[Freesurfer] FSFAST error: ERROR: fast_selxavg3() failed\n

[ERIK JAHNER]

Hello FreeSurfer Developers, This is Erik Jahner, I’m attempting to complete the final step in the tutorial concerning FSFast Functional connectivity walkthrough (http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough ), but for I get the following error when I run the following command:selxavg3-sess -s subj439rest -a fc.lpccseed.surf.lhMon Jul  4 11:01:41 PDT 2016rawfunc2surf-sess completed Started at Mon Jul 4 11:01:40 PDT 2016Ended   at Mon Jul  4 11:01:41 PDT 2016preproc-sess done---/Applications/freesurfer/LagStructure/subj439restMon Jul  4 11:01:41 PDT 2016anadir = /Applications/freesurfer/LagStructure/subj439rest/rest/fc.lpccseed.surf.lhDoGLMFit = 1DoContrasts = 1UpdateNeeded = 1- matlab output matlab: Command not found.--ERROR: fast_selxavg3() failed\n I've searched the list and no similar errors have been reported. I have tried to reinstall MATLAB; I have tried following the instructions to install the runtime environment; I have tried redoing all analysis from scratch. I have noticed that STEP 5 does not work unless I change the -cfg from “L_Posteriorcingulate.config” to “mean.L_Posteriorcingulate.config”. I don’t think this is the problem, but I thought I would point it out. My session directory is “subj439rest”Instead of titling the sub directory “bold”, I titled it “rest” 1) FreeSurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.02) Platform: OSX Yousemite3) uname -a: Darwin ERIKs-iMac.local 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr 19 18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_644) selxavg3-sess-rest-fc.lpccseed.surf.lh-160704110140.log: see attached___Here are the command lines I put in for steps 4-8, incase this is of some use:STEP 4fcseed-config -segid 1010 -fcname L_Posteriorcingulate.dat -fsd rest -mean -cfg mean.L_Posteriorcingulate.configSTEP 5fcseed-sess  -s subj439rest -cfg mean.L_Posteriorcingulate.configSTEP 6fcseed-config -wm -fcname wm.dat -fsd rest -pca -cfg wm.config fcseed-sess -s subj439rest -cfg wm.configfcseed-config -vcsf -fcname vcsf.dat -fsd rest -pca -cfg vcsf.config fcseed-sess -s subj439rest -cfg vcsf.configSTEP7mkanalysis-sess -analysis fc.lpccseed.surf.lh -surface fsaverage lh -fwhm 5 -notask -taskreg L_Posteriorcingulate.dat 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5  -mcextreg -polyfit 5 -nskip 4 -fsd rest -TR 2 -per-runSTEP 8selxavg3-sess -s subj439rest -a fc.lpccseed.surf.lhselxavg3-sess log file
/Applications/freesurfer/fsfast/bin/selxavg3-sess
-s subj439rest -a fc.lpccseed.surf.lh
$Id: selxavg3-sess,v 1.57.2.1 2011/12/09 20:06:47 greve Exp $
uid=0(root) gid=0(wheel) 
groups=0(wheel),701(com.apple.sharepoint.group.1),1(daemon),2(kmem),3(sys),4(tty),5(operator),8(procview),9(procmod),12(everyone),20(staff),29(certusers),61(localaccounts),80(admin),702(com.apple.sharepoint.group.2),33(_appstore),98(_lpadmin),100(_lpoperator),204(_developer),395(com.apple.access_ftp),101(com.apple.access_screensharing-disabled),399(com.apple.access_ssh)
/Applications/freesurfer/LagStructure
Darwin ERIKs-iMac.local 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr 19 
18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64
Mon Jul  4 11:01:40 PDT 2016
preproc-sess -s subj439rest -d /Applications/freesurfer/LagStructure -a 
fc.lpccseed.surf.lh -nolog
--
preproc-sess logfile is /dev/null
--
$Id: preproc-sess,v 1.45.2.3 2013/01/22 22:09:10 greve Exp $
root
setenv FREESURFER_HOME /Applications/freesurfer
setenv SUBJECTS_DIR /Applications/freesurfer/subjects
Darwin ERIKs-iMac.local 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr 19 
18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64
/Applications/freesurfer/LagStructure
/Applications/freesurfer/fsfast/bin/preproc-sess
-s subj439rest -d /Applications/freesurfer/LagStructure -a fc.lpccseed.surf.lh 
-nolog
Mon Jul  4 11:01:40 PDT 2016
instem   f 
mc   1 f fmcpr 
stc  0 fmcpr
sm   0   
mask 1   brain
subj439rest Template -
mktemplate-sess -s subj439rest -d /Applications/freesurfer/LagStructure -fsd 
rest -nolog -update
 
Session: /Applications/freesurfer/LagStructure/subj439rest 
Mon Jul  4 11:01:40 PDT 2016
Detected input format at nii.gz
subj439rest Update not needed
  Run: 007 
  Mon Jul  4 11:01:40 PDT 2016
  subj439rest 007 Update not needed
Mon Jul  4 11:01:40 PDT 2016
mktemplate-sess completed 
subj439rest Mask 
mkbrainmask-sess -maskstem brain -fsd rest -s subj439rest -d 
/Applications/freesurfer/LagStructure -nolog -update

/Applications/freesurfer/LagStructure/subj439rest 
Mon Jul  4 

Re: [Freesurfer] LGI

[Mahtab Farahbakhsh]

I have the very same problem! Hope to be able to solve it with the guidance 
from Freesurfer.

Best Regards,
Mahtab.



Friday, July 8, 2016, 01:43 +0100 from walidyassi...@gmail.com  
:
>Hello,
>
>Sorry for raising this questions again. I posted this questions a while ago 
>(Twice), but i haven't gotten an answer yet.
>Can i at least know if i can tweak something for this to work? or just give 
>up? 
>I tried downgrading Xquatrz, to 2.7.8, but it still doesn't work! My matlab is 
>2016a, could this be the problem?
>
>
>Thank you for letting me know
>
>WY
>
>On Sat, Jun 25, 2016 at 10:39 AM, Walid Yassin  < walidyassi...@gmail.com > 
>wrote:
>>Hello again,
>>
>>Sorry for posting twice, but does someone know what might be the problem?
>>Thank you in advance.
>>I’m trying to run recon-all -lgi - s Subjectname  on my data but i am
getting this error!
>>***

Error in dsearchn (line 79)
[d(i),t(i)] = min(sum((x-yi).^2,2));

Error in mesh_vertex_nearest (line 29)
nearestIndex = dsearchn(vertices,points);


Error in reorganize_verticeslist (line 28)

[nextindex,nextvalue]=mesh_vertex_nearest(mesh_total.vertices(remaininglist,:),mesh_total.vertices(verticeslist(start_vertex),:));


Error in make_roi_paths (line 93)
reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer, perim,
verticeslist, step);


>>
ERROR:  make_roi_paths did not complete successfully!


***


*I checked the archives and saw a reply by Marie to someone who had the
same problem.*
*She recommended changing the info inside “SearchProjectionByPial.m" in the
~/Application/freesurfer/matlab directory to:*



***

function [verticeslist]=SearchProjectionOnPial(mesh_total,mesh_outer,perim,
step)

% step is typically set between 5 and 10. Default is 7, increasing it will
% limit redundancies in the resulting path file.

verticeslist=[];
si=max(size(perim));
for t=1:step:si

[nearestIndexMT,nearestValuesMT]=mesh_vertex_nearest(mesh_total.vertices,mesh_outer.vertices(perim(t),:));
verticeslist= [verticeslist nearestIndexMT];
end
verticeslist=unique(vertices list);

***


Which i did, but i am still getting this error!*
Any recommendations on what to do next? I am running MATLAB_R2016.

Thank you in advance,

WY
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>
>
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>at
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>but does not contain patient information, please contact the sender and 
>properly
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Re: [Freesurfer] question about volume of the hippocampus

[kjunji]

Dear Douglas N Greve

Following your comments, I could open aseg.stats, and obtain the 
hippocampus volume.
Thank you for your grateful advise.

Yours sincerely,
Junji Komatsu



2016-07-08 02:50 に Douglas N Greve さんは書きました:
> aseg.stats is just a text file, so you can view it with any text viewer
> (eg, the unix more or less commands, vi, emacs)
> 
> On 07/07/2016 06:41 AM, kju...@med.kanazawa-u.ac.jp wrote:
>> Dear freesurfer developers.
>> 
>> I am working at department of neurology in university Hospital, Japan.
>> I am beginner of freesurfer, please forgive me to ask you a basic
>> question.
>> 
>> I want to measure the volume of the hippocampus in my patients.
>> I was able to segment the MRI successfully and display the image in
>> freeviewer.
>> However, I could not recognize the way to obtain the volume of the
>> hippocampus.
>> 
>> *I saw the "mail acheive"
>> (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg14679.html),
>> however, I could not understand the way to look at the the aseg.stats.
>> 
>> Could you teach me the way for obtaining the volume of the 
>> hippocampus?
>> I and very looking forward to hearing from you.
>> 
>> Yours sincerely,
>> Junji Komatsu
>> ___
>> 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
> 
> 
> 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] LGI

[Walid Yassin]

Hello,

Sorry for raising this questions again. I posted this questions a while ago
(Twice), but i haven't gotten an answer yet.
Can i at least know if i can tweak something for this to work? or just give
up?
I tried downgrading Xquatrz, to 2.7.8, but it still doesn't work! My matlab
is 2016a, could this be the problem?


Thank you for letting me know

WY

On Sat, Jun 25, 2016 at 10:39 AM, Walid Yassin 
wrote:

> Hello again,
>
> Sorry for posting twice, but does someone know what might be the problem?
>
> Thank you in advance.
>
> I’m trying to run recon-all -lgi - s Subjectname  on my data but i am
> getting this error!
>
> ***
>
> Error in dsearchn (line 79)
> [d(i),t(i)] = min(sum((x-yi).^2,2));
>
> Error in mesh_vertex_nearest (line 29)
> nearestIndex = dsearchn(vertices,points);
>
>
> Error in reorganize_verticeslist (line 28)
>
> [nextindex,nextvalue]=mesh_vertex_nearest(mesh_total.vertices(remaininglist,:),mesh_total.vertices(verticeslist(start_vertex),:));
>
>
> Error in make_roi_paths (line 93)
> reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer, perim,
> verticeslist, step);
>
>
> >>
> ERROR:  make_roi_paths did not complete successfully!
>
>
> ***
>
>
> *I checked the archives and saw a reply by Marie to someone who had the
> same problem.*
> *She recommended changing the info inside “SearchProjectionByPial.m" in the
> ~/Application/freesurfer/matlab directory to:*
>
>
>
> ***
>
> function [verticeslist]=SearchProjectionOnPial(mesh_total,mesh_outer,perim,
> step)
>
> % step is typically set between 5 and 10. Default is 7, increasing it will
> % limit redundancies in the resulting path file.
>
> verticeslist=[];
> si=max(size(perim));
> for t=1:step:si
>
> [nearestIndexMT,nearestValuesMT]=mesh_vertex_nearest(mesh_total.vertices,mesh_outer.vertices(perim(t),:));
> verticeslist= [verticeslist nearestIndexMT];
> end
> verticeslist=unique(vertices list);
>
> ***
>
>
> Which i did, but i am still getting this error!*
> Any recommendations on what to do next? I am running MATLAB_R2016.
>
> Thank you in advance,
>
> WY
>
>
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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] fornix segmentation using recon-all

[Hari Guragain]

Dear Freesurfer Experts,

I am interested to get the volume information of the structure "fornix" in
the aseg.stats file.
I would appreciate if there is any such argument that can be used along
with the recon-all to get the volume information of the fornix like below.
Till now, I have been using

·   *recon-all -autorecon-all -subjid **your_subject_name*

Any suggestions will be appreciated.


# ColHeaders  Index SegId NVoxels Volume_mm3 StructName normMean normStdDev
normMin normMax normRange
  1   4  6489 6958.2  Left-Lateral-Ventricle34.8514
 11.576715.82.67.

Thank you,

Hari Guragain
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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
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Re: [Freesurfer] fslaverage/MNI coordinates

[Li, Baojuan]

Thank you so much!

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: Thursday, July 07, 2016 1:45 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] fslaverage/MNI coordinates

I've just added your use case to this page. See Case 8.
http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems

On 07/06/2016 05:09 PM, Li, Baojuan wrote:
> Hi Doug,
>
> Thank you so much! Because I will do the analysis using SPM, I need the 
> coordinates in MNI152 space. I found a transformation between them:
>
> M = [0.9975   -0.00730.0176   -0.0429
> 0.01461.0009   -0.00241.5496
>-0.0130   -0.00930.99711.1840
> 000  1.]
> Is this transformation correct?
> I guess I can then get the MNI152  coordinates in this way:
>
>   P305 = [MNI305x MNI305y MNI305z 1]';
>   P152 = M*P305
>
> Am I correct?
>
> Best wishes,
> Baojuan
>
> 
> 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: Wednesday, July 06, 2016 4:44 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] fslaverage/MNI coordinates
>
> Hi Baojuan, that coordinate will be mni305 space. Is that what you want?
>
> On 07/06/2016 04:17 PM, Li, Baojuan wrote:
>> Dear Freesurfer experts,
>>
>>
>> I am using MNE (with MEG data) to define my ROIs for a connectivity
>> analysis. I am going through the following steps to get the MNI
>> coordinates of the regions:
>>
>> 1. Morph the subject's brain to fslaverage;
>>
>> 2. Load the inflated surface of fslaverage to MNE analyze;
>>
>> 3. Look for regions that are activated during my task;
>>
>> 3. Use view>show coordinates to show the coordinates of the vertex;
>>
>> 4. The surface RAS (MRI) coordinates are shown;
>>
>> 5. Used these coordinates as MNI coordinates.
>>
>> Because I was using SPM in the past and am quite new to freesurfer, I
>> strongly hope someone can help me to check if I have done it
>> correctly. Thank you so much for your help!
>>
>> Best wishes,
>> Baojuan
>>
>>
>> ___
>> 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
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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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
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Re: [Freesurfer] XQuartz 2.7.9 update results in errors

[Robert C Welsh]

Hi Zeke,

I’m seeing the same issue (running xquartz 2.7.9 on MacBooPro10,1). XQuartz 
2.7.8 works, 2.7.9 breaks both freeview, tkmedit, qdec

I’ve also submitted bug report to xquartz, 
https://bugs.freedesktop.org/show_bug.cgi?id=96849 


The errors thrown are:


rcwelsh@mnemosyne:/home/Software/fs_install/bin$ qdec
X Error of failed request:  BadValue (integer parameter out of range for 
operation)
  Major opcode of failed request:  150 (GLX)
  Minor opcode of failed request:  3 (X_GLXCreateContext)
  Value in failed request:  0x0
  Serial number of failed request:  1184
  Current serial number in output stream:  1185


rcwelsh@mnemosyne:/home/Software/fs_install/bin$ tkmedit
X Error of failed request:  GLXBadContext
  Major opcode of failed request:  150 (GLX)
  Minor opcode of failed request:  6 (X_GLXIsDirect)
  Serial number of failed request:  26
  Current serial number in output stream:  25


rcwelsh@mnemosyne:/home/Software/fs_install/bin$ freeview
X Error: BadValue (integer parameter out of range for operation) 2
  Extension:150 (Uknown extension)
  Minor opcode: 3 (Unknown request)
  Resource id:  0x0
X Error: GLXBadContext 160
  Extension:150 (Uknown extension)
  Minor opcode: 5 (Unknown request)
  Resource id:  0x18001d8
[0]PETSC ERROR: 

[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably 
memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see 
http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
 ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find 
memory corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run 
[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: - Error Message 

[0]PETSC ERROR: Signal received!
[0]PETSC ERROR: 

[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 
2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR: 

[0]PETSC ERROR: Unknown Name on a linux-gnu named mnemosyne by rcwelsh Thu Jul  
7 14:56:12 2016
[0]PETSC ERROR: Libraries linked from 
/autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt
[0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010
[0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc 
--with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 
--with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 
CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
[0]PETSC ERROR: 

[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown 
file
[unset]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
X Error: GLXBadContextTag 164
  Extension:150 (Uknown extension)
  Minor opcode: 1 (Unknown request)
  Resource id:  0x960005


-Robert

--

Hello Kate,

Thanks for the information. We have seen similar behavior with previous 
XQuartz releases in the past as well. This tends to "freeze" certain 
vesion of OSX with certain versions of XQuartz. I will take a closer 
look but this is usually something that we have to deal with.
-Zeke

On 06/20/2016 08:34 PM, Kate Mills wrote:
> Hi All,
>
> My lab is having difficulty loading the freeview gui after updating to
> the latest version of XQuartz (2.7.9). We were wondering if others have
> experienced this issue? We have reverted by to XQuartz 2.7.8 on our
> machines for now. In case relevant, this errors seems to span Mac OS
> versions.
>
> Thank you!
>
> Kate
>
>
>
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> 
>
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Associate Professor
Department of Radiology
Department of Psychiatry
University of Michigan
rcwe...@umich.edu

Associate 

Re: [Freesurfer] Inflation of one hemi only

[Kang, XJ]

For the normal inflated brain, wmparc.mgz has values: 0~85, 251~255, 
1000~1035, 2000~2035, 3000~3035, 4000~4035, and 5001, 5002.


I have two unfinished one hemi inflation brains, one wmparc.mgz has 
values 0 ~176, and the other has 0~156. No other values found.


On 7/7/2016 11:25 AM, Bruce Fischl wrote:

what values does the wmparc have?
On Thu, 7 Jul 2016, Kang, XJ wrote:



Thank you for your reply.

The image "wmparc.mgz" does not have the correct values. I am not 
sure if
that because of the interruption of the procedures or not. Also I 
need to

use some other files.

Thank you for your explanations. I will wait for the future 
corrections on

the problem.

On 7/7/2016 11:11 AM, Bruce Fischl wrote:
  Hi XJ

  this is a known problem but we haven't gotten to fixing it yet.
  Do you need it to complete that step? It is pretty close to the
  end so it may be that the error doesn't effect you
  cheers
  Bruce

  On Thu, 7 Jul 2016, Kang, XJ wrote:

Hi,

I am trying to inflate right hemisphere only using
the commands:

recon-all -autorecon2 -hemi rh  -subjid 160526
recon-all -autorecon3 -hemi rh  -subjid 160526

The inflation stopped at the step:
mris_volmask --label_left_white 2
--label_left_ribbon 3 --label_right_white
41 --label_right_ribbon 42 --save_ribbon 160526

SUBJECTS_DIR is /home/sata3/FreeSurfer/Subjects
MRISread(/home/sata3/FreeSurfer/Subjects/160526/surf/lh.white):
could not
open file

The program "mris_volmask" needs to read "lh.white",
which is not generated.
Any expert has any suggestions? Maybe I didn't use
the commands correctly?

Thank you for your help.

XJ Kang




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Re: [Freesurfer] Inflation of one hemi only

[Bruce Fischl]

what values does the wmparc have?
On Thu, 7 Jul 2016, Kang, XJ wrote:



Thank you for your reply.

The image "wmparc.mgz" does not have the correct values. I am not sure if
that because of the interruption of the procedures or not. Also I need to
use some other files.

Thank you for your explanations. I will wait for the future corrections on
the problem.

On 7/7/2016 11:11 AM, Bruce Fischl wrote:
  Hi XJ

  this is a known problem but we haven't gotten to fixing it yet.
  Do you need it to complete that step? It is pretty close to the
  end so it may be that the error doesn't effect you
  cheers
  Bruce

  On Thu, 7 Jul 2016, Kang, XJ wrote:

Hi,

I am trying to inflate right hemisphere only using
the commands:

recon-all -autorecon2 -hemi rh  -subjid 160526
recon-all -autorecon3 -hemi rh  -subjid 160526

The inflation stopped at the step:
mris_volmask --label_left_white 2
--label_left_ribbon 3 --label_right_white
41 --label_right_ribbon 42 --save_ribbon 160526

SUBJECTS_DIR is /home/sata3/FreeSurfer/Subjects
MRISread(/home/sata3/FreeSurfer/Subjects/160526/surf/lh.white):
could not
open file

The program "mris_volmask" needs to read "lh.white",
which is not generated.
Any expert has any suggestions? Maybe I didn't use
the commands correctly?

Thank you for your help.

XJ Kang




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Re: [Freesurfer] Inflation of one hemi only

[Kang, XJ]

Thank you for your reply.

The image "wmparc.mgz" does not have the correct values. I am not sure 
if that because of the interruption of the procedures or not. Also I 
need to use some other files.


Thank you for your explanations. I will wait for the future corrections 
on the problem.


On 7/7/2016 11:11 AM, Bruce Fischl wrote:

Hi XJ

this is a known problem but we haven't gotten to fixing it yet. Do you 
need it to complete that step? It is pretty close to the end so it may 
be that the error doesn't effect you

cheers
Bruce

On Thu, 7 Jul 2016, Kang, XJ wrote:


Hi,

I am trying to inflate right hemisphere only using the commands:

recon-all -autorecon2 -hemi rh  -subjid 160526
recon-all -autorecon3 -hemi rh  -subjid 160526

The inflation stopped at the step:
mris_volmask --label_left_white 2 --label_left_ribbon 3 
--label_right_white

41 --label_right_ribbon 42 --save_ribbon 160526

SUBJECTS_DIR is /home/sata3/FreeSurfer/Subjects
MRISread(/home/sata3/FreeSurfer/Subjects/160526/surf/lh.white): could 
not

open file

The program "mris_volmask" needs to read "lh.white", which is not 
generated.
Any expert has any suggestions? Maybe I didn't use the commands 
correctly?


Thank you for your help.

XJ Kang





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Re: [Freesurfer] FS V6.0 GTM PVC ROI definition

[Douglas N Greve]

On 06/20/2016 08:25 PM, Pradeep wrote:
> Hello Freesrufer Team,
>
> I am trying to use the Partial volume correction procedure implemented 
> in the freesurfer 6 beta version and have a few questions.
>
> In your recent Neuroimaging paper, the left and right hemispheres were 
> combined by taking the average of the two as they did not show any 
> age-by-hemisphere interaction.
>
> I might have interpreted the Supplementary figure 1 incorrectly, but 
> the Geometric transfer matrix seem to show around 52 ROI's, So were 
> the L and R ROIs combined for the PVC results you reported in  that 
> paper? Or were the same 52 used for the general PVC in the FS pipeline?
They were combined only after the PVC calculation. For the figure, I 
changed the GTM to show the combined GTM.
>
> Do you have any concrete results to examine the effects of the size 
> variation over the ROIs used for PVC?
Not sure what you mean here. You can get the variance reduction factor 
for each ROI in the gtm.stats.dat file. This indicates how much noise 
reduction you can expect (assuming gaussian noise, etc) in each ROI 
given the size and anatomical distribution of the ROIs and PSF.
> Should a threshold be set for the sizes of these ROIs?
What do you mean?
>
> How were the white matter hypo-intensities dealt with while generating 
> the ROI masks?
I merged them with WM. I tried it with and without, and it did not make 
much of a difference.
doug
>
>
> Thanks,
> Pradeep
>
>
>
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] BrainSeg Volume Clarification

[Douglas N Greve]

There are several ROIs you could be missing such as choroid plexus, 
vessel. Also, the BrainSegVol does not include partial volume correction 
which the aseg volumes will include, so you might be slightly off.

On 06/23/2016 12:47 PM, Cook, Bernie wrote:
>
> All,
>
>
> Upon looking at online forums and the FreeSurfer wiki, I have come to 
> the understanding that "BrainSeg" volume in the aseg.stats file 
> includes all cortical and subcortical gray matter, cerebellar gray 
> matter; cortical, subcortical and cerebellar white matter and white 
> matter hypointensities; and all ventricle volumes, but excludes the 
> brain stem.
>
>
> When using the aseg.stats file for included subject "bert" to check my 
> understanding of which volumes are used, I cannot seem to produce 
> identical "BrainSegVol-to-TIV" ratios.
>
>
> I am adding the following volumes, all in mm^3, to obtain the brain 
> volume:
>
> TotalGrayVol: 658087.056198
>
> CorticalWhiteMatterVol: 485627.161537
>
> Left-Lateral-Ventricle: 6562.6
>
> Left-Inf-Lat-Vent: 228.3
>
> Left-Cerebellum-White-Matter: 15708.2
>
> 3rd-Ventricle: 997.5
>
> 4th Ventricle: 1714.2
>
> Right-Lateral-Ventricle: 6039.9
>
> Right-Inf-Lat-Vent: 160.3
>
> Right-Cerebellum-White-Matter: 15694.5
>
> 5th-Ventricle: 14.1
>
> WM-hypointensities: 1002.6
>
>
> Sum of individual measures: 1191836.418
>
> Output of BrainSegVol: 1193318
>
>
> And when normalizing the subject's brain volume by the eTIV measure 
> (1594882.911364), I obtain the following:
>
> Individual measures: 0.7473
>
> BrainSegVol-to-eTIV: 0.7482
>
>
> Is there a reason that these two measurements are slightly off?  I'm 
> wondering whether there's certain volumes used for BrainSegVol that I 
> missed, or ones that I included that would not be present in the 
> output.  Moreover, I'm wondering whether this could potentially be a 
> result of using surface volumes (BrainSegVol) versus using both 
> surface and voxel-space calculations (my addition method).
>
>
> Any help is appreciated.  Thank you in advance.
>
>
> Best,
>
> *
> *
> *1455168447449_PastedImage*
> Bernard L. Cook
> Biomedical Engineering | Class of 2017
> BMES at Ohio State | Professional Development Chair '16-'17
> IBRC| Undergraduate Research Assistant
>
> 440-623-4710
> cook.1...@osu.edu 
>
>
>
>
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
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Re: [Freesurfer] continuity in volumes converted from labels

[Bruce Fischl]

I'm not sure I totally understand. What kind of continuity do you 
require? That every voxel has at least one adjacent voxel with the same 
label?

On Thu, 7 Jul 2016, Douglas N Greve wrote:

> Sorry, I can't think of an easy way to do this. It is possible for two
> adjacent vertices to be in two voxels that only share an edge or a
> corner and not necessarily a face. Maybe if you increase the size of the
> mesh (and so reduce the distance between vertices) you will not run into
> this problem. I don't know of a command off hand that will do this, but
> I think Bruce may have something.
>
> On 06/24/2016 07:33 AM, MIKHAEL Shadia wrote:
>>
>> Hello,
>>
>>
>> I am interested in the cortical parcellations at the pial (grey
>> matter) and white matter layers
>>
>>
>> I have extracted grey matter (pial) and white matter (white) labels
>> for a gyrus (right superior frontal gyrus, label 2028)
>>
>> mri_annotation2label --subject s1/12copy --hemi rh --labelbase
>> ./12copy/label/rh.cortex --surface pial
>>
>> mri_annotation2label --subject s1/12copy --hemi rh --labelbase
>> ./12copy/label/rh.cortex --surface white
>>
>>
>> then converted the above 2 files (renamed to ...-wm and ...-gm) for
>> the superior frontal gyrus  to nifti's for viewing in other applications
>>
>> mri_label2vol --label ./label/rh.cortex-028.label --o
>> rh-cortex-028-rsfg-wm.nii --identity --temp ./mri/T1.mgz
>>
>> mri_label2vol --label ./label/rh.cortex-028.label --o
>> rh-cortex-028-rsfg-gm.nii --identity --temp ./mri/T1.mgz
>>
>>
>> My goal is to run some statistics on 2 nifti's, which requires
>> continuity in the nonzero voxels, in at least 1 of the 3 directions
>> (x/y/z). This isn't the case for this gyri, particularly at the pial
>> layer (shown in blue in the attachment). Is there a way in which this
>> could be achieved? Have I missed any steps?
>>
>>
>> Many thanks in advance.
>>
>> Shads
>>
>>
>>
>>
>> The University of Edinburgh is a charitable body, registered in
>> Scotland, with registration number SC005336.
>>
>>
>> ___
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>
>
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Re: [Freesurfer] Inflation of one hemi only

[Bruce Fischl]

Hi XJ

this is a known problem but we haven't gotten to fixing it yet. Do you 
need it to complete that step? It is pretty close to the end so it may be 
that the error doesn't effect you

cheers
Bruce

On Thu, 7 Jul 2016, Kang, XJ wrote:


Hi,

I am trying to inflate right hemisphere only using the commands:

recon-all -autorecon2 -hemi rh  -subjid 160526
recon-all -autorecon3 -hemi rh  -subjid 160526

The inflation stopped at the step:
mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white
41 --label_right_ribbon 42 --save_ribbon 160526

SUBJECTS_DIR is /home/sata3/FreeSurfer/Subjects
MRISread(/home/sata3/FreeSurfer/Subjects/160526/surf/lh.white): could not
open file

The program "mris_volmask" needs to read "lh.white", which is not generated.
Any expert has any suggestions? Maybe I didn't use the commands correctly?

Thank you for your help.

XJ Kang

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Re: [Freesurfer] Design Matrix Creation

[Douglas N Greve]

I don't think you can do that. A subject must belong to both a gender 
and a dx class, so you have to do it as an interaction.


On 07/06/2016 03:38 PM, Timothy Hendrickson wrote:
> Hi Doug,
> I just wanted to make sure that we were on the same page. I may have been a 
> little unclear in

> what I would ideally like to do.
> For #2 what I would like to do is take into account age slopes and total 
> intracranial slopes for

>   gender, and age slopes and total intracranial slopes for diagnosis.
> I was not implying that I wanted diagnosis and gender to interact.
>
> Assuming that you understood this previously could you please explain why you 
> would model

> the matrix this way? I do not fully understand.
>
> Respectfully,
>
> -Tim
> >I did not get the same matrix. Here's how I would do it
> >Columns 1-16 model the intercepts for all your classes
> >Columns 17-20 model the ages for your gender-x-diagnosis subclasses
> >Columns 21-24 model the ICV for your gender-x-diagnosis subclasses
> On 07/06/2016 02:04 PM, Timothy Hendrickson wrote:
> > Freesurfer Support,
> >
> > Thank you for your support with my previous line of questions regarding
> > design matrix creation.
> > I have manually created another design matrix and want to ensure that I
> > designed it correctly.
> >
> > An example of my FSGD file is as follows below:
> > Class SITE 1-Male-Control
> > Class SITE 1-Male-PATIENT
> > Class SITE 1-Female-Control
> > Class SITE 1-Female-PATIENT
> > Class SITE 2-Male-Control
> > Class SITE 2-Male-PATIENT
> > Class SITE 2-Female-Control
> > Class SITE 2-Female-PATIENT
> > Class SITE 3-Male-Control
> > Class SITE 3-Male-PATIENT
> > Class SITE 3-Female-Control
> > Class SITE 3-Female-PATIENT
> > Class SITE 4-Male-Control
> > Class SITE 4-Male-PATIENT
> > Class SITE 4-Female-Control
> > Class SITE 4-Female-PATIENT
> > Variables age_at_scan total_intracranial_volume
> > study site levels = 1, 2, 3, 4
> > gender levels = Male, Female
> > diagnosis levels = PATIENT, Control
> > age_at_scan = covariate age
> > total_intracranial_volume = covariate total intracranial volume
> >
> > What I would ideally like to do is:
> >
> > 1) Take into account offset differences amongst diagnosis, gender, and study
> > site.
> >
> > 2) Allowing a difference in age slope, and total intracranial volume slope
> > amongst the diagnosis and gender levels.
> >
> > 3) Modeling the age slope and total intracranial volume slope as the same 
> > for
> > the study site levels.
> > Let's image that the first participant is from site 1, Male, and control, 
> > and
> > is 12 and has a TIV of 30,000.
> > The second participant is from site 2, Female, and PATIENT, and is 14, and
> > has a TIV of 25,000.
> > My understanding of the design matrix would be as follows:
> > 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 0 3 0 0 0
> > 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 14 0 0 0 25000
> > -Tim
> >
> > >Yes, create your matrix manually.
> > >
> > >Those matrix lines are not quite right. The ages are in the correct
> > >column, but you need a 1 somewhere in columns 1-8 to indicate the class
> > >(ie, site/dx) that the subject is in.
> > On 05/26/2016 12:57 PM, Timothy Hendrickson wrote:
> > > Hi Doug,
> > >
> > > Thank you for such a prompt response. Just to be clear you are
> > > recommending that I manually create the matrix file right?
> > >
> > > If so I want to ensure that I am understanding how to design the
> > > matrix file properly.
> > >
> > > Let's imagine that the first participant is a control and is 13 and
> > > the second is a patient and is 15. My understanding is that the matrix
> > > file would be as follows:
> > > 0 0 0 0 0 0 0 0 13 0
> > > 0 0 0 0 0 0 0 0 0 15.
> > >
> > > -Tim
> > > Previous correspondences are below:
> > >
> > > You'll need a regressor for each of the 8 classes you describe below.
> > > You can use mri_glmfit to generate this (Xg.dat file)
> > > You'll need two more regressors for age, one for each diagnosis. If a
> > > subject (ie, row) is a control then the two values will be AGE 0. If the
> > > subject of the row is a patient, then the two values will be 0 AGE. You
> > > can then set up a Controls-Patients age (ie, interaction between dx and
> > > age) contrast like
> > > [0 0 0 0 0 0 0 0 1 -1]
> > > On 05/24/2016 02:30 PM, Timothy Hendrickson wrote:
> > > >
> > > > Freesurfer Support,
> > > >
> > > > I'd like to create a design matrix for a group analysis outside of the
> > > > DODS and DOSS models. I understand that in order to do this the -X
> > > > flag must be used. However, I have been unable to find examples of how
> > > > to do this.
> > > >
> > > > I am hoping to reveal a difference in thickness or gyrification
> > > > amongst a clinical population. The data set contains two factors:
> > > > diagnosis, and study site and one covariate: age. Diagnosis has two
> > > > levels: controls, and patients. Study site has four levels, one level
> > > > for each location the data has been collected from.
> > > >
> 

Re: [Freesurfer] mapping a surface from fsaverage_sym to the subject's native surface

[Douglas N Greve]

I answered this yesterday


On 07/06/2016 01:47 PM, Douglas N Greve wrote:
>
> It would be something like
> mris_apply_reg --src lh.data-from-fsavgsym.mgh --streg 
> $SUBJECTS_DIR/fsaverage_sym/surf/lh.sphere.reg 
> $SUBJECTS_DIR/yoursubject/surf/lh.fsaverage_sym.sphere.reg --o 
> lh.data-from-fsavgsym-on-yoursubject.mgh
>
>
> On 07/04/2016 10:34 AM, Ali-Reza Mohammadi-Nejad wrote:
>> Dear Freesurfer experts,
>>
>> Based on the FS wiki, I calculated the cortical thickness difference 
>> between the lh and rh of a subject.
>> Now, I want to use the “mris_apply_reg” command to map the 
>> “left-right  difference” from fsaverage_sym back to the subject's 
>> native surface.
>> Unfortunately, I did not find the appropriate options of this command 
>> to do this work.
>> Thanks for any help.
>> Best regards, 

On 07/07/2016 01:05 PM, ali reza mohammadi nejad wrote:
> Dear Freesurfer experts,
>>
>> Based on the FS wiki, I calculated the cortical thickness difference 
>> between the lh and rh of a subject.
>> Now, I want to use the “mris_apply_reg” command to map the 
>> “left-right  difference” from fsaverage_sym back to the subject's 
>> native surface.
>> Unfortunately, I did not find the appropriate options of this command 
>> to do this work.
>> Thanks for any help.
>> Best regards,
>> Ali-Reza
>> Ali-Reza Mohammadi-Nejad
>> Pre-doctoral research fellow
>> Radiology and Neurology Research
>> Henry Ford Health System
>> Detroit, MI 48202, USA
>
>
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[Freesurfer] Inflation of one hemi only

[Kang, XJ]

Hi,

I am trying to inflate right hemisphere only using the commands:

recon-all -autorecon2 -hemi rh  -subjid 160526
recon-all -autorecon3 -hemi rh  -subjid 160526

The inflation stopped at the step:
mris_volmask --label_left_white 2 --label_left_ribbon 3 
--label_right_white 41 --label_right_ribbon 42 --save_ribbon 160526


SUBJECTS_DIR is /home/sata3/FreeSurfer/Subjects
MRISread(/home/sata3/FreeSurfer/Subjects/160526/surf/lh.white): could 
not open file


The program "mris_volmask" needs to read "lh.white", which is not 
generated. Any expert has any suggestions? Maybe I didn't use the 
commands correctly?


Thank you for your help.

XJ Kang
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Re: [Freesurfer] continuity in volumes converted from labels

[Douglas N Greve]

Sorry, I can't think of an easy way to do this. It is possible for two 
adjacent vertices to be in two voxels that only share an edge or a 
corner and not necessarily a face. Maybe if you increase the size of the 
mesh (and so reduce the distance between vertices) you will not run into 
this problem. I don't know of a command off hand that will do this, but 
I think Bruce may have something.

On 06/24/2016 07:33 AM, MIKHAEL Shadia wrote:
>
> Hello,
>
>
> I am interested in the cortical parcellations at the pial (grey 
> matter) and white matter layers
>
>
> I have extracted grey matter (pial) and white matter (white) labels 
> for a gyrus (right superior frontal gyrus, label 2028)
>
> mri_annotation2label --subject s1/12copy --hemi rh --labelbase 
> ./12copy/label/rh.cortex --surface pial
>
> mri_annotation2label --subject s1/12copy --hemi rh --labelbase 
> ./12copy/label/rh.cortex --surface white
>
>
> then converted the above 2 files (renamed to ...-wm and ...-gm) for 
> the superior frontal gyrus  to nifti's for viewing in other applications
>
> mri_label2vol --label ./label/rh.cortex-028.label --o 
> rh-cortex-028-rsfg-wm.nii --identity --temp ./mri/T1.mgz
>
> mri_label2vol --label ./label/rh.cortex-028.label --o 
> rh-cortex-028-rsfg-gm.nii --identity --temp ./mri/T1.mgz
>
>
> My goal is to run some statistics on 2 nifti's, which requires 
> continuity in the nonzero voxels, in at least 1 of the 3 directions 
> (x/y/z). This isn't the case for this gyri, particularly at the pial 
> layer (shown in blue in the attachment). Is there a way in which this 
> could be achieved? Have I missed any steps?
>
>
> Many thanks in advance.
>
> Shads
>
>
>
>
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>
>
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Re: [Freesurfer] PVE correction tool on Freesurfer 6

[Douglas N Greve]

Hi Subin, I just created this page this morning
http://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer
do you want to take a look and see if it answers your questions. As for 
#2, yes you still need to run gtmseg.

On 06/26/2016 07:45 AM, Lee Subin Kristine wrote:
>
> Hello,
>
> I am trying to use PVE correction on preprocessed PET data downloaded 
> from the Alzheimer's Disease Neuroimaging Initiative(ADNI) database.
> I have a couple of questions:
>
>
> 1) I am using the co-registered, averaged image of the dynamic images, 
> and it seems from your answers here 
> (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg43435.html) 
> that
>  
> for static PET images, #3~5 will be different. Could you explain how I 
> would need to enter the command differently?
>
> 2) I already have segmentations of my MRI images obtained via 
> FreeSurfer(v.5.2)'s cortical parcellation. Would I still have to do 
> procedure #1 (gtmeseg --s subject) ? I did try using xcerebralseg 
> because it seemed from the help command that in my case where I 
> already have some FS segmentations that I should use this one:
>
> /You can use your own segmentation or a modified FS segmentation. //
> //It will be easiest if you modify apas+head.mgz to insert your//
> //segmentations. apas+head.mgz is created by gtmseg but you can//
> //create it with //
> /
> /xcerebralseg --s $subject --o $SUBJECTS_DIR/$subject/mri/apas+head.mgz/
>
> However when I do try I got the following error:
>
> /ERROR: could not open 
> /usr/local/freesurfer/subjects/002_S_4213/stats/002_S_4213/mri/apas+head.stats
>  
> for writing//
> //Errno: No such file or directory/
>
>
>
> Thanks a lot in advance,
>
> Regards,
> Subin
>
>
>
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Re: [Freesurfer] question about volume of the hippocampus

[Douglas N Greve]

aseg.stats is just a text file, so you can view it with any text viewer 
(eg, the unix more or less commands, vi, emacs)

On 07/07/2016 06:41 AM, kju...@med.kanazawa-u.ac.jp wrote:
> Dear freesurfer developers.
>
> I am working at department of neurology in university Hospital, Japan.
> I am beginner of freesurfer, please forgive me to ask you a basic
> question.
>
> I want to measure the volume of the hippocampus in my patients.
> I was able to segment the MRI successfully and display the image in
> freeviewer.
> However, I could not recognize the way to obtain the volume of the
> hippocampus.
>
> *I saw the "mail acheive"
> (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg14679.html),
> however, I could not understand the way to look at the the aseg.stats.
>
> Could you teach me the way for obtaining the volume of the hippocampus?
> I and very looking forward to hearing from you.
>
> Yours sincerely,
> Junji Komatsu
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>

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Re: [Freesurfer] make_average_template error

[Douglas N Greve]

Try setting the SUBJECTS_DIR to an absolute path, eg,
setenv SUBJECTS_DIR `pwd`


On 07/07/2016 05:28 AM, Chatzi, Vasiliki wrote:
>
>
>  *
> Hello freesurfer developers,
> I am trying to compute the average_subject template described in
> the freesurfer wiki
> (https://surfer.nmr.mgh.harvard.edu/fswiki/make_average_subject).
> I have located all the subjects' directories in one folder named
> All_data_baseline. Then I set SUBJECTS_DIR to this folder using
> the command setevn  SUBJECTS_DIR ./ ,and then I defined the
> subjects using the command setenv SUBJECTS = (subject1 subject2
> ...). Finally I run the command make_average_subject --out
> avgsubject. The directory avgsubject was created but then I
> received the following error:
>
> error.log:
> MRISread (.//subject1/surf/lh.sphere.reg): could not open file
> mris_make_template: could not read surface file
> .//subject1/surf/lh.sphere.reg
>
>
> error as it appears on the terminal:
> output subject: avgsubject
> mri_add_xform_to_header -c auto .//avgsubject/mri/mni305.cor.mgz
> .//avgsubject/mri/mni305.cor.mgz
> INFO: extension is mgz
>
> tee: .//avgsubject/scripts/make_average_surface.log: No such file
> or directory
> #@# Making lh registration template -
> tee: .//avgsubject/scripts/make_average_surface.log: No such file
> or directory
> /homedirectory/All_data_baseline/avgsubject
> tee: .//avgsubject/scripts/make_average_surface.log: No such file
> or directory
> mris_make_template -norot -annot aparc lh sphere.reg subject1
>
> tee: .//avgsubject/scripts/make_average_surface.log: No such file
> or directory
> not aligning hemispheres before averaging.
> zeroing medial wall in aparc
> creating new parameterization...
>
> processing subject subject1 (1 of 313)
> reading spherical surface .//subject1/surf/lh.sphere.reg...
> MRISread(.//subject1/surf/lh.sphere.reg): could not open file
> No such file or directory
> mris_make_template: could not read surface file
> .//subject1/surf/lh.sphere.reg
> No such file or directory
> ERROR: make_average_surface
>
> I did search the make_average_subject --help and the mail archive
> but I have not yet found a solution. Please accept my apologies if
> there is one but I have not noticed.
>
> I am using version freesurfer-5.3.0 in a Linux 7.1 with 48 core
> memory.
>
> I was wondering if you could possibly provide any advice for
> troubleshooting this error.
>
> Best wishes,
> Vasiliki
>
>
>
>
>
>
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Re: [Freesurfer] fslaverage/MNI coordinates

[Douglas N Greve]

I've just added your use case to this page. See Case 8.
http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems

On 07/06/2016 05:09 PM, Li, Baojuan wrote:
> Hi Doug,
>
> Thank you so much! Because I will do the analysis using SPM, I need the 
> coordinates in MNI152 space. I found a transformation between them:
>
> M = [0.9975   -0.00730.0176   -0.0429
> 0.01461.0009   -0.00241.5496
>-0.0130   -0.00930.99711.1840
> 000  1.]
> Is this transformation correct?
> I guess I can then get the MNI152  coordinates in this way:
>   
>   P305 = [MNI305x MNI305y MNI305z 1]';
>   P152 = M*P305
>
> Am I correct?
>
> Best wishes,
> Baojuan
>
> 
> 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: Wednesday, July 06, 2016 4:44 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] fslaverage/MNI coordinates
>
> Hi Baojuan, that coordinate will be mni305 space. Is that what you want?
>
> On 07/06/2016 04:17 PM, Li, Baojuan wrote:
>> Dear Freesurfer experts,
>>
>>
>> I am using MNE (with MEG data) to define my ROIs for a connectivity
>> analysis. I am going through the following steps to get the MNI
>> coordinates of the regions:
>>
>> 1. Morph the subject's brain to fslaverage;
>>
>> 2. Load the inflated surface of fslaverage to MNE analyze;
>>
>> 3. Look for regions that are activated during my task;
>>
>> 3. Use view>show coordinates to show the coordinates of the vertex;
>>
>> 4. The surface RAS (MRI) coordinates are shown;
>>
>> 5. Used these coordinates as MNI coordinates.
>>
>> Because I was using SPM in the past and am quite new to freesurfer, I
>> strongly hope someone can help me to check if I have done it
>> correctly. Thank you so much for your help!
>>
>> Best wishes,
>> Baojuan
>>
>>
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> --
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> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
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>
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Re: [Freesurfer] LGI Summary Statistics

[Douglas N Greve]

It is not the same. You would have to weight by the number of vertices. 
You can also run mris_anatomical_stats passing the ?h.cortex.label as 
the label and the lgi overlay as the input

On 07/06/2016 02:57 PM, Timothy Hendrickson wrote:
> Freesurfer Support,
>
> I have seen previous message threads on extracting LGI measurements 
> across ROIs, however I have yet to find anything which would provide a 
> summary LGI across an entire hemsphere.
> Other measurements like cortical thickness have a measurement like 
> this. Is there a measurement like this for LGI?
>
> If I take the mean of all of the ROIs would that be equivalent to a 
> hemispheric LGI measure?
>
> Thanks!
>
> -Tim
>
> Timothy Hendrickson
> Department of Psychiatry
> University of Minnesota
> Mobile: 507-259-3434 (texts okay)
>
>
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[Freesurfer] mapping a surface from fsaverage_sym to the subject's native surface

[ali reza mohammadi nejad]

Dear Freesurfer experts,
> 
> Based on the FS wiki, I calculated the cortical thickness difference between 
> the lh and rh of a subject.
> Now, I want to use the “mris_apply_reg” command to map the “left-right  
> difference” from fsaverage_sym back to the subject's native surface.
> Unfortunately, I did not find the appropriate options of this command to do 
> this work.
> Thanks for any help.
>  
> Best regards,
> Ali-Reza
>  
> Ali-Reza Mohammadi-Nejad
> Pre-doctoral research fellow
> Radiology and Neurology Research
> Henry Ford Health System 
> Detroit, MI 48202, USA
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[Freesurfer] FOV Size Discrepancy

[Tamara Tavares]

Hello!

I was hoping someone can provide me with some clarification on an issue I
have been having with the FOV size.

I have a database of scans which I am running through recon-all
cross-sectionally. The majority of the scans have an FOV of 256x256x208;
however, when I run them through recon-all I get an error message
indicating that the FOV is larger than 256 (282x282x228). When I use the
-cw256 flag, recon-all runs through successfully. I do not understand why
recon-all thinks the FOV is larger then it is. I double checked that the
FOV size is 256 using the mri_info command line and the database
information. Does anyone know why recon-all is listing a larger FOV size?

Thank you in advance for your help.

Tamara
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Re: [Freesurfer] Question about Thalamus segmentation

[Bruce Fischl]

nope, we don't have anything to segment thalamic nuclei yet. It's one of 
the things we are interested in pursuing, but haven't gotten to it yet
On 
Thu, 7 Jul 2016, Dorsa Haji Ghaffari wrote:

> Hi,
> I am trying to segment the thalamus into its nuclei such as VLA , VLP and
> VIM. I see those labels available in the atlas but I do not get any of them
> in my segmentation. Does anyone have any idea how to do that?
> 
> Thank you
> 
> Dorsa
> 
>
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Re: [Freesurfer] TRACULA group stats visualization

[Derek Pisner]

Sure thing. fmajor mean.txt file is attached.


Thanks a bunch,
-Derek

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki 
[ayend...@nmr.mgh.harvard.edu]
Sent: Thursday, July 07, 2016 4:48 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] TRACULA group stats visualization

Hi Derek - this is strange. The dev and 5.3 version of freeview should
display them differently. Can you send me one of those mean.txt files?

a.y

On Wed, 6 Jul 2016, Derek Pisner wrote:

> Hi Anastasia,
>
> This occurs for me on both stable and dev versions of freview and trac-all 
> -stat
>
> -Derek
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki 
> [ayend...@nmr.mgh.harvard.edu]
> Sent: Monday, July 04, 2016 12:47 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] TRACULA group stats visualization
>
> Hi Derek - Are you by any chance using the dev version of freeview?
>
> a.y
>
> On Fri, 1 Jul 2016, Derek Pisner wrote:
>
>> Dear Anastasia,
>> I am running into an issue with the trac-all -stat option on our 
>> longitudinal TRACULA data.
>>
>> Everything runs smoothly through all earlier stages, and I checked 
>> individual subjects' merged outputs in freeview with -tv mode. Everything 
>> looks fine.
>>
>> Also, then when I run trac-all -c dmric_config -stat, everything finishes 
>> without error.
>>
>> But then when I open the results with the command:
>> freeview -v $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz -w 
>> /data/blt/TRACULA/tractography_output/stats.long/*.path.mean.txt
>>
>> I get the image seen in the attached .png file. Any idea what might be 
>> causing this?
>>
>> Many thanks in advance for you help.
>>
>> Best,
>> Derek
>>
>>
>>
>>
>
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>
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#!ascii label
273
1 54.9828 -112.501 134.663 0
2 54.8962 -112.723 134.277 0
3 54.0067 -113.333 135.846 0
4 53.8695 -113.932 136.691 0
5 53.488 -114.202 136.28 0
6 53.4998 -114.438 135.639 0
7 53.632 -112.881 136.864 0
8 53.3387 -112.84 136.552 0
9 53.0535 -113.161 136.031 0
10 52.9872 -113.197 135.736 0
11 52.8514 -113.258 135.182 0
12 52.4076 -113.371 134.821 0
13 52.2039 -113.531 134.275 0
14 52.1372 -113.697 133.98 0
15 52.0764 -113.804 133.217 0
16 51.8519 -113.722 132.737 0
17 51.7159 -113.81 132.038 0
18 51.6539 -113.897 131.42 0
19 51.5181 -113.984 131.109 0
20 51.3017 -113.883 130.785 0
21 51.3861 -114.038 130.187 0
22 51.1757 -114.051 129.486 0
23 51.1854 -114.098 129.097 0
24 51.191 -114.043 128.46 0
25 51.2034 -114.111 127.835 0
26 51.4293 -114.06 127.592 0
27 51.3601 -114.142 126.947 0
28 51.37 -114.23 126.088 0
29 51.4519 -114.289 125.551 0
30 51.6811 -114.268 125.169 0
31 51.835 -114.279 124.435 0
32 51.9185 -114.331 123.889 0
33 52.2176 -114.398 123.35 0
34 52.5197 -114.503 122.581 0
35 52.524 -114.463 122.161 0
36 53.0479 -114.374 121.687 0
37 53.114 -114.364 121.276 0
38 53.3473 -114.501 120.582 0
39 53.8011 -114.525 120.43 0
40 53.8766 -114.583 119.812 0
41 54.3976 -114.613 119.485 0
42 54.7717 -114.673 119.028 0
43 54.9236 -114.726 118.395 0
44 55.2803 -113.186 120.859 0
45 55.7019 -113.144 120.469 0
46 55.9703 -113.171 120.184 0
47 56.4664 -113.232 119.667 0
48 56.6804 -113.292 119.236 0
49 56.789 -112.336 121.61 0
50 57.1244 -112.444 121.202 0
51 57.468 -111.296 123.863 0
52 57.5774 -110.19 126.032 0
53 57.7526 -110.28 125.502 0
54 58.1686 -110.318 124.941 0
55 58.5142 -110.392 124.715 0
56 58.8735 -110.535 124.181 0
57 59.051 -110.578 124.062 0
58 59.3363 -110.624 123.756 0
59 59.6364 -110.645 123.25 0
60 60.1 -110.692 123.017 0
61 60.5096 -110.734 122.772 0
62 60.9678 -110.682 122.446 0
63 61.3771 -110.716 122.329 0
64 61.6718 -110.668 122.256 0
65 61.9056 -109.866 123.949 0
66 62.063 -108.816 126.077 0
67 62.3246 -108.75 126.048 0
68 62.896 -108.687 126.098 0
69 63.1635 -108.724 125.928 0
70 63.4838 -108.704 125.751 0
71 63.7405 -108.677 125.802 0
72 64.2219 -108.634 125.899 0
73 64.4849 -108.658 125.845 0
74 65.1619 -107.993 127.811 0
75 65.4599 -107.961 127.848 0
76 65.8393 -107.168 129.594 0
77 66.0783 -107.132 129.646 0
78 66.363 -107.148 129.738 0
79 66.6837 

Re: [Freesurfer] question about exporting volumes

[Krieger, Donald N.]

Hi Dorsa,

ImageJ and the people on the ImageJ mailing list may be helpful in transforming 
one of the standard output formats provided by freeview, e.g. nii, to a 
standard input format provided by COMSOL.
Here's a useful link.
  http://imagej.nih.gov/ij/list.html 

HTH - Don


> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
> boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
> Sent: Thursday, July 07, 2016 12:29 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] question about exporting volumes
> 
> You can view it in freesurfer with
> cd $SUBJECTS_DIR/subject/mri
> freeview -v orig.mgz -v
> aseg.mgz:lut=$FREESURFER_HOME/FreeSurferColorLUT.txt:opacity=.3:colormap
> =lut
> 
> I don't know anything about COMSOL
> 
> 
> On 07/07/2016 12:25 PM, Dorsa Haji Ghaffari wrote:
> > Thank you. I want to view the thalamus as a volume in freesurfer. Do
> > you know how to do that? also by exporting I mean exporting it as a
> > volume and then import it into COMSOL as a geometry.
> >
> > Thank you for your help!
> >
> > Dorsa
> >
> >
> > On Wed, Jul 6, 2016 at 7:50 PM, Douglas N Greve
> > > wrote:
> >
> > what do you mean isolate? what do you mean export? You can create a
> > binary mask in nifti format with mri_binarize --i aseg.mgz --match
> > 10 49
> > --o thalamus.mask.nii.gz
> >
> >
> > On 07/06/2016 04:46 PM, Dorsa Haji Ghaffari wrote:
> > >
> > >
> > >
> > > Hi,
> > >
> > > I was able to segment the MRI successfully, now I am trying to
> > isolate
> > > the thalamus and export it out of FS as a volume. Is there a way
> > to do
> > > that in FS?
> > >
> > > Thank you
> > >
> > > Dorsa
> > >
> > >
> > >
> > > ___
> > > 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
> >
> >
> > 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.
> >
> >
> >
> >
> > ___
> > 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/
> 
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Re: [Freesurfer] question about exporting volumes

[Douglas N Greve]

You can view it in freesurfer with
cd $SUBJECTS_DIR/subject/mri
freeview -v orig.mgz -v 
aseg.mgz:lut=$FREESURFER_HOME/FreeSurferColorLUT.txt:opacity=.3:colormap=lut

I don't know anything about COMSOL


On 07/07/2016 12:25 PM, Dorsa Haji Ghaffari wrote:
> Thank you. I want to view the thalamus as a volume in freesurfer. Do 
> you know how to do that? also by exporting I mean exporting it as a 
> volume and then import it into COMSOL as a geometry.
>
> Thank you for your help!
>
> Dorsa
>
>
> On Wed, Jul 6, 2016 at 7:50 PM, Douglas N Greve 
> > wrote:
>
> what do you mean isolate? what do you mean export? You can create a
> binary mask in nifti format with mri_binarize --i aseg.mgz --match
> 10 49
> --o thalamus.mask.nii.gz
>
>
> On 07/06/2016 04:46 PM, Dorsa Haji Ghaffari wrote:
> >
> >
> >
> > Hi,
> >
> > I was able to segment the MRI successfully, now I am trying to
> isolate
> > the thalamus and export it out of FS as a volume. Is there a way
> to do
> > that in FS?
> >
> > Thank you
> >
> > Dorsa
> >
> >
> >
> > ___
> > 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
>
>
> 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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> 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
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Re: [Freesurfer] question about exporting volumes

[Dorsa Haji Ghaffari]

Thank you. I want to view the thalamus as a volume in freesurfer. Do you
know how to do that? also by exporting I mean exporting it as a volume and
then import it into COMSOL as a geometry.

Thank you for your help!

Dorsa


On Wed, Jul 6, 2016 at 7:50 PM, Douglas N Greve 
wrote:

> what do you mean isolate? what do you mean export? You can create a
> binary mask in nifti format with mri_binarize --i aseg.mgz --match 10 49
> --o thalamus.mask.nii.gz
>
>
> On 07/06/2016 04:46 PM, Dorsa Haji Ghaffari wrote:
> >
> >
> >
> > Hi,
> >
> > I was able to segment the MRI successfully, now I am trying to isolate
> > the thalamus and export it out of FS as a volume. Is there a way to do
> > that in FS?
> >
> > Thank you
> >
> > Dorsa
> >
> >
> >
> > ___
> > 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/
>
> ___
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>
>
> 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
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> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
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Re: [Freesurfer] mri_segstats

[Douglas N Greve]

The first one

On 07/06/2016 08:22 PM, Alshikho, Mohamad J. wrote:
>
> Dear FS experts,
>
> I have PET image "pet.anat.mgz" in subject space. I want to calculate 
> the mean PET signal for every parcellate and segment in the atlas 
> "wmparc.mgz".
>
> _Which one of the following commands is more accurate? _
>
> __
>
> 1.mri_segstats --seg $SUBJECTS_DIR/${subj}/mri/wmparc.mgz --ctab 
> $FREESURFER_HOME/FREESURFERColorLUT.txt --i PET.anat.mgz --sum 
> PET.wmparc.stats
>
> 2.mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv 
> mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/ 
> PET.anat.mgz--in-intensity-name norm --in-intensity-units MR --subject 
> ${subj} --surf-wm-vol --ctab 
> /usr/local/freesurfer/stable5_3_0/WMParcStatsLUT.txt --etiv
>
> Best,
>
> Mohamad
>
>
>
> ___
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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

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[Freesurfer] Question about Thalamus segmentation

[Dorsa Haji Ghaffari]

Hi,

I am trying to segment the thalamus into its nuclei such as VLA , VLP and
VIM. I see those labels available in the atlas but I do not get any of them
in my segmentation. Does anyone have any idea how to do that?

Thank you

Dorsa
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[Freesurfer] Error with local Gyrification Index (lGI)

[Mahtab Farahbakhsh]

Dear FreeSurfer,

I am trying to calculate LGI for my images, but it seems like that it
doesn't work. I have tried everything, but it's still giving me the same
error.

I'm using FreeSurfer on a mac and my Matlab version is R2016a.

When I try to run "recon-all -s  -localGI", I get this error: ERROR:
Matlab is required to run mris_compute_lgi!.

I have done these so far:
PATH=/Applications/MATLAB_R2016a.app/bin/matlab:$PATH
export PATH

And my $PATH is:
/Applications/MATLAB_R2016a.app/bin/matlab:/usr/local/fsl/bin:/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/local/fsl/bin:/Applications/freesurfer/mni/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/opt/X11/bin:
No such file or directory

And when I write getmatlab, I get this:
ERROR: Cannot find matlab.
Does not exist or is not in path.

My original Matlab is in the /Applications folder and I also have a folder
named "matlab" in my FreeSurfer folder.

Would you please guide me what I should do?

Best Regards,
Mahtab.
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Re: [Freesurfer] Recon-all error after El Capitain update

[dgw]

It's hard to fully diagnose, without the command you called, but it
looks like you have your SUBJECTS_DIR and SUBJECT variable wrong, and
perhaps command syntax. Take another look at your command.

hth
d

On Thu, Jul 7, 2016 at 2:59 AM,   wrote:
> Hi list,
>
> after update with El Capitain, recon-all -all produce the error reported
> below.
>
>
> Thanks
>
> srclabel =
> /Applications/freesurfer/subjects/subject_prova/subj/fsaverage/label/lh.BA1.label
>
> srcsubject = fsaverage
>
> trgsubject = SUBJECTS_DIR
>
> trglabel = ./lh.BA1.label
>
> regmethod = surface
>
>
> srchemi = lh
>
> trghemi = lh
>
> trgsurface = white
>
> srcsurfreg = sphere.reg
>
> trgsurfreg = sphere.reg
>
> usehash = 1
>
> Use ProjAbs  = 0, 0
>
> Use ProjFrac = 0, 0
>
> DoPaint 0
>
>
> SUBJECTS_DIR/Applications/freesurfer/subjects/subject_prova/subj
>
> FREESURFER_HOME /Applications/freesurfer
>
> Loading source label.
>
> No such file or directory
>
> ERROR reading
> /Applications/freesurfer/subjects/subject_prova/Control89/fsaverage/label/lh.BA1.label
>
> Darwin iMac-di-Stefano.local 15.5.0 Darwin Kernel Version 15.5.0:
> root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64
>
>
> recon-all -s SUBJECTS_DIR exited with ERRORS
>
>
> ___
> 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] mris_preproc subject-volume mismatch

[Raney, Talia L.]

It worked with the register.dat files. Thank you! 

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: Wednesday, July 06, 2016 2:07 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_preproc subject-volume mismatch

Ah, the problem is with using an lta with 5.3 mris_preproc. I've put
version 6 mris_preproc here
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_preproc
try that and see if it works. Alternatively, you could convert the lta
files to register.dat files


On 07/06/2016 02:02 PM, Raney, Talia L. wrote:
> Hmm, it says that there is one frame in each of the subjects.
> 
> 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: Wednesday, July 06, 2016 1:54 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mris_preproc subject-volume mismatch
>
> It must be that one of the ces files has multiple frames. Try running
> mri_info --nframes ces.nii.gz
> on all of the ces files to see how many frames are in each
>
> On 07/06/2016 01:39 PM, Raney, Talia L. wrote:
>> mris_preproc --target fsaverage --hemi lh --iv 
>> WADG77j/restingstate/fc.lh-entorhinal.space.lh/lh-entorhinal/ces.nii.gz 
>> WADG77j/restingstate/bb.register.lta --iv 
>> WADG77k/restingstate/fc.lh-entorhinal.space.lh/lh-entorhinal/ces.nii.gz 
>> WADG77k/restingstate/bb.register.lta --projfrac 0.5 --out lh.ces.mgh
>> ERROR: number of input volumes (2) does not equal number of subjects (8)
>> It apparently thinks one volume is 4 subjects but when checking 
>> bb.register.lta, it doesn't appear to be the case.
>> Thanks!
>> Talia
>> 
>> 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: Wednesday, July 06, 2016 1:19 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] mris_preproc subject-volume mismatch
>>
>> can you send the terminal output?
>>
>> On 07/06/2016 11:32 AM, Raney, Talia L. wrote:
>>> Hi FreeSurfer users,
>>> I'm trying to use mri-preproc to do a group fMRI analysis(based on the 
>>> tutorial). However, I keep getting an error that the number of input 
>>> volumes does not equal number of subjects. It seems one volume is counted 
>>> as 4 subjects. I'm wondering what the command determines to be the subject 
>>> list when you use the --iv flag.
>>> For reference, I'm basing it off of this command:
>>> mris_preproc --target fsaverage --hemi lh \
>>>  --iv  fbirn-101/ces.nii fbirn-101/bb.register.lta \
>>>  --iv  fbirn-103/ces.nii fbirn-103/bb.register.lta \
>>>  --iv  fbirn-104/ces.nii fbirn-104/bb.register.lta \
>>>  --iv  fbirn-105/ces.nii fbirn-105/bb.register.lta \
>>>  --iv  fbirn-106/ces.nii fbirn-106/bb.register.lta \
>>>  --projfrac 0.5 \
>>>  --out lh.ces.mgh
>>> Thanks!
>>> Talia
>>> ___
>>> 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
> 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
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: 

Re: [Freesurfer] recon-all exited with error: reading lh.BA1_exvivo.label

[Vaz pandolfo, Renata]

Okay, I changed some other things and now the recon-all is running.
I will see how it looks tomorrow.

I used:
recon-all -all \
> -i
~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/co_T1_20110815.nii.gz
-s new_trial_20110815 \
> -sd ~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/  \
> -T2
~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/o20160524_143200t2tirmcordarkfluidhipp3mmGRAPPAs006a1001.nii.gz
\
> -T2pial -hippocampal-subfields-T1

Thanks!


On Thu, Jul 7, 2016 at 2:15 PM, Vaz pandolfo, Renata  wrote:

> Thank you!
>
> But now the error is:
>
> ERROR: cannot find
> o20160524_143200t2tirmcordarkfluidhipp3mmGRAPPAs006a1001.nii.gz
> Linux lundb2 4.4.0-24-generic #43-Ubuntu SMP Wed Jun 8 19:27:37 UTC 2016
> x86_64 x86_64 x86_64 GNU/Linux
>
> recon-all -s 20110815 exited with ERRORS at Do 7. Jul 14:14:09 CEST 2016
>
> Maybe I have to put the whole path?
>
> On Thu, Jul 7, 2016 at 2:10 PM, Krieger, Donald N. 
> wrote:
>
>> Hi Renata,
>>
>>
>>
>> Is there a problem with the “-s” argument, i.e. the “/” in  - s 20110815/
>>
>>
>>
>> HTH - Don
>>
>>
>>
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [mailto:
>> freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *Vaz pandolfo,
>> Renata
>> *Sent:* Thursday, July 07, 2016 8:05 AM
>> *To:* freesurfer@nmr.mgh.harvard.edu
>> *Subject:* [Freesurfer] recon-all exited with error: reading
>> lh.BA1_exvivo.label
>>
>>
>>
>> Dear FreeSurfer developers,
>>
>> I am running recon-all on a healthy subject and I am also trying to get
>> the hippocampal subfields segmentation.
>> On the mri directory there is no hippocampus output, and the recon-all
>> exited with errors.
>> From my understanding, the error is with the lh.BA1_exvivo.label:
>>
>> SUBJECTS_DIR
>> /home/lub_jungs/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815
>> FREESURFER_HOME /usr/local/freesurfer
>> Loading source label.
>> Invalid argument
>> ERROR reading
>> /home/lub_jungs/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/fsaverage/label/lh.BA1_exvivo.label
>>
>> The command I used was:
>> recon-all -all \
>> -i
>> ~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/co_T1_20110815.nii.gz
>> -s 20110815/ \
>> -sd ~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/  \
>> -T2 o20160524_143200t2tirmcordarkfluidhipp3mmGRAPPAs006a1001.nii.gz \
>> -T2pial -hippocampal-subfields-T1
>>
>>
>> When trying to solve the problem, I noticed that I could have run a
>> separate command for the hippocampal subfields and I ran this one:
>>
>>
>> recon-all \
>> -s 20110815/ \
>> -sd ~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/  \
>> -hippocampal-subfields-T1T2
>> ~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/o20160524_143200t2tirmcordarkfluidhipp3mmGRAPPAs006a1001.nii.gz
>> 20110815_T2
>>
>> Since the previous data had errors, I didn't really expect this to work,
>> but I tried it anyways.
>>
>> It exited "without errors", but on the log there was the following error
>> twice:
>>
>> Error:Cannot find CTF archive
>> /usr/local/freesurfer/bin/segmentSubjectT1T2_autoEstimateAlveusML.ctf
>>
>> Extra info:
>>
>> Freesurfer version: freesurfer-Linux-centos6_x86_64-dev-20160616-8264611
>>
>> uname -a: Linux lundb2 4.4.0-24-generic #43-Ubuntu SMP Wed Jun 8 19:27:37
>> UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
>>
>> logs: recon-all and hippocampal-subfields-T1T2 attached
>>
>> If anyone has had the same problem, could you please tell me how to solve
>> it?
>> And if I am doing something wrong, please tell me the correct way so I
>> can continue with the analysis.
>>
>>
>>
>> Thank you!
>>
>> Renata
>>
>> ___
>> 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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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] recon-all exited with error: reading lh.BA1_exvivo.label

[Vaz pandolfo, Renata]

Thank you!

But now the error is:

ERROR: cannot find
o20160524_143200t2tirmcordarkfluidhipp3mmGRAPPAs006a1001.nii.gz
Linux lundb2 4.4.0-24-generic #43-Ubuntu SMP Wed Jun 8 19:27:37 UTC 2016
x86_64 x86_64 x86_64 GNU/Linux

recon-all -s 20110815 exited with ERRORS at Do 7. Jul 14:14:09 CEST 2016

Maybe I have to put the whole path?

On Thu, Jul 7, 2016 at 2:10 PM, Krieger, Donald N. 
wrote:

> Hi Renata,
>
>
>
> Is there a problem with the “-s” argument, i.e. the “/” in  - s 20110815/
>
>
>
> HTH - Don
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [mailto:
> freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *Vaz pandolfo,
> Renata
> *Sent:* Thursday, July 07, 2016 8:05 AM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* [Freesurfer] recon-all exited with error: reading
> lh.BA1_exvivo.label
>
>
>
> Dear FreeSurfer developers,
>
> I am running recon-all on a healthy subject and I am also trying to get
> the hippocampal subfields segmentation.
> On the mri directory there is no hippocampus output, and the recon-all
> exited with errors.
> From my understanding, the error is with the lh.BA1_exvivo.label:
>
> SUBJECTS_DIR
> /home/lub_jungs/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815
> FREESURFER_HOME /usr/local/freesurfer
> Loading source label.
> Invalid argument
> ERROR reading
> /home/lub_jungs/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/fsaverage/label/lh.BA1_exvivo.label
>
> The command I used was:
> recon-all -all \
> -i
> ~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/co_T1_20110815.nii.gz
> -s 20110815/ \
> -sd ~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/  \
> -T2 o20160524_143200t2tirmcordarkfluidhipp3mmGRAPPAs006a1001.nii.gz \
> -T2pial -hippocampal-subfields-T1
>
>
> When trying to solve the problem, I noticed that I could have run a
> separate command for the hippocampal subfields and I ran this one:
>
>
> recon-all \
> -s 20110815/ \
> -sd ~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/  \
> -hippocampal-subfields-T1T2
> ~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/o20160524_143200t2tirmcordarkfluidhipp3mmGRAPPAs006a1001.nii.gz
> 20110815_T2
>
> Since the previous data had errors, I didn't really expect this to work,
> but I tried it anyways.
>
> It exited "without errors", but on the log there was the following error
> twice:
>
> Error:Cannot find CTF archive
> /usr/local/freesurfer/bin/segmentSubjectT1T2_autoEstimateAlveusML.ctf
>
> Extra info:
>
> Freesurfer version: freesurfer-Linux-centos6_x86_64-dev-20160616-8264611
>
> uname -a: Linux lundb2 4.4.0-24-generic #43-Ubuntu SMP Wed Jun 8 19:27:37
> UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
>
> logs: recon-all and hippocampal-subfields-T1T2 attached
>
> If anyone has had the same problem, could you please tell me how to solve
> it?
> And if I am doing something wrong, please tell me the correct way so I can
> continue with the analysis.
>
>
>
> Thank you!
>
> Renata
>
> ___
> 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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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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] recon-all exited with error: reading lh.BA1_exvivo.label

[Krieger, Donald N.]

Hi Renata,

Is there a problem with the “-s” argument, i.e. the “/” in  - s 20110815/

HTH - Don

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Vaz pandolfo, 
Renata
Sent: Thursday, July 07, 2016 8:05 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon-all exited with error: reading lh.BA1_exvivo.label

Dear FreeSurfer developers,
I am running recon-all on a healthy subject and I am also trying to get the 
hippocampal subfields segmentation.
On the mri directory there is no hippocampus output, and the recon-all exited 
with errors.
From my understanding, the error is with the lh.BA1_exvivo.label:

SUBJECTS_DIR
/home/lub_jungs/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Invalid argument
ERROR reading 
/home/lub_jungs/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/fsaverage/label/lh.BA1_exvivo.label

The command I used was:
recon-all -all \
-i 
~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/co_T1_20110815.nii.gz
 -s 20110815/ \
-sd ~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/  \
-T2 o20160524_143200t2tirmcordarkfluidhipp3mmGRAPPAs006a1001.nii.gz \
-T2pial -hippocampal-subfields-T1


When trying to solve the problem, I noticed that I could have run a separate 
command for the hippocampal subfields and I ran this one:

recon-all \
-s 20110815/ \
-sd ~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/  \
-hippocampal-subfields-T1T2 
~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/o20160524_143200t2tirmcordarkfluidhipp3mmGRAPPAs006a1001.nii.gz
  20110815_T2
Since the previous data had errors, I didn't really expect this to work, but I 
tried it anyways.
It exited "without errors", but on the log there was the following error twice:

Error:Cannot find CTF archive 
/usr/local/freesurfer/bin/segmentSubjectT1T2_autoEstimateAlveusML.ctf
Extra info:
Freesurfer version: freesurfer-Linux-centos6_x86_64-dev-20160616-8264611
uname -a: Linux lundb2 4.4.0-24-generic #43-Ubuntu SMP Wed Jun 8 19:27:37 UTC 
2016 x86_64 x86_64 x86_64 GNU/Linux
logs: recon-all and hippocampal-subfields-T1T2 attached
If anyone has had the same problem, could you please tell me how to solve it?
And if I am doing something wrong, please tell me the correct way so I can 
continue with the analysis.

Thank you!
Renata
___
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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.

Re: [Freesurfer] TRACULA tract group comparison p-values

[Anastasia Yendiki]

Hi Barbara - I don't believe that freeview has an option to show colorbars 
for heat maps that are loaded onto waypoints (if that's what you're 
trying to display). We should definitely add it in the future.

Best,
a.y

On Wed, 6 Jul 2016, Barbara Kreilkamp wrote:

> Dear Freesurfers,
>
> I am looking for a way to add a colorbar to my p-value tract cores
> generated through TRACULA.
>
> When I load up the images as described in the tutorial here
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics
>
> I only get a colorbar from 0 to 28.5 which cannot reflect pvalues, and
> there is no option to select my textfile with the p-values unfortunately.
>
> Would you please help?
>
> Thanks ever so,
>
> Barbara
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
___
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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
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] TRACULA group stats visualization

[Anastasia Yendiki]

Hi Derek - this is strange. The dev and 5.3 version of freeview should 
display them differently. Can you send me one of those mean.txt files?

a.y

On Wed, 6 Jul 2016, Derek Pisner wrote:

> Hi Anastasia,
>
> This occurs for me on both stable and dev versions of freview and trac-all 
> -stat
>
> -Derek
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki 
> [ayend...@nmr.mgh.harvard.edu]
> Sent: Monday, July 04, 2016 12:47 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] TRACULA group stats visualization
>
> Hi Derek - Are you by any chance using the dev version of freeview?
>
> a.y
>
> On Fri, 1 Jul 2016, Derek Pisner wrote:
>
>> Dear Anastasia,
>> I am running into an issue with the trac-all -stat option on our 
>> longitudinal TRACULA data.
>>
>> Everything runs smoothly through all earlier stages, and I checked 
>> individual subjects' merged outputs in freeview with -tv mode. Everything 
>> looks fine.
>>
>> Also, then when I run trac-all -c dmric_config -stat, everything finishes 
>> without error.
>>
>> But then when I open the results with the command:
>> freeview -v $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz -w 
>> /data/blt/TRACULA/tractography_output/stats.long/*.path.mean.txt
>>
>> I get the image seen in the attached .png file. Any idea what might be 
>> causing this?
>>
>> Many thanks in advance for you help.
>>
>> Best,
>> Derek
>>
>>
>>
>>
>
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>
>
>
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Re: [Freesurfer] Coordinates in TRACULA group analysis

[Anastasia Yendiki]

Hi Anri - Is there an error in the stats/*.log files for the different 
tracts?


a.y

On Tue, 5 Jul 2016, Anri WATANABE wrote:


Dear Anastasia, 

I use TRACULA to obtain diffusion measures at each voxel in a certain pathway 
for group analysis, but
there aren't stats/*.path.mean.txt files. I found .log files 
(_PP.avg33_mni_bbr.log) which exist
1 file per 1 tract, except corticospinal tract which has 2 .log files.

Command: trac-all –stat –c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.example

Error log: Loading output reference volume from 
/Applications/freesurfer/subjects/cvs_avg35

corRead(): can't open file /Applications/freesurfer/subjects/cvs_avg35/COR-.info

ERROR: Could not read /Applications/freesurfer/subjects/cvs_avg35


I attached dmrirc.example (configuration file) and /scripts/trac-all.log.


Thanks in advance,
Anri




**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里
**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
**

2016-06-03 9:51 GMT+09:00 Anri WATANABE :
  Hi, Anastasia.
There aren't any .log files but text files like 
lh.ilf_AS.avg33_mni_bbr.FA_Avg.txt. I guess text
files complete all pathways and measures.

**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里
**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
**

2016-06-02 3:03 GMT+09:00 Anastasia Yendiki :

  Thanks, Anri. So the previous steps seem to have run fine. Are there any 
.log files
  created in the stats/ folder, which is created by trac-all -stat?

  On Wed, 1 Jun 2016, Anri WATANABE wrote:

Hi Anastasia, This is a /scripts/trac-all.log of one 
subject of
the group.

Thanks,
Anri


**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里

**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine

**

2016-05-31 22:55 GMT+09:00 Anastasia Yendiki
:

      Hi Anri - Can you also send your log file 
(scripts/trac-all.log)?
I'll need to see what
      exactly was running when the error occurred. Thanks!

      a.y

      On Sat, 28 May 2016, Anri WATANABE wrote:

            Hello Anastasia,sorry for few information and let me 
tell you
command and
            error log.
            Command: trac-all –stat –c
$TUTORIAL_DATA/diffusion_tutorial/dmrirc.example

            Error log: Loading output reference volume from
            /Applications/freesurfer/subjects/cvs_avg35

            corRead(): can't open file
            /Applications/freesurfer/subjects/cvs_avg35/COR-.info

            ERROR: Could not read
/Applications/freesurfer/subjects/cvs_avg35


            dmrirc.example (configuration file) is attached to this
e-mail.

            Thanks in advance,
            Anri



           

**
            京都府立医科大学附属病院
            精神科・心療内科
            渡辺 杏里
           

**
            Anri WATANABE, M.D.
            Department of Psychiatry,
            University Hospital, Kyoto Prefectural University of 
Medicine
           

**

            2016-05-27 22:57 GMT+09:00 Anastasia Yendiki
:

                  Hi Anri - I do not know what command line you ran 
and
what your
            configuration file looks like, so it is very
                  hard for me to suggest solutions.

                  Best,
                  a.y

                  On Fri, 27 May 2016, Anri WATANABE wrote:

                        Hi 

[Freesurfer] question about volume of the hippocampus

[kjunji]

Dear freesurfer developers.

I am working at department of neurology in university Hospital, Japan.
I am beginner of freesurfer, please forgive me to ask you a basic 
question.

I want to measure the volume of the hippocampus in my patients.
I was able to segment the MRI successfully and display the image in 
freeviewer.
However, I could not recognize the way to obtain the volume of the 
hippocampus.

*I saw the "mail acheive" 
(http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg14679.html), 
however, I could not understand the way to look at the the aseg.stats.

Could you teach me the way for obtaining the volume of the hippocampus?
I and very looking forward to hearing from you.

Yours sincerely,
Junji Komatsu
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[Freesurfer] make_average_template error

[Chatzi, Vasiliki]

  *
Hello freesurfer developers,
I am trying to compute the average_subject template described in the freesurfer 
wiki (https://surfer.nmr.mgh.harvard.edu/fswiki/make_average_subject).
I have located all the subjects' directories in one folder named 
All_data_baseline. Then I set SUBJECTS_DIR to this folder using the command 
setevn  SUBJECTS_DIR ./ ,and then I defined the subjects using the command 
setenv SUBJECTS = (subject1 subject2 ...). Finally I run the command 
make_average_subject --out avgsubject. The directory avgsubject was created but 
then I received the following error:

error.log:
MRISread (.//subject1/surf/lh.sphere.reg): could not open file
mris_make_template: could not read surface file .//subject1/surf/lh.sphere.reg


error as it appears on the terminal:
output subject: avgsubject
mri_add_xform_to_header -c auto .//avgsubject/mri/mni305.cor.mgz 
.//avgsubject/mri/mni305.cor.mgz
INFO: extension is mgz

tee: .//avgsubject/scripts/make_average_surface.log: No such file or directory
#@# Making lh registration template -
tee: .//avgsubject/scripts/make_average_surface.log: No such file or directory
/homedirectory/All_data_baseline/avgsubject
tee: .//avgsubject/scripts/make_average_surface.log: No such file or directory
mris_make_template -norot -annot aparc lh sphere.reg subject1

tee: .//avgsubject/scripts/make_average_surface.log: No such file or directory
not aligning hemispheres before averaging.
zeroing medial wall in aparc
creating new parameterization...

processing subject subject1 (1 of 313)
reading spherical surface .//subject1/surf/lh.sphere.reg...
MRISread(.//subject1/surf/lh.sphere.reg): could not open file
No such file or directory
mris_make_template: could not read surface file .//subject1/surf/lh.sphere.reg
No such file or directory
ERROR: make_average_surface

I did search the make_average_subject --help and the mail archive but I have 
not yet found a solution. Please accept my apologies if there is one but I have 
not noticed.

I am using version freesurfer-5.3.0 in a Linux 7.1 with 48 core memory.

I was wondering if you could possibly provide any advice for troubleshooting 
this error.

Best wishes,
Vasiliki



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[Freesurfer] Freeview: how to change spline color bar

[Barbara Kreilkamp]

Dear Freesurfers,

How would I be able to use a different colormap under point sets please?

I can only find "solid color" and "heatmap" but a blue to red colorbar 
would suit my needs more.

Any assistance is greatly appreciated.

Thank you,

Best wishes,

Barbara

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[Freesurfer] Recon-all error after El Capitain update

[stdp82]

Hi list,
after update with El Capitain, recon-all -all produce the error reported below.

Thanks
srclabel = 
/Applications/freesurfer/subjects/subject_prova/subj/fsaverage/label/lh.BA1.label
srcsubject = fsaverage
trgsubject = SUBJECTS_DIR
trglabel = ./lh.BA1.label
regmethod = surface


srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0


SUBJECTS_DIR/Applications/freesurfer/subjects/subject_prova/subj
FREESURFER_HOME /Applications/freesurfer
Loading source label.
No such file or directory
ERROR reading 
/Applications/freesurfer/subjects/subject_prova/Control89/fsaverage/label/lh.BA1.label
Darwin iMac-di-Stefano.local 15.5.0 Darwin Kernel Version 15.5.0: 
root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64


recon-all -s SUBJECTS_DIR exited with ERRORS___
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