Dear Sahil,
could you send the full command-line and unthresholded view of
*_clustere_tstat_fwep ?
How the data showed in screenshot 1 were produced?
How are the actual p-values of your clusters in *_clustere_tstat_fwep?
You can also use -saveglm and inspect the files containing values of GLM fit.
You can load the *dpv_tstat.mgz file and threshold it by your cluster-forming
threshold (I suppose that you should correctly convert z value to t-value), to
see your initial clusters after thresholding.
Regards,
Antonin
Thanks a lot Anderson and Antonin, that's really useful.
Actually, I am having trouble in interpreting the results. Could you please
share any document explaining all these tests/outputs and their
interpretation in simple terms?
Here I am attaching a screen shot: (1) Simple partial correlations (I
adjusted the color bar between 0.30 and 0.35 to visualize the high
correlation coefficients, which is ~0.35) and (2) Results I get when I
used cluster
extent stats: *dpv_tstat
But I do not see any significant clusters when I view
*_clustere_tstat_fwep, *_dpv_tstat_fwep, which is very unexpected in my
data set.
So basically I really doubt if I am running the stats correctly because PCC
looks high at that big cluster (shown in PCC in attached screen shot).
Could you please suggest if there is any alternative (less stronger) stat
flag I can use here while running PALM command?
I would be more than happy sharing any required files to interpret the
results.
Thanks.
On Wed, Mar 8, 2017 at 10:20 AM, Sahil Bajaj <sahil.br...@gmail.com> wrote:
> Thanks a lot Anderson and Antonin, that's really useful.
>
> Actually, I am having trouble in interpreting the results. Could you
> please share any document explaining all these tests/outputs and their
> interpretation in simple terms?
>
> Here I am attaching two screen shots: (1) Results I get when I used cluster
> extent stats: *dpv_tstat and (2). Simple partial correlations (I adjusted
> the color bar between 0.30 and 0.35 to visualize the high correlation
> coefficients, which is ~0.35).
> I do not see any significant clusters when I view *_clustere_tstat_fwep,
> *_dpv_tstat_fwep, which is very unexpected in my data set.
>
> So basically I really doubt if I am running the stats correctly because
> PCC looks high at that big cluster (shown in PCC in attached screen shot).
>
> Could you please suggest if there is any alternative (less stronger) stat
> flag I can use here while running PALM command?
>
> I would be more than happy sharing any required files to interpret the
> results.
>
> Thanks.
>
> On Wed, Mar 8, 2017 at 9:27 AM, Martin Juneja <mj70...@gmail.com> wrote:
>
>> Hi Antonin and Anderson,
>>
>> That's wonderful ! I am able to run PALM now, without any problem.
>>
>> Thank you so much for your help and time, I really appreciate that.
>>
>> Best,
>> MJ
>>
>>
>>
>> On Wed, Mar 8, 2017 at 6:30 AM, Anderson M. Winkler <
>> wink...@fmrib.ox.ac.uk> wrote:
>>
>>> Hi all,
>>>
>>> That's exactly as Antonin says -- I have very little to add :-)
>>>
>>> Only a few suggestions:
>>>
>>> - With surfaces, both cluster and TFCE statistics tend to be slow.
>>> Consider using the tail approximation ("-approx tail -n 500
>>> -nouncorrected")
>>>
>>> - Include -logp, so that the p-values are in log-10 scale. Significant
>>> p-values are then those above 1.3 (i.e., -log10(0.05). This will help to
>>> make the figures nicer later.
>>>
>>> All the best,
>>>
>>> Anderson
>>>
>>>
>>>
>>> On 8 March 2017 at 00:19, Antonin Skoch <a...@ikem.cz> wrote:
>>>
>>>> Dear Sahil,
>>>>
>>>> I suppose, for qcache 1.3 the equivalent cluster-forming threshold
>>>> z-value is
>>>>
>>>> two-tailed test:
>>>> qnorm(1-10^-1.3/2)=1.958949
>>>>
>>>> for one-tailed test:
>>>> qnorm(1-10^-1.3)=1.643704
>>>>
>>>> (qnorm is R function call for quantile function of normal distribution,
>>>> you can compute this by using other methods or use statistical z-tables)
>>>>
>>>> And, the directionality of the hypothesis is I suppose specified by the
>>>> sign of your contrast vector, as I wrote in my previous mail.
>>>>
>>>> As for the output files, you can look at the documentation:
>>>>
>>>> https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM/UserGuide#Output_files
>>>>
>>>> For example, if you are looking for the p-values, used cluster extent
>>>> inference and used t-contrast, the file with FWER-corrected p-values would
>>>> be something like
>>>>
>>>> output_basename_clustere_tstat_fwep.mgz
>>>>
>>>> Antonin
>>>>
>>>>
>>>>
>>>>
>>>> Hello Martin and Antonin,
>>>>
>>>> I was following this conversation very closely to understand how to use
>>>> PALM in FreeSurfer.
>>>>
>>>> Can any of you please confirm in case I am interested in checking
>>>> correlation between gyrification index (LGI) and behavioral measure using
>>>> two tailed, p < 0.05:
>>>> Step 1: I used --cache 1.3
>>>> Step 2: Because (1-10^-1.3)= 0.95, so I will have to use -C 0.95 in palm
>>>> command
>>>>
>>>> Could you please confirm if thats correct and the output *_tstat.mgz is
>>>> the
>>>> final two-tailed corrected significant correlation map between LGI and
>>>> behavioral data?
>>>>
>>>> Thanks a lot for this wonderful discussion.
>>>> Sahil
>>>>
>>>> PS: For one-tailed: it will be -C -0.95 in palm command, correct?
>>>>
>>>>
>>>>
>>>> On Tue, Mar 7, 2017 at 3:48 PM, Antonin Skoch <a...@ikem.cz> wrote:
>>>>
>>>> > Dear Martin,
>>>> >
>>>> > after -s option, there have to be 2 arguments, as I specified in my
>>>> > previous
>>>> > mail:
>>>> >
>>>> > -s fsaverage/surf/lh.white fsaverage/surf/lh.white.avg.area.mgh
>>>> >
>>>> > And beware that -C has to have negative sign, if your hypothesis is
>>>> > one-tailed negative.
>>>> >
>>>> > Antonin
>>>> >
>>>> >
>>>> >
>>>> > Hi Antonin,
>>>> >
>>>> > Thank you so much for this detailed explanation, that's really useful.
>>>> >
>>>> > Following your instructions, I ran:
>>>> >
>>>> > palm -i lh.MEQ_LGI.10.mgh -s fsaverage/surf/lh.white.avg.area.mgh -d
>>>> > check.csv -t Contrast_MEQ.csv -n 5000 -m lh.MEQ_LGI.glmdir/mask.mgh -o
>>>> > myresults -Cstat extent -C 3.719016
>>>> >
>>>> > but I am getting following error:
>>>> >
>>>> > Running PALM alpha104 using MATLAB 9.0.0.341360 (R2016a) with the
>>>> > following
>>>> > options:
>>>> > -i lh.MEQ_LGI.10.mgh
>>>> > -s fsaverage/surf/lh.white.avg.area.mgh
>>>> > -d check.csv
>>>> > -t Contrast_MEQ.csv
>>>> > -n 5000
>>>> > -m lh.MEQ_LGI.glmdir/mask.mgh
>>>> > -o myresults
>>>> > -Cstat extent
>>>> > -C 3.719016
>>>> > Loading surface 1/1: fsaverage/surf/lh.white.avg.area.mgh
>>>> > Reading input 1/1: lh.MEQ_LGI.10.mgh
>>>> >
>>>> > Struct contents reference from a non-struct array object.
>>>> >
>>>> > Error in palm_takeargs (line 1632)
>>>> > if any(size(plm.srf{s}.data.vtx,
>>>> > 1) == ...
>>>> >
>>>> > Error in palm_core (line 33)
>>>> > [opts,plm] = palm_takeargs(varargin{:});
>>>> >
>>>> > Error in palm (line 81)
>>>> > palm_core(varargin{:});
>>>> >
>>>> > Could you please help me in resolving this error?
>>>> >
>>>> > Thanks much.
>>>> >
>>>> > On Tue, Mar 7, 2017 at 2:55 PM, Antonin Skoch <a...@ikem.cz> wrote:
>>>> >
>>>> > > Dear Martin,
>>>> > >
>>>> > > input -i input file is
>>>> > >
>>>> > > lh.MEQ_LGI.10.mgh file in your glmdir directory (for left hemisphere).
>>>> > >
>>>> > > As you could read in following messages in the referenced thread in
>>>> > > FSL
>>>> > > discussion forum, cluster-forming threshold need to be specified in z,
>>>> > > not
>>>> > > in t.
>>>> > >
>>>> > > Therefore, you would have to select cluster forming threshold and
>>>> > > specify
>>>> > > it as a z score.
>>>> > >
>>>> > > I think that your z-score for your original mri_glmfit-sim commandline
>>>> > > argument
>>>> > >
>>>> > > --cache 4 neg
>>>> > >
>>>> > > will be -qnorm(1-10^-4)=-3.719016. (I am not perfectly sure since I
>>>> > > never
>>>> > > tried negative one-side hypothesis testing in PALM).
>>>> > >
>>>> > > You could also use other statistics, such as cluster mass, or TFCE.
>>>> > > See
>>>> > > PALM user guide.
>>>> > >
>>>> > > Do not include -pmethodp none and -pmethodr none, since you would need
>>>> > > the
>>>> > > partitioning due your non-orthogonal design matrix.
>>>> > >
>>>> > > ?h.white.avg.area.mgh file (which you will find under fsaverage
>>>> > > directory)
>>>> > > goes as second argument after -s option.
>>>> > >
>>>> > > Therefore I suppose the commandline for cluster extent inference with
>>>> > > cluster forming threshold p=0.0001, negative one-sided hypothesis,
>>>> > > left
>>>> > > hemisphere, will be hopefully something like
>>>> > >
>>>> > > palm
>>>> > > -i y.mgh
>>>> > > -s fsaverage/surf/lh.white fsaverage/surf/lh.white.avg.area.mgh
>>>> > > -d Xg.csv
>>>> > > -t your_contrasts.csv
>>>> > > -n number_of_permutations
>>>> > > -m mask.mgh
>>>> > > -o output_basename
>>>> > > -Cstat extent
>>>> > > -C -3.719016
>>>> > > -saveglm
>>>> > > -savedof
>>>> > > -savemetrics
>>>> > >
>>>> > > The last 3 commandline options are only for diagnostical purposes.
>>>> > >
>>>> > > The output is surface overlay you can visualize in freeview.
>>>> > >
>>>> > > I use following code snippet for the reporting significant clusters in
>>>> > > MNI
>>>> > > coordinates:
>>>> > >
>>>> > > # PALM output cluster extent p maps have 1 outside cluster - problem
>>>> > > with
>>>> > > mri_surfcluster and also for display in freeView
>>>> > > #here we set values 1 to 0 in pmaps.
>>>> > > #done by binarizing and subtracting
>>>> > > if [[ $# -ne 2 ]]; then
>>>> > > echo "get cluster summary of PALM statistics. Expecting 2 arguments:
>>>> > > 1-
>>>> > > input p-map, 2- hemisphere (lh/rh)"
>>>> > > exit
>>>> > > fi
>>>> > > mri_binarize --i $1 --min 1 --o p_bin.mgz
>>>> > > mris_calc --output ${1%%.mgz}_filtered.mgz $1 sub p_bin.mgz
>>>> > > mri_surfcluster --in ${1%%.mgz}_filtered.mgz --subject fsaverage
>>>> > > --hemi $2
>>>> > > --surf white --annot aparc --thmin 0.000000001 --thmax 0.05 --mask
>>>> > > mask.mgh
>>>> > > --sum ${1%%.mgz}_cluster.summary --nofixmni
>>>> > > rm p_bin.mgz
>>>> > >
>>>> > > They are not Bonferroni-corrected for 2 hemispheres (--2spaces).
>>>> > >
>>>> > > Regarding your design and contrast:
>>>> > >
>>>> > > Design has to be matrix of values. You can use qdec to produce Xg.dat
>>>> > > file
>>>> > > with design matrix, then rename it to Xg.csv to be correctly readable
>>>> > > by
>>>> > > PALM.
>>>> > >
>>>> > > Regards,
>>>> > >
>>>> > > Antonin
>>>> > >
>>>> > >
>>>> > >
>>>> > >
>>>> > >
>>>> > > Hi Antonin,
>>>> > >
>>>> > > As you suggested in discussion forum, I tried to run following command
>>>> > > after mri_glmfit:
>>>> > >
>>>> > > palm -s fsaverage/surf/lh.white -n 10000 -m mask.mgh -Cstat extent -C
>>>> > > 1.974975 -pmethodp none -pmethodr none -twotail -d Design_MEQ.txt -t
>>>> > > Contrast_MEQ.txt
>>>> > >
>>>> > > Running PALM alpha104 using MATLAB 9.0.0.341360 (R2016a) with the
>>>> > > following
>>>> > > options:
>>>> > >
>>>> > > -s fsaverage/surf/lh.white
>>>> > >
>>>> > > -n 10000
>>>> > >
>>>> > > -m mask.mgh
>>>> > >
>>>> > > -Cstat extent
>>>> > >
>>>> > > -C 1.974975
>>>> > >
>>>> > > -pmethodp none
>>>> > >
>>>> > > -pmethodr none
>>>> > >
>>>> > > -twotail
>>>> > >
>>>> > > -d Design.txt
>>>> > >
>>>> > > -t Contrast.txt
>>>> > >
>>>> > > Found FSL in /usr/share/fsl/5.0
>>>> > >
>>>> > > Found FreeSurfer in /usr/local/freesurfer
>>>> > >
>>>> > > Found SPM in /usr/local/spm12
>>>> > >
>>>> > > Error using palm_takeargs (line 1141)
>>>> > >
>>>> > > Missing input data (missing "-i").
>>>> > >
>>>> > > Error in palm_core (line 33)
>>>> > >
>>>> > > [opts,plm] = palm_takeargs(varargin{:});
>>>> > >
>>>> > > Error in palm (line 81)
>>>> > >
>>>> > > palm_core(varargin{:});
>>>> > >
>>>> > > Looks like error is because its missing -i input here, I am not sure
>>>> > > what's
>>>> > > input file here?
>>>> > >
>>>> > > Also, I am trying to correlate LGI versus behavioral score, regressing
>>>> > > out
>>>> > > the effect of sex and age. So I just wanted to confirm if my
>>>> > > design.txt and
>>>> > > contrast.txt files are correct here. Please find both following:
>>>> > >
>>>> > > Design file (Variables Behav, Age) as following:
>>>> > >
>>>> > > S001 Male 60 36
>>>> > >
>>>> > > S003 Female 73 29
>>>> > >
>>>> > > S004 Male 48 39
>>>> > >
>>>> > > .......so on......
>>>> > >
>>>> > > Contrast file as following:
>>>> > > 0 0 0.5 0.5 0 0 (same as *.mtx file used for glm_fit)
>>>> > >
>>>> > > Thank you so much for your help and time.
>>>> > >
>>>> > > On Tue, Mar 7, 2017 at 10:49 AM, Martin Juneja <mj70...@gmail.com>
>>>> > > wrote:
>>>> > >
>>>> > > > Hi Antonin,
>>>> > > >
>>>> > > > Thanks a lot for your reply.
>>>> > > >
>>>> > > > Somehow, in the link you sent, I could not find any response to your
>>>> > > > email. But I can see your email to Anderson and command line
>>>> > > > parameters.
>>>> > > >
>>>> > > > As I am not an expert in using FreeSurfer, so would it be possible
>>>> > > > for you
>>>> > > > to share detailed step-by-step guide and PALM command after I run
>>>> > > > mri_glmfit
>>>> > > > command and how and where to include '?h.white.avg.area.mgh' file?
>>>> > > >
>>>> > > > I would really appreciate any help.
>>>> > > >
>>>> > > > On Mon, Mar 6, 2017 at 4:28 PM, Antonin Skoch <a...@ikem.cz> wrote:
>>>> > > >
>>>> > > >> Dear Martin,
>>>> > > >>
>>>> > > >> I think yes, you can use PALM with FreeSurfer surfaces, see my
>>>> > > >> conversation with Anderson on FSL list:
>>>> > > >>
>>>> > > >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1604&L=FSL
>>>>
>>>> >
>>>> > >
>>>> > > >> &D=0&1=FSL&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4&P=239088
>>>> > > >>
>>>> > > >> but beware not to forget to include average the vertex area
>>>> > > >> (?h.white.avg.area.mgh) file.
>>>> > > >>
>>>> > > >> Antonin
>>>> > > >>
>>>> > > >>
>>>> > > >> If you don't have an orthogonal design, then you can't use
>>>> > > >> mri_glmfit-sim. I think you can use PALM:
>>>> > > >>
>>>> > > >> https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM
>>>> > > >>
>>>> > > >> I have not tried it yet.
>>>> > > >>
>>>> > > >> Anderson, can you use PALM with surfaces?
>>>> > > >>
>>>> > > >>
>>>> > > >>
>>>> > > >>
>>>> > > >>
>>>> > > >>
>>>> > > >> On 03/06/2017 05:23 PM, Martin Juneja wrote:
>>>> > > >> > Hi Dr. Greve,
>>>> > > >> >
>>>> > > >> > I tried to run: mri_glmfit-sim --glmdir lh.MEQ_LGI.glmdir --sim
>>>> > > >> > perm
>>>> > > >> > 1000 3 permcsd --sim-sign abs --cwpvalthresh .05
>>>> > > >> > It gives error that ERROR: design matrix is not orthogonal,
>>>> > > >> > cannot be
>>>> > > >> > used with permutation.
>>>> > > >> >
>>>> > > >> > But when I run: mri_glmfit-sim --glmdir lh.MEQ_LGI.glmdir --sim
>>>> > > >> > perm
>>>> > > >> > 1000 3 permcsd --sim-sign abs --cwpvalthresh .05 --perm-force, it
>>>> > > >> > works.
>>>> > > >> >
>>>> > > >> > I am not sure whether I will have to make the design matrix
>>>> > > >> > orthogonal. If so, could you please tell me how that can be done?
>>>> > > >> >
>>>> > > >> > Or using --perm-force should be fine?
>>>> > > >> >
>>>> > > >> > Thanks.
>>>> > > >> >
>>>> > > >> > On Mon, Mar 6, 2017 at 1:58 PM, Douglas N Greve
>>>> > > >> > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu
>>>> > > >> > <gr...@nmr.mgh.harvard.edu>
>>>> > > >> > <gr...@nmr.mgh.harvard.edu>
>>>> > > >> > <gr...@nmr.mgh.harvard.edu>
>>>> > > >> > <gr...@nmr.mgh.harvard.edu>>> wrote:
>>>> > > >> >
>>>> > > >> > This is a problem with using LGI in that it is already
>>>> > > >> > extremely
>>>> > > >> > smooth
>>>> > > >> > that the smoothness exceeds the limit of the look up table
>>>> > > >> > that we
>>>> > > >> > supply. I recommend that you not use a gaussian-based
>>>> > > >> > correction
>>>> > > >> > for
>>>> > > >> > LGI. Instead, use permutation (see mri_glmfit-sim --help).
>>>> > > >> >
>>>> > > >> >
>>>> > > >> >
>>>> > > >> > On 03/06/2017 01:36 PM, Martin Juneja wrote:
>>>> > > >> > > Hello everyone,
>>>> > > >> > >
>>>> > > >> > > I am trying to extract clusters showing significant
>>>> > > >> > correlation
>>>> > > >> > > between LGI and a behavioral measure. I am able to extract
>>>> > > >> > PCC
>>>> > > >> > and
>>>> > > >> > > sig.mgh but at the last step when I try to run simulation
>>>> > > >> > command
>>>> > > >> > to
>>>> > > >> > > view corrected results and I run:
>>>> > > >> > >
>>>> > > >> > > mri_glmfit-sim --glmdir lh.MEQ_LGI.glmdir --cache 4 neg
>>>> > > >> > --cwp
>>>> > > >> > 0.05
>>>> > > >> > > --2spaces
>>>> > > >> > >
>>>> > > >> > > I get following error:
>>>> > > >> > >
>>>> > > >> > > ERROR: cannot find
>>>> > > >> > >
>>>> > > >> >
>>>> > > >> >
>>>> > > >> > /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm35/neg/th40/mc-z.csd
>>>> > > >> >
>>>> > > >> > >
>>>> > > >> > > But I can see mc-z.csd file in fwhm30 etc.
>>>> > > >> > >
>>>> > > >> > > Full message on terminal window is attached following.
>>>> > > >> > >
>>>> > > >> > > Any help would be really appreciated.
>>>> > > >> > >
>>>> > > >> > > ----- Full message ----
>>>> > > >> > >
>>>> > > >> > > cmdline mri_glmfit.bin --y lh.MEQ_LGI.10.mgh --fsgd
>>>> > > >> > MEQ.fsgd
>>>> > > >> > dods --C
>>>> > > >> > > Corr-MEQ-cor.mtx --surf fsaverage lh --cortex --glmdir
>>>> > > >> > lh.MEQ_LGI.glmdir
>>>> > > >> > >
>>>> > > >> > > WARNING: unrecognized mri_glmfit cmd option mri_glmfit.bin
>>>> > > >> > >
>>>> > > >> > > SURFACE: fsaverage lh
>>>> > > >> > >
>>>> > > >> > > log file is lh.MEQ_LGI.glmdir/cache.mri_glmfit-sim.log
>>>> > > >> > >
>>>> > > >> > > /usr/local/freesurfer/bin/mri_glmfit-sim
>>>> > > >> > >
>>>> > > >> > > --glmdir lh.MEQ_LGI.glmdir --cache 4 neg --cwp 0.05
>>>> > > >> > --2spaces
>>>> > > >> > >
>>>> > > >> > > $Id: mri_glmfit-sim,v 1.60 2016/04/30 15:13:36 greve Exp $
>>>> > > >> > >
>>>> > > >> > > Mon Mar 6 11:11:13 MST 2017
>>>> > > >> > >
>>>> > > >> > > setenv SUBJECTS_DIR
>>>> > > >> > > /data/emot/Freesurfer/FreeSurferSegmentation/SB_AgingAll
>>>> > > >> > >
>>>> > > >> > > FREESURFER_HOME /usr/local/freesurfer
>>>> > > >> > >
>>>> > > >> > > Original mri_glmfit command line:
>>>> > > >> > >
>>>> > > >> > > cmdline mri_glmfit.bin --y lh.MEQ_LGI.10.mgh --fsgd
>>>> > > >> > MEQ.fsgd
>>>> > > >> > dods --C
>>>> > > >> > > Corr-MEQ-cor.mtx --surf fsaverage lh --cortex --glmdir
>>>> > > >> > lh.MEQ_LGI.glmdir
>>>> > > >> > >
>>>> > > >> > > DoSim = 0
>>>> > > >> > >
>>>> > > >> > > UseCache = 1
>>>> > > >> > >
>>>> > > >> > > DoPoll = 0
>>>> > > >> > >
>>>> > > >> > > DoPBSubmit = 0
>>>> > > >> > >
>>>> > > >> > > DoBackground = 0
>>>> > > >> > >
>>>> > > >> > > DiagCluster = 0
>>>> > > >> > >
>>>> > > >> > > gd2mtx = dods
>>>> > > >> > >
>>>> > > >> > > fwhm = 35.073391
>>>> > > >> > >
>>>> > > >> > > ERROR: cannot find
>>>> > > >> > >
>>>> > > >> >
>>>> > > >> >
>>>> > > >> > /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm35/neg/th40/mc-z.csd
>>>> > > >> >
>>>> > > >> > >
>>>> > > >> > >
>>>> > >
>>>> > >
>>>>
>>>>
>>>>
>>>> _______________________________________________
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>>>
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