Re: [Freesurfer] mergecontrasts-sess group map

2012-11-29 Thread Douglas N Greve

You'll have to run mri_vol2surf on each one separately to bring it into 
the fsaverage space, then mri_concat to stack all of the maps into one 
file. At that point you can compute a mean (also with mri_concat). 
Generally, one does not do group analysis on sig maps though.
doug


On 11/27/2012 05:08 PM, Alexandra Tanner wrote:
> Hi Doug and Freesurfers,
>
> I recently used mergecontrasts-sess to merge two contrasts of an analysis
> in 50 different subjects. The command ran on each subject individually and
> created a sig.nii and sig.ovpl file within a merged contrast folder for
> each subject. I'd now like to look at an average map of the merged
> contrasts across all 50 subjects.
> Does anyone know how to go about getting this average map for my group of
> 50 subjects?
>
> Command I ran to get the sig.nii/sig.ovpl file for each subject:
> mergecontrasts-sess -mergedcontrast Merge_7vFix_1vFix -conjunction andor
> -analysis SIRP_Stable5 -contrast Cond7vFix 3 pos 0 -contrast Cond1vFix 3
> pos 0 -map sig -sf
> /cluster/roffman/users/Stable5_PerRun/Subject_Files/50_MTH_Subjects -df
> /cluster/roffman/users/Stable5_PerRun
>
> Any help would be greatly appreciated!
>
> Thanks,
> Alex
>
>

-- 
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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] mergecontrasts-sess group map

2012-11-29 Thread Alexandra Tanner

Hi Doug,

Thanks for the response! Just out of curiosity, what map is typically used
for group analyses? Should I have used a map other than sig on the
individual subject level as well?

Thanks!
Alex


>
> You'll have to run mri_vol2surf on each one separately to bring it into
> the fsaverage space, then mri_concat to stack all of the maps into one
> file. At that point you can compute a mean (also with mri_concat).
> Generally, one does not do group analysis on sig maps though.
> doug
>
>
> On 11/27/2012 05:08 PM, Alexandra Tanner wrote:
>> Hi Doug and Freesurfers,
>>
>> I recently used mergecontrasts-sess to merge two contrasts of an
>> analysis
>> in 50 different subjects. The command ran on each subject individually
>> and
>> created a sig.nii and sig.ovpl file within a merged contrast folder for
>> each subject. I'd now like to look at an average map of the merged
>> contrasts across all 50 subjects.
>> Does anyone know how to go about getting this average map for my group
>> of
>> 50 subjects?
>>
>> Command I ran to get the sig.nii/sig.ovpl file for each subject:
>> mergecontrasts-sess -mergedcontrast Merge_7vFix_1vFix -conjunction andor
>> -analysis SIRP_Stable5 -contrast Cond7vFix 3 pos 0 -contrast Cond1vFix 3
>> pos 0 -map sig -sf
>> /cluster/roffman/users/Stable5_PerRun/Subject_Files/50_MTH_Subjects -df
>> /cluster/roffman/users/Stable5_PerRun
>>
>> Any help would be greatly appreciated!
>>
>> Thanks,
>> Alex
>>
>>
>
> --
> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
>
>

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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] mergecontrasts-sess group map

2012-11-29 Thread Douglas N Greve
Usually the contrast effects size (ces) (in SPM this is the CON image, 
in FSL it is the COPE image). Univariate maps are usually passed up to 
the group level (the conjunction done with mergecontrasts is multivariate).
doug


On 11/29/2012 01:05 PM, Alexandra Tanner wrote:
> Hi Doug,
>
> Thanks for the response! Just out of curiosity, what map is typically used
> for group analyses? Should I have used a map other than sig on the
> individual subject level as well?
>
> Thanks!
> Alex
>
>
>> You'll have to run mri_vol2surf on each one separately to bring it into
>> the fsaverage space, then mri_concat to stack all of the maps into one
>> file. At that point you can compute a mean (also with mri_concat).
>> Generally, one does not do group analysis on sig maps though.
>> doug
>>
>>
>> On 11/27/2012 05:08 PM, Alexandra Tanner wrote:
>>> Hi Doug and Freesurfers,
>>>
>>> I recently used mergecontrasts-sess to merge two contrasts of an
>>> analysis
>>> in 50 different subjects. The command ran on each subject individually
>>> and
>>> created a sig.nii and sig.ovpl file within a merged contrast folder for
>>> each subject. I'd now like to look at an average map of the merged
>>> contrasts across all 50 subjects.
>>> Does anyone know how to go about getting this average map for my group
>>> of
>>> 50 subjects?
>>>
>>> Command I ran to get the sig.nii/sig.ovpl file for each subject:
>>> mergecontrasts-sess -mergedcontrast Merge_7vFix_1vFix -conjunction andor
>>> -analysis SIRP_Stable5 -contrast Cond7vFix 3 pos 0 -contrast Cond1vFix 3
>>> pos 0 -map sig -sf
>>> /cluster/roffman/users/Stable5_PerRun/Subject_Files/50_MTH_Subjects -df
>>> /cluster/roffman/users/Stable5_PerRun
>>>
>>> Any help would be greatly appreciated!
>>>
>>> Thanks,
>>> Alex
>>>
>>>
>> --
>> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>>
>>
>

-- 
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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] mergecontrasts-sess group map

2012-11-29 Thread Alexandra Tanner
Thanks for the clarification! So I will rerun mergecontrasts-sess using
the ces image on my subjects and then run mri_vol2surf and mri_concat to
get the group map. Thanks for your help!

Best,
Alex

> Usually the contrast effects size (ces) (in SPM this is the CON image,
> in FSL it is the COPE image). Univariate maps are usually passed up to
> the group level (the conjunction done with mergecontrasts is
> multivariate).
> doug
>
>
> On 11/29/2012 01:05 PM, Alexandra Tanner wrote:
>> Hi Doug,
>>
>> Thanks for the response! Just out of curiosity, what map is typically
>> used
>> for group analyses? Should I have used a map other than sig on the
>> individual subject level as well?
>>
>> Thanks!
>> Alex
>>
>>
>>> You'll have to run mri_vol2surf on each one separately to bring it into
>>> the fsaverage space, then mri_concat to stack all of the maps into one
>>> file. At that point you can compute a mean (also with mri_concat).
>>> Generally, one does not do group analysis on sig maps though.
>>> doug
>>>
>>>
>>> On 11/27/2012 05:08 PM, Alexandra Tanner wrote:
 Hi Doug and Freesurfers,

 I recently used mergecontrasts-sess to merge two contrasts of an
 analysis
 in 50 different subjects. The command ran on each subject individually
 and
 created a sig.nii and sig.ovpl file within a merged contrast folder
 for
 each subject. I'd now like to look at an average map of the merged
 contrasts across all 50 subjects.
 Does anyone know how to go about getting this average map for my group
 of
 50 subjects?

 Command I ran to get the sig.nii/sig.ovpl file for each subject:
 mergecontrasts-sess -mergedcontrast Merge_7vFix_1vFix -conjunction
 andor
 -analysis SIRP_Stable5 -contrast Cond7vFix 3 pos 0 -contrast Cond1vFix
 3
 pos 0 -map sig -sf
 /cluster/roffman/users/Stable5_PerRun/Subject_Files/50_MTH_Subjects
 -df
 /cluster/roffman/users/Stable5_PerRun

 Any help would be greatly appreciated!

 Thanks,
 Alex


>>> --
>>> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>> Outgoing:
>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>>
>>>
>>>
>>
>
> --
> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
>
>

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addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] mergecontrasts-sess group map

2012-11-29 Thread Douglas N Greve

Hi Alex, unfortunately, you cannot compute a conjunction with the CES. 
That's the problem with trying to do group-wise multi-variate analysis. 
Another thing you can do is to do a group analysis with each contrast 
separately, then do a conjunction of the group sig maps.
doug

On 11/29/2012 03:39 PM, Alexandra Tanner wrote:
> Thanks for the clarification! So I will rerun mergecontrasts-sess using
> the ces image on my subjects and then run mri_vol2surf and mri_concat to
> get the group map. Thanks for your help!
>
> Best,
> Alex
>
>> Usually the contrast effects size (ces) (in SPM this is the CON image,
>> in FSL it is the COPE image). Univariate maps are usually passed up to
>> the group level (the conjunction done with mergecontrasts is
>> multivariate).
>> doug
>>
>>
>> On 11/29/2012 01:05 PM, Alexandra Tanner wrote:
>>> Hi Doug,
>>>
>>> Thanks for the response! Just out of curiosity, what map is typically
>>> used
>>> for group analyses? Should I have used a map other than sig on the
>>> individual subject level as well?
>>>
>>> Thanks!
>>> Alex
>>>
>>>
 You'll have to run mri_vol2surf on each one separately to bring it into
 the fsaverage space, then mri_concat to stack all of the maps into one
 file. At that point you can compute a mean (also with mri_concat).
 Generally, one does not do group analysis on sig maps though.
 doug


 On 11/27/2012 05:08 PM, Alexandra Tanner wrote:
> Hi Doug and Freesurfers,
>
> I recently used mergecontrasts-sess to merge two contrasts of an
> analysis
> in 50 different subjects. The command ran on each subject individually
> and
> created a sig.nii and sig.ovpl file within a merged contrast folder
> for
> each subject. I'd now like to look at an average map of the merged
> contrasts across all 50 subjects.
> Does anyone know how to go about getting this average map for my group
> of
> 50 subjects?
>
> Command I ran to get the sig.nii/sig.ovpl file for each subject:
> mergecontrasts-sess -mergedcontrast Merge_7vFix_1vFix -conjunction
> andor
> -analysis SIRP_Stable5 -contrast Cond7vFix 3 pos 0 -contrast Cond1vFix
> 3
> pos 0 -map sig -sf
> /cluster/roffman/users/Stable5_PerRun/Subject_Files/50_MTH_Subjects
> -df
> /cluster/roffman/users/Stable5_PerRun
>
> Any help would be greatly appreciated!
>
> Thanks,
> Alex
>
>
 --
 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing:
 ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/



>> --
>> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>>
>>
>

-- 
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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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



Re: [Freesurfer] mergecontrasts-sess group map

2012-11-30 Thread Alexandra Tanner
Hi Doug,

So if I run a group analysis with each contrast separately, would I then
be running mri_concat to do a conjunction of the group sig maps? Also, can
I merge more than 2 contrasts at once when using mri_concat? Thanks!

Alex

>
> Hi Alex, unfortunately, you cannot compute a conjunction with the CES.
That's the problem with trying to do group-wise multi-variate analysis.
Another thing you can do is to do a group analysis with each contrast
separately, then do a conjunction of the group sig maps.
> doug
>
> On 11/29/2012 03:39 PM, Alexandra Tanner wrote:
>> Thanks for the clarification! So I will rerun mergecontrasts-sess using
the ces image on my subjects and then run mri_vol2surf and mri_concat
to
>> get the group map. Thanks for your help!
>> Best,
>> Alex
>>> Usually the contrast effects size (ces) (in SPM this is the CON image,
in FSL it is the COPE image). Univariate maps are usually passed up to
the group level (the conjunction done with mergecontrasts is
>>> multivariate).
>>> doug
>>> On 11/29/2012 01:05 PM, Alexandra Tanner wrote:
 Hi Doug,
 Thanks for the response! Just out of curiosity, what map is typically
used
 for group analyses? Should I have used a map other than sig on the
individual subject level as well?
 Thanks!
 Alex
> You'll have to run mri_vol2surf on each one separately to bring it into
> the fsaverage space, then mri_concat to stack all of the maps into one
> file. At that point you can compute a mean (also with mri_concat).
Generally, one does not do group analysis on sig maps though. doug
> On 11/27/2012 05:08 PM, Alexandra Tanner wrote:
>> Hi Doug and Freesurfers,
>> I recently used mergecontrasts-sess to merge two contrasts of an
analysis
>> in 50 different subjects. The command ran on each subject
>> individually
>> and
>> created a sig.nii and sig.ovpl file within a merged contrast folder
for
>> each subject. I'd now like to look at an average map of the merged
contrasts across all 50 subjects.
>> Does anyone know how to go about getting this average map for my group
>> of
>> 50 subjects?
>> Command I ran to get the sig.nii/sig.ovpl file for each subject:
mergecontrasts-sess -mergedcontrast Merge_7vFix_1vFix -conjunction
andor
>> -analysis SIRP_Stable5 -contrast Cond7vFix 3 pos 0 -contrast Cond1vFix
>> 3
>> pos 0 -map sig -sf
>> /cluster/roffman/users/Stable5_PerRun/Subject_Files/50_MTH_Subjects
-df
>> /cluster/roffman/users/Stable5_PerRun
>> Any help would be greatly appreciated!
>> Thanks,
>> Alex
> --
> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>> --
>>> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing:
>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> --
> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
>
>



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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] mergecontrasts-sess group map

2012-11-30 Thread Douglas N Greve
yesand yes
doug

On 11/30/2012 10:53 AM, Alexandra Tanner wrote:
> Hi Doug,
>
> So if I run a group analysis with each contrast separately, would I then
> be running mri_concat to do a conjunction of the group sig maps? Also, can
> I merge more than 2 contrasts at once when using mri_concat? Thanks!
>
> Alex
>
>> Hi Alex, unfortunately, you cannot compute a conjunction with the CES.
> That's the problem with trying to do group-wise multi-variate analysis.
> Another thing you can do is to do a group analysis with each contrast
> separately, then do a conjunction of the group sig maps.
>> doug
>>
>> On 11/29/2012 03:39 PM, Alexandra Tanner wrote:
>>> Thanks for the clarification! So I will rerun mergecontrasts-sess using
> the ces image on my subjects and then run mri_vol2surf and mri_concat
> to
>>> get the group map. Thanks for your help!
>>> Best,
>>> Alex
 Usually the contrast effects size (ces) (in SPM this is the CON image,
> in FSL it is the COPE image). Univariate maps are usually passed up to
> the group level (the conjunction done with mergecontrasts is
 multivariate).
 doug
 On 11/29/2012 01:05 PM, Alexandra Tanner wrote:
> Hi Doug,
> Thanks for the response! Just out of curiosity, what map is typically
> used
> for group analyses? Should I have used a map other than sig on the
> individual subject level as well?
> Thanks!
> Alex
>> You'll have to run mri_vol2surf on each one separately to bring it into
>> the fsaverage space, then mri_concat to stack all of the maps into one
>> file. At that point you can compute a mean (also with mri_concat).
> Generally, one does not do group analysis on sig maps though. doug
>> On 11/27/2012 05:08 PM, Alexandra Tanner wrote:
>>> Hi Doug and Freesurfers,
>>> I recently used mergecontrasts-sess to merge two contrasts of an
> analysis
>>> in 50 different subjects. The command ran on each subject
>>> individually
>>> and
>>> created a sig.nii and sig.ovpl file within a merged contrast folder
> for
>>> each subject. I'd now like to look at an average map of the merged
> contrasts across all 50 subjects.
>>> Does anyone know how to go about getting this average map for my group
>>> of
>>> 50 subjects?
>>> Command I ran to get the sig.nii/sig.ovpl file for each subject:
> mergecontrasts-sess -mergedcontrast Merge_7vFix_1vFix -conjunction
> andor
>>> -analysis SIRP_Stable5 -contrast Cond7vFix 3 pos 0 -contrast Cond1vFix
>>> 3
>>> pos 0 -map sig -sf
>>> /cluster/roffman/users/Stable5_PerRun/Subject_Files/50_MTH_Subjects
> -df
>>> /cluster/roffman/users/Stable5_PerRun
>>> Any help would be greatly appreciated!
>>> Thanks,
>>> Alex
>> --
>> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing:
>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
 --
 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing:
 ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>> --
>> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>>
>>
>
>
>

-- 
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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Freesurfer@nmr.mgh.harvard.edu
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