commandline:
mri_glmfit --glmdir $SUBJECTS_DIR/qdec/rmanova/ --y
$SUBJECTS_DIR/81kids_template/GLMprep/40kids-lh.thickness-rmanova.sm10.mgh
--fsgd $SUBJECTS_DIR/qdec/rmanova/2014.03.27-40kids-rmanova.fsgd doss --C
$SUBJECTS_DIR/qdec/rmanova/C-pre-vs-post.mtx
terminal output:
gdfReadHeader: rea
Sorry, I had a typo in the fsgd file. This is the correct command line and
terminal output:
mri_glmfit --glmdir $SUBJECTS_DIR/qdec/rmanova/ --y
$SUBJECTS_DIR/81kids_template/GLMprep/40kids-lh.thickness-rmanova.sm10.mgh
--fsgd $SUBJECTS_DIR/qdec/rmanova/2014.03.27-40kids-rmanova.fsgd doss --C
$
Hello,
As a PhD student, I often use Freesurfer software and more precisely QDEC. A
great question arises in connection with my last work. After drawing ROIs, I
extricated values thanks to a " .levels" and a creation of a "stat" folder for
each participant (aparcstat2table).
My question is : c
Hi Bruce,
Thanks very much for your email. Yes, I want to color each area with the
same color accroding the Z scores, and on the fsaverage surface. I have one
solution which transfer Z scores to RGB for displaying, but I think that
solution would not be suitable for cases with both positive and ne
hi
can we use mris_make_face_parcellation for fMRI data? or is there any way to do
random volumetric parcellation for fMRI?
and if you can advise how to generate .tri file
many thanks..
fati
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Hi fati
the tri files are just pre-generated super-sampled icosahedra. Not sure
what you mean about using it for fmri data. Certainly you can use it to
parcellate the cortex from structural data and then average fmri data
within each parcel - is that what you mean?
cheers
Bruce
On Tue, 28 Mar 2
Dear Freesurfer experts,
Does anyone have any experience on surface PVC in DTI? Concretely, I'm
analysing cortical mean diffusivity (all on surface) and I am wondering whether
the PVC pipeline for PET (petsurfer) would work on that case.
Thanks for your help,
Edu V.
_
Hi Marine, I'm having a hard time following what you are trying to do.
It sounds like you have done a thickenss analysis where you have found
some clusters, but after that I'm not sure what you are asking. Please
elaborate.
doug
On 3/28/17 6:07 AM, Lisa Delalande wrote:
Hello,
As a PhD st
Thank you, Dr. Greve.
when I ran >2000 subjects in Version 5.3, I received this error message
"##ERROR: gdfReadV1: the number of inputs in FSGD file exceeds the maximum
allowed 2000##"
In your previous post about mri_glmfit,
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-September/0
version 6 should be able to go up to 20,000
On 03/28/2017 11:45 AM, Wang, Xin wrote:
> Thank you, Dr. Greve.
> when I ran >2000 subjects in Version 5.3, I received this error message
> "##ERROR: gdfReadV1: the number of inputs in FSGD file exceeds the maximum
> allowed 2000##"
> In your previou
I'm not sure what's in your FSGD file, but you design matrix has 41
columns and your contrast matrix has 80. I'm guessing that you have 40
subjects and that you created the contrast matrix based on DODS and not
DOSS (see the web page on the rmanova about creating contrasts)
On 03/28/2017 03:
Try annotval2surfoverlay.m in v6. If you don't have v6, you can get it
from here
https://gate.nmr.mgh.harvard.edu/safelinks/greve/annotval2surfoverlay.m
On 03/27/2017 05:47 PM, Bruce Fischl wrote:
> so you want to color each parcellation unit with the same color on say
> the fsaverage surface
This is how it should work:
WM edits in the base should affect surfaces in the base, these surfaces
should be used as initialization for the long processing and fix most of
the things there. If not , you need to edit the cross, because WM edits
are copied into long from cross.
Using the -us
Hello is it possible to just create the left hemisphere with white and grey
matter intact?
Youssif AlKheder
Youssif Alkheder
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The i
do you mean the subject only has a left hemi or that you just don't want
to process the right hemi? If the latter, then you can specify -hemi lh
On 03/28/2017 02:16 PM, yusif Al-kheder wrote:
> Hello is it possible to just create the left hemisphere with white and grey
> matter intact?
>
> Yous
can you explain more about what you are trying to do?
On Tue, 28 Mar 2017,
yusif Al-kheder wrote:
> Hello is it possible to just create the left hemisphere with white and grey
> matter intact?
>
> Youssif AlKheder
>
> Youssif Alkheder
> ___
> Freesurf
Yes it's the latter would the command be mri2mesh -hemi lh *subject name *nii
file?
Youssif Alkheder
> On Mar 28, 2017, at 2:38 PM, Douglas N Greve
> wrote:
>
> do you mean the subject only has a left hemi or that you just don't want
> to process the right hemi? If the latter, then you can s
what is mri2mesh? If it is not our program, then you're on your own
On 03/28/2017 03:04 PM, yusif Al-kheder wrote:
> Yes it's the latter would the command be mri2mesh -hemi lh *subject name *nii
> file?
>
> Youssif Alkheder
>
>> On Mar 28, 2017, at 2:38 PM, Douglas N Greve
>> wrote:
>>
>> do y
Sorry for the confusion I got mixed up between simnibs and FreeSurfer, how
would I be able to recreate just the left hemisphere of the brain using
FreeSurfer?
Youssif
> On Mar 28, 2017, at 3:05 PM, Douglas N Greve
> wrote:
>
> what is mri2mesh? If it is not our program, then you're on your
Hello,
i am on el capitan 10.11.6 , XQuartz 2.7.8
I named the old Applictions/freesurfer directory something else and
installed freesurfer 6.0 and sourced through the script, i also changed the
subject directory
but otherwise i think this is a clean install of FS 6.0
I am running trac-all -p
This error is related a new security feature implemented in OS X El Capitan:
https://support.apple.com/en-gb/HT204899
You should not be getting this error with version FS6.0, but if you are
you can always get around it by disabling SIP:
http://osxdaily.com/2015/10/05/disable-rootless-syste
I will try to disable SIP
(although i dont want to restart the system because i am curious if this XL
defect will ever be corrected running 80 plus hours now... lol)
attached is the trac -all.log
On Tue, Mar 28, 2017 at 12:40 PM, Z K wrote:
> This error is related a new security feature implem
use -hemi lh when running recon-all
On 03/28/2017 03:09 PM, yusif Al-kheder wrote:
> Sorry for the confusion I got mixed up between simnibs and FreeSurfer, how
> would I be able to recreate just the left hemisphere of the brain using
> FreeSurfer?
>
> Youssif
>
>> On Mar 28, 2017, at 3:05 PM, D
Thanks for the response. I ran the command again with FWHM 6, but am getting a
'MatrixAlloc(2368,100): allocation failed' error.
mri_gtmpvc --i OutBrick_run_008.nii --reg template.reg.lta --psf 6 --seg
gtmseg.mgz --default-seg-merge --o gtmpvc.output
This is the output log file-
$Id: mri_
Thanks for the log file. I believe this is a real bug on OSX platforms.
I should have a fix by tomorrow.
-Zeke
On 03/28/2017 03:46 PM, VA Research wrote:
> I will try to disable SIP
>
> (although i dont want to restart the system because i am curious if this
> XL defect will ever be corrected ru
Dear FS experts:
How can I get the whole cerebral WM and cortex volume.
I am using following command:
asegstats2table --subjects 10001 --segno 2 3 41 42 24 --tablefile
10001_WB_table
It shows that no 2,3, 41,42 segment NO, however, they can be found in
the FreeSurferColorLUT.txt
file.
thanks
L
Don't use those IDs. Just run it with a single ID (eg, 17). The ouput
file will then have a bunch of other columns called CortexVol,
SubCortGray, CerebralWhiteMatter, etc
On 03/28/2017 04:01 PM, shi yao wang wrote:
> Dear FS experts:
> How can I get the whole cerebral WM and cortex volume.
>
>
disabled SIP got it working
briefly why would SIP (files system not accessible) halt the trac-all?
On Tue, Mar 28, 2017 at 12:59 PM, Z K wrote:
> Thanks for the log file. I believe this is a real bug on OSX platforms.
> I should have a fix by tomorrow.
>
> -Zeke
>
> On 03/28/2017 03:46 PM, VA
freesurfer depends on certain environment variables to run properly, but
SIP prevents the passing of those environment variables at runtime,
namely LD_LIBRARY_PATH. This causes the error.
I have uploaded a fix to our server. If SIP was still enabled, running
'sudo -E fs_update' would update a s
thanks! after the trac-all prep is done
i would like to re enable the SIP , update FS
and give it a try!, I'll let you know if it works ok
thanks again for all your help!!!
On Tue, Mar 28, 2017 at 2:50 PM, Z K wrote:
> freesurfer depends on certain environment variables to run properly, but
>
Hi Mailing List,
If you are comparing two matlab based linear mixed effects models (vertex-wise)
with the same number of random effects (e.g. model with random effect for time
vs. model with random effect for age at baseline), which segmentation should
you use to estimate the parameters for bot
dear freesurfer experts：
I ran my subjects and i found there were lots of pial leave in the
brainmask and affects the cortical surface, by following the troubleshooting
tutorial i use the g-cut flag, the pial was cut while some brain matters were
cut, too, and i found in my data fix the c
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