Re: [Freesurfer] identity.nofile

[Douglas Greve]

Can you load another label, eg, lh.cortex.label? Also, I noticed that 
there is a space between "label=" and "/data/..." in the command line 
below. That space should not be there, so if it was there when you ran 
the command try again without the space.


On 4/19/16 9:19 PM, Trisanna Sprung-Much wrote:

Hi Doug

I tried again in the terminal and got this:
*
trisanna@kaplan:~$ freeview -f 
/data-01/trisanna/freesurfer/icbm-102/surf/lh.pial:label= 
/data-01/trisanna/freesurfer/icbm-102/label/labeltest.label *
[0]PETSC ERROR: 

[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, 
probably memory access out of range

[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see 
http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC 
ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple 
to find memory corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, 
and run

[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: - Error Message 


[0]PETSC ERROR: Signal received!
[0]PETSC ERROR: 

[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 
17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124

[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR: 

[0]PETSC ERROR: Unknown Name on a linux-gnu named kaplan by trisanna 
Tue Apr 19 21:13:58 2016
[0]PETSC ERROR: Libraries linked from 
/autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt

[0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010
[0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc 
--with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 
--with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 
COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
[0]PETSC ERROR: 

[0]PETSC ERROR: User provided function() line 0 in unknown directory 
unknown file

[unset]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0


--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Tue, Apr 19, 2016 at 8:59 PM, Trisanna Sprung-Much 
> wrote:


Hi Doug

I thought this was the case as well but when I try manually in
Freeview and select the correct label, Freeview crashes and gives
this error in the terminal:

trisanna@kaplan:~$ freeview
*** Error in `freeview.bin': double free or corruption (out):
0x29080920 ***
Abort (core dumped)


--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Tue, Apr 19, 2016 at 6:17 PM, Douglas N Greve
> wrote:

I don't think that is the problem. The problem is that it
cannot find
the file. Try giving it the whole path

On 04/19/2016 05:45 PM, Bruce Fischl wrote:
> Hi Trisanna
>
> if your output is .mgz it isn't a label file. Labels are
stored in
> .label names and are text files. The .mgz is a scalar field
over the
> surface (that is, a vector with a single value at each surface
> location). In freeview you can view it as:
>
> freeview -f lh.inflated:overlay=surfaceoverlay.mgz
>
>
> cheers
> Bruce
>
> On Tue, 19 Apr 2016, Trisanna Sprung-Much wrote:
>
>> Hi Doug
>>
>> So I ran mri_vol2surf and generated my .mgz surface overlay
using
>> --regheader as you suggested. I than ran mri_cor2label
using that
>> .mgz file.
>> This also completed successfully. However, when I then try
to open
>> the pial
>> surface and the corresponding new label in freeview, it says it
>> cannot read
>> the label. Below is what I ran. I tried the same thing for
the inflated
>> surface.
>>
>> I put labelid as "1" as I was unsure as to what to put.
Could this have
>> affected the label creation?
>>
>> Trisanna
>>
>>
>> trisanna@kaplan:~$ mri_vol2surf --mov
>> /data-01/trisanna/freesurfer/icbm-102/mri/labels5.mnc --o
>> 

Re: [Freesurfer] identity.nofile

[Bruce Fischl]

Hi Trisanna

your output is a .mgz file, which is *not* a label. Try loading it as an 
overlay. The label format is different (ascii for one thing, and only part 
of the surface for another).


cheers
Bruce

On Tue, 19 Apr 2016, Trisanna Sprung-Much wrote:


Hi Doug

I thought this was the case as well but when I try manually in Freeview and
select the correct label, Freeview crashes and gives this error in the
terminal:

trisanna@kaplan:~$ freeview
*** Error in `freeview.bin': double free or corruption (out):
0x29080920 ***
Abort (core dumped)


--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology


On Tue, Apr 19, 2016 at 6:17 PM, Douglas N Greve 
wrote:
  I don't think that is the problem. The problem is that it cannot
  find
  the file. Try giving it the whole path

  On 04/19/2016 05:45 PM, Bruce Fischl wrote:
  > Hi Trisanna
  >
  > if your output is .mgz it isn't a label file. Labels are
  stored in
  > .label names and are text files. The .mgz is a scalar field
  over the
  > surface (that is, a vector with a single value at each surface
  > location). In freeview you can view it as:
  >
  > freeview -f lh.inflated:overlay=surfaceoverlay.mgz
  >
  >
  > cheers
  > Bruce
  >
  > On Tue, 19 Apr 2016, Trisanna Sprung-Much wrote:
  >
  >> Hi Doug
  >>
  >> So I ran mri_vol2surf and generated my .mgz surface overlay
  using
  >> --regheader as you suggested. I than ran mri_cor2label using
  that
  >> .mgz file.
  >> This also completed successfully. However, when I then try to
  open
  >> the pial
  >> surface and the corresponding new label in freeview, it says
  it
  >> cannot read
  >> the label. Below is what I ran. I tried the same thing for
  the inflated
  >> surface.
  >>
  >> I put labelid as "1" as I was unsure as to what to put. Could
  this have
  >> affected the label creation?
  >>
  >> Trisanna
  >>
  >>
  >> trisanna@kaplan:~$ mri_vol2surf --mov
  >> /data-01/trisanna/freesurfer/icbm-102/mri/labels5.mnc --o
  >> /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz
  --regheader
  >> icbm-102 --hemi lh --surf pial
  >> srcvol =
  /data-01/trisanna/freesurfer/icbm-102/mri/labels5.mnc
  >> srcreg unspecified
  >> srcregold = 0
  >> srcwarp unspecified
  >> surf = pial
  >> hemi = lh
  >> reshape = 0
  >> interp = nearest
  >> float2int = round
  >> GetProjMax = 0
  >> INFO: float2int code = 0
  >> INFO: changing type to float
  >> Done loading volume
  >> Computing registration from header.
  >>   Using /data-01/trisanna/freesurfer/icbm-102/mri/orig.mgz as
  target
  >> reference.
  >> Reading surface
  /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial
  >> Done reading source surface
  >> Mapping Source Volume onto Source Subject Surface
  >>  1 0 0 0
  >> using old
  >> Done mapping volume to surface
  >> Number of source voxels hit = 85413
  >> Writing to
  /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz
  >> Dim: 169941 1 1
  >>
  >>
  >> trisanna@kaplan:~$ mri_cor2label --i
  >> /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz --id
  1 --l
  >> /data-01/trisanna/freesurfer/icbm-102/label/labeltest --surf
  lh.pial
  >> $Id: mri_cor2label.c,v 1.12 2011/03/02 00:04:14 nicks Exp $
  >> Loading mri
  /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz
  >> --- Vox2RAS of input volume ---
  >> -1.000   0.000   0.000   84970.500;
  >>  0.000   0.000   1.000  -0.500;
  >>  0.000  -1.000   0.000   0.500;
  >>  0.000   0.000   0.000   1.000;
  >> Scanning the volume
  >> Found 1651 label voxels
  >> Writing label file
  /data-01/trisanna/freesurfer/icbm-102/label/labeltest
  >> Centroid: -56170.34   -0.50    0.50
  >> mri_cor2label completed SUCCESSFULLY
  >>
  >>
  >> trisanna@kaplan:~$ freeview -f
  >>
  /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial:label=labeltest
  >> No such file or directory
  >> freeview.bin: could not open label file labeltest.label
  >> No such file or directory
  >> LabelRead failedNo such file or directory
  >> en label file labeltest.label
  >>
  >>
  >>
  >> --
  >> Ph.D. CandidateMcGill University
  >> Integrated Program in Neuroscience
  >> Psychology
  >>
  >>
  >> On Tue, Apr 19, 2016 at 4:15 PM, Trisanna Sprung-Much
  >>  wrote:
  >>       many thanks - will give this a go!
  >>
  >> --
  >> Ph.D. CandidateMcGill University
  >> Integrated Program in Neuroscience
  >> Psychology
  >>
  >>
  >> On Tue, Apr 

Re: [Freesurfer] identity.nofile

[Trisanna Sprung-Much]

Hi Doug

I tried again in the terminal and got this:

*trisanna@kaplan:~$ freeview -f
/data-01/trisanna/freesurfer/icbm-102/surf/lh.pial:label=
/data-01/trisanna/freesurfer/icbm-102/label/labeltest.label *
[0]PETSC ERROR:

[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
probably memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see
http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to
find memory corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and
run
[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: - Error Message

[0]PETSC ERROR: Signal received!
[0]PETSC ERROR:

[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26
CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR:

[0]PETSC ERROR: Unknown Name on a linux-gnu named kaplan by trisanna Tue
Apr 19 21:13:58 2016
[0]PETSC ERROR: Libraries linked from
/autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt
[0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010
[0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc
--with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1
--with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3
CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
[0]PETSC ERROR:

[0]PETSC ERROR: User provided function() line 0 in unknown directory
unknown file
[unset]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0


--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Tue, Apr 19, 2016 at 8:59 PM, Trisanna Sprung-Much <
trisanna.sprung-m...@mail.mcgill.ca> wrote:

> Hi Doug
>
> I thought this was the case as well but when I try manually in Freeview
> and select the correct label, Freeview crashes and gives this error in the
> terminal:
>
> trisanna@kaplan:~$ freeview
> *** Error in `freeview.bin': double free or corruption (out):
> 0x29080920 ***
> Abort (core dumped)
>
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Tue, Apr 19, 2016 at 6:17 PM, Douglas N Greve <
> gr...@nmr.mgh.harvard.edu> wrote:
>
>> I don't think that is the problem. The problem is that it cannot find
>> the file. Try giving it the whole path
>>
>> On 04/19/2016 05:45 PM, Bruce Fischl wrote:
>> > Hi Trisanna
>> >
>> > if your output is .mgz it isn't a label file. Labels are stored in
>> > .label names and are text files. The .mgz is a scalar field over the
>> > surface (that is, a vector with a single value at each surface
>> > location). In freeview you can view it as:
>> >
>> > freeview -f lh.inflated:overlay=surfaceoverlay.mgz
>> >
>> >
>> > cheers
>> > Bruce
>> >
>> > On Tue, 19 Apr 2016, Trisanna Sprung-Much wrote:
>> >
>> >> Hi Doug
>> >>
>> >> So I ran mri_vol2surf and generated my .mgz surface overlay using
>> >> --regheader as you suggested. I than ran mri_cor2label using that
>> >> .mgz file.
>> >> This also completed successfully. However, when I then try to open
>> >> the pial
>> >> surface and the corresponding new label in freeview, it says it
>> >> cannot read
>> >> the label. Below is what I ran. I tried the same thing for the inflated
>> >> surface.
>> >>
>> >> I put labelid as "1" as I was unsure as to what to put. Could this have
>> >> affected the label creation?
>> >>
>> >> Trisanna
>> >>
>> >>
>> >> trisanna@kaplan:~$ mri_vol2surf --mov
>> >> /data-01/trisanna/freesurfer/icbm-102/mri/labels5.mnc --o
>> >> /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz --regheader
>> >> icbm-102 --hemi lh --surf pial
>> >> srcvol = /data-01/trisanna/freesurfer/icbm-102/mri/labels5.mnc
>> >> srcreg unspecified
>> >> srcregold = 0
>> >> srcwarp unspecified
>> >> surf = pial
>> >> hemi = lh
>> >> reshape = 0
>> >> interp = nearest
>> >> float2int = round
>> >> GetProjMax = 0
>> >> INFO: float2int code = 0
>> >> INFO: changing type to float
>> >> Done loading volume
>> >> Computing registration from header.
>> >>   Using /data-01/trisanna/freesurfer/icbm-102/mri/orig.mgz as target
>> >> reference.
>> >> Reading surface /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial
>> >> Done reading source surface
>> >> Mapping Source Volume onto 

Re: [Freesurfer] identity.nofile

[Trisanna Sprung-Much]

Hi Doug

I thought this was the case as well but when I try manually in Freeview and
select the correct label, Freeview crashes and gives this error in the
terminal:

trisanna@kaplan:~$ freeview
*** Error in `freeview.bin': double free or corruption (out):
0x29080920 ***
Abort (core dumped)


--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Tue, Apr 19, 2016 at 6:17 PM, Douglas N Greve 
wrote:

> I don't think that is the problem. The problem is that it cannot find
> the file. Try giving it the whole path
>
> On 04/19/2016 05:45 PM, Bruce Fischl wrote:
> > Hi Trisanna
> >
> > if your output is .mgz it isn't a label file. Labels are stored in
> > .label names and are text files. The .mgz is a scalar field over the
> > surface (that is, a vector with a single value at each surface
> > location). In freeview you can view it as:
> >
> > freeview -f lh.inflated:overlay=surfaceoverlay.mgz
> >
> >
> > cheers
> > Bruce
> >
> > On Tue, 19 Apr 2016, Trisanna Sprung-Much wrote:
> >
> >> Hi Doug
> >>
> >> So I ran mri_vol2surf and generated my .mgz surface overlay using
> >> --regheader as you suggested. I than ran mri_cor2label using that
> >> .mgz file.
> >> This also completed successfully. However, when I then try to open
> >> the pial
> >> surface and the corresponding new label in freeview, it says it
> >> cannot read
> >> the label. Below is what I ran. I tried the same thing for the inflated
> >> surface.
> >>
> >> I put labelid as "1" as I was unsure as to what to put. Could this have
> >> affected the label creation?
> >>
> >> Trisanna
> >>
> >>
> >> trisanna@kaplan:~$ mri_vol2surf --mov
> >> /data-01/trisanna/freesurfer/icbm-102/mri/labels5.mnc --o
> >> /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz --regheader
> >> icbm-102 --hemi lh --surf pial
> >> srcvol = /data-01/trisanna/freesurfer/icbm-102/mri/labels5.mnc
> >> srcreg unspecified
> >> srcregold = 0
> >> srcwarp unspecified
> >> surf = pial
> >> hemi = lh
> >> reshape = 0
> >> interp = nearest
> >> float2int = round
> >> GetProjMax = 0
> >> INFO: float2int code = 0
> >> INFO: changing type to float
> >> Done loading volume
> >> Computing registration from header.
> >>   Using /data-01/trisanna/freesurfer/icbm-102/mri/orig.mgz as target
> >> reference.
> >> Reading surface /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial
> >> Done reading source surface
> >> Mapping Source Volume onto Source Subject Surface
> >>  1 0 0 0
> >> using old
> >> Done mapping volume to surface
> >> Number of source voxels hit = 85413
> >> Writing to /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz
> >> Dim: 169941 1 1
> >>
> >>
> >> trisanna@kaplan:~$ mri_cor2label --i
> >> /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz --id 1 --l
> >> /data-01/trisanna/freesurfer/icbm-102/label/labeltest --surf lh.pial
> >> $Id: mri_cor2label.c,v 1.12 2011/03/02 00:04:14 nicks Exp $
> >> Loading mri /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz
> >> --- Vox2RAS of input volume ---
> >> -1.000   0.000   0.000   84970.500;
> >>  0.000   0.000   1.000  -0.500;
> >>  0.000  -1.000   0.000   0.500;
> >>  0.000   0.000   0.000   1.000;
> >> Scanning the volume
> >> Found 1651 label voxels
> >> Writing label file /data-01/trisanna/freesurfer/icbm-102/label/labeltest
> >> Centroid: -56170.34   -0.500.50
> >> mri_cor2label completed SUCCESSFULLY
> >>
> >>
> >> trisanna@kaplan:~$ freeview -f
> >> /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial:label=labeltest
> >> No such file or directory
> >> freeview.bin: could not open label file labeltest.label
> >> No such file or directory
> >> LabelRead failedNo such file or directory
> >> en label file labeltest.label
> >>
> >>
> >>
> >> --
> >> Ph.D. CandidateMcGill University
> >> Integrated Program in Neuroscience
> >> Psychology
> >>
> >>
> >> On Tue, Apr 19, 2016 at 4:15 PM, Trisanna Sprung-Much
> >>  wrote:
> >>   many thanks - will give this a go!
> >>
> >> --
> >> Ph.D. CandidateMcGill University
> >> Integrated Program in Neuroscience
> >> Psychology
> >>
> >>
> >> On Tue, Apr 19, 2016 at 3:48 PM, Douglas N Greve
> >>  wrote:
> >>   yes, but the surface overlay is in mgz (or nii.gz) format
> >>
> >>   On 04/19/2016 03:05 PM, Trisanna Sprung-Much wrote:
> >>   > Hi Doug
> >>   >
> >>   > below is the email I had written last Friday. I thought
> >>   it got lost in
> >>   > the mix. I was told by Bruce to use identity.nofile as
> >>   the
> >>   > transformation since my labels and T1s are already in
> >>   the same space
> >>   > and I just want to resample my labels to the surfaces.
> >>   >
> >>   > *I will try, as you suggest, --regheader *
> >>   >
> >>   > When I do "mri_cor2label --help" it says it uses surface
> >>   overlays or
> >>   > volumes. *I am not sure why I want to 

[Freesurfer] Convert retenotopic areas from brainvoyger to Freesurfer

[Lilia Jorge]

Hello


I intend to compute cortical thickness in retinotopic areas. However
retinotopic areas were delimited in BrainVoyager and the cortical thickness
maps with FreeSurfer.

There are any way to reconcile data from the two softawares?

-- 
Com os melhores cumprimentos,

Lília Jorge
___
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.

Re: [Freesurfer] identity.nofile

[Douglas N Greve]

I don't think that is the problem. The problem is that it cannot find 
the file. Try giving it the whole path

On 04/19/2016 05:45 PM, Bruce Fischl wrote:
> Hi Trisanna
>
> if your output is .mgz it isn't a label file. Labels are stored in 
> .label names and are text files. The .mgz is a scalar field over the 
> surface (that is, a vector with a single value at each surface 
> location). In freeview you can view it as:
>
> freeview -f lh.inflated:overlay=surfaceoverlay.mgz
>
>
> cheers
> Bruce
>
> On Tue, 19 Apr 2016, Trisanna Sprung-Much wrote:
>
>> Hi Doug
>>
>> So I ran mri_vol2surf and generated my .mgz surface overlay using
>> --regheader as you suggested. I than ran mri_cor2label using that 
>> .mgz file.
>> This also completed successfully. However, when I then try to open 
>> the pial
>> surface and the corresponding new label in freeview, it says it 
>> cannot read
>> the label. Below is what I ran. I tried the same thing for the inflated
>> surface.
>>
>> I put labelid as "1" as I was unsure as to what to put. Could this have
>> affected the label creation?
>>
>> Trisanna
>>
>>
>> trisanna@kaplan:~$ mri_vol2surf --mov
>> /data-01/trisanna/freesurfer/icbm-102/mri/labels5.mnc --o
>> /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz --regheader
>> icbm-102 --hemi lh --surf pial
>> srcvol = /data-01/trisanna/freesurfer/icbm-102/mri/labels5.mnc
>> srcreg unspecified
>> srcregold = 0
>> srcwarp unspecified
>> surf = pial
>> hemi = lh
>> reshape = 0
>> interp = nearest
>> float2int = round
>> GetProjMax = 0
>> INFO: float2int code = 0
>> INFO: changing type to float
>> Done loading volume
>> Computing registration from header.
>>   Using /data-01/trisanna/freesurfer/icbm-102/mri/orig.mgz as target
>> reference.
>> Reading surface /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial
>> Done reading source surface
>> Mapping Source Volume onto Source Subject Surface
>>  1 0 0 0
>> using old
>> Done mapping volume to surface
>> Number of source voxels hit = 85413
>> Writing to /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz
>> Dim: 169941 1 1
>>
>>
>> trisanna@kaplan:~$ mri_cor2label --i
>> /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz --id 1 --l
>> /data-01/trisanna/freesurfer/icbm-102/label/labeltest --surf lh.pial
>> $Id: mri_cor2label.c,v 1.12 2011/03/02 00:04:14 nicks Exp $
>> Loading mri /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz
>> --- Vox2RAS of input volume ---
>> -1.000   0.000   0.000   84970.500;
>>  0.000   0.000   1.000  -0.500;
>>  0.000  -1.000   0.000   0.500;
>>  0.000   0.000   0.000   1.000;
>> Scanning the volume
>> Found 1651 label voxels
>> Writing label file /data-01/trisanna/freesurfer/icbm-102/label/labeltest
>> Centroid: -56170.34   -0.500.50
>> mri_cor2label completed SUCCESSFULLY
>>
>>
>> trisanna@kaplan:~$ freeview -f
>> /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial:label=labeltest
>> No such file or directory
>> freeview.bin: could not open label file labeltest.label
>> No such file or directory
>> LabelRead failedNo such file or directory
>> en label file labeltest.label
>>
>>
>>
>> -- 
>> Ph.D. CandidateMcGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Tue, Apr 19, 2016 at 4:15 PM, Trisanna Sprung-Much
>>  wrote:
>>   many thanks - will give this a go!
>>
>> -- 
>> Ph.D. CandidateMcGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Tue, Apr 19, 2016 at 3:48 PM, Douglas N Greve
>>  wrote:
>>   yes, but the surface overlay is in mgz (or nii.gz) format
>>
>>   On 04/19/2016 03:05 PM, Trisanna Sprung-Much wrote:
>>   > Hi Doug
>>   >
>>   > below is the email I had written last Friday. I thought
>>   it got lost in
>>   > the mix. I was told by Bruce to use identity.nofile as
>>   the
>>   > transformation since my labels and T1s are already in
>>   the same space
>>   > and I just want to resample my labels to the surfaces.
>>   >
>>   > *I will try, as you suggest, --regheader *
>>   >
>>   > When I do "mri_cor2label --help" it says it uses surface
>>   overlays or
>>   > volumes. *I am not sure why I want to generate a volume
>>   with
>>   > mri_vol2surf* - shouldn't I generate a surface overlay
>>   that I can then
>>   > create as a label using mri_cor2label?
>>   >
>>   > many thanks
>>   >
>>   > Trisanna
>>   >
>>   >
>>   >
>>   > thanks Bruce
>>   >
>>   > I could not find identity.nofile anywhere, when I ran
>>   mri_vol2surf I
>>   > got the following error
>>   >
>>   > trisanna@kaplan:~$ mri_vol2surf --mov
>>   > /data-01/trisanna/freesurfer/icbm-112/mri/labels5.mgz
>>   --o
>>   > /data-01/trisanna/freesurfer/icbm-112 --reg
>>   identity.nofile --hemi lh
>>   > srcvol =
>>   

Re: [Freesurfer] identity.nofile

[Bruce Fischl]

Hi Trisanna

if your output is .mgz it isn't a label file. Labels are stored in .label 
names and are text files. The .mgz is a scalar field over the surface (that 
is, a vector with a single value at each surface location). In freeview you 
can view it as:


freeview -f lh.inflated:overlay=surfaceoverlay.mgz


cheers
Bruce

On Tue, 19 Apr 2016, Trisanna Sprung-Much wrote:


Hi Doug

So I ran mri_vol2surf and generated my .mgz surface overlay using
--regheader as you suggested. I than ran mri_cor2label using that .mgz file.
This also completed successfully. However, when I then try to open the pial
surface and the corresponding new label in freeview, it says it cannot read
the label. Below is what I ran. I tried the same thing for the inflated
surface.

I put labelid as "1" as I was unsure as to what to put. Could this have
affected the label creation?

Trisanna


trisanna@kaplan:~$ mri_vol2surf --mov
/data-01/trisanna/freesurfer/icbm-102/mri/labels5.mnc --o
/data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz --regheader
icbm-102 --hemi lh --surf pial
srcvol = /data-01/trisanna/freesurfer/icbm-102/mri/labels5.mnc
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = pial
hemi = lh
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
INFO: changing type to float
Done loading volume
Computing registration from header.
  Using /data-01/trisanna/freesurfer/icbm-102/mri/orig.mgz as target
reference.
Reading surface /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial
Done reading source surface
Mapping Source Volume onto Source Subject Surface
 1 0 0 0
using old
Done mapping volume to surface
Number of source voxels hit = 85413
Writing to /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz
Dim: 169941 1 1


trisanna@kaplan:~$ mri_cor2label --i
/data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz --id 1 --l
/data-01/trisanna/freesurfer/icbm-102/label/labeltest --surf lh.pial
$Id: mri_cor2label.c,v 1.12 2011/03/02 00:04:14 nicks Exp $
Loading mri /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz
--- Vox2RAS of input volume ---
-1.000   0.000   0.000   84970.500;
 0.000   0.000   1.000  -0.500;
 0.000  -1.000   0.000   0.500;
 0.000   0.000   0.000   1.000;
Scanning the volume
Found 1651 label voxels
Writing label file /data-01/trisanna/freesurfer/icbm-102/label/labeltest
Centroid: -56170.34   -0.50    0.50
mri_cor2label completed SUCCESSFULLY


trisanna@kaplan:~$ freeview -f
/data-01/trisanna/freesurfer/icbm-102/surf/lh.pial:label=labeltest
No such file or directory
freeview.bin: could not open label file labeltest.label
No such file or directory
LabelRead failedNo such file or directory
en label file labeltest.label



--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology


On Tue, Apr 19, 2016 at 4:15 PM, Trisanna Sprung-Much
 wrote:
  many thanks - will give this a go!

--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology


On Tue, Apr 19, 2016 at 3:48 PM, Douglas N Greve
 wrote:
  yes, but the surface overlay is in mgz (or nii.gz) format

  On 04/19/2016 03:05 PM, Trisanna Sprung-Much wrote:
  > Hi Doug
  >
  > below is the email I had written last Friday. I thought
  it got lost in
  > the mix. I was told by Bruce to use identity.nofile as
  the
  > transformation since my labels and T1s are already in
  the same space
  > and I just want to resample my labels to the surfaces.
  >
  > *I will try, as you suggest, --regheader *
  >
  > When I do "mri_cor2label --help" it says it uses surface
  overlays or
  > volumes. *I am not sure why I want to generate a volume
  with
  > mri_vol2surf* - shouldn't I generate a surface overlay
  that I can then
  > create as a label using mri_cor2label?
  >
  > many thanks
  >
  > Trisanna
  >
  >
  >
  > thanks Bruce
  >
  > I could not find identity.nofile anywhere, when I ran
  mri_vol2surf I
  > got the following error
  >
  > trisanna@kaplan:~$ mri_vol2surf --mov
  > /data-01/trisanna/freesurfer/icbm-112/mri/labels5.mgz
  --o
  > /data-01/trisanna/freesurfer/icbm-112 --reg
  identity.nofile --hemi lh
  > srcvol =
  /data-01/trisanna/freesurfer/icbm-112/mri/labels5.mgz
  > srcreg = identity.nofile
  > srcregold = 0
  > srcwarp unspecified
  > surf = white
  > hemi = lh
  > reshape = 0
  > interp = nearest
  > float2int = round
  > GetProjMax = 0
  > INFO: float2int code = 0
  > INFO: changing type to float
  > Done loading volume
  > regio_read_register(): No such file or directory
  > Could not open identity.nofile
  >
  >
  >
  > On Fri, Apr 15, 2016 at 8:40 AM, Bruce Fischl
  > 

Re: [Freesurfer] identity.nofile

[Trisanna Sprung-Much]

Hi Doug

So I ran mri_vol2surf and generated my .mgz surface overlay using
--regheader as you suggested. I than ran mri_cor2label using that .mgz
file. This also completed successfully. *However, when I then try to open
the pial surface and the corresponding new label in freeview, it says it
cannot read the label. *Below is what I ran. I tried the same thing for the
inflated surface.

I put labelid as "1" as I was unsure as to what to put. Could this have
affected the label creation?

Trisanna


trisanna@kaplan:~$ mri_vol2surf --mov
/data-01/trisanna/freesurfer/icbm-102/mri/labels5.mnc --o
/data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz --regheader
icbm-102 --hemi lh --surf pial
srcvol = /data-01/trisanna/freesurfer/icbm-102/mri/labels5.mnc
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = pial
hemi = lh
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
INFO: changing type to float
Done loading volume
Computing registration from header.
  Using /data-01/trisanna/freesurfer/icbm-102/mri/orig.mgz as target
reference.
Reading surface /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial
Done reading source surface
Mapping Source Volume onto Source Subject Surface
 1 0 0 0
using old
Done mapping volume to surface
Number of source voxels hit = 85413
Writing to /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz
Dim: 169941 1 1


trisanna@kaplan:~$ mri_cor2label --i
/data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz --id 1 --l
/data-01/trisanna/freesurfer/icbm-102/label/labeltest --surf lh.pial
$Id: mri_cor2label.c,v 1.12 2011/03/02 00:04:14 nicks Exp $
Loading mri /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz
--- Vox2RAS of input volume ---
-1.000   0.000   0.000   84970.500;
 0.000   0.000   1.000  -0.500;
 0.000  -1.000   0.000   0.500;
 0.000   0.000   0.000   1.000;
Scanning the volume
Found 1651 label voxels
Writing label file /data-01/trisanna/freesurfer/icbm-102/label/labeltest
Centroid: -56170.34   -0.500.50
mri_cor2label completed SUCCESSFULLY


trisanna@kaplan:~$ freeview -f
/data-01/trisanna/freesurfer/icbm-102/surf/lh.pial:label=labeltest
No such file or directory
freeview.bin: could not open label file labeltest.label
No such file or directory
LabelRead failedNo such file or directory
en label file labeltest.label



--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Tue, Apr 19, 2016 at 4:15 PM, Trisanna Sprung-Much <
trisanna.sprung-m...@mail.mcgill.ca> wrote:

> many thanks - will give this a go!
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Tue, Apr 19, 2016 at 3:48 PM, Douglas N Greve <
> gr...@nmr.mgh.harvard.edu> wrote:
>
>> yes, but the surface overlay is in mgz (or nii.gz) format
>>
>> On 04/19/2016 03:05 PM, Trisanna Sprung-Much wrote:
>> > Hi Doug
>> >
>> > below is the email I had written last Friday. I thought it got lost in
>> > the mix. I was told by Bruce to use identity.nofile as the
>> > transformation since my labels and T1s are already in the same space
>> > and I just want to resample my labels to the surfaces.
>> >
>> > *I will try, as you suggest, --regheader *
>> >
>> > When I do "mri_cor2label --help" it says it uses surface overlays or
>> > volumes. *I am not sure why I want to generate a volume with
>> > mri_vol2surf* - shouldn't I generate a surface overlay that I can then
>> > create as a label using mri_cor2label?
>> >
>> > many thanks
>> >
>> > Trisanna
>> >
>> >
>> >
>> > thanks Bruce
>> >
>> > I could not find identity.nofile anywhere, when I ran mri_vol2surf I
>> > got the following error
>> >
>> > trisanna@kaplan:~$ mri_vol2surf --mov
>> > /data-01/trisanna/freesurfer/icbm-112/mri/labels5.mgz --o
>> > /data-01/trisanna/freesurfer/icbm-112 --reg identity.nofile --hemi lh
>> > srcvol = /data-01/trisanna/freesurfer/icbm-112/mri/labels5.mgz
>> > srcreg = identity.nofile
>> > srcregold = 0
>> > srcwarp unspecified
>> > surf = white
>> > hemi = lh
>> > reshape = 0
>> > interp = nearest
>> > float2int = round
>> > GetProjMax = 0
>> > INFO: float2int code = 0
>> > INFO: changing type to float
>> > Done loading volume
>> > regio_read_register(): No such file or directory
>> > Could not open identity.nofile
>> >
>> >
>> >
>> > On Fri, Apr 15, 2016 at 8:40 AM, Bruce Fischl
>> > > wrote:
>> > Hi Trisanna
>> >
>> > you can give the transformation "file" named identity.nofile and it
>> > will assume that the transform is the identity. You can then use
>> > mri_vol2label to sample the label onto the surface and visualize it
>> with:
>> >
>> > freeview -f lh.inflated:label=lh.labels.label
>> >
>> > or some such
>> >
>> > cheers
>> > Bruce
>> >
>> > On Thu, 14 Apr 2016, Trisanna Sprung-Much wrote:
>> >
>> > Hi there
>> >
>> > Just to reiterate my point above, when I open a surface created in
>> > Freesurfer with my labels.mgz 

Re: [Freesurfer] white matter edits not incorporated

[dgw]

Hi Bruce,

Thanks! I'll give it a whirl.

d

On Tue, Apr 19, 2016 at 5:24 PM, Bruce Fischl
 wrote:
> Hi Daniel
>
> the problems isn't that it it's ignoring the wm edits, it is that it starts
> the orig surface out there, but then retracts to the (same) visible
> gray/white boundary that it found in the first place. For this type of
> lesion I think what you should do is also edit those voxels in the aseg.mgz
> and change them to right-lesion. This should freeze the white surface there
> I think. If it doesn't, let me know and I'll fix it.
>
> cheers
> Bruce
>
>
> On Tue, 19 Apr 2016, dgw wrote:
>
>> Here is the log for the most recent -autorecon2-wm call:
>>
>> Thanks!
>> d
>>
>> On Tue, Apr 19, 2016 at 4:56 PM, Bruce Fischl
>>  wrote:
>>> can you send us the recon-all.log? I don't see an obvious reason why it
>>> wouldn't have worked
>>> On Tue, 19 Apr 2016, dgw wrote:
>>>
 Just to follow up, I have tried several different options with
 recon-all to get the white matter edits to stick on this participant,
 and it doesn't seem to be working:

 re-editing wm.mgz and running recon-all -autorecon2-wm
 re-editing wm.mgz and running recon-all -make all

 I can't seem to get any appreciable change in the white matter
 surface. I have attached a screenshot, for an example.

 hth
 d


 On Mon, Apr 18, 2016 at 10:30 AM, dgw  wrote:
> Hi,
>
> I recently edited a brain with a gyral cyst, carefully filling the
> cyst with white matter in the wm.mgz. Unfortunately after running:
> /usr/local/freesurfer/stable5_3_0/bin/recon-all
> -autorecon2-wm -autorecon3 -subjid nmr01002 -FLAIRpial -openmp 8
>
> none of the edits were incorporated.
>
> Is the FLAIRpial flag incompatible with autorecon2-wm?
>
> Is there some other misake?
>
> I followed this guide
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits_freeview
>
> Thanks,
> Dan

>>> ___
>>> 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.
>>>
>>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] white matter edits not incorporated

[Bruce Fischl]

Hi Daniel

the problems isn't that it it's ignoring the wm edits, it is that it starts 
the orig surface out there, but then retracts to the (same) visible 
gray/white boundary that it found in the first place. For this type of 
lesion I think what you should do is also edit those voxels in the aseg.mgz 
and change them to right-lesion. This should freeze the white surface there 
I think. If it doesn't, let me know and I'll fix it.

cheers
Bruce


On Tue, 19 Apr 2016, dgw wrote:

> Here is the log for the most recent -autorecon2-wm call:
>
> Thanks!
> d
>
> On Tue, Apr 19, 2016 at 4:56 PM, Bruce Fischl
>  wrote:
>> can you send us the recon-all.log? I don't see an obvious reason why it
>> wouldn't have worked
>> On Tue, 19 Apr 2016, dgw wrote:
>>
>>> Just to follow up, I have tried several different options with
>>> recon-all to get the white matter edits to stick on this participant,
>>> and it doesn't seem to be working:
>>>
>>> re-editing wm.mgz and running recon-all -autorecon2-wm
>>> re-editing wm.mgz and running recon-all -make all
>>>
>>> I can't seem to get any appreciable change in the white matter
>>> surface. I have attached a screenshot, for an example.
>>>
>>> hth
>>> d
>>>
>>>
>>> On Mon, Apr 18, 2016 at 10:30 AM, dgw  wrote:
 Hi,

 I recently edited a brain with a gyral cyst, carefully filling the
 cyst with white matter in the wm.mgz. Unfortunately after running:
 /usr/local/freesurfer/stable5_3_0/bin/recon-all
 -autorecon2-wm -autorecon3 -subjid nmr01002 -FLAIRpial -openmp 8

 none of the edits were incorporated.

 Is the FLAIRpial flag incompatible with autorecon2-wm?

 Is there some other misake?

 I followed this guide
 https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits_freeview

 Thanks,
 Dan
>>>
>> ___
>> 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.
>>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] white matter edits not incorporated

[Bruce Fischl]

can you send us the recon-all.log? I don't see an obvious reason why it 
wouldn't have worked
On Tue, 19 Apr 2016, dgw wrote:

> Just to follow up, I have tried several different options with
> recon-all to get the white matter edits to stick on this participant,
> and it doesn't seem to be working:
>
> re-editing wm.mgz and running recon-all -autorecon2-wm
> re-editing wm.mgz and running recon-all -make all
>
> I can't seem to get any appreciable change in the white matter
> surface. I have attached a screenshot, for an example.
>
> hth
> d
>
>
> On Mon, Apr 18, 2016 at 10:30 AM, dgw  wrote:
>> Hi,
>>
>> I recently edited a brain with a gyral cyst, carefully filling the
>> cyst with white matter in the wm.mgz. Unfortunately after running:
>> /usr/local/freesurfer/stable5_3_0/bin/recon-all
>> -autorecon2-wm -autorecon3 -subjid nmr01002 -FLAIRpial -openmp 8
>>
>> none of the edits were incorporated.
>>
>> Is the FLAIRpial flag incompatible with autorecon2-wm?
>>
>> Is there some other misake?
>>
>> I followed this guide
>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits_freeview
>>
>> Thanks,
>> Dan
>
___
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.

Re: [Freesurfer] white matter edits not incorporated

[dgw]

Just to follow up, I have tried several different options with
recon-all to get the white matter edits to stick on this participant,
and it doesn't seem to be working:

re-editing wm.mgz and running recon-all -autorecon2-wm
re-editing wm.mgz and running recon-all -make all

I can't seem to get any appreciable change in the white matter
surface. I have attached a screenshot, for an example.

hth
d


On Mon, Apr 18, 2016 at 10:30 AM, dgw  wrote:
> Hi,
>
> I recently edited a brain with a gyral cyst, carefully filling the
> cyst with white matter in the wm.mgz. Unfortunately after running:
> /usr/local/freesurfer/stable5_3_0/bin/recon-all
> -autorecon2-wm -autorecon3 -subjid nmr01002 -FLAIRpial -openmp 8
>
> none of the edits were incorporated.
>
> Is the FLAIRpial flag incompatible with autorecon2-wm?
>
> Is there some other misake?
>
> I followed this guide
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits_freeview
>
> Thanks,
> Dan
___
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.

Re: [Freesurfer] identity.nofile

[Trisanna Sprung-Much]

many thanks - will give this a go!

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Tue, Apr 19, 2016 at 3:48 PM, Douglas N Greve 
wrote:

> yes, but the surface overlay is in mgz (or nii.gz) format
>
> On 04/19/2016 03:05 PM, Trisanna Sprung-Much wrote:
> > Hi Doug
> >
> > below is the email I had written last Friday. I thought it got lost in
> > the mix. I was told by Bruce to use identity.nofile as the
> > transformation since my labels and T1s are already in the same space
> > and I just want to resample my labels to the surfaces.
> >
> > *I will try, as you suggest, --regheader *
> >
> > When I do "mri_cor2label --help" it says it uses surface overlays or
> > volumes. *I am not sure why I want to generate a volume with
> > mri_vol2surf* - shouldn't I generate a surface overlay that I can then
> > create as a label using mri_cor2label?
> >
> > many thanks
> >
> > Trisanna
> >
> >
> >
> > thanks Bruce
> >
> > I could not find identity.nofile anywhere, when I ran mri_vol2surf I
> > got the following error
> >
> > trisanna@kaplan:~$ mri_vol2surf --mov
> > /data-01/trisanna/freesurfer/icbm-112/mri/labels5.mgz --o
> > /data-01/trisanna/freesurfer/icbm-112 --reg identity.nofile --hemi lh
> > srcvol = /data-01/trisanna/freesurfer/icbm-112/mri/labels5.mgz
> > srcreg = identity.nofile
> > srcregold = 0
> > srcwarp unspecified
> > surf = white
> > hemi = lh
> > reshape = 0
> > interp = nearest
> > float2int = round
> > GetProjMax = 0
> > INFO: float2int code = 0
> > INFO: changing type to float
> > Done loading volume
> > regio_read_register(): No such file or directory
> > Could not open identity.nofile
> >
> >
> >
> > On Fri, Apr 15, 2016 at 8:40 AM, Bruce Fischl
> > > wrote:
> > Hi Trisanna
> >
> > you can give the transformation "file" named identity.nofile and it
> > will assume that the transform is the identity. You can then use
> > mri_vol2label to sample the label onto the surface and visualize it with:
> >
> > freeview -f lh.inflated:label=lh.labels.label
> >
> > or some such
> >
> > cheers
> > Bruce
> >
> > On Thu, 14 Apr 2016, Trisanna Sprung-Much wrote:
> >
> > Hi there
> >
> > Just to reiterate my point above, when I open a surface created in
> > Freesurfer with my labels.mgz (converted from minc) in Freeview (i.e. no
> > transformations have been performed) I get the following snapshot
> > #1. Clearly, my original labels are aligned with the surface, as they
> > should
> > be since Freesurfer did not alter the space. So, how can I use
> mrivol2surf
> > to resample the surface such that the vertices carry the label info? What
> > output format should I use in mrivol2surf? How can I open this output in
> > Freeview?
> >
> > For instance, when I try a .dat that creates no transformation and
> > save the
> > output as .mgz and use Overlay in Freeview, I get snapshot #2. So,
> > something
> > is going wrong in my mrivol2surf command.
> >
> > My apologies for the questions
> > Trisanna
> >
> >
> >
> > --
> > Ph.D. Candidate
> > McGill University
> > Integrated Program in Neuroscience
> > Psychology
> >
> >
> > On Tue, Apr 19, 2016 at 1:23 PM, Douglas N Greve
> > > wrote:
> >
> > I'm not sure what identity.nofile is or what you are trying to do (no
> > previous info in the email). If whatever you are trying to map to the
> > surface is already in anatomical space (so no registration
> necessary),
> > then you can use --regheader with mri_vol2surf. mri_cor2label will
> > take
> > a volume format as input (ie, mgz, nii.gz ,etc)
> >
> > On 04/19/2016 01:17 PM, Trisanna Sprung-Much wrote:
> > >
> > > Hi All!
> > >
> > > Could someone please tell me how to run mri_vol2surf using
> > > identity.nofile as the transformation? I cannot find any
> > documentation
> > > on identity.nofile
> > >
> > > Additionally, if my next step is to use the output of
> > mri_vol2surf in
> > > mri_cor2label, which takes surface overlays OR volumes, what format
> > > should my output be for mri_vol2surf?
> > >
> > > many thanks!
> > >
> > > Trisanna
> > >
> > > --
> > > Ph.D. Candidate
> > > McGill University
> > > Integrated Program in Neuroscience
> > > Psychology
> > >
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > 
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > gr...@nmr.mgh.harvard.edu 
> > Phone Number: 617-724-2358 
> > Fax: 617-726-7422 
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > 

Re: [Freesurfer] fcseed-sess ERROR: could not determine file for .../fmcpr

[Douglas N Greve]

That means that there are no voxels in the final ROI in native 
functional space. You should check your registration and also see how 
big your original ROI is.

On 04/15/2016 11:32 PM, Julio Alberto González Torre wrote:
> I performed the preprocessing again with -per-run parameter. 
> Everything ok in that step.
>
> The, when I run the fcseed-sess command, I've got new errors.
>
> Segmentation fault
>
> MRIalloc(0, 1, 1): bad parm
>
> I have attached the log file.
>
> 2016-04-15 17:56 GMT+02:00 Raney, Talia L.  >:
>
> Hi Julio,
> You're right in that the problem is occurring in a later step.
> However, the fmcpr file is created during preprocessing. When you
> do the preprocessing step, it doesn't show an error occurring in
> the logs(this happened to me too because it said that preproc-sess
> was completed but fcseed-sess gave me this error that it could not
> determine the fmcpr file).
> You're right that you have to use the per-run parameter during
> preproc-sess. I think this will fix the problem if everything else
> is set up correctly.
> Best,
> Talia
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> 
> [freesurfer-boun...@nmr.mgh.harvard.edu
> ] on behalf of
> Julio Alberto González Torre [al099...@uji.es
> ]
> Sent: Friday, April 15, 2016 11:42 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] fcseed-sess ERROR: could not determine
> file for   .../fmcpr
>
> Hi Talia. Thanks for the quick answer.
>
> But the preprocessing finished correctly without errors as I can
> check on all the log files generated in the same project folder.
> "subjectname" and $SUBJECTS_DIR are correctly placed.
>
> The problem is a later step (STEP 5,
> 
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough),
> when I try to create FC seeds for an individual.
>
> As long as I can read in previously threads, the problem may be
> the parameter "-per-session", so now I'm trying to do it with
> "-per-run" parameter to check if the error remains. But I was
> unable to find a definitive fix for this error.
>
> 2016-04-15 14:09 GMT+02:00 Raney, Talia L.   >>:
> Hi Julio,
> In the past I received this error because the subject was not
> preprocessed correctly. Make sure you have a link to the subject's
> structural recon folder in the resting state folder. In order to
> do this, you have to create a txt file(in this case it would
> 02_resting/subjectname) and within that txt file you put the name
> of the recon directory. After doing this, make sure that the
> $SUBJECTS_DIR is where the subject's recon folder is or else it
> won't fully run preprocessing.
> Hope this helps!
> Best,
> Talia
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> 
>  >
> [freesurfer-boun...@nmr.mgh.harvard.edu
> 
>  >] on behalf of
> Julio Alberto González Torre [al099...@uji.es
>  >]
> Sent: Thursday, April 14, 2016 6:42 PM
> To: Freesurfer support list
> Subject: [Freesurfer] fcseed-sess ERROR: could not determine file
> for   .../fmcpr
>
> Hi Freesurfer users.
>
> I am currently performing the steps of Functional Connectivity
> Walkthrough. And after resolving the problems in the first steps,
> specially in the preprocessing command (missing AFNI files), I'm
> now stuck in the 5th step: Creating the FC seeds for each subject.
>
> In the 4th step I've created the parameters for a region of
> interest. In this case, cheking the FreeSurferColorLUT.txt, I run
> this command to create the parameters for Left CA1 of Hippocampus
> (after the reconstruction, I performed the hippocampal subfields):
>
> fcseed-config -segid 552 -fcname L_CA1.dat -fsd rest -mean -cfg
> mean.L_CA1.config
>
> In the 5th step, when I run the fcseed-sess command, I obtain this
> error and I'm unable to figure out why:
>
> fcseed-sess -s con_algon -cfg L_CA1.config
>
> ERROR: could not determine file for
> 
> /Users/acad1215inv/Desktop/ALBERTO/08_Conectividad/CONECTIVIDAD/02_resting/con_algon/rest/009/fmcpr
> stem2fname
>   

Re: [Freesurfer] Segmentation Fault during mri_glmfit-sim

[Douglas N Greve]

There is nothing obvious going wrong. If the exact same command 
sometimes fails and sometimes works, then it may be a problem on your 
system. In any event, without a reproducible error, I can't really debug it.

On 04/15/2016 08:31 PM, Elijah Mak wrote:
>
> On another note, I am running into a puzzling "Segmentation fault" 
> error with the following command:
>
> mri_glmfit-sim --glmdir  lh_ad_hc.glmdir  --cache 2 neg --cwp  0.05 
> --2spaces
>
> 
>
> Reading source surface 
> /Users/MacPro/Documents/NIMROD_DTI//fsaverage/surf/lh.white
>
> Done reading source surface
>
> Reading annotation 
> /Users/MacPro/Documents/NIMROD_DTI//fsaverage/label/lh.aparc.annot
>
> reading colortable from annotation file...
>
> colortable with 36 entries read (originally 
> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
>
> Segmentation fault
>
> 
>
> Strangely, I can't seem to reproduce this error consistently too. 
> Sometimes, after a pause of few minutes, the exact same command works! 
> This happens on smoothed and non-smooth PET data.
>
> I have attached the text outputs resulting from both scenarios 1) 
> seg_fault and 2) no_seg_fault (about 10 minutes between each execution).
>
> The mri_glmfit-sim version is v .53.2.2 2015/08/28 19:00:13
> I am running this on a Mac Pro with 64 GB RAM.
>
> Thanks again
>
> Best Wishes,
> Elijah
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
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.

Re: [Freesurfer] PET voxelwise

[Douglas N Greve]

On 04/15/2016 08:31 PM, Elijah Mak wrote:
> No, more like running the voxelwise comparisons only on voxels that 
> have positive BP between 2 group.  Is that possible?
I'm still not sure what you mean by "positive BP between 2 group". Do 
you mean masking out voxels where either group is less than 0? This is 
not possible in mri_glmfit, but you could do it post hoc.
>
> On another note, I am running into a puzzling "Segmentation fault" 
> error with the following command:
Moving this to another thread
>
> mri_glmfit-sim --glmdir  lh_ad_hc.glmdir  --cache 2 neg --cwp  0.05 
> --2spaces
>
> 
>
> Reading source surface 
> /Users/MacPro/Documents/NIMROD_DTI//fsaverage/surf/lh.white
>
> Done reading source surface
>
> Reading annotation 
> /Users/MacPro/Documents/NIMROD_DTI//fsaverage/label/lh.aparc.annot
>
> reading colortable from annotation file...
>
> colortable with 36 entries read (originally 
> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
>
> Segmentation fault
>
> 
>
> Strangely, I can't seem to reproduce this error consistently too. 
> Sometimes, after a pause of few minutes, the exact same command works! 
> This happens on smoothed and non-smooth PET data.
>
> I have attached the text outputs resulting from both scenarios 1) 
> seg_fault and 2) no_seg_fault (about 10 minutes between each execution).
>
> The mri_glmfit-sim version is v .53.2.2 2015/08/28 19:00:13
> I am running this on a Mac Pro with 64 GB RAM.
>
> Thanks again
>
> Best Wishes,
> Elijah
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
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.

Re: [Freesurfer] mkanalysis-sess stimulusdelay parameter

[Douglas N Greve]

That was set assuming that the data have been slice-time corrected to 
the middle of the TR.

On 04/19/2016 02:31 PM, Joseph Dien wrote:
> I’m taking a look at the effects of stimulus delay settings in one of 
> my datasets so I was surprised to notice that the default setting 
> of mkanalysis-sess is a delay of -TR/2 seconds.  What is the reasoning 
> for this?  If, as I expect, it was just empirically found that it 
> worked better than without, my question is whether this decision was 
> made on the basis of all the event-related options or just some subset 
> of them?  I’m worried that this might be an optimization that isn’t 
> appropriate for my particular parameter choices (FS 5.3, spmhrf0). 
>  Any comments would be appreciated.
>
> Cheers!
>
> Joe
>
>
> 
>
> Joseph Dien, PhD
> Senior Research Scientist
> Maryland Neuroimaging Center
> University of Maryland, College Park
> http://joedien.com
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
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.

Re: [Freesurfer] identity.nofile

[Douglas N Greve]

yes, but the surface overlay is in mgz (or nii.gz) format

On 04/19/2016 03:05 PM, Trisanna Sprung-Much wrote:
> Hi Doug
>
> below is the email I had written last Friday. I thought it got lost in 
> the mix. I was told by Bruce to use identity.nofile as the 
> transformation since my labels and T1s are already in the same space 
> and I just want to resample my labels to the surfaces.
>
> *I will try, as you suggest, --regheader *
>
> When I do "mri_cor2label --help" it says it uses surface overlays or 
> volumes. *I am not sure why I want to generate a volume with 
> mri_vol2surf* - shouldn't I generate a surface overlay that I can then 
> create as a label using mri_cor2label?
>
> many thanks
>
> Trisanna
>
>
>
> thanks Bruce
>
> I could not find identity.nofile anywhere, when I ran mri_vol2surf I 
> got the following error
>
> trisanna@kaplan:~$ mri_vol2surf --mov 
> /data-01/trisanna/freesurfer/icbm-112/mri/labels5.mgz --o 
> /data-01/trisanna/freesurfer/icbm-112 --reg identity.nofile --hemi lh
> srcvol = /data-01/trisanna/freesurfer/icbm-112/mri/labels5.mgz
> srcreg = identity.nofile
> srcregold = 0
> srcwarp unspecified
> surf = white
> hemi = lh
> reshape = 0
> interp = nearest
> float2int = round
> GetProjMax = 0
> INFO: float2int code = 0
> INFO: changing type to float
> Done loading volume
> regio_read_register(): No such file or directory
> Could not open identity.nofile
>
>
>
> On Fri, Apr 15, 2016 at 8:40 AM, Bruce Fischl 
> > wrote:
> Hi Trisanna
>
> you can give the transformation "file" named identity.nofile and it 
> will assume that the transform is the identity. You can then use 
> mri_vol2label to sample the label onto the surface and visualize it with:
>
> freeview -f lh.inflated:label=lh.labels.label
>
> or some such
>
> cheers
> Bruce
>
> On Thu, 14 Apr 2016, Trisanna Sprung-Much wrote:
>
> Hi there
>
> Just to reiterate my point above, when I open a surface created in
> Freesurfer with my labels.mgz (converted from minc) in Freeview (i.e. no
> transformations have been performed) I get the following snapshot
> #1. Clearly, my original labels are aligned with the surface, as they 
> should
> be since Freesurfer did not alter the space. So, how can I use mrivol2surf
> to resample the surface such that the vertices carry the label info? What
> output format should I use in mrivol2surf? How can I open this output in
> Freeview?
>
> For instance, when I try a .dat that creates no transformation and 
> save the
> output as .mgz and use Overlay in Freeview, I get snapshot #2. So, 
> something
> is going wrong in my mrivol2surf command.
>
> My apologies for the questions
> Trisanna
>
>
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Tue, Apr 19, 2016 at 1:23 PM, Douglas N Greve 
> > wrote:
>
> I'm not sure what identity.nofile is or what you are trying to do (no
> previous info in the email). If whatever you are trying to map to the
> surface is already in anatomical space (so no registration necessary),
> then you can use --regheader with mri_vol2surf. mri_cor2label will
> take
> a volume format as input (ie, mgz, nii.gz ,etc)
>
> On 04/19/2016 01:17 PM, Trisanna Sprung-Much wrote:
> >
> > Hi All!
> >
> > Could someone please tell me how to run mri_vol2surf using
> > identity.nofile as the transformation? I cannot find any
> documentation
> > on identity.nofile
> >
> > Additionally, if my next step is to use the output of
> mri_vol2surf in
> > mri_cor2label, which takes surface overlays OR volumes, what format
> > should my output be for mri_vol2surf?
> >
> > many thanks!
> >
> > Trisanna
> >
> > --
> > Ph.D. Candidate
> > McGill University
> > Integrated Program in Neuroscience
> > Psychology
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
> Phone Number: 617-724-2358 
> Fax: 617-726-7422 
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
> Outgoing:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu 
> 

Re: [Freesurfer] identity.nofile

[Bruce Fischl]

sorry for the confusion. Some of our tools use identity.nofile, but these 
use --regheader


cheers
Bruce

On Tue, 19 Apr 2016, Trisanna 
Sprung-Much wrote:



Hi Doug

below is the email I had written last Friday. I thought it got lost in the
mix. I was told by Bruce to use identity.nofile as the transformation since
my labels and T1s are already in the same space and I just want to resample
my labels to the surfaces.

I will try, as you suggest, --regheader

When I do "mri_cor2label --help" it says it uses surface overlays or
volumes. I am not sure why I want to generate a volume with mri_vol2surf -
shouldn't I generate a surface overlay that I can then create as a label
using mri_cor2label?

many thanks

Trisanna



thanks Bruce
I could not find identity.nofile anywhere, when I ran mri_vol2surf I got the
following error

trisanna@kaplan:~$ mri_vol2surf --mov
/data-01/trisanna/freesurfer/icbm-112/mri/labels5.mgz --o
/data-01/trisanna/freesurfer/icbm-112 --reg identity.nofile --hemi lh
srcvol = /data-01/trisanna/freesurfer/icbm-112/mri/labels5.mgz
srcreg = identity.nofile
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
INFO: changing type to float
Done loading volume
regio_read_register(): No such file or directory
Could not open identity.nofile[cleardot.gif]



On Fri, Apr 15, 2016 at 8:40 AM, Bruce Fischl 
wrote:
Hi Trisanna

you can give the transformation "file" named identity.nofile and it will
assume that the transform is the identity. You can then use mri_vol2label to
sample the label onto the surface and visualize it with:

freeview -f lh.inflated:label=lh.labels.label

or some such

cheers
Bruce

On Thu, 14 Apr 2016, Trisanna Sprung-Much wrote:

Hi there

Just to reiterate my point above, when I open a surface created in
Freesurfer with my labels.mgz (converted from minc) in Freeview (i.e. no
transformations have been performed) I get the following snapshot
#1. Clearly, my original labels are aligned with the surface, as they should
be since Freesurfer did not alter the space. So, how can I use mrivol2surf
to resample the surface such that the vertices carry the label info? What
output format should I use in mrivol2surf? How can I open this output in
Freeview?

For instance, when I try a .dat that creates no transformation and save the
output as .mgz and use Overlay in Freeview, I get snapshot #2. So, something
is going wrong in my mrivol2surf command.

My apologies for the questions
Trisanna



--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology


On Tue, Apr 19, 2016 at 1:23 PM, Douglas N Greve 
wrote:
  I'm not sure what identity.nofile is or what you are trying to
  do (no
  previous info in the email). If whatever you are trying to map
  to the
  surface is already in anatomical space (so no registration
  necessary),
  then you can use --regheader with mri_vol2surf. mri_cor2label
  will take
  a volume format as input (ie, mgz, nii.gz ,etc)

  On 04/19/2016 01:17 PM, Trisanna Sprung-Much wrote:
  >
  > Hi All!
  >
  > Could someone please tell me how to run mri_vol2surf using
  > identity.nofile as the transformation? I cannot find any
  documentation
  > on identity.nofile
  >
  > Additionally, if my next step is to use the output of
  mri_vol2surf in
  > mri_cor2label, which takes surface overlays OR volumes, what
  format
  > should my output be for mri_vol2surf?
  >
  > many thanks!
  >
  > Trisanna
  >
  > --
  > Ph.D. Candidate
  > McGill University
  > Integrated Program in Neuroscience
  > Psychology
  >
  >
  >
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
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.



___
Freesurfer 

Re: [Freesurfer] identity.nofile

[Trisanna Sprung-Much]

Hi Doug

below is the email I had written last Friday. I thought it got lost in the
mix. I was told by Bruce to use identity.nofile as the transformation since
my labels and T1s are already in the same space and I just want to resample
my labels to the surfaces.

*I will try, as you suggest, --regheader *

When I do "mri_cor2label --help" it says it uses surface overlays or
volumes. *I am not sure why I want to generate a volume with mri_vol2surf*
- shouldn't I generate a surface overlay that I can then create as a label
using mri_cor2label?

many thanks

Trisanna



thanks Bruce

I could not find identity.nofile anywhere, when I ran mri_vol2surf I got
the following error

trisanna@kaplan:~$ mri_vol2surf --mov /data-01/trisanna/freesurfer/icbm-112/
mri/labels5.mgz --o /data-01/trisanna/freesurfer/icbm-112 --reg
identity.nofile --hemi lh
srcvol = /data-01/trisanna/freesurfer/icbm-112/mri/labels5.mgz
srcreg = identity.nofile
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
INFO: changing type to float
Done loading volume
regio_read_register(): No such file or directory
Could not open identity.nofile



On Fri, Apr 15, 2016 at 8:40 AM, Bruce Fischl 
wrote:
Hi Trisanna

you can give the transformation "file" named identity.nofile and it will
assume that the transform is the identity. You can then use mri_vol2label
to sample the label onto the surface and visualize it with:

freeview -f lh.inflated:label=lh.labels.label

or some such

cheers
Bruce

On Thu, 14 Apr 2016, Trisanna Sprung-Much wrote:

Hi there

Just to reiterate my point above, when I open a surface created in
Freesurfer with my labels.mgz (converted from minc) in Freeview (i.e. no
transformations have been performed) I get the following snapshot
#1. Clearly, my original labels are aligned with the surface, as they should
be since Freesurfer did not alter the space. So, how can I use mrivol2surf
to resample the surface such that the vertices carry the label info? What
output format should I use in mrivol2surf? How can I open this output in
Freeview?

For instance, when I try a .dat that creates no transformation and save the
output as .mgz and use Overlay in Freeview, I get snapshot #2. So, something
is going wrong in my mrivol2surf command.

My apologies for the questions
Trisanna



--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Tue, Apr 19, 2016 at 1:23 PM, Douglas N Greve 
wrote:

> I'm not sure what identity.nofile is or what you are trying to do (no
> previous info in the email). If whatever you are trying to map to the
> surface is already in anatomical space (so no registration necessary),
> then you can use --regheader with mri_vol2surf. mri_cor2label will take
> a volume format as input (ie, mgz, nii.gz ,etc)
>
> On 04/19/2016 01:17 PM, Trisanna Sprung-Much wrote:
> >
> > Hi All!
> >
> > Could someone please tell me how to run mri_vol2surf using
> > identity.nofile as the transformation? I cannot find any documentation
> > on identity.nofile
> >
> > Additionally, if my next step is to use the output of mri_vol2surf in
> > mri_cor2label, which takes surface overlays OR volumes, what format
> > should my output be for mri_vol2surf?
> >
> > many thanks!
> >
> > Trisanna
> >
> > --
> > Ph.D. Candidate
> > McGill University
> > Integrated Program in Neuroscience
> > Psychology
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> 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.
>
>
___
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

Re: [Freesurfer] CA2 hippocampal subfield in FS6.0

[Eugenio Iglesias]

Yes!

Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer

- Original Message -
From: "Patrick Sezen" 
To: "Freesurfer support list" 
Sent: Monday, April 18, 2016 7:20:46 PM
Subject: [Freesurfer] CA2 hippocampal subfield in FS6.0

Dear FreeSurfers,

I was running the FS 6.0 hippocampal subsegmentation and was wondering
where the CA2 subfield disappeared to. Version 5.3 had a CA2-3 label,
but in 6.0 I can only find CA3, is it implicated that CA2 is part of CA3
as well in 6.0?

Sincerely,
Patrick Sezen



___
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.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] mkanalysis-sess stimulusdelay parameter

[Joseph Dien]

I’m taking a look at the effects of stimulus delay settings in one of my 
datasets so I was surprised to notice that the default setting of 
mkanalysis-sess is a delay of -TR/2 seconds.  What is the reasoning for this?  
If, as I expect, it was just empirically found that it worked better than 
without, my question is whether this decision was made on the basis of all the 
event-related options or just some subset of them?  I’m worried that this might 
be an optimization that isn’t appropriate for my particular parameter choices 
(FS 5.3, spmhrf0).  Any comments would be appreciated.

Cheers!

Joe




Joseph Dien, PhD
Senior Research Scientist
Maryland Neuroimaging Center
University of Maryland, College Park
http://joedien.com

___
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.

Re: [Freesurfer] identity.nofile

[Douglas N Greve]

I'm not sure what identity.nofile is or what you are trying to do (no 
previous info in the email). If whatever you are trying to map to the 
surface is already in anatomical space (so no registration necessary), 
then you can use --regheader with mri_vol2surf. mri_cor2label will take 
a volume format as input (ie, mgz, nii.gz ,etc)

On 04/19/2016 01:17 PM, Trisanna Sprung-Much wrote:
>
> Hi All!
>
> Could someone please tell me how to run mri_vol2surf using 
> identity.nofile as the transformation? I cannot find any documentation 
> on identity.nofile
>
> Additionally, if my next step is to use the output of mri_vol2surf in 
> mri_cor2label, which takes surface overlays OR volumes, what format 
> should my output be for mri_vol2surf?
>
> many thanks!
>
> Trisanna
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
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.

Re: [Freesurfer] MatrixMultiply: m2 is null error, trying to convert MNI152 ROI to FreeSurfer label

[Douglas N Greve]

are you sure the label file is really a label file? Does the same thing 
happen if you specify -l labelfile on the command line?

On 04/18/2016 05:08 PM, DeCross, Stephanie N. wrote:
> I can open the nii.gz output of the first step (vol2vol) just fine. But the 
> .label output of the second step (cor2label) won't open in tksurfer or 
> freeview. When I try to open it in freeview from the command line (freeview 
> -l ) I get:
>
> [0]PETSC ERROR: 
> 
> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, 
> probably memory access out of range
> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> [0]PETSC ERROR: or see 
> http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
>  ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to 
> find memory corruption errors
> [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
> [0]PETSC ERROR: to get more information on the crash.
> [0]PETSC ERROR: - Error Message 
> 
> [0]PETSC ERROR: Signal received!
> [0]PETSC ERROR: 
> 
> [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 
> CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> [0]PETSC ERROR: See docs/index.html for manual pages.
> [0]PETSC ERROR: 
> 
> [0]PETSC ERROR: Unknown Name on a linux-gnu named 
> anderson.nmr.mgh.harvard.edu by sdecross Mon Apr 18 17:03:37 2016
> [0]PETSC ERROR: Libraries linked from 
> /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt
> [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010
> [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc 
> --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 
> --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 
> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
> [0]PETSC ERROR: 
> 
> [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown 
> file
> [unset]: aborting job:
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
>
>
>
> When I try to open the .label file in tksurfer by putting in the command line 
> "tksurfer fsaverage lh inflated" and then opening the label menu, the 
> tksurfer command line reads this before it automatically closes:
>
> subject is fsaverage
> hemiis lh
> surface is inflated
> surfer: current subjects dir: 
> /autofs/cluster/maury/users/gcoombs/College_Risk/SUBJECTS_DIR_FS53
> surfer: not in "scripts" dir ==> using cwd for session root
> surfer: session root data dir ($session) set to:
> surfer: 
> /autofs/cluster/maury/users/gcoombs/College_Risk/fcMRI/ROIs/AllROIs/temp/VoltoSurf
> checking for nofix files in 'inflated'
> Reading image info 
> (/autofs/cluster/maury/users/gcoombs/College_Risk/SUBJECTS_DIR_FS53/fsaverage)
> Reading 
> /autofs/cluster/maury/users/gcoombs/College_Risk/SUBJECTS_DIR_FS53/fsaverage/mri/orig.mgz
> surfer: Reading header info from 
> /autofs/cluster/maury/users/gcoombs/College_Risk/SUBJECTS_DIR_FS53/fsaverage/mri/orig.mgz
> surfer: vertices=163842, faces=327680
> surfer: single buffered window
> surfer: tkoInitWindow(fsaverage)
> surfer: using interface /usr/local/freesurfer/stable5_3_0/tktools/tksurfer.tcl
> Reading /usr/local/freesurfer/stable5_3_0/tktools/tkm_common.tcl
> Reading /usr/local/freesurfer/stable5_3_0/tktools/tkm_wrappers.tcl
> Reading /usr/local/freesurfer/stable5_3_0/lib/tcl/fsgdfPlot.tcl
> Reading /usr/local/freesurfer/stable5_3_0/tktools/tkUtils.tcl
> Successfully parsed tksurfer.tcl
> reading white matter vertex locations...
> %   0 nonzero vertices found 
> label stat field identically zero - setting to 1
> 12304 unassigned vertices in label - building spatial LUT...
> assigning vertex numbers to label...
> MatrixMultiply: m2 is null!
>
>
> Thanks,
> Stephanie
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Wednesday, April 13, 2016 5:10 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] MatrixMultiply: m2 is null error, trying to convert 
> MNI152 ROI to FreeSurfer label
>
> what is your tksurfer command line? Can you send all the terminal output
> from tksurfer? Does it work in freeview?
>
> On 04/13/2016 11:20 AM, DeCross, Stephanie N. wrote:
>> Hi,
>>
>> I’m trying to take an ROI in MNI152 

[Freesurfer] identity.nofile

[Trisanna Sprung-Much]

Hi All!

Could someone please tell me how to run mri_vol2surf using identity.nofile
as the transformation? I cannot find any documentation on identity.nofile

Additionally, if my next step is to use the output of mri_vol2surf in
mri_cor2label, which takes surface overlays OR volumes, what format should
my output be for mri_vol2surf?

many thanks!

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology
___
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.

Re: [Freesurfer] preproc-sess error opening tmp brain_mask

[Douglas N Greve]

Can you run

/mkbrainmask-sess//-debug -s FS_T1_501 //-fsd bold/  |& tee dng.log
and send me dng.log ?

doug


On 04/18/2016 04:51 PM, Mcnorgan, Christopher wrote:
> du -h /tmp/ shows 256GB available, so that doesn’t seem to be it. Is 
> the “not found” error telling me that a binary is not found, or that 
> some expected output file is not found? I was looking for /bin/imtest 
> and /bin/remove_ext, and those binaries indeed do not exist, but we’ve 
> run Freesurfer on another dataset (but on another workstation, but 
> neither were those two binaries to be found on that workstation).
>> Is your /tmp space full?
>>
>> On 04/15/2016 12:54 PM, Mcnorgan, Christopher wrote:
>> >//>/I was hoping the developers might be able to help with a problem I'm 
>> >/>/having with a sub-step of preproc-sess./
>> >/I executed the following: />//>/preproc-sess -s FS_T1_501 -surface 
>> self lhrh -fwhm 6 -per-run -fsd bold />//>/In the relevant output, I 
>> see mktemplate-sess completed, followed by a />/call to 
>> mkbrainmask-sess, which eventually reported: />//>/# -- Using 
>> FSL's BET to Extract Brain-- # 
>> />//home/chris/ubfs/cpmcnorg/openfmri/booth/FS_T1_501/bold />/bet.fsl 
>> /tmp/mkbrainmask_2623/in.nii /tmp/mkbrainmask_2623/brain -m -f 0.1 
>> />//usr/local/freesurfer/bin/bet.fsl: 1: 
>> />//usr/local/freesurfer/bin/bet.fsl: /bin/remove_ext: not found 
>> />//usr/local/freesurfer/bin/bet.fsl: 1: 
>> />//usr/local/freesurfer/bin/bet.fsl: /bin/remove_ext: not found 
>> />//usr/local/freesurfer/bin/bet.fsl: 1: 
>> />//usr/local/freesurfer/bin/bet.fsl: /bin/imtest: not found 
>> />//usr/local/freesurfer/bin/bet.fsl: 153: [: =: unexpected operator 
>> />//usr/local/freesurfer/bin/bet.fsl: 231: 
>> />//usr/local/freesurfer/bin/bet.fsl: /bin/bet2: not found/
>
>
> /**
> * Chris McNorgan
> * Assistant Professor
> * Department of Psychology
> * University at Buffalo,
> * The State University of New York
> * http://ccnlab.buffalo.edu/
> * Office: 716.645.0236
> * Lab: 716.645.0222
> **/
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
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.

Re: [Freesurfer] entorhinal & temporal pole thickness measurements

[Bruce Fischl]

Hi Mihaela

adolescent girls probably have thicker cortex than older kids/adults. One 
thing to watch our for is dura/tentorium. Particularly when the cortex is 
thick it can be adjacent to cortical gray matter and difficult/impossible 
to avoid including in the cortical ribbon unless you have something in 
addition to a T1 (FLAIR, T2SPACE, T2*)


cheers
Bruce


On Tue, 19 Apr 
2016, Mihaela Stefan wrote:



Dear Freesurfers,
We noticed that some subjects in our study have the average cortical
thickness values in entorhinal and temporal pole above 4 mm. They are
adolescent girls so they're pretty young but we wonder if these values are
accurate. Visually, their segmentations seem good.

In an older email, Bruce was recommending using _exvivo.stats instead of
aparc for entorhinal measurements:
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg26364.html 

Is there a similar recommendation for the temporal pole? There doesn't seem
to be any stats files apart from aparc concerning this region.

Thanks!
Mihaela 

___
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.

[Freesurfer] entorhinal & temporal pole thickness measurements

[Mihaela Stefan]

Dear Freesurfers,

We noticed that some subjects in our study have the average cortical
thickness values in entorhinal and temporal pole above 4 mm. They are
adolescent girls so they're pretty young but we wonder if these values are
accurate. Visually, their segmentations seem good.

In an older email, Bruce was recommending using _exvivo.stats instead of
aparc for entorhinal measurements:
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg26364.html

Is there a similar recommendation for the temporal pole? There doesn't seem
to be any stats files apart from aparc concerning this region.

Thanks!
Mihaela
___
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.

Re: [Freesurfer] temporal lobe pial surface problem

[Xiaomin Yue]

OK.  I will do it.  
Xiaomin

Date: Tue, 19 Apr 2016 10:56:15 -0400
From: fis...@nmr.mgh.harvard.edu
To: yu...@hotmail.com
CC: freesurfer@nmr.mgh.harvard.edu; macar...@libero.it
Subject: Re: [Freesurfer] temporal lobe pial surface problem

then you need to put some control points in the white matter. 70 is way 
too low
On Tue, 19 Apr 2016, Xiaomin Yue wrote:
 
> The white matter in the anterior temporal lobe is around 70, the gray matter
> is about 30.  The number is read from brain.finalsurfs.mgz.
> Xiaomin
> 
> > Date: Tue, 19 Apr 2016 09:29:50 -0400
> > From: fis...@nmr.mgh.harvard.edu
> > To: freesurfer@nmr.mgh.harvard.edu
> > CC: macar...@libero.it; yu...@hotmail.com
> > Subject: Re: [Freesurfer] temporal lobe pial surface problem
> >
> > yes, you can do that for both mris_make_surfaces and mri_segment, but
> > that will only help if you've removed the majority of the bias field. Is
> > anterior temporal white matter near 110? If so, what is the gray matter
> > at?
> > On Tue, 19 Apr 2016, Falk Lüsebrink wrote:
> >
> > > Hi Xiaomin,
> > > currently I don't have access to my notes, however, if I remember
> correctly,
> > > you can specify thresholds in mris_make_surfaces for consideration in
> the
> > > surface placement. This obviously works well only if the contrast
> between
> > > WM/GM/CSF is high enough.
> > >
> > > If you are interested and nobody jumps in giving you the according
> flags,
> > > let me know.
> > >
> > > Best,
> > > Falk
> > >
> > >___
> _
> > > Von: freesurfer-boun...@nmr.mgh.harvard.edu
> > > [freesurfer-boun...@nmr.mgh.harvard.edu]" im Auftrag von "Xiaomin Yue
> > > [yu...@hotmail.com]
> > > Gesendet: Dienstag, 19. April 2016 01:13
> > > An: Freesurfer support list
> > > Cc: macar...@libero.it
> > > Betreff: Re: [Freesurfer] temporal lobe pial surface problem
> > >
> > > Hi Jon,
> > > Thanks for your answers.   There is gray-white contrast in the temporal
> > > lobe, but same as you said that the gray-csf is low.  Attached is a
> > > screenshot.  let's me know if you need more information. 
> > >
> > > Xiaomin
> > >
> > > > Date: Mon, 18 Apr 2016 17:43:47 -0400
> > > > From: j...@nmr.mgh.harvard.edu
> > > > To: yu...@hotmail.com
> > > > CC: freesurfer@nmr.mgh.harvard.edu; macar...@libero.it
> > > > Subject: Re: [Freesurfer] temporal lobe pial surface problem
> > > >
> > > >
> > > > hi Xiaomin,
> > > >
> > > > it is tough to say what might be causing the problem since a lot can
> go
> > > > wrong in the anterior temporal lobes at 7T. you say that your contrast
> is
> > > > low there? it is possible to have OK gray-white contrast but low
> overall
> > > > signal levels (so poor gray-CSF contrast) due to dielectric effects as
> > > > bruce mentioned, which can make the MP2RAGE ratio images noisy in that
> > > > region. also some adiabatic inversion pulses break down around the
> > > > temporal poles due to the B0 inhomogeneity around the ear canals. if
> you
> > > > could send a screenshot we'd have a better chance at diagnosing the
> > > > problem.
> > > >
> > > >
> > > > -jon
> > > >
> > > >
> > > >
> > > >
> > > > On Mon, 18 Apr 2016, Xiaomin Yue wrote:
> > > >
> > > > > Hi Jon Polimeni,
> > > > > Do you have any suggestions on the following questions?
> > > > > Thanks,Xiaomin
> > > > >
> > > > > Date: Fri, 15 Apr 2016 12:07:48 -0400
> > > > > From: fis...@nmr.mgh.harvard.edu
> > > > > To: freesurfer@nmr.mgh.harvard.edu
> > > > > CC: macar...@libero.it; j...@nmr.mgh.harvard.edu
> > > > > Subject: Re: [Freesurfer] temporal lobe pial surface problem
> > > > >
> > > > > Hi Xiaomin
> > > > >
> > > > > it's really hard to say without seeing more detail in your images.
> Do
> > > you
> > > > > have contrast in the temporal lobe? Frequently it goes away at 7T
> due to
> > > > > dielectric effects. I'll cc Jon Polimeni who is our 7T (among other
> > > > > things!) expert.
> > > > >
> > > > > cheers
> > > > > Bruce
> > > > >
> > > > >
> > > > > On Fri, 15 Apr 2016, Xiaomin Yue wrote:
> > > > >
> > > > > > Hi Bruce,
> > > > > > I have done the recon-all (fs5.3) with the data collected from a
> 7T
> > > scanner
> > > > > > using MP2Rage. The recon went well without problem. But the the
> > > temporal
> > > > > > reconstruction looks clearly not correct (see attached). I tried
> to
> > > push
> > > > > > the pial surface outside by editing the white matter evidenced in
> the
> > > > > > attached figures, but has no effect to genera correct pial
> surface. I
> > > do
> > > > > > realize that the contrast is low in the anterior temporal lobes.
> > > However, I
> > > > > > am wondering if there are expert parameters I can use to push the
> pial
> > > > > > surface into the right place. If that isn't a option, can I use
> some
> > > other
> > > > > > images collected during the MP2rage scan to help the segmentation
> in
> > > the
> > > > > > anterior temporal lobe? Those extract scans are: inv1_nd,
> inv1_phs_nd,
> > > ,

Re: [Freesurfer] Preprocessing task data with multiple B0-corrected runs

[Shea, Conor]

One of the tasks we use has three runs, and so each run has a specific B0 map.  
We're wondering how we can concatenate the three runs back together again for 
the Group analysis, since FSFAST is technically now considering each run to be 
a separate "task."

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: Tuesday, April 12, 2016 6:22 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Preprocessing task data with multiple B0-corrected 
runs

Can you tell me more about your design? Does each run have a separate task? Do 
you want to test across tasks?

On 04/12/2016 11:53 AM, Shea, Conor wrote:
> Thanks so much.  So, then, how does the Group Level Analysis work?  How do I 
> concatenate the runs together again, now that we've separated them into 
> different tasks?
>
> Conor
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N 
> Greve
> Sent: Friday, April 08, 2016 12:05 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Preprocessing task data with multiple 
> B0-corrected runs
>
> Unfortunately, I only programmed it assuming that you would have only one B0 
> map per session. There are a couple of work-arounds. One is to create a 
> different session for each run. This is probably easiest but makes the group 
> analysis a little trickier.
>
> On 04/05/2016 04:48 PM, Shea, Conor wrote:
>> Dear Doug,
>>
>> I'm trying to use FSFAST to analyze task data with multiple runs.  Before 
>> using the preproc-sess pipeline, I ran B0 correction on each of the runs, so 
>> I have 3 different b0dcmap files.  I'm trying to figure out the best way to 
>> run preprocessing on the three runs simultaneously using preproc-sess, but I 
>> don't know how to get FSFAST to use each run's specific b0dcmap in the 
>> preprocessing of each run's data.  FSFAST wants the b0dcmap files to be in 
>> the task folder, but how can it differentiate between the three b0dcmap 
>> files if they're not in the run folders?
>>
>> Thanks,
>> Conor
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: 
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

--
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/

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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.

Re: [Freesurfer] temporal lobe pial surface problem

[Bruce Fischl]

then you need to put some control points in the white matter. 70 is way 
too low

On Tue, 19 Apr 2016, Xiaomin Yue wrote:


The white matter in the anterior temporal lobe is around 70, the gray matter
is about 30.  The number is read from brain.finalsurfs.mgz.
Xiaomin

> Date: Tue, 19 Apr 2016 09:29:50 -0400
> From: fis...@nmr.mgh.harvard.edu
> To: freesurfer@nmr.mgh.harvard.edu
> CC: macar...@libero.it; yu...@hotmail.com
> Subject: Re: [Freesurfer] temporal lobe pial surface problem
>
> yes, you can do that for both mris_make_surfaces and mri_segment, but
> that will only help if you've removed the majority of the bias field. Is
> anterior temporal white matter near 110? If so, what is the gray matter
> at?
> On Tue, 19 Apr 2016, Falk Lüsebrink wrote:
>
> > Hi Xiaomin,
> > currently I don't have access to my notes, however, if I remember
correctly,
> > you can specify thresholds in mris_make_surfaces for consideration in
the
> > surface placement. This obviously works well only if the contrast
between
> > WM/GM/CSF is high enough.
> >
> > If you are interested and nobody jumps in giving you the according
flags,
> > let me know.
> >
> > Best,
> > Falk
> >
> >___
_
> > Von: freesurfer-boun...@nmr.mgh.harvard.edu
> > [freesurfer-boun...@nmr.mgh.harvard.edu]" im Auftrag von "Xiaomin Yue
> > [yu...@hotmail.com]
> > Gesendet: Dienstag, 19. April 2016 01:13
> > An: Freesurfer support list
> > Cc: macar...@libero.it
> > Betreff: Re: [Freesurfer] temporal lobe pial surface problem
> >
> > Hi Jon,
> > Thanks for your answers.   There is gray-white contrast in the temporal
> > lobe, but same as you said that the gray-csf is low.  Attached is a
> > screenshot.  let's me know if you need more information. 
> >
> > Xiaomin
> >
> > > Date: Mon, 18 Apr 2016 17:43:47 -0400
> > > From: j...@nmr.mgh.harvard.edu
> > > To: yu...@hotmail.com
> > > CC: freesurfer@nmr.mgh.harvard.edu; macar...@libero.it
> > > Subject: Re: [Freesurfer] temporal lobe pial surface problem
> > >
> > >
> > > hi Xiaomin,
> > >
> > > it is tough to say what might be causing the problem since a lot can
go
> > > wrong in the anterior temporal lobes at 7T. you say that your contrast
is
> > > low there? it is possible to have OK gray-white contrast but low
overall
> > > signal levels (so poor gray-CSF contrast) due to dielectric effects as
> > > bruce mentioned, which can make the MP2RAGE ratio images noisy in that
> > > region. also some adiabatic inversion pulses break down around the
> > > temporal poles due to the B0 inhomogeneity around the ear canals. if
you
> > > could send a screenshot we'd have a better chance at diagnosing the
> > > problem.
> > >
> > >
> > > -jon
> > >
> > >
> > >
> > >
> > > On Mon, 18 Apr 2016, Xiaomin Yue wrote:
> > >
> > > > Hi Jon Polimeni,
> > > > Do you have any suggestions on the following questions?
> > > > Thanks,Xiaomin
> > > >
> > > > Date: Fri, 15 Apr 2016 12:07:48 -0400
> > > > From: fis...@nmr.mgh.harvard.edu
> > > > To: freesurfer@nmr.mgh.harvard.edu
> > > > CC: macar...@libero.it; j...@nmr.mgh.harvard.edu
> > > > Subject: Re: [Freesurfer] temporal lobe pial surface problem
> > > >
> > > > Hi Xiaomin
> > > >
> > > > it's really hard to say without seeing more detail in your images.
Do
> > you
> > > > have contrast in the temporal lobe? Frequently it goes away at 7T
due to
> > > > dielectric effects. I'll cc Jon Polimeni who is our 7T (among other
> > > > things!) expert.
> > > >
> > > > cheers
> > > > Bruce
> > > >
> > > >
> > > > On Fri, 15 Apr 2016, Xiaomin Yue wrote:
> > > >
> > > > > Hi Bruce,
> > > > > I have done the recon-all (fs5.3) with the data collected from a
7T
> > scanner
> > > > > using MP2Rage. The recon went well without problem. But the the
> > temporal
> > > > > reconstruction looks clearly not correct (see attached). I tried
to
> > push
> > > > > the pial surface outside by editing the white matter evidenced in
the
> > > > > attached figures, but has no effect to genera correct pial
surface. I
> > do
> > > > > realize that the contrast is low in the anterior temporal lobes.
> > However, I
> > > > > am wondering if there are expert parameters I can use to push the
pial
> > > > > surface into the right place. If that isn't a option, can I use
some
> > other
> > > > > images collected during the MP2rage scan to help the segmentation
in
> > the
> > > > > anterior temporal lobe? Those extract scans are: inv1_nd,
inv1_phs_nd,
> > ,
> > > > > t1, inv2_nd, invs_phas_nd,
> > > > >
> > > > > thanks very much.
> > > > >
> > > > > Xiaomin
> > > > >
> > > > >
> > > >
> > > > ___
> > > > 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 

Re: [Freesurfer] temporal lobe pial surface problem

[Xiaomin Yue]

The white matter in the anterior temporal lobe is around 70, the gray matter is 
about 30.  The number is read from brain.finalsurfs.mgz.
Xiaomin

> Date: Tue, 19 Apr 2016 09:29:50 -0400
> From: fis...@nmr.mgh.harvard.edu
> To: freesurfer@nmr.mgh.harvard.edu
> CC: macar...@libero.it; yu...@hotmail.com
> Subject: Re: [Freesurfer] temporal lobe pial surface problem
> 
> yes, you can do that for both mris_make_surfaces and mri_segment, but 
> that will only help if you've removed the majority of the bias field. Is 
> anterior temporal white matter near 110? If so, what is the gray matter 
> at?
> On Tue, 19 Apr 2016, Falk Lüsebrink wrote:
> 
> > Hi Xiaomin,
> > currently I don't have access to my notes, however, if I remember correctly,
> > you can specify thresholds in mris_make_surfaces for consideration in the
> > surface placement. This obviously works well only if the contrast between
> > WM/GM/CSF is high enough.
> > 
> > If you are interested and nobody jumps in giving you the according flags,
> > let me know.
> > 
> > Best,
> > Falk
> > 
> > 
> > Von: freesurfer-boun...@nmr.mgh.harvard.edu
> > [freesurfer-boun...@nmr.mgh.harvard.edu]" im Auftrag von "Xiaomin Yue
> > [yu...@hotmail.com]
> > Gesendet: Dienstag, 19. April 2016 01:13
> > An: Freesurfer support list
> > Cc: macar...@libero.it
> > Betreff: Re: [Freesurfer] temporal lobe pial surface problem
> > 
> > Hi Jon,
> > Thanks for your answers.   There is gray-white contrast in the temporal
> > lobe, but same as you said that the gray-csf is low.  Attached is a
> > screenshot.  let's me know if you need more information. 
> > 
> > Xiaomin
> > 
> > > Date: Mon, 18 Apr 2016 17:43:47 -0400
> > > From: j...@nmr.mgh.harvard.edu
> > > To: yu...@hotmail.com
> > > CC: freesurfer@nmr.mgh.harvard.edu; macar...@libero.it
> > > Subject: Re: [Freesurfer] temporal lobe pial surface problem
> > >
> > >
> > > hi Xiaomin,
> > >
> > > it is tough to say what might be causing the problem since a lot can go
> > > wrong in the anterior temporal lobes at 7T. you say that your contrast is
> > > low there? it is possible to have OK gray-white contrast but low overall
> > > signal levels (so poor gray-CSF contrast) due to dielectric effects as
> > > bruce mentioned, which can make the MP2RAGE ratio images noisy in that
> > > region. also some adiabatic inversion pulses break down around the
> > > temporal poles due to the B0 inhomogeneity around the ear canals. if you
> > > could send a screenshot we'd have a better chance at diagnosing the
> > > problem.
> > >
> > >
> > > -jon
> > >
> > >
> > >
> > >
> > > On Mon, 18 Apr 2016, Xiaomin Yue wrote:
> > >
> > > > Hi Jon Polimeni,
> > > > Do you have any suggestions on the following questions?
> > > > Thanks,Xiaomin
> > > >
> > > > Date: Fri, 15 Apr 2016 12:07:48 -0400
> > > > From: fis...@nmr.mgh.harvard.edu
> > > > To: freesurfer@nmr.mgh.harvard.edu
> > > > CC: macar...@libero.it; j...@nmr.mgh.harvard.edu
> > > > Subject: Re: [Freesurfer] temporal lobe pial surface problem
> > > >
> > > > Hi Xiaomin
> > > >
> > > > it's really hard to say without seeing more detail in your images. Do
> > you
> > > > have contrast in the temporal lobe? Frequently it goes away at 7T due to
> > > > dielectric effects. I'll cc Jon Polimeni who is our 7T (among other
> > > > things!) expert.
> > > >
> > > > cheers
> > > > Bruce
> > > >
> > > >
> > > > On Fri, 15 Apr 2016, Xiaomin Yue wrote:
> > > >
> > > > > Hi Bruce,
> > > > > I have done the recon-all (fs5.3) with the data collected from a 7T
> > scanner
> > > > > using MP2Rage. The recon went well without problem. But the the
> > temporal
> > > > > reconstruction looks clearly not correct (see attached). I tried to
> > push
> > > > > the pial surface outside by editing the white matter evidenced in the
> > > > > attached figures, but has no effect to genera correct pial surface. I
> > do
> > > > > realize that the contrast is low in the anterior temporal lobes.
> > However, I
> > > > > am wondering if there are expert parameters I can use to push the pial
> > > > > surface into the right place. If that isn't a option, can I use some
> > other
> > > > > images collected during the MP2rage scan to help the segmentation in
> > the
> > > > > anterior temporal lobe? Those extract scans are: inv1_nd, inv1_phs_nd,
> > ,
> > > > > t1, inv2_nd, invs_phas_nd,
> > > > >
> > > > > thanks very much.
> > > > >
> > > > > Xiaomin
> > > > >
> > > > >
> > > >
> > > > ___
> > > > 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
> 

Re: [Freesurfer] temporal lobe pial surface problem

[Xiaomin Yue]

Hi Bruce,
the data was uploaded to the ftp site.  The file name is xyueSubj.mgz.
thanks,Xiaomin 

From: fis...@nmr.mgh.harvard.edu
Date: Mon, 18 Apr 2016 22:58:30 -0400
To: freesurfer@nmr.mgh.harvard.edu
CC: macar...@libero.it
Subject: Re: [Freesurfer] temporal lobe pial surface problem

It's tough to make out much from the snapshots, if you upload the entire 
subject dir to our ftp site I'll take a lookCheersBruce
On Apr 18, 2016, at 7:13 PM, Xiaomin Yue  wrote:




Hi Jon,
Thanks for your answers.   There is gray-white contrast in the temporal lobe, 
but same as you said that the gray-csf is low.  Attached is a screenshot.  
let's me know if you need more information. 
Xiaomin
> Date: Mon, 18 Apr 2016 17:43:47 -0400
> From: j...@nmr.mgh.harvard.edu
> To: yu...@hotmail.com
> CC: freesurfer@nmr.mgh.harvard.edu; macar...@libero.it
> Subject: Re: [Freesurfer] temporal lobe pial surface problem
> 
> 
> hi Xiaomin,
> 
> it is tough to say what might be causing the problem since a lot can go
> wrong in the anterior temporal lobes at 7T. you say that your contrast is
> low there? it is possible to have OK gray-white contrast but low overall
> signal levels (so poor gray-CSF contrast) due to dielectric effects as
> bruce mentioned, which can make the MP2RAGE ratio images noisy in that
> region. also some adiabatic inversion pulses break down around the
> temporal poles due to the B0 inhomogeneity around the ear canals. if you
> could send a screenshot we'd have a better chance at diagnosing the
> problem.
> 
> 
> -jon
> 
> 
> 
> 
> On Mon, 18 Apr 2016, Xiaomin Yue wrote:
> 
> > Hi Jon Polimeni,
> > Do you have any suggestions on the following questions?
> > Thanks,Xiaomin
> >
> > Date: Fri, 15 Apr 2016 12:07:48 -0400
> > From: fis...@nmr.mgh.harvard.edu
> > To: freesurfer@nmr.mgh.harvard.edu
> > CC: macar...@libero.it; j...@nmr.mgh.harvard.edu
> > Subject: Re: [Freesurfer] temporal lobe pial surface problem
> >
> > Hi Xiaomin
> >
> > it's really hard to say without seeing more detail in your images. Do you
> > have contrast in the temporal lobe? Frequently it goes away at 7T due to
> > dielectric effects. I'll cc Jon Polimeni who is our 7T (among other
> > things!) expert.
> >
> > cheers
> > Bruce
> >
> >
> >   On Fri, 15 Apr 2016, Xiaomin Yue wrote:
> >
> > > Hi Bruce,
> > > I have done the recon-all (fs5.3) with the data collected from a 7T 
> > > scanner
> > > using MP2Rage.  The recon went well without problem.  But the the temporal
> > > reconstruction looks clearly not correct (see attached).  I tried to push
> > > the pial surface outside by editing the white matter evidenced in the
> > > attached figures, but has no effect to genera correct pial surface.  I do
> > > realize that the contrast is low in the anterior temporal lobes.  
> > > However, I
> > > am wondering if there are expert parameters I can use to push the pial
> > > surface into the right place.  If that isn't a option, can I use some 
> > > other
> > > images collected during the MP2rage scan to help the segmentation in the
> > > anterior temporal lobe?  Those extract scans are: inv1_nd, inv1_phs_nd, ,
> > > t1, inv2_nd, invs_phas_nd,
> > >
> > > thanks very much.
> > >
> > > Xiaomin
> > >
> > >
> >
> > ___
> > 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.
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
  
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] how to add skull and scalp and how to convert RAS coordinates

[Chiara Bulgarelli]

Dear FreeSurfer users, 
I am a PhD student from Birkbeck University and I am trying to segment some 
structural images of infants data.

After the classical segmentation done with the ‘-recon all’ function, I am 
stuck with two issues:
1. How can I add the CSF, the skull and the scalp in my model? I know that with 
FS you can get just WM and GM.
2. How can I convert the RAS coordinates to MNI ones?

I have been trying to look at these topics on line and on the FreeSurfer 
website, but I haven’t find anything useful so far.

Many thanks in advance for your help!

Best Regards
Chiara


Chiara Bulgarelli
PhD Student, Centre for Brain and Cognitive Development
Birkbeck College, University of London

cbulg...@mail.bbk.ac.uk // bulgarelli.chia...@gmail.com






___
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.

Re: [Freesurfer] Fwd: Exporting TIFF and rotating volume with tkmedit in Ubuntu 14.04

[Bruce Fischl]

Hi Nasos

tkmedit has been deprecated for a few years. Can you try freeview?

cheers
Bruce
On Tue, 
19 Apr 2016, Nasos Petridis wrote:

> Hello,
>
> Recently, I started using freesurfer on a Ubuntu system. I've noticed
> two issues, when using tkmedit, for example:
>
> tkmedit subj_name  norm.mgz  -segmentation aparc.a2009s+aseg.mgz
>
> (i) When I try to save TIFF (Tools > Save TIFF), a TIFF file is
> created, and it can be opened in any image viewing program but is
> black. It's worth noting that when I try to save a cortical thickness
> surface view as tiff, using tksurfer tools, it works fine.
>
> (ii) When I try to rotate the volume (Tools > Volume > Rotate Volume),
> I cannot enter an angle in the "Degrees" dialogue box, ie I type the
> number but no number appears neither doe the cursor move.
>
> I've tried both freesurfer 5.3 Linux distributions  (centos4, centos6)
> with no difference. I'm running Ubuntu 14.04LTS.
>
> Do I need to install any packages in Ubuntu? Any suggestion how to
> tackle those two issues would be greatly appreciated.
>
> Many thanks,
>
> Nasos
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Export Freesurfer labels to SPM ROIs

[Mohamed Abdelhack]

Hello FS community,

I have made some custom labels based on retinotopy data and I wish to
export these as SPM ROIs so that I can use some specific tools.
I grouped the labels into an annotation file and I used mri_label2vol to
convert it into nifti, I then imported it into matlab and I get a volume
with each pixels corresponding to a number.

How can I confirm if the coordinates that I have used to export these
labels are aligned well with the data in SPM coordinate system?

Thank you,
Mohamed,
___
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.

Re: [Freesurfer] temporal lobe pial surface problem

[Falk Lüsebrink]

Hi Xiaomin,

currently I don't have access to my notes, however, if I remember correctly, 
you can specify thresholds in mris_make_surfaces for consideration in the 
surface placement. This obviously works well only if the contrast between 
WM/GM/CSF is high enough.

If you are interested and nobody jumps in giving you the according flags, let 
me know.

Best,
Falk


Von: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu]" im Auftrag von "Xiaomin Yue 
[yu...@hotmail.com]
Gesendet: Dienstag, 19. April 2016 01:13
An: Freesurfer support list
Cc: macar...@libero.it
Betreff: Re: [Freesurfer] temporal lobe pial surface problem

Hi Jon,

Thanks for your answers.   There is gray-white contrast in the temporal lobe, 
but same as you said that the gray-csf is low.  Attached is a screenshot.  
let's me know if you need more information.

Xiaomin

> Date: Mon, 18 Apr 2016 17:43:47 -0400
> From: j...@nmr.mgh.harvard.edu
> To: yu...@hotmail.com
> CC: freesurfer@nmr.mgh.harvard.edu; macar...@libero.it
> Subject: Re: [Freesurfer] temporal lobe pial surface problem
>
>
> hi Xiaomin,
>
> it is tough to say what might be causing the problem since a lot can go
> wrong in the anterior temporal lobes at 7T. you say that your contrast is
> low there? it is possible to have OK gray-white contrast but low overall
> signal levels (so poor gray-CSF contrast) due to dielectric effects as
> bruce mentioned, which can make the MP2RAGE ratio images noisy in that
> region. also some adiabatic inversion pulses break down around the
> temporal poles due to the B0 inhomogeneity around the ear canals. if you
> could send a screenshot we'd have a better chance at diagnosing the
> problem.
>
>
> -jon
>
>
>
>
> On Mon, 18 Apr 2016, Xiaomin Yue wrote:
>
> > Hi Jon Polimeni,
> > Do you have any suggestions on the following questions?
> > Thanks,Xiaomin
> >
> > Date: Fri, 15 Apr 2016 12:07:48 -0400
> > From: fis...@nmr.mgh.harvard.edu
> > To: freesurfer@nmr.mgh.harvard.edu
> > CC: macar...@libero.it; j...@nmr.mgh.harvard.edu
> > Subject: Re: [Freesurfer] temporal lobe pial surface problem
> >
> > Hi Xiaomin
> >
> > it's really hard to say without seeing more detail in your images. Do you
> > have contrast in the temporal lobe? Frequently it goes away at 7T due to
> > dielectric effects. I'll cc Jon Polimeni who is our 7T (among other
> > things!) expert.
> >
> > cheers
> > Bruce
> >
> >
> > On Fri, 15 Apr 2016, Xiaomin Yue wrote:
> >
> > > Hi Bruce,
> > > I have done the recon-all (fs5.3) with the data collected from a 7T 
> > > scanner
> > > using MP2Rage. The recon went well without problem. But the the temporal
> > > reconstruction looks clearly not correct (see attached). I tried to push
> > > the pial surface outside by editing the white matter evidenced in the
> > > attached figures, but has no effect to genera correct pial surface. I do
> > > realize that the contrast is low in the anterior temporal lobes. However, 
> > > I
> > > am wondering if there are expert parameters I can use to push the pial
> > > surface into the right place. If that isn't a option, can I use some other
> > > images collected during the MP2rage scan to help the segmentation in the
> > > anterior temporal lobe? Those extract scans are: inv1_nd, inv1_phs_nd, ,
> > > t1, inv2_nd, invs_phas_nd,
> > >
> > > thanks very much.
> > >
> > > Xiaomin
> > >
> > >
> >
> > ___
> > 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.
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Fwd: Exporting TIFF and rotating volume with tkmedit in Ubuntu 14.04

[Nasos Petridis]

Hello,

Recently, I started using freesurfer on a Ubuntu system. I've noticed
two issues, when using tkmedit, for example:

tkmedit subj_name  norm.mgz  -segmentation aparc.a2009s+aseg.mgz

(i) When I try to save TIFF (Tools > Save TIFF), a TIFF file is
created, and it can be opened in any image viewing program but is
black. It's worth noting that when I try to save a cortical thickness
surface view as tiff, using tksurfer tools, it works fine.

(ii) When I try to rotate the volume (Tools > Volume > Rotate Volume),
I cannot enter an angle in the "Degrees" dialogue box, ie I type the
number but no number appears neither doe the cursor move.

I've tried both freesurfer 5.3 Linux distributions  (centos4, centos6)
with no difference. I'm running Ubuntu 14.04LTS.

Do I need to install any packages in Ubuntu? Any suggestion how to
tackle those two issues would be greatly appreciated.

Many thanks,

Nasos
___
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.