Hi there,
I have a a couple of question related to the output generated by the
‘mri_volcluster' command.
1) It seems that the command automatically assumes that my voxels are 8 mm^3.
Is there a way to specify my voxel size when I run the command?
2) The output is given in Talairach coordinat
Hi,
I'm trying to use the mri_volcluster command to make label files from a
single volume of binary voxel clusters. Once I have split the volume into
individual label files I want to convter the label files back into
individual cluster volumes (I am trying to use mri_label2vol to do this).
T
Hi,
I'm trying to use the mri_volcluster command to make label files from a single
volume of binary voxel clusters. Once I have split the volume into individual
label files I want to convter the label files back into individual cluster
volumes (I am trying to use mri_label2vol to do this). T
On 08/10/2015 10:47 AM, Morenikeji Adebayo wrote:
> Hi there,
>
> I have a a couple of question related to the output generated by the
> ‘mri_volcluster' command.
>
> 1) It seems that the command automatically assumes that my voxels are
> 8 mm^3. Is there a way to specify my voxel size when I
Hi there,
The command I submitted is:
mri_volcluster --in merged_encode_Young_NEUT_hit_V_miss_n41.nii.gz --thmin 1.3
--minsizevox 5 --sign neg --sum adebayo_young_neut_p.05 —fsaverage
How would I:
1) Specify the voxel size
2) Have the results output in MNI?
Thanks,
Keji
> On Aug 10, 2015,
Hi there,
Just following up. Any advice would be much appreciated!
Thanks,
Keji
> On Aug 10, 2015, at 1:50 PM, Morenikeji Adebayo
> wrote:
>
> Hi there,
>
> The command I submitted is:
> mri_volcluster --in merged_encode_Young_NEUT_hit_V_miss_n41.nii.gz --thmin
> 1.3 --minsizevox 5 --sign n
It will produce results in the voxel size and space of
merged_encode_Young_NEUT_hit_V_miss_n41.nii.gz
How was that file produced? What space is it in?
On 08/10/2015 01:50 PM, Morenikeji Adebayo wrote:
> Hi there,
>
> The command I submitted is:
> mri_volcluster --in merged_encode_Young_NEUT_hit_
Hi FS Community,
I am using the mri_volcluster command but for some reason the --sumfile
shows up as an unknown flag. Is there another way to get a summary text
file?
(I am using FS 5.3 stable.)
Thank you for your time!
Best,
Panos
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Hi
I have a few questions regarding the use of “mri_volcluster” for
clusterwise thresholding. Essentially, we have a volume of pvalues
obtained from a two tailed t-test comparing beta values from condition A vs
condition B.
When I ran this command:
mri_volcluster --in transformedP.nii --sum
Hello,
Does the frame flag refer to offsets? If so, would frame 5 be the same as
offset 5 (6 seconds)?
Thank you,
Dave Brohawn
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Hi
Can you please post an example of "mri_volcluster" use with fsfast?
more specifically, when i run :
mri_volcluster \
--in
/space/engram/12/users/pman/rk_fmri/Y15_111504/bold/rk_enc_sm5/RNeg_vs_Fix/sig \
--in_type bfloat \
--reg
/space/engram/12/users/pman/rk_fmri/Y15_111504/bold/rk_enc_sm
I would probably use --ocn with mri_volcluster to create a single volume
in which each voxel value is the cluster number it belongs to. Then
split them out like:
mri_binarize --i ocn.mgh --match 1 --o cluster-0001.mgh
doug
Gregory Dierksen wrote:
Hi,
I'm trying to use the mri_volcluster c
It is --sum, not --sumfile
doug
On 09/25/2013 12:44 PM, pfot...@nmr.mgh.harvard.edu wrote:
> Hi FS Community,
>
> I am using the mri_volcluster command but for some reason the --sumfile
> shows up as an unknown flag. Is there another way to get a summary text
> file?
> (I am using FS 5.3 stable.)
I see, thanks Doug!
> It is --sum, not --sumfile
> doug
>
>
> On 09/25/2013 12:44 PM, pfot...@nmr.mgh.harvard.edu wrote:
>> Hi FS Community,
>>
>> I am using the mri_volcluster command but for some reason the --sumfile
>> shows up as an unknown flag. Is there another way to get a summary text
>> f
Hello all,
I'm trying to run mri_volcluster on our third-level functional data
and one of the required flagged arguments is the register.dat file.
Our data preprocessing/registration was done in FSL, not Freesurfer,
so we don't have this particular file. Is there anything we can do to
get around t
It is more straightforward if you use -log10(p). If you want to do an
unsigned test, then run it twice, once with pos and once with neg, then
multiply the resulting cluster-wise p-values by 2.
doug
On 10/21/2014 02:11 AM, Joo Tan wrote:
>
> Hi
>
>
> I have a few questions regarding the use of “
basically, yes. It is the 0-based frame number. The time of this frame
will depend on your TR and prestim.
doug
Dave Brohawn wrote:
Hello,
Does the frame flag refer to offsets? If so, would frame 5 be the same as
offset 5 (6 seconds)?
Thank you,
Dave Brohawn
___
You are using the wrong register.dat file. Use the one in Y15_111504/bold
doug
Paymon Hosseini wrote:
Hi
Can you please post an example of "mri_volcluster" use with fsfast?
more specifically, when i run :
mri_volcluster \
--in
/space/engram/12/users/pman/rk_fmri/Y15_111504/bold/rk_enc_
Hi Huiting, you don't need to give it a register.dat. That only gives
you access to label locations of your clusters. If this is something you
want, you can use $FREESURFER_HOME/average/mni152.register.dat.
doug
Huiting Liu wrote:
> Hello all,
>
> I'm trying to run mri_volcluster on our third-le
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Hello FreeSurfer experts,
I am trying to run mri_volcluster with the following command to later create
masks of clustered regions from functional data. I get an error saying that the
option --mindistance is not recognized, even though this option is
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Dear Freesurfer support,
My name is Vicente and I have a question for you regarding mri_volcluster. I am
interested in using mri_volcluster to correct for multiple comparison after
generating a probability distribution function (pdf) via simulation t
Hello All,
I've been using fslstats to create a mask of voxels reaching a certain
threshold and then using mri_volcluster to reduce the mask down to just
clusters above 3 voxels. Now we're trying to filter them down to just those
clusters that have more than 3 contiguous voxels in a single directi
Hello,
I was wondering if there is a Freesurfer command for getting neuroanatomical
labels for the output clusters of mri_volcluster.
thank you very much for your help,
paymon
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Try --mindist not --mindistance
On 8/9/18 9:08 AM, Yagmur Ozdemir 19 wrote:
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Hello FreeSurfer experts,
I am trying to run mri_volcluster with the following command to later
create masks of clustered regions from functional data. I get an error
saying that
Does running it with --label not work?
On Mon, 31 Jul 2006, Paymon Hosseini wrote:
Hello,
I was wondering if there is a Freesurfer command for getting neuroanatomical
labels for the output clusters of mri_volcluster.
thank you very much for your help,
paymon
_
doug
i think he's asking about what you were thinking of implementing with
a similar flag to the --annot one that you added to mri_surfcluster.
frida
On Jul 31, 2006, at 5:34 PM, Doug Greve wrote:
Does running it with --label not work?
On Mon, 31 Jul 2006, Paymon Hosseini wrote:
Hello,
Oh, no that does not exist yet. There are some issues as to whether
it's really valid as the volumetric analysis that preceeds
mri_volcluster is linear whereas the aseg.mgz is produced with a
nonlinear registration. I'm looking into something intermediate that
could give you something close to th
Hi all,
I was going through the FSFAST TUTORIAL from wiki(
https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorial?action=highlight&value=TUTORIAL).
I got the follwoing error during mri_volcluster,
"NOT Adjusting threshold for 1-tailed test
ERROR: you must specify a pos or neg sign with --fwhm
To use --fwhm you have to specify the sign of the contrast (this
implements the gaussian random fields). If a sign is not given in the
wiki, can you fix it?
doug
pkun...@nmr.mgh.harvard.edu wrote:
> Hi all,
>
> I was going through the FSFAST TUTORIAL from wiki(
> https://surfer.nmr.mgh.harvard.
Nevermind, it works fine now with after i added "--sign < >" flag to the
mri_volcluster ..command.
thanks
pratap
Original Message ----
Subject: [Freesurfer] mri_volcluster --ERROR: you must specify a pos or
neg sign with --fwhm
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