Re: [Freesurfer] WG: WG: [Fwd: WG: missing temporal lobes]

[Bruce Fischl]

Hi Kristina

can you please post to the list so others can answer? If you add control 
points to the temporal WM where you are missing gm it should recover most 
if not all of it. Hippocampus is not neocortical and isn't supposed to be 
included. The surfaces are somewhat arbitrary there, and excluded from all 
subsequent calculations (like total cortical area/volume)


cheers
Bruce

On Tue, 27 May 2014, 
Mayer Kristina wrote:



Dear Bruce
How can I get the Hippocampus and the missing parts of GM of the temporal lobe 
into the PIAL (sufrace mask)? How can I convince freesurfer those parts are 
belonging to gray matter?

Cheers,
Kristina

Von: Mayer Kristina
Gesendet: Freitag, 23. Mai 2014 16:11
An: Freesurfer support list; freesurfer-boun...@nmr.mgh.harvard.edu
Betreff: AW: [Freesurfer] WG: [Fwd: WG:  missing temporal lobes]


Von: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu]" im Auftrag von "Bruce 
Fischl [fis...@nmr.mgh.harvard.edu]
Gesendet: Freitag, 23. Mai 2014 14:52
An: Freesurfer support list
Betreff: Re: [Freesurfer] WG: [Fwd: WG:  missing temporal lobes]

Hi Kristina

don't add CPs to the gray matter - that will mess everything up!
Bruce
On Fri, 23
May 2014, Mayer Kristina wrote:




Dear Bruce
My dataset is very young (around 2 years of age), I suppose the contrast
and size is just different from the default-template of freesurfer. Is
there a way to exchange the template (I am thinking of a probabilistic
map) without creating an own atlas first?
Attached you find screenshots of my work and the recon-log of the same
subject.
I first run all recon-all steps. Then I added CP where WM was missing. I
also added CP in GM region where lost of GM was missing (temporal lobe) to
get the pial right. Then I tried to remove the WM which came out too much,
for I placed CP in GM regions.
Is there another way for it?

Best,
Kristina

log 0001339:
Fri May 16 08:50:00 CEST 2014
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
/media/n-NAS_MRI/freesurfer-subjects-dir/0001336
setenv SUBJECTS_DIR /media/n-NAS_MRI/freesurfer-subjects-dir
-autorecon2-cp -autorecon3 -subjid 0001336
Linux cs2.kispi.int 3.13.5-103.fc19.x86_64 #1 SMP Mon Mar 3 18:46:36 UTC
2014 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 64 kbytes
maxproc  1024
maxlocks unlimited
maxsignal514103
maxmessage   819200
maxnice  0
maxrtprio0
maxrttimeunlimited

FSL_BIN=/usr/local/fsl/bin
SSH_AGENT_PID=4883
XDG_SESSION_ID=35
HOSTNAME=cs2.kispi.int
SELINUX_ROLE_REQUESTED=
FS_OVERRIDE=0
GPG_AGENT_INFO=/home/maykr/.gnupg/S.gpg-agent:4883:1
GLADE_PIXMAP_PATH=:
TERM=xterm-256color
XDG_MENU_PREFIX=xfce-
SHELL=/bin/bash
HISTSIZE=1000
SSH_CLIENT=127.0.0.1 40762 22
FSLMULTIFILEQUIT=TRUE
PERL5LIB=/media/n-NAS_MRI/Fontan/programs/ibeat/tools:/media/n-NAS_MRI/Fontan/programs/ibeat/tools:/media/n-NAS_MRI/Fontan/programs/ibeat/tools:/usr/local/freesurfer/mni/lib/perl5/5.8.5
SELINUX_USE_CURRENT_RANGE=
WINDOWID=46782934
OS=Linux
XAPPLRESDIR=/media/n-NAS_MRI/Fontan/programs/ibeat/MCR/v715/X11/app-defaults
QT_GRAPHICSSYSTEM_CHECKED=1
http_proxy=http://proxy.uzh.ch:3128/
LOCAL_DIR=/usr/local/freesurfer/local
USER=maykr
LS_COLORS=rs=0:di=38;5;27:ln=38;5;51:mh=44;38;5;15:pi=40;38;5;11:so=38;5;13:do=38;5;5:bd=48;5;232;38;5;11:cd=48;5;232;38;5;3:or=48;5;232;38;5;9:mi=05;48;5;232;38;5;15:su=48;5;196;38;5;15:sg=48;5;11;38;5;16:ca=48;5;196;38;5;226:tw=48;5;10;38;5;16:ow=48;5;10;38;5;21:st=48;5;21;38;5;15:ex=38;5;34:*.tar=38;5;9:*.tgz=38;5;9:*.arc=38;5;9:*.arj=38;5;9:*.taz=38;5;9:*.lha=38;5;9:*.lzh=38;5;9:*.lzma=38;5;9:*.tlz=38;5;9:*.txz=38;5;9:*.tzo=38;5;9:*.t7z=38;5;9:*.zip=38;5;9:*.z=38;5;9:*.Z=38;5;9:*.dz=38;5;9:*.gz=38;5;9:*.lrz=38;5;9:*.lz=38;5;9:*.lzo=38;5;9:*.xz=38;5;9:*.bz2=38;5;9:*.bz=38;5;9:*.tbz=38;5;9:*.tbz2=38;5;9:*.tz=38;5;9:*.deb=38;5;9:*.rpm=38;5;9:*.jar=38;5;9:*.war=38;5;9:*.ear=38;5;9:*.sar=38;5;9:*.rar=38;5;9:*.alz=38;5;9:*.ace=38;5;9:*.zoo=38;5;9:*.cpio=38;5;9:*.7z=38;5;9:*.rz=38;5;9:*.cab=38;5;9:*.jpg=38;5;13:*.jpeg=38;5;13:*.gif=38;5;13:*.bmp=38;5;13:*.pbm=38;5;13:*.pgm=38;5;13:*.ppm=38;5;13:*.tga=38;5;13:*.xbm=38;5;13:*.xpm=38;5;13:*.tif=38;5;13:*.tiff=38;5;13:*.png=38;5;13:*.svg=38;5;13:*.svgz=38;5;13:*.mng=38;5;13:*.pcx=38;5;13:*.mov=38;5;13:*.mpg=38;5;13:*.mpeg=38;5;13:*.m2v=38;5;13:*.mkv=38;5;13:*.ogm=38;5;13:*.mp4=38;5;13:*.m4v=38;5;13:*.mp4v=38;5;13:*.vob=38;5;13:*.qt=38;5;13:*.nuv=38;5;13:*.wmv=38;5;13:*.asf=38;5;13:*.rm=38;5;13:*.rmvb=38;5;13:*.flc=38;5;13:*.avi=38;5;13:*.fli=38;5;13:*.flv=38;5;13:*.gl=38;5;13:*.dl=38;5;13:*.xcf=38;5;13:*.xwd=38;5;13:*.yuv=38;5;13:*.cgm=38;5;13:*.emf=38;5;13:*.axv=38;5;13:*.anx=38;5;13:*.ogv=38;5;13:*.ogx=38;5;13:*.aac=38;5;45:*.au=38;5;45:*.flac=38;5;45:*.mid=38;5;45:*.mid

[Freesurfer] FW: WG: WG: [Fwd: WG: missing temporal lobes], calculation CSF

[Mayer Kristina]

Oh, I see. So in the calculation of total GM in aseg.stats does it include the 
hippocampus, although it is not showing on the masks for surface of GM or PIAL?
I also tried to calculate total intracranial CSF (ventricles + outer liquor 
spaces). Is following calculation correct:
e TIV   -   BrainSegNotVent   =  total intracranial CSF

These calculations are voxels based. I rather prefer a surface based 
calculation of total intracranial CSF. Is this faisible with freesurfer?

Thanks a lot!
Cheers, Kristina

-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] 
Sent: Tuesday, May 27, 2014 2:24 PM
To: Mayer Kristina
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: WG: [Freesurfer] WG: [Fwd: WG: missing temporal lobes]

Hi Kristina

can you please post to the list so others can answer? If you add control 
points to the temporal WM where you are missing gm it should recover most 
if not all of it. Hippocampus is not neocortical and isn't supposed to be 
included. The surfaces are somewhat arbitrary there, and excluded from all 
subsequent calculations (like total cortical area/volume)

cheers
Bruce

On Tue, 27 May 2014, 
Mayer Kristina wrote:

> Dear Bruce
> How can I get the Hippocampus and the missing parts of GM of the temporal 
> lobe into the PIAL (sufrace mask)? How can I convince freesurfer those parts 
> are belonging to gray matter?
>
> Cheers,
> Kristina
> 
> Von: Mayer Kristina
> Gesendet: Freitag, 23. Mai 2014 16:11
> An: Freesurfer support list; freesurfer-boun...@nmr.mgh.harvard.edu
> Betreff: AW: [Freesurfer] WG: [Fwd: WG:  missing temporal lobes]
>
> 
> Von: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu]" im Auftrag von "Bruce 
> Fischl [fis...@nmr.mgh.harvard.edu]
> Gesendet: Freitag, 23. Mai 2014 14:52
> An: Freesurfer support list
> Betreff: Re: [Freesurfer] WG: [Fwd: WG:  missing temporal lobes]
>
> Hi Kristina
>
> don't add CPs to the gray matter - that will mess everything up!
> Bruce
> On Fri, 23
> May 2014, Mayer Kristina wrote:
>
>>
>>
>> Dear Bruce
>> My dataset is very young (around 2 years of age), I suppose the contrast
>> and size is just different from the default-template of freesurfer. Is
>> there a way to exchange the template (I am thinking of a probabilistic
>> map) without creating an own atlas first?
>> Attached you find screenshots of my work and the recon-log of the same
>> subject.
>> I first run all recon-all steps. Then I added CP where WM was missing. I
>> also added CP in GM region where lost of GM was missing (temporal lobe) to
>> get the pial right. Then I tried to remove the WM which came out too much,
>> for I placed CP in GM regions.
>> Is there another way for it?
>>
>> Best,
>> Kristina
>>
>> log 0001339:
>> Fri May 16 08:50:00 CEST 2014
>> FREESURFER_HOME /usr/local/freesurfer
>> Actual FREESURFER_HOME /usr/local/freesurfer
>> /media/n-NAS_MRI/freesurfer-subjects-dir/0001336
>> setenv SUBJECTS_DIR /media/n-NAS_MRI/freesurfer-subjects-dir
>> -autorecon2-cp -autorecon3 -subjid 0001336
>> Linux cs2.kispi.int 3.13.5-103.fc19.x86_64 #1 SMP Mon Mar 3 18:46:36 UTC
>> 2014 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 64 kbytes
>> maxproc  1024
>> maxlocks unlimited
>> maxsignal514103
>> maxmessage   819200
>> maxnice  0
>> maxrtprio0
>> maxrttimeunlimited
>>
>> FSL_BIN=/usr/local/fsl/bin
>> SSH_AGENT_PID=4883
>> XDG_SESSION_ID=35
>> HOSTNAME=cs2.kispi.int
>> SELINUX_ROLE_REQUESTED=
>> FS_OVERRIDE=0
>> GPG_AGENT_INFO=/home/maykr/.gnupg/S.gpg-agent:4883:1
>> GLADE_PIXMAP_PATH=:
>> TERM=xterm-256color
>> XDG_MENU_PREFIX=xfce-
>> SHELL=/bin/bash
>> HISTSIZE=1000
>> SSH_CLIENT=127.0.0.1 40762 22
>> FSLMULTIFILEQUIT=TRUE
>> PERL5LIB=/media/n-NAS_MRI/Fontan/programs/ibeat/tools:/media/n-NAS_MRI/Fontan/programs/ibeat/tools:/media/n-NAS_MRI/Fontan/programs/ibeat/tools:/usr/local/freesurfer/mni/lib/perl5/5.8.5
>> SELINUX_USE_CURRENT_RANGE=
>> WINDOWID=46782934
>> OS=Linux
>> XAPPLRESDIR=/media/n-NAS_MRI/Fontan/programs/ibeat/MCR/v715/X11/app-defaults
>> QT_GRAPHICSSYSTEM_CHECKED=1
>> http_proxy=http://proxy.uzh.ch:3128/
>> LOCAL_DIR=/usr/local/freesurfer/local
>> USER=maykr
>> LS_COLORS=rs=0:di=38;5;27:ln=38;5;51:mh=44;38;5;15:pi=40;38;5;11:so=38;5;13:do=38;5;5:bd=48;5;232;38;5;11:cd=48;5;232;38;5;3:or=48;5;232;38;5;9:mi=05;48;5;232;38;5;15:su=48;5;196;38;5;15:sg=48;5;11;38;5;16:ca=48;5;196;38;5;226:tw=48;5;10;38;5;16:ow=48;5;10;38;5;21:st=48;5;21;38;5;15:ex=38;5;34:*.tar=38;5;9:*.tgz=38;5;9:*.arc=38;5;9:*.arj=38;5;9:*.taz=38;5;9:*.lha=38;5;9:*.lzh=38;5;9:*.lzma=38;5;9:*.tlz=38;5;9:*.txz=38;5;9:*.tzo=38;5;9:*.t7z=38;5;9:*.zip=38;5;9:*.z=38;5;9:*.Z=38;5;9:*.dz=38;5;9:*.gz=38;5;9:*.lrz=38

Re: [Freesurfer] FW: WG: WG: [Fwd: WG: missing temporal lobes], calculation CSF

[Louis Nicholas Vinke]

Hi Kristina,
This page has the details I believe you are looking for:

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

-Louis


On Tue, 27 May 2014, Mayer Kristina wrote:


Oh, I see. So in the calculation of total GM in aseg.stats does it include the 
hippocampus, although it is not showing on the masks for surface of GM or PIAL?
I also tried to calculate total intracranial CSF (ventricles + outer liquor 
spaces). Is following calculation correct:
e TIV   -   BrainSegNotVent   =  total intracranial CSF

These calculations are voxels based. I rather prefer a surface based 
calculation of total intracranial CSF. Is this faisible with freesurfer?

Thanks a lot!
Cheers, Kristina

-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
Sent: Tuesday, May 27, 2014 2:24 PM
To: Mayer Kristina
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: WG: [Freesurfer] WG: [Fwd: WG: missing temporal lobes]

Hi Kristina

can you please post to the list so others can answer? If you add control
points to the temporal WM where you are missing gm it should recover most
if not all of it. Hippocampus is not neocortical and isn't supposed to be
included. The surfaces are somewhat arbitrary there, and excluded from all
subsequent calculations (like total cortical area/volume)

cheers
Bruce

On Tue, 27 May 2014,
Mayer Kristina wrote:


Dear Bruce
How can I get the Hippocampus and the missing parts of GM of the temporal lobe 
into the PIAL (sufrace mask)? How can I convince freesurfer those parts are 
belonging to gray matter?

Cheers,
Kristina

Von: Mayer Kristina
Gesendet: Freitag, 23. Mai 2014 16:11
An: Freesurfer support list; freesurfer-boun...@nmr.mgh.harvard.edu
Betreff: AW: [Freesurfer] WG: [Fwd: WG:  missing temporal lobes]


Von: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu]" im Auftrag von "Bruce 
Fischl [fis...@nmr.mgh.harvard.edu]
Gesendet: Freitag, 23. Mai 2014 14:52
An: Freesurfer support list
Betreff: Re: [Freesurfer] WG: [Fwd: WG:  missing temporal lobes]

Hi Kristina

don't add CPs to the gray matter - that will mess everything up!
Bruce
On Fri, 23
May 2014, Mayer Kristina wrote:




Dear Bruce
My dataset is very young (around 2 years of age), I suppose the contrast
and size is just different from the default-template of freesurfer. Is
there a way to exchange the template (I am thinking of a probabilistic
map) without creating an own atlas first?
Attached you find screenshots of my work and the recon-log of the same
subject.
I first run all recon-all steps. Then I added CP where WM was missing. I
also added CP in GM region where lost of GM was missing (temporal lobe) to
get the pial right. Then I tried to remove the WM which came out too much,
for I placed CP in GM regions.
Is there another way for it?

Best,
Kristina

log 0001339:
Fri May 16 08:50:00 CEST 2014
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
/media/n-NAS_MRI/freesurfer-subjects-dir/0001336
setenv SUBJECTS_DIR /media/n-NAS_MRI/freesurfer-subjects-dir
-autorecon2-cp -autorecon3 -subjid 0001336
Linux cs2.kispi.int 3.13.5-103.fc19.x86_64 #1 SMP Mon Mar 3 18:46:36 UTC
2014 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 64 kbytes
maxproc  1024
maxlocks unlimited
maxsignal514103
maxmessage   819200
maxnice  0
maxrtprio0
maxrttimeunlimited

FSL_BIN=/usr/local/fsl/bin
SSH_AGENT_PID=4883
XDG_SESSION_ID=35
HOSTNAME=cs2.kispi.int
SELINUX_ROLE_REQUESTED=
FS_OVERRIDE=0
GPG_AGENT_INFO=/home/maykr/.gnupg/S.gpg-agent:4883:1
GLADE_PIXMAP_PATH=:
TERM=xterm-256color
XDG_MENU_PREFIX=xfce-
SHELL=/bin/bash
HISTSIZE=1000
SSH_CLIENT=127.0.0.1 40762 22
FSLMULTIFILEQUIT=TRUE
PERL5LIB=/media/n-NAS_MRI/Fontan/programs/ibeat/tools:/media/n-NAS_MRI/Fontan/programs/ibeat/tools:/media/n-NAS_MRI/Fontan/programs/ibeat/tools:/usr/local/freesurfer/mni/lib/perl5/5.8.5
SELINUX_USE_CURRENT_RANGE=
WINDOWID=46782934
OS=Linux
XAPPLRESDIR=/media/n-NAS_MRI/Fontan/programs/ibeat/MCR/v715/X11/app-defaults
QT_GRAPHICSSYSTEM_CHECKED=1
http_proxy=http://proxy.uzh.ch:3128/
LOCAL_DIR=/usr/local/freesurfer/local
USER=maykr
LS_COLORS=rs=0:di=38;5;27:ln=38;5;51:mh=44;38;5;15:pi=40;38;5;11:so=38;5;13:do=38;5;5:bd=48;5;232;38;5;11:cd=48;5;232;38;5;3:or=48;5;232;38;5;9:mi=05;48;5;232;38;5;15:su=48;5;196;38;5;15:sg=48;5;11;38;5;16:ca=48;5;196;38;5;226:tw=48;5;10;38;5;16:ow=48;5;10;38;5;21:st=48;5;21;38;5;15:ex=38;5;34:*.tar=38;5;9:*.tgz=38;5;9:*.arc=38;5;9:*.arj=38;5;9:*.taz=38;5;9:*.lha=38;5;9:*.lzh=38;5;9:*.lzma=38;5;9:*.tlz=38;5;9:*.txz=38;5;9:*.tzo=38;5;9:*.t7z=38;5;9:*.zip=38;5;9:*.z=38;5;9:*.Z=38;5;9:*.dz=38;5;9:*.gz=38;5;9:*.lrz=38;5;9:*.lz=38;5;9:*.lzo=38;5;9:*.xz=38;5;9:*.bz2=38;5;9:*.bz=38;5;9:*.t

Re: [Freesurfer] FW: WG: WG: [Fwd: WG: missing temporal lobes], calculation CSF

[Mayer Kristina]

Dear Louis,

I got my information from the same page. As eTIV is a totally different 
algorithm, I am not sure if it is faisible to calculate total CSF from this 
parameters. 
As eTIV isn't representing voxels should I rather use the following:

eTIV - BrainSegNotVentSurf = total intracranial CSF

Or is there a more sophisticated method (sorry I did not find anything 
described on the freesurfer wiki about it)?

Thanks in advance,
Kristina

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Louis Nicholas 
Vinke
Sent: Tuesday, May 27, 2014 3:22 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] FW: WG: WG: [Fwd: WG: missing temporal lobes], 
calculation CSF

Hi Kristina,
This page has the details I believe you are looking for:

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

-Louis


On Tue, 27 May 2014, Mayer Kristina wrote:

> Oh, I see. So in the calculation of total GM in aseg.stats does it include 
> the hippocampus, although it is not showing on the masks for surface of GM or 
> PIAL?
> I also tried to calculate total intracranial CSF (ventricles + outer liquor 
> spaces). Is following calculation correct:
>   e TIV   -   BrainSegNotVent   =  total intracranial CSF
>
> These calculations are voxels based. I rather prefer a surface based 
> calculation of total intracranial CSF. Is this faisible with freesurfer?
>
> Thanks a lot!
> Cheers, Kristina
>
> -Original Message-
> From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
> Sent: Tuesday, May 27, 2014 2:24 PM
> To: Mayer Kristina
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: WG: [Freesurfer] WG: [Fwd: WG: missing temporal lobes]
>
> Hi Kristina
>
> can you please post to the list so others can answer? If you add control
> points to the temporal WM where you are missing gm it should recover most
> if not all of it. Hippocampus is not neocortical and isn't supposed to be
> included. The surfaces are somewhat arbitrary there, and excluded from all
> subsequent calculations (like total cortical area/volume)
>
> cheers
> Bruce
>
> On Tue, 27 May 2014,
> Mayer Kristina wrote:
>
>> Dear Bruce
>> How can I get the Hippocampus and the missing parts of GM of the temporal 
>> lobe into the PIAL (sufrace mask)? How can I convince freesurfer those parts 
>> are belonging to gray matter?
>>
>> Cheers,
>> Kristina
>> 
>> Von: Mayer Kristina
>> Gesendet: Freitag, 23. Mai 2014 16:11
>> An: Freesurfer support list; freesurfer-boun...@nmr.mgh.harvard.edu
>> Betreff: AW: [Freesurfer] WG: [Fwd: WG:  missing temporal lobes]
>>
>> 
>> Von: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu]" im Auftrag von "Bruce 
>> Fischl [fis...@nmr.mgh.harvard.edu]
>> Gesendet: Freitag, 23. Mai 2014 14:52
>> An: Freesurfer support list
>> Betreff: Re: [Freesurfer] WG: [Fwd: WG:  missing temporal lobes]
>>
>> Hi Kristina
>>
>> don't add CPs to the gray matter - that will mess everything up!
>> Bruce
>> On Fri, 23
>> May 2014, Mayer Kristina wrote:
>>
>>>
>>>
>>> Dear Bruce
>>> My dataset is very young (around 2 years of age), I suppose the contrast
>>> and size is just different from the default-template of freesurfer. Is
>>> there a way to exchange the template (I am thinking of a probabilistic
>>> map) without creating an own atlas first?
>>> Attached you find screenshots of my work and the recon-log of the same
>>> subject.
>>> I first run all recon-all steps. Then I added CP where WM was missing. I
>>> also added CP in GM region where lost of GM was missing (temporal lobe) to
>>> get the pial right. Then I tried to remove the WM which came out too much,
>>> for I placed CP in GM regions.
>>> Is there another way for it?
>>>
>>> Best,
>>> Kristina
>>>
>>> log 0001339:
>>> Fri May 16 08:50:00 CEST 2014
>>> FREESURFER_HOME /usr/local/freesurfer
>>> Actual FREESURFER_HOME /usr/local/freesurfer
>>> /media/n-NAS_MRI/freesurfer-subjects-dir/0001336
>>> setenv SUBJECTS_DIR /media/n-NAS_MRI/freesurfer-subjects-dir
>>> -autorecon2-cp -autorecon3 -subjid 0001336
>>> Linux cs2.kispi.int 3.13.5-103.fc19.x86_64 #1 SMP Mon Mar 3 18:46:36 UTC
>>> 2014 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 64 kbytes
>>> maxproc  1024
>>> maxlocks unlimited
>>> maxsignal514103
>>> maxmessage   819200
>>> maxnice  0
>>> maxrtprio0
>>> maxrttimeunlimited
>>>
>>> FSL_BIN=/usr/local/fsl/bin
>>> SSH_AGENT_PID=4883
>>> XDG_SESSION_ID=35
>>> HOSTNAME=cs2.kispi.int
>>> SELINUX_ROLE_REQUESTED=
>>> FS_OVERRIDE=0
>>> GPG_AGENT_INFO=/home/maykr/.gnupg/S.gpg-agent:4883:1
>>> GLADE_PIXMAP_PATH=:
>>> TERM=xterm-256color
>>> XDG_MENU_PRE

Re: [Freesurfer] mris_convert to GIFTI misaligned in freeview

[Franz Liem]

Hi Michael,

I had a similar problem a while ago. Maybe this might help.
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg31152.html

Best,
Franz

Am 23.05.2014 um 05:38 schrieb Harms, Michael:

> 
> Hi,
> I converted a surface to GIFTI
> e.g.,
> mris_convert lh.white lh.white.gii
> 
> lh.white and lh.white.gii align when they are both loaded in 'tkmedit'.
> However, they do not align when loaded simultaneously in 'freeview'.
> 
> Of possible relevance: When I loaded lh.white.gii into 'freeview', I got the 
> following message in the terminal:
> "Did not find any volume geometry information in the surface"
> 
> Is this possibly a bug of some sort in the display of GIFTI surfaces within 
> 'freeview'?
> 
> This was all done with FS 5.3.
> 
> thanks,
> -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
> 
>  
> 
> The materials in this message are private and may contain Protected 
> Healthcare Information or other information of a sensitive nature. If you are 
> not the intended recipient, be advised that any unauthorized use, disclosure, 
> copying or the taking of any action in reliance on the contents of this 
> information is strictly prohibited. If you have received this email in error, 
> please immediately notify the sender via telephone or return mail.
> 
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Re: [Freesurfer] High Intensity Spots and Surfacing Issues

[Bruce Fischl]

Hi Jon

definitely not control points. I guess you would have to draw stuff in, 
but that kind of intensity patch is so far from our expectations it may 
be hard. Any idea where it comes from?

Bruce
On Tue, 27 May 
2014, Jonathan Holt wrote:



Hi all,
this is a recurring issue that I'm hoping I can find a solution to. Pictured
is a brain with a particularly high intensity area that seems to defy
surfacing. Is there a way to work around this?

See attached image 

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Re: [Freesurfer] High Intensity Spots and Surfacing Issues

[Jonathan Holt]

No idea, I think it’s due to the scanner, but could be wrong. Drawing in WM 
voxels? 
On May 27, 2014, at 10:20 AM, Bruce Fischl  wrote:

> Hi Jon
> 
> definitely not control points. I guess you would have to draw stuff in, but 
> that kind of intensity patch is so far from our expectations it may be hard. 
> Any idea where it comes from?
> Bruce
> On Tue, 27 May 2014, Jonathan Holt wrote:
> 
>> Hi all,
>> this is a recurring issue that I'm hoping I can find a solution to. Pictured
>> is a brain with a particularly high intensity area that seems to defy
>> surfacing. Is there a way to work around this?
>> See attached image 
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Re: [Freesurfer] High Intensity Spots and Surfacing Issues

[Bruce Fischl]

yes, that's what I meant. It looks too far in the interior to be a B0 
effect. Do you see it in all your subjects? What sequence/scanner are you 
using?On Tue, 27 May 2014, Jonathan Holt wrote:



No idea, I think it’s due to the scanner, but could be wrong. Drawing in WM 
voxels?
On May 27, 2014, at 10:20 AM, Bruce Fischl  wrote:


Hi Jon

definitely not control points. I guess you would have to draw stuff in, but 
that kind of intensity patch is so far from our expectations it may be hard. 
Any idea where it comes from?
Bruce
On Tue, 27 May 2014, Jonathan Holt wrote:


Hi all,
this is a recurring issue that I'm hoping I can find a solution to. Pictured
is a brain with a particularly high intensity area that seems to defy
surfacing. Is there a way to work around this?
See attached image

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[Freesurfer] Registration and Surface Flattening

[Caka]

Thank you Bruce,

I convert the fsaverage flat map into a ascii file, using:   mris_convert  -p  
lh.cortex.patch.flat  lh.cortex.patch.flat.asc.
Now I need to read these two files.

(1) I used read_patch.m to read lh.cortex.patch.flat. But an error came out, it 
said ‘ Error using ==> read_patch at 28, could not open file …’.
(2) I couldn’t find a read_patch_asc.m script in Freesurfer, as is suggested in 
https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg35813.html
(3) I found a read_asc.m instead, but when I used it to read the 
lh.cortex.patch.flat.asc, an error occurred: ‘Error using ==> fgets,  Invalid 
file identifier. Use open to generate a valid file identifier’.

Could you please give me some advices?Thank you very much!

Best regards,
Qiongmin


Original email---
Hi Qiongmin

1. I think this is a bug in the open GL code that is outside of our 
control. We will try to track it down

2. The flat maps aren't really any different than say the inflated 
fsaverage surface. If you can generate group (or individual maps) in 
fsaverage space you can display them on the flat maps.

3. The index of each vertex in the flattened space is stored in the patch 
files so you can always look up what vertex it was on inflated, sphere, 
etc...

cheers
Bruce


On Mon, 26 May 2014, Caka 
wrote:

> Dear Bruce, Doug and all,
> Thanks for your suggestion, it helped a lot.
> 
> (1) I load the fsaverage surface (lh.inflated) in tksurfer, and then load
> the fsaverage patch (lh.cortex.patch.flat). The flat map was shown for
> several seconds, and then ?an error occurred and tksurfer was shut down. The
> terminal said: ?tksurfer.bin:tnl/t_vertex.c:407: update_input_ptrs:
> Assertion ?a[j].inputstride == vptr-> stride? failed. Abort(core dumped)?.
> ?Could you give me some advice?
> I use a 'CentOS release 6.2' system. The freesurfer is
> ?freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0?.?
> 
> (2) Indeed, I want to flatten all cortical thickness surfaces of 140
> subjects onto the ?lh.cortex.patch.flat? of fsaverage. I just don?t
> understand your idea how to do this. After I load ?lh.cortex.patch.flat? of
> fsaverage, the tksurfer only shows this flat map (now it lasted for several
> seconds and crashed), so how can I ' load whatever overlay you want in the
> same way you would on the inflated surface??
> Does it mean that I load the individual flat map on the individual inflated
> surface? But I haven?t got the individual flat map yet.?
> 
> (3) I am wondering if there are some table recording the transformation
> relationships between the fsaverage surface vertices and the flat map
> vertices? If so, then I think all I need to do is extracting the cortical
> thickness value of every vertex in individual inflated surface, and then
> putting into the corresponding vertex in the flat map.?
> 
> Thank you very much!?
> 
> Best regards,
> Qiongmin?
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Re: [Freesurfer] mris_convert to GIFTI misaligned in freeview

[Matt Glasser]

Yes the HCP pipelines have to take care of this as well so that the
surfaces and volume align outside of FreeSurfer.

Peace,

Matt.

On 5/27/14, 8:35 AM, "Franz Liem"  wrote:

>Hi Michael,
>
>I had a similar problem a while ago. Maybe this might help.
>http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg31152.html
>
>Best,
>Franz
>
>Am 23.05.2014 um 05:38 schrieb Harms, Michael:
>
>> 
>> Hi,
>> I converted a surface to GIFTI
>> e.g.,
>> mris_convert lh.white lh.white.gii
>> 
>> lh.white and lh.white.gii align when they are both loaded in 'tkmedit'.
>> However, they do not align when loaded simultaneously in 'freeview'.
>> 
>> Of possible relevance: When I loaded lh.white.gii into 'freeview', I
>>got the following message in the terminal:
>> "Did not find any volume geometry information in the surface"
>> 
>> Is this possibly a bug of some sort in the display of GIFTI surfaces
>>within 'freeview'?
>> 
>> This was all done with FS 5.3.
>> 
>> thanks,
>> -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
>> 
>>  
>> 
>> The materials in this message are private and may contain Protected
>>Healthcare Information or other information of a sensitive nature. If
>>you are not the intended recipient, be advised that any unauthorized
>>use, disclosure, copying or the taking of any action in reliance on the
>>contents of this information is strictly prohibited. If you have
>>received this email in error, please immediately notify the sender via
>>telephone or return mail.
>> 
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> 
>> 
>> The information in this e-mail is intended only for the person to whom
>>it is
>> addressed. If you believe this e-mail was sent to you in error and the
>>e-mail
>> contains patient information, please contact the Partners Compliance
>>HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>>in error
>> but does not contain patient information, please contact the sender and
>>properly
>> dispose of the e-mail.
>
>
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Re: [Freesurfer] Registration and Surface Flattening

[Bruce Fischl]

Hi Qiongmin

why are you trying to read the patches into matlab?

Also, can you send us your full matlab command that generated the error? 
Sounds like you passed the incorrect file name



cheers
Bruce
On Tue, 27 May 2014, 
Caka wrote:



Thank you Bruce,

I convert the fsaverage flat map into a ascii file, using:   mris_convert
 -p  lh.cortex.patch.flat  lh.cortex.patch.flat.asc.
Now I need to read these two files.

(1) I used read_patch.m to read lh.cortex.patch.flat. But an error came out,
it said ‘ Error using ==> read_patch at 28, could not open file …’.
(2) I couldn’t find a read_patch_asc.m script in Freesurfer, as is suggestedin 
https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg35813.h
tml
(3) I found a read_asc.m instead, but when I used it to read the
lh.cortex.patch.flat.asc, an error occurred: ‘Error using ==> fgets,
 Invalid file identifier. Use open to generate a valid file identifier’.

Could you please give me some advices?Thank you very much!

Best regards,
Qiongmin


Original email---
Hi Qiongmin

1. I think this is a bug in the open GL code that is outside of our 
control. We will try to track it down

2. The flat maps aren't really any different than say the inflated 
fsaverage surface. If you can generate group (or individual maps) in 
fsaverage space you can display them on the flat maps.

3. The index of each vertex in the flattened space is stored in the patch 
files so you can always look up what vertex it was on inflated, sphere, 
etc...

cheers
Bruce


On Mon, 26 May 2014, Caka 
wrote:

  Dear Bruce, Doug and all,
  Thanks for your suggestion, it helped a lot.

  (1) I load the fsaverage surface (lh.inflated) in tksurfer, and
  then load
  the fsaverage patch (lh.cortex.patch.flat). The flat map was
  shown for
  several seconds, and then ?an error occurred and tksurfer was
  shut down. The
  terminal said: ?tksurfer.bin:tnl/t_vertex.c:407:
  update_input_ptrs:
  Assertion ?a[j].inputstride == vptr-> stride? failed. Abort(core
  dumped)?.
  ?Could you give me some advice?
  I use a 'CentOS release 6.2' system. The freesurfer is
  ?freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0?.?

  (2) Indeed, I want to flatten all cortical thickness surfaces of
  140
  subjects onto the ?lh.cortex.patch.flat? of fsaverage. I just
  don?t
  understand your idea how to do this. After I load
  ?lh.cortex.patch.flat? of
  fsaverage, the tksurfer only shows this flat map (now it lasted
  for several
  seconds and crashed), so how can I ' load whatever overlay you
  want in the
  same way you would on the inflated surface??
  Does it mean that I load the individual flat map on the
  individual inflated
  surface? But I haven?t got the individual flat map yet.?

  (3) I am wondering if there are some table recording the
  transformation
  relationships between the fsaverage surface vertices and the
  flat map
  vertices? If so, then I think all I need to do is extracting the
  cortical
  thickness value of every vertex in individual inflated surface,
  and then
  putting into the corresponding vertex in the flat map.?

  Thank you very much!?

  Best regards,
  Qiongmin?


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[Freesurfer] Registration of Functional Data to the Inflated Brain

[Sherryse Corrow]

Hi FreeSurfer Team,

Please help out a FreeSurfer newbie!  We are having an issue with mapping our 
functional data onto the inflated brain.  When we finish the mapping, it seems 
that much of the data is showing up in white-matter space, and therefore, 
cannot be seen on the external surface of the brain. We later discovered that 
we were likely using the wrong registration matrix. However, it doesn’t seem 
like the one we are supposed to use is being produced during recon-all.  I am 
new to FreeSurfer and would greatly appreciate some assistance!

To provide you with more detail.

Problem: When we run the command line below, and then open the folder
experiment.feat/reg/freesurfer, there is no
anat2exf.register.dat file.  However, there is a file called:
anat2exf.register.dat.init.

Command Line: Reg-feat2anat -feat OurFeatDirectory.feat -subject P143

Terminal Output: There is no terminal output.  No error of any kind.

Log File: Attached.

Thanks,
Sherryse

P.S. We submitted this issue previously but were not getting a response, so we 
tried again in case our thread wasn’t working properly.


--
Sherryse Corrow, Ph.D. / Postdoctoral Fellow
Human Vision and Eye Movement Lab
Department of Ophthalmology & Visual Sciences
UBC/VGH Eye Care Centre
360A-2550 Willow Street
Vancouver, BC, V5Z 3N9
Tel: 604-875-4111 ext 67672
Cell: 604-315-6717
sherryse.cor...@eyecarecentre.org


anat2exf.register.dat.fslregister.log
Description: anat2exf.register.dat.fslregister.log
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Re: [Freesurfer] High Intensity Spots and Surfacing Issues

[Jonathan Holt]

we used an SPGR sequence on a GE 3T, it was 7-10 years old at the time. it’s 
not on every subject, but on the handful of subjects that do present this 
issue, it’s definitely stubborn and I’ve been unable to fix it as of yet.


On May 27, 2014, at 10:28 AM, Bruce Fischl  wrote:

> yes, that's what I meant. It looks too far in the interior to be a B0 effect. 
> Do you see it in all your subjects? What sequence/scanner are you using?On 
> Tue, 27 May 2014, Jonathan Holt wrote:
> 
>> No idea, I think it’s due to the scanner, but could be wrong. Drawing in WM 
>> voxels?
>> On May 27, 2014, at 10:20 AM, Bruce Fischl  
>> wrote:
>> 
>>> Hi Jon
>>> 
>>> definitely not control points. I guess you would have to draw stuff in, but 
>>> that kind of intensity patch is so far from our expectations it may be 
>>> hard. Any idea where it comes from?
>>> Bruce
>>> On Tue, 27 May 2014, Jonathan Holt wrote:
>>> 
 Hi all,
 this is a recurring issue that I'm hoping I can find a solution to. 
 Pictured
 is a brain with a particularly high intensity area that seems to defy
 surfacing. Is there a way to work around this?
 See attached image
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> 
>>> 
>>> The information in this e-mail is intended only for the person to whom it is
>>> addressed. If you believe this e-mail was sent to you in error and the 
>>> e-mail
>>> contains patient information, please contact the Partners Compliance 
>>> HelpLine at
>>> http://www.partners.org/complianceline . If the e-mail was sent to you in 
>>> error
>>> but does not contain patient information, please contact the sender and 
>>> properly
>>> dispose of the e-mail.
>> 
>> 
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>> 
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Re: [Freesurfer] Registration of Functional Data to the Inflated Brain

[Bruce Fischl]

Hi Sherryse

you only need to register the anatomicals to the funtionals once, then 
sample the functional data onto the surface using mri_vol2surf. This will 
create a surface overlay that can be visualized on any of the surfaces 
for that subject (e.g. lh.white, lh.pial, lh.inflated)


cheers
Bruce
On Tue, 27 May 
2014, Sherryse Corrow wrote:



Hi FreeSurfer Team, 

Please help out a FreeSurfer newbie!  We are having an issue with mapping
our functional data onto the inflated brain.  When we finish the mapping, it
seems that much of the data is showing up in white-matter space, and
therefore, cannot be seen on the external surface of the brain. We later
discovered that we were likely using the wrong registration matrix. However,
it doesn’t seem like the one we are supposed to use is being produced during
recon-all.  I am new to FreeSurfer and would greatly appreciate some
assistance!  

To provide you with more detail. 

Problem: When we run the command line below, and then open the folder
experiment.feat/reg/freesurfer, there is no
anat2exf.register.dat file.  However, there is a file called:
anat2exf.register.dat.init.

Command Line: Reg-feat2anat -feat OurFeatDirectory.feat -subject P143

Terminal Output: There is no terminal output.  No error of any kind.

Log File: Attached.

Thanks,
Sherryse

P.S. We submitted this issue previously but were not getting a response, so
we tried again in case our thread wasn’t working properly. 


-- 
Sherryse Corrow, Ph.D. / Postdoctoral Fellow
Human Vision and Eye Movement Lab
Department of Ophthalmology & Visual Sciences
UBC/VGH Eye Care Centre
360A-2550 Willow Street
Vancouver, BC, V5Z 3N9
Tel: 604-875-4111 ext 67672
Cell: 604-315-6717
sherryse.cor...@eyecarecentre.org

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Re: [Freesurfer] How to obtain stats on custom anatomical ROI in freeview/freesurfer

[Ruopeng Wang]

Hi Lucette,

Are you saying that the label file saved by freeview can not be loaded 
by other tools in freesurfer? Can you post the complete commands and 
output that did not work?


Best,
Ruopeng

On 05/27/2014 02:03 AM, Lucette Cysique wrote:

Dear Ruopeng and colleagues,

I am interested in following same tracing protocol for the amygdala as 
in "Neuroimage. 2012 April 2; 60(2): 1226–1235: "A reliable protocol 
for the manual segmentation of the human amygdala and its subregions 
using ultra-high resolution MRI”


I would like as they did use freeview because it has some versatility 
and resolution that other programs do not have.


I have however one issue
Once I have created my ROI in freeview it ends up being by default a 
.label file. I create my ROI using ROIs and edit ROI tools and simply 
save it.
I have tried to use “mri_label2vol” to get my ROI file (e.g., 
right_amygdala.label) into a volume file from which I thought I could 
then compute stats using “mri_segstats”
But it does not work, as it seems that the initial .label file does 
not have the current format? Or required info? My command line output 
that it cannot read my .label file


Thanks for your assistance
Lucette


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[Freesurfer] dt_recon error

[Weber, Wade (weberw)]

Hi all,

I have been trying to work with DTI data in FreeSurfer for the first time. We 
acquire our data on a 4T Varian and reconstruct into AFNI format (BRIK/HEAD 
files).  I set up the bval and bvec files successfully and ran the "dt_recon" 
script.  It seemed to run fine until I got an fslregister error saying "G-W 
contrast is negative but expecting positive."  It says to try running with the 
"--T1" flag.  The problem is that I'm not sure which line I put the flag into.  
I tried re-running the dt_recon line again with the --T1 flag, but it did not 
work.

I know I may not be giving enough information, so if anyone needs more 
information, just let me know what you want to know.

Thanks in advance!

Wade Weber
University of Cincinnati


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[Freesurfer] "average" brain files

[Borzello, Mia]

Hi Freesurfers,

I was wondering if the SurferOutput files for the average subject's brain were 
somewhere tobe downloaded on the wiki or within the toolbox?

Thanks,
m
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Re: [Freesurfer] unpacking error

[Douglas N Greve]

What is the model of the scanner? I think there is an error in there 
because it can' find the parameters it needs. You can also try something 
like

mri_convert 160 11147SACC000.MR.RESEARCH_NEURO. test.mgh

this might print something more informative to the terminal. You can 
also try

mri_probedicom --i 11147SACC000.MR.RESEARCH_NEURO.

doug


On 05/23/2014 10:18 AM, Caroline Lewis wrote:
> That doesn't sound good. Does tag 28, 30 mean the voxel size is 
> missing, why would this be? It is a Siemens dicom from a 3T scanner - 
> not sure which model but I can find out.
>
> Do you have any idea why I am getting errors for some runs in the 
> scan. info file as such?:
>
> 7 t1_mprage_tra_p2_iso_1.0 err0   0   0 160 
> 11147SACC000.MR.RESEARCH_NEURO.
>
> Thanks Doug,
>
> Caroline
>
>
> On Thu, May 22, 2014 at 6:52 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>
> hmmm, if it does not have tag 28 30, then something is really wrong.
> This is a Siemens dicom, right? What scanner?
> doug
>
>
> On 05/22/2014 06:05 PM, Caroline Lewis wrote:
> > Thanks Douglas. Now I am running into other errors. I ran the
> command:
> >
> > unpacksdcmdir -src 0008 -targ 0008/mri/orig -fsfast \
> > ? -run 8 bold nii 001.nii
> >
> > ERROR: reading
> >
> 
> 0008/11147SACC000.MR.RESEARCH_NEURO.8.1.2014.05.13.14.42.14.530.48877356.dcm
> > tag 28 30
> >
> > Also, some of the runs in the "scan.info 
> " file say
> > "err" where it should say "ok"
> >
> > Do you have any idea why I'm getting these errors?
> >
> > Thanks,
> >
> > Caroline
> >
> >
> > On Thu, May 22, 2014 at 4:16 PM, Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>
>  >> wrote:
> >
> > Remove the \<>
> >
> > On 05/22/2014 03:45 PM, Caroline Lewis wrote:
> > > Hi,
> > >
> > > I am trying to unpack dicom files and convert them to
> nifti, but am
> > > running into an error. I ran the following command with no
> issue:
> > > unpacksdcmdir -src dicomdir -targ  targetdir -scanonly
> > targetdir/scan.info  
>  
> > >
> > >
> > > however, when I try to run the next command to actually unpack
> > the data:
> > >
> > > unpacksdcmdir -src 0008 -targ NIFTI -fsfast \
> > > ? -run 7 3danat mgz 001.mgz \<>
> > >
> > > I get the following error message: Missing name for redirect.
> > > Thanks,
> > >
> > > Caroline
> > >
> > >
> > > ___
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> 
> >  >
> > > 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
> 
> > 
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> 
> > 
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> >
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>  >
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> >
> >
> > The information in this e-mail is intended only for the
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> > whom it is
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Re: [Freesurfer] R: Re: R: Re: R: Re: Problem of size

[Douglas N Greve]

Why not just use the wmparc.mgz created by recon-all?
doug

On 05/22/2014 12:04 PM, Andrea Tateo wrote:
>  Hi FreeSurfer expert,
>
> after that I have used the command "recon-all"
>
> I would like to obtain wm-lh and wm-rh information ( for example 
> wm-lh-bankssts,wm-lh-caudalanteriorcingulate,wm-lh-caudalmiddlefrontal, ...).
>
> I have read that mri_aparc2aseg command can help me, but when I use it 
> I have two problems:
>
> 1)   When I use the command mri_aparc2aseg --s 
> subject  I obtain as output the image "aparc+aseg.mgz" 
> which contains information only about cortical label.
>
> 2)  When I use the command mri_aparc2aseg --s subject --a.2005 
> I get the following message:  ERROR: Option --a2005 unknown
>
>
> Can you help me?
>
> Moreover, the recon-all output in directory /mri is:
>
>
> aparc.a2009s+aseg.mgz,  aparc+aseg.mgz, aseg.auto.mgz, 
> aseg.auto_noCCseg.label_intensities.txt ,  aseg.auto_noCCseg.mgz
> aseg.mgz, brain.finalsurfs.mgz, brainmask.auto.mgz, 
> brainmask.mgz,brain.mgz, ctrl_pts.mgz, filled.mgz,
> lh.ribbon.mgz,
> mri_nu_correct.mni.log,norm.mgz,nu.mgz, nu_noneck.mgz,
> orig,   orig.mgz,  rawavg.mgz, rh.ribbon.mgz,ribbon.mgz,
> segment.dat   ,   T1.mgz,talairach.label_intensities.txt , 
> talairach.log, talairach_with_skull.log, transforms,
> wm.asegedit.mgz,
> wm.mgz,wmparc.mgz , wm.seg.mgz
>
>
> Do you think  that the searched information is here?
>
> Thanks for your help.
> Best regards,
>
> Andrea
>
>
>
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Re: [Freesurfer] Longitudinal design

[Tudor Popescu]

Hi Martin,
Wasn't sure whether you'd seen my reply below, look forward to hear back
your thoughts, thanks!
Tudor
On 25 May 2014 21:40, "Tudor Popescu"  wrote:

> Thanks very much Martin and Bruce. I guess I'd misread the Wiki (my own
> fault, not the text's), and am glad to hear that the longitudinal pipeline
> is in fact perfectly suitable for my needs here.
>
> Having run the first 2 steps (cross and base), I'm a bit unclear how the
> output so far has to be manually inspected. It says in the tutorial
>  that you
> should load each subject's base volume + surfs in freeview and then "move
> back and forth a few slices". However, even just loading each base in this
> manner takes ~1 min on my PC (CoreDuo, 4GB, Ubuntu Virtualbox in Windows
> 7), and then moving with PgUp/PgDn between all coronal slices (starting
> from the default slice=128, going all the way posterior and then all the
> way anterior) is excruciatingly slow. All of this would have to be repeated
> for all my 72 subjects - is there any way to optimise this manual
> inspection?
>
> Also, if the surfs turn out to not follow the volume correctly, presumably
> the thing to do is white surface correction + re-running recon. But what
> should one do if, due to an erroneous averaging between timepoints, you see
> blurs/ghosts in your base template?
>
> Many thanks!
> Tudor
>
>
> On 9 May 2014 21:33, Martin Reuter  wrote:
>
>>  Hi Tudor,
>>
>> the longitudinal pipeline in FS is actually one of the best on the planet
>> as far as I know :-). If there is any contradictory information on the
>> wiki, can you point me to that so I can see what causes the misconception.
>> Really: compared to independent processing, it significantly increases
>> sensitivity. Also we have designed it to be unbiased with respect to a
>> single time point or directionality. It is quite mature by now.
>>
>> You should definitely use the longitudinal pipeline for the analysis of
>> your data. Now to your questions
>>
>> 1. QDEC: I am not too familiar with qdec. You can definitely try the
>> 2-stage approach described on the wiki. There you first compute a measure
>> of change (e.g. hippocampal volume change during your week) and then
>> compare that measure across groups similar to a cross sectional
>> volume/thickness analysis. You can also use our tools to run a linear mixed
>> effects model if you want to do that (it is more involved and requires you
>> to use matlab tools). In your case, you probably have 2 time points for all
>> subjects and the time distance is probably the same for all subjects, so
>> the 2-stage approach should be fine.
>>
>> 2. The image processing is done via the longitudinal pipeline (three
>> steps: cross, base, long), to prepare the data look at the description of
>> the 2-stage model
>> http://freesurfer.net/fswiki/LongitudinalTwoStageModel
>> and also the longitudinal tutorial
>> http://freesurfer.net/fswiki/FsTutorial/LongitudinalTutorial
>>
>> 3. At the recon all level in FS you get (after the 3 steps) measurement
>> for all time points. So you would compare those results across time in the
>> stats.
>>
>> Hope that helps, Martin
>>
>>
>> On 05/08/2014 08:14 AM, Tudor Popescu wrote:
>>
>> Sorry for the repeat, wasn't sure whether this was received the first
>> time.
>> Tudor
>>
>>
>> On 6 May 2014 19:55, Tudor Popescu  wrote:
>>
>>>Dear FS list,
>>>
>>>  I have structural data from a learning study (pre&post-training scans,
>>> with 3 groups). Although the training was only one week, I'm guessing from
>>> an analysis point of view, this still qualifies as longitudinal. I want to
>>> check for
>>>
>>>- the main within-subjects effect of time point (pre&post)
>>>- the main between-subjects effect of group (treatment A, treatment
>>>B, control),
>>>- the time x group interaction
>>>
>>> I intend to look at thickness, surface area, volume, and lGI.
>>>
>>>  I read on the wiki
>>>  that
>>> FS is currently not optimal for longitudinal analyses. I intend my
>>> FreeSurfer analysis to supplement a VBM analysis done in FSL. In case it is
>>> in fact a good idea to do this, my questions (not covered in the
>>> 'longitudinal' wiki page) are:
>>>
>>>  1) Can QDEC be used for such an analysis, and if so, what would be
>>> different as compared to a cross-sectional (no temporal/within factor)
>>> study?
>>>
>>>  2) Also, is the pre-processing stage any different?
>>>
>>> 3) In FSL, for longitudinal designs you do stats on images obtained as
>>> the difference between consecutive time points. Does this have to be done
>>> in FreeSurfer as well, and if so, is it done at the recon-all level or only
>>> at the stats (QDEC) level?
>>>
>>>  Thanks!
>>>
>>> Tudor
>>>
>>>
>>>
>>
>>
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Re: [Freesurfer] bbregister and FLAIR

[Douglas N Greve]

Hi Kayle, can you try the following

bbregister --s SLOTS007 --mov flair.mgz --init-header --reg reg.test.dat 
--t2 --lta reg.test.lta

this should hopefully generate a good registration. If it does, then I 
can find a work-around for you
doug



On 05/23/2014 03:05 PM, Kayle Sawyer wrote:
> Hello,
>
> We have been examining the pial surface adjustment with FLAIR scans, 
> and the improvement is quite dramatic. There are MANY areas where the 
> pial surface was clearly wrong and has been substantially improved, 
> considerably reducing (often eliminating) the need for manual pial 
> corrections. I suggest everyone who uses FreeSurfer surfaces acquire a 
> FLAIR scan if they can (see attached for the sequence we’re using).
>
> However, for most of our participants, we have run into a serious 
> problem with bbregister.
>
> We're running recon-all with two input volumes:
> -i MEMPRAGE_scan -FLAIR FLAIR_scan
>
> Recon-all completes successfully, however the results do not look good 
> due to a bad 'bbregister' registration step.
>
> The MEMPRAGE and FLAIR runs were acquired within the same scanning 
> session and they're very well registered to begin with. However, the 
> 'bbregister' step seems to not work well, and they end up grossly 
> misaligned.
>
> Here is an example (on the Martinos network):
> [kslays@ficus ~]$
> source /usr/local/freesurfer/nmr-stable53-env;
> setenv SUBJECTS_DIR /autofs/space/ficus_004/users/SLOTS_subjects;
> cd $SUBJECTS_DIR;
>
> recon-all -all -subjid SLOTS007 \
> -i $SUBJECTS_DIR/SLOTS007/3danat/006/MEMPRAGE_RMS.mgz \
> -FLAIR $SUBJECTS_DIR/SLOTS007/flair/007/flair.mgz \
> -FLAIRpial -mprage -3T -pctsurfcon -qcache -hippo-subfields
>
>
> Check input volume registration (looks good):
>
> tkregister2 --targ SLOTS007/mri/orig/001.mgz \
> --mov SLOTS007/mri/orig/FLAIRraw.mgz \
> --reg NULL --regheader
>
> Check bbregister output (looks bad):
>
> tkregister2 --mov SLOTS007/mri/orig/FLAIRraw.mgz \
> --reg SLOTS007/mri/transforms/FLAIRraw.dat --surf
>
> How do we correct the bbregister step?
>
> Thanks in advance for your input.
> -Kayle
>
> P.S. If you would like to see other examples, feel free to look at 
> other recons in the same directory. Here is an example where 
> bbregister worked, and the pial corrections are dramatic:
> freeview -v SLOTS005/mri/FLAIR.mgz \
> -f SLOTS005/surf/lh.white:edgecolor=yellow \
> SLOTS005/surf/rh.white:edgecolor=yellow \
> SLOTS005/surf/lh.pial:edgecolor=red \
> SLOTS005/surf/rh.pial:edgecolor=red \
> SLOTS005/surf/lh.woFLAIR.pial:edgecolor=green \
> SLOTS005/surf/rh.woFLAIR.pial:edgecolor=green \
> -ras -37 -46 -42
>
>
>
> Kayle Sawyer, PhD
>
> Athinoula A. Martinos Center for Biomedical Imaging
> MGH East Campus, Charlestown Navy Yard
> Building 149, South Central 1113 - Seat F
> 149 13th Street
> Boston, MA 02129
> OFFICE:(617) 726-8791
>
> Laboratory of Neuropsychology
> Boston University School of Medicine L-815
> 72 E. Concord St
> Boston, MA 02118
> OFFICE:(617) 638-4803
>
> VA Boston Healthcare System Jamaica Plain
> 150 South Huntington Ave 151-A, D11-126
> Boston, MA 02130
> OFFICE:(857) 364-4003
> FAX: (857) 364-5829
>
>
>
>
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Re: [Freesurfer] Error: no dicom files found

[Douglas N Greve]

Are they siemens dicoms? If not, use dcmunpack. If so, what is the 
command you ran and terminal output?


On 05/26/2014 11:34 AM, Caroline Lewis wrote:
> Hi,
>
> I am trying to use the unpacksdcmdir command to convert my dicom files 
> to mgz/nifti, and when i run the command:
>
> unpacksdcmdir -src DTI -targ DTI -scanonly DTI/scan.info 
> 
>
> I get an error message saying there are no dicom files found in the 
> folder, whereas all of the dicom files for that sequence are in that 
> folder (and when I use ls, all of the dcm files are listed). Can 
> anyone help me as to why I am getting this error?
>
> Thanks,
>
> Caroline
>
>
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Fax: 617-726-7422

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Re: [Freesurfer] URGENT: Error in analyse

[Douglas N Greve]

Does it print out anything else? An alternative is to use the command 
line stream (create your own fsgd file, run mris_preproc, smooth, 
mri_glmfit, mri_glmfit-sim)
doug




On 05/27/2014 06:38 AM, Saloni Sharma wrote:
> I am attaching a screen shot of the error, if it helps!
>
>
> On 26 May 2014 17:14, Saloni Sharma  > wrote:
>
> yes exactly, if I click analyze without the gender it works fine.
> No thats okay, what do you need from me again?
>
>
> On 26 May 2014 17:11, Bruce Fischl  > wrote:
>
> so if you click "analyze" without gender it works fine? Sorry,
> I missed
> that. I think you'll need to wait for Doug or Nick to reply,
> but you might
> send your qdec file and the group.levels files
>
> sorry
> Bruce
>
> On Mon, 26 May 2014, Saloni Sharma wrote:
>
> > Hey Bruce,
> >
> > Yes, that directory exists, as I said if I only choose
> groups(high stress
> > and low stress) as the discrete variables its runs fine and
> analyses, it
> > only shows the error if I add more factors (like gender)
> into the software.
> >
> > My subjects directory is set to
> > export
> SUBJECTS_DIR=/tallaght-disk4/IMAGEN/Saloni_data/freesurfer_output/
> >
> > and yes I have run recon-all-qcache on all my subjects.
> >
> > Saloni
> >
> >
> > On 26 May 2014 16:58, Bruce Fischl
>  > wrote:
> >   Hi Saloni
> >
> >   Does that directory exist? What is your SUBJECTS_DIR
> set to? And
> >   have you
> >   run recon-all -qcache on all your subjects?
> >
> >   cheers
> >   Bruce
> >   On Mon, 26 May 2014, Saloni Sharma wrote:
> >
> >   > Dear Freesurfers,
> >   >
> >   > So I have followed all the instructions given on
> your website
> >   in order to
> >   > use qdec. When i analyse the images only using a file
> >   group.levels that
> >   > defines the two groups I'm comparing the analysis
> runs fine
> >   and gives me
> >   > results, but when I add gender, for instance, as a
> discrete
> >   factor, it loads
> >   > the data successfully but when I click analyse it
> shows the
> >   following error:
> >   >
> >   > Error in Analyze: Couldn't
> 
> openfile/tallaght-disk4/IMAGEN/Saloni_data/freesurfer_output/72882642/surf/
> >   lh.t
> >   > hickness.fwhm10.fsaverage.mgh
> >   >
> >   > Please guide me as to what is going wrong and what I
> can do to
> >   fix it. I
> >   > would appreciate a quick response as my thesis
> submission is
> >   due in two
> >   > weeks and I cannot proceed until this problem is sorted.
> >   >
> >   > Thanks and regards,
> >   > Saloni
> >   >
> >   >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > The information in this e-mail is intended only for the
> person to whom
> > it is
> > addressed. If you believe this e-mail was sent to you in
> error and the
> > e-mail
> > contains patient information, please contact the Partners
> Compliance
> > HelpLine at
> > http://www.partners.org/complianceline . If the e-mail was
> sent to you
> > in error
> > but does not contain patient information, please contact the
> sender
> > and properly
> > dispose of the e-mail.
> >
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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
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Re: [Freesurfer] Registration of Functional Data to the Inflated Brain

[Douglas N Greve]

recon-all will not produce the registration file you are looking for. It 
should be produced by reg-feat2anat. Try running it with --debug as the 
first argument and post the terminal output to the list
doug



On 05/27/2014 12:10 PM, Sherryse Corrow wrote:
> Hi FreeSurfer Team,
>
> Please help out a FreeSurfer newbie! We are having an issue with 
> mapping our functional data onto the inflated brain. When we finish 
> the mapping, it seems that much of the data is showing up in 
> white-matter space, and therefore, cannot be seen on the external 
> surface of the brain. We later discovered that we were likely using 
> the wrong registration matrix. However, it doesn’t seem like the one 
> we are supposed to use is being produced during recon-all. I am new to 
> FreeSurfer and would greatly appreciate some assistance!
>
> To provide you with more detail.
>
> Problem: When we run the command line below, and then open the folder
> experiment.feat/reg/freesurfer, there is no
> anat2exf.register.dat file. However, there is a file called:
> anat2exf.register.dat.init.
>
> Command Line: Reg-feat2anat -feat OurFeatDirectory.feat -subject P143
>
> Terminal Output: There is no terminal output. No error of any kind.
>
> Log File: Attached.
>
> Thanks,
> Sherryse
>
> P.S. We submitted this issue previously but were not getting a 
> response, so we tried again in case our thread wasn’t working properly.
>
>
> -- 
> Sherryse Corrow, Ph.D. / Postdoctoral Fellow
> Human Vision and Eye Movement Lab
> Department of Ophthalmology & Visual Sciences
> UBC/VGH Eye Care Centre
> 360A-2550 Willow Street
> Vancouver, BC, V5Z 3N9
> Tel: 604-875-4111 ext 67672
> Cell: 604-315-6717
> sherryse.cor...@eyecarecentre.org 
> 
>
>
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-- 
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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
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Re: [Freesurfer] dt_recon error

[Douglas N Greve]

Did it actually fail? If not, does the registration look ok? That msg 
should just be a warning
doug

On 05/27/2014 02:06 PM, Weber, Wade (weberw) wrote:
>
> Hi all,
>
> I have been trying to work with DTI data in FreeSurfer for the first 
> time. We acquire our data on a 4T Varian and reconstruct into AFNI 
> format (BRIK/HEAD files). I set up the bval and bvec files 
> successfully and ran the “dt_recon” script. It seemed to run fine 
> until I got an fslregister error saying “G-W contrast is negative but 
> expecting positive.” It says to try running with the “--T1” flag. The 
> problem is that I’m not sure which line I put the flag into. I tried 
> re-running the dt_recon line again with the --T1 flag, but it did not 
> work.
>
> I know I may not be giving enough information, so if anyone needs more 
> information, just let me know what you want to know.
>
> Thanks in advance!
>
> Wade Weber
>
> University of Cincinnati
>
>
>
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-- 
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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
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Re: [Freesurfer] URGENT: Error in analyse

[Saloni]

It prints out fine and gives results if I only use it to analyse two 
groups(differentiated on stress levels) but if I add gender as a discrete 
variable or even as a continuous one along with the groups it shows this error. 

Sent from my iPhone

> On 27 May 2014, at 23:40, Douglas N Greve  wrote:
> 
> 
> Does it print out anything else? An alternative is to use the command 
> line stream (create your own fsgd file, run mris_preproc, smooth, 
> mri_glmfit, mri_glmfit-sim)
> doug
> 
> 
> 
> 
>> On 05/27/2014 06:38 AM, Saloni Sharma wrote:
>> I am attaching a screen shot of the error, if it helps!
>> 
>> 
>> On 26 May 2014 17:14, Saloni Sharma > > wrote:
>> 
>>yes exactly, if I click analyze without the gender it works fine.
>>No thats okay, what do you need from me again?
>> 
>> 
>>On 26 May 2014 17:11, Bruce Fischl >> wrote:
>> 
>>so if you click "analyze" without gender it works fine? Sorry,
>>I missed
>>that. I think you'll need to wait for Doug or Nick to reply,
>>but you might
>>send your qdec file and the group.levels files
>> 
>>sorry
>>Bruce
>> 
>>>On Mon, 26 May 2014, Saloni Sharma wrote:
>>> 
>>> Hey Bruce,
>>> 
>>> Yes, that directory exists, as I said if I only choose
>>groups(high stress
>>> and low stress) as the discrete variables its runs fine and
>>analyses, it
>>> only shows the error if I add more factors (like gender)
>>into the software.
>>> 
>>> My subjects directory is set to
>>> export
>>SUBJECTS_DIR=/tallaght-disk4/IMAGEN/Saloni_data/freesurfer_output/
>>> 
>>> and yes I have run recon-all-qcache on all my subjects.
>>> 
>>> Saloni
>>> 
>>> 
>>> On 26 May 2014 16:58, Bruce Fischl
>>>> wrote:
>>>  Hi Saloni
>>> 
>>>  Does that directory exist? What is your SUBJECTS_DIR
>>set to? And
>>>  have you
>>>  run recon-all -qcache on all your subjects?
>>> 
>>>  cheers
>>>  Bruce
  On Mon, 26 May 2014, Saloni Sharma wrote:
 
 Dear Freesurfers,
 
 So I have followed all the instructions given on
>>your website
>>>  in order to
 use qdec. When i analyse the images only using a file
>>>  group.levels that
 defines the two groups I'm comparing the analysis
>>runs fine
>>>  and gives me
 results, but when I add gender, for instance, as a
>>discrete
>>>  factor, it loads
 the data successfully but when I click analyse it
>>shows the
>>>  following error:
 
 Error in Analyze: Couldn't
>>
>> openfile/tallaght-disk4/IMAGEN/Saloni_data/freesurfer_output/72882642/surf/
>>>  lh.t
 hickness.fwhm10.fsaverage.mgh
 
 Please guide me as to what is going wrong and what I
>>can do to
>>>  fix it. I
 would appreciate a quick response as my thesis
>>submission is
>>>  due in two
 weeks and I cannot proceed until this problem is sorted.
 
 Thanks and regards,
 Saloni
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> 
>>> 
>>> The information in this e-mail is intended only for the
>>person to whom
>>> it is
>>> addressed. If you believe this e-mail was sent to you in
>>error and the
>>> e-mail
>>> contains patient information, please contact the Partners
>>Compliance
>>> HelpLine at
>>> http://www.partners.org/complianceline . If the e-mail was
>>sent to you
>>> in error
>>> but does not contain patient information, please contact the
>>sender
>>> and properly
>>> dispose of the e-mail.
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>> 
>> 
>> 
>> 
>> 
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> 
> -- 
> 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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