Re: [Freesurfer] segmentation
Ok, thanks. Is the new mris_make_surfaces included with the latest release? >>> Bruce Fischl <[EMAIL PROTECTED]> 2/26/2007 5:29 PM >>> you can certainly get cortical gray by using the ?h.cortex.label that's generated automatically by the new mris_make_surfaces. The whole notion of a gray/white boundary is a myth. There's about 1/2mm of slack in which there are gradually more and more cell bodies (moving up from the wm) until it's only cell bodies and no wm. On Mon, 26 Feb 2007, Sasha Wolosin wrote: > Well, since at the neuronal level there is some degree of white matter > present in the cortex, in whole brain segmentation cortical gray matter > is often reported (plus subcortical gray), which is different from the > freesurfer output of cortical "gray matter volume" because it may > exclude small amounts of white matter embedded within the cortex. We > would like to know if there is any way to obtain a comparable measure in > freesurfer. > >>>> Bruce Fischl <[EMAIL PROTECTED]> 2/26/2007 3:49 PM >>> > what does that mean? > On Mon, 26 Feb 2007, Sasha Wolosin wrote: > >> In freesurfer, is there any way to run a gray/white matter > segmentation >> within the cortex? >> Thanks, >> Sasha >> >> >> >> Disclaimer: >> The materials in this e-mail are private and may contain Protected > Health Information. Please note that e-mail is not necessarily > confidential or secure. Your use of e-mail constitutes your > acknowledgment of these confidentiality and security limitations. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying, distribution, or the taking of any action in > reliance on the contents of this information is strictly prohibited. If > you have received this e-mail in error, please immediately notify the > sender via telephone or return e-mail. >> ___ >> 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
Re: [Freesurfer] segmentation
Well, since at the neuronal level there is some degree of white matter present in the cortex, in whole brain segmentation cortical gray matter is often reported (plus subcortical gray), which is different from the freesurfer output of cortical "gray matter volume" because it may exclude small amounts of white matter embedded within the cortex. We would like to know if there is any way to obtain a comparable measure in freesurfer. >>> Bruce Fischl <[EMAIL PROTECTED]> 2/26/2007 3:49 PM >>> what does that mean? On Mon, 26 Feb 2007, Sasha Wolosin wrote: > In freesurfer, is there any way to run a gray/white matter segmentation > within the cortex? > Thanks, > Sasha > > > > Disclaimer: > The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. > ___ > 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
[Freesurfer] segmentation
In freesurfer, is there any way to run a gray/white matter segmentation within the cortex? Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] folding index on surface
Ok, that is what I thought- thanks. Sasha >>> Bruce Fischl <[EMAIL PROTECTED]> 2/19/2007 4:19 PM >>> Hi Sasha, the folding index is computed across the whole surface, so how would you display it? You can display H, K, k1 and k2 if you want (you can compute them with mris_curvature -w ...) Bruce On Mon, 19 Feb 2007, Sasha Wolosin wrote: > Dear all, > Is it possible to display folding index on the cortical surface? > Thanks, > Sasha > > > > Disclaimer: > The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. > ___ > 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
[Freesurfer] folding index on surface
Dear all, Is it possible to display folding index on the cortical surface? Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mris_preproc and thickness
Dear all, Does "--meas thickness" as an input for mris_preproc always specify to use the ?h.thickness file in the surf folder? Is there a way to specify a different thickness file as input for mris_preproc? Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] thickness standard deviation
I understand that thickness may vary greatly across the entire surface, but shouldn't we expect some stability within smaller regions (e.g. those in the Desikan/Killany atlas)? >>> Bruce Fischl <[EMAIL PROTECTED]> 8/24/2006 4:40 pm >>> Hi Sasha, the standard deviation across the surface isn't a very meaningful number, since the thickness isn't spatially stationary. cheers, Bruce On Thu, 24 Aug 2006, Sasha Wolosin wrote: > Dear all, > I am interested in measuring mean thickness within ROI in MPRAGEs of > children. My mean thickness values tend to be around 3.3 mm, with a > standard deviation of about 1mm. I am concerned that these standard > deviations are somewhat high. What typical values should I be expecting > for standard deviation? > Thanks, > Sasha > > > > Disclaimer: > The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. > ___ > 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
[Freesurfer] thickness standard deviation
Dear all, I am interested in measuring mean thickness within ROI in MPRAGEs of children. My mean thickness values tend to be around 3.3 mm, with a standard deviation of about 1mm. I am concerned that these standard deviations are somewhat high. What typical values should I be expecting for standard deviation? Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] thickness maps
Dear all, When I load ?h.thick files as an overlay in tksurfer I notice that values at the thickest points are all listed as having a thickness of exactly 5. Is this a max cutoff in the actual values, or is it just that tksurfer won't display larger values? Is there a better way to visualize thickness files? Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] viewing subcortical structures
thanks. Regarding subcortical segmentation in general, if I am using a Philips scanner should I be using the flag -cross-sequence when calling mri_ca_label? >>> Doug Greve <[EMAIL PROTECTED]> 7/18/2006 10:54 am >>> It is relatively new. You can get it from: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_binarize doug On Tue, 18 Jul 2006, Sasha Wolosin wrote: > Thanks! I don't have mri_binarize though. Is it included in 3.0.3? I > am currently running stable 3.0.1 > > >>>> Doug Greve <[EMAIL PROTECTED]> 7/17/2006 7:14 pm >>> > One way to do it is with mri_binarize: > > mri_binarize --i aseg.mgz --min 1.5 --max 2.5 --o wm-lh.mask.nii > > This will find all the voxels whose value is between 1.5 and 2.5 and > set > them to 1 in the output. In this case, it will make a binary mask of > the > left cerebral white matter as that has a code of 2 (from > FreeSurferColorLUT.txt). > > The output can be saved in any mri_convert output format (ie, mgh, mgz, > > analyze, nifti, etc). > > doug > > > Sasha Wolosin wrote: > >> Dear all, >> Does aseg save out masks of the various subcortical regions > measured? >> If so, is it possible to visualize and/or edit these in > tkmedit/scuba, >> or export them to an external format? >> Thanks, >> Sasha >> >> >> >> Disclaimer: >> The materials in this e-mail are private and may contain Protected > Health Information. Please note that e-mail is not necessarily > confidential or secure. Your use of e-mail constitutes your > acknowledgment of these confidentiality and security limitations. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying, distribution, or the taking of any action in > reliance on the contents of this information is strictly prohibited. If > you have received this e-mail in error, please immediately notify the > sender via telephone or return e-mail. >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> > > -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] viewing subcortical structures
Thanks! I don't have mri_binarize though. Is it included in 3.0.3? I am currently running stable 3.0.1 >>> Doug Greve <[EMAIL PROTECTED]> 7/17/2006 7:14 pm >>> One way to do it is with mri_binarize: mri_binarize --i aseg.mgz --min 1.5 --max 2.5 --o wm-lh.mask.nii This will find all the voxels whose value is between 1.5 and 2.5 and set them to 1 in the output. In this case, it will make a binary mask of the left cerebral white matter as that has a code of 2 (from FreeSurferColorLUT.txt). The output can be saved in any mri_convert output format (ie, mgh, mgz, analyze, nifti, etc). doug Sasha Wolosin wrote: >Dear all, > Does aseg save out masks of the various subcortical regions measured? > If so, is it possible to visualize and/or edit these in tkmedit/scuba, >or export them to an external format? >Thanks, >Sasha > > > >Disclaimer: >The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. >___ >Freesurfer mailing list >Freesurfer@nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] viewing subcortical structures
Dear all, Does aseg save out masks of the various subcortical regions measured? If so, is it possible to visualize and/or edit these in tkmedit/scuba, or export them to an external format? Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] details on subcortical segmentation
Dear all, I am interested in learning more about the details of subcortical segmentation, in particular how the basal ganglia structure boundaries are determined. Is there any literature I may refer to? Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] surface area
Thanks. Can I make mris_anatomical_stats use the pial surface instead? >>> Doug Greve <[EMAIL PROTECTED]> 6/29/2006 1:29 pm >>> White. doug Sasha Wolosin wrote: >Dear all, > Are the regional surface areas computed by mris_anatomical_stats >using the ?h.white surface or the ?h.pial surface? >Thanks, >Sasha > > > >Disclaimer: >The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. >___ >Freesurfer mailing list >Freesurfer@nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] surface area
Dear all, Are the regional surface areas computed by mris_anatomical_stats using the ?h.white surface or the ?h.pial surface? Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] volumes
is there a way to compute the volumes contained within the ?h.pial and ?h.white surfaces? >>> Bruce Fischl <[EMAIL PROTECTED]> 6/23/2006 4:41 pm >>> it's the volume of the wm.mgz, and it's deprecated. Use the various wm volumes in the aseg files (or aseg.stats) instead. cheers, Bruce On Fri, 23 Jun 2006, Sasha Wolosin wrote: > Dear All, > Is the total white matter volume computed by mris_anatomical_stats > the total volume inside the gray/white surface? Or does it exclude > subcortical structures? i.e. is total brain volume = total gray matter > volume + total white matter volume ? > Thanks, > Sasha > > > Sasha Wolosin > Research Assistant > Developmental Cognitive Neurology > Kennedy Krieger Institute > 707 N. Broadway > Baltimore, MD 21205 > ph: (443) 923-9270 > [EMAIL PROTECTED] > > > > Disclaimer: > The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. > ___ > 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
[Freesurfer] volumes
Dear All, Is the total white matter volume computed by mris_anatomical_stats the total volume inside the gray/white surface? Or does it exclude subcortical structures? i.e. is total brain volume = total gray matter volume + total white matter volume ? Thanks, Sasha Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 [EMAIL PROTECTED] Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] measures of folding
Dear All, We are interested in degree of cortical folding within our subject populations. Would someone please help me to better understand what the measures "MeanCurv", "GausCurv", "FoldInd" and "CurvInd" in the ?h.aparc.stats files mean? Also, are whole brain stats reported elsewhere? Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] eTIV bug
Dear all, I have processed all my data using Stable v3.0.1. Does the eTIV bug effect any other volume measures? If I want to compute eTIV for my data, should I install the lates version and re-run mri_label_volume -eTIV ? Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] smoothing kernel
Dear all, In group analysis, how should I determine which value to use for the Gaussian fwhm smoothing kernel? Is there a recommended number? Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] aseg.stats question
Dear all, I would like to know what some of the abbreviations of areas in the aseg.stats file stand for, in particular: Left-F3orb Left-lOg Left-aOg Left-mOg Left-pOg Left-Stellate Left-Porg Left-Aorg and "Right-Thalamus" vs "Right-Thalamus-Proper" Where may I find documentation on these names? Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] interaction effects
Is it possible to run an ANOVA or multiple linear regression in freesurfer? >>> Doug Greve <[EMAIL PROTECTED]> 4/25/2006 11:17 am >>> Still valid. Sasha Wolosin wrote: >Is running a t-test contrast still valid if I don't have equal numbers >in the four groups (Male Treatment, Male Control, Female Treatment, >Female Control) or should I be running an F test instead? > >Sasha > > > >>>>Doug Greve <[EMAIL PROTECTED]> 4/14/2006 3:18 pm >>> >>>> >>>> > >Yes, you just need to come up with the the contrast matrix taht tests >what you want to test. If the contrast matrix has one row, then it's a > >t-test. If there are more than one, then it's an F test. You example is > >actually a t-test, I think, just: > > >(MaleTreatment-MaleControl) - (FemaleTreatment-FemaleControl) > >for a contrast of: +1 -1 -1 +1 > > >doug > > >Sasha Wolosin wrote: > > > >>Dear FreeSurfers, >> >> I am interested in examining interaction effects between two sets >> >> >of > > >>classes where each covers all the data, let's say Male/Female and >>Treatment/Control. I know mri_glmfit can be used to run t-test >>comparisons between groups (e.g. All Treatment vs. All Control , or >> >> >Male > > >>& Control vs. Male & Treatment), but can mri_glmfit be used to >> >> >examine > > >>interaction effects between these two sets of classes (for surface >>data)? >> >>my FSGD file looks like this: >> GroupDescriptorFile 1 >> Class MaleTreatment >> Class MaleControl >> Class FemaleTreatment >> Class FemaleControl >> Input subjid1a MaleTreatment >> Input subjid1b FemaleTreatment >> Input subjid2a FemaleControl >> Input subjid2b MaleControl >> etc... >> >>Thanks, >>Sasha >> >>Sasha Wolosin >>Research Assistant >>Developmental Cognitive Neurology >>Kennedy Krieger Institute >>707 N. Broadway >>Baltimore, MD 21205 >>ph: (443) 923-9270 >>[EMAIL PROTECTED] >> >> >> >>Disclaimer: >>The materials in this e-mail are private and may contain Protected >> >> >Health Information. Please note that e-mail is not necessarily >confidential or secure. Your use of e-mail constitutes your >acknowledgment of these confidentiality and security limitations. If you >are not the intended recipient, be advised that any unauthorized use, >disclosure, copying, distribution, or the taking of any action in >reliance on the contents of this information is strictly prohibited. If >you have received this e-mail in error, please immediately notify the >sender via telephone or return e-mail. > > >>___ >>Freesurfer mailing list >>Freesurfer@nmr.mgh.harvard.edu >>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> >> >> > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] interaction effects
Is running a t-test contrast still valid if I don't have equal numbers in the four groups (Male Treatment, Male Control, Female Treatment, Female Control) or should I be running an F test instead? Sasha >>> Doug Greve <[EMAIL PROTECTED]> 4/14/2006 3:18 pm >>> Yes, you just need to come up with the the contrast matrix taht tests what you want to test. If the contrast matrix has one row, then it's a t-test. If there are more than one, then it's an F test. You example is actually a t-test, I think, just: (MaleTreatment-MaleControl) - (FemaleTreatment-FemaleControl) for a contrast of: +1 -1 -1 +1 doug Sasha Wolosin wrote: >Dear FreeSurfers, > > I am interested in examining interaction effects between two sets of >classes where each covers all the data, let's say Male/Female and >Treatment/Control. I know mri_glmfit can be used to run t-test >comparisons between groups (e.g. All Treatment vs. All Control , or Male >& Control vs. Male & Treatment), but can mri_glmfit be used to examine >interaction effects between these two sets of classes (for surface >data)? > >my FSGD file looks like this: > GroupDescriptorFile 1 > Class MaleTreatment > Class MaleControl > Class FemaleTreatment > Class FemaleControl > Input subjid1a MaleTreatment > Input subjid1b FemaleTreatment > Input subjid2a FemaleControl > Input subjid2b MaleControl > etc... > >Thanks, >Sasha > >Sasha Wolosin >Research Assistant >Developmental Cognitive Neurology >Kennedy Krieger Institute >707 N. Broadway >Baltimore, MD 21205 >ph: (443) 923-9270 >[EMAIL PROTECTED] > > > >Disclaimer: >The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. >___ >Freesurfer mailing list >Freesurfer@nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] physical sizes too big
Dear FreeSurfer, During mri_convert, I get the following warning, and then an error during mri_em_register in -autorecon2. Would greatly appreciate any help, Thanks, Sasha WARNING ===== The physical sizes are (307.20 mm, 307.20 mm, 186.00 mm), which cannot fit in 256^3 mm^3 volume. The resulting volume will have 308 slices. The freesurfer tools should be able to handle more than 256 slices. If you find problems, please let us know (freesurfer@nmr.mgh.harvard.edu). == [EMAIL PROTECTED] EM Registration Fri Apr 7 15:08:40 EDT 2006 /data/subjects/2154/mri mri_em_register -mask brainmask.mgz nu.mgz /freesurfer/average/RB_all_2006-02-15.gca transforms/talairach.lta using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/freesurfer/average/RB_all_2006-02-15.gca'... setting gca type = Normal gca type average std = 7.4 using min determinant for regularization = 5.5 0 singular and 1662 ill-conditioned covariance matrices regularized reading 'nu.mgz'... Segmentation fault Linux localhost.localdomain 2.6.9-22.0.2.ELsmp #1 SMP Tue Jan 17 06:12:06 CST 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Fri Apr 7 15:08:49 EDT 2006 Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] renaming
Dear all, I am using freesurfer stable 3.0.1. If I want to rename a subject after the subject has been fully processed, are there any extra steps I would need to take to ensure that the subjects files are referenced correctly in group analysis/ future processing? Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] aparc2aseg -hemi
Dear FreeSurfers, I am using freesurfer stable 3.0.1 for 64-bit linux, and I would like to run aparc2aseg on just the right hemisphere. I ran "recon-all -hemi rh -subjid 2600test -autorecon-all" and when it got to aparc2aseg it exited with the following error: MRISread(/data/subjects/2600test/surf/lh.white): could not open file No such file or directory I then tried to run mri_aparc2aseg separately using the flag "-hemi rh" and it said option "-hemi" is unknown. Does aparc2aseg require both hemispheres be run through all the previous steps? Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] interaction effects
great, thanks! >>> Doug Greve <[EMAIL PROTECTED]> 4/14/2006 3:18 pm >>> Yes, you just need to come up with the the contrast matrix taht tests what you want to test. If the contrast matrix has one row, then it's a t-test. If there are more than one, then it's an F test. You example is actually a t-test, I think, just: (MaleTreatment-MaleControl) - (FemaleTreatment-FemaleControl) for a contrast of: +1 -1 -1 +1 doug Sasha Wolosin wrote: >Dear FreeSurfers, > > I am interested in examining interaction effects between two sets of >classes where each covers all the data, let's say Male/Female and >Treatment/Control. I know mri_glmfit can be used to run t-test >comparisons between groups (e.g. All Treatment vs. All Control , or Male >& Control vs. Male & Treatment), but can mri_glmfit be used to examine >interaction effects between these two sets of classes (for surface >data)? > >my FSGD file looks like this: > GroupDescriptorFile 1 > Class MaleTreatment > Class MaleControl > Class FemaleTreatment > Class FemaleControl > Input subjid1a MaleTreatment > Input subjid1b FemaleTreatment > Input subjid2a FemaleControl > Input subjid2b MaleControl > etc... > >Thanks, >Sasha > >Sasha Wolosin >Research Assistant >Developmental Cognitive Neurology >Kennedy Krieger Institute >707 N. Broadway >Baltimore, MD 21205 >ph: (443) 923-9270 >[EMAIL PROTECTED] > > > >Disclaimer: >The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. >___ >Freesurfer mailing list >Freesurfer@nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] {Disarmed} stats
Great, thanks! >>> Nick Schmansky <[EMAIL PROTECTED]> 4/14/2006 3:29 pm >>> Sasha, Some of the algorithms rely on a random number generator, which is why you will see small variations in results when re-processing a subject. What we do for our own testing scheme is to pass a seed value to the binaries that rely on random number generation. You can do this also by creating a file called expert-options, containing the following: mris_fix_topology -seed 1234 mris_sphere -seed 1234 mris_ca_label -seed 1234 and then include this parameter with recon-all: -expert expert-options which will cause the three binaries to seed their random number generator with the same number, thus ensuring an identical run from run to run. It is not strictly necessary to do this, though, as the differences resulting from the random effects are small. Nick On Fri, 2006-04-14 at 14:39 -0400, Sasha Wolosin wrote: > Dear FreeSurfers, > > We are running FreeSurfer on CentOS 4.2 and are currently in the > process of updating from CentOS 4.2 to 4.3. To check stability, we ran > the same data on multiple machines with the different versions of CentOS > using recon-all. We also ran the same data twice on the same machine > (on the following day, with no changes made). We actually found slight > differences in the ROI stats for the data run twice on the same machine, > (in addition to slight differences between machines.) While these > differences do not seem to be significant, we are concerned about them > because we do not know of any reason to expect random effects in our > analysis. > > here is an example of the differences found: > [EMAIL PROTECTED] subjects]$ grep -s caudalmid 2606/stats/lh.aparc.stats > caudalmiddlefrontal 3873 2648 6807 2.155 0.735 > 0.119 0.023 41.641 3.388 > [EMAIL PROTECTED] subjects]$ grep -s caudalmid > apr11run2606/stats/lh.aparc.stats > caudalmiddlefrontal 3877 2644 6994 2.212 0.736 > 0.118 0.023 41.228 3.411 > > Does anyone know what may cause these differences? Is there any standard > method you would use to test for stability other than looking at data > such as these? Thanks! > -Sasha > > > > Disclaimer: > The materials in this e-mail are private and may contain Protected Health > Information. Please note that e-mail is not necessarily confidential or > secure. Your use of e-mail constitutes your acknowledgment of these > confidentiality and security limitations. If you are not the intended > recipient, be advised that any unauthorized use, disclosure, copying, > distribution, or the taking of any action in reliance on the contents of this > information is strictly prohibited. If you have received this e-mail in > error, please immediately notify the sender via telephone or return e-mail. > email message attachment > On Fri, 2006-04-14 at 14:39 -0400, Sasha Wolosin wrote: > > logo > > Oxford University Press | USA > > The World's Largest University Press: Excellence, > > Tradition,Innovation > > Online Catalog | Catalogs by Mail | Subscribe Today | About > > Us | > > Search Author Title ISBN # Keyword Corporate Info > > > > Chodová Planá > > Coordinates: 49 50 N 12 44 E > > Annual beer production: 2,378,000 gallons (90,000 hectoliters) > > Geographic Theme: Location > > > > > > Clever advertisers may have come up with the slogan: "Heineken > > refreshes the parts other beers cannot reach" for a Dutch company, > > but it took Czech ingenuity to turn a tagline into reality. Perhaps > > in an effort to cater to a local population that leads the world in > > per capita beer consumption, the Chodovar Family Brewery in Western > > Bohemia recently began offering a unique type of therapy in the form > > of Real Beer Baths. Bizarre as the notion of soaking in a hot tub of > > yeast and herbs may sound to some, the owners certainly chose their > > location well*the geothermal activity beneath this forested region > > of the country has drawn people to its salubrious spas and mineral > > springs for centuries. > > > > - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > > - > > > > Explore a little closer to home with the new Atlas of the United > > States. > > > > > > > > - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > > - > > > > View a sample page of our featured Regions in the News. > > > > Marvel at the magnitude of Texas here. > > > > For an example of Oxford's city mapping, click here. > > > > Plus, br
[Freesurfer] {Disarmed} stats
Dear FreeSurfers, We are running FreeSurfer on CentOS 4.2 and are currently in the process of updating from CentOS 4.2 to 4.3. To check stability, we ran the same data on multiple machines with the different versions of CentOS using recon-all. We also ran the same data twice on the same machine (on the following day, with no changes made). We actually found slight differences in the ROI stats for the data run twice on the same machine, (in addition to slight differences between machines.) While these differences do not seem to be significant, we are concerned about them because we do not know of any reason to expect random effects in our analysis. here is an example of the differences found: [EMAIL PROTECTED] subjects]$ grep -s caudalmid 2606/stats/lh.aparc.stats caudalmiddlefrontal 3873 2648 6807 2.155 0.735 0.119 0.023 41.641 3.388 [EMAIL PROTECTED] subjects]$ grep -s caudalmid apr11run2606/stats/lh.aparc.stats caudalmiddlefrontal 3877 2644 6994 2.212 0.736 0.118 0.023 41.228 3.411 Does anyone know what may cause these differences? Is there any standard method you would use to test for stability other than looking at data such as these? Thanks! -Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. --- Begin Message --- Title: Oxford University Press Ben's Place of the Week Oxford University Press | USA The World's Largest University Press: Excellence, Tradition,Innovation Online Catalog | Catalogs by Mail | Subscribe Today | About Us | Search Author Title ISBN # Keyword Corporate Info Chodová Planá Coordinates: 49 50 N 12 44 E Annual beer production: 2,378,000 gallons (90,000 hectoliters) Geographic Theme: Location Clever advertisers may have come up with the slogan: Heineken refreshes the parts other beers cannot reach for a Dutch company, but it took Czech ingenuity to turn a tagline into reality. Perhaps in an effort to cater to a local population that leads the world in per capita beer consumption, the Chodovar Family Brewery in Western Bohemia recently began offering a unique type of therapy in the form of Real Beer Baths. Bizarre as the notion of soaking in a hot tub of yeast and herbs may sound to some, the owners certainly chose their location wellthe geothermal activity beneath this forested region of the country has drawn people to its salubrious spas and mineral springs for centuries. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Explore a little closer to home with the new Atlas of the United States. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - View a sample page of our featured Regions in the News. Marvel at the magnitude of Texas here. For an example of Oxford's city mapping, click here. Plus, browse all the other great titles that Oxford publishes by visiting our website. To send a message to Ben Keene, email him at: [EMAIL PROTECTED]. Fun Stuff: Our very own Ben Keene created this quiz so you can test your geography knowlege. Take it now but don't look at the answers until you're finished! Oxford University Press | 198 Madison Avenue | New York, NY 10016 | Update Your Preferences | Unsubscribe | Customer Service --- End Message --- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] interaction effects
Dear FreeSurfers, I am interested in examining interaction effects between two sets of classes where each covers all the data, let's say Male/Female and Treatment/Control. I know mri_glmfit can be used to run t-test comparisons between groups (e.g. All Treatment vs. All Control , or Male & Control vs. Male & Treatment), but can mri_glmfit be used to examine interaction effects between these two sets of classes (for surface data)? my FSGD file looks like this: GroupDescriptorFile 1 Class MaleTreatment Class MaleControl Class FemaleTreatment Class FemaleControl Input subjid1a MaleTreatment Input subjid1b FemaleTreatment Input subjid2a FemaleControl Input subjid2b MaleControl etc... Thanks, Sasha Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 [EMAIL PROTECTED] Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] contrast.mat file
What format should my contrast.mat file be for group analysis? e.g. if my contrast vector is [1,-1], should the contrast.mat file be a text file with [1 -1] as the first line? or 1 -1 as the first line? Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] fsaverage
Is fsaverage used in recon-all processing? Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] fix vertex area
Regarding stable 3.0.1: Have there been any changes in recon-all processing? i.e. Should I re-run subjects processed with recon-all in stable 3 if I want to upgrade to stable 3.0.1? Thanks, Sasha >>> Doug Greve <[EMAIL PROTECTED]> 3/13/2006 5:00 pm >>> If you ran it outside of recon-all then you should re-run it. Sorry. On Mon, 13 Mar 2006, Sasha Wolosin wrote: > Dear all, > I ran the 'mris_make_surfaces' script after running recon-all, but I > forgot to include 'setenv FIX_VERTEX_AREA' in my set up file. I saved a > back-up of the surf folder created by recon-all. Will I need to re-run > mris_make_surfaces? > Thanks, > Sasha > > Sasha Wolosin > Research Assistant > Developmental Cognitive Neurology > Kennedy Krieger Institute > 707 N. Broadway > Baltimore, MD 21205 > ph: (443) 923-9270 > [EMAIL PROTECTED] > > > > Disclaimer: > The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] fix vertex area
Dear all, I ran the 'mris_make_surfaces' script after running recon-all, but I forgot to include 'setenv FIX_VERTEX_AREA' in my set up file. I saved a back-up of the surf folder created by recon-all. Will I need to re-run mris_make_surfaces? Thanks, Sasha Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 [EMAIL PROTECTED] Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] talairach subject
Dear all, I noticed that there is no talairach subject included in the new release subject's directory. Is the talairach subject no longer needed? Or must it be downloaded separately? Thanks! Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] cluster thresholding
Dear all, Has the January dev release incorporated the new corrections for multiple comparisons in group analysis, e.g. cluster thresholding? Thanks, Sasha Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 [EMAIL PROTECTED] Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] newest dev question
Dear all, Is the latest January dev release compatible with the previous one (Oct 2005) with regards to surface-based measures? Are there any differences in the segmentation algorithms or in the implementation of these algorithms which might cause differences in the surface files? Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] notes on Jan 2006 release
Can the aseg from the current dev release (Oct 3rd, 2005) be used to get subcortical measurements from data acquired on Philips scanner? Or is the new aseg only available in the upcoming release? Thanks, Sasha >>> Bruce Fischl <[EMAIL PROTECTED]> 1/23/2006 2:42 pm >>> Hi Sasha, in the newest version of the aseg we've made a lot of progress on this front, and labeling across different platforms is pretty much comparable to labeling on the same platform. cheers, Bruce On Mon, 23 Jan 2006, Sasha Wolosin wrote: > Dear all, > > In the notes on the Jan 2006 release it was mentioned that the > subcortical atlas is built from the Siemens scans, and thus might not be > reliable for GE scans. How might this subcortical atlas handle data > aqcuired on a Philips scanner? > > thanks, > Sasha > > > > Disclaimer: > The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. > ___ > 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
[Freesurfer] notes on Jan 2006 release
Dear all, In the notes on the Jan 2006 release it was mentioned that the subcortical atlas is built from the Siemens scans, and thus might not be reliable for GE scans. How might this subcortical atlas handle data aqcuired on a Philips scanner? thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_convert ascii
great, thanks! >>> Doug Greve <[EMAIL PROTECTED]> 1/19/2006 11:29 AM >>> Use mris_convert (note the 's' in the name, not mri_convert) doug Sasha Wolosin wrote: >Dear all, > Is there a way to convert FreeSurfer surface files to ASCII? In the most recent listserve, it was mentioned that mri_convert can be used to convert FreeSurfer surface files to ASCII format, but I could not figure it out- I thought mri_convert could only handle volumes. >Thanks, >Sasha > > > >Disclaimer: >The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. > >___ >Freesurfer mailing list >Freesurfer@nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mri_convert ascii
Dear all, Is there a way to convert FreeSurfer surface files to ASCII? In the most recent listserve, it was mentioned that mri_convert can be used to convert FreeSurfer surface files to ASCII format, but I could not figure it out- I thought mri_convert could only handle volumes. Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] multiple comparisons
When I set FDR = .05, or anything under .85, and select "set threshold using FDR" the min threshold is always set to 4.03, which is about p= .0001, correct? Would you normally require such low p-values for this type of analysis? Why would such varied FDRs result in the same min threshold? We do not see any results when the min>2.0 (p=.01), so this is very problematic for us. Also, at just over FDR = .85 (I realize this is absurdly high) the min threshold jumps down to 1.23, do you have any idea why this jump might occur? Thanks, Sasha >>> Bruce Fischl <[EMAIL PROTECTED]> >>> .05 is fairly standard I think. On Mon, 9 Jan 2006, Sasha Wolosin wrote: > Is this something you apply frequently at MGH? What FDR value would you > typically require? > >>>> Doug Greve <[EMAIL PROTECTED]> >>> > > Currently, mris_glm does not attempt to correct for multiple > comparisons, though this feature will be in the next release. In the > mean time, you can correct for multiple comparisons using FDR in > tksurfer. > > > > Sasha Wolosin wrote: > >> Dear all, >> I would like to learn more about group analysis using mris_glm. How >> does the program correct for the problem of multiple comparisons? Is >> there any way to determine the rate of false positives? >> Thanks, >> Sasha >> >> Sasha Wolosin >> Research Assistant >> Developmental Cognitive Neurology >> Kennedy Krieger Institute >> 707 N. Broadway >> Baltimore, MD 21205 >> ph: (443) 923-9270 >> [EMAIL PROTECTED] >> >> >> >> Disclaimer: >> The materials in this e-mail are private and may contain Protected > Health Information. Please note that e-mail is not necessarily > confidential or secure. Your use of e-mail constitutes your > acknowledgment of these confidentiality and security limitations. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying, distribution, or the taking of any action in > reliance on the contents of this information is strictly prohibited. If > you have received this e-mail in error, please immediately notify the > sender via telephone or return e-mail. >> ___ >> 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
Re: [Freesurfer] multiple comparisons
Is this something you apply frequently at MGH? What FDR value would you typically require? >>> Doug Greve <[EMAIL PROTECTED]> >>> Currently, mris_glm does not attempt to correct for multiple comparisons, though this feature will be in the next release. In the mean time, you can correct for multiple comparisons using FDR in tksurfer. Sasha Wolosin wrote: >Dear all, > I would like to learn more about group analysis using mris_glm. How >does the program correct for the problem of multiple comparisons? Is >there any way to determine the rate of false positives? >Thanks, >Sasha > >Sasha Wolosin >Research Assistant >Developmental Cognitive Neurology >Kennedy Krieger Institute >707 N. Broadway >Baltimore, MD 21205 >ph: (443) 923-9270 >[EMAIL PROTECTED] > > > >Disclaimer: >The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. >___ >Freesurfer mailing list >Freesurfer@nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] multiple comparisons
Dear all, I would like to learn more about group analysis using mris_glm. How does the program correct for the problem of multiple comparisons? Is there any way to determine the rate of false positives? Thanks, Sasha Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 [EMAIL PROTECTED] Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tksurfer
I am loading the GDF file from the menu interface. Tksurfer runs correctly before loading the file, including when I load an overlay, but it quits immediately after loading any GDF file. >>> Kevin Teich <[EMAIL PROTECTED]> >>> Are you loading the GDF file from the menu interface, or from a commandline tool? Does tksurfer run correctly before you load the file? Does it run correctly for other subjects, and with other GDF files? On Tue, Jan 03, 2006 at 09:29:30AM -0500, Sasha Wolosin wrote: > Dear all, > I am running into some problems with tksurfer in the x86_64 dev > release (oct 03). Whenever I attempt to load a group descriptor file > the program quits. Below is the command line output. Any idea what > might be happening? > Thanks, > Sasha > > surfer: current subjects dir: /data/final_surfs_30_60_20 > surfer: not in "scripts" dir ==> using cwd for session root > surfer: session root data dir ($session) set to: > surfer: /data/final_surfs_30_60_20 > surfer: Reading header info from > /data/final_surfs_30_60_20/average_306020_all//mri/T1.mgz > surfer: vertices=163842, faces=327680 > surfer: single buffered window > surfer: using interface /freesurfer_dev/lib/tcl/tksurfer.tcl > Reading /freesurfer_dev/lib/tcl/tkm_common.tcl > Reading /freesurfer_dev/lib/tcl/tkm_wrappers.tcl > Reading /freesurfer_dev/lib/tcl/fsgdfPlot.tcl > Reading /freesurfer_dev/lib/tcl/tkUtils.tcl > Read /freesurfer_dev/surface_labels.txt, found 95 structures > Successfully parsed tksurfer.tcl > % surfer: Interpreting overlay volume > /data/final_surfs_30_60_20/stats_all_30/sigt_Group_doss-thickness-100rh.mgz > as encoded value file. > min value=-3.646420 > max value=4.032682 > gdfReadHeader: reading > /data/final_surfs_30_60_20/stats_all_30/y_doss-thickness-100rh_000.fsgd > INFO: ignoring tag Creator > INFO: ignoring tag SmoothSteps > INFO: ignoring tag SUBJECTS_DIR > INFO: ignoring tag SynthSeed > > > > Disclaimer: > The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] tksurfer
Dear all, I am running into some problems with tksurfer in the x86_64 dev release (oct 03). Whenever I attempt to load a group descriptor file the program quits. Below is the command line output. Any idea what might be happening? Thanks, Sasha surfer: current subjects dir: /data/final_surfs_30_60_20 surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /data/final_surfs_30_60_20 surfer: Reading header info from /data/final_surfs_30_60_20/average_306020_all//mri/T1.mgz surfer: vertices=163842, faces=327680 surfer: single buffered window surfer: using interface /freesurfer_dev/lib/tcl/tksurfer.tcl Reading /freesurfer_dev/lib/tcl/tkm_common.tcl Reading /freesurfer_dev/lib/tcl/tkm_wrappers.tcl Reading /freesurfer_dev/lib/tcl/fsgdfPlot.tcl Reading /freesurfer_dev/lib/tcl/tkUtils.tcl Read /freesurfer_dev/surface_labels.txt, found 95 structures Successfully parsed tksurfer.tcl % surfer: Interpreting overlay volume /data/final_surfs_30_60_20/stats_all_30/sigt_Group_doss-thickness-100rh.mgz as encoded value file. min value=-3.646420 max value=4.032682 gdfReadHeader: reading /data/final_surfs_30_60_20/stats_all_30/y_doss-thickness-100rh_000.fsgd INFO: ignoring tag Creator INFO: ignoring tag SmoothSteps INFO: ignoring tag SUBJECTS_DIR INFO: ignoring tag SynthSeed Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] cma colors
Dear all, I am interested in using the CMA parcellation. Is the atlas lh.curvature.buckner40.filled.desikan_killany.gcs equivalent to the CMA parcellation? Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] threshold
Dear all, In group analysis, how are the various thresholds (min, mid, max) related to p-values? Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] CMA parcellation
Dear all, I am interested in using the CMA parcellation to create ROI's. Is it possible to create ?h.aparc.annot files using the CMA parcellation scheme instead of the surface-based parcellation scheme? Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] autorecon2-wm
Dear all, When we run autorecon2-wm it doesn't seem to be reading the editing done in the Edit WM With ASeg step. Looking at wm.mgz, none of the filling that we see after autorecon2 is present after autorecon2-wm. What's going wrong? Thanks, Marin Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] talairach
Dear all, We are having some difficulties getting accurate talairach.xfm files. After running recon-all, the final objective function value for most of our brains was above .2 We then regenerated the transform using brain.mgz. This helped, but our final objective function values are still above .1, some are above 1.5 There don't seem to be any bright neck regions left in the brain volumes, so we don't think bright neck regions are causing the problem. Manual inspection shows that the fuzzy talairach brain is slightly smaller than the subjects' brains, but seems to be in the correct orientation. Is there anything else we should try before manually adjusting the xform? Is there any objective way to evaluate a manually adjusted xform? Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] talairach
Dear all, I am trying to improve talairach registration and I noticed the following suggestion in the freesurfer wiki: "If you suspect that the bad transform is the result of a bright neck region, edit the volume to erase the neck and run mritotal on the edited volume. This can be accomplished through simple volume editing: set all the regions to zero where y is greater than a certain value (around 170). This generally works better than using the brain volume. Check your transform using tkmedit" I would like to try this, but I don't know which command to use. Could someone please fill me in? Also, after fixing the talairach registration, is it necessary to re-run -autorecon2? Or is it sufficient to over-write the header files and talairach.xfm? Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. --- Begin Message --- The Abstract Submission Deadline has been extended!The OHBM Executive Council has decided to extend the abstract submission deadline for the 12th Annual Meeting of the Organization for Human Brain Mapping in Florence, Italy, June 11-15, 2006. Please note that the Abstract Submission deadline is now January 8, 2006 at 11:59 p.m. CST. Click here to submit an abstract. Though you are not required to register for the meeting prior to submitting an abstract, the presenter of the abstract must register for the meeting. To take advantage of the lowest registration fee, register online at MailScanner has detected a possible fraud attempt from "www.llmsi.com" claiming to be MailScanner has detected a possible fraud attempt from "www.llmsi.com" claiming to be www.humanbrainmapping.org by March 15, 2006. Watch for an email announcing the opening of the registration site. We hope you will join us for what promises to be a memorable meeting from both a scientific and social perspective! If you have any comments, questions or suggestions, please feel free to contact us at [EMAIL PROTECTED].Sincerely,Maurizio Corbetta, Program CommitteePietro Pietrini, Local Organizing ChairPeter Bandettini, Chair, OHBMTo be removed from this mailing list, please click here. --- End Message --- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] skull stripping
Dear all, To improve skull stripping, I adjusted the watershed threshold using wsthresh, but this did not work well with our data. Do you have any other suggestions for improving skull stripping when there is too much membrane included? Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] warning
Dear all, I see this warning for several different commands, does anyone know what this means? INFO: Volume /tmp/mritotal_32685/nu_8_dxyz.mnc cannot be found. Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] 64 vs 32
So why aren't they included in the 64-bit stable? How long would you expect these steps to take? Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] 64 vs 32
Dear all, I have run several subjects on a 64-bit machine using the stable release. I recently installed the 32-bit stable version on a 32-bit machine. I noticed that running stage1 on the 32-bit version took much longer than running stage1 on the 64-bit machine (several hours, actually). So I looked at the recon-all scripts for each version and I noticed that they were different. The 32-bit version includes the extra steps DoGCAReg, DoCANormalize, DoCAReg, and DoCALabel. Does anyone know why this is? Below are the stage1 lists for each version. Thanks, Sasha 32-bit version: case "-stage1": set DoMotionCor = 1; set DoTalairach = 1; set DoNuIntensityCor = 1; set DoNormalization = 1; set DoSkullStrip = 1; set DoSegmentation = 1; set DoGCAReg = 1; set DoCANormalize= 1; set DoCAReg = 1; set DoCALabel= 1; set DoFill = 1; set DoTessellate = 1; set SvInitOrigSurf = 1; set DoSmooth1= 1; set DoInflate1 = 1; set SvInitInflated = 1; breaksw 64-bit version: case "-stage1": set DoMotionCor = 1; set DoTalairach = 1; set DoNuIntensityCor = 1; set DoNormalization = 1; set DoSkullStrip = 1; set DoSegmentation = 1; set DoFill = 1; set DoTessellate = 1; set SvInitOrigSurf = 1; set DoSmooth1= 1; set DoInflate1 = 1; set SvInitInflated = 1; breaksw Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Re: mris_ca_label 32vs64 (Satrajit Ghosh)
Dear all, I have also noticed a discrepancy between the stable 32 and the stable 64. The FreeSurferEnv.csh files are quite different. Why is that? Are there any other differences? Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] tkmedit
Dear all, My brains appear too bright after skull stripping, so I tried to fix this with the following command: tkmedit 2316_corffe brain -mm-main 0 255 But the --mm-main option did not have an effect unless I set the max to be lower than the actual max (which was about 170 in this case) The brightness/contrast gui in the tkmedit menu does not allow me to increase the max either. I am using the stable release for x86_64 machines. Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] labels
great, thanks Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] labels
If the atlas is not included, how am I able to run mris_ca_label? Is the atlas you are referring to different from the ?h.atlas2002_simple.gcs file found in /freesurfer/average? Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] labels
so for the stable release should I run both mris_ca_label and mris_anatomical_stats? I'm not sure I understand how to use mris_anatomical_stats to get all the information- is it necessary to specify a surface file? Also, can I view the thickness map of an individual subject? Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] labels
I looked through the recon-all.log file, but I could not find any references to mris_ca_label or mris_anatomical_stats, do you know what else I can search for? I found this warning in several places, but I don't know if it is related: INFO: Volume /tmp/mritotal_12360/orig_8_dxyz.mnc cannot be found. In the recon-all.status file there is another warning: Euler: NHoles = WARNING: Number of holes is not zero This subject was previously manually edited with an older version (oct 2003 release). I made four copies of the subject and ran each of the following in both the 2003 release and the latest stable release: recon-all -subjid subject -stage3 -stage4a -stage4b recon-all -subjid subject -all I only saw the warnings in subjects run with the stable release, (in the 2003 release NHoles =0). Could I be missing some files? Thanks, Sasha >>> Xiao Han <[EMAIL PROTECTED]> >>> If you run "recon-all -all ...", then mris_ca_label and mris_anatomical_stats should be included as the final two steps. You can check the recon-all.log file under each subject's script directory to see why mris_ca_label wasn't executed in your previous run of recon-all. -Xiao On Mon, 14 Nov 2005, Sasha Wolosin wrote: > That might have been what happened. I loaded the annotation to the > other surfaces, but they also looked strange. Then I re-ran > mris_ca_label and the labels look normal. > > So are mris_ca_label and mris_anatomical_stats not part of the recon-all > script (I am using the stable release)? > > Thanks, > Sasha > > > >>>> Xiao Han <[EMAIL PROTECTED]> >>> > hmm, that's wierd. > Did you recomputed the white surface after the annotation file was > generated? > You can try to load the annotation to other surfaces of the same > hemisphere, like ?h.sphere, ?h.sphere.reg, to see whether the same > scattered appearance still exists. > > -Xiao > > > On Mon, 14 Nov 2005, Sasha Wolosin wrote: > >> I double-checked, the correct hemisphere is loaded >> >>>>> Xiao Han <[EMAIL PROTECTED]> >>> >> It's not normal. >> It's very likely that you load a rh annotation to a lh surface or the >> other way around. Pls double check. >> >> -Xiao >> >> On Mon, 14 Nov 2005, Sasha Wolosin wrote: >> >>> Dear all, >>> >>> When I load the ?h.aparc.annot with the ?h.white surface in > tksurfer, >>> the labels look very scattered, is this normal? (please see attached >>> jpeg) >>> >>> Thanks, >>> Sasha >>> >>> >>> >>> Disclaimer: >>> The materials in this e-mail are private and may contain Protected >> Health Information. Please note that e-mail is not necessarily >> confidential or secure. Your use of e-mail constitutes your >> acknowledgment of these confidentiality and security limitations. If > you >> are not the intended recipient, be advised that any unauthorized use, >> disclosure, copying, distribution, or the taking of any action in >> reliance on the contents of this information is strictly prohibited. > If >> you have received this e-mail in error, please immediately notify the >> sender via telephone or return e-mail. >>> >> >> >> > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] labels
Dear all, When I load the ?h.aparc.annot with the ?h.white surface in tksurfer, the labels look very scattered, is this normal? (please see attached jpeg) Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. <> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mris_fix_topology
Hi Bruce, yep, the cerebellum was attatched, so I guess that must have been the problem. Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mris_fix_topology
Dear all, I ran into a problem with the mris_fix_topology step of recon-all. Below is the output of mris_fix_topology. Does anyone know what this might mean? Any help is greatly appreciated, Thanks, Sasha Fix Topology lh Wed Nov 9 23:53:11 EST 2005 /data/Sasha_subjects/0248_corffe/scripts mris_fix_topology 0248_corffe lh * Setting options * Topology Correction Parameters retessellation mode : greedy search ordering dependant retessellation: 0 initial patch selection : 0 use precomputed edge table :0 smooth retessellated patch :0 match retessellated patch : 0 verbose mode : 0 * reading input surface /data/Sasha_subjects/0248_corffe/surf/lh.qsphere... INFO: Volume /tmp/mritotal_24375/nu_8_dxyz.mnc cannot be found. INFO: found the orig volume info on /data/Sasha_subjects/0248_corffe/mri/filled in the surface data. before topology correction, eno=-1360 (nv=257430, nf=517668, ne=776458, g=681) using quasi-homeomorphic spherical map to tessellate cortical surface... Too many intersected faces for face 347232 (171859, 173622, 173623) No such file or directory reading T1 volume from T1... reading wm segmentation from wm... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 14 iterations marking ambiguous vertices... ERROR: mris_fix_topology exited with non-zero status -- Filesystem 1K-blocks Used Available Use% Mounted on /dev/sdb7136908624 11451328 118388296 9% /data -- recon-all exited with errors at Wed Nov 9 23:55:36 EST 2005 Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] analyze format
yes, it is the orientation field I need to set. I found a lossless way
to re-orient my data using another program before passing it to
freesurfer, so I guess I can use that, but I would prefer to do it all
in one step with freesurfer, is the -i{ijk}d method lossless?
Thanks,
Sasha
Disclaimer:
The materials in this e-mail are private and may contain Protected Health
Information. Please note that e-mail is not necessarily confidential or secure.
Your use of e-mail constitutes your acknowledgment of these confidentiality and
security limitations. If you are not the intended recipient, be advised that
any unauthorized use, disclosure, copying, distribution, or the taking of any
action in reliance on the contents of this information is strictly prohibited.
If you have received this e-mail in error, please immediately notify the sender
via telephone or return e-mail.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] analyze format
Dear all, When converting from analyze format is there any way to get mri_convert to read in orientation information from the analyze header file? Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Re: Freesurfer Digest, Vol 21, Issue 3
Regarding this issue with the old version of mris_anatomical_stats, will problems with rh.area effect any of the other results? Or are there any bugs effecting other anatomical stats besides rh.area? Message: 2 Date: Wed, 02 Nov 2005 12:58:06 -0500 From: Doug Greve <[EMAIL PROTECTED]> Subject: Re: [Freesurfer] area file To: Marie Schaer <[EMAIL PROTECTED]> Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=us-ascii; format=flowed We found a problem with this computation about a year ago (11/12/2004 to be specific). I think I sent an email about it to the list. Any releases prior to that date will have this error in the area computations. Can you try it with a more recent release? Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 [EMAIL PROTECTED] Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] help with mris_ca_label
thanks, I created a label directory and that solved the problem. It looks like all our subjects are missing a label directory. Do you know why that might happen? Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 [EMAIL PROTECTED] >>> Bruce Fischl <[EMAIL PROTECTED]> 11/02/05 1:46 PM >>> Hi Sasha, it gets written into the label dir by default. Are you sure that directory exists (should be at the same level as surf) Bruce On Wed, 2 Nov 2005, Sasha Wolosin wrote: > I'm having trouble specifying the output file when running > mris_ca_label- should it be in the surf folder or somewhere else? > (output below) > Thanks, > Sasha > > [EMAIL PROTECTED] surf]$ pwd > /home/wolosin/subjects/dec1877J_prac/surf > [EMAIL PROTECTED] surf]$ mris_ca_label dec1877J_prac rh rh.sphere.reg > /freesurfer/ average/rh.atlas2002_simple.gcs rh.aparc.annot > reading atlas from /freesurfer/average/rh.atlas2002_simple.gcs... > reading color table from GCSA file > input 1: CURVATURE FILE, flags 0, avgs 0, name sulc > input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature > labeling surface... > relabeling using gibbs priors... > 000: 9230 changed, 125897 examined... > 001: 2224 changed, 34779 examined... > 002:681 changed, 11344 examined... > 003:275 changed, 3817 examined... > 004:160 changed, 1602 examined... > 005: 76 changed, 937 examined... > 006: 31 changed, 434 examined... > 007: 18 changed, 193 examined... > 008: 15 changed, 103 examined... > 009: 7 changed, 86 examined... > 010: 2 changed, 46 examined... > 011: 3 changed, 16 examined... > 012: 0 changed, 10 examined... > 000: 286 total segments, 189 labels (2604 vertices) changed > 001: 107 total segments, 12 labels (195 vertices) changed > 002: 95 total segments, 0 labels (0 vertices) changed > 10 filter iterations complete (10 requested, 121 changed) > writing output to rh.aparc.annot... > could not write annot file > /home/wolosin/subjects/dec1877J_prac/surf/../label/rh .aparc.annot > No such file or directory > mris_ca_label: could not write annot file rh.aparc.annot for > dec1877J_prac > No such file or directory > [EMAIL PROTECTED] surf]$ > > Sasha Wolosin > Research Assistant > Developmental Cognitive Neurology > Kennedy Krieger Institute > 707 N. Broadway > Baltimore, MD 21205 > ph: (443) 923-9270 > [EMAIL PROTECTED] > > > > Disclaimer: > The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] help with mris_ca_label
I'm having trouble specifying the output file when running mris_ca_label- should it be in the surf folder or somewhere else? (output below) Thanks, Sasha [EMAIL PROTECTED] surf]$ pwd /home/wolosin/subjects/dec1877J_prac/surf [EMAIL PROTECTED] surf]$ mris_ca_label dec1877J_prac rh rh.sphere.reg /freesurfer/ average/rh.atlas2002_simple.gcs rh.aparc.annot reading atlas from /freesurfer/average/rh.atlas2002_simple.gcs... reading color table from GCSA file input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... relabeling using gibbs priors... 000: 9230 changed, 125897 examined... 001: 2224 changed, 34779 examined... 002:681 changed, 11344 examined... 003:275 changed, 3817 examined... 004:160 changed, 1602 examined... 005: 76 changed, 937 examined... 006: 31 changed, 434 examined... 007: 18 changed, 193 examined... 008: 15 changed, 103 examined... 009: 7 changed, 86 examined... 010: 2 changed, 46 examined... 011: 3 changed, 16 examined... 012: 0 changed, 10 examined... 000: 286 total segments, 189 labels (2604 vertices) changed 001: 107 total segments, 12 labels (195 vertices) changed 002: 95 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 121 changed) writing output to rh.aparc.annot... could not write annot file /home/wolosin/subjects/dec1877J_prac/surf/../label/rh .aparc.annot No such file or directory mris_ca_label: could not write annot file rh.aparc.annot for dec1877J_prac No such file or directory [EMAIL PROTECTED] surf]$ Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 [EMAIL PROTECTED] Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] help with mris_ca_label
is that *_trans_toSulc.gcs or *.atlas2002_simple.gcs? Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 [EMAIL PROTECTED] >>> "Brian T. Quinn" <[EMAIL PROTECTED]> 11/01/05 7:38 PM >>> canonical surface refers to *.sphere.reg (found in $SUBJECTS_DIR/$s/surf) classifier is *.gcs (found in $FREESURFER_HOME/average) On Tue, 1 Nov 2005, Sasha Wolosin wrote: > Dear all, > In calling mris_ca_label, what does 'canonical surface' and > 'classifier' refer to? > Thanks, > Sasha > > Sasha Wolosin > Research Assistant > Developmental Cognitive Neurology > Kennedy Krieger Institute > 707 N. Broadway > Baltimore, MD 21205 > ph: (443) 923-9270 > [EMAIL PROTECTED] > > > > Disclaimer: > The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- brian t. quinn ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] help with mris_ca_label
Dear all, In calling mris_ca_label, what does 'canonical surface' and 'classifier' refer to? Thanks, Sasha Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 [EMAIL PROTECTED] Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tkregister2
In the meantime, is there any benefit to processing brains, or would most of the reconstruction steps need to be re-run after this problem is fixed? How much of the reconstruction needs to be re-run after manually fixing a bad talairach.xfm? Thanks, Sasha >>> Doug Greve <[EMAIL PROTECTED]> 10/18/2005 8:08 PM >>> OK. We've replicated this problem here. I'll work on it to find out what's going on. doug On Tue, 18 Oct 2005, Sasha Wolosin wrote: > yes, the surface does not align with the anatomical. > >>>> Doug Greve <[EMAIL PROTECTED]> 10/18/2005 2:20 PM >>> > > So the surface does not align with the anatomical? > > > > On Tue, 18 Oct 2005, Sasha Wolosin wrote: > >> My subject's anatomical scan seems to be relatively well aligned > with >> the fuzzy talairach brain, but the green 'orig' surface is > completely >> off. How is this possible? Why do we need the surface at all if > it's >> not used for alignment? >> >> The tutorial advises using the 'final objective function value' > from >> mritotal.log to determine if the registration is off before making > any >> edits. If the registration needs to be modified, and if it's > important >> to have an accurate talairach.xfm, how do I determine if it is > aligned >> sufficiently after making edits? >> >> Thanks, >> Sasha >> >>>>> Doug Greve <[EMAIL PROTECTED]> 10/18/2005 12:23 PM >>> >> >> >> Hit the "compare" button to flip back and forth between the > talairach >> brain and your subjects anatomical. >> >> >> On Tue, 18 Oct 2005, Sasha Wolosin wrote: >> >>> How can I check the registration if I can't see the surface? >>> -Sasha >>> >>>>>> Doug Greve <[EMAIL PROTECTED]> 10/18/2005 12:07 PM >>> >>> >>> If you don't have a surface, then don't run it with --surf. It's >>> important to have an accurate talairach.xfm. >>> >>> doug >>> >>> >>> >>> >>> On Mon, 17 Oct 2005, Sasha Wolosin wrote: >>> >>>> Dear Nick, >>>> >>>> I recently installed the dev release from October 3rd, but >> tkregister2 still does not work after autorecon1. (It will not load > the >> orig volume because rh.orig and lh.orig do not yet exist in the surf >> folder for the subject) Am I not using the correct inputs for this >> step (my inputs are the same as that of the tutorial)? How > important >> is it to have a correct registration before running autorecon2? >>>> >>>> Here is the script for a subject who has only been run with >> autorecon1: >>>> >>>> % [EMAIL PROTECTED] mri]$ tkregister2 --mgz --s 2333 --fstal > --surf >> orig >>>> surfname set to orig >>>> INFO: no target volume specified, assuming FreeSurfer orig volume. >>>> target volume orig >>>> movable volume (null) >>>> reg file (null) >>>> LoadVol1 >>>> $Id: tkregister2.c,v 1.38 2005/09/15 17:43:48 greve Exp $ >>>> Diagnostic Level -1 >>>> talairach.xfm - >>>> 1.020 -0.138 0.036 -2.498; >>>> 0.151 1.100 -0.045 -8.636; >>>> -0.033 0.052 1.156 -11.535; >>>> 0.000 0.000 0.000 1.000; >>>> WARNING: can't find the talairach xform >> '/freesurfer/subjects/2333/mri/transforms/talairach.xfm' >>>> WARNING: transform is not loaded into mri >>>> INFO: loading target /freesurfer_subjects/2333/mri/orig.mgz >>>> WARNING: can't find the talairach xform >> '/freesurfer/subjects/2333/mri/transforms/talairach.xfm' >>>> WARNING: transform is not loaded into mri >>>> INFO: changing target type to float >>>> Ttarg: >>>> -1.000 0.000 0.000 128.538; >>>> 0.000 0.000 1.000 -132.197; >>>> 0.000 -1.000 0.000 137.708; >>>> 0.000 0.000 0.000 1.000; >>>> INFO: loading movable /freesurfer_subjects/talairach/mri/orig.mgz >>>> INFO: changing move type to float >>>> Tmov: >>>> -1.000 0.000 0.000 128.000; >>>> 0.000 0.000 1.000 -128.000; >>>> 0.000 -1.000 0.000 128.000; >>>> 0.000 0.000 0.000 1.000; >>>> mkheaderreg = 0, float2int = 0 >>>> I
Re: [Freesurfer] tkregister2
yes, the surface does not align with the anatomical. >>> Doug Greve <[EMAIL PROTECTED]> 10/18/2005 2:20 PM >>> So the surface does not align with the anatomical? On Tue, 18 Oct 2005, Sasha Wolosin wrote: > My subject's anatomical scan seems to be relatively well aligned with > the fuzzy talairach brain, but the green 'orig' surface is completely > off. How is this possible? Why do we need the surface at all if it's > not used for alignment? > > The tutorial advises using the 'final objective function value' from > mritotal.log to determine if the registration is off before making any > edits. If the registration needs to be modified, and if it's important > to have an accurate talairach.xfm, how do I determine if it is aligned > sufficiently after making edits? > > Thanks, > Sasha > >>>> Doug Greve <[EMAIL PROTECTED]> 10/18/2005 12:23 PM >>> > > > Hit the "compare" button to flip back and forth between the talairach > brain and your subjects anatomical. > > > On Tue, 18 Oct 2005, Sasha Wolosin wrote: > >> How can I check the registration if I can't see the surface? >> -Sasha >> >>>>> Doug Greve <[EMAIL PROTECTED]> 10/18/2005 12:07 PM >>> >> >> If you don't have a surface, then don't run it with --surf. It's >> important to have an accurate talairach.xfm. >> >> doug >> >> >> >> >> On Mon, 17 Oct 2005, Sasha Wolosin wrote: >> >>> Dear Nick, >>> >>> I recently installed the dev release from October 3rd, but > tkregister2 still does not work after autorecon1. (It will not load the > orig volume because rh.orig and lh.orig do not yet exist in the surf > folder for the subject) Am I not using the correct inputs for this > step (my inputs are the same as that of the tutorial)? How important > is it to have a correct registration before running autorecon2? >>> >>> Here is the script for a subject who has only been run with > autorecon1: >>> >>> % [EMAIL PROTECTED] mri]$ tkregister2 --mgz --s 2333 --fstal --surf > orig >>> surfname set to orig >>> INFO: no target volume specified, assuming FreeSurfer orig volume. >>> target volume orig >>> movable volume (null) >>> reg file (null) >>> LoadVol1 >>> $Id: tkregister2.c,v 1.38 2005/09/15 17:43:48 greve Exp $ >>> Diagnostic Level -1 >>> talairach.xfm - >>> 1.020 -0.138 0.036 -2.498; >>> 0.151 1.100 -0.045 -8.636; >>> -0.033 0.052 1.156 -11.535; >>> 0.000 0.000 0.000 1.000; >>> WARNING: can't find the talairach xform > '/freesurfer/subjects/2333/mri/transforms/talairach.xfm' >>> WARNING: transform is not loaded into mri >>> INFO: loading target /freesurfer_subjects/2333/mri/orig.mgz >>> WARNING: can't find the talairach xform > '/freesurfer/subjects/2333/mri/transforms/talairach.xfm' >>> WARNING: transform is not loaded into mri >>> INFO: changing target type to float >>> Ttarg: >>> -1.000 0.000 0.000 128.538; >>> 0.000 0.000 1.000 -132.197; >>> 0.000 -1.000 0.000 137.708; >>> 0.000 0.000 0.000 1.000; >>> INFO: loading movable /freesurfer_subjects/talairach/mri/orig.mgz >>> INFO: changing move type to float >>> Tmov: >>> -1.000 0.000 0.000 128.000; >>> 0.000 0.000 1.000 -128.000; >>> 0.000 -1.000 0.000 128.000; >>> 0.000 0.000 0.000 1.000; >>> mkheaderreg = 0, float2int = 0 >>> Input registration matrix >>> 1.020 -0.138 0.036 -2.498; >>> 0.151 1.100 -0.045 -8.636; >>> -0.033 0.052 1.156 -11.535; >>> 0.000 0.000 0.000 1.000; >>> subject = 2333 >>> Reading lh surface orig >>> MRISread(/freesurfer_subjects/2333/surf/lh.orig): could not open > file >>> No such file or directory >>> tkregister2: could not read surface orig >>> No such file or directory >>> [EMAIL PROTECTED] mri]$ >>> >>> If I instead run the command: >>> tkregister2 --mgz --s 2333 --fstal >>> tkregister2 does load, but there is no green orig outline to guide > any corrections. >>> >>> If I run tkregister2 after running autorecon2, it also loads, but > the registration is all wrong. (It was about as far off as the tutorial > subject) Here is the out
Re: [Freesurfer] tkregister2
My subject's anatomical scan seems to be relatively well aligned with the fuzzy talairach brain, but the green 'orig' surface is completely off. How is this possible? Why do we need the surface at all if it's not used for alignment? The tutorial advises using the 'final objective function value' from mritotal.log to determine if the registration is off before making any edits. If the registration needs to be modified, and if it's important to have an accurate talairach.xfm, how do I determine if it is aligned sufficiently after making edits? Thanks, Sasha >>> Doug Greve <[EMAIL PROTECTED]> 10/18/2005 12:23 PM >>> Hit the "compare" button to flip back and forth between the talairach brain and your subjects anatomical. On Tue, 18 Oct 2005, Sasha Wolosin wrote: > How can I check the registration if I can't see the surface? > -Sasha > >>>> Doug Greve <[EMAIL PROTECTED]> 10/18/2005 12:07 PM >>> > > If you don't have a surface, then don't run it with --surf. It's > important to have an accurate talairach.xfm. > > doug > > > > > On Mon, 17 Oct 2005, Sasha Wolosin wrote: > >> Dear Nick, >> >> I recently installed the dev release from October 3rd, but tkregister2 still does not work after autorecon1. (It will not load the orig volume because rh.orig and lh.orig do not yet exist in the surf folder for the subject) Am I not using the correct inputs for this step (my inputs are the same as that of the tutorial)? How important is it to have a correct registration before running autorecon2? >> >> Here is the script for a subject who has only been run with autorecon1: >> >> % [EMAIL PROTECTED] mri]$ tkregister2 --mgz --s 2333 --fstal --surf orig >> surfname set to orig >> INFO: no target volume specified, assuming FreeSurfer orig volume. >> target volume orig >> movable volume (null) >> reg file (null) >> LoadVol1 >> $Id: tkregister2.c,v 1.38 2005/09/15 17:43:48 greve Exp $ >> Diagnostic Level -1 >> talairach.xfm - >> 1.020 -0.138 0.036 -2.498; >> 0.151 1.100 -0.045 -8.636; >> -0.033 0.052 1.156 -11.535; >> 0.000 0.000 0.000 1.000; >> WARNING: can't find the talairach xform '/freesurfer/subjects/2333/mri/transforms/talairach.xfm' >> WARNING: transform is not loaded into mri >> INFO: loading target /freesurfer_subjects/2333/mri/orig.mgz >> WARNING: can't find the talairach xform '/freesurfer/subjects/2333/mri/transforms/talairach.xfm' >> WARNING: transform is not loaded into mri >> INFO: changing target type to float >> Ttarg: >> -1.000 0.000 0.000 128.538; >> 0.000 0.000 1.000 -132.197; >> 0.000 -1.000 0.000 137.708; >> 0.000 0.000 0.000 1.000; >> INFO: loading movable /freesurfer_subjects/talairach/mri/orig.mgz >> INFO: changing move type to float >> Tmov: >> -1.000 0.000 0.000 128.000; >> 0.000 0.000 1.000 -128.000; >> 0.000 -1.000 0.000 128.000; >> 0.000 0.000 0.000 1.000; >> mkheaderreg = 0, float2int = 0 >> Input registration matrix >> 1.020 -0.138 0.036 -2.498; >> 0.151 1.100 -0.045 -8.636; >> -0.033 0.052 1.156 -11.535; >> 0.000 0.000 0.000 1.000; >> subject = 2333 >> Reading lh surface orig >> MRISread(/freesurfer_subjects/2333/surf/lh.orig): could not open file >> No such file or directory >> tkregister2: could not read surface orig >> No such file or directory >> [EMAIL PROTECTED] mri]$ >> >> If I instead run the command: >> tkregister2 --mgz --s 2333 --fstal >> tkregister2 does load, but there is no green orig outline to guide any corrections. >> >> If I run tkregister2 after running autorecon2, it also loads, but the registration is all wrong. (It was about as far off as the tutorial subject) Here is the output: >> >> [EMAIL PROTECTED] /freesurfer_subjects]$ tkregister2 --mgz --s 2338 --fstal --surf orig >> surfname set to orig >> INFO: no target volume specified, assuming FreeSurfer orig volume. >> target volume orig >> movable volume (null) >> reg file (null) >> LoadVol1 >> $Id: tkregister2.c,v 1.38 2005/09/15 17:43:48 greve Exp $ >> Diagnostic Level -1 >> talairach.xfm - >> 1.131 -0.107 0.009 -12.066; >> 0.107 1.119 -0.133 -2.885; >> 0.003 0.141 1.186 -27.267; >> 0.000 0.000 0.000 1.000; >> WARNING: can't find the talairach xfor
Re: [Freesurfer] tkregister2
How can I check the registration if I can't see the surface? -Sasha >>> Doug Greve <[EMAIL PROTECTED]> 10/18/2005 12:07 PM >>> If you don't have a surface, then don't run it with --surf. It's important to have an accurate talairach.xfm. doug On Mon, 17 Oct 2005, Sasha Wolosin wrote: > Dear Nick, > > I recently installed the dev release from October 3rd, but tkregister2 still > does not work after autorecon1. (It will not load the orig volume because > rh.orig and lh.orig do not yet exist in the surf folder for the subject) Am > I not using the correct inputs for this step (my inputs are the same as that > of the tutorial)? How important is it to have a correct registration before > running autorecon2? > > Here is the script for a subject who has only been run with autorecon1: > > % [EMAIL PROTECTED] mri]$ tkregister2 --mgz --s 2333 --fstal --surf orig > surfname set to orig > INFO: no target volume specified, assuming FreeSurfer orig volume. > target volume orig > movable volume (null) > reg file (null) > LoadVol1 > $Id: tkregister2.c,v 1.38 2005/09/15 17:43:48 greve Exp $ > Diagnostic Level -1 > talairach.xfm - > 1.020 -0.138 0.036 -2.498; > 0.151 1.100 -0.045 -8.636; > -0.033 0.052 1.156 -11.535; > 0.000 0.000 0.000 1.000; > WARNING: can't find the talairach xform > '/freesurfer/subjects/2333/mri/transforms/talairach.xfm' > WARNING: transform is not loaded into mri > INFO: loading target /freesurfer_subjects/2333/mri/orig.mgz > WARNING: can't find the talairach xform > '/freesurfer/subjects/2333/mri/transforms/talairach.xfm' > WARNING: transform is not loaded into mri > INFO: changing target type to float > Ttarg: > -1.000 0.000 0.000 128.538; > 0.000 0.000 1.000 -132.197; > 0.000 -1.000 0.000 137.708; > 0.000 0.000 0.000 1.000; > INFO: loading movable /freesurfer_subjects/talairach/mri/orig.mgz > INFO: changing move type to float > Tmov: > -1.000 0.000 0.000 128.000; > 0.000 0.000 1.000 -128.000; > 0.000 -1.000 0.000 128.000; > 0.000 0.000 0.000 1.000; > mkheaderreg = 0, float2int = 0 > Input registration matrix > 1.020 -0.138 0.036 -2.498; > 0.151 1.100 -0.045 -8.636; > -0.033 0.052 1.156 -11.535; > 0.000 0.000 0.000 1.000; > subject = 2333 > Reading lh surface orig > MRISread(/freesurfer_subjects/2333/surf/lh.orig): could not open file > No such file or directory > tkregister2: could not read surface orig > No such file or directory > [EMAIL PROTECTED] mri]$ > > If I instead run the command: > tkregister2 --mgz --s 2333 --fstal > tkregister2 does load, but there is no green orig outline to guide any > corrections. > > If I run tkregister2 after running autorecon2, it also loads, but the > registration is all wrong. (It was about as far off as the tutorial subject) > Here is the output: > > [EMAIL PROTECTED] /freesurfer_subjects]$ tkregister2 --mgz --s 2338 --fstal > --surf orig > surfname set to orig > INFO: no target volume specified, assuming FreeSurfer orig volume. > target volume orig > movable volume (null) > reg file (null) > LoadVol1 > $Id: tkregister2.c,v 1.38 2005/09/15 17:43:48 greve Exp $ > Diagnostic Level -1 > talairach.xfm - > 1.131 -0.107 0.009 -12.066; > 0.107 1.119 -0.133 -2.885; > 0.003 0.141 1.186 -27.267; > 0.000 0.000 0.000 1.000; > WARNING: can't find the talairach xform > '/freesurfer/subjects/2338/mri/transforms/talairach.xfm' > WARNING: transform is not loaded into mri > INFO: loading target /freesurfer_subjects/2338/mri/orig.mgz > WARNING: can't find the talairach xform > '/freesurfer/subjects/2338/mri/transforms/talairach.xfm' > WARNING: transform is not loaded into mri > INFO: changing target type to float > Ttarg: > -1.000 0.000 0.000 136.359; > 0.000 0.000 1.000 -135.309; > -0.000 -1.000 0.000 159.346; > 0.000 0.000 0.000 1.000; > INFO: loading movable /freesurfer_subjects/talairach/mri/orig.mgz > INFO: changing move type to float > Tmov: > -1.000 0.000 0.000 128.000; > 0.000 0.000 1.000 -128.000; > 0.000 -1.000 0.000 128.000; > 0.000 0.000 0.000 1.000; > mkheaderreg = 0, float2int = 0 > Input registration matrix > 1.131 -0.107 0.009 -12.066; > 0.107 1.119 -0.133 -2.885; > 0.003 0.141 1.186 -27.267; > 0.000 0.000 0.000 1.000; > subject = 2338 > Reading lh surface ori
Re: [Freesurfer] tkregister2
Dear Nick,
I recently installed the dev release from October 3rd, but tkregister2 still
does not work after autorecon1. (It will not load the orig volume because
rh.orig and lh.orig do not yet exist in the surf folder for the subject) Am I
not using the correct inputs for this step (my inputs are the same as that of
the tutorial)? How important is it to have a correct registration before
running autorecon2?
Here is the script for a subject who has only been run with autorecon1:
% [EMAIL PROTECTED] mri]$ tkregister2 --mgz --s 2333 --fstal --surf orig
surfname set to orig
INFO: no target volume specified, assuming FreeSurfer orig volume.
target volume orig
movable volume (null)
reg file (null)
LoadVol1
$Id: tkregister2.c,v 1.38 2005/09/15 17:43:48 greve Exp $
Diagnostic Level -1
talairach.xfm -
1.020 -0.138 0.036 -2.498;
0.151 1.100 -0.045 -8.636;
-0.033 0.052 1.156 -11.535;
0.000 0.000 0.000 1.000;
WARNING: can't find the talairach xform
'/freesurfer/subjects/2333/mri/transforms/talairach.xfm'
WARNING: transform is not loaded into mri
INFO: loading target /freesurfer_subjects/2333/mri/orig.mgz
WARNING: can't find the talairach xform
'/freesurfer/subjects/2333/mri/transforms/talairach.xfm'
WARNING: transform is not loaded into mri
INFO: changing target type to float
Ttarg:
-1.000 0.000 0.000 128.538;
0.000 0.000 1.000 -132.197;
0.000 -1.000 0.000 137.708;
0.000 0.000 0.000 1.000;
INFO: loading movable /freesurfer_subjects/talairach/mri/orig.mgz
INFO: changing move type to float
Tmov:
-1.000 0.000 0.000 128.000;
0.000 0.000 1.000 -128.000;
0.000 -1.000 0.000 128.000;
0.000 0.000 0.000 1.000;
mkheaderreg = 0, float2int = 0
Input registration matrix
1.020 -0.138 0.036 -2.498;
0.151 1.100 -0.045 -8.636;
-0.033 0.052 1.156 -11.535;
0.000 0.000 0.000 1.000;
subject = 2333
Reading lh surface orig
MRISread(/freesurfer_subjects/2333/surf/lh.orig): could not open file
No such file or directory
tkregister2: could not read surface orig
No such file or directory
[EMAIL PROTECTED] mri]$
If I instead run the command:
tkregister2 --mgz --s 2333 --fstal
tkregister2 does load, but there is no green orig outline to guide any
corrections.
If I run tkregister2 after running autorecon2, it also loads, but the
registration is all wrong. (It was about as far off as the tutorial subject)
Here is the output:
[EMAIL PROTECTED] /freesurfer_subjects]$ tkregister2 --mgz --s 2338 --fstal
--surf orig
surfname set to orig
INFO: no target volume specified, assuming FreeSurfer orig volume.
target volume orig
movable volume (null)
reg file (null)
LoadVol1
$Id: tkregister2.c,v 1.38 2005/09/15 17:43:48 greve Exp $
Diagnostic Level -1
talairach.xfm -
1.131 -0.107 0.009 -12.066;
0.107 1.119 -0.133 -2.885;
0.003 0.141 1.186 -27.267;
0.000 0.000 0.000 1.000;
WARNING: can't find the talairach xform
'/freesurfer/subjects/2338/mri/transforms/talairach.xfm'
WARNING: transform is not loaded into mri
INFO: loading target /freesurfer_subjects/2338/mri/orig.mgz
WARNING: can't find the talairach xform
'/freesurfer/subjects/2338/mri/transforms/talairach.xfm'
WARNING: transform is not loaded into mri
INFO: changing target type to float
Ttarg:
-1.000 0.000 0.000 136.359;
0.000 0.000 1.000 -135.309;
-0.000 -1.000 0.000 159.346;
0.000 0.000 0.000 1.000;
INFO: loading movable /freesurfer_subjects/talairach/mri/orig.mgz
INFO: changing move type to float
Tmov:
-1.000 0.000 0.000 128.000;
0.000 0.000 1.000 -128.000;
0.000 -1.000 0.000 128.000;
0.000 0.000 0.000 1.000;
mkheaderreg = 0, float2int = 0
Input registration matrix
1.131 -0.107 0.009 -12.066;
0.107 1.119 -0.133 -2.885;
0.003 0.141 1.186 -27.267;
0.000 0.000 0.000 1.000;
subject = 2338
Reading lh surface orig
Done reading surface
Reading rh surface orig
Done reading surface
Zoom Factor = 2
FOV = 256
Opening window 2338
Setting scale
tkregister2: interface: /freesurfer/lib/tcl/tkregister2.tcl
tkregister.tcl: startup done
tkregister.tcl: default macro interface (to change: macro,mini,micro)
tkregister.tcl: or: setenv tkregisterinterface {macro,mini,micro}
Looking through the script I noticed it never mentions the path to the
correct .xfm file, which is in the subjects directory (the subjects directory
is /freesurfer_subjects, not /freesurfer/subjects) But I copied the .xfm file
to the folder it was looking for, and the registration was still just as far
off.
Any help is greatly appreciated,
Thanks,
Sasha
Sasha Wolosin
Research Assistant
Developmental Cognitive Neurology
Kennedy Krieger Institute
707 N. Broadway
Baltimore, MD 2
[Freesurfer] Fwd: public distribution
Oh, sorry, I see now that I need to use ftp to access the files, nevermind my question. >>> Sasha Wolosin 10/14/2005 9:57 AM >>> Dear all, Has the tutorial data been relocated? I cannot find it on https://surfer.nmr.mgh.harvard.edu/pub/dist Many Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] public distribution
Dear all, Has the tutorial data been relocated? I cannot find it on https://surfer.nmr.mgh.harvard.edu/pub/dist Many Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] control points
Dear all, I am trying to add control points for a subject in order to improve normalization and skull stripping, but I found that the control points I added did not have much effect on the end result. I know control points should be added at points that the user feels sure are inside the white matter boundary, and that there should be about 20 spread out throughout the volume, but I am still uncertain as to how to choose them effectively. Should they be closer to the white/gray boundary? Or closer to the center? I believe I would be able to choose these points more effectively if I understood how FreeSurfer uses control points. Is it used as a high or low cut-off thresh-hold? Or is it more complex than that? Is location taken into account or is it just the intensity values that are used? Any help is greatly appreciated. Thank you, Sasha Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 [EMAIL PROTECTED] Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] new stable release
Dear all, I am having trouble installing/setting up the stable release v2.1 for CentOS 4 x86_64. I seem to be missing all the mni and fsl tools, they are not included in my freesurfer home folder. Should I just copy these from the dev version? When I try to run setup I get this error: [EMAIL PROTECTED] /freesurfer]$ source SetUpFreeSurfer.csh Setting up enviroment for FreeSurfer/FS-FAST $Id: FreeSurferEnv.csh,v 1.3.6.6 2005/07/29 17:40:57 kteich Exp $ FREESURFER_HOME /freesurfer FSFAST_HOME /freesurfer/fsfast FSL_DIR /freesurfer/fsl SUBJECTS_DIR/freesurfer/subjects WARNING: /freesurfer/fsl/bin does not exist. Any help is greatly appreciated. Thanks, Sasha Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 [EMAIL PROTECTED] Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] tkregister2
Dear all, I am having trouble running tkregister2. I get an error when I run tkregister2 on a subject after running autorecon1 (see below.) However, I also get an error when I run it on bert. It seems tkregister2 is searching for COR files, but I am using mgz format. Am I not using the correct flags? My subjects directory contains the talairach subject included in the dev release. Do I need to download talairach separately? Here is the output for subject 2335 and bert: [EMAIL PROTECTED] talairach]$ tkregister2 --mgz --s 2335 --fstal INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume (null) reg file (null) LoadVol1 $Id: tkregister2.c,v 1.37 2005/08/29 21:38:09 greve Exp $ Diagnostic Level -1 talairach.xfm - 1.002 0.050 -0.017 -3.539; -0.053 1.034 -0.076 -12.275; 0.014 0.081 1.091 -14.424; 0.000 0.000 0.000 1.000; corRead(): can't open file /freesurfer/subjects/talairach/mri/orig/COR-.info ERROR: could not read /freesurfer/subjects/talairach/mri/orig as 0 [EMAIL PROTECTED] subjects]$ tkregister2 --mgz --s bert --fstal INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume (null) reg file (null) LoadVol1 $Id: tkregister2.c,v 1.37 2005/08/29 21:38:09 greve Exp $ Diagnostic Level -1 talairach.xfm - 1.154 -0.024 0.046 -5.813; 0.014 0.941 0.131 -21.893; -0.048 -0.155 1.123 -0.730; 0.000 0.000 0.000 1.000; WARNING: can't find the talairach xform '/autofs/space/minerva_001/users/nicks/subjects/bert/mri/transforms/talairach.xfm' WARNING: transform is not loaded into mri corRead(): can't open file /freesurfer/subjects/talairach/mri/orig/COR-.info ERROR: could not read /freesurfer/subjects/talairach/mri/orig as 0 [EMAIL PROTECTED] subjects]$ Any help is greatly appreciated. Thanks, Sasha Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 [EMAIL PROTECTED] Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_normalize
I haven't conformed it, so I'll try that- thanks. -Sasha >>> Bruce Fischl <[EMAIL PROTECTED]> 9/9/2005 3:42 PM >>> Hi Sasha, the problem is that the orig.mgz volume hasn't been "conformed". Did you generate it with recon-all? It should be 1mm isotropic, 256mm^3 and UCHAR instead of SHORT. You could do (from the mri subdir): mv orig.mgz orig_unconformed.mgz mri_convert --conform orig_unconformed orig.mgz then go on your merry way Bruce On Fri, 9 Sep 2005, Sasha Wolosin wrote: > OK, this time it worked: > [EMAIL PROTECTED] /freesurfer]# cd $SUBJECTS_DIR/2332/mri > [EMAIL PROTECTED] mri]# ls > aseg fillednormsegment.dat transforms > brain flash nu.mgz T1 wm > brain.mgz fsamples origT1.mgz wm-init.mgz > error.log mri rawavg.mgz tmp wm.mgz > [EMAIL PROTECTED] mri]# cd orig > [EMAIL PROTECTED] orig]# mri_info orig.mgz > Volume information for orig.mgz > type: MGH >dimensions: 256 x 256 x 124 > voxel sizes: 0.9375, 0.9375, 1.5000 > type: SHORT (4) > fov: 240.000 >xstart: -112.5, xend: 112.5 >ystart: -112.5, yend: 112.5 >zstart: -139.5, zend: 139.5 >TR: 35.00 msec, TE: 6.00 msec, TI: 0.00 msec, flip angle: 45.00 > degrees > nframes: 1 > ras xform present >xform info: x_r = -0.9981, y_r = -0.0056, z_r = 0.0616, c_r = > 0.4646 : x_a = -0.0615, y_a = -0.0131, z_a = -0.9980, c_a = > 0.9575 : x_s = 0.0064, y_s = -0., z_s = 0.0127, c_s = >15.7709 > talairach xfm : /home/wolosin/subjects/2332/mri/transforms/talairach.xfm > Orientation LIP > Primary Slice Direction coronal > > voxel to ras transform: > -0.9357 -0.0052 0.0923 115.1803 > -0.0576 -0.0122 -1.4970 102.7195 >0.0060 -0.9374 0.0190 133.8122 >0. 0. 0. 1. > > voxel-to-ras determinant 1.31836 > > ras to voxel transform: > -1.0646 -0.0656 0.0068 128.4501 > -0.0060 -0.0139 -1.0666 144.8367 >0.0410 -0.6653 0.008562.4846 >0. 0. 0. 1. > [EMAIL PROTECTED] orig]# > > thanks, > Sasha > > Sasha Wolosin > Research Assistant > Developmental Cognitive Neurology > Kennedy Krieger Institute > 707 N. Broadway > Baltimore, MD 21205 > ph: (443) 923-9270 >>>> Bruce Fischl <[EMAIL PROTECTED]> 09/09/05 1:48 PM >>> > sorry, you have to run it from the subject's mri dir (or use the full > path) > > On Fri, 9 Sep 2005, Sasha Wolosin wrote: > >> Here is the result: >> >> [EMAIL PROTECTED] /freesurfer]# mri_info orig.mgz >> zcat: /freesurfer/orig.mgz.gz: No such file or directory >> mghRead(/freesurfer/orig.mgz, -1): read error >> >> thanks, >> Sasha >> >> Sasha Wolosin >> Research Assistant >> Developmental Cognitive Neurology >> Kennedy Krieger Institute >> 707 N. Broadway >> Baltimore, MD 21205 >> ph: (443) 923-9270 >>>>> Bruce Fischl <[EMAIL PROTECTED]> 09/09/05 1:23 PM >>> >> Hi Sasha, >> >> can you do: >> >> mri_info orig.mgz >> >> and send us the results? >> >> thanks, >> Bruce >> On Fri, 9 Sep 2005, Sasha Wolosin wrote: >> >>> I am still having problems with mri_normalize. I have downloaded the >>> latest snapshot- but I still get an error: >>> >>> [EMAIL PROTECTED] mri]$ mri_normalize orig.mgz T1.mgz >>> reading from orig.mgz... >>> normalizing image... >>> talairach transform >>> 1.103 0.048 -0.007 -4.504; >>> -0.051 1.166 0.004 -13.012; >>> 0.007 -0.003 1.090 -15.454; >>> 0.000 0.000 0.000 1.000; >>> INFO: Modifying talairach volume c_(r,a,s) based on average_305 >>> building Voronoi diagram... >>> performing soap bubble smoothing... >>> 3d normalization pass 1 of 2 >>> white matter peak found at 110 >>> Segmentation fault >>> >>> >>> I thought it might be a problem with the talairach transform, but I can't >>> figure out how to view this properly. >>> >>> [EMAIL PROTECTED] subjects]$ tkregister2 --mgz --s 2335 --fstal --surf >>> orig.mgz >>> surfname set to orig.mgz >>> INFO: no target volume specified, assuming FreeSurfer orig volume. >>> target volume orig >>> movable volume (null) >>> reg file (null) >>>
Fwd: Re: [Freesurfer] mri_normalize
Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 --- Begin Message --- OK, this time it worked: [EMAIL PROTECTED] /freesurfer]# cd $SUBJECTS_DIR/2332/mri [EMAIL PROTECTED] mri]# ls aseg fillednormsegment.dat transforms brain flash nu.mgz T1 wm brain.mgz fsamples origT1.mgz wm-init.mgz error.log mri rawavg.mgz tmp wm.mgz [EMAIL PROTECTED] mri]# cd orig [EMAIL PROTECTED] orig]# mri_info orig.mgz Volume information for orig.mgz type: MGH dimensions: 256 x 256 x 124 voxel sizes: 0.9375, 0.9375, 1.5000 type: SHORT (4) fov: 240.000 xstart: -112.5, xend: 112.5 ystart: -112.5, yend: 112.5 zstart: -139.5, zend: 139.5 TR: 35.00 msec, TE: 6.00 msec, TI: 0.00 msec, flip angle: 45.00 degrees nframes: 1 ras xform present xform info: x_r = -0.9981, y_r = -0.0056, z_r = 0.0616, c_r = 0.4646 : x_a = -0.0615, y_a = -0.0131, z_a = -0.9980, c_a = 0.9575 : x_s = 0.0064, y_s = -0., z_s = 0.0127, c_s = 15.7709 talairach xfm : /home/wolosin/subjects/2332/mri/transforms/talairach.xfm Orientation LIP Primary Slice Direction coronal voxel to ras transform: -0.9357 -0.0052 0.0923 115.1803 -0.0576 -0.0122 -1.4970 102.7195 0.0060 -0.9374 0.0190 133.8122 0. 0. 0. 1. voxel-to-ras determinant 1.31836 ras to voxel transform: -1.0646 -0.0656 0.0068 128.4501 -0.0060 -0.0139 -1.0666 144.8367 0.0410 -0.6653 0.008562.4846 0. 0. 0. 1. [EMAIL PROTECTED] orig]# thanks, Sasha Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 >>> Bruce Fischl <[EMAIL PROTECTED]> 09/09/05 1:48 PM >>> sorry, you have to run it from the subject's mri dir (or use the full path) On Fri, 9 Sep 2005, Sasha Wolosin wrote: > Here is the result: > > [EMAIL PROTECTED] /freesurfer]# mri_info orig.mgz > zcat: /freesurfer/orig.mgz.gz: No such file or directory > mghRead(/freesurfer/orig.mgz, -1): read error > > thanks, > Sasha > > Sasha Wolosin > Research Assistant > Developmental Cognitive Neurology > Kennedy Krieger Institute > 707 N. Broadway > Baltimore, MD 21205 > ph: (443) 923-9270 >>>> Bruce Fischl <[EMAIL PROTECTED]> 09/09/05 1:23 PM >>> > Hi Sasha, > > can you do: > > mri_info orig.mgz > > and send us the results? > > thanks, > Bruce > On Fri, 9 Sep 2005, Sasha Wolosin wrote: > >> I am still having problems with mri_normalize. I have downloaded the latest >> snapshot- but I still get an error: >> >> [EMAIL PROTECTED] mri]$ mri_normalize orig.mgz T1.mgz >> reading from orig.mgz... >> normalizing image... >> talairach transform >> 1.103 0.048 -0.007 -4.504; >> -0.051 1.166 0.004 -13.012; >> 0.007 -0.003 1.090 -15.454; >> 0.000 0.000 0.000 1.000; >> INFO: Modifying talairach volume c_(r,a,s) based on average_305 >> building Voronoi diagram... >> performing soap bubble smoothing... >> 3d normalization pass 1 of 2 >> white matter peak found at 110 >> Segmentation fault >> >> >> I thought it might be a problem with the talairach transform, but I can't >> figure out how to view this properly. >> >> [EMAIL PROTECTED] subjects]$ tkregister2 --mgz --s 2335 --fstal --surf >> orig.mgz >> surfname set to orig.mgz >> INFO: no target volume specified, assuming FreeSurfer orig volume. >> target volume orig >> movable volume (null) >> reg file (null) >> LoadVol1 >> $Id: tkregister2.c,v 1.35 2005/07/12 19:50:28 greve Exp $ >> Diagnostic Level -1 >> talairach.xfm ----- >> 1.103 0.048 -0.007 -4.504; >> -0.051 1.166 0.004 -13.012; >> 0.007 -0.003 1.090 -15.454; >> 0.000 0.000 0.000 1.000; >> ERROR: cannot determine type of /home/wolosin/subjects/talairach/mri/orig >> >> Do you know what I am missing? >> Any advice is greatly appreciated, >> Thanks, >> Sasha >> >> Sasha Wolosin >> Research Assistant >> Developmental Cognitive Neurology >> Kennedy Krieger Institute >> 707 N. Broadway >> Baltimore, MD 21205 >> ph: (443) 923-9270 >> >> >> >> Disclaimer: >> The materials in this e-mail are private and may contain Protected Health &
[Freesurfer] mri_normalize
I am still having problems with mri_normalize. I have downloaded the latest snapshot- but I still get an error: [EMAIL PROTECTED] mri]$ mri_normalize orig.mgz T1.mgz reading from orig.mgz... normalizing image... talairach transform 1.103 0.048 -0.007 -4.504; -0.051 1.166 0.004 -13.012; 0.007 -0.003 1.090 -15.454; 0.000 0.000 0.000 1.000; INFO: Modifying talairach volume c_(r,a,s) based on average_305 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 1 of 2 white matter peak found at 110 Segmentation fault I thought it might be a problem with the talairach transform, but I can't figure out how to view this properly. [EMAIL PROTECTED] subjects]$ tkregister2 --mgz --s 2335 --fstal --surf orig.mgz surfname set to orig.mgz INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume (null) reg file (null) LoadVol1 $Id: tkregister2.c,v 1.35 2005/07/12 19:50:28 greve Exp $ Diagnostic Level -1 talairach.xfm - 1.103 0.048 -0.007 -4.504; -0.051 1.166 0.004 -13.012; 0.007 -0.003 1.090 -15.454; 0.000 0.000 0.000 1.000; ERROR: cannot determine type of /home/wolosin/subjects/talairach/mri/orig Do you know what I am missing? Any advice is greatly appreciated, Thanks, Sasha Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] recon-all
ted yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Number of iterations: 8 CV of field change: 0.000890052 [EMAIL PROTECTED]:/home/wolosin/subjects/2332/mri/] [2005-09-08 16: 35:30] running: /usr/pubsw/packages/mni/current/bin/make_template -quiet -shrink 3 nu3.mnc /us r/tmp/nu_correct_2295//template.mnc Transforming slices: ..Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Transforming slices: Done mri_convert nu4.mnc nu.mgz mri_convert nu4.mnc nu.mgz reading from nu4.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998088, -0.0614863, 0.00638348) j_ras = (-0.00559035, -0.0130627, -0.999899) k_ras = (0.0615663, -0.998022, 0.0126937) writing to nu.mgz... - Talairach Thu Sep 8 16:35:36 EDT 2005 /home/wolosin/subjects/2332/mri talairach2 2332 .mgz INFO: registering 2332 Thu Sep 8 16:35:36 EDT 2005 mri_convert nu.mgz nu.mnc mri_convert nu.mgz nu.mnc reading from nu.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998088, -0.0614863, 0.00638348) j_ras = (-0.00559035, -0.0130627, -0.999899) k_ras = (0.0615663, -0.998022, 0.0126937) writing to nu.mnc... mritotal -verbose -debug -clobber -protocol icbm nu.mnc transforms/talairach.xfm mri_add_xform_to_header /home/wolosin/subjects/2332/mri/transforms/talairach.xfm /home/wolosin/subjects/2332/mri/orig.mgz /home/wolosin/subjects/2332/mri/orig.m gz INFO: extension is mgz Thu Sep 8 16:36:16 EDT 2005 - Intensity Normalization Thu Sep 8 16:36:16 EDT 2005 /home/wolosin/subjects/2332/mri mri_normalize nu.mgz T1.mgz reading from nu.mgz... normalizing image... building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 1 of 2 Segmentation fault ERROR: mri_normalize exited with non-zero status recon-all exited with errors at Thu Sep 8 16:37:02 EDT 2005 Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Re: new Freesurfer version
I ran mri_convert with the input as the folder name followed by / and that seems to be working fine, but when I run csurf I still get the same error, and when I run tkmedit I get the error below: [EMAIL PROTECTED] /freesurfer]# mri_convert -it dicom -ot mgz /freesurfer/subjects/2333/mri/orig/2333_crsg/ /freesurfer/subjects/2333/mri/orig/001.mgz mri_convert -it dicom -ot mgz /freesurfer/subjects/2333/mri/orig/2333_crsg/ /freesurfer/subjects/2333/mri/orig/001.mgz reading from /freesurfer/subjects/2333/mri/orig/2333_crsg/... 124 DICOM 3.0 files in list Found 124 DICOM Files WARNING: NumberOfFrames 0 != Found Count of slices 124. reading DICOM image... - DICOM meta-header file name /freesurfer/subjects/2333/mri/orig/2333_crsg/001Date and time study date 20030617 study time 153907. series time 155302.26 acquisition time155302.26 Identification patient nameLittle,Britney manufacturerPhilips Medical Systems Dimensions number of rows 256 number of columns 256 number of frames124 pixel width 0.9375 pixel height0.9375 slice thickness 1.5 field of view 240 image number1 (might be not reliable) Acquisition parameters echo time 6.3 repetition time 35 inversion time not found echo number 1 flip angle 0.785398 bits allocated 16 Spatial information first image position-127.793 -89.0762 120.125 last image position -113.357 94.0528 137.314 image orientation 0.996907 -0.0785857 5.7501e-10 0.00732152 0.0928779 -0.995651 - TR=35.00, TE=6.00, TI=0.00, flip angle=45.00 i_ras = (-0.996907, 0.0785857, 5.7501e-10) j_ras = (-0.00732152, -0.0928779, -0.995651) k_ras = (-0.0782441, -0.992571, 0.0931655) writing to /freesurfer/subjects/2333/mri/orig/001.mgz... [EMAIL PROTECTED] /freesurfer]# csurf csurf: logfile: /freesurfer/subjects/2333/scripts/csurf.log [EMAIL PROTECTED] /freesurfer]# tkmedit 2332 orig Reading /freesurfer/lib/tcl/tkm_common.tcl Reading /freesurfer/lib/tcl/tkm_wrappers.tcl [EMAIL PROTECTED] /freesurfer]# tkmedit 2333 orig corRead(): can't open file /freesurfer/subjects/2333/mri/orig/COR-.info Error: Loading volume orig Couldn't read the anatomical volume. Tkmedit couldn't read the volume you specified. This could be because the image format wasn't recognized, or it couldn't find the proper header, or the file(s) were unreadable, or it was the wrong size. [EMAIL PROTECTED] /freesurfer]# Thanks, Sasha >> Jenni Pacheco <[EMAIL PROTECTED]> 08/29/05 5:24 PM >>> Hi Sasha, try this as your mri_convert command, see if it works: mri_convert -it dicom -ot mgz 2332_crsg/ 001.mgz Jenni On Mon, 29 Aug 2005, Sasha Wolosin wrote: > Here is the full command and output > When I try to open the orig volume, I get the error: > "First orig image: > /freesurfer/subjects/2332/mri/orig/COR-001 not found" > > [EMAIL PROTECTED] /freesurfer]# cd subjects/2332/mri/orig > [EMAIL PROTECTED] orig]# ls > 2332_analyze 2332_crsg > [EMAIL PROTECTED] orig]# mri_convert -it dicom -ot mgz 2332_crsg/001 001.mgz > mri_convert -it dicom -ot mgz 2332_crsg/001 001.mgz > reading from 2332_crsg/001... > 124 DICOM 3.0 files in list > Found 124 DICOM Files > WARNING: NumberOfFrames 0 != Found Count of slices 124. > reading DICOM image... > - > DICOM meta-header > > file name 2332_crsg/001 > Date and time >study date 20030630 >study time 101639. >series time 104735.12 >acquisition time104735.12 > Identification >patient name... >manufacturerPhilips Medical Systems > Dimensions >number of rows 256 >number of columns 256 >number of frames124 >pixel width 0.9375 >pixel height0.9375 >slice thickness 1.5 >field of view 240 >image number1 (might be not reliable) > Acquisition parameters >echo time 6.3 >repetition time 35 >inversion time not found >echo number 1 >flip angle 0.785398 >bits allocated 16 > Spatial information >first image p
[Freesurfer] mgz format
Sorry to send this twice, but I should have elaborated: I am trying to convert files to mgz format. I was able to run mri_convert, but when I run csurf and attempt to open the orig volume, I get the error: "First orig image: /freesurfer/subjects/2332/mri/orig/COR-001 not found" Does anyone know why this may happen? Here is the command and output: [EMAIL PROTECTED] /freesurfer]# cd subjects/2332/mri/orig [EMAIL PROTECTED] orig]# ls 2332_analyze 2332_crsg [EMAIL PROTECTED] orig]# mri_convert -it dicom -ot mgz 2332_crsg/001 001.mgz mri_convert -it dicom -ot mgz 2332_crsg/001 001.mgz reading from 2332_crsg/001... 124 DICOM 3.0 files in list Found 124 DICOM Files WARNING: NumberOfFrames 0 != Found Count of slices 124. reading DICOM image... - DICOM meta-header file name 2332_crsg/001 Date and time study date 20030630 study time 101639. series time 104735.12 acquisition time104735.12 Identification patient name... manufacturerPhilips Medical Systems Dimensions number of rows 256 number of columns 256 number of frames124 pixel width 0.9375 pixel height0.9375 slice thickness 1.5 field of view 240 image number1 (might be not reliable) Acquisition parameters echo time 6.3 repetition time 35 inversion time not found echo number 1 flip angle 0.785398 bits allocated 16 Spatial information first image position-114.756 -101.936 133.356 last image position -126.115 82.1994 135.698 image orientation 0.998088 0.0614863 0.00638348 0.00559035 0.0130627 -0.999899 - TR=35.00, TE=6.00, TI=0.00, flip angle=45.00 i_ras = (-0.998088, -0.0614863, 0.00638348) j_ras = (-0.00559035, -0.0130627, -0.999899) k_ras = (0.0615663, -0.998022, 0.0126937) writing to 001.mgz... [EMAIL PROTECTED] orig]# csurf Thanks, Sasha Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Re: new Freesurfer version
Here is the full command and output When I try to open the orig volume, I get the error: "First orig image: /freesurfer/subjects/2332/mri/orig/COR-001 not found" [EMAIL PROTECTED] /freesurfer]# cd subjects/2332/mri/orig [EMAIL PROTECTED] orig]# ls 2332_analyze 2332_crsg [EMAIL PROTECTED] orig]# mri_convert -it dicom -ot mgz 2332_crsg/001 001.mgz mri_convert -it dicom -ot mgz 2332_crsg/001 001.mgz reading from 2332_crsg/001... 124 DICOM 3.0 files in list Found 124 DICOM Files WARNING: NumberOfFrames 0 != Found Count of slices 124. reading DICOM image... - DICOM meta-header file name 2332_crsg/001 Date and time study date 20030630 study time 101639. series time 104735.12 acquisition time104735.12 Identification patient name... manufacturerPhilips Medical Systems Dimensions number of rows 256 number of columns 256 number of frames124 pixel width 0.9375 pixel height0.9375 slice thickness 1.5 field of view 240 image number1 (might be not reliable) Acquisition parameters echo time 6.3 repetition time 35 inversion time not found echo number 1 flip angle 0.785398 bits allocated 16 Spatial information first image position-114.756 -101.936 133.356 last image position -126.115 82.1994 135.698 image orientation 0.998088 0.0614863 0.00638348 0.00559035 0.0130627 -0.999899 - TR=35.00, TE=6.00, TI=0.00, flip angle=45.00 i_ras = (-0.998088, -0.0614863, 0.00638348) j_ras = (-0.00559035, -0.0130627, -0.999899) k_ras = (0.0615663, -0.998022, 0.0126937) writing to 001.mgz... [EMAIL PROTECTED] orig]# csurf Thanks, Sasha Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 >>> Bruce Fischl <[EMAIL PROTECTED]> 08/29/05 4:50 PM >>> p.s. in general please include the full command line and output, otherwise it's really hard to help you. Also, if you send these things to the freesurfer list your response time will get a lot better as there are a bunch of people who answer questions on it On Mon, 29 Aug 2005, Sasha Wolosin wrote: > Hi Nick, > > We now have the libraries installed, and we have managed to get freesurfer > running on FC4, and I am able to convert from dicom to COR by typing: > mri_convert -it dicom -ot cor 2332_crsg/001 001 > > but I am having trouble converting to/ opening files in mgz format. When I > specify the output type as mgz instead of cor, I get a "segmentation fault" > and when I try to open the orig volume in csurf I get the error: > "First orig image: > /freesurfer/subjects/2332/mri/orig/COR-001 not found" > > Is this version of freesurfer not set up to use mgz files yet? Or is there > some setting I must change? > > Thanks, > Sasha > > > > Sasha Wolosin > Research Assistant > Developmental Cognitive Neurology > Kennedy Krieger Institute > 707 N. Broadway > Baltimore, MD 21205 > ph: (443) 923-9270 >>>> Nick Schmansky <[EMAIL PROTECTED]> 08/24/05 4:15 PM >>> > Sasha, > > Hi, Freesurfer requires the following libraries, which are sometimes > (and sometimes not) included in Linux distributions: > > tcl, tk, tix, blt, gsl, tiff, jpeg, and glut > > Usually, a sysadmin will install these, but we are finding that a lot of > people do not have the tcl/tk/tix/blt tools installed and working (and > that work well with freesurfer). > > So for now, you will need to install the tcl/tk/tix/blt tools. Or you > can try downloading a source code bundle, called fs_supportlibs.tar.gz > from our distribution site: > > http://www.bic.mni.mcgill.ca/software/distribution/ > > to untar/unzip, type: > > tar zxvf fs_supportlibs.tar.gz > > then type > > cd fs_supportlibs > setenv LIBS_DIR /usr > > then to build tcl and tk: > > ./build-tcltk.csh > > and tix and blt: > > ./build-tix.csh > ./build-blt > > Upon completion, you should see the libs in the /usr/lib directory. > I can't guarantee this will work well for you, some build engineer > skills are required if problems are encountered. You may want to have > your sysadmin do it. > > We are considering including some of these libs in the next release. > > As for not finding the nu_correct command, this seems to be more basic > proble
Fwd: Re: [Freesurfer] mri_watershed
Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270--- Begin Message --- Hi Xiao, That seems to be it, thanks. The actual values are the same. I looked at the brightness/contrast settings for the skull-stripped brain and noticed that they had been automatically adjusted. So I matched the orig volume brightness/contrast range to the brain brightness/contrast range, and now they look identical- problem solved! Thanks, Sasha Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 >>> Xiao Han <[EMAIL PROTECTED]> 08/19/05 1:37 PM >>> Hi Sasha, If you use tkmedit to visualize the results, then the contrast change you saw may be just due to the display problem (not exactly a problem) of tkmedit. You can move the mouse around the image to actually see whether the image intensity values were changed or not. I used mri_watershed a lot, and never saw it changed the original image intensity (in the brain region). But tkmedit will adjust its display contrast according to the dynamic range of the original image. So once skull is removed, the max and min intensity values of the image are very likely to be different, and the image will then look differently in tkmedit. -Xiao On Fri, 19 Aug 2005, florent segonne wrote: > Dear Sasha, > > mri_watershed was initially designed to skull strip orig images, without any > preprocessing step, such as intensity normalization or contrast modification. > So, This certainly seems like a reasonable thing to do. > > However, mri_watershed might normalize intensities during the process but > should NOT generate skull-stripped images with different intensities. We'll > quickly look into this and let you know if this is a bug that needs to be > fixed. > > Cheers, > > Florent > > On Fri, 19 Aug 2005, Sasha Wolosin wrote: > >> We use an anatomical analysis program called Brain Image in our lab. We >> would like to speed up our analysis in Brain Image by replacing manual >> skull stripping with FreeSurfer's automated skull strip program. For this >> we would need to do a skull strip alone, without adjusting intensity values >> or contrast. Is this possible? Is this a reasonable thing to do? >> I have run mri_watershed with the input from orig on several subjects, >> and the output volume looks much brighter than the orig volume. Does >> mri_watershed normalize intensities or change the contrast in order to >> strip the skull? >> >> Thanks, >> Sasha >> >> Sasha Wolosin >> Research Assistant >> Developmental Cognitive Neurology >> Kennedy Krieger Institute >> 707 N. Broadway >> Baltimore, MD 21205 >> ph: (443) 923-9270 >> >> >> >> Disclaimer: >> The materials in this e-mail are private and may contain Protected Health >> Information. Please note that e-mail is not necessarily confidential or >> secure. Your use of e-mail constitutes your acknowledgment of these >> confidentiality and security limitations. If you are not the intended >> recipient, be advised that any unauthorized use, disclosure, copying, >> distribution, or the taking of any action in reliance on the contents of >> this information is strictly prohibited. If you have received this e-mail >> in error, please immediately notify the sender via telephone or return >> e-mail. >> >> ___ >> 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 > > > --- End Message --- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mri_watershed
We use an anatomical analysis program called Brain Image in our lab. We would like to speed up our analysis in Brain Image by replacing manual skull stripping with FreeSurfer's automated skull strip program. For this we would need to do a skull strip alone, without adjusting intensity values or contrast. Is this possible? Is this a reasonable thing to do? I have run mri_watershed with the input from orig on several subjects, and the output volume looks much brighter than the orig volume. Does mri_watershed normalize intensities or change the contrast in order to strip the skull? Thanks, Sasha Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mri_convert dicom
I'm having some trouble running mri_convert. I keep getting an error message, do you know what this means (see below)? Thanks. [EMAIL PROTECTED] FreeSurferPractice]$ mri_convert -it dicom -ot cor CRSG_2332/001 2332_skullstrip/mri/orig/001 mri_convert -it dicom -ot cor CRSG_2332/001 2332_skullstrip/mri/orig/001 reading from CRSG_2332/001... 124 DICOM 3.0 files in list Found 124 DICOM Files reading DICOM image... FreeElementData: 137302584 unrecognizedSegmentation fault Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mri_convert
Does mri_convert cause any loss in resolution when converting from DICOM to COR format? What about from DICOM to MGZ? Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] skull strip
Is it possible to do skull stripping without motion correction or intensity normalization? Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
