[Freesurfer] stats question

[j janssen]

Hi,

i read the following in a paper and would like to do the same:

"At each vertex in each hemisphere, the proportion of total variance in
cortical thickness (CT) accounted for by 2 linear regression models was
compared: One that did not include an age-by-group interaction term, Model
1: [CT = intercept + (group * b1) + (age * b2)] and one that did, Model 2:
[CT = intercept + (group * b1) + (age * b2) + (group * age * b3)]. This
resulted in an F ratio map for each hemisphere showing the degree to which
the inclusion of an age-by-group term increased the proportion of CT
variance that was accounted for."

i have set up the matrices for the 2 models. my questions:
1. do you think that i should test the effect of age in model 1 (contrast:
0 0 1) and the effect of age * group in model 2 (contrast 0 0 0 1 -1)? if
not, what do you suggest?

2. do you have any idea how to combine these two analyses in a resulting F
ratio map?

thanks,
-joost
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] error longitudinal processing

[j janssen]

Hi (Martin),

- version 5.1 (Ubuntu 64b)
- command: long_mris_slopes --qdec ./qdec/long.qdec.table.n114.dat --meas
thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack
--do-label --time ISI_years --qcache fsaverage
- attached: first 3 lines of qdec table containing the info for subject
11298
- attached: on screen error output.
- i have 2 timepoints/subject.

things go awry in the "SUBJECT 11298  Running Within-Subject GLM" step (see
attachment):

Reshaping mriglm->mask...
ERROR: mri_reshape: number of elements cannot change

what am i doing wrong?

-joost
jjanssen@neurojoost:/media/LA-PUBLIC/REDES_LONGITUDINAL_BRAINVISA$ 
long_mris_slopes --qdec ./qdec/long.qdec.table.n114.dat --meas thickness --hemi 
lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time ISI_years 
--qcache fsaverage
Parsing the qdec table: ./qdec/long.qdec.table.n114.dat

Working in SUBJECTS_DIR: /media/LA-PUBLIC/REDES_LONGITUDINAL_BRAINVISA


Subject-Template: 11298


INFO: 2 TPs in 11298 , mean age: 0.915


===
SUBJECT 11298  Intersecting Within-Subject Cortex Label

cp 
/media/LA-PUBLIC/REDES_LONGITUDINAL_BRAINVISA/11298.long.11298/label/lh.cortex.label
 /media/LA-PUBLIC/REDES_LONGITUDINAL_BRAINVISA/11298/label/lh.long.cortex.label



mris_label_calc intersect 
/media/LA-PUBLIC/REDES_LONGITUDINAL_BRAINVISA/11298_2.long.11298/label/lh.cortex.label
 /media/LA-PUBLIC/REDES_LONGITUDINAL_BRAINVISA/11298/label/lh.long.cortex.label 
/media/LA-PUBLIC/REDES_LONGITUDINAL_BRAINVISA/11298/label/lh.long.cortex.label

LabelWrite: saving to 
/media/LA-PUBLIC/REDES_LONGITUDINAL_BRAINVISA/11298/label/lh.long.cortex.label



===
SUBJECT 11298  mapping label to QCache

mri_label2label --srclabel 
/media/LA-PUBLIC/REDES_LONGITUDINAL_BRAINVISA/11298/label/lh.long.cortex.label 
--srcsubject 11298 --trglabel 
/media/LA-PUBLIC/REDES_LONGITUDINAL_BRAINVISA/11298/label/lh.long.cortex.fsaverage.label
 --trgsubject fsaverage --regmethod surface --hemi lh


srclabel = 
/media/LA-PUBLIC/REDES_LONGITUDINAL_BRAINVISA/11298/label/lh.long.cortex.label
srcsubject = 11298
trgsubject = fsaverage
trglabel = 
/media/LA-PUBLIC/REDES_LONGITUDINAL_BRAINVISA/11298/label/lh.long.cortex.fsaverage.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR/media/LA-PUBLIC/REDES_LONGITUDINAL_BRAINVISA
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Found 115366 points in source label.
Starting surface-based mapping
Reading source registration 
 /media/LA-PUBLIC/REDES_LONGITUDINAL_BRAINVISA/11298/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /media/LA-PUBLIC/REDES_LONGITUDINAL_BRAINVISA/fsaverage/surf/lh.white
Reading target registration 
 /media/LA-PUBLIC/REDES_LONGITUDINAL_BRAINVISA/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  115366 nlabel points
Performing mapping from target back to the source label
Number of reverse mapping hits = 55920
Checking for and removing duplicates
Writing label file 
/media/LA-PUBLIC/REDES_LONGITUDINAL_BRAINVISA/11298/label/lh.long.cortex.fsaverage.label
 171286
LabelWrite: saving to 
/media/LA-PUBLIC/REDES_LONGITUDINAL_BRAINVISA/11298/label/lh.long.cortex.fsaverage.label
mri_label2label: Done




===
SUBJECT 11298  Stackinbg Within-Subject Maps

mri_concat 
/media/LA-PUBLIC/REDES_LONGITUDINAL_BRAINVISA/11298.long.11298/surf/lh.thickness
 
/media/LA-PUBLIC/REDES_LONGITUDINAL_BRAINVISA/11298_2.long.11298/surf/lh.thickness
 --o 
/media/LA-PUBLIC/REDES_LONGITUDINAL_BRAINVISA/11298/surf/lh.long.thickness-stack.mgh

ninputs = 2
Checking inputs
nframestot = 2
Allocing output
Done allocing
nframes = 2
Writing to 
/media/LA-PUBLIC/REDES_LONGITUDINAL_BRAINVISA/11298/surf/lh.long.thickness-stack.mgh



===
SUBJECT 11298  Running Within-Subject GLM

Writing ./tmp-11298_lh_thickness_FC4k2V/X-long.mat ...

mri_glmfit --y 
/media/LA-PUBLIC/REDES_LONGITUDINAL_BRAINVISA/11298/surf/lh.long.thickness-stack.mgh
 --X ./tmp-11298_lh_thickness_FC4k2V/X-long.mat --allow-zero-dof  
--no-contrasts-ok --surf 11298 lh --label 
/media/LA-PUBLIC/REDES_LONGITUDINAL_BRAINVISA/11298/label/lh.long.cortex.label 
--glmdir ./tmp-11298_lh_thickness_FC4k2V/glm

Reading source surface 
/media/LA-PUBLIC/REDES_LONGITUDINAL_BRAINVISA/11298/surf/lh.white
Number of vertices 127120
Number of faces254236
Total area 83204.789062
AvgVtxArea   0.654537
AvgVtxDist   0.885641
StdVtxDist   0.257092

$Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25

Re: [Freesurfer] error longitudinal processing

[j janssen]

Hi Martin,

changing the dir-names and qdec table to:

fsid fsid-base ISI_years Group Gender Age ICV
11298_1 11298_template 0 patient F 16 1441
11298_2 11298_template 1.83 patient F 17.92 1396

solved my problem.

-joost




On Sun, Jul 1, 2012 at 4:33 PM, j janssen  wrote:

> Hi Martin,
>
> thanks.
>
> i changed 11298 to 11298_1 and got the same error. are you suggesting that
> some recon-all error may have happened because of the file names? no error
> messages were reported in any of the log files, all (cross-sectional and
> longitudinal) finished without error. does the error point to two
> intra-subject surfaces which should have the same # of vertices but do not
> have so? if so, which surfaces?
>
> thanks,
> -joost
>
>
>
>
> On Fri, Jun 29, 2012 at 8:50 PM, Martin Reuter <
> mreu...@nmr.mgh.harvard.edu> wrote:
>
>> Hi Joost,
>>
>> the tp id cannot be the same as the base id:
>>
>> fsid fsid-base ISI_years Group Gender Age ICV
>> 11298 11298 0 patient F 16 1441
>> 11298_2 11298 1.83 patient F 17.92 1396
>>
>> I am amazed that you were able to process it this way?
>>
>> So either call the first time point
>> 11298_1
>> or call the base 11298_base in both cases.
>>
>> Also make sure your longitudinal processing is correct (I mean the
>> recon-all, not the post processing that you are trying here).
>>
>> Best, Martin
>>
>> On Fri, 2012-06-29 at 13:35 +0200, j janssen wrote:
>> > Hi (Martin),
>> >
>> > - version 5.1 (Ubuntu 64b)
>> > - command: long_mris_slopes --qdec ./qdec/long.qdec.table.n114.dat
>> > --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc
>> > --do-stack --do-label --time ISI_years --qcache fsaverage
>> > - attached: first 3 lines of qdec table containing the info for
>> > subject 11298
>> > - attached: on screen error output.
>> > - i have 2 timepoints/subject.
>> >
>> > things go awry in the "SUBJECT 11298  Running Within-Subject GLM" step
>> > (see attachment):
>> >
>> > Reshaping mriglm->mask...
>> > ERROR: mri_reshape: number of elements cannot change
>> >
>> > what am i doing wrong?
>> >
>> > -joost
>> >
>> > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Extraction Longitudinal Stats

[j janssen]

Hi Martin,

lot's of small changes can make a big change but from your phrasing i
assume this isn't the case. what has changed? i would like to have the new
(long_mris_slope) script.

thanks,
-joost


On Tue, Jul 3, 2012 at 6:30 PM, Martin Reuter
wrote:

> Hi Yolanda,
>
> take a look at the longitudinal tutorial:
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial
>
> There is a section that hints at the post-processing as far as we have
> implemented it. Based on a longitudinal qdec table you can run
> long_mris_slopes to create rate or percent change maps for each subject
> and then run qdec on these for the cross sectional comparison.
>
> Also I can make available a newer version of that script as lots of
> small things have changed since last year, let me know.
>
> Best, Martin
>
>
> On Tue, 2012-07-03 at 15:58 +0200, Yolanda Vives wrote:
> > Hi Martin,
> >
> > I would like to compare also a Control vs. an Experimental group
> > (pre-post), but instead of using ROIs, I am interested in a
> > whole-brain paired t-test analysis between the two groups. Which data
> > should I take? Would it be possible to process ?.long.base with qcache
> > and take the "rh.thickness.fwhm20.fsaverage.mgh" files? Or maybe could
> > I use QDEC with ?.long.base after qcache?
> >
> > Thank you,
> > Yolanda
> >
> > 2012/4/12 Martin Reuter 
> > Yes, just extract the stats on each time point as done in a
> > cross
> > sectional analysis (but instead on the ?.long.base
> > directories) do a
> > paired t (or a t on the difference) to see if there is
> > increase or
> > decrease.
> >
> > If you look at one of the reported ROI's (e.g. caudate volume,
> > or
> > pre-central thickness) you can directly get the values from
> > the stats
> > files. If you have your own ROI's you need to use segstats to
> > get the
> > stats for them.
> >
> > Cheers, Martin
> >
> > On Wed, 2012-04-11 at 19:19 +0200, Dídac Vidal wrote:
> > > Hi everybody,
> > > I have a question about FS longitudinal post-processing.
> > Currently I
> > > obtained some corrected results comparing a Control vs. an
> > > Experimental group (pre-post).
> > > What i would like to know is if there's a thinning in the
> > control
> > > group or a increase in the thickness of the experimental
> > group.
> > > I tought in create a label and extract the individual values
> > of both
> > > timepoints and then do a t test in order to see if the mean
> > differs to
> > > 0.
> > > How I can do that?; There is an easier way to do it?
> > > Thanks in advance
> > >
> > > --
> > > Dídac Vidal Piñeiro
> > >
> > > Dept. Psychiatry and Clinical Psychobiology
> > > Faculty of Medicine
> > > University of barcelona
> > >
> > >
> >
> > > ___
> > > 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
> >
> >
> > The information in this e-mail is intended only for the person
> > to whom it is
> > addressed. If you believe this e-mail was sent to you in error
> > and the e-mail
> > contains patient information, please contact the Partners
> > Compliance HelpLine at
> > http://www.partners.org/complianceline . If the e-mail was
> > sent to you in error
> > but does not contain patient information, please contact the
> > sender and properly
> > dispose of the e-mail.
> >
> >
> >
> >
>
> ___
> 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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] T-value intensity overlayed onto 2009 Destrieux Parcellations

[j janssen]

Hi,

not 100% sure what you want but perhaps this:

http://brainder.org/2011/07/05/freesurfer-brains-in-arbitrary-colours

is what you're looking for?

-joost





On Tue, Aug 14, 2012 at 11:13 PM, Douglas N Greve  wrote:

> Try touching ?h.orig.nofix, ie,
> touch rh.orig.nofix lh.orig.nofix
>
> then re-running with -make all
>
> doug
>
> On 08/14/2012 05:08 PM, David Vazquez wrote:
> >
> > Hi,
> >
> > We would like to visually display some t-values onto a brain using the
> > 2009 Destrieux freesurfer parcellations.  We have our own t-values for
> > each parcellation.  We would like to display a color-coded spm map for
> > all parcellations, and would like each parcellation to represent the
> > same intensity, instead of voxel by voxel, as was done by Watkins et
> > al. (2001).
> >
> > Has anyone done this?  Or have a clue where to find the relevant options?
> >
> > Thank you,
> >
> > David Vazquez
> >
> >
> > Watkins, K.E., Paus, T., Lerch, J.P., Zijdenbos, A., Collins, D.L.,
> > Neelin, P., Taylor, J., Worsley., K.J., and Evans, A.C. (2001).
> > Stuctural Asymmetries in the human brain: A voxel-pased Statistical
> > Analysis of 142 MRI scans. /Cerebral Cortex, 11/(9), 868-877.
> >
> >
> >
> > ___
> > 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
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] cortical surface area related measures

[j janssen]

Regarding Winkler et al.:

http://brainder.org/2012/06/02/facewise-brain-cortical-surface-area-scripts-now-available/
On Aug 21, 2012 11:00 PM, "Gregory Kirk"  wrote:

>
> Hi folks, I wanted to make sure i have everything straight w.r.t. the
> surface area measures.
>
> as i see there are 4 ways implemented ( somewhere ) to do cortical surface
> area analysis.
>
> 1. areal expansion
>
> 2. Local Gyrification Index
>
> 3. direct vertex based true surface area glm, Winkler AM et. al
>
> 4. roi based, i.e. based on the surface areas of the parcellation units in
> lh.aparc.a2009s.stats etc.
>
>
> 1. recent pub, Lisa T. Eyler et. al used the areal expansion method.
> was this done exactly as would be achived by using the area tab on qdec
> and setting up a glm ?
> Dale published surface area specifying some details of implementation but
> i was not sure
> if this was exactly what is implemented in qdec ?
>
> 2. LGI seems to me this is the ratio of two areas, that of the hull to the
> area inscribed by projecting
> the border of the hull onto the grey/white surface. In an e-mail Nick said
> LGI is a curvature based measure and that
> confused me a bit. gyrification is of course related to curvature but it
> seems the quantities actually calculated here are ratios of areas, which
> gives local info on surface area differences.
>
> 3. the winkler stuff is i think not publicly available yet at this time ?
>
> 4. straightforward enough not withstanding ICV corrections, etc.
>
> any words of clarification before i start trying some analysis on my group
> ?
>
> thank you
>
> Greg
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] question mris_preproc

[j janssen]

Hi,

freesurfer-x86_64-redhat-linux-gnu-stable5-20110522

$Id: mris_preproc,v 1.66 2012/12/06 16:06:17 mreuter Exp $

after recon-all i ran recon-all -s $subject -qcache

this generates lh.area.fsaverage.mgh which only contains values 0 and
higher while negative values exist for the lh.area of the same subject.

is this normal and if so, why?

thanks,
-joost
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] question TRACULA

[j janssen]

Hi,

TRACULA gives pathstats.txt which includes *weighted* averages, mentioned
on the wiki as: "weighted average over the entire support of the path
distribution".

question: weighted for what (is it the probability)?

thanks,
-joost
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Cortical Normalization Questions

[j janssen]

Hi Michael and others,

maybe it's this one:

http://bjp.rcpsych.org/content/196/5/414.1.long

best,
-joost


On Fri, Mar 23, 2012 at 2:15 AM, Michael Harms wrote:

>
> Hi Jeff,
> I personally like the idea of using average thickness as a covariate to
> control for a reduction in "whole brain" thickness, and have used that
> approach in a paper.  If the Abstract that you mentioned indicated that
> this is flawed, I'd be curious to know what the reason was...
>
> cheers,
> -MH
>
> On Thu, 2012-03-22 at 21:00 -0400, Bruce Fischl wrote:
> > Hi Jeff
> >
> > yes, I think this is still our recommendation for thickness, although
> > perhaps David Salat can verify. As far as surface area, you might get
> > Anderson Winkler to send you a preprint of his newly accepted paper on
> > surface area comparisons and how to do them properly. I would have said
> > normalize by the 2/3 root of ICV (maybe David can comment on this as
> well)
> >
> > cheers
> > Bruce
> >
> >
> > On Thu, 22 Mar 2012, Jeff Sadino wrote:
> >
> > > Hello,
> > > For cortical thickness normalizations, Bruce said not to normalize
> based on a HBM
> > > abstract
> > > (
> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06646.html).
>  Is
> > > this still the consensus?
> > >
> > > For cortical volume, it is pretty standard to normalize to eTIV.
> > >
> > > For cortical surface area (jacobian), I couldn't find any information
> on the wiki.
> > >  Does anyone have any recommendations?
> > >
> > > Thank you,
> > > Jeff
> > >
> > >
> > ___ Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The
> information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail contains patient information, please contact the Partners Compliance
> HelpLine at http://www.partners.org/complianceline . If the e-mail was
> sent to you in error but does not contain patient information, please
> contact the sender and properly dispose of the e-mail.
>
> ___
> 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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] lGI differences without variation in other cortical morphometric variables

[j janssen]

Hi,

I am comparing a group of patients with controls. I extracted:
> cortical volume, surface area, cortical thickness and gyrification
> index for each subject's lobe.
> Comparisons between this variables with Total Intracranial Volume as a
> covariate indicated a difference in frontal and temporal lobes lGI.
>

what happens if you do not adjust for intracranial volume? if your patients
have abnormal sized lobes then this may be obscured by controlling for head
size.


> However, differences were not significant for any of the other
> variables.
>
> I can´t understand these results from a biological perspective. I was
> expecting that if a difference exist in lGI it would also manifest in
> surface area or volume.
>

this paper: http://www.ncbi.nlm.nih.gov/pubmed/18267953

tells us that it is possible for smaller sized brains to have higher
folding compared to bigger sized brains. however, it also states that it's
much more probable for bigger sized brains to have a higher degree of
folding, indeed a strong relationship is shown between brain volume,
cortical surface and folding (Figs. 3 and 4c) over large parts of the
cortex.

hth,
-joost



> Can someone help me with an explanation for this?
>
> Thank you.
>
> ines
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Freesurfer and FSL

[j janssen]

Hi,

this is not a direct comparison but at least indicates similar volumes in
FSL-FIRST and Freesurfer.

br J Psychiatry. 2012 Jan;200(1):30-6.

hth,
-joost



On Sun, May 27, 2012 at 2:09 PM, Martin Reuter
wrote:

> Hi Ana,
>
> Sorry I can't help more. Have never compared fsl and FS directly. Keep in
> mind that any consistent differences may also depend on the software
> version.
> Maybe other people on the list have done some comparisons.
>
> Best Martin
>
> On May 26, 2012, at 13:59, Ana Arruda  wrote:
>
> > Thanks for your help Martin.
> >
> > However I don't have just a single subject with that discrepancy. My
> data has 18 subjects and most of the results obtained with Freesurfer are
> bigger than FSL.
> >
> > Thank you again,
> >
> > Ana
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] localGI exits with error

[j janssen]

Hi,

i am using version 4.0.5. for two brains out of a larger study, localGI
exits with errors, the error message is similar in both brains and looks
like:

lGI for vertex number 49901 of the outer mesh is 1.9168
lGI for vertex number 50001 of the outer mesh is 2.4523
ratio saved at 50001
lGI for vertex number 50101 of the outer mesh is 3.2668
... remeasuring lGI value for vertex iV = 50201. It may take a few minutes.
WARNING -- Problem for vertex iV = 50201, lGI value is aberrantly high
(lGI=43.3799)...
...lGI computation will be stopped. This may be caused by topological
defects, check mris_euler_number on the pial surface.

mris_euler_number ?h.pial gives 0 defects. i ran localGI on both brains
several times and got the same error message at the same vertex number (for
lh). empirically, surfaces look reasonable.

a similar message was posted some time ago:

http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07281.html

but no reply.

any ideas?

thanks,
-joost
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] labels to surface

[j janssen]

Hi,

using version 4.0.5.

i want to convert the lh.Medial_wall.label found in the fsaverage label
subdir into a mask which consists of 1 x v vector, with value 1 inside the
mask, 0 outside the mask and v=#vertices. should i follow mri_label2vol and
thereafter mri_vol2surf? i guess i am looking for a way to put binary masks
on surface data.

thanks,
-joost
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] question mri_glmfit

[j janssen]

Hi,

using version 4.0.5

i ran the command:
mri_glmfit --y qdec/N83_only_boys.mgh --fsgd qdec/qdec.fsgd doss --surf
fsaverage lh --C qdec/diff-1-2.txt --glmdir stats/

it worked.

then i did:

mri_glmfit --y qdec/N83_only_boys.mgh --fsgd qdec/qdec.fsgd doss --surf
fsaverage lh --C qdec/diff-1-2.txt --sim perm 1000 1.3 stats/newperm_lh
--glmdir stats/newperm_lh/

output:

gdfReadHeader: reading qdec/qdec.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 Age 15.4819
Class Means of each Continuous Variable
1 control 15.0882
2 patient 15.7551
INFO: gd2mtx_method is doss
Reading source surface
/home/neuro/joost/redes/maranon/freesurfer/fsaverage/surf/lh.white
reading group avg surface area 822 cm^2 from file
Reading in average area
/home/neuro/joost/redes/maranon/freesurfer/fsaverage/surf/lh.white.avg.area.mgh
simbase stats/perm_lh
Number of vertices 163842
Number of faces327680
Total area 65416.648438
AvgVtxArea   0.399267
AvgVtxDist   0.721953
StdVtxDist   0.195470

$Id: mri_glmfit.c,v 1.138.2.1 2007/09/12 15:38:19 nicks Exp $
cwd /home/neuro/joost/redes/maranon/freesurfer
cmdline mri_glmfit --y qdec/N83_only_boys.mgh --fsgd qdec/qdec.fsgd doss
--surf fsaverage lh  --C qdec/diff-1-2.txt --sim perm 1000 1.3 stats/perm_lh
--glmdir stats/
sysname  Linux
hostname fedoraneuro.lim.local
machine  x86_64
user neuro
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y/home/neuro/joost/redes/maranon/freesurfer/qdec/N83_only_boys.mgh
logyflag 0
usedti  0
FSGD qdec/qdec.fsgd
glmdir stats/
DoFFx 0
Loading y from
/home/neuro/joost/redes/maranon/freesurfer/qdec/N83_only_boys.mgh
Matrix condition is 404.504
search space = 82220
ERROR: design matrix is not orthogonal, cannot be used with permutation.
If this something you really want to do, run with --perm-force

mri_info N83_only_boys.mgh gives 83 frames.

what´s wrong with my design matrix?

thanks!
-joost


qdec.fsgd
Description: Binary data
1 -1 0
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] converting modified labels from annot

[j janssen]

Hi,

using version 4.0.5.

i used mri_extract_label on the aparc+aseg.mgz file to extract and convert
labels into volume nifti files, which i can view and use outside FreeSurfer.
works fine.

however, i have manually edited some surface labels, following the
instructions found here:
https://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer_labeledit?action=fullsearch&context=180&value=mris_annot_to_segmentation&titlesearch=Titles

these instructions result in a modified .annot file, which i have. my
question: what is the best way to get a nifti volume for the modified
(manually edited) label? ideally, this nifti volume should be exactly the
same as done with mri_extract_label except for the modified part.

thanks,
-joost
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] tksurfer display question

[j janssen]

Hi,

using version 4.0.5

look at the attached picture. its the result of:

tksurfer code lh inflated -aparc aparc -gray

i have selected one region (yellow outline). i would like to
- fill this region and some other regions, *but not all regions*!
- give the filled regions different color-labelings
- i would like to display them (outlined and filled regions) at the *same*
time.

i have tried numerous ways, without result. any suggestions?

thanks,
-joost
<>___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] question on tksurfer tcl

[j janssen]

Hi,

using version 4.0.5

my goal: to display in tksurfer an inflated brain with curvature and an
*outlined* label, using a tcl-script.

there are probably numerous ways, i did:

 tksurfer "subject" rh inflated -gray -tcl tksurf.tcl

where tksurf.tcl contains:

make_lateral_view
rotate_brain_x -90
redraw
labl_load "label-file"
set gaLinkedVars(redrawlockflag) 0
SendLinkedVarGroup redrawlock
set gaLinkedVars(labelstyle) 1
SendLinkedVarGroup view
save_tiff "tiff_file.tiff"

all works except for the label to be outlined. any suggestions?

thanks!
-joost
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] surface

[j janssen]

Hi,

here's an email from Don Hagler from February 2009:

 It seems to me that vertex areas in the native subject space are not
> meaningful.  The orig surfaces should be uniformly tesselated; however,
> topology correction and final surface finding should introduce complicated
> and probably uninteresting variation.
>

i couldn't find a direct reply to this remark, hence my question:
is this true? and if so, does this imply that native space surface
measurements (as given in the aparc.stats file) are uninteresting for
statistical analysis?

best,
-joost
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Covariate for results of cortical parcellation

[j janssen]

Hi,

you could try including average cortical thickness over the entire
> hemisphere as a covariate. This was Mike Harms' suggestion, and I think a
> good one.


why is it a good one? for cortical thickness: i'm not so sure. my 2 cents
(and i may be wrong!):
- controlling for intracranial volume is done to remove differences due to
overall size variability.
- the relationship between thickness and size is much less strong than
between volume and size (or surface and size).
- suppose your groups differ in mean thickness, if you would like to include
mean thickness as a covariate in a mapping study (vertex-wise comparisons)
of cortical thickness you would have to show that the group-difference in
mean thickness is due to an effect that's spread out over the whole cortex
(an overall effect, not localized), otherwise the mean thickness covariate
is not a good estimator of the overall size factor that you'd like to
remove.

check Peter Kochunov's recent publications on this.

-joost




cheers
> Bruce
>
>
>
> On Thu, 8 Apr 2010, Liukarl wrote:
>
>
>> Hello, Freesurfer experts:
>>
>> I noticed for analyzing the results from autorecon2, the intracranial
>> volume are controlled as covariate in some publications. Is there any
>> corresponding covariate for cortical results from autorecon3, cortical
>> thickness, surface, and volume?
>>
>> In my current study, there are two group: one is a group with less optimal
>> developmental environment and the other is control. I noticed that without
>> any covariate, the r square from cortical measure and group variable was
>> really low, only accounting for 2%. Is any standard way to analyze the
>> cortical data?
>>
>>
>> Thanks!
>>
>> Karl
>> _
>> MSN十年回馈，每位用户可免费获得价值25元的卡巴斯基反病毒软件2010激活码，快来领取！
>> http://kaba.msn.com.cn/?k=1
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Question about cortical surface area

[j janssen]

Hi,

what's the reason that FS's default surface for measuring surface area is
the white matter surface and not the pial surface? why isn't surface area
measured on the intermediate surface (average of gray.and white which should
be less biased by sulci and gyri, i think)?

thanks,
-joost

>
> > On Wed, Apr 28, 2010 at 5:48 PM, Michael Harms
> >  wrote:
> >
> > Hi Massieh,
> > There were some posts related to this a while back.
> > If I recall correctly, the vertex-wise area measure (and
> > likewise the
> > vertex-wise volume measure) is highly dependent on the local
> > mesh
> > triangulation, and thus is not really a meaningful variable
> > from a
> > biological perspective.  So, you would be better off analyzing
> > the area
> > of a whole label.
> >
> > Best,
> > -Mike H.
> >
> >
> >
> > On Wed, 2010-04-28 at 09:54 -0400, Massieh Moayedi wrote:
> > > Hi everyone,
> > >
> > > I had two questions:
> > >
> > > 1) I was wondering if it's ok to run a glm to compare
> > cortical surface
> > > areas between two groups on a vertex-wide basis (just like a
> > thickness
> > > analysis).  Or is it better to extract the area of a label
> > (as is the
> > > output of mri_anatomical_stats)?
> > >
> > > 2) The mri_anatomical_stats output includes 4 measures of
> > curvature:
> > > MeanCurv, GausCurv, Van Essen Folding index and Curvature
> > Index.  There
> > > was some discussion as to which of these was most
> > appropriate for
> > > comparing sulcal folding (that is, essentially what they
> > measure,
> > > correct?)- was there ever any final consensus?
> > >
> > > Thank you.
> > >
> > > Regards,
> > >
> > > Massieh Moayedi B.Sc. (Hons)
> > > PhD Student
> > > Dr. Karen Davis' Lab
> > > Institute of Medical Science
> > > University of Toronto
> > >
> > > Brain, Imaging and Behaviour- Systems Neuroscience
> > > MP 14-301
> > > Toronto Western Research Institute
> > > University Health Network
> > > 399 Bathurst Street
> > > Toronto, Ontario
> > > Canada M5T 2S8
> > > Tel: 416-603-5882
> > >
> > > massih.moay...@utoronto.ca
> > > mmoay...@uhnres.utoronto.ca
> > > http://individual.utoronto.ca/PSMJC
> > >
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > >
> > >
> > > The information in this e-mail is intended only for the
> > person to whom it is
> > > addressed. If you believe this e-mail was sent to you in
> > error and the e-mail
> > > contains patient information, please contact the Partners
> > Compliance HelpLine at
> > > http://www.partners.org/complianceline . If the e-mail was
> > sent to you in error
> > > but does not contain patient information, please contact the
> > sender and properly
> > > dispose of the e-mail.
> >
> > ___
> > 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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Re: can not see the pial surface using tksurfer

[j janssen]

Hi,

i can not see the pial surface using tksurfer. i´m using Fedora core 7, 64
bits, with version:
freesurfer-Linux-centos4_x86_64-stable-pub-v4.0.3-full.tar.gz,
with nvidia card.

when i enter:
ldd /usr/local/freesurfer/bin/tksurfer.bin
i get:
linux-vdso.so.1 =>  (0x7fff463fd000)
libtix8.1.8.4.so => not found
libtk8.4.so => /usr/lib64/libtk8.4.so (0x003678a0)
libtcl8.4.so => /usr/lib64/libtcl8.4.so (0x00367860)
libGLU.so.1 => /usr/lib64/libGLU.so.1 (0x2aaca000)
libXmu.so.6 => /usr/lib64/libXmu.so.6 (0x003c3560)
libGL.so.1 => /usr/lib64/libGL.so.1 (0x003c2d20)
libXext.so.6 => /usr/lib64/libXext.so.6 (0x003c2840)
libX11.so.6 => /usr/lib64/libX11.so.6 (0x003c27c0)
libexpat.so.0 => /lib64/libexpat.so.0 (0x003c2880)
libjpeg.so.62 => /usr/lib64/libjpeg.so.62 (0x003c2f20)
libtiff.so.3 => /usr/lib64/libtiff.so.3 (0x00367e80)
libz.so.1 => /lib64/libz.so.1 (0x003c2640)
libcrypt.so.1 => /lib64/libcrypt.so.1 (0x003c3820)
libdl.so.2 => /lib64/libdl.so.2 (0x003c2600)
libpthread.so.0 => /lib64/libpthread.so.0 (0x003c26c0)
libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x003ed0a0)
libm.so.6 => /lib64/libm.so.6 (0x003ed0e0)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x003c3320)
libc.so.6 => /lib64/libc.so.6 (0x003c2580)
libXt.so.6 => /usr/lib64/libXt.so.6 (0x003c38e0)
libXxf86vm.so.1 => /usr/lib64/libXxf86vm.so.1 (0x003c3ae0)
libdrm.so.2 => /usr/lib64/libdrm.so.2 (0x003c2d60)
libXau.so.6 => /usr/lib64/libXau.so.6 (0x003c2740)
libXdmcp.so.6 => /usr/lib64/libXdmcp.so.6 (0x003c2700)
/lib64/ld-linux-x86-64.so.2 (0x003c2540)
libSM.so.6 => /usr/lib64/libSM.so.6 (0x003c2fa0)
libICE.so.6 => /usr/lib64/libICE.so.6 (0x003c3020)

starting tksurfer:
[EMAIL PROTECTED] subjects]$ tksurfer bert rh pial
gives:
surfer: current subjects dir: /usr/local/freesurfer/subjects
surfer: not in "scripts" dir ==> using cwd for session root
surfer: session root data dir ($session) set to:
surfer: /usr/local/freesurfer/subjects
surfer: Reading header info from
/usr/local/freesurfer/subjects/bert/mri/T1.mgz
surfer: vertices=131277, faces=262550
Loading /usr/local/freesurfer/surface_labels.txt
surfer: ### redraw failed: no gl window open
surfer: single buffered window
surfer: using interface /usr/local/freesurfer/lib/tcl/tksurfer.tcl
Reading /usr/local/freesurfer/lib/tcl/tkm_common.tcl
Reading /usr/local/freesurfer/lib/tcl/tkm_wrappers.tcl
Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl
Reading /usr/local/freesurfer/lib/tcl/tkUtils.tcl
Successfully parsed tksurfer.tcl
reading white matter vertex locations...

can you help?

thanks!
-joost






On Fri, Apr 25, 2008 at 4:05 PM, Nick Schmansky <[EMAIL PROTECTED]>
wrote:

> If you have an Nvidia graphics card, you will need to update the driver.
>
> Try running nvidia-installer --update, as root (preferably have your
> sysadmin do this).
>
> Nick
>
> On Fri, 2008-04-25 at 21:25 +0800, yczhang wrote:
> > Hi,
> > when I launched the command tksurfer to see the constructed pial
> > surface,
> > only a very small part of the surface can been seen in the window.
> > I do not know how to fix the problem.
> > Thanks!
> >
> >
> > __
> > yczhang
> > 2008-04-25
> > ___
> > 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 mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Re: can not see the pial surface using tksurfer

[j janssen]

Hi,

the second option (copying tksurfer.bin) worked.

thanks!
-joost


On Wed, Apr 30, 2008 at 4:09 PM, Nick Schmansky <[EMAIL PROTECTED]>
wrote:

> Joost,
>
> Try both of these things:
>
>  - update the nvidia driver from their website (or run nvidia-installer
> --update, which does this for you).
>
>  - copy tksurfer.bin from here:
>
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/stable/centos4_x86_64
>
> to here:
> $FREESURFER_HOME/bin
>
> Nick
>
>
> On Wed, 2008-04-30 at 12:31 +0200, j janssen wrote:
> > Hi,
> >
> > i can not see the pial surface using tksurfer. i´m using Fedora core
> > 7, 64 bits, with version: freesurfer-Linux-centos4_x86_64-stable-pub-
> > v4.0.3-full.tar.gz, with nvidia card.
> >
> > when i enter:
> > ldd /usr/local/freesurfer/bin/tksurfer.bin
> > i get:
> > linux-vdso.so.1 =>  (0x7fff463fd000)
> > libtix8.1.8.4.so => not found
> > libtk8.4.so => /usr/lib64/libtk8.4.so (0x003678a0)
> > libtcl8.4.so => /usr/lib64/libtcl8.4.so (0x00367860)
> > libGLU.so.1 => /usr/lib64/libGLU.so.1 (0x2aaca000)
> > libXmu.so.6 => /usr/lib64/libXmu.so.6 (0x003c3560)
> > libGL.so.1 => /usr/lib64/libGL.so.1 (0x003c2d20)
> > libXext.so.6 => /usr/lib64/libXext.so.6 (0x003c2840)
> > libX11.so.6 => /usr/lib64/libX11.so.6 (0x003c27c0)
> > libexpat.so.0 => /lib64/libexpat.so.0 (0x003c2880)
> > libjpeg.so.62 => /usr/lib64/libjpeg.so.62 (0x003c2f20)
> > libtiff.so.3 => /usr/lib64/libtiff.so.3 (0x00367e80)
> > libz.so.1 => /lib64/libz.so.1 (0x003c2640)
> > libcrypt.so.1 => /lib64/libcrypt.so.1 (0x003c3820)
> > libdl.so.2 => /lib64/libdl.so.2 (0x003c2600)
> > libpthread.so.0 => /lib64/libpthread.so.0 (0x003c26c0)
> > libstdc++.so.6 => /usr/lib64/libstdc++.so.6
> > (0x003ed0a0)
> > libm.so.6 => /lib64/libm.so.6 (0x003ed0e0)
> > libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x003c3320)
> > libc.so.6 => /lib64/libc.so.6 (0x003c2580)
> > libXt.so.6 => /usr/lib64/libXt.so.6 (0x003c38e0)
> > libXxf86vm.so.1 => /usr/lib64/libXxf86vm.so.1
> > (0x003c3ae0)
> > libdrm.so.2 => /usr/lib64/libdrm.so.2 (0x003c2d60)
> > libXau.so.6 => /usr/lib64/libXau.so.6 (0x003c2740)
> > libXdmcp.so.6 => /usr/lib64/libXdmcp.so.6 (0x003c2700)
> > /lib64/ld-linux-x86-64.so.2 (0x003c2540)
> > libSM.so.6 => /usr/lib64/libSM.so.6 (0x003c2fa0)
> > libICE.so.6 => /usr/lib64/libICE.so.6 (0x003c3020)
> >
> > starting tksurfer:
> > [EMAIL PROTECTED] subjects]$ tksurfer bert rh pial
> > gives:
> > surfer: current subjects dir: /usr/local/freesurfer/subjects
> > surfer: not in "scripts" dir ==> using cwd for session root
> > surfer: session root data dir ($session) set to:
> > surfer: /usr/local/freesurfer/subjects
> > surfer: Reading header info
> > from /usr/local/freesurfer/subjects/bert/mri/T1.mgz
> > surfer: vertices=131277, faces=262550
> > Loading /usr/local/freesurfer/surface_labels.txt
> > surfer: ### redraw failed: no gl window open
> > surfer: single buffered window
> > surfer: using interface /usr/local/freesurfer/lib/tcl/tksurfer.tcl
> > Reading /usr/local/freesurfer/lib/tcl/tkm_common.tcl
> > Reading /usr/local/freesurfer/lib/tcl/tkm_wrappers.tcl
> > Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl
> > Reading /usr/local/freesurfer/lib/tcl/tkUtils.tcl
> > Successfully parsed tksurfer.tcl
> > reading white matter vertex locations...
> >
> > can you help?
> >
> > thanks!
> > -joost
> >
> >
> >
> >
> >
> >
> > On Fri, Apr 25, 2008 at 4:05 PM, Nick Schmansky
> > <[EMAIL PROTECTED]> wrote:
> > If you have an Nvidia graphics card, you will need to update
> > the driver.
> >
> > Try running nvidia-installer --update, as root (preferably
> > have your
> > sysadmin do this).
> >
> > Nick
> >
> >
> > On Fri, 2008-04-25 at 21:25 +0800, yczhang wrote:
> > > Hi,
> > > when I launched the command tksurfer to see the constructed
> > pial
> > 

[Freesurfer] Fwd: FindFacePath

[j janssen]

Hi,

after a bit more digging i´ve concluded that the orginal topology fixer
(mris_fix_topology) failed because:
mris_euler_number ../surf/lh.orig

gave

(euler number != 2)

therefore it tries:
mris_topo_fixer -mgz -warnings "subjid" lh

which runs for some time and then exits:
ERROR: _FindFacePath: could not find path!

any ideas?

- the scan looks (is) crappy due to movement artifacts, which may well be
the cause.

best,
-joost




-- Forwarded message ------
From: j janssen <[EMAIL PROTECTED]>
Date: Tue, Sep 16, 2008 at 2:05 PM
Subject: FindFacePath
To: freesurfer@nmr.mgh.harvard.edu



Hi,

using Freesurfer version 4.05 i have a brain that runs through autorecon1
(without errors according to log) but exits with errors during autorecon2.
the error given is:
"ERROR: _FindFacePath: could not find path!"

other brains in the same set do not give this error message, therefore i
assume it must have something to do with the specific brain.

i´ve attached the log-file.

i realize this is little info, let me know what else you need for diagnosis.

thanks,
-joost
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] mri_robust_register

[j janssen]

Hi,

- using version 4.5

in the v4.5 standard longitudinal processing stream with 2 images
mri_robust_register creates halfway space transformations using the 2
time point's norm.mgz files.

i would like to apply the halfway transformations (mri_convert -at) to
the 2 time point's _original_ (001.mgz) images. can i do this and if
so, how?

or should i create new halfway transformations with something like:
mri_robust_register --mov timepoint1_001.mgz --dst timepoint2_001.mgz
--lta v1to2.lta --halfmov h1.mgz --halfdst h2.mgz --halfmovlta h1.lta
--halfdstlta h2.lta --iscale

thanks,
-joost
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] merging average cortical thickness data

[j janssen]

Hi Tina,

> (e.g. to compute a general cortical thickness average for
> the inferior frontal gyrus using the pars orbitalis, pars opercularis and
> pars triangularis data).

instead of "merging" existing thickness-data you could create a new
label that constitutes your regions of interest. something like:

1. mri_annotation2label, gives you the labels.
2. mri_mergelabels, merge only the labels you are interested in.
3. mris_anatomical_stats, use the newly created label (e.g. inferior
frontal gyrus) to compute thickness, surface area, volume etc.

>Average cortical thickness= [(part 1 cortical thickness*part 1 surface area) + 
>(part 2 cortical thickness*part 2 surface area) + …]/ >(part 1 surface area + 
>part 2 surface area + …)

my 2 cents:
1. if you have an a priori hypothesis dealing with the mean thickness
of certain region (e.g. inferior frontal gyrus, IFG) then your should
calculate the mean thickness of IFG. if you have an a priori
hypothesis about the mean thickness of a certain part of the IFG then
you should calculate the mean thickness for that part. i think your
approach doesn't follow this, you are going from subregions to IFG
thereby weighing for surface area of the subregions, what's your a
priori reason for doing this? why not measure the pars-regions
directly and forget about IFG?

2. the linear relationship between thickness and surface area. e.g. if
mean thickness is equal in all subregions that make up the IFG, you
give more weight to the region with a larger surface area, why?

best,
-joost




On Thu, Dec 23, 2010 at 4:00 AM, Bruce Fischl
 wrote:
> Hi Tina,
>
> I think weighting by surface area is a reasonable approach.
>
> cheers
> Bruce
> On Wed, 22 Dec 2010, tina roostaei wrote:
>
>> Dear all,
>>
>> I have access to a dataset of freesurfer segmentation  products (i.e.
>> cortical
>> volume, surface area, cortical thickness average  and standard deviation)
>> for a
>> number of patients. I wanted to merge the  data of some segmented parts
>> (e.g. to
>> compute a general cortical  thickness average for the inferior frontal
>> gyrus
>> using the pars orbitalis, pars opercularis and pars triangularis data).
>> I wanted to know if it is right to compute the average cortical thickness
>> using
>> the following formula:
>> Average cortical thickness= [(part 1 cortical thickness*part 1 surface
>> area) +
>> (part 2 cortical thickness*part 2 surface area) + ÿÿ]/ (part 1 surface
>> area +
>> part 2 surface area + ÿÿ)
>> BTW,  I also checked whether the cortical volume equals ÿÿsurface
>> area*average
>> cortical thicknessÿÿ, to see if I could use the following formula
>>  instead:
>> Average cortical thickness= (part 1 cortical volume + part 2  cortical
>> volume +
>> ÿÿ)/ (part 1 surface area + part 2 surface area + ÿÿ)
>> But it simply proved wrong.
>>
>> Any suggestion is greatly appreciated.
>>
>> Thanks in advance.
>> Tina
>>
>>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>

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

[Freesurfer] question on contrast matrix

[j janssen]

FreeSurfer version: 4.5

Background: we have 6 subjects, each subject has 1 scan per site,
there are 6 sites (so each subject has 6 scans).

Aim: to assess whether thickness is different per site: a F-test.

what we did so far:

we used mri_glmfit with the following .fsdg file (here we only show
the Input of the first 2 subjects)

GroupDescriptorFile 1
Title scanner
MeasurementName thickness
Class Site1
Class Site2
Class Site3
Class Site4
Class Site5
Class Site6
Input Subject1 Site1
Input Subject1 Site2
Input Subject1 Site3
Input Subject1 Site4
Input Subject1 Site5
Input Subject1 Site6
Input Subject2 Site1
Input Subject2 Site2
Input Subject2 Site3
Input Subject2 Site4
Input Subject2 Site5
Input Subject2 Site6
.
.
Input Subject6 Site6

we used the following .mtx file for mri_glmfit:

1 -1 0 0 0 0
0 1 -1 0 0 0
0 0 1 -1 0 0
0 0 0 1 -1 0
0 0 0 0 1 -1

we doubt that this is correct since our contrasts do handle the
subjects at each site as an independent group, i.e. it does not take
into account that each subject had 6 different scans (one at each
site). any advice on how we should set up our contrast matrix? i
repeat: our aim is to do a F-test to assess whether thickness is
affected by site.

thanks,
-joost
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] surface to native space

[j janssen]

Hi,

FS version 4.5

- goal: to transfer the ?h.pial to native ('pre-conformed') space.
thus to the space of the image _before_ any FS processing.

- what we have done so far:
1) if we convert the T1.mgz (from the FS mri-dir, mri_convert T1.mgz
T1.nii) to nifti it coincides perfectly with the native space image.
2) if we then overlay the ?h.pial over the T1.nii it does _not_ match,
i.e. it looks like mri_convert includes a translation that shifts the
surface with respect to the volume.

question: how can we achieve our goal, i.e. get the surface in native
space (a perfect overlap with T1.nii)?

thanks,
-joost
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.