Re: [Freesurfer] Freesurfer surface circle of pre-defined size

[Satrajit Ghosh]

hi sarah,

you'll get a much quicker response posting PySurfer related questions to:

nipy-de...@neuroimaging.scipy.org

cheers,

satra

On Fri, Jul 26, 2013 at 12:57 PM,  wrote:

> Hello Freesurfer Experts,
>
> We would like to use PySurfer's function plot_label_foci.py to
> automatically create circular labels of a pre-defined radius (eg. 14mm) on
> the fsaverage surface of freesurfer.
>
> What are the specified units of "n_steps" in the command line argument
> "utils.coord_to_label(subject_id, coord, label='coord', hemi='lh',
> n_steps=50"?
>
> Thank you,
> Sarah
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Re: [Freesurfer] qdec question: discrepancy in sig. clusters

[Douglas Greve]

Hi Maria, can you tar up the qdec output folder and send it to our file 
drop? I'm traveling now, so it might be the 1st week of august before I 
can take a look. You can also go into the qdec output folder and run 
tksurfer to show you the results.

doug


On 7/26/13 1:37 PM, Maria Kharitonova wrote:
> Hello,
>
> I have another newbie question. I'm running qdec, trying to compare cortical 
> thickness in children with and without ADHD. However, I'm seeing a 
> discrepancy between the clusters that are significant according to the 
> terminal (after applying the Monte-Carlo simulation with default parameters; 
> output below) and the ones that pop up when I hit "Find clusters and goto 
> Max". For example, I'm seeing 4 regions in the terminal: 
> medialorbitalfrontal, inferiorparietal, caudalmiddlefrontal, and precentral. 
> However, when I hit "Find clusters and goto Max", I only see the Frontalpole.
>
> Using mri_surfcluster to extrat thickness measures only extracts it for the 
> frontalpole, and not for the 4 ROIs listed in the terminal. I would like to 
> be able to extract stats on those 4 that are listed in the terminal, if 
> possible.
>
> Can you please help me reconcile the 2 types of output? Thanks!
>
> *** terminal output:
>
> # Input  
> /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/FS_5.3_final/qdec/dx_age_icv_nuis_lh/rh-Diff-CONTROL-ADHD-Cor-thickness-age/sig.mgh
> # Frame Number  0
> # srcsubj fsaverage
> # hemi rh
> # surface white
> # annot aparc
> # SUBJECTS_DIR 
> /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/FS_5.3_final
> # Minimum Threshold 2
> # Maximum Threshold infinity
> # Threshold Signabs
> # AdjustThreshWhenOneTail 1
> # CW PValue Threshold: 0.05
> # Area Threshold0 mm^2
> # CSD thresh  2.00
> # CSD nreps1
> # CSD simtype  null-z
> # CSD contrast NA
> # CSD confint  90.00
> # Overall max 4.75828 at vertex 134555
> # Overall min -2.56762 at vertex 93241
> # NClusters  4
> # Total Cortical Surface Area 65020.8 (mm^2)
> # FixMNI = 1
> #
> # ClusterNo  Max   VtxMax   Size(mm^2)  TalX   TalY   TalZCWPCWPLow   
>  CWPHi   NVtxs   Annot
> 14.758  134555   1015.59  8.7   58.2   -5.8  0.00010  0.0 
>  0.00020  1292  medialorbitofrontal
> 23.968  135840466.91 40.0  -66.8   25.9  0.01790  0.01620 
>  0.01960   750  inferiorparietal
> 33.954  115431497.60 29.3   21.4   39.9  0.01150  0.01010 
>  0.01290   900  caudalmiddlefrontal
> 43.242  133890439.44 49.4   -5.1   22.0  0.02520  0.02320 
>  0.02720   932  precentral
>
> Simulation complete.
>
>
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[Freesurfer] qdec question: discrepancy in sig. clusters

[Maria Kharitonova]

Hello,

I have another newbie question. I'm running qdec, trying to compare cortical 
thickness in children with and without ADHD. However, I'm seeing a discrepancy 
between the clusters that are significant according to the terminal (after 
applying the Monte-Carlo simulation with default parameters; output below) and 
the ones that pop up when I hit "Find clusters and goto Max". For example, I'm 
seeing 4 regions in the terminal: medialorbitalfrontal, inferiorparietal, 
caudalmiddlefrontal, and precentral. However, when I hit "Find clusters and 
goto Max", I only see the Frontalpole.

Using mri_surfcluster to extrat thickness measures only extracts it for the 
frontalpole, and not for the 4 ROIs listed in the terminal. I would like to be 
able to extract stats on those 4 that are listed in the terminal, if possible. 

Can you please help me reconcile the 2 types of output? Thanks!

*** terminal output:

# Input  
/net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/FS_5.3_final/qdec/dx_age_icv_nuis_lh/rh-Diff-CONTROL-ADHD-Cor-thickness-age/sig.mgh
# Frame Number  0
# srcsubj fsaverage
# hemi rh
# surface white
# annot aparc
# SUBJECTS_DIR 
/net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/FS_5.3_final
# Minimum Threshold 2
# Maximum Threshold infinity
# Threshold Signabs
# AdjustThreshWhenOneTail 1
# CW PValue Threshold: 0.05 
# Area Threshold0 mm^2
# CSD thresh  2.00
# CSD nreps1
# CSD simtype  null-z
# CSD contrast NA
# CSD confint  90.00
# Overall max 4.75828 at vertex 134555
# Overall min -2.56762 at vertex 93241
# NClusters  4
# Total Cortical Surface Area 65020.8 (mm^2)
# FixMNI = 1
# 
# ClusterNo  Max   VtxMax   Size(mm^2)  TalX   TalY   TalZCWPCWPLow
CWPHi   NVtxs   Annot
   14.758  134555   1015.59  8.7   58.2   -5.8  0.00010  0.0  
0.00020  1292  medialorbitofrontal
   23.968  135840466.91 40.0  -66.8   25.9  0.01790  0.01620  
0.01960   750  inferiorparietal
   33.954  115431497.60 29.3   21.4   39.9  0.01150  0.01010  
0.01290   900  caudalmiddlefrontal
   43.242  133890439.44 49.4   -5.1   22.0  0.02520  0.02320  
0.02720   932  precentral

Simulation complete.


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Re: [Freesurfer] functional connectivity, group averages

[Douglas Greve]

yes, use isxconcat-sess (after you have done the 1st level analysis of 
course). To use the r-rvalue, add "-m pcc" to the isxconcat-sess command 
line

doug




On 7/25/13 1:54 PM, Mario Ortega wrote:

Hi Team,
I have a question on making a group average of subjects for functional 
connectivity.
In detail, I want to make a surface overlay that is the average 
correlation (r-value) of a certain subject group. What commands would 
be used for this? simply isxconcat-sess? I could not find much info on 
the FSFAST or Functional webpages.

Thanks,
Mario


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Re: [Freesurfer] HypoIntense Lesions

[Fotiadis, Panagiotis]

Ok, thanks for your reply!

Best,
Panos

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Friday, July 26, 2013 12:35 PM
To: Fotiadis, Panagiotis
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] HypoIntense Lesions

no, segmenting lesions is hard and can't be done with a simple threshold
On
Fri, 26 Jul 2013, Fotiadis, Panagiotis wrote:

> Hi Bruce,
>
> I see. In that case, do you happen to know if there is another way to get 
> clusters with orig as the input? Maybe by setting a threshold instead of a 
> match?
>
> Thanks again,
> Panos
> 
> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
> Sent: Friday, July 26, 2013 12:18 PM
> To: Fotiadis, Panagiotis
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] HypoIntense Lesions
>
> Hi Panos
>
> when you run it with the orig you are getting voxels that happen to have
> an intensity of 77 and have nothing to do with lesions. Run it on the
> aseg
>
> Bruce
> On Fri, 26 Jul 2013, Fotiadis, Panagiotis wrote:
>
>> Hi Doug and Bruce,
>>
>> When I am running mri_binarize with aseg.mgz as input and --match 77 I get 
>> clusters, but when I run the same thing with the orig.mgz as input, I get 
>> individual voxels and not any clusters are forming. Could you please explain 
>> to me why is this happening and whether there is a way to get clusters with 
>> orig.mgz as input?
>>
>> Thank you for your time.
>> Panos
>> 
>> From: Fotiadis, Panagiotis
>> Sent: Monday, June 10, 2013 4:03 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: RE: [Freesurfer] HypoIntense Lesions
>>
>> Great, thank you!
>>
>> Panos
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Monday, June 10, 2013 3:40 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] HypoIntense Lesions
>>
>> Hi Panos, I don't know an automatic way to do it. You could label it by
>> hand on tkmedit or freeview.
>> doug
>>
>>
>> On 06/10/2013 03:31 PM, Fotiadis, Panagiotis wrote:
>>> Hi Doug,
>>>
>>> Thanks for your response, it was really helpful. In addition to the 
>>> previous comments, I have some subjects that have a hematoma that is not 
>>> shown in the aseg.mgz file, and hence is not shown as a hypointense cluster 
>>> after doing the analysis provided below. Do you know if there is any other 
>>> way to extract information (such as outlining it and/or acquiring its 
>>> volume) about something like?
>>>
>>> Thanks again,
>>> Panos
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
>>> [gr...@nmr.mgh.harvard.edu]
>>> Sent: Monday, June 10, 2013 12:18 PM
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] HypoIntense Lesions
>>>
>>> On 06/10/2013 12:12 PM, Fotiadis, Panagiotis wrote:
 Hi Doug and Bruce,

 Don't worry about it! Actually, Bruce, tools for labeling hypo-intense T1 
 would work great as well. Do you know where I could look for them?
>>> This is already done in recon-all (aseg.mgz and aseg.stats)
 In addition, Doug besides the WM hypointensities in the aseg.stats is 
 there something that shows the number of lesions, instead of the volume 
 (or the volume that corresponds to each lesion)?
>>> That is not output by default, but you can get it relatively easily in
>>> two steps:
>>> mri_binarize --i aseg.mgz --o wmhypo.mgz --match 77  -->> This
>>> creates a binary image
>>> Then run mri_volcluster with --in wmhypo.mgz --thmin .5. The number and
>>> volume of each lesion will be in the summary file
>>> doug
 Thanks for your help,
 Panos
 
 From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
 Sent: Monday, June 10, 2013 11:52 AM
 To: Fotiadis, Panagiotis
 Cc: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] HypoIntense Lesions

 Hi Panos

 sorry, forgot to respond to this. We have tools for labeling
 hyper-intense T2/hypo-intense T1. Not sure about the hypointense SWI. It
 might work on those if you also had a good T1 and some training data. Doug
 might know

 cheers
 Bruce


 On Mon, 10 Jun 2013, Fotiadis, Panagiotis
 wrote:

> Hi FreeSurfer Community,
>
> I was wondering whether there is an automatic tool that outlines the 
> hypointense lesions in a SWI scan.
>
> Thank you,
> Panos
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Re: [Freesurfer] selxavg3-sess： Matlab cannot display graphics

[Douglas Greve]

Hi James, does everything run to completion? If so, then you can ignore 
those warnings.

doug




On 7/26/13 8:35 AM, Wang Zhiwei wrote:


Hi all,

When I run selxavg3-sess for any analysis, the following information 
is always appearing. Can you please give some suggestions how to fix 
that? Any thoughts would be very appreciated!


--

--- matlab output 

Warning: Unable to open display 'iconic'.  You will not be able to 
display graphics on the screen.


Warning: No window system found.  Java option 'MWT' ignored.

< M A T L A B (R) >

Copyright 1984-2012 The MathWorks, Inc.

R2012b (8.0.0.783) 64-bit (glnxa64)

August 22, 2012

No window system found. Java option 'MWT' ignored.

To get started, type one of these: helpwin, helpdesk, or demo.

For product information, visit www.mathworks.com.

>> >> >> >> >> >> >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m

>> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >>

Thanks!

James



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Re: [Freesurfer] J_white

[Douglas Greve]

Hi Linn, what do you mean that you cannot select it? Is it grayed out?
doug


On 7/26/13 4:20 AM, Linn Mittlestein wrote:

Dear freesurfer experts,

I am currently do group analysis in qdec, and I canot select jacobian 
white from the drop down menu, I thought this would be an option? Do I 
do have additional steps to get these values?


Kind Regards,

Linn


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[Freesurfer] Freesurfer surface circle of pre-defined size

[sarahp]

Hello Freesurfer Experts,

We would like to use PySurfer's function plot_label_foci.py to
automatically create circular labels of a pre-defined radius (eg. 14mm) on
the fsaverage surface of freesurfer.

What are the specified units of "n_steps" in the command line argument
"utils.coord_to_label(subject_id, coord, label='coord', hemi='lh',
n_steps=50"?

Thank you,
Sarah
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Re: [Freesurfer] spmregister error

[Douglas Greve]

what version of spm are you using? Look in your ~/matlab/startup.m file 
to see. If you are using version 5 or less, then add --img
doug


On 7/26/13 11:19 AM, Marco Loggia wrote:
> Hello Doug,
>
> I am encountering the error below when running spmregister. Where do you
> think is the issue? Thanks!
>
> Best,
> Marco
>
>
>
> bash-4.1$ spmregister --mov "$file".nii --s PBR_"$subj" --reg tmp.dat
> --fsvol merged.lrrev
>
> Log file is ./spmregister.log
> Fri Jul 26 10:52:49 EDT 2013
> --mov rsl_CLBP001_f1_1_3627_5427_nas_suv.nii --s PBR_CLBP001 --reg tmp.dat
> --fsvol merged.lrrev
> $Id: spmregister,v 1.39.2.1 2012/10/30 20:05:17 greve Exp $
> matlab matlab
> fmt nii
> UseSPMGetSpace 1
> --
> /autofs/cluster/hookerlab/Studies/PBR/Marco/CLBP001/PET/Sum_single_frame/PET_recon_SUV/rsl_files
> mri_convert
> /autofs/cluster/vitaly/marco/PBR28/data/fs/PBR_CLBP001/mri/merged.lrrev.mgz
> ./tmp.spmreg.10617/refvol.spmregister.nii -ic 0 0 0
> mri_convert
> /autofs/cluster/vitaly/marco/PBR28/data/fs/PBR_CLBP001/mri/merged.lrrev.mgz
> ./tmp.spmreg.10617/refvol.spmregister.nii -ic 0 0 0
> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> reading from
> /autofs/cluster/vitaly/marco/PBR28/data/fs/PBR_CLBP001/mri/merged.lrrev.mgz...
> TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (-0.0414768, -0.991189, -0.125791)
> j_ras = (-0.0799847, 0.128789, -0.988441)
> k_ras = (-0.995933, 0.030936, 0.084622)
> writing to ./tmp.spmreg.10617/refvol.spmregister.nii...
> --
> /autofs/cluster/hookerlab/Studies/PBR/Marco/CLBP001/PET/Sum_single_frame/PET_recon_SUV/rsl_files
> mri_convert rsl_CLBP001_f1_1_3627_5427_nas_suv.nii
> ./tmp.spmreg.10617/movvol.spmregister.nii -ic 0 0 0 --frame 0
> mri_convert rsl_CLBP001_f1_1_3627_5427_nas_suv.nii
> ./tmp.spmreg.10617/movvol.spmregister.nii -ic 0 0 0 --frame 0
> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> reading from rsl_CLBP001_f1_1_3627_5427_nas_suv.nii...
> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (1, 0, 0)
> j_ras = (0, -1, 0)
> k_ras = (0, 0, -1)
> keeping frame 0
> writing to ./tmp.spmreg.10617/movvol.spmregister.nii...
> Matlab file is ./tmp.spmreg.10617/spmregister.10617.m
> monly   = 0;
> targvol = './tmp.spmreg.10617/refvol.spmregister.nii';
> srcvol  = './tmp.spmreg.10617/movvol.spmregister.nii';
> errfile  = './tmp.spmreg.10617/spmregister.10617.err';
> fmt = 'nii';
>
> if(exist('spm_coreg') ~= 2)
>fprintf('ERROR: cannot find spm_coreg.m. Make sure that the SPM\n');
>fprintf('   package is in your matlab path (check ~/matlab/startup)\n');
>fp = fopen(errfile,'w');
>fprintf(fp,'ERROR: cannot find spm_coreg.m. Make sure that the SPM\n');
>fprintf(fp,'   package is in your matlab path (check ~/matlab/startup)\n');
>fclose(fp);
>return; quit;
> end
>
> fprintf('fmt %s\n',fmt);
> which spm_coreg
>
> % This is a hack to try to determine which version of spm is being run. If
> % spm8 is being run with analyze as input, a left-right reveral will occur.
> % This searches for "spm8" in the spm path, not perfect, but hopefully good
> % enough. It does not appear that spm offers a "version" command.
> IsSPM8 = length(findstr(dirname(which('spm_coreg')),'spm8'));
> if(IsSPM8 & strcmp(fmt,'img'))
>fprintf('\n\n');
>fprintf('ERROR: you appear to be using spm8. If so, re-run this with
> --nii\n');
>fprintf('\n\n');
>fp = fopen(errfile,'a');
>fprintf(fp,'ERROR: you appear to be using spm8. If so, re-run this with
> --nii\n');
>fclose(fp);
>return; quit; exit; % These do nothing when run from a csh script
> end
>
> global defaults
> spm_defaults  % load spm2's default fields
>
> fprintf('INFO: Assuming RAS coordinate system\n');
> defaults.analyze.flip = 0;
>
> %===
> % coregistration  defaults
> %===
>
> defaults.coreg.estimate.cost_fun = 'nmi';
> defaults.coreg.estimate.sep  = [4 2];
> defaults.coreg.estimate.tol  = [0.02 0.02 0.02 0.001 0.001 0.001 0.01
> 0.01 0.01 0.001 0.001 0.001];
> defaults.coreg.estimate.fwhm = [7 7];
> defaults.coreg.estimate.params = [0 0 0 0 0 0];
> defaults.coreg.estimate.graphics = 0; % dont crate ps file
>
>
> %===
> % coregister files
> %===
>
> disp(sprintf('using %s as the target image',targvol));
> disp(sprintf('using %s as the source image',srcvol));
>
> [pth1,nam1,ext1] = fileparts(deblank(targvol));
> [pth2,nam2,ext2] = fileparts(deblank(srcvol));
>
> %tmp = spm_get('Files',pth1,[nam1 ext1]);
> tmp = sprintf('%s/%s%s',pth1,nam1,ext1);
> VG= spm_vol(tmp); % target image
> if(isempty(VG))
>fprintf('ERROR: loading target %s\n',targvol);
>fp = fopen(er

Re: [Freesurfer] HypoIntense Lesions

[Bruce Fischl]

no, segmenting lesions is hard and can't be done with a simple threshold
On 
Fri, 26 Jul 2013, Fotiadis, Panagiotis wrote:

> Hi Bruce,
>
> I see. In that case, do you happen to know if there is another way to get 
> clusters with orig as the input? Maybe by setting a threshold instead of a 
> match?
>
> Thanks again,
> Panos
> 
> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
> Sent: Friday, July 26, 2013 12:18 PM
> To: Fotiadis, Panagiotis
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] HypoIntense Lesions
>
> Hi Panos
>
> when you run it with the orig you are getting voxels that happen to have
> an intensity of 77 and have nothing to do with lesions. Run it on the
> aseg
>
> Bruce
> On Fri, 26 Jul 2013, Fotiadis, Panagiotis wrote:
>
>> Hi Doug and Bruce,
>>
>> When I am running mri_binarize with aseg.mgz as input and --match 77 I get 
>> clusters, but when I run the same thing with the orig.mgz as input, I get 
>> individual voxels and not any clusters are forming. Could you please explain 
>> to me why is this happening and whether there is a way to get clusters with 
>> orig.mgz as input?
>>
>> Thank you for your time.
>> Panos
>> 
>> From: Fotiadis, Panagiotis
>> Sent: Monday, June 10, 2013 4:03 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: RE: [Freesurfer] HypoIntense Lesions
>>
>> Great, thank you!
>>
>> Panos
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Monday, June 10, 2013 3:40 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] HypoIntense Lesions
>>
>> Hi Panos, I don't know an automatic way to do it. You could label it by
>> hand on tkmedit or freeview.
>> doug
>>
>>
>> On 06/10/2013 03:31 PM, Fotiadis, Panagiotis wrote:
>>> Hi Doug,
>>>
>>> Thanks for your response, it was really helpful. In addition to the 
>>> previous comments, I have some subjects that have a hematoma that is not 
>>> shown in the aseg.mgz file, and hence is not shown as a hypointense cluster 
>>> after doing the analysis provided below. Do you know if there is any other 
>>> way to extract information (such as outlining it and/or acquiring its 
>>> volume) about something like?
>>>
>>> Thanks again,
>>> Panos
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
>>> [gr...@nmr.mgh.harvard.edu]
>>> Sent: Monday, June 10, 2013 12:18 PM
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] HypoIntense Lesions
>>>
>>> On 06/10/2013 12:12 PM, Fotiadis, Panagiotis wrote:
 Hi Doug and Bruce,

 Don't worry about it! Actually, Bruce, tools for labeling hypo-intense T1 
 would work great as well. Do you know where I could look for them?
>>> This is already done in recon-all (aseg.mgz and aseg.stats)
 In addition, Doug besides the WM hypointensities in the aseg.stats is 
 there something that shows the number of lesions, instead of the volume 
 (or the volume that corresponds to each lesion)?
>>> That is not output by default, but you can get it relatively easily in
>>> two steps:
>>> mri_binarize --i aseg.mgz --o wmhypo.mgz --match 77  -->> This
>>> creates a binary image
>>> Then run mri_volcluster with --in wmhypo.mgz --thmin .5. The number and
>>> volume of each lesion will be in the summary file
>>> doug
 Thanks for your help,
 Panos
 
 From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
 Sent: Monday, June 10, 2013 11:52 AM
 To: Fotiadis, Panagiotis
 Cc: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] HypoIntense Lesions

 Hi Panos

 sorry, forgot to respond to this. We have tools for labeling
 hyper-intense T2/hypo-intense T1. Not sure about the hypointense SWI. It
 might work on those if you also had a good T1 and some training data. Doug
 might know

 cheers
 Bruce


 On Mon, 10 Jun 2013, Fotiadis, Panagiotis
 wrote:

> Hi FreeSurfer Community,
>
> I was wondering whether there is an automatic tool that outlines the 
> hypointense lesions in a SWI scan.
>
> Thank you,
> Panos
> ___
> 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


>>> --
>>> Douglas N. Greve, Ph.D.
>>> MGH-NMR Center
>>> gr...@nmr.mgh.harvard.edu
>>> Phone Number: 617-724-2358
>>> Fax: 617-726-7422
>>>
>>> Bugs: sur

Re: [Freesurfer] spmregister error

[Douglas Greve]

That probably just means that you have run out of space in the directory 
you are running it from. Run
quota -v
to see
doug


On 7/26/13 11:27 AM, Marco Loggia wrote:
> Hi again,
>
> interestingly, if I run the same command using the full fsvol path I get
> the 'Disk quota exceeded' message... I wonder if even the message I wrote
> you about in my previous email has something to do with disk space.
>
> I will try free up some room and try spmregister again!
> Marco
>
> bash-4.1$ spmregister --mov "$file".nii --s PBR_"$subj" --reg tmp.dat
> --fsvol
> /autofs/cluster/vitaly/marco/PBR28/data/fs/PBR_CLBP001/mri/merged.lrrev.mgz
> mkdir: cannot create directory `./tmp.spmreg.11238': Disk quota exceeded
> Log file is ./spmregister.log
> Fri Jul 26 11:21:20 EDT 2013
> tee: ./spmregister.log: Disk quota exceeded
> --mov rsl_CLBP001_f1_1_3627_5427_nas_suv.nii --s PBR_CLBP001 --reg tmp.dat
> --fsvol
> /autofs/cluster/vitaly/marco/PBR28/data/fs/PBR_CLBP001/mri/merged.lrrev.mgz
> tee: ./spmregister.log: Disk quota exceeded
> $Id: spmregister,v 1.39.2.1 2012/10/30 20:05:17 greve Exp $
> tee: ./spmregister.log: Disk quota exceeded
> matlab matlab
> tee: ./spmregister.log: Disk quota exceeded
> fmt nii
> tee: ./spmregister.log: Disk quota exceeded
> UseSPMGetSpace 1
> tee: ./spmregister.log: Disk quota exceeded
> ERROR:
> /autofs/cluster/vitaly/marco/PBR28/data/fs/PBR_CLBP001/mri//autofs/cluster/vitaly/marco/PBR28/data/fs/PBR_CLBP001/mri/merged.lrrev.mgz.mgz
> not found in either COR or MGZ formats
>
>> Hello Doug,
>>
>> I am encountering the error below when running spmregister. Where do you
>> think is the issue? Thanks!
>>
>> Best,
>> Marco
>>
>>
>>
>> bash-4.1$ spmregister --mov "$file".nii --s PBR_"$subj" --reg tmp.dat
>> --fsvol merged.lrrev
>>
>> Log file is ./spmregister.log
>> Fri Jul 26 10:52:49 EDT 2013
>> --mov rsl_CLBP001_f1_1_3627_5427_nas_suv.nii --s PBR_CLBP001 --reg tmp.dat
>> --fsvol merged.lrrev
>> $Id: spmregister,v 1.39.2.1 2012/10/30 20:05:17 greve Exp $
>> matlab matlab
>> fmt nii
>> UseSPMGetSpace 1
>> --
>> /autofs/cluster/hookerlab/Studies/PBR/Marco/CLBP001/PET/Sum_single_frame/PET_recon_SUV/rsl_files
>> mri_convert
>> /autofs/cluster/vitaly/marco/PBR28/data/fs/PBR_CLBP001/mri/merged.lrrev.mgz
>> ./tmp.spmreg.10617/refvol.spmregister.nii -ic 0 0 0
>> mri_convert
>> /autofs/cluster/vitaly/marco/PBR28/data/fs/PBR_CLBP001/mri/merged.lrrev.mgz
>> ./tmp.spmreg.10617/refvol.spmregister.nii -ic 0 0 0
>> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
>> reading from
>> /autofs/cluster/vitaly/marco/PBR28/data/fs/PBR_CLBP001/mri/merged.lrrev.mgz...
>> TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
>> i_ras = (-0.0414768, -0.991189, -0.125791)
>> j_ras = (-0.0799847, 0.128789, -0.988441)
>> k_ras = (-0.995933, 0.030936, 0.084622)
>> writing to ./tmp.spmreg.10617/refvol.spmregister.nii...
>> --
>> /autofs/cluster/hookerlab/Studies/PBR/Marco/CLBP001/PET/Sum_single_frame/PET_recon_SUV/rsl_files
>> mri_convert rsl_CLBP001_f1_1_3627_5427_nas_suv.nii
>> ./tmp.spmreg.10617/movvol.spmregister.nii -ic 0 0 0 --frame 0
>> mri_convert rsl_CLBP001_f1_1_3627_5427_nas_suv.nii
>> ./tmp.spmreg.10617/movvol.spmregister.nii -ic 0 0 0 --frame 0
>> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
>> reading from rsl_CLBP001_f1_1_3627_5427_nas_suv.nii...
>> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
>> i_ras = (1, 0, 0)
>> j_ras = (0, -1, 0)
>> k_ras = (0, 0, -1)
>> keeping frame 0
>> writing to ./tmp.spmreg.10617/movvol.spmregister.nii...
>> Matlab file is ./tmp.spmreg.10617/spmregister.10617.m
>> monly   = 0;
>> targvol = './tmp.spmreg.10617/refvol.spmregister.nii';
>> srcvol  = './tmp.spmreg.10617/movvol.spmregister.nii';
>> errfile  = './tmp.spmreg.10617/spmregister.10617.err';
>> fmt = 'nii';
>>
>> if(exist('spm_coreg') ~= 2)
>>fprintf('ERROR: cannot find spm_coreg.m. Make sure that the SPM\n');
>>fprintf('   package is in your matlab path (check ~/matlab/startup)\n');
>>fp = fopen(errfile,'w');
>>fprintf(fp,'ERROR: cannot find spm_coreg.m. Make sure that the SPM\n');
>>fprintf(fp,'   package is in your matlab path (check
>> ~/matlab/startup)\n');
>>fclose(fp);
>>return; quit;
>> end
>>
>> fprintf('fmt %s\n',fmt);
>> which spm_coreg
>>
>> % This is a hack to try to determine which version of spm is being run. If
>> % spm8 is being run with analyze as input, a left-right reveral will
>> occur.
>> % This searches for "spm8" in the spm path, not perfect, but hopefully
>> good
>> % enough. It does not appear that spm offers a "version" command.
>> IsSPM8 = length(findstr(dirname(which('spm_coreg')),'spm8'));
>> if(IsSPM8 & strcmp(fmt,'img'))
>>fprintf('\n\n');
>>fprintf('ERROR: you appear to be using spm8. If so, re-run this with
>> --nii\n');
>>fprintf('\n\n');
>>fp = fopen(errfile,'a');
>>fprintf(fp,'ERROR: you appear to be using spm8. If so, re-run this with
>> --nii\n');
>

Re: [Freesurfer] HypoIntense Lesions

[Fotiadis, Panagiotis]

Hi Bruce,

I see. In that case, do you happen to know if there is another way to get 
clusters with orig as the input? Maybe by setting a threshold instead of a 
match?

Thanks again,
Panos

From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Friday, July 26, 2013 12:18 PM
To: Fotiadis, Panagiotis
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] HypoIntense Lesions

Hi Panos

when you run it with the orig you are getting voxels that happen to have
an intensity of 77 and have nothing to do with lesions. Run it on the
aseg

Bruce
On Fri, 26 Jul 2013, Fotiadis, Panagiotis wrote:

> Hi Doug and Bruce,
>
> When I am running mri_binarize with aseg.mgz as input and --match 77 I get 
> clusters, but when I run the same thing with the orig.mgz as input, I get 
> individual voxels and not any clusters are forming. Could you please explain 
> to me why is this happening and whether there is a way to get clusters with 
> orig.mgz as input?
>
> Thank you for your time.
> Panos
> 
> From: Fotiadis, Panagiotis
> Sent: Monday, June 10, 2013 4:03 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: RE: [Freesurfer] HypoIntense Lesions
>
> Great, thank you!
>
> Panos
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Monday, June 10, 2013 3:40 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] HypoIntense Lesions
>
> Hi Panos, I don't know an automatic way to do it. You could label it by
> hand on tkmedit or freeview.
> doug
>
>
> On 06/10/2013 03:31 PM, Fotiadis, Panagiotis wrote:
>> Hi Doug,
>>
>> Thanks for your response, it was really helpful. In addition to the previous 
>> comments, I have some subjects that have a hematoma that is not shown in the 
>> aseg.mgz file, and hence is not shown as a hypointense cluster after doing 
>> the analysis provided below. Do you know if there is any other way to 
>> extract information (such as outlining it and/or acquiring its volume) about 
>> something like?
>>
>> Thanks again,
>> Panos
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Monday, June 10, 2013 12:18 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] HypoIntense Lesions
>>
>> On 06/10/2013 12:12 PM, Fotiadis, Panagiotis wrote:
>>> Hi Doug and Bruce,
>>>
>>> Don't worry about it! Actually, Bruce, tools for labeling hypo-intense T1 
>>> would work great as well. Do you know where I could look for them?
>> This is already done in recon-all (aseg.mgz and aseg.stats)
>>> In addition, Doug besides the WM hypointensities in the aseg.stats is there 
>>> something that shows the number of lesions, instead of the volume (or the 
>>> volume that corresponds to each lesion)?
>> That is not output by default, but you can get it relatively easily in
>> two steps:
>> mri_binarize --i aseg.mgz --o wmhypo.mgz --match 77  -->> This
>> creates a binary image
>> Then run mri_volcluster with --in wmhypo.mgz --thmin .5. The number and
>> volume of each lesion will be in the summary file
>> doug
>>> Thanks for your help,
>>> Panos
>>> 
>>> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
>>> Sent: Monday, June 10, 2013 11:52 AM
>>> To: Fotiadis, Panagiotis
>>> Cc: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] HypoIntense Lesions
>>>
>>> Hi Panos
>>>
>>> sorry, forgot to respond to this. We have tools for labeling
>>> hyper-intense T2/hypo-intense T1. Not sure about the hypointense SWI. It
>>> might work on those if you also had a good T1 and some training data. Doug
>>> might know
>>>
>>> cheers
>>> Bruce
>>>
>>>
>>> On Mon, 10 Jun 2013, Fotiadis, Panagiotis
>>> wrote:
>>>
 Hi FreeSurfer Community,

 I was wondering whether there is an automatic tool that outlines the 
 hypointense lesions in a SWI scan.

 Thank you,
 Panos
 ___
 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
>>>
>>>
>> --
>> 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/
>>
>> ___

Re: [Freesurfer] HypoIntense Lesions

[Bruce Fischl]

Hi Panos

when you run it with the orig you are getting voxels that happen to have 
an intensity of 77 and have nothing to do with lesions. Run it on the 
aseg

Bruce
On Fri, 26 Jul 2013, Fotiadis, Panagiotis wrote:

> Hi Doug and Bruce,
>
> When I am running mri_binarize with aseg.mgz as input and --match 77 I get 
> clusters, but when I run the same thing with the orig.mgz as input, I get 
> individual voxels and not any clusters are forming. Could you please explain 
> to me why is this happening and whether there is a way to get clusters with 
> orig.mgz as input?
>
> Thank you for your time.
> Panos
> 
> From: Fotiadis, Panagiotis
> Sent: Monday, June 10, 2013 4:03 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: RE: [Freesurfer] HypoIntense Lesions
>
> Great, thank you!
>
> Panos
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Monday, June 10, 2013 3:40 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] HypoIntense Lesions
>
> Hi Panos, I don't know an automatic way to do it. You could label it by
> hand on tkmedit or freeview.
> doug
>
>
> On 06/10/2013 03:31 PM, Fotiadis, Panagiotis wrote:
>> Hi Doug,
>>
>> Thanks for your response, it was really helpful. In addition to the previous 
>> comments, I have some subjects that have a hematoma that is not shown in the 
>> aseg.mgz file, and hence is not shown as a hypointense cluster after doing 
>> the analysis provided below. Do you know if there is any other way to 
>> extract information (such as outlining it and/or acquiring its volume) about 
>> something like?
>>
>> Thanks again,
>> Panos
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Monday, June 10, 2013 12:18 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] HypoIntense Lesions
>>
>> On 06/10/2013 12:12 PM, Fotiadis, Panagiotis wrote:
>>> Hi Doug and Bruce,
>>>
>>> Don't worry about it! Actually, Bruce, tools for labeling hypo-intense T1 
>>> would work great as well. Do you know where I could look for them?
>> This is already done in recon-all (aseg.mgz and aseg.stats)
>>> In addition, Doug besides the WM hypointensities in the aseg.stats is there 
>>> something that shows the number of lesions, instead of the volume (or the 
>>> volume that corresponds to each lesion)?
>> That is not output by default, but you can get it relatively easily in
>> two steps:
>> mri_binarize --i aseg.mgz --o wmhypo.mgz --match 77  -->> This
>> creates a binary image
>> Then run mri_volcluster with --in wmhypo.mgz --thmin .5. The number and
>> volume of each lesion will be in the summary file
>> doug
>>> Thanks for your help,
>>> Panos
>>> 
>>> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
>>> Sent: Monday, June 10, 2013 11:52 AM
>>> To: Fotiadis, Panagiotis
>>> Cc: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] HypoIntense Lesions
>>>
>>> Hi Panos
>>>
>>> sorry, forgot to respond to this. We have tools for labeling
>>> hyper-intense T2/hypo-intense T1. Not sure about the hypointense SWI. It
>>> might work on those if you also had a good T1 and some training data. Doug
>>> might know
>>>
>>> cheers
>>> Bruce
>>>
>>>
>>> On Mon, 10 Jun 2013, Fotiadis, Panagiotis
>>> wrote:
>>>
 Hi FreeSurfer Community,

 I was wondering whether there is an automatic tool that outlines the 
 hypointense lesions in a SWI scan.

 Thank you,
 Panos
 ___
 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
>>>
>>>
>> --
>> 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/
>>
>> ___
>> 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
>>
>>
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> F

Re: [Freesurfer] HypoIntense Lesions

[Fotiadis, Panagiotis]

Hi Doug and Bruce,

When I am running mri_binarize with aseg.mgz as input and --match 77 I get 
clusters, but when I run the same thing with the orig.mgz as input, I get 
individual voxels and not any clusters are forming. Could you please explain to 
me why is this happening and whether there is a way to get clusters with 
orig.mgz as input?

Thank you for your time.
Panos

From: Fotiadis, Panagiotis
Sent: Monday, June 10, 2013 4:03 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] HypoIntense Lesions

Great, thank you!

Panos

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Monday, June 10, 2013 3:40 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] HypoIntense Lesions

Hi Panos, I don't know an automatic way to do it. You could label it by
hand on tkmedit or freeview.
doug


On 06/10/2013 03:31 PM, Fotiadis, Panagiotis wrote:
> Hi Doug,
>
> Thanks for your response, it was really helpful. In addition to the previous 
> comments, I have some subjects that have a hematoma that is not shown in the 
> aseg.mgz file, and hence is not shown as a hypointense cluster after doing 
> the analysis provided below. Do you know if there is any other way to extract 
> information (such as outlining it and/or acquiring its volume) about 
> something like?
>
> Thanks again,
> Panos
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Monday, June 10, 2013 12:18 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] HypoIntense Lesions
>
> On 06/10/2013 12:12 PM, Fotiadis, Panagiotis wrote:
>> Hi Doug and Bruce,
>>
>> Don't worry about it! Actually, Bruce, tools for labeling hypo-intense T1 
>> would work great as well. Do you know where I could look for them?
> This is already done in recon-all (aseg.mgz and aseg.stats)
>> In addition, Doug besides the WM hypointensities in the aseg.stats is there 
>> something that shows the number of lesions, instead of the volume (or the 
>> volume that corresponds to each lesion)?
> That is not output by default, but you can get it relatively easily in
> two steps:
> mri_binarize --i aseg.mgz --o wmhypo.mgz --match 77  -->> This
> creates a binary image
> Then run mri_volcluster with --in wmhypo.mgz --thmin .5. The number and
> volume of each lesion will be in the summary file
> doug
>> Thanks for your help,
>> Panos
>> 
>> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
>> Sent: Monday, June 10, 2013 11:52 AM
>> To: Fotiadis, Panagiotis
>> Cc: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] HypoIntense Lesions
>>
>> Hi Panos
>>
>> sorry, forgot to respond to this. We have tools for labeling
>> hyper-intense T2/hypo-intense T1. Not sure about the hypointense SWI. It
>> might work on those if you also had a good T1 and some training data. Doug
>> might know
>>
>> cheers
>> Bruce
>>
>>
>> On Mon, 10 Jun 2013, Fotiadis, Panagiotis
>> wrote:
>>
>>> Hi FreeSurfer Community,
>>>
>>> I was wondering whether there is an automatic tool that outlines the 
>>> hypointense lesions in a SWI scan.
>>>
>>> Thank you,
>>> Panos
>>> ___
>>> 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
>>
>>
> --
> 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/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
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] correspondance between broadmann areas and freesurfer labels

[Anastasia Yendiki]

You can search recon-all.log for the command that generates those stats 
and appply it to the ?h.BA.thresh.annot instead of ?h.BA.annot.


On Fri, 26 Jul 2013, Satrajit Ghosh wrote:


thanks guys. any thoughts on when the ba*.stats files will use these? right
now i agree with bruce that they are biased by the predictability of the
region. less accurate prediction -> greater volume.
cheers,

satra


On Fri, Jul 26, 2013 at 10:28 AM, Anastasia Yendiki
 wrote:

  There is a *.thresh.label version of all the BA labels in 5.3,
  but I don't think it's used by default. You can try using those
  labels instead.

  On Fri, 26 Jul 2013, Satrajit Ghosh wrote:

hi bruce,
currently 5.3, but the data i was looking at was
processed with 5.1 and in
that right ba44/45 was always larger.

cheers,

satra


On Fri, Jul 26, 2013 at 9:47 AM, Bruce Fischl

wrote:
      Hi Satra,

      what version are you using? I think Anastasia
implemented a
      thresholded version in 5.3, but perhaps she
can comment.
      Bruce
      On Fri, 26 Jul 2013, Satrajit Ghosh wrote:

            hi bruce,
            related to this question, how are the
stats/volumes
            of the BAs computed?

            cheers,

            satra

            On Fri, Jul 26, 2013 at 9:33 AM, Bruce
Fischl
            
            wrote:
                  Hi Laouchedi

                  that is a big research question!
The answer is
            a qualified yes,
                  but it depends strongly on what
labels you
            mean. In general we
                  find that the closer you are to
primary areas
            like V1/M1, the
                  stronger the correspondence is. We
do supply
            some explicit
                  estimates of Brodmann areas, have
you looked
            at them?

                  Bruce


                  On Fri, 26 Jul 2013, LAOUCHEDI
MAKHLOUF wrote:

                        Hi
                            i used freesurfer labels
in a study
            and i want
                        to identify the broadmann
                        areas corresponding to some
labels, is
            there any
                        correspondence between the
                        two ?

                        Thanks


                 
           
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Re: [Freesurfer] spmregister error

[Marco Loggia]

Hi again,

interestingly, if I run the same command using the full fsvol path I get
the 'Disk quota exceeded' message... I wonder if even the message I wrote
you about in my previous email has something to do with disk space.

I will try free up some room and try spmregister again!
Marco

bash-4.1$ spmregister --mov "$file".nii --s PBR_"$subj" --reg tmp.dat
--fsvol
/autofs/cluster/vitaly/marco/PBR28/data/fs/PBR_CLBP001/mri/merged.lrrev.mgz
mkdir: cannot create directory `./tmp.spmreg.11238': Disk quota exceeded
Log file is ./spmregister.log
Fri Jul 26 11:21:20 EDT 2013
tee: ./spmregister.log: Disk quota exceeded
--mov rsl_CLBP001_f1_1_3627_5427_nas_suv.nii --s PBR_CLBP001 --reg tmp.dat
--fsvol
/autofs/cluster/vitaly/marco/PBR28/data/fs/PBR_CLBP001/mri/merged.lrrev.mgz
tee: ./spmregister.log: Disk quota exceeded
$Id: spmregister,v 1.39.2.1 2012/10/30 20:05:17 greve Exp $
tee: ./spmregister.log: Disk quota exceeded
matlab matlab
tee: ./spmregister.log: Disk quota exceeded
fmt nii
tee: ./spmregister.log: Disk quota exceeded
UseSPMGetSpace 1
tee: ./spmregister.log: Disk quota exceeded
ERROR:
/autofs/cluster/vitaly/marco/PBR28/data/fs/PBR_CLBP001/mri//autofs/cluster/vitaly/marco/PBR28/data/fs/PBR_CLBP001/mri/merged.lrrev.mgz.mgz
not found in either COR or MGZ formats

> Hello Doug,
>
> I am encountering the error below when running spmregister. Where do you
> think is the issue? Thanks!
>
> Best,
> Marco
>
>
>
> bash-4.1$ spmregister --mov "$file".nii --s PBR_"$subj" --reg tmp.dat
> --fsvol merged.lrrev
>
> Log file is ./spmregister.log
> Fri Jul 26 10:52:49 EDT 2013
> --mov rsl_CLBP001_f1_1_3627_5427_nas_suv.nii --s PBR_CLBP001 --reg tmp.dat
> --fsvol merged.lrrev
> $Id: spmregister,v 1.39.2.1 2012/10/30 20:05:17 greve Exp $
> matlab matlab
> fmt nii
> UseSPMGetSpace 1
> --
> /autofs/cluster/hookerlab/Studies/PBR/Marco/CLBP001/PET/Sum_single_frame/PET_recon_SUV/rsl_files
> mri_convert
> /autofs/cluster/vitaly/marco/PBR28/data/fs/PBR_CLBP001/mri/merged.lrrev.mgz
> ./tmp.spmreg.10617/refvol.spmregister.nii -ic 0 0 0
> mri_convert
> /autofs/cluster/vitaly/marco/PBR28/data/fs/PBR_CLBP001/mri/merged.lrrev.mgz
> ./tmp.spmreg.10617/refvol.spmregister.nii -ic 0 0 0
> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> reading from
> /autofs/cluster/vitaly/marco/PBR28/data/fs/PBR_CLBP001/mri/merged.lrrev.mgz...
> TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (-0.0414768, -0.991189, -0.125791)
> j_ras = (-0.0799847, 0.128789, -0.988441)
> k_ras = (-0.995933, 0.030936, 0.084622)
> writing to ./tmp.spmreg.10617/refvol.spmregister.nii...
> --
> /autofs/cluster/hookerlab/Studies/PBR/Marco/CLBP001/PET/Sum_single_frame/PET_recon_SUV/rsl_files
> mri_convert rsl_CLBP001_f1_1_3627_5427_nas_suv.nii
> ./tmp.spmreg.10617/movvol.spmregister.nii -ic 0 0 0 --frame 0
> mri_convert rsl_CLBP001_f1_1_3627_5427_nas_suv.nii
> ./tmp.spmreg.10617/movvol.spmregister.nii -ic 0 0 0 --frame 0
> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> reading from rsl_CLBP001_f1_1_3627_5427_nas_suv.nii...
> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (1, 0, 0)
> j_ras = (0, -1, 0)
> k_ras = (0, 0, -1)
> keeping frame 0
> writing to ./tmp.spmreg.10617/movvol.spmregister.nii...
> Matlab file is ./tmp.spmreg.10617/spmregister.10617.m
> monly   = 0;
> targvol = './tmp.spmreg.10617/refvol.spmregister.nii';
> srcvol  = './tmp.spmreg.10617/movvol.spmregister.nii';
> errfile  = './tmp.spmreg.10617/spmregister.10617.err';
> fmt = 'nii';
>
> if(exist('spm_coreg') ~= 2)
>   fprintf('ERROR: cannot find spm_coreg.m. Make sure that the SPM\n');
>   fprintf('   package is in your matlab path (check ~/matlab/startup)\n');
>   fp = fopen(errfile,'w');
>   fprintf(fp,'ERROR: cannot find spm_coreg.m. Make sure that the SPM\n');
>   fprintf(fp,'   package is in your matlab path (check
> ~/matlab/startup)\n');
>   fclose(fp);
>   return; quit;
> end
>
> fprintf('fmt %s\n',fmt);
> which spm_coreg
>
> % This is a hack to try to determine which version of spm is being run. If
> % spm8 is being run with analyze as input, a left-right reveral will
> occur.
> % This searches for "spm8" in the spm path, not perfect, but hopefully
> good
> % enough. It does not appear that spm offers a "version" command.
> IsSPM8 = length(findstr(dirname(which('spm_coreg')),'spm8'));
> if(IsSPM8 & strcmp(fmt,'img'))
>   fprintf('\n\n');
>   fprintf('ERROR: you appear to be using spm8. If so, re-run this with
> --nii\n');
>   fprintf('\n\n');
>   fp = fopen(errfile,'a');
>   fprintf(fp,'ERROR: you appear to be using spm8. If so, re-run this with
> --nii\n');
>   fclose(fp);
>   return; quit; exit; % These do nothing when run from a csh script
> end
>
> global defaults
> spm_defaults  % load spm2's default fields
>
> fprintf('INFO: Assuming RAS coordinate system\n');
> defaults.analyze.flip = 0;
>
> %=

[Freesurfer] spmregister error

[Marco Loggia]

Hello Doug,

I am encountering the error below when running spmregister. Where do you
think is the issue? Thanks!

Best,
Marco



bash-4.1$ spmregister --mov "$file".nii --s PBR_"$subj" --reg tmp.dat
--fsvol merged.lrrev

Log file is ./spmregister.log
Fri Jul 26 10:52:49 EDT 2013
--mov rsl_CLBP001_f1_1_3627_5427_nas_suv.nii --s PBR_CLBP001 --reg tmp.dat
--fsvol merged.lrrev
$Id: spmregister,v 1.39.2.1 2012/10/30 20:05:17 greve Exp $
matlab matlab
fmt nii
UseSPMGetSpace 1
--
/autofs/cluster/hookerlab/Studies/PBR/Marco/CLBP001/PET/Sum_single_frame/PET_recon_SUV/rsl_files
mri_convert
/autofs/cluster/vitaly/marco/PBR28/data/fs/PBR_CLBP001/mri/merged.lrrev.mgz
./tmp.spmreg.10617/refvol.spmregister.nii -ic 0 0 0
mri_convert
/autofs/cluster/vitaly/marco/PBR28/data/fs/PBR_CLBP001/mri/merged.lrrev.mgz
./tmp.spmreg.10617/refvol.spmregister.nii -ic 0 0 0
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from
/autofs/cluster/vitaly/marco/PBR28/data/fs/PBR_CLBP001/mri/merged.lrrev.mgz...
TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.0414768, -0.991189, -0.125791)
j_ras = (-0.0799847, 0.128789, -0.988441)
k_ras = (-0.995933, 0.030936, 0.084622)
writing to ./tmp.spmreg.10617/refvol.spmregister.nii...
--
/autofs/cluster/hookerlab/Studies/PBR/Marco/CLBP001/PET/Sum_single_frame/PET_recon_SUV/rsl_files
mri_convert rsl_CLBP001_f1_1_3627_5427_nas_suv.nii
./tmp.spmreg.10617/movvol.spmregister.nii -ic 0 0 0 --frame 0
mri_convert rsl_CLBP001_f1_1_3627_5427_nas_suv.nii
./tmp.spmreg.10617/movvol.spmregister.nii -ic 0 0 0 --frame 0
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from rsl_CLBP001_f1_1_3627_5427_nas_suv.nii...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (1, 0, 0)
j_ras = (0, -1, 0)
k_ras = (0, 0, -1)
keeping frame 0
writing to ./tmp.spmreg.10617/movvol.spmregister.nii...
Matlab file is ./tmp.spmreg.10617/spmregister.10617.m
monly   = 0;
targvol = './tmp.spmreg.10617/refvol.spmregister.nii';
srcvol  = './tmp.spmreg.10617/movvol.spmregister.nii';
errfile  = './tmp.spmreg.10617/spmregister.10617.err';
fmt = 'nii';

if(exist('spm_coreg') ~= 2)
  fprintf('ERROR: cannot find spm_coreg.m. Make sure that the SPM\n');
  fprintf('   package is in your matlab path (check ~/matlab/startup)\n');
  fp = fopen(errfile,'w');
  fprintf(fp,'ERROR: cannot find spm_coreg.m. Make sure that the SPM\n');
  fprintf(fp,'   package is in your matlab path (check ~/matlab/startup)\n');
  fclose(fp);
  return; quit;
end

fprintf('fmt %s\n',fmt);
which spm_coreg

% This is a hack to try to determine which version of spm is being run. If
% spm8 is being run with analyze as input, a left-right reveral will occur.
% This searches for "spm8" in the spm path, not perfect, but hopefully good
% enough. It does not appear that spm offers a "version" command.
IsSPM8 = length(findstr(dirname(which('spm_coreg')),'spm8'));
if(IsSPM8 & strcmp(fmt,'img'))
  fprintf('\n\n');
  fprintf('ERROR: you appear to be using spm8. If so, re-run this with
--nii\n');
  fprintf('\n\n');
  fp = fopen(errfile,'a');
  fprintf(fp,'ERROR: you appear to be using spm8. If so, re-run this with
--nii\n');
  fclose(fp);
  return; quit; exit; % These do nothing when run from a csh script
end

global defaults
spm_defaults% load spm2's default fields

fprintf('INFO: Assuming RAS coordinate system\n');
defaults.analyze.flip = 0;

%===
% coregistration  defaults
%===

defaults.coreg.estimate.cost_fun = 'nmi';
defaults.coreg.estimate.sep  = [4 2];
defaults.coreg.estimate.tol  = [0.02 0.02 0.02 0.001 0.001 0.001 0.01
0.01 0.01 0.001 0.001 0.001];
defaults.coreg.estimate.fwhm = [7 7];
defaults.coreg.estimate.params   = [0 0 0 0 0 0];
defaults.coreg.estimate.graphics = 0; % dont crate ps file


%===
% coregister files
%===

disp(sprintf('using %s as the target image',targvol));
disp(sprintf('using %s as the source image',srcvol));

[pth1,nam1,ext1] = fileparts(deblank(targvol));
[pth2,nam2,ext2] = fileparts(deblank(srcvol));

%tmp = spm_get('Files',pth1,[nam1 ext1]);
tmp = sprintf('%s/%s%s',pth1,nam1,ext1);
VG  = spm_vol(tmp); % target image
if(isempty(VG))
  fprintf('ERROR: loading target %s\n',targvol);
  fp = fopen(errfile,'a');
  fprintf(fp,'ERROR: loading target %s\n',targvol);
  fclose(fp);
  return; quit;
end
% tmp = spm_get('Files',pth2,[nam2 ext2])
tmp = sprintf('%s/%s%s',pth2,nam2,ext2);
VF  = spm_vol(tmp); % source image
if(isempty(VF))
  fprintf('ERROR: loading source %s\n',srcvol);
  fp = fopen(errfile,'a');
  fprintf(fp,'ERROR: loading source %s\n',srcvol);
  fclose(fp);
  return; quit;
end

fprintf('\n\nINFO: ignore warn

Re: [Freesurfer] correspondance between broadmann areas and freesurfer labels

[Satrajit Ghosh]

thanks guys. any thoughts on when the ba*.stats files will use these? right
now i agree with bruce that they are biased by the predictability of the
region. less accurate prediction -> greater volume.

cheers,

satra


On Fri, Jul 26, 2013 at 10:28 AM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:

>
> There is a *.thresh.label version of all the BA labels in 5.3, but I don't
> think it's used by default. You can try using those labels instead.
>
>
> On Fri, 26 Jul 2013, Satrajit Ghosh wrote:
>
>  hi bruce,
>> currently 5.3, but the data i was looking at was processed with 5.1 and in
>> that right ba44/45 was always larger.
>>
>> cheers,
>>
>> satra
>>
>>
>> On Fri, Jul 26, 2013 at 9:47 AM, Bruce Fischl > >
>> wrote:
>>   Hi Satra,
>>
>>   what version are you using? I think Anastasia implemented a
>>   thresholded version in 5.3, but perhaps she can comment.
>>   Bruce
>>   On Fri, 26 Jul 2013, Satrajit Ghosh wrote:
>>
>> hi bruce,
>> related to this question, how are the stats/volumes
>> of the BAs computed?
>>
>> cheers,
>>
>> satra
>>
>> On Fri, Jul 26, 2013 at 9:33 AM, Bruce Fischl
>> 
>> wrote:
>>   Hi Laouchedi
>>
>>   that is a big research question! The answer is
>> a qualified yes,
>>   but it depends strongly on what labels you
>> mean. In general we
>>   find that the closer you are to primary areas
>> like V1/M1, the
>>   stronger the correspondence is. We do supply
>> some explicit
>>   estimates of Brodmann areas, have you looked
>> at them?
>>
>>   Bruce
>>
>>
>>   On Fri, 26 Jul 2013, LAOUCHEDI MAKHLOUF wrote:
>>
>> Hi
>> i used freesurfer labels in a study
>> and i want
>> to identify the broadmann
>> areas corresponding to some labels, is
>> there any
>> correspondence between the
>> two ?
>>
>> Thanks
>>
>>
>>
>> __**_
>>   Freesurfer mailing list
>>   Freesurfer@nmr.mgh.harvard.edu
>>
>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**
>> freesurfer 
>>
>>
>>   The information in this e-mail is intended
>> only for the person
>>   to whom it is
>>   addressed. If you believe this e-mail was sent
>> to you in error
>>   and the e-mail
>>   contains patient information, please contact
>> the Partners
>>   Compliance HelpLine at
>>   
>> http://www.partners.org/**complianceline.
>>  If
>> the e-mail was sent
>>   to you in error
>>   but does not contain patient information,
>> please contact the
>>   sender and properly
>>   dispose of the e-mail.
>>
>>
>>
>>
>>
>>
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] correspondance between broadmann areas and freesurfer labels

[Anastasia Yendiki]

There is a *.thresh.label version of all the BA labels in 5.3, but I don't 
think it's used by default. You can try using those labels instead.


On Fri, 26 Jul 2013, Satrajit Ghosh wrote:


hi bruce,
currently 5.3, but the data i was looking at was processed with 5.1 and in
that right ba44/45 was always larger.

cheers,

satra


On Fri, Jul 26, 2013 at 9:47 AM, Bruce Fischl 
wrote:
  Hi Satra,

  what version are you using? I think Anastasia implemented a
  thresholded version in 5.3, but perhaps she can comment.
  Bruce
  On Fri, 26 Jul 2013, Satrajit Ghosh wrote:

hi bruce,
related to this question, how are the stats/volumes
of the BAs computed?

cheers,

satra

On Fri, Jul 26, 2013 at 9:33 AM, Bruce Fischl

wrote:
      Hi Laouchedi

      that is a big research question! The answer is
a qualified yes,
      but it depends strongly on what labels you
mean. In general we
      find that the closer you are to primary areas
like V1/M1, the
      stronger the correspondence is. We do supply
some explicit
      estimates of Brodmann areas, have you looked
at them?

      Bruce


      On Fri, 26 Jul 2013, LAOUCHEDI MAKHLOUF wrote:

            Hi
                i used freesurfer labels in a study
and i want
            to identify the broadmann
            areas corresponding to some labels, is
there any
            correspondence between the
            two ?

            Thanks


     
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      addressed. If you believe this e-mail was sent
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Re: [Freesurfer] correspondance between broadmann areas and freesurfer labels

[Bruce Fischl]

those are the probabilistic estimates of the Brodmann areas (that is, the 
files in the label dir named h.BA*.label)


cheers
Bruce

On Fri, 26 Jul 2013, LAOUCHEDI MAKHLOUF wrote:


Hi
   thank you for the reply. Yes, i have looked at them, in fact i used the
freesurfer parcels as nodes in a TBI connectivity study and i want to report
my results both in terms of the freesurfer components and broadmann areas. 
i just asked, if since, some probabilistic map of broadmann areas exist ?

Thanks


De : Bruce Fischl 
À : LAOUCHEDI MAKHLOUF 
Cc : "freesurfer@nmr.mgh.harvard.edu" 
Envoyé le : Vendredi 26 juillet 2013 15h33
Objet : Re: [Freesurfer] correspondance between broadmann areas and
freesurfer labels

Hi Laouchedi

that is a big research question! The answer is a qualified yes, but it
depends strongly on what labels you mean. In general we find that the
closer you are to primary areas like V1/M1, the stronger the correspondence
is. We do supply some explicit estimates of Brodmann areas, have you looked
at them?

Bruce


On Fri, 26 Jul 2013, LAOUCHEDI MAKHLOUF
wrote:

> Hi
>     i used freesurfer labels in a study and i want to identify the
broadmann
> areas corresponding to some labels, is there any correspondence between
the
> two ?
>
> Thanks
>
>


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HelpLine at
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Re: [Freesurfer] correspondance between broadmann areas and freesurfer labels

[LAOUCHEDI MAKHLOUF]

Hi
   thank you for the reply. Yes, i have looked at them, in fact i used the 
freesurfer parcels as nodes in a TBI connectivity study and i want to report my 
results both in terms of the freesurfer components and broadmann areas.  i just 
asked, if since, some probabilistic map of broadmann areas exist ?

Thanks 




 De : Bruce Fischl 
À : LAOUCHEDI MAKHLOUF  
Cc : "freesurfer@nmr.mgh.harvard.edu"  
Envoyé le : Vendredi 26 juillet 2013 15h33
Objet : Re: [Freesurfer] correspondance between broadmann areas and freesurfer 
labels
 

Hi Laouchedi

that is a big research question! The answer is a qualified yes, but it 
depends strongly on what labels you mean. In general we find that the 
closer you are to primary areas like V1/M1, the stronger the correspondence 
is. We do supply some explicit estimates of Brodmann areas, have you looked 
at them?

Bruce


On Fri, 26 Jul 2013, LAOUCHEDI MAKHLOUF 
wrote:

> Hi
>     i used freesurfer labels in a study and i want to identify the broadmann
> areas corresponding to some labels, is there any correspondence between the
> two ?
> 
> Thanks
> 
>


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Re: [Freesurfer] correspondance between broadmann areas and freesurfer labels

[Bruce Fischl]

if it's not the thresholded version that might reflect the fact that it 
is less well-predicted and so the borders are more spread out

Bruce
On Fri, 26 Jul 
2013, Satrajit Ghosh wrote:



hi bruce,
currently 5.3, but the data i was looking at was processed with 5.1 and in
that right ba44/45 was always larger.

cheers,

satra


On Fri, Jul 26, 2013 at 9:47 AM, Bruce Fischl 
wrote:
  Hi Satra,

  what version are you using? I think Anastasia implemented a
  thresholded version in 5.3, but perhaps she can comment.
  Bruce
  On Fri, 26 Jul 2013, Satrajit Ghosh wrote:

hi bruce,
related to this question, how are the stats/volumes
of the BAs computed?

cheers,

satra

On Fri, Jul 26, 2013 at 9:33 AM, Bruce Fischl

wrote:
      Hi Laouchedi

      that is a big research question! The answer is
a qualified yes,
      but it depends strongly on what labels you
mean. In general we
      find that the closer you are to primary areas
like V1/M1, the
      stronger the correspondence is. We do supply
some explicit
      estimates of Brodmann areas, have you looked
at them?

      Bruce


      On Fri, 26 Jul 2013, LAOUCHEDI MAKHLOUF wrote:

            Hi
                i used freesurfer labels in a study
and i want
            to identify the broadmann
            areas corresponding to some labels, is
there any
            correspondence between the
            two ?

            Thanks


     
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      addressed. If you believe this e-mail was sent
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      contains patient information, please contact
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Re: [Freesurfer] correspondance between broadmann areas and freesurfer labels

[Satrajit Ghosh]

hi bruce,

currently 5.3, but the data i was looking at was processed with 5.1 and in
that right ba44/45 was always larger.

cheers,

satra


On Fri, Jul 26, 2013 at 9:47 AM, Bruce Fischl wrote:

> Hi Satra,
>
> what version are you using? I think Anastasia implemented a thresholded
> version in 5.3, but perhaps she can comment.
> Bruce
>
> On Fri, 26 Jul 2013, Satrajit Ghosh wrote:
>
>  hi bruce,
>> related to this question, how are the stats/volumes of the BAs computed?
>>
>> cheers,
>>
>> satra
>>
>> On Fri, Jul 26, 2013 at 9:33 AM, Bruce Fischl > >
>> wrote:
>>   Hi Laouchedi
>>
>>   that is a big research question! The answer is a qualified yes,
>>   but it depends strongly on what labels you mean. In general we
>>   find that the closer you are to primary areas like V1/M1, the
>>   stronger the correspondence is. We do supply some explicit
>>   estimates of Brodmann areas, have you looked at them?
>>
>>   Bruce
>>
>>
>>   On Fri, 26 Jul 2013, LAOUCHEDI MAKHLOUF wrote:
>>
>> Hi
>> i used freesurfer labels in a study and i want
>> to identify the broadmann
>> areas corresponding to some labels, is there any
>> correspondence between the
>> two ?
>>
>> Thanks
>>
>>
>>   __**_
>>   Freesurfer mailing list
>>   Freesurfer@nmr.mgh.harvard.edu
>>   
>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer
>>
>>
>>   The information in this e-mail is intended only for the person
>>   to whom it is
>>   addressed. If you believe this e-mail was sent to you in error
>>   and the e-mail
>>   contains patient information, please contact the Partners
>>   Compliance HelpLine at
>>   
>> http://www.partners.org/**complianceline.
>>  If the e-mail was sent
>>   to you in error
>>   but does not contain patient information, please contact the
>>   sender and properly
>>   dispose of the e-mail.
>>
>>
>>
>>
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Re: [Freesurfer] correspondance between broadmann areas and freesurfer labels

[Bruce Fischl]

Hi Satra,

what version are you using? I think Anastasia implemented a thresholded 
version in 5.3, but perhaps she can comment.

Bruce
On Fri, 26 Jul 2013, Satrajit 
Ghosh wrote:



hi bruce,
related to this question, how are the stats/volumes of the BAs computed?

cheers,

satra

On Fri, Jul 26, 2013 at 9:33 AM, Bruce Fischl 
wrote:
  Hi Laouchedi

  that is a big research question! The answer is a qualified yes,
  but it depends strongly on what labels you mean. In general we
  find that the closer you are to primary areas like V1/M1, the
  stronger the correspondence is. We do supply some explicit
  estimates of Brodmann areas, have you looked at them?

  Bruce


  On Fri, 26 Jul 2013, LAOUCHEDI MAKHLOUF wrote:

Hi
    i used freesurfer labels in a study and i want
to identify the broadmann
areas corresponding to some labels, is there any
correspondence between the
two ?

Thanks


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  to you in error
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Re: [Freesurfer] correspondance between broadmann areas and freesurfer labels

[Satrajit Ghosh]

hi bruce,

related to this question, how are the stats/volumes of the BAs computed?

cheers,

satra

On Fri, Jul 26, 2013 at 9:33 AM, Bruce Fischl wrote:

> Hi Laouchedi
>
> that is a big research question! The answer is a qualified yes, but it
> depends strongly on what labels you mean. In general we find that the
> closer you are to primary areas like V1/M1, the stronger the correspondence
> is. We do supply some explicit estimates of Brodmann areas, have you looked
> at them?
>
> Bruce
>
>
> On Fri, 26 Jul 2013, LAOUCHEDI MAKHLOUF wrote:
>
>  Hi
>> i used freesurfer labels in a study and i want to identify the
>> broadmann
>> areas corresponding to some labels, is there any correspondence between
>> the
>> two ?
>>
>> Thanks
>>
>>
> ___
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>
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>
>
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Re: [Freesurfer] correspondance between broadmann areas and freesurfer labels

[Bruce Fischl]

Hi Laouchedi

that is a big research question! The answer is a qualified yes, but it 
depends strongly on what labels you mean. In general we find that the 
closer you are to primary areas like V1/M1, the stronger the correspondence 
is. We do supply some explicit estimates of Brodmann areas, have you looked 
at them?


Bruce


On Fri, 26 Jul 2013, LAOUCHEDI MAKHLOUF 
wrote:



Hi
    i used freesurfer labels in a study and i want to identify the broadmann
areas corresponding to some labels, is there any correspondence between the
two ?

Thanks

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Re: [Freesurfer] are many *.dat files written out to disk in /mri and then deleted when autorecon completes?

[Bruce Fischl]

Hi Albert

that sounds pretty mysterious and probably some left-over debugging code 
that you somehow activated. Can you check to make sure that you don't 
have an environment variable named DIAG defined? And what do the various 
Ns run from and too (that is, what are the names of the files)? Any idea 
which step is creating them?


Bruce


On Fri, 26 Jul 2013, Montillo, Albert (GE Global Research) 
wrote:




After importing a subject’s data (T1 single time point)

I run a script with these commands:

recon-all –s  -autorecon1

recon-all –s  -autorecon2

recon-all –s  -autorecon3

 

 

I did this twice, once on each of two linux machines.

I am using the same exact input intensity T1 data and importing the data
into separate subject names (e1859_workingBak  and e1858_nonworking) so
there is no collision.

 

Why am I getting many (really 1000’s ) of  v1_1.dat files in the
$SUBJECTS_DIR//mri   of one of the machines, even though the input
data is the same?

They are named vNNN_N.dat where N is a digit . Contents of one of these
files is below.

The contents of the subject folders are represented below using the du –k .
command. Now in this nonworking case the job terminated early (run time
limit on the job which I can fix ) ; however I am curious: are all of these
*.dat files  (40GB worth!) written out all the time and then deleted at the
end of the recon tasks?

This happens on one red-hat linux machine (cluster ) but not on another for
the same subject data

Is this normal behavior? Are the dat files written out normally and then
deleted later in the processing (since I don’t see them in the run that
completed).

 

Contents of a subject after a successful run to completion:

[e1858_workingBak]$ du -k .

1176    ./scripts

16  ./mri/transforms/bak

108200  ./mri/transforms

14088   ./mri/orig

176068  ./mri

149940  ./surf

16  ./tmp

35228   ./label

1096    ./touch

544 ./stats

16      ./src

16  ./trash

16  ./bem

364132  .

 

 

Contents of same MRI input data to a different subject name, whose
processing (same as above) terminated prematurely:

[e1858_nonworking]$ du -k .

800 ./scripts

16  ./mri/transforms/bak

108200  ./mri/transforms

14088   ./mri/orig

41027804    ./mri

29252   ./surf

16  ./tmp

16  ./label

360 ./touch

16  ./stats

16  ./src

16  ./trash

16  ./bem

41058328    .

 

 

This is when the processing of e1858_nonworking got terminated:

[scripts]$ tail recon-all-status.log

#@# Intensity Normalization2 Thu Jul 25 19:20:22 EDT 2013

#@# Mask BFS Thu Jul 25 19:24:53 EDT 2013

#@# WM Segmentation Thu Jul 25 19:24:56 EDT 2013

#@# Fill Thu Jul 25 19:27:47 EDT 2013

#@# Tessellate lh Thu Jul 25 19:28:47 EDT 2013

#@# Smooth1 lh Thu Jul 25 19:28:56 EDT 2013

#@# Inflation1 lh Thu Jul 25 19:29:01 EDT 2013

#@# QSphere lh Thu Jul 25 19:29:37 EDT 2013

#@# Fix Topology lh Thu Jul 25 19:35:03 EDT 2013

#@# Make White Surf lh Thu Jul 25 19:55:20 EDT 2013

 

This is the contents of one (v1_1.dat ) of the many *.dat files  in /mri

[mri]$ tail v1_1.dat

12.014513 223.051927 250.208421

12.052258 222.911943 252.203797

12.090005 222.771944 254.199159

12.127751 222.631960 256.194520

12.165498 222.491960 258.189912

12.203243 222.351976 260.185273

12.240990 222.211977 262.180635

12.278736 222.071992 264.175996

12.316483 221.931993 266.171358

12.354229 221.791994 268.166750


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[Freesurfer] selxavg3-sess： Matlab cannot display graphics

[Wang Zhiwei]

Hi all,

 

When I run selxavg3-sess for any analysis, the following information is
always appearing. Can you please give some suggestions how to fix that? Any
thoughts would be very appreciated!

--

--- matlab output 

Warning: Unable to open display 'iconic'.  You will not be able to display
graphics on the screen.

Warning: No window system found.  Java option 'MWT' ignored.

 

< M A T L A B (R) >

  Copyright 1984-2012 The MathWorks, Inc.

R2012b (8.0.0.783) 64-bit (glnxa64)

  August 22, 2012

 

No window system found.  Java option 'MWT' ignored.

To get started, type one of these: helpwin, helpdesk, or demo.

For product information, visit www.mathworks.com.

>> >> >> >> >> >> >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m

>> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >>

 

Thanks!

 

James

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[Freesurfer] correspondance between broadmann areas and freesurfer labels

[LAOUCHEDI MAKHLOUF]

Hi
    i used freesurfer labels in a study and i want to identify the broadmann 
areas corresponding to some labels, is there any correspondence between the two 
?

Thanks
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[Freesurfer] J_white

[Linn Mittlestein]

Dear freesurfer experts,

I am currently do group analysis in qdec, and I canot select jacobian white
from the drop down menu, I thought this would be an option? Do I do have
additional steps to get these values?

Kind Regards,

Linn
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