In the aseg, 24=CSF is comprised of some indeterminant ventricle space
in the middle of the brain. It is small and not well defined. In
synthseg, it represents that region but is mostly comprised of
extracerebral CSF as you have noted.
On 5/29/2025 5:24 PM, Emma Rodrigues wrote:
Exte
External Email - Use Caution
Dear FreeSurfer Experts,
I hope this email finds you well.
I'm reaching out to request clarification regarding label 24 – CSF in the
FreeSurfer software. From my observations, this label appears to correspond to
a region near the third ventricle. Ho
Douglas N. Greve
*Sent:* Tuesday, April 15, 2025 1:51 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] clarification - recon-all output data
But what are you comparing? Eg, thickness, or the white surface (somehow)?
On 4/15/2025 1:26 PM, Stefanie Bradley wrote:
Exte
Yes, you should be able to use fsaverage for your age cohort.
From: Greve, Douglas N.,Ph.D.
Sent: Tuesday, April 15, 2025 1:14 PM
To: freesurfer@nmr.mgh.harvard.edu ; Zollei,
Lilla,Ph.D.
Subject: Re: [Freesurfer] clarification - recon-all output data
I'
ch subject (in common
space?) with overlays as well.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
Sent: Tuesday, April 15, 2025 1:51 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] clarification - recon-all output
fanie
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* Tuesday, April 15, 2025 1:14 PM
*To:* freesurfer@nmr.mgh.harvard.edu ;
Zollei, Lilla,Ph.D.
*Subject:* Re: [Freesurfer] clarific
Sent: Tuesday, April 15, 2025 1:14 PM
To: freesurfer@nmr.mgh.harvard.edu ; Zollei,
Lilla,Ph.D.
Subject: Re: [Freesurfer] clarification - recon-all output data
I'm not sure I know what you mean. Why do you want to map them to fsaverage?
I'm cc'ing Lilla about the age question
O
vard.edu
on behalf of Douglas N. Greve
*Sent:* Monday, April 14, 2025 10:12 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] clarification - recon-all output data
All outputs from recon-all are in native space
On 4/12/2025 5:57 PM, Stefanie Bradley wrote:
External
hanks,
Stefanie
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
Sent: Monday, April 14, 2025 10:12 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] clarification - recon-all output data
All outputs from recon-all are in n
All outputs from recon-all are in native space
On 4/12/2025 5:57 PM, Stefanie Bradley wrote:
External Email - Use Caution
Hi there,
I wanted to clarify about the recon-all output: is it in the subject's
native space or is everything already mapped to fsaverage space?
For example, i
External Email - Use Caution
Hi there,
I wanted to clarify about the recon-all output: is it in the subject's native
space or is everything already mapped to fsaverage space?
For example, is aparc.stats based on the brain in the subject's native space or
has the cortical surfac
External Email - Use Caution
Dears,
I'm Gabriella, a PhD student in Neuroscience and Imaging.
I am currently working on coregistering anatomical scans with DTI scans (FA and
MD maps) using bbregister. However, there are some details in the pipeline that
I find unclear.
First, is
bject: Re: [Freesurfer] Clarification about .annot file format
Is this the offending line? or is there more?
value = (A * 2563) + (B * 2562) + (G * 256) + (R)
On 9/28/18 1:03 PM, Christopher Markiewicz wrote:
External Email - Use Caution
Hi Doug,
The relevant wiki page is:
tember 28, 2018 12:47:36 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Clarification about .annot file format
Thanks Chris, can you point us to the offending wiki page?
doug
On 9/28/18 12:44 PM, Christopher Markiewicz wrote:
: Friday, September 28, 2018 12:47:36 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Clarification about .annot file format
Thanks Chris, can you point us to the offending wiki page?
doug
On 9/28/18 12:44 PM, Christopher Markiewicz wrote:
External Email - Use Caution
Hi
t;
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of paul mccarthy
<mailto:pauldmccar...@gmail.com>
Sent: Thursday, September 20, 2018 11:39:53 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Clarification about .annot file format
gotten something wrong.
Best,
Chris Markiewicz
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of paul mccarthy
Sent: Thursday, September 20, 2018 11:39:53 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Clarification about .annot file format
External Email - Use Caution
Howdy,
There is a discussion regarding the .annot file format over at the nibabel
github repository, regarding the interpretation of the flag/alpha value:
https://github.com/nipy/nibabel/issues/649
If one wishes to create an .annot file with colours
correct
On 03/06/2018 01:41 PM, Avideh Gharehgazlou wrote:
> Hi,
>
> Thank you so much for the clarification, so values listed under “CWP”
> column in "mc-z.abs.th13.sig.cluster.summary" file are my corrected
> p-values to be reported? (in this case having run monte carlo for
> multiple compar
Hi,
Thank you so much for the clarification, so values listed under “CWP” column in
"mc-z.abs.th13.sig.cluster.summary" file are my corrected p-values to be
reported? (in this case having run monte carlo for multiple comparison
correction)
CONFIDENTIALITY NOTICE: This e-mail message, including
On 03/06/2018 12:03 PM, Douglas N. Greve wrote:
>
>
> On 03/06/2018 10:14 AM, Avideh Gharehgazlou wrote:
>> Hi,
>>
>> I have a 2 questions regarding properly interpreting results from
>> QDEC. Will you please clarify the following for me?
>>
>> 1. What is the difference between stats table gener
Hi,
I have a 2 questions regarding properly interpreting results from QDEC. Will
you please clarify the following for me?
1. What is the difference between stats table generated after correcting for
multiple comparisons (i.e. monte carlo), vs the stats table generated after
clicking "find clus
yes and yes
On 12/07/2017 02:23 PM, Taylor, Johnmark wrote:
> Thanks once again for all the help on this. I am running the GLM in
> native space, typically so that I can get the beta values to use in an
> MVPA analysis. So it sounds like if you specify per-run
> motion-correction and registrat
Thanks once again for all the help on this. I am running the GLM in native
space, typically so that I can get the beta values to use in an MVPA
analysis. So it sounds like if you specify per-run motion-correction and
registration, and don't tell it to resample to anything (e.g., the MNI
brain or th
Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> <https://gate.nmr.mgh.harvard.edu/filedrop2>
> www.nmr.mgh
r.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
>
>
> --
>
> Message
On 12/03/2017 06:35 PM, Taylor, Johnmark wrote:
> Hello,
>
> A few quick questions about the "Per-Run" option in preproc-sess. I
> understand that in this option, each run's images are registered to
> the middle timepoint of that run, rather than the first timepoint of
> the first run. I was w
Hello,
A few quick questions about the "Per-Run" option in preproc-sess. I
understand that in this option, each run's images are registered to the
middle timepoint of that run, rather than the first timepoint of the first
run. I was wondering, though:
1) Why is this the preferred option instead o
Hi Tamara,
this should finish the longitudinal recon-all. It picks it up from
where you edited and completes the rest. It needs to know about the name
of the time point and the name of the base to access files from there
(e.g. to map initial surfaces from base ect).
Best, Martin
On 07/24
Hello,
I have made edits to aseg files in the longitudinal outputs
(participantID.long.participantID-temp). I am beginning the reconstruction
phase and as suggested by a response to an earlier post I am running:
recon-all -long tpN1 template ID -autorecon2-noaseg -autorecon3, where tpN1
is cross-s
with 5.2 and beyond "SubcorticalGray" does not include cerebellum GM. See
http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats
On 03/10/2017 05:27 AM, elisa ferrari wrote:
>
> Hello,
>
> I examined data from a public database (ABIDE) processed both with
> freesurfer 5.1 and freesurfer 6.0
Hi,
Images from different scanners can look very differently (intensity, scaling, non linearities). Also acquisition parameters can change images and bias results.
This warning exists to make sure users understand that whatever they get out of the analysis could be completely driven by acquisition
My apologies as I misstated some of the data in my first email,
The voxel sizes are relatively similar, (two of the acquisitions are 1mm vs one
with 0.9mm).
Whereas the FOV is different between the scans being 256x256x176 on one
acquisition, 224x256x176 on the second and 240x240x180 on the thir
19, 2014 9:45 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Clarification regarding group specific average
template creation
I take it back, mris_make_subject does create the .tifs you would need
for mris_register. I still doubt it will change much, but feel free to
try it out and let
___
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
[fis...@nmr.mgh.harvard.edu]
Sent: Thursday, December 18, 2014 3:46 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Clarification regarding group specific average
template creation
essing stream?
Thanks,
-Prad
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
[fis...@nmr.mgh.harvard.edu]
Sent: Thursday, December 18, 2014 3:46 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Clarification regarding gr
: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
[fis...@nmr.mgh.harvard.edu]
Sent: Thursday, December 18, 2014 3:46 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Clarification regarding group specific average
template creation
Hi Prad
no, everything is still ni fsaverage space. You would need to run
mris_make_template to create a new template, then rerun mris_register
cheers
Bruce
On Thu, 18 Dec 2014, Bharadwaj,
Pradyumna - (prad) wrote:
Hello,
My question is regarding the registration procedure using a gro
Hello,
My question is regarding the registration procedure using a group specific
average template.
I ran recon-all for my group(with >100 subjects), created an average subject
using make_average_subject and then used recon-all qcache by referencing the
average template that I just created. I
Nope, there's no flipping in tracula. But, *both* the gradient vectors and
the DWIs are converted to LAS orientation as the first step in the
preprocessing. This makes the FSL tools that are run later in the
preprocessing (dtifit and bedpostx) run smoothly without any flipping.
On Mon, 26 Au
Hi,
After much searching, it appears to be pretty uniform that the product DTI
sequence performed on GE requires the y gradient to be flipped. For the
datasets with which I am working diffusion toolkit, vistalab and
exploredti all require the y gradient to be flipped. However, Tracula
makes appro
Dear List Members,
I am planning to use the eTIV for a group analysis using segmentation
volumes and I need to confirm that the eTIV ( aka ICV) generated in
freesurfer is NOT dependent on the skull strip? Specifically, I wanted to
make sure one does not need to QC the skull strips to make sure al
Chris,
going forward, yes, i would recommend installing centos6. you can use
the centos4 freesurfer build in the meantime, until the centos6
freesurfer build (the faster one) is ready. you dont have to rerun your
subjects if your happy with the current results. the next release
doesnt have any
Hi Nick,
So would you recommend I install Centos 6 on the new workstation?
In addition, I've run recon-all on a large study group (>100); I take it I'll
have to re-run all of them?
Thanks,
Chris
Chris,
yes, the centos5 build freesurfer 5.1 will work on centos6 (we use it
i
Chris,
yes, the centos5 build freesurfer 5.1 will work on centos6 (we use it
in-house). when the v5.2 release of freesurfer is ready (hopefully at
the end of may) you will want to use the centos6 build, as it will get a
bit better performance because of the compiler and some openmp options.
n.
H i Nick,
Will the centos5 build of v5.1 work with centos6? I'm getting a new
workstation and want to know which version of centos is better to install.
On 04/10/2012 10:08 AM, Nick Schmansky wrote:
> Wil,
>
> Hi, the contents of that 'misc' directory is just a filedrop of sorts to
> supply fixes
Wil,
Hi, the contents of that 'misc' directory is just a filedrop of sorts to
supply fixes to individuals who need particular updates. We dont supply
formal patches, as it gets too unwieldy to track versions. Rather bug
fixes are documented (mostly!) on the ReleaseNotes page with links to
fixes.
Hi-
It would appear the stable release for centos6 is ready for primetime
'stable5.1-bin.tgz'; Is this correct? There is an updated version of
'mri_info' based on file size
(ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos6_x86_64/).
mri_info in 'stable5.1-bin.tgz': 978
Dear Freesurfer team,
I was a little confused by the recent e-mails about total GM and WM.
If you could help clarify the below mentioned, I would really appreciate it (am
using freesurfer: stable 4 version).
1) For cortical thickness analysis, there is no necessity to normalize each
parcellat
Hello,
The "unknown" parcellation in /h.aparc.annot includes vertices of the
white/pial surface that correspond to the insula, medial temporal cortex
(including hippocampus and amygdala), and the midline.
How are the vertices that "cut" through the hippocampus, amygdala, and
midline treated durin
Two more thing:
please include the # of subjects that you have analyzed, and any clinically
relevant study that uses FreeSurfer can be included (included DTI and
fMRI).
thanks again,
Bruce
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