date:20190107

[Freesurfer] FreeSurfer crashing

2019-01-07 Thread vittal korann

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Hello FreeSurfer Developers,

I'm attempting to run recon-all on schizophrenia patients and
controls. For some reason freesurfer is crashing.

I wanted to know the reason for frequent crashing.

I'm using Ubuntu 16.04 LTS and
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.

Below I have attached the recon-all.log file for your reference.

Kindly help me to sort this out.

Thank you

Regards
*Vittal*
Tue Jan  8 01:59:38 EST 2019
/usr/local/freesurfer/subjects/insp019
/usr/local/freesurfer/bin/recon-all
-i /home/milkyway2/Desktop/INSP-019-NR-1-Structural.nii -s insp019 -all
subjid insp019
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Linux milkyway2 4.15.0-43-generic #46~16.04.1-Ubuntu SMP Fri Dec 7 13:31:08 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
cputime  unlimited
filesize unlimited
datasize unlimited
stacksize8192 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
vmemoryuse   unlimited
descriptors  1024 
memorylocked 64 kbytes
maxproc  128124 
maxlocks unlimited
maxsignal128124 
maxmessage   819200 
maxnice  0 
maxrtprio0 
maxrttimeunlimited

  totalusedfree  shared  buff/cache   available
Mem:   32859472  94740430511832  100636 140023631292176
Swap:  33473532   033473532


program versions used
$Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
$Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2019/01/08-06:59:38-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $  User: root  Machine: milkyway2  Platform: Linux  PlatformVersion: 4.15.0-43-generic  CompilerName: GCC  CompilerVersion: 40400 
FLIRT version 5.5
$Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
mri_convert --version 
stable5
ProgramName: tkregister2_cmdl  ProgramArguments: --all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2019/01/08-06:59:38-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $  User: root  Machine: milkyway2  Platform: Linux  PlatformVersion: 4.15.0-43-generic  CompilerName: GCC  CompilerVersion: 40400 
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
ProgramName: mri_make_uchar  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2019/01/08-06:59:38-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $  User: root  Machine: milkyway2  Platform: Linux  PlatformVersion: 4.15.0-43-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2019/01/08-06:59:39-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $  User: root  Machine: milkyway2  Platform: Linux  PlatformVersion: 4.15.0-43-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2019/01/08-06:59:39-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $  User: root  Machine: milkyway2  Platform: Linux  PlatformVersion: 4.15.0-43-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2019/01/08-06:59:39-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $  User: root  Machine: milkyway2  Platform: Linux  PlatformVersion: 4.15.0-43-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segment  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2019/01/08-06:59:39-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $  User: root  Machine: milkyway2  Platform: Linux  PlatformVersion: 4.15.0-43-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_label2label  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2019/01/08-06:59:39-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $  User: root  Machine: milkyway2  Platform: Linux  PlatformVersion: 4.15.0-43-generic  CompilerName: GCC  CompilerVersion: 40400 


 === NUMBER OF OPENMP THREADS = 1 === 
ProgramName: mri_em_register  ProgramArguments: -all-info  ProgramVersion: $Name: stable5

[Freesurfer] T1 hypointensities

2019-01-07 Thread Rockers, Elijah D.

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Hello,


Are the WM-hypointensities segmented in the same way as the rest of the 
subcortical regions? i.e., using the probablistic atlas referenced in the 2002 
Fischl et al paper?


Thanks,

- Eli

Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & 
World Report as the No. 1 hospital in Texas for patient care. Houston Methodist 
is nationally ranked in 8 specialties and is designated as a Magnet hospital 
for excellence in nursing.  Visit us at  houstonmethodist.org. Follow us at  
twitter.com/MethodistHosp and facebook.com/HoustonMethodist.  
***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist 
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the sender and delete all copies of the message. Thank you.
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Re: [Freesurfer] LME

2019-01-07 Thread Tefera, Getaneh B

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Dear Kersten,

I have a question about how to interpret  cortical thickness difference between 
groups.

I have three groups(A, B, and C) and five time points(t=0,0.5, 1,2,3).

To see the difference between group A and group B,  I constructed the following 
contrast matrix using the tutorial  provided by Freesurfer

C = [zeros(1,3) [1 0 0] zeros(1,4)];
CM.C=[zeros(1,3) [1 0 0] zeros(1,4)];

I run the following functions

rhstats = lme_mass_fit_Rgw(X,[1 2],rhY,ni,rhTh0,rhRgs,rhsphere);
F_rhstats = lme_mass_F(rhstats,CM);
fs_write_fstats(F_rhstats,rhmri,'/backup/cross/rh_AB_cross_sig.mgh','sig');

nv=length(rhstats);
Beta2 = zeros(1,nv);
for i=1:nv
  if ~isempty(rhstats(i).Bhat)
  Beta2(i) = rhstats(i).Bhat(2);
   end;
end;

rhmri1 = rhmri;
rhmri1.volsz(4) = 1;
fs_write_Y(Beta2,rhmri1,'/backup/cross/rh_AB_cross_rhBeta2.mgh');

[detvtx,sided_pval,pth] = 
lme_mass_FDR2(F_rhstats.pval,F_rhstats.sgn,rhcortex,0.05,0);

fs_write_Y(sided_pval,rhmri1,'/backup/cross/rh_AB_cross_spval.mgh');

When I view rh_AB_cross_sig.mgh using tksurfer I see regions with red and blue 
color .

1) How do I know the difference between the two groups for 5 time points?
2) Does red means thickness of group A is larger than thickness of group B?

With regards

Getaneh

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Diers, Kersten 
/DZNE
Sent: Friday, January 12, 2018 9:50 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] LME

Hi Getaneh,

thanks for the additional information.

I suspect that one source of confusion was that we have to distinguish
the univariate and the mass-univariate processing stream in the LME
toolbox. 

The univariate stream is about a single measure like left or right or
bilateral hippocampal volume, whereas the mass-univariate stream does
statistical modeling and testing for all vertices in a hemisphere, for
example to evaluate cortical thickness.

For a large part of my previous replies I was assuming that we are
talking about the univariate stream, where we need to use the
'lme_fit_FS' script. In contrast, the 'lme_mass_fit_Rgw' script, among
others, is used for estimation in the mass-univariate stream.

In that sense, it is not surprising to get error messages when using
the 'lme_fit_FS' script with mass-univariate vertex data as in your
example.

The bad news is that power analysis is only implemented for the
univariate stream, but not the mass-univariate stream. This is because
mass-univariate processing returns thousands of different estimates for
phisq and Dhat, among others, one for each vertex in a hemisphere. We
can get them from the data structure returned by 'lme_mass_fit_Rgw',
but they are simply too many to submit to the power analysis. 

In that sense, I currently see no viable way for power analysis for
cortical thickness data within the LME toolbox unless we can reduce it
to using estimates of a single (as opposed to multi-vertex) effect and
its variabilty.

Likewise, it is not surprising that estimates for Dhat and phisqhat are
different for e.g. the left and right hippocampus. One might speculate,
though, that they should be somewhat similar, and I would be somewhat
suprised if sample size calculations based on them result in very
different sample size estimates.

I have one more remark about the lme_plannedSampleSize script: I would
only recommend using it prospectively. As far as I can see it is not
intended nor can it be meaningfully used retrospectively, i.e. for
assessing the properties of a study that has already been conducted. 

Best regards,

Kersten


-Original Message-
From: "Tefera, Getaneh B" 
Reply-to: Freesurfer support list 
To: freesurfer@nmr.mgh.harvard.edu 
Cc: "Tefera, Getaneh B" 
Subject: Re: [Freesurfer] LME
Date: Thu, 11 Jan 2018 21:09:21 +0100

Hi Kersten,

I am sorry I did not make the question more specific.

I have three groups. I want see the power analysis by checking the
sample size calculation for the cortical thickness analysis .

[sz1,sz2] = lme_plannedSampleSize(Zi,ZiCol,Dhat,phisqhat,effsz,...
 dr,pw,alpha,gr
_pr)


my question is how can I get Dhat ( Estimated
random effects covariance matrix) and phisqhat (Estimated intra-subject
variability) to calculate the sample size of the pairs  .

Based on your suggestion to get Dhat and phisqhat I have to run "
lme_fit_FS(X,[1,2],y ,ni)"

When I run

lme_fit_FS(X,[1,2],y ,ni), where  Y is obtained from the following

[Y,mri] = fs_read_Y('lh.thickness_sm10.mgh'),  I get error.

Which function with what argument is good to use to find Dhat and
phisqhat?

Are these values the same for left and right cortical thickness data?

I am  sorry for the inconvenience .


with regards

Getaneh



From: freesurfer-boun...@nmr.mgh.harvard.edu  on behalf of Diers, Kersten /DZNE

Re: [Freesurfer] mris_apply_reg failing for area/volume

2019-01-07 Thread James Michael Roe

External Email - Use Caution

Thanks for the quick reply. Have sent the file to you now


- James



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Greve, Douglas N.,Ph.D. 

Sent: 07 January 2019 17:42
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_apply_reg failing for area/volume


What is $SUBJECTS_DIR/${template}/surf/lh.sphere.reg ? If template is not 
fsaverage_sym, can you send this file to me too?


On 1/7/19 5:21 AM, James Michael Roe wrote:

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Dear freesurfer experts

I am still unable to register RH area and volume files to the LH of a 
symmetrical template for a number of longitudinally processed subs. This is 
only the case when using the --jac flag (all run fine without).
There appears to be quite good correspondence (although not perfect) between 
whether the LONG sub fails and whether the BASE of that sub fails with the same 
error. Some CROSS subs also fail, though there appears to be little 
correspondence.

I would greatly appreciate any help you can give me.

To recap, the command I am running is:

#right to left
mris_apply_reg \
--src $SUBJECTS_DIR/$sub/surf/rh.area \
--trg $concatdir/rh.lh.area.${sub}.${template}.nii.gz \
--streg $SUBJECTS_DIR/$sub/xhemi/surf/lh.${template}.sphere.reg
$SUBJECTS_DIR/${template}/surf/lh.sphere.reg \
--jac


#right to right
mris_apply_reg \
--src $SUBJECTS_DIR/$sub/surf/rh.area \
--trg $concatdir/rh.rh.area.${sub}.${template}.nii.gz \
--streg $SUBJECTS_DIR/$sub/surf/rh.${template}.sphere.reg
$SUBJECTS_DIR/${template}/surf/rh.sphere.reg \
--jac


Attached is the output for one CROSS sub (with fsaverage_sym as template) and 
one LONG (with another symmetrical template) to show that the error is not 
template-specific.


Thank you in advance!


- James




From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 on behalf of James Michael Roe 

Sent: 12 November 2018 10:52
To: Freesurfer support list
Subject: Re: [Freesurfer] mris_apply_reg failing for area/volume

External Email - Use Caution

Hi again Doug

FYI have sent the files as requested

James


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 on behalf of Greve, Douglas N.,Ph.D. 

Sent: 08 November 2018 15:01
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_apply_reg failing for area/volume

Not sure what is going on. Can you send me the input rh.area file as
well as lh.40tvs8ref_sym_20.sphere.reg and
40tvs8ref_sym_20/surf/lh.sphere.reg? You can post them here

https://gate.nmr.mgh.harvard.edu/filedrop2

When it asks you for an email, use 
gr...@nmr.mgh.harvard.edu and not my
email above






On 11/08/2018 08:21 AM, James Michael Roe wrote:


 External Email - Use Caution

Hi Doug

Here is the output file


James Michael Roe
PhD. Candidate
Center for Lifespan Changes in Brain and Cognition
Department of Psychology
University of Oslo
PB 1094 Blindern
0317 Oslo
Mobile: 958 49 437


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 on behalf of Greve, Douglas N.,Ph.D. 

Sent: 07 November 2018 19:02
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_apply_reg failing for area/volume

Can you send the terminal output that includes the error?

On 11/06/2018 06:36 PM, James Michael Roe wrote:


  External Email - Use Caution

Hi Bruce

I realise that my last message made it sound as though the problem was fixed.
However, I was only confirming that the files load fine in freeview (are not 
corrupted) as asked.
The issue of many subs area and volume files failing to register when using 
--jac is still unsolved

Appreciate the support.

Thanks

James


From: James Michael Roe
Sent: 31 October 2018 19:45
To: Freesurfer support list
Subject: Re: [Freesurfer] mris_apply_reg failing for area/volume

Hi Bruce

Can confirm that both files (rh.area & rh.volume) load fine in freeview

Thanks for the help!

James

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 on behalf of Bruce Fischl 

Sent: 29 October 2018 15:43
To: Freesurfer support list
Subject: Re: [Freesurfer] mris_apply_reg failing for area/volume

Hi James

can you verify that the

Re: [Freesurfer] Pial surface error (failing dura removal)

2019-01-07 Thread Rusche, Johann

Hi Douglas,

Thanks for your swift reply. I just shared a link to a Partners Dropbox folder 
with you as our group (lazargp) does not have a folder in /cluster/outgoing.

No T2 or FLAIR unfortunately. Other than MPRAGE T1 we only have fMRI and DTI 
scans.

Thanks,
Johann


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Greve, Douglas N.,Ph.D. 
[dgr...@mgh.harvard.edu]
Sent: Monday, January 07, 2019 11:05 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Pial surface error (failing dura removal)

Do you have a T2 or a FLAIR? Can you upload the subject so we can take a look?

On 1/6/19 6:20 PM, Rusche, Johann wrote:

Dear Freesurfers,

I have been processing my T1 dataset through the longitudinal pipeline with the 
-3T flag (scanned at Martinos). Unfortunately in 50% of all subjects large 
areas of dura are being included in the pial surface.

Both gcut and adjustment of watershed parameters (down to 5) did not bring 
significant improvements. I understand intensity characteristics are very 
similar for GM and dura. However, I wonder whether you can recommend a more 
elegant solution than painfully recon-editing all brainmasks by hand.

Attached is a screenshot depicting the issue with and without gcut. I am using 
stable v6.0. Thanks for your time!

Best,
Johann

__
Johann Rusche

Graduate Research Student, Lazar Lab
Department of Psychiatry – Neurosciences
Massachusetts General Hospital




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Re: [Freesurfer] Calculating volume using pial files

2019-01-07 Thread Bruce Fischl


Hi Da-Yea

mris_volume can be used to compute the volume of any closed surface.

cheers
Bruce
On Mon, 
7 Jan 2019, Song, Da-Yea wrote:




External Email - Use Caution

Hello,

 

I’m trying to calculate the volume using pial files. Is there a way to
convert ?h.pial files into nii formats? Or is there a command to calculate
the volume?

 

Thank you so much in advance for your help.

 

Best regards,

Da-Yea Song  


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Re: [Freesurfer] Calculating volume using pial files

2019-01-07 Thread Rusche, Johann

Have you tried aparcstats2table?

This command does not convert, but it extracts all the stats which allows you 
to play with the volume and any other stats.

https://surfer.nmr.mgh.harvard.edu/fswiki/aparcstats2table

Johann



From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Song, Da-Yea 
[so...@kennedykrieger.org]
Sent: Monday, January 07, 2019 12:48 PM
To: 'freesurfer@nmr.mgh.harvard.edu'
Subject: [Freesurfer] Calculating volume using pial files


External Email - Use Caution
Hello,

I’m trying to calculate the volume using pial files. Is there a way to convert 
?h.pial files into nii formats? Or is there a command to calculate the volume?

Thank you so much in advance for your help.

Best regards,
Da-Yea Song

Disclaimer:


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Please note that e-mail communication is not encrypted by default. You have the 
right to request further emails be encrypted by notifying the sender. Your 
continued use of e-mail constitutes your acknowledgment of these 
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information is strictly prohibited. If you have received this e-mail in error, 
please immediately notify the sender via telephone or return e-mail.
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[Freesurfer] Calculating volume using pial files

2019-01-07 Thread Song, Da-Yea

External Email - Use Caution

Hello,

I'm trying to calculate the volume using pial files. Is there a way to convert 
?h.pial files into nii formats? Or is there a command to calculate the volume?

Thank you so much in advance for your help.

Best regards,
Da-Yea Song

--
Disclaimer:


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Please note that e-mail communication is not encrypted by default. You have the 
right to request further emails be encrypted by notifying the sender. Your 
continued use of e-mail constitutes your acknowledgment of these 
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recipient, be advised that any unauthorized use, disclosure, copying, 
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information is strictly prohibited. If you have received this e-mail in error, 
please immediately notify the sender via telephone or return e-mail.
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Re: [Freesurfer] (no subject)

2019-01-07 Thread Larissa Bechtle

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Hi Ruopeng,

Thank you very much for your quick answer and advice. So I am going to update 
freeview! 
Thanks! 
Larissa

Gesendet mit der WEB.DE Mail App

Am 07.01.19 um 17:35 schrieb Ruopeng Wang

> Hi Larissa,
> 
> The latest development version of freeview supports drawing labels on 
> surface. You can take a look here on how to update freeview:
> 
> https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview
> 
> In the latest version, you can draw paths on surface and use custom fill 
> to create/edit labels, just like in tksurfer.
> 
> Best,
> Ruopeng
> 
> On 1/7/19 11:22 AM, Larissa Bechtle wrote:
> >  External Email - Use Caution
> >
> > Hi everybody,
> >   
> > after finishing my group analysis I am currently trying to run a ROI 
> > analysis.
> > However I have some problems/general questions.
> > I am trying to draw a ROI on fsaverage in order to use the mri_label2label 
> > command afterwards.
> > I opened Freeview, clicked on "load surface" first and then chose 
> > lh.inflated_avg  (fsaverage -> surf) which worked fine but  I cant choose 
> > "New ROI" (in order to crate the ROI).
> >   
> > So is it possible to draw a ROI when focussing only on the surface? And if 
> > this is the case why cant I? Did I chose the wrong file?
> > I am really thankful for any help!!
> >   
> > Larissa
> >   
> >
> > ___
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> > Freesurfer@nmr.mgh.harvard.edu
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> >
> >
> ___
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Re: [Freesurfer] mris_apply_reg failing for area/volume

2019-01-07 Thread Greve, Douglas N.,Ph.D.

What is $SUBJECTS_DIR/${template}/surf/lh.sphere.reg ? If template is not 
fsaverage_sym, can you send this file to me too?


On 1/7/19 5:21 AM, James Michael Roe wrote:

External Email - Use Caution

Dear freesurfer experts

I am still unable to register RH area and volume files to the LH of a 
symmetrical template for a number of longitudinally processed subs. This is 
only the case when using the --jac flag (all run fine without).
There appears to be quite good correspondence (although not perfect) between 
whether the LONG sub fails and whether the BASE of that sub fails with the same 
error. Some CROSS subs also fail, though there appears to be little 
correspondence.

I would greatly appreciate any help you can give me.

To recap, the command I am running is:

#right to left
mris_apply_reg \
--src $SUBJECTS_DIR/$sub/surf/rh.area \
--trg $concatdir/rh.lh.area.${sub}.${template}.nii.gz \
--streg $SUBJECTS_DIR/$sub/xhemi/surf/lh.${template}.sphere.reg
$SUBJECTS_DIR/${template}/surf/lh.sphere.reg \
--jac


#right to right
mris_apply_reg \
--src $SUBJECTS_DIR/$sub/surf/rh.area \
--trg $concatdir/rh.rh.area.${sub}.${template}.nii.gz \
--streg $SUBJECTS_DIR/$sub/surf/rh.${template}.sphere.reg
$SUBJECTS_DIR/${template}/surf/rh.sphere.reg \
--jac


Attached is the output for one CROSS sub (with fsaverage_sym as template) and 
one LONG (with another symmetrical template) to show that the error is not 
template-specific.


Thank you in advance!


- James




From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 on behalf of James Michael Roe 

Sent: 12 November 2018 10:52
To: Freesurfer support list
Subject: Re: [Freesurfer] mris_apply_reg failing for area/volume

External Email - Use Caution

Hi again Doug

FYI have sent the files as requested

James


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 on behalf of Greve, Douglas N.,Ph.D. 

Sent: 08 November 2018 15:01
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_apply_reg failing for area/volume

Not sure what is going on. Can you send me the input rh.area file as
well as lh.40tvs8ref_sym_20.sphere.reg and
40tvs8ref_sym_20/surf/lh.sphere.reg? You can post them here

https://gate.nmr.mgh.harvard.edu/filedrop2

When it asks you for an email, use 
gr...@nmr.mgh.harvard.edu and not my
email above






On 11/08/2018 08:21 AM, James Michael Roe wrote:


 External Email - Use Caution

Hi Doug

Here is the output file


James Michael Roe
PhD. Candidate
Center for Lifespan Changes in Brain and Cognition
Department of Psychology
University of Oslo
PB 1094 Blindern
0317 Oslo
Mobile: 958 49 437


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 on behalf of Greve, Douglas N.,Ph.D. 

Sent: 07 November 2018 19:02
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_apply_reg failing for area/volume

Can you send the terminal output that includes the error?

On 11/06/2018 06:36 PM, James Michael Roe wrote:


  External Email - Use Caution

Hi Bruce

I realise that my last message made it sound as though the problem was fixed.
However, I was only confirming that the files load fine in freeview (are not 
corrupted) as asked.
The issue of many subs area and volume files failing to register when using 
--jac is still unsolved

Appreciate the support.

Thanks

James


From: James Michael Roe
Sent: 31 October 2018 19:45
To: Freesurfer support list
Subject: Re: [Freesurfer] mris_apply_reg failing for area/volume

Hi Bruce

Can confirm that both files (rh.area & rh.volume) load fine in freeview

Thanks for the help!

James

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 on behalf of Bruce Fischl 

Sent: 29 October 2018 15:43
To: Freesurfer support list
Subject: Re: [Freesurfer] mris_apply_reg failing for area/volume

Hi James

can you verify that the various files (e.g.
/cluster/projects/p23/projects/Memory_Project/James/AgeSym/long_recons_FXhemi/010_NDev/1000409_02_10_02_11.long.base_1000409_11/surf/rh.area)

are intact by loading them into freeview? For the area file you will of
course have to load it as an overlay not as a surface (since it isn't a
surface)

cheers
Bruce
On Mon, 29 Oct 2018, James Michael Roe

Re: [Freesurfer] (no subject)

2019-01-07 Thread Ruopeng Wang

Hi Larissa,

The latest development version of freeview supports drawing labels on 
surface. You can take a look here on how to update freeview:

https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview

In the latest version, you can draw paths on surface and use custom fill 
to create/edit labels, just like in tksurfer.

Best,
Ruopeng

On 1/7/19 11:22 AM, Larissa Bechtle wrote:
>  External Email - Use Caution
>
> Hi everybody,
>   
> after finishing my group analysis I am currently trying to run a ROI analysis.
> However I have some problems/general questions.
> I am trying to draw a ROI on fsaverage in order to use the mri_label2label 
> command afterwards.
> I opened Freeview, clicked on "load surface" first and then chose 
> lh.inflated_avg  (fsaverage -> surf) which worked fine but  I cant choose 
> "New ROI" (in order to crate the ROI).
>   
> So is it possible to draw a ROI when focussing only on the surface? And if 
> this is the case why cant I? Did I chose the wrong file?
> I am really thankful for any help!!
>   
> Larissa
>   
>
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Re: [Freesurfer] [PETSurfer] Intensity normalization of PET images without PVE correction

2019-01-07 Thread Greve, Douglas N.,Ph.D.



On 1/7/19 11:18 AM, Matthieu Vanhoutte wrote:

External Email - Use Caution

I used the following command to obtain only rescaled voxel-wise PET image (with 
no PVC):
mri_gtmpvc --i PET.nii.gz --reg Pet2T1.register.dof6.lta --psf 0 --no-tfe --seg 
gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --rbv --o  nopvc

If I omitted --rbv or --mgx option I didn't get the rescaled voxel-wise PET 
image (without PVC). Could I obtain the rescaled voxel-wise PET image (without 
PVC) just by dividing each voxel of the native PET image by the mean of the 
reference region ?
Yes

Best,
Matt

Le lun. 7 janv. 2019 à 16:01, Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> a écrit :
I'm not sure what you mean. If you are turning off PVC, why are you computing 
RBV and MGX? What is your command line? What do you mean that these options 
don't seem to work?

On 12/21/18 2:22 PM, Matthieu Vanhoutte wrote:

External Email - Use Caution

Hi Douglas,

Thanks for helping.

To have an only rescaled voxel-wise PET image, these options seem to work only 
when -rbv method is used and not -mgx.

Do you know why ?

Best,
Matthieu


Le mar. 18 déc. 2018 à 17:58, Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> a écrit :
You will need to set --psf 0 and --no-tfe to fully turn off PVC.

On 12/18/18 4:50 AM, Matthieu Vanhoutte wrote:

External Email - Use Caution

Hi Douglas,

Could you help me on this point ?

Best,
Matthieu


Le mer. 12 déc. 2018 à 10:50, Matthieu Vanhoutte 
mailto:matthieuvanhou...@gmail.com>> a écrit :
Dear Douglas,

Is it possible to use mri_gtmpvc command in order to intensity normalize PET 
images without applying PVE correction by setting --psf to 0 ?

Best,
Matthieu



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Re: [Freesurfer] [PETSurfer] Intensity normalization of PET images without PVE correction

2019-01-07 Thread Matthieu Vanhoutte

External Email - Use Caution

I used the following command to obtain only rescaled voxel-wise PET image
(with no PVC):
*mri_gtmpvc --i PET.nii.gz --reg Pet2T1.register.dof6.lta --psf 0 --no-tfe
--seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --rbv --o  nopvc*

If I omitted *--rbv *or* --mgx* option I didn't get the rescaled voxel-wise
PET image (without PVC). Could I obtain the rescaled voxel-wise PET image
(without PVC) just by dividing each voxel of the native PET image by the
mean of the reference region ?

Best,
Matt

Le lun. 7 janv. 2019 à 16:01, Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> a écrit :

> I'm not sure what you mean. If you are turning off PVC, why are you
> computing RBV and MGX? What is your command line? What do you mean that
> these options don't seem to work?
>
> On 12/21/18 2:22 PM, Matthieu Vanhoutte wrote:
>
> External Email - Use Caution
> Hi Douglas,
>
> Thanks for helping.
>
> To have an only rescaled voxel-wise PET image, these options seem to work
> only when -rbv method is used and not -mgx.
>
> Do you know why ?
>
> Best,
> Matthieu
>
>
> Le mar. 18 déc. 2018 à 17:58, Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> a écrit :
>
>> You will need to set --psf 0 and --no-tfe to fully turn off PVC.
>>
>> On 12/18/18 4:50 AM, Matthieu Vanhoutte wrote:
>>
>> External Email - Use Caution
>> Hi Douglas,
>>
>> Could you help me on this point ?
>>
>> Best,
>> Matthieu
>>
>>
>> Le mer. 12 déc. 2018 à 10:50, Matthieu Vanhoutte <
>> matthieuvanhou...@gmail.com> a écrit :
>>
>>> Dear Douglas,
>>>
>>> Is it possible to use mri_gtmpvc command in order to intensity normalize
>>> PET images without applying PVE correction by setting --psf to 0 ?
>>>
>>> Best,
>>> Matthieu
>>>
>>
>>
>> ___
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>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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[Freesurfer] (no subject)

2019-01-07 Thread Larissa Bechtle

External Email - Use Caution

Hi everybody,
 
after finishing my group analysis I am currently trying to run a ROI analysis.
However I have some problems/general questions.
I am trying to draw a ROI on fsaverage in order to use the mri_label2label 
command afterwards.
I opened Freeview, clicked on "load surface" first and then chose 
lh.inflated_avg  (fsaverage -> surf) which worked fine but  I cant choose "New 
ROI" (in order to crate the ROI).
 
So is it possible to draw a ROI when focussing only on the surface? And if this 
is the case why cant I? Did I chose the wrong file?
I am really thankful for any help!!
 
Larissa
 

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Re: [Freesurfer] [PETsurfer] Use of MGX and RBV partial volume correction

2019-01-07 Thread Greve, Douglas N.,Ph.D.


For MGX, the field of view is reduced to reduce computation and space usage; 
this requires a new registration matrix. For RBV, the voxel size is changed in 
addition. In both cases, a new registration is computed from the input 
registration


On 12/21/18 2:29 PM, Matthieu Vanhoutte wrote:

External Email - Use Caution

Hi Douglas,

Thanks for these clarifications. I have however one misunderstanding.

When sampling PVC corrected PET image onto surface:
- I use bbpet2anat.lta when MGX was used as specified un tutorial
- I use rbv2anat.lta when RBV was used

But why not to use template.reg.lta computed by mri_coreg ? What are the 
differences between those different files ?

Best,
Matthieu

Le mar. 18 déc. 2018 à 18:13, Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> a écrit :


On 12/7/18 9:29 AM, Matthieu Vanhoutte wrote:
>  External Email - Use Caution
>
> Hi Douglas,
>
> Thanks for these clarifications. I added some others questions inline below.
>
> Best,
> Matthieu
>
>> Le 6 déc. 2018 à 17:25, Greve, Douglas N.,Ph.D. 
>> mailto:dgr...@mgh.harvard.edu>> a écrit :
>>
>>
>>
>> On 11/30/2018 07:15 AM, Matthieu Vanhoutte wrote:
>>>  External Email - Use Caution
>>>
>>> Hi Douglas,
>>>
>>> Thank you for answering. Please find below new questions.
>>> Bien cordialement,
>>>
>>>
>>> Le ven. 30 nov. 2018 à 00:00, Greve, Douglas N.,Ph.D.
>>> mailto:dgr...@mgh.harvard.edu> 
>>> >> a écrit :
>>>
>>> Hi Matthieu, sorry for the delay
>>>
>>> On 11/29/2018 12:50 PM, Matthieu Vanhoutte wrote:
External Email - Use Caution

 Dear Freesurfer's experts,

 I tried to use PETSurfer to correct partial volume effect on my
>>> FDG PET images, testing both Muller-Gartner and RBV corrections.
 I ran the commands specified in PETSurfer website and used the
>>> two following commands for both MGX and RBV corrections respectively:
 mri_gtmpvc --i PET.nii.gz --reg register.dof6.lta --psf-col 5.51
>>> --psf-row 5.51 --psf-slice 5.9 --seg gtmseg.mgz
>>> --default-seg-merge --auto-mask PSF .01 --mgx .01 --o ./gtmpvc.output
 mri_gtmpvc --i PET.nii.gz --reg register.dof6.lta --psf-col 5.51
>>> --psf-row 5.51 --psf-slice 5.9 --seg gtmseg.mgz
>>> --default-seg-merge --auto-mask PSF .01 --rbv --o rbv.output.orig
 1) However, I found that cortical output mgx.ctxgm.nii.gz of MGX
>>> correction encompass more than just GM and values at the
>>> boundaries of mgx.ctxgm.nii.gz seem to me very high or aberrant.
>>> This is expected. The MG method gives you a value every place that
>>> there
>>> is GM signal *in the PET volume after partial volume effects*. So
>>> basically, if you were to take the cortical ribbon and smooth it
>>> by your
>>> PSF, every non-zero voxel has some GM in it (which is why the
>>> edges are
>>> so high). When you run it with --mgx .01, it will exclude voxels that
>>> have less than 1% GM after smoothing. If you you are disturbed by the
>>> wide ribbon, just make the threshold higher. In theory, every point
>>> along the surface normal gives you a valid answer, but the further
>>> from
>>> the center of the ribbon, the noisier it is going to be, so we
>>> generally
>>> only sample it at the center (--projfrac 0.5 to mri_vol2surf).
>>>
>>>
>>> Basically, please find below the mgx.ctxgm with threshold set at 0.01:
>>> image.png
>>>
>>> Then threshold set at 0.1:
>>> image.png
>>>
>>> Values at some parts of the cortex (olfactory, visual) are not the
>>> same between the two thresholds. In the first one in these parts of
>>> the brain, values are higher than the second and seem kind of
>>> aberrant. Is there no reason to prefer a threshold at 0.1 than 0.01 ?
>>> For example, in (Douglas et al., 2016, NeuroImage) a threshold of 0.3
>>> has been found to be optimal: how determine visually or quantitatively
>>> this optimal threshold ?
>> So when you click on the same voxel in both images, you get different
>> values? Or is it just that the color scale is changing? The threshold
>> should not change the values, just what is in or out of the final mask.
>> The threshold of 0.3 was chosen mainly because it worked for the ROI
>> analysis. In general, you should use GTM instead of MG for ROI analysis.
>> For surface-based analysis, the threshold is not critical because the GM
>> PVF is generally pretty high in cortex. It will make more of a
>> difference in subcortical analysis.
> Yes, thresholding at 0.01 and 0.1 gave me different values in the same voxel 
> in both images. Whereas when thresholding between 0.1 and 0.3 gave me same 
> values. What could it be due to ?
I don't know. Are the differences widespread or just a voxel near the edge?
>
> GTM is always computed in the *.stat file whatever the method specified in 
> mri_gtmpvc command ?
Yes, the GTM is the basis for all the methods.

Re: [Freesurfer] Pial surface error (failing dura removal)

2019-01-07 Thread Greve, Douglas N.,Ph.D.

Do you have a T2 or a FLAIR? Can you upload the subject so we can take a look?

On 1/6/19 6:20 PM, Rusche, Johann wrote:

Dear Freesurfers,

I have been processing my T1 dataset through the longitudinal pipeline with the 
-3T flag (scanned at Martinos). Unfortunately in 50% of all subjects large 
areas of dura are being included in the pial surface.

Both gcut and adjustment of watershed parameters (down to 5) did not bring 
significant improvements. I understand intensity characteristics are very 
similar for GM and dura. However, I wonder whether you can recommend a more 
elegant solution than painfully recon-editing all brainmasks by hand.

Attached is a screenshot depicting the issue with and without gcut. I am using 
stable v6.0. Thanks for your time!

Best,
Johann

__
Johann Rusche

Graduate Research Student, Lazar Lab
Department of Psychiatry – Neurosciences
Massachusetts General Hospital




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Re: [Freesurfer] Robust PET signal projection

2019-01-07 Thread Greve, Douglas N.,Ph.D.

No. You can use mri_concat with --mtx option, where the argument to --mtx is an 
asci matrix that is square and diagonal with the weighting factors on the 
diagonal. You could also use mri_glmfix with the --X option, where X is an 
ascii column matrix of weighting factors (make sure that the the sum.^2 = 1)

On 12/21/18 2:31 PM, Matthieu Vanhoutte wrote:

External Email - Use Caution

Thanks Douglas.

Is there a way to compute a weighted average in one command with fscalc ?

Best,
Matthieu


Le mar. 18 déc. 2018 à 18:03, Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> a écrit :
you can use mri_vol2surf to sample at different depths. If you want a simple 
average across cortex, then you can use --projfrac-avg .35 .65 .05
If you want to do more sophisticated weighting, then you will have to sample at 
each layer and then combine the files (eg, fscalc). Unless you have very small 
voxels, it probably will not make a difference.

On 12/18/18 4:50 AM, Matthieu Vanhoutte wrote:

External Email - Use Caution

Dear experts,

Is there any advice on this point ?

Best,
Matthieu


Le mer. 12 déc. 2018 à 10:47, Matthieu Vanhoutte 
mailto:matthieuvanhou...@gmail.com>> a écrit :
Dear Freesurfer's experts,

In order to have a robust PET signal projection, is it possible compute the 
projected PET signal as a weighted average of the PET signal intersecting with 
the surfaces ranging from 35 to 65% of the cortical tickness with a step t=5% ?

More weight would be given to the surfaces located near the mid distance 
between the pial and white surfaces as they have a higher probability to be 
well located within the cortex (using a normal distribution for example).

Thank you for helping.

Best,
Matthieu



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Re: [Freesurfer] [PETSurfer] Intensity normalization of PET images without PVE correction

2019-01-07 Thread Greve, Douglas N.,Ph.D.

I'm not sure what you mean. If you are turning off PVC, why are you computing 
RBV and MGX? What is your command line? What do you mean that these options 
don't seem to work?

On 12/21/18 2:22 PM, Matthieu Vanhoutte wrote:

External Email - Use Caution

Hi Douglas,

Thanks for helping.

To have an only rescaled voxel-wise PET image, these options seem to work only 
when -rbv method is used and not -mgx.

Do you know why ?

Best,
Matthieu


Le mar. 18 déc. 2018 à 17:58, Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> a écrit :
You will need to set --psf 0 and --no-tfe to fully turn off PVC.

On 12/18/18 4:50 AM, Matthieu Vanhoutte wrote:

External Email - Use Caution

Hi Douglas,

Could you help me on this point ?

Best,
Matthieu


Le mer. 12 déc. 2018 à 10:50, Matthieu Vanhoutte 
mailto:matthieuvanhou...@gmail.com>> a écrit :
Dear Douglas,

Is it possible to use mri_gtmpvc command in order to intensity normalize PET 
images without applying PVE correction by setting --psf to 0 ?

Best,
Matthieu



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Re: [Freesurfer] Longitudinal Hippocampal Subfields - error during segmentation {Disarmed}

2019-01-07 Thread Rachel Phillips

External Email - Use Caution

Version 6.0


Thanks,

Rachel


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Iglesias Gonzalez, 
Eugenio 
Sent: Monday, January 7, 2019 2:50:57 AM
To: freesurfer@nmr.mgh.harvard.edu; Freesurfer support list
Cc: Courtney Haswell
Subject: Re: [Freesurfer] Longitudinal Hippocampal Subfields - error during 
segmentation {Disarmed}


External Email - Use Caution

Hi Rachel
This is very weird. What exact version are you using? 6.0 or dev?
Cheers
Eugenio

Juan Eugenio Iglesias

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

Research staff
Martinos Center for Biomedical Imaging
Massachusetts General Hospital and Harvard Medical School

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


MailScanner has detected a possible fraud attempt from " 
www.jeiglesias.com




From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Rachel Phillips 

Sent: Friday, January 4, 2019 7:43:45 PM
To: freesurfer@nmr.mgh.harvard.edu
Cc: Courtney Haswell
Subject: [Freesurfer] Longitudinal Hippocampal Subfields - error during 
segmentation


External Email - Use Caution

Hello,


I have run a longitudinal sample (up to 4 timepoints per subject) through the 
Freesurfer 6.0 longitudinal processing pipeline, and currently I am attempting 
to produce the longitudinal hippocampal subfield segmentation with the 
following command: longHippoSubfieldsT1.sh  [SubjectsDirectory]. I am 
receiving the following error: "Error using SegmentSubfeldsT1Longitudinal (line 
441) The vector of prior probabilities in the mesh nodes must always sum to one 
over all classes".


Below is an example of the output that precedes this error:


[> In SegmentSubfieldsT1Longitudinal at 418]
Reading contexts of file 
/usr/local/packages/freesurfer_v6.0.0/average/HippoSF/atlas/compressionLookupTable.txt
--
Making Lateral-nucleus map to reduced label 1
Making Paralaminar-nucleus map to reduced label 1
Making Basal-nucleus map to reduced label 1
Making Accessory-Basal-nucleus map to reduced label 1
Making Corticoamygdaloid-transitio map to reduced label 1
Making Central-nucleus map to reduced label 1
Making Cortical-nucleus map to reduced label 1
Making Medial-nucleus map to reduced label 1
Making Anterior-amygdaloid-area-AAA map to reduced label 1
--
Making alveus map to reduced label 2
Making Hippocampal_tail map to reduced label 2
Making HATA map to reduced label 2
Making fimbria map to reduced label 2
Making parasubiculum map to reduced label 2
Making hippocampal-fissure map to reduced label 2
--
Making Left-Cerebral-Cortex map to reduced label 3
--
Making Left-Cerebral-White-Matter map to reduced label 4
--
Making Left-Lateral-Ventricle map to reduced label 5
--
Making Left-choroid-plexus map to reduced label 6
--
Making Unknown map to reduced label 7
--
Making Left-VentralDC map to reduced label 8
--
Making Left-Putamen map to reduced label 9
--
Making Left-Pallidum map to reduced label 10
--
Making Left-Thalamus-Proper map to reduced label 11
--
Making Left-Accumbens-area map to reduced label 12
--
Making Left-Caudate map to reduced label 13
Error using SegmentSubfieldsT1Longitudinal (line 441)
The vector of prior probabilities in the mesh nodes must always sum to one over 
all classes

Any guidance on this error would be greatly appreciated.

Thanks,
Rachel
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Re: [Freesurfer] mris_apply_reg failing for area/volume

2019-01-07 Thread James Michael Roe

External Email - Use Caution

Dear freesurfer experts

I am still unable to register RH area and volume files to the LH of a 
symmetrical template for a number of longitudinally processed subs. This is 
only the case when using the --jac flag (all run fine without). 
There appears to be quite good correspondence (although not perfect) between 
whether the LONG sub fails and whether the BASE of that sub fails with the same 
error. Some CROSS subs also fail, though there appears to be little 
correspondence.

I would greatly appreciate any help you can give me.

To recap, the command I am running is:

#right to left
mris_apply_reg \
--src $SUBJECTS_DIR/$sub/surf/rh.area \
--trg $concatdir/rh.lh.area.${sub}.${template}.nii.gz \
--streg $SUBJECTS_DIR/$sub/xhemi/surf/lh.${template}.sphere.reg
$SUBJECTS_DIR/${template}/surf/lh.sphere.reg \
--jac


#right to right
mris_apply_reg \
--src $SUBJECTS_DIR/$sub/surf/rh.area \
--trg $concatdir/rh.rh.area.${sub}.${template}.nii.gz \
--streg $SUBJECTS_DIR/$sub/surf/rh.${template}.sphere.reg
$SUBJECTS_DIR/${template}/surf/rh.sphere.reg \
--jac


Attached is the output for one CROSS sub (with fsaverage_sym as template) and 
one LONG (with another symmetrical template) to show that the error is not 
template-specific.


Thank you in advance!


- James




From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of James Michael Roe 

Sent: 12 November 2018 10:52
To: Freesurfer support list
Subject: Re: [Freesurfer] mris_apply_reg failing for area/volume

External Email - Use Caution

Hi again Doug

FYI have sent the files as requested

James


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Greve, Douglas N.,Ph.D. 

Sent: 08 November 2018 15:01
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_apply_reg failing for area/volume

Not sure what is going on. Can you send me the input rh.area file as
well as lh.40tvs8ref_sym_20.sphere.reg and
40tvs8ref_sym_20/surf/lh.sphere.reg? You can post them here

https://gate.nmr.mgh.harvard.edu/filedrop2

When it asks you for an email, use gr...@nmr.mgh.harvard.edu and not my
email above






On 11/08/2018 08:21 AM, James Michael Roe wrote:
>  External Email - Use Caution
>
> Hi Doug
>
> Here is the output file
>
>
> James Michael Roe
> PhD. Candidate
> Center for Lifespan Changes in Brain and Cognition
> Department of Psychology
> University of Oslo
> PB 1094 Blindern
> 0317 Oslo
> Mobile: 958 49 437
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Greve, Douglas N.,Ph.D. 
> 
> Sent: 07 November 2018 19:02
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mris_apply_reg failing for area/volume
>
> Can you send the terminal output that includes the error?
>
> On 11/06/2018 06:36 PM, James Michael Roe wrote:
>>   External Email - Use Caution
>>
>> Hi Bruce
>>
>> I realise that my last message made it sound as though the problem was fixed.
>> However, I was only confirming that the files load fine in freeview (are not 
>> corrupted) as asked.
>> The issue of many subs area and volume files failing to register when using 
>> --jac is still unsolved
>>
>> Appreciate the support.
>>
>> Thanks
>>
>> James
>>
>> 
>> From: James Michael Roe
>> Sent: 31 October 2018 19:45
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] mris_apply_reg failing for area/volume
>>
>> Hi Bruce
>>
>> Can confirm that both files (rh.area & rh.volume) load fine in freeview
>>
>> Thanks for the help!
>>
>> James
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>  on behalf of Bruce Fischl 
>> 
>> Sent: 29 October 2018 15:43
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] mris_apply_reg failing for area/volume
>>
>> Hi James
>>
>> can you verify that the various files (e.g.
>> /cluster/projects/p23/projects/Memory_Project/James/AgeSym/long_recons_FXhemi/010_NDev/1000409_02_10_02_11.long.base_1000409_11/surf/rh.area)
>>
>> are intact by loading them into freeview? For the area file you will of
>> course have to load it as an overlay not as a surface (since it isn't a
>> surface)
>>
>> cheers
>> Bruce
>> On Mon, 29 Oct 2018, James Michael Roe wrote:
>>
>>>   External Email - Use Caution
>>>
>>>
>>> Dear freesurfer experts
>>>
>>>
>>>
>>> I’m running the following commands to register RH area and volume files per 
>>> sub to both hemispheres
>>> of a symmetrical template following Xhemi routines.
>>>
>>> The commands have already worked for many subs, but are failing to write 
>>> the target file for a
>>> number of others (and all run fine without the –-jac flag)
>>>
>>>
>>> #right to left
>>>
>>> mris_apply_reg \
>>>
>>> --src $SUBJECTS_DIR/$sub/surf/rh.area \
>>>
>>> --trg $concatdir/rh.lh.area.${sub}.${template}.nii.gz \
>>>
>>>

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