[Freesurfer] amygdala segmentation using additional scan error

[오진영]

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Hello, freesurfer experts

I'm trying to run segmentation of hippocampal subfields and nuclei of
amygdala with additional scan.
I already ran segmentation of hippocampal subfields and nuclei of amygdala
with only T1 image, using segmentHA_T1.sh command and succeeded.
After success of segmentation of amygdala with T1 image, I tried to run
segmentation again with additional scan(T2 image) to get more reliable
results.
However, when I use command segmentHA_T2.sh, I got the following error:

Error in segmentSubjectT1T2_autoEstimateAlveusML (line 2628)


And the last few lines before the error are below:

*Fitting mesh to image data mask took 264.2808 seconds*

*Transforming points*

*Transforming points*

*Wrote image to file image1.mgz*

*Wrote image to file image2.mgz*

*INFO: dst volume info differs from the one stored in lta.  gets modified
now.*

*volume geometry:*

*extent  : (232, 469, 208)*

*voxel   : ( 0.,  0.,  0.)*

*x_(ras) : ( 0., -1.,  0.)*

*y_(ras) : ( 0.,  0., -1.)*

*z_(ras) : ( 1.,  0.,  0.)*

*c_(ras) : (-21.1788, -1.8961,  3.8447)*

*file: T2isotropic.mgz*

*volume geometry:*

*extent  : (256, 256, 256)*

*voxel   : ( 1.,  1.,  1.)*

*x_(ras) : ( 0., -1.,  0.)*

*y_(ras) : ( 0.,  0., -1.)*

*z_(ras) : ( 1.,  0.,  0.)*

*c_(ras) : ( 2.3212,  8.6039, -21.1553)*

*file: /Users/mnd_mac/Desktop/JY_surfer/sub_05_T2.nii*

*Constructing image-to-world transform from header information (asmr1.mgz)*

*Constructing image-to-world transform from header information
(/Users/mnd_mac/Desktop/JY_surfer//recon_sub_05/tmp/hippoSF_T1T2_v21_T2_left/imageDump.mgz)*

*Wrote image to file asmr2.mgz*

*This file does not contain MRI parameters*

*This file does not contain MRI parameters*

*This file does not contain MRI parameters*

*In an assignment  A(:) = B, the number of elements in A and B must be the
same.*


*Error in segmentSubjectT1T2_autoEstimateAlveusML (line 2628)*




*MATLAB:subsassignnumelmismatch*

*Darwin MnD-macui-iMac.local 17.7.0 Darwin Kernel Version 17.7.0: Thu Jun
21 22:53:14 PDT 2018; root:xnu-4570.71.2~1/RELEASE_X86_64 x86_64*

and I have no idea how to solve this problem out.

I use the dev version of freesurfer.
T1 scan image and T2 scan image of participant were taken on the same day.

If you have any recommendations, please send me the email back.

Thanks!

Jinyoung
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Re: [Freesurfer] [External] Re: SurfaceRAS to Vertex coordinate system

[Bruce Fischl]

Hi Joel

there is internal code for this where we create a spatial lookup/hash 
table and use it to find the closest vertex, but it is just a set of c 
functions.


cheers
Bruce


On Tue, 4 Sep 2018, Bruss, Joel E wrote:



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Ah, that makes sense.  Short of calculating a Euclidean distance between every 
surface RAS and my
point I'd like on the surface, then grabbing the one with the shortest 
distance, is there a
function/utility in FreeSurfer that will generate the closest vertex for me?


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of
Ehsan Tadayon 
Sent: Tuesday, September 4, 2018 2:05:05 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] [External] Re: SurfaceRAS to Vertex coordinate system 
 

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[cbb23410d862335b08d6bf64e91c01427a4b6868.png?u=375924]
  There is no linear transformation between the two. Vertex coordinate is 
equal to
  surfaceRAS when the point that you have selected is actually one of the 
vertices on the
  chosen surface. However, if the point is not on the surface, it finds the 
nearest
  vertex. So, you can read your surface  ( in matlab : [vertices, faces] =
  read_surf('lh.pial') ) and then find the vertex that is closest to your 
selected point
  (surfaceRAS). This is the vertex that you see in the Freeview. 

 
Ehsan. 



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Re: [Freesurfer] [External] Re: SurfaceRAS to Vertex coordinate system

[Bruss, Joel E]

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Ah, that makes sense.  Short of calculating a Euclidean distance between every 
surface RAS and my point I'd like on the surface, then grabbing the one with 
the shortest distance, is there a function/utility in FreeSurfer that will 
generate the closest vertex for me?


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Ehsan Tadayon 

Sent: Tuesday, September 4, 2018 2:05:05 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] [External] Re: SurfaceRAS to Vertex coordinate system


External Email - Use Caution


There is no linear transformation between the two. Vertex coordinate is equal 
to surfaceRAS when the point that you have selected is actually one of the 
vertices on the chosen surface. However, if the point is not on the surface, it 
finds the nearest vertex. So, you can read your surface  ( in matlab : 
[vertices, faces] = read_surf('lh.pial') ) and then find the vertex that is 
closest to your selected point (surfaceRAS). This is the vertex that you see in 
the Freeview.

Ehsan.



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Re: [Freesurfer] long_mris_slopes: error: cannot create a table with longitudinal pc1

[Shatil, Anwar Shahadat]

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Hi Martin/Doug:

Still looking for an answer. Could not find a way to list the percentage change 
values for each subject in a tabular form.

Thanks,

Anwar

On 2018-08-30, 12:15 PM, "Shatil, Anwar Shahadat"  
wrote:

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Hello Martin:

I am using freesurfer 6.0.0 and the long_mris_slopes version 1.42 (that 
came with it by default).

If I omit --out-pc1 but keep --do-pc1 still do not get any output as a .dat 
or .stats file. I only get .mgh file in surf folder.

I need percentage change values of tp2 from tp1 for each subject in a 
tabular form.

Best,

Anwar

On 2018-08-30, 3:22 AM, "Martin Reuter"  
wrote:

Hi Anwar,

what FS version are you using?

Also what happens if you omit the --out-pc1 but keep the --do-pc1 ?
Also no output with that ending? It should write it to the default
location.

Best, Martin





On Wed, 2018-08-29 at 16:45 +, Shatil, Anwar Shahadat wrote:
> External Email - Use Caution
> Dear Doug:
>
> I am trying to get a table containing pc1 values for each subject in
> a longitudinal study and failed to extract this. I use the code
> below:
>
> long_mris_slopes --qdec ./qdec/long.qdec.table.2.dat --meas thickness
> --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label
> --time years --qcache fsaverage --sd
> /Users/richardaviv/Desktop/Longitudinal_FS --out-pc1 out-pc1.dat
>
> It says
> long_mris_slopes: error: no such option: --out-pc1
>
>
> However in the --help file it says:
>
> Within-Subject Output:
> Pass these to overwrite the default names:
>
> --out-avg=OUT_AVG   filename to store temporal average in
> /stats/ (default:
> long..-avg.dat)
> --out-rate=OUT_RATE
> filename to store rate in
> /stats/
> (default: long..-rate.dat)
> --out-pc1fit=OUT_PC1FIT
> filename to store pct. change (to tp1fit) in
> /stats/ (default:
> long..-pc1fit.dat)
> --out-pc1=OUT_PC1   filename to store pct. change (to tp1) in
> /stats/ (default:
> long..-pc1.dat)
> --out-spc=OUT_SPC   filename to store sym. pct. change in
> /stats/ (default:
> long..-spc.dat)
> --out-resid=OUT_RESID
> filename to store residual in
> /stats/ (default:
> long..-resid.dat),
> requires
> --resid 
> --out-stack=OUT_STACK
> filename to store stacked measure file
> /stats/ (default:
> long..-stack.dat)
>
>   Stacked Tables:
> To output tables with results from all subjects
>
> --stack-avg=STACK_AVG
> full filename to stack temporal average
> tables
> (default no stacking)
> --stack-rate=STACK_RATE
> full filename to stack rate tables (default
> no
> stacking)
> --stack-pc1fit=STACK_PC1FIT
> full filename to stack pct. change to tp1fit
> tables
> (default no stacking)
> --stack-pc1=STACK_PC1
> full filename to stack pct. change to tp1
> tables
> (default no stacking)
> --stack-spc=STACK_SPC
> full filename to stack sym. pct. tables
> (default no
> stacking)
> --stack-resid=STACK_RESID
> full filename to stack residual tables
> (default no
> stacking)
>
>
> Am I writing the code wrong?? I never got any long..-
> pc1.dat file in /stats/ folder except bunch of mgh files
> in /surf/ folder.
>
> Thanks,
>
> Anwar
> --
>
> Anwar S. Shatil
>
> Research Assistant
> Department of Medical Imaging
> Sunnybrook Health Sciences Centre
> Room AB204, 2075 Bayview Avenue
> Toronto, ON M4N 3M5
> Tel: 416.480.6100 ext. 89617
> Email: a

Re: [Freesurfer] [External] Re: SurfaceRAS to Vertex coordinate system

[Ehsan Tadayon]

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> There is no linear transformation between the two. Vertex coordinate is
> equal to surfaceRAS when the point that you have selected is actually one
> of the vertices on the chosen surface. However, if the point is not on the
> surface, it finds the nearest vertex. So, you can read your surface  ( in
> matlab : [vertices, faces] = read_surf('lh.pial') ) and then find the
> vertex that is closest to your selected point (surfaceRAS). This is the
> vertex that you see in the Freeview.


Ehsan.
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[Freesurfer] strange eTIV values

[Miguel Ángel Rivas Fernández]

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Hello Freesurfer experts,


When I exported the Destrieux and Desikian-Killiany volume values from
Freesurfer to SPSS I obtained "strange" eTIV values with 16 digits as
follows:

101,632,104,008.
134,253,072,953.
155,967,056,944.
142,085,122,028.
181,105,664,397.
118,051,287,519.
896,135,067,103.

With how many decimals Freesurfer exports the eTIV values ?, that is, what
is the precision of this measure? I do not know how many decimals this
measure has.

Another doubt, it is necessary to make some kind of numerical
transformation on the eTIV values before including it as a covariate in the
statistical analysis (for example, a logarithmic transformation).


Best,

-- 
*Miguel Ángel Rivas Fernández*
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Re: [Freesurfer] [External] Re: SurfaceRAS to Vertex coordinate system

[Bruss, Joel E]

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Close, but still not what I'm looking for.  I start with orig.mgz file and have 
RAS.  I can convert that to voxel coordinates.  I can then convert that to 
TkReg RAS/SurfaceRAS coordinates, but what I'm looking for is the Vertex 
coordinate.  For example, looking at FreeView, I see the following four 
coordinates (on Rhemi, for example):


RAS: 54, -78, 1

TkReg RAS (orig): 55, -61, -18

orig: 50 [73, 146, 67]

rh.pial: SurfaceRAS [55, -61, -18]

rh.pial: Vertex 11660 [53.91, -60.35, -18.31]


I can convert back and forth between the top three with ease.  I can't figure 
out how to get the last coordinate (Vertex).


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Ehsan Tadayon 

Sent: Tuesday, September 4, 2018 12:00:53 PM
To: Freesurfer support list
Subject: [External] Re: [Freesurfer] SurfaceRAS to Vertex coordinate system


External Email - Use Caution


Hi Joel,

you need to find the corresponding voxel ( using ras2vox transformation matrix) 
and then apply your vox2ras-tkr matrix to it. it would give you the tkrRAS 
coordinate.

cheers,
Ehsan.



On Tue, Sep 4, 2018 at 12:40 PM Bruss, Joel E 
mailto:joel-br...@uiowa.edu>> wrote:

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If I load, say, orig.mgz and lh.pial, in FreeView and lay my cursor on a point, 
I can see  RAS (and surfaceRAS) as well as TKReg RAS (orig) coordinates.  
Following the steps laid out on the CoordinateSystems web page I can convert 
back and forth between those coordinate systems.  However, I can't figure out 
what I need to do to calculate the Vertex coordinates.  I can load lh.pial in 
matlab and see the (+1) vertex number and coordinates, but I'd like to figure 
out the best way to get from Vertex x/y/z to TkReg RAS or SurfaceRAS.  Is there 
an easy formula to calculate this?  Thanks in advance for any and all responses.


-Joel



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Re: [Freesurfer] SurfaceRAS to Vertex coordinate system

[Ehsan Tadayon]

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Hi Joel,

you need to find the corresponding voxel ( using ras2vox transformation
matrix) and then apply your vox2ras-tkr matrix to it. it would give you the
tkrRAS coordinate.

cheers,
Ehsan.



On Tue, Sep 4, 2018 at 12:40 PM Bruss, Joel E  wrote:

> External Email - Use Caution
>
> If I load, say, orig.mgz and lh.pial, in FreeView and lay my cursor on a
> point, I can see  RAS (and surfaceRAS) as well as TKReg RAS (orig)
> coordinates.  Following the steps laid out on the CoordinateSystems
> web page I can convert back and forth between those coordinate systems.
> However, I can't figure out what I need to do to calculate the Vertex
> coordinates.  I can load lh.pial in matlab and see the (+1) vertex number
> and coordinates, but I'd like to figure out the best way to get from Vertex
> x/y/z to TkReg RAS or SurfaceRAS.  Is there an easy formula to calculate
> this?  Thanks in advance for any and all responses.
>
>
> -Joel
>
>
> --
> Notice: This UI Health Care e-mail (including attachments) is covered by
> the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and is
> intended only for the use of the individual or entity to which it is
> addressed, and may contain information that is privileged, confidential,
> and exempt from disclosure under applicable law. If you are not the
> intended recipient, any dissemination, distribution or copying of this
> communication is strictly prohibited. If you have received this
> communication in error, please notify the sender immediately and delete or
> destroy all copies of the original message and attachments thereto. Email
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> --
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[Freesurfer] Stats Error

[Song, Da-Yea]

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Hello,

I'm extracting some stats from recon-all but noticed that it would stop running 
in the middle (error message: end: Not in while/foreach) . Any suggestions on 
how I could solve this problem would be greatly appreciated! Thank you so much 
in advance.

Best regards,
Da-Yea


computing statistics for each annotation in rantaFL.annot.
reading volume 
/g5/dcn/freesurfer_testing/subjects//3095_3T_011216_0/mri/wm.mgz...
reading input surface 
/g5/dcn/freesurfer_testing/subjects//3095_3T_011216_0/surf/lh.white...
Using TH3 vertex volume calc
Total face volume 249500
Total vertex volume 245871 (mask=0)
reading input pial surface 
/g5/dcn/freesurfer_testing/subjects//3095_3T_011216_0/surf/lh.pial...
reading input white surface 
/g5/dcn/freesurfer_testing/subjects//3095_3T_011216_0/surf/lh.white...
reading colortable from annotation file...
colortable with 11 entries read (originally /freesurfer/FrontalLobeColorLUT.txt)
atlas_icv (eTIV) = 1377325 mm^3(det: 1.414413 )
lhCtxGM: 245607.578 244866.000  diff=  741.6  pctdiff= 0.302
rhCtxGM: 253269.330 252721.000  diff=  548.3  pctdiff= 0.217
lhCtxWM: 199421.968 199714.500  diff= -292.5  pctdiff=-0.147
rhCtxWM: 198426.788 199552.500  diff=-1125.7  pctdiff=-0.567
SubCortGMVol  53103.000
SupraTentVol  962619.664 (961451.000) diff=1168.664 pctdiff=0.121
SupraTentVolNotVent  951172.664 (950004.000) diff=1168.664 pctdiff=0.123
BrainSegVol  1091475.000 (1088903.000) diff=2572.000 pctdiff=0.236
BrainSegVolNotVent  1076628.000 (1076311.664) diff=316.336 pctdiff=0.029
BrainSegVolNotVent  1076628.000
CerebellumVol 126436.000
VentChorVol   11447.000
3rd4th5thCSF   3400.000
CSFVol   828.000, OptChiasmVol   188.000
MaskVol 1502516.000
structure is "anterior_cingulate"
number of vertices  = 3531
total surface area  = 2414 mm^2
total gray matter volume= 6657 mm^3
average cortical thickness  = 2.742 mm +- 0.824 mm
average integrated rectified mean curvature = 0.116
average integrated rectified Gaussian curvature = 0.017
folding index   = 37
intrinsic curvature index   = 2.5
structure is "dlpfc"
number of vertices  = 10762
total surface area  = 7059 mm^2
total gray matter volume= 20651 mm^3
average cortical thickness  = 2.426 mm +- 0.665 mm
average integrated rectified mean curvature = 0.125
average integrated rectified Gaussian curvature = 0.025
folding index   = 150
intrinsic curvature index   = 10.8
structure is "frontal_eye_field"
number of vertices  = 1371
total surface area  = 927 mm^2
total gray matter volume= 2587 mm^3
average cortical thickness  = 2.654 mm +- 0.526 mm
average integrated rectified mean curvature = 0.111
average integrated rectified Gaussian curvature = 0.020
folding index   = 12
intrinsic curvature index   = 1.0
structure is "inferolateral_pfc"
number of vertices  = 4430
total surface area  = 2928 mm^2
total gray matter volume= 9914 mm^3
average cortical thickness  = 2.662 mm +- 0.654 mm
average integrated rectified mean curvature = 0.124
average integrated rectified Gaussian curvature = 0.022
folding index   = 64
intrinsic curvature index   = 4.1
structure is "lateral_OFC"
number of vertices  = 5859
total surface area  = 3926 mm^2
total gray matter volume= 11128 mm^3
average cortical thickness  = 2.493 mm +- 0.732 mm
average integrated rectified mean curvature = 0.128
average integrated rectified Gaussian curvature = 0.029
folding index   = 74
intrinsic curvature index   = 6.6
structure is "medial_OFC"
number of vertices  = 1871
total surface area  = 1217 mm^2
total gray matter volume= 3722 mm^3
average cortical thickness  = 2.641 mm +- 0.791 mm
average integrated rectified mean curvature = 0.121
average integrated rectified Gaussian curvature = 0.036
folding index   = 27
intrinsic curvature index   = 2.9
structure is "mpfc"
number of vertices  = 6801
total surface area  = 4531 mm^2
total gray matter volume= 15597 mm^3
average cortical thickness  = 2.761 mm +- 0.652 mm
average integrated rectified mean curvature = 0.127
average integrated rectified Gaussian curvature = 0.027
folding index   = 86
intrinsic curvature index   = 7.4
structure is "primary_motor"
number of vertices  = 6578
total surface area  = 3910 mm^2
total gra

[Freesurfer] SurfaceRAS to Vertex coordinate system

[Bruss, Joel E]

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If I load, say, orig.mgz and lh.pial, in FreeView and lay my cursor on a point, 
I can see  RAS (and surfaceRAS) as well as TKReg RAS (orig) coordinates.  
Following the steps laid out on the CoordinateSystems web page I can convert 
back and forth between those coordinate systems.  However, I can't figure out 
what I need to do to calculate the Vertex coordinates.  I can load lh.pial in 
matlab and see the (+1) vertex number and coordinates, but I'd like to figure 
out the best way to get from Vertex x/y/z to TkReg RAS or SurfaceRAS.  Is there 
an easy formula to calculate this?  Thanks in advance for any and all responses.


-Joel



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Re: [Freesurfer] Freesurfer download issue

[Hoopes, Andrew]

Unfortunately, the disk that hosts the ftp data has died, so resolving this 
might take a bit longer than expected. The new disk should be repopulated 
within the next few days. Sorry about that everyone.

Best,
Andrew


On 9/3/18, 11:24 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Bruce Fischl"  wrote:

Hi All

we had a (planned) power outage this weekend and things may still be 
down. We should have everything back up by tomorrow

cheers
Bruce



On Sun, 2 Sep 2018, Mengxue Kang wrote:

> 
> External Email - Use Caution
> 
> Hello,
> 
> I am trying to download FreeSurfer from
> "http://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall"; and I can't 
open the download page. It
> keeps returning an error message below:
> 
> This site can’t be reached
> The webpage 
atftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Darwin-OSX-stable-pub-v6.0.0.
> dmg might be temporarily down or it may have moved permanently to a new 
web address.
> ERR_FTP_FAILED
> 
> Is there any other way to download the software?
> Thank you very much. 
> 
> Regards,
> Mengxue
> 
>


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Re: [Freesurfer] fsaverage for a Left vs Right hemisphere Longitudinal

[Douglas Greve]

I'm not sure what this is referring to, but you should be very careful 
flipping images. If you want to compare left and right, then use the 
xhemi tool https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi


On 9/4/18 10:41 AM, Martin Reuter wrote:

Hi Xiaoyu,

please keep the previous conversation as inline citation below so I 
know what we discussed before.


What I mean is to process every subject only once and not twice (with 
flipped images, if that is what you did?).


Then run xhemi analysis on the subject-level. Invert the sign of the 
left-right difference depending on which is the diseased hemi. Then do 
a regular analysis on that. Nothing paired.


Best, Martin



On 30. Aug 2018, at 18:29, Wang, Xiaoyu 
> wrote:




Thanks Martin,
Yes, I did mean to have the right hemisphere added to the left 
hemisphere as a new time point.

Can you explain on what you mean by run every subject only once?
Do you mean to run xhemi for all of the subjects and then run a 
paired analysis?

Xiaoyu
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Re: [Freesurfer] NIFTI to pial.vtk space

[Douglas Greve]

what is your mris_convert command line?

On 9/3/18 4:10 PM, M. Jordan wrote:


External Email - Use Caution

Hello,

I have a CT NIFTI coregistered to the MRI NIFTI used for reconAll. 
When I export the .pial files to .vtk using mris_convert, they are 
shifted with respect to the MRI. Is there a way to process the CT 
NIFTI in such a way that it will match the .vtk pial files?


Thank you!



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Re: [Freesurfer] fsaverage for a Left vs Right hemisphere Longitudinal

[Martin Reuter]

Hi Xiaoyu, 

please keep the previous conversation as inline citation below so I know what 
we discussed before. 

What I mean is to process every subject only once and not twice (with flipped 
images, if that is what you did?). 

Then run xhemi analysis on the subject-level. Invert the sign of the left-right 
difference depending on which is the diseased hemi. Then do a regular analysis 
on that. Nothing paired. 

Best, Martin



> On 30. Aug 2018, at 18:29, Wang, Xiaoyu  
> wrote:
> 
> 
> 
> 
> Thanks Martin,
>  
> Yes, I did mean to have the right hemisphere added to the left hemisphere as 
> a new time point.
>  
> Can you explain on what you mean by run every subject only once?
> Do you mean to run xhemi for all of the subjects and then run a paired 
> analysis?
>  
> Xiaoyu
>  
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Re: [Freesurfer] Is voxel size resampled during recon-all? And different voxel size in longitudinal studies

[Martin Reuter]

Hi Dani, 

the regular FreeSurfer stream samples everything to 1mm isotropic. This is of 
course problematic, if you have one group scanned at 1mm and the other at a 
different resolution (as group differences could be affected by the different 
resolutions). You would never know how much of what you get is group and how 
much is resolution. 

Similarly this is problematic if you switch scanner, software, head-coil, 
resolution in a longitudinal study. Effects cannot be separated any longer and 
all you can report in a paper is that what you find is longitudinal effect plus 
resolution effects and you don’t know how much is which. 

FreeSurfers longitudinal stream therefore requires inputs to be the same 
resolution. This safety feature (to prevent potentially meaningless analysis) 
can be circumvented by manually sampling images first - at your own risk. If 
you go that way, you should at least also interpolate the 1mm images to a new 
position (at least then both images will have interpolation artefacts, so that 
differences are only the acquisition resolution and not additionally 
interpolation artefacts in one of the time points). 

As an example, taking the same image twice, mapping one to a different location 
and back again produces interpolation artefacts that are significant and at 
orders comparable with 1 year of neurodegenerative disease. 

Best, Martin





> On 30. Aug 2018, at 18:22, Daniel Ferreira  wrote:
> 
> 
> 
> 
> Dear colleagues,
> 
> I was wondering if resampling voxel size is done during recon-all.
> 
> Also, I have data with voxel resolution of 1x1x1 mm at baseline and 
> 1,2x1,2x1,2 at follow-up. I was wondering if recon-all does any computation 
> by default (or can be performed by any way) that minimizes these differences 
> in somehow.
> 
> Thank you very much
> 
> Dani
> 
> -- 
> Daniel Ferreira, PhD, Assistant Professor
> 
> Division of Clinical Geriatrics; Department of Neurobiology, Care Sciences 
> and Society
> 
> Karolinska Institutet (Sweden)
> 
> Address: Blickagången 16, 141 52 Huddinge | phone: +46 720128047 | email: 
> daniel.ferreira.padi...@ki.se 
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[Freesurfer] MNI to native space using mri_cvs_register and applyMorph

[Ehsan Tadayon]

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Hi,

I'm tyring to transform a bunch of MNI coordinates to subject's space using
mri_cvs_register and applyMorph. I have run the mri_cvs_register but
could'nt find detailed description of applyMorph.  I appreciate any input
on what command should be run to transform an MNI152 coordinate back to
subject's space.

thanks
Ehsan.
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[Freesurfer] Tools for FreeSurfer QC based on quality metrics?

[ts+ml]

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Dear FreeSurfer experts,


Which tools would you recommend to compute quality metrics for FreeSurfer 6 
output?

I would like to complement visual QC of the FreeSurfer segmentation output for 
structural images with automated metrics, e.g., outlier detection for the 
volume or CNR of certain subcortical structures or surface-based measures. Are 
there any tools for this? I guess I'm looking for something similar to the 
QATools for FreeSurfer 5 but for the latest FreeSurfer version.


All the best,

-- 
Tim Schäfer

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