Re: [Freesurfer] ANOVA(analysis of variance)

//www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > -- *** Ilana Hairston ,PhD Research Assistant Professor 4250

[Freesurfer] flipped orientation in tksurfer and tkmedit

-- ** Ilana Hairston ,PhD Research Assistant Professor 4250 Plymouth Rd. (rm 2439) Psychiatry Department, Addiction Research Center University of Michigan, Ann Arbor MI 48109-2700 Tel: 734-232-0232; Mobile: 650-906-8449 Reminder: Women do 66% of the work worldwide, earn 10

Re: [Freesurfer] FW: flipped orientation in tksurfer and tkmedit

u [mailto: > freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve > Sent: Wednesday, September 14, 2011 6:10 PM > To: Ilana Hairston > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] flipped orientation in tksurfer and tkmedit > > When you say on the

[Freesurfer] Fwd: FW: flipped orientation in tksurfer and tkmedit

compare the 2 side by side, the brains should be mirror images. Ours are not, they are the same. Make sense? On Tue, Sep 20, 2011 at 2:26 PM, Ilana Hairston wrote: > could you check this? > this a followup on my original email after looking at 110???yl with Barbara > and Steve. > thanks

Re: [Freesurfer] Fwd: FW: flipped orientation in tksurfer and tkmedit

Ilana -- ** Ilana Hairston ,PhD Research Assistant Professor 4250 Plymouth Rd. (rm 2439) Psychiatry Department, Addiction Research Center University of Michigan, Ann Arbor MI 48109-2700 Tel: 734-232-0232; Mobile: 650-906-8449 Reminder: Women do 66% of the work worldwide, earn 1

[Freesurfer] Fwd: Fwd: FW: flipped orientation in tksurfer and tkmedit

. Thanks i. -- Forwarded message -- From: Chelsea Cummiford Date: Thu, Sep 22, 2011 at 4:35 PM Subject: Re: [Freesurfer] Fwd: FW: flipped orientation in tksurfer and tkmedit To: Ilana Hairston [chelsea@hypnos ilanagroup]$ recon-all -all -subjid FlippedFS091205dc/ Subject Stamp: freesu

Re: [Freesurfer] Fwd: Fwd: FW: flipped orientation in tksurfer and tkmedit

nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/xhemireg> > > Ilana Hairston wrote: > >> Hi Doug, >> Sorry, that this is turning into a saga. >> The xhemireg command ran, but then recon-all failed (we used recon-all >> -all). >> Also it seems there are missing

[Freesurfer] SetUp file error

setup files and they don't have typo in them. what should i do? thanks ilana -- ******* Ilana Hairston ,PhD Research Assistant Professor 4250 Plymouth Rd. Psychiatry Department, Addiction Research Center University of Michigan, Ann Arbor MI 48109-2700 Tel: 734-232-02

Re: [Freesurfer] orientation of the data

was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > -- *** Ilana Hairston ,PhD Research Assistant Professor 4250 Plymouth Rd. (rm 2439) Psychi

[Freesurfer] contrast correction

Hi there, We have been doing contrast correction using mri_nu_correct.mni (e.g., mri_nu_correct.mni --i FS090620ll/mri/orig/001.mgz --o FS090620ll/mri/orig/nu2.mgz --n 2). My question is, after subsequent corrections (control points, white matter) do we need to specify nu2.mgz as the target file fo

Re: [Freesurfer] Talairach failure

ard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >>>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>>

Re: [Freesurfer] contrast correction

-i FS090620ll/mri/orig/nu2.mgz > -force) > > > thanks > ilana > -- *** Ilana Hairston ,PhD Research Assistant Professor 4250 Plymouth Rd. (rm 2439) Psychiatry Department, Addiction Research Center University of Michigan, Ann Arbor MI 48

Re: [Freesurfer] contrast correction

n 4 May 2010 17:01, Bruce Fischl wrote: > Hi Ilana > > that won't work. I guess you could try copying nu2.mgz to nu.mgz and > trying -make all (assuming you have a new enough version of recon-all) > > cheers > Bruce > On > Tue, 4 May 2010, Ilana Hairston wrote: >

[Freesurfer] recon error

Hi there, I am new to free surfer, and am trying to analyse brains of kids ages 8-11. running recon1 i get the following error message: ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0., pval=0. < threshold=0.0050) Looking at past mailings seems you re

Re: [Freesurfer] wm correction issues

Hi there. > we have been doing some white matter corrections, based on the wiki > instructions. After filling in some missing voxels we ran ...autorecon2-wm > autorecon3 ... but it doesn't look like the white matter was corrected. > > thanks > ilana > -- ***

Re: [Freesurfer] retinotopy: MGH vs UCSD

ontain patient information, please contact the sender and > properly > dispose of the e-mail. > > -- *** Ilana Hairston ,PhD Research Assistant Professor 4250 Plymouth Rd. (rm 2439) Psychiatry Department, Addiction Research Center University of Michigan, Ann Arbor MI 48

[Freesurfer] computer shut down

Hi There, If a recon stopped half way, because of a power outage. Is there a way to continue the process, rather than start from scratch? thanks ilana ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/list

[Freesurfer] label 28 error

Hi there, We've been getting this label 28 error more often recently, and found that by adding '-no-ca-align' to the end of recon-all command, the error went away and visually the brain looks OK (at least first pass). Does this make sense? thanks ilana -- **

Re: [Freesurfer] QDEC table loading errors

mr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compl

[Freesurfer] error loading averaged brain in QDEC

ta file as a surface! What am i missing? Note - the data was originally processed using FS version 4.5. thanks ilana -- *** Ilana Hairston ,PhD Research Assistant Professor 4250 Plymouth Rd. (rm 2439) Psychiatry Department, Addiction Research Center University of Mi

[Freesurfer] error loading averaged brain in QDEC (2)

quot;avgsubject" was the output name of the averaged subject template). Indeed, there are ?h.?.fwhm?.fsaverage.mgh in my subject folders (presumable from the previous preproc), but no new ones. thanks ilana -- ******* Ilana Hairston ,PhD Research Assistant Professor 4

[Freesurfer] error loading averaged brain in QDEC

plate). Indeed, there are only *h.*.fwhm*.fsaverage.mgh in my subject folders (presumably from the previous preproc), but no new ones with 'avgsubject'. What am i doing wrong? thanks ilana -- *** Ilana Hairston ,PhD Research Assistant Professor 4250 Plymouth

[Freesurfer] two issues with the processing stream

: could not find path! *We looked it up on the freesurfer wiki and there is an entry about this error, but the answer perhaps was not posted. thanks ilana -- *** Ilana Hairston ,PhD Research Assistant Professor 4250 Plymouth Rd. (rm 2439) Psychiatry Department

[Freesurfer] two issues with the processing stream

Hi there, we are having two unrelated problems with a couple of files: 1. A brain running extremely slow, after initial processing. i.e. we ran recon-all, made some edits (control points etc.) and now for some reason the second round is taking days. 2. An error message*: ERROR: _FindFacePath: co

[Freesurfer] Aseg tables

that are labeled as hippocampus or such, is labeled correctly, but i can't seem to find an annotation table that contains aseg.volume. thx ilana -- ******* Ilana Hairston ,PhD Research Assistant Professor 4250 Plymouth Rd. (rm 2439) Psychiatry Department, Addictio

Re: [Freesurfer] two issues with the processing stream

pology fixing, check > the inflated.nofix file and see if there is a huge defect. > > 2. This is also a topology fixer problem. Nick: isn't it only in the new > fixer? > > Bruce > > > > On Mon, 17 Jan 2011, Ilana Hairston wrote: > > Hi there, >> we ar

[Freesurfer] statistical question

Hi there, This is a bit outside the pure technical questions. My subject pool has both boys and girls, with the boys having larger intracranial volume. My results when controlling for gender and intracranial volume however are not the same (obviously, one is a dichotomous variable, the other contin

Re: [Freesurfer] Recon-all Error: _FindFacePath

what does "old topo fixer" mean? thanks ilana On 15 February 2011 09:55, Bruce Fischl wrote: > Hi Nasim, > > can you tar and gzip the entire subject dir and send it to us? I'll try > to track it down. In the mean time if you just rerun with the old topo > fixer it should work. Nick can post the

[Freesurfer] creating labels in tksurfer

Hi there, I'm having difficulty creating labels in tksurfer (v4.5). I followed the "Creating Labels" instructions on the Wiki, however clicking Fill on the closed path didn't seem to do anything. I used save label anyway, and tried to load this new label again, and even though it says "7681 nonze

Re: [Freesurfer] creating labels in tksurfer

t; recon-all with -make all on that subject and see if it needs to recreate > anything. > > Not sure what's up with your label, but things can act strangely when the > surfaces are out of date > > cheers > Bruce > > On Fri, 1 Apr 2011, Ilana Hairston wrote: > >

Re: [Freesurfer] creating labels in tksurfer

label display is turned on in the > tksurfer interface (the default may be off). It's one of the buttons on the > top right. > > cheers > Bruce > > > On Sat, 2 Apr 2011, Ilana Hairston wrote: > >> sorry for the delay (can't ftp from the server). the file

[Freesurfer] question regarding clusterwise correction for multiple comparisons

Hi there, After running mri_glmfit with several different contrasts, all stored in the same folder (e.g., gender controlling for age: 1 -1 0 0; interaction of gender with age: 0 0 1 -1, etc.), i am interested in correcting for only one of the effects (e.g., gender). However, the mri_glmfit-sim do

[Freesurfer] analysis questions

-- *** Ilana Hairston ,PhD Research Assistant Professor 4250 Plymouth Rd. (rm 2439) Psychiatry Department, Addiction Research Center University of Michigan, Ann Arbor MI 48109-2700 Tel: 734-232-0232; Mobile: 650-906-8449 Reminder: Women do 66% of the work

[Freesurfer] analysis questions

-- *** Ilana Hairston ,PhD Research Assistant Professor 4250 Plymouth Rd. (rm 2439) Psychiatry Department, Addiction Research Center University of Michigan, Ann Arbor MI 48109-2700 Tel: 734-232-0232; Mobile: 650-906-8449 Reminder: Women do 66% of the work

[Freesurfer] display issue on MacBook Pro 13"

Hi there, I'm traveling and using my laptop for freesurfer. For some reason the displayed windows are greater than my screen (at least for tksurfer), leaving boxes such as FDR correction, Apply outside range. I'm using the highest possible resolution. Is there something that can be adjusted on X11

Re: [Freesurfer] Interpreting results from Qdec

Exporting ROI volumes/thickness values may not be significant because the analysis in qdec (glm) includes the whole cortical surface. But, I have a follow up question to this question. In the plotted graph the abscissa reports F values. Which basically mean that the significant ROI reflects the

[Freesurfer] two questions

or within aparc annotations. 3. Is there a way to set FDR separately for positive and negative values? thanks ilana Ilana Hairston hairstons...@gmail.com * Our ignorance is not so vast as our failure to use what we know. —M. King Hubbert, peak o

[Freesurfer] ERROR: gdfOffsetSlope:

Hi there, When i load he group descriptor file i get the following error: "cannot determine the offset and slope for the given group descriptor because the design matrix creation method is unknown" Why is that? Thanks ilana -- *** peligro! flaca pero mala! ***

Re: [Freesurfer] overlay properties tksurfer window incomplete...

i had a similar problem with my macbook (i think), and was told to use spacebar in lieu of enter. On 23 May 2011, at 01:04, Gonzalo Rojas Costa wrote: > Hi: > > I have an ubuntu based computer with Freesurfer 5, and it seems that > because the font size or the screen resolution, the lowes

[Freesurfer] analysis interpretion question

Hi there, I have two behavioural variables that are inversely related to each other. One was correlated with thinning of the posterior insula (using glm_mri), while the other is positively correlated with the putamen volume (extracting aseg tables and running in SPSS). The region of the insula