date:20161014

[Freesurfer] How to get numerical r values from analysis

2016-10-14 Thread Marissa Pifer

Hi freesurfer experts,

I've run into a problem of not being able to generate the numerical results
of the analysis I've run through qdec.After I ran the analysis in qdec I
opened the overlay in tksurfer, applied a label, and found a significant
negative correlation between cortical thickness and one of our variables. I
cannot figure out how to get the numerical r value of this correlation. How
can I get this value?

Thanks in advance

Marissa
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Re: [Freesurfer] Quantifying volumes

2016-10-14 Thread Douglas Greve

How did you create the label ?

On 10/14/16 12:43 PM, Josue Luiz Dalboni Da Rocha wrote:

Dear Doug,

From the curvature file of the ROI (selected portion of surface), we 
extract the volume using this 2 command lines:

mri_binarize --i $D_load/lh_masked_all.curv --max -.001 --o 
$D_load/lh_masked_all_bin.mgh
mri_segstats --seg $D_load/lh_masked_all_bin.mgh --id 1 --i 
$SUBJECTS_DIR/$subj/surf/lh.volume --accumulate --sum 
$D_load/lh_masked_all_bin.txt

From the label file of the same ROI, we extract the volume using the 
following command line:
mris_anatomical_stats -l 
$SUBJECTS_DIR/$subj/label/labelsAtlas2009/lh_masked_all.label -f 
$outD/lh_masked_all_Volume $subj lh

As the '.curv' file and the '.label' file represent the same ROI, we 
were expecting to get the same volume (total gray matter volume of the 
selected portion of surface). But the results using the first method 
are always about 3 time higher than using the second method.

We would like to understand what is going on, because for some 
selected portions of ROI we just have the '.curv' file to extract the 
volume from.

Thank you very much for your help!

Best regards,
Josue

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas Greve 

*Sent:* Friday, October 14, 2016 5:54 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] Quantifying volumes

please send command lines

On 10/14/16 6:36 AM, Damien MARIE wrote:

Hi,

Just adding a word about the e-mail of ma colleague Josue. What he 
meant is that he extracted volumes for exactly the same ROI (a 
merging of destrieux labels of Hechl’s gyrus, Heschl's sulcus and 
planum temporale) using 1- a .curv file of this ROI, mri_binarize and 
mri_segstats  or 2- a .label file of this ROI and mris_anatomical_stats.

We get a different volume output (ratio of difference between the 2 
methods = approx. 2.5, similar to mean thickness I would say…), so we 
would like to understand what is happening exactly.

Using the method 1, it’s actually a surface measurement we get no?

Would that be possible to convert a .cuvr file to a .label file ?

Thank you and best,
Damien

Josue Luiz Dalboni Da Rocha Wed, 12 Oct 2016 07:26:32 -0700
Dear Doug,

Thank you very much for your advice!
We get to extract results for the volumes from a ".curv file encoded 
ROI" using

your recommended command lines (mri_binarize and mri_segstats ), but
unfortunately the results are much smaller (around 3 times) than when we
extract total gray matter volumes from a respective ".label file 
encoded ROI"

using mris_anatomical_stats .
Example:
Volumes from a ".curv file encoded ROI" using your recommended 
command lines

(mri_binarize and mri_segstats):
Subject1 = 1090
Subject2 = 1181
Subject3 = 713
Subject4 = 1230
Volumes from a respective ".label file encoded ROI" 
(mris_anatomical_stats):

Subject1 = 3497
Subject2 = 3786
Subject3 = 2268
Subject4 = 3491

Are the volumes extracted from a ".curv file encoded ROI" (using 
mri_binarize

and mri_segstats) an estimation of the total gray matter volumes?
Why these values are differing that much?

Thank you very much,
Josue Dalboni

From: freesurfer-boun...@nmr.mgh.harvard.edu 

> 
on behalf of Douglas N Greve

>
Sent: Wednesday, October 5, 2016 5:19 PM
To: freesurfer@nmr.mgh.harvard.edu 

Subject: Re: [Freesurfer] Quantifying volumes

I would binarize the curv file with

mri_binarize --i lh.yourcurvfile --abs --min .001 --o
lh.yourcurvfilebin.mgh

Then compute the volume with

mri_segstats --seg lh.yourcurvfilebin.mgh --id 1 --i lh.volume
--accumulate --sum lh.vol.yourcurv.sum

On 10/05/2016 09:09 AM, Josue Luiz Dalboni Da Rocha wrote:
> Dear Douglas,
>
> I have a ".curv" file that contains the curvature information 
inside an

> automatically delineated ROI and 0 everywhere else.
> I would like to calculate the volume of this ROI,
>
> Can I extract statistics directly from the ".curv" file?
>
> Best regards,
> Josue
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 

> > on behalf of Douglas N Greve

> >
> Sent: Tuesday, October 4, 2016 9:41 PM
> To: freesurfer@nmr.mgh.harvard.edu 

> Subject: Re: [Freesurfer] Quantifying volumes
>
> What is the nature of the segmentation? Is it just a binary (1=in,
> 0=out) segmentation? And what file format? In general we don't use .w
> anymore, but it can be converted into something else.
>
> doug
>
>
>

Re: [Freesurfer] group analysis

2016-10-14 Thread Douglas Greve

Both contrasts are right. You might want to change the value from 0.5 to 
1/6, but that won't affect the actual p-values (only the gamma values). 
The 2nd contrast is correct, but it maybe difficult to interpret if the 
first contrast has an effect. Technically, you should verify that there 
is no interaction between group and continuous covariates. If there is 
no effect, then re-run with DOSS (the non-interaction model).

On 10/12/16 1:01 PM, charles laidi wrote:

Dear Douglas and Trisanna,

Thank you very much for your explanations.

I just would like to be sure of what I am doing since there is no 
example on the wiki as complex as mine.

If I have the following classes :

Diagnosis : Patient or Control
Gender : Male or Female
Site : Site1 or Site2 or Site3

NregressorsDODS = Nclasses*(Nvariables+1) = 6*(0+1) = 2*2*3*(1+1) = 24
Regressor1: ones for PatientMaleSite1 subjects, 0 otherwise. Codes 
intercept for Group 1
Regressor2: ones for PatientMaleSite2 subjects, 0 otherwise. Codes 
intercept for Group 2
Regressor2: ones for PatientMaleSite3 subjects, 0 otherwise. Codes 
intercept for Group 3

Regressor12: ones for ControlFemaleSite3 subjects, 0 otherwise. Codes 
intercept for Group 12
Regressor13: age for PatientMaleSite1 subjects, 0 otherwise. Codes age 
slope for Group 1
Regressor14: age for PatientMaleSite2 subjects, 0 otherwise. Codes age 
slope for Group 2

...
Regressor24: age for ControlFemaleSite3 subjects, 0 otherwise. Codes 
age slope for Group 12

*I assume my FSGDF file should look like : *

GroupDescriptorFile 1
Title analysis
Class PatientMaleSite1
Class PatientMaleSite2
Class PatientMaleSite3
Class PatientFemaleSite1
Class PatientFemaleSite2
Class PatientFemaleSite3
Class ControlMaleSite1
Class ControlMaleSite2
Class ControlMaleSite3
Class ControlFemaleSite1
Class ControlFemaleSite2
Class ControlFemaleSite3
Variables Age
Input subject1 PatientMaleSite1 30
Input subject2 PatientFemaleSite2 45
Input subject3 PatientFemaleSite3 85
Input subject4 PatientFemaleSite4 75
...

As for the contrast analysis :

If my question is : *is there a difference between Patient and 
Controls age slope regressing out the effects of gender and site? *

_Contrast1 patient-control.slope.mtx_

0 0 0 0 0 0 0 0 0 0 0 0 0.5 0.5 0.5 0.5 0.5 0.5 -0.5 -0.5 -0.5 -0.5 
-0.5 -0.5

with all regressor1 to regressor12 equal to *0*
with regressor13 to 18 equal to *0.5 *(regressor with Patient in it)
with regressor19 to 24 equal to *- 0.5* (regressor with Controls in it)

If my question is :*is there a difference between cortical thickness 
in patients and controls, regressing out the effects of age, gender 
and site ? *

_Contrast2 patient-controls.mtx_

0.5 0.5 0.5 0.5 0.5 0.5 -0.5 -0.5 -0.5 -0.5 -0.5 -0.5 0 0 0 0 0 0 0 0 
0 0 0 0

with all regressor1 to regressor6 equal to *0.5
*with all regressor7 to regressor12 equal to -*0.5*
with all regressor13 to regressor24 equal to *0*

Thank you very much in advance for your help and sorry for taking your 
time.

Best,

Charles

2016-10-05 17:44 GMT+02:00 Douglas N Greve >:

This is a straightforward extension to the FSGD examples. You have 3
discrete factors (2 diagnosis, 2 gender, 6 centers), this yields
2*2*6=24 classes. With one covariate, you would have 24 covariate
regressors (one for each class) for a total of 48. You would then need
to create a contrast matrix that tests for an interaction between
diagnosis and age which is also a straight-forward extension to the
examples.

Having said that, I think that 48 regressors is a lot unless you have
about 500 subjects. It is also possible to have a less agressive model
and just have two regressors, one for each diagnosis. But you'd
have to
create the design matrix yourself as this is outside of the FSGD
specification.

On 10/05/2016 09:22 AM, charles laidi wrote:
> Dear FreeSurfers,
>
> I would like to study the interaction between age and cortical
> thickness in patients and controls.
> My hypothesis is that there is an interaction and that cortical
> thickness is decreasing faster with age in patients than in
controls.
> I have both Male and Female included in 6 different centers.
> I would like to consider also Gender and Site (6 centers) as
confounds.
>
> My understanding is that I should perform a surface based group
> analysis with freesurfer.
>
> I am not able to find an example for my problem in the documentation
> https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G0V

>
> Would anyone had some tips to build the Fsgd file and the
contrast file ?
>
> Thank you very much in advance.
>
> Best,
>
> Charles
>
>
>
> ___
> Freesurfer mailing list
>

Re: [Freesurfer] MRI_segstats for adc.nii from dt recon - increasing decimal digits

2016-10-14 Thread Douglas Greve


You can add --mul 1000 to multiply everything by 1000


On 10/11/16 4:47 PM, Chung, Yoonho wrote:


Hi!


I ran mri_segstats as instructed in the wiki to extract ADC values 
from adc.nii. And as you can see below in my output, I think the 
decimal digits are truncated and missing the following decimal values. 
Is there an option or other way to get around this problem and extract 
ADC values from the ROIS with greater precision?  Thank you!


mri_segstats \
 --seg $SUBJECTS_DIR/$subj/mri/wmparc2diff.mgz \
 --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt \
 --id 251 --id 3021 --id 3024 --id 3030 --id 12 --id 4 \
 --i adc.nii --sum adc.stat
# ColHeaders  Index SegId NVoxels Volume_mm3 StructName Mean StdDev 
Min Max Range
29 3001   344 2752.0 wm-lh-bankssts 
0.0007 0.0001 0.0006 0.0009 0.0003
 30 3002   450 3600.0 wm-lh-caudalanteriorcingulate  
0.0009 0.0003 0.0006 0.0026 0.0020
 31 3003   851 6808.0 wm-lh-caudalmiddlefrontal  
0.0007 0.0001 0.0005 0.0010 0.0005
 32 3005   337 2696.0 wm-lh-cuneus   
0.0008 0.0001 0.0006 0.0011 0.0005
 33 300682  656.0 wm-lh-entorhinal   
0.0009 0.0001 0.0008 0.0016 0.0008





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Re: [Freesurfer] No cluster remains significant after multiple comparisons

2016-10-14 Thread Douglas Greve



It may be the case that the result are not significant. If you have an 
apriori region then you can analyze only in that region rather than 
doing a whole-brain analysis. That will make the result more significant.



On 10/9/16 4:08 PM, Karamfil Bahchevanov wrote:

Hello Freesurfer experts,

I'm really struggling with my study.
I have a 27 scans that I analyze in QDEC. Scans are from Siemens 
machine, mprage protocol, TR1620, TE 4.3, FOV 240*256, acq. matrix 
232*256, slice thickness 0,9mm.
After I enter model and have some initial significant clusters 
(threshold 2 - 5) I run multiple comparisons, and none have survived 
the procedures, no matter method or significance -  FDR 
(0.1-0.05-0.01) or Monte-Carlo(0.05-0.01-0.01). This repeats no matter 
of the tested variables and the initial significancy and size of the 
clusters.
I'm really confused of that and could not find an explanation, except 
that my study is really non-significant. However, the significant 
results I get are in the regions that I expect to be, that are 
reported previously and they also explain my results. If they happen 
to survive, but that never is the case (In fact one survived, but I 
entered wrong variables and model was wrong).
What could be the reason? Outliers? Really non-significant results 
(which I doubt as I said already)? Should I recheck the quality of the 
processed scans?  I also made my own average, hoping to improve things 
somehow, but QDEC doesn't allow me to run multiple comparisons with it.
Anyway, is it mistake to discuss the results when they don't survive 
simulation, as they fit with initial hipothesis and what I'm testing. 
I have to point that there are only few significant clusters, that 
could not be explained with what I'm testing and tested population, so 
in fact the "noise" is very small.

Any help will be of great value,

Thanks



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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
dispose of the e-mail.

Re: [Freesurfer] Quantifying volumes

2016-10-14 Thread Josue Luiz Dalboni Da Rocha

Dear Doug,

From the curvature file of the ROI (selected portion of surface), we extract 
the volume using this 2 command lines:

mri_binarize --i $D_load/lh_masked_all.curv --max -.001 --o 
$D_load/lh_masked_all_bin.mgh
mri_segstats --seg $D_load/lh_masked_all_bin.mgh --id 1 --i 
$SUBJECTS_DIR/$subj/surf/lh.volume --accumulate --sum 
$D_load/lh_masked_all_bin.txt

From the label file of the same ROI, we extract the volume using the following 
command line:
mris_anatomical_stats -l 
$SUBJECTS_DIR/$subj/label/labelsAtlas2009/lh_masked_all.label -f 
$outD/lh_masked_all_Volume $subj lh

As the '.curv' file and the '.label' file represent the same ROI, we were 
expecting to get the same volume (total gray matter volume of the selected 
portion of surface). But the results using the first method are always about 3 
time higher than using the second method.

We would like to understand what is going on, because for some selected 
portions of ROI we just have the '.curv' file to extract the volume from.

Thank you very much for your help!

Best regards,
Josue

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas Greve 

Sent: Friday, October 14, 2016 5:54 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Quantifying volumes

please send command lines

On 10/14/16 6:36 AM, Damien MARIE wrote:
Hi,

Just adding a word about the e-mail of ma colleague Josue. What he meant is 
that he extracted volumes for exactly the same ROI (a merging of destrieux 
labels of Hechl’s gyrus, Heschl's sulcus and planum temporale) using 1- a .curv 
file of this ROI, mri_binarize and mri_segstats  or 2- a .label file of this 
ROI and mris_anatomical_stats.

We get a different volume output (ratio of difference between the 2 methods = 
approx. 2.5, similar to mean thickness I would say…), so we would like to 
understand what is happening exactly.

Using the method 1, it’s actually a surface measurement we get no?

Would that be possible to convert a .cuvr file to a .label file ?

Thank you and best,
Damien

Josue Luiz Dalboni Da Rocha Wed, 12 Oct 2016 07:26:32 -0700
Dear Doug,

Thank you very much for your advice!
We get to extract results for the volumes from a ".curv file encoded ROI" using
your recommended command lines (mri_binarize and mri_segstats ), but
unfortunately the results are much smaller (around 3 times) than when we
extract total gray matter volumes from a respective ".label file encoded ROI"
using mris_anatomical_stats .
Example:
Volumes from a ".curv file encoded ROI" using your recommended command lines
(mri_binarize and mri_segstats):
Subject1 = 1090
Subject2 = 1181
Subject3 = 713
Subject4 = 1230
Volumes from a respective ".label file encoded ROI" (mris_anatomical_stats):
Subject1 = 3497
Subject2 = 3786
Subject3 = 2268
Subject4 = 3491

Are the volumes extracted from a ".curv file encoded ROI" (using mri_binarize
and mri_segstats) an estimation of the total gray matter volumes?
Why these values are differing that much?

Thank you very much,
Josue Dalboni

From: freesurfer-boun...@nmr.mgh.harvard.edu
> on behalf 
of Douglas N Greve
>
Sent: Wednesday, October 5, 2016 5:19 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Quantifying volumes

I would binarize the curv file with

mri_binarize --i lh.yourcurvfile --abs --min .001 --o
lh.yourcurvfilebin.mgh

Then compute the volume with

mri_segstats --seg lh.yourcurvfilebin.mgh --id 1 --i lh.volume
--accumulate --sum lh.vol.yourcurv.sum

On 10/05/2016 09:09 AM, Josue Luiz Dalboni Da Rocha wrote:
> Dear Douglas,
>
> I have a ".curv" file that contains the curvature information inside an
> automatically delineated ROI and 0 everywhere else.
> I would like to calculate the volume of this ROI,
>
> Can I extract statistics directly from the ".curv" file?
>
> Best regards,
> Josue
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> > on 
> behalf of Douglas N Greve
> >
> Sent: Tuesday, October 4, 2016 9:41 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Quantifying volumes
>
> What is the nature of the segmentation? Is it just a binary (1=in,
> 0=out) segmentation? And what file format? In general we don't use .w
> anymore, but it can be converted into something else.
>
> doug
>
>
> On 10/03/2016 12:35 PM, Josue Luiz Dalboni Da Rocha wrote:
>> Dear Douglas,
>>
>>
>> I have a segmented gyrus curvature file (.curv or .w) and I would like
>> to calculate the

Re: [Freesurfer] Quantifying volumes

2016-10-14 Thread Douglas Greve


please send command lines


On 10/14/16 6:36 AM, Damien MARIE wrote:

Hi,

Just adding a word about the e-mail of ma colleague Josue. What he 
meant is that he extracted volumes for exactly the same ROI (a merging 
of destrieux labels of Hechl’s gyrus, Heschl's sulcus and planum 
temporale) using 1- a .curv file of this ROI, mri_binarize and 
mri_segstats  or 2- a .label file of this ROI and mris_anatomical_stats.


We get a different volume output (ratio of difference between the 2 
methods = approx. 2.5, similar to mean thickness I would say…), so we 
would like to understand what is happening exactly.


Using the method 1, it’s actually a surface measurement we get no?

Would that be possible to convert a .cuvr file to a .label file ?

Thank you and best,
Damien


Josue Luiz Dalboni Da Rocha Wed, 12 Oct 2016 07:26:32 -0700
Dear Doug,

Thank you very much for your advice!
We get to extract results for the volumes from a ".curv file encoded 
ROI" using

your recommended command lines (mri_binarize and mri_segstats ), but
unfortunately the results are much smaller (around 3 times) than when we
extract total gray matter volumes from a respective ".label file 
encoded ROI"

using mris_anatomical_stats .
Example:
Volumes from a ".curv file encoded ROI" using your recommended command 
lines

(mri_binarize and mri_segstats):
Subject1 = 1090
Subject2 = 1181
Subject3 = 713
Subject4 = 1230
Volumes from a respective ".label file encoded ROI" 
(mris_anatomical_stats):

Subject1 = 3497
Subject2 = 3786
Subject3 = 2268
Subject4 = 3491

Are the volumes extracted from a ".curv file encoded ROI" (using 
mri_binarize

and mri_segstats) an estimation of the total gray matter volumes?
Why these values are differing that much?

Thank you very much,
Josue Dalboni

From: freesurfer-boun...@nmr.mgh.harvard.edu 
> 
on behalf of Douglas N Greve

>
Sent: Wednesday, October 5, 2016 5:19 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Quantifying volumes

I would binarize the curv file with

mri_binarize --i lh.yourcurvfile --abs --min .001 --o
lh.yourcurvfilebin.mgh

Then compute the volume with

mri_segstats --seg lh.yourcurvfilebin.mgh --id 1 --i lh.volume
--accumulate --sum lh.vol.yourcurv.sum


On 10/05/2016 09:09 AM, Josue Luiz Dalboni Da Rocha wrote:
> Dear Douglas,
>
> I have a ".curv" file that contains the curvature information inside an
> automatically delineated ROI and 0 everywhere else.
> I would like to calculate the volume of this ROI,
>
> Can I extract statistics directly from the ".curv" file?
>
> Best regards,
> Josue
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 

> > on behalf of Douglas N Greve

> >
> Sent: Tuesday, October 4, 2016 9:41 PM
> To: freesurfer@nmr.mgh.harvard.edu 


> Subject: Re: [Freesurfer] Quantifying volumes
>
> What is the nature of the segmentation? Is it just a binary (1=in,
> 0=out) segmentation? And what file format? In general we don't use .w
> anymore, but it can be converted into something else.
>
> doug
>
>
> On 10/03/2016 12:35 PM, Josue Luiz Dalboni Da Rocha wrote:
>> Dear Douglas,
>>
>>
>> I have a segmented gyrus curvature file (.curv or .w) and I would like
>> to calculate the volume (and other statistics) of this gyrus.
>>
>>
>> I currently only know mris_anatomical_stats to perform that, but
>> requiring a '.label' file.
>>
>>
>> Can I extract statistics directly from the ".curv" file?
>>
>>
>> Or can I convert directly from .curv to .label in order to extract
>> these statistics?
>>
>>
>> As another option, is it feasible to convert the '.curv' file to nifti
>> volume (mri_surf2vol), binarize it (mri_binarize), and then convert to
>> label (mri_cor2label)?
>>
>>
>> What does the output nifti file from 'mri_surf2vol' contain? Does it
>> contain the complete volume behind the surface? Or does it only
>> contain the surface over the 3D space?
>>
>>
>> Thank you very much in advance for your help!
>>
>>
>> Best regards,
>>
>> Josue
>>
>>
>>
>> ___
>> 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
>

Re: [Freesurfer] Warping an ROI from one subject to another

2016-10-14 Thread Douglas Greve

So the result of step 4 looks ok on the volume but not on the surface? 
How are you putting the volume-based ROI back on the surface?  This is 
tricky because now it will be a 1mm thin label. You should use 
mri_vol2surf for this, maybe selecting the --projfrac-max to make sure 
that it grabs the value.



On 10/5/16 5:47 PM, Joel Bruss wrote:

Doug-

I'm sooo close but something isn't right.  I've run:

1)mri_vol2sur to sampel the ROI in subA surface space

2) mri_cor2label to convert it to a label

3) mri_label2lable to push it to subB

4) mri_label2vol to get back to a a volume

Steps 1-3 look great.  The output of step 4, loaded on subB inflated
surface looks cut off.  I suspect this is because it's actually down in
volume space now?  If I load the ROI over the wmparc file for subB, it
fits, it's just that I only have a strip of voxels on the WM surface
only.  I chose  the wmparc.mgz file for subB for both "--temp" and
''--regheader."  The result is the same if specify "--surf pial" or
choose nothing, it's also the same if I chose orig.mgz or brainmask.mgz
for the temp/header options.  How do I get the ROI to "fill in" like it
is in subA, originally?

I've attached a composite of the steps I've run.  I really hate to keep
pestering the listserv with this.  My apologies.

-Joel

On 10/04/2016 03:03 PM, Douglas N Greve wrote:

mri_label2vol will transfer it into the volume, no need for surf2vol

On 10/04/2016 03:54 PM, Joel Bruss wrote:

Doug (Bruce and Trisanna)-

Thank you all for your help.  I do, indeed, have a volume, then label,
and see now how to load and view this properly.  I've gotten through 
the

"label2label" step and now have a label (from subA)  in subB space.  If
I now want to back-project this label to subB's input MRI volume, would
I run the following?

(Assuming I invert the steps I did to get the original binary mask to
subA's surface, as a label)

mri_label2vol --label $SUBJECTS_DIR/subA/tmpdir/rh.roi_to_subB.label \
--subject subB \
--temp brainmask.mgz \
--regheader brainmask.mgz \
--o $SUBJECTS_DIR/subA/tmpdir/roi_to_subB.mgz \
--surf pial

mri_surf2vol --surfval $SUBJECTS_DIR/subA/tmpdir/roi_to_subB.mgz \
--volregidentity subB --template $SUBJECTS_DIR/subB/mri/orig.mgz 
--hemi rh \

--o $SUBJECTS_DIR/subA/tmpdir/roi_to_subB_orig.mgz


"label2vol" works but I'm now stuck on the "surf2vol" command.  I 
end up

with the following error:

ERROR: dimension inconsistency in source data
  Number of surface vertices = 128997
 Number of value vertices = 16777216

-Joel





On 10/04/2016 02:45 PM, Douglas N Greve wrote:

The rh.roiS.mgh file is a surface overlay (ie, one value per vertex),
not a surface itself (which would have a list of vertices, the XYZ for
each, and neighborhood relations). When you loaded rh.roiS.mgh as a
surface overlay, did you change the threshold to be 0.5? The 
default is

2, and if your ROI is binary (0,1), then no voxels would ever appear
above threshold


On 10/03/2016 03:20 PM, Joel Bruss wrote:

Sorry, it sent before I finished. I'll try this again.

On 09/30/2016 02:00 PM, Douglas N Greve wrote:

First, bring up the ROI on the volume along with the surface in the
volume. You can do this with FreeView. Make sure that the ROI 
intersects

the surface.

Yes, this looks fine

Then run mri_vol2surf so sample the binary ROI volume onto
the surface.

This is what I ran:

mri_vol2surf  --src $SUBJECTS_DIR/subA/tmpdir/roi.mgz \
--out $SUBJECTS_DIR/subA/tmpdir/rh.roiS.mgh \


You can view the ROI on the surface by loading it as an
overlay.
This is a volume or a surface now? Is it just a volume resampled 
to the


surface space?  I can't get it to load in freeview as a surface 
(it just

crashes), and it doesn't look like anything as an overlay.



Then run mri_cor2label using the surface-sampled ROI as input
and specifying --surf (see the --help) to make this a surface-based
label.

I next ran this:
mri_cor2label --id 1 --c $SUBJECTS_DIR \
--i $SUBJECTS_DIR/subA/tmpdir/rh.roiS.mgh \
--l $SUBJECTS_DIR/subA/tmpdir/rh.roi.label \
--surf subA rh

You can also view this label in the surface in freeview.

At this point, it just kept loading and loading and loading and I'd
finally have to kill the process.  I never could visualize this 
output.

  Finally,
run mri_label2label using the --regmethod surface

At this point, I must just be feeding bad data into good commands:
mri_label2vol --label 
$SUBJECTS_DIR/subA/tmpdir/rh.roi_to_subB.label \

--subject subB \
--temp brainmask.mgz \
--regheader brainmask.mgz \
--o $SUBJECTS_DIR/subA/tmpdir/roi_to_subB.mgz \
--surf pial

I don't know where things went wrong or how to view the output to 
diagnose.





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Re: [Freesurfer] GLM in groups with unequal size

2016-10-14 Thread Douglas Greve

It will not

On 10/13/16 10:34 AM, Eelco van Duinkerken wrote:
Ah sorry for the low level of info. I am aiming to do a simple group 
comparison, where I'm comparing thickness between controls and obese 
or T2DM patients, regressing out the effect of age, sex and, 
hypertension. So I created one thickness file with fwhm 10 containing 
all participants of the 3 groups.

The contrast file looks like this:

1 0 -1 0 0 0 for controls vs T2DM
1 -1 0 0 0 0 for controls vs obese
0 1 -1 0 0 0 for obese vs T2DM, although there I do not expect 
something to happen

And the GLM works fine (differences in the first and second contrast), 
but I was wondering whether the fact that the groups are unbalanced 
might influence the results in some way.

Thanks,

Eelco

2016-10-13 11:17 GMT-03:00 Bruce Fischl >:

Hi Eelco

it depends on how you setup your GLM. Are you trying to regress
out the effects of obesity in some way? If you give us more
details I expect someone else can answer your question (Doug!)

cheers
Bruce

On Thu, 13 Oct 2016, Eelco van Duinkerken wrote:

Thanks for the quick reply!
So if I understand correctly, the power of say the controls
vs. diabetes
(indeed it is type 2 diabetes) comparison is constrained by
the sample size
of the obese group?

2016-10-13 11:02 GMT-03:00 Bruce Fischl
>:
  Hi Eelco

  it isn't really a question of whether our implementation is
  senstitive to
  this. It's that in general your power will be
constrained by the
  size of
  the smaller group (I assume this is Type 2 diabetes by
the way).

  cheers
  Bruce

  On Thu, 13 Oct 2016, Eelco van Duinkerken wrote:

  > Hi all,
  > I am using FS with data from 2 different studies that were
  acquired on the
  > same MRI-machine with the same T1 and FLAIR sequences.
  Unfortunately, the
  > group sizes are not very balanced, with 31 controls,
16 obese
  and 32
  > diabetes patients.
  >
  > Is the GLM for thickness used in FS very sensitive to this
  unequal group
  > size?
  >
  >
  > Thanks for the help,
  >
  > Eelco
  >
  >
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Eelco van Duinkerken, PhD
Pontifícia Universidade Católica | Department of Psychology |
R. Marquês de São Vicente 225 | Gávea, Rio de Janeiro - RJ |
CEP 22451-900 |
Brasil |
E-mail: e.vanduinker...@vumc.nl
 | Phone: +55-21-35271855
 |
http://lattes.cnpq.br/7180895567820901

&
VU University Medical Center | Department of Medical Psychology |
De Boelelaan 1117 | 1081 HV | Amsterdam | The Netherlands

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Pontifícia

Re: [Freesurfer] GLM in groups with unequal size

2016-10-14 Thread Douglas Greve

It will be constrained by the group with the smaller number of subjects. 
There is not anything wrong with unequal group sizes, but it is less 
efficient than if you had split your acquisitions evenly.

On 10/13/16 10:17 AM, Bruce Fischl wrote:

Hi Eelco

it depends on how you setup your GLM. Are you trying to regress out 
the effects of obesity in some way? If you give us more details I 
expect someone else can answer your question (Doug!)

cheers
Bruce

On Thu, 13 Oct 2016, Eelco van Duinkerken wrote:

Thanks for the quick reply!
So if I understand correctly, the power of say the controls vs. diabetes
(indeed it is type 2 diabetes) comparison is constrained by the 
sample size

of the obese group?

2016-10-13 11:02 GMT-03:00 Bruce Fischl :
  Hi Eelco

  it isn't really a question of whether our implementation is
  senstitive to
  this. It's that in general your power will be constrained by the
  size of
  the smaller group (I assume this is Type 2 diabetes by the way).

  cheers
  Bruce

  On Thu, 13 Oct 2016, Eelco van Duinkerken wrote:

  > Hi all,
  > I am using FS with data from 2 different studies that were
  acquired on the
  > same MRI-machine with the same T1 and FLAIR sequences.
  Unfortunately, the
  > group sizes are not very balanced, with 31 controls, 16 obese
  and 32
  > diabetes patients.
  >
  > Is the GLM for thickness used in FS very sensitive to this
  unequal group
  > size?
  >
  >
  > Thanks for the help,
  >
  > Eelco
  >
  >
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--
Eelco van Duinkerken, PhD
Pontifícia Universidade Católica | Department of Psychology |
R. Marquês de São Vicente 225 | Gávea, Rio de Janeiro - RJ | CEP 
22451-900 |

Brasil |
E-mail: e.vanduinker...@vumc.nl | Phone: +55-21-35271855 |
http://lattes.cnpq.br/7180895567820901
&
VU University Medical Center | Department of Medical Psychology |
De Boelelaan 1117 | 1081 HV | Amsterdam | The Netherlands

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Re: [Freesurfer] Cortical Thickness Zero Values

2016-10-14 Thread Douglas Greve

The entire medial wall has thickness values of 0 because there is no 
cortex there. There needs to be a surface in that area because we need a 
closed surface.



On 10/12/16 8:10 PM, Taha Abdullah wrote:

Hello All,

Quick question, I ran recon-all with the qcache option and after 
converting the ?.thickness.fsaverage.mgh to an ascii text file via 
mri_convert I am noticing some vertices have 0mm thickness and it 
varies, for example, one subject had 53 vertices labeled as zeros 
while another had over 9,000 vertices. Is there a method I can use to 
have a thickness value for each of the 163000+ vertices? I am not sure 
if this is a possible registration issue to mni305.


Thanks in advance,
Taha
--
/Taha Abdullah/
/Department of Physiology,/
/Northwestern University Feinberg School of Medicine
/
/MS in Physiology and Biophysics, Georgetown University 2015/
/Work Cell: (312)-451-8468/


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Re: [Freesurfer] issue with unpacksdcmdir

2016-10-14 Thread Douglas Greve

Could be. Can you run dcmunpack instead of unpacksdcmdir? You should be 
able to use the same command line. Let me know how it goes.


doug


On 10/13/16 5:25 PM, Marco Loggia wrote:

Hello Doug and Freesurfers,

We are having trouble unpacking DTI data collected in Bay7.

Data are here: cd /autofs/eris/marco/tmp/seun

The error I get is this one, which prevents the nii file from being 
created:


ERROR: mri_convert
child killed: segmentation violation

It looks like the problem doesn’t occur for other data (E.g., BOLD, 
MPRAGE), so could it be only DTI-specific?


More details are below, and the infodump.dat file is attached. Thanks!
Marco


##
olaf:marco[195] cd /autofs/eris/marco/tmp/seun
olaf:marco[196] unpacksdcmdir -src DTI_sevoEEG_006/ -targ . -generic 
-run 10 dti nii dti.nii -unpackerr


$Id: unpacksdcmdir,v 1.23 2008/12/15 21:42:16 greve Exp $

/autofs/eris/marco/tmp/seun
-src DTI_sevoEEG_006/ -targ . -generic -run 10 dti nii dti.nii -unpackerr

Thu Oct 13 17:13:49 EDT 2016

mri_convert -all-info
ProgramName: mri_convert  ProgramArguments: -all-info  ProgramVersion: 
$Name: stable5 $  TimeStamp: 2016/10/13-21:13:49-GMT  BuildTimeStamp: 
May 14 2013 15:52:47  CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 
21:55:16 mreuter Exp $  User: marco  Machine: olaf Platform: Linux  
PlatformVersion: 2.6.32-642.3.1.el6.x86_64  CompilerName: GCC 
CompilerVersion: 40400


olaf
Linux olaf 2.6.32-642.3.1.el6.x86_64 #1 SMP Tue Jul 12 18:30:56 UTC 
2016 x86_64 x86_64 x86_64 GNU/Linux


Thu Oct 13 17:13:49 EDT 2016
Log File is ./unpack.log
INFO: Logfile is ./unpack.log
SkipMoCo 0
Scanning source directory ...
INFO: summary file is ./dicomdir.sumfile
INFO: status file is ./parse.status
Scanning directory Thu Oct 13 17:13:49 EDT 2016
mri_parse_sdcmdir --sortbyrun --d DTI_sevoEEG_006/ --o 
./dicomdir.sumfile --status ./parse.status
0   2   4   6   8  10  12  15  17  19  21  23 26  28  30  32  34  36  
38  41  43  45  47  49  52  54 56  58  60  63  65  67  69  71  73  75  
78  80  82  84 86  89  91  93  95  97 100

Done scanning Thu Oct 13 17:14:01 EDT 2016
--
 10 ep2d_diff_mgh_30dir_b1000_2000_10b0_tensor err  128 128  64  70 
MR.1.3.12.2.1107.5.2.38.51006.2015051409122443188606899

unpacking config --
{10 dti nii dti.nii}
---
-
Run 10 -
Thu Oct 13 17:14:01 EDT 2016
10 dti nii dti.nii
INFO: this run has an error, but trying anyway
mri_convert 
DTI_sevoEEG_006//MR.1.3.12.2.1107.5.2.38.51006.2015051409122443188606899 
./dti/dti.nii --sdcmlist ./dti/flf -ot nii --nspmzeropad 3 --in_type 
siemens_dicom

ERROR: mri_convert
child killed: segmentation violation



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Re: [Freesurfer] graphic board question

2016-10-14 Thread dgw

The last time I tried, I was using 5.1.0, but the graphics requirements 
are very modest and I don't believe they have increased. In the past 
there were some issues, with bad drivers on linux (I don't think this is 
an issue any longer on linux).

hth
d

On 10/14/16 10:57 AM, Dix Meiberth wrote:
> Thanks for your reply, did you use the newest release for your
> analyses?
>
> Best,
>
> DM
>
> -Ursprüngliche Nachricht- Von:
> freesurfer-boun...@nmr.mgh.harvard.edu
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von dgw
> Gesendet: Freitag, 14. Oktober 2016 16:24 An:
> freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] graphic
> board question
>
> The graphics card will not be an issue. I have used much slower
> integrated graphics without any problem.
>
> hth d
>
> On 10/14/16 9:05 AM, Dix Meiberth wrote:
>> Dear all,
>>
>>
>>
>> I'm thinking about starting a cortical thickness analysis.
>> Therefore I would like to buy a new machine, namely an Apple iMac
>> 21,5"
>>
>> including: 2,8 GHz Quad-Core Intel Core i5 (Turbo Boost up to 3,3
>> GHz); 8 GB 1867 MHz LPDDR3 RAM (on-board); Intel Iris Pro Graphics
>> 6200
>>
>>
>>
>> The Apple support told me that the graphic board may not be
>> sufficient to perform FS analyses as the Intel Iris Pro Graphics
>> 6200 card does not include an extern video memory.
>>
>> Does anyone of you has experience if the machine is in fact not
>> sufficient? Thanks in advance and
>>
>>
>>
>> best regards,
>>
>>
>>
>> DM
>>
>>
>>
>> ___ Freesurfer mailing
>> list Freesurfer@nmr.mgh.harvard.edu
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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.
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Re: [Freesurfer] How to use -openmp flag/ Please help

2016-10-14 Thread Douglas Greve

Also, don't use -qcache until after you have run and manually inspected 
your analysis


On 10/13/16 3:29 PM, Z K wrote:
> You provided us with very little information to help you solve your
> problem. Please read the "How to describe you problem" section of our wiki:
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
> However, after looking at your exact command, it appears you are using
> the "long dash" (or em dash) for your command line switches instead of
> the standard hyphen. Try using the standard hyphen as that worked for me.
>
> -Zeke
>
> On 10/13/2016 03:16 PM, Farzaneh keyvanfard wrote:
>> Dear expert
>>
>> I'm beginner in using Freesurfer and I really need your help.
>> However I've read all related responded questions about paralleling
>> process. I found -openmp N flag to do that, but I don't understand its
>> correct location in 'recon-all'. I used it as follows but it doesn't
>> work. Also I want to use -qcache flag in addition to -openmp N. Would
>> you please kindly let me know in which order, these flags should be
>> used? I really appreciate your kind help.
>>
>>
>> recon-all -i SerieMR-0002.dcm -subjid Results -all –openmp 8 –qcache
>> /
>> 
>> /
>> I'm looking forward to hearing from you.
>>
>> Best Regards*
>>
>> F. Keyvanfard*
>>
>>
>>
>> F.Keyvanfard
>> 
>>
>>
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Re: [Freesurfer] graphic board question

2016-10-14 Thread Dix Meiberth

Thanks for your reply, did you use the newest release for your analyses?

Best,

DM

-Ursprüngliche Nachricht-
Von: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von dgw
Gesendet: Freitag, 14. Oktober 2016 16:24
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] graphic board question

The graphics card will not be an issue. I have used much slower integrated 
graphics without any problem.

hth
d

On 10/14/16 9:05 AM, Dix Meiberth wrote:
> Dear all,
>
>
>
> I'm thinking about starting a cortical thickness analysis. Therefore I 
> would like to buy a new machine, namely an Apple iMac 21,5"
>
> including: 2,8 GHz Quad-Core Intel Core i5 (Turbo Boost up to 3,3 
> GHz);
> 8 GB 1867 MHz LPDDR3 RAM (on-board); Intel Iris Pro Graphics 6200
>
>
>
> The Apple support told me that the graphic board may not be sufficient 
> to perform FS analyses as the Intel Iris Pro Graphics 6200 card does 
> not include an extern video memory.
>
> Does anyone of you has experience if the machine is in fact not 
> sufficient? Thanks in advance and
>
>
>
> best regards,
>
>
>
> DM
>
>
>
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> Partners Compliance HelpLine at http://www.partners.org/complianceline 
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>
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Re: [Freesurfer] graphic board question

2016-10-14 Thread dgw

The graphics card will not be an issue. I have used much slower 
integrated graphics without any problem.

hth
d

On 10/14/16 9:05 AM, Dix Meiberth wrote:
> Dear all,
>
>
>
> I’m thinking about starting a cortical thickness analysis. Therefore I
> would like to buy a new machine, namely an Apple iMac 21,5"
>
> including: 2,8 GHz Quad-Core Intel Core i5 (Turbo Boost up to 3,3 GHz);
> 8 GB 1867 MHz LPDDR3 RAM (on-board); Intel Iris Pro Graphics 6200
>
>
>
> The Apple support told me that the graphic board may not be sufficient
> to perform FS analyses as the Intel Iris Pro Graphics 6200 card does not
> include an extern video memory.
>
> Does anyone of you has experience if the machine is in fact not
> sufficient? Thanks in advance and
>
>
>
> best regards,
>
>
>
> DM
>
>
>
> ___
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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
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[Freesurfer] graphic board question

2016-10-14 Thread Dix Meiberth

Dear all,

I'm thinking about starting a cortical thickness analysis. Therefore I would 
like to buy a new machine, namely an Apple iMac 21,5"
including: 2,8 GHz Quad-Core Intel Core i5 (Turbo Boost up to 3,3 GHz); 8 GB 
1867 MHz LPDDR3 RAM (on-board); Intel Iris Pro Graphics 6200

The Apple support told me that the graphic board may not be sufficient to 
perform FS analyses as the Intel Iris Pro Graphics 6200 card does not include 
an extern video memory.
Does anyone of you has experience if the machine is in fact not sufficient? 
Thanks in advance and

best regards,

DM
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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] Quantifying volumes

2016-10-14 Thread Damien MARIE

Hi,

Just adding a word about the e-mail of ma colleague Josue. What he meant is 
that he extracted volumes for exactly the same ROI (a merging of destrieux 
labels of Hechl’s gyrus, Heschl's sulcus and planum temporale) using 1- a .curv 
file of this ROI, mri_binarize and mri_segstats  or 2- a .label file of this 
ROI and mris_anatomical_stats.

We get a different volume output (ratio of difference between the 2 methods = 
approx. 2.5, similar to mean thickness I would say…), so we would like to 
understand what is happening exactly. 

Using the method 1, it’s actually a surface measurement we get no?

Would that be possible to convert a .cuvr file to a .label file ?

Thank you and best,
Damien

Josue Luiz Dalboni Da Rocha Wed, 12 Oct 2016 07:26:32 -0700
Dear Doug,

Thank you very much for your advice!
We get to extract results for the volumes from a ".curv file encoded ROI" using 
your recommended command lines (mri_binarize and mri_segstats ), but 
unfortunately the results are much smaller (around 3 times) than when we 
extract total gray matter volumes from a respective ".label file encoded ROI" 
using mris_anatomical_stats .
Example:
Volumes from a ".curv file encoded ROI" using your recommended command lines 
(mri_binarize and mri_segstats):
Subject1 = 1090
Subject2 = 1181
Subject3 = 713
Subject4 = 1230
Volumes from a respective ".label file encoded ROI" (mris_anatomical_stats):
Subject1 = 3497
Subject2 = 3786
Subject3 = 2268
Subject4 = 3491

Are the volumes extracted from a ".curv file encoded ROI" (using mri_binarize 
and mri_segstats) an estimation of the total gray matter volumes?
Why these values are differing that much?

Thank you very much,
Josue Dalboni

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N Greve 

Sent: Wednesday, October 5, 2016 5:19 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Quantifying volumes

I would binarize the curv file with

mri_binarize --i lh.yourcurvfile --abs --min .001 --o
lh.yourcurvfilebin.mgh

Then compute the volume with

mri_segstats --seg lh.yourcurvfilebin.mgh --id 1 --i lh.volume
--accumulate --sum lh.vol.yourcurv.sum

On 10/05/2016 09:09 AM, Josue Luiz Dalboni Da Rocha wrote:
> Dear Douglas,
>
> I have a ".curv" file that contains the curvature information inside an 
> automatically delineated ROI and 0 everywhere else.
> I would like to calculate the volume of this ROI,
>
> Can I extract statistics directly from the ".curv" file?
>
> Best regards,
> Josue
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Douglas N Greve 
> 
> Sent: Tuesday, October 4, 2016 9:41 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Quantifying volumes
>
> What is the nature of the segmentation? Is it just a binary (1=in,
> 0=out) segmentation? And what file format? In general we don't use .w
> anymore, but it can be converted into something else.
>
> doug
>
>
> On 10/03/2016 12:35 PM, Josue Luiz Dalboni Da Rocha wrote:
>> Dear Douglas,
>>
>>
>> I have a segmented gyrus curvature file (.curv or .w) and I would like
>> to calculate the volume (and other statistics) of this gyrus.
>>
>>
>> I currently only know mris_anatomical_stats to perform that, but
>> requiring a '.label' file.
>>
>>
>> Can I extract statistics directly from the ".curv" file?
>>
>>
>> Or can I convert directly from .curv to .label in order to extract
>> these statistics?
>>
>>
>> As another option, is it feasible to convert the '.curv' file to nifti
>> volume (mri_surf2vol), binarize it (mri_binarize), and then convert to
>> label (mri_cor2label)?
>>
>>
>> What does the output nifti file from 'mri_surf2vol' contain? Does it
>> contain the complete volume behind the surface? Or does it only
>> contain the surface over the 3D space?
>>
>>
>> Thank you very much in advance for your help!
>>
>>
>> Best regards,
>>
>> Josue
>>
>>
>>
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> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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>
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> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient

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