find these values
>> somewhere else like in stats files?
>>
>> 2- Is FreeSurfer compute metric distortion for a specific ROI (e.g. ROIs
>> segmented in parcellation )
>> according following equation? and if that's the case where can I find
>> these values of metric
>> distortion?
>>
>>
>> Metric distortion = k ∗ area of a triangle on registered sphere/
>> area of triangle on original gray/white interface surface
>>
>> Where k = total surface area of original gray/white interface surface/
>> total surface area of individual sphere
>>
>> could you help me to solve the problem, I am looking forward to receive
>> your answer. Thank you for
>> your help.
>>
>> Best Regards,
>> Nazanin
>>
>>
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[Freesurfer] cortical marker

2017-09-28 Thread N Saf 
Dear FreeSurfer experts,

I have 2 questions:
1- I try to measure average convexity for temporal lobe by FreeSurfer, I
can see the values for each vertex when I overlay the e.g. lh.sulc in
lh.inflated, but I wonder if I can find these values somewhere else like in
stats files?

2- Is FreeSurfer compute metric distortion for a specific ROI (e.g. ROIs
segmented in parcellation ) according following equation? and if that's the
case where can I find these values of metric distortion?


Metric distortion = k ∗ area of a triangle on registered sphere/
area of triangle on original gray/white interface surface

Where k = total surface area of original gray/white interface surface/
total surface area of individual sphere

could you help me to solve the problem, I am looking forward to receive
your answer. Thank you for your help.

Best Regards,
Nazanin
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[Freesurfer] Freeview

2017-04-08 Thread N Saf 
Dear FreeSurfer experts,

I have two questions please.

1- I cannot understand the concept of "existing labels". Why few labels
(such as #19) do exist in the LUT, but they cannot be overlaid on the
brain? What should I do if I need to map one of those labels on the brain
that disappear when I press the button of "existing labels"?

2- I can see that the 5 label is named as ctx-lh-G-front-middle, and
the 1109 label is named as ctx-lh-G-frontal-middle. Is there any difference
between these two? If yes, what is the difference? If no, why their name is
different?
 (The 1109 label disappears when pressing the existing labels button)

Sincerely yours,
Nazanin
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Re: [Freesurfer] Freeview

2017-02-21 Thread N Saf 
Thank you very much ,it was a great help .

Best Regards,
Nazanin

On Tue, Feb 21, 2017 at 7:34 PM, Ruopeng Wang <rpw...@nmr.mgh.harvard.edu>
wrote:

> Just open FreeSurferColorLUT.txt file in your freesurfer installation
> directory, you should be able to figure the format.
>
> On Feb 21, 2017, at 10:59 AM, N Saf <nali...@gmail.com> wrote:
>
> Dear Ruopeng,
>
> Thank you for the fast response ,where can I learn how to create my custom
> lookup table step by step ? and what the format of this file is?any help
> will be very appreciated.
>
> Best Regards,
> Nazanin
>
> On Tue, Feb 21, 2017 at 6:45 PM, Ruopeng Wang <rpw...@nmr.mgh.harvard.edu>
> wrote:
>
>> Hi Nazanin,
>>
>> To change color you will need to modify the look up table, i.e., load
>> your own look up table. There is no way to only display a few selected
>> labels. As a workaround, you may try applying a look up table with only a
>> few labels in it.
>>
>> Best,
>> Ruopeng
>>
>> > On Feb 21, 2017, at 5:20 AM, N Saf <nali...@gmail.com> wrote:
>> >
>> > Dear Experts,
>> >
>> > I load the T1 and aseg file in freeveiw and select the lookup table
>> ,and show as isosurface in 3D view for a label .Is it possible to change
>> the color(for example label 13 is blue but I want to show it as
>> yellow!).another question is that if I want to show multiple labels which
>> are not in the range how should I do it ? for example I want to see labels
>> 11 & 13 & 30  but not the lables between ,how can I do it?thanks for your
>> support.
>> >
>> >
>> > Best Regards,
>> > Nazanin
>> > ___
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>> > Freesurfer@nmr.mgh.harvard.edu
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>>
>>
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Re: [Freesurfer] Freeview

2017-02-21 Thread N Saf 
Dear Ruopeng,

Thank you for the fast response ,where can I learn how to create my custom
lookup table step by step ? and what the format of this file is?any help
will be very appreciated.

Best Regards,
Nazanin

On Tue, Feb 21, 2017 at 6:45 PM, Ruopeng Wang <rpw...@nmr.mgh.harvard.edu>
wrote:

> Hi Nazanin,
>
> To change color you will need to modify the look up table, i.e., load your
> own look up table. There is no way to only display a few selected labels.
> As a workaround, you may try applying a look up table with only a few
> labels in it.
>
> Best,
> Ruopeng
>
> > On Feb 21, 2017, at 5:20 AM, N Saf <nali...@gmail.com> wrote:
> >
> > Dear Experts,
> >
> > I load the T1 and aseg file in freeveiw and select the lookup table ,and
> show as isosurface in 3D view for a label .Is it possible to change the
> color(for example label 13 is blue but I want to show it as
> yellow!).another question is that if I want to show multiple labels which
> are not in the range how should I do it ? for example I want to see labels
> 11 & 13 & 30  but not the lables between ,how can I do it?thanks for your
> support.
> >
> >
> > Best Regards,
> > Nazanin
> > ___
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> > Freesurfer@nmr.mgh.harvard.edu
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[Freesurfer] Freeview

2017-02-21 Thread N Saf 
Dear Experts,

I load the T1 and aseg file in freeveiw and select the lookup table ,and
show as isosurface in 3D view for a label .Is it possible to change the
color(for example label 13 is blue but I want to show it as
yellow!).another question is that if I want to show multiple labels which
are not in the range how should I do it ? for example I want to see labels
11 & 13 & 30  but not the lables between ,how can I do it?thanks for your
support.


Best Regards,
Nazanin
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Re: [Freesurfer] Question

2017-01-19 Thread N Saf 
Dear Bruce,

I read this article "Atlas Renormalization for Improved Brain MR Image
Segmentation Across Scanner Platforms(2007)" and I wonder if theses steps
"normalization" and "normalization2" do the Atlas Renormalization which
mentioned at that article or should I use another command myself to do the
Atlas Renormalization that the article proposed? (sorry if the question is
basic)


Best,
Nazanin

On Fri, Jan 20, 2017 at 9:16 AM, N Saf <nali...@gmail.com> wrote:

> Dear Bruce,
>
> thank you for your comprehensive explanation.
>
> Best,
> Nazanin
>
>
> On Thu, Jan 19, 2017 at 7:00 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
> wrote:
>
>> Hi Nazanin
>>
>> there is no easy way to display a partial volume. You can still use
>> Dice/Jaccard on the hard segmentations, but we have found that the partial
>> volume correction improves e.g. test/retest reliability and probably
>> accuracy, although that is harder to prove.
>>
>> cheers
>> Bruce
>>
>>
>>
>> On Thu, 19 Jan 2017, N Saf wrote:
>>
>> Dear Bruce
>>>
>>> is there any 3D image file which shows the segmentation regions after
>>> this
>>> correction ?and if there is not is it right to use aseg.mgz file for
>>> reporting Dice or Jaccard Index (I have manual segmentation as gold
>>> standard)?
>>>
>>> Best Regards,
>>> Nazanin
>>>
>>>
>>>
>>>
>>> On Wed, Jan 18, 2017 at 5:18 PM, Bruce Fischl <
>>> fis...@nmr.mgh.harvard.edu>
>>> wrote:
>>>   Hi Nazanin
>>>
>>>   the volumes reported in the aseg.stats file have been corrected
>>>   for partial volume effects.
>>>
>>>   cheers
>>>   Bruce
>>>   On Wed, 18 Jan 2017, N Saf wrote:
>>>
>>> Dear FreeSurfers,
>>> I have a question about aseg file. I load the aseg
>>> file of bert subject in
>>> itk-snap and read the volume for 17 and 53 label but
>>> it is a bit larger of
>>> the volume in bert stats file. I do the same for
>>> some of my subjects too and
>>> I see the same result .I don't know why it is like
>>> that ?would you please
>>> clear the reason for me.because I need to  compare
>>> the FreeSurfer result and
>>> I should use of aseg file labels but I'm afraid the
>>> comparison I'm doing is
>>> not valid.
>>>
>>> Sincerely yours,
>>> Nazanin
>>>
>>>
>>>
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>>>
>>>
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>>> it is
>>> addressed. If you believe this e-mail was sent to you in error and the
>>> e-mail
>>> contains patient information, please contact the Partners Compliance
>>> HelpLine at
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>>> but does not contain patient information, please contact the sender
>>> and properly
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>>>
>>>
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Re: [Freesurfer] Question

2017-01-19 Thread N Saf 
Dear Bruce,

thank you for your comprehensive explanation.

Best,
Nazanin


On Thu, Jan 19, 2017 at 7:00 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:

> Hi Nazanin
>
> there is no easy way to display a partial volume. You can still use
> Dice/Jaccard on the hard segmentations, but we have found that the partial
> volume correction improves e.g. test/retest reliability and probably
> accuracy, although that is harder to prove.
>
> cheers
> Bruce
>
>
>
> On Thu, 19 Jan 2017, N Saf wrote:
>
> Dear Bruce
>>
>> is there any 3D image file which shows the segmentation regions after this
>> correction ?and if there is not is it right to use aseg.mgz file for
>> reporting Dice or Jaccard Index (I have manual segmentation as gold
>> standard)?
>>
>> Best Regards,
>> Nazanin
>>
>>
>>
>>
>> On Wed, Jan 18, 2017 at 5:18 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu
>> >
>> wrote:
>>   Hi Nazanin
>>
>>   the volumes reported in the aseg.stats file have been corrected
>>   for partial volume effects.
>>
>>   cheers
>>   Bruce
>>   On Wed, 18 Jan 2017, N Saf wrote:
>>
>> Dear FreeSurfers,
>> I have a question about aseg file. I load the aseg
>> file of bert subject in
>> itk-snap and read the volume for 17 and 53 label but
>> it is a bit larger of
>> the volume in bert stats file. I do the same for
>> some of my subjects too and
>> I see the same result .I don't know why it is like
>> that ?would you please
>> clear the reason for me.because I need to  compare
>> the FreeSurfer result and
>> I should use of aseg file labels but I'm afraid the
>> comparison I'm doing is
>> not valid.
>>
>> Sincerely yours,
>> Nazanin
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
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>> it is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender
>> and properly
>> dispose of the e-mail.
>>
>>
>>
>>
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Re: [Freesurfer] Question

2017-01-18 Thread N Saf 
Dear Bruce

is there any 3D image file which shows the segmentation regions after this
correction ?and if there is not is it right to use aseg.mgz file for
reporting Dice or Jaccard Index (I have manual segmentation as gold
standard)?

Best Regards,
Nazanin




On Wed, Jan 18, 2017 at 5:18 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:

> Hi Nazanin
>
> the volumes reported in the aseg.stats file have been corrected for
> partial volume effects.
>
> cheers
> Bruce
>
> On Wed, 18 Jan 2017, N Saf wrote:
>
> Dear FreeSurfers,
>> I have a question about aseg file. I load the aseg file of bert subject in
>> itk-snap and read the volume for 17 and 53 label but it is a bit larger of
>> the volume in bert stats file. I do the same for some of my subjects too
>> and
>> I see the same result .I don't know why it is like that ?would you please
>> clear the reason for me.because I need to  compare the FreeSurfer result
>> and
>> I should use of aseg file labels but I'm afraid the comparison I'm doing
>> is
>> not valid.
>>
>> Sincerely yours,
>> Nazanin
>>
>>
>>
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[Freesurfer] Question

2017-01-18 Thread N Saf 
Dear FreeSurfers,

I have a question about aseg file. I load the aseg file of bert subject in
itk-snap and read the volume for 17 and 53 label but it is a bit larger of
the volume in bert stats file. I do the same for some of my subjects too
and I see the same result .I don't know why it is like that ?would you
please clear the reason for me.because I need to  compare the FreeSurfer
result and I should use of aseg file labels but I'm afraid the comparison
I'm doing is not valid.

Sincerely yours,
Nazanin
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Re: [Freesurfer] dice coefficient computing

2017-01-10 Thread N Saf 
Dear Bruce,

Thank you very much,you are a life saver..

Best,
Nazanin

On Mon, Jan 9, 2017 at 11:05 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:

> yes, you can use mri_convert as follows:
>
> mri_convert -rl rawavg.mgz -rt nearest aseg.mgz aseg.resliced.mgz
>
> assuming the rawavg.mgz has the 208x176x176 dimensions (which it should)
>
> cheers
> Bruce
> On Mon, 9 Jan 2017, N Saf wrote:
>
> Dear Bruce,
>>
>> thank you for your fast reply ,I think I could not explain the problem
>> correctly . I want the number of slices in aseg file convert from
>> 256x256x256 to 208x176x176(the
>> subject size) so I can enable to compute the dice coefficient with my
>> Matlab code ? any suggestions how can I make it possible?
>>
>>
>> Best Regards,
>> Nazanin
>>
>> On Mon, Jan 9, 2017 at 5:51 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
>> wrote:
>>   Hi Nazanin
>>
>>   all our segmentations are in subject space, so it should be pretty
>> straightforward
>>
>>   cheers
>>   Bruce
>>   On Mon, 9 Jan 2017, N Saf wrote:
>>
>> Dear freesurfers,
>>
>> I analysis my T1 MRI with FreeSurfer (aseg.mgz 256x256x256)
>> and I have
>> manual segmentation for hippocampus in my subject
>> space(208x176x176)as well.
>> I want to compute the dice coefficient with one simple Matlab
>> code. how can
>> I do it correctly ?if I want to  bring the aseg to subject
>> space , which
>> command with which options is the best way to do it correctly
>> ?any help can
>> be appreciated.(I did it for the FSL segmentation result but
>> it was simple
>> because the result is in my subject space).
>>
>> Best Regards,
>> Nazanin
>>
>>
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>> in error
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>> dispose of the e-mail.
>>
>>
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Re: [Freesurfer] dice coefficient computing

2017-01-09 Thread N Saf 
Dear Bruce,

thank you for your fast reply ,I think I could not explain the problem
correctly . I want the number of slices in aseg file convert from
256x256x256 to 208x176x176(the subject size) so I can enable to compute the
dice coefficient with my Matlab code ? any suggestions how can I make it
possible?


Best Regards,
Nazanin

On Mon, Jan 9, 2017 at 5:51 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:

> Hi Nazanin
>
> all our segmentations are in subject space, so it should be pretty
> straightforward
>
> cheers
> Bruce
>
> On Mon, 9 Jan 2017, N Saf wrote:
>
> Dear freesurfers,
>>
>> I analysis my T1 MRI with FreeSurfer (aseg.mgz 256x256x256) and I have
>> manual segmentation for hippocampus in my subject space(208x176x176)as
>> well.
>> I want to compute the dice coefficient with one simple Matlab code. how
>> can
>> I do it correctly ?if I want to  bring the aseg to subject space , which
>> command with which options is the best way to do it correctly ?any help
>> can
>> be appreciated.(I did it for the FSL segmentation result but it was simple
>> because the result is in my subject space).
>>
>> Best Regards,
>> Nazanin
>>
>>
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[Freesurfer] dice coefficient computing

2017-01-09 Thread N Saf 
Dear freesurfers,

I analysis my T1 MRI with FreeSurfer (aseg.mgz 256x256x256) and I have
manual segmentation for hippocampus in my subject space(208x176x176)as
well. I want to compute the dice coefficient with one simple Matlab code.
how can I do it correctly ?if I want to  bring the aseg to subject space ,
which command with which options is the best way to do it correctly ?any
help can be appreciated.(I did it for the FSL segmentation result but it
was simple because the result is in my subject space).

Best Regards,
Nazanin
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[Freesurfer] mri_cvs_register

2016-12-24 Thread N Saf 
Dear Freesurfers,

I try to register my subject with cvs atlas in mni space I use this command
mri_cvs_register --mov subject.nii --mni

I got this error:
Using m3z type morph files.
amir : at least one mean and/or Gaussian curvature file is missing (.H, .K)
/home/nazanin/freesurfer/subjects/amir/surf: No such file or directory.


should I first do some processing with freesurfer for my subject and then
use this command ??? and if so what is the minimum processing I should run
before using mri_cvs_register command?I saw a similar question in mailing
list but I did not find the answer ,in advance I apologize if it can be
repetitive.another question is that if it's possible to register my subject
with the probability map of cvs atlas ??


Best Regards,
Nazanin
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Re: [Freesurfer] change the algorithm

2016-06-20 Thread N Saf 
Dear Bruce,

thank you for your fast and helpful response.

I have read in some papers (e.g. paper1
<https://scholar.google.com/scholar?hl=en=Validation+of+hippocampal+volumes+measured+using+a+manual+method+and+two+automated+methods+%28FreeSurfer+and+IBASPM%29+in+chronic+major+depressive+disorder=_sdt=1%2C5_sdtp=>
,paper2
<https://scholar.google.com/scholar?q=Evaluation+of+Hippocampal+Volume+Based+on+Various+Inversion+Time+in+Normal+Adults+by+Manual+Tracing+and+Automated+Segmentation+Methods==en_sdt=0%2C5>)
that FreeSurfer overestimates hippocampus volume a little  compared to the
manual segmentation. I know this is to be expected, but I wanted to see if
there are some parameters that I can work with to reduce this problem as
much as possible.can I access to probabilities which computed for
subcortical segmentation  from training data  in FreeSurfer ?

Sincerely,
Nazanin

On Sun, Jun 19, 2016 at 7:21 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:

> Hi Nazanin
>
> no, sorry, that isn't possible. Our accuracy is improved by the fact that
> we model all subcortical structures simultaneously.
>
> As for your second question you need to be more specific. Are you finding
> some inaccuracies that you want to correct?
>
> cheers
> Bruce
>
>
>
> On Sun, 19 Jun 2016, N Saf wrote:
>
> Dear Freesurfer,
>>
>> I wonder if it is possible to segment just one sub-cortical structures
>> like
>> hippocampus by changing the algorithm (e.g. according to spatial prior
>> knowledge divided the image to some sub-images and do analysis just on
>> that
>> sub-image which we sure the hippocampus located)and by that reducing the
>> processing time ? and another general question I have is that in
>> sub-cortical segmentation commands 1to12 commands of -all flag  which
>> parameters can I change to affect the outputs?
>>
>> Sincerely,
>> Nazanin
>>
>>
>>
>>
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[Freesurfer] change the algorithm

2016-06-19 Thread N Saf 
Dear Freesurfer,

I wonder if it is possible to segment just one sub-cortical structures like
hippocampus by changing the algorithm (e.g. according to spatial prior
knowledge divided the image to some sub-images and do analysis just on that
sub-image which we sure the hippocampus located)and by that reducing the
processing time ? and another general question I have is that in
sub-cortical segmentation commands 1to12 commands of -all flag  which
parameters can I change to affect the outputs?

Sincerely,
Nazanin
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