External Email - Use Caution
Hello,
Just wanted to re-circulate this – thanks again!
Best,
Panos
From: Fotiadis, Panagiotis
Date: Monday, June 10, 2024 at 10:44 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: TRACULA multiple sessions output question
Hello,
First of all
External Email - Use Caution
Hello,
First of all, thank you for the fantastic software! I have a cohort of
individuals with multiple DWI sessions each, and I have been using TRACULA with
a configuration file similar to that of Example 3 (“Cross-sectional study,
multiple diffusi
behalf of Fischl, Bruce R.,PHD
Date: Tuesday, January 23, 2024 at 12:26 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] MRIread and RAS orientation
Does fslorient resample or just change the ras2vox?
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Fotiadis, Panagiotis
Sent
MATLAB. And the
index starts from 1.
Best,
Yujing
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of Fotiadis, Panagiotis
Sent: Tuesday, January 23, 2024 1:54 AM
To
,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Fotiadis, Panagiotis
Sent: Tuesday, January 23, 2024 1:54 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] MRIread and RAS orientation
External Email - Use Caution
Hello,
I have two nifti files that are both
External Email - Use Caution
Hello,
I have two nifti files that are both in the same MNI space, the former of which
is saved in LAS orientation while the other in RAS orientation (as showcased by
the “Orientation” field of mri_info). I just wanted to verify: When loading
both o
ve.
-Paul
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Fotiadis, Panagiotis
Sent: Wednesday, September 21, 2022 5:07 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Voxel to mm coordinates
External Email - Use Caution
Hello,
I was wondering what the best wa
External Email - Use Caution
Hello,
I was wondering what the best way would be to extract the coordinates of each
voxel in my nifti volume in mm. I have used MRIread to load the nifti volume
into Matlab (=mri) and wanted to essentially create a new variable that takes
each (vox
: [Freesurfer] Cortical depth at each cortical voxel
Hi Panos,
Please see my responses interleaved.
Best,
Iman
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Fotiadis, Panagiotis
Sent: Monday, April 25, 2022 10:48 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Cortical depth at
To: Freesurfer support list
Subject: [External] Re: [Freesurfer] Cortical depth at each cortical voxel
Of course! Please let me know if you have any questions about the toolbox.
Best,
Iman
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Fotiadis, Panagiotis
Sent: Thursday, April 21
-boun...@nmr.mgh.harvard.edu
On Behalf Of Fotiadis, Panagiotis
Sent: Thursday, April 21, 2022 11:48 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Cortical depth at each cortical voxel
Hi FS experts,
I was wondering whether there was a way to assign each cortical voxel within
the T1w
External Email - Use Caution
Hi FS experts,
I was wondering whether there was a way to assign each cortical voxel within
the T1w (volumetric) scan an index corresponding to its “cortical depth.” I
have essentially taken the cortical ribbon .mgz file, assigned each cortical
voxe
or
0*offset+1*slope = slope
If you add a covariate, then the contrast would be [0 0 1]
On 8/11/2020 3:13 AM, Fotiadis, Panagiotis wrote:
External Email - Use Caution
Hi Doug,
That’s extremely helpful, thank you! And just to verify:
1. Since I have 1 group and I just want to compare
gz --o my.glm --surf fsaverage lh
On 8/10/2020 1:29 AM, Fotiadis, Panagiotis wrote:
External Email - Use Caution
Hello FS experts,
I have a cohort of subjects for whom I created cortical thickness and T1w/T2w
signal ratio surface maps, projected them to fsaverage’s surface, smoothed
th
External Email - Use Caution
Hello FS experts,
I have a cohort of subjects for whom I created cortical thickness and T1w/T2w
signal ratio surface maps, projected them to fsaverage’s surface, smoothed
them, and then created average thickness and T1w/T2w maps using mris_preproc.
vnew = zeros(size(v))
left_hippo_ind = find(v == 17);
for i=1:length(left_hippo_ind)
vnew(i) = i
end
On Mon, 8 Jul 2019,
Fotiadis, Panagiotis wrote:
> Hi Bruce,
>
> Thanks for your response! Within aseg, however, there is a group of
d.edu on behalf of Bruce
Fischl" wrote:
Hi Panos
I'm not sure I understand. Isn't that already what the aseg is? E.g.
voxel intensity 17 means left hippocampus?
Bruce
On Sun, 7 Jul 2019, Fotiadis,
Panagiotis wrote:
>
> Hell
Hello,
I was wondering whether there is a way to assign a different intensity value on
each voxel within a parcellation file (such as aseg.mgz). What I’m essentially
trying to do is create a file (using the aseg.mgz file as a template) where
each voxel represents a different ROI. I can think of
RAGE. That automatically outputs a quantitative T1 map using
the two inversion technique. The results are much more accurate than using
multiple flip angles
On 8/8/18 5:00 PM, Fotiadis, Panagiotis wrote:
Hello,
I am interested in doing some T1-mapping analyses on some ex vivo brains. We
have
Hello,
I am interested in doing some T1-mapping analyses on some ex vivo brains. We
have collected flash sequences under multiple flip angles (5, 10, 15, 20, 25
and 30). How would you suggest that I proceed? Should I use the mri_ms_fitparms
to come up with the T1 maps for each subject and then
Bruce Fischl
Sent: Thursday, August 2, 2018 11:13:02 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Ex vivo segmentations
yes, use vol2surf. I'm not sure what you want to do with the results, but
certainly matlab will give you the max flexibility
On Thu, 2 Aug 2018,
Fotiadis, Panag
AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Ex vivo segmentations
Hi Panos
we typically use mri_expand to move the surface inwards and outwards, then
sample with the resulting surfaces.
cheers
Bruce
On Thu, 2 Aug 2018, Fotiadis, Panagiotis
wrote:
>
> Hi Bruce,
>
>
> I had
lf of Fotiadis, Panagiotis
Sent: Monday, July 30, 2018 4:33 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Ex vivo segmentations
Cool. Thanks again!
Panagiotis Fotiadis
Senior Imaging Research Technologist
J. P. Kistler Stroke Research Center, Department of Neurology
Massachusetts Ge
Bruce Fischl
Sent: Monday, July 30, 2018 4:29:35 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Ex vivo segmentations
as I said, I don't think I would trust the ex vivo thicknesses. Definitely
not in an absolute sense
On Mon, 30 Jul 2018,
Fotiadis, Panagiotis wrote:
>
&g
t: Re: [Freesurfer] Ex vivo segmentations
Hi Panos
I think you can trust the white surface (more or less), it's the pial
that is tougher. So you might sample say 1mm out from the white and not
use the pial at all
cheers
Bruce
On Mon, 30 Jul 2018, Fotiadis, Panagiotis wrote:
>
> Hi Bruce,
n Mon, 30 Jul 2018, Fotiadis, Panagiotis wrote:
>
> Hi Bruce and Doug,
>
>
> I have processed a few ex vivo brains with the help of the ex vivo freesurfer
> pipeline (outlined
> in https://surfer.nmr.mgh.harvard.edu/fswiki/ExvivoRecon), and have extracted
> their cortical
Hi Bruce and Doug,
I have processed a few ex vivo brains with the help of the ex vivo freesurfer
pipeline (outlined in https://surfer.nmr.mgh.harvard.edu/fswiki/ExvivoRecon),
and have extracted their cortical thickness. So far the range of the cortical
thicknesses have been approximately betwe
essor (--pvr) in mri_glmfit (and the
whole process might be iffy). why not just analyze the lesion load vs mean
cortical thickness for an ROI?
On 5/31/18 3:07 PM, Fotiadis, Panagiotis wrote:
Hi Doug,
No worries at all! Thanks for your input, I will go ahead and do that.
In addition to calculating
-3869
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of Fotiadis, Panagiotis
<mailto:pfotia...@mgh.harvard.edu>
Sent: Friday, May 25, 2018 10:
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Fotiadis, Panagiotis
Sent: Friday, May 25, 2018 10:49:10 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Regional comparisons between cortical thickness and white
matter hyperintensity
Hello,
I'm inter
Hello,
I'm interested in looking into the association of cortical thickness and white
matter hyperintensity from a regional perspective. Specifically, I would like
to create a figure that depicts in which ROIs does cortical thinning correlate
significantly with increased white matter hyperinte
Just wanted to re-circulate this.
Thanks in advance!
Panos
Panagiotis Fotiadis
Research Technologist II
J. P. Kistler Stroke Research Center
Massachusetts General Hospital
175 Cambridge Street, Suite 300
Boston, MA, 02114
T: (617) 643-3869
From: Fotiadis
Hello FS team,
Is there any way to download FreeView as a standalone application on a Windows
computer, or would I need to download freesurfer as a whole and then VPN?
Thanks in advance!
Panos
Panagiotis Fotiadis
Research Technologist II
J. P. Kistler Stroke Research Center
Massachusetts Genera
file. Does that work for you? This is not an atlas per se (ie, it is not
what is used when creating the aseg)
On 03/15/2017 02:10 PM, Fotiadis, Panagiotis wrote:
> Hi FS team,
>
> I was wondering whether you know where I can find the MNI305 altas
> (with labels that correspond to cor
Hi FS team,
I was wondering whether you know where I can find the MNI305 altas (with labels
that correspond to cortical/subcortical parcellations). I have found the
average MNI305 brain under the $FREESURFER_HOME directory, but if I'm not
mistaken this is just the average brain and not the labe
/2017 01:18 PM, Fotiadis, Panagiotis wrote:
> Hi Doug and Bruce,
>
> I was wondering whether you know where I can download the version 6
> mris_preproc!
>
> Thanks in advance,
> Panos
>
> Panagiotis Fotiadis
> Research Technologist II
> J. P. Kistler Stroke Resear
Hi Doug and Bruce,
I was wondering whether you know where I can download the version 6
mris_preproc!
Thanks in advance,
Panos
Panagiotis Fotiadis
Research Technologist II
J. P. Kistler Stroke Research Center
Massachusetts General Hospital
175 Cambridge Street, Suite 300
Boston, MA, 02114
T: (61
Hi FS Community,
Does the "Total cortical white matter volume" parameter in the aseg.stats file
represent the total wm volume in the brain?
Thank you in advance,
Panos
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Great, thanks Bruce!
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
[fis...@nmr.mgh.harvard.edu]
Sent: Friday, September 27, 2013 9:36 AM
To: pfot...@nmr.mgh.harvard.edu
Cc: freesurfer@nmr.mg
Ok, thanks for your reply!
Best,
Panos
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
[fis...@nmr.mgh.harvard.edu]
Sent: Friday, July 26, 2013 12:35 PM
To: Fotiadis, Panagiotis
Cc
26, 2013 12:18 PM
To: Fotiadis, Panagiotis
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] HypoIntense Lesions
Hi Panos
when you run it with the orig you are getting voxels that happen to have
an intensity of 77 and have nothing to do with lesions. Run it on the
aseg
Bruce
On Fri, 26
a way to get clusters with
orig.mgz as input?
Thank you for your time.
Panos
From: Fotiadis, Panagiotis
Sent: Monday, June 10, 2013 4:03 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] HypoIntense Lesions
Great, thank you!
Panos
Actually, never mind, I found a way through bet!
Panos
From: Fotiadis, Panagiotis
Sent: Wednesday, July 24, 2013 10:08 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Binary mask of the skull
Hi,
I was wondering whether there was a command (or a flag in
Hi,
I was wondering whether there was a command (or a flag in a command such as
mri_binarize) that can give me the binary mask of my subject's skull. I was
thinking of creating a binary ask of the subject's brain and then one of the
brain and the skull and subtracting them, but I was wondering
] Skull stripped MNI305
yes, mni305
doug
On 07/22/2013 04:28 PM, Fotiadis, Panagiotis wrote:
> Thanks Doug, that looks great! In addition, is the specific fsaverage brain
> in the MNI space?
>
> Panos
>
> From: freesurfer-boun...@n
: Monday, July 22, 2013 12:24 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Skull stripped MNI305
Try $SUBJECTS_DIR/fsaverage/mri/brain.mgz
doug
On 07/19/2013 03:06 PM, Fotiadis, Panagiotis wrote:
> Hi,
>
> I was wondering if there is a skull stripped version of the file
>
Hi,
I was wondering if there is a skull stripped version of the file
/usr/local/freesurfer/stable5_0_0/average/mni305.cor.mgz stored anywhere. I
tried applying bet and mri_watershed on the mni305.cor.mgz file (with different
frequencies as well) but there were still parts of the skull showing.
: [Freesurfer] Motion Correction Options
On 07/18/2013 10:13 AM, Fotiadis, Panagiotis wrote:
> Hi,
>
> I had two questions concerning motion correction:
>
> 1) Besides the motion correction pipeline followed in the recon-all process,
> is there any other motion correctio
Hi,
I had two questions concerning motion correction:
1) Besides the motion correction pipeline followed in the recon-all process, is
there any other motion correction pipeline that is available for use?
2) If I have only one scan is there a way to apply motion correction on it?
Because from wh
ur time and help!
Best,
Panos
From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Wednesday, July 17, 2013 11:54 AM
To: Fotiadis, Panagiotis
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] SWI acquisition question
Hi Panos
sorry, I think this is pretty far outside our expe
:00 PM
To: Fotiadis, Panagiotis
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Motion correction in recon-all
Hi Panos,
The motion correction itself is carried out using the mri_robust_template
binary. The motion correction step also includes an mri_convert command to
conform the
Hi FS Community,
I was wondering which command(s) is(are) being used in the "Motion Correction"
part of the recon-all process, to merge the mri/orig/XXX.mgz files and correct
for any motion.
Thank you for your time!
Best,
Panos
___
Freesurfer mailing
: [Freesurfer] HypoIntense Lesions
Hi Panos, I don't know an automatic way to do it. You could label it by
hand on tkmedit or freeview.
doug
On 06/10/2013 03:31 PM, Fotiadis, Panagiotis wrote:
> Hi Doug,
>
> Thanks for your response, it was really helpful. In addition to the previous
...@nmr.mgh.harvard.edu]
Sent: Monday, June 10, 2013 12:18 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] HypoIntense Lesions
On 06/10/2013 12:12 PM, Fotiadis, Panagiotis wrote:
> Hi Doug and Bruce,
>
> Don't worry about it! Actually, Bruce, tools for labeling hypo-intense T1
f the volume (or the
volume that corresponds to each lesion)?
Thanks for your help,
Panos
From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Monday, June 10, 2013 11:52 AM
To: Fotiadis, Panagiotis
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Frees
Hi FreeSurfer Community,
I was wondering whether there is an automatic tool that outlines the
hypointense lesions in a SWI scan.
Thank you,
Panos
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Hi FreeSurfer Community,
I was wondering whether there is an automatic tool that outlines the
hypointense lesions in a SWI scan.
Thank you,
Panos
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listin
Subject: Re: [Freesurfer] Group Analysis Question
yes, I think so. Maybe others can comment.
On 06/03/2013 02:49 PM, Fotiadis, Panagiotis wrote:
> Ok, great, it seems in this case that even though the overlays in both cases
> are very similar, the kurtosis in the second analysis (Disea
] Group Analysis Question
yes
On 06/03/2013 02:26 PM, Fotiadis, Panagiotis wrote:
> I see. Would it be correct to say that better kurtosis would be illustrated
> as less significant clusters in the kurtosis.mgh overlay?
>
> Panos
>
> Fro
.
doug
On 06/03/2013 01:20 PM, Fotiadis, Panagiotis wrote:
> I see. Yes from the one hand the results that I got make a lot more sense in
> the second type of analysis, compared to the first one, however, there are
> some somewhat important difference between the two analyses. If th
AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Group Analysis Question
I would not expect them to be identical but similar. If they change a
lot there may be an issue with your data.
doug
On 6/3/13 11:11 AM, Fotiadis, Panagiotis wrote:
> Hey Doug,
>
> I have ru
Hey Doug,
I have run a group analysis on my data with two different ways. (The input is
cortical thickness.) In the first analysis, I specified 4 groups
(Diseased_Male, Diseased_Female, Healthy_Male, and Healthy_Female) whereas in
the second, just two groups (Diseased, Healthy). One of the comp
Analysis
mri_glmfit does not do it. Run mris_preproc. See the tutorial
doug
On 05/31/2013 01:13 PM, Fotiadis, Panagiotis wrote:
> Hey Doug,
>
> Is there any need to co-register the subjects (of the two cohorts) destined
> for group analysis to the fsaverage space first in order t
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Fotiadis, Panagiotis
Sent: Friday, May 31, 2013 12:28 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Group Analysis
Thanks!
Panos
From
] Group Analysis
yes
doug
On 05/31/2013 12:16 PM, Fotiadis, Panagiotis wrote:
> Hey Doug,
>
> Great, but besides the unbalanced numbers in each cohort, the fact that we
> have a cross sectional analysis instead of a longitudinal one doesn't matter
> right? Would it be correct
e you asking whether theunbalanced design will leadto one
slope being different than another just because the numbers are
different? That is not a problem. You can simply follow the instructions
on the wiki.
doug
On 05/31/2013 11:26 AM, Fotiadis, Panagiotis wrote:
> Hey Doug,
>
>
Hey Doug,
Sorry for the overwhelming amount of questions. I wanted to confirm something.
Suppose you want to do group analysis between two groups say a healthy cohort
vs a diseased cohort. Each cohort has ~40 and ~30 subjects each (different
people), and you want to compare how for instance the
Great, thank you for your help!
Panos
From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Sent: Thursday, May 30, 2013 5:39 PM
To: Fotiadis, Panagiotis
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Correction for multiple comparisons error
Fotiadis, Panagiotis
Sent: Thursday, May 30, 2013 4:50 PM
To: Douglas N Greve
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Correction for multiple comparisons error
Great, thanks!
Panos
From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Sent
Great, thanks!
Panos
From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Sent: Thursday, May 30, 2013 4:47 PM
To: Fotiadis, Panagiotis
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Correction for multiple comparisons error
yes
On 05/30/2013 04
the --2spaces flag does not
apply)?
Best,
Panos
From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Sent: Thursday, May 30, 2013 4:29 PM
To: Fotiadis, Panagiotis
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Correction for multiple
Definitely, just uploaded it!
Panos
From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Sent: Thursday, May 30, 2013 4:10 PM
To: Fotiadis, Panagiotis
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Correction for multiple comparisons error
hmm
Hey Doug,
I was wondering whether you had a chance to give this a look!
Thanks again,
Panos
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Fotiadis, Panagiotis
Sent: Tuesday, May 28, 2013 1:38 PM
To
Hi!
I have been running the mri_glmfit-sim command to do the correction for
multiple comparisons for my group analysis and for some voxel-based thresholds
(not all) there is an error that comes up when reading the colortable from the
annotation file:
reading colortable from annotation file...
Hi FreeSurfer experts,
I was wondering whether there is an average b0 scan in the fsaverage space or
in the MNI space?
Thank you,
Panagiotis.
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Subject: Re: [Freesurfer] Correction for multiple comparisons question
On 05/13/2013 11:11 AM, Fotiadis, Panagiotis wrote:
> Thanks for the clarifications, Doug!
>
> 1) I am using FS stable version 5.0.0, so I'm assuming that the --2spaces
> flag has probably been implemented for t
du
Subject: Re: [Freesurfer] Correction for multiple comparisons question
Hi Panagiotis,
On 5/12/13 9:32 PM, Fotiadis, Panagiotis wrote:
> Hi Freesurfer experts,
>
> I was wondering about three things concerning the use of the mri_glmfit-sim
> command:
>
> 1) I tried running i
Hi Freesurfer experts,
I was wondering about three things concerning the use of the mri_glmfit-sim
command:
1) I tried running it with the --2spaces flag in order to Bonferroni correct
over the two hemispheres but it tells me that the specific flag is not
recognized. Is there another way to co
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