Re: [Freesurfer] segmentation

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 i

Re: [Freesurfer] segmentation

lude 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: &g

[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 cons

Re: [Freesurfer] folding index on surface

m 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 Info

[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 a

[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 Pro

Re: [Freesurfer] thickness standard deviation

on 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 va

[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 st

[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 th

Re: [Freesurfer] viewing subcortical structures

rfer.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 PROT

Re: [Freesurfer] viewing subcortical structures

gh, 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 >

[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 Inf

[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 Protec

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.whi

[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 confidentia

Re: [Freesurfer] volumes

s) 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 gr

[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

[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,

[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

[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 necess

[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?

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 g

Re: [Freesurfer] interaction effects

tment-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

[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

[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: Th

[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

Re: [Freesurfer] interaction effects

n 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 >cla

Re: [Freesurfer] {Disarmed} stats

006-04-14 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 &

[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 machin

[Freesurfer] interaction effects

nput 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 [EM

[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 Protecte

[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 secu

Re: [Freesurfer] fix vertex area

utside 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

[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 Wolosi

[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 Informa

[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

[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

Re: [Freesurfer] notes on Jan 2006 release

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

[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 th

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

[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

Re: [Freesurfer] multiple comparisons

L 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]> >>> > > Currentl

Re: [Freesurfer] multiple comparisons

ime, 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

[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

Re: [Freesurfer] tksurfer

enu 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 th

[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_3

[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

[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

[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 Pro

[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

[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 ab

[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

[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 a

[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

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

[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

[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 Informatio

[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

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

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

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 Dis

Re: [Freesurfer] labels

us 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_ana

[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-mai

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 co

[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 mr

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:

[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 ne

[Freesurfer] Re: Freesurfer Digest, Vol 21, Issue 3

nk 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

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

Re: [Freesurfer] help with mris_ca_label

le 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 PROT

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

[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

Re: [Freesurfer] tkregister2

CTED]> 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 PR

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 relative

Re: [Freesurfer] tkregister2

anks, 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

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 Mo

Re: [Freesurfer] tkregister2

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 21205 ph: (443) 923-9270 [EMAIL PROTECTED] >>> Nick Schmansky <[EMAIL PROTECTED]> 09/15/05

[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 Disclai

[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

[Freesurfer] control points

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

[Freesurfer] new stable release

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

[Freesurfer] tkregister2

airach/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

Re: [Freesurfer] mri_normalize

otropic, 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] /fr

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

[Freesurfer] mri_normalize

annot 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

[Freesurfer] recon-all

ors 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 t

Re: [Freesurfer] Re: new Freesurfer version

t;> 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 i

[Freesurfer] mgz format

348) 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

[Freesurfer] Re: new Freesurfer version

-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 Wolosi

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

[Freesurfer] mri_watershed

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-ma

[Freesurfer] mri_convert dicom

2/001 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 Balt

[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 sec

[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