have to help you with
this, but it might well do better for your acquisitions)
Cheers
Bruce
From: Edan Daniel
Sent: Monday, February 21, 2022 11:14 AM
To: Fischl, Bruce
Cc: Freesurfer support list
Subject: Re: [Freesurfer] autorecon2-wm not reflecting edits in white matter
segmentation (7.1.1
th v7.
Many thanks!!!
Edan @ PrincetonBrainDevLab
On Mon, Feb 21, 2022 at 5:04 PM Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>> wrote:
If this is not something you have to do a lot of, you can put a repositioning
point. See the release notes.
On 2/21/2022 1:10 PM, Fischl, Bruce wrote:
Hi Ed
In python you should be able to do (assuming you have a list of subject ids in
subject_list):
import nibabel as nib
file_list = [os.path.join(os.getenv(‘SUBJECTS_DIR’), subject) for subject in
subject_list]
mri_list = [nib.load(fname) for fname in file_list]
even for 1000 subjects it won’t ta
Oops, slight edit
import nibabel as nib
file_list = [os.path.join(os.getenv(‘SUBJECTS_DIR’), subject, ‘mri’,
‘brainmask.mgz’)for subject in subject_list]
mri_list = [nib.load(fname) for fname in file_list]
On Feb 22, 2022, at 9:53 PM, Fischl, Bruce wrote:
In python you should be able to
Sorry, can you explain a bit more about what you want to do. What does
“demonstrate morphological variation” mean? Just quantify variability? Are
there any variables that you are correlating it with (e.g. disease status,
cognitive measure, etc…)? I don’t understand what you are trying to do
Chee
I see. Well, you will probably want some combination of cortical thickness maps
and subcortical volumes at the least, although of course other information
might be important as well (connectivity, myelin content, etc…). These things
have different shapes (in the python sense) so you’ll have to s
Hi Noam
Have you tried running it without -parallel? It looks like it is waiting for
some other PID to finish
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Peled, Noam
Sent: Thursday, February 24, 2022 12:36 PM
To: Freesurfer support list
Subject: [Freesurfer] Neverending mr
why are there multiple frames? What it in them?
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Knut J Bjuland
Sent: Saturday, February 26, 2022 1:33 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Checking for (invalid) multi-frame inputs...
FYI
From: Talley, Edmund (NIH/NINDS) [E]
Sent: Wednesday, March 2, 2022 1:08 PM
To: Talley, Edmund (NIH/NINDS) [E]
Subject: Neurotechnology Job Opportunity for the BRAIN Initiative
External Email - Use Caution
I’m writing with information on a rare opening for a Neurotechnology Progra
FYI
-Original Message-
From: Oula
Sent: Wednesday, March 16, 2022 10:08 AM
To: Fischl, Bruce ; Iglesias Gonzalez, Eugenio
Subject: Postdoc position
External Email - Use Caution
Hi guys,
The postdoc position in the LF&NIH project is now open for applications.
Hi Dongyue
A couple of things. I’m not sure which column you mean in the aparc.stats, but
the default values are usually for the white surface not the pial. But more
importantly, what are you trying to achieve by computing the mean area? That
will be a function of the tessellation I think, no
Hi KC
Are you naming the file “license.txt” or “licence.txt”. We look for the former,
not the latter. And is there a .license.txt in that directory? And if so, where
did it come from?
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Koustav Chatterjee
Sent: Saturday, Marc
Hi KC
Where did you get the license.txt file originally? Can you try requesting
another? I’ll leave the freeview question for Ruopeng.
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Koustav Chatterjee
Sent: Monday, March 28, 2022 11:04 PM
To: Freesurfer support list
S
Hi Ali
We keep track of the vertex index of the flat maps, so you should just be able
to use it to look up the coordinate of whatever other (white, pial) surface you
want, then see what volumetric coordinates it is at
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Ali
sday, March 30, 2022 11:45 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] FREESURFER Maintaining vertex Id during
transformations
External Email - Use Caution
Hi Bruce,
If I have the coordinate on the flat map how do I get the corresponding vertex
ID? And then from that same ID get
FYI
From: Irene Costantini
Sent: Wednesday, April 6, 2022 4:08 AM
To: Fischl, Bruce ; Boas, David ; Hof,
Patrick
Cc: Mora, Jocelyn S.
Subject: Postdoc positions
External Email - Use Caution
Dear all,
we are currently trying to recruit two Postdocs to work on advanced microscopy
FYI
---
Dear colleagues,
We are excited to announce that Neuromatch Academy (NMA) is offering two
courses this year from July 11th to July 29th 2022 which will run in parallel
online. Applications for students and teaching assistants are now open until
April 20th, 2022
Hi Luqi
You need to send us the complete command line you ran and the entire output of
the command, plus the FS version number you are using.
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of lqcheng2017
Sent: Tuesday, April 12, 2022 9:09 AM
To: freesurfer
Subject: [Fre
I think you mean “th3” not “thr3”. It is interpreting it as an option to use a
different thickness file (specified by the next thing on the command line,
which is “-mgz”.
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of lqcheng2017
Sent: Tuesday, April 12, 2022 11:22 PM
worked when I changed "thr3" to "th3". Thanks again.
Best,
Luqi
On 4/13/2022 21:46，Fischl,
Bruce<mailto:bfis...@mgh.harvard.edu> wrote：
I think you mean “th3” not “thr3”. It is interpreting it as an option to use a
different thickness file (specified by the next thing o
There is a link at the bottom of every fs list email you can use to remove
yourself
On Apr 14, 2022, at 8:49 PM, wangjinjing992 wrote:
External Email - Use Caution
Dear Sir or Madam,
I am sorry to disburb you. Recently, when I filled my personal information in
Freesurfer Support L
.
Aaron
On Apr 17, 2022, at 9:59 AM, Fischl, Bruce
mailto:bfis...@mgh.harvard.edu>> wrote:
Hi Aaron
We explicitly exclude amygdala/hippocampus from the surface models since they
aren’t neocortical. Hippocampus of course has some internal structure that
could be modeled that way (and ha
What is inside your mri folder? And make sure you are not running out of disk
space as that would cause the 0 length files
Cheers
Bruce
On Apr 17, 2022, at 9:04 PM, HYE JUNG YOUN wrote:
External Email - Use Caution
Hi,
Just re-sending this message in case it didn’t go through to the
Is this for a subject that you can’t load the wm.mgz for? It doesn’t show any
errors. Is the wm.mgz zero length? I don’t see how those things can both be
true unless you overwrote it at some point. If you haven’t manually edited this
subject maybe you should just rerun it?
From: freesurfer-boun
Just give freeview the path to whatever volume or surface you want to visualize
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Jabeur Mouna
Sent: Wednesday, April 27, 2022 5:45 AM
To: Freesurfer support list
Subject: [Freesurfer] (no subject)
External Email -
Why not just flatten it and save it as a .mgz? Then I think it should be
straightforward
-Original Message-
From: Greve, Douglas N.,Ph.D.
Sent: Wednesday, April 27, 2022 10:42 AM
To: freesurfer@nmr.mgh.harvard.edu; Fischl, Bruce
Subject: Re: [Freesurfer] Resampling of surface-based
Right, I meant flatten the matrix into a vector/vertex, do the cross-subject
mapping, then reshape it back to a matrix
-Original Message-
From: Greve, Douglas N.,Ph.D.
Sent: Wednesday, April 27, 2022 12:24 PM
To: Fischl, Bruce ; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer
If you have 2 volumes that share an RAS coordinate system but have different
voxel geometry you can use the -rl ("reslice like") option:
mri_convert -rl template.mgz vol_to_convert.nii vol_like_template.mgz
cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Zeng, Victor (B
Hi Alberto
Usually that means that you missed some cuts and there are still attachments.
Occasionally it is due to a local minimum. You can try changing the distance
preservation matrix to be bigger with longer range distances. Something like
-distances 20 20 (out to 20 neighbors and 20 at eac
Hi Sam
We need more information. What do you mean by “freesurfer space”? Is it on an
individual subject or fsaverage? Volume or surface? How did you create it?
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Sam W
Sent: Friday, June 3, 2022 9:12 AM
To: Freesurfer suppor
an individual subject. I always assumed (maybe
wrongly) that labels correspond to surfaces and are defined in freesurfer's
conformed space.
Best regards,
Sam
On Fri, Jun 3, 2022 at 4:33 PM Fischl, Bruce
mailto:bfis...@mgh.harvard.edu>> wrote:
Hi Sam
We need more information. What
U_gxbaLIl7SQeLo9fLKXARb5PZ9X-IHyfQhf_PIcOb6l4jJqZME_CByZqGbYbpvpD3tYyXIg3Q5SZyGvjmG_QnzD_xw6Q/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsAnat-to-NativeAnat>)
can I do the same with freesurfer labels?
Best regards,
Sam
On Fri, Jun 3, 2022 at 4:59 PM Fischl, Bruce
mailto:bfis...@mgh.harvard.edu>> wrote:
Sure. You can either change it in the environment, or pass it to recon-all with
-sd
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Mostafa Fakhri
Sent: Saturday, June 25, 2022 9:35 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] change the $SUBJECTS_DIR
mri_convert file.mgz file.nii.gz
should do the trick
cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Rachel Wagner
Sent: Tuesday, June 28, 2022 2:00 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Converting File Type
External Email - Use Caution
He
The brain.mgz doesn't exist in that location. How did you create it? Maybe it
in a subject's dir?
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Rachel Wagner
Sent: Tuesday, June 28, 2022 2:26 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Error Opening File
Ex
Can you summarize what you are trying to do? What kind of overlay are you
trying to visualize and what exactly do you mean by a "3D image"?
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Rachel Wagner
Sent: Thursday, June 30, 2022 2:48 PM
To: Freesurfer support list
Subject: Re: [Fr
Sure, just run your subject through recon-all, then use mri_binarize or
mri_extract_label to pull the cc labels out of the aseg.
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Mostafa Fakhri
Sent: Sunday, July 3, 2022 1:31 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject:
--mov
rReslice_Combined_roi_meanRD.nii --bold \ --s bert \ --init-rr --lta
register.lta
However, my results still look very grainy. Is there a better way to do this?
Thank you again,
Rachel Wagner
From: Fischl, Bruce<mailto:bfis...@mgh.harvard.edu>
Sent: June 30, 2022 9:09 PM
To
:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Fischl, Bruce
mailto:bfis...@mgh.harvard.edu>>
Sent: Sunday, July 3, 2022 6:37:42 PM
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Frees
deep) considerably -
is there any way for me to do that?
From: Fischl, Bruce<mailto:bfis...@mgh.harvard.edu>
Sent: July 3, 2022 7:44 PM
To: Freesurfer support list<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] How to project SPM image
I see, and what's wrong with th
ii --bold \ inflated -overlay
--s fsaverage \ --init-rr --lta register.lta
From: Fischl, Bruce<mailto:bfis...@mgh.harvard.edu>
Sent: July 4, 2022 3:45 PM
To: Freesurfer support list<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] How to project SPM image
Well you can
The NIH-funded MGH Metabolic Imaging Core is seeking to fill a position of
full-time Research Technician I role in the field of metabolic imaging. As part
of the research group, the incumbent will work in a highly dynamic clinical
research environment in metabolism, focused on body composition,
Hi Carl
This happens in a small fraction of cases that have an outlier folding pattern
(an extra fold) in perirolandic cortex. You can fix it by manually drawing a
central sulcus label on the surface, saving it, then rerunning mris_register
witih (from the help):
-L
Spec
Hi Yiyu
Can you clarify what you are trying to do? Take an individual coordinate or
list of them and transform them? Or transform an entire volume? And what kind
of coordinates do you want at the end? Voxel indices? RAS?
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of
There is a button on the interface that looks like a little camera that saves
snapshots
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Rachel Wagner
Sent: Thursday, July 7, 2022 2:57 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Export Image
Exte
Hi Rachel
It depends on what you mean by "higher quality". I think if you change the
magnification on the save snapshot window it will increase the effective
resolution of the image, regardless of what format you save it in (png, tif,
jpg) , but maybe Ruopeng has a better idea?
Cheers
Bruce
Hi Danielle
I believe that the template volume has the geometry/direction cosines to use
for the output.
Note that this is an *old* binary and not really used any longer so I’m not
sure it works ☹.
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Danielle Carrol
Sent: Wednesd
Thank you all,
Danielle
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of Fischl, Bruce
Sent: Wednesday, July 27, 2022 9:54 AM
To: Freesurfer support list
mailto:freesurfer@nm
What is the output of the first command? And if you bring up the ?h.sphere.reg
does it align better with the atlas? You can use mrisp_paint or just look at
fsaverage on the sphere
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Trolle, Carl
Sent: Wednesday, August 3, 2022 9:25 AM
To:
Yes, definitely something wrong. For the paint you want to specify which frame
in the tiff with #3 I believe (so
$FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif#3). We
store information in 3-frame sets, with means, variances and dofs in that
order for each of inflated, sulc
You should paint the template onto the sphere that is registered (i.e.
sphere.reg), at which point it should look similar to the individual subject's
sulc pattern.
And by "bounce" I just meant send it to me
Cheers,
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Trolle, Carl
S
Hi Carl
Can you upload your subject including the central sulcus labels you drew?
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Trolle, Carl
Sent: Friday, August 12, 2022 12:12 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Shift in cortical parcellation,
I don’t think we ever write out the mid-sagittal plane, but we do compute it
when we segment the callosum. You could set the lateral distance to extend the
callosum to 0 with -t 0 and then it will only label cc voxels in the
mid-sagittal plane
From: freesurfer-boun...@nmr.mgh.harvard.edu
On B
Hi Carl
Did you try outputting files with names that won't be overwritten by recon-all
for the sphere.reg and annot files and see if they are correct?
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Trolle, Carl
Sent: Sunday, August 28, 2022 4:32 PM
To: freesurfer@nmr.m
Hi Ruifeng
I think they are similar, but you would have to ask Neuromorphometrics about
the differences. Our protocol was published in the Neuron 2002 paper and the
papers it cites, which I think is also where the Neuromorphometrics’ protocol
came from
Cheers
Bruce
From: freesurfer-boun...@nm
this field, and don't know if my question is clear to you.
Thanks again.
On Tue, Aug 30, 2022 at 1:29 PM Fischl, Bruce
mailto:bfis...@mgh.harvard.edu>> wrote:
Hi Ruifeng
I think they are similar, but you would have to ask Neuromorphometrics about
the differences. Our protocol was
2022 at 2:37 PM Fischl, Bruce
mailto:bfis...@mgh.harvard.edu>> wrote:
Yes, that can definitely be the case. Some boundaries are not visible (in e.g.
the accumbens) and so the border is defined by geometric means. Other times the
definition of what is in or not in a structure can cha
command do I need to run with -t 0?
Best regards,
Sam
On Sat, Aug 27, 2022 at 3:44 AM Fischl, Bruce
mailto:bfis...@mgh.harvard.edu>> wrote:
I don’t think we ever write out the mid-sagittal plane, but we do compute it
when we segment the callosum. You could set the lateral distance to exte
But it did what it was supposed to do, so you must be overwriting it later
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Trolle, Carl
Sent: Thursday, September 1, 2022 3:46 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Shift in cortical parcellation, issues wi
Hi Mostafa
autorecon2-cp assumes that you have previously run autorecon2. What are you
trying to do here? If you just want to run through the end of autrecon2, remove
the “-cp” from your command line
cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Mostafa Fakhri
Sent:
I think so, but it may be that later stages (like surface deformation) can be
used to refine the wm.seg.mgz so it is more accurate.
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Mostafa Fakhri
Sent: Wednesday, September 7, 2022 2:53 AM
To: freesurfer@nmr.mgh.harvard.ed
Yes, I think that is correct
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Ellie Shaw
Sent: Wednesday, September 7, 2022 7:32 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] ERROR! FOV=288.000 > 256
External Email - Use Caution
Hi,
Thank you for your help!
Hi Yoonho
1. It mostly applies to the nonlinear warp as the “further” an anatomy it is
from our atlas the longer it will take to compute. And yes, that is reasonable
definition of cnr (although you would need some squares/sqrts or abs). The
higher the CNR the better the segmentation and the
Not everything that is faced can be changed. But nothing can be changed until
it is faced"
-- James Baldwin.
In these troubling times, it is increasingly obvious that silence is tantamount
to complicity. If we do not object to objectionable events, we are tacitly
condoning them, and as such we
Thanks Jenifer
Bruce
From: Juranek, Jenifer
Sent: Sunday, June 7, 2020 10:14 AM
To: freesurfer@nmr.mgh.harvard.edu
Cc: Fischl, Bruce R,
Subject: Freesurfer statement
External Email - Use Caution
I pledge to do better. I pledge to pursue systemic change as passionately as I
pursue
Main, Germany
> On June 6, 2020 at 4:36 PM "Fischl, Bruce R," wrote:
>
>
> Not everything that is faced can be changed. But nothing can be changed until
> it is faced"
>
> -- James Baldwin.
>
> In these troubling times, it is increasingly obvious that s
External Email - Use Caution
Don’t you want a surface to print, not a volume? What would printing the
aseg/aparc mean?
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Magang Visa
Sent: Tuesday, August 15, 2023 8:20 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Frees
External Email - Use Caution
Hi Jason
There are morphological tools built into freeview, so you could select a single
vertex, make a label from it, then dilate it as many times as you want. That
will of course give you the graph distance not the actual surface geodesic, but
mig
External Email - Use Caution
Hi Haley
I'm not sure I understand how you ran SynthSeg in matlab, but we supply .m
files for reading/writing volumes (MRIread and MRIwrite). You probably want to
read in the existing aseg to get the header, then replace the data with the
segmentati
External Email - Use Caution
This happens in one case or in all 292? You should follow the processing stream
backwards to see where things first went wrong. It could be the skull
stripping, but it might also be one of the inputs to it is already incorrect
like the T1.mgz or tra
External Email - Use Caution
Hi Sebastien
Do you know why they don't align in RAS coords? That seems a bit worrisome to
me. I think you can try what you are suggesting easily enough in matlab or
python. Read both in, replace the header in one with the header of the other
then s
External Email - Use Caution
Actually there is a whole Bayesian segmentation on the surface procedure that
generates the individual subject parcellation so it definitely won’t be the
same as just mapping fsaverage
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On B
ntion!
Best,
Leo
Em dom., 10 de set. de 2023 às 14:19, Fischl, Bruce R.,PHD
mailto:bfis...@mgh.harvard.edu>> escreveu:
External Email - Use Caution
Actually there is a whole Bayesian segmentation on the surface procedure that
generates the individual subject parcellation so it definite
to the subjects' native surfaces. This
should ensure that the parcellations for all subjects are generated in the same
way, right?
Many thanks again!
Best,
Leo
Em dom., 10 de set. de 2023 às 15:55, Fischl, Bruce R.,PHD
mailto:bfis...@mgh.harvard.edu>> escreveu:
External
Hi Mudathir
No particular rationale. It is configurable if you want more/less
Cheers
Bruce
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of FMU
Sent: Thursday, December 14, 2023 5:25 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] The Corpus Call
Hi Yunus
The ones with “pial” in them are from the pial surface for things like
curvature and surface area, the ones without are from the white surface. The
rest of the name indicates which cortical parcellation the statistics are
summarized in (e.g. the lh.aparc.pial.stats contains statistics
Hi Anna
Parcellation is more than just format conversion - you need to map it onto the
details of an individual subject's anatomy. In addition, the DKT atlas is only
cortical. If you want subcortical regions in addition you should run recon-all
as it will produce both.
Cheers
Bruce
From: Arkh
Do you acquire any other scans, like an mprage, in the same session? If so, the
easiest thing to do would be to push that through our recon-all pipeline, then
register your MPF images to either the mprage or to surfaces using bbregister
and you can transfer whatever parcellations/segmentations y
A T1-weighted FLASH should work. When you say “it did not work” what do you
mean? Can you give us some details?
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of ERNEST KISSI
Sent: Thursday, January 11, 2024 3:54 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer]
time series should be
pretty straightforward if that is what you want (although Doug will know the
commands better than I do)
Cheers
Bruce
From: Arkhipova Anna, MUDr.
Sent: Friday, January 19, 2024 10:08 AM
To: Fischl, Bruce R.,PHD ;
Freesurfer@nmr.mgh.harvard.edu; fischl
Cc: phlus...@up
I agree with Eugenio - it doesn't do any resampling. Just reads in the data as
is
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Huang, Yujing
Sent: Tuesday, January 23, 2024 8:49 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] MRIread and RAS orientation
I'm
with MRIread, regardless of
the orientation?
---
Thank you all again!
Best,
Panos
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Fischl, Bruce R.,PHD
It is whatever volume you gave as input to recon-all. If you tell us which
statistics you want to regenerate for another volume we can tell you know what
commands to run.
cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of ERNEST KISSI
Sent: Wednesday, January 24, 2024 9:05
Hi Abeoseh
You need to take a look at the output and see what is causing the large defect.
It is usually something like a big piece of skull left around.
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Flemister, Abeoseh B.
Sent: Thursday, January 25, 2024 10:33 AM
To:
Hi Ernest
Take a look at mri_segstats. I think it should do what you want (and it has an
extensive help with examples, thanks to Doug)
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of ERNEST KISSI
Sent: Thursday, January 25, 2024 11:31 AM
To: Freesurfer support list
Sub
Hi Anna
The DK atlas (or DKT?) gets written into the aparc+aseg.mgz volume, but the DKT
parts of it only consist of cortex. The subcortical labels are the normal ones
(caudate, putamen, etc...)
Cheers
Bruce
From: Arkhipova Anna, MUDr.
Sent: Monday, January 29, 2024 10:21 AM
To: Fischl, Bruce
Hi Melissa
mris_euler_number
writes out a bunch of stuff, including the Euler number:
mris_euler_number ~/links/subjects/bruce.dev/surf/lh.orig.nofix
euler # = v-e+f = 2g-2: 154526 - 463668 + 309112 = -30 --> 16 holes
F =2V-4: 309112 != 309052-4 (-64)
2E=3F:9273
Hi Linn
The text you cite is how we measure it. It is the signed distance each points
moves to get from the white to the inflated surface, where outwards movement is
positive (along the surface normal direction) and inwards distance is negative.
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.ha
You can try
mri_compute_volume_fractions
USAGE: mri_compute_volume_fractions
--o outstem : output will be outstem.{cortex,subcort_gm,wm,csf}.mgz
--reg regfile : can be LTA or reg.dat (if reg.dat, then need template volume)
--regheader subject
.
.
.
Which should output a multi-frame MG
Can you clarify what you mean by “measure the intensities for the grey matter
regions”? You could for example compute the mean gray matter intensity within
each cortical parcel and each subcortical structure. Is that what you want?
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of ERNE
Of ERNEST KISSI
Sent: Wednesday, February 21, 2024 11:14 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Grey Matter Intensities
External Email - Use Caution
Yes, please
That's exactly what I mean.
On Wed, Feb 21, 2024, 6:44 PM Fischl, Bruce R.,PHD
mailto
gray matter ratio
: lh.w-g.pct and rh.w-g.pct and I have a file for the white matter so I think I
may be able to create a code to calculate the gray matter.
On Wed, Feb 21, 2024 at 7:21 PM Fischl, Bruce R.,PHD
mailto:bfis...@mgh.harvard.edu>> wrote:
I think that is exactly one of the outp
I guess if nothing else you can cite the 2012 FreeSurfer paper
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Shounak Nandi
Sent: Monday, March 4, 2024 2:50 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Citing the bert dataset
External Email - Use Caution
Hi,
What was your recon-all command line? You need to give it a directive (like
-all), otherwise it will just create a subject directory tree and put the
001.mgz in the orig dir
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Naama Zur
Sent: Sunday, March 17, 2024 5:13 PM
T
Can you post some pictures? The norm.mgz, the wm.mgz, the lh.orig.nofix, the
aseg.mgz, that kind of thing? Something is badly wrong….
Bruce
On Apr 10, 2024, at 7:05 PM, Bhole, Salil wrote:
External Email - Use Caution
Hello,
I have tried to process this MRI a few times now and it a
issue, however, the same issue persisted. Thank
you for your help!
Best,
Salil
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Fischl,
Yes, we support surface-based smoothing. Check out the help for mri_surf2surf
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Jiaen Liu
Sent: Thursday, April 11, 2024 2:14 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] surface-based filtering
Exter
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of Fischl, Bruce R.,PHD
Sent: Thursday, April 11, 2024 14:24
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subjec
: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Fischl, Bruce R.,PHD
Sent: Thursday, April 11, 2024 15:50
To: Freesurfer support list
Subject: Re: [Freesurfer] surface-based filtering
Hi Jiaen
I’m not sure what you mean by “stacked smoothing”. I think the N in nsmooth is
the number of
Hi Shahar
Can you look at the input to that step? Usually it means something prior has
gone wrong (like the skull stripping remove the entire brain or something). And
maybe post a couple of images of the processing (the orig.mgz, the T1.mgz, the
brainmask.mgz, …)
Cheers
Bruce
From: freesurfer
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