Hi Ladan
that is a warning burried in the depths of some numerical optimization
libraries we use that I don't think matters. Did you kill the recon job?
I think it was running fine and you should let it go to completion then
take a look at the results
cheers
Bruce
On Wed, 28 Dec 2016, Ladan
Hi Paul
it's hard to diagnose from one slice. If you upload the subject and send
us voxel coords of this region we will take a look.
cheers
Bruce
On Wed, 28 Dec 2016,
miracle ozzoude wrote:
Hello Freesurfer, I was wondering if anyone knows how to correct an
underestimation of white matter
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
On Thu, 29 Dec
2016, miracle ozzoude wrote:
Thanks bruce. How do I upload the subject?Best,
Paul
On Thu, Dec 29, 2016 at 1:28 PM, Bruce Fischl
wrote:
Hi Paul
it's hard to diagnose from one slice. If you uploa
Hi Kevin
yes, I think that should work.
cheers
Bruce
On Fri, 30 Dec 2016, Kevin Aquino wrote:
Hi all,
When V6 is released I'd want to re-run all my (10) subjects through
recon-all again (they were processed with v6 alpha). I'd like to keep all my
wm edits, mask and control points, is it as e
Hi Ladan
the column of -1s means that the label hasn't been sampled onto to the
surface, and shouldn't matter if you are doing a volumetric analysis.
cheers
Bruce
On
Sun, 1 Jan 2017, Ladan Shahshahani wrote:
> Dear experts,
>
> I'm trying to create labels for subcortical regions. I want to us
Hi Antonin,
yes, we came across that bug and have fixed it (it's one of the reasons
that we didn't release before Christmas)
Thanks for catching it thouggh
Bruce
On Wed, 4 Jan 2017, Antonin Skoch wrote:
> Dear experts,
>
> while testing V6beta version I encountered problem with aseg. In one s
use -openmp 8
instead
cheers
Bruce
On Wed, 4 Jan 2017, Li,Tengfei wrote:
Hello,
Is there some way to use multithread in recon-all to speed up?
I searched the freesurfer website and try using
recon-all -autorecon-all -itkthreads 8 -subjid SUBID
It simply gives an error mess
Hi Robert
disk space and permissions are really the only two things I can think of.
Can you try writing it somewhere else? Or using .mgz as output (or .nii
without the .gz)?
cheers
Bruce
On Wed, 4 Jan 2017, Wujek, Robert
wrote:
> I'm trying to convert a group of .dcm files to .nii.gz, but I'
Hi Lucette
how do you do the editing? Looks like it was in some other package, which
probably accounts for the error. You should be able to fix it by
cding into the mri dir and running:
mri_convert -rt nearest -rl orig.mgz aseg.your_edits.mgz aseg.mgz
cheers
Bruce
On
Thu, 5 Jan 2017, Luce
."
Today's Topics:
1. V6 beta freeview - stopped loading remaining files when one
is missing (Antonin Skoch)
2. freeview V6beta - reposition surface option (Antonin Skoch)
3. Re: mri_convert error message (Bruce Fischl)
4. Re: V6 beta freeview - stopped loading remaining
Hi László
sorry, no there definitely isn't since the aparc+aseg is pretty much the
output of everything we do.
cheers
Bruce
On Sat, 7 Jan 2017, Halász László wrote:
Dear fellow Freesurfer users,
I just wanted to ask whether there is simpler and shorter way for getting
aparc+aseg without ru
Hi Nazanin
all our segmentations are in subject space, so it should be pretty
straightforward
cheers
Bruce
On Mon, 9 Jan 2017, N Saf wrote:
Dear freesurfers,
I analysis my T1 MRI with FreeSurfer (aseg.mgz 256x256x256) and I have
manual segmentation for hippocampus in my subject space(208x17
PM, Bruce Fischl wrote:
Hi Nazanin
all our segmentations are in subject space, so it should be pretty
straightforward
cheers
Bruce
On Mon, 9 Jan 2017, N Saf wrote:
Dear freesurfers,
I analysis my T1 MRI with FreeSurfer (aseg.mgz
Hi Paul
for 1 and 2, these are run internally to recon-all and don't need to be
run again afterwards. 3. looks right to me
cheers
Bruce
On Mon, 9 Jan 2017, miracle
ozzoude wrote:
-- Forwarded message --
From: miracle ozzoude
Date: Mon, Jan 9, 2017 at 11:06 AM
Subject: mri
hmmm, you had 3 numbered questions below, which is what my response
referred to
On Mon, 9 Jan 2017, miracle ozzoude wrote:
Thanks bruce for your response. Please, which of my questions did you answer
since I listed 4. Best,
Miracle
On Mon, Jan 9, 2017 at 2:46 PM, Bruce Fischl wrote
html
Best,
Paul
On Mon, Jan 9, 2017 at 2:55 PM, Bruce Fischl
wrote:
hmmm, you had 3 numbered questions below, which is what my
response referred to
On Mon, 9 Jan 2017, miracle ozzoude wrote:
Thanks bruce for your response. Please, which of my
questio
Hi Antonin
the reason we didn't answer your post about the reposition tool is that
it is really under development and for internal use only. You are
welcome to try it out, but we don't have the bandwidth to support it at the
moment.
cheers
Bruce
On Mon, 9 Jan 2017, Antonin Skoch wrote:
Hi Paul
it's to help with cortex where the deep layers are heavily myelinated and
the gray/white boundary isn't as big a jump in contrast as
infragranular/supragranular. It usually is only needed for hires data
cheers
Bruce
On Mon, 9 Jan 2017, miracle ozzoude wrote:
hello Bruce, I have ano
yes, and you shouldn't need a starting value (not sure what that even
means)
On Mon, 9 Jan 2017, miracle ozzoude wrote:
Thanks for your response bruce. Do you think I can use it for 3T scans and
do i need to specify a specific starting value?
Best,
Paul
On Mon, Jan 9, 2017 at 5:00 PM,
Hi Jerome
Do you mean the hippocampal subfield segmentation or the aseg whole hippocampus
one?
CheerS
Bruce
> On Jan 9, 2017, at 6:37 PM, Jerome Maller wrote:
>
> Jerome
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mg
Hi Paul
sorry, this is something that Ruopeng put together for me to mess around
with - there isn't any documentation
cheers
Bruce
On Tue, 10 Jan 2017, miracle ozzoude
wrote:
Hello Freesurfer, I would like to learn how to use the reposition surface
tool in freeview. Specifically, what para
Hi Lawrence
can you send us the full command line and screen output of what you ran?
thanks
Bruce
On
Wed, 11 Jan 2017, shi yao wang wrote:
Dear FS teams:
when I running FS, there is a message like this:
Error:Cannot find CTF archive
/usr/local/freesurfer/bin/segmentSubjectT1_autoEstimate
Hi Paul
it's hard to answer your questions without knowing what you are trying to
achieve
cheers
Bruce
On Wed, 11 Jan 2017, miracle ozzoude wrote:
Hello freesurfer,
I have several questions about mris_expand command. I know it can be used to
expand or shrink a point on a surface by a fixed
Hi Aziz
yes, you ran out of RAM. That said, a defect with 66K vertices is pretty
big - more than 1/3 of a typical surface. You should check to make sure
nothing big is wrong (hemis attached, skull left around, etc). Look
at the inflated.nofix surface and it should be obvious what the defec
1.mgz without other files.
Best Regards,
Aziz.
On Thu, Jan 12, 2017 at 8:55 PM, Bruce Fischl
wrote:
Hi Aziz
yes, you ran out of RAM. That said, a defect with 66K vertices
is pretty big - more than 1/3 of a typical surface. You should
check to make sure nothing big is
try.
Thank you,
Aziz.
On Thu, Jan 12, 2017 at 10:32 PM, Bruce Fischl
wrote:
Hi Aziz
it will be in the subject's surf dir. You can visualize it via:
freeview -f $SUBJECTS_DIR//surf/lh.inflated.nofix
cheers
Bruce
On Thu, 12 Jan 2017, Aziz Nanthaamorn
Hi Tamara
sorry, not easily - we have no visualization tools for the cortical
atlases (*.gcs files)
cheers
Bruce
On Thu, 12 Jan 2017, Tamara Tavares wrote:
> Hello,
>
> I was wondering whether it is possible to view the atlases that are used to
> construct the cortical surface ROIs in a visual
Hi Martin
I guess you could do it in tksurfer. This functionality hasn't been
addded to freeview yet
cheers
Bruce
On Tue, 10 Jan 2017, Martin Juneja wrote:
Hi,
I was wondering if there is any way to edit annot file e.g. I would like to
edit lh.Yeo2011_7Networks_N1000.annot file in such a way
Hi Chris
are you talking about recon-all -hires ...? That has worked for me without
cropping to 256.
cheers
Bruce
On Fri, 13 Jan 2017, Chris Adamson wrote:
In the git version I’m trying to use the -hires option on an image. It
initially says that I need the cw256 option to restrict the FO
Hi Zhivago
1) You can project from inside the ?h.white surface if projfrac<0 and
outside pial if projfrac>1. <<0 and >>1 won't make much sense though as it
starts to get arbitrary.
2) The default projfrac, as documented in the -help response, is 0.
3) Yes, 0-->white matter boundary. 1--> pia
yes, I believe so
On Sun, 15 Jan 2017, Zhivago wrote:
Hi,
Are the lh.ribbon & rh.ribbon volumes the GM estimate from reconall? Can I
used these as GM voxels?
Thanks,
Zhivago...
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mai
ll be helpful.
3) Is mri_vol2surf the only way to view activation maps on inflated surfaces
or any surface?
Cheers,
Zhivago...
On Sun, Jan 15, 2017 at 9:23 PM, Bruce Fischl
wrote:
Hi Zhivago
1) You can project from inside the ?h.white surface if
projfrac<0 and outside pial if
Hi Erik
it's all empirical, but I would think much over 1.5mm in and direction
would make it of limited value
Bruce
On Mon, 16 Jan 2017, Erik O'Hanlon wrote:
> Dear Freesurfer experts,
>
> I'm wondering if there is a minimum voxel size for the T2 iamge to be
> included in the recon_all. My T1
10:02 PM, Bruce Fischl
wrote:
1) This is up to you. Jon Polimeni had a nice paper
describing the trade-off between accurately representing
the local neural response (which is best at the white
border) and statistical power (which is best nearer the
pial surface).
Hi Nazanin
the volumes reported in the aseg.stats file have been corrected for
partial volume effects.
cheers
Bruce
On Wed, 18 Jan 2017, N Saf wrote:
Dear FreeSurfers,
I have a question about aseg file. I load the aseg file of bert subject in
itk-snap and read the volume for 17 and 53 label
Hi Sneha
how much RAM do you have in your machine? And what is the resolution of
your data?
cheers
Bruce
On Wed, 18 Jan 2017, Sneha Pandya wrote:
Hi all,
I have successfully ran recon-all on my subjects with multiple T1s. We want
to use flair to refine pial surfaces as for all the subject
recon-all -autorecon3 with -bbr-init-header flag.
Thanks,
Sneha
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Bruce Fischl
Sent: Wednesday, January 18, 2017 11:09:36 AM
To: Freesurfer support list
Subject: Re
urfer-boun...@nmr.mgh.harvard.edu
on behalf of Bruce Fischl
Sent: Wednesday, January 18, 2017 12:20 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] mris_make_surfaces error with bbr-init-header
hmmm, can you send us the recon-all.log file?
On Wed, 18 Jan 2017, Sneha Pandya wrote:
&
hen replying, please edit your Subject line so it is more
specific
than "Re: Contents of Freesurfer digest..."
Today's Topics:
1. Re: mris_make_surfaces error with bbr-init-header (Sneha
Pandya)
2. Re: mris_make_surfaces error with bbr-ini
Email)
On Wed, Jan 18, 2017 at 2:33 PM, Bruce Fischl
wrote:
Hi Alex
you get to decide whether to average your data or not. It's a
totally empirical question which one is better - why don't you
run them each and v
Email)
On Wed, Jan 18, 2017 at 2:56 PM, Bruce Fischl
wrote:
average what? The different voxel size images?
On Wed, 18 Jan 2017, Alex Cohen wrote:
I will likely end up running each separately on several
subjects to get a
handle o
can you please include the entire correspondence. We get a lot of emails
and it's hard for us to keep track otherwise
thanks
Bruce
On Wed, 18 Jan 2017, Aya
Kabbara wrote:
>
> Thank you..
>
> Actually, I realized that using tksurfer I can do a manual parcellation.
> However, I need an automati
, Jan 18, 2017 at 5:18 PM, Bruce Fischl
wrote:
Hi Nazanin
the volumes reported in the aseg.stats file have been corrected
for partial volume effects.
cheers
Bruce
On Wed, 18 Jan 2017, N Saf wrote:
Dear FreeSurfers,
I have a question about
Hmmm, not sure what's going on. Can you try this:
cd /mnt/Local_Data/Reliability/Matt/5514syxa_110502_3Tnu_HFBd_wmseg/scripts
setenv DIAG 0x04048
mris_sphere -w 0 -seed 1234 ../surf/lh.inflated ../surf/lh.sphere
and send us the output?
On Thu, 19 Jan 2017,
Sanjana Shellikeri wrote:
Hi Fr
Hi Nabin
note that tksurfer is deprecated - we are not developing it anymore.
That said, I thing you can type:
select_vertex_by_vno
at the tcl prompt, where is the number of the vertex you want to select
cheers
Bruce
On Fri, 20 Jan 2017, Nabin Koirala wrote:
Dear freesurfer team,
I wa
Hi Fabrice,
what would converting a thickness file (which has one value for each point
on the surface) to a volume mean? Would you want just a strand of voxels
with the thickness values at the gray/white boundary? At the pial surface?
Would you want the ribbon filled with the same value? If you
Hi Gabor,
it depends on the cause. Typically we fix this by placing control points
in the subjacent WM that is < 110
cheers
Bruce
On Wed, 18 Sep 2013, Gabor Perlaki wrote:
Dear all,
In the suggested workflow there is clear deescription of how to correct pial
surface including non-cortex wi
Hi Damien,
yes, that's correct. The sulc is the integrated dot product between the
movement vector and the surface normal, so things that move consistently
outwards (like sulci) will be positive, and gyri will be negative.
cheers
Bruce
On Sat,
21 Sep 2013, Damien MARIE wrote:
Hello everyo
Hi Daniel
you could do this in tksurfer, but I don't think there is a commandline
facility for it (although you could write a matlab script to do so). In
tksurfer, I would:
1. Load the label.
2. Copy label statistics to overlay
3. Delete the label
4. Load the parcellation you want to use
5. U
sure, glad to help
Bruce
On Sun, 22 Sep 2013, Yang, Daniel wrote:
Hi Bruce,
Cool! This works nicely! Thanks so much!
Best,
Daniel
--
Yung-Jui "Daniel" Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454
On 9/22/13 10:07 AM, "Bruce
Hi Daniel,
yes, mri_label2label will do this, at least the current dev version and
maybe 5.3:
mri_label2label | grep dilate
--dilate Ndilate the label N times before writing
cheers
Bruce
On Mon, 23 Sep 2013, Yang, Daniel wrote:
Hi FreeSurfer Experts,
Is it possible to dilate a la
Hi Amirhossein
as long as the surfaces are correct (yellow and red lines), then you
don't need to worry about the segmentation, as it is the surfaces that
define the thickness
cheers
Bruce
On Mon, 23 Sep 2013, amirhossein manzouri wrote:
Hi,
In the attached Slice image of a processed brain
Hi Andrew
sorry, not yet. It is on our list though
Bruce
On Mon, 23 Sep 2013,
O'Shea,Andrew wrote:
Hello FS-Experts,
I was wondering if there has been any work done to subdivide the thalamus
segmentation (aseg volume) into smaller sub-sections,
similar to what has been done with the hipp
Hi Daniel
you can give it to mris_anatomical_stats with the -l command
cheers
Bruce
On Mon,
23 Sep 2013, Yang, Daniel wrote:
Dear FreeSurfer Experts,
Is there a way to use command line to obtain the stats (e.g., area) for a given
label?
Thanks!
Daniel
--
Yung-Jui "Daniel" Yang, PhD
Po
Hi Krista,
which V1 label are you talking about? And when you say holes when you load
it onto the 3D brain with tksurfer, what exactly do you mean? Can you send
us a snapshot?
Bruce
On Mon, 23 Sep 2013,
krista kelly wrote:
Hi all,
I'm having trouble with V1 labels that are mapped automa
there is an opacity slider in freeview you can use for this
cheers
Bruce
On Tue, 24 Sep
2013, Jonathan Holt wrote:
> Is there any way to accomplish this?
>
> Jon
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.ha
jon
> On Sep 24, 2013, at 12:22 PM, Bruce Fischl wrote:
>
>> there is an opacity slider in freeview you can use for this
>>
>> cheers
>> Bruce
>> On Tue, 24 Sep 2013, Jonathan Holt wrote:
>>
>>> Is there any way to accomplish this?
>>>
Hi Jon
no, I don't think we use the orig surface for anything we report.
cheers
Bruce
On Wed, 25
Sep 2013, Jonathan Holt wrote:
> I'm curious whether or not freesurfer, when calculating surface values, takes
> the original surface into account? If not, which surfaces are included in
> this ca
Hi Panos
that means that you reran one of the surfaces but not the other. Try
running recon-all -make all, which should check to see if the
surfaces/volumes are up-to-date and rebuild them if needed. Note that
having an euler number of 2 doesn't mean the surfaces match, they also need
to have
Hi Francesco
recon-all assumes that all the control points are in the single file
/tmp/control.dat. Why are you separating them? Can you combine
them?
cheers
Bruce
On Thu, 26 Sep 2013, Francesco Siciliano wrote:
Hello,
I am currently having an issue getting my recon's to recognize multiple
Hi Jon,
I don't think it is, although you might be able to use mri_copy_values to
copy the edits from one volume to the other.
cheers
Bruce
On Thu, 26 Sep 2013, Jonathan
Holt wrote:
> I'd like to know whether or not this is possible. I am unable, at this
> point to figure it out. In the
ues works?
>
> jon
> On Sep 26, 2013, at 12:08 PM, Bruce Fischl wrote:
>
>> Hi Jon,
>>
>> I don't think it is, although you might be able to use mri_copy_values to
>> copy the edits from one volume to the other.
>>
>> cheers
>> Bruce
>
probably because there isn't one. I think it is:
mri_copy_values < output volume>
On Thu,
26 Sep 2013,
Jonathan Holt wrote:
> I apologize I was looking for syntax, I can't seem to find the help/manual
>
> jon
> On Sep 26, 2013, at 12:12 PM, Bruce Fischl wrote:
> subsequent edits. Is it not possible to have multiple sets of control points
> recognized during a recon-all?
>
> Thanks,
> Francesco
>
> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
> Sent: Thursday, September 26, 2013 12:06 PM
continue to add to one
> .dat file?
>
> Thanks,
> Francesco
>
> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
> Sent: Thursday, September 26, 2013 12:50 PM
> To: Francesco Siciliano
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: R
Hi Joy-Loi
read_curv.m should do the trick.
cheers
Bruce
On Fri, 27 Sep 2013, Joy-Loi Chepkoech
wrote:
> Dear FreeSurfer experts,
>
> I am looking for a way to read a subject's cortical thickness and
> volume, and surface area at each vertex into a vector that is readable
> by matlab.
> How s
Hi Panos
yes, mri_convert will do this with -odt int
cheers
Bruce
On Fri, 27 Sep 2013,
pfot...@nmr.mgh.harvard.edu wrote:
> Hi FS Community,
>
> I was wondering whether there is a way to convert a FLOAT type niftii file
> to an INT type niftii file.
> Thanks in advance!
>
> Best,
> Panos
>
Hi Paul
not really. It is a nonlinear transform to our own atlas, which is
loosely in MNI space. Doug can probably give you a more precise answer
cheers
Bruce
On
Fri, 27 Sep 2013, Paul Beach wrote:
Hello Freesurfer community,
I have a question about the file talairach.m3z, which is found i
Hi Michael
that looks pretty bad! What is the resolution of the T2? The T1 that you
overlay on also looks somewhat blurry - what was it?
Bruce
On Fri, 27 Sep
2013, Michael Waskom wrote:
Hi, just to make the problem a bit more transparent, I took a second
screenshot of the slices with the
>
> On 9/27/13 12:58 PM, "Bruce Fischl" wrote:
>
>> Hi Michael
>>
>> that looks pretty bad! What is the resolution of the T2? The T1 that you
>> overlay on also looks somewhat blurry - what was it?
>>
>> Bruce
>>
>>
>> On Fri,
r
to modify the –nsigma_above and -nsigma_below flags for
mris_make_surfaces when using -T2pial?
Peace,
Matt.
From: Michael Waskom
Date: Friday, September 27, 2013 2:20 PM
To: Matt Glasser
Cc: Bruce Fischl ,
"Freesurfer@nmr.mgh.harvard.edu"
Subject: Re: [Freesurfer] Major
hmmm, maybe Nick or Doug can investigate, although we are crazy busy at
the moment
On Sat, 28 Sep 2013, Michael Waskom wrote:
>
> On Sat, Sep 28, 2013 at 5:28 AM, Bruce Fischl
> wrote:
> hmmm. That would be strange and would result in complete failure
>
>
> I a
1. sorry, not easily that I can think of
2. I guess you could try mri_robust_register on the brain.mgz, output the
halfway volumes, then count ones that are 0 in the post and not 0 in the
pre (and probably are brain in the aseg of the pre)
cheers
Bruce
On Mon, 30 Sep 2013, Germeyan, Sierra (NI
Hi Arnaud
why would transparency help? You should be able to view the overlay on
any surface without transparency (the overlay defines the colors
displayed on the surface). Can you explain further why the normal display
in tksurfer doesn't do what you want?
cheers
Bruce
On Tue, 1 Oct 2013,
yes, bbregister should do this just fine with T2 contrast specified
cheers
Bruce
On Tue,
1 Oct 2013, Ayaz, Muhammad wrote:
Dear All,
Can I co-register SWI with FLAIR images using Freesurfer?
thanks
Ayaz
_
not able to see the snapshots.
Thanks!
Krista
On Mon, Sep 23, 2013 at 5:10 PM, Bruce Fischl
wrote:
Hi Krista,
which V1 label are you talking about? And when you say holes
when you load it onto the 3D brain with tksurfer, what exactly
do you mean? Can you send us a snapshot
Hi Caspar
try putting control points in the white matter where the pial surface
doesn't get out far enough.
cheers
Bruce
On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote:
> Hi Freesurfer Experts,
> I am working on a fairly noisy and inhomogeneous MPRAGE T1 and I am having
> trouble getting the p
e grey matter intensity (the white surface looks pretty good)?Caspar
>
> On Thursday, October 3, 2013, Bruce Fischl wrote:
> Hi Caspar
>
> try putting control points in the white matter where the pial
> surface doesn't get out far enough.
>
> cheers
h. Can you tell us more about the acquisition?
On Thu, 3 Oct 2013,
Caspar M. Schwiedrzik wrote:
the white matter is mostly between 100 and 110 in these regions. at least in
the center of the wm, the voxels are almost all 110.
caspar
2013/10/3 Bruce Fischl
is the WM in those
where the pial surface starts to fail is when the gray matter
values drop from above 90 to below 90.
Caspar
2013/10/3 Bruce Fischl
h. Can you tell us more about the acquisition?
On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote:
the white matter is mostly between 100
drop from above 90 to below 90.
Caspar
2013/10/3 Bruce Fischl
h. Can you tell us more about the
acquisition?
On Thu, 3 Oct 2013, Caspar M. Schwiedrzik
wrote:
the white matter is mostly b
yes, and all the z values should be zero if it has been flattened. Note
that the coordinates in the flat space are pretty arbitrary
cheers
Bruce
On Thu, 3
Oct 2013, Oya, Hiroyuki wrote:
Hello,
read_patch (patch_name) gives x,y and z values. Are these vertex RAS?
Thank you.
Hiroyuki
something I'm doing wrong?
Please let me know you're not able to see the
snapshots.
Thanks!
Krista
On Mon, Sep 23, 2013 at 5:10 PM, Bruce Fischl
wrote:
Hi Krista,
how long have you waited?
On Fri, 4 Oct 2013, Marcos Martins da Silva wrote:
Hi, Freesurfers
I am getting some interesting hippocampal surfaces with the following steps:
1- recon-all -all -hippo-subfields
2- mri-concat (only CA1, CA23, CA4DG and the tail complement volumes)
3- a custom OCTAVE
Hi Tara
if you upload the subject we will track it down
cheers
Bruce
On Fri, 4 Oct 2013, Tara Ann
Miskovich wrote:
> Hello Freesurfer experts,
>
> I am having difficulty when trying to extract LGI values from a specific
> label I made. mris_anatomical seems to work when I run it with an annota
Hi Jon
voxels deleted with tkmedit are set to 1, not 0, so try that
Bruce
On Fri, 4 Oct 2013, Jonathan Holt wrote:
> I'm trying to apply voxel deletions made to the brainmask.mgz to the wm.mgz.
> As I understand it, if I run
>
> mri_copy_values brainmask.mgz 0 wm.mgz
>
> all of the 0 value voxe
oblem. See occipital lobe.
Caspar
2013/10/3 Bruce Fischl
Hi Caspar,
that's probably part of the problem. Is this human data?
If you actually run it at 1mm (conforming it) does it work
better?
Bruce
On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote:
I
Hi Sarah
what ROIs do you mean? And did you correct for the reduced surface area
in fsaverage w.r.t. the individual surfaces? If not, it's not surprising
that fsaverage ROIs have less surface area. It is an average surface and
less folded than any individual.
cheers
Bruce
On Mon, 7 Oct 201
on Freesurfer Wiki how
to merge the
labels into an annot file but not how to make the labels from the binary masks.
Thank you for your attention.
2013/10/4 Bruce Fischl
how long have you waited?
On Fri, 4 Oct 2013, Marcos Martins da Silva wrote:
Hi, Freesurfers
Hi Francesco
where do you save the file control.dat? It must be in the directory
$SUBJECTS_DIR/$subject/tmp/control.dat
otherwise recon-all won't find it
cheers
Bruce
On Mon, 7 Oct 2013, Francesco
Siciliano wrote:
> Hello,
> I am still having issues getting all of my control points to be ef
/7 Bruce Fischl
Hi Caspar
I'm not sure what to tell you. There are bright spots and rings out near
the pial
surface that are probably part of your problem, and the images even in
the zoom
look really inhomogenous. I don't think we ever have to add thousands o
>
> -Francesco
> ________
> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
> Sent: Monday, October 07, 2013 12:47 PM
> To: Francesco Siciliano
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] [FreeSurfer] control points
>
> Hi Francesc
and how many do you see in the control.dat file? Sounds like they aren't
getting saved to disk somehow
On Mon, 7 Oct 2013, Francesco Siciliano
wrote:
> I counted at least 28 control points on the brainmask when I loaded the set
> and my log indicates that freesurfer read 22 control points.
what version are you running?
On Mon, 7 Oct 2013, Francesco Siciliano wrote:
> Hello,
> After doing manual editing to the surface of a brain (brainmask.mgz, wm.mgz,
> and brain.finalsurfs.mgz) through freeview, I noticed that the volumes of
> some subcortical structures (specifically the hippocamp
you check if you
really received the file? If not, I will try again using plain ftp.
Thank you again for your help.
Marcos.
Em Seg, 2013-10-07 às 09:21 -0400, Bruce Fischl escreveu:
hmmm, I guess you should upload the subject so that we can track it down
On
Mon, 7 Oct 2013, Marcos Martins da Sil
instead of 8).
Thank you again.
Em Seg, 2013-10-07 as 20:47 -0400, Bruce Fischl escreveu:
sorry, I don't think it completed as unzip can't find the end of directory
mark in the file. Try our filedrop instead:
https://gate.nmr.mgh.harvard.edu/filedrop2/
cheers
Bruce
On
Mon, 7 Oct 20
Hi Olof
what are the dimensions of the volumes that fail? If you upload one we will
take a look. Is it a display problem or is the volume actually cropped? Try
looking at the .mgz in different viewers (freeview, fslview) and see if it
is still an issue
cheers
Bruce
On Tue, 8 Oct 2013, Erik
on my analysis. Please, could you check if
you really received the file? If not, I will try again using plain
ftp.
Thank you again for your help.
Marcos.
Em Seg, 2013-10-07 às 09:21 -0400, Bruce Fischl escreveu:
hmmm, I guess you should upload the subject so that we can track it down
On
Mon, 7 Oct
Hi Daniel
no, I don't think so. What would a correction index be?
cheers
Bruce
On Wed, 9 Oct 2013,
Daniel Moadel wrote:
> Dear Freesurfer friends,
>
> I am wondering if there is a confidence value or correction index for the
> volumetric data in aseg.stats. Thanks for your help!
>
> Daniel Mo
quality of the scans? Sorry if that
> is redundant. Thanks again,
> Daniel
>
>
> On Wed, Oct 9, 2013 at 4:35 PM, Bruce Fischl
> wrote:
> Hi Daniel
>
> no, I don't think so. What would a correction index be?
>
> cheers
> Bruc
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