Dear Doug,
Unfortunately, it doesn't make a difference if I'm using a dot or comma or
simply type in 2 or 3 as a threshold. The terminal output always shows me the
converted version with a comma 2.3 -- 2,3 or 2 -- 2,0 which is not recognized
by the command.
Maybe I have to change the default
Dear Bruce!
Thanks a lot for the response. I try to get an idea about the minimal time
needed to get the subcortical volumes.
Best wishes,
Luke
Re: [Freesurfer] subcortical segmentation only
Bruce Fischl Wed, 10 Dec 2014 05:22:18 -0800
Hi Luke
you can run -autorecon1 and -autorecon2 if
Dear Remi!
Would you mind to send me the new mri_tessellate?
Best wishes,
Luke
Re: [Freesurfer] use of high res T1 for subcortical segmentation
Remi Gau Wed, 10 Dec 2014 06:29:04 -0800
Hey,
Someone corrects me if I am wrong, but it seems that the number of
vertices currently allowed
Dear experts,
I had a question regarding the output of my Qdec analyses. When I run a
Monte Carlo Z simulation on my results, I get the following output:
# ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZCWP
CWPLowCWPHi NVtxs Annot
12.930 94685921.76-48.9
Thank you very much!
The map opened by rtview seems correct. As a new learner of retinotopic
analysis, I have one more basic quesion: What do the three files
(imag.nii.gz, real.nii.gz and fsig.nii.gz) represent? Hope some experienced
one can reply me!
Mingxia
On Thu, Dec 11, 2014 at 12:14 AM,
Hello,everyone
Your reply said I can't use alphasim with qdec.By the way ,Could I use
alphasim in other ways in FreeSurfer,for example command line ?
Best regards.
Xin-Fa Shi.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
mri_extract_label
Usage: mri_extract_label [options] input volume label 1 label 2 ...
output name
Options:
-s sigma apply a Gaussian smoothing kernel
-t xform file apply the transform in xform file to extracted
volume
-exit_none_foundexit 1 if label(s) not
if you tell us what hardware/software platform you want it for we can
post the current version, which I think has a limit of 10,000,000
vertices and twice that many faces. Presumably that is enough?
cheers
Bruce
On Thu, 11
Dec 2014, lukas.sch...@ukb.uni-bonn.de wrote:
Dear Remi!
Would
Hello,
Has anyone had a chance to look at this? I still haven't been able to solve
the problem.
Thanks!
Lindsay
On Mon, Dec 1, 2014 at 2:41 PM, lindsay hanford lindsay.hanf...@gmail.com
wrote:
Hello Freesurfer Experts!
I am encountering the dreaded mri_glmfit error: matrix is
Hi Bruce!
I am working on a Mac, OS 10.10.1, FS version:
freesurfer-Darwin-lion-stable-pub-v5.3.0
All the best,
Luke
Re: [Freesurfer] use of high res T1 for subcortical segmentation
Bruce Fischl Thu, 11 Dec 2014 05:36:52 -0800
if you tell us what hardware/software platform you want it
Hi Bruce,
Thank you very much for this information. Deleting the rh.sphere file and
re-running -make all did fix this issue and the brain now looks great. I
wanted to confirm this so that if anyone else has the same issue they will
know what might work to fix it.
I had a question about the
Hi Ezra
I have no idea why this would have happened. That's plenty of disk space
and RAM.
sorry
Bruce
On Thu, 11 Dec 2014, Wegbreit, Ezra wrote:
Hi Bruce,
Thank you very much for this information. Deleting the rh.sphere file and
re-running -make all did fix this issue and the brain now
imag is the imaginary (sine) part of the signal
real is the real part (cosine)
fsig is the significance (-log10(p)) where p is computed from an F test
of the real and imag components
On 12/11/2014 05:09 AM, zhang mingxia wrote:
Thank you very much!
The map opened by rtview seems correct. As
Hi Mohamad - What you did with your binarization was that you lowered the
threshold all the way to zero, i.e., included all the voxels that had any
probability 0 to be in the tract. This means that you included more
voxels than the default, which is to threshold at 20% of the max
probability.
Hi Cat - Currently the only stats that are produced automatically are
FA/MD/RD/AD. But if you have volumes of other parameters, you could always
use the tracts from trac-all and extract mean values of those parameters
within each tract with something like mri_segstats, fslastats, etc.
Best,
Hi Amanda - The final masks used by tracula are derived from the
structural and not the diffusion data, i.e., they are the whole-brain
FreeSurfer segmentations (from mri/aparc+aseg.mgz) mapped onto diffusion
space and dilated slightly. It may be that there was something wrong with
the
Hi - Any format that can be handled by mri_convert (run mri_convert
--help to see the list) can be run through freesurfer and tracula. If
mri_convert doesn't work on your format, you'll have to find a converter
that can convert it into one of the formats on that list (like nifti).
Hope this
Hi Anri - This is not a command itself, it's an option of the trac-all
command. So you need to run:
trac-all -qa -c the_name_of_your_configuration_file
Or, if you just run the entire preprocessing:
trac-all -prep -c the_name_of_your_configuration_file
then the motion QA
Hi Emad - Those missing voxels in the mask in the middle of the corpus
callosum could very well be what's not allowing that tract to be
preconstructed.
The file used to create the brain mask from the freesurfer recon is not
mri/brainmask.mgz, but mri/aparc+aseg.mgz, which is mapped to
Hi Thomas - No bother at all! If you search for the word error in your
trac-all.log, you'll see that it couldn't find the MNI template, which
means that some of the pre-processing steps did not complete. You can
either remove the mnitemp line from your configuration file (so that it
uses the
Hi - The fact that the first 2 parameters are all zero (translation and
rotation) means that it didn't find the file that it expects to derive
those parameters from. Currently, this is the eddy_correct log file that
contains the affine registration matrices from each DWI volume to the
first
Hi Kate - The screenshot looks more like a low-b image from a diffusion
scan than a field map. In case this helps, the phase map data will have
either 2 volumes (2 phase maps acquired at different echo times) or 1
volume (the difference of 2 such phase maps).
Best,
a.y
On Thu, 11 Dec 2014,
I am sorry, I am a bit confused. What am I supposed to be specifying under
the b0mlist and b0plist?
I thought that it was the B0 low-b image from diffusion.
Thank you!
On Thu, Dec 11, 2014 at 2:25 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
Hi Kate - The screenshot looks more
No, those are field maps used to correct for inhomogeneities in the main
magnetic field (which in MRI lingo is referred to as the B0 field, not to
be confused with the b=0 images). You can skip that correction (you have
to skip it if you don't have field maps).
On Thu, 11 Dec 2014,
Your FSGD file appears to have been made under windows or using an
editor that is not simple text. The contrast matrix looks ok.
doug
On 12/01/2014 02:41 PM, lindsay hanford wrote:
Hello Freesurfer Experts!
I am encountering the dreaded mri_glmfit error: matrix is
ill-conditioned or
No
On 12/11/2014 06:48 AM, Xinfa Shi wrote:
Hello,everyone
Your reply said I can't use alphasim with qdec.By the way ,Could I use
alphasim in other ways in FreeSurfer,for example command line ?
Best regards.
Xin-Fa Shi.
___
Freesurfer
You should run mri_glmfit-sim from the command line passing it the QDEC
glmdir as output and the same thresholds you used in QDEC. This will
create several output files one of which will include the means inside
each cluster. Run it with --help to get more info.
doug
On 12/10/2014 12:16 PM,
Once you have the CWP image loaded, the Threshold value sets the CWP.
doug
On 12/03/2014 10:12 AM, Claire Morley wrote:
Hi Freesurfer Experts,
I was wondering if there is a way for me to adjust the default CWP of
p .01 to p .05 on Qdec? I saw that it is possible using cwpvalthresh
.05 with
Hi all,
I'd like to know whether there is a command line that I could use to extract
the level of smoothness in my data, the same way qdec does it automatically,
i.e. writing the fwhm.dat that is then used to define which precomputed CSD
file should be used in the Monte Carlo Simulation. Is
Hi Marie, you can use mris_fwhm, something like
mris_fwhm --i y.mgh --subject fsaverage --hemi lh --cortex --dat fwhm.dat
doug
On 12/11/14 8:40 PM, Marie Schaer wrote:
Hi all,
I'd like to know whether there is a command line that I could use to extract
the level of smoothness in my data,
Thanks, Anastasia.
I'm worried about that a quality assessment step is not run because there
are no presentation about -qa when I type trac-all in terminal (other
steps are presented.)
Do you mean QA step will be run even if no mention about it?
Thanks in advance,
Anri
Awesome Doug, that's exactly what I wanted, thanks a lot for the prompt answer!
Have a nice evening,
Marie
On Dec 11, 2014, at 6:38 PM, Douglas Greve gr...@nmr.mgh.harvard.edu
wrote:
Hi Marie, you can use mris_fwhm, something like
mris_fwhm --i y.mgh --subject fsaverage --hemi lh
I tried to run trac-all -qa -c the_name_of_my_configuration_file after trac-all
-corr -c the_name_of_my_configuration_file, but it failed.
I pasted the log below and do you have any advices?
Thank you,
Anri
[watanabeanris-Mac-Pro:~] watanabeanri% trac-all -corr -c
33 matches
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