Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30085 discussions

Re: [Freesurfer] Filling Big Ventricles
by Matt Clarkson 13 Nov '09

13 Nov '09

Hi Bruce, I agree with your point, however this method was instigated by a previous person at our institution, so I'm looking at it afresh. Also, the addition of regions 4, 43, 5 and 44 does do "something". I agree though that when I look at wm.mgz using tkmedit on a vanilla FreeSurfer run, it appears that the white matter is a grey colour, and that the vents have been filled with white (colour 255). So, is it possible that a previous version of FreeSurfer did not by default try and fill the vents in, and now version 4.5 does by default attempt to fill the vents in? Cheers Matt ----- Original Message ----- From: "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> To: "Matt Clarkson" <clarkson(a)drc.ion.ucl.ac.uk> Cc: freesurfer(a)nmr.mgh.harvard.edu Sent: Friday, November 13, 2009 2:25:16 PM GMT +00:00 GMT Britain, Ireland, Portugal Subject: Re: [Freesurfer] Filling Big Ventricles Hi Matt, the -bigventricles stuff is something I messed with for a while, but didn't get to work robustly and haven't gotten back to it. I'm not sure I understand your fix though. If the aseg properly labels the ventricles, then they should be filled in the wm.mgz, and if the aseg doesn't, then your fix doesn't help. Do you manually correct before doing this? cheers, Bruce On Fri, 13 Nov 2009, Matt Clarkson wrote: > Hi there, > > we have various Alzheimer cases, where the FreeSurfer pipeline can occasionally struggle to correctly segment the ventricles, which results in white matter and pial surfaces "leaking" into the ventricles. > > I have tried using -bigventricles passed into the autorecon2 stage, but I can't tell if its doing much. I checked the log files, and you can see -bigventricles passed to several binaries such as mri_ca_register and mri_ca_label, so the flag is definitely being passed from the command line. > > Is the -bigventricles meant to be used in this way, and what should it be doing? > > Also, I notice that the binary mri_edit_wm_with_aseg has a flag -fillven, but I can't find the documentation to say what it does and if I should be using it. > > So, we have previously used a technique whereby we run freesurfer once then create a vents image like: > mri_binarize --i aparc+aseg.mgz --match 4 --match 43 --match 5 --match 44 --o vents.mgz --binval 255 > > and then add this into the wm.mgz to fill some holes in. I have attached two .png files to illustrate the effect. In this example, I have chosen the slice where the surfaces just start to leak into the ventricles. So, on these snapshots, the problem looks quite small, but on other subsequent slices, you can get fairly large leakage into the ventricles. > > So, with these options, what would be the best way to cope with very abnormal ventricles? > > Many thanks in advance. > > Matt Clarkson > > Senior Research Associate > Dementia Research Centre > UCL > Institute Of Neurology > Queen Square > London WC1N 3BG > > m.clarkson(a)ucl.ac.uk > Tel: 08451 555 000 ext. 723653 > Fax: 020 7676 2066 > > >

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Filling Big Ventricles
by Matt Clarkson 13 Nov '09

13 Nov '09

Hi there, we have various Alzheimer cases, where the FreeSurfer pipeline can occasionally struggle to correctly segment the ventricles, which results in white matter and pial surfaces "leaking" into the ventricles. I have tried using -bigventricles passed into the autorecon2 stage, but I can't tell if its doing much. I checked the log files, and you can see -bigventricles passed to several binaries such as mri_ca_register and mri_ca_label, so the flag is definitely being passed from the command line. Is the -bigventricles meant to be used in this way, and what should it be doing? Also, I notice that the binary mri_edit_wm_with_aseg has a flag -fillven, but I can't find the documentation to say what it does and if I should be using it. So, we have previously used a technique whereby we run freesurfer once then create a vents image like: mri_binarize --i aparc+aseg.mgz --match 4 --match 43 --match 5 --match 44 --o vents.mgz --binval 255 and then add this into the wm.mgz to fill some holes in. I have attached two .png files to illustrate the effect. In this example, I have chosen the slice where the surfaces just start to leak into the ventricles. So, on these snapshots, the problem looks quite small, but on other subsequent slices, you can get fairly large leakage into the ventricles. So, with these options, what would be the best way to cope with very abnormal ventricles? Many thanks in advance. Matt Clarkson Senior Research Associate Dementia Research Centre UCL Institute Of Neurology Queen Square London WC1N 3BG m.clarkson(a)ucl.ac.uk Tel: 08451 555 000 ext. 723653 Fax: 020 7676 2066

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nu_correct problem.
by Mr k hanimireddy 13 Nov '09

13 Nov '09

Hi Bruce, I got a problem with mri_nu_correct in recon-all process. After mri_nu_corret step, nu.mgz looks oversmoothed. Could you please let me know why this is happening and how can I get rid of this? This is happening with few images only. I attached original (001.mgz), nu corrected (nu.mgz) images and mri_nu_correct.mni.log file for your reference. Thanks in advance! Reddy. The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. http://in.yahoo.com/

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recon without normalization
by africa millan 12 Nov '09

12 Nov '09

Hello, Another question:If during the first recon-all, freesurfer makes skullstripping and normalization automatically... Is there any way to run the first recon-all without automatic normalization? Is it possible? Thanks Af. _________________________________________________________________ Descubre todas las formas en que puedes estar en contacto con amigos y familiares. http://www.microsoft.com/windows/windowslive/default.aspx

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FW: brightness problem
by africa millan 12 Nov '09

12 Nov '09

Hello everybody, Yesterday I sent a message about a brightness problem. If anybody has an answer or any idea about it, It would be very helpful for me. Thank you for your help. Af. From: africa_millan(a)hotmail.es To: freesurfer(a)nmr.mgh.harvard.edu Subject: brightness problem Date: Wed, 11 Nov 2009 11:37:19 +0100 Hello everybody, When I open the wm.mgz file of a subject to check the result of the first automatic segmentation that freesurfer runs, I get the image that I've attached in this message ( the image is named "1st recon"). As you can see,there are problems with the differentation between the grey and the white matter maybe because of the high brigthness of the image. But when I check the original image of the subject, the brightness is ok. The thing is that if I compare the original image (orig.mgz) with the file rawavg.mgz of the same subject that Freesurfer generates,I realize that the second one (rawavg.mgz) has an increased brightness. I've also attached a file that corresponds to the comparation between the brightness of the original image and the brightness of the rawavg.mgz file of the same subject (the file is named "comparation1"), the recon-all.log and the recon-all-status.log files where you can check that the recon-all finished without any problem or without any error message. There is any way to avoid the increased brightness of the rawavg.mgz? Thank you for your help. Af. 49 habitantes, 49 expertos en Windows 7. Así es Sietes, ¡Visítalo! _________________________________________________________________ Convierte las fotos que más te gustan en tu nuevo fondo de escritorio para el ordenador. Es fácil y además gratis http://wallpapers.msn.com/es-es

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creat own template
by Guang Zeng 12 Nov '09

12 Nov '09

Hi, there, I have two questions, 1. I have read "The surface registration and templates" at FreeSurfer WIKI, and I am going to creat our own registration template. Is there a shell script available somewhere to do this? 2. What are the files in the folder of ../freesurfer/subjects/fsaverage. Are they the results of crosse-sectional FS anlysis using the average of Buckner40 as input. Why there is no wmparc.mgz in /mri Thannks a lot! Guang _________________________________________________________________ Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. http://clk.atdmt.com/GBL/go/171222985/direct/01/

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Cortical thickness measurements from T2 data sets
by Magerkurth, Olaf 12 Nov '09

12 Nov '09

Dear Sirs and Madams, we are planning a study measuring cortical thickness in children. Due to better contrast bettween white matter and cortex in infants we generally use T2 images in 3 planes. Is it possible to measure the cortical thickness slice by slice without the availabilit yof 3D datasets? Thank you very much Olaf Magerkurth Hinweis: Der Inhalt von dieser E-Mail und jeglichen Anhaengen dazu sind ausschliesslich fuer den Empfaenger bestimmt. Die E-Mail und jegliche Anhaenge koennen vertrauliche Informationen enthalten und sind durch Gesetze, Reglemente und/oder vertraglichen Verpflichtungen geschuetzt. Sollten Sie diese E-Mail versehentlich empfangen haben, duerfen Sie weder davon Gebrauch machen noch den Inhalt von der E-Mail oder von jeglichen Anhaengen dazu preisgeben. In so einem Fall informieren Sie bitte den Absender der E-Mail und vernichten Sie den Inhalt und alle zugehoerigen Anhaenge.

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Question on pial surface intersecting wm limits and on qdec
by Hugo Ferreira 11 Nov '09

11 Nov '09

Dear all, I've two questions which I couldn't get answered in your wiki tutorials. I hope you can help me. - I have some processed images that have in the medial part of the brain intersection of the pial matter and the grey matter (see image in attachment). From the tutorial I could only learn about removing dura segmented as pial matter and filling in wm on lesions/ventricles. In my case if I delete voxels I'll loose wm/gm information is there anything I can do? - Also, there are cases where the pial matter does not cover the full gm, particularly at the base of the skull and at the temporal lobes (see attachment). What do you recommend me to do? One thing though is that the annotation seems to be ok (see attachs). So do I really have to correct for the pial and wm surface, as I'm asking above, as I'm interested in studying both cortical thicknesses and subcortical volumes of gm structures, wm and ventricles, or do not have to worry about it? Regarding QDEC, when preprocessing/preparing images for analysis do we have to have all the fsaverage folder together with all the subjects (lets say patients and controls), or can I have the fsaverage folder in two or more subfolders were I have segregated patient subjects and control subjects? This is to ask you also, do the fsaverage folder is changed by the qdec -cache processing or is it used only as a template for each subject (patient and control), and data is only created in patient/control individual subject folders? Many thanks and best regards, Hugo Ferreira

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restricting mri_glmfit to cortical regions
by Prapti Gautam 11 Nov '09

11 Nov '09

Dear Freesurfers, I have a question regarding thickness analyses using mri_glmfit. I am interested in correlating cognitive performance with a specific region in the brain and to increase the power of my analyses I want to conduct mri_glmfit on only my ROI. I was just wondering if it is possible to restrict mri_glmfit to certain regions of the brain instead of running them on the entire cortical surface and how I would I go about doing so. Thanks for your help, Prapti

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brightness problem
by africa millan 11 Nov '09

11 Nov '09

Hello everybody, When I open the wm.mgz file of a subject to check the result of the first automatic segmentation that freesurfer runs, I get the image that I've attached in this message ( the image is named "1st recon"). As you can see,there are problems with the differentation between the grey and the white matter maybe because of the high brigthness of the image. But when I check the original image of the subject, the brightness is ok. The thing is that if I compare the original image (orig.mgz) with the file rawavg.mgz of the same subject that Freesurfer generates,I realize that the second one (rawavg.mgz) has an increased brightness. I've also attached a file that corresponds to the comparation between the brightness of the original image and the brightness of the rawavg.mgz file of the same subject (the file is named "comparation1"), the recon-all.log and the recon-all-status.log files where you can check that the recon-all finished without any problem or without any error message. There is any way to avoid the increased brightness of the rawavg.mgz? Thank you for your help. Af. _________________________________________________________________ Deja que Sietes te enseñe todo los secretos de Windows http://www.sietesunpueblodeexpertos.com/

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Freesurfer