hi doug and fellow FS users,
i am going thru the recon_checker.log file to look into anat SNR, mWM, stdWM
and voxWM.the ones with lowest SNR are seemed to be marked with
arrowmay i know the reason why some of them have lowest SNR and they are
marked with arrow in front of em?..the data
hi doug n fellow fs users,
whenever we try to load a fsaverage surface in freeview, it shows me following
message:
"Surface does not contain valid volume geometry information. It may not align
with volumes and other surfaces"
this message is limited only to fsaverage surfaces.
was just wo
hi doug,
i am loading 917 subjects in qdec.i already made qdec.table.dat which
consist the list of subjid, age, gender, lh & rh thickness..
for some reason, it is only displaying the first subject.others are not
been detected by qdec.
i also looked into tutorial and compared th
hi,
i am trying to do group analysis in qdec...my fixed factor = gender; continuous
factors= age, lhthickness and rhthickness
for some reason i am coming across two following issues over and over:
1- the qdec shows fixed factors are gender, lh thickness and rhthickness while
covariate as age
I
- Original Message -
From: "Nick Schmansky"
To: "Kushal Kapse"
Cc: "Freesurfer Mailinglist"
Sent: Monday, June 11, 2012 3:49:23 PM
Subject: Re: [Freesurfer] qdec issue
kk,
can you send me your qdec.table.data? qdec automatically assigns a
factor as a fixed fctor if
as per my experience in grp analysis with cortical thickness, age and
gender.i would suggest you to use qdec and select the gender as fixed
factor and age/IQ as continuous factor...once you do tht, qdec will define the
contrast for you to see "correlation between thickness and age, accountin
mike
if all male, then it may be worth observing how age of all those
male-individuals correlate with cortical thickness..
kk
- Original Message -
From: mdkrue...@uwalumni.com
To: "Kushal Kapse"
Cc: "freesurfer"
Sent: Wednesday, June 13, 2012 11:49:29 AM
Subj
hi fellas,
i am trying to run mri_cnr command in freesurfer to compute and see CNR for
gray/white/csf the command gives following info as help:
-bash-3.2$ mri_cnr
usage: mri_cnr [options]...
-s
i understand that 'surf directory'= subjects 'surf' folder ; but i am not able
thanks Dr. B.that helped a lot
- Original Message -
From: "Bruce Fischl"
To: "Kushal Kapse"
Cc: "freesurfer"
Sent: Monday, June 18, 2012 2:27:29 PM
Subject: Re: [Freesurfer] mri_cnr
Hi KK
this is something i wrote for myself, but you are welcome to
for multiple subjects to run for -qcache, i wud suggest use this
http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/Scripts/Two
substitute "-all" with "-qcache"..you can also pick specific measure and
fwhm if you dont want all others to be ran.
hope this helps
kk
- Origin
e -measure thickness
-fwhm 10; done
hope this helps
kk
- Original Message -
From: mdkrue...@uwalumni.com
To: "Kushal Kapse"
Cc: "freesurfer"
Sent: Wednesday, June 20, 2012 2:57:30 PM
Subject: Re: [Freesurfer] qdec analysis sequence
Kushal -
This helps immensely! Jus
hi miro,
as per me, i would suggest to divide ICV with TotalGrayVol and other aseg.stats
files' global measures to remove the invariability across these measures.
divide ICV to
totalgrayvol,corticalwhitemattervolume,supratenorialvol,subcorticalgrayvol...this
will remove any in-variability with
hi fellow FS users,
i am running bbregister (bbregister --s 083010_004498 --mov
083010_004498/bbl1_frac2back1_231.nii.gz --bold --reg register.dat --init-fsl).
it shows me following error:
FSLOUTPUTTYPE NIFTI
tkreg2FSL: mov det = -27, ref det = -1
FSLDIR: Undefined variable.
i did run bbregis
u have FSL installed.
doug
On 06/21/2012 04:16 PM, Kushal Kapse wrote:
> hi fellow FS users,
>
> i am running bbregister (bbregister --s 083010_004498 --mov
> 083010_004498/bbl1_frac2back1_231.nii.gz --bold --reg register.dat
> --init-fsl).
>
> it shows me following error:
&g
hi FS users;
have two questions which i am having issue across ss and pial/wm/orig surf
boundaries
1- it has happened that sometimes the sagittal view of individual was flipped
from left to right. but the pial/wm boundaries look good. was wondering why
this happened only for countable ppl? i t
kka...@mail.med.upenn.edu
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> Hi Everyone,
>
> I am new to FreeSurfer, and having some issues with what I believe should be
> a pretty basic operation.
>
> My goal is to register a 4D functional time series to FS average space for
> further connectivity analysis in Matlab (similar to the recent Yeo et al. J
> Neurophy
- Forwarded Message -
From: "Kushal Kapse"
To: "Bruce Fischl"
Sent: Thursday, May 24, 2012 9:14:55 AM
Subject: Re: [Freesurfer] fMRI time series in surface space
hi Bruce,
what if I have .feat files from FSL which have already been processed for
functional ana
- Forwarded Message -
From: "Kushal Kapse"
To: "Douglas N Greve"
Sent: Thursday, May 24, 2012 11:45:14 AM
Subject: Re: [Freesurfer] fMRI time series in surface space
run preprocessing of FS-FAST and do sampling on surface seems a good way to
give a tryi am ha
hi,
i am performing feat2surf after i successfully performed
reg-feat2anat...for some reason it gives me "ERROR: cannot find any .img,
.nii, .nii.gz files"although the stats file is in reg folder.may i
please get suggestion on how to proceed from here
thanks
kk
___
i got it fixed...thanks
- Original Message -
From: "Douglas N Greve"
To: freesurfer@nmr.mgh.harvard.edu
Sent: Thursday, May 24, 2012 2:58:32 PM
Subject: Re: [Freesurfer] feat2surf
Please send the command line and full terminal output.
doug
On 05/24/2012 02:47 PM, Kushal K
surf so you can do it all with one command).
doug
On 05/24/2012 08:35 AM, Kushal Kapse wrote:
>> Hi Everyone,
>>
>> I am new to FreeSurfer, and having some issues with what I believe should be
>> a pretty basic operation.
>>
>> My goal is to register a 4D funct
: "Douglas N Greve"
To: "Kushal Kapse"
Cc: freesurfer@nmr.mgh.harvard.edu
Sent: Friday, May 25, 2012 3:53:31 PM
Subject: Re: [Freesurfer] fMRI time series in surface space
Hi Kushal, please be sure to include the entire terminal output. These
kinds of things are hard to trac
not find target reference for orig.mgz"..
please let me know
thanks
kk
- Original Message -
From: "Douglas N Greve"
To: "Kushal Kapse"
Cc: freesurfer@nmr.mgh.harvard.edu
Sent: Friday, May 25, 2012 4:08:35 PM
Subject: Re: [Freesurfer] fMRI time series in su
@doug
no doug...this "orig.mgz"error was before segmentation fault error started
showing up.hence i wanna see if why it gave that lemme take a look and
will keep u updated
- Original Message -
From: "Douglas N Greve"
To: "Kushal Kapse"
Cc: frees
/controls/15546_03908//register.dat/mri/orig.mgz,
-1): could not open file
i didnt understand when u said in last email "where "subject" comes from the
register.dat file".would you please explain me this
thanks
kk
- Original Message -
From: "Kushal Kapse&qu
orig.mgz file is on 15446_03908/mri/orig.mgz
yes the subject name and the directory path is correct
- Original Message -
From: "Douglas N Greve"
To: "Kushal Kapse"
Cc: freesurfer@nmr.mgh.harvard.edu
Sent: Friday, May 25, 2012 4:52:37 PM
Subject: Re: [Freesurfer]
well...
it seems the seg fault occured due to i was using a 4D func file and not
3ddoes the vol2surf does only on 3d func data ?how would i do that for
4D time series?
please let me know
thanks
kk
- Original Message -
From: "Douglas N Greve"
To: "Ku
yes ..the registration is nicely aligned and i did check the green-lines
alignment in tkregister2
is their any other reason for it showing segmentation fault
- Original Message -
From: "Douglas N Greve"
To: "Kushal Kapse"
Cc: freesurfer@nmr.mgh.harvard.edu
doug,
did try new version..it worked fine...but seems tht new version doesnt support
.w as output format; like in the tutorial online.what output format does
the new version vol2surf likes?
thanks
kk
- Original Message -
From: "Douglas N Greve"
To: "Kushal Kapse&q
i tried .nii.gz and they didnt work.i will try .mgz file and keep u
updated,...
thanks
kk
- Original Message -
From: "Douglas Greve"
To: "Kushal Kapse"
Cc: freesurfer@nmr.mgh.harvard.edu
Sent: Friday, May 25, 2012 8:23:47 PM
Subject: Re: [Freesurfer] fMRI ti
uglas Greve"
To: "Kushal Kapse"
Cc: freesurfer@nmr.mgh.harvard.edu
Sent: Friday, May 25, 2012 8:23:47 PM
Subject: Re: [Freesurfer] fMRI time series in surface space
I don't think it ever supported w files ... you can use mgh /mgz format.
It will also produce nifti files, but
"
To: "Kushal Kapse"
Cc: freesurfer@nmr.mgh.harvard.edu
Sent: Tuesday, May 29, 2012 8:54:40 AM
Subject: Re: [Freesurfer] fMRI time series in surface space
Hi Kushal, you cannot use .w file for 4D outputs. Use this cmd:
mri_vol2surf.linux --src func.nii.gz --reg register.dat --hemi
functionaltosurface..i have been
trying numerous ways looking at the output by working on tutorial of
"functional to surface resampling"...but havent been successful...please
lemme know
thanks
kk
- Original Message -
From: "Douglas Greve"
To: "Kushal Kapse"
Cc: frees
hi doug,
now it works finei can check the activations of a particular condition on
surfacethanks for all you help
kk
- Original Message -
From: "Douglas Greve"
To: "Kushal Kapse"
Cc: freesurfer@nmr.mgh.harvard.edu
Sent: Tuesday, May 29, 2012 9:
uld i do tht in matlab.
for eg: a voxel (12, 24, 64) would be what and how on its surface?
please let me know
thanks
kk
- Original Message -
From: "Douglas N Greve"
To: "Kushal Kapse"
Cc: freesurfer@nmr.mgh.harvard.edu
Sent: Friday, May 25, 2012 5:59:59 PM
Sub
x27; is it talking about as i have clearly imported
qdec.table.dat
thanks
kk
- Original Message -
From: "Douglas Greve"
To: "Kushal Kapse"
Cc: freesurfer@nmr.mgh.harvard.edu
Sent: Tuesday, May 29, 2012 6:45:07 PM
Subject: Re: [Freesurfer] fMRI time series in surfac
hi doug,
we i am working parallel with tutorial and working on our own data
- Original Message -
From: "Douglas N Greve"
To: "Kushal Kapse"
Cc: freesurfer@nmr.mgh.harvard.edu
Sent: Thursday, May 31, 2012 5:15:06 PM
Subject: Re: [Freesurfer] fMRI time series in
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