Hi Courtney
Can you send us your command line and a recon-all.log?
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Courtney Haswell
Sent: Wednesday, December 2, 2020 9:24 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Recon-all error
External Email
Sure, try the bbregister tool
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Karan Desai
Sent: Tuesday, December 1, 2020 10:46 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Aligning functional and structural scans with FsFast
External Email - Use
Hi Paul
Have you tried using the wmseg?
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of miracle ozzoude
Sent: Wednesday, December 2, 2020 1:35 PM
To: Douglas N Greve
Subject: [Freesurfer] Fwd: extracting mask for basal ganglia, deep grey, and
centrum semiovale
Have you looked at the T1.mgz?
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Julia Yang
Sent: Wednesday, December 2, 2020 8:37 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mri_watershed error: problem in the COG calcuation
External Email - Use Caution
Hi,
Wh
Hi Courtney
Can you send us the recon-all.log file and the full screen output from one job
that failed?
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Courtney Haswell
Sent: Thursday, December 3, 2020 9:52 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] rec
Make sure it looks reasonable (that there is a brain in there, and the
intensities look ok). You can send it to us if you want
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Julia Yang
Sent: Wednesday, December 2, 2020 10:27 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] m
Hi Antonín
You can specify what surfaces to use in mris_thickness:
mris_thickness -pial -white …
cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Antonín Škoch
Sent: Wednesday, December 9, 2020 6:16 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Computing
You probably want to mask the medial wall
Bruce
On Dec 9, 2020, at 11:31 PM, Antonín Škoch wrote:
External Email - Use Caution
Hi, Bruce,
in the meantime, I found the old thread
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg05989.html
which suggests to set -N 20 p
Hi Antonin
Sorry for the trouble. We can add a -mask option to it going forward
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Antonín Škoch
Sent: Friday, December 11, 2020 1:16 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Computing thickness from woT2
HI Fahimeh
You need to give us a lot more information. What kind of scans did you acquire?
Were they the same across time? Were they on the same scanner? Were any
upgrades or similar performed in between the scans. We don’t generally find
growth like this in adult populations
Cheers
Bruce
Fro
Hi Stephanie
Do you know why you have multiple frames? You can always extract a frame via:
cd $SUBJECTS_DIR/$subject/mri/orig
mv 001.mgz 001.multiframe.mgz
mri_convert -nth 0 001.multiframe.mgz 001.mgz
assuming you know that frame 0 is the correct one. You might have to do this
for 002 also, af
Hi Jim
You should be able to use mris_expand with a negative distance to generate this
surface.
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Gugger, James J
Sent: Tuesday, December 22, 2020 11:42 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Superficial
Hi,
Those aren't surfaces - they are scalar fields over surfaces. You can visualize
them by first loading any surface you want (e.g. lh.inflated), then use the
"load curvature" or "load overlay" functions in freeview to visualize them on
the surface.
Cheers
Bruce
From: freesurfer-boun...@nmr
Hi Dylan
Sorry, did anyone ever answer this? The .lta files contain the transform but
also information on the coordinate systems that they are in. I think that the
standard talairach one is voxel to voxel, so it would indeed change with the
image fov. There are tools for converting ltas to ras-
p.s. oh, and the .lta format is ascii so you can just look at it to see if it
is vox2vox or ras2ras
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Tisdall, Dylan
Sent: Thursday, December 24, 2020 11:41 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesur
Hi Octavian
1. Yes, there is a write_annotation.m that you can use.
2. We output an annot of the max probability labels at each point I think
called BA_exvivo.thresh.annot
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Octavian Lie
Sent: Friday, January 8, 2021
.annot files
External Email - Use Caution
Thank you, Bruce, as always. The BA_exvivo.thresh.annot does not annotate all
the vertices, see attached BA.png. Is there a complete Brodmann map like in the
atlas image? Thank you, Octavian
On Fri, Jan 8, 2021 at 10:37 AM Fischl, Bruce
mailto:bfis
the LUT table by matching annot vertex indices to col 1 in the
LUT. Is there any .m file that can do that? If not, I can write one, but wanted
to check, thank you.
Octavian
On Fri, Jan 8, 2021 at 11:03 AM Fischl, Bruce
mailto:bfis...@mgh.harvard.edu>> wrote:
Alas there is not – there are
Hi Fleur
FreeSurfer provides tools that take an approximately isotropic T1-weighted
input volume with voxel dimensions around .7-1.5mm and reconstructs models of
most macroscopically visible structures. There are other algorithms around that
take a set of orthogonal anisotropic acquisitions and
Yes, that should work
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Trisanna Sprung-Much
Sent: Monday, January 18, 2021 5:01 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] making labels in Freeview/Freesurfer 7.1.1
External Email - Use Caution
Hi there
The
Hi Andy
I think the rh.white.H is generated by mris_curvature. Does that help?
Cheers,
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Andy Worth
Sent: Tuesday, January 19, 2021 5:29 PM
To: Freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Cannot find rh.white.H
Ex
Hi Simone
You can do this all in freeview. If you give it -ss it will save a
snapshot to that file and exit. Check out the help. There is something like
–view lateral or medial that you can use. I think everything you have below has
a command line switch, but if you can’t find one post again a
Can you send us the full output?
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of KennethSPrice
Sent: Sunday, January 24, 2021 5:01 PM
To: Freesurfer support list
Subject: [Freesurfer] command terminated by signal 11?
External Email - Use Caution
Hell Freesurfers,
When runni
Hi Stephanie
I’m not sure you can really compare their accuracy. Thickness is easier to
interpret though and is also a point measure and relatively insensitive to head
size, so is frequently an easier surrogate biomarker than surface area. That
said, we have done studies of surface area change
Hi Trisanna
Yes, I’m pretty sure that would work. That is, using the current freeview on
older versions of recon data.
Cheers
Bruce
p.s. one addendum – you should not have to blur the labels after registration,
assuming your manually labeled dataset is big enough
From: freesurfer-boun...@nmr.
:
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of "Fischl, Bruce"
mailto:bfis...@mgh.harvard.edu>>
Reply-To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Tuesday, January 26, 2021 at 1:22 PM
To: Freesurfer support list
mailto:fr
Hi Rahul
That typically means that something has gone wrong, like too much skull being
left around. The timing of the defect correction is quadratic in the size of
the largest defect, so quite fast for small ones, but very very slow for big
ones (and less likely to be correct when done). Look
all
Hi Bruce,
Is it possible to do a zoom call for troubleshooting with me and my PI today?
Rahul
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on beha
Hi Michele
I guess after running the long you could launch a cross recon on the spatially
registered time points. You’ll have to be careful about extra interpolations
though
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Michele Valotti
Sent: Wednesday, February 3, 20
Hi Katie
Can you give us more info? What command line did you run? Can you send us the
recon-all.log file from the subject so we can see what step it is on? Usually
this means the topology fixer is trying to fix something giant, like the
cerebellum attached to cortex or skull left around or som
#x27;ve attached the recon-all.log below and it mentions there is an Error that
says "don't know how to get DWI parameters from.
Is there anyway you can help me debug this issue. I know this process shouldn't
be taking so long.
Best,
Katie
On Sun, Feb 7, 2021 at 2:38 PM Fischl, Br
see which is the best looking series and then I upload those
dicoms into iEEGview in order to do segmentation-->coregistration--> and then
electrode localization.
Best,
Katie
On Mon, Feb 8, 2021 at 11:05 AM Fischl, Bruce
mailto:bfis...@mgh.harvard.edu>> wrote:
Hi Katie
I defer to oth
not CT?
-Katie
On Mon, Feb 8, 2021 at 12:25 PM Fischl, Bruce
mailto:bfis...@mgh.harvard.edu>> wrote:
Well, we only process MRI, not CT, so definitely don’t give us a CT! And
generally you need a T1-weighted MRI that is about 1mm isotropic
From:
freesurfer-boun...@nmr.mgh.harvard.
Hi Gunes
Just set it in your environment before calling mri_em_register. For example
setenv OMP_NUM_THREADS 1
in csh/tcsh or
export OMP_NUM_THREADS=1
in bash. I think you can also give -openmp 1 to recon-all (hopefully that will
also work)
cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harva
DICOMS labeled IM-0027-0001
all the way to IM-0027-0255 (so 255 dicoms total). Its been running for about
20 hours now. I've attached the new recon-all.log file below.
On Mon, Feb 8, 2021 at 1:48 PM Fischl, Bruce
mailto:bfis...@mgh.harvard.edu>> wrote:
Hi Katie
I don’t know what
Hi Kristi
I use mris_spherical_average for this, but I think Doug has something better
documented
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Kristi Drudik
Sent: Friday, February 19, 2021 11:37 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Sulcal probabil
Did you try mris_spherical_average? I have definitely used it for this (among
other things). I assume you saved the sulcal labels to a .label file?
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Kristi Drudik
Sent: Tuesday, February 23, 2021 2:30 PM
To: Freesurfer suppo
r-boun...@nmr.mgh.harvard.edu>>
On Behalf Of Fischl, Bruce
Sent: February 23, 2021 8:09 PM
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Sulcal probability maps
Did you try mris_spherical_average? I have definitely used it for this (among
having some trouble running this command.
Best,
Kristi
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Fischl, Bruce
Sent: February 25, 2021 11:57 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Sulcal probability maps
Sorry, it doesn’t have the greatest help
lf Of Fischl, Bruce
Sent: February 26, 2021 12:14 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Sulcal probability maps
fname is the name of the file you want to load for every subject (the label
file name in your case). Subject 1 is the FS id of the first subject you want
to load (follow
...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of Fischl, Bruce
Sent: February 26, 2021 12:28 PM
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Sulcal probability maps
...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of Fischl, Bruce
Sent: February 26, 2021 2:46 PM
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Sulcal probability maps
>>
On Behalf Of Fischl, Bruce
Sent: February 26, 2021 3:45 PM
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Sulcal probability maps
Oh yes, that is your problem. mris_spherical_average assumes they are in
subject space
From
You should register them using bbregister, then use mri_vol2vol to resample
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of ??
Sent: Saturday, March 6, 2021 7:17 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Freesurfer consult
External Email - Use
Hi Alberto
1. And 4. Are not properties of single surfaces – they are computed from the
white and the pial. For 2 and 3 that is really up to you
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Alberto Del Cerro Leon
Sent: Monday, March 8, 2021 7:02 AM
To: Freesurfer
Hi Raquel
The log says:
Command terminated by signal 9
Which is a message from the Linux scheduler, and usually means you ran out of
ram. It looks like you have 5G on that machine and some of it was in use at the
time. Can you find a machine with more ram to try it on? Or free up the memory
b
Hi Akila
You haven't told it to do anything, so all it does is create the directory
structure and import the data. You need to add a directive like "- all" to the
recon-all command line
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of A.R. Sekar
Sent: Tuesday, March 16,
Hi Carolin
Yes, I guess send along images using all 3 orientations. There has to be some
white matter there somewhere….
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Caroline Chwiesko
Sent: Friday, March 19, 2021 12:28 AM
To: Freesurfer support list
Subject: [Freesurf
HI Mudathir
Looks like mri_vol2surf doesn’t want the full path in the “surf” parameter –
just stuff after the “lh.”.
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of ·
Sent: Friday, March 19, 2021 2:21 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] e
Hi Stef
This is usually the result of a incorrectly fixed topological defect. You can
confirm this if the area is present in the ?h.orig.nofix and not in the
?h.orig. The fix depends on the source of the defect. It might be as simple as
drawing a single voxel back into the wm.mgz, but might ne
Hi Yusheng
lh.area is not a surface. It is a scalar overlay that can be loaded onto a
surface. Try loading lh.inflated or lh.white then load area or thickness on top
of it using file load overlay or curvature
Cheers
Bruce
> On Mar 22, 2021, at 10:30 PM, 超级无敌 wrote:
>
> Yusheng
___
?h.orig.nofix, but not in ?h.orig have intensities above 100, but
some are as low as 86. Additionally, it also looks to me as if wm.mgz is also
missing some voxels. What kind of intervention would you recommend?
Many thanks,
Stef
From:
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of &
Hi Arman
You can use mri_extract_labels or mri_binarize – match. The labels are in
$FREESUFER_HOME/FreeSurferColorLUT.txt
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Arman Avesta
Sent: Tuesday, March 23, 2021 9:53 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Free
instead of ?h.orig.nofix first.
Do I need to convert the /?h.defect_labels first? If so, how? I tried running
mris_convert -c lh.defect_labels lh.defect_labels.asc from the surf directory,
but it just prints the help message.
Stef
From:
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf o
Sure, I guess you can just run mri_average. I think also if you specify the
file name for the transform as identity.nofile to any binary that takes an lta
file, the code will internally create an identity transform.
I won’t look pretty though….
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harv
Hi
I'm not entirely sure what the question is, but if you run recon-all on
appropriate input data you will get a DKT parcellation as one of the outputs
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of 1248742467
Sent: Thursday, March 25, 2021 10:59 PM
To: freesurfer
Sub
ar 19, 2021 at 7:26 AM Fischl, Bruce
mailto:bfis...@mgh.harvard.edu>> wrote:
Hi Carolin
Yes, I guess send along images using all 3 orientations. There has to be some
white matter there somewhere….
Cheers
Bruce
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...
On Fri, Mar 26, 2021 at 3:20 PM Fischl, Bruce
mailto:bfis...@mgh.harvard.edu>> wrote:
Hi Carolin
Where did you upload the images?
Bruce
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
u very much for your help with this!
Cheers
Carolin
On Sat, Mar 27, 2021 at 8:35 AM Fischl, Bruce
mailto:bfis...@mgh.harvard.edu>> wrote:
Hi Carolin
What did you name them? Also, we won’t really be able to diagnose things unless
you upload the entire tarred/gzipped subject directory
Hi Ellen
It is certainly possible. Have you looked at the surfaces for those subjects?
Cheers
Bruce
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Ellen Ji
Sent: Tuesday, March 30, 2021 5:44 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Aborm
Hi Ornaith
The mapping uses the vertex index. That is, the vertex index is stored in the
flatmap, so you should always be able to recover it, then look up the location
of that vertex on any other surface (of the same hemisphere/subject)
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
Hi Noam
You can always use the -rl switch in mri_convert (rl == "reslice
like"). So for example
mri_convert -rl rawavg.mgz orig.mgz orig_back_to_raw.mgz
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Peled, Noam
Sent: Tuesday, April 6, 2021 2:52 PM
To: freesurfer@nmr.mgh.harvard.e
When I load in the data to
MATLAB as discussed - the only thing that I have access to are the coordinates
of the vertices - not the vertex index. How can I recover the vertex indices
as well?
Thanks again.
Kind Regards,
Ornaith
On Tue, 6 Apr 2021 at 19:31, Fischl, Bruce
mailto:bfis...@mgh.
Mon, Mar 29, 2021 at 3:32 PM Caroline Chwiesko
mailto:cchwi...@uci.edu>> wrote:
RAS: 6.11, 57.54, 60.36
brainmask [120, 98, 191]
Talairach 115.59, 127.61, 202.35
On Mon, Mar 29, 2021 at 3:08 PM Fischl, Bruce
mailto:bfis...@mgh.harvard.edu>> wrote:
Thanks. What are the voxel coords of
Hi Yoonho
That warning is usually benign. Does the recon finish ok?
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Yoonho Hwang
Sent: Friday, April 9, 2021 2:49 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] MCSRCH error using sample data (001.mgz and 002.mg
Did you use mri_surf2surf to map the data from fsaverage to a surface in the
subject space first?
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Ren, Xueying
Sent: Monday, April 12, 2021 9:21 PM
To: Freesurfer support list
Subject: [Freesurfer] question about mapping fsaverage surfa
ailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Fischl, Bruce
mailto:bfis...@mgh.harvard.edu>>
Sent: Monday, April 12, 2021 10:17 PM
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] question about mapping fsaverage surface
Hi Mason
Yes, you can use mri_vol2surf to go native vol->native surf, then mri_surf2surf
to go native surf->group surf
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Mason Wells
Sent: Monday, April 19, 2021 5:45 AM
To: Freesurfer support list ;
freesurfer-boun...@nmr.
/lh.pial:edgecolor=red \ subject1/surf/rh.white:edgecolor=yellow \
subject1/surf/rh.pial:edgecolor=red
Nothing stood out to me. Is there anything else you suggest I investigate? What
could explain a negative folding index?
Best,
Ellen
On 3/31/2021 12:18 AM, Fischl, Bruce wrote:
> Hi Ellen
>
&
ers,
Mason
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
mailto:bfis...@mgh.harvard.edu>>
Sent: Monday, April 19, 2021 4
u>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Fischl, Bruce
mailto:bfis...@mgh.harvard.edu>>
Sent: Monday, April 19, 2021 5:06 PM
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Native volume to fs_average surface
Hi Stephan
I think there has always been topology fixing. The ?h.orig should be created
prior to the fixing then corrected I believe, but if you have big topological
defects you probably want to figure out why and correct them. Have you
visualize the ?h.inflated.nofix or the ?h.orig.nofix? If t
You just need to rerun mris_register using the options I included in my
previous email. This will recreate the ?h.sphere.reg, after which you can
recreate the parcellation
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Fraser Smith
Sent: Monday, April 26, 2021 9:33 AM
T
Hi Pål
Thickness and curvature are overlays, not surfaces. Load a surface then load
them as either overlays or curvature files.
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Pål Gunnar Larsson
Sent: Monday, April 26, 2021 9:50 AM
To: 'Freesurfer support list'
Subjec
Hi Alexandria
The file given in the -l option should be an ascii label file, not a volume.
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Jensen, Alexandria
Sent: Monday, April 26, 2021 4:26 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_anatomical
ODI values for each ROI in the DKT
atlas.
Alexandria
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
mailto:bfis...@mgh.harvard.edu
t map. But how do i know the vertex number of each vertex in
the pial surface? Are they in order ?
Also, what coordinate system is the pial surface in when its read into
FreeSurfer? Is it RAS or surface RAS?
Kind Regards,
Ornaith
On Wed, 7 Apr 2021 at 20:02, Fischl, Bruce
mailto
surface analysis
External Email - Use Caution
Hi Bruce,
Thanks a lot for this. What is the difference between RAS and surface RAS?
Do I need to convert the surface RAS into RAS to be dealing in the volume space?
Kind Regards,
Ornaith
On Tue, 27 Apr 2021 at 15:44, Fischl, Bruce
mailto:bfis
Yes, I believe so depending on which parcellation you are using
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Nils B.
Sent: Thursday, April 29, 2021 9:55 AM
To: Freesurfer support list
Subject: [Freesurfer] mris_anatomical_stats
External Email - Use Caution
Dear Supp
Hi Maria
Have you looked at the aseg.auto_noCCseg.mgz? Sounds like something went wrong
in your processing and you need to track backwards to see where it started
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Maria Baena Perez
Sent: Friday, April 30, 2021 7:10 AM
To:
Was the aseg correct in the cross? If you can upload this subject (all the
cross and long timepoints) we can take a look
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Malo Gaubert
Sent: Monday, May 3, 2021 10:19 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Frees
Hi Ileana
Have you examined the input to the mri_normalize call? It should be in the log
file. If it looks normal then maybe tar/gzip the subject dir and send it to us?
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Camerino, I.L. (Ileana)
Sent: Tuesday, May 4, 2021 9:
Can you take a look at the volume that was the input to mri_normalize and see
if it looks ok? And check the talairach
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Corinna Bauer
Sent: Wednesday, May 5, 2021 5:25 PM
To: Mailing Freesurfer List
Subject: [Freesurfer] error at 3d norma
at 3d normalization pass 1 of 2 stage with
MP2RAGE data
External Email - Use Caution
Hi Bruce,
The nu.mgz input into mri_normalize looks ok to me (screenshot attached), as
does the talairach registration.
Corinna
On Wed, May 5, 2021 at 5:39 PM Fischl, Bruce
mailto:bfis
Hi John,
It depends on how you sample from the volume to the surface, but yes, in
general voxels in the white matter (and deep gray matter and csf and bone,
etc….) won’t show up on the surface
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of John Gelburg
Sent: Friday, M
(as when you configure an overlay), where the least
likely vertices are drawn in blue and the most likely vertices are drawn in red?
Thank you very much for your help!
Best,
Kristi
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Fischl, Bruce
Sent: February 26, 2021 4:59 PM
To
Hi Sara
You can assemble all the BA labels on fsaverage into a .annot file and display
it that way if you want. mris_label2annot should do the trick. Just give it
all the appropriate either with/without thresh (?h.BA*_exvivo.label or
?h.BA*_exvivo.thresh.label)
Or just load the individual lab
:
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
mailto:bfis...@mgh.harvard.edu>>
Sent: Saturday, May 15, 2021 11:45 AM
To: freesurfer@nmr.mgh.harvard.edu
r-boun...@nmr.mgh.harvard.edu>>
on behalf of Fischl, Bruce
mailto:bfis...@mgh.harvard.edu>>
Sent: Saturday, May 15, 2021 2:58 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [External] Re: [Freesurfer] Overlay of MGH clusters on Broadmann atlas
Hi Sar
ine Avenue, 02215 Boston, MA, USA
Phone Nr: +1-339-229-7645
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
mailto:bfis...@
...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Fischl, Bruce
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Sent: Saturday, May 15, 2021 5:47 PM
To: Freesurfer support list
Subject: [External] Re: [Freesurf
...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Fischl, Bruce
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Sent: Saturday, May 15, 2021 6:04 PM
To: Freesurfer support list
Subject: [External] Re: [Freesurfer] Overlay
r-boun...@nmr.mgh.harvard.edu>>
on behalf of Fischl, Bruce
mailto:bfis...@mgh.harvard.edu>>
Sent: Sunday, May 16, 2021 10:31 AM
To: Freesurfer support list
Subject: [External] Re: [Freesurfer] Overlay of MGH clusters on Broadmann atlas
Hi Sara
Why do you need MNI at all? Why not just do it in indivi
to
.func.gii. .annot can be converted to .label.gii with mris_convert.
Matt.
From:
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of "Fischl, Bruce"
mailto:bfis...@mgh.harvard.edu>>
Reply-To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date
-7645
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
mailto:bfis...@mgh.harvard.edu>>
Sent: Sunday, May 16, 2021 10:54 PM
To:
All of our binaries read any of our supported formats, so that should be fine
as like as the direction cosines are correct
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of A.R. Sekar
Sent: Wednesday, May 19, 2021 7:12 AM
To: Freesurfer support list
Subject: Re: [Freesurf
Hi Kristi
I don't think it does any blurring unless you tell it to. The output should
reflect the actual alignment of those labels
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Kristi Drudik
Sent: Thursday, May 20, 2021 12:48 PM
To: Freesurfer support list
Subject: R
ould I tell the command “mris_spherical_average” to blur the
output? Also, how can I display the probability values in a colour scale?
Thank you very much!
Best,
Kristi
From:
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of "Fischl, Bruce"
mailto:bfis...@mgh.
...@nmr.mgh.harvard.edu>>
on behalf of "Fischl, Bruce"
mailto:bfis...@mgh.harvard.edu>>
Reply-To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Thursday, May 20, 2021 at 1:35 PM
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of Fischl, Bruce
Sent: May 20, 2021 2:15 PM
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] blurring average label files
Almost. -prior takes two parameters. The second is the file
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