Hi Doug,
Thank you for the custom permutation script; it is very helpful.
However, it is still not clear how to use mri_mcsim to create tables with
different thresholds. I understand how to use it to restrict the search space
and how to use it on different subjects, but I don't see any option
Hi Janani, if you want help, please provide more complete information.
Eg, what command was not found? What is the terminal output?
On 09/13/2017 07:07 AM, M Janani wrote:
> No.
> When we ran the unsetenv FS_LOAD_DWI, we got command not found error.
>
> Thanks,
> Janani
>
> -Original
On 09/13/2017 12:59 PM, Alexopoulos, Dimitrios wrote:
> For further clarification, what are the main differences between the '
> BrainSegVol' and eTIV'.
>
> I understand the eTIV is determined from amount of scaling in the talariach
> transformation file and is not a voxel count. Does it
There is actually an option called --thresh where you can give it a
threshold to use. Somehow it did not make it onto the help docs
On 09/13/2017 11:39 AM, Jahn, Andrew wrote:
> Hi Doug,
>
> Thank you for the custom permutation script; it is very helpful.
>
> However, it is still not clear how
For further clarification, what are the main differences between the '
BrainSegVol' and eTIV'.
I understand the eTIV is determined from amount of scaling in the talariach
transformation file and is not a voxel count. Does it include extra axial CSF?
BrainSegVol is total aseg/aparc voxel count
Yes, that should work, except you will need to add --perm-resid. See the
--help
On 09/13/2017 02:33 PM, Martin Juneja wrote:
> Hi experts,
>
> To calculate simulations on LGI measures, I ran:
> mri_glmfit-sim --glmdir lh.MEQ_LGI.glmdir --sim perm 1000 3 permcsd
> --sim-sign abs --cwpvalthresh
Thank you Dr Bruce,
The stat values for every BA are generated using the command
mris_anatomical_stats. I found this command in the stats file for one of the
BAs.
In this stats file I see values for gray matter volume, thickness ,... etc.
If I move SUV map or FA map to surface using the
you should be able to use mris_anatomical_stats I believe
cheers
Bruce
On Wed, 13 Sep
2017, John Anderson wrote:
Thank you Dr Bruce,
The stat values for every BA are generated using the command
mris_anatomical_stats. I found this
command in the stats file for one of the BAs.
In this stats
Hi Jake
if you upload a subject and send us the voxel coords you are looking at
one of us will take a look
cheers
Bruce
On Wed, 13 Sep 2017, Jake Rieke wrote:
We are using Freesurfer v6.0
Biomedical Engineer, Brain Rehabilitation Research CenterMalcolm Randall VA
Medical Center, 1601 SW
Bruce,
I've uploaded one of our subjects to the FileDrop
http://gate.nmr.mgh.harvard.edu/filedrop2/?p=31qhh4docnq
The areas we're concerned with are temporal regions. [151,150,131] is one
instance of these unknown entorhinal regions.
Aidan
On Wed, Sep 13, 2017 at 2:43 PM, Bruce Fischl
It seems that this command doesn't accept input files. Are there any commands
in Freesurfer that can do similar job?
> Original Message
> Subject: Re: [Freesurfer] BA Labels
> Local Time: September 13, 2017 3:11 PM
> UTC Time: September 13, 2017 7:11 PM
> From:
mri_segstats with the --slabel option
On 09/13/2017 03:14 PM, John Anderson wrote:
> It seems that this command doesn't accept input files. Are there any
> commands in Freesurfer that can do similar job?
>
>
>> Original Message
>> Subject: Re: [Freesurfer] BA Labels
>> Local
Dear FS experts,
I have SUV maps for subjects within two groups. I moved these SUV maps into
surface then I concatenated the images in the order of two groups then I used
the compiled file in a glm analysis to check the difference between the two
groups.
I aim to use V1 Atlas to derive the SUV
Hi John
if you have run recon-all you should have a bunch of ex vivo BA labels in
the label dir.
cheers
Bruce
On Wed, 13 Sep 2017, John Anderson wrote:
Dear FS experts,
I have SUV maps for subjects within two groups. I moved these SUV maps into
surface then I
concatenated the images in the
Hi experts,
To calculate simulations on LGI measures, I ran:
mri_glmfit-sim --glmdir lh.MEQ_LGI.glmdir --sim perm 1000 3 permcsd
--sim-sign abs --cwpvalthresh .05
But it gives error: ERROR: design matrix is not orthogonal, cannot be used
with permutation.
I came across a post where its
Hello,
I ran a longitudinal analysis cortical structure in Freesurfer version 5.3. I'd
now like to compute hippocampus subfields using the new beta version of the
"Segmentation of hippocampal subfields and nuclei of the amygdala" tool
dear mr. greve,
dear fs community,
REGARDING CSF and CSFVol:
i still don’t understand the whole CSF and CSFVol thing.
it seems to be impossible that CSFVol ist the volume of the CSF label because
CSFVol is bigger than CSF.
additional to this aspect the value of the CSF label is a volume
Hi Douglas,
As you recommended, I ran unsetenv FS_LOAD_DWI command in the terminal,
but I got Bash command not found error.
Could you please help me in resolving this error.
Thanks,
Janani
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
No.
When we ran the unsetenv FS_LOAD_DWI, we got command not found error.
Thanks,
Janani
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: 12 September 2017 21:42
To:
We are using Freesurfer v6.0
Biomedical Engineer, Brain Rehabilitation Research Center
Malcolm Randall VA Medical Center, 1601 SW Archer Road, Gainesville, FL
32608
Phone: 1-352-376-1611 ext. 5249, E-mail: jakeri...@gmail.com
On Thu, Sep 7, 2017 at 6:17 PM, Douglas N Greve
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