[Freesurfer] Post-doctoral position in brain development in NeuroSpin, Paris
The team of brain development imaging (Gif-sur-Yvette, France) offers a 2-year post-doctoral position from September 2013, on the study of cortical and white matter maturation in infants using complementary multi-modal imaging methods. The team research is focused on the cerebral bases of cognitive functions in healthy babies and on the relationships between functional development and the anatomical maturation of cerebral networks with emphasis on language and vision. The team has performed pioneer works on language perception with functional MRI (Dehaene-Lambertz et al, Science 2002), on correlations between white matter development and its functional efficiency (respectively assessed by diffusion tensor imaging DTI and event-related potentials; Dubois et al, J. Neuroscience 2008), and on cortical maturation (Leroy el al, J. Neuroscience 2011). The post-doctoral candidate will integrate this research topic, combining anatomical MRI, DTI, mappings of T1 and T2 relaxation times and EEG in healthy infants to assess the structural and functional organization of the developing brain. Applicants should possess solid technical background in imaging techniques (MRI, EEG, MEG) and in post-processing tools or in signal processing and computational science. Knowledge (or at least a strong interest) in human cognition and brain development would be appreciated. Applications should be sent to Jessica Dubois (jessica.dub...@cea.fr) and Ghislaine Dehaene-Lambertz (ghislaine.deha...@cea.fr). The Cognitive Neuroimaging Unit (INSERM-CEA U992) is implemented in the NeuroSpin centre, localized in the suburb of Paris. This centre gathers varied research laboratories on cognitive neuroscience, biophysics, imaging and post-processing methodologies, etc. The platform is organized around non-invasive techniques which are particularly suitable for imaging infants and children (3T MRI, mock MRI scanner, EEG and MEG installations). Lab website: www.unicog.org tab Kids lab NeuroSpin website: http://www-dsv.cea.fr/en/institutes/institute-of-biomedical-imaging-i2bm/departments/neurospin-neurospin ___ 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] Measure outer surface area
Dear all, how can I measure the surface area of the outer surface computed to calculate lgi? I've tried mris_anatomical_stats subject lh pial-outer-smoothed but that doesn't work (since it doesn't match lh.pial). Any idea would be greatly appreciated. Thank you, Irene ___ 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] Inter-hemispheric registration issue
Dear Doug, thanks for putting mri_vol2vol on the ftp site, and sorry for bothering you again with this. I did as suggested, but I still get an error, now when attempting to run xhemireg. Apparently nu.mgz is missing. Please find the log attached. Thank you very much again, Irene Le vendredi 18 mai 2012 à 11:24 -0400, Douglas N Greve a écrit : > You'll need a new version of mri_vol2vol, which I have put on that ftp site. > doug > > On 05/18/2012 04:25 AM, Irene Altarelli wrote: > > Thanks for your help, Doug. > > > > It seems as if there is another script problem then, because when > > running the command I get the following error message (log also > > attached): > > ERROR: Option --keep-precision unknown > > > > I'm using Fs version 5, and the version of xhemireg I have downloaded > > is: v 1.22 2012/01/20 20:12:32. > > > > Should that --keep-precision option be removed from the script? > > > > Thank you, > > Irene > > > > > > > > Le mercredi 16 mai 2012 à 11:16 -0400, Douglas N Greve a écrit : > >> Irene, this is a problem with the script. The work-around is to run > >> xhemireg before running surfreg with the --xhemi option. > >> > >> doug > >> > >> On 05/16/2012 01:56 AM, Irene Altarelli wrote: > >>> Dear Doug, > >>> > >>> here is what I get. > >>> > >>> First, I ran surfreg --s aa_tris --t fsaverage_sym --lh and got the > >>> attached log file. Here is the terminal output: > >>> > >>> setenv SUBJECTS_DIR /home/ialtarelli/DATABASE/Karla5/ > >>> cd /home/ialtarelli > >>> /home/ialtarelli/freesurfer/bin/surfreg --s aa_tris --t fsaverage_sym > >>> --lh > >>> > >>> Linux lscp-iao1 2.6.32-5-amd64 #1 SMP Mon Jan 16 16:22:28 UTC 2012 > >>> x86_64 GNU/Linux > >>> #@# lh mardi 15 mai 2012, 19:23:56 (UTC+0200) > >>> #CMD# mris_register -curv -annot > >>> aparc.annot /home/ialtarelli/DATABASE/Karla5//aa_tris/surf/lh.sphere > >>> /home/ialtarelli/DATABASE/Karla5//fsaverage_sym/lh.reg.template.tif > >>> /home/ialtarelli/DATABASE/Karla5//aa_tris/surf/lh.fsaverage_sym.sphere.reg > >>> using smoothwm curvature for final alignment > >>> zeroing medial wall in aparc.annot > >>> $Id: mris_register.c,v 1.56 2010/02/28 23:08:04 fischl Exp $ > >>> $Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $ > >>> reading surface > >>> from /home/ialtarelli/DATABASE/Karla5//aa_tris/surf/lh.sphere... > >>> reading colortable from annotation file... > >>> colortable with 36 entries read > >>> (originally > >>> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) > >>> reading template parameterization > >>> from > >>> /home/ialtarelli/DATABASE/Karla5//fsaverage_sym/lh.reg.template.tif... > >>> ripping medial wall... > >>> writing registered surface > >>> to > >>> /home/ialtarelli/DATABASE/Karla5//aa_tris/surf/lh.fsaverage_sym.sphere.reg... > >>> curvature mean = 0.007, std = 0.603 > >>> curvature mean = 0.030, std = 0.806 > >>> curvature mean = 0.024, std = 0.853 > >>> curvature mean = 0.009, std = 0.826 > >>> curvature mean = 0.011, std = 0.936 > >>> curvature mean = 0.003, std = 0.836 > >>> curvature mean = 0.005, std = 0.972 > >>> curvature mean = 0.001, std = 0.837 > >>> curvature mean = 0.001, std = 0.988 > >>> curvature mean = -0.032, std = 0.312 > >>> curvature mean = 0.032, std = 0.124 > >>> curvature mean = 0.079, std = 0.315 > >>> curvature mean = 0.031, std = 0.151 > >>> curvature mean = 0.049, std = 0.489 > >>> curvature mean = 0.031, std = 0.165 > >>> curvature mean = 0.028, std = 0.631 > >>> curvature mean = 0.031, std = 0.171 > >>> curvature mean = 0.011, std = 0.749 > >>> 159: 0 negative triangles > >>> surfreg-Run-Time-Hours aa_tris lh 0 0,90 > >>> mardi 15 mai 2012, 20:17:58 (UTC+0200) > >>> surfreg done > >>> > >>> Then, I ran surfreg --s aa_tris --t fsaverage_sym --lh --xhemi and the > >>> terminal output is just: > >>> > >>> ERROR: cannot > >>> find /home/ialtarelli/DATABASE/Karla5//aa_tris/xhemi/surf/lh.sphere > >>> > >>> without any log file, at least I can't find any modified file
Re: [Freesurfer] Inter-hemispheric registration issue
My command was: xhemireg --s ac_copie The terminal output is identical to the log file (attached), ending by: #@# Talairach Tue May 29 18:24:25 CEST 2012 /home/ialtarelli/DATABASE/Karla5/ac_copie/xhemi/mri talairach_avi --i nu.mgz --xfm transforms/talairach.auto.xfm ERROR: input volume nu.mgz does not exist Linux lscp-iao1 2.6.32-5-amd64 #1 SMP Mon Jan 16 16:22:28 UTC 2012 x86_64 GNU/Linux recon-all -s ac_copie/xhemi exited with ERRORS at Tue May 29 18:24:26 CEST 2012 Should I skip that by using the --no-tal flag? Thanks! Irene Le samedi 02 juin 2012 à 10:57 -0400, Douglas Greve a écrit : > Can you send your cmd and terminal output? > doug > > On 6/2/12 9:46 AM, Irene Altarelli wrote: > > Dear Doug, > > > > thanks for putting mri_vol2vol on the ftp site, and sorry for bothering > > you again with this. I did as suggested, but I still get an error, now > > when attempting to run xhemireg. Apparently nu.mgz is missing. > > > > Please find the log attached. > > > > Thank you very much again, > > Irene > > > > > > > > Le vendredi 18 mai 2012 à 11:24 -0400, Douglas N Greve a écrit : > >> You'll need a new version of mri_vol2vol, which I have put on that ftp > >> site. > >> doug > >> > >> On 05/18/2012 04:25 AM, Irene Altarelli wrote: > >>> Thanks for your help, Doug. > >>> > >>> It seems as if there is another script problem then, because when > >>> running the command I get the following error message (log also > >>> attached): > >>> ERROR: Option --keep-precision unknown > >>> > >>> I'm using Fs version 5, and the version of xhemireg I have downloaded > >>> is: v 1.22 2012/01/20 20:12:32. > >>> > >>> Should that --keep-precision option be removed from the script? > >>> > >>> Thank you, > >>> Irene > >>> > >>> > >>> > >>> Le mercredi 16 mai 2012 à 11:16 -0400, Douglas N Greve a écrit : > >>>> Irene, this is a problem with the script. The work-around is to run > >>>> xhemireg before running surfreg with the --xhemi option. > >>>> > >>>> doug > >>>> > >>>> On 05/16/2012 01:56 AM, Irene Altarelli wrote: > >>>>> Dear Doug, > >>>>> > >>>>> here is what I get. > >>>>> > >>>>> First, I ran surfreg --s aa_tris --t fsaverage_sym --lh and got the > >>>>> attached log file. Here is the terminal output: > >>>>> > >>>>> setenv SUBJECTS_DIR /home/ialtarelli/DATABASE/Karla5/ > >>>>> cd /home/ialtarelli > >>>>> /home/ialtarelli/freesurfer/bin/surfreg --s aa_tris --t fsaverage_sym > >>>>> --lh > >>>>> > >>>>> Linux lscp-iao1 2.6.32-5-amd64 #1 SMP Mon Jan 16 16:22:28 UTC 2012 > >>>>> x86_64 GNU/Linux > >>>>> #@# lh mardi 15 mai 2012, 19:23:56 (UTC+0200) > >>>>> #CMD# mris_register -curv -annot > >>>>> aparc.annot /home/ialtarelli/DATABASE/Karla5//aa_tris/surf/lh.sphere > >>>>> /home/ialtarelli/DATABASE/Karla5//fsaverage_sym/lh.reg.template.tif > >>>>> /home/ialtarelli/DATABASE/Karla5//aa_tris/surf/lh.fsaverage_sym.sphere.reg > >>>>> using smoothwm curvature for final alignment > >>>>> zeroing medial wall in aparc.annot > >>>>> $Id: mris_register.c,v 1.56 2010/02/28 23:08:04 fischl Exp $ > >>>>> $Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $ > >>>>> reading surface > >>>>> from /home/ialtarelli/DATABASE/Karla5//aa_tris/surf/lh.sphere... > >>>>> reading colortable from annotation file... > >>>>> colortable with 36 entries read > >>>>> (originally > >>>>> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) > >>>>> reading template parameterization > >>>>> from > >>>>> /home/ialtarelli/DATABASE/Karla5//fsaverage_sym/lh.reg.template.tif... > >>>>> ripping medial wall... > >>>>> writing registered surface > >>>>> to > >>>>> /home/ialtarelli/DATABASE/Karla5//aa_tris/surf/lh.fsaverage_sym.sphere.reg... > >>>>> curvature mean = 0.007, std = 0.603 > >>>>> curvature mean = 0.030, std = 0.806 > >>>>> curvature mean = 0.024,
[Freesurfer] ROI from left to right hemi - cortical thickness
Dear all, I have a ROI on the left hemisphere and I'd like to extract cortical thickness values from the homologous region in the right hemisphere. For this I applied the interhemispheric registration process and got my ROI mapped into the right hemisphere in /subject/xhemi/label. However when I tried to run mris_anatomical_stats on /subject/xhemi it failed, as there is no wm.mgz file in /subject/xhemi/mri. Any suggestion would be greatly appreciated. Thank you, Irene -- Irene Altarelli Laboratoire de Sciences Cognitives et Psycholinguistique Ecole Normale Supérieure 29, rue d'Ulm 75230 Paris Cedex 05 tel. +33 (0)1 44 32 26 23 ___ 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] ROI from left to right hemi - cortical thickness
Dear all, I have a ROI on the left hemisphere and I'd like to extract cortical thickness values from the homologous region in the right hemisphere. For this I applied the interhemispheric registration process and got my ROI mapped into the right hemisphere in /subject/xhemi/label. However when I tried to run mris_anatomical_stats on /subject/xhemi it failed, as there is no wm.mgz file in /subject/xhemi/mri. Any suggestion would be greatly appreciated. Thank you, Irene -- Irene Altarelli Laboratoire de Sciences Cognitives et Psycholinguistique Ecole Normale Supérieure 29, rue d'Ulm 75230 Paris Cedex 05 tel. +33 (0)1 44 32 26 23 ___ 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] ROI from left to right hemi - cortical thickness
Dear Doug, thanks for your answer. I guess I got confused by the output of the interhemispheric registration. So, to be sure I understood correctly: are you suggesting that I should 1) run mri_label2label --srcsubject suj1 --trgsubject suj1/xhemi --srclabel $SUBJECT_DIR/suj1/label/lh.mylabel.label --trglabel $SUBJECT_DIR/suj1/xhemi/label/lh.mylabel.label --regmethod surface --surfreg sphere --hemi lh 2) copy the newly created label /suj1/xhemi/label/lh.mylabel.label to suj1/label/rh.mylabel.label and calculate stats from that one? Thanks again! Have a nice day, Irene Le lundi 16 juillet 2012 à 10:49 -0400, Douglas N Greve a écrit : > Hi Irene, what are the instructions you are following? If you have > mapped the lh.roi to the LH of the xhemi subject (making it the RH), > then you can copy it to subject/label/rh.roi and run the normal stats. > doug > > On 07/09/2012 04:31 AM, Irene Altarelli wrote: > > Dear all, > > > > I have a ROI on the left hemisphere and I'd like to extract cortical > > thickness values from the homologous region in the right hemisphere. For > > this I applied the interhemispheric registration process and got my ROI > > mapped into the right hemisphere in /subject/xhemi/label. > > However when I tried to run mris_anatomical_stats on /subject/xhemi it > > failed, as there is no wm.mgz file in /subject/xhemi/mri. > > > > Any suggestion would be greatly appreciated. > > > > Thank you, > > Irene > > > > > > > > > -- Irene Altarelli Laboratoire de Sciences Cognitives et Psycholinguistique Ecole Normale Supérieure 29, rue d'Ulm 75230 Paris Cedex 05 tel. +33 (0)1 44 32 26 23 ___ 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] cortical thickness asymmetries
Dear Freesurfer experts, have cortical thickness asymmetries ever been looked at using Destrieux parcellation scheme, either in adults or (even better) in children? Thanks! Irene -- Irene Altarelli Laboratoire de Sciences Cognitives et Psycholinguistique Ecole Normale Supérieure 29, rue d'Ulm 75230 Paris Cedex 05 tel. +33 (0)1 44 32 26 23 ___ 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] Longitudinal pipeline question
Dear Martin, thanks for your quick reply. I am using version 5.1. I only have two timepoints per subject and I took the snapshots from the independent runs. What bothers me is that the difference is not present in the 001.mgz images, but seems to appear later in the workflow. Thanks again, Irene Le jeudi 03 novembre 2011 à 10:40 -0400, Martin Reuter a écrit : > Hi Irene, > > both images should be smoothed the same. You only have two time points > in each subject? Which FreeSurfer version are you using? And these > images are from the *.long.base directories (or are they from the > independent runs)? > > -Martin > > On Thu, 2011-11-03 at 15:20 +0100, Irene Altarelli wrote: > > Dear Fs experts, > > > > I am running a longitudinal dataset through the longitudinal pipeline, > > and noticed that for one subject, although we kept everything the same > > (sequence, coil etc) the two timepoints' brainmasks look different: > > timepoint one (in the attached snapshot, gs_tp1) looks as if it has been > > smoothed, compared to timepoint two (gs_tp2). I have checked some other > > images from this subject, and the same seems to occur for orig.mgz, but > > not for rawavg.mgz. > > > > Any idea on what could be causing the difference would be greatly > > appreciated. > > > > Thanks in advance, > > Irene > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > 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. > > -- Irene Altarelli Laboratoire de Sciences Cognitives et Psycholinguistique Ecole Normale Supérieure 29, rue d'Ulm 75230 Paris Cedex 05 tel. +33 (0)1 44 32 26 23 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] different interpolation smoothing in conform step
Dear Martin, the RAS coordinates and voxel to ras transforms are indeed slightly different. Should I change this and if so, how? Please find the output of mri_info for each of the two acquisitions at the end of this email. Thanks again! Irene *** Volume information for gsTP1/mri/rawavg.mgz type: MGH dimensions: 256 x 256 x 176 voxel sizes: 1., 1., 1. type: FLOAT (3) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -88.0, zend: 88.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = 0., y_r = -0.0436, z_r = 0.9990, c_r =-3.5493 : x_a = -1., y_a = 0., z_a = 0., c_a =12.8739 : x_s = 0., y_s = 0.9990, z_s = 0.0436, c_s = -16.0490 talairach xfm : Orientation : PSR Primary Slice Direction: sagittal voxel to ras transform: 0. -0.0436 0.9990 -85.8823 -1. 0. 0. 140.8739 0. 0.9990 0.0436 -147.7657 0. 0. 0. 1. voxel-to-ras determinant -1 ras to voxel transform: -0. -1. -0. 140.8739 -0.0436 0. 0.9990 143.8789 0.9990 -0. 0.043692.2460 0. 0. 0. 1. *** Volume information for gsTP2/mri/rawavg.mgz type: MGH dimensions: 256 x 256 x 176 voxel sizes: 1., 1., 1. type: FLOAT (3) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -88.0, zend: 88.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = 0., y_r = 0., z_r = 1., c_r =-1.5339 : x_a = -1., y_a = 0., z_a = 0., c_a =11.5254 : x_s = 0., y_s = 1., z_s = 0., c_s = -19.3390 talairach xfm : Orientation : PSR Primary Slice Direction: sagittal voxel to ras transform: 0. 0. 1. -89.5339 -1. 0. 0. 139.5254 0. 1. 0. -147.3390 0. 0. 0. 1. voxel-to-ras determinant -1 ras to voxel transform: -0. -1. -0. 139.5254 -0. -0. 1. 147.3390 1. 0. 0.89.5339 0. 0. 0. 1. Selon Martin Reuter : > Hi Irene, > > since those images are not from the longitudinal runs, it really is a > cross sectional question: > > You have two images and the raw average look both similarly noisy, but > the orig (which is the first image in the recon-all stream) is smoother > for one than the other. > > That means that the conform step (that interpolates the isotropic orig > from the rawavg) introduces the different smoothing. Not sure why it is > different. > You can check (with mri_info) the voxel sizes of your rawavg and the RAS > coordinates. If they are the same, smoothing should also be the same. > > Best, Martin > > On Thu, 2011-11-03 at 17:48 +0100, Irene Altarelli wrote: > > Dear Martin, > > > > thanks for your quick reply. > > > > I am using version 5.1. I only have two timepoints per subject and I > > took the snapshots from the independent runs. What bothers me is that > > the difference is not present in the 001.mgz images, but seems to appear > > later in the workflow. > > > > Thanks again, > > Irene > > > > Le jeudi 03 novembre 2011 à 10:40 -0400, Martin Reuter a écrit : > > > Hi Irene, > > > > > > both images should be smoothed the same. You only have two time points > > > in each subject? Which FreeSurfer version are you using? And these > > > images are from the *.long.base directories (or are they from the > > > independent runs)? > > > > > > -Martin > > > > > > On Thu, 2011-11-03 at 15:20 +0100, Irene Altarelli wrote: > > > > Dear Fs experts, > > > > > > > > I am running a longitudinal dataset through the longitudinal pipeline, > > > > and noticed that for one subject, although we kept everything the same > > > > (sequence, coil etc) the two timepoints' brainmasks look different: > > > &
Re: [Freesurfer] different interpolation smoothing in conform step
> > > > > > > Thanks again! > > > > Irene > > > > > > > > > > > > > > > > > *** > > > > > > > > Volume information for gsTP1/mri/rawavg.mgz > > > > type: MGH > > > > dimensions: 256 x 256 x 176 > > > >voxel sizes: 1., 1., 1. > > > > type: FLOAT (3) > > > >fov: 256.000 > > > >dof: 0 > > > > xstart: -128.0, xend: 128.0 > > > > ystart: -128.0, yend: 128.0 > > > > zstart: -88.0, zend: 88.0 > > > > TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: > > > > 0.00 > > > > degrees > > > >nframes: 1 > > > >PhEncDir: UNKNOWN > > > > ras xform present > > > > xform info: x_r = 0., y_r = -0.0436, z_r = 0.9990, c_r = > > > -3.5493 > > > > : x_a = -1., y_a = 0., z_a = 0., c_a = > > > 12.8739 > > > > : x_s = 0., y_s = 0.9990, z_s = 0.0436, c_s = > > > -16.0490 > > > > > > > > talairach xfm : > > > > Orientation : PSR > > > > Primary Slice Direction: sagittal > > > > > > > > voxel to ras transform: > > > > 0. -0.0436 0.9990 -85.8823 > > > >-1. 0. 0. 140.8739 > > > > 0. 0.9990 0.0436 -147.7657 > > > > 0. 0. 0. 1. > > > > > > > > voxel-to-ras determinant -1 > > > > > > > > ras to voxel transform: > > > >-0. -1. -0. 140.8739 > > > >-0.0436 0. 0.9990 143.8789 > > > > 0.9990 -0. 0.043692.2460 > > > > 0. 0. 0. 1. > > > > > > > > > > > > > > > > > > > > > > > > > *** > > > > > > > > > > > > > > > > Volume information for gsTP2/mri/rawavg.mgz > > > > type: MGH > > > > dimensions: 256 x 256 x 176 > > > >voxel sizes: 1., 1., 1. > > > > type: FLOAT (3) > > > >fov: 256.000 > > > >dof: 0 > > > > xstart: -128.0, xend: 128.0 > > > > ystart: -128.0, yend: 128.0 > > > > zstart: -88.0, zend: 88.0 > > > > TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: > > > > 0.00 > > > > degrees > > > >nframes: 1 > > > >PhEncDir: UNKNOWN > > > > ras xform present > > > > xform info: x_r = 0., y_r = 0., z_r = 1., c_r = > > > -1.5339 > > > > : x_a = -1., y_a = 0., z_a = 0., c_a = > > > 11.5254 > > > > : x_s = 0., y_s = 1., z_s = 0., c_s = > > > -19.3390 > > > > > > > > talairach xfm : > > > > Orientation : PSR > > > > Primary Slice Direction: sagittal > > > > > > > > voxel to ras transform: > > > > 0. 0. 1. -89.5339 > > > >-1. 0. 0. 139.5254 > > > > 0. 1. 0. -147.3390 > > > > 0. 0. 0. 1. > > > > > > > > voxel-to-ras determinant -1 > > > > > > > > ras to voxel transform: > > > >-0. -1. -0. 139.5254 > > > >-0. -0. 1. 147.3390 > > > > 1. 0. 0.89.5339 > > > > 0. 0. 0. 1. > > > > > > > > > > > > > > > > > > > > Selon Martin Reuter : > > > > > > > > > Hi Irene, > > > > > > > > > > since those images are not from the longitudinal runs, it really is a > > > > > cross sectional question: > > > > > > > > > > Yo
[Freesurfer] Postdoc position in neuroanatomical MRI of developmental dyslexia
Applications are invited for a postdoc position in the team of Franck Ramus, LSCP, Institut d'Etudes Cognitives, Ecole Normale Supérieure, Paris, France. The successful candidate will investigate neuroanatomical differences between dyslexic and control children, using high-quality 3T MRI images from diffusion and T1 sequences that have already been collected as part of an imaging and genetics project. The position is available from January 1st. Candidates should have a PhD and extensive research experience in cognitive neuroscience. Expertise with the analysis of neuroanatomical images will be a strong asset. Net salary will be a minimum of 2000â¬/month and will depend on the experience of the candidate. Further details and informal enquiries may be directed to Franck Ramus (franck.ra...@ens.fr). Applicants should send a letter of application, clearly outlining the candidate's expertise and research interests, along with a CV, and names of 2-3 references to franck.ra...@ens.fr, by February 1st. The position will remain open until a suitable candidate has been found. ___ 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] Inter-hemispheric registration issue
Dear all, I'm trying to use the new script for the inter-hemisphere analysis, in Fs version 5.0. I have downloaded the files as suggested (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21706.html). Surfreg seems to be running fine (surfreg --s subject --t fsaverage_sym --lh), but I have problems then with the --xhemi option. Some files appear to be missing, I get the following error messages: ERROR: cannot find /path/subject/xhemi/surf/lh.sphere ERROR: cannot find /path/subject/xhemi/surf/lh.smoothwm ERROR: cannot find /path/subject/xhemi/surf/lh.sphere ERROR: cannot find /path/subject/xhemi/label/lh.aparc.annot lh.fsaverage_sym.sphere.reg is created in $subject as it should (please find the surfreg log below). Thank you in advance, Irene Log file for surfreg samedi 12 mai 2012, 17:36:31 (UTC+0200) setenv SUBJECTS_DIR /home/ialtarelli/DATABASE/Karla5/ cd /home/ialtarelli /home/ialtarelli/freesurfer/bin/surfreg --s aa_copie --t fsaverage_sym --lh Linux lscp-iao1 2.6.32-5-amd64 #1 SMP Mon Jan 16 16:22:28 UTC 2012 x86_64 GNU/Linux #@# lh samedi 12 mai 2012, 17:36:31 (UTC+0200) #CMD# mris_register -curv -annot aparc.annot /home/ialtarelli/DATABASE/Karla5//aa_copie/surf/lh.sphere /home/ialtarelli/DATABASE/Karla5//fsaverage_sym/lh.reg.template.tif /home/ialtarelli/DATABASE/Karla5//aa_copie/surf/lh.fsaverage_sym.sphere.reg using smoothwm curvature for final alignment zeroing medial wall in aparc.annot $Id: mris_register.c,v 1.56 2010/02/28 23:08:04 fischl Exp $ $Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $ reading surface from /home/ialtarelli/DATABASE/Karla5//aa_copie/surf/lh.sphere... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) reading template parameterization from /home/ialtarelli/DATABASE/Karla5//fsaverage_sym/lh.reg.template.tif... ripping medial wall... writing registered surface to /home/ialtarelli/DATABASE/Karla5//aa_copie/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.007, std = 0.603 curvature mean = 0.030, std = 0.806 curvature mean = 0.024, std = 0.853 curvature mean = 0.009, std = 0.826 curvature mean = 0.011, std = 0.936 curvature mean = 0.003, std = 0.836 curvature mean = 0.005, std = 0.972 curvature mean = 0.001, std = 0.837 curvature mean = 0.001, std = 0.988 curvature mean = -0.032, std = 0.312 curvature mean = 0.032, std = 0.124 curvature mean = 0.079, std = 0.315 curvature mean = 0.031, std = 0.151 curvature mean = 0.049, std = 0.489 curvature mean = 0.031, std = 0.165 curvature mean = 0.028, std = 0.631 curvature mean = 0.031, std = 0.171 curvature mean = 0.011, std = 0.749 159: 0 negative triangles surfreg-Run-Time-Hours aa_copie lh 0 0,84 samedi 12 mai 2012, 18:26:49 (UTC+0200) surfreg done -- Irene Altarelli Laboratoire de Sciences Cognitives et Psycholinguistique Ecole Normale Supérieure 29, rue d'Ulm 75230 Paris Cedex 05 tel. +33 (0)1 44 32 26 23 ___ 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] Inter-hemispheric registration issue
Thanks for your help, Doug. It seems as if there is another script problem then, because when running the command I get the following error message (log also attached): ERROR: Option --keep-precision unknown I'm using Fs version 5, and the version of xhemireg I have downloaded is: v 1.22 2012/01/20 20:12:32. Should that --keep-precision option be removed from the script? Thank you, Irene Le mercredi 16 mai 2012 à 11:16 -0400, Douglas N Greve a écrit : > Irene, this is a problem with the script. The work-around is to run > xhemireg before running surfreg with the --xhemi option. > > doug > > On 05/16/2012 01:56 AM, Irene Altarelli wrote: > > Dear Doug, > > > > here is what I get. > > > > First, I ran surfreg --s aa_tris --t fsaverage_sym --lh and got the > > attached log file. Here is the terminal output: > > > > setenv SUBJECTS_DIR /home/ialtarelli/DATABASE/Karla5/ > > cd /home/ialtarelli > > /home/ialtarelli/freesurfer/bin/surfreg --s aa_tris --t fsaverage_sym > > --lh > > > > Linux lscp-iao1 2.6.32-5-amd64 #1 SMP Mon Jan 16 16:22:28 UTC 2012 > > x86_64 GNU/Linux > > #@# lh mardi 15 mai 2012, 19:23:56 (UTC+0200) > > #CMD# mris_register -curv -annot > > aparc.annot /home/ialtarelli/DATABASE/Karla5//aa_tris/surf/lh.sphere > > /home/ialtarelli/DATABASE/Karla5//fsaverage_sym/lh.reg.template.tif > > /home/ialtarelli/DATABASE/Karla5//aa_tris/surf/lh.fsaverage_sym.sphere.reg > > using smoothwm curvature for final alignment > > zeroing medial wall in aparc.annot > > $Id: mris_register.c,v 1.56 2010/02/28 23:08:04 fischl Exp $ > >$Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $ > > reading surface > > from /home/ialtarelli/DATABASE/Karla5//aa_tris/surf/lh.sphere... > > reading colortable from annotation file... > > colortable with 36 entries read > > (originally > > /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) > > reading template parameterization > > from /home/ialtarelli/DATABASE/Karla5//fsaverage_sym/lh.reg.template.tif... > > ripping medial wall... > > writing registered surface > > to > > /home/ialtarelli/DATABASE/Karla5//aa_tris/surf/lh.fsaverage_sym.sphere.reg... > > curvature mean = 0.007, std = 0.603 > > curvature mean = 0.030, std = 0.806 > > curvature mean = 0.024, std = 0.853 > > curvature mean = 0.009, std = 0.826 > > curvature mean = 0.011, std = 0.936 > > curvature mean = 0.003, std = 0.836 > > curvature mean = 0.005, std = 0.972 > > curvature mean = 0.001, std = 0.837 > > curvature mean = 0.001, std = 0.988 > > curvature mean = -0.032, std = 0.312 > > curvature mean = 0.032, std = 0.124 > > curvature mean = 0.079, std = 0.315 > > curvature mean = 0.031, std = 0.151 > > curvature mean = 0.049, std = 0.489 > > curvature mean = 0.031, std = 0.165 > > curvature mean = 0.028, std = 0.631 > > curvature mean = 0.031, std = 0.171 > > curvature mean = 0.011, std = 0.749 > > 159: 0 negative triangles > > surfreg-Run-Time-Hours aa_tris lh 0 0,90 > > mardi 15 mai 2012, 20:17:58 (UTC+0200) > > surfreg done > > > > Then, I ran surfreg --s aa_tris --t fsaverage_sym --lh --xhemi and the > > terminal output is just: > > > > ERROR: cannot > > find /home/ialtarelli/DATABASE/Karla5//aa_tris/xhemi/surf/lh.sphere > > > > without any log file, at least I can't find any modified file in the > > subject's folder. > > > > > > Hope this helps make things clearer. > > Many thanks in advance! > > Irene > > > > > > Le mardi 15 mai 2012 à 15:19 -0400, Douglas N Greve a écrit : > >> Can you send me the command line and terminal output? Did you run > >> xhemireg first? Should not have had to ... > >> > >> On 05/15/2012 03:02 PM, irene.altare...@ens.fr wrote: > >>> Dear Doug, > >>> > >>> where would that log file be? As the /subject/xhemi fails to be created > >>> the log > >>> normally appearing in there cannot be found.. Sorry if I misunderstood > >>> something. > >>> > >>> Thanks, > >>> Irene > >>> > >>> > >>> Selon Douglas N Greve: > >>> > >>>> Hi Irene, can you send the log file for the command that is failing? > >>>> doug > >>>> > >>>> On 05/15/2012 01:28 PM, Irene Altarelli wrote: > >>>>> Dear all, > >>>>> > >>>>> I'm trying to use the new script for the inter-h
[Freesurfer] White matter hypointensities
Hi Freesurfers, I heard about tools for segmenting wm hypotensities from multi-spectral data. We have various sequences (T1, T2 and Flair) from a group of patients and controls and would be interested in looking at hypointensities. So I was wondering if these tools are accessible somewhere. Thanks very much in advance, Irene Le mercredi 12 mai 2010 à 20:06 -0400, Bruce Fischl a écrit : > Hi Victor > > we treat it as any other label - it's manually labeled in the training > subjects and propagated into the aseg. Koen Van Leemput (ccd) has some > tools for segmenting them from multi-spectral data that probably works > better though (they aren't that well defined only on a T1). > > cheers > Bruce > > On Wed, 12 May 2010, Laluz, > Victor wrote: > > > Hello guys, > > > > I am curious as to how white matter hypointensities (on T1 mprage) are > > measured automatically for the aseg.stats file in FS? A group at UCSF is > > interested in using this measure for a study and would like to have a nice > > explanation or citation to describe how it is generated. > > > > I have looked through what I think the likely citations would be on the > > Freesurfer techniques article listing and came up empty. > > > > Thanks! > > > > Victor > > > > Victor Laluz : Imaging Coordinator : UCSF Memory and Aging Center > > > > > ___ > 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. > > -- Irene Altarelli Laboratoire de Sciences Cognitives et Psycholinguistique Ecole Normale Supérieure 29, rue d'Ulm 75005 Paris tel. +33 (0)1 44 32 26 23 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] problem with labels
Dear Freesurfers, I have a problem with labels. I select a given Talairach coordinate that interests me, draw an approximately circular label around it in tksurfer, and save it. When I open that same label in tkmedit, the central Talairach coordinate is changed and the whole label is somewhat shifted. Am I missing something? Should I use mri_label2vol or some other command? Thanks very much in advance! Irene -- Irene Altarelli Laboratoire de Sciences Cognitives et Psycholinguistique Ecole Normale Supérieure 29, rue d'Ulm 75005 Paris tel. +33 (0)1 44 32 26 23 ___ 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] Visualizing SPM Results on Template FreeSurfer Brain
Dear Doug and Freesurfer experts, I have a question related to the previous post. I have two groups (patients and controls), for which I have both functional and T1 data. I'd like to look at differences in cortical thickness between the groups inside some clusters of functional activation. Would it be wrong to overlay the activations (spmT.img maps) on fsaverage, convert them into labels (through Fill Stats) and use label2label to map them to each subject's surface? Thanks very much! Irene Le mardi 15 mars 2011 à 16:08 -0400, Douglas N Greve a écrit : > After you've gone into MNI space with all of your subjects, then > visualizing the results on the surface are of questionable value. If you > just want to take a peek, then it's not a big deal, but I would not > recommend reporting them in a publication. If your results are in the > mni152 space, you can try > > tksurfer fsaverage lh inflated -aparc -mni152reg yourfile.img > > doug > > Andrew Jahn wrote: > > Hello, > > > > I have second-level results in .img/.hdr format that I have just run > > through SPM. I was wondering whether there is a way to visualize > > these results onto a template FreeSurfer surface model in MNI space. > > Is this possible, or can you only visualize second-levels which have > > been processed through FreeSurfer? > > > > > > Thanks, > > > > -Andrew > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- Irene Altarelli Laboratoire de Sciences Cognitives et Psycholinguistique Ecole Normale Supérieure 29, rue d'Ulm 75005 Paris tel. +33 (0)1 44 32 26 23 ___ 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] flipping left-right
Dear Fs experts, I've been processing a whole group of subjects, manually correcting the surfaces, and I just noticed that a small part of that sample was badly oriented (right-left). Should I flip the initial images and reprocess/recorrect them...? Would the result of mris_reverse be as good? Thanks very much for your help! Irene -- Irene Altarelli Laboratoire de Sciences Cognitives et Psycholinguistique Ecole Normale Supérieure 29, rue d'Ulm 75005 Paris tel. +33 (0)1 44 32 26 23 ___ 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] Wm segmentation problem
Dear Freesurfers, we are processing a dataset of children through recon-all, applying manual corrections when needed. For one subject, after manual correction and running autorecon2-cp, we observe errors in wm segmentation, bilaterally, with portions of gm included in wm - as can be seen in the attached picture. This concerns most of the coronal slices. We have been checking that control points were not misplaced and they look ok to us. What do you think is happening there and is there anything we can try before manually correcting these errors? Thanks very much in advance, Irene -- Irene Altarelli Laboratoire de Sciences Cognitives et Psycholinguistique Ecole Normale Supérieure 29, rue d'Ulm 75005 Paris tel. +33 (0)1 44 32 26 23 <>___ 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] Wm segmentation problem
Dear Khoa and Bruce, thanks for replying so fast. The wm.mgz does not look correct either. I have uploaded the subject using the second option. Thanks again, Irene Le lundi 06 juin 2011 à 07:46 -0400, Khoa Nguyen a écrit : > Hi Irene, > > Is the wm segmentation correct in the wm.mgz? If you want, you can upload > the subject and I can take a look. > > You can try using this website > http://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange > > If that doesn't work, try this one > https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > -Khoa > > On Mon, 6 Jun 2011, Irene Altarelli wrote: > > > Dear Freesurfers, > > > > we are processing a dataset of children through recon-all, applying > > manual corrections when needed. > > > > For one subject, after manual correction and running autorecon2-cp, we > > observe errors in wm segmentation, bilaterally, with portions of gm > > included in wm - as can be seen in the attached picture. This concerns > > most of the coronal slices. We have been checking that control points > > were not misplaced and they look ok to us. > > > > What do you think is happening there and is there anything we can try > > before manually correcting these errors? > > > > Thanks very much in advance, > > Irene > > > > > > > > > ___ > 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. > > -- Irene Altarelli Laboratoire de Sciences Cognitives et Psycholinguistique Ecole Normale Supérieure 29, rue d'Ulm 75005 Paris tel. +33 (0)1 44 32 26 23 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
