Freesurfer

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Re: [Freesurfer] Control point edits adversely affect cortical surfaces using FS 5.1
by Vanessa Louise Cropley 16 Oct '12

16 Oct '12

Dear Bruce/freesurfer community, Thank-you for offering to take a look at our data. I have uploaded two files to the ftp. They are called Subject_Before_CP.zip and Subject_After_Cpedit.zip. Please let me know if you haven't received them. I uploaded these last Friday but haven't as yet had a reply. I did this as a test as I assumed that a single ctrl point in WM would have no effect on the surfaces. The 1 ctrl point was added to the LH WM in temporal cortex (slice 120). Thank-you for your help, it would be great if we could find a solution to this problem. - Vanessa On 12/10/12 1:24 AM, "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> wrote: > Hi Vanessa > > if you can upload an example (the entire subject dir) before adding the > single control point you refer to, and after adding it we'll track it down. > > thanks > Bruce > > > > On Thu, 11 Oct 2012, Vanessa Louise Cropley wrote: > >> Hi all, >> >> I have seen others post a similar problem on the freesurfer mailing list but >> I could not find a solution. >> >> When I edit a volume using control points, I am noticing that the use of CP >> edits adversely effects the wm/gm surfaces in the resulting re-processed >> image. Like others have reported, the surfaces are adversely affected in >> locations distant from the CP edits. The temporal lobes are particularly >> affected. >> >> We are using freesurfer 5.1. >> I have noticed the following things: >> >> 1. The problem occurs irrespective of the number of control points added, >> i.e. whether >100 or <10 control points added >> 2. The problem occurred when only one CP was added in a voxel that was >> clearly wm >> 3. The problem did not occur after reprocessing with FS 4.5 >> 4. I have tried the flag to disable mri_ca_normalize when reprocessing with >> ?autorecon2. This did not seem to help. I used the command: recon-all >> ?nocanorm ?autorecon2-cp ?subjid $SUBJ >> >> I have screenshots available that illustrate the changes in the surfaces >> after reprocessing. >> >> Could anyone help with this problem? >> >> Thank-you, >> >> Vanessa >> > _______________________________________________ > 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. > > ------ End of Forwarded Message

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DODS and group age interaction
by Mahinda Yogarajah 16 Oct '12

16 Oct '12

Dear Experts, I have 2 groups - controls (22 subjects) and patients (19 subjects) with mean ages that are not significantly different, though ranges/median are. I want to compare cortical thickness between groups while allowing for age (age as nuisance factor) but also want to see if there is an interaction between age and group (age as continuous variable). I have demeaned the age across both controls and patients and then used qdec. 1) Using DODS and demeaned ages I find that there is an age-gp interaction such that patients have quicker thickness decline with age than controls. This survives FDR 0.05 and monte carlo VWP 0.005 CWP 0.05. Is this finding valid given that I used demeaned ages (rather than absolute ages) to look for interaction or does it make no difference ? 2) When I come to look to see whether there is a gp difference in thickness I enter age as a nuisance variable in qdec (as opposed to continuous variable above) and use DODS with demeaned age variable across gp. Am I safe to interpret my findings normally given age-gp interaction or is is not safe - if it is not safe how can I look for gp differences or it ok to interpret results provided gp differences are not in regions where I see an interaction ? Thanks. Mahinda

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Re: [Freesurfer] Freesurfer 1mm Isotropic standard and the Future
by Joshua Lee 16 Oct '12

16 Oct '12

Hi Everyone, Back in May I was very excited to learn that there was some movement toward allowing Freesurfer to utilize the higher than 1mm iso. resolutions of some of our structural images, which could be fantastic help in subcortical segmentations. Is this something that is still in the works for the next release? gratefully, Joshua - Joshua Lee Graduate Student Center for Mind and Brain & Department of Psychology University of California, Davis 530.747.3805 On Thu, May 31, 2012 at 5:49 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > Hi Joshua > > sorry, I haven't found the time to really work on it. I spent a couple of > hours and found some problems, but haven't found the time to fix them > > Bruce > > On Thu, 31 May 2012, Joshua Lee wrote: > > Hi Bruce, >> >> I'm just checking in to see how it turned out with the subcortical >> segmentation using the high resolution images I sent. >> Best, >> >> Joshua >> >> >> >> >> >> >> - >> Joshua Lee >> Graduate Student >> Center for Mind and Brain & >> Department of Psychology >> University of California, Davis >> 530.747.3805 >> >> >> On Tue, May 15, 2012 at 5:29 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu >> > >> wrote: >> you need to call mris_make_surfaces directly. It's a bit >> complicated as you need to intensity normalize and register the >> hires volume to the surfaces first. I have an example script if >> anyone is interested, but no one has used it yet but me I don't >> think (unless Matt Glasser has gotten his version working, which >> on second thought he probably has) >> >> On Mon, 14 May 2012, Michael Waskom wrote: >> >> Hi Bruce, >> Is there a flag for this on recon-all? áOr do you >> >> need to use >> mri_make_surfaces directly? >> >> Best, >> Michael >> >> On Mon, May 14, 2012 at 2:09 PM, Bruce Fischl >> <fischl(a)nmr.mgh.harvard.edu> >> wrote: >> á á áHi Joshua >> >> á á áyes, we already have upgraded >> mris_make_surfaces to take higher >> á á áres data >> á á áand refine the surfaces with it. Haven't tried >> it on the aseg >> á á áyet, but if >> á á áyou upload a sample dataset I could see how >> hard it is. >> >> á á ácheers >> á á áBruce >> á á áOn Mon, 14 May 2012, >> á á áJoshua Lee wrote: >> >> á á á> Dear Freesurfers, >> á á á> >> á á á> Over the last years, MR imaging technology >> hasimproved such >> á á áthat sub 1-mm >> á á á> isotropic scans can be obtained with good >> signal to noise >> á á ácharacteristics. >> á á á> For example, our lab uses 0.7mm isotropic >> structural MR >> á á áimages. I understand >> á á á> that the Freesurfer pipeline will up-sample >> these to 1mm >> á á áisotropic, but it >> á á á> seems a shame that so much information is >> left unused which >> á á ácould be used to >> á á á> improve the accuracy of sub-cortical and >> cortical >> á á ásegmentation. My question >> á á á> is whether there are any plans at Freesurfer >> to change the >> á á áreference >> á á á> standard resolution from 1mm isotropic, or >> provide another >> á á ásolution that can >> á á á> help researchers make the most of your >> technology. >> á á á> >> á á á> Sincerely, >> á á á> >> á á á> >> á á á> Joshua >> á á á> - >> á á á> Joshua >> á á á> >> á á á> >> á á á> >> >> ______________________________**_________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** >> freesurfer <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<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<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<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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Installation difficulties (Mac)
by Julia Nantes 16 Oct '12

16 Oct '12

I have downloaded the FreeSurfer software onto a Mac computer. I did the setenv/source steps and got this output: Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer/ FSFAST_HOME /Applications/freesurfer//fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer//subjects MNI_DIR /Applications/freesurfer//mni Next, I obtained a license and finally got the text to go into a pico .license file after doing this: [Lisa-Koskis-iMac:~] rsussex% sudo -s Password: [Lisa-Koskis-iMac:~] root# cd /Applications/freesurfer/ [Lisa-Koskis-iMac:/Applications/freesurfer] root# pico $FREESURFER_HOME .license FREESURFER_HOME: Undefined variable. [Lisa-Koskis-iMac:/Applications/freesurfer] root# pico .license [Lisa-Koskis-iMac:/Applications/freesurfer] root# ls ASegStatsLUT.txt SetUpFreeSurfer.sh fsfast AUTHORS Simple_surface_labels2009.txt lib DefectLUT.txt VERSION matlab FreeSurferColorLUT.txt WMParcStatsLUT.txt mni FreeSurferEnv.csh average sessions FreeSurferEnv.sh bin subjects LICENSE build-stamp.txt tkmeditParcColorsCMA NOTICE data tktools README diffusion trctrain SegmentNoLUT.txt docs SetUpFreeSurfer.csh fsafd [Lisa-Koskis-iMac:/Applications/freesurfer] root# cd ../.. [Lisa-Koskis-iMac:/] root# cd /Applications/freesurfer//subjects/ [Lisa-Koskis-iMac:/Applications/freesurfer/subjects] root# ls README bert fsaverage fsaverage4 fsaverage6 rh.EC_average sample-002.mgz V1_average cvs_avg35 fsaverage3 fsaverage5 lh.EC_average sample-001.mgz [Lisa-Koskis-iMac:/Applications/freesurfer/subjects] root# tkmedit bert orig.mgz tkmedit: Command not found. [Lisa-Koskis-iMac:/Applications/freesurfer/subjects] root# qdec qdec: Command not found. Since the 'Testing your FreeSurfer installation" commands from the wiki page are not working, I may not have installed this properly. Any insights as to how this could be resolved would be much appreciated. Thank you, Julia

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Re: [Freesurfer] error measuring LGI
by Gabriel Gonzalez Escamilla 16 Oct '12

16 Oct '12

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3 Factor glm group analysis
by hhal5293＠uni.sydney.edu.au 16 Oct '12

16 Oct '12

Hello, We are currently doing a longitudinal Group Analysis using FreeSurfer, and were wondering if there is a way to run a 3 factor design (time is 2 levels, group is 2 levels, subject is 10 levels) using the mri_glmfit model, as i want to test the time by group interaction? Is there a way of writing this model in an FSDG file? If we can't do this using mri_glmfit, is it possible to do this using QDEC? Regards, Harry

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pctsurfcon question
by Phil Greer 16 Oct '12

16 Oct '12

I do not have a question on how to use the program, the wiki covered that well. My question is about the formula embedded in the program to calculate the contrast. The formula is ((wm-gm)/((wm+gm)/2))*100 This creates a dynamic range of -200 to +200. Which the last time I checked is not really a percent as the command name implies. Was there some reasoning behind this that I am missing? Phil Greer University of Pittsburgh

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error measuring LGI
by Gabriel Gonzalez Escamilla 16 Oct '12

16 Oct '12

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Can I get verification of some scripts I wrote to parallelize recon-all?
by Chris Adamson 15 Oct '12

15 Oct '12

Hey all, Can I send through some shell scripts that I wrote to run all the hemisphere-specific steps so that the lh and rh steps are run together. If I could send them through to make sure I'm doing autorecon2-wm and autorecon3-pial correctly? Thank you. Chris. -- Dr Christopher Adamson, PhD (Melb.), B Software Engineering (Hons., Monash) Research Officer Developmental Imaging, Critical Care and Neurosciences Murdoch Childrens Research Institute The Royal Children’s Hospital Flemington Road Parkville Victoria 3052 Australia T 9906 6780 M XXXX XXX XXX E chris.adamson(a)mcri.edu.au www.mcri.edu.au ______________________________________________________________________ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com ______________________________________________________________________

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mistake in webpage SubCortGray description??
by Fernando Ventrice 15 Oct '12

15 Oct '12

Dear all, I think in the following webpage there is a very small mistake: http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats It states that SubCortGray is the sum of the thalamus, caudate, putamen, pallidum, hippocampus, amygdala, accumbens, and VentralDC from both hemispheres. But I think SubCortGray sums all those areas plus the Cerebellum-Cortex from both hemispheres and the Brain-Stem. Please tell me if this is correct. Best, Fernando Ventrice El contenido del presente mensaje y el de sus adjuntos, es confidencial, privado y de uso exclusivo de los destinatarios a los cuales está dirigido, pudiendo contener información legalmente protegida. Queda prohibida la revisión, divulgación, publicación, modificación, copia, distribución o acción en relación con esta información, por personas o entidades distintas al destinatario. Si usted, por alguna razón, lo ha recibido por error, por favor tenga la amabilidad de eliminarlo de su sistema. Las opiniones contenidas, son exclusivas de su autor, y no representa necesariamente, la opinión de FLENI. http://www.fleni.org.ar

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