[Freesurfer] MRIread (load_nifti)- Out of memory

[Ilaria Sani]

Dear All,

I'm trying to load a pretty big diffusion MRI dataset (320x320x260x122).
I'm running matlab 2015a 64bit on a linux machine.

I'm using MRIread, which in turn calls load_nifti.
I'm getting the following error:

Error using  +
Out of memory. Type HELP MEMORY for your options.

Error in load_nifti (line 158)
  hdr.vol = hdr.vol * hdr.scl_slope  + hdr.scl_inter;

Error in MRIread (line 158)
hdr = load_nifti(fspec,headeronly);

When I load half dataset (320x320x260x61) it works ok.
I tried to increase the Maximum array size in Matalb (default 1,000 - now 
10,000), but I'm still getting the error.
I tried to change machine (which runs matlab 2013a on linux) and it worked fine.

I think this is due to some matlab settings.
Can anyone help?

Thanks a lot,
Ilaria


---
Ilaria Sani, PhD
Postdoctoral Fellow, Freiwald Lab
The Rockefeller University
1230 York Ave., New York, NY 10065.
Phone: (212) 327 7699
Fax: (212) 327 7698
Email: 
isan...@rockefeller.edu

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[Freesurfer] long mri_ca_register error

[Chris Adamson]

Freesurfer devs,

In freesurfer 6 stable I'm having a problem at the careg stage of the long. The 
relevant recon-all log is pasted below. Could you point me to where to debug 
this problem?

Cheers,

Chris.

mri_ca_register -rusage 
136_S_0426_20070604.long.136_S_0426/touch/rusage.mri_ca_register.dat 
-bigventricles -smoothness 0.5 -levels 2 -A 1 -l 
*base*/transforms/talairach.m3z identity.nofile -align-after -mask 
brainmask.mgz norm.mgz 
/usr/local/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca 
transforms/talairach.m3z

handling expanded ventricles...
l_smoothness = 0.50
levels = 2
smoothing gradient with 1 averages...
reading previously computed atlas xform 
/isilon/data/addo/ADNI3T/freesurfer6/136_S_0426/mri/transforms/talairach.m3z 
and applying inverse registration identity.nofile
renormalizing sequences with structure alignment, equivalent to:
-renormalize
-regularize_mean 0.500
-regularize 0.500
using MR volume brainmask.mgz to mask input volume...

== Number of threads available to mri_ca_register for OpenMP = 2 ==
reading 1 input volumes...
logging results to talairach.log
reading input volume 'norm.mgz'...
reading GCA '/usr/local/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca'...
label assignment complete, 0 changed (0.00%)
TransformSample: gcam has not been inverted!
freeing gibbs priors...done.
average std[0] = 5.0
setting orig areas to linear transform determinant scaled 8.40
writing talairach.invalid.mgz
writing talairach.status.mgz
registering ventricular system...
using threshold 45.0 from atlas ventricle (20.1 +- 5.0) and caudate (70.0 +- 
5.0) distributions for initial ventricular estimate
No such file or directory
TransformSample: gcam has not been inverted!
No such file or directory
TransformSample: gcam has not been inverted!
No such file or directory
TransformSample: gcam has not been inverted!
No such file or directory
TransformSample: gcam has not been inverted!
No such file or directory
TransformSample: gcam has not been inverted!
No such file or directory
TransformSample: gcam has not been inverted!
No such file or directory
TransformSample: gcam has not been inverted!
No such file or directory
TransformSample: gcam has not been inverted!
No such file or directory
TransformSample: gcam has not been inverted!
No such file or directory
TransformSample: gcam has not been inverted!
No such file or directory
TransformSample: gcam has not been inverted!
No such file or directory

Dr Chris Adamson
Senior Research Officer
Developmental Imaging, Clinical Sciences

Murdoch Childrens Research Institute
The Royal Children's Hospital
Flemington Road, Parkville, VIC 3052 Australia
E chris.adam...@mcri.edu.au
www.mcri.edu.au


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Re: [Freesurfer] Re. display SPM results on inflated surface? {Disarmed}

[Kevin Aquino]

Hi Douglas,

I am wondering, where did you find the mini 152 T1 map? :)

Regarding this...
Would it be better to instead run recon-all on a higher-res MNI atlas? and
then run mri_vol2surf for that segmentation?






Cheers,


*Dr Kevin Aquino*
Research fellow,
Sir Peter Mansfield Magnetic Resonance Center, The University of
Nottingham.

Honorary Research Fellow
School of Physics, Faculty of Science, University of Sydney

*E* kevin.aqu...@nottingham.ac.uk, aqu...@physics.usyd.edu.au | *W*
https://kevinaquino.github.io 

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On Thu, Mar 23, 2017 at 7:53 AM, Douglas Greve 
wrote:

> Just map your mni152-spm volume to the surface with mri_vol2surf and
> --regheader, eg,
>
> mri_vol2surf --mov yourspm152.nii.gz --hemi lh --projfrac 0.5 --s mni152
> --o lh.yourspm152.nii.gz
>
> then visualize
>
> tksurferfv mni152 lh inflated -ov lh.yourmni152.nii.gz
>
>
> On 3/22/17 3:46 PM, Schoot, Lotte wrote:
> > Thanks so much, I appreciate the help.
> > However, I am not sure what I am supposed to do with the output of the
> recon-all process.
> > Can I simply use the .dat file that is outputted there in MRI_vol2surf?
> >
> > Lotte
> >
> >
> > Date: Wed, 22 Mar 2017 13:01:42 -0400
> > From: Douglas Greve 
> > Subject: Re: [Freesurfer] display SPM results on inflated surface?
> > To: freesurfer@nmr.mgh.harvard.edu
> > Message-ID: <41134c50-bb0b-792c-c52b-b6850bcec...@nmr.mgh.harvard.edu>
> > Content-Type: text/plain; charset="windows-1252"
> >
> > If you have the T1 for the mni152 (which is somewhere in the bowels of
> the spm distribution), then you just run recon-all on it. I've done this
> for myself, so you can just download the result (which I have not checked
> thoroughly) from here https://gate.nmr.mgh.harvard.
> edu/safelinks/greve/mni152.tar.gz
> >
> >
> >
> > On 3/21/17 1:27 PM, Schoot, Lotte wrote:
> >> Hi Doug and others,
> >>
> >> A while ago, I got this reply to my question below (thanks!). I tried
> to look in to it, but I am a bit confused (probably because I am very new
> to Freesurfer).
> >> My results are on the MNI 152, but I don't understand what you mean
> with 'run the mni152 through freesurfer'. Is this the process to get the
> register.dat file that is required in mri_vol2surf?
> >> What would you recommend to get the register.dat file? Is it possible
> to use bbregister for that? I have tried this, but I don't know whether it
> is correct:
> >>
> >> bbregister --s fsaverage --mov con_0001.nii --init-spm --reg
> >> register.dat --bold
> >>
> >>
> >> Thanks!
> >> Lotte
> >>
> >>
> >>> If your results are on the MNI152, you can run the mni152 through
> >>> freesurfer, then use mri_vol2surf to map the data to the surface then
> >>> view it with freeview (or tksurfer). You should not confuse this with
> >>> doing the fMRI analysis on the surface. You will not have the
> >>> benefits of surface-based analysis
> >>
> >> On 02/15/2017 03:37 PM, Schoot, Lotte wrote:
> >>> /Hi all, />//>/I was wondering if you knew of a way to display SPM
> >>> results onto the />/inflated surface in Freesurfer. />//>/I have
> >>> tried using SurfRend but there seem to be problems which might />/be
> >>> due to the fact the results are obtained with SPM12 and SurfRend
> >>> />/was designed to work with SPM5. />//>/Thanks, />/Lotte
> >>> />//>//>/___
> >>> />/Freesurfer mailing list />/Freesurfer at nmr.mgh.harvard.edu
> >> 
> >> />/https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer /
> >> --
> >> Douglas N. Greve, Ph.D.
> >> MGH-NMR Center
> >> greve at nmr.mgh.harvard.edu
> >> 
> >> Phone Number: 617-724-2358
> >> Fax: 617-726-7422
> >>
> >>
> >> ___
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Re: [Freesurfer] Petsc Error in Freesurfer v6.0

[Chris Adamson]

I get these pincher errors as well in VirtualBox.
One thing that may fix it is to disable 3D acceleration for the graphics in the 
VM settings.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Michael ONeill
Sent: Thursday, 23 March 2017 11:56 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Petsc Error in Freesurfer v6.0

Hello Freesurfer Developers,

I've just installed Freesurfer v6.0 and attempted to run the commands printed 
below in order to test the installation:

freeview -v \

bert/mri/T1.mgz \

bert/mri/wm.mgz \

bert/mri/brainmask.mgz \

bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \

-f \

bert/surf/lh.white:edgecolor=blue \

bert/surf/lh.pial:edgecolor=red \

bert/surf/rh.white:edgecolor=blue \

bert/surf/rh.pial:edgecolor=red

Running this resulted in the a PETSC error which i have attached in .txt file.
I'm running Ubuntu 16.04 64bit in virtual box on a windows host.
I've tried numerous solutions including using the latest dev build of 
freesurfer v6.0 (as of 23/03/2017), installing the latest version of PETSC and 
doubling the amount of RAM available to the guest OS from 12GB to 24GB.
But unfortunately none of these approaches worked and the issue still persists.

I'm very eager to start using Freesurfer v6.0 and this seems to, hopefully, be 
the last rock in the road.
Any help you could offer would be appreciated.

Kind Regards,

Michael




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[Freesurfer] R: Re: R: Re: Whole preprocessing with FAST without to perform a seed based analysis

[stdp82]

Hi, 
as you advise I have run selxavg3-sess with the -svres option.I found a folder 
called "res" which contain "res-001.nii". Is it the f.nii fully 
processed?ThanksStefano



Messaggio originale

Da: "Douglas Greve" 

Data: 14-mar-2017 17.38

A: 

Ogg: Re: [Freesurfer] R: Re: Whole preprocessing with FAST without to perform a 
seed based analysis




  
  

You can't  on either occasion just using preproc-sess. You can
  create an analysis with those components, then run selxavg3-sess
  with the -svres option. This will create a folder called eres with
  volumes that have had all the nuisance variables and low
  freqeuncies regressed out




On 3/14/17 12:32 PM, std...@virgilio.it
  wrote:



  Thanks.
  1- By using only preproc-sess, how can I perform "band pass
filtering"?
  2- And how can I take in account the nuisance variables: the
CSF from which the top 5 principle components, the white matter
from which the top 5 principle components, motion correction
parameters (-mcextreg), 5th order polynomial. How can I
eliminate the first 4 time points?
  Regards
  Stefano
  

  Messaggio originale

  Da: "Douglas Greve" 

  Data: 14-mar-2017 16.14

  A: 

  Ogg: Re: [Freesurfer] Whole preprocessing with FAST without to
  perform a seed based analysis

  

  
  
just use preproc-sess

  
  

  On 3/14/17 10:45 AM, std...@virgilio.it
wrote:

  
  

  Hi list,
  in FS-FAST, on rs-fMRI data, is possible to run
selxavg3-sess without -a option?
  I would use whole the FS-FAST to preprocess my data.
I would include the mkanalysis-sess step but I would not
perform a seed-based analysis. 
  Thanks
  Stefano






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[Freesurfer] QDEC-volume, thickness and area

[Lim, Lena]

Dear Freesurfer Experts,

1) I have 2 groups (A & B), which do not differ in terms of gender ratio. If 
there were no significant regions for Group-Gender interaction in mean cortical 
thickness in the QDEC analysis, can I conclude that gender does not influence 
the effect of group on thickness? The differences between A and B on mean 
thickness is not affected by Gender? Is this valid or do I need to add Gender 
as a covariate even though the group do not differ on gender ratio?

2) A reviewer pointed that it is not right to test for group differences in 
volume once I have tested for thickness and area, especially when there is a 
cluster where A and B do not differ significantly in thickness and area but 
they differ significantly in volume...Is this right?

Please kindly advise.

Many thanks,

Lena


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[Freesurfer] ERROR: nu_correct

[Das S.]

Dear Freesurfer  Developers,
I was trying to use the recon-all -autorecon1 -subjid bert and got an error. 
When I checked I found the error was coming while executing the below command:
nu_correct -clobber ./tmp.mri_nu_correct.mni.7555/nu0.mnc 
./tmp.mri_nu_correct.mni.7555/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.7555/0/ 
-iterations 1000 -distance 50

When I executed the command separately I got below error message:

Can't use 'defined(@array)' (Maybe you should just omit the defined()?) at 
/usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 165.
nu_correct: crashed while running nu_estimate_np_and_em (termination 
status=65280)
ERROR: nu_correct


Can you please suggest why the error is coming and how to remove it.
Many thanks
Sarbani

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Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 Cross and Long Streams

[Antonin Skoch]

Dear David,

I did not see your data, but maybe couple of relevant remarks could be useful:

1.
By default the wm.mgz edits are not propagated from cross to the base, but from 
the cross to long. And surfaces in long are initialized from the base. 
Therefore the wm.mgz has to be OK both in the cross and in the base. My view 
and current experience is, that this means that in many cases it is probably 
necessary to edit wm.mgz both in cross and base. This would explain your 
observation that the wm.mgz edits in cross are not propagated to the base and 
the edits in base (but not in cross) are not seen in the long. 

I implemented a custom script which transfers  INTERSECTION of the wm.mgz edits 
from all cross points to the base. I think that to transfer the intersection of 
edits is safe approach to prevent to introduce errors in wm.mgz in base due to 
the false propagation of wm.mgz edits from cross to base in case of significant 
changes in the anatomy between cross and base. My  preliminary testing shows 
that this approach works well and saves time in wm.mgz editing of large errors 
which are consistently present in all timepoints. But in case of significant 
errors, the wm.mgz in the base still needs some additional editing. Therefore I 
think that there is not any single intervention point in wm.mgz edits.

 I was discussing the approach of transferring wm.mgz edits with Martin Reuter 
in the following thread:

http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51092.html

2.
When there are spots in the cross, where wm.mgz edits do not take an effect, I 
would suggest to inspect the brain.finalsurfs.mgz to see if there is sufficient 
contrast of the white/gray matter. In many such cases where I observe my wm.mgz 
edits do not take an effect, there is local issue with insufficient white/gray 
matter contrast. The white surface placement is primarily driven by the local 
gradient of intensity in brain.finalsurfs.mgz, the boundaries/edits of wm.mgz 
play only supplementary role (as an starting point for gradient search, via 
?h.orig, at least in default invocation of mris_make_surfaces, AFAIK).

If I have enough clues where the white surface should lie (i.e. from FLAIR) and 
there is insufficient white/gray matter contrast (typically there are spots in 
gray matter with spuriously high signal intensity, similar to white matter), I 
am currently experimenting with workaround, by directly editing gray matter 
voxels of 001.mgz in problematic spots by setting their values to typical gray 
matter values to enforce better white surface placement.
I decided to place my edits just in the beginning to the recon-all stream 
(001.mgz) to ensure the edits are not overwritten in case of new recon-all 
rerun.

Maybe other experts could comment on my workaround approach, it would also help 
me out.

Regards,

Antonin Skoch



I believe what I am seeing in the long stream is the edits not properly taking 
effect.I uploaded a subject with two timepoints, and only baseline edits to the 
wm as 
dsemanek2.zip about a week and a half ago. There doesn’t seem to be any 
significant changes to the surfaces in the base or either of the long runs. I 
will redo this subject on my end with some more extreme edits for testing to 
see if I can “force” something.

Thanks again for looking,

David P. Semanek, HCISPP
Research Technician, Posner Lab
Division of Child and Adolescent Psychiatry
Columbia University Medical Center
New York State Psychiatric Institute
1051 Riverside Drive, Pardes Bldg. Rm. 2424
New York, NY 10032
PH: (646) 774-5885

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From: Martin Reuter 
Date: Wednesday, April 5, 2017 at 2:19 AM
To: David Semanek 
Cc: "freesurfer@nmr.mgh.harvard.edu" , "Hoopes, 
Andrew" 
Subject: Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 
Cross and Long Streams

Hi David,

so edits are affecting the surfaces in cross, just not as much as you would 
like. We need to check if there is a problem there.

For the longitudinal stream, edits in the base should affect surfaces in the 
base, which in turn will affect surfaces in the long. In long, surfaces would 
start from a better starting position. Furthermore, wm edits from cross should 
be propagated to long, to make sure that surfaces don’t move back to the wrong 
position. So far the theory.
If you don’t see any effect of WM 

[Freesurfer] Selxavg3-sess Looking for (and can't find) "fmc.sm0"

[Taylor, Johnmark]

Hello,

I am getting an odd bug on selxavg3-sess. I am getting the error message,

*ERROR: cannot find [rest of file path]/fmc.sm0*

I am indicating zero smoothing in mkanalysis-sess ("-fwhm 0"). I am
confused because the output of preproc-sess for no smoothing is
fmc.nii.gz, *NOT
*fmc.sm0.nii.gz when doing analyses in native volume space, so I am not
sure why selxavg-sess is looking for the wrong file path. For reference,
here is my call to mkanalysis-sess:

mkanalysis-sess -analysis analysis_name -fsd bold -runlistfile runlist.txt
-native -nuisreg mcextreg 3 -fwhm 0 -event-related -nconditions 8
-paradigm spiralpara.par -spmhrf 0 -refeventdur 12 -TR 1.5
-polyfit 2 -nskip 8

I am using Freesurfer 5.3, if that helps. The analysis works fine when I
apply 3mm smoothing (I've done preprocessing for both the 0mm and 3mm
options).

Thank you very much, and cheers,

JohnMark
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[Freesurfer] QDEC-volume, thickness and area

[Lim, Lena]

Dear Freesurfer Experts,

1) I have 2 groups (A & B), which do not differ in terms of gender ratio. If 
there were no significant regions for Group-Gender interaction in mean cortical 
thickness in the QDEC analysis, can I conclude that gender does not influence 
the effect of group on thickness? The differences between A and B on mean 
thickness is not affected by Gender? Is this valid or do I need to add Gender 
as a covariate even though the group do not differ on gender ratio?

2) A reviewer pointed that it is not right to test for group differences in 
volume once I have tested for thickness and area, especially when there is a 
cluster where A and B do not differ significantly in thickness and area but 
they differ significantly in volume...Is this right?

Please kindly advise.

Many thanks,

Lena


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Re: [Freesurfer] mri_watershed seed point

[Antonin Skoch]

Dear Kristen,

looking at the source code of mri_watershed, the seed point has to be specified 
in the format:
-s i j k

and the option can be specified more than once when you want to add more seed 
points (30 seed points is maximum).

i.e., when you want to input seed points in coordinates 50,60,70, and 
80,90,100, the option would be:
-s 50 60 70 -s 80 90 100

Regards,

Antonin Skoch



Hello FreeSurfer Community,

I am attempting to use mri_watershed to create BEM surfaces, but for some of my 
subjects part of the cerebellum is being cut off.  Adjusting the threshold was 
not sufficient, so I attempted to add a seed point in the cerebellum using the 
following command:mri_watershed -atlas -useSRAS -surf ./surfout -s [105 182 81] 
./T1.mgz 
./brainvol

The coordinates for the seed point are from the T1.mgz image.  I reran 
mri_watershed and the seed point does not seem to be taken into consideration 
so I'm thinking that the input format I used may be wrong.  Could someone 
please tell me if I am not using the proper input format?  And what format to 
use if I wish to add multiple seed points?  Command output is attached.

Thanks in advance!

Kristen___
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[Freesurfer] How to generate binary mask image using FreeSurfer's “mri_volsynth”?

[Karan Vahi]

Dear Freesurfers,


I am trying to implement the methods mentioned in this paper to deal with
partial volume effects when quantifying metabolites: https://www.ncbi.
nlm.nih.gov/pmc/articles/PMC4849426/#__sec2title



The first step it mentions is: A binary mask must first be created, which
represents the 3D SVS voxel. A binary mask is an image where each voxel
contains either 1 or 0; in this case, the SVS voxel would be represented by
a value of 1 and all other voxels 0. There are multiple ways to create a
binary mask; one example, which was used successfully in this work, is the
“mask()” function within Matlab9 and the FreeSurfer (Fischl)10 application
“mri_volsynth.”



When I am trying the following command in FreeSurfer:

mri_volsynth --dim 3 4 5 2 --vol try.IMA



I am getting this output:

[image: Inline image 1]



But, I don’t know where it is saving the output file. And, I am also not
sure whether I am using mri_volsynth correctly. What is --dim nc nr ns nf
in https://surfer.nmr.mgh.harvard.edu/fswiki/mri_volsynth?

Also which pixels suppose to be 1's and which 0's?


Any help is appreciated.
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[Freesurfer] mri_watershed seed point

[Kanoff, Kristen Elise]

Hello FreeSurfer Community,

I am attempting to use mri_watershed to create BEM surfaces, but for some of my 
subjects part of the cerebellum is being cut off.  Adjusting the threshold was 
not sufficient, so I attempted to add a seed point in the cerebellum using the 
following command:

mri_watershed -atlas -useSRAS -surf ./surfout -s [105 182 81] ./T1.mgz 
./brainvol

The coordinates for the seed point are from the T1.mgz image.  I reran 
mri_watershed and the seed point does not seem to be taken into consideration 
so I'm thinking that the input format I used may be wrong.  Could someone 
please tell me if I am not using the proper input format?  And what format to 
use if I wish to add multiple seed points?  Command output is attached.

Thanks in advance!

Kristen


Kristen Kanoff
Clinical Research Coordinator II
Department of Neurology
Massachusetts General Hospital
Boston, MA
Ph: 617-726-3958
osboxes@osboxes:~/Documents/freesurfer/subjects/iDBS002/mri$ mri_watershed 
-atlas -useSRAS -surf ./surfout -s [105 182 81] ./T1.mgz ./brainvol

Mode:  Atlas analysis
Mode:  use surfaceRAS to save surface vertex positions
Mode:  Saving out BEM surfaces

*
The input file is ./T1.mgz
The output file is ./brainvol

*WATERSHED**
Sorting...
  T1-weighted MRI image
  modification of the preflooding height to 15 percent
  Count how many 110 voxels are present :  176432

  Find the largest 110-component...
 heap usage = 336340 Kbytes.
 current max segment has 154566 voxels
 removing small segments (less than 1 percent of maxarea).
 heap usage = 130864 Kbytes.
 removing small segments (less than 1 percent of maxarea).done
  And identify it as the main brain basin...done
  Main component: 154566 voxels
  first estimation of the COG coord: x=128 y=122 z=94 r=81
  first estimation of the main basin volume: 2241917 voxels
  global maximum in x=146, y=114, z=55, Imax=255
  CSF=24, WM_intensity=110, WM_VARIANCE=5
  WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 
  preflooding height equal to 15 percent
done.
Analyze...

  main basin size=34171332 voxels, voxel volume =1.000 
 = 34171332 mmm3 = 34171.332 cm3
done.
PostAnalyze...
  ambiguous basin, merged: at least 12 ambiguous voxels; size: 1490 voxels
  ambiguous basin, merged: at least 4 ambiguous voxels; size: 60 voxels
  ambiguous basin, merged: at least 11 ambiguous voxels; size: 1280 voxels
  ambiguous basin, merged: at least 7 ambiguous voxels; size: 260 voxels
  ambiguous basin, merged: at least 10 ambiguous voxels; size: 913 voxels
  ambiguous basin, merged: at least 7 ambiguous voxels; size: 307 voxels
  * 6 basin(s) merged in 4 iteration(s)
  * 4310 voxel(s) added to the main basin
  ambiguous basin, non merged: 6 ambiguous voxels; size: 2335 voxels
done.

TEMPLATE DEFORMATION

  second estimation of the COG coord: x=128,y=120, z=92, r=12891 iterations
 couldn't find WM with original limits - expanding ^^

   GLOBAL  CSF_MIN=1, CSF_intensity=2, CSF_MAX=31 , nb = 43064
 Problem with the least square interpolation in GM_MIN calculation.
   
 CSF_MAX  TRANSITION  GM_MIN  GM
GLOBAL 
  before analyzing :31,  29,28,   54
  after  analyzing :20,  29,29,   35
  mri_strip_skull: done peeling brain
  highly tesselated surface with 10242 vertices
  matching...59 iterations

*VALIDATION*
curvature mean = -0.013, std = 0.011
curvature mean = 67.196, std = 9.490

Rigid alignment...
  scanning 32.00 degree nbhd, min sse =  6.39 at ( 0.00,  8.00,  8.00)
  scanning 16.00 degree nbhd, min sse =  6.10 at ( 0.00, -4.00, -4.00)
  scanning  8.00 degree nbhd, min sse =  6.10 at ( 0.00,  0.00,  0.00)
  scanning  4.00 degree nbhd, min sse =  6.08 at ( 1.00,  1.00,  1.00)
done
  before rotation: sse = 6.68, sigma = 13.72
  after  rotation: sse = 6.08, sigma = 10.80
Localization of inacurate regions: Erosion-Dilation steps
  the sse mean is  7.43, its var is 10.75   
  before Erosion-Dilatation  6.23% of inacurate vertices
  after  Erosion-Dilatation  9.18% of inacurate vertices
  Validation of the shape of the surface done.
Scaling of atlas fields onto current surface fields

FINAL ITERATIVE TEMPLATE DEFORMATION
Compute Local values csf/gray
Fine Segmentation...40 iterations

  mri_strip_skull: done peeling brain

Brain Size = 1413043 voxels, voxel volume = 1.000 mm3
   = 1413043 mmm3 = 1413.043 cm3

  outer skin surface matching...187 iterations

**
Saving ./brainvol
done
mri_watershed utimesec513.928000
mri_watershed 

Re: [Freesurfer] ROI seed size

[Bruce Fischl]

Hi Erik

I see. I defer to Thomas on this issue

Bruce

On Wed, 5 Apr 2017, ERIK JAHNER 
wrote:



Hi Bruce,

Thanks for the quick response. Sorry, I meant 6mm radius (for regions such as 
fusiform face area and visual word form area). I am using the same seeds that 
are suggested to be associated with reading in the following study. I am 
wondering whether any guidelines have been set for determining seed size on 
surface from comparable volume based studies when that seed is a sphere or cube 
of voxels. I will be doing something similar using the peak coordinates of the 
components DMN suggested by Yeo 2011.

Koyama, M. S., Kelly, C., Shehzad, Z., Penesetti, D., Castellanos, F. X., & 
Milham, M. P. (2010). Reading Networks at Rest. Cerebral Cortex, 20(11), 2549–2559. 
http://doi.org/10.1093/cercor/bhq005

Many thanks
Erik Jahner


Sent from my iPad


On Apr 5, 2017, at 7:12 AM, freesurfer-requ...@nmr.mgh.harvard.edu wrote:

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Today's Topics:

  1. Re: Can anyone help with this error - trying to compare 2
 scans in same person (Martin Reuter)
  2.  Generate stat file of ROI voxel sizes (Ostrowski, Lauren)
  3. Reminder: 3.5-year Postdoc Position in Social Neuroscience at
 Bangor University, UK (Kami Koldewyn)
  4. Re: Custom color maps (dg wakeman)
  5. Re: ROI seed size (Bruce Fischl)
  6. PROGRAM DIRECTOR POSITION IN COGNITIVE NEUROSCIENCE AT NSF:
 Application deadline May 11, 2017 (Uri Hasson)
  7. Re: wm.mgz Edits Ignored With Current Dataset in FS 5.3/6
 Cross and Long Streams (David Semanek)
  8. Re: wm.mgz Edits Ignored With Current Dataset in FS 5.3/6
 Cross and Long Streams (Octavian Lie)
  9. Re: Comparing LME models (Bronwyn Overs)
 10. Re: Registration of both the brain and the "surf" files to
 the same template. (Douglas Greve)
 11. Re: Volume to Surface mapping looks great for Vols created in
 FSL but not SPM (Douglas Greve)
 12. Re: Volume to Surface mapping looks great for Vols created in
 FSL but not SPM (Rita Elena Loiotile)
 13. Re: wm.mgz Edits Ignored With Current Dataset in FS5.3/6
 Cross and Long Streams (Martin Reuter)
 14. Surface Integral Questions (Levman, Jacob)
 15. Re: Volume to Surface mapping looks great for Vols created in
 FSL but not SPM (Douglas Greve)
 16. Re: Qdec effect sizes, correlation coefficient (Douglas Greve)
 17. Changing the Orientation of Scan Slices (Imagesincluded)
 (Jeffrey Crawford)


--

Message: 1
Date: Tue, 4 Apr 2017 18:17:16 +0200
From: Martin Reuter 
Subject: Re: [Freesurfer] Can anyone help with this error - trying to
   compare 2 scans in same person
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <1dec67aa-6ef5-1ea2-4241-b578b5213...@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

Hi Brad,


the base commands needs a space before -tp


recon-all -base 005_IHD_1_base -tp 005_IHD_1 -tp 005_IHD_1_post -all


check if the directory 005_IHD_1_base exists.
Also check if this file exits:
/usr/local/freesurfer/subjects/005_IHD_1_base/mri/transforms/talairach.auto.xfm

Best, Martin


On 04/04/2017 05:55 PM, Brad Matushewski wrote:

*From:*freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *Brad
Matushewski
*Sent:* March 30, 2017 2:38 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* [Freesurfer] Trying to compare 2 scans from same person, 6
months apart.

First scan is 005_IHD_1

Second scan is 005_IHD_1_post

These were in $SUBJECTS / ihd

I moved them into $SUBJECTS

(i.e. no subfolder within $SUBJECTS folder).

I am following this;

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

FsTutorial/LongProcessing - Free Surfer Wiki


surfer.nmr.mgh.harvard.edu

Processing your data consists of three steps: First, run all your data
independently (we also say cross sectionally) using "recon-all -all"
(i.e. all time points for ...

I ran a normal recon all on both scans first.

I then ran this command:

recon-all -base 005_IHD_1_base-tp 005_IHD_1 -tp 005_IHD_1_post -all

and all seemed well.

I then tried to run this command.

recon-all -long   -all

This is how I entered the command:

recon-all -long 005_IHD_1 005_IHD_1_base -all

It resulted in errors...here is the last bit of the error log:

Applying LTAtransformInterp (resample_type 5)
MRItoBSpline degree 

Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 Cross and Long Streams

[David Semanek]

I believe what I am seeing in the long stream is the edits not properly taking 
effect.

I uploaded a subject with two timepoints, and only baseline edits to the wm as 
dsemanek2.zip about a week and a half ago. There doesn’t seem to be any 
significant changes to the surfaces in the base or either of the long runs. I 
will redo this subject on my end with some more extreme edits for testing to 
see if I can “force” something.

Thanks again for looking,

David P. Semanek, HCISPP
Research Technician, Posner Lab
Division of Child and Adolescent Psychiatry
Columbia University Medical Center
New York State Psychiatric Institute
1051 Riverside Drive, Pardes Bldg. Rm. 2424
New York, NY 10032
PH: (646) 774-5885

IMPORTANT NOTICE:  This e-mail is meant only for the use of the intended 
recipient.  It may contain confidential information which is legally privileged 
or otherwise protected by law.  If you received this e-mail in error or from 
someone who was not authorized to send it to you, you are strictly prohibited 
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PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS 
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From: Martin Reuter 
Date: Wednesday, April 5, 2017 at 2:19 AM
To: David Semanek 
Cc: "freesurfer@nmr.mgh.harvard.edu" , "Hoopes, 
Andrew" 
Subject: Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 
Cross and Long Streams

Hi David,

so edits are affecting the surfaces in cross, just not as much as you would 
like. We need to check if there is a problem there.

For the longitudinal stream, edits in the base should affect surfaces in the 
base, which in turn will affect surfaces in the long. In long, surfaces would 
start from a better starting position. Furthermore, wm edits from cross should 
be propagated to long, to make sure that surfaces don’t move back to the wrong 
position. So far the theory.
If you don’t see any effect of WM edits (in the base) on surfaces (in the base) 
then there is a problem. This step should be basically identical to how we 
treat edits in cross.

Best, Martin


On 04 Apr 2017, at 23:13, David Semanek 
> wrote:

Thanks for looking into this. I have uploaded another two subject folders as 
dsemanek3.zip, this time from a single time point for the same subject having 
been run through the cross stream of recon-all, the one with “test” appended at 
the end has had white matter edits on sagittal slices 126-142.

So, I have been able to get the surfaces to change in a single cross run as 
demonstrated in this upload. For this test, I did some edits that are typical 
on this dataset. Although the surfaces did change to reflect the edits, in a 
couple of places the surfaces did not change enough, and still encompassed 
space in the wm volume which had the white matter voxels removed.

For the first pass through these data before I realized there was a potential 
problem, I had initially edited the cross folders for the subjects and then ran 
the base, expecting the edits to be transferred over, but they did not seem to 
be. So I am still left with two issues: 1) incomplete incorporation of cross 
edits on the cross folders, 2) so far being unable to find an intervention 
point which will change the surfaces in the long stream, I have edited the base 
and then ran the long folders and these were not carried over as demonstrated 
in my previous uploads.

Thanks again,

David P. Semanek, HCISPP
Research Technician, Posner Lab
Division of Child and Adolescent Psychiatry
Columbia University Medical Center
New York State Psychiatric Institute
1051 Riverside Drive, Pardes Bldg. Rm. 2424
New York, NY 10032
PH: (646) 774-5885

IMPORTANT NOTICE:  This e-mail is meant only for the use of the intended 
recipient.  It may contain confidential information which is legally privileged 
or otherwise protected by law.  If you received this e-mail in error or from 
someone who was not authorized to send it to you, you are strictly prohibited 
from reviewing, using, disseminating, distributing or copying the e-mail.  
PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS 
MESSAGE FROM YOUR SYSTEM.  Thank you for your cooperation.

From: Martin Reuter 
>
Date: Tuesday, April 4, 2017 at 11:20 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
>
Subject: Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 
Cross and Long Streams

So the way to debug this is to test if we can replicate the problem of WM edits 
not taking effect in a regular cross sectional stream.
If true this means that there 

[Freesurfer] Ventricle-to-Brain Ratio

[Gullickson, James]

Hello all,

I want to calculate a Ventricle-to-Brain ratio (VBR) as a measure of
parenchymal atrophy using Freesurfer version 5.3.0. I have tried to go
about this using the aseg.stats output (using asegstats2table), but am
running into inconsistencies.

The basic calculation for VBR is:

(Total Ventricular Volume/Total Brain Volume) * 100

i.e. Bigler, E. D. (2013). Traumatic brain injury, neuroimaging, and
neurodegeneration. *Frontiers in human neuroscience*, *7*, 395.


What is the best way to get Total Ventricular Volume (TVV) and Total Brain
Volume (TBV) for this calculation? I have tried several ways, which lead to
different values:

TVV = left lateral ventricle + left inf lateral ventricle + right lateral
ventricle + right inf lateral ventricle + 3rd ventricle + 4th ventricle +
5th ventricle + choroid plexus

which gives me a different result than

TVV = BrainSegVol - BrainSegVolNotVent


and for TBV

TBV = TotalGrayVol + CorticalWhiteMatterVol

which differs from

TBV = BrainSegVolNotVent


Thank you for your help,

James Gullickson
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Re: [Freesurfer] Changing the Orientation of Scan Slices (Images included)

[Douglas N Greve]

you can try playing with the --reorder flag in mri_convert


On 04/05/2017 10:11 AM, Jeffrey Crawford wrote:
>
> Hello everyone!
>
> I have two types of scans of the same participant. One was an Axial 
> scan (Image 1) and the other is a Cortical Scan (Image 2), both with 
> the same dimensions (256 by 256 by 124). As you can see, the 
> orientation of the axial scan has the coronal in the top left, the 
> sagittal in the top right, and the axial below. The coronal scan has 
> the axial in the top left, the sagittal in the top right (in an odd 
> orientation) and the cortical on the bottom.
>
> Is it possible in Freesurfer to convert the cortical scan, so that it 
> presents itself in the same order and orientation as the axial scan?
>
> I realize that this would mean that the converted cortical scan would 
> have different dimensions, but I think that is just fine for my purposes.
>
> I would much appreciate any and all opinions,
>
> Jeff
>
>
>
> ___
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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
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] Generate stat file of ROI voxel sizes

[Douglas N Greve]

You can  use mri_segstats to generate a file for each subject (use the 
ROI volume as the --seg). Then use asegstats2table to create your final 
table


On 04/04/2017 12:18 PM, Ostrowski, Lauren wrote:
> Hello experts,
>
> We are looking to generate a stat file containing the number of voxels 
> in a series of ROIs. We have a collection of about 300 different 
> user-defined cortical ROI nifti volumes (not from aseg) and need to 
> retrieve the number of voxels in each ROI for further analysis, but so 
> far haven't been able to come up with an algorithm to do so. Any help 
> is much appreciated!
>
> Thank you,
> Lauren Ostrowski
>
>
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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
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] Qdec effect sizes, correlation coefficient

[Douglas Greve]

yes


On 4/3/17 1:34 PM, Juan Baldermann wrote:
> Is ist correct that the pcc.mgh file give's me pearson's correlation 
> coeeficient for each vertex?
>
> Best, Carlos
>
>
> 
> Dr. med. Juan Carlos Baldermann
> Wissenschaftlicher Mitarbeiter, Assistenzarzt
> AG Neurobiologie und Neuromodulation psychischer Erkrankungen
>
> Klinik für Psychiatrie und Psychotherapie
> Universitätsklinikum Köln
> Kerpener Str. 62
> D - 50937 Köln
> Telefon: 0221- 478 86211
> Email: juan.balderm...@uk-koeln.de
> __
>
>
> VERTRAULICHKEITSHINWEIS:
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> 
> Von: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] im Auftrag von Douglas N 
> Greve [gr...@nmr.mgh.harvard.edu]
> Gesendet: Montag, 13. März 2017 21:07
> An: freesurfer@nmr.mgh.harvard.edu
> Betreff: Re: [Freesurfer] Qdec effect sizes, correlation coefficient
>
> if you use the version 6 of mri_glmfit, it will automatically output the
> pcc.mgh file. If you want a cohen's D, then you can
>
> cd glmdir/contrast
>
> fscalc gamma.mgh div ../rstd.mgh -o cohensd.mgh
>
>
>
> On 03/13/2017 01:45 PM, Juan Baldermann wrote:
>> Dear all,
>>
>> I did a correlation analysis in qdec and now I want to report effect
>> sizes of my significant clustes. How can I extract a correlation
>> coefficient for this type of analyis? Or any other effect size? I saw
>> that i can derive them from the pcc.mgh file, but this somehow didn't
>> work in matlab...does the gamma.mgh file also have effect sizes per
>> cluster?
>>
>> Kind regards
>> Carlos
>>
>>
>> 
>> Dr. med. Juan Carlos Baldermann
>> Wissenschaftlicher Mitarbeiter, Assistenzarzt
>> AG Neurobiologie und Neuromodulation psychischer Erkrankungen
>> Klinik für Psychiatrie und Psychotherapie
>> Universitätsklinikum Köln
>> Kerpener Str. 62
>> D - 50937 Köln
>> Telefon: 0221- 478 86211
>> Email: juan.balderm...@uk-koeln.de
>> __
>>
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>> uns bitte umgehend. Danke! CONFIDENTIALITY NOTICE : This email and any
>> documents which may accompany it, contains information, which is
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>> addressed, and which may contain information that is privileged,
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>> this communication in error, please contact us immediately. Thank you!
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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
>
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Re: [Freesurfer] Volume to Surface mapping looks great for Vols created in FSL but not SPM

[Douglas Greve]

If you have a 3mm MNI152 space, then you should run bbregister to 
fsaverage to create a new register.dat file. Alternatively, you can 
register it directly to 32k_fs_LR and cut out the middle man (make sure 
to use --9 to account for scaling). Please ignore my comment about 
fsaverage. In that case it was actually fine.




On 4/4/17 9:40 PM, Rita Elena Loiotile wrote:

Hi Doug,

Thanks for the email.  It is in 3mm space, so I guess I should 
reslice.  Can you please clarify the comment about fsaverage?  Does 
the --mni152reg flag not apply to that subject?  I'm not sure what you 
mean about the inclusion indicating ambiguity.


Thanks again,
Rita

On Tue, Apr 4, 2017 at 9:21 PM, Douglas Greve 
> wrote:


The --mni152reg flag is only appropriate if the mov file is in the
2mm mni152 space. The inclusion of fsaverage as the source subject
indicates some ambiguity about this


On 4/3/17 1:56 PM, Rita Elena Loiotile wrote:

Hi,

I'm trying to compare analyses that I've done entirely on the
surface to analyses I've done in the volume.  I'm comparing the
analyses by projecting the volume analyses to the surface (HCP's
32k_fs_LR).

The commands I'm using are:
mri_vol2surf --mov $niftiFile --mni152reg --hemi ${hemi}
--projfrac-max 0 1 0.2 --o ${giftiFile}.$hemi.gii;
mri_surf2surf --srcsubject fsaverage --srcsurfval
${giftiFile}.$hemi.gii --trgsubject 32k_fs_LR --trgsurfval
${giftiFile}.$hemi.gii --hemi ${hemi};It seems that the FSL
volumes look identical to the surface analysis, when mapped. (Our
surface analysis is mainly FSL-based, so this makes sense.)
The SPM mapping, however, looks very odd. It isn't just that the
intensity differs, but the localization of high intensity areas
also varies. It seems that everything is shifted a bit superior
and, possibly, posterior to the true location (as seen on the
surface analysis).
I'm wondering if I'm doing anything obviously wrong in my command
usage. The brains were normalized to the MNI ICBM 152 template in
SPM. I *think* it's suitable to use the -mni152reg flag in the
command.

I can attach pictures of the comparison if you'd like.

Thanks in advance,
Rita


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[Freesurfer] Surface Integral Questions

[Levman, Jacob]

Hi FreeSurfer community,


I have several questions regarding FreeSurfer's surface integral measurements. 
Perhaps there is a documentation page that answers these questions that someone 
can point me to that I haven't been able to find, or perhaps someone knows the 
answers to these questions off the top of their head.


I understand that the negative surface integral corresponds to gyral regions 
and the positive surface integral corresponds to sulcal regions, but how do 
these differ from the Natural Surface Integral?


Additionally:

Integrals add up a series of underlying measurements, what is the measurement 
they are adding here - ie. is it a sum of local curvature measurements?

What is the AreaNorm Natural Surface Integral?

What is the Mean Natural Surface Integral?

What is K, k1 and their differences from H, C, k2 etc.


Thanks so much for your help!


Jacob Levman, PhD

Boston Children's Hospital

Harvard Medical School

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Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 Cross and Long Streams

[Martin Reuter]

Hi David, 

so edits are affecting the surfaces in cross, just not as much as you would 
like. We need to check if there is a problem there. 

For the longitudinal stream, edits in the base should affect surfaces in the 
base, which in turn will affect surfaces in the long. In long, surfaces would 
start from a better starting position. Furthermore, wm edits from cross should 
be propagated to long, to make sure that surfaces don’t move back to the wrong 
position. So far the theory. 
If you don’t see any effect of WM edits (in the base) on surfaces (in the base) 
then there is a problem. This step should be basically identical to how we 
treat edits in cross. 

Best, Martin


> On 04 Apr 2017, at 23:13, David Semanek  > wrote:
> 
> Thanks for looking into this. I have uploaded another two subject folders as 
> dsemanek3.zip, this time from a single time point for the same subject having 
> been run through the cross stream of recon-all, the one with “test” appended 
> at the end has had white matter edits on sagittal slices 126-142.
>  
> So, I have been able to get the surfaces to change in a single cross run as 
> demonstrated in this upload. For this test, I did some edits that are typical 
> on this dataset. Although the surfaces did change to reflect the edits, in a 
> couple of places the surfaces did not change enough, and still encompassed 
> space in the wm volume which had the white matter voxels removed.
>  
> For the first pass through these data before I realized there was a potential 
> problem, I had initially edited the cross folders for the subjects and then 
> ran the base, expecting the edits to be transferred over, but they did not 
> seem to be. So I am still left with two issues: 1) incomplete incorporation 
> of cross edits on the cross folders, 2) so far being unable to find an 
> intervention point which will change the surfaces in the long stream, I have 
> edited the base and then ran the long folders and these were not carried over 
> as demonstrated in my previous uploads.
>  
> Thanks again,
>  
> David P. Semanek, HCISPP
> Research Technician, Posner Lab
> Division of Child and Adolescent Psychiatry
> Columbia University Medical Center
> New York State Psychiatric Institute
> 1051 Riverside Drive, Pardes Bldg. Rm. 2424
> New York, NY 10032
> PH: (646) 774-5885
>  
> IMPORTANT NOTICE:  This e-mail is meant only for the use of the intended 
> recipient.  It may contain confidential information which is legally 
> privileged or otherwise protected by law.  If you received this e-mail in 
> error or from someone who was not authorized to send it to you, you are 
> strictly prohibited from reviewing, using, disseminating, distributing or 
> copying the e-mail.  PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN 
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>  
> From: Martin Reuter  >
> Date: Tuesday, April 4, 2017 at 11:20 AM
> To: "freesurfer@nmr.mgh.harvard.edu " 
> >
> Subject: Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 
> 5.3/6 Cross and Long Streams
>  
> So the way to debug this is to test if we can replicate the problem of WM 
> edits not taking effect in a regular cross sectional stream.
> If true this means that there is a bug to the way WM edits are considered in 
> FS6.0. It is unlikely that we missed that, but can happen. Probably something 
> else is going on here.
>  
> For that it would be good to have a single time point (cross sectional step) 
> with WM edits send over, so that Andrew can take a look at that.
>  
> Best, Martin
>  
>  
> On 04/04/2017 05:03 PM, David Semanek wrote:
> I used –uselongbasewmedits only as a test to see if I could get some 
> condition under which the wm edits would be taken into account when the 
> surfaces were generated.
>  
> I did not use that flag for the data I uploaded. The wm edits to base did not 
> influence the base wm surfaces or the cross wm surfaces. The cross wm edits 
> (not uploaded) did not influence cross, base, or long wm surfaces.
>  
> I’ve found no condition under which wm edits have influenced the white matter 
> surface in any of my data.
>  
> Best,
>  
> David P. Semanek, HCISPP
> Research Technician, Posner Lab
> Division of Child and Adolescent Psychiatry
> Columbia University Medical Center
> New York State Psychiatric Institute
> 1051 Riverside Drive, Pardes Bldg. Rm. 2424
> New York, NY 10032
> PH: (646) 774-5885
>  
> IMPORTANT NOTICE:  This e-mail is meant only for the use of the intended 
> recipient.  It may contain confidential information which is legally 
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