Dear Freesurfers,
I am setting up the configuration file to run Tracula preproc. I have some
doubts on some variables...
*
pedir: on my DTI protocol I have "PhaseEncodingDirection": "j-",so I assume it
is AP
*
epifactor : I took it from "EchoTrainLength": 48
*
echospacing: shall I take it
Dear Freesurfers,
I am setting up the configuration file to run Tracula preproc. I have some
doubts on certain variables...
*
pedir: on my DTI protocol I have "PhaseEncodingDirection": "j-",so I assume it
is AP
*
epifactor : I took it from "EchoTrainLength": 48
*
echospacing: shall I take
Hello Freesurfers,
I am trying to launch trac-all -prep on Ubuntu 22 but I am getting this error:
-bash: /home/local/PARTNERS/vb922/freesurfer/bin/trac-all: /bin/tcsh: bad
interpreter: No such file or directory
Can you please help me figure out what is going on?
Thank you,
Valeria
_
Dear Freesurfers,
Do you know how to fix this error in trac-all? (I'm using Ubuntu 18.04)
#@# Inter-subject registration Wed Dec 4 22:37:52 CET 2024
/home/vbarletta/ants-2.5.4/bin/antsRegistrationSyNQuick.sh -d 3 -m
trac/R01121_SCAN/dmri/dtifit_FA.nii.gz -f
/home/vbarletta/tester/freesurfer/trc
Dear Freesurfers,
I am trying to run trac-all on Freesurfer 7.4.1 but I am obtaining this output:
eddy_openmp --imain=trac/R01121_SCAN/dmri/dwi_orig_las.nii.gz
--mask=trac/R01121_SCAN/dmri/lowb_orig_las_brain_mask.nii.gz
--bvecs=trac/R01121_SCAN/dmri/dwi_orig_las.bvecs
--bvals=trac/R01121_SCAN/
urfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
Sent: Tuesday, February 23, 2021 9:10 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] WM volume
Yes, that is the right value. We changed the name of it in more recent versions
to CerebralWhiteMatter
On 2/22/2021 4:12 PM
Dear Freesurfers,
In what file inside the patient_name/stats folder do I find the total white
matter volume?
In the file "aseg.stats" there is something called lh/rh "cortical white matter
volume", is that the right value to look at?
Thank you,
Valeria Barletta, MD
Massachusetts General Hospita
, 2021 5:24 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] question on GLM
0 0 0 0 0.5 0.5 -0.5 -0.5
will compute control-patient slope accounting for gender
On 1/8/2021 7:49 AM, Barletta, Valeria wrote:
Good morning Freesurfers!
I am building a GLM with 4 classes (control_F
Good morning Freesurfers!
I am building a GLM with 4 classes (control_F, control_M, patient_F, patient_M)
to check for differences in cortical thickness between patients and control
accounting for the effect of gender and age on cortical thickness.
How should my contrast be?
Thanks a lot,
Val
Good evening Freesurfers!
I am building a GLM with 4 classes (control_F, control_M, patient_F, patient_M)
to check for differences in cortical thickness between patients and control
accounting for the effect of gender and age on cortical thickness.
How should my contrast be?
Thanks a lot,
Vale
Hello Freesurfers,
I need to perform a GLM in 25 patients versus 19 controls but I need the
comparison to be done only on normal appearing cortex (in patients), thus
excluding cortical lesions.
* Is it possible to concatenate binary masks projected to surface? What
command shall I use?
*
that all you need?
On 5/19/2020 11:36 AM, Barletta, Valeria wrote:
Dear Freesurfers,
We need to analyze PET data after correcting for partial volume effect in the
cortex, white matter and subarachnoid space. Is Freesurfer's partial volume
correction working on all these areas or only the
Dear Freesurfers,
We need to analyze PET data after correcting for partial volume effect in the
cortex, white matter and subarachnoid space. Is Freesurfer's partial volume
correction working on all these areas or only the grey matter volume and
surface? Is there a way to use gtmseg on the white
Dear Freesurfers,
We need to analyze PET data after correcting for partial volume effect in the
cortex, white matter and subarachnoid space. Is Freesurfer's partial volume
correction working on all these areas or only the grey matter volume and
surface? Is there a way to use gtmseg on the white
Dear Freesurfers,
I am trying to apply the bias correction on the 7T MEMPRAGE through the unified
segmentation algorithm on SPM12, as a primary step to do the submillimetric
recon on Freesurfer, as you suggested here:
https://surfer.nmr.mgh.harvard.edu/fswiki/HighFieldRecon
For some reason, I ca
e for the single voxel?
From: Greve, Douglas N.,Ph.D.
Sent: Thursday, December 5, 2019 12:40 PM
To: Barletta, Valeria ; Freesurfer support list
Subject: Re: [Freesurfer] Question on GLM - correlation
On 12/4/19 11:51 AM, Barletta, Valeria wrote:
> Ok I did it
From: Barletta, Valeria
Sent: Friday, September 27, 2019 12:30 PM
To: freesurfer-boun...@nmr.mgh.harvard.edu
Subject: question on mris_calc
Dear Freesurfers,
I am trying to perform an operation with .mgh files by using mris_calc. This is
my operation
Dear Freesurfers,
We need to install the last version of Freesurfer, but we need to keep the wm
edits that we made with version 5.3
How can this be done? Is there any specific command?
Thanks a lot,
Vale
___
Freesurfer mailing list
Freesurfer@nmr.mgh.ha
Dear Freesurfers,
Where in the /mri/stats folder can I find the total cortical surface in mm2?
Is it in the ?h.aparc.stats or in the ?h.curv.stats?
Thank you,
Valeria
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.har
: [Freesurfer] problem with reconstruction
Hi Vale
do you want to tar, gzip and ftp us that entire subject dir so we can
take a look?
cheers
Bruce
On Wed, 19 Jun 2019, Barletta, Valeria wrote:
>
> Dear Freesurfers,
>
>
> I am having issues with a reconstruction which is giving me giant de
4 Jun 2019,
Barletta, Valeria wrote:
>
> Dear Freesurfers,
> I am getting this type of error in the Terminal when I open my images on
> Freesurfer:
>
> MRISreadNewCurvature: incompatible vertex number in file
> /autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv
Dear Freesurfers,
I am getting this type of error in the Terminal when I open my images on
Freesurfer:
MRISreadNewCurvature: incompatible vertex number in file
/autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3/MSTAT_MS_001_B/surf/lh.curv
No such file or directory
could not re
Dear Freesurfers,
Is there a way to turn N .mgh files in to a single output .mgh file in which
each vertex is the mean of the corresponding vertices in my input files?
For example, input lh.Ctrl029.fsaverage.mgh , lh.Ctrl030.fsaverage.mgh ,
lh.Ctrl031.fsaverage.mgh , lh.Ctrl032.fsaverage.mgh
it looks like a volume in that it has columns,
row, and slices, but the underlying data is interpreted as a
surface-based map
On 5/22/19 12:33 PM, Barletta, Valeria wrote:
>
> That is a great solution, thank you!
>
>
> How exactly can I apply this whole thing to .mgh surface-bas
/dist/freesurfer/6.0.0-patch/hcp/
On 5/23/19 2:59 PM, Barletta, Valeria wrote:
>
> Dear Freesurfers,
>
> I tried to launch "recon-all -all" for an high-resolution 7T 0.75
> isotropic MEMPRAGE, but the process got stuck on a XL defect in rh,
> numbered 54, measuring over
Dear Freesurfers,
I tried to launch "recon-all -all" for an high-resolution 7T 0.75 isotropic
MEMPRAGE, but the process got stuck on a XL defect in rh, numbered 54,
measuring over 20,000 voxels!!
How do I check, and eventually fix, this defect?
Thank you,
Vale
_
...@nmr.mgh.harvard.edu
on behalf of Greve, Douglas N.,Ph.D.
Sent: Wednesday, May 22, 2019 10:47:19 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] question on surface analysis
On 5/22/2019 10:19 AM, Barletta, Valeria wrote:
Dear Freesurfer,
I have a surface file containing values of a cortical
Dear Freesurfer,
I have a surface file containing values of a cortical myelination index
(rh.MS075_CME.mgh), and a lesion mask (rh.surf_CL03.mgh)
What I need to do is:
- Masking the surface file with the lesion mask, to create a new lesion mask
that contains the myelination index values from
hiing below 1 (eg, 0.5)
On 5/20/19 2:40 PM, Barletta, Valeria wrote:
>
> Dear Freesurfers,
>
> I am trying to obtain clusters of vertices whit a certain value over a
> threshold inside a lesion mask projected to the surface, with the command:
>
>
> mri_surfcluster --subject
Dear Freesurfers,
I am trying to obtain clusters of vertices whit a certain value over a
threshold inside a lesion mask projected to the surface, with the command:
mri_surfcluster --subject MS075_R01_07_R1year --hemi lh --in
lh.MS075_R01_07_R1year.subjspace.mgh --surf lh.pial --mask
lh.surf_m
You will need to create your own color table
On 2/19/19 3:21 PM, Barletta, Valeria wrote:
>
> Dear Freesurfers,
>
> I have a 3D volume mask of cortical lesions with 8 different clusters
> (8 cortical lesions).
>
> I projected this mask to the cortex and obtained a .mgh file wi
Dear Freesurfers,
I have a 3D volume mask of cortical lesions with 8 different clusters (8
cortical lesions).
I projected this mask to the cortex and obtained a .mgh file with the command
vol2surf:
mri_vol2surf --src $path_to_lesion/$subj/combined-$lesion.nii.gz --out
$path_to_output/$subj/su
2:05:58 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] surf2vol ERROR
you have a typo. It's not "-identify" it is "--identity"
On Sun, 17 Feb
2019, Barletta, Valeria wrote:
>
> Sure... There is also a screenshot attached
>
>
> panarea:/autofs/sp
eesurfer support list
> Subject: Re: [Freesurfer] surf2vol ERROR
> Hi Vale
>
> mri_surf2vol is to take take from the surface to the volume within one
> subject. Why do you need a trgsubject? You can compute the registration
> with e.g. bbregister. Maybe I'm not understanding wh
ster. Maybe I'm not understanding what you are trying to
do
cheers
Bruce
On Sat, 16 Feb 2019, Barletta, Valeria wrote:
>
> Dear all,
>
> I am trying to register surfaces to a volume by this command:
>
> mri_surf2vol --subject MS089_R01_29 --hemi rh --rh.MS089_R01_29.su
Dear all,
I am trying to register surfaces to a volume by this command:
mri_surf2vol --subject MS089_R01_29 --hemi rh --rh.MS089_R01_29.subjspace.mgh
--hemi lh --surfval lh.MS089_R01_29.subjspace.mgh --o CME_MS089_R01_29.nii.gz
--merge combined-CL.nii.gz --trgsubj MS089_R01_29
And am obtainin
own. Use FreeSurferColorsLUT.txt as your template
On 2/15/19 1:08 PM, Barletta, Valeria wrote:
Ok thank you, it works but there is a problem... The command mris_label2annot
requires a ColorTable file.
As I tried to use FreeSurferColorLUT.txtI got a list of all regions I did
not need.
What kin
ile ???
You can make separate labels (mri_cor2label with --surf option), then
use mris_label2annot
On 2/14/19 3:32 PM, Barletta, Valeria wrote:
>
> Yes sure,
> I need to extract values from discrete cortical lesions, but I have
> masks of all lesions together projected to the cortical surfac
cortical lesions mask --> annotation file ???
not sure what you mean, can you elaborate?
On 2/14/19 2:05 PM, Barletta, Valeria wrote:
>
> Dear Freesurfers,
>
> I need to extract annotation files from my cortical lesion masks
> projected to the surface.
>
> Do you know
Dear Freesurfers,
I need to extract annotation files from my cortical lesion masks projected to
the surface.
Do you know whether this is possible?
Thank you,
Valeria
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harv
permutation if you are using such
a low clusterwise threshold. See
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm
The monte carlo simulation is not valid at such low thresholds
On 2/14/19 11:50 AM, Barletta, Valeria wrote:
>
> Dear Freesurfers,
>
> I am perf
Dear Freesurfers,
I am trying to run the command trac-all -prep -c but I'm getting this error:
error while loading shared libraries: libnetcdf.so.6: cannot open shared object
file: No such file or directory
Can you help me?
Thank you,
Vale
___
0
1 0 -1 0 0 0
thank you,
Valeria
From: Barletta, Valeria
Sent: Friday, December 7, 2018 2:23:10 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: glm analysis
Dear Freesurfers,
I am trying to run a GLM analysis with 3 groups (1)long disease duration MS,
2
Dear Freesurfers,
I am trying to run a GLM analysis with 3 groups (1)long disease duration MS,
2)short disease duration MS, 3)healthy controls) and 1 variable (age).
According to the formula provided on freewiki:
N classes (N of variables + 1),
is this contrast matrix correct?
1 -1 0 0 0 0
/Ctrl034_R01_07/surf/overlay/rh.T1_mp2rage_depth0.5_fwhm3.mgh
to the surface then recreated the surfaces after editing?
cheers
Bruce
On Mon, 5 Nov 2018, Barletta, Valeria wrote:
> Dear FreeSurfers,
> I am trying to apply surface processes to concatenate my cohort, but for some
> subjects I a
Dear FreeSurfers,
I am trying to apply surface processes to concatenate my cohort, but for some
subjects I am getting this error:
mri_surf2surf --srcsubject Ctrl034_R01_07 --srchemi rh --srcsurfreg sphere.reg
--trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg --tval
/autofs/space/alicu
b etc
from copy paste that mess things up.
Best, Martin
On Wed, 2018-08-29 at 13:51 +, Barletta, Valeria wrote:
> Dear Freesurfers,
> I am trying to re-launch a longitudinal time point after edits by
> using the command:
>
> recon-all -long MS069_R01_01_Bay8_3T_03102014.lon
Dear Freesurfers,
I am trying to re-launch a longitudinal time point after edits by using the
command:
recon-all -long MS069_R01_01_Bay8_3T_03102014.long.MS069_base MS069_base -all
But I am obtaining this type of error:
Unmatched ".
I also tried to launch it on Launchpad but I have an error al
3:58 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] brain parenchymal fraction
you'll have to be more specific about what "brain surface contour" means.
On 7/26/18 3:46 PM, Barletta, Valeria wrote:
> Dear Freesurfers,
> I need to extract the brain parenchy
Dear Freesurfers,
I need to extract the brain parenchymal fraction to check brain atrophy in my
patients.
The BPF is defined as "the ratio of brain parenchymal tissue volume to the
total volume contained within the brain surface contour".
In the text file aseg.stats, I found this info:
# Measur
Hi Freesurfers,
We are trying to apply the PVC process to our PET images.
We proceeded through step3 as indicated on fswiki, and obtained the files:
- gtm.nii
- nopvc.nii
- mgx.gm.nii
How can we obtain the corrected uptake values from these files?
Can we obtain a corrected volume file for voxel bas
Hi Freesurfers,
I sent this help request some days ago but had some problems in receiving the
reply because of mailing list subscription issues...
Sorry for submitting this request again:
I used the command mris_preproc to have all the surfaces of my cohort
concatenated in fs average and I obtai
Hi Freesurfers,
I used the command mris_preproc to have all the surfaces of my cohort
concatenated in fs average and I obtained this error message from several of my
subjects:
#@# 3/11 MS073_R01_05/Bay8_3T/fs/MS073_R01_05 Fri May 11 14:24:58 EDT 2018
--
---
mri_s
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