[Freesurfer] wm and ctx labels - mri_aparc2aseg
Hi FreeSurfer expert, after that I have used the command "recon-all" I would like to obtain wm-lh and wm-rh information ( for example wm-lh-bankssts,wm-lh-caudalanteriorcingulate,wm-lh-caudalmiddlefrontal, ...). I have read that mri_aparc2aseg command can help me, but when I use it I have two problems: 1) When I use the command mri_aparc2aseg --s subject I obtain as output the image "aparc+aseg.mgz" which contains information only about cortical label. 2) When I use the commandmri_aparc2aseg --s subject --a.2005 I get the following message: ERROR: Option --a2005 unknown Can you help me? Moreover, the recon-all output in directory /mri is: aparc.a2009s+aseg.mgz, aparc+aseg.mgz,aseg.auto.mgz, aseg.auto_noCCseg.label_intensities.txt , aseg.auto_noCCseg.mgz aseg.mgz, brain.finalsurfs.mgz, brainmask.auto.mgz, brainmask.mgz, brain.mgz,ctrl_pts.mgz, filled.mgz,lh.ribbon.mgz, mri_nu_correct.mni.log,norm.mgz,nu.mgz,nu_noneck.mgz,orig, orig.mgz, rawavg.mgz, rh.ribbon.mgz,ribbon.mgz, segment.dat , T1.mgz,talairach.label_intensities.txt , talairach.log, talairach_with_skull.log, transforms, wm.asegedit.mgz, wm.mgz,wmparc.mgz , wm.seg.mgz Do you think that the searched information is here? Thanks for your help. Best regards, Andrea ___ 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] R: Re: R: Re: R: Re: Problem of size
Hi FreeSurfer expert, after that I have used the command "recon-all" I would like to obtain wm-lh and wm-rh information ( for example wm-lh-bankssts,wm-lh-caudalanteriorcingulate,wm-lh-caudalmiddlefrontal, ...). I have read that mri_aparc2aseg command can help me, but when I use it I have two problems: 1) When I use the command mri_aparc2aseg --s subject I obtain as output the image "aparc+aseg.mgz" which contains information only about cortical label. 2) When I use the commandmri_aparc2aseg --s subject --a.2005 I get the following message: ERROR: Option --a2005 unknown Can you help me? Moreover, the recon-all output in directory /mri is: aparc.a2009s+aseg.mgz, aparc+aseg.mgz,aseg.auto.mgz, aseg.auto_noCCseg.label_intensities.txt , aseg.auto_noCCseg.mgz aseg.mgz, brain.finalsurfs.mgz, brainmask.auto.mgz, brainmask.mgz, brain.mgz,ctrl_pts.mgz, filled.mgz,lh.ribbon.mgz, mri_nu_correct.mni.log,norm.mgz,nu.mgz,nu_noneck.mgz,orig, orig.mgz, rawavg.mgz, rh.ribbon.mgz,ribbon.mgz, segment.dat , T1.mgz,talairach.label_intensities.txt , talairach.log, talairach_with_skull.log, transforms, wm.asegedit.mgz, wm.mgz,wmparc.mgz , wm.seg.mgz Do you think that the searched information is here? Thanks for your help. Best regards, Andrea ___ 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] R: Re: R: Re: R: Re: Problem of size
Endless thanks. I'll try and update you. Andrea Messaggio originale Da: fis...@nmr.mgh.harvard.edu Data: 9-apr-2014 17.16 A: "Andrea Tateo" Cc: "Freesurfer support list" Ogg: Re: R: Re: R: Re: [Freesurfer] Problem of size on the recon-all command line On Wed, 9 Apr 2014, Andrea Tateo wrote: > I use > « recon-all -debug -s 001 -autorecon-all» > > > and after > > « mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o 001_rawavg.mgz > --regheader aseg.mgz » > > Where can I specify"-cw256" ? > > > > Messaggio originale > Da: fis...@nmr.mgh.harvard.edu > Data: 9-apr-2014 16.56 > A: "Andrea Tateo" > Cc: "Freesurfer support list" > Ogg: Re: R: Re: [Freesurfer] Problem of size > > Hi Andrea > > will it fit in 256? You can try specifying -cw256 > > cheers > Bruce > > > On Wed, 9 Apr 2014, Andrea Tateo wrote: > > > > > Hi Bruce, > > > > thanks for the quick response. > > > > I report the full error message: > > > > > >WARNING==== > === > > == > > The physical sizes are (256.00 mm, 256.00 mm, 312.00 mm), which cannot fit > > in 256^3 mm^3 volume. > > The resulting volume will have 312 slices. > > If you find problems, please let us know (freesurfer@nmr.mgh.harvard.edu). > >=== > > > == > > > > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ > > readingfrom/lustre/home/tateo/Simulazione_FREESURF_GRID_2/Segmentazione/SUB_1006_3 > /001 > > /mri/rawavg.mgz... > > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > > i_ras = (-1, 0, -0) > > j_ras = (0, 0, -1) > > k_ras = (-0, 1, -0) > > Original Data has (1, 1, 1) mm size and (256, 256, 312) voxels. > > Data is conformed to 1 mm size and 312 voxels for all directions > > changing data type from float to uchar (noscale = 0)... > > MRIchangeType: Building histogram > > Reslicing using trilinear interpolation > > writingto/lustre/home/tateo/Simulazione_FREESURF_GRID_2/Segmentazione/SUB_1006_3/0 > 01 > > /mri/orig.mgz... > > > > > > ERROR! FOV=312.000 > 256 > > Include the flag -cw256 with recon-all! > > > > > > Thank you very much > > > > Andrea > > > > > > > > > > > > > > Messaggio originale > > Da: fis...@nmr.mgh.harvard.edu > > Data: 9-apr-2014 14.45 > > A: "Andrea Tateo", "Freesurfer support > > list" > > Ogg: Re: [Freesurfer] Problem of size > > > > Hi Andrea > > > > what size are your voxels? Do you really need an FOV that big? If not, > > you could extract the central 256mm using mri_extract. And I believe this > > is just a warning - does recon-all complete? > > > > cheers > > Bruce > > > > > > > > On Wed, 9 Apr 2014, > > Andrea Tateo wrote: > > > > > > > > Hi FreeSurfer expert, > > > > > > I have a problem with command "recon-all". > > > > > > In recon-all.log I can read: > > > > > > «The physical sizes are (256.00 mm, 256.00 mm, 312.00 mm), which cannot > > fit > > > in 256^3 mm^3 volume. > > > > > > The resulting volume will have 312 slices. > > > > > > If you find problems, please let us know > > (freesurfer@nmr.mgh.harvard.edu).» > > > > > > I hope are there anyone to help me. > > > > > > Thank for your help. > > > > > > Andrea > > > > > > > > > > > > > > > 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 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] R: Re: R: Re: Problem of size
I use « recon-all -debug -s 001 -autorecon-all» and after « mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o 001_rawavg.mgz --regheader aseg.mgz » Where can I specify"-cw256" ? Messaggio originale Da: fis...@nmr.mgh.harvard.edu Data: 9-apr-2014 16.56 A: "Andrea Tateo" Cc: "Freesurfer support list" Ogg: Re: R: Re: [Freesurfer] Problem of size Hi Andrea will it fit in 256? You can try specifying -cw256 cheers Bruce On Wed, 9 Apr 2014, Andrea Tateo wrote: > > Hi Bruce, > > thanks for the quick response. > > I report the full error message: > > > WARNING=== > == > The physical sizes are (256.00 mm, 256.00 mm, 312.00 mm), which cannot fit > in 256^3 mm^3 volume. > The resulting volume will have 312 slices. > If you find problems, please let us know (freesurfer@nmr.mgh.harvard.edu). > === > == > > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ > reading > from/lustre/home/tateo/Simulazione_FREESURF_GRID_2/Segmentazione/SUB_1006_3/001 > /mri/rawavg.mgz... > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-1, 0, -0) > j_ras = (0, 0, -1) > k_ras = (-0, 1, -0) > Original Data has (1, 1, 1) mm size and (256, 256, 312) voxels. > Data is conformed to 1 mm size and 312 voxels for all directions > changing data type from float to uchar (noscale = 0)... > MRIchangeType: Building histogram > Reslicing using trilinear interpolation > writing > to/lustre/home/tateo/Simulazione_FREESURF_GRID_2/Segmentazione/SUB_1006_3/001 > /mri/orig.mgz... > > > ERROR! FOV=312.000 > 256 > Include the flag -cw256 with recon-all! > > > Thank you very much > > Andrea > > > > > > > Messaggio originale > Da: fis...@nmr.mgh.harvard.edu > Data: 9-apr-2014 14.45 > A: "Andrea Tateo", "Freesurfer support > list" > Ogg: Re: [Freesurfer] Problem of size > > Hi Andrea > > what size are your voxels? Do you really need an FOV that big? If not, > you could extract the central 256mm using mri_extract. And I believe this > is just a warning - does recon-all complete? > > cheers > Bruce > > > > On Wed, 9 Apr 2014, > Andrea Tateo wrote: > > > > > Hi FreeSurfer expert, > > > > I have a problem with command "recon-all". > > > > In recon-all.log I can read: > > > > «The physical sizes are (256.00 mm, 256.00 mm, 312.00 mm), which cannot > fit > > in 256^3 mm^3 volume. > > > > The resulting volume will have 312 slices. > > > > If you find problems, please let us know > (freesurfer@nmr.mgh.harvard.edu).» > > > > I hope are there anyone to help me. > > > > Thank for your help. > > > > Andrea > > > > > > > > > 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 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] R: Re: Problem of size
Hi Bruce, thanks for the quick response. I report the full error message: WARNING =====The physical sizes are (256.00 mm, 256.00 mm, 312.00 mm), which cannot fit in 256^3 mm^3 volume.The resulting volume will have 312 slices.If you find problems, please let us know (freesurfer@nmr.mgh.harvard.edu).===== $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $reading from /lustre/home/tateo/Simulazione_FREESURF_GRID_2/Segmentazione/SUB_1006_3/001/mri/rawavg.mgz...TR=0.00, TE=0.00, TI=0.00, flip angle=0.00i_ras = (-1, 0, -0)j_ras = (0, 0, -1)k_ras = (-0, 1, -0)Original Data has (1, 1, 1) mm size and (256, 256, 312) voxels.Data is conformed to 1 mm size and 312 voxels for all directionschanging data type from float to uchar (noscale = 0)...MRIchangeType: Building histogramReslicing using trilinear interpolationwriting to /lustre/home/tateo/Simulazione_FREESURF_GRID_2/Segmentazione/SUB_1006_3/001/mri/orig.mgz... ERROR! FOV=312.000 > 256Include the flag -cw256 with recon-all! Thank you very much Andrea Messaggio originale Da: fis...@nmr.mgh.harvard.edu Data: 9-apr-2014 14.45 A: "Andrea Tateo", "Freesurfer support list" Ogg: Re: [Freesurfer] Problem of size Hi Andrea what size are your voxels? Do you really need an FOV that big? If not, you could extract the central 256mm using mri_extract. And I believe this is just a warning - does recon-all complete? cheers Bruce On Wed, 9 Apr 2014, Andrea Tateo wrote: > > Hi FreeSurfer expert, > > I have a problem with command "recon-all". > > In recon-all.log I can read: > > «The physical sizes are (256.00 mm, 256.00 mm, 312.00 mm), which cannot fit > in 256^3 mm^3 volume. > > The resulting volume will have 312 slices. > > If you find problems, please let us know (freesurfer@nmr.mgh.harvard.edu).» > > I hope are there anyone to help me. > > Thank for your help. > > Andrea > > > 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 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] Problem of size
Hi FreeSurfer expert,I have a problem with command "recon-all". In recon-all.log I can read:«The physical sizes are (256.00 mm, 256.00 mm, 312.00 mm), which cannot fit in 256^3 mm^3 volume.The resulting volume will have 312 slices.If you find problems, please let us know (freesurfer@nmr.mgh.harvard.edu).»I hope are there anyone to help me.Thank for your help.Andrea ___ 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] R: Re: R: Re: problem with nu_correct
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Hello Zeke,
I must make a clarification: I use
freesurfer on a PC cluster.
I have submitted the same image several
times and on different machines.
Sometimes it was killed sometimes
not.
If I submit a second time the failed
job it may happen that it is terminated with success.
thank you very much
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Messaggio originale
Da: zkauf...@nmr.mgh.harvard.edu
Data: 24-lug-2013 21.53
A: "Andrea Tateo"
Cc:
Ogg: Re: R: Re: [Freesurfer] problem with nu_correct
Andrea,
Hmmm. I am not able to duplicate this error on my end using local data.
A few things:
1) What happens when you type "nu_evaluate -help"? Do you get help
output or does it crash?
2) Does this error occur for all subjects or just this one used for this
particular recon?
3) Does the brain image look "normal", meaning is there anything
obviously wrong with the input data, which you can see by opening it
with Freeview?
-Zeke
On 07/24/2013 11:22 AM, Andrea Tateo wrote:
> Hello zkaufman,
>
> thanks for your involvement
>
> Andrea
>
>
>
> Messaggio originale
> Da: zkauf...@nmr.mgh.harvard.edu
> Data: 24-lug-2013 16.52
> A: "Andrea Tateo"
> Cc:
> Ogg: Re: [Freesurfer] problem with nu_correct
>
> Hello Andrea,
>
> Can you please attach the entire recon-all.log file? It will be located
> in $SUBJECT_DIR/subject_name/scripts/recon-all.log
>
> -Zeke
>
> On 07/24/2013 09:35 AM, Andrea Tateo wrote:
> > Hi FreeSurfer expert,
> >
> > I have a problem with command "recon-all".
> >
> > In recon-all.log I can to read
> >
> > nu_correct: crashed while running nu_evaluate (termination status=9)
> >
> > Thank for your help
> >
> >
> > ___
> > 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
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] R: Re: problem with nu_correct
Hello zkaufman, thanks for your involvement Andrea Messaggio originale Da: zkauf...@nmr.mgh.harvard.edu Data: 24-lug-2013 16.52 A: "Andrea Tateo" Cc: Ogg: Re: [Freesurfer] problem with nu_correct Hello Andrea, Can you please attach the entire recon-all.log file? It will be located in $SUBJECT_DIR/subject_name/scripts/recon-all.log -Zeke On 07/24/2013 09:35 AM, Andrea Tateo wrote: > Hi FreeSurfer expert, > > I have a problem with command "recon-all". > > In recon-all.log I can to read > > nu_correct: crashed while running nu_evaluate (termination status=9) > > Thank for your help > > > ___ > 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. recon-all.log Description: Binary data ___ 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] problem with nu_correct
Hi FreeSurfer expert, I have a problem with command "recon-all". In recon-all.log I can to read nu_correct: crashed while running nu_evaluate (termination status=9) Thank for your help ___ 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] Problem with recon-all - nu_currect
Dear FS experts, I have a problem with the command "recon-all". In many cases when I use it on the same brain's MRI, on the CLUSTER COMPUTING INFRASTRUCTURE, about 40% of my jobs finish without erros while the other are killed at the command "nu_currect", as you can see from the file.log in attachment. Do you have any suggestions? Thanks a lot for your help. Best regardes, Andrea Thu May 23 13:58:52 CEST 2013 /lustre/home/tateo/Simulazione_FREESURF_GRID/Segmentazione/SUB_Or_test_16/001 /opt/exp_soft/mag/freesurfer/bin/recon-all -debug -s 001 -autorecon-all subjid 001 setenv SUBJECTS_DIR /lustre/home/tateo/Simulazione_FREESURF_GRID/Segmentazione/SUB_Or_test_16 FREESURFER_HOME /opt/exp_soft/mag/freesurfer Actual FREESURFER_HOME /opt/exp_soft/mag/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Linux pccms114.ba.infn.it 2.6.18-348.1.1.el5 #1 SMP Thu Jan 24 13:25:42 CET 2013 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize10240 kbytes coredumpsize 0 kbytes memoryuseunlimited vmemoryuse unlimited descriptors 32768 memorylocked 32 kbytes maxproc 386293 total used free sharedbuffers cached Mem: 49448428 462321603216268 0 900488 29561664 -/+ buffers/cache: 15770008 33678420 Swap: 16779884 613964 16165920 program versions used $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 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: 2013/05/23-11:58:53-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400 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: 2013/05/23-11:58:53-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400 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: 2013/05/23-11:58:53-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-11:58:53-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize.c,v 1.73 2011/03/11 20:55:38 fischl Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-11:58:53-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_watershed.cpp,v 1.96 2011/03/16 21:23:49 nicks Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-11:58:54-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-11:58:54-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-11:58:54-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_label2label.c,v 1.40.2.1 2011/05/19 17:21:56 greve Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-11:58:54-GMT BuildTimeSt
[Freesurfer] Problem with recon-all
Dear FS experts, I have a problem with the command "recon-all". In many cases when I use it on the same brain's MRI, on the CLUSTER COMPUTING INFRASTRUCTURE, about 40% of my jobs finish without erros while the other are killed at the command "nu_currect", as you can see from the file.log in attachment. Do you have any suggestions? Thanks a lot for your help. Best regardes, Andrea Thu May 23 13:58:52 CEST 2013 /lustre/home/tateo/Simulazione_FREESURF_GRID/Segmentazione/SUB_Or_test_16/001 /opt/exp_soft/mag/freesurfer/bin/recon-all -debug -s 001 -autorecon-all subjid 001 setenv SUBJECTS_DIR /lustre/home/tateo/Simulazione_FREESURF_GRID/Segmentazione/SUB_Or_test_16 FREESURFER_HOME /opt/exp_soft/mag/freesurfer Actual FREESURFER_HOME /opt/exp_soft/mag/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Linux pccms114.ba.infn.it 2.6.18-348.1.1.el5 #1 SMP Thu Jan 24 13:25:42 CET 2013 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize10240 kbytes coredumpsize 0 kbytes memoryuseunlimited vmemoryuse unlimited descriptors 32768 memorylocked 32 kbytes maxproc 386293 total used free sharedbuffers cached Mem: 49448428 462321603216268 0 900488 29561664 -/+ buffers/cache: 15770008 33678420 Swap: 16779884 613964 16165920 program versions used $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 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: 2013/05/23-11:58:53-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400 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: 2013/05/23-11:58:53-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400 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: 2013/05/23-11:58:53-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-11:58:53-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize.c,v 1.73 2011/03/11 20:55:38 fischl Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-11:58:53-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_watershed.cpp,v 1.96 2011/03/16 21:23:49 nicks Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-11:58:54-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-11:58:54-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-11:58:54-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_label2label.c,v 1.40.2.1 2011/05/19 17:21:56 greve Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-11:58:54-GMT BuildTimeStamp: May
[Freesurfer] R: Re: ERROR: nu_correct
It could be Let me check Thank you very much Andrea Messaggio originale Da: fis...@nmr.mgh.harvard.edu Data: 20-gen-2013 15.13 A: "Andrea Tateo" Cc: "freesurfer@nmr.mgh.harvard.edu" Ogg: Re: [Freesurfer] ERROR: nu_correct Sounds like it ran out of memory. Is that possible?Bruce On Jan 20, 2013, at 4:14 AM, Andrea Tateo wrote: Hi freesurfer experts, my jobs are finished with this output Processing:.DoneKilledERROR: nu_correct Can you help me? endless thanks Andrea___ 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 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] ERROR: nu_correct
Hi freesurfer experts, my jobs are finished with this output Processing:.DoneKilledERROR: nu_correct Can you help me? endless thanks Andrea ___ 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] Info change size nii
Hello FS experts, I have a problem to solve. I have a binary image.nii to estimate the segmentation of freesurfer. His size is 70,30,70 but format nii includes other information: resolution, origin, ... so, when I convert image.nii to image.mgz, I see an image of size256, 256, 256, (256 slides for orientation). I need to have the image.nii of size 256,256,256 voxels. there is a FreeSurfer's command which allows me to convert to image.nii with size 256 256 256 (if I convert image.nii to image.mgz, the image.mgz has size 256, 256,256) Thank you very much Andrea ___ 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.
Re: [Freesurfer] convert size
Sorry if I bother you again, actually I would like to convert from 256,128,256 to 256,256,256 and from 181,145,181 to 256,256,256. Can you tell me the complete command and not just the option. -rl if volume is 256,256,256? thank you vary much Andrea Messaggio originale Da: fis...@nmr.mgh.harvard.edu Data: 10-dic-2012 14.36 A: "Andrea Tateo" Cc: Ogg: Re: [Freesurfer] convert size Hi Andrea I think there is a typo in your email as your sizes are the same. If you have a volume you would like to reslice it like you can use the -rl option to do what you want. cheers Bruce On Mon, 10 Dec 2012, Andrea Tateo wrote: > Hello FS experts, > I would like to to convert binary images from size 256,256,256 voxels to > size 256, 256, 256. > > Is there any FreeSurfer's module to make it? > > Thank you very much > > Andrea > > 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 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] R: Re: convert size
Soory if I bother you again, actually I would like to convert from 256,128,256 to 256,256,256 and from 181,145,181 to 256,256,256. Can you tell me the complete command and not just the option. thanks immensely Andrea Messaggio originale Da: fis...@nmr.mgh.harvard.edu Data: 10-dic-2012 14.36 A: "Andrea Tateo" Cc: Ogg: Re: [Freesurfer] convert size Hi Andrea I think there is a typo in your email as your sizes are the same. If you have a volume you would like to reslice it like you can use the -rl option to do what you want. cheers Bruce On Mon, 10 Dec 2012, Andrea Tateo wrote: > Hello FS experts, > I would like to to convert binary images from size 256,256,256 voxels to > size 256, 256, 256. > > Is there any FreeSurfer's module to make it? > > Thank you very much > > Andrea > > 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 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] convert size
Hello FS experts, I would like to to convert binary images from size 256,256,256 voxels to size 256, 256, 256. Is there any FreeSurfer's module to make it? Thank you very much Andrea ___ 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] R: Re: R: Re: R: Re: different MRI size
This is my dataset.I don't know another Tenx Messaggio originale Da: fis...@nmr.mgh.harvard.edu Data: 7-dic-2012 17.09 A: "Andrea Tateo" Ogg: Re: R: Re: R: Re: [Freesurfer] different MRI size why do you have different matrix sizes? And I can't tell resolution without knowing the FOV. Ideally no voxel dimension is bigger than about 1.3-1.4mm. cheers Bruce p.s. please cc the list so that others can answer! On Fri, 7 Dec 2012, Andrea Tateo wrote: > > > My data set has two types of MR-images: > first 256, 124, 256 > > second 181, 145, 181 > > > > > > > Messaggio originale > Da: fis...@nmr.mgh.harvard.edu > Data: 7-dic-2012 15.56 > A: "Andrea Tateo" > Ogg: Re: R: Re: [Freesurfer] different MRI size > > Sure. What are the voxel sizes? > > On Dec 7, 2012, at 9:52 AM, Andrea Tateo > wrote: > > Thank you Bruce for answering. > > > My images have size: 256, 124, 256 and181, 145, 181 > I would like to have FS-output with same input's size to evaluate > DICE index. > > (The manual segmentation of comparison are images with sizes 256, > 124, 256 and181, 145, 181) > > Thank you for your time > > > > > > > Messaggio originale > Da: fis...@nmr.mgh.harvard.edu > Data: 7-dic-2012 14.20 > A: "Andrea Tateo" > Cc: > Ogg: Re: [Freesurfer] different MRI size > > Hi Andrea > > sure, recon-all will handle whatever you give it and resample to > 256^3, > but the accuracy will degrade as the resolution worsens. What > resolution > are your images? > > cheers > Bruce > On Fri, 7 Dec > 2012, Andrea Tateo wrote: > > > Hello FS experts, > > I would like to study MRI, by using FS, to extract binary images > of > > hippocampi. > > > > My data images have sizes different from 256,256,256. > > > > Is there any FS procedure to generate images 256, 256, 256 from > my data > > set? > > > > Does FS work only on images 256, 256, 256 ? > > > > Thank you very much > > > > Andrea > > > > > > > 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 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] different MRI size
Hello FS experts, I would like to study MRI, by using FS, to extract binary images of hippocampi. My data images have sizes different from 256,256,256. Is there any FS procedure to generate images 256, 256, 256 from my data set? Does FS work only on images 256, 256, 256 ? Thank you very much Andrea ___ 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] Info extraction hippocampus
Hello FS experts, I would like to extract from head's MRI a bunary image showing only hippocampus. I used command: ### mri_convert FILE_NAME.nii path/directory/NAME_OUTPUT.mgz recon-all -s SUBJECT_name -autorecon-all mri_extract_label aseg.mgz 17 53 hippocampi.mgz # This command spends more then 12 computing houres. I would like to spend less computing time. Is there any procedure? thanks All the best Andre Tateo ___ 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] Info FreeSurfer
Hello, I am working on segmentation of the hippocampus and I need a comparing method. I am approaching for the first time to FreeSurfer method. I would like your courteous help. I have three questions for you: 1 - I have input a MRI-image.nii showing all head. As output I would like a binary image showing only left and right hippocampus. I used the following command: ### mri_convert FILE_NAME.nii path/directory/NAME_OUTPUT.mgz recon-all -s SUBJECT_name -autorecon-all ### How can I extract the required binary image? 2 - Is it possible to comput only hippocampus region (to reduce the processing time)? 3 - Is it possible to give as input only an ristrected region of the subject's head? Best regards Andre Tateo ___ 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.
