Freesurfer December 2011

freesurfer@nmr.mgh.harvard.edu

98 participants
157 discussions

Re: [Freesurfer] aparc.a2009s+aseg problem
by Michael Harms 30 Dec '11

30 Dec '11

For some reason the beginning section of the recon-all.log that you sent is missing (i.e,. the part containing the actual command that you ran). What was the exact recon-all command that you used? From the log file, only the very first mri_convert was performed. Was your command perhaps recon-all -i <input.nii> -s <subjname> If so, you need to include the -all flag to actually run all the rest of the recon-all stream. cheers, -MH On Fri, 2011-12-30 at 13:55 +0000, LAOUCHEDI MAKHLOUF wrote: > Hi Michael > i looked in and the file doesn't contain a section > called "Cortical Parc 2" . what do you think is the problem ? i > attached the log > > thanks > > > > --- En date de : Jeu 29.12.11, Michael Harms <mharms(a)conte.wustl.edu> > a écrit : > > De: Michael Harms <mharms(a)conte.wustl.edu> > Objet: Re: [Freesurfer] aparc.a2009s+aseg problem > À: "LAOUCHEDI MAKHLOUF" <laoumakhl(a)yahoo.fr> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Date: Jeudi 29 décembre 2011, 18h17 > > > That is a job log from your cluster, which isn't helpful to > the issue at > hand. > > You need to look in <subjdir>/scripts/recon-all.log, which > contains a > complete log of the entire recon-all processing stream. > > cheers, > -MH > > On Thu, 2011-12-29 at 17:10 +0000, LAOUCHEDI MAKHLOUF wrote: > > Hi Michael > > i looked in the job.log file (i am using a > condor > > cluster) that i attached, and there is no such section! > > > > thanks > > > > --- En date de : Jeu 29.12.11, Michael Harms > <mharms(a)conte.wustl.edu> > > a écrit : > > > > De: Michael Harms <mharms(a)conte.wustl.edu> > > Objet: Re: [Freesurfer] aparc.a2009s+aseg problem > > À: "LAOUCHEDI MAKHLOUF" <laoumakhl(a)yahoo.fr> > > Cc: freesurfer(a)nmr.mgh.harvard.edu > > Date: Jeudi 29 décembre 2011, 18h01 > > > > > > The problem is apparently that the > Xh.aparc.a2009s.annot > > wasn't created. > > > > Look in scripts/recon-all.log and make sure that the > section > > "Cortical > > Parc 2" is present, and if it is, look for clues as > to why > > the .annot > > wasn't created. > > > > cheers, > > -MH > > > > On Thu, 2011-12-29 at 16:03 +0000, LAOUCHEDI > MAKHLOUF wrote: > > > hi everyone > > > i run recon-all on 27 subjects > using the > > 5.1 > > > version, and i don't find aparc.a2009s+aseg.mgz > neither > > > lh.aparc.a2009s.annot so i can't use the command > > mri_aparc2aseg > > > ( mri_aparc2aseg --s subject --a2009s). what must > i do to > > have > > > aparc.a2009s+aseg.mgz. > > > > > > thanks > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)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(a)nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

wm edit freeview
by Sabin Khadka 29 Dec '11

29 Dec '11

Dear all, Is there any documentation on doing em edit using freeview. Thanks, SK

2 1

Re: [Freesurfer] aparc.a2009s+aseg problem
by Michael Harms 29 Dec '11

29 Dec '11

That is a job log from your cluster, which isn't helpful to the issue at hand. You need to look in <subjdir>/scripts/recon-all.log, which contains a complete log of the entire recon-all processing stream. cheers, -MH On Thu, 2011-12-29 at 17:10 +0000, LAOUCHEDI MAKHLOUF wrote: > Hi Michael > i looked in the job.log file (i am using a condor > cluster) that i attached, and there is no such section! > > thanks > > --- En date de : Jeu 29.12.11, Michael Harms <mharms(a)conte.wustl.edu> > a écrit : > > De: Michael Harms <mharms(a)conte.wustl.edu> > Objet: Re: [Freesurfer] aparc.a2009s+aseg problem > À: "LAOUCHEDI MAKHLOUF" <laoumakhl(a)yahoo.fr> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Date: Jeudi 29 décembre 2011, 18h01 > > > The problem is apparently that the Xh.aparc.a2009s.annot > wasn't created. > > Look in scripts/recon-all.log and make sure that the section > "Cortical > Parc 2" is present, and if it is, look for clues as to why > the .annot > wasn't created. > > cheers, > -MH > > On Thu, 2011-12-29 at 16:03 +0000, LAOUCHEDI MAKHLOUF wrote: > > hi everyone > > i run recon-all on 27 subjects using the > 5.1 > > version, and i don't find aparc.a2009s+aseg.mgz neither > > lh.aparc.a2009s.annot so i can't use the command > mri_aparc2aseg > > ( mri_aparc2aseg --s subject --a2009s). what must i do to > have > > aparc.a2009s+aseg.mgz. > > > > thanks > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)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(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

1 0

aparc.a2009s+aseg problem
by LAOUCHEDI MAKHLOUF 29 Dec '11

29 Dec '11

hi everyone i run recon-all on 27 subjects using the 5.1 version, and i don't find aparc.a2009s+aseg.mgz neither lh.aparc.a2009s.annot so i can't use the command mri_aparc2aseg ( mri_aparc2aseg --s subject --a2009s). what must i do to have aparc.a2009s+aseg.mgz. thanks

2 1

Corpus callosum aseg division...
by Gonzalo Rojas Costa 29 Dec '11

29 Dec '11

Hi: Any reference about how freesurfer divides the corpus callosum in CC_Posterior, CC_Mid_Posterior, CC_Central, CC_Mid_Anterior, CC_Anterior ?... Sincerely, Gonzalo Rojas Costa

2 1

Setting Up Source File Automatically
by James, Brian 28 Dec '11

28 Dec '11

Hi - I am trying to setup the FreeSurfer program so that when I open the terminal it sources the file automatically. As per the instructions, I have changed my .tcshrc file in my Home Directory so that both the setenv and source commands are in there. I have also permanently changed my shell type to tcsh. However, when I open my terminal, it doesn't start automatically. I must type 'tcsh' and then it runs. What am I missing? Thanks. Brian James Technical Applications Analyst North Bay Regional Health Centre<http://www.nbrhc.on.ca/> The information contained in this electronic transmission is intended for the person(s) or entity to whom it is addressed. Delivery of this message to any person other than the intended recipient(s) is not intended in any way to waive confidentiality. This material may contain confidential or personal information which may be subject to the provisions of Ontario's Personal Health Information Protection Act. Any review, retransmission, dissemination or other use of this information by entities other than the intended recipient is prohibited. If you receive this in error, please contact the sender and delete the material immediately. L'information contenue dans ce message ?lectronique est destin?e uniquement au destinataire ou aux destinataires vis?s. La transmission de ce message ? une personne autre que son destinataire ou ses destinataires vis?s ne supprime en rien l'obligation d'en respecter la confidentialit?. Ce message peut contenir des renseignements de nature confidentielle ou personnelle qui pourraient ?tre soumis aux dispositions de la Loi de 2004 sur la protection des renseignements personnels sur la sant?. L'examen, la retransmission, la diffusion et toute autre utilisation de l'information contenue dans ce message par des personnes autres que le destinataire ou les destinataires vis?s sont interdits. Si vous recevez ce message par erreur, veuillez le supprimer imm?diatement et en avertir l'exp?diteur.

2 2

recon-all problem
by LAOUCHEDI MAKHLOUF 28 Dec '11

28 Dec '11

Hi everyone I run freesurfer recon-all command with the flag -all and I have this error ERROR:mpr2mni305 failed, see transforms/talairach_avi.log Some one have any idea? Thanks this is the whole process: Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /var/spool/pbs/tmpdir/168794.gridgate.scg.nuigalway.ie/https_3a_2f_2flcglb11.jinr.ru_3a9000_2fkuCIe3Owzqt9NMK8dnWJIg/ws22493/.tmp/a62dcf35-8a80-4ffe-b336-6fa96f009a56/systemExecTask2949236199702543515/6559183/6559183/mri/orig/001.mgz /var/spool/pbs/tmpdir/168794.gridgate.scg.nuigalway.ie/https_3a_2f_2flcglb11.jinr.ru_3a9000_2fkuCIe3Owzqt9NMK8dnWJIg/ws22493/.tm mri_convert /var/spool/pbs/tmpdir/168794.gridgate.scg.nuigalway.ie/https_3a_2f_2flcglb11.jinr.ru_3a9000_2fkuCIe3Owzqt9NMK8dnWJIg/ws22493/.tmp/a62dcf35-8a80-4ffe-b336-6fa96f009a56/systemExecTask2949236199702543515/6559183/6559183/mri/rawavg.mgz /var/spool/pbs/tmpdir/168794.gridgate.scg.nuigalway.ie/https_3a_2f_2flcglb11.jinr.ru_3a9000_2fkuCIe3Owzqt9NMK8dnWJIg/ws22493/.tmp/a62dcf35-8a80-4ffe-b336-6fa96f009a56/systemExecTask2949236199702543515/6559183/6559183/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /var/spool/pbs/tmpdir/168794.gridgate.scg.nuigalway.ie/https_3a_2f_2flcglb11.jinr.ru_3a9000_2fkuCIe3Owzqt9NMK8dnWJIg/ws22493/.tmp/a62dcf35-8a80-4ffe-b336-6fa96f009a56/systemExecTask2949236199702543515/6559183/6559183/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, 1, 0) k_ras = (-0, -0, 1) Original Data has (1.33, 1, 1) mm size and (128, 256, 256) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /var/spool/pbs/tmpdir/168794.gridgate.scg.nuigalway.ie/https_3a_2f_2flcglb11.jinr.ru_3a9000_2fkuCIe3Owzqt9NMK8dnWJIg/ws22493/.tmp/a62dcf35-8a80-4ffe-b336-6fa96f009a56/systemExecTask2949236199702543515/6559183/6559183/mri/orig.mgz... mri_add_xform_to_header -c /var/spool/pbs/tmpdir/168794.gridgate.scg.nuigalway.ie/https_3a_2f_2flcglb11.jinr.ru_3a9000_2fkuCIe3Owzqt9NMK8dnWJIg/ws22493/.tmp/a62dcf35-8a80-4ffe-b336-6fa96f009a56/systemExecTask2949236199702543515/6559183/6559183/mri/transforms/talairach.xfm /var/spool/pbs/tmpdir/168794.gridgate.scg.nuigalway.ie/https_3a_2f_2flcglb11.jinr.ru_3a9000_2fkuCIe3Owzqt9NMK8dnWJIg/ws22493/.tmp/a62dcf35-8a80-4ffe-b336-6fa96f009a56/systemExecTask2949236199702543515/6559183/6559183/mri/orig.mgz /var/spool/pbs/tmpdir/168794.gridgate.scg.nuigalway.ie/https_3a_2f_2flcglb11.jinr.ru_3a9000_ ERROR: mpr2mni305 failed, see transforms/talairach_avi.log Linux wn033.grid.scg.nuigalway.ie 2.6.18-274.7.1.el5 #1 SMP Thu Oct 20 15:20:36 EDT 2011 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 6559183 exited with ERRORS at Wed Dec 28 16:21:01 GMT 2011 For more details, see the log file /var/spool/pbs/tmpdir/168794.gridgate.scg.nuigalway.ie/https_3a_2f_2flcglb11.jinr.ru_3a9000_2fkuCIe3Owzqt9NMK8dnWJIg/ws22493/.tmp/a62dcf35-8a80-4ffe-b336-6fa

2 1

FA interpretation from cvs registration for group analysis
by Antonella Kis 28 Dec '11

28 Dec '11

Dear Lilla, I will appreciate a lot if you can help me understand what is the meaning of the results after running after running mri_cvs_register and the GLM group analysis. More exactly, I followed all the instructions from the webpage: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Diffusion and I wonder if based on the cluster's colours I can say something about my FA values in one group related to the other one. More exactly I am looking to understand if I have an increase in the FA value for the controls versus patients or the FA in patients is larger than in the control group. My contrast matrix is C = [+1.00000 -1.00000 ] and I have 30 controls and 32 patients. What is the age range for the cvs_avg35 space? I wonder if is the best space to register my subjects if they are children with age between 6-14. Thank you very much! Antonella

2 6

Question after preprocessing in FreeSurfer.
by Long 27 Dec '11

27 Dec '11

Dear all, Hi, I am a beginner of FreeSurfer. Recently I have run recon-all and preproc-sess on my MRI and fMRI images. Next I'd like to convert surface images to AFNI-SUMA and convert fMRI images to volume space. I found that the T1 image and its surface maps were not normalized and the fMRI images were normalized into MNI305 in surface space. So my question is, how to normalize the T1 surface maps by using talairach.xfm, so I can view the normalized surface maps in SUMA, and how to convert surface space fMRI images (i.e., fmcpr.up.sm5.fsaverage.lh.nii.gz) to the volume space? Thank you in advance! Best, Xiangyu

1 0

freeview auditory cortex etc.
by Klein, Holger 25 Dec '11

25 Dec '11

Dear freesurfers, 1) I have a little question concerning Freeview: As attachment there are 3 screenshots, which show a label of the 2009 atlas (Primary auditory cortex). I used brain.mgz as "input" volume and chose the label in the ROI tab in freeview - but the screenshots look like as if there is a vast part of the labeled cortex not colored. I'm wondering why the other cortical voxels - which definitely belong to Heschl-Gyrus (A1) - are not marked? I thought that a label marks all the pixels/voxels (also in 2D view) between the white matter surface and the pial surface that belong to the chosen cortical structure. Am I mistaken by interpreting the meaning of a label in this way? 2) Actually I got stuck when trying to find a good 3D-view of Heschl'Gyrus (lh.G_temp_sup-G_T_transv.label) cause it is hidden in the deep Sylvian fissure. Is there a possibility to get a better view on this label (e.g. transparent view of the surrounding brain structures)? I attached another screenshot (Schneider, Cortex) which was taken from a colleague of mine working with brainvoyager - is it possible to create something like this in freesurfer/freeview? Looking forward to answers, thanks a lot... Holger

1 0

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer December 2011