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Hi Freesurfer Experts,
I am designing some new hardware for a mini-cluster running Freesurfer
and other neuroimaging toolboxes and wanted to better understand
requirements from Freesurfer.
1) Is there a minimum amount of ram per core that is needed/
Do you correct for multiple contrasts and if not, is there any particular
reason why not.
Thanks,
Ajay
On Wed, Aug 3, 2016 at 2:45 AM, Ajay Kurani
wrote:
> Hi Doug,
>Thank you very much for your update regarding this issue.
>
> 1)Just curious, will LGI be included in this report
ocation,I can upload the stats file if that is easier.
Thanks,
Ajay
On Sat, Sep 17, 2016 at 10:03 PM, Ajay Kurani
wrote:
> Hi Anderson,
>Thanks for the help. When viewing my results they looked very
> strange. Upon further investigation it looks as though the mask I supplied
cortical
thickness, would the mask need to be a volume file which is between the
pial and white matter surfaces or would it just need to be the pial surface
(lh.pial / rh.pial), or something else? Any suggestions on the best way to
create this?
Thanks,
Ajay
On Sat, Sep 17, 2016 at 1:03 PM, Ajay Kurani
Hello Freesurfer Experts,
I was running permutation simulations on cortical thickness data and I
had an issue with non-orthogonal covariates with mri_glmfit-sim -perm. I
then tried FSL's PALM which is an extension of randomize to calculate
threshold free stats. I saved the output as logp(which
Hi Doug,
Thanks for the follow up. Do you recommend using a covariate such as
mean thickness or is a covariate not necessary for cortical thickness
analysis?
Thanks,
Ajay
On Thu, Sep 8, 2016 at 2:00 PM, Ajay Kurani
wrote:
> Hi Freesurfer Experts,
>I am comparing a control group
Hi Freesurfer Experts,
I am comparing a control group and 2 patient groups (HC vs Group1, HC vs
Group2, Group1 vs Group2). I am interested in seeing what is the most
appropriate covariate to use for both a cortical thickness analysis and LGI
analysis. I do not expect major changes in brain sha
et the 5% FPR. One question is if the non-orthogonal data
affects this analysis as well for this model?
Thanks,
Ajay
On Thu, Aug 25, 2016 at 12:18 PM, Ajay Kurani
wrote:
> Hi Freesurfer Experts,
>I am trying to use freesurfer's mri_glmfit-sim tool to run permutation
> testing on c
Hi Freesurfer Experts,
I am trying to use freesurfer's mri_glmfit-sim tool to run permutation
testing on cortical thickness data (as recommended by Doug in my previous
post:
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg48653.html )
Most of the tutorials I found were not relat
long tails are not taken into account?
Thanks,
Ajay
On Mon, Aug 1, 2016 at 11:43 PM, Ajay Kurani
wrote:
> Hello Freesurfer Experts,
>Recently there were two article published regarding clusterwise
> simulations for volumetric fmri analyses and potential errors for
> underestimat
Hello Freesurfer Experts,
Recently there were two article published regarding clusterwise
simulations for volumetric fmri analyses and potential errors for
underestimating clusterwise extent thresholds.
1) http://www.pnas.org/content/113/28/7900.full.pdf?with-ds=yes
2) biorxiv.org/content/early
to if A > B or B>A? I
guess with the blue and red color bars I thought directionality was
implied.
Or would one need to do a subsequent one tailed test (Pos A>B; Neg B>A)d in
order to determine directionality of thickness results?
Thanks,
Ajay
On Mon, May 9, 2016 at 3:11 PM, Ajay Ku
hanks,
Ajay
On Sun, May 8, 2016 at 7:33 PM, Ajay Kurani
wrote:
> Hi Doug,
>Thanks for the explanation. In using p=0.05 with my thickness files
> (smoothed 15mm translates to FWHM=21mm), I looked at fwhm21/abs/th13/ cdf
> file.
>
> In regards to Qdec , if I choose abs, do
n Friday, May 6, 2016, Ajay Kurani wrote:
> Hi Doug,
>I wanted to figure out what is the minimum cluster extent for a given
> monte carlo simulation (ie when you choose p=0.5/T=1.3). I saw the
> following tutorial :
> https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteC
asure (ie measuring the
smoothness of the input thicknesss image)? Is there a way to see what
cluster minimum is used?
Thanks,
Ajay
On Thu, May 5, 2016 at 3:49 PM, Ajay Kurani
wrote:
> Hi Doug,
>Thanks for the clarification. So in the case of cortical thickness,
> qcache
rh.pial?
Best,
Ajay
On Thu, May 5, 2016 at 2:53 PM, Ajay Kurani
wrote:
> Hi Doug,
>Thanks for the quick reply.
>
> Is there a difference from qcache/mris_fwhm with mris_smooth and
> mri_surf2surf -fwhm ? If so, which is recommended for cortical thickness
> analysis?
Hi Doug,
Thanks for the quick reply.
Is there a difference from qcache/mris_fwhm with mris_smooth and
mri_surf2surf -fwhm ? If so, which is recommended for cortical thickness
analysis?
Thanks,
Ajay
On Wed, May 4, 2016 at 11:18 PM, Ajay Kurani
wrote:
> Hi Freesurfer Experts,
>J
(based on the earlier email) so I am not sure if there is a freesurfer tool
to check the smoothness level or if the qcache smoothness levels make sense
for cortical thickness.
Thanks,
Ajay
On Wed, May 4, 2016 at 5:41 PM, Ajay Kurani
wrote:
> Hi Freesurfer Experts,
>I am trying t
Hi Freesurfer Experts,
I am trying to understand the difference between qcache option and
mris_fwhm and which is appropriate for a cortical thickness analysis. I
processed my files with qcache and have lh.thickness.fsaverage.fwhm15.gii
(converted) files. I used an afni tool SurfFWHM to estima
?
Thanks,
Ajay
On Thu, Apr 21, 2016 at 9:15 AM, Ajay Kurani
wrote:
> Hi Freesurfer Experts,
>
> I have used freesurfer smoothed images (lh.thickness.fsaverage.fwhm15.gii)
> to perform a cortical thickness analysis. I used qdec with a surface-based
> morphometric analysis to compare tw
Hi Freesurfer Experts,
I have used freesurfer smoothed images (lh.thickness.fsaverage.fwhm15.gii)
to perform a cortical thickness analysis. I used qdec with a surface-based
morphometric analysis to compare two groups. As my discrete fixed factor I
used group membership. As Nuisance factors I used
Hello Freesurfer Experts,
I am having a bit of trouble with the hippocampal subfield analysis
using the Freesurfer 6.0 program.
My data is organized as /AnalysisFolder/Group/Subject/Anatomical/SUB_FS ..
where SUBJECTS_DIR=/AnalysisFolder/Group/Subject/Anatomical/ and my subject
specific folder
Thanks for clarifying Bruce.
Just curious is there any freesurfer commands to convert this internal
surface file into a .mgh file for external use? For example mri_surf2vol
or mri_surf2label etc?
Thanks,
Ajay
On Wed, Apr 6, 2016 at 5:17 PM, Ajay Kurani
wrote:
> Hello Freesurfer Expe
Wed, Apr 6, 2016 at 12:59 PM, Ajay Kurani
wrote:
> Hello Freesurfer Experts,
>As a follow up question for bbregister, I used the --tmp and --epi-mask
> options, but I did not see a mask in the directory. I wanted to see if
> there is any way to output the B0/edge excluded epi-
ile a label,
annotation surface etc?
Thanks,
Ajay
On Mon, Mar 21, 2016 at 1:03 PM, Ajay Kurani
wrote:
> Hi Freesurfer experts,
>I wanted to create a Freesurfer surface on some of the aseg ROIs. I
> was able to run mri_tesselate, mris_smooth, mris_inflate and mris_sphere
> some o
, Ajay Kurani
wrote:
> Hi Freesurfer Experts,
>I was running bbregister and came across an issue. I have used
> previous versions of bbregister (FS 5.3.0 with spm8) with the --init-spm at
> it worked perfectly for a specific subject.
>
> I recently installed FS dev 6.0 w
Hi Freesurfer Experts,
I was running bbregister and came across an issue. I have used previous
versions of bbregister (FS 5.3.0 with spm8) with the --init-spm at it
worked perfectly for a specific subject.
I recently installed FS dev 6.0 with SPM12b and ran bbregister --init-spm
option with th
to flip these thickness files to the opposite hemisphere
(files already warped to symmetric space)
Thanks,
Ajay
On Mon, Mar 28, 2016 at 5:05 PM, Ajay Kurani
wrote:
> Hi Doug,
>I attached a .png file to show an example. The Yellow outline is the
> right and left caudate surface. Th
, causing the same pixel
shift issue???
Based on what I can find is it best to run the following:
surfreg --s sub001 --t fsaverage_sym --lh --xhemi
Would this flip my lh.thickness.fwhm10.fsaverage_sym.mgh file to the
other hemisphere?
Thanks,
Ajay
On Mon, Mar 28, 2016 at 1:30 PM, Ajay Kurani
wrote
Hello Freesurfer Experts,
I processed all of my brains through freesurfer 6.0 dev for Linux and
warped the surfaces to standardized space. For a handful of subjects I
want to perform a left right flip of the cortical thickness files
(standardized space) for a group analysis. What is the best
Hi Freesurfer experts,
I wanted to create a Freesurfer surface on some of the aseg ROIs. I was
able to run mri_tesselate, mris_smooth, mris_inflate and mris_sphere some
of the subcortical volumes for creating a surface.
The mri_sphere had a big chunk that was deleted and so I wanted to run
mri
Hello Freesurfer experts,
I am using the nightly build of Freesurfer 6.0 (Dec 18, 2015) on Ubuntu
14.04 with a high resolution image (0.5mm isotropic). I set
OMP_NUM_THREADS=16 and then passed the -openmp 16 and -itkthreads 16 flags
in my autorecon 2 line command. Autorecon1 and the beginning
; for this dataset, they will not be geometrically acccurate in the vicinity
> of the huge (>200,000 vertices!) defects.
>
> cheers
> Bruce
>
>
> On Wed, 2 Dec 2015, Ajay Kurani wrote:
>
> Hi Bruce,
>>
>> The template is the ICBM 2009b nonlinear
id running it's normal genetic
> algorithm as it would take days (or weeks) to finish, since it scales with
> the square of the number of vertices. I haven't figured out what is going
> wrong yet, but hopefully will have a code fix soon.
>
> cheers
> Bruce
>
>
>
> On
gt;
>> cp ?h.orig.nofix ?h.orig
>>
>> cp ?h.inflated.nofix ?h.inflated
>>
>>
>>
>> with ? being l or r depending your hemisphere. After the fixing stage the
>> surfaces got damaged somehow, therefore you have to recreate it them. I’m
>> not
>
> Hi Ajay
>
> are you sure you didn't run out of disk space? That error is a sanity
> check on the surfaces that should never occur
>
> cheers
> Bruce
> On Sun, 29 Nov 2015, Ajay
> Kurani wrote:
>
> > Hello Freesurfer experts,
> >I am trying to
:48
> An: Freesurfer support list
> Betreff: Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure
> (mris_euler_number) using high res (0.5mm isotropic) T1 image
>
> Hi Ajay
>
> are you sure you didn't run out of disk space? That error is a sanity
> check on the surfaces that shou
Hello Freesurfer experts,
I am trying to run Freesurfer 6.0 beta (downloaded 10/15/15 version)
with the -hires flag to process an MNI template image which is 0.5mm
isotropic. Stage 1 ran well and on stage 2 there is an error during
pocessing:
Command run:
recon-all -s ICBM -autorecon2 -openmp
Hi Bruce,
1) I was also concerned 3mm may be too thick but I will try a few subjects
to see how it goes.
2) Hi Eugenio I wanted to see if you can give a bit of insight into the
hippocampal issue.
3) Bruce, sorry for the confusion. I was referring to sqrt(T1w*B1 x
T2w*B1) ~ B1 bias field estimat
think that using these
scans would be ok since the bias field is supposed to be smooth, however I
wanted to see your thoughts regarding using the T2 scans of this resolution
for the B1 bias-field estimation.
Any guidance to any of these questions would be much appreciated!
Sincerely,
Ajay Kurani
Hello Freesurfer experts,
I wanted to see if the nightly dev builds of freesurfer are v6.0 with
the new hippocampal subfields or if that download is in another section?
If so can you send me the proper download location? Also is CUDA support
still at 5.0 with this version or is there any update
Hello Freesurfer experts,
I have a question regarding the use of the -T2 and -FLAIR flags in
freesurfer. I have 2 scans: 1 whole brain MPRAGE and 1 partial brain FLAIR
(bottom of cerebellum/brainstem gets cut off on some subjects). I wanted
to see if freesurfer would still be able to run corre
Dear Freesurfer users,
I wanted to see if anyone knows what part of the file NIFIT header
mri_vol2vol or mri_convert uses to write transform information from
register.dat acquired from bbregister? I used the following commands to
register the anatiomcal brain.mgz to the last time point of my EPI
Dear Freesurfer users,
I had a question regarding how to combine multiple register.dat files
into one file. Essentially, I have a T1 image which I created masks for in
native space. I then import the T1 image into freesurfer and run through
the recon-all pipeline. Subsequently, I use bbregist
Hi all,
I used freesurfer to process my anatomical scans, followed by BBregister
to align my resting state scan to the anatomical and finally afni to
process the resting state fmri scans. After recon-all I used bbregister:
*bbregister -s ${sub}_FS --mov ${sub}.RS.nii --reg $sub_RS_register.dat
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