Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30093 discussions

tracula longitudinal
by Cat Chong 30 Jan '13

30 Jan '13

Hello Experts, Please forgive another question. I have run 59 people through the recon-all freesurfer longitudinal stream with 2 timepoints (tp1id, tp2id). I want to run these subjects through "tracula" next, since the same people also received repeated Tensor imaging. To process everybody through tracula, I would use each person's original (cross-sectional) recon-all output and not the template or -long recon-all output, correct? Best regards, Catherine

2 1

Delay
by Varghese Chikku 30 Jan '13

30 Jan '13

Dear All, I ran a test subject on VM and the process took 20 hrs to complete.But the same images on Mc pro took 58 hours.VM is 8GB and Mpro is 16 GB.I have noticed this delay happening in the past as well,where VM takes 20-24 for a single patient and Mc takes 24-30 for the same.But,this time ,its was so unexpected.Why is this happening?.Which would be more accurate,and does it mean that more time FS take,the better the results? Many thanks Chikku

3 7

Re: [Freesurfer] beta
by Bruce Fischl 30 Jan '13

30 Jan '13

thanks Fidel we will certainly take you up on it in the next submission Bruce On Wed, 30 Jan 2013, Fidel Vila wrote: > Sorry to hear about this. If there is anything it can be done at a "FS-virtual-community" level that could support the funding request, I'd be supportive of it. > > Fidel > On 2013-01-30, at 9:43, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > >> thanks Joshua >> >> I wish study sections agreed with you. We will probably put in another support grant in the next year when I work up the energy to write one (they are quite dull). I'll probably request support letters at that time. >> >> cheers >> Bruce >> >> >> On Wed, 30 Jan 2013, Joshua Lee wrote: >> >>> This news is most unfortunate. We all appreciate the Freesurfer team's work. Freesurfer, and project's like >>> these, provide a substantial multiplier effect to the productivity of the neuroscience community. There >>> should be more funding for these types of neuroscience research infrastructure. >>> - >>> Joshua >>> On Wed, Jan 30, 2013 at 7:50 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: >>> Hi Ed >>> >>> I mean that the grant funding FreeSurfer maintainance didn't get renewed. We certainly will >>> continue support and development, but it does have a substantial negative impact on the >>> engineering we can do, such as getting rid of the 1mm restrictions. >>> >>> cheers >>> Bruce >>> >>> On Wed, 30 Jan 2013, Ed Gronenschild wrote: >>> >>> Hi Bruce, >>> What do you mean: no support anymore or no new development? >>> >>> Cheers, >>> Ed >>> >>> On 30 Jan 2013, at 13:41, Jacobs H (NP) wrote: >>> >>> Message: 7 >>> Date: Mon, 21 Jan 2013 19:19:25 -0500 (EST) >>> From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >>> Subject: Re: [Freesurfer] beta >>> To: Colin Reveley <reveley(a)gmail.com> >>> Cc: Joshua Lee >>> <jkilee(a)ucdavis.edu>, freesurfer(a)nmr.mgh.harvard.edu, >>> Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> >>> Message-ID: >>> <alpine.LRH.2.00.1301211918340.29285(a)entry.nmr.mgh.harvard.edu> >>> Content-Type: text/plain; charset="iso-8859-1" >>> >>> Hi Colin >>> >>> yes, but we simply don't have the person power to do it at the >>> moment. Our >>> FS support grant ends in a month and is not going to get >>> renewed, so it's >>> going to be hard to do anytime soon. >>> >>> sorry >>> Bruce >>> _______________________________________________ >>> 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 >> >> >> 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. > > >

1 0

mris_pmake
by Andrew Bock 30 Jan '13

30 Jan '13

Dear all, I am trying to calculate the distance from a reference vertex to all other vertices in a surface mesh (or ideally to a subset of vertices), moving along the actual surface (e.g. smoothwm). I am able to loop through the pairs of vertices in which I'm interested, using mris_pmake in each loop, but this is quite time consuming. I have tried using '--mpmProg autodijk' as described in the mris_pmake help file, but have been unsuccessful at getting this command to work. The current code I am using for each pair is: mris_pmake --subject <subject> --surface0 smoothwm --curv0 sulc --curv1 sulc --mpmOverlay euclidean --mpmProg pathFind --mpmArgs startVertex:###,endVertex:### Any suggestions to cut down my processing time, while still calculating along the surface, would be greatly appreciated. Andrew

2 1

tracula batch processing
by Cat Chong 30 Jan '13

30 Jan '13

Hello Experts, Unfortunately I am currently only able to run tracula on a personal computer, System Version: Mac OS X 10.6.7 (10J869) Kernel Version: Darwin 10.7.0. I have no problem running a single subject on the dmrirc_single subject configuration file. When I try to run several subjects as described in the configuration file on the tracula tutorial page http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula it finishes without errors but only the first subject gets processed. Do you have any ideas of what I am doing wrong? cheers, Cat

2 1

Re: [Freesurfer] mean cortical thickness of significant clusters in qdec
by Douglas Greve 30 Jan '13

30 Jan '13

Oh, sorry, I thought you said you were using mri_glmfit-sim (which does not have an FDR option). Are you using the FDR in QDEC? If so, it will display the voxel-wise threshold that realizes the FDR threshold. You can then run mri_glmfit-sim --cache threshold sign --cwpvalthresh .99 where threshold is the voxelwise threshold from FDR and sign is either abs (absolute), pos, or neg. Setting cwpvalthresh=.99 tell it to report all clusters doug On 1/30/13 8:09 AM, Richter, Julia wrote: > No it is not...or I just do not find it. > > Might it be that I only get the xxx.y.ocn.dat if I correct for multiple comparisons with Monte Carlo? If yes, is there any possibility that I get this xxx.y.ocn.dat when correcting with FDR? > > Many thanks, Julia > > -----Ursprüngliche Nachricht----- > Von: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Douglas N Greve > Gesendet: Dienstag, 29. Januar 2013 18:46 > An: freesurfer(a)nmr.mgh.harvard.edu > Betreff: Re: [Freesurfer] mean cortical thickness of significant clusters in qdec > > Hi Julia, it should just be created when mri_glmfit-sim runs. Is it not? > doug > > > On 01/29/2013 11:03 AM, Richter, Julia wrote: >> Dear FreeSurfer experts, >> >> I did a group analysis in qdec, found several significant clusters and >> would now like to extract the mean cortical thickness of each >> significant cluster. I know that I have to run mri_glmfit-sim to do >> this, but I do not understand which commands I need to get the >> xxx.y.ocn.dat as output by running mri_glmfit-sim. >> >> Any ideas? Any help is appreciated. J >> >> Best wishes, Julia >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > 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. > > >

1 0

TRACULA
by stdp82＠virgilio.it 29 Jan '13

29 Jan '13

Hi Anastasia, I put my files in a folder /Application/freesurfer/subjects/subject_prova/Diff01/ File are these:data.nii.gz (DWI data, 16 directions)TI_CON_01.nii.gz (T1 structural images)bvals.txt and bvecs.txt (as you can see in the previously attacked files). Could error depends from the use of the . or , that was used to separate the decimal?Is corrects the name of the 4 files in the Diff01 folder (FSL.nii.gz and its directory)I have previously used this data in FSL for TBSS. I only inverted the matrix of bvals (FLS:1x16, fs:16x1) and (FSL:3x16; fs:16x3)Is the configuration file good? Thank you very much for you kindness and avaibility. Stefano ----Messaggio originale---- Da: ayendiki(a)nmr.mgh.harvard.edu Data: 29-gen-2013 15.42 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: R: Re: TRACULA Hi Stefano - Are the files that you're attaching the ones from the dmri directory or are they the original files that you specified in your configuration file? I'm guessing they're not the dmri/bv??s files because then they'd be formatted in rows and not columns. Without seeing the bvecs from your dmri directory my best guess for what could be causing the error is this: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg26026.html a.y On Tue, 29 Jan 2013, stdp82(a)virgilio.it wrote: > > Hi list, > > I'm trying to run trac-all on one subject and have a problem with the > bvecs file at the -prep stage. > After dtifit is started an error massage occurs: Error: bvecs and bvals don' > t have the same number of entries: > > [iMac-di-Stefano:/Applications/freesurfer/subjects] Stefano% trac-all -prep > -c /Users/Stefano/Desktop/dmrirc_single_subject > INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/subject_prova > INFO: Diffusion root is /Applications/freesurfer/subjects/subject_prova > Actual FREESURFER_HOME /Applications/freesurfer > trac-preproc -c /Applications/freesurfer/subjects/subject_prova/Diff01/scrip > ts/dmrirc.local -log /Applications/freesurfer/subjects/subject_prova/Diff01/ > scripts/trac-all.log -cmd /Applications/freesurfer/subjects/subject_prova/Di > ff01/scripts/trac-all.cmd > #------------------------------------- > /Applications/freesurfer/bin/trac-preproc > #------------------------------------- > #@# Image corrections Mar 29 Gen 2013 13:51:50 CET > mri_convert /Applications/freesurfer/subjects/subject_prova/Diff01/data.nii. > gz /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.nii. > gz > mri_convert /Applications/freesurfer/subjects/subject_prova/Diff01/data.nii. > gz /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.nii. > gz > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ > reading from /Applications/freesurfer/subjects/subject_prova/Diff01/data.nii > .gz... > TR=1000.00, 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) > writing to /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_o > rig.nii.gz... > cp /Applications/freesurfer/subjects/subject_prova/Diff01/bvecs.txt /Applica > tions/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.mghdti.bvecs > cp /Applications/freesurfer/subjects/subject_prova/Diff01/bvals.txt /Applica > tions/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.mghdti.bvals > flip4fsl /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_ori > g.nii.gz /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_ori > g_flip.nii.gz > INFO: input image orientation is LAS > INFO: input image determinant is -1 > fslswapdim /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_o > rig.nii.gz x y z /Applications/freesurfer/subjects/subject_prova/Diff01/dmri > /dwi_orig_flip.nii.gz > fslorient -forceradiological /Applications/freesurfer/subjects/subject_prova > /Diff01/dmri/dwi_orig_flip.nii.gz > INFO: found /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_ > orig.mghdti.bvals, converting to FSL format > INFO: found /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_ > orig.mghdti.bvecs, converting to FSL format > mv -f /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig_f > lip.mghdti.bvecs /Applications/freesurfer/subjects/subject_prova/Diff01/dmri > /bvecs > mv -f /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig_f > lip.mghdti.bvals /Applications/freesurfer/subjects/subject_prova/Diff01/dmri > /bvals > eddy_correct /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi > _orig_flip.nii.gz /Applications/freesurfer/subjects/subject_prova/Diff01/dmr > i/dwi.nii.gz 0 > processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t > mp0000 > processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t > mp0001 > processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t > mp0002 > processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t > mp0003 > processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t > mp0004 > processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t > mp0005 > processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t > mp0006 > processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t > mp0007 > processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t > mp0008 > processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t > mp0009 > processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t > mp0010 > processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t > mp0011 > processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t > mp0012 > processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t > mp0013 > processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t > mp0014 > processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t > mp0015 > mv -f /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvecs /App > lications/freesurfer/subjects/subject_prova/Diff01/dmri/bvecs.norot > xfmrot /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi.ecclo > g /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvecs.norot /A > pplications/freesurfer/subjects/subject_prova/Diff01/dmri/bvecs > fslroi /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi.nii.g > z /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb.nii.gz 0 > 1 > fslmaths /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb.ni > i.gz -Tmean /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb > .nii.gz > bet /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb.nii.gz > /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb_brain.nii.g > z -m -f 0.3 > mv -f /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb_brain > _mask.nii.gz /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/d > iff > #------------------------------------- > #@# Inter-subject registration Mar 29 Gen 2013 14:05:11 CET > flirt -in /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb_b > rain.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -ou > t /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb_brain_mni > .nii.gz -omat /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/xf > ms/diff2mni.mat -cost mutualinfo > convert_xfm -omat /Applications/freesurfer/subjects/subject_prova/Diff01/dmr > i/xfms/mni2diff.mat -inverse /Applications/freesurfer/subjects/subject_prova > /Diff01/dmri/xfms/diff2mni.mat > #------------------------------------- > #@# Masks Mar 29 Gen 2013 14:06:35 CET > #------------------------------------- > #@# Tensor fit Mar 29 Gen 2013 14:06:35 CET > dtifit -k /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi.ni > i.gz -m /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/diff/l > owb_brain_mask.nii.gz -r /Applications/freesurfer/subjects/subject_prova/Dif > f01/dmri/bvecs -b /Applications/freesurfer/subjects/subject_prova/Diff01/dmr > i/bvals -o /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dtifi > t > Error: bvecs and bvals don't have the same number of entries > Darwin iMac-di-Stefano.local 12.2.1 Darwin Kernel Version 12.2.1: Thu Oct 18 > 12:13:47 PDT 2012; root:xnu-2050.20.9~1/RELEASE_X86_64 x86_64 > > I checked the dmri/bvals and dmri/bvecs and attached them. > > Thank you very much. > > Stefano > > > ----Messaggio originale---- > Da: ayendiki(a)nmr.mgh.harvard.edu > Data: 29-gen-2013 0.44 > A: <stdp82(a)virgilio.it> > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] R: Re: R: Re: R: R: Re: TRACULA > > > Hi Stefano - The file that you defined as your gradient vector file (set > bvecfile = ...) doesn't exist. This file has to exist. > > Hope this helps, > a.y > > On Tue, 29 Jan 2013, stdp82(a)virgilio.it wrote: > > > Hi Anastasia, > > > > I have prepared this configuration file: > > > > > > # > > # Set locations of diffusion DICOMs, diffusion output, FreeSurfer recons > > # > > # This file contains commands that will be run by trac-all before an > > analysis. > > # It is used to set all parameters needed for the analysis. > > # > > # Remove a parameter from your dmrirc file if you want to use the default > > value. > > # Parameters that don't have default values must be specified. > > # > > # Any other commands that you might want to run before an analysis can be > > added > > # to this file. > > # > > # Original Author: Anastasia Yendiki > > # CVS Revision Info: > > # $Author: ayendiki $ > > # $Date: 2010/12/15 08:36:00 $ > > # $Revision: 1.1 $ > > # > > # Copyright (C) 2010 > > # The General Hospital Corporation (Boston, MA). > > # All rights reserved. > > # > > # Distribution, usage and copying of this software is covered under the > > # terms found in the License Agreement file named 'COPYING' found in the > > # FreeSurfer source code root directory, and duplicated here: > > # https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOpenSourceLicense > > # > > # General inquiries: freesurfer(a)nmr.mgh.harvard.edu > > # > > # FreeSurfer SUBJECTS_DIR > > # setenv SUBJECTS_DIR $FREESURFER_HOME/subjects/subject_prova > > # Output directory where trac-all results will be saved > > set dtroot = $SUBJECTS_DIR > > # Subject IDs > > set subjlist = (Diff01) > > set runlist = (1) > > # Input diffusion DICOMs (file names relative to dcmroot) > > set dcmroot = $SUBJECTS_DIR > > set dcmlist = (Diff01/data.nii.gz) > > set bvalfile = $SUBJECTS_DIR/bvals.txt > > set bvecfile = $SUBJECTS_DIR/bvecs.txt > > set nb0 = 1 > > set doeddy = 1 > > set dorotbvecs = 1 > > set thrbet = 0.3 > > set doregflt = 1 > > set doregbbr = 1 > > set doregmni = 1 > > set mnitemp = Users/Stefano/Desktop/MNI152_T1_1mm_brain.nii.gz > > set trainfile = > > $TUTORIAL_DATA/diffusion_tutorial/scripts/subj,train,difftutorial32.txt > > # Paths to reconstruct > > # Default: All paths > > set pathlist = (lh.cst_AS rh.cst_AS \ > > lh.ilf_AS rh.ilf_AS \ > > lh.unc_AS rh.unc_AS \ > > fmajor_PP fminor_PP \ > > lh.atr_PP rh.atr_PP \ > > lh.cab_PP rh.cab_PP \ > > lh.ccg_PP rh.ccg_PP \ > > lh.slfp_PP rh.slfp_PP \ > > lh.slft_PP rh.slft_PP) > > > > # Number of path control points > > # Default: 5 > > set ncpts = 5 > > > > When I run this, I have: > > > > [iMac-di-Stefano:/Applications/freesurfer/subjects] Stefano% trac-all > -prep > > -c /Users/Stefano/Desktop/dmrirc_single_subject > > INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/subject_prova > > INFO: Diffusion root is /Applications/freesurfer/subjects/subject_prova > > Actual FREESURFER_HOME /Applications/freesurfer > > trac-preproc-c/Applications/freesurfer/subjects/subject_prova/Diff01/scripts/dmrirc.loc > al > >-log/Applications/freesurfer/subjects/subject_prova/Diff01/scripts/trac-all > .log > >-cmd/Applications/freesurfer/subjects/subject_prova/Diff01/scripts/trac-all > .cmd > > #------------------------------------- > > /Applications/freesurfer/bin/trac-preproc > > #------------------------------------- > > #@# Image corrections Mar 29 Gen 2013 00:32:23 CET > > mri_convert > >/Applications/freesurfer/subjects/subject_prova/Diff01/data.nii.gz/Applicat > ions/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.nii.gz > > mri_convert > >/Applications/freesurfer/subjects/subject_prova/Diff01/data.nii.gz/Applicat > ions/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.nii.gz > > > > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ > > reading from > > /Applications/freesurfer/subjects/subject_prova/Diff01/data.nii.gz... > > TR=1000.00, 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) > > writingto/Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.nii. > gz > > ... > > cp/Applications/freesurfer/subjects/subject_prova/bvecs.txt/Applications/free > surfer/subjects/subject_prova/Diff01/dmri/dwi_orig.mghdti > > .bvecs > > cp: /Applications/freesurfer/subjects/subject_prova/bvecs.txt: No such > file > > or directory > > Darwin iMac-di-Stefano.local 12.2.1 Darwin Kernel Version 12.2.1: Thu Oct > 18 > > 12:13:47 PDT 2012; root:xnu-2050.20.9~1/RELEASE_X86_64 x86_64 > > > > I apologize but I need to have your help. > > > > Thank you very much, > > > > > > Stefano > > > > > > > > ----Messaggio originale---- > > Da: ayendiki(a)nmr.mgh.harvard.edu > > Data: 28-gen-2013 20.03 > > A: <stdp82(a)virgilio.it> > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > Ogg: Re: [Freesurfer] R: Re: R: R: Re: TRACULA > > > > > > Hi Stefano - Type "which trac-all" to find out where trac-all lives on > > your computer, then copy the updated version over it. > > > > a.y > > > > On Mon, 28 Jan 2013, stdp82(a)virgilio.it wrote: > > > > > Thank you very much for you kindness Anastasia. > > > The folder that contains .nii.gz file is correct? > > > I'm looking the recommended trac-all update. Where can I put it? > > > > > > Stefano > > > > > > > > > ----Messaggio originale---- > > > Da: ayendiki(a)nmr.mgh.harvard.edu > > > Data: 28-gen-2013 16.45 > > > A: <stdp82(a)virgilio.it> > > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > > Ogg: Re: [Freesurfer] R: R: Re: TRACULA > > > > > > > > > Hi Stefano - The argument of the -c option is a configuration file, not > a > > > directory. For more info on trac-all and setting up the configuration > > > file, please see the trac-all wiki page: > > > http://www.freesurfer.net/fswiki/trac-all > > > and tracula tutorials: > > > http://www.freesurfer.net/fswiki/FsTutorial/Tracula > > > > > > a.y > > > > > > On Mon, 28 Jan 2013, stdp82(a)virgilio.it wrote: > > > > > > > Hi and thank you very much for your availability. > > > > Now, I'm running tracula as following: > > > > > > > > trac-all -prep -c > /Applications/freesurfer/subjects/subject_prova/CON_01 > > > > > > > > my CON_01 forder contains: data.nii.gz (DWI), bvals and bvecs (as used > > in > > > > > previous FSL analysis) and T1-images.nii.gz. File.niii.gz are the > same > > > > that I have previously used in FSL analysis. > > > > > > > > Please, my questions are: > > > > a- Are correct the command and the files (dyrectory positioning and > > their > > > > extensions)? > > > > b- Now my computer seem to running but after 1 h from the start, I > > > visualize > > > > on my desktop this message "Your Mac 0SX has no more space available > for > > > > application memory". > > > > My pc is a iMAC OS X Mountain Lion. 2.7 GHz Intel Core i5; 8GB 1600 > MHz > > > > DDR3; NVIDIA GeForce DT640M 512 MB; 762,42 GB are free on a total of > > > 999,35 > > > > I have download the package for (Snow)Leopard (10.5/6.x) Intel. > > > > > > > > Thanks, > > > > > > > > > > > > Stefano > > > > > > > > > > > > ----Messaggio originale---- > > > > Da: ayendiki(a)nmr.mgh.harvard.edu > > > > Data: 27-gen-2013 19.36 > > > > A: <stdp82(a)virgilio.it> > > > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > > > Ogg: Re: [Freesurfer] TRACULA > > > > > > > > Hi Stefano - The -prep option doesn't take an argument. Please run > > > > trac-all with no arguments to see usage info. > > > > > > > > a.y > > > > > > > > > Hi list, > > > > > I'm trying to run a test subject with TRACULA. > > > > > I placed a folder in /Applications/freesurfer/subject/subject_prova > > > which > > > > > contains these files: data.nii.gz (DWI), bvals and bvecs (as used in > > > > > previous FSL analysis) and T1-images.in > > > > > /Applications/freesurfer/subject/subject_prova > > > > > This is the command that I'm running:[iMac-di-Stefano:~] Stefano% > > > trac-all > > > > > -prep $FREESURFER_HOME/subjects/subject_prova/CON_01 --i > > > > > $FREESURFER_HOME/subjects/subject_prova > > > > > ERROR: flag > > > > > > > /Applications/freesurfer/subjects/subject_prova/CON_01unrecognized-prep > > > > > /Applications/freesurfer/subjects/subject_prova/CON_01 --i > > > > > /Applications/freesurfer/subjects/subject_prova > > > > > Please, give me an help. > > > > > > > > > > Thanks in advance, > > > > > > > > > > Stefano _______________________________________________ > > > > > 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 > > > > > > > > > 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 > > > > > > 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 > > > 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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entorhinal cortex volume question
by Cat Chong 29 Jan '13

29 Jan '13

Hello experts, I am very new to freesurfer so please excuse my basic question: We want to get measurements of entorhinal cortex volumes on a group of people. I found these results listed in ?h.aparc.stats. I also noticed another ?h.entorhinal_exvivo.stats, with different results. Which should I use for a group analysis of entorhinal volume and surface area, and why are the results very different? very best regards, catherine

3 4

diluting a mask using inflated brain
by Jodie Davies-Thompson 29 Jan '13

29 Jan '13

Dear Freesurfer users and experts, We are attempting to grow a mask that we have created in FSL, to expand it into white matter. At first, we tried this in FSL using the dilM command which dilated the size of the mask by n voxels. We then multiplied this by a segmented white matter mask (again, created in FSL) so only the white matter voxels were included. However, a problem with this method, is that if a mask is over a gyri (as most of our masks are), then diluting the mask in a non-inflated brain causes some voxels from an adjacent gyri to be included. What we would like to be able to do, is to dilute the mask using the inflated white matter brain created by Freesurfer, and then to take this back into FSL space; thereby, allowing us to create a mask of which includes the true surrounding white matter rather than white matter from adjacent gyri. Hope this makes sense!? Does anyone know how to do this or could point us in the right direction? Cheers, Jodie - --- Jodie Davies-Thompson, Postdoctoral Fellow Department of Ophthalmology & Visual Sciences UBC/VGH Eye Care Centre 2550 Willow Street Vancouver, BC, V5Z 3N9 Canada Tel: 604-875-4111<Tel:604-875-411> ext 69003

3 2

Postdoctoral Position in Australia
by Nicolas Cherbuin 29 Jan '13

29 Jan '13

Post-doc position available immediately within the Centre for Research on Ageing, Health and Wellbeing, College of Medicine, Biology and the Environment, Australian National University, Canberra, Australia. We are seeking a junior Postdoctoral Fellow to join a small collaborative team working on research aimed at characterising normal brain ageing in mid-life and into old age. This research includes using large neuroimaging datasets, studying cognitive correlates of age-related brain changes, identifying predictors and risk factors for brain and cognitive ageing, and test theoretical models of neuro-cognitive ageing. Working closely with Dr Nicolas Cherbuin, the research involves, processing and analysing structural brain scans and conducting research with a dynamic multi-disciplinary team. The successful applicant will hold a PhD in Psychology or equivalent and will have a research record in a field relevant to the project with demonstrated experience in processing and analysing neuroimaging data using FSL/Freesurfer or equivalent. An interest in ageing/lifespan development research will be highly regarded. Applications are required to be lodged online, please submit a summary of claims against the selection criteria along with your CV. Full details can be found here: http://jobs.anu.edu.au/PositionDetail.aspx?p=3120 Enquiries: Dr Nicolas Cherbuin Phone: 02 61253858 Email: nicolas.cherbuin(a)anu.edu.au Nicolas Cherbuin PhD ARC Research Fellow Director of the NeuroImaging and Brain Lab Centre for Research on Ageing, Health and Wellbeing College of Medicine Biology and Environment 62A Eggleston Road Australian National University Canberra ACT 0200 P: +61 2 6125 3858 F: +61 2 6125 1558 E: nicolas.cherbuin(a)anu.edu.au W: ageing.anu.edu.au/research/projects/nimbl.php CRICOS Provider #00120C

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