[Freesurfer] MRISalloc error during automatic reconstruction

[Julia Ströhlein]

External Email - Use Caution

Dear experts,

while running one of my subjects, I got this error:

 

MRISalloc(732595, 480): could not allocate vertices 

Cannot allocate memory 

Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10

20:41:14 UTC 2012 i686 i686 i386 GNU/Linux

 

recon-all -s P_04 exited with ERRORS at Mon Feb  4 16:40:03 EST 2019

 

Do you know what went wrong and how I can fix this?

Best regards,

Julia

 

 



 

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Second order (square) link function for GLM

[Abhinav Yadav]

External Email - Use Caution

Hello,

  I am trying to do GLM analysis for cortical thickness with a behavioral
score. I wanted to explore square fit in the GLM. Basically wanted to see
weather the behaviour is related in a quadratic function instead of linear
one.

  Couldn't find any option for this is GLM fit.

   I was thinking of feeding a squareroot values of the behavioural
parameter in the GLM as an alternative. But not sure weather that will
work. Please any one can help me with this.

Thanks,
Abhinav
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Converting MNI152 coorindates to fsaverage space

[Wu Jianxiao]

External Email - Use Caution

Dear Tim,

The best way to do this would be to create a volume file (e.g. each
location of interest is labelled as 1), and then projecting that
volume file to the fsaverage surface. For the projection step, you can
use the script `CBIG_RF_projectVol2fsaverage_single.m` from
`bin/scripts_final_proj` (or `CBIG_RF_projectMNI2fsaverage.m` from
`bin/standalone_scripts_for_MNI_fsaverage_projection`. Make sure you
choose 'nearest' interpolation if you want discrete results.


On 2/12/19, Tim Schäfer  wrote:
> External Email - Use Caution
>
> Dear Thomas,
>
> thanks for your reply and suggestion. I had a look at the tool and its paper
> on it and I think it could be helpful. If I got it correctly, use case #8 at
> https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems is referred to
> as 'the affine method' in the paper, but it is inferior the the non-linear
> warp method presented in the Wu2017_RegistrationFusion paper.
>
> About using the github repo: The MNI152 coords I have are in a text file and
> they represent locations within the cortex, so I have no volume file that I
> want to project. But from a quick look at the repo, what I could do is to
> use the displacement fields (or whatever you want to call them) under
> bin/final_warps_FS5.3/?h.avgMapping_allSub_RF_ANTs_MNI152_orig_to_fsaverage.mat
> to look up the surface coords in fsaverage. Is that correct?
>
> Thanks,
>
> Tim
>
>> On February 11, 2019 at 1:45 AM Thomas Yeo  wrote:
>>
>>
>> External Email - Use Caution
>>
>> Hi Tim,
>>
>> Case #8 is transforming between MNI152 and MNI305 spaces. MNI305 is
>> different from fsaverage: one is a volumetric space and one is a surface
>> space.
>>
>> If you are indeed looking for a transformation between MNI152 volumetric
>> space and fsaverage surface space, you can consider the following:
>> https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/registration/Wu2017_RegistrationFusion
>>
>> Regards,
>> Thomas
>>
>> On Sat, Feb 9, 2019 at 11:11 PM Tim Schäfer  wrote:
>>
>> > External Email - Use Caution
>> >
>> > > Dear list,
>> > >
>> > > I have some points of interest (volume coordinates, e.g. '5.9, -27.7,
>> > 49.7') in MNI152 space. I would like to transform them to fsaverage
>> > space.
>> > >
>> > > How should I do that?
>> > >
>> >
>> > To answer my own question, this seems to be explained as use case #8 on
>> > the following website (at the bottom):
>> >
>> > https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
>> >
>> > To be precise, the website explains the transformation in the opposite
>> > direction, so one should use the inverse of the matrix given on the
>> > website.
>> >
>> > --
>> > Tim
>> >
>> > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Tim
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


-- 
Regards,
*Wu* Jianxiao
Institute for Neuroscience and Medicine, Brain and Behaviour (INM-7)
Forschungszentrum Jülich

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Why in the aseg.stats file the nvoxel value doesn't equal to the volume or follow a arithmetic correlation?

[Bruce Fischl]

Hi Yongxiang

we compute partial-volume corrected volumes by estimating the mixing 
fraction of every border voxel. This significantly increases reliability 
(and presumably accuracy)


cheers
Bruce
On Tue, 12 Feb 2019, 赵永翔 wrote:



External Email - Use Caution

Hi all.
I was puzzled when I checked the the aseg.stats in the fs_output_folder after I 
run the routuine
recon-all cmd.(fs6.0_linux)
In this stat file  I found that the nvoxel value doesn't equal to the volumes 
of each subcortical
segmentation. They even doesn't follow a arithmetic correlation.
But the header reads that the voxel is equal to 1 mm^3 in volume.
So why?
I wiil be greatly appreciated if somebody could tell me if there is anything 
wrong with my ideas.


the sample of my aseg.stat file(some lines) is appended here.

# Title Segmentation Statistics 
# 
# generating_program mri_segstats
# cvs_version $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
# VoxelVolume_mm3 1 
# ColHeaders  Index SegId NVoxels Volume_mm3 StructName normMean normStdDev 
normMin normMax
normRange  
  1   4     18001    18343.9  Left-Lateral-Ventricle            37.8841     
9.3238    24.   
90.    66. 
  2   5      1641     1672.0  Left-Inf-Lat-Vent                 45.0488    
11.6523    23.   
82.    59. 
  3   7     16241    16825.4  Left-Cerebellum-White-Matter      84.3527     
5.6642    29.   
98.    69. 
  4   8     52760    52711.2  Left-Cerebellum-Cortex            66.2411     
9.4589    25.   
91.    66. 
  5  10      7246     6891.5  Left-Thalamus-Proper              91.3607     
9.1942    41. 
 107.    66. 
  6  11      3246     3140.1  Left-Caudate                      85.8783     
7.9460    53. 
 107.    54. 
  7  12      4285     4264.4  Left-Putamen                      91.0488     
4.3328    63. 
 104.    41. 
  8  13      2022     2006.2  Left-Pallidum                    100.0514     
4.3088    75. 
 118.    43. 
  9  14      2969     3048.2  3rd-Ventricle                     39.8787     
8.2650    26.   
81.    55. 
 10  15      1552     1705.4  4th-Ventricle                     40.3808     
9.6486    23.   
79.    56. 
 11  16     19144    18890.9  Brain-Stem                        83.6324    
10.1835    34. 
 108.    74. 
 12  17      3738     3442.8  Left-Hippocampus                  74.7269     
8.1358    40.   
97.    57. 
 13  18      1100     1054.6  Left-Amygdala                     76.2536     
7.1347    43.   
95.    52. 
 14  24      1791     1694.4  CSF                               51.9894    
11.2187    32.   
94.    62. 
 15  26       278      249.5  Left-Accumbens-area               85.4928     
6.2711    54.   
93.    39. 
 16  28      4171     3992.6  Left-VentralDC                    92.5809    
11.1675    41. 
 116.    75. 
 17  30         0        0.0  Left-vessel                        0.     
0.     0.   
 0.     0. 
 18  31       928      888.8  Left-choroid-plexus               52.3438    
10.8472    31.   
78.    47. 
 19  43     20737    20900.1  Right-Lateral-Ventricle           37.1717     
8.9953    25.   
92.    67. 
 20  44      5481     5495.9  Right-Inf-Lat-Vent                37.8816     
9.1653    26.   
79.    53. 
 21  46     16633    17143.0  Right-Cerebellum-White-Matter     83.6901     
5.3551    40.   
99.    59. 
 22  47     54353    54454.1  Right-Cerebellum-Cortex           66.2976     
9.1862    20.   
89.    69. 
 23  49      6416     6042.8  Right-Thalamus-Proper             89.1852     
9.9130    37. 
 106.    69. 
 24  50      3294     3062.4  Right-Caudate                     87.1703     
8.2085    53. 
 107.    54. 
 25  51      3794     3796.8  Right-Putamen                     92.5113     
4.1020    62. 
 104.    42. 
 26  52      2124     2028.5  Right-Pallidum                   102.1172     
4.1392    75. 
 118.    43. 
 27  53      2980     2742.1  Right-Hippocampus                 73.9638     
9.4803    28.   
96.    68. 
 28  54      1299     1132.8  Right-Amygdala                    69.1655    
14.6045    28.   
98.    70. 
 29  58       273      223.8  Right-Accumbens-area              88.0403     
5.5989    64.   
99.    35. 
 30  60      3924     3713.0  Right-VentralDC                   92.1210    
12.3974    35. 
 117.    82. 
 31  62        13       24.5  Right-vessel                      60.4615     
6.2930    48.   
71.    23. 
 32  63      1302     1224.4  Right-choroid-plexus              51.1751    
10.0901    31.   
79.    48. 
 33  72         0        0.0  5th-Ventricle                      0.     
0.     0.   
 0.     0. 
 34  77      1508 

[Freesurfer] Why in the aseg.stats file the nvoxel value doesn't equal to the volume or follow a arithmetic correlation?

[赵永翔]

External Email - Use Caution

Hi all.
I was puzzled when I checked the the aseg.stats in the fs_output_folder after I 
run the routuine recon-all cmd.(fs6.0_linux)
In this stat file  I found that the nvoxel value doesn't equal to the volumes 
of each subcortical segmentation. They even doesn't follow a arithmetic 
correlation.
But the header reads that the voxel is equal to 1 mm^3 in volume.
So why?
I wiil be greatly appreciated if somebody could tell me if there is anything 
wrong with my ideas.




the sample of my aseg.stat file(some lines) is appended here.


# Title Segmentation Statistics 
# 
# generating_program mri_segstats
# cvs_version $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
# VoxelVolume_mm3 1 
# ColHeaders  Index SegId NVoxels Volume_mm3 StructName normMean normStdDev 
normMin normMax normRange  
  1   4 1800118343.9  Left-Lateral-Ventricle37.8841 
9.323824.90.66. 
  2   5  1641 1672.0  Left-Inf-Lat-Vent 45.0488
11.652323.82.59. 
  3   7 1624116825.4  Left-Cerebellum-White-Matter  84.3527 
5.664229.98.69. 
  4   8 5276052711.2  Left-Cerebellum-Cortex66.2411 
9.458925.91.66. 
  5  10  7246 6891.5  Left-Thalamus-Proper  91.3607 
9.194241.   107.66. 
  6  11  3246 3140.1  Left-Caudate  85.8783 
7.946053.   107.54. 
  7  12  4285 4264.4  Left-Putamen  91.0488 
4.332863.   104.41. 
  8  13  2022 2006.2  Left-Pallidum100.0514 
4.308875.   118.43. 
  9  14  2969 3048.2  3rd-Ventricle 39.8787 
8.265026.81.55. 
 10  15  1552 1705.4  4th-Ventricle 40.3808 
9.648623.79.56. 
 11  16 1914418890.9  Brain-Stem83.6324
10.183534.   108.74. 
 12  17  3738 3442.8  Left-Hippocampus  74.7269 
8.135840.97.57. 
 13  18  1100 1054.6  Left-Amygdala 76.2536 
7.134743.95.52. 
 14  24  1791 1694.4  CSF   51.9894
11.218732.94.62. 
 15  26   278  249.5  Left-Accumbens-area   85.4928 
6.271154.93.39. 
 16  28  4171 3992.6  Left-VentralDC92.5809
11.167541.   116.75. 
 17  30 00.0  Left-vessel0. 
0. 0. 0. 0. 
 18  31   928  888.8  Left-choroid-plexus   52.3438
10.847231.78.47. 
 19  43 2073720900.1  Right-Lateral-Ventricle   37.1717 
8.995325.92.67. 
 20  44  5481 5495.9  Right-Inf-Lat-Vent37.8816 
9.165326.79.53. 
 21  46 1663317143.0  Right-Cerebellum-White-Matter 83.6901 
5.355140.99.59. 
 22  47 5435354454.1  Right-Cerebellum-Cortex   66.2976 
9.186220.89.69. 
 23  49  6416 6042.8  Right-Thalamus-Proper 89.1852 
9.913037.   106.69. 
 24  50  3294 3062.4  Right-Caudate 87.1703 
8.208553.   107.54. 
 25  51  3794 3796.8  Right-Putamen 92.5113 
4.102062.   104.42. 
 26  52  2124 2028.5  Right-Pallidum   102.1172 
4.139275.   118.43. 
 27  53  2980 2742.1  Right-Hippocampus 73.9638 
9.480328.96.68. 
 28  54  1299 1132.8  Right-Amygdala69.1655
14.604528.98.70. 
 29  58   273  223.8  Right-Accumbens-area  88.0403 
5.598964.99.35. 
 30  60  3924 3713.0  Right-VentralDC   92.1210
12.397435.   117.82. 
 31  6213   24.5  Right-vessel  60.4615 
6.293048.71.23. 
 32  63  1302 1224.4  Right-choroid-plexus  51.1751
10.090131.79.48. 
 33  72 00.0  5th-Ventricle  0. 
0. 0. 0. 0. 
 34  77  1508 1452.2  WM-hypointensities74.0351
13.044537.   107.70. 
 35  78 00.0  Left-WM-hypointensities0. 
0. 0. 0. 0. 



Thank 

Re: [Freesurfer] registration and resampling in native space

[Bruce Fischl]

Hi Francesca

check out the --no-resample option in mri_vol2vol. It just changes the 
header, so I think should do what you want.


cheers
Bruce


On Tue, 12 Feb 2019, Francesca Strappini wrote:



External Email - Use Caution

Dear Freesurfer's experts,

I would like to register some functional data to the T1, that were collected in 
separate days.
I used bbregister:

bbregister --s sub3 --mov func_data.nii.gz - --reg register.dat --init-coreg 
--t1

Now, I would like to resample the data based on the register.dat without 
upsampling and keeping the
same FoV (3x3x3 mm; 64 64 50). Is it doable?

Thanks!
Best


--
Francesca Strappini, Ph.D.
Neurobiology Department
Weizmann Institute of Science
234 Herzl Street, Rehovot 7610001 Israel
Tel.: +972 58 444 2584
E-mail: francesca.strapp...@weizmann.ac.il

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] registration and resampling in native space

[Francesca Strappini]

External Email - Use Caution

Dear Freesurfer's experts,

I would like to register some functional data to the T1, that were
collected in separate days.
I used bbregister:

bbregister --s sub3 --mov func_data.nii.gz - --reg register.dat
--init-coreg --t1

Now, I would like to resample the data based on the register.dat without
upsampling and keeping the same FoV (3x3x3 mm; 64 64 50). Is it doable?

Thanks!
Best



-- 
Francesca Strappini, Ph.D.
Neurobiology Department
Weizmann Institute of Science
234 Herzl Street, Rehovot 7610001 Israel
Tel.: +972 58 444 2584
E-mail: francesca.strapp...@weizmann.ac.il
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] zero values when run recon-all with T2pial flag (V6.0)

[Greve, Douglas N.,Ph.D.]

When you say that, eg, BrainSegVolNotVent is zero, is this in the 
aseg.stats file? In looking at your log, it appears that 
BrainSegVolNotVent is non-zero, eg,

BrainSegVolNotVent  1304558.000


On 2/11/19 5:51 PM, Morgan Botdorf wrote:
>
> External Email - Use Caution
>
> Yes, attached is the recon-all.log file for one subject.
>
> -Morgan
>
> -- 
>
> Morgan Botdorf, M.S.
>
> Graduate Student
>
> Neurocognitive Development Lab
>
> University of Maryland, College Park
>
> mbotd...@terpmail.umd.edu 
>
>
> >Date: Thu, 7 Feb 2019 22:29:43 +
> >From: "Greve, Douglas N.,Ph.D."  >
> >Subject: Re: [Freesurfer] zero values when run recon-all with T2pial
> >       flag (V6.0)
> >To: "freesurfer@nmr.mgh.harvard.edu 
> " 
> mailto:freesurfer@nmr.mgh.harvard.edu>>
> >Message-ID: <6ea86bbf-6001-e95d-dcee-84cc8ba5d...@mgh.harvard.edu 
> >
> >Content-Type: text/plain; charset="utf-8"
>
> >
>
> >I have not. Can you send the recon-all.log file?
>
>
> >On 2/1/19 6:01 PM, Morgan Botdorf wrote:
> >
> > External Email - Use Caution
> >
> > Dear all,
> >
> > I recently ran recon-all on data using the T2pial flag to improve the
> > pial surface (using version 6.0). The T2 images seemed to improve the
> > pial surfaces; however, when I extract stats using the Destrieux
> > atlas, I get zero values for several regions and for
> > BrainSegVolNotVent and eTIV. If I run recon-all without the T2 image,
> > I get data for these regions,?BrainSegVolNotVent, and eTIV. Has anyone
> > run into similar issues using the T2pial flag or have an idea of what
> > may be causing this problem?
> >
> > Thank you in advance?for your help!
> >
> > Morgan
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Question

[Bruce Fischl]

yes, I imagine it should be fine, depending on resolution and CNR. Try 
running them through recon-all and see. Generally surfaces are ok with 
post-contrast also, although thickness might be messed up by the contrast 
brightening the dura.


cheers
Bruce
On Mon, 11 Feb 2019, alireza gazani 
wrote:




External Email - Use Caution

Hello,
I have a question and I couldn't find any answer in the archive. We have 
clinical T-1
(post-contrast) images, can we use them for subcortical analysis? 
I know they can't be used for cortical thickness analysis.

Thank you!

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Hypointensities in Freesurfer

[Miguel Ángel Rivas Fernández]

External Email - Use Caution

Hi Douglas,

have you had occasion to review this matter? I was thinking that we also
have FLAIR and T2 images...

Thanks in advance for your help.


Best,

El vie., 8 feb. 2019 a las 18:36, Miguel Ángel Rivas Fernández (<
miguelrivasf...@gmail.com>) escribió:

> Hi,
>
> Yes, I would like to know the x,y,z MNI coordinates of lesions for each
> subject.
>
>
> BEST,
>
> El vie., 8 feb. 2019 18:34, Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> escribió:
>
>> not sure what you want. MNI coords for each lesion?
>>
>> On 2/8/19 7:21 AM, Miguel Ángel Rivas Fernández wrote:
>>
>> External Email - Use Caution
>>
>> Hi Freesurfer devs,
>>
>>
>> I saw that Freesurfer export measures of hypointensities. I was wondering
>> if it´s possible to know where are located this brain lesions using as
>> reference some neuroanatomical atlas.
>>
>>
>> Best,
>>
>> --
>> *Miguel Ángel Rivas Fernández*
>>
>> ___
>> Freesurfer mailing 
>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

-- 
*Miguel Ángel Rivas Fernández*
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Question

[alireza gazani]

External Email - Use Caution

Hello,

I have a question and I couldn't find any answer in the archive. We have
clinical T-1 (post-contrast) images, can we use them for subcortical
analysis?
I know they can't be used for cortical thickness analysis.

Thank you!
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] mri_segstat: same output with two different label

[Greve, Douglas N.,Ph.D.]

If mri_diff says that there is no difference, then there is something 
wrong. Double check that your contrasts are correct.


On 2/10/19 9:47 AM, Francesca Strappini wrote:
>
> External Email - Use Caution
>
> Thanks a lot for the reply!
> If I run mri_diff order/z.nii.gz disorder/z.nii.gz I indeed get zero.
> However, if I perform the contrast "order minus disorder" I get 0.1, 
> so I should see some difference although very small, right?
> These are the outputs:
>
> francesca@francesca-desktop:/opt/freesurfer/fsfast/OrderDisorder/AB/bold/AB_OrderDisorder_lh$
>  
> mri_segstats --i order/z.nii.gz --slabel AB lh 
> /opt/freesurfer/subjects/AB/label/lh.V2dorsal_AB.label --sfavg 
> lh.V2dorsal_AB_order_avg --snr --sum lh.V2dorsal_AB_order_sum
>
> $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
> cwd
> cmdline mri_segstats --i order/z.nii.gz --slabel AB lh 
> /opt/freesurfer/subjects/AB/label/lh.V2dorsal_AB.label --sfavg 
> lh.V2dorsal_AB_order_avg --snr --sum lh.V2dorsal_AB_order_sum
> sysname  Linux
> hostname francesca-desktop
> machine  x86_64
> user     francesca
> UseRobust  0
> Constructing seg from label
> Loading order/z.nii.gz
> Vertex Area is 0.65781 mm^3
> Generating list of segmentation ids
> Found   2 segmentations
> Computing statistics for each segmentation
>
> Reporting on   2 segmentations
> Using PrintSegStat
> Computing spatial average of each frame
>   0  1
> Writing to lh.V2dorsal_AB_order_avg
> 0 -0.950279
> 1 1.31525
> mri_segstats done
>
> francesca@francesca-desktop:/opt/freesurfer/fsfast/OrderDisorder/AB/bold/AB_OrderDisorder_lh$
>  
> mri_segstats --i disorder/z.nii.gz --slabel AB lh 
> /opt/freesurfer/subjects/AB/label/lh.V2dorsal_AB.label --sfavg 
> lh.V2dorsal_AB_disorder_avg --snr --sum lh.V2dorsal_AB_disorder_sum
>
> $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
> cwd
> cmdline mri_segstats --i disorder/z.nii.gz --slabel AB lh 
> /opt/freesurfer/subjects/AB/label/lh.V2dorsal_AB.label --sfavg 
> lh.V2dorsal_AB_disorder_avg --snr --sum lh.V2dorsal_AB_disorder_sum
> sysname  Linux
> hostname francesca-desktop
> machine  x86_64
> user     francesca
> UseRobust  0
> Constructing seg from label
> Loading disorder/z.nii.gz
> Vertex Area is 0.65781 mm^3
> Generating list of segmentation ids
> Found   2 segmentations
> Computing statistics for each segmentation
>
> Reporting on   2 segmentations
> Using PrintSegStat
> Computing spatial average of each frame
>   0  1
> Writing to lh.V2dorsal_AB_disorder_avg
> 0 -0.950279
> 1 1.31525
> mri_segstats done
>
> mri_segstats --i order-vs-disorder/z.nii.gz --slabel AB lh 
> /opt/freesurfer/subjects/AB/label/lh.V2dorsal_AB.label --sfavg 
> lh.V2dorsal_AB_orderVsdisorder_avg --snr --sum 
> lh.V2dorsal_AB_orderVsdisorder_sum
>
> $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
> cwd
> cmdline mri_segstats --i order-vs-disorder/z.nii.gz --slabel AB lh 
> /opt/freesurfer/subjects/AB/label/lh.V2dorsal_AB.label --sfavg 
> lh.V2dorsal_AB_orderVsdisorder_avg --snr --sum 
> lh.V2dorsal_AB_orderVsdisorder_sum
> sysname  Linux
> hostname francesca-desktop
> machine  x86_64
> user     francesca
> UseRobust  0
> Constructing seg from label
> Loading order-vs-disorder/z.nii.gz
> Vertex Area is 0.65781 mm^3
> Generating list of segmentation ids
> Found   2 segmentations
> Computing statistics for each segmentation
>
> Reporting on   2 segmentations
> Using PrintSegStat
> Computing spatial average of each frame
>   0  1
> Writing to lh.V2dorsal_AB_orderVsdisorder_avg
> 0 0.119339
> 1 -1.93788
> mri_segstats done
>
> Thanks again for the help!
> Best
> Francesca
>
>
>
> Il giorno mar 22 gen 2019 alle ore 20:55 Greve, Douglas N.,Ph.D. 
> mailto:dgr...@mgh.harvard.edu>> ha scritto:
>
> I don't know what is happening. If the two z-maps are really
> different,
> then it should have given different values. Run this
> mri_diff order/z.nii.gz disorder/z.nii.gz
> Does it indicate that there is a difference? If so, can you run
> your two
> mri_segment commands and send me the terminal output of each?
> As for the two mean intensity values, one (Seg0001) is from inside
> your
> ROI and the other (Seg) is outside. You can have it exclude
> Seg
> with --excludeid 0
>
>
> On 1/20/19 10:00 AM, Francesca Strappini wrote:
> >
> > External Email - Use Caution
> >
> > Dear Freesurfer's experts,
> >
> > I'm trying to run a ROIs mean intensity analysis using mri_segstat.
> > I'm using as an input contrast maps created with mkcontrast-sess
> and
> > selxavg3-sess (block-design experiment) and as masks, some labels
> > created on the surface with a retinotopic analysis.
> >
> > I noticed that all my outputs with the same label have the same
> > values, regardless of the contrast map that I'm giving as an input.
> > However, if I plot the contrast maps on the surface I can
> clearly see
> > that there are 

Re: [Freesurfer] reporting fsl PALM results

[Greve, Douglas N.,Ph.D.]

This is the purpose of fsplam. fspalm is just a frontend for palm meant 
to produce the output your would have gotten if you had run 
mri_glmfit-sim. If you don't want to run fspalm, then look inside it for 
the commands that do this.

On 2/11/19 9:05 AM, C.P.E. Rollins wrote:
>  External Email - Use Caution
>
> Hi Douglas,
> I'm using FSL PALM, but am wondering if there is a way to produce a file
> like the something.y.ocn.dat file from fspalm. That is, I would like to
> calculate the mean thickness for each subject and cluster from FSL PALM
> outputs.
> Thanks again
> Colleen
>
> On 2019-02-08 11:16, C.P.E. Rollins wrote:
>> Dear Freesurfer Developers,
>> I'm using PALM to run permutation analyses to correct for multiple
>> comparisons on Freesurfer cortical thickness and LGI data. fspalm from
>> a command like "mri_glmfit-sim --glmdir lh.lgi.glmdir --perm 1000 2
>> pos --cwp .05 --2spaces" produces output files including *.cluster.mgh
>> - map of signifcant clusters, *.cluster.summary - text file of of
>> cluster table (incl. sizes, cluster annotation, MNI coordinates, and
>> significance), and *.y.ocn.dat – text file containing LGI or cortical
>> thickness values for each subject from significant clusters. I was
>> wondering if PALM produces similar output? From my understanding the
>> *clustere_tstat_fwep.mgz file from PALM would be equivalent to the
>> *.cluster.mgh from fspalm, but is there any way to get a text file of
>> the cluster table or of the LGI/CT values for each subject from
>> significant clusters?I would like to report significant clusters (ie.
>> coordinates or parcellation, cluster size, pvalue) in a table and also
>> to extract the average lgi/thickness from significant clusters for
>> each subject.
>>
>> Thanks very much
>> Colleen
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] lh.PDDvsHC.thinckness.00.mris_preproc

[Greve, Douglas N.,Ph.D.]

can you send the full mri_surf2surf terminal output?

On 2/11/19 8:08 AM, ?? wrote:
>
> ?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2External Email - Use Caution
>
> Hello FreeSurfer Developers,
>
> I didn't cache the data during recon-all, so I ran the
>
> >following:
>
> >
>
> >  ?0?2?0?2?0?2?0?2?0?2mris_preproc ?Cfsgd PDDvsHC.fsgd --target 
> > fsaverage
>
> >--hemi lh
>
> >   --meas thickness --out lh.MMSE-AD.thickness.00.mgh
>
> >
>
> >   It seemed to run smoothly (I've attached the log below)
>
> >so I
>
> >   ran the next step:
>
> >
>
> >   mri_surf2surf --hemi lh --s fsaverage --sval
>
> >   lh.PDDvsHC.thickness.00.mgh --fwhm 10 --cortex --tval
>
> >   lh.PDDvsHC.thickness.10.mgh
>
> >
>
> >   I got the following error:
>
> >
>
> >   Reading source surface reg
>
> >  
>
> >   freesurfer/subjects/fsaverage/surf/lh.sphere.reg
>
> >   Loading source data
>
> >  
>
> >  
>
> mghRead(/Users/cengzhou/Desktop/volumetric_FS/FS/lh.PDDvsHC.thickness.00.mgh, 
> -1): could not open file
>
> recon-all.log: see attached
>
> Platform: mac os 10
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] "CorticalWhiteMatterVol" ?

[Greve, Douglas N.,Ph.D.]

All the white matter in the cerebrum (so all white matter excluding WM 
in cerebellum, brainstem, or diencephalon). We have changed the name to 
CerebralWhiteMatterVol

On 2/11/19 10:37 AM, Gonzalo Rojas Costa wrote:
>  External Email - Use Caution
>
> Hi:
>
>What is the meaning of the "CorticalWhiteMatterVol" measure?
>
>Sincerely,
>
>
> Gonzalo Rojas Costa
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] PETSurfer: "mri_gtmpvc --psf 0 --no-tfe" voxel-wise output

[Greve, Douglas N.,Ph.D.]

It will not used trilinear interp. Try it with nearest neighbor

On 2/10/19 11:55 AM, Matthieu Vanhoutte wrote:
>  External Email - Use Caution
>
> Dear Douglas,
>
> Before using "mri_gtmpvc --psf 0 --no-tfe -- rbv" according your advice to 
> obtain voxel-wise output rescaled without PVC correction, I have done 
> sequentially the different steps to obtain this output. However, when 
> comparing voxel-wise rescaled output (rbv.nii.gz) between the two methods, 
> final values at each voxel are not the same…
>
> To obtain first rescaled voxel-wise output I have used sequentially these 
> steps:
> 1.Concatenate transforms from PET space to gtmseg.mgz
> 2.Register native PET into gtmseg space (trilin. interpolation)
> 3.Compute mean PET inside reference regions (with regions masks from 
> gtmseg.mgz)
> 4.Compute intensity normalized PET images in gtmseg space
>
> Doesn’t the "mri_gtmpvc --psf 0 --no-tfe -- rdv" command use these same steps 
> ?
>
> Best,
> Matthieu
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Converting MNI152 coorindates to fsaverage space

[Tim Schäfer]

External Email - Use Caution

Dear Thomas,

thanks for your reply and suggestion. I had a look at the tool and its paper on 
it and I think it could be helpful. If I got it correctly, use case #8 at 
https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems is referred to as 
'the affine method' in the paper, but it is inferior the the non-linear warp 
method presented in the Wu2017_RegistrationFusion paper.

About using the github repo: The MNI152 coords I have are in a text file and 
they represent locations within the cortex, so I have no volume file that I 
want to project. But from a quick look at the repo, what I could do is to use 
the displacement fields (or whatever you want to call them) under 
bin/final_warps_FS5.3/?h.avgMapping_allSub_RF_ANTs_MNI152_orig_to_fsaverage.mat 
to look up the surface coords in fsaverage. Is that correct?

Thanks,

Tim

> On February 11, 2019 at 1:45 AM Thomas Yeo  wrote:
> 
> 
> External Email - Use Caution
> 
> Hi Tim,
> 
> Case #8 is transforming between MNI152 and MNI305 spaces. MNI305 is
> different from fsaverage: one is a volumetric space and one is a surface
> space.
> 
> If you are indeed looking for a transformation between MNI152 volumetric
> space and fsaverage surface space, you can consider the following:
> https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/registration/Wu2017_RegistrationFusion
> 
> Regards,
> Thomas
> 
> On Sat, Feb 9, 2019 at 11:11 PM Tim Schäfer  wrote:
> 
> > External Email - Use Caution
> >
> > > Dear list,
> > >
> > > I have some points of interest (volume coordinates, e.g. '5.9, -27.7,
> > 49.7') in MNI152 space. I would like to transform them to fsaverage space.
> > >
> > > How should I do that?
> > >
> >
> > To answer my own question, this seems to be explained as use case #8 on
> > the following website (at the bottom):
> >
> > https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
> >
> > To be precise, the website explains the transformation in the opposite
> > direction, so one should use the inverse of the matrix given on the website.
> >
> > --
> > Tim
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Tim

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] hippocampus subfield division

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Dear Yixin,
Yes, give segmentHA_T1.sh a shot. You need to install the development version 
of FreeSurfer, though.
Cheers,
/Eugenio

--
Juan Eugenio Iglesias

ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London

Research staff
Martinos Center for Biomedical Imaging
Massachusetts General Hospital

Research Affiliate
Computer Science and Artificial Intelligence Laboratory (CSAIL)
Massachusetts Institute of Technology

Lecturer on Radiology
Harvard Medical School

http://www.jeiglesias.com


From:  on behalf of Yixin Ma 

Reply-To: Freesurfer support list 
Date: Monday, 11 February 2019 at 10:01
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] hippocampus subfield division


External Email - Use Caution
Hi Freesurfer experts,

I'm writing to ask about the hippocampus subfield division again. Last time, I 
gave you an example of the subject that I failed to run the hippocampal 
subfield division, and you told me that you were able to run the hippocampus 
subfield on your laptop. I was using the older command of recon-all -all -s 
bert -hippocampal-subfields-T1. Should I try to use the newer version: 
segmentHA_T1.sh bert [SUBJECTS_DIR]. Is that possible FreeSurfer upgrading is 
the reason that I failed to run a subject on my server recently (but I was able 
to run it before). Also, can I ask where can I find the file of segmentHA_T1.sh?

Thanks for your help.

Cheers,

Yixin
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] "CorticalWhiteMatterVol" ?

[Gonzalo Rojas Costa]

External Email - Use Caution

Hi:

  What is the meaning of the "CorticalWhiteMatterVol" measure?

  Sincerely,


Gonzalo Rojas Costa

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] hippocampus subfield division

[Yixin Ma]

External Email - Use Caution

Hi Freesurfer experts,

I'm writing to ask about the hippocampus subfield division again. Last
time, I gave you an example of the subject that I failed to run the
hippocampal subfield division, and you told me that you were able to run
the hippocampus subfield on your laptop. I was using the older command of
recon-all -all -s bert -hippocampal-subfields-T1. Should I try to use the
newer version: segmentHA_T1.sh bert [SUBJECTS_DIR]. Is that possible
FreeSurfer upgrading is the reason that I failed to run a subject on my
server recently (but I was able to run it before). Also, can I ask where
can I find the file of segmentHA_T1.sh?

Thanks for your help.

Cheers,

Yixin
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] reporting fsl PALM results

[C.P.E. Rollins]

External Email - Use Caution

Hi Douglas,
I'm using FSL PALM, but am wondering if there is a way to produce a file 
like the something.y.ocn.dat file from fspalm. That is, I would like to 
calculate the mean thickness for each subject and cluster from FSL PALM 
outputs.
Thanks again
Colleen

On 2019-02-08 11:16, C.P.E. Rollins wrote:
> Dear Freesurfer Developers,
> I'm using PALM to run permutation analyses to correct for multiple
> comparisons on Freesurfer cortical thickness and LGI data. fspalm from
> a command like "mri_glmfit-sim --glmdir lh.lgi.glmdir --perm 1000 2
> pos --cwp .05 --2spaces" produces output files including *.cluster.mgh
> - map of signifcant clusters, *.cluster.summary - text file of of
> cluster table (incl. sizes, cluster annotation, MNI coordinates, and
> significance), and *.y.ocn.dat – text file containing LGI or cortical
> thickness values for each subject from significant clusters. I was
> wondering if PALM produces similar output? From my understanding the
> *clustere_tstat_fwep.mgz file from PALM would be equivalent to the
> *.cluster.mgh from fspalm, but is there any way to get a text file of
> the cluster table or of the LGI/CT values for each subject from
> significant clusters?I would like to report significant clusters (ie.
> coordinates or parcellation, cluster size, pvalue) in a table and also
> to extract the average lgi/thickness from significant clusters for
> each subject.
> 
> Thanks very much
> Colleen

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] lh.PDDvsHC.thinckness.00.mris_preproc

[??]

External Email - Use Caution

Hello FreeSurfer Developers,

I didn't cache the data during recon-all, so I ran the

> following:

> 

>mris_preproc ?Cfsgd PDDvsHC.fsgd --target fsaverage

> --hemi lh

>--meas thickness --out lh.MMSE-AD.thickness.00.mgh

> 

>It seemed to run smoothly (I've attached the log below)

> so I

>ran the next step:

> 

>mri_surf2surf --hemi lh --s fsaverage --sval

>lh.PDDvsHC.thickness.00.mgh --fwhm 10 --cortex --tval

>lh.PDDvsHC.thickness.10.mgh

> 

>I got the following error:

> 

>Reading source surface reg

>  

>freesurfer/subjects/fsaverage/surf/lh.sphere.reg

>Loading source data

>  

>  

mghRead(/Users/cengzhou/Desktop/volumetric_FS/FS/lh.PDDvsHC.thickness.00.mgh, 
-1): could not open file



recon-all.log: see attached

Platform: mac os 10

lh.PDDvsHC.thinckness.00.mris_preproc.log
Description: Binary data


error.log
Description: Binary data
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer