Re: [Freesurfer] Loading thickness data in python

[Satrajit Ghosh]

hi sebastian,

I would now like to create my own curvature overlay (similar to the
> thickness file) by assigning non-zero values to neighboring verteces to a
> selected vertex and zero to others. My question is: is there any way I can
> save a numpy array to a "morphometric" file using nibabel or a different
> package?
>

unfortunately write support is more sparse, but for something like this it
would not be difficult to add. a pull request on nibabel would be quite
welcome. you might even be able to peek at the matlab code to speed up the
translation to python.

cheers,

satra

On 15 July 2013 15:58, Satrajit Ghosh  wrote:
>
>> hi sebastian,
>>
>> you simply need to read the geometry file and the morphometry vector and
>> the two pieces will give you what you need.
>>
>> the geometry file gives you the relation between vertex indices via the
>> faces array.
>>
>> ```
>> def return_neighbors(faces, vertex_index):
>> faces_containing_vertex = np.nonzero((faces ==
>> vertex_index).sum(axis=1))[0]
>> neighbors = np.setdiff(faces[faces_containg_vertex, :].flatten(),
>> vertex_index)
>> return neighbors
>> ```
>>
>> cheers,
>>
>> satra
>>
>> On Mon, Jul 15, 2013 at 9:52 AM, Sebastian Urchs <
>> sebastian.ur...@gmail.com> wrote:
>>
>>> Hi Satra,
>>>
>>> thank you very much. I believe I have to rephrase my question as I
>>> didn't completely think it through. I need to find neighboring vertices to
>>> a specified vertex and then read out their thickness values. I don't think
>>> I can do this directly from the morphometry vector that pysurfer gives me.
>>>
>>> Thanks again, I'll send another mail to the mailinglist.
>>>
>>> Best,
>>> Sebastian
>>>
>>>
>>> On 15 July 2013 15:22, Satrajit Ghosh  wrote:
>>>
 hi sebastian,

 please take a look at pysurfer (https://github.com/nipy/pysurfer) and
 nibabel (https://github.com/nipy/nibabel).

 the relevant code is here:

 https://github.com/nipy/nibabel/blob/master/nibabel/freesurfer/io.py

 cheers,

 satra

 On Mon, Jul 15, 2013 at 9:11 AM, Sebastian Urchs <
 sebastian.ur...@gmail.com> wrote:

> Hi,
>
> I am trying to figure out how to load thickness data into python such
> that I would be able to identify the thickness at a given mesh node and
> also identify surrounding nodes. I searched the mailinglist and found this
> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07307.html 
> but
> this unfortunately did not solve my question as I was unable to find a
> downloadable version of pymgh.
>
> Is there some python package that you could point me to and that
> allows me to load thickness data and do analysis in python?
>
> Thanks in advance!
> Sebastian
>
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Re: [Freesurfer] Artefactual skull stripping for some subjects

[Bruce Fischl]

Hi Tudor,

yes, it got through. It's on our list of things to get to, we just 
haven't gotten there yet

Bruce
On Wed, 17 Jul 2013, Tudor Popescu wrote:


Dear Bruce,

Could you please let me know whether my message of last week, in which I
uploaded the subject's vols&surfs, have reached the list? I haven't received
a reply about those questions and was wondering whether that email maybe got
rejected due to the large size of the attachments. The questions should be
visible in plaintext below, please let me know if I should upload the files
on a sharing server

Thanks!
Tudor

On 15 July 2013 19:51, Tudor Popescu  wrote:
  Hi again,

  I was wondering whether my previous message was received, since
  it had rather large attachments. I look forward to receiving a
  reply with regards to my questions!

  Thank you,
  Tudor

  On 12 July 2013 16:03, Tudor Popescu  wrote:
Thanks Bruce. So the massive chunks that appear as
missing in freeview, e.g. at coronal slice 153, show
correctly in tkmedit, although the surfaces don't
exist there. If I mouse above that area,
brainmask.mgz intensities (which seem to be always
identical to T1.mgz ones) seem quite normal to me,
i.e. they're not all 0 but vary in a range centred
around ~100.

As for the segmentation (aseg) - not quite sure
where I need to look for that. I attach here the
main volumes & surfaces of this subject. Could my
"-wsthresh 35" recon not have replaced the existing
one?

Many thanks again!
Tudor

PS: why does freeview show the coordinates in the
order [x z y] instead of [x y z]? I.e., as I move
from anterior to posterior, I'd expect the middle
coordinate to decrease, rather than the third one.

PPS: what is the difference between brain.mgz and
brainmask.mgz? Is it to do with conformity and
intensity correction, just like the difference
between 001.mgz and T1.mgz? I would have thought
that brainmask.mgz would be a binary image (a mask
consisting of 0s and 1s), rather than a regular
(skull-stripped) structural.

On 11 July 2013 21:40, Bruce Fischl
 wrote:
  Hi Tudor

  can you cc the list so others can
  answer? What are the intensities in the
  excluded right temporal wm in the
  brainmask.mgz? What is the aseg like
  there? Looks like an intensity
  normalization failure, but I'm not sure
  why. If you want to upload the subject
  I'll take a look
  Bruce
  On Thu, 11 Jul 2013, Tudor Popescu
  wrote:

Hi Bruce,

Sorry, wasn't sure whether
you'd seen my previous
message. So in the
meantime, after the
following command for
subject C06 (whose
artefactual
skull strip I previously
included as a screenshot)
completed without error,

recon-all -skullstrip
-wsthresh 35 -clean-bm
-subjid C06

..the volumes&surfaces still
look bad (see screenshot and
recon log
attached).

C06 is just one of several
subjects for which this has
happened. Is there
anything else I can try?
Thanks!

Tudor

On 9 July 2013 13:33, Tudor
Popescu 
wrote:
      Thanks for clarifying
this Doug!

      Please let me know if
anyone has suggestions about
my other
      questions below, re
skull stripping.

      Cheers!
      T

      On 8 July 2013 18:01,
Douglas N Greve
     

wrote:

            001.mgz ->
raw.mgz -> orig.mgz ->
nu.mgz -> T1.mgz

            If you only have
one run, then 001 and raw
are the
         

Re: [Freesurfer] Artefactual skull stripping for some subjects

[Tudor Popescu]

Dear Bruce,

Could you please let me know whether my message of last week, in which I
uploaded the subject's vols&surfs, have reached the list? I haven't
received a reply about those questions and was wondering whether that email
maybe got rejected due to the large size of the attachments. The questions
should be visible in plaintext below, please let me know if I should upload
the files on a sharing server

Thanks!
Tudor

On 15 July 2013 19:51, Tudor Popescu  wrote:

> Hi again,
>
> I was wondering whether my previous message was received, since it had
> rather large attachments. I look forward to receiving a reply with regards
> to my questions!
>
> Thank you,
> Tudor
>
>
> On 12 July 2013 16:03, Tudor Popescu  wrote:
>
>> Thanks Bruce. So the massive chunks that appear as missing in freeview,
>> e.g. at coronal slice 153, show correctly in tkmedit, although the surfaces
>> don't exist there. If I mouse above that area, brainmask.mgz intensities
>> (which seem to be always identical to T1.mgz ones) seem quite normal to me,
>> i.e. they're not all 0 but vary in a range centred around ~100.
>>
>> As for the segmentation (aseg) - not quite sure where I need to look for
>> that. I attach here the main volumes & surfaces of this subject. Could my
>> "-wsthresh 35" recon not have replaced the existing one?
>>
>> Many thanks again!
>> Tudor
>>
>> PS: why does freeview show the coordinates in the order [x z y] instead
>> of [x y z]? I.e., as I move from anterior to posterior, I'd expect the
>> middle coordinate to decrease, rather than the third one.
>>
>> PPS: what is the difference between brain.mgz and brainmask.mgz? Is it to
>> do with conformity and intensity correction, just like the difference
>> between 001.mgz and T1.mgz? I would have thought that brainmask.mgz would
>> be a binary image (a mask consisting of 0s and 1s), rather than a regular
>> (skull-stripped) structural.
>>
>>
>> On 11 July 2013 21:40, Bruce Fischl  wrote:
>>
>>> Hi Tudor
>>>
>>> can you cc the list so others can answer? What are the intensities in
>>> the excluded right temporal wm in the brainmask.mgz? What is the aseg like
>>> there? Looks like an intensity normalization failure, but I'm not sure why.
>>> If you want to upload the subject I'll take a look
>>> Bruce
>>>
>>> On Thu, 11 Jul 2013, Tudor Popescu wrote:
>>>
>>>  Hi Bruce,

 Sorry, wasn't sure whether you'd seen my previous message. So in the
 meantime, after the following command for subject C06 (whose artefactual
 skull strip I previously included as a screenshot) completed without
 error,

 recon-all -skullstrip -wsthresh 35 -clean-bm -subjid C06

 ..the volumes&surfaces still look bad (see screenshot and recon log
 attached).

 C06 is just one of several subjects for which this has happened. Is
 there
 anything else I can try? Thanks!

 Tudor

 On 9 July 2013 13:33, Tudor Popescu  wrote:
   Thanks for clarifying this Doug!

   Please let me know if anyone has suggestions about my other
   questions below, re skull stripping.

   Cheers!
   T

   On 8 July 2013 18:01, Douglas N Greve
wrote:

 001.mgz -> raw.mgz -> orig.mgz -> nu.mgz -> T1.mgz

 If you only have one run, then 001 and raw are the
 same
 orig.mgz is the first conformed volume

 doug



 On 07/08/2013 12:38 PM, Tudor Popescu wrote:
 > Thanks Bruce. I have looked at that part of the
 wiki but I was
 > wondering whether the screenshots at all suggest
 that all artefacts
 > are likely to be the result of the same problem,
 and that e.g.
 > re-running recon for all subjects with a
 watershed>25 and with the
 > -no-wsgcaatlas flag might be the thing to do in
 this case, rather than
 > manually editing slices in tkmedit.
 >
 > So after making these corrections to all affected
 subjects, before
 > proceeding to analyses, is a visual inspection in
 freeview of the
 > brain.mgz of all subjects enough? It seems like
 some of these
 > skull-stripping errors are quite subtle and can be
 easily missed (as I
 > have, in fact, when I checked the output after my
 first recon-all).
 >
 > the T1.mgz is intensity corrected and
 conformed (the orig.mgz is
 > just conformed).
 >
 > So are both derived from 001.mgz? Otherwise, what
 is the difference
 > between 001.mgz and orig.mgz?
  

Re: [Freesurfer] beta weights from FS-Fast analysis

[Douglas N Greve]

Oh, right, the nuisance regressors are given a separate regressor for 
each run. I had forgotten!

On 07/17/2013 04:55 PM, Joseph Dien wrote:
>
> On Jul 17, 2013, at 4:50 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>>
>> On 07/17/2013 04:48 PM, Joseph Dien wrote:
>>> The single nuisance regressor models the difference between the merged
>>> runs.  So if the first run had a mean of 90 and the second run had a
>>> mean of 110 then the merged run mean would be 100.  The nuisance
>>> regressor has 1s for the volumes of the first run and -1s for the
>>> volumes of the second run so it ends up with a beta value of 10, thus
>>> accounting for the difference between these two sets of volumes.  I
>>> think it does make sense.
>> Do you do this in a single regressor? So you would have a +1 -1 pattern
>> repeated 4 times? I think to make it work, you would need 4 regressors.
>> In any event, FSFAST will do the right thing, so maybe it is not 
>> important.
>>>
>
> Looking at the X.X file, it did create four nuisance regressors.  I'm 
> really impressed with how well FSFAST handles all this!  :)
>
>
>>> In any case, while it was necessary to do so for my original SPM
>>> analyses since it uses a separate covariates for each run, after
>>> working through the FSFAST procedures with your help I see that is not
>>> the case for FSFAST (a single regressor models a given condition in
>>> all the runs).  I'll try doing as you suggest to see what difference
>>> it makes.
>>>
>>> It is indeed cognitive areas and the manipulations are subtle social
>>> cognition manipulations so perhaps not surprising after all.
>>>
>>> I'll send you the paradigm file separately.
>>>
>>> Thanks for taking the time to look into this!
>>>
>>> Joe
>>>
>>>
>>> On Jul 17, 2013, at 4:38 PM, Douglas N Greve
>>> mailto:gr...@nmr.mgh.harvard.edu> 
>>> > wrote:
>>>

 It is not necessary or beneficial to combine the runs in this way.
 FSFAST will do all this for you and keep account of all the runs and
 transitions. FSFAST will put in regressors to fit each of the run 
 means.
 The single regressor you have is not the right way to hand this (at
 least I don't understand how it works). It could be that the low %
 signal change is related to the colinearity between the task waveform
 and the mean regressors. Can you set things up in the way that FSFAST
 expects them and don't use any nuisance regressors?

 Also, in what area are you looking at the percent change? .02% sounds
 very small, but may be if it is in some cognitive area, maybe it is ok.
 If it is in visual cortex, then it looks way too low.

 Also, can you send the paradigm file?

 doug




 On 07/17/2013 04:27 PM, Joseph Dien wrote:
> It's a little complicated.  Basically there were eight runs,
> comprising four conditions (me, we, you1, you2) each with two
> adjoining runs.  For the analysis, I merged each of the pairs into a
> single run and added a nuisance regressor to account for the
> difference in run means.  There were a total of four different kinds
> of boxcars (AR, CS, EM, MP).  So 4x4=16 conditions.  There was also a
> covariate of non-interest to mark the switch point for each boxcar,
> one for each run, so 20 total.
>
> The 7 nuisance regressors are six movement covariates plus one to
> account for merging eight runs into four (it consists of 1 for the
> first half and -1 for the second, so the difference in the run means).
> I'm using the movement covariates from a prior SPM run since
> ARTdetect (for detecting bad volumes) isn't set up for AFNI style
> data.  From all published accounts the different movement detection
> routines yield similar enough results that it shouldn't be a problem
> (consistent with what I found when I compared them for this dataset).
>
> You're thinking that collinearity could have reduced the effect sizes?
> When I correlate the X.X regressor matrix, the 20 predictors don't
> correlate by more than about .2 at worst.  I do see greater
> correlations with some of the nuisance regressors (as high as the .4
> range).  Are my betas unusually small for FSFAST analyses?  They did
> come up clusterwise significant at least. Or should I not worry?  I'm
> not sure what to expect from FSFAST analyses.
>
> Thanks!
>
> Joe
>
>
> On Jul 17, 2013, at 3:58 PM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu> 
> 
> > wrote:
>
>> why do you have 20 conditions? And what are the 7 nuisance 
>> regressors?
>>
>> On 07/17/2013 03:54 PM, Joseph Dien wrote:
>>> It's a boxcar design so 20.265.
>>>
>>> mkanalysis-sess -fsd bold -analysis CPA.sm05.lh -surface 
>>> fsaverage lh
>>> -fwhm

[Freesurfer] recon-all steps specified into volume and surface based stream?

[Martina Papmeyer]

Dear FreeSurfer experts,

I was wondering if there is anywhere a table or hint, suggesting which  
particular steps of all the recon-all steps (i.e.  
https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable) are part  
of the volume-based or the surface-based stream or both? I also found  
this diagram  
https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllBlockDiagram but I'm  
unsure if the colours are supposed to give me any clues.

I'm familiar with the broad processing stages of the two streams off  
course but would very much love to understand the details better :)

Thank you very much for your help, Martina

-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.


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[Freesurfer] Cortical surface

[pablo najt]

Dear Freesurfer experts,  I am 
interested in running cortical surface area on longitudinal data from MRI scans 
and run multisubject comparisons (patients vs controls). I would like to ask 
you where could I find either a tutorial or a guide for performing such 
analysis. Also I am not familiar with freesurfer, so I am not sure which type 
of preprocessing should be undertaken.I would greatly appreciate your valuable 
help on this topic.Pablo 
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Re: [Freesurfer] beta weights from FS-Fast analysis

[Joseph Dien]

It's a little complicated.  Basically there were eight runs, comprising four 
conditions (me, we, you1, you2) each with two adjoining runs.  For the 
analysis, I merged each of the pairs into a single run and added a nuisance 
regressor to account for the difference in run means.  There were a total of 
four different kinds of boxcars (AR, CS, EM, MP).  So 4x4=16 conditions.  There 
was also a covariate of non-interest to mark the switch point for each boxcar, 
one for each run, so 20 total.

The 7 nuisance regressors are six movement covariates plus one to account for 
merging eight runs into four (it consists of 1 for the first half and -1 for 
the second, so the difference in the run means).  I'm using the movement 
covariates from a prior SPM run since ARTdetect (for detecting bad volumes) 
isn't set up for AFNI style data.  From all published accounts the different 
movement detection routines yield similar enough results that it shouldn't be a 
problem (consistent with what I found when I compared them for this dataset).

You're thinking that collinearity could have reduced the effect sizes?  When I 
correlate the X.X regressor matrix, the 20 predictors don't correlate by more 
than about .2 at worst.  I do see greater correlations with some of the 
nuisance regressors (as high as the .4 range).  Are my betas unusually small 
for FSFAST analyses?  They did come up clusterwise significant at least. Or 
should I not worry?  I'm not sure what to expect from FSFAST analyses.

Thanks!

Joe


On Jul 17, 2013, at 3:58 PM, Douglas N Greve  wrote:

> why do you have 20 conditions? And what are the 7 nuisance regressors?
> 
> On 07/17/2013 03:54 PM, Joseph Dien wrote:
>> It's a boxcar design so 20.265.
>> 
>> mkanalysis-sess -fsd bold -analysis CPA.sm05.lh -surface fsaverage lh 
>> -fwhm 5 -event-related-paradigm CPA1.par -nconditions 20 -spmhrf 0 -TR 
>> 2 -refeventdur 20.265 -polyfit 2 -per-run -force -nuisreg nuisreg2.dat 
>> 7 -tpexclude tpexclude.dat
>> 
>> On Jul 17, 2013, at 3:50 PM, Douglas N Greve 
>> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>> 
>>> when you ran mkanalysis-sess, what did you set --refeventdur to?
>>> On 07/17/2013 02:50 PM, Joseph Dien wrote:
 then I get on the order of .02% difference between the contrasted 
 conditions.
 The run mean values are in my expected ballpark of about 100 or so.
 The condition betas are just very very small.
 Or perhaps this is typical of FSFAST analyses?
 
 On Jul 17, 2013, at 2:00 PM, Douglas N Greve 
 mailto:gr...@nmr.mgh.harvard.edu> 
 > wrote:
 
> 
> The beta's have already been scaled. What do you get if you just
> beta/runmean ?
> 
> 
> 
> On 07/17/2013 01:45 PM, Joseph Dien wrote:
>> I implemented the ROI percent signal change formula following the
>> MarsBaR FAQ (http://marsbar.sourceforge.net/faq.html) but the values
>> I'm getting seem too small (on the order of .0002%).  Basically the
>> formula is the (beta * peak absolute value of the canonical HRF
>> regressor * 100)/(run mean).  No derivatives in this case as it is a
>> boxcar design.
>> 
>> I took the mean across all the runs since FSFAST uses the same
>> regressor across the entire experiment (unlike SPM).
>> I used the X.runflac(1).flac.ev(m).Xirf values for the canonical HRF
>> as you suggested (where m equals the condition+1).
>> 
>> Is it possible that I'm missing something in the scaling here?
>> Especially with a boxcar design, the signal change should be much
>> larger than this for a significant cluster, I think.  For example, the
>> peak HRF value for one of the conditions is 0.0092.  If the betas are
>> already scaled according to the peak value, then it would come out as
>> .02%, which is more reasonable, although still too small.
>> 
>> Thanks for your help with this!
>> 
>> Joe
>> 
>> 
>> 
>> On May 31, 2013, at 5:02 PM, Douglas N Greve
>> mailto:gr...@nmr.mgh.harvard.edu> 
>>  
>> > wrote:
>> 
>>> 
>>> Oh, right, it is probably not there for subcortical. I don't know 
>>> what I
>>> would have to do to write it out. It won't be something that happens
>>> before I get back from HBM. Can you remind me after HBM?
>>> doug
>>> 
>>> On 05/31/2013 04:44 PM, Joseph Dien wrote:
 It looks like the corrected vertex p-values
 (ex: cache.th13.abs.sig.voxel.nii.gz) are only available for the
 surface-based lh and rh spaces.  For the subcortical volume-based
 analysis I don't see the corresponding corrected voxel p-values 
 being
 available?
 
 On May 31, 2013, at 2:46 PM, Joseph Dien >>>  
 
 > 

Re: [Freesurfer] beta weights from FS-Fast analysis

[Joseph Dien]

It's a boxcar design so 20.265.

  mkanalysis-sess -fsd bold -analysis CPA.sm05.lh -surface fsaverage lh 
-fwhm 5 -event-related  -paradigm CPA1.par -nconditions 20 -spmhrf 0 -TR 2 
-refeventdur 20.265 -polyfit 2 -per-run -force -nuisreg nuisreg2.dat 7 
-tpexclude tpexclude.dat

On Jul 17, 2013, at 3:50 PM, Douglas N Greve  wrote:

> when you ran mkanalysis-sess, what did you set --refeventdur to?
> On 07/17/2013 02:50 PM, Joseph Dien wrote:
>> then I get on the order of .02% difference between the contrasted conditions.
>> The run mean values are in my expected ballpark of about 100 or so.
>> The condition betas are just very very small.
>> Or perhaps this is typical of FSFAST analyses?
>> 
>> On Jul 17, 2013, at 2:00 PM, Douglas N Greve > > wrote:
>> 
>>> 
>>> The beta's have already been scaled. What do you get if you just
>>> beta/runmean ?
>>> 
>>> 
>>> 
>>> On 07/17/2013 01:45 PM, Joseph Dien wrote:
 I implemented the ROI percent signal change formula following the
 MarsBaR FAQ (http://marsbar.sourceforge.net/faq.html) but the values
 I'm getting seem too small (on the order of .0002%).  Basically the
 formula is the (beta * peak absolute value of the canonical HRF
 regressor * 100)/(run mean).  No derivatives in this case as it is a
 boxcar design.
 
 I took the mean across all the runs since FSFAST uses the same
 regressor across the entire experiment (unlike SPM).
 I used the X.runflac(1).flac.ev(m).Xirf values for the canonical HRF
 as you suggested (where m equals the condition+1).
 
 Is it possible that I'm missing something in the scaling here?
 Especially with a boxcar design, the signal change should be much
 larger than this for a significant cluster, I think.  For example, the
 peak HRF value for one of the conditions is 0.0092.  If the betas are
 already scaled according to the peak value, then it would come out as
 .02%, which is more reasonable, although still too small.
 
 Thanks for your help with this!
 
 Joe
 
 
 
 On May 31, 2013, at 5:02 PM, Douglas N Greve
 mailto:gr...@nmr.mgh.harvard.edu> 
 > wrote:
 
> 
> Oh, right, it is probably not there for subcortical. I don't know what I
> would have to do to write it out. It won't be something that happens
> before I get back from HBM. Can you remind me after HBM?
> doug
> 
> On 05/31/2013 04:44 PM, Joseph Dien wrote:
>> It looks like the corrected vertex p-values
>> (ex: cache.th13.abs.sig.voxel.nii.gz) are only available for the
>> surface-based lh and rh spaces.  For the subcortical volume-based
>> analysis I don't see the corresponding corrected voxel p-values being
>> available?
>> 
>> On May 31, 2013, at 2:46 PM, Joseph Dien > 
>> 
>> > wrote:
>> 
>>> 
>>> On May 31, 2013, at 12:11 PM, Douglas N Greve
>>> mailto:gr...@nmr.mgh.harvard.edu> 
>>> 
>>> > wrote:
>>> 
 
 On 05/31/2013 01:49 AM, Joseph Dien wrote:
> I was able to make more progress so I'm mostly good at this point but
> I have a remaining question:
> 
> I assume the contents of sig.nii.gz (which I assume are the vertex
> p-values) are not FWE corrected.  Is it possible to get FWE-corrected
> vertex p-values?  Or are only clusterwise corrections available?
 There should be something like cache.th13.abs.sig.voxel.mgh which is
 corrected on a voxelwise basis (the th13 is just part of the name
 but it
 should be the same regardless of the threshold you choose)
 doug
>>> 
>>> Excellent!  Thanks!  :)
>>> 
> 
> Thanks again for your patience!
> 
> Joe
> 
> On May 30, 2013, at 4:37 PM, Joseph Dien  
> 
> 
> > wrote:
> 
>> Just to make sure I'm doing this right, I'm going to summarize what
>> I've taken away from your answers and to ask some new questions. In
>> order to present the results, I need two things:
>> 
>> 1) A set of histograms (with error bars) for each cluster figure to
>> show the % signal change for each of the four contrasts of interest.
>> The cache.th20.pos.y.ocn.dat file only gives it for the condition
>> where the cluster was significant so I can't use that.
>> So I could use mri_label2vol to convert cache.th20.neg.sig.ocn.annot
>> from the group level analysis to generate a mask for each cluster of
>> interest.
>> Then I could extract the value of the vo

Re: [Freesurfer] Gray matter missed in the pial layer after mri_segment

[ye tian]

Hello Erin,

Thank you so much for asking. I have been curious to know this, too.

Sincerely,
Ye


On Wed, Jul 17, 2013 at 12:41 PM, Erin Browning  wrote:

> Hello--
>
> We have a set of scans with bad artifact throughout the temporal lobe and
> the superior cortex. We've had to do the normalization steps (n3
> correction, normalization) manually on most of these scans to preserve the
> gm/wm boundary. Now, when we run mri_segment, it leaves out some gray
> matter along the pial border. Is there a correction for this? Mri_segment
> has wlo and whi and ghi, but no glo, and it doesn't look like there's a
> method to add gray matter to the pial boundary like there is to remove it.
>
> Thank you,
> Erin Browning
>
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>
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Re: [Freesurfer] Q) Medial_wall.label

[Bruce Fischl]

Hi Yune

you are better off using the ?h.cortex.label file to mask in what is 
needed for each subject


cheers
Bruce

On Wed, 17 Jul 2013, Yune Lee wrote:


Hello freesurfer experts, 
For visualization purpose (i.e., displaying group maps), I applied a mask
for medial wall regions using the files (e.g., rh.Medial_wall.label or
lh.Medial.wall.label), which I found in fsaverage/label/ directory. 

However, I noticed a somewhat imperfect medial wall masking in both
hemispheres, such that 
transversing lines are seen in unthresholded t maps for both
hemispheres (see attached ). 

Those lines eventually disappear when I increased threshold, but I wonder
why this happened. 

Any ideas? 

best,
yune 




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Re: [Freesurfer] beta weights from FS-Fast analysis

[Joseph Dien]

then I get on the order of .02% difference between the contrasted conditions.
The run mean values are in my expected ballpark of about 100 or so.
The condition betas are just very very small.
Or perhaps this is typical of FSFAST analyses?

On Jul 17, 2013, at 2:00 PM, Douglas N Greve  wrote:

> 
> The beta's have already been scaled. What do you get if you just 
> beta/runmean ?
> 
> 
> 
> On 07/17/2013 01:45 PM, Joseph Dien wrote:
>> I implemented the ROI percent signal change formula following the 
>> MarsBaR FAQ (http://marsbar.sourceforge.net/faq.html) but the values 
>> I'm getting seem too small (on the order of .0002%).  Basically the 
>> formula is the (beta * peak absolute value of the canonical HRF 
>> regressor * 100)/(run mean).  No derivatives in this case as it is a 
>> boxcar design.
>> 
>> I took the mean across all the runs since FSFAST uses the same 
>> regressor across the entire experiment (unlike SPM).
>> I used the X.runflac(1).flac.ev(m).Xirf values for the canonical HRF 
>> as you suggested (where m equals the condition+1).
>> 
>> Is it possible that I'm missing something in the scaling here? 
>> Especially with a boxcar design, the signal change should be much 
>> larger than this for a significant cluster, I think.  For example, the 
>> peak HRF value for one of the conditions is 0.0092.  If the betas are 
>> already scaled according to the peak value, then it would come out as 
>> .02%, which is more reasonable, although still too small.
>> 
>> Thanks for your help with this!
>> 
>> Joe
>> 
>> 
>> 
>> On May 31, 2013, at 5:02 PM, Douglas N Greve 
>> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>> 
>>> 
>>> Oh, right, it is probably not there for subcortical. I don't know what I
>>> would have to do to write it out. It won't be something that happens
>>> before I get back from HBM. Can you remind me after HBM?
>>> doug
>>> 
>>> On 05/31/2013 04:44 PM, Joseph Dien wrote:
 It looks like the corrected vertex p-values
 (ex: cache.th13.abs.sig.voxel.nii.gz) are only available for the
 surface-based lh and rh spaces.  For the subcortical volume-based
 analysis I don't see the corresponding corrected voxel p-values being
 available?
 
 On May 31, 2013, at 2:46 PM, Joseph Dien >>> 
 > wrote:
 
> 
> On May 31, 2013, at 12:11 PM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu> 
> > wrote:
> 
>> 
>> On 05/31/2013 01:49 AM, Joseph Dien wrote:
>>> I was able to make more progress so I'm mostly good at this point but
>>> I have a remaining question:
>>> 
>>> I assume the contents of sig.nii.gz (which I assume are the vertex
>>> p-values) are not FWE corrected.  Is it possible to get FWE-corrected
>>> vertex p-values?  Or are only clusterwise corrections available?
>> There should be something like cache.th13.abs.sig.voxel.mgh which is
>> corrected on a voxelwise basis (the th13 is just part of the name
>> but it
>> should be the same regardless of the threshold you choose)
>> doug
> 
> Excellent!  Thanks!  :)
> 
>>> 
>>> Thanks again for your patience!
>>> 
>>> Joe
>>> 
>>> On May 30, 2013, at 4:37 PM, Joseph Dien >> 
>>> 
>>> > wrote:
>>> 
 Just to make sure I'm doing this right, I'm going to summarize what
 I've taken away from your answers and to ask some new questions. In
 order to present the results, I need two things:
 
 1) A set of histograms (with error bars) for each cluster figure to
 show the % signal change for each of the four contrasts of interest.
 The cache.th20.pos.y.ocn.dat file only gives it for the condition
 where the cluster was significant so I can't use that.
 So I could use mri_label2vol to convert cache.th20.neg.sig.ocn.annot
 from the group level analysis to generate a mask for each cluster of
 interest.
 Then I could extract the value of the voxels from each
 subject's cespct file for each contrast, average them across the
 cluster ROI, then average them across each subject, to generate the
 histogram?
 This would suffice to give me the %age signal change?
 I would be doing these computations in Matlab using MRIread.
 
 2) A results table with the headings:
 
 Cluster p (FWE corrected)
 Cluster size
 Peak Voxel p (FWE corrected)
 Peak Voxel T
 Peak Voxel Coords
 BA
 Anatomical Landmark
 
 I can get the first two from
 the cache.th20.pos/neg.sig.cluster.summary files from the group 
 level
 analysis.
 I can get the peak voxel coordinates from the summary files as well.
 I can use this to get

Re: [Freesurfer] beta weights from FS-Fast analysis

[Joseph Dien]

I implemented the ROI percent signal change formula following the MarsBaR FAQ 
(http://marsbar.sourceforge.net/faq.html) but the values I'm getting seem too 
small (on the order of .0002%).  Basically the formula is the (beta * peak 
absolute value of the canonical HRF regressor * 100)/(run mean).  No 
derivatives in this case as it is a boxcar design.

I took the mean across all the runs since FSFAST uses the same regressor across 
the entire experiment (unlike SPM).
I used the X.runflac(1).flac.ev(m).Xirf values for the canonical HRF as you 
suggested (where m equals the condition+1). 

Is it possible that I'm missing something in the scaling here?  Especially with 
a boxcar design, the signal change should be much larger than this for a 
significant cluster, I think.  For example, the peak HRF value for one of the 
conditions is 0.0092.  If the betas are already scaled according to the peak 
value, then it would come out as .02%, which is more reasonable, although still 
too small.

Thanks for your help with this!

Joe



On May 31, 2013, at 5:02 PM, Douglas N Greve  wrote:

> 
> Oh, right, it is probably not there for subcortical. I don't know what I 
> would have to do to write it out. It won't be something that happens 
> before I get back from HBM. Can you remind me after HBM?
> doug
> 
> On 05/31/2013 04:44 PM, Joseph Dien wrote:
>> It looks like the corrected vertex p-values 
>> (ex: cache.th13.abs.sig.voxel.nii.gz) are only available for the 
>> surface-based lh and rh spaces.  For the subcortical volume-based 
>> analysis I don't see the corresponding corrected voxel p-values being 
>> available?
>> 
>> On May 31, 2013, at 2:46 PM, Joseph Dien > > wrote:
>> 
>>> 
>>> On May 31, 2013, at 12:11 PM, Douglas N Greve 
>>> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>>> 
 
 On 05/31/2013 01:49 AM, Joseph Dien wrote:
> I was able to make more progress so I'm mostly good at this point but
> I have a remaining question:
> 
> I assume the contents of sig.nii.gz (which I assume are the vertex
> p-values) are not FWE corrected.  Is it possible to get FWE-corrected
> vertex p-values?  Or are only clusterwise corrections available?
 There should be something like cache.th13.abs.sig.voxel.mgh which is
 corrected on a voxelwise basis (the th13 is just part of the name 
 but it
 should be the same regardless of the threshold you choose)
 doug
>>> 
>>> Excellent!  Thanks!  :)
>>> 
> 
> Thanks again for your patience!
> 
> Joe
> 
> On May 30, 2013, at 4:37 PM, Joseph Dien  
> > wrote:
> 
>> Just to make sure I'm doing this right, I'm going to summarize what
>> I've taken away from your answers and to ask some new questions. In
>> order to present the results, I need two things:
>> 
>> 1) A set of histograms (with error bars) for each cluster figure to
>> show the % signal change for each of the four contrasts of interest.
>> The cache.th20.pos.y.ocn.dat file only gives it for the condition
>> where the cluster was significant so I can't use that.
>> So I could use mri_label2vol to convert cache.th20.neg.sig.ocn.annot
>> from the group level analysis to generate a mask for each cluster of
>> interest.
>> Then I could extract the value of the voxels from each
>> subject's cespct file for each contrast, average them across the
>> cluster ROI, then average them across each subject, to generate the
>> histogram?
>> This would suffice to give me the %age signal change?
>> I would be doing these computations in Matlab using MRIread.
>> 
>> 2) A results table with the headings:
>> 
>> Cluster p (FWE corrected)
>> Cluster size
>> Peak Voxel p (FWE corrected)
>> Peak Voxel T
>> Peak Voxel Coords
>> BA
>> Anatomical Landmark
>> 
>> I can get the first two from
>> the cache.th20.pos/neg.sig.cluster.summary files from the group level
>> analysis.
>> I can get the peak voxel coordinates from the summary files as well.
>> I can use this to get the peak voxel p from the group
>> level sig.nii.gz file.  Is this FWE corrected?  If not, how can I get
>> this information?
>> I can use these coordinates to get the peak voxel T by getting the
>> value from the group level F.nii.gz file and taking its square root.
>> How can I get the sign of the T statistic?
>> I can use the Lancaster transform to convert the MNI305 peak voxel
>> coordinates into the Atlas coordinates to look up the putative BA and
>> landmarks (unless there is a better way with Freesurfer?  I'm seeing
>> some references to some BA labels in the forum but it doesn't look
>> like this is a complete set yet?).
>> 
>> Sorry for all these questions!  I got some nice results from FSFAST
>> and would like to get them written up.
>> 
>>

[Freesurfer] Crash in mri_register_ca during recon-all -base id -tp id1 -tp id2 -all

[Knut J Bjuland]

Hi,
I have some trouble running recon-all longitudinal pipelines. When 
recon-all comes to mri_register_ca it crashes without giving a message, 
even tough 8g ram was available. I have run the program with -debug. Is 
there any other option I may use? The system is running Rocks 6.0 
(Mamba), and it uses Slurm queue system.

Can I use the FreeSurfer 5.3 longitudinal process with data processed 
with FreeSurfer 5.1? I wish to use the new Longitudinal linear mixed 
effects model  MATLAB tools.

Knut J
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[Freesurfer] Gray matter missed in the pial layer after mri_segment

[Erin Browning]

Hello--

We have a set of scans with bad artifact throughout the temporal lobe and
the superior cortex. We've had to do the normalization steps (n3
correction, normalization) manually on most of these scans to preserve the
gm/wm boundary. Now, when we run mri_segment, it leaves out some gray
matter along the pial border. Is there a correction for this? Mri_segment
has wlo and whi and ghi, but no glo, and it doesn't look like there's a
method to add gray matter to the pial boundary like there is to remove it.

Thank you,
Erin Browning
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Re: [Freesurfer] SWI acquisition question

[Fotiadis, Panagiotis]

Hi Bruce,

Don't worry about it!
In addition, I was wondering about something else as well. I've been using 
MRIcron to analyze some of my Susceptibility Clinical Scans and even though 
they used to open fine, some of them (like the one I have attached in this 
email) appear distorted in a way. In the images I attached the "Original" one 
is how the Susceptibility clinical image should appear like, and the 
"Distorted" is how it appears for some of my subjects. Would you happen to know 
why is this happening?
Thanks again for your time and help!

Best,
Panos

From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Wednesday, July 17, 2013 11:54 AM
To: Fotiadis, Panagiotis
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] SWI acquisition question

Hi Panos

sorry, I think this is pretty far outside our expertise, and it would be
hard in any case to try to figure out what happened to give you these
strange looking results. I certainly don't have any insight

sorry,
Bruce
On Wed, 17 Jul
2013, Fotiadis, Panagiotis wrote:

> Hi FS Community,
>
> I was wondering whether anyone had a chance to look into this. Thanks again 
> for your time!
>
> Best,
> Panos
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Fotiadis, Panagiotis
> Sent: Tuesday, July 16, 2013 2:00 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: [Freesurfer] SWI acquisition question
>
> Hi FreeSurfer community,
>
> I am analyzing some SWI scans of some old subjects. For most of my subjects 
> when a SWI was acquired, the resulting files that I would get would be a 
> Magnitude image, a Phase image, a mIP image, and the SWI image. However, I 
> have a couple of subjects for whom I get only the mIP and the SWI images, and 
> the SWI image looks more blurry than it's supposed to be. I was wondering:
>
> 1) Why do I get only the mIP and the SWI images for those subjects and not 
> the magnitude and phase images as well,
> 2) Is it normal for the mIP to look like that? Usually it looks different, and
> 3) Why is the final SWI image more blurry than usual? By looking at the 
> image, I believe that maybe the head coil was not properly connected to the 
> scanner at the time of the acquisition but I don't know whether that would be 
> a sufficient explanation.
>
> I have attached two attachments: One of the resulting mIP and one of the 
> equivalent blurry SWI of the same subject.
>
> Thank you in advance for your help and time!
>
> Best,
> Panos
>
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Re: [Freesurfer] kvlQuantifyHippocampalSubfieldSegmentations.sh empty text files

[Jasmeet Hayes]

That worked, thanks for your help!


On Wed, Jul 17, 2013 at 12:00 PM, Juan Eugenio Iglesias <
igles...@nmr.mgh.harvard.edu> wrote:

>  OK, then the question is why kvlQuantifyPosteriorProbabilityImages is
> producing an empty file
> I think the problem is that kvlQuantifyHippocampalSubfieldSegmentations.sh
> behaves in a different way depending on the number arguments, etc. I would
> suggest that you go back to the original version of the script, and use it
> the way it's described in
> http://ftp.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation,
> that is, setting the environment variable SUBJECTS_DIR and calling the
> script without arguments.
> Kind regards,
> /Eugenio
>
>
>
>
> On 07/17/2013 11:46 AM, Jasmeet Hayes wrote:
>
> Hi Eugenio,
>
>  We are using version 5.1. I attached our script. We added to line 60,
> setting the subject directory. We also changed the statFileName (see line
> 291 on the attached script).  I should also note that the volumeStats_left
> and right text files within each subject's mri folder is empty. Thanks for
> your help.
>
>
> On Wed, Jul 17, 2013 at 11:16 AM, Juan Eugenio Iglesias <
> igles...@nmr.mgh.harvard.edu> wrote:
>
>>  Hi Jasmeet,
>> what modification did you exactly make? Whih version of FreeSurfer is
>> this?
>> Cheers,
>> /Eugenio
>>
>>
>> On 07/17/2013 10:22 AM, Jasmeet Hayes wrote:
>>
>>  Dear Freesurfer experts,
>>
>>  I tried running the kvlQuantifyHippocampalSubfieldSegmentations.sh
>> script and get two text files (left & right stats) but the only information
>> in the text files is the subject ID number.
>>
>>  However, on my terminal window, I can see the volume output for each
>> subfield and for each subject (see below for an example of 1 subject). And
>> there were no errors after running the script.
>>
>>  Every subject in the folder went through the hippocampal subfield recon
>> procedure, and I have verified that there were no errors (each subject's
>> folder has the left and right posterior_* files).
>>
>>  We made a slight modification to the kvl script, only to change the
>> Subject directory. Any ideas about what might be the problem? Thanks!
>> -Jasmeet
>>
>>  cd .. Quantifying subject er002_recon/ right Doing right side cd mri
>> THIS IS THE COMPRESSION LOOKUP TABLE FILE
>> /Applications/freesurfer/data/GEMS/compressionLookupTable.txt PWD before
>> running KVLQuantifyPosteriorProb IS:
>> /Volumes/VA_Imaging/Projects/jpannuhayes/emoreg/HIPPOCAMPAL_SUBFIELDS/er002_recon/mri
>> kvlQuantifyPosteriorProbabilityImages
>> /Applications/freesurfer/data/GEMS/compressionLookupTable.txt
>> posterior_Right-Hippocampus.mgz posterior_right_presubiculum.mgz
>> posterior_right_CA1.mgz posterior_right_CA2-3.mgz
>> posterior_right_fimbria.mgz posterior_right_subiculum.mgz
>> posterior_right_CA4-DG.mgz posterior_right_hippocampal_fissure.mgz >
>> volumeStats_right.txt volumeInVoxels: Right-Hippocampus: 3094.49
>> right_presubiculum: 4373.15 right_CA1: 2483.23 right_CA2-3: 8192.11
>> right_fimbria: 740.934 right_subiculum: 5402.79 right_CA4-DG: 4688.93
>> right_hippocampal_fissure: 541.872 cd .. cd ..
>>
>>
>>  ___
>> Freesurfer mailing 
>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> --
>> -
>> Juan Eugenio Iglesias, 
>> PhDhttp://www.jeiglesias.comigles...@nmr.mgh.harvard.edu
>> Athinoula A. Martinos Center for Biomedical Imaging
>> 149 Thirteenth Street, Suite 2301
>> Charlestown, Massachusetts 2129
>> U.S.A.
>>
>> 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.
>>
>
>
> --
> -
> Juan Eugenio Iglesias, 
> PhDhttp://www.jeiglesias.comigles...@nmr.mgh.harvard.edu
> Athinoula A. Martinos Center for Biomedical Imaging
> 149 Thirteenth Street, Suite 2301
> Charlestown, Massachusetts 2129
> U.S.A.
>
>
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Re: [Freesurfer] Missing flirt.fsl file in bin folder

[Z K]

Hello,

Individuals who downloaded Freesurfer v5.3 for snow leopard (32bit) will 
be missing six fsl routines. A patch has been created and can be 
downloaded from this link:

ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/freesurfer_fsl.tar.gz

To apply the patch, simply extract the contents of the above file into 
the "/Applications/freesurfer/bin" directory. This should result in six 
new files in the "/Applications/freesurfer/bin" directory all with the 
.fsl extension.

-Zeke



On 07/17/2013 09:33 AM, Gundran, Andrew wrote:
> Hello freesurfers,
>
> I’ve been trying to run tracula on freesurfer and it seems that when I get to 
> the point where it uses FSL’s flirt I receive an error. I looked into it 
> further and it seems I am missing a file to run flirt:
>
> $FREESURFER_HOME/bin/flirt.fsl
>
> It seems that I somehow do not have that file to complete tracula.  I was 
> hoping someone could help with this or perhaps send me the file?
>
>
> I am using freesurfer-
> Darwin-snowleopard-i686-stable-pub-v5.3.0-
> MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0:
>
> Hope to hear from someone soon,
> Andrew
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Re: [Freesurfer] convert DK atlas ROI to .nii.gz in MNI space

[Douglas N Greve]

does htis answer your question? It is from running mri_label2vol with --help
doug

--temp tempvolid

Template volume. The output volume will have the same size and geometry
as the template. Template must have geometry information (ie, direction
cosines and voxel sizes). Required.



On 07/17/2013 12:11 PM, Yang, Daniel wrote:
> Hi Doug,
>
> Can I ask a basic question about mri_label2vol? in mri_label2vol, what 
> should be the input for "--temp"? I understand it's supposed to be the 
> template image. If it's the native space, should it be rawavg.mgz or 
> orig.mgz for that individual?
>
> Great thanks!
>
> Best,
> Daniel
>
> -- 
> Yung-Jui "Daniel" Yang, PhD
> Postdoctoral Researcher
> Yale Child Study Center
> New Haven, CT
> (203) 737-5454
>
> On 7/16/13 9:13 PM, "Douglas Greve"  > wrote:
>
>
> use
>
> $FREESURFER_HOME/average/mni152.register.dat
>
> doug
>
> On 7/16/13 8:36 PM, Yang, Daniel wrote:
>> Dear FreeSurfer Experts,
>>
>> I am interested in a specific ROI in the DK atlas, and I know
>> that I can use tkregister2 to obtain a register.dat, and then
>> mri_annotation2label + mri_label2vol to convert the annotation of
>> the ROI to an .nii.gz.
>>
>> However, it seems that the end product is in the TAL space? If
>> yes, how can I convert it to the MNI 152 space?
>>
>> Many thanks!!
>>
>> Best,
>> Daniel
>> -- 
>> Yung-Jui "Daniel" Yang, PhD
>> Postdoctoral Researcher
>> Yale Child Study Center
>> New Haven, CT
>> (203) 737-5454
>>
>>
>> ___
>> Freesurfer mailing list
>> 
>> freesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>

-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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

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Re: [Freesurfer] convert DK atlas ROI to .nii.gz in MNI space

[Yang, Daniel]

Hi Doug,

Can I ask a basic question about mri_label2vol? in mri_label2vol, what should 
be the input for "--temp"? I understand it's supposed to be the template image. 
If it's the native space, should it be rawavg.mgz or orig.mgz for that 
individual?

Great thanks!

Best,
Daniel

--
Yung-Jui "Daniel" Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454

On 7/16/13 9:13 PM, "Douglas Greve" 
mailto:gr...@nmr.mgh.harvard.edu>> wrote:


use

$FREESURFER_HOME/average/mni152.register.dat

doug

On 7/16/13 8:36 PM, Yang, Daniel wrote:
Dear FreeSurfer Experts,

I am interested in a specific ROI in the DK atlas, and I know that I can use 
tkregister2 to obtain a register.dat, and then mri_annotation2label + 
mri_label2vol to convert the annotation of the ROI to an .nii.gz.

However, it seems that the end product is in the TAL space? If yes, how can I 
convert it to the MNI 152 space?

Many thanks!!

Best,
Daniel
--
Yung-Jui "Daniel" Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454



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Re: [Freesurfer] kvlQuantifyHippocampalSubfieldSegmentations.sh empty text files

[Juan Eugenio Iglesias]

OK, then the question is why kvlQuantifyPosteriorProbabilityImages is 
producing an empty file
I think the problem is that 
kvlQuantifyHippocampalSubfieldSegmentations.sh behaves in a different 
way depending on the number arguments, etc. I would suggest that you go 
back to the original version of the script, and use it the way it's 
described in 
http://ftp.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation, 
that is, setting the environment variable SUBJECTS_DIR and calling the 
script without arguments.

Kind regards,
/Eugenio



On 07/17/2013 11:46 AM, Jasmeet Hayes wrote:

Hi Eugenio,

We are using version 5.1. I attached our script. We added to line 60, 
setting the subject directory. We also changed the statFileName (see 
line 291 on the attached script).  I should also note that the 
volumeStats_left and right text files within each subject's mri folder 
is empty. Thanks for your help.



On Wed, Jul 17, 2013 at 11:16 AM, Juan Eugenio Iglesias 
mailto:igles...@nmr.mgh.harvard.edu>> 
wrote:


Hi Jasmeet,
what modification did you exactly make? Whih version of FreeSurfer
is this?
Cheers,
/Eugenio


On 07/17/2013 10:22 AM, Jasmeet Hayes wrote:

Dear Freesurfer experts,

I tried running the
kvlQuantifyHippocampalSubfieldSegmentations.sh script and get two
text files (left & right stats) but the only information in the
text files is the subject ID number.

However, on my terminal window, I can see the volume output for
each subfield and for each subject (see below for an example of 1
subject). And there were no errors after running the script.

Every subject in the folder went through the hippocampal subfield
recon procedure, and I have verified that there were no errors
(each subject's folder has the left and right posterior_* files).

We made a slight modification to the kvl script, only to change
the Subject directory. Any ideas about what might be the problem?
Thanks! -Jasmeet

cd .. Quantifying subject er002_recon/ right Doing right side cd
mri THIS IS THE COMPRESSION LOOKUP TABLE FILE
/Applications/freesurfer/data/GEMS/compressionLookupTable.txt PWD
before running KVLQuantifyPosteriorProb IS:

/Volumes/VA_Imaging/Projects/jpannuhayes/emoreg/HIPPOCAMPAL_SUBFIELDS/er002_recon/mri
kvlQuantifyPosteriorProbabilityImages
/Applications/freesurfer/data/GEMS/compressionLookupTable.txt
posterior_Right-Hippocampus.mgz posterior_right_presubiculum.mgz
posterior_right_CA1.mgz posterior_right_CA2-3.mgz
posterior_right_fimbria.mgz posterior_right_subiculum.mgz
posterior_right_CA4-DG.mgz
posterior_right_hippocampal_fissure.mgz > volumeStats_right.txt
volumeInVoxels: Right-Hippocampus: 3094.49 right_presubiculum:
4373.15 right_CA1: 2483.23 right_CA2-3: 8192.11 right_fimbria:
740.934 right_subiculum: 5402.79 right_CA4-DG: 4688.93
right_hippocampal_fissure: 541.872 cd .. cd ..


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-- 
-

Juan Eugenio Iglesias, PhD
http://www.jeiglesias.com
igles...@nmr.mgh.harvard.edu  
Athinoula A. Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, Massachusetts 2129
U.S.A.

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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
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dispose of the e-mail.




--
-
Juan Eugenio Iglesias, PhD
http://www.jeiglesias.com
igles...@nmr.mgh.harvard.edu
Athinoula A. Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, Massachusetts 2129
U.S.A.

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Re: [Freesurfer] SWI acquisition question

[Bruce Fischl]

Hi Panos

sorry, I think this is pretty far outside our expertise, and it would be 
hard in any case to try to figure out what happened to give you these 
strange looking results. I certainly don't have any insight

sorry,
Bruce
On Wed, 17 Jul 
2013, Fotiadis, Panagiotis wrote:

> Hi FS Community,
>
> I was wondering whether anyone had a chance to look into this. Thanks again 
> for your time!
>
> Best,
> Panos
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Fotiadis, Panagiotis
> Sent: Tuesday, July 16, 2013 2:00 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: [Freesurfer] SWI acquisition question
>
> Hi FreeSurfer community,
>
> I am analyzing some SWI scans of some old subjects. For most of my subjects 
> when a SWI was acquired, the resulting files that I would get would be a 
> Magnitude image, a Phase image, a mIP image, and the SWI image. However, I 
> have a couple of subjects for whom I get only the mIP and the SWI images, and 
> the SWI image looks more blurry than it's supposed to be. I was wondering:
>
> 1) Why do I get only the mIP and the SWI images for those subjects and not 
> the magnitude and phase images as well,
> 2) Is it normal for the mIP to look like that? Usually it looks different, and
> 3) Why is the final SWI image more blurry than usual? By looking at the 
> image, I believe that maybe the head coil was not properly connected to the 
> scanner at the time of the acquisition but I don't know whether that would be 
> a sufficient explanation.
>
> I have attached two attachments: One of the resulting mIP and one of the 
> equivalent blurry SWI of the same subject.
>
> Thank you in advance for your help and time!
>
> Best,
> Panos
>
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Re: [Freesurfer] bvecs error from Tracula

[amirhossein manzouri]

The format of my bval file was wrong so I edited your file and tried and it
worked, also bvec should be in three columns as you have mentioned before.


On Wed, Jul 17, 2013 at 5:11 PM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:

>
> Good to hear! Can you please share with all of us what was wrong with your
> original files? It may help others who have the same problem in the future.
> Thanks!
>
>
> On Wed, 17 Jul 2013, amirhossein manzouri wrote:
>
>  Thanks Anastasia,
>> IT HELPED!
>>
>>
>> On Tue, Jul 16, 2013 at 5:25 PM, Anastasia Yendiki <
>> ayend...@nmr.mgh.harvard.edu>
>> wrote:
>>
>>   Hi Amirhossein - I'm attaching sample files.
>>
>>   a.y
>>
>>   On Tue, 16 Jul 2013, amirhossein manzouri wrote:
>>
>> Hi Anastasia,
>> I have tried both , 3-row and 3-column format and still
>> wrong bvecc and bval
>> from flip4fsl. Could you please send me a sample of your
>> original files so I
>> can compare?
>>
>>
>> On Mon, Jul 15, 2013 at 7:44 PM, Anastasia Yendiki
>>  wrote:
>>
>>   Hi Amirhossein - Are your original bvecs/bvals in
>> 3-row format
>>   instead of 3-column format?
>>
>> 
>> http://surfer.nmr.mgh.harvard.**edu/fswiki/FsTutorial/Tracula
>>
>>   Thanks,
>>   a.y
>>
>>   On Mon, 15 Jul 2013, amirhossein manzouri wrote:
>>
>> Dear Experts,
>> I am running trac-all -prep -c dmrirc on my
>> DWI
>> data. After flip4fsl step I get the attached
>> bval
>> and bvec file which the bvec one is wrong so
>> the
>> process exits
>> with error in dtifit. I have also attached
>>  original
>> bvec and bval.
>>
>> --
>> Best regards,
>> Amirhossein Manzouri
>>
>>
>>
>>
>>
>>
>>
>> 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.
>>
>>
>>
>>
>> --
>> Best regards,
>> Amirhossein Manzouri
>>
>>
>>
>>
>>
>>
>>
>> --
>> Best regards,
>> Amirhossein Manzouri
>>
>>
>>
>>
>>


-- 
Best regards,
Amirhossein Manzouri
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Re: [Freesurfer] kvlQuantifyHippocampalSubfieldSegmentations.sh empty text files

[Jasmeet Hayes]

Hi Eugenio,

We are using version 5.1. I attached our script. We added to line 60,
setting the subject directory. We also changed the statFileName (see line
291 on the attached script).  I should also note that the volumeStats_left
and right text files within each subject's mri folder is empty. Thanks for
your help.


On Wed, Jul 17, 2013 at 11:16 AM, Juan Eugenio Iglesias <
igles...@nmr.mgh.harvard.edu> wrote:

>  Hi Jasmeet,
> what modification did you exactly make? Whih version of FreeSurfer is this?
> Cheers,
> /Eugenio
>
>
> On 07/17/2013 10:22 AM, Jasmeet Hayes wrote:
>
> Dear Freesurfer experts,
>
>  I tried running the kvlQuantifyHippocampalSubfieldSegmentations.sh
> script and get two text files (left & right stats) but the only information
> in the text files is the subject ID number.
>
>  However, on my terminal window, I can see the volume output for each
> subfield and for each subject (see below for an example of 1 subject). And
> there were no errors after running the script.
>
>  Every subject in the folder went through the hippocampal subfield recon
> procedure, and I have verified that there were no errors (each subject's
> folder has the left and right posterior_* files).
>
>  We made a slight modification to the kvl script, only to change the
> Subject directory. Any ideas about what might be the problem? Thanks!
> -Jasmeet
>
>  cd .. Quantifying subject er002_recon/ right Doing right side cd mri
> THIS IS THE COMPRESSION LOOKUP TABLE FILE
> /Applications/freesurfer/data/GEMS/compressionLookupTable.txt PWD before
> running KVLQuantifyPosteriorProb IS:
> /Volumes/VA_Imaging/Projects/jpannuhayes/emoreg/HIPPOCAMPAL_SUBFIELDS/er002_recon/mri
> kvlQuantifyPosteriorProbabilityImages
> /Applications/freesurfer/data/GEMS/compressionLookupTable.txt
> posterior_Right-Hippocampus.mgz posterior_right_presubiculum.mgz
> posterior_right_CA1.mgz posterior_right_CA2-3.mgz
> posterior_right_fimbria.mgz posterior_right_subiculum.mgz
> posterior_right_CA4-DG.mgz posterior_right_hippocampal_fissure.mgz >
> volumeStats_right.txt volumeInVoxels: Right-Hippocampus: 3094.49
> right_presubiculum: 4373.15 right_CA1: 2483.23 right_CA2-3: 8192.11
> right_fimbria: 740.934 right_subiculum: 5402.79 right_CA4-DG: 4688.93
> right_hippocampal_fissure: 541.872 cd .. cd ..
>
>
> ___
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>
>
> --
> -
> Juan Eugenio Iglesias, 
> PhDhttp://www.jeiglesias.comigles...@nmr.mgh.harvard.edu
> Athinoula A. Martinos Center for Biomedical Imaging
> 149 Thirteenth Street, Suite 2301
> Charlestown, Massachusetts 2129
> U.S.A.
>
>  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.
>


kvlQuantifyHippocampalSubfieldSegmentations.sh
Description: Bourne shell script
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Re: [Freesurfer] kvlQuantifyHippocampalSubfieldSegmentations.sh empty text files

[Juan Eugenio Iglesias]

Hi Jasmeet,
what modification did you exactly make? Whih version of FreeSurfer is this?
Cheers,
/Eugenio

On 07/17/2013 10:22 AM, Jasmeet Hayes wrote:

Dear Freesurfer experts,

I tried running the kvlQuantifyHippocampalSubfieldSegmentations.sh 
script and get two text files (left & right stats) but the only 
information in the text files is the subject ID number.


However, on my terminal window, I can see the volume output for each 
subfield and for each subject (see below for an example of 1 subject). 
And there were no errors after running the script.


Every subject in the folder went through the hippocampal subfield 
recon procedure, and I have verified that there were no errors (each 
subject's folder has the left and right posterior_* files).


We made a slight modification to the kvl script, only to change the 
Subject directory. Any ideas about what might be the problem? Thanks! 
-Jasmeet


cd .. Quantifying subject er002_recon/ right Doing right side cd mri 
THIS IS THE COMPRESSION LOOKUP TABLE FILE 
/Applications/freesurfer/data/GEMS/compressionLookupTable.txt PWD 
before running KVLQuantifyPosteriorProb IS: 
/Volumes/VA_Imaging/Projects/jpannuhayes/emoreg/HIPPOCAMPAL_SUBFIELDS/er002_recon/mri 
kvlQuantifyPosteriorProbabilityImages 
/Applications/freesurfer/data/GEMS/compressionLookupTable.txt 
posterior_Right-Hippocampus.mgz posterior_right_presubiculum.mgz 
posterior_right_CA1.mgz posterior_right_CA2-3.mgz 
posterior_right_fimbria.mgz posterior_right_subiculum.mgz 
posterior_right_CA4-DG.mgz posterior_right_hippocampal_fissure.mgz > 
volumeStats_right.txt volumeInVoxels: Right-Hippocampus: 3094.49 
right_presubiculum: 4373.15 right_CA1: 2483.23 right_CA2-3: 8192.11 
right_fimbria: 740.934 right_subiculum: 5402.79 right_CA4-DG: 4688.93 
right_hippocampal_fissure: 541.872 cd .. cd ..



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-
Juan Eugenio Iglesias, PhD
http://www.jeiglesias.com
igles...@nmr.mgh.harvard.edu
Athinoula A. Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, Massachusetts 2129
U.S.A.

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Re: [Freesurfer] bvecs error from Tracula

[Anastasia Yendiki]

Good to hear! Can you please share with all of us what was wrong with your 
original files? It may help others who have the same problem in the 
future. Thanks!


On Wed, 17 Jul 2013, amirhossein manzouri wrote:


Thanks Anastasia, 
IT HELPED!


On Tue, Jul 16, 2013 at 5:25 PM, Anastasia Yendiki 

wrote:

  Hi Amirhossein - I'm attaching sample files.

  a.y

  On Tue, 16 Jul 2013, amirhossein manzouri wrote:

Hi Anastasia, 
I have tried both , 3-row and 3-column format and still
wrong bvecc and bval
from flip4fsl. Could you please send me a sample of your
original files so I
can compare?


On Mon, Jul 15, 2013 at 7:44 PM, Anastasia Yendiki
 wrote:

      Hi Amirhossein - Are your original bvecs/bvals in
3-row format
      instead of 3-column format?
     
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula

      Thanks,
      a.y

      On Mon, 15 Jul 2013, amirhossein manzouri wrote:

            Dear Experts, 
            I am running trac-all -prep -c dmrirc on my
DWI
            data. After flip4fsl step I get the attached
bval
            and bvec file which the bvec one is wrong so
the
            process exits
            with error in dtifit. I have also attached
 original
            bvec and bval.

            --
            Best regards,
            Amirhossein Manzouri 

             





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.




--
Best regards,
Amirhossein Manzouri 

 





--
Best regards,
Amirhossein Manzouri 

 


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Re: [Freesurfer] Freesurfer installation

[Z K]

Pablo,

That page "describes how to setup a personal laptop for usage in the 
Freesurfer course." It does not apply to a standard freesurfer 
installation.

Try opening a new terminal and typing "bash" before the "export" and 
"source" commands you give below.

-Zeke


On 07/17/2013 10:27 AM, pablo najt wrote:
> Dear Freesurfer experts,
>
>   I have a question regarding the installation/running of FreeSurfer.
>
> I have been trying to install freesurfer in a macbook pro (snow leopard)
> but no success.
>
> I followed the webpage from freesurfer (link below).
>
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PersonalLaptopSetup
>
>
> But after the installations when I open the terminal nothing happens.
>
>
> I also tried to launch freesurfer this way:
>
> export FREESURFER_HOME=/Applications/freesurfer
>
> source $FREESURFER_HOME/SetUpFreeSurfer.sh
>
> If I do this I get:
>
> command not found
>
> command not found
>
> command not found
>
>
> Any advice on how to finally set up the software would be great help.
>
> Thank you in anticipation.
>
> Pablo
>
>
>
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>
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[Freesurfer] Freesurfer installation

[pablo najt]

Dear Freesurfer experts,
 I have a question regarding the installation/running of FreeSurfer.
I have been trying to install freesurfer in a macbook pro (snow leopard) but no 
success. 
I followed the webpage from freesurfer (link below). 


https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PersonalLaptopSetup


But after the installations when I open the terminal nothing happens.


I also tried to launch freesurfer this way:
export FREESURFER_HOME=/Applications/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh
If I do this I get:
command not found
command not found
command not found


Any advice on how to finally set up the software would be great help.
Thank you in anticipation.Pablo   ___
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[Freesurfer] kvlQuantifyHippocampalSubfieldSegmentations.sh empty text files

[Jasmeet Hayes]

Dear Freesurfer experts,

I tried running the kvlQuantifyHippocampalSubfieldSegmentations.sh script
and get two text files (left & right stats) but the only information in the
text files is the subject ID number.

However, on my terminal window, I can see the volume output for each
subfield and for each subject (see below for an example of 1 subject). And
there were no errors after running the script.

Every subject in the folder went through the hippocampal subfield recon
procedure, and I have verified that there were no errors (each subject's
folder has the left and right posterior_* files).

We made a slight modification to the kvl script, only to change the Subject
directory. Any ideas about what might be the problem? Thanks! -Jasmeet

cd .. Quantifying subject er002_recon/ right Doing right side cd mri THIS
IS THE COMPRESSION LOOKUP TABLE FILE
/Applications/freesurfer/data/GEMS/compressionLookupTable.txt PWD before
running KVLQuantifyPosteriorProb IS:
/Volumes/VA_Imaging/Projects/jpannuhayes/emoreg/HIPPOCAMPAL_SUBFIELDS/er002_recon/mri
kvlQuantifyPosteriorProbabilityImages
/Applications/freesurfer/data/GEMS/compressionLookupTable.txt
posterior_Right-Hippocampus.mgz posterior_right_presubiculum.mgz
posterior_right_CA1.mgz posterior_right_CA2-3.mgz
posterior_right_fimbria.mgz posterior_right_subiculum.mgz
posterior_right_CA4-DG.mgz posterior_right_hippocampal_fissure.mgz >
volumeStats_right.txt volumeInVoxels: Right-Hippocampus: 3094.49
right_presubiculum: 4373.15 right_CA1: 2483.23 right_CA2-3: 8192.11
right_fimbria: 740.934 right_subiculum: 5402.79 right_CA4-DG: 4688.93
right_hippocampal_fissure: 541.872 cd .. cd ..
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[Freesurfer] Propagating changes to segmentation

[Liane Hunter]

Hello,

I have a question about propagating changes to segmentation. Once I have
saved my edits what is the appropriate command to propagate these changes
for both cortical and subcortical changes that I have made.

The workflow instructs that after segmentation edits are made to run

 -normalization -maskbfs -segmentation -autorecon2-wm -autorecon3 to the wm.
mgz file. However the instructions indicate to open brainmask.mgz to make
edits.  Should I make changes on the wm.mgz file?

Any clarification on this topic would be much appreciated.

-- 
Liane Hunter
MD/Ph.D Candidate
Albert Einstein College of Medicine
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[Freesurfer] Missing flirt.fsl file in bin folder

[Gundran, Andrew]

Hello freesurfers,

I’ve been trying to run tracula on freesurfer and it seems that when I get to 
the point where it uses FSL’s flirt I receive an error. I looked into it 
further and it seems I am missing a file to run flirt:

$FREESURFER_HOME/bin/flirt.fsl

It seems that I somehow do not have that file to complete tracula.  I was 
hoping someone could help with this or perhaps send me the file?


I am using freesurfer-
Darwin-snowleopard-i686-stable-pub-v5.3.0-
MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0:

Hope to hear from someone soon,
Andrew 
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Re: [Freesurfer] bvecs error from Tracula

[amirhossein manzouri]

Thanks Anastasia,
IT HELPED!


On Tue, Jul 16, 2013 at 5:25 PM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:

>
> Hi Amirhossein - I'm attaching sample files.
>
> a.y
>
>
> On Tue, 16 Jul 2013, amirhossein manzouri wrote:
>
>  Hi Anastasia,
>> I have tried both , 3-row and 3-column format and still wrong bvecc and
>> bval
>> from flip4fsl. Could you please send me a sample of your original files
>> so I
>> can compare?
>>
>>
>> On Mon, Jul 15, 2013 at 7:44 PM, Anastasia Yendiki
>>  wrote:
>>
>>   Hi Amirhossein - Are your original bvecs/bvals in 3-row format
>>   instead of 3-column format?
>>   
>> http://surfer.nmr.mgh.harvard.**edu/fswiki/FsTutorial/Tracula
>>
>>   Thanks,
>>   a.y
>>
>>   On Mon, 15 Jul 2013, amirhossein manzouri wrote:
>>
>> Dear Experts,
>> I am running trac-all -prep -c dmrirc on my DWI
>> data. After flip4fsl step I get the attached bval
>> and bvec file which the bvec one is wrong so the
>> process exits
>> with error in dtifit. I have also attached  original
>> bvec and bval.
>>
>> --
>> Best regards,
>> Amirhossein Manzouri
>>
>>
>>
>>
>>
>>
>>
>> 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.
>>
>>
>>
>>
>> --
>> Best regards,
>> Amirhossein Manzouri
>>
>>
>>
>>
>>


-- 
Best regards,
Amirhossein Manzouri
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Re: [Freesurfer] convert DK atlas ROI to .nii.gz in MNI space

[Yang, Daniel]

Hi Doug,

Thanks very much!!

Best,
Daniel

On Jul 16, 2013, at 9:14 PM, "Douglas Greve" 
mailto:gr...@nmr.mgh.harvard.edu>> wrote:


use

$FREESURFER_HOME/average/mni152.register.dat

doug

On 7/16/13 8:36 PM, Yang, Daniel wrote:
Dear FreeSurfer Experts,

I am interested in a specific ROI in the DK atlas, and I know that I can use 
tkregister2 to obtain a register.dat, and then mri_annotation2label + 
mri_label2vol to convert the annotation of the ROI to an .nii.gz.

However, it seems that the end product is in the TAL space? If yes, how can I 
convert it to the MNI 152 space?

Many thanks!!

Best,
Daniel
--
Yung-Jui "Daniel" Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454



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