The --cache is completely independent of --qcache (it was an unfortunate
name for me to give it). The --cache means that the simulations have
already been run. Think about a statistics text book that has a table of
t-values, DOF, and corresponding p-values. I created a similar table
that we d
Dear Prof. Greve
Thanks for the quick responses.
My questions are now resolved.
Here is my last question regarding permutation testing.
I cannot figure out what the '--cache' flag stands for.
I've already done my data using recon-all with '-qcache' flag.
Should I use '--cache' flag option in mri_
Hi Rebecca, this is intentional. The whole brain is divided up into left
cortical hemi, right hemi, and subcortical structures. the MNI305 is
only supposed to handle the subcortical structures. If you want a brain
volume with cortical and subcortical, you can use vlrmerge to merge the
volume,
Hi experts,
When I'm pre-processing the 4D whole brain BOLD images using "preproc-sess
-sf -mni305 -fwhm 5 -fsd bold -per-run" , the results of registration from
BOLD images to the MNI305 template are always only a small part of the
original images. I tried to use another T1_152 template instea
Does that file exist?
doug
On 7/10/13 8:25 PM, Aaron Tanenbaum wrote:
Thank you fore responding.
I ran recon-all and it worked fine. however when i run bbregister i
get an error
"ERROR: cannot find /usr/lib/fsl/etc/flirtsch/xyztrans.sch". I have
installed fsl 5.0 and FSLDIR set right
i am runn
FREESURFER_HOME should point to the absolute/full path to the
installation directory
doug
On 7/10/13 10:00 PM, Stéphane Poulin wrote:
> Hello Freesurfer experts
>
> I have just installed Freesurfer and tried to run recon-all command.
>
> I get these "command not found" errors.
>
> Any idea?
>
>
Hello Freesurfer experts
I have just installed Freesurfer and tried to run recon-all command.
I get these "command not found" errors.
Any idea?
Stephane
Last login: Wed Jul 10 21:42:55 on ttys001
[silicium:~] stephanep% cd /Volumes/Macintosh_HD_Donnees/Applications/
[silicium:/Volumes/Macintos
Thank you fore responding.
I ran recon-all and it worked fine. however when i run bbregister i get an
error
"ERROR: cannot find /usr/lib/fsl/etc/flirtsch/xyztrans.sch". I have
installed fsl 5.0 and FSLDIR set right
i am running this in ubuntu 12.04 using freesurfer 5.3. am I doing some
thing wrong
What directory are you in? Is your registration file (diff2anat.bbr.mat)
in the same directory as where you are calling the command from?
Lilla
On Wed, 10 Jul 2013, Hoptman, Matthew wrote:
Hi Lilla,
Unfortunately, when I run:
mri_vol2vol --targ ../../../cvs_avg35_inMNI152/mri/norm.mgz --m3z
Hi Lilla,
Unfortunately, when I run:
mri_vol2vol --targ ../../../cvs_avg35_inMNI152/mri/norm.mgz --m3z
../../cvs/cvs_avg35_inMNI152/final_CVSmorph_tocvs_avg35_inMNI152.m3z
--noDefM3zPath --reg diff2anat.bbr.mat --mov ../dtifit_FA.nii.gz --o
diffvol2CVS.nii.gz --no-save-reg
I now get:
Using the
Hey all, I want to announce a little tool I've been working on. I wanted
to be able to put Freesurfer stats into our REDCap databases so our
group can more easily analyze these measures against behavioral data. I
wrote a tiny little python package that you can find at
github.com/sburns/recon-st
Hi Jason
what does the aseg look like? Is that labeled as ventricle (incorrectly)?
Bruce
On
Wed, 10 Jul 2013, Jason Tourville wrote:
Hello freesurfers,
In the attached pic, the red cross hairs fall in the calcarine fissure (right
hemisphere). In this scan (and some others I've
reviewed rece
Sounds good!
Regarding creating a new volume and computing contrasts from it, what do you
mean? I didn't follow that.
Thanks!
Joe
On Jul 10, 2013, at 1:33 PM, Douglas N Greve wrote:
>
> On 07/10/2013 01:29 PM, Joseph Dien wrote:
>> Sorry, not following what you are suggesting?
>>
>> I wa
Sorry, not following what you are suggesting?
I want the second derivative for calculating the Calhoun et al 2004 derivative
boost measure.
My understanding is that to the extent that the BOLD signal deviates from the
canonical hrf, the amplitude of the primary regressor will be attenuated and
Hi Ines, there should not be any difference. You can upload the two QDEC
output folders to
https://gate.nmr.mgh.harvard.edu/filedrop2
And I'll take a look
doug
On 07/10/2013 08:13 AM, Mürner-Lavanchy, Ines wrote:
> Dear experts,
>
> is there a limitation concerning the number of variables in
I'm thinking of generating a modified beta.nii.gz file where the primary betas
have been replaced with the Calhoun et al (2004) derivative boost measure.
What do you think? Also, please note my question below about the second
derivative as it is causing me concern about my analysis. Thanks!
SURFACE INFO
type: MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE
num vertices: 143704
num faces : 287404
num strips : 0
surface area: 125661
AvgVtxArea 0.874440
AvgVtxDist 1.078393
StdVtxDist 0.419625
ctr : (0.000782013, 0.000
and how about:
mris_info s000_open_brain_sanlm_+TIR_normlalized/surf/lh.sphere
On Wed, 10
Jul 2013, fatma zribi wrote:
Dear Bruce,
this is the result:
-rwxrwxr-x 1 zribi.f scalp 5175759 Jun 21 14:57
s000_open_brain_sanlm_+TIR_normlalized/surf/lh.sphere
2013/7/10 Bruce Fischl
Hi Fa
Dear Bruce,
this is the result:
-rwxrwxr-x 1 zribi.f scalp 5175759 Jun 21 14:57
s000_open_brain_sanlm_+TIR_normlalized/surf/lh.sphere
2013/7/10 Bruce Fischl
> Hi Fatma
>
> this not what we meant. From here please run:
> cd ..
> ls -l s000_open_brain_sanlm_+TIR_**normlalized/surf/lh.sphere
>
>
Hi Aaron
the first thing you'll need to do is find an anatomical volume that is in
the atlas coordinates (or maybe is the atlas) and run recon-all on it.
Then you can run bbregister to register the time series to the recon and
mri_vol2surf to sample it onto the surface.
cheers
Bruce
On Wed
You will need to register your volume with the anatomical with
bbregister. bbregister will take a "template" which should be the time
point you used for motion correction. Then run mri_vol2surf to create a
new data set sampled on the surface
doug
On 07/10/2013 12:32 PM, Aaron Tanenbaum wrote
Hi Fatma
this not what we meant. From here please run:
cd ..
ls -l s000_open_brain_sanlm_+TIR_normlalized/surf/lh.sphere
cheers
Bruce
On Wed, 10 Jul 2013, fatma
zribi wrote:
-- Forwarded message --
From: fatma zribi
Date: 2013/7/10
Subject: Re: [Freesurfer] Fwd: how to us
Hi Bianca, it is not currently possible to this since it expects to have
one cycle duration. You can analyze them separately, then create a field
sign map outside of the regular stream.
doug
On 07/10/2013 10:58 AM, Bianca van Kemenade wrote:
> Dear Freesurfers,
>
> When I only had 3 runs of po
Hola Freesurfers,
I am new to Freesurfer and still learning the basics. I have been given a
project and have not found a way to do it. Part of this task involves
taking a 4dfp volume time series and convert it to a time series of a
surface. This 4dfp I have is a statistical analysis mapped on to a
-- Forwarded message --
From: fatma zribi
Date: 2013/7/10
Subject: Re: [Freesurfer] Fwd: how to use mris_register?
To: Bruce Fischl
Copie1/s000_open_brain_sanlm_+TIR_normlalized$ ls -l
total 704
drwxrwxr-x 2 zribi.f scalp 4096 Jul 5 17:12 bem
drwxrwxr-x 2 zribi.f scalp 4096 Ju
I meant can you run it and send us the results? If we can't open the file
it is not an FS issue, but something with the file system. Run ls -l with
the same path that you are giving mris_register
Bruce
On Wed, 10 Jul 2013, fatma zribi wrote:
Hi Bruce,
Yes i can run ls -l in the directory
Hi Bruce,
Yes i can run ls -l in the directory
2013/7/10 Bruce Fischl
> Hi Fatma
>
> are you sure you don't have a typo in the path? Can you run ls -l on that
> file?
> Bruce
>
> On Wed, 10 Jul 2013, fatma zribi wrote:
>
>
>>
>> -- Forwarded message --
>> From: fatma zribi
>> D
mri_label2label is what we would typically use. You can probably use
bbregister to generate the registration from the old session to the new
anatomicals
On Wed, 10 Jul 2013, Bianca
van Kemenade wrote:
Flag -reassign is unrecognised unfortunately when I add it to the tksurfer-sess
command I
Flag -reassign is unrecognised unfortunately when I add it to the
tksurfer-sess command I posted before. I tried it with tksurfer P2_BK rh
inflated -reassign, there at least it ran. However if I then use the
tksurfer-sess command again and load the labels I can only see that the
labels changed a bi
you can try adding -reassign, but the label must be in the same coords as
the anatomical for this to work. You'll know right away if it did or not
though
cheers
Bruce
On Wed, 10 Jul 2013, Bianca van Kemenade wrote:
Hi Bruce,
Thank you for your reply. I coregistered the new data beforehand in
Hi Bruce,
Thank you for your reply. I coregistered the new data beforehand in SPM (to
the structural of the old session). So I didn't do anything to the label. I
displayed the structural with tksurfer-sess -c eccen -fthresh 0.5 -a
rtopy.self.lh -s P2_BK (since I wanted to display my eccentricity d
On 07/10/2013 01:26 AM, amirhossein manzouri wrote:
> Dear Doug and FS experts,
> I am trying to use Xhemi tool to study asymmetry in the brain. I have
> done the exact procedure you mentioned in WiKi for a group of 40 controls.
> 1) Is lh.lh-rh.thickness.sm00.mgh the stack of voxel-wise cortical
Hi Bianca
how did you coregister the data? Did you map the label so that it is in
the coords of the new session? If so, try specifying -reassign on the
tksurfer command line. That will discard the vertex indices in the label
(which refer to the first session surfaces) and reassign vertex number
Dear Freesurfers,
When I only had 3 runs of polar angle data for retinotopic mapping, I used
for example this command to make the analysis:
mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2 -retinotopy 12
-paradigm rtopy.par -fwhm 5 -fsd bold
For some new subjects I have 3 runs of polar an
Hi Fatma
are you sure you don't have a typo in the path? Can you run ls -l on that
file?
Bruce
On Wed, 10 Jul 2013, fatma zribi wrote:
-- Forwarded message --
From: fatma zribi
Date: 2013/7/10
Subject: Re: [Freesurfer] how to use mris_register?
To: Bruce Fischl
Hi Bruce,
-- Forwarded message --
From: fatma zribi
Date: 2013/7/10
Subject: Re: [Freesurfer] how to use mris_register?
To: Bruce Fischl
Hi Bruce,
Thank you very much for your help but it still don't work.
mris_register s000_open_brain_sanlm_+TIR_normlalized/surf/lh.sphere
avg_all_subj
Rune,
I have not seen this error before. Can you please type mri_convert on
the command line and tell me what, if any, output is produced.
-Zeke
On 07/10/2013 05:14 AM, Rune Frandsen wrote:
I have just installed Freesurfer and wanted to try tkmedit
I get a Segfault error and it asked me to wr
I mean send your email to the FreeSurfer list as well so that others can
answer (which I'll do on this email).
Are you sure you don't have a typo in your command line? You typed
"normlalized" instead of "normalized"
cheers
Bruce
On Wed, 10 Jul 2013, fatma zribi wrote:
Hi Bruce,
i didn't
Dear experts,
is there a limitation concerning the number of variables in qdec (in
qdec.table.dat)?
I obtained different results when I included about 30 variables vs. only 10
variables in qdec.table.dat for exactly the same analysis, involving only 2 of
the variables (I did not include the ot
Hi list,
I have been trying to test out bias correction on hi-res post mortem
animal MRI data. (which is not going through regular FS analysis pipeline)
Is there any option for not changing the resolution ?
from mri_nu_correct.mni.log:
Original Data has (0.234375, 0.234375, 0.43) mm size a
I have just installed Freesurfer and wanted to try tkmedit
I get a Segfault error and it asked me to write to this mail.
The .xdebug_tkmedit is
tkmedit started: Wed Jul 10 10:53:23 2013
/usr/local/freesurfer/tktools/tkmedit.bin
$Id: tkmedit.c,v 1.343 2011/03/01 01:41:22 nicks Exp $ $Name: s
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