Hi Freesurfer experts,
I would like to register my test subjects to fsaverage and extract WM
surface parcellation info into ascii files
I think the surface registration and parcellation annotation is done
correctly:
*mri_surf2surf* --hemi lh --srcsubject MY_SBJ --sval-annot aparc
Hi I am reposting a previous message about difficulty to install Bernal's
Linear Mixed Effects Models. I am in doubt if I should log in as a guest (I
assume so). Anyway I have tried this and I get a .dmg installation file that
seems to be corrupted as it does not allow me to install.
Any help
Dear Freesurfer experts,
I have two question about my freesurfer results.
1. I performed recon-all analyses on my data and found all the data's maximal
value of cortical thickness is 5. Is there any standardization procedure in
the recon-all that normalize the maximum value to 5? In addition,
Yes, it does. However, I am able to start Freeview whiteout any argument from
matlab 2015b on Mac X 10.10.5.
If I use this commandsystem('freeview -f
/Applications/freesurfer/subjects/fsaverage/surf/lh.white’); in matlab ferview
crash, but I use this command system(‘freeview’) I am able to
sorry, I dont' think we have a binary for this, but it should be easy
enough in matlab with read_annotation
cheers
Bruce
On Wed, 16 Sep 2015, xtong wrote:
> Hi Freesurfer experts,
>
> I would like to register my test subjects to fsaverage and extract WM
> surface parcellation info into ascii
Hi Feng
I'll answer 1. and leave 2 for someone else (Doug?). We have a hard limit
on the max thickness of 5 but no lower bound other than 0 of course. This
prevents large values due to surface inaccuracies.
cheers
Bruce
On Wed, 16 Sep 2015, chenhf_uestc wrote:
Dear Freesurfer experts,
Dear Experts,
I tried to extract freesurfer cortical values for a ROI defined in a spm-vbm
analysis following the instructions
(https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness) and got
stuck at step 2. Please could you kindly assist?
[spjwker@nanlnx2 FSL]0% cd
That is not going to work because you have way more regressors than you
have data points.
doug
On 9/16/15 9:05 AM, Kallirroi Retzepi wrote:
> Hello,
> I am trying to run glm-fit on a total of 36 subjects - there are 8
> categorical variables (group, smoking, gender etc) and one continuous
>
Hi, freesurfer developers.
In some cases, I found that the recon-all script stops after running
mris_remove_intersection.
Here's an example of the recon-all.log in those cases:
---
Hello,
I am trying to run glm-fit on a total of 36 subjects - there are 8
categorical variables (group, smoking, gender etc) and one continuous
(age).
I want to test group effect, regressing out all other variables.
There are (correct me if I am mistaken)
- 256 classes (2^8)
- 256 *(1+1)=512
Dear Experts,
I need some help regarding saving the brain images in Freesurfer/Qdec please:
1) Can I save the brain regions shown in Qdec group analysis as other files and
view them in MRIcroN etc or does it only allow us to save the images as tiff
files (inflated medial, inflated lateral,
Please change the subject of your message to "Problem installing installing
Freesurfer on Mac ".
-Jorge
De: pablo najt
Para: "freesurfer@nmr.mgh.harvard.edu"
Enviado: Miércoles 16 de septiembre de 2015 3:32
Asunto: [Freesurfer]
For #2, that option won't do anything, but it probably needs to be there.
On 9/16/15 8:28 AM, Bruce Fischl wrote:
Hi Feng
I'll answer 1. and leave 2 for someone else (Doug?). We have a hard
limit on the max thickness of 5 but no lower bound other than 0 of
course. This prevents large values
you don't have write permission to that folder. Get write permission or
put the reg file in a different place
On 9/16/15 9:45 AM, Lim, Lena wrote:
Dear Experts,
I tried to extract freesurfer cortical values for a ROI defined in a
spm-vbm analysis following the instructions
Hi Lena, QDEC does not have that much functionality, so you may have to
move to tksurfer or freeview. More answers below.
On 9/16/15 10:05 AM, Lim, Lena wrote:
Dear Experts,
I need some help regarding saving the brain images in Freesurfer/Qdec
please:
1) Can I save the brain regions shown
Dear Jorge, I am testing 3 groups (HC, BD, relative) and want to apply your
model. Now I am in doubt if I would be able to use qdec? Or if this instead
will not be viable as I have 3 groups is not possible with qdec?ThanksPablo
Date: Thu, 10 Sep 2015 13:44:36 +
From: jbernal0...@yahoo.es
please remember to cc the list, thanks. Also remember to include
previous correspondence. 50 is still greater than 36 so that won't work.
You can probably get away with 4, maybe 6.
On 09/16/2015 11:53 AM, Retzepi, Kallirroi wrote:
> So I should:
> 1. keep in the FSGD file only the relevant
not possible with qdec
On 09/16/2015 11:29 AM, pablo najt wrote:
>
> Dear Jorge, I am testing 3 groups (HC, BD, relative) and want to apply
> your model. Now I am in doubt if I would be able to use qdec? Or if
> this instead will not be viable as I have 3 groups is not possible
> with qdec?
>
Hi Anastasia,
How the script "dmri_pathstats" compute the weighted FA, MD, AD, and RD values?
I checked the command "dmri_pathstats" inside the file "trac-all.log" but I was unable to figure out how this weighting is working. Is it by multiplying the mean DTI metrics by the number of voxel?
note that bbregister does not output "xfm" files but either
tkregister-style .dat files and .lta files.
You can use lta_convert to convert to/from different formats. You can
convert the .dat file to an lta (or output an lta directly), and convert
the fsl to lta. Then use mri_concatenate_lta to
it seems that it stopped after a cp, not after the
mris_remove_intersection call, no?
On Wed, 16 Sep 2015,
Nakyoung Kim wrote:
Hi, freesurfer developers.
In some cases, I found that the recon-all script stops after running
mris_remove_intersection.
Here's an example of the recon-all.log
give it the .img as input, not the .hdr. Note that using analyze is not
recommended though! It doesn't store direction cosines so you will never be
sure that there is no left/right flip unless you have a fiducial marker
like a vitamin E tablet
cheers
Bruce
On Wed, 16 Sep 2015, A-reum Min
Dear freesurfer experts,
I want to concatenate *.xfm transformation from bbregister with *.mat from
flirt. For that I need to convert .xfm to .mat. Any idea how can that be done?
Thanks,
Sneha
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Thanks.
On 09/16/2015 08:26 AM, Bruce Fischl wrote:
> sorry, I dont' think we have a binary for this, but it should be easy
> enough in matlab with read_annotation
>
> cheers
> Bruce
> On Wed, 16 Sep 2015, xtong wrote:
>
>> Hi Freesurfer experts,
>>
>> I would like to register my test subjects to
Thanks!
On Tue, Sep 15, 2015 at 6:21 PM, Douglas N Greve
wrote:
> check out this page
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
>
>
>
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