Freesurfer October 2009

freesurfer@nmr.mgh.harvard.edu

99 participants
151 discussions

nu_correct or mri_nu_correct
by McLean John (NHS Greater Glasgow & Clyde) 16 Oct '09

16 Oct '09

> Hi, > > What's the difference between applying nu_correct and mri_nu_correct? > > Many thanks > John ******************************************************************************************************************** This message may contain confidential information. If you are not the intended recipient please inform the sender that you have received the message in error before deleting it. Please do not disclose, copy or distribute information in this e-mail or take any action in reliance on its contents: to do so is strictly prohibited and may be unlawful. Thank you for your co-operation. NHSmail is the secure email and directory service available for all NHS staff in England and Scotland NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and GSI recipients NHSmail provides an email address for your career in the NHS and can be accessed anywhere For more information and to find out how you can switch, visit www.connectingforhealth.nhs.uk/nhsmail ********************************************************************************************************************

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Segmentation fault ...
by Erick Jorge Canales 16 Oct '09

16 Oct '09

Dear experts, The recon-all process of some of my subjects (15 from 100) exited with ERRORS ... I got in the recon-all file of one of them the following report: ... Reporting on 49 segmentations #-------------------------------------------- #@# Cortical ribbon mask Sat Aug 29 13:09:43 CEST 2009 /mnt/HDD1/FreeSurfer_Cortical/Results/Prueba/Cont_FreeSurf_BMJGR19839SC/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance Cont_FreeSurf_BMJGR19839SC SUBJECTS_DIR is /mnt/HDD1/FreeSurfer_Cortical/Results/Prueba Segmentation fault Linux uifsl5 2.6.26-1-amd64 #1 SMP Thu Oct 9 14:16:53 UTC 2008 x86_64 GNU/Linux recon-all exited with ERRORS at Sat Aug 29 13:19:32 CEST 2009 ... Is there any way to fix this problem? My computer have 8 cores and 16 Gb of RAM, in general I have been running 6 recon-all jobs concurrently. I'm running this version: freesurfer-Linux-centos4_x86_64-stable-pub-v4.1.0 Many thanks in advance, Regards, Erick

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Re: [Freesurfer] processing time for autorecon1 in Freesurfer v4.5
by Chris Hyatt 16 Oct '09

16 Oct '09

autorecon2 takes about 15.5 hours on the Blade 2.0 GHz running FS v4.5 versus 9.8 hours on the 3.2 GHz computer running v4.0.5, but this is in line with the increased clock speed of the second computer (1.6x faster than the Blade). Thanks, Chris >>> Bruce Fischl 10/16/09 7:25 AM >>> are all the steps taking longer, or are some binaries longer than others On Thu, 15 Oct 2009, Alexander Zaitsev (CNI) wrote: > We are having the same issue after upgrade to FreeSurfer 4.5. > It takes more than 1.5 hrs for the jobs that used to complete in less > than 30 minutes. > > Alex Zaitsev > > Chris Hyatt wrote: >> >> We recently installed a Dell Blade server cluster running Freesurfer >> v4.5 under CentOS 64-bit Linux, with each Blade server having two >> Intel Xeon E5405 quad core CPUs, running at 2.0 GHz, 2x6144 KB cache >> and 16 GB of RAM, with a swap file of size between 8-16 GB. >> >> Using a single Blade server of this cluster, a single subject takes >> between 70 and 100 minutes to complete the Freesurfer autorecon1 >> stage, which seems overly long. >> >> We also have another computer, running an older version of Freesurfer >> (v4.0.5) under Fedora 64-bit Linux. This computer is similar to a >> single Blade server - it has two Xeon X5482 quad core CPUs, running at >> 3.2 GHz, 2x6144 KB cache and also with 16 GB RAM with a swap file of >> 16 GB. This computer can complete autorecon1 stage in about 18 minutes. >> >> The only real difference with this computer and the Blade computers >> that I aware of is the clock speed (3.2 vs 2.0 GHz, 1.6x faster), so >> the Dell Blade computers should be able to complete autorecon1 in no >> worse than about 30 minutes. >> >> Does anyone have an idea as to why Freesurfer v4.5 is running so slow >> on our Dell Blade cluster? Has anyone found the newest version of >> Freesurfer (v4.5) slower than v4.0.5? Thanks in advance for your help. >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> 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 > > >

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averaging DTI sequences
by Jose Luis Cantero Lorente 16 Oct '09

16 Oct '09

Dear Freesurfers, I have 2 identical DTI sequences for each patient (adquired within the same session), but would like to work with the average DTI sequence in all my subsequent analysis. How to obtain the average of both DTI sequences with Freesurfer, and convert the resulting file into .nii? Does the resulting nii file change the brain hemispheries? Thanks in advance. Best regards, Jose --- Jose L. Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla - Spain - Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcanlor(a)upo.es http://www.upo.es/neuroaging/en/

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test message
by Christophe Destrieux 15 Oct '09

15 Oct '09

-- Christophe Destrieux Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé 37032 Tours - France tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07

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Re: [Freesurfer] images with poor resolution
by Dana W. Moore 15 Oct '09

15 Oct '09

Hi Nick, After trying all of the steps below, the surfaces are much improved, but the pial surface still has problems, particularly in the temporal lobes (see below). So, maybe this is the best we can do with this image. Thank you for helping out with this. Thanks, Dana [] At 06:58 PM 10/5/2009, Nick Schmansky wrote: >Dana, > >First I would run: > >recon-all -s subid -clean > >to remove any prior control points and edits. > >Then I would open nu.mgz: > >tkmedit subjid nu.mgz > >and *sparingly* put control points well into white matter areas on a few >different slices. you only need a half dozen or so. to add control >points, see: > >http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints > >except you will add them to nu.mgz, to make sure that T1.mgz gets >created properly. > >Then create a file name xopts.txt containing these lines: > >mri_normalize -gentle > >Then run: > >recon-all -s subjid -autorecon1 -expert <path_to>/xopts.txt > >and when done, open brainmask.mgz > >tkmedit subjid brainmask.mgz > >and check again to get a sense of the low value for white matter and >high value for gray matter, then run: > >recon-all -s subjid -autorecon2 -seg-wlo wlo -seg-ghi ghi > >replacing wlo and ghi with those values. > >if the surfaces still look bad, you can add a line to the xopts.txt >file : > >mris_make_surfaces -max_gray val -min_gray_at_white_border val > >replacing the two 'val's with something you find appropriate, then run: > >recon-all -s subjid -autorecon2-pial -autorecon3 \ > -expert <path_to>/xopts.txt > >good luck! > >Nick > > >On Mon, 2009-10-05 at 16:56 -0400, Dana W. Moore wrote: > > Hi Nick, > > > > Below is Bruce's response to a problem I'm having with the gray/white > > segmentation. (Pasted below, you can see the brainmask.mgz volume and > > surfaces--the entire brain is labeled as white matter). I could use > > some guidance in carrying out his advice. He says to adjust the > > intensity normalization using control points and then use expert opts > > for mri_segment and mris_make_surfaces. > > > > When I look at the brain.mgz volume, the white matter tends to have an > > intensity of 110, as it should, but the gray matter at times goes as > > high as 115. I was thinking, I could set ghi to 115 and wlo to 110. > > Then, I am not sure how to actually run the corrections and what > > language to use to implement the control points and mri_segment > > adjustments. I will save control points and then run: recon-all > > -autorecon2-cp -autorecon3 -subjed <subject>. Can I somehow include > > the mri_segment adjustments into this command, or do I have to run > > that separately? > > > > I am also not sure how options for mris_make_surfaces might help. > > > > I appreciate your help with this! > > > > Thanks, > > dana > > > > > > > > > > [] > > > > At 04:40 PM 10/2/2009, Bruce Fischl wrote: > > > Hi Dana, > > > > > > it looks like the gray/white density estimation failed. Try setting > > > them with the expert opts for mri_segment and mris_make_surfaces > > > (Nick can point you in the right direction if you can't figure it > > > out). Things like max gm at white border and such. > > > > > > cheers, > > > Bruce > > > > > > p.s. it also looks like the intensity normalization went too far due > > to the low contrast. You'll probably need to add some control points > > and run it with the -gentle option > > > > > > > > > On Fri, 2 Oct 2009, Dana W. Moore wrote: > > > > > > > Hi everyone, > > > > > > > > I am trying to salvage some images that were done with poor > > > > gray/white boundary contrasts. First, FreeSurfer includes an area > > > > of dura in the skull strip. I tried adjusting the watershed but > > > > it made no differences. FreeSurfer is subsequently unable to > > > > detect the gray/white boundary and labels the dura as cortex: > > > > > > > > [] > > > > > > > > > > > > > > > > Looking at the raw images, the gray/white boundaries are faint but > > > > visible. Is there anything I can adjust to try to make this work > > > > with FreeSurfer? > > > > > > > > Thanks, > > > > Dana > > > > > > > > > > > > Dana W. Moore, Ph.D. > > > > Neuropsychology Fellow > > > > Cornell Neuropsychology Service > > > > Weill Medical College of Cornell University > > > > New York Presbyterian Hospital > > > > Department of Neurology & Neuroscience > > > > 428 East 72nd Street, Suite 500 > > > > New York, NY 10021 > > > > Phone: 212-746-2823 > > > > Fax: 212-746-5584 > > > > Email: dwm2003(a)med.cornell.edu > > > > Dana W. Moore, Ph.D. > > Neuropsychology Fellow > > Cornell Neuropsychology Service > > Weill Medical College of Cornell University > > New York Presbyterian Hospital > > Department of Neurology & Neuroscience > > 428 East 72nd Street, Suite 500 > > New York, NY 10021 > > Phone: 212-746-2823 > > Fax: 212-746-5584 > > Email: dwm2003(a)med.cornell.edu > > > > Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology Service Weill Medical College of Cornell University New York Presbyterian Hospital Department of Neurology & Neuroscience 428 East 72nd Street, Suite 500 New York, NY 10021 Phone: 212-746-2823 Fax: 212-746-5584 Email: dwm2003(a)med.cornell.edu

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Re: [Freesurfer] transverse gyrus and translucent brain renderings (fwd)
by Bruce Fischl 15 Oct '09

15 Oct '09

>From Christophe.... ------------------------ Hi Narly > Hello Christophe, hello all, > > I would like to know if the way that the transverse gyrus is labelled in > freesurfer, and specifically the fact that in the case of multiple > transverse gyri only the more anterior transverse temporal gyrus (ie; > Heschl's gyrus) is included, has changed across different releases of > freesurfer, or if it differs between the different atlases used by > freesurfer. I ask this because I see a somewhat different pattern of > results in this part of the brain when comparing output generated by > freesurfer version 3.0.5 and version 4.4. > the changed occured in 2005; but both atalases (atlas2002_simple.gcs and atlas2005_simple.gcs) were distributed for a while) In the 2002 version the parcellation was indeed different : * When several transverse temporal gyri were present they were grouped together in a common label with the sulcus limiting them (G_temp_sup-G_temp_transv_and_interm_S) * The sulcus posterior to this label was then labeled "S_temporal_transverse" I hope that it helped > More generally, I would like to know if there is any version of > freesurfer, or any atlas, that includes multiple transverse gyri when they > exist (ie; that does NOT exclude the more posterior one in cases of > multiple transverse gyri). > > thanks in advance and best wishes, > Narly. -- Christophe Destrieux Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé 37032 Tours - France tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07

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Re: [Freesurfer] isxconcat-sess
by Maximilien Chaumon 15 Oct '09

15 Oct '09

Hi freesurfers, I've been running isxconcat-sess with this line chaumon[/homes/11/chaumon/data] (nmr-std-env) isxconcat-sess -sf subjlist.txt -analysis Analyse_Simple_Confidence -c High_confidence__Low_confidence_vs_HSF_gabor__LSF_gabor -o AVG08 I was expecting to find a directory called osgm in the specified analysis directory with which I could feed data to mri_glmfit, but I can't find it. /homes/11/chaumon/bomba/AVG08/Analyse_Simple_Confidence/High_confidence__Low_confidence_vs_HSF_gabor__LSF_gabor The log file is attached. I don't find "error" in the text. Where am I wrong? Is there any mri_glmfit-sess like script somewhere? It's going to be pretty tough to find each parameter to feed to mri_glmfit... Thanks, Max

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process dying during longitudinal reconstruction
by Dana W. Moore 15 Oct '09

15 Oct '09

Hi everyone, I am trying to run the longitudinal stream on some images. I have 3 timepoints, and 2 of them finished the stream just fine, but a third quits during autorecon1 during the 3rd and final longitudinal step. There is no error message or anything, it just stops. The log file is attached--any insight into what is going wrong will be appreciated. Thanks, Dana

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Inflation Transformation
by Tina Jeon 15 Oct '09

15 Oct '09

Hello FreeSurfers, I have inflated a couple surfaces less so that the gyri and sulci are more prominent on the surface using the parameters: mris_smooth -a 70 -n 70 -nw ./subj/surf/lh.white ./subj/surf/lh.smoothwm mris_inflate -n 5 ./subj/surf/lh.smoothwm ./subj/surf/lh.inflated mris_curvature -w -a 70 -thresh .999 -distances 10 10 ./subj/surf/lh.inflated Which seemed to do the trick, however, when I viewed the surfaces on the 3D surface generator Amira, I realized that inflating less caused the left and right surfaces to shift toward each other when viewed on the same coordinate system. The left and right surfaces must have been translated somewhere in the inflation process. How do I put them back into the correct coordinate space that the pial and white surfaces are? Thank you. Tina Jeon, M.S. Project Supervisor UT Southwestern Medical Center Advanced Imaging Research Center 2201 Inwood Road, NE 3.2 Dallas, Texas 75390-8568 Office (214) 645-2766 Fax (214) 645-2744 Cell (310) 592-1853 tina.jeon(a)utsouthwestern.edu

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Freesurfer October 2009