Trisanna, has this issue been resolved?
doug
On 06/30/2016 01:26 PM, Trisanna Sprung-Much wrote:
> Hi Bruce
>
> <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote:> here is the output of my mri_vol2surf for a volumetric spam created in
> minc tools. When I then overlay this result in Freeview, it displays a
> Min of 127 and a Max of 255.
>
> trisanna@kaplan:~$ mri_vol2surf --mov
> /data-01/trisanna/freesurfer/MNI_average_2009a_asymm/spam_for_label_id_4_blur_minc1.mnc
> --o
> /data-01/trisanna/freesurfer/MNI_average_2009a_asymm/spam_for_label_id_4_blur_overlay.mgz
> --hemi lh --surf pial --regheader MNI_average_2009a_asymm
> srcvol =
> /data-01/trisanna/freesurfer/MNI_average_2009a_asymm/spam_for_label_id_4_blur_minc1.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/MNI_average_2009a_asymm/mri/orig.mgz as
> target reference.
> Reading surface
> /data-01/trisanna/freesurfer/MNI_average_2009a_asymm/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 = 95521
> Writing to
> /data-01/trisanna/freesurfer/MNI_average_2009a_asymm/spam_for_label_id_4_blur_overlay.mgz
> Dim: 152257 1 1
>
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Wed, Jun 29, 2016 at 8:10 PM, Bruce Fischl
>
> Can you send the full output of that command?
>
> On Jun 29, 2016, at 2:54 PM, Trisanna Sprung-Much
> <trisanna.sprung-much@mail.mcgill.ca
> <mailto:trisanna.sprung-much@mail.mcgill.ca>> wrote:
>
>> Hi Bruce
>>
>> I simply use
>>
>> mri_vol2surf --mov spam.mnc --output overlayspam.mgz --regheader
>> subject --hemi lh --surf pial
>>
>> Trisanna
>>
>> --
>> Ph.D. Candidate
>> McGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Wed, Jun 29, 2016 at 1:23 PM, Bruce Fischl
>> <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>
>> wrote:
>>
>> how do you create the overlay?
>> On Wed, 29 Jun 2016, Trisanna Sprung-Much wrote:
>>
>> Hi Bruce
>>
>> To create the spam I used minctools:
>>
>> mincaverage input.mnc output.mnc
>>
>> I blurred the spam using
>>
>> mincblur input.mnc output.mnc -fwhm 3
>>
>> When I open the spams using minc software, the % shown is
>> from about 10-40%
>> (i.e. the max overlap). For some reason when I create an
>> overlay from this
>> it displays the % from 1-255.
>>
>> Trisanna
>>
>> --
>> Ph.D. CandidateMcGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Wed, Jun 29, 2016 at 12:20 PM, Bruce Fischl
>> <fischl@nmr.mgh.harvard.edu
>> <mailto:fischl@nmr.mgh.harvard.edu>>
>> <mailto:fischl@nmr.mgh.harvard.edu>>>> wrote:
>> Hi Trisanna
>>
>> what commands did you use to generate the
>> volumetric probability
>> map?
>>
>> Bruce
>>
>>
>>
>> On Wed, 29 Jun 2016, Trisanna Sprung-Much wrote:
>>
>> Hi Bruce
>> So, when I take a probability map formed using
>> linear volumetric
>> registration with minc tools and saved as
>> .mnc and
>> convert it to an
>> overlay.mgz and open it in Freeview, the
>> probability
>> seems to be out of 255
>> (See the image attached). This is different
>> from my
>> Freesurfer generated
>> probability maps where I use -p in the
>> mri_average
>> command.
>>
>> Is there a way to change these probability values
>> that are displaying from
>> 1-255?
>>
>> many thanks
>>
>> Trisanna
>>
>> --
>> Ph.D. CandidateMcGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Mon, Jun 27, 2016 at 10:28 AM, Bruce Fischl
>> <fischl@nmr.mgh.harvard.edu
>> <mailto:trisanna.sprung-much@mail.mcgill.ca>>>> wrote:
>> Hi Trisanna
>>
>> we need more information if you want us to
>> help you. What does
>> "very odd mean"? If you do it in .mgz
>> do you
>> get a different
>> answer than in .mnc? If so, why not just
>> compute them in .mgz
>> and convert to .mnc at the end?
>>
>> cheers
>> Bruce
>>
>>
>> On Mon, 27 Jun 2016, Trisanna Sprung-Much
>> wrote:
>>
>> any ideas?
>> Thanks!
>>
>> Trisanna
>>
>> --
>> Ph.D. CandidateMcGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Wed, Jun 22, 2016 at 10:22 PM,
>> Trisanna
>> Sprung-Much
>>
>> <trisanna.sprung-much@mail.mcgill.ca
>> wrote:
>> thanks Bruce - I had found that
>> option for my
>> fsaverage maps and
>> it worked.
>> What about if I am importing
>> probability
>> maps formed
>> as .mnc and
>> creating overlays from them? The
>> percentages seem to
>> be very odd for
>> min and max threshold.
>>
>> Trisanna
>>
>> --
>> Ph.D. CandidateMcGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Wed, Jun 22, 2016 at 9:32 PM,
>> Bruce
>> Fischl
>> <fischl@nmr.mgh.harvard.edu
>> <mailto:fischl@nmr.mgh.harvard.edu>>>> <mailto:fischl@nmr.mgh.harvard.edu>> wrote:
>> Hi Trisanna
>>
>> if you are using
>> mri_average you
>> can give it
>> -p as the
>> first argument and it will
>> compute
>> a percent
>> at the end
>> Bruce
>> On Wed, 22 Jun 2016, Trisanna
>> Sprung-Much
>> wrote:
>>
>> Hi Bruce
>>
>> Is there is a way to set the
>> probability of an
>> overlay between 0 and 1?
>> Would this have to be done when
>> creating the
>> overlay
>> using mri_vol2surf?
>>
>> thanks
>>
>> Trisanna
>>
>> --
>> Ph.D. CandidateMcGill
>> University
>> Integrated Program in
>> Neuroscience
>> Psychology
>>
>>
>> On Mon, Jun 20, 2016 at
>> 12:11 PM,
>> Bruce Fischl
>> <fischl@nmr.mgh.harvard.edu
>> <mailto:fischl@nmr.mgh.harvard.edu>>>> wrote:
>> Hi Trisanna
>>
>> the binaries that take
>> mandatory
>> command-line
>> arguments (i.e.
>> without a -- or - in
>> front
>> of them)
>> require
>> all options to be
>> given before the
>> mandatory
>> arguments
>>
>> cheers
>> Bruce
>>
>> On Mon, 20 Jun 2016,
>> Trisanna
>> Sprung-Much
>> wrote:
>>
>> thanks, Bruce. Yes in
>> the end
>> through
>> trial and
>> error I tried
>> "mri_average
>> -noconform
>> input output"
>> and it worked.
>> I was
>> surprised that I had
>> to put the
>> -noconform first as
>> normally one can put
>> the argument
>> anywhere in the
>> command.
>>
>> Best
>>
>> Trisanna
>>
>> --
>> Ph.D. CandidateMcGill
>> University
>> Integrated Program in
>> Neuroscience
>> Psychology
>>
>>
>> On Mon, Jun 20,
>> 2016
>> at 9:27 AM,
>> Bruce
>> Fischl
>>
>> <fischl@nmr.mgh.harvard.edu
>> <mailto:trisanna.sprung-much@mail.mcgill.ca>>>> wrote:
>> yes, your last
>> file on the
>> command
>> line should
>> be the output file
>> (the average)
>>
>> cheers
>> Bruce
>>
>> On Mon, 20 Jun
>> 2016,
>> Trisanna
>> Sprung-Much
>> wrote:
>>
>> As a follow-up,
>> here is the
>> mri_info for one
>> of my overlays
>> in the
>> folder
>> and the output
>> file that
>> mri_average seems to
>> create (if I don't
>> specify an
>> output and it
>> re-writes my
>> last
>> file). The
>> dimensions are off:
>> Any ideas?
>>
>> Trisanna
>>
>>
>> Tgtrisanna@kaplan:/data-01/trisanna/freesurfer/fsaverage/DISPLAY_overlay
>> s
>> _
>> f
>> sa
>>
>> vee_left/aalf_lh$ mri_info
>>
>>
>> fsaverage_overlay_aalf_icbm-102_left.mgz
>> Volume
>> information for
>>
>> fsaverage_overlay_aalf_icbm-102_left.mgz
>> type:
>> MGH
>> dimensions:
>> 163842 x 1 x
>> 1
>> voxel sizes:
>> 1.0000,
>> 1.0000,
>> 1.0000
>> type:
>> FLOAT (3)
>> fov:
>> 163842.000
>> dof:
>> 0
>> xstart:
>> -81921.0,
>> xend:
>> 81921.0
>> ystart:
>> -0.5, yend:
>> 0.5
>> zstart:
>> -0.5, zend:
>> 0.5
>> TR:
>> 0.00 msec,
>> TE:
>> 0.00 msec, TI:
>> 0.00 msec, flip
>> angle:
>> 0.00
>> degrees
>> nframes:
>> 1
>> PhEncDir:
>> UNKNOWN
>> ras xform
>> present
>> xform info:
>> x_r =
>> 1.0000,
>> y_r =
>> 0.0000, z_r =
>> 0.0000, c_r =
>> 0.5000
>> :
>> x_a =
>> 0.0000,
>> y_a =
>> 1.0000, z_a =
>> 0.0000, c_a =
>> -17.5000
>> :
>> x_s =
>> 0.0000,
>> y_s =
>> 0.0000, z_s =
>> 1.0000, c_s =
>> 18.5000
>>
>> talairach xfm :
>> Orientation :
>> RAS
>> Primary Slice
>> Direction:
>> axial
>>
>> voxel to ras
>> transform:
>>
>> 1.0000
>> 0.0000
>> 0.0000
>> -81920.5000
>>
>> 0.0000
>> 1.0000
>> 0.0000
>> -18.0000
>>
>> 0.0000
>> 0.0000
>> 1.0000
>> 18.0000
>>
>> 0.0000
>> 0.0000
>> 0.0000
>> 1.0000
>>
>> voxel-to-ras
>> determinant 1
>>
>> ras to voxel
>> transform:
>>
>> 1.0000
>> -0.0000
>> -0.0000
>> 81920.5000
>>
>> -0.0000
>> 1.0000
>> -0.0000
>> 18.0000
>>
>> -0.0000
>> -0.0000
>> 1.0000
>> -18.0000
>>
>> 0.0000
>> 0.0000
>> 0.0000
>> 1.0000
>>
>>
>> trisanna@kaplan:/data-01/trisanna/freesurfer/fsaverage/DISPLAY_overlays_
>> f
>> s
>> a
>>
>>
>> verage_left/aalf_lh$
>> mri_info
>>
>>
>> fsaverage_overlay_aalf_icbm-350_left.mgz
>> Volume
>> information for
>>
>> fsaverage_overlay_aalf_icbm-350_left.mgz
>> type:
>> MGH
>> dimensions:
>> 256 x 256 x
>> 256
>> voxel sizes:
>> 1.0000,
>> 1.0000,
>> 1.0000
>> type:
>> FLOAT (3)
>> fov:
>> 256.000
>> dof:
>> 0
>> xstart:
>> -128.0,
>> xend:
>> 128.0
>> ystart:
>> -128.0,
>> yend:
>> 128.0
>> zstart:
>> -128.0,
>> zend:
>> 128.0
>> TR:
>> 0.00 msec,
>> TE:
>> 0.00 msec, TI:
>> 0.00 msec, flip
>> angle:
>> 0.00
>> degrees
>> nframes:
>> 1
>> PhEncDir:
>> UNKNOWN
>> ras xform
>> present
>> xform info:
>> x_r =
>> -1.0000,
>> y_r =
>> 0.0000, z_r =
>> 0.0000, c_r =
>> 0.5000
>> :
>> x_a =
>> 0.0000,
>> y_a =
>> 0.0000, z_a =
>> 1.0000, c_a =
>> -17.5000
>> :
>> x_s =
>> 0.0000,
>> y_s =
>> -1.0000, z_s =
>> 0.0000, c_s =
>> 18.5000
>>
>> talairach xfm :
>> Orientation :
>> LIA
>> Primary Slice
>> Direction:
>> coronal
>>
>> --
>> Ph.D. CandidateMcGill
>> University
>> Integrated Program in
>> Neuroscience
>> Psychology
>>
>>
>> On Mon, Jun 20,
>> 2016
>> at 12:32 AM,
>> Trisanna
>> Sprung-Much
>>
>>
>> <trisanna.sprung-much@mail.mcgill.ca
>> <mailto:Freesurfer@nmr.mgh.harvard.edu>>> wrote:
>> Hi Dr. Fischl
>> I ran the following
>> mri_average
>> and
>> consistently get
>> this message. It
>> seems to be trying to
>> read my
>> output as
>> one of the
>> input volumes. If I
>> don't specify an
>> output it
>> re-writes my
>> last file in
>> the input folder
>> and when I try
>> to open
>> this it
>> doesn't
>> work at all.
>>
>> What exactly does
>> MRIchangeType
>> mean?
>>
>>
>>
>> (navigated to folder
>> with all .mgz
>> volumes want to
>> average)
>> mri_average *.mgz
>> test.mgz
>> --noconform
>>
>> 1 of 51: reading
>>
>>
>> fsaverage_overlay_aalf_icbm-102_left.mgz...
>> embedding and
>> interpolating volume
>> MRIchangeType:
>> Building histogram
>> 2 of 51: reading
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>>
>> fsaverage_overlay_aalf_icbm-103_left.mgz...
>> embedding and
>> interpolating volume
>> MRIchangeType:
>> Building histogram
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>> fsaverage_overlay_aalf_icbm-104_left.mgz...
>> embedding and
>> interpolating volume
>> MRIchangeType:
>> Building histogram
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>> fsaverage_overlay_aalf_icbm-105_left.mgz...
>> embedding and
>> interpolating volume
>> MRIchangeType:
>> Building histogram
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>> fsaverage_overlay_aalf_icbm-106_left.mgz...
>> embedding and
>> interpolating volume
>> MRIchangeType:
>> Building histogram
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>> fsaverage_overlay_aalf_icbm-107_left.mgz...
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>> interpolating volume
>> MRIchangeType:
>> Building histogram
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>> embedding and
>> interpolating volume
>> MRIchangeType:
>> Building histogram
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>> embedding and
>> interpolating volume
>> MRIchangeType:
>> Building histogram
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>> fsaverage_overlay_aalf_icbm-110_left.mgz...
>> embedding and
>> interpolating volume
>> MRIchangeType:
>> Building histogram
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>> fsaverage_overlay_aalf_icbm-111_left.mgz...
>> embedding and
>> interpolating volume
>> MRIchangeType:
>> Building histogram
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>> fsaverage_overlay_aalf_icbm-112_left.mgz...
>> embedding and
>> interpolating volume
>> MRIchangeType:
>> Building histogram
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>> fsaverage_overlay_aalf_icbm-113_left.mgz...
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>> interpolating volume
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>> Building histogram
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>> fsaverage_overlay_aalf_icbm-114_left.mgz...
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>> interpolating volume
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>> Building histogram
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>> fsaverage_overlay_aalf_icbm-115_left.mgz...
>> embedding and
>> interpolating volume
>> MRIchangeType:
>> Building histogram
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>> fsaverage_overlay_aalf_icbm-116_left.mgz...
>> embedding and
>> interpolating volume
>> MRIchangeType:
>> Building histogram
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>> fsaverage_overlay_aalf_icbm-117_left.mgz...
>> embedding and
>> interpolating volume
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>> Building histogram
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>> fsaverage_overlay_aalf_icbm-118_left.mgz...
>> embedding and
>> interpolating volume
>> MRIchangeType:
>> Building histogram
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>> fsaverage_overlay_aalf_icbm-119_left.mgz...
>> embedding and
>> interpolating volume
>> MRIchangeType:
>> Building histogram
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>> fsaverage_overlay_aalf_icbm-120_left.mgz...
>> embedding and
>> interpolating volume
>> MRIchangeType:
>> Building histogram
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>> fsaverage_overlay_aalf_icbm-121_left.mgz...
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>> interpolating volume
>> MRIchangeType:
>> Building histogram
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>> fsaverage_overlay_aalf_icbm-122_left.mgz...
>> embedding and
>> interpolating volume
>> MRIchangeType:
>> Building histogram
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>> fsaverage_overlay_aalf_icbm-123_left.mgz...
>> embedding and
>> interpolating volume
>> MRIchangeType:
>> Building histogram
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>> fsaverage_overlay_aalf_icbm-124_left.mgz...
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>> interpolating volume
>> MRIchangeType:
>> Building histogram
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>> fsaverage_overlay_aalf_icbm-125_left.mgz...
>> embedding and
>> interpolating volume
>> MRIchangeType:
>> Building histogram
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>> fsaverage_overlay_aalf_icbm-126_left.mgz...
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>> interpolating volume
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>> Building histogram
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>> fsaverage_overlay_aalf_icbm-127_left.mgz...
>> embedding and
>> interpolating volume
>> MRIchangeType:
>> Building histogram
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>> fsaverage_overlay_aalf_icbm-131_left.mgz...
>> embedding and
>> interpolating volume
>> MRIchangeType:
>> Building histogram
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>>
>> fsaverage_overlay_aalf_icbm-133_left.mgz...
>> embedding and
>> interpolating volume
>> MRIchangeType:
>> Building histogram
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>> fsaverage_overlay_aalf_icbm-134_left.mgz...
>> embedding and
>> interpolating volume
>> MRIchangeType:
>> Building histogram
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>> fsaverage_overlay_aalf_icbm-135_left.mgz...
>> embedding and
>> interpolating volume
>> MRIchangeType:
>> Building histogram
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>> fsaverage_overlay_aalf_icbm-137_left.mgz...
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>> interpolating volume
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>> interpolating volume
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>> Building histogram
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>> interpolating volume
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>> Building histogram
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>> fsaverage_overlay_aalf_icbm-142_left.mgz...
>> embedding and
>> interpolating volume
>> MRIchangeType:
>> Building histogram
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>> fsaverage_overlay_aalf_icbm-143_left.mgz...
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>> interpolating volume
>> MRIchangeType:
>> Building histogram
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>> fsaverage_overlay_aalf_icbm-144_left.mgz...
>> embedding and
>> interpolating volume
>> MRIchangeType:
>> Building histogram
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>>
>> fsaverage_overlay_aalf_icbm-145_left.mgz...
>> embedding and
>> interpolating volume
>> MRIchangeType:
>> Building histogram
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>> fsaverage_overlay_aalf_icbm-146_left.mgz...
>> embedding and
>> interpolating volume
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>> Building histogram
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>> fsaverage_overlay_aalf_icbm-150_left.mgz...
>> embedding and
>> interpolating volume
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>> Building histogram
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>> fsaverage_overlay_aalf_icbm-158_left.mgz...
>> embedding and
>> interpolating volume
>> MRIchangeType:
>> Building histogram
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>>
>> fsaverage_overlay_aalf_icbm-200_left.mgz...
>> embedding and
>> interpolating volume
>> MRIchangeType:
>> Building histogram
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>>
>> fsaverage_overlay_aalf_icbm-201_left.mgz...
>> embedding and
>> interpolating volume
>> MRIchangeType:
>> Building histogram
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>>
>> fsaverage_overlay_aalf_icbm-203_left.mgz...
>> embedding and
>> interpolating volume
>> MRIchangeType:
>> Building histogram
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>> fsaverage_overlay_aalf_icbm-204_left.mgz...
>> embedding and
>> interpolating volume
>> MRIchangeType:
>> Building histogram
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>>
>> fsaverage_overlay_aalf_icbm-205_left.mgz...
>> embedding and
>> interpolating volume
>> MRIchangeType:
>> Building histogram
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>>
>> fsaverage_overlay_aalf_icbm-209_left.mgz...
>> embedding and
>> interpolating volume
>> MRIchangeType:
>> Building histogram
>> 48 of 51: reading
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>>
>> fsaverage_overlay_aalf_icbm-340_left.mgz...
>> embedding and
>> interpolating volume
>> MRIchangeType:
>> Building histogram
>> 49 of 51: reading
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>>
>> fsaverage_overlay_aalf_icbm-347_left.mgz...
>> embedding and
>> interpolating volume
>> MRIchangeType:
>> Building histogram
>> 50 of 51: reading
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>> fsaverage_overlay_aalf_icbm-350_left.mgz...
>> embedding and
>> interpolating volume
>> MRIchangeType:
>> Building histogram
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>> test.mgz...
>> mghRead(/data-01/trisanna/freesurfer/fsaverage/DISPLAY_overlays_fsaverage_l
>>
>>
>>
>>
>> eft/aalf_lh/test.mgz,
>> -1): could
>> not
>>
>>
>> _______________________________________________
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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