Hi Sandro
can you clarify what you mean? Do you want to run recon-all on each one
separately? That would be fine. Or do you mean somehow average all the
different res volumes into a single recon?
cheers
Bruce
On Sat, 11 Jul 2015, Sandro
Marini wrote:
Dear FreeSurfer experts,
we have col
,
Sandro
Message: 11
Date: Sat, 11 Jul 2015 10:04:20 -0400 (EDT)
From: Bruce Fischl
Subject: Re: [Freesurfer] voxel of different size
To: Freesurfer support list
Message-ID:
Content-Type: text/plain; charset="utf-8"
Hi Sandro
you can change formats with mri_convert:
mri_convert vol.nii.gz vol.mgz
but you shouldn't need to - all our tools will read nifti just fine. Doug's
question was whether your mask was in the right coordinates, regardless of
whether it was in mgz or nifti.
cheers
Bruce
On Sun, 12 Jul 2015,
Hi Niels
is that the entire error? Does it not say what volume produces the error?
That was a bug we had briefly some time ago, but I didn't think it made it
into anything we released. If you can track down which volume is causing
this problem you can just load it into matlab with load_mgh.m
vard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: zondag 12 juli 2015 16:44
To: Freesurfer support list
Subject: Re: [Freesurfer] Computing SA from an older FS version
Hi Niels
is that the entire error? Does it not say what volume produces the error?
Th
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: maandag 13 juli 2015 14:46
To: Freesurfer support list
Subject: Re: [Freesurfer] Computing SA from an older FS version
Hi Niels
the matlab commands should be:
>> [v, M,mr] = load_mgh('wm.mgz') ;
>&g
Hi Pawel
does this happen in both versions? If so, upload a bad subject and we
will take a look
cheers
Bruce
On Tue, 14 Jul 2015, Wrobel, Pawel wrote:
> Dear FreeSurfer Team!
>
> We have a question concerning corrections with white-matter-points.
>
> We are currently working on a T1 data set. A
can you run mris_info on
/scratch/lfs/aoshea/testAndrew/dotsonFSprocessed//EX03/surf/rh.white
and/or view it in freeview to make sure it isn't corrupted?
On
Wed, 15 Jul 2015, O'Shea,Andrew wrote:
Hello all,
I am having an issue where the mris anatomical stats command is failing and
only prin
icode1
talairach_flag 0
rescale 0.00
nvertices 106524
nfaces 213044
total_area 69696.328125
group_avg_vtxarea_loaded 0
avgvtxarea 0.654278
avgvtxdist 0.886314
stdvtxdist 0.266572
vtx0xyz 18.017620 -83.093475 36.833847
[aoshea@gator1 ~]$
On 7/15/15, 12:05 PM, "Bruce
Hi Amirhossein
we will reformat them all to 1mm iso during recon-all. Hopefully those
differences are small enough not to cause a bias.
cheers
Bruce
On Thu, 16 Jul 2015,
amirhossein manzouri wrote:
Hi FS,
MR images of two of my subjects in a group have been acquired with different
T1 pro
ay 13, 2015 at 8:38 AM, Bruce Fischl
wrote:
the gad will make the dura more likely to be segmented as wm and
might require more manual interventions, but if you are willing
to put in the time it should still be usable.
cheers
Bruce
On Wed, 13 May 2015, Santosh
Hi Itamar
no, I never got to the bottom of this. Zeke: do you know anything about it?
Bruce
On Sat, 18 Jul
2015, Itamar Kahn wrote:
Dear Bruce et al.,
I encountered the dreadful t_vertex assertion failed error. I’ve seen on the
list it showed up a while ago. Did you figure out which packag
(PNL)
> Brigham and Women's Hospital
>
>
>
> Message: 6
> Date: Tue, 14 Jul 2015 11:33:57 -0400 (EDT)
> From: Bruce Fischl
> Subject: Re: [Freesurfer] Correction with white-matter-points
> To: Freesurfer support list
> Message-ID:
>
> Content-Type: TEX
Hi Kristi
yes, that is correct. Everything is stored in native space and all
processing is done there until you start doing group-level stuff
cheers
Bruce
On Fri, 17 Jul 2015,
Kristi Griffiths wrote:
Dear FS experts,
I am new to freesurfer and have a few basic questions.
I have
Hi Bingjiang
did you acquire any field maps? If so, you can them to undistort the EPIs
cheers
Bruce
On Tue, 21 Jul 2015, Bingjiang Lyu wrote:
> Dear all,
> I've got the automaticlly parcellated 'aparc.a2009s+aseg.nii' file for
> individual T1 image, and I want to calculate functional connectiv
Hi Sam
if you want us to help you, you need to provide us with the full
command line and screen output (at least!)
cheers
Bruce
On Tue, 21 Jul 2015, Sam Zorowitz
wrote:
Hi all,
I am using mri_watershed to create skull surfaces for a cohort of subjects
for whom we were unable to collect a F
Hi Silas
what do you want to do with the labels? As for whether to do it on
fsaverage or individuals, you could start with fsaverage and map it to
your other subjects and see how accurate it looks
cheers
Bruce
On Tue, 21 Jul 2015, Silas
wrote:
> Dear Freesurfer team,
> I've created my own lab
Hi Stefano
can you send us the command that was run and the full output?
Bruce
On Wed, 22 Jul
2015, std...@virgilio.it wrote:
> Hi list,
>
> mri_convert command line did not provide output file.
>
> This error was produced during the first computations of trac-all -prep
> command line.
>
>
Hi Silas
I think we already provide the information you want as we tabulate the
thickness of the different parcels in the various files in each subject's
stats dir. If you want to do the same thing with a different set of labels
draw the labels on fsaverage, use mri_label2label to map them to
Hi Tony
if you run recon-all it will do everything needed. You could stop after
mri_ca_label I suppose, but then you won't be able to use the surfaces to
correct white matter and cortex.
cheers
Bruec
On Wed, 22 Jul 2015, Tony
Koroulakis wrote:
> Dear Freesurfer Team,
>
> I am inquiring as t
actors) : diagnosis
continuous (covariate) : age , Left-Lateral-Ventricle
---
which one click before analyze?
2015-04-05 21:41 GMT+09:00 Bruce Fischl
:
I'm glad it worked out
Bruce
On Sun, 5 Apr 2015, A-reum M
HI Alessia
you can turn the aparc file into separate labels using
mri_annotation2label, then load different parcels as individual labels
cheers
Bruce
On Thu, 23 Jul 2015, Alessia
Sarica wrote:
> Dear all,
>
> this is to know if you can suggest me the right way for visualizing on
> FreeSurfer
Hi Kalyan
usually improving the wm surfaces results in improved pial surfaces. If
not, it typically means something went wrong. If you upload a subject and
email me and Ani the coordinates of a spot (or spots) you are having
trouble, we will take a look
cheers
Bruce
On Thu, 23 Jul 2015, Trip
Hi Antonin
that's a good point and something we probably need to fix.
Bruce
On Fri, 24 Jul
2015, Antonin Skoch wrote:
> Dear Kalyan,
>
> do you use standard pial surface reconstruction via T1 images, or optional
> pial
> surface refinement with T2/FLAIR images?
>
> I had similar problems wit
p.s. although in this case I think it won't hurt to always pass that
parameter since it is only used for the flair/pial stuff
On Fri, 24 Jul
2015, Antonin Skoch wrote:
> Dear Kalyan,
>
> do you use standard pial surface reconstruction via T1 images, or optional
> pial
> surface refinement with
Hi Antonin
not sure - if you upload the subject I'll take a look
Bruce
On Fri, 24 Jul 2015,
Antonin Skoch wrote:
> Dear experts,
>
> I came several times across the situation when pial surface from one
> hemisphere
> is crossing the surface of other hemishpere (see the attached screenshot). Is
Hi Antonin
I think that the current flair/pial stuff will correct small errors in
the wm placement, but this one is probably too large and is really a
skull stripping problem. Have you tried gcuts? If the dura is attached to
the wm then the mris_make_surfaces step will not usually fix it.
sorr
you could try binarizing the brainmask.mgz
cheers
Bruce
On Fri, 24 Jul
2015, Liang Wang wrote:
Hi folks,
I would like to create a brain outline based on the generated pial surface. This
outline will completely cover the whole cortex (ignoring gyrus and sulcus info)
and is treated as a brain o
Hi Caspar
we tried to replicate this and couldn't. Can you upload the subject(s)
involved in this and send us the exact command line that shows the
problem?
cheers
Bruce
On Fri, 24 Jul 2015, Caspar M. Schwiedrzik wrote:
-- Forwarded message --
From: Caspar M. Schwiedrzik
you can use mri_morphometry and use the close operation to get rid of
some holes
On Sat, 25 Jul 2015, Liang Wang wrote:
Thanks Bruce. I applied mri_binarize to brainmask.mgz with specified threshold
and got many holes in the mask. In addition, brainmask.mgz includes the
cerebellum. I would like
yes, I guess so
On Fri, 24 Jul 2015, joseph veliz wrote:
> We need to subdivide regions of the VentralDC that would carry onto the
> aparc+aseg.mgz.
>
> Would this involve just editing the aseg.mgz?
>
>
> On Fri, Jul 24, 2015 at 9:27 AM, Douglas Greve
> wrote:
> For surface ROIs, you'll
Hi Joseph
if you have lots to get through you might be better off running two with 4
cores at a time. Speed increase is pretty good through 4 last time Nick
tested, but then the benefits fall off a bit
Bruce
On Fri, 24 Jul 2015, joseph veliz wrote:
> What is the best set up to utilize the mul
Maybe Zeke or Ruopeng know?
> On Jul 26, 2015, at 5:17 PM, A-reum Min wrote:
>
> Hi, Bruce
>
> When i use a Qdec, this message(12.png) show up..
> How can i solve this problem?
>
> 2015-07-23 22:57 GMT+09:00 Bruce Fischl :
>> 1. No, each subject has a differe
Hi Eric
the optimal smoothing kernel more or less matches the size of the effect,
so it's impossible to say a priori. A bigger kernel is better if there is
more widespread subtle thinning
cheers
Bruce
On Mon, 27 Jul 2015, Erik Lindberg
wrote:
> Dear freesufers,
> I quick question about smoot
it depends on which gm you are looking at. For cortex you can use the
brain.mgz, for any subcortical structure you can use the norm
cheers
Bruce
On Mon, 27 Jul
2015, Jacek Manko wrote:
I can't recommend anything in that case, since I am just relying on available,
but very scanty documentat
hmmm, that usually means you ran out of memory, which is surprising given
that that step doesn't take very much. Were there other jobs running on
the same machine?
On Mon, 27 Jul 2015, Park, Jung Mi wrote:
Hello Freesurfer expert
I got an error message while running recon-all.
1) subject na
there is probably an error before that. Can you send the entire
recon-all.log?
On Mon, 27 Jul 2015, Park, Jung Mi wrote:
Hello Freesurfer expert
Running recon-all abruptly stopped with this error message at NMR center;
mri_ca_register -invert-and-save transforms/talairach.m3z
Loading, Inve
Hi Chris
if you send me all the inputs to mri_ca_label and your exact command line
I'll see if I can replicate it and either fix it or send you a new
version. Or you can try the current dev version and see if it fixes
things
cheers
Bruce
On Wed, 29 Jul 2015, Chris Adamson wrote:
Devs,
Hi Antonin
if it is correct in the orig.nofix but not correct in the orig that means
it was an incorrectly fixed topological defect that you need to manually
correct. I'll see if we can find someone here to take a look.
Bruce
On Wed, 29 Jul
2015, Antonin Skoch wrote:
Dear experts,
during
Hi Owais
do you mean the wmparc.mgz or the aparc+aseg.mgz? You can use
mris_divide_parcellation or mris_make_face_parcellation to subdivide or
make an isotropic finer scale one if you want. I believe that you can then
create a new aparc+aseg from one of those and then the wmparc from that to
g
yes, specify -max on the command line
to mris_thickness and mris_make_surfaces (you can do this in recon-all with
expert options)
cheers
Bruce
On Wed, 29 Jul 2015, Jesse
Bledsoe wrote:
> Hi FreeSurfer community,
>
> I would like to see if FreeSurfer could be used to improve clinical detect
-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Thursday, 30 July 2015 12:03 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] dev version of mri_ca_label memory leak?
Hi Chris
if you send me all the inputs to mri_ca_label and your
Hi Caspar
the dev version of label2label doesn't have this problem. If you let us
know your hardware/software environment Zeke can get you a new binary that
should fix this issue
cheers
Bruce
On Thu, 30 Jul
2015, Caspar M. Schwiedrzik wrote:
Hi Bruce and Doug,
thanks for looking into th
Hi Andre
why would changing the surfaces affect ICV? We estimate ICV using Randy
Buckner's method of looking at the determinant of the Talairach transform,
which is totally insensitive to the surface placement.
cheers
Bruce
p.s. I think it's more common to include ICV as a regression factor
Hi Lena
you need to run the hippocampal subfield code. Depending on what version
you are running it could mean adding something like:
-hippocampal-subfields-
and removing the -autorecon-all
cheers
Bruce
On Thu, 30 Jul 2015, Lim, Lena wrote:
Dear Freesurfer experts,
My colleague (who
Hi Katherine
you can try changing permissions on the .license file if you own it:
chmod +w $FREESURFER_HOME/.license
if you don't you'll have to get the owner (or a sysadmin) to change it
cheers
Bruce
On Fri, 31
Jul 2015, Petrilli Paolino, Katherine wrote:
Hi,
I've been having problem
mgh.harvard.edu
When replying, please edit your Subject line so it is more
specific
than "Re: Contents of Freesurfer digest..."
Today's Topics:
1. Re: recon-all -white does not respect wm edits (Antonin
Skoch)
2. Re: wm parcellation freesu
HI Pantea
our atlases contain a lot more information than that and can't easily fit
into nifti (e.g. the Markov probabilities). Plus the fact that the gcs is
on the surface and not in 3D (it is on the surface of the sphere)
cheers
Bruce
On Fri, 31
Jul 2015, Pantea Moghimi wrote:
Hi,
I wa
Hi Jon
you need to send us the exact command line you are using for the
conversion and the counting
cheers
Bruce
On Fri, 31 Jul 2015, Jonathan Plasencia wrote:
> I've converted the aseg.mgz file to .nii (need data in nii to do some
> further work on the data). However, the number of voxels for
why are you specifying the output orientation? That is probably causing
resampling
On Fri, 31 Jul 2015,
Jonathan Plasencia wrote:
>
> We are using the following line:
>
>
> mri_convert aseg.mgz aseg.nii --out_orientation RAS
>
>
>
> Best,
>
> Jonathan Plasencia
> Graduate Student
> NSF G
ellow
School of Biological and Health Systems Engineering
Arizona State University
Email: jplas...@asu.edu
Phone: (480)861-7017
On Fri, Jul 31, 2015 at 12:54 PM, Bruce Fischl
wrote:
why are you specifying the output orientation? That is probably
causing
resampling
On F
hmm, something seems to be wrong maybe the the ?h.sphere. Can you try
recreating it
cheers
Bruce
On Sun, 2 Aug 2015, Fidel Alfaro Almagro wrote:
Hi all,
I received an error in one of the steps of recon-all. The error is "No such
file or directory" at the end of one of the registration processe
the same, I am guessing that any non-deterministic
process would have the same output.
Is there a a way to automatically know if there was a problem in the sphere
creation?
Cheers.
2015-08-02 16:27 GMT+01:00 Bruce Fischl :
hmm, something seems to be wrong maybe the the ?h.sphere. Can
Thanks,
Lena
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: 30 July 2015 18:02
To: Freesurfer support list
Subject: Re: [Freesurfer] Help with Freesurfer preprocessing pls
Hi Le
ginal Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: 03 August 2015 15:38
To: Freesurfer support list
Subject: Re: [Freesurfer] Help with Freesurfer preprocessing pls
Hi Lena
those aren't files that you
d.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: 03 August 2015 16:04
To: Freesurfer support list
Subject: Re: [Freesurfer] Help with Freesurfer preprocessing pls
no! Don't delete those files - we need them. Just don't include them in your
for loop
cheers
Bruce
subjects I have
so far ?
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: 03 August 2015 16:41
To: Freesurfer support list
Subject: Re: [Freesurfer] Help with Freesurfer preprocessing pls
I
original T1 MRI? If it is possible to do so that would be nice, otherwise I
will probably try to run the entire recon -all with the new voxel size.
Thanks,
Owais
On Wed, Jul 29, 2015 at 11:25 AM, Bruce Fischl
wrote:
Hi Owais
do you mean the wmparc.mgz or the aparc+aseg.mgz?
Jonathan Plasencia
Graduate Student
NSF Graduate Research Fellow
School of Biological and Health Systems
Engineering
Arizona State University
Email: jplas...@asu.edu
Phone: (480)861-7017
On Fri, Jul 31, 2015 at 12
le is based off the mgz file. If this is the
case then yes to your first question).
I'll send a mgz file and its stats file directly to your personal email in a
minute:
fis...@nmr.mgh.harvard.edu
Best,
Jon
On Mon, Aug 3, 2015 at 1:18 PM, Bruce Fischl
wrote:
and you are saying that ase
minute:
>>
>> fis...@nmr.mgh.harvard.edu <mailto:fis...@nmr.mgh.harvard.edu>
>>
>> Best,
>>
>> Jon
>>
>> On Mon, Aug 3, 2015 at 1:18 PM, Bruce Fischl
>> mailto:fis...@nmr.mgh.harvard.edu>> wrote:
>>
>> and you are saying tha
Hi Brent
are you saying you just multiplied the gray matter intensities by some
scale factor (>1)?
Bruce
On Tue, 4 Aug 2015, Brent Womble wrote:
Hi everyone,
I've been making synthetic brains to test how Freesurfer handles various
structural changes.
One of the changes I'm testing is increa
k=padarray(k,padsize_pre,1,'pre');
%Restrict the kernel to the gray mask
b=k.*c1;
b(~c1)=1;
%%Apply the kernel to the original image
c=b.*a;
%Write to .nii
raw.img=c;
save_nii(raw,[pwd,'/', num2str(i), '/dense-sy
a uniform
darkening of the gray matter.
On Tue, 4 Aug 2015, Brent Womble wrote:
Yes, I'm multiplying the image intensities by a scaling factor. Sorry if
that wasn't clear.
-Brent
On Aug 4, 2015 12:09, "Bruce Fischl" wrote:
Hi Brent
a quick look and it seems that
Just doing those structures should be fine
Bruce
> On Aug 4, 2015, at 10:46 PM, prasser wrote:
>
> Hi,
>
>
>
> If I am only interested in the gm thickness (ThickAvg) of a specific
> structure/s (e.g. precentral) is it sufficient to only QC these specific
> structures/s or does the wm and
Hi Saeed
if you specify -w to mris_inflate or mris_sphere it will save snapshots
of the process every nth iteration
cheers
Bruce
On Wed, 5 Aug 2015,
Saeed Mahdizadeh Bakhshmand wrote:
> Hello,
>
> Since surface deformation from WM to inflated surface is a gradual process,
> I assume that in
you can use convert to take the multiple tiff files that are written and
output a dynamic gifti
On Wed, 5 Aug 2015, Saeed
Mahdizadeh Bakhshmand wrote:
> Thanks Bruce, and Is there an easy way to make a movie of this deformation?
>
> On Wed, Aug 5, 2015 at 1:06 PM, Bruce Fischl
the easiest thing to do is to read them into matlab and write them back
out. I think that strips all the tags (which is where the subject name is
stored)
On Wed, 5 Aug 2015, Nate Vack wrote:
Thanks!
One complication I'm seeing is that when I uncompress, say, an .mgz file,
the old subject numbe
Will it be captured from a
specified perspective and 1 tiff for each volume?And these tiff files will
be combined to generate animated gif? What is "dynamic gifti"?
On Wed, Aug 5, 2015 at 3:08 PM, Bruce Fischl
wrote:
you can use convert to take the multiple tiff files that a
Hi Maryam
try specifying -f on the mri_cc command line (as the first option)
cheers
Bruce
On Thu, 6
Aug 2015, Syeda Maryam wrote:
> Hi everyone,
>
> So I've been going through the list trying to see if someone has encountered
> the same problem as me with regards to segmentation of the fornix
s it possible to separate the two?
> Thanks in advance!
>
> Regards,
> Maryam
>
>
>
> On Thursday, August 6, 2015 1:22 PM, Bruce Fischl
> wrote:
>
>
> Hi Maryam
>
> try specifying -f on the mri_cc command line (as the first option)
>
> cheers
> B
sure, you can use mris_anatomical_stats with the label (-l) and specify
sulc instead of thickness on the command line
Bruce
On Thu, 6 Aug 2015, Yang,
Daniel wrote:
> Dear FreeSurfer Experts,
>
> Is there a way to obtain sulcal depth in a given region (label) for a
> particular subject?
>
> Man
r gyrus dataset first
because it was simplest.
On Tue, Aug 4, 2015 at 12:58 PM, Bruce Fischl
wrote:
What you really want to simulate is an underlying
geometric deformation (like atrophy) that gets propagated
through an image formation model to create an atrophic
image. I don
; GrayVol ThickAvg ThickStd
>
> When sulc is used instead of thickness, do you know what the meaning of
> these three variables is changed to?
>
> Many thanks,
> Daniel
>
> On 8/6/15, 1:35 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
> Bruce Fischl" fi
no, the scalar overlays are stored separately (e.g. lh.curv, lh.sulc,
etc...)
On Thu, 6 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote:
Hello,
Is scalar overlay information embedded into surface file itself? When I open
them in freeview they are loaded with color overlays (sulcus/gyrus), but
when
load them as "curvature" files
cheers
Bruce
On Thu, 6 Aug 2015, Saeed Mahdizadeh Bakhshmand
wrote:
And are they treated as label files (e.g. lh.aparc.annot ) in the label
directory? And how they can be added to the tksurfer snapshot procedure?
On Thu, Aug 6, 2015 at 4:04 PM, Br
here? I set w to 5 and
> all of the iterations are spheres!
>
> Thanks,
> Saeed
>
> On Wed, Aug 5, 2015 at 1:06 PM, Bruce Fischl
> wrote:
> Hi Saeed
>
> if you specify -w to mris_inflate or mris_sphere it will
> save snapshots
> of
.
On Aug 6, 2015 7:45 PM, "Bruce Fischl" wrote:
yes, because it is unfolding on the sphere to recover metric
properties.
-w 1 gives you every iteration. You will need to show curvature
or you
won't see anything
On Thu, 6 Aug 2015, Saeed Mahdiza
Hi Jurgen
why not just use the defaced T1 as a mask for the DTI?
Bruce
On Fri, 7 Aug 2015,
Jürgen Hänggi wrote:
Dear FS experts
I have to anonymize T1-w. and DTI images. I run mri_deface for T1-w. images
successfully,
but I am wondering whether there is any easy way to also deface DTI imag
information for mris_sphere?
This page seems to e incomplete in that aspect.
Many Thanks,
Saeed
On Fri, Aug 7, 2015 at 10:36 AM, Bruce Fischl
wrote:
Hi Saeed
we normally project onto the sphere, but if you want to generate
a movie to show the idea you can give mris_sphere the flag -i
save your time for more technical
questions. Documentation doesn't correlate with how great FS and it's
support community is.
On Fri, Aug 7, 2015 at 11:11 AM, Bruce Fischl
wrote:
I guess only by looking at the code. We have tried to flesh out
most of the documentation but ha
Hi Gonzalo
Jon and Kyoko (both ccd) have put together a 7T stream, and should be
able to help you out
cheers
Bruce
On Sat, 8 Aug 2015, Gonzalo Rojas Costa wrote:
Hi:
Must I use any recon-all option for 7T images ?...
Sincerely,
Gonzalo Rojas Costa
--
Gonzalo Rojas Costa
Laboratory f
Hi Carina
it should be something like:
freeview -f /lh.inflated:overlay=mc-z.abs.2.sig.cluster.mgh
assuming mc-z.abs.2.sig.cluster.mgh is in your current directory
cheers
Bruce
On Sun, 9 Aug 2015, car...@van-vlodrop.de
wrote:
Hi Lilla,
I still have the problem to display my surface creat
sorry, had an old address for Kyoko
On Sun, 9 Aug 2015, Bruce Fischl wrote:
Hi Gonzalo
Jon and Kyoko (both ccd) have put together a 7T stream, and should be able to
help you out
cheers
Bruce
On Sat, 8 Aug 2015, Gonzalo Rojas Costa wrote:
Hi:
Must I use any recon-all option for
Hi Andre
it's up to you. The aparc and .aparc.DKTatlas40 are probably pretty
similar, although we haven't looked at the .aparc.DKTatlas40 much. The
aparc.a2009s contains more, smaller parcels, and so is probably less
reliable but might correspond more closely to an anatomical hypothesis you
h
001/t1.mgz, -1)
> could not open file"
>
> Any suggestions?
> Thank you.
> AS
> ___
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
> [fis...@nmr.mgh.harvard.edu
Hi Emma
can you clarify? Did you process one subject in a directory then overwrite
it with a second? If so you probably can't recover it without rerunning
recon-all.
cheers
Bruce
On Mon, 10 Aug 2015, Emma Thompson wrote:
> Hi,
> I'm re-posting my query in case it got buried on the listserve
yes, it should
Bruce
On Mon, 10 Aug 2015, Nate Vack wrote:
On Fri, Aug 7, 2015 at 2:45 PM Douglas N Greve
wrote:
On 08/07/2015 03:11 PM, Nate Vack wrote:
> Thanks. Any other file types I should look for tags in?
I think the surfaces have the subject name imbedded in them.
Hi Joseph,
no it shouldn't matter to us what the angle is as long as it's in
approximately the right orientation. You could reorient the volumes in
freeview if you wanted, but I don't think it's necessary
cheers
Bruce
On Mon, 10 Aug 2015, fmri wrote:
> Hello FreeSurfer experts,
>
> When MRI
Hi Vincent
you aren't creating a surface - you are creating a scalar overlay on the
surface. Try something like:
freeview -f lh.inflated:overlay=output.mgh
not that the MNI transform doesn't do a very good job aligning cortex so
the results will spread over adjacent gyri and such
cheers
Br
g and endling you told
me, freeview opens with the error message 'failed to load surface' and in
the command field it says 'MRISread failed'.
Do you have any idea of how it is possible to avoid this error?
Best regards, Carina
Gesendet: Sonntag, 09. August 2015 um 16:33 Uh
to redo anything (e.g., recon-all), does that sound
correct to you?
Thanks so much for your help!
On Mon, Aug 10, 2015 at 3:44 PM, Bruce Fischl
wrote:
Hi Emma
can you clarify? Did you process one subject in a directory then
overwrite
it with a second? If so you pro
Ruopeng should be able to help you out
cheers
Bruce
On Tue, 11 Aug 2015, fmri wrote:
> Is there a wiki instruction block on how to reorient all volumes?
>
> Thanks
>
> On Aug 11, 2015, at 6:13 AM, Bruce Fischl wrote:
>
>> Hi Joseph,
>>
>> no it shouldn'
oops, had a typo in Ruopeng's address.
On Tue, 11 Aug 2015, Bruce Fischl
wrote:
>
> Ruopeng should be able to help you out
>
> cheers
> Bruce
> On Tue, 11 Aug 2015, fmri wrote:
>
>> Is there a wiki instruction block on how to reorient all volumes?
>>
>
wrote:
Hi Bruce,
I send you a screenshot of my command field with my command line and the
following error message.
Thank you very much for your help.
Carina
Gesendet: Dienstag, 11. August 2015 um 16:54 Uhr Von: "Bruce Fischl"
An: "Freesurfer support list"
Betreff: Re: [F
Hi Chester
the voxel coords reflect positioning in the scanner and so there is a lot
of variability in them depending on landmarking, head size, etc...
cheers
Bruce
On Thu,
13 Aug 2015, Chester Dolph wrote:
I used mri_binarize to get a mask of the hippocampus from aseg.mgz and then
used m
can you use vol2surf to generate a .mgz/.mgh file instead? We have
deprecated the use of .w files
On Thu, 13 Aug
2015, Ivan Alvarez wrote:
> Dear all,
>
> I am wondering if there is a facility for loading .w overlay files in
> Freeview? In the surface section of the GUI, the overlay tab is for
Hi Jan
have you asked the HCP/Wash U group? I bet that they would know. Maybe Mike
Harms or Matt Glasser can chime in?
Bruce
On Thu, 13
Aug 2015, Jan Willem Koten wrote:
Dear ladies and possibly gentlemen as well,
I have got a rather nasty question. I would like to import the followi
FreeSurfer formats), however I don’t
provide Caret support either having not used it in years (I can be more
helpful with Connectome Workbench stuff). Donna on the Caret list can
perhaps provide further help.
Peace,
Matt.
On 8/13/15, 12:12 PM, "Bruce Fischl"
wrote:
Hi Jan
have you asked th
Hi Matt
can you tell us what your goal is for this analysis? You could use the
longitudinal tools depending on what you are up to
cheers
Bruce
On Fri, 14 Aug 2015,
Hibert, Matthew Louis wrote:
Hi Freesurfers,
I've scanned the same subject with 2 different head coils and reconstructed
the
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