:
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: May 20, 2021 3:22 PM
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer
:
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: May 20, 2021 5:08 PM
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] blur
Hi Aldo
Usually we just run recon-all with -all instead of the individual -autorecon
options. This will give you pretty much everything, including GM and WM
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Camargo, Aldo
Sent: Sunday, May 23, 2021 11:25 PM
To: Freesurfer
Hi Arunan
That is a giant defect and means something large (but possibly easily fixable)
went wrong. Have you looked at the subject? We have a tutorial on our website
for fixing topological defects, but in this case it will be something very
large (like a lot of the skull attached, or the 2 hem
Hi Nate
I guess it depends on how they were created. If it the ima/dicom creation
doesn't change either the direction cosines or the image data I don't think it
should be a problem.
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Nathan Hostetler
Sent: Wednesday, May 26, 2021
Or the ?h.inflated.nofix can be helpful as well
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Douglas N. Greve
Sent: Tuesday, June 1, 2021 5:57 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_fix_topology taking ages
I mean mris_fix_topology. Try loading the ?h.
Contact Dr. Quiroz If you are interested in the postdoc opportunity below
Bruce
From: all-boun...@nmr.mgh.harvard.edu On
Behalf Of Quiroz, Yakeel T.,Ph.D.
Sent: Tuesday, June 1, 2021 8:44 PM
To: a...@nmr.mgh.harvard.edu
Subject: [All] Postdoctoral position at the Multicultural Alzheimer's
Prev
smoothwm.nofix has a lot of holes), do you know if is there
any way to solve it? Could the data be modified in some way to get through this
step?
Thanks a lot for your great help!! Best wishes,
Diana Ortega.
El mié, 2 jun 2021 a las 3:13, Fischl, Bruce
(mailto:bfis...@mgh.harvard.edu>>) escrib
Hi Fatemeh
You need to give us significantly more information if you want us to be able to
help you
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Fatemeh Ahmadi
Sent: Monday, June 7, 2021 12:09 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] error in trian
Hi Evan
Is it a volumetric atlas or a surface one?
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Evan Collins
Sent: Saturday, June 12, 2021 11:33 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Inquiry about creating .label files from .nii file
Ex
from .nii file
External Email - Use Caution
Hi Bruce,
It is volumetric.
Thanks!
On Sat, Jun 12, 2021 at 11:47 AM Fischl, Bruce
mailto:bfis...@mgh.harvard.edu>> wrote:
Hi Evan
Is it a volumetric atlas or a surface one?
Cheers
Bruce
From:
freesurfer-boun...@nmr.mgh.harva
External Email - Use Caution
Thanks for the info. I have the atlas surface (with vertex data) saved as a
.vtk. Would the mris_sample_parc work with this input file type?
On Sat, Jun 12, 2021 at 1:01 PM Fischl, Bruce
mailto:bfis...@mgh.harvard.edu>> wrote:
I see. And what do you want to do wi
Sat, Jun 12, 2021 at 2:08 PM Fischl, Bruce
mailto:bfis...@mgh.harvard.edu>> wrote:
If you already have it on the surface you don’t need it, do you?
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harva
Sulc is the integrated dot product of the movement vector with the (outwards
pointing) surface normal during inflation. In gyral regions the movement vector
is consistently inwards and has a negative dot product with the surface normal,
which is why it is negative.
As for your second question,
Yes, if it is high enough quality
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of 1248742467
Sent: Monday, June 14, 2021 9:32 PM
To: freesurfer
Subject: [Freesurfer] the white matter surface is from the individual sMRI?
External Email - Use Caution
Hello, Fs
ca
Maybe a better way to think about curvature is that it indicates whether the
surface is locally above (positive) or below (negative) the tangent plane
On Jun 14, 2021, at 10:29 PM, Fischl, Bruce wrote:
Sulc is the integrated dot product of the movement vector with the (outwards
pointing
We produce 3 cortical parcellations based on different manual labelings. They
should be named *parc*.annot in the subject's label dir.
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of 1248742467
Sent: Tuesday, June 15, 2021 2:36 AM
To: freesurfer
Subject: [Freesurfer] wh
Hi Harriet
Is that a parcellation overlaid on the brain? Usually this means something was
not regenerated when you reran (like the parcellation). Try just recreating it
an see if it fixes your problems. Should just take a couple of min to run just
the parcellation stage
Cheers
Bruce
From: fre
Hi Rosalia
Does /home/rosalia/Desktop/ARTICO/sub-001_ses-BSL_T1w exist? Shouldn’t it have
an extension like .nii.gz or .mgz?
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Rosalia Dacosta Aguayo
Sent: Monday, June 21, 2021 10:49 AM
To: Freesurfer support list
Subject:
Caution
Hi Bruce,
Yes, I noticed that I did not include the extension by error.
Sorry for this childish error.
Kind regards,
Rosie
On Mon, Jun 21, 2021 at 5:06 PM Fischl, Bruce
mailto:bfis...@mgh.harvard.edu>> wrote:
Hi Rosalia
Does /home/rosalia/Desktop/ARTICO/sub-001_ses-BSL_T1w
Hi Spencer
Are 01.nii and 02.nii MRI volumes for different subjects? Do you have only a
single volume/subject? If so, you would recon-all on each one individually.
Something like:
recon-all -i /01.nii -s subj01 -sdir -all
if you have 8 cores and enough ram you can run 8 subjects at the same t
When replying, please edit your Subject line so it is more specific than "Re:
Contents of Freesurfer digest..."
Today's Topics:
1. Re: External 3D View Issue (Fischl, Bruce)
2. Yeo atlas for children! (Martin Juneja)
3. Running Freesurfer in the D
Hi Julia
I’m not sure what a group-level dice map would be. Maybe you are talking about
an accuracy map? Like how often a single point is in one label vs. another? For
individual cortical labels you can generate this for each label across subjects
using mris_spherical_average. If you really mea
Hi Lara
Can you send us some pictures? The answer depends on why the white matter
surface is settling at the wrong place
Bruce
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Lara Foland-Ross
Sent: Wednesday, June 23, 2021 7:11 PM
To: freesurfer@nmr.mgh.har
I guess doing it in matlab would be easiest
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Hye Min Shin
Sent: Friday, June 25, 2021 1:24 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Calculating group-wise Dice Similarity Coefficient
and corresponding surface map
Hi Rosie
I’m not sure what you mean by “control point errors”. The things control points
are intended to correct, like B1- shading, can cause topological defects, so
adding control points can fix the topology as well
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Rosa
control point errors
External Email - Use Caution
Hi Bruce,
Sorry, I refer to topological defects and white mater segmentation errors. What
should I correct first?
Kind regards,
Rosie
On Sat, Jun 26, 2021 at 6:25 PM Fischl, Bruce
mailto:bfis...@mgh.harvard.edu>> wrote:
Hi Rosie
I
Hi Vector
The .thresh files are indeed thresholded so that the label has the average area
of that label across subjects in our training set
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Zeng, Victor (BIDMC -
Keshavan - Psychiatry)
Sent: Monday, June 28, 2021 9:28 AM
T
oun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Fischl, Bruce
mailto:bfis...@mgh.harvard.edu>>
Sent: Monday, June 28, 2021 10:00 AM
To: Freesurfer support list
Subject: [External] Re: [Freesurfer] The differences in stats between BA_exvivo
and BA
Hi Guy
We don't automatically deface, nor do we transform into a normalized coordinate
system by default. We do "conform" - make the input data 1mm isotropic and
256^3, but it remains in the same RAS coordinate system
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Guy
Hi Lisa
Is the subject fsaverage symlinked in your SUBJECTS_DIR? Also, the argument to
-s is typically just an identifier, not a path then and identifier. That is, it
should be more like:
recon-all -s subid
instead of
recon-all -s imagedir/subid
I’m not sure if this is the source of your pro
Hi Daniel
Tksurfer has been deprecated for a long time. Have you tried freeview instead?
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Drucker, Daniel
Sent: Thursday, July 15, 2021 10:21 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] /usr/pubsw reference i
Hi Jamie
Where did the original .nii file come from? Seems like something might be wrong
with it. Do you have the dicoms it came from you can try? What if you try to
visualize the nifty directly?
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Podell, Jamie
Sent: Satur
Hi AJ
No, not easily. Maybe you can tell us your overall goal to see if we can help?
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of AJ
Sent: Wednesday, July 21, 2021 1:27 AM
To: Freesurfer support list
Subject: [Freesurfer] Intensity equalization
External Ema
Hi Robin
If you run-recon-all you will get a map that we call “sulc” for each subject.
When we generated our original manual parcellations we used it to guide where
to place the boundary between a sulcus and a gyrus. Essentially we used the
zero-crossing of sulc. Load it on an white surface and
Hi Rosie
Recon-all won’t delete edits unless you explicitly tell it to. That said,
control points my affect the region you are working on (and possibly correct
some defects!)
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Rosalia Dacosta Aguayo
Sent: Wednesday, July 2
order matter, right? That is, first do control points and once
corrected, then do wm_segmentation edits, right?
Sorry for insisting, but this is very important to me.
Kind regards,
Rosie
On Wed, Jul 21, 2021 at 4:44 PM Fischl, Bruce
mailto:bfis...@mgh.harvard.edu>> wrote:
Hi Rosie
Rec
Hi Don
By far the easiest way to do this is to find the locations of the points on the
sphere then compute the length of the great circle arc connecting them, then
correct by the ratio of the sqrt of the areas of the two surfaces.
Alternatively I think Rudolph may have had some tools for comput
, 09:40 Fischl, Bruce
mailto:bfis...@mgh.harvard.edu>> wrote:
Hi AJ
No, not easily. Maybe you can tell us your overall goal to see if we can help?
Cheers
Bruce
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:fre
Hi Franchesca
It’s hard to say without seeing your data so we can diagnose what went wrong.
If you upload a representative dataset we will take a look
Cheers
Bruce
From: Franchesca Kuhney
Sent: Wednesday, July 28, 2021 7:46 AM
To: Freesurfer support list
Cc: Fischl, Bruce
Subject: Re
Can you load
/Users/amhaun01/Documents/HERIdata/anatomy/AX_FSPGR_BRAVO_NEW_acpc.nii in
freeview? Maybe run ls -l on it?
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Andrew
Sent: Friday, July 30, 2021 1:44 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] niiRead: error o
- Use Caution
Bruce, thank you for this response. In fact I had the T1 path wrong despite
having read it over and over 20 times.. listing directory contents indeed
revealed my error…
-andrew
On Jul 30, 2021, at 13:38, Fischl, Bruce
mailto:bfis...@mgh.harvard.edu>> wrote:
Can you load
Hi Frank
Do you know why there are multiple frames? What kind of MRI acquisition are you
trying to use as input? Most standard T1-weighted series only have a single
frame
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Frank Chau
Sent: Monday, August 2, 2021 3:49 PM
To: freesu
Hi Ammar
In the mri dir there are segmented volumed called aseg.mgz and aparc+aseg.mgz
where every voxel has an index into the FreeSurferColorLUT.txt lookup file
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Ammar Shujaa
Sent: Tuesday, August 3, 2021 4:19 AM
To: frees
Hi Paul
Have you run recon-all on your data? If so, then there will be .annot files
that you can use to look up what parcellation unit is at that coordinate in any
given subject. Or closest to that coordinate as in general it may not be in
the cortex
Cheers
Bruce
From: freesurfer-boun...@nmr
That defect is about half the size of a normal surface model, so I don’t think
it will complete successfully! Doug is right about the bias fields, both
transmit and receive, so you usually have to at least do something on the
acquisition end to get a good-enough image. I’ll include Jon Polimeni
Hi Noam
can you convert them with any dicom converter to any other format? dcm2nii?
That kind of thing?
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Peled, Noam
Sent: Thursday, September 2, 2021 12:19 PM
To: Freesurfer support list
Subject:
wonder why mri_convert failed.
Thanks!
Noam
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: Thursday, September 2, 2021 12:44 PM
To: Freesurfer
Hi Rahul
Sorry, meant to respond to your previous post. The defects can change with
different versions and don't necessarily reflect things being "better" or
"worse". Sometimes even a single voxel difference in the wm segmentation can
create a giant defect. Can you investigate a bit and see wh
It is quite likely that in the next year or two we will be releasing versions
that have GPU support, so getting a card with a reasonable amount of RAM would
be a good idea
Cheers
Bruce
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Tim Schäfer
Sent: Thurs
Hi Blue
That message is almost certainly generated by the *.nii bit. Can you path to an
actual file instead of a wildcard? If you need multiple inputs you have to give
multiple -i options (like -I file1.nii -i file2.nii …)
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of ???
S
Hi Isaac
Yes, you can use mris_fill on the two surfaces, then intersect the resulting
volumes. We use the binary mri_ribbon that does this for you, you can try that
out instead if you want.
Cheers
Bruce
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of I. K
between the output of mri_ribbon and an
atlas ROI.
Is there a tool in freesurfer for this (preferred option to keep within the
same ecosystem) or would I be best off using something like fslmaths with the
-mas flag?
Thanks again for your help!
Isaac
> On 30 Sep 2021, at 3:19 pm, Fischl, Br
Can you just read it in with python or something and write it out in one of our
supported formats (like .lta)?
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Douglas N. Greve
Sent: Friday, October 8, 2021 1:36 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject:
Hi Paul
mri_vol2label maps the volume into an ascii label structure but has no
knowledge of surfaces. You then need to run mri_label2label with options like
–sample to sample it onto a surface
cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Paul Dhami
Sent: Sunday, Oct
And you can use read_annotation.m in $FREESURFER_HOME/matlab to load it
Cheers
Bruce
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Tim Schäfer
Sent: Monday, October 11, 2021 4:32 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Question about fsav
FYI
-- Forwarded message -
From: Stern, Chantal E mailto:chan...@bu.edu>>
Date: Thu, Oct 14, 2021 at 6:11 PM
Subject: Re: Research Computing Position in Kilachand
Hi Everyone,
We are still looking to fill this position. Please post or send to anyone who
might be interested!
Be
Hi Wei
The DKT and aparc are estimates from folding patterns, based on different
neuroanatomist’s conventions. The exvivo ones are based on direct observation
of highres ex vivo images where we can see the borders and likely to be more
accurate in my opinion. The first one is all vertices that
Hi Arian
Tksurfer has been deprecated for a long time. Can you try freeview instead?
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Arian Klows
Sent: Wednesday, November 3, 2021 1:07 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] tksurfer
External Email -
FYI
-Original Message-
From: Jeff Fessler
Sent: Thursday, November 4, 2021 8:56 PM
Cc: fess...@umich.edu
Subject: Faculty opening in ECE at University of Michigan in Image Analysis
External Email - Use Caution
Dear Colleague,
This year, the Electrical and Computer Engi
You need to tell recon-all what to do. Try adding -all at the end
On Nov 11, 2021, at 10:33 PM, a Chinese reader wrote:
External Email - Use Caution
Hello FreeSurfer Developers,
I'm attempting to compute the thickness of the grey matter ,but for some of my
subjects I get the follow
Hi Nilab
Can you send us an example? Usually you can fix this using expert options to
constrain the range of intensities that white matter is allowed to take
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Nilab Nasrullah
Sent: Thursday, November 18, 2021 8:01 AM
To: fr
Hi Noam
How much ram do you have in the machine? Is anything else big running? You can
also examine that defect and see what is going on. 9000 vertices is pretty big
so something significant like a chunk of skull might be fixable
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On B
edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of Fischl, Bruce
Sent: Thursday, November 18, 2021 9:29 PM
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] recon-all reconbatchjobs Segmentation fault
Hi Noam
How much ram do you have
Hi Rosie
It really depends on what your hypotheses are, but if you are covarying for age
and gender in thickness you probably want to do so in an analysis of volume as
well. The only real difference are (1) thickness doesn’t really need TBV
covariation, and (2) thickness is a more localizable q
Hi KC
1. Volumes are typically correlated with TIV and so if you don’t care about
TIV itself you probably want to include it as a nuisance variable (both
cortical and subcortical)
2. Thickness does not show this correlation and typically does not need to
be correlated. Surface area does,
Hi AJ
you might try SynthSeg, as that is one of the advantages of it - it isn't
biased towards any particular MRI sequence
cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of AJ
Sent: Thursday, November 25, 2021 9:00 PM
To: Freesurfer suppor
Sorry, what is the “sb” in sbTIV? I’m sure you can use it from samseg, or just
use samseg for the segmentation as well if you want, since it is agnostic with
respect to MRI sequence as well.
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of AJ
Sent: Saturday, November 27,
Subject: Re: [Freesurfer] SynthSeg
External Email - Use Caution
Many thanks.
Best
AJ
On Sat, Nov 27, 2021, 20:04 Fischl, Bruce
mailto:bfis...@mgh.harvard.edu>> wrote:
Sorry, what is the “sb” in sbTIV? I’m sure you can use it from samseg, or just
use samseg for the segmentation a
Hi Achille
I don't think any attachments came through.
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of
achille.teil...@chu-lyon.fr
Sent: Monday, November 29, 2021 2:40 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Visualization error in freeview from recon
That is the DKT atlas so you should look at lh.aparc.DKTatlas.annot in the
label dir
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of 1248742467
Sent: Tuesday, November 30, 2021 12:41 AM
To: freesurfer
Subject: [Freesurfer] Which file should be used as the result of auto
Hi Ali
No, there is no auto-cutting. You need to cut your own patch
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Alison McDonnell
Sent: Tuesday, November 30, 2021 2:01 PM
To: Freesurfer support list
Subject: [Freesurfer] FREESURFER issue making flatmap
External Ema
Hi KC
I think that not all regions occur in all subjects. I know that is true of
Christophe’s parcellation and think it is also true of Ron and Rahul’s, but
I’ll cc Ron who can comment
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Koustav Chatterjee
Sent: Wednesday,
ldn't
determine the file type as can be seen in the screenshot I attached in my
original email. I don't know why it wouldn't let me open it?
Thanks,
Ali
On Tue, 30 Nov 2021 at 20:06, Fischl, Bruce
mailto:bfis...@mgh.harvard.edu>> wrote:
Hi Ali
No, there is no auto-cutting. You
Sorry, had Ron’s old email address. Hopefully this one works
From: Fischl, Bruce
Sent: Wednesday, December 1, 2021 9:59 AM
To: Freesurfer support list
Cc: ron_killiany Ron KILLIANY (rkilli...@cajal-1.bu.edu)
Subject: RE: [Freesurfer] Queries on DK Atlas and No of regions
Hi KC
I think that
these files should I use if I would like to consider
Desikan-Killiany atlas?
Thanks you for your help.
Regards
On Wed, 1 Dec, 2021, 8:29 pm Fischl, Bruce,
mailto:bfis...@mgh.harvard.edu>> wrote:
Hi KC
I think that not all regions occur in all subjects. I know that is true of
Christ
External Email - Use Caution
Hi Bruce,
I used the command line you said and freeview opened but gave an error message
saying it failed to load the surface but in my folder i have an lh.inflated
file.
Thanks,
Ali
On Wed, 1 Dec 2021 at 15:05, Fischl, Bruce
mailto:bfis...@mgh.harvard.edu>>
at 15:00, Fischl, Bruce
mailto:bfis...@mgh.harvard.edu>> wrote:
Hi Ali
Can you send us the full command line and output in text?
Cheers
Bruce
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu&
Hi Trisanna
Can you run mris_sphere on it to create a spherical surface? You could then
register that to our atlas using mris_register. You will need to create a bunch
of files that we expect though like ?h.curv, ?h.sulc, etc... You might also
need to specify a volume, but I expect any conform
- Use Caution
Hi Bruce, I will try mris_sphere! But since this is a chimp average, when you
say then register it to your atlas- is this something I should do?
Trisanna
Sent from my Bell Samsung device over Canada's largest network.
Original message ----
From: &quo
alaxy
Original message
From: "Fischl, Bruce" mailto:bfis...@mgh.harvard.edu>>
Date: 2021-12-04 11:12 a.m. (GMT-05:00)
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] question about surface registration to an average
surface
O
: Freesurfer support list
Subject: Re: [Freesurfer] FREESURFER issue making flatmap
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IM-0001 is the subject name. should i instead be doing freeview -f
$SUBJECTS_DIR/$subjects/IM-0001 ?
On Thu, 2 Dec 2021 at 17:42, Fischl, Bruce
mailto:bfis...@mgh.harvard.edu
n Mon 6 Dec 2021, 15:24 Fischl, Bruce,
mailto:bfis...@mgh.harvard.edu>> wrote:
No, it should be:
freeview -f $SUBJECTS_DIR/IM-0001/surf/lh.inflated
the $ means to dereference a variable, so it was trying to find an environment
var named IM
cheers
Bruce
From:
freesurfer-boun...@nmr.mgh.
No such file or directory
error: mris_flatten: could not read surface file /Users/ali/lh.smoothwm
I can see the lh.full.patch file and smoothwm file in the surf folder.
Thanks
On Mon, 6 Dec 2021 at 15:35, Fischl, Bruce
mailto:bfis...@mgh.harvard.edu>> wrote:
It should be displayed by defa
working but think it'll get confusing if i change before then
Thanks
On Mon, 6 Dec 2021 at 16:56, Fischl, Bruce
mailto:bfis...@mgh.harvard.edu>> wrote:
Hi Ali
Can you send us the full command line and output in general? What directory are
you running that from? If not the surf dir th
Hi Sumit
Can you post some images? It looks like the topo fixer ran out of memory:
CORRECTING DEFECT 0 (vertices=2851, convex hull=1075, v0=1654)
An extra large defect has been detected...
This often happens because cerebellum or dura has not been removed from wm.mgz.
This may cause recon-all to
Hi Ali
mris_convert converts surface while mri_convert converts volumes (in general
these prefixes hold across all our binaries – the mris_ ones do surfaces and
the mri_ ones do volumes).
To convert a patch you need to tell mris_convert that it is a patch and not a
complete surface by giving t
n Thu, 9 Dec 2021 at 15:33, Fischl, Bruce
mailto:bfis...@mgh.harvard.edu>> wrote:
Hi Ali
mris_convert converts surface while mri_convert converts volumes (in general
these prefixes hold across all our binaries – the mris_ ones do surfaces and
the mri_ ones do volumes).
To convert a patch
Hi Travis
It is because you have a space “ “ in your path:
Processed Data
If you rename the path to
Processed_Data
It should work fine
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of William McCuddy AZ-Phoenix
Sent: Saturday, December 11, 2021 3:13 PM
To: freesurfer@nmr.mgh.h
Caution
wow, that did the trick! recon-all is off and running. Thank you for catching
this!
Travis
On Sat, Dec 11, 2021 at 1:24 PM Fischl, Bruce
mailto:bfis...@mgh.harvard.edu>> wrote:
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Hi Travis
It is because you have a space
HI Evie
You can try thresholding the premotor area, or removing the intersection with
precentral gyrus (or both)
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Tsolaki, Evangelia C.
Sent: Monday, December 13, 2021 3:18 PM
To: Freesurfer support list
Subject: Re: [Free
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Hi Jee Won
Can you send us the recon-all.log file? And ideally an example orig.mgz that we
can try things on
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Kang, Jee Won
Sent: Tuesday, December 21, 2021 9:19 AM
To: freesurf
Hi Knut
Including Ron in the conversation. Of course outside striate cortex the mapping
between folding and function isn’t so straightforward.
And Happy New Year to all!
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Knut J Bjuland
Sent: Saturday, January 1, 2022 8:03 AM
To:
Hi Rahul
If you have run the qcache stuff you can just run mri_average on all the
individual subject thickness files since they are all mapped to fsaverage, then
display them on fsaverage
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Yash Patel
Sent: Saturday, Januar
Hi Knut
Can you be more specific about what you mean by extrastriate cortex? Do you
mean all visual cortex that is not V1?
Bruce
From: Knut J Bjuland
Sent: Wednesday, January 19, 2022 8:43 AM
To: Fischl, Bruce ; Freesurfer Mailing List
Subject: Re: [Freesurfer] In the Desikan-Killiani
, January 20, 2022 9:56 AM
To: Fischl, Bruce ; Freesurfer Mailing List
Cc: Killiany, Ronald
Subject: Re: [Freesurfer] In the Desikan-Killiani parcellatino scheme, which
parcellations contain the extrastriate cortex?
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Hi Bruce,
We're using FreeSurfer data
Hi Anna
Where did you install FreeSurfer? That is where the env variable
FREESURFER_HOME should point. What does:
ls $FREESURFER_HOME
show you?
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Pusok, Anna
Sent: Thursday, February 17, 2022 6:40 PM
To: Freesurfer support list
Hi Edan
Sometimes control points can be more effective than editing the wm,
particularly if the intensities in that region are not what we expect (like if
the wm and gm are darker than what we try to set them to). Can you post an
image or two?
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.har
.
Cheers
Bruce
From: Edan Daniel
Sent: Friday, February 18, 2022 12:15 AM
To: Freesurfer support list ; Fischl, Bruce
Subject: Re: [Freesurfer] autorecon2-wm not reflecting edits in white matter
segmentation (7.1.1, 7.2.0)
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Hi Bruce!
We are focusing on the
Hi Francisco
My guess is that some of the versions you are using outputted the raw sulc (in
mm) and some z-normalized it. So you can either take all your sulc files and
z-normalize them, or rerun mris_inflate on all your subjects and give it the
flag
-mm
You can also add -sulc
So you don’t o
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