Aug 6, 2015 at 4:20 PM, Bruce Fischl
wrote:
load them as "curvature" files
cheers
Bruce
On Thu, 6 Aug 2015, Saeed Mahdizadeh
Bakhshmand wrote:
And are they t
Hi Lars
can you give more details? What prevents you from entering values? Do you
get any errors when tksurfer loads?
cheers
Bruce
On Sat,
15 Aug 2015, Lars M. Rimol wrote:
>
> Hi all,
>
> I have installed FS 5.3 on an Ubuntu 14.04 system and find that I am unable
> to set threshold
> valu
Hi Fidel
How do you know it is wrong? Have you looked at the minc and the nifti in
freeview?
Cheers
Bruce
> On Aug 15, 2015, at 10:19 PM, Schumman Resonance wrote:
>
> Hi freesurfers,
>
> I want to convert minc files to nii to work with them in ITK-SNAP
> segmentation software.
>
> I have
What is the source file you are trying to convert? You need to specify a file
not a directory. If it is dicom, give it one file in the right series
Cheers
Bruce
> On Aug 16, 2015, at 2:34 PM, Hugh Pemberton wrote:
>
> Hi freesurfer team,
>
> I think this is a very basic error with the mri_
No I don't think so,
Sorry
Bruce
> On Aug 17, 2015, at 12:45 PM, Saeed Mahdizadeh Bakhshmand
> wrote:
>
> Hello Experts,
>
> Is there any command that can map both hemispheres of the brain into one
> single sphere? It will be equal to combining two inflated hemispheres into
> one spherical
Hi Feng
we compute many transforms for many reasons. The em reg is computed once
in the image with skull to help with skull stripping, then again to the GCA
atlas to initialize the nonlinear transform for computing the aseg
segmentation.
cheers
Bruce
On Tue, 18 Aug 2015, chenhf_uestc wrote
Hi John
the MEFLASH never achieved as good cortical contrast as the memprage, so
for cotical stuff we still recomment memprage. And yes, feeding the RMS to
recon-all will be fine. If you can get a readout/bandwidth matched T2-space
or FLAIR that can be a pretty big help as well for avoiding du
into recon-all at the same time as the MEMPRAGE as a second series?
best,
John
On 8/18/15, at Tue,Aug 18 - 8:32:00 PM, Bruce Fischl
wrote:
Hi John
the MEFLASH never achieved as good cortical contrast as the memprage, so for
cotical stuff we still recomment memprage. And yes, feeding th
transform from native space to MNI305
(We perform recon-all in the native space)? Best, Feng
发件人：Bruce Fischl
发送时间：2015-08-18 22:09
主题：Re: [Freesurfer] Query about transformations in the recon-all
收件人："Frees
Hi James
the same vertex index can be used within-subject and within-hemisphere (so
e.g. lh.pial, lh.white and lh.inflated all can be indexed with the same #s)
cheers
Bruce
On Sat, 22 Aug 2015, james pardon wrote:
> Dear All,
>
> I would be grateful if someone could help me to find the correp
Hi Jennifer
sorry for the lack of response - do you want to upload your subject data
(the entire subject directory) and we will take a look?
cheers
Bruce
On Mon, 24 Aug 2015, Kriegel, Jennifer Lynn
Sarai wrote:
Hi,
I apologize for asking this question again, but I’m still not recei
Hi Priyanka
that is what mri_extract_label is designed to do. This facilitates making
density maps in a common space. If you want to get the original label #
back you can use something like:
mri_binarize --match 128 --binval or something like that
cheers
Bruce
On Tue, 25 Aug 2015, Priyank
of course
On Tue, 25 Aug 2015, Priyanka wrote:
> Thanks Bruce. Just wanted to make sure I've got the correct output.
>
> Really appreciate the help.
>
> Thanks again,
> Priyanka Mehta
>
>> On Aug 25, 2015, at 4:44 PM, Bruce Fischl wrote:
>>
>> Hi Priy
Hi Joe
what version are you using? That looks a lot like a bug I fixed a month
or two ago (the hippocampal stuff). The cortex I'm not so sure about. Some
of it might be dura
cheers
Bruce
On Tue, 25 Aug 2015, fmri wrote:
> Dear Freesurfer experts,
>
> on aparc+aseg.mgz there is Hippocampus lab
;
> freesurfer-Darwin-lion-dev-20150701
>
>
> On Aug 25, 2015, at 3:11 PM, Bruce Fischl wrote:
>
>> Hi Joe
>>
>> what version are you using? That looks a lot like a bug I fixed a month
>> or two ago (the hippocampal stuff). The cortex I'm not so sure about. S
t;> hasn't it?
>>
>> On Tue, 25 Aug 2015, fmri wrote:
>>
>>> Version
>>>
>>> freesurfer-Darwin-lion-dev-20150701
>>>
>>>
>>> On Aug 25, 2015, at 3:11 PM, Bruce Fischl wrote:
>>>
>>>> Hi Joe
>>>>
&g
we have toold for doing this but they aren't documented (mris_expand,
mri_compute_layer_fractions, mris_compute_layer_intensities). This is what
Rebecca Shafee used in her recent two-compartment paper
http://www.ncbi.nlm.nih.gov/pubmed/25449739
cheers
Bruce
On Wed, 26 Aug 2015, Douglas Greve
:37, Bruce Fischl
wrote:
we have toold for doing this but they aren't documented (mris_expand,
mri_compute_layer_fractions, mris_compute_layer_intensities). This is
what
Rebecca Shafee used in her recent two-compartment paper
http://www.ncbi.nlm.nih.gov/pubmed/25449739
cheers
Bruce
Hi Emma
not yet, sorry
Bruce
On Wed, 26 Aug 2015, Emma Thompson wrote:
> Dear Freesurfers,
> Is it possible to segment using freesurfer specific thalamic nuclei, for
> example, the VPL?
>
>
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.e
Hi Alexander
I doubt it actually has a whole. We have automated topology correction
that prevents this. You can use mris_euler_number to check.
I am a bit surprised that you only have 30-something images. That is
typically not nearly enough to cover the brain at high-enough resolution
for go
Hi Cat
do those file exist? What does ls -l tell you for them?
Bruce
On Wed, 26 Aug 2015, Cat Chong wrote:
Dear Experts,
I am trying to use Freeview to view volumes using the command listed on the
website: http://freesurfer.net/fswiki/FsTutorial/OutputData_freeview but the
only volume that l
MF\Domain Users 0 Aug 26 09:12 brainmask.mgz
On Wednesday, August 26, 2015 12:04 PM, Bruce Fischl
wrote:
Hi Cat
do those file exist? What does ls -l tell you for them?
Bruce
On Wed, 26 Aug 2015, Cat Chong wrote:
> Dear Experts,
>
> I am trying to use Freeview to vie
did you run recon-all? If so, check the recon-all.log for errors
On Wed, 26 Aug 2015, Cat Chong wrote:
no, seems to be plenty left.. 240 TB
On Wednesday, August 26, 2015 12:23 PM, Bruce Fischl
wrote:
they are empty (zero size). Maybe your disk filled up?
On Wed, 26 Aug 2015, Cat Chong
Typically we use an mprage with 1mm isotropic resolution, but depending on
your coil/field strength you might want it to be a bit lower res to improve
CNR (say 1.1mm isotropic,which as 20% more SNR than 1mm)
On Wed, 26 Aug 2015,
Alexander van Dijk wrote:
Thanks Michael.
Yes, it was a clin
Hi Jen
I guess you would just use freeview to do the manual editing and then rerun
the autorecon2/3 stages that come later.
cheers
Bruce
On Thu, 27 Aug 2015, Jennifer Eastman wrote:
> Hello All,
>
> I am hoping to make some edits to subcortical segmentations, and while I have
> found instruct
Hi Michael
IBSR is not part of the FreeSurfer training set, but does use the same
manual labeling protocol.
cheers
Bruce
On Thu, 27 Aug 2015, Michaël Sdika wrote:
Hi,
Does anyone known if (and how) the 43 structures IBSR dataset and
FreeSurfer are related ?
The subcortical segmentation of f
> On Aug 26, 2015, at 7:06 AM, Bruce Fischl wrote:
>
>> it would fix the hippocampal problems and maybe the cortical ones as well
>>
>> cheers
>> Bruce
>> On
>> Tue, 25 Aug 2015, fmri wrote:
>>
>>> I have already processed 88 subjects in this
Hi Niels
why are you surprised that the pial surface has significantly more
surface area than the white? It would seem like it must.
Bruce
On Fri, 28 Aug 2015, Gerrits, Niels wrote:
Dear Experts,
With your help, I recalculated the surface area, now using the pial surface
instead of the wm
Hi Matthieu
I believe you can use
freeview -f lh.inflated:annot=lh.aparc.annot
check out freeview -help. It lists this type of option
cheers
Bruce
On Fri, 28 Aug 2015, Matthieu
Vanhoutte wrote:
> I launched freeview, then added manually lh.pial and rh.pial of
> fsaverage_sym. A this point al
Hi Jürgen and Ali
I don't think it has anything to do with the quality of the data, but we
are also happy to take a look if you upload one subject. This seems more
like an installation issue, and I would think it would happen on every
subject. Did someone upgrade perl at somepoint? Or just som
Hi Katarina
it looks like that file might be corrupted. Where did you get it from?
Can you view it in freeview? Maybe that partition was full when you copied
it there or something similar?
cheers
Bruce
On Mon, 31 Aug 2015, Katarina Trojacanec wrote:
Dear experts,
After running recon-all
Hi Michael
does /Applications/freesurfer/.license exist? Do you have permission to
read it? Don't name the file license.txt - rename it to .license
cheers
Bruce
On Mon, 31 Aug 2015, Amlung, Michael wrote:
Hi All,
This is my first time using the software. I have installed FreeSurfer on a
M
at 4:05 PM, Bruce Fischl
wrote:
Hi
Jürgen and Ali
I don't think it has anything to do with the quality of the data, but
we are also happy to take a look if you upload one subject. This seems
more like an installation issue, and I would think it would happen on
every subject. Did someo
Hi Cristina
sorry, while thalamic nuclei are of interest to us we haven't developed
anything for labeling them yet.
cheers
Bruce
On Mon, 31 Aug 2015, Lois Gomez, Cristina wrote:
Dear all,
I am interested in analyzing thalamic sub-nuclei separately, instead of the
whole thalamus. I've
Hi Andre
sorry, we haven't gotten to 9 and 46 yet
Bruce
On Tue, 1 Sep 2015, Son, Andre
wrote:
Hello,
I’d like to study measurements of Brodmann Areas 9 and 46 but they don’t
seem to be included in the FS package.
Do you know if there are any regions that FS generates that can be used
i
you need to use mris_expand to generate the family of intermediate
surfaces
cheers
Bruce
On Tue, 1 Sep 2015, Yun Wang wrote:
Hi all experts,
I have the error message when trying to use mri_compute_layer_fractions.
mri_compute_layer_fractions $SUBJECTS_DIR/fMRI/register.lta
$SUBJECTS_DIR/wh
no, you just need to name them in the way that
mri_compute_layer_fractions is expecting (e.g. lh.gwdist000 for white,
etc...)
On Tue, 1 Sep 2015, Yun Wang wrote:
> I do have 5 intermediate surfaces, should I combine them together?
>
>> On Sep 1, 2015, at 10:43, Bruce Fischl wrot
:
mri_compute_layer_fractions: could not load lh surface 5
from/Users/emilyUS/Documents/Cortical_layer/Data/anatomical/Rest-Anatomical/out
put/surf/lh.gwdist005
I do not have lh.gwdist005. How can I set up the number in this code?
On Sep 1, 2015, at 11:08, Bruce Fischl
wrote:
no
Hi Lena
Sure, but you will need to run all your subjects through recon-all first. The
if the ROI is in MNI space you can use mri_label2label to map it to our group
space fsaverage.
Cheers
Bruce
> On Sep 4, 2015, at 9:27 AM, Lim, Lena wrote:
>
> Sorry, I haven’t heard any replies so am re-post
Hi David
I don't think there's an easy way to do it all at once unless you apply
the transform to the orig.mgz then rerun recon-all (which will not be the
same as applying it to the outputs)
sorry
Bruce
On Fri, 4 Sep 2015, David Grayson wrote:
Hi all,
I would like to take a single subj
Hi Noam
yes, you should be able to run mri_pretess (or mri_mc) on any volume to
generate a tessellation of any label in the volume you specify
cheers
Bruce
On Thu, 3 Sep
2015, Peled, Noam wrote:
> Hello,
> Is there a way to run mri_pretess on fsaverage? It has no mri/norm.mgz file.
> I'm tryin
image file names?) --hemi lh –regmethod
surface
How do I next do the group comparison on the ROI?
Many thanks again,
Lena
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: 04 September 2015 15:25
To
Hi Chester
if you upload the dataset we will take a look
cheers
Bruce
On Fri, 4 Sep 2015, CHESTER DOLPH wrote:
Hello,
I have one brain in a large dataset that is not skull stripping properly. I
have tried the changing watershed parameters using the freesurfer tutorial,
but brainmask.mgz does
Hi Deborrah
I think we fixed this in the dev version
cheers
Bruce
On Fri, 4 Sep 2015, Deborrah
Castillo wrote:
Hi,
After doing cortical edits (removing part of the dura) and running RECON23,
the pial (red line) and white surface (yellow line) are crossing each other
(please see attached ima
Hi John
sorry, meant to respond but spaced it. Have you checked out the
wmparc.mgz? It may have what you need.
cheers
Bruce
On Sat, 5 Sep 2015, John Anderson
wrote:
Hi Freesurfers,
I am interested in studying the difference between the outer and deep white
matter volume in my study groups.
or Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419
Sent: Saturday, September 05, 2015 at 4:23 PM
From: "Bruce Fischl"
To: "Freesurfer support list&quo
ard.edu
> Subject: Re: [Freesurfer] Segmenting deep and outer white matter
> The best thing is to take a look at the wmparc. It was not really designed to
> be deep and superficial. There is only one "deep" WM seg which is called
> "Unsgemented White Matter" or so
if it's saved as a surface you can get it from mris_anatomical_stats. If
you want only a region within the surface, create a label and use the -l
option
cheers
Bruce
On Tue, 8 Sep 2015, Jockwitz, Christiane wrote:
Dear all,
I would like to extract the surface area from the outer smoothed
Hi Yun
1. No, the surfaces are not binary. They exist in in a continuum, so aren't
limited by the resolution of the underlying volumes. You should be able to
visualize them over the volumes using
freeview -v -f
2. mri_compute_layer_fractions computes the volume fractions of each
compartme
Hi Sebastien
it's pretty hard to tell what's going on from a couple of slices. What was
the command line you used? If you upload the subject I'll take a look (I'll
need the exact command lines you ran as well).
cheers
Bruce
On Tue, 8
Sep 2015, Sebastien Proulx wrote:
My images don’t se
p.s. you can try increasing the resolution of the intermediate volumes
using the -r switch. The default is 0.5. Try 0.25 (although this will
take 8 times the memory and time I think). Make sure to put the -r 0.25
before before the mandatory options. If this does make things look
significantly b
Hi Michael
sure, send us the recon-all.log. We don't get many segfaults, and usually
they are because you ran out of RAM or disk space. Were you running other
things on the machine at the same time? We will need this info:
https://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
cheers
Bruce
ng some sulci
properly (Bruce Fischl)
9. Help with recon-all (Amlung, Michael)
10. Re: mri_compute_volume_fractions not filling some sulci
properly (Bruce Fischl)
11. Re: Help with recon-all (Bruce Fischl)
12. TrackVis Transforms (Thomas Potrusil)
13. Re: TrackVis Transforms (Anas
Hi Sam
are you running this from a unix/linux command line? The >> usually means
matlab. In any case, it looks like $CTAB is not being expanded by the
shell. Try using echo to see what the actual command is.
cheers
Bruce
On Thu, 10 Sep 2015,
Sam Zorowitz wrote:
> Hi all,
>
> I am trying to
ginal Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
Sent: Thursday, September 10, 2015 10:06 AM
To: Sebastien Proulx
Subject: Re: [Freesurfer] mri_compute_volume_fractions not filling some sulci
properly
how much ram do you have in the machine? You probably need more. Also, ca
.
Best,
Sam
On Thu, Sep 10, 2015 at 9:00 AM, Bruce Fischl
wrote:
Hi Sam
are you running this from a unix/linux command line? The >> usually means
matlab. In any case, it looks like $CTAB is not being expanded by the
shell. Try using echo to see what the actual c
chine at 16GB. Would that be enough? Are there work around, since
going higher than 11.9GB might cause problem (memory swapping) between my
virtual machine and my native os.
-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
Sent: Thursday, September 10, 2015 10:15
Hi Jefferson
it sounds like one of your volumes has a different type. Maybe some of
the seg_edited.mgz are int and some uchar? Or maybe this is true of the
brain.mgz? Not sure, it is a bit of a confusing error message. if you can
narrow it down so it happens when you use only one or two subjec
Yi Yi-Yu
the volumes are partial-volume corrected.
cheers
Bruce
On Thu, 10 Sep 2015, Yi-Yu Chou
wrote:
> Dear Freesurfer experts,
> I was wondering why the volumes for each ROI reported in aseg.stats differ
> from the number of voxles
> counted using aparc+aseg.mgz (which is after surface-base
..
Thanks again,
David
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Friday, September 04, 2015 5:25 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] generating new FREESURFER dire
Hi Bronwyn
I think that means that the aseg failed in that region since it is caudate
and would have been filled if it had been correct. Can you check the aseg?
I'm pretty surprised as I don't think I've ever seen us mislabel caudate
there. You can upload it and we will take a look if you like.
changing names of the wm surface to pial surface would allow me to test this
idea?
Thanks a lot for your precious help!
Sébastien
-Original Message-----
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
Sent: Thursday, September 10, 2015 10:28 AM
To: Sebastien Proulx
Cc: freesurfer@nmr.
Hi John
I'm actually not sure how fslstats works. I'll cc MJ so he can answer that
part of it. When we measure volume (e.g. in the stats files) we do partial
volume correction as opposed to counting voxels, which we have found to be
more accurate and repeatable.
cheers
Bruce
On Sat, 12 Sep
sorry, I dont' think we have a binary for this, but it should be easy
enough in matlab with read_annotation
cheers
Bruce
On Wed, 16 Sep 2015, xtong wrote:
> Hi Freesurfer experts,
>
> I would like to register my test subjects to fsaverage and extract WM
> surface parcellation info into ascii fi
Hi Feng
I'll answer 1. and leave 2 for someone else (Doug?). We have a hard limit
on the max thickness of 5 but no lower bound other than 0 of course. This
prevents large values due to surface inaccuracies.
cheers
Bruce
On Wed, 16 Sep 2015, chenhf_uestc wrote:
Dear Freesurfer experts,
I
it seems that it stopped after a cp, not after the
mris_remove_intersection call, no?
On Wed, 16 Sep 2015,
Nakyoung Kim wrote:
Hi, freesurfer developers.
In some cases, I found that the recon-all script stops after running
mris_remove_intersection.
Here's an example of the recon-all.log in
;>> >
>>> > both(GLM, Qdec) group analysis program results
are
>>> not same. What
>>> > is differences
>>> >
>>> > between two analysis program? How can
Hi Feng
can you load that file into tksurfer/freeview? It sounds like something
is wrong with it. You should also just run ls -l on it and see if it looks
reasonable in terms of size and permissions
cheers
Bruce
On Thu, 17 Sep 2015, chenhf_uestc wrote:
Dear Freesurfer expert,
How could I
Hi,
you should copy the list on this type of email so others can answer.
Bruce
On Thu, 17 Sep 2015, Nakyoung Kim wrote:
oops, I didn't notice there's a cp after mris_remove_intersection.
Thanks for your advice.
I found a small error in recon-all script as follows:
--
Hi John
what parts of the basal ganglia do you want? We label
caudate/putamen/pallidum/accumbens separately. You can combine them all
together and get one ROI if you want. They should all be in the wmparc.mgz
cheers
Bruce
On Mon, 21 Sep 2015, John Anderson
wrote:
Hi Experts,
I want to do
Hi Richard,
yes, that all sounds good to me. The other thing you can do if you have the
data is use a T2 or flair to improve the dura removal.
cheers
Bruce
On Wed, 23 Sep 2015, Parker, Richard wrote:
Greetings Freesurfer Gurus,
I'm having a little trouble with a small minority of my s
Hi Jonathan
just a warning that Doug is likely to be out of contact for a few days so
please repost this type of question sometime next week.
cheers
Bruce
On Wed, 23 Sep 2015, Jonathan DuBois wrote:
Hi Doug,
Thanks for sending me this information. I ran gtmseg, and bbregister
successfully
Hi Angela
you can load it into matlab with read_curv. If you have the surface and the
tal xform (or transform the surface before loading it into matlab) you can
find the point on the surface that is closest to a given tal coord and read
out the sulc at that point
cheers
Bruce
On Wed, 23 Sep 20
Hi Jinsong
do you mean some of the values are not 1? By default I believe vol2vol uses
trilinear interpolation. Try including the option --nearest to use nearest
neighbor instead
cheers
Bruce
On Wed, 23 Sep 2015, Jinsong Tang wrote:
Hello,
I am try to convert some binary mask (0,1) to na
Hi Roberta
the surface indices are preserved in the flat maps and can be used to
lookup the coordinates on any of the surfaces.
cheers
Bruce
On Thu, 24 Sep 2015, Roberta
Santoro wrote:
> Dear list,
>
> I have created flat maps of Freesurfer ROIs and manipulated them in Matlab to
> extract onl
Feel free to upload a representative subject and we will take a look
Cheers
Bruce
> On Sep 24, 2015, at 11:54 AM, Martin Reuter
> wrote:
>
> Hi Garret,
> this is not really a longitudinal question, rather what accuracy can be
> expected and when do you need to do aseg edits. I therefore chan
cd $SUBJECTS_DIR/$subject/mri
set hemi=lh
mri_label2vol --labe ${hemi}.perirhinal_exvivo.thresh.label \
--regheader \
../mri/norm.mgz \
--fill-ribbon \
--subject $subject \
--hemi $hemi \
--o ${hemi}.peri.nii.gz
should do the trick
cheers
Bruce
On
when you say "it does not work either', what do you mean? Please remember
to send us the entire screen output of commands you are asking about
On Thu,
24 Sep 2015, Myriam Oliver wrote:
> Dear Freesurfers,
>
> I wanted to ask you if you know how can I convert a .mgh file to a .obj
> file.
>
> I
27;], []);
right_files = SurfStatListDir([cd filesep 'rh.white.transform'], []);
f = [left_files, right_files];
avsurf = SurfStatAvSurf(f);
The error is:
Error using + Matrix dimensions must agree.
Error in SurfStatAvSurf (line 36)
surf.coord=fun(surf.coord,double(s.coord
are they only high on the pial and not on the white? I would have guessed
that they would be high on both, and further that it is due to the topology
correction and the quirks of the way we retesselate. One easy way to find
out if this is true is if the vertex index is near the end of the list
you want to extract the time series from an fMRI volume in say "deep" and
"superficial" V1? If so, then I think what you want is 3 intermediate
surfaces between white and pial, then sample using surfaces 1 and 3 (but
not 2, which would be the boundary between the top half and the bottom
half).
functional data in
one or multiple ROI.
Thanks!
Yun
On Sep 25, 2015, at 10:59, Bruce Fischl wrote:
you want to extract the time series from an fMRI volume in say "deep" and
"superficial" V1? If so, then I think what you want is 3 intermediate surfaces between
white a
I use this?
—mask:the label that I want use V1?
On Sep 25, 2015, at 11:18, Bruce Fischl wrote:
Hi Yun
just specify the surface you want in mri_vol2surf to generate a time series
per-vertex on each surface, then you can average each of those within the V1
ROI if you want.
cheers
Bruce
Hi Martin
you will need to get the transform into either .lta .xfm or .dat format,
after which you can use mris_transform or mri_surf2surf I believe.
LTA format is specified here:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LtaFormat
cheers
Bruce
On Sun,
27 Sep 2015, Martin Tisdall wr
Hi Martin
what do you mean by "convert"? What is the volume? If it's a T1-weighted
MRI then you can use recon-all, but it's not so much a conversion as a
reconstruction.
cheers
Bruce
On Sun, 27 Sep 2015, Martin Tisdall wrote:
> Could you talk me through the best way to convert a volume to a su
erently would also like to know the best way of producing a
> surface to represent blood vessels from a thresholded ct angiogram volume
> where vowels will have different intensity values rather single label.
> Thanks Martin
>
>> On 28 Sep 2015, at 01:08, Bruce Fischl wrote:
thanks both for your responses, they were very very useful!
So, at the end I was not transforming properly (from the individual space to
the average).
After doing it, it works!
Many thanks!
2015-09-25 8:59 GMT-04:00 Bruce Fischl :
Hi Myriam
sorry, I don't know SurfStat at all so
Hi Ali
using Thomas' parcellation won't change the vertex-wise thickness values,
but of course if you want to average within his ROIs you can generate stats
files with that information.
Sorry, does that answer you question?
cheers
Bruce
On Mon, 28 Sep 2015,
Ali Radaideh wrote:
Thanks a
that is certainly wrong. What does it look like on the surface? You can
upload the subject if you want and we will take a look
On Mon, 28 Sep 2015,
Jacobs H (NP) wrote:
Dear Doug,
By looking at it in Freeview. Anatomically, I would expect that the entorhinal
cortex would not be localized so
Hi Feng
they are different atlases made up of a different set of manually labeled
subjects but they share the same colortable
cheers
Bruce
On Tue, 29 Sep 2015,
chenhf_uestc wrote:
Dear Freesurfer experts,
In the stats folder of subject in the SUBJECTS_DIR, I found the files of
lh.aparc.D
that will generate a parcellation on the individual subject surface of
Thomas Yeo's 17-network clustering. It won't do anything with the thickness
though. What are you trying to do?
On Tue, 29 Sep 2015, Ali Radaideh wrote:
mri_surf2surf --srcsubject fsaverage --trgsubject scz10 --hemi rh
--sv
Hi Mahinda
1. The subvoxel accuracy has been verified experimentally in Dianas Rosas'
paper:
http://www.ncbi.nlm.nih.gov/pubmed/11889230
where she measured the thickness under a microscope (ex vivo) and compared
it to our results and found they agreed within a couple of hundred microns.
It
Hi Feng
the area of the triangls is oriented to detected changes in the jacobian.
That said, they should be positive definite (you can verify
thismris_remove_intersection on the ?h.sphere.reg to make sure that this is
the case. Perhaps Anderson or Doug can comment?
cheers
Bruce
On Tue, 29 Se
Hi Feng
it depends on where the tumor is
cheers
Bruce
On Wed, 30 Sep 2015, chenhf_uestc wrote:
Hi, freesurfer experts,
If my data came from the patients with brain tumors, could I perform
recon-all analyses to calculate cortical thickness, surface area and so on.
If not, could I mask the bra
can you try chmod a+x on one of them and see if it can then be executed?
e.g.:
chmod a+x /home/tle7/freesurfer/bin/mri_convert
/home/tle7/freesurfer/bin/mri_convert
and see if you get an error. If not, you probably downloaded the wrong
hardware version
cheers
Bruce
On Tue, 29 Sep 2015, Ti
Hi Kie Woo
can you run mris_euler_number on those surfaces to see if they are
topologically correct?
cheers
Bruce
On Thu, 1 Oct 2015, Nam, Kie Woo wrote:
Dear experts,
I’m trying to calculate local gyrifcation index using CIVET’s surface file
(‘.obj’).
First, I’ve success
Hi Satra
it will probably reject this by default, which you can get around be
reslicing one of them to be like the other. Or "conforming" both of them.
cheers
Bruce
On
Tue, 31 May 2016, Satrajit Ghosh wrote:
> hi folks,
> does recon-all work if the input T1s for the same participant have diffe
Hi Shyam
can you add arrows to show where you don't think the surfaces are
accurate?
And are the green circles meant to be control points? If so, I'm
surprised that didn't break everything since they need to be added to the
interior of the WM.
cheers
Bruce
On Tue, 31 May 2016, Limachia,
nts?
Thanks,
Shyam
On 5/31/16, 3:33 PM, "Bruce Fischl" wrote:
Hi Shyam
can you add arrows to show where you don't think the surfaces are
accurate?
And are the green circles meant to be control points? If so, I'm
surprised that didn't break everything since they need
low/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep
> 4/005.mgz' to bspline ...
> MRItoBSpline degree 3
> Standard error:
> ERROR: MultiRegistration::loadMovables: images have different voxel sizes.
> Currently not supported, maybe first make conform?
>
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