Dear all,
the current module in FreeSurfer works with 1mm T1 data, by relying on strong
shape priors. So, at this point, feeding the algorithm data from a 3T scanner
or a 1.5T scanner is pretty much the same.
Joshua, it is indeed inaccurate to say that the method relies on a generated
hippocampa
Thank you very much!
A last question, please. Therefore, do you are working also on SLF I and SLF II
implementation in TRACULA? If yes, how much time might be required to do it?
(I'm writing a paper and I may wait these new tracts).
Stefano
Messaggio originale
Da: fis...@nmr.mgh.harv
I think there is - look in the view menu. There is also something in
freeview that Ruopeng can point you at.
cheers
Bruce
On Sun, 27 Apr 2014, prasser wrote:
> Thanks for your reply.
>
> Yes, I can upload the data. Is there a private area I can upload to?
>
> Also, is there a flag that enables
Thanks Eugenio.
On Mon, Apr 28, 2014 at 3:18 AM, Eugenio Iglesias wrote:
> Dear all,
> the current module in FreeSurfer works with 1mm T1 data, by relying on
> strong shape priors. So, at this point, feeding the algorithm data from a
> 3T scanner or a 1.5T scanner is pretty much the same.
> Josh
Hi Corinna,
try to open
/home/Documents/longitudinal_morph/meta/test_subject_2ndpostop/mri/orig/001.mgz
in freeview to see if maybe the file is corrupted.
Best, Martin
On 04/25/2014 03:46 PM, Corinna Bauer wrote:
Hello,
I am on the recon-all -long step of the longitudinal processing stream
Hi Martin,
Neither freeview nor tkmedit could open the 001.mgz file. It could not read
262144 bytes at slice 4. At this point is my best option to re-run this
time point from the beginning?
Corinna
On Mon, Apr 28, 2014 at 9:18 AM, Martin Reuter
wrote:
> Hi Corinna,
>
> try to open
>
> /home/D
Hi Maia
it's hard to know from just these images, but I wonder whether the high
background noise level at the top of the image is messing up 5.1. You
might try cropping that out and seeing if things get better.
cheers
Bruce
On Fri, 25 Apr
2014, Maia Pujara wrote:
Hi all,
After running 200
Bruce,
I dont see any WM connections that jump out at me. Could I upload it and have a
second opinion?
Jon
On Apr 25, 2014, at 11:33 PM, Bruce Fischl wrote:
> Hi Jon
>
> in this kind of case the default method did the wrong thing (closing the hole
> instead of cutting the handle). You need t
Hi Corinna,
the 001.mgz is the first file created in the cross sectional stream
(when you import your dicom) it is the input image to the stream and
just the dicom converted into mgz format. If it is corrupted, you should
rerun this cross sectional time point (just to be safe), the base and
t
sure
On Mon, 28 Apr 2014, Jonathan Holt wrote:
Bruce,
I dont see any WM connections that jump out at me. Could I upload it and have a
second opinion?
Jon
On Apr 25, 2014, at 11:33 PM, Bruce Fischl wrote:
Hi Jon
in this kind of case the default method did the wrong thing (closing the hole
No, I mean using the --cache option which will use precomputed tables
rather than generating new ones
On 04/24/2014 08:01 PM, Jacqueline Elaine Fitzgerald wrote:
> Hi Doug,
>
> Thank you for your reply. By precomputed do you mean the FDR in the
> GUI? Apologies I'm still new to the program!
>
>
Use mri_cor2label
On 04/28/2014 01:11 PM, std...@virgilio.it wrote:
> Hi list,
>
> I'd like to obtained .labels of thalami to use it in FSL.
>
> How can I do it?
>
> Thanks,
>
>
> Stefano
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.
My apology. Here, the responce
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg32645.html
Messaggio originale
Da: std...@virgilio.it
Data: 28-apr-2014 19.11
A:
Ogg: [Freesurfer] labels of thalami
Hi list,
I'd like to obtained .labels of thalami to use it in FSL.
H
Thank you very much!!
Messaggio originale
Da: gr...@nmr.mgh.harvard.edu
Data: 28-apr-2014 19.21
A:
Ogg: Re: [Freesurfer] labels of thalami
Use mri_cor2label
On 04/28/2014 01:11 PM, std...@virgilio.it wrote:
> Hi list,
>
> I'd like to obtained .labels of thalami to use it in FSL.
>
>
Hi list,
I'd like to obtained .labels of thalami to use it in FSL.
How can I do it?
Thanks,
Stefano ___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mai
Hi FS experts,
I was wondering what the best way to extract an ROI from an anatomical
volume would be. For instance, I would like to create a volume of only the
wm-lh-precentral based on the orig.mgz volume and on the segmentation map
wmparc.mgz. I know that something similar can be done with the
John,
Have you tried the Centos6_x86_64 build of freesurfer on Fedora 19? The
Centos4_x86_64 build is built against a rather old kernel, and likely to
go away soon anyway.
Generally a debug build is not of much use for tkmedit seg-faults. If
you still have trouble after trying the centos6 build
Hi Panos
so you want an intensity volume that is zero everywhere except in a
label? If so, try mri_mask
cheers
Bruce
On Mon, 28 Apr 2014, pfot...@nmr.mgh.harvard.edu wrote:
> Hi FS experts,
>
> I was wondering what the best way to extract an ROI from an anatomical
> volume would be. For instan
My apologies, but how can I visualize and check the labels obtained by
mri_cor2label?
Thanks,
Stefano
Messaggio originale
Da: std...@virgilio.it
Data: 28-apr-2014 19.23
A:
Ogg: [Freesurfer] R: Re: labels of thalami
Thank you very much!!
Messaggio originale
Da: gr..
Load them in tkmedit
On 04/28/2014 01:46 PM, std...@virgilio.it wrote:
> My apologies, but how can I visualize and check the labels obtained
> by mri_cor2label?
>
> Thanks,
>
>
> Stefano
>
> Messaggio originale
> Da: std...@virgilio.it
> Data: 28-apr-2014 19.23
> A:
> Ogg: [Freesurfer] R
The matrix in the lta is probably not the right one. Try using
lta_convert or tkregister2 to change it to a register.dat file (which is
what is expected in your formula)
doug
On 04/25/2014 12:28 PM, ISAAC PEDISICH wrote:
> Hi All,
>
> I am attempting to transform sets of coordinates from subjec
Try running
tkmedit fsaverage orig.mgz -reg
$FREESURFER_HOME/average/mni152.register.dat -overlay rIPL.nii -fminmax .1 1
to see if they mask lands in the right place. If it does not, then your
input data are not in mni152 space
On 04/25/2014 10:38 PM, charujing123 wrote:
> Hi doug,
> Thanks
Look for spuriousWMconnections.tar
jon
On Apr 28, 2014, at 12:03 PM, Bruce Fischl wrote:
> sure
> On Mon, 28 Apr 2014, Jonathan Holt wrote:
>
>> Bruce,
>>
>> I dont see any WM connections that jump out at me. Could I upload it and
>> have a second opinion?
>>
>> Jon
>> On Apr 25, 2014, at 1
On 04/26/2014 07:06 AM, charujing123 wrote:
> Hi all,
> I have done group analysis and see it in freeview. Also I can see my
> sig.cluster.summary file to find clusters those survived. As I know,
> the MNIX MNIY MNIZ in the cluster summary file is coordinates for the
> maximum. The coordinate s
On 04/26/2014 02:54 PM, Kaveh Kohan wrote:
> Dear All,
>
> This probably a newbie question, so I apologize if it is a naive one,
> please bear with me.
>
> I have on value for each ROI on the surface of brain and one value for
> each sub-cortical structures. Those ROIs and sub-cortical structur
Also robust register (at least the standard version that you use) is not
designed to do cross modal registration. So I am amazed it can register
a CT to an MRI at all (if that is what you are doing). To get a better
registration try
- using a different cost functions, e.g.
--cost nmi (normaliz
Hi Bruce,
Yes, that's exactly what I needed, thanks a lot!
Best,
Panos
> Hi Panos
>
> so you want an intensity volume that is zero everywhere except in a
> label? If so, try mri_mask
>
> cheers
> Bruce
>
> On Mon, 28 Apr 2014, pfot...@nmr.mgh.harvard.edu wrote:
>
>> Hi FS experts,
>>
>> I was w
There should be a ?h.volume file. Are you sure there is not? You can
specify -meas volume when you run mris_preproc
doug
On 04/27/2014 08:35 PM, Yizhou Ma wrote:
> Dear freesurfer experts,
>
> I am working on a project on cortical asymmetry and I have analyzed
> vertex-wise cortical thickness/
Hi Doug,
Thanks for the response.
I'm not seeing lta_convert as an executable that I can run. I have
freesurfer v5.3.0 installed - is there another version that I should be
using?
For using tkregister2, I'm a bit confused as to what I should be doing. I
had assumed (erroneously, it seems) that the
FYI, it is bbregister not bb_register :-)
On 04/28/2014 02:51 PM, Martin Reuter wrote:
> Also robust register (at least the standard version that you use) is not
> designed to do cross modal registration. So I am amazed it can register
> a CT to an MRI at all (if that is what you are doing). To
Thanks Doug. I have ?h.volume in subject/surf but not in
subject/xhemi/surf. I followed this page
http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi and I think it is a problem
with surfreg rather than mris_preproc. Can I just copy the ?h.volume from
subject/surf to subject/xhemi/surf?
Best,
Cherry
Then something went wrong along the way. Check the xhemi/xhemireg.?h.log
to see if there is an error. If not, send the log file to me
On 04/28/2014 04:14 PM, Yizhou Ma wrote:
> Thanks Doug. I have ?h.volume in subject/surf but not in
> subject/xhemi/surf. I followed this page
> http://surfer.n
When you say the content is the same, do you mean exactly the same or
just the matrix? Also, what coordinate system are you trying to go to?
The equation you have below takes CRS in the CT and maps it to tkrRAS in
the anatomical. If you want to map the CRS in the anat then use
inv(Tanat) * inv
Sorry - I meant just the matrix.
I'm trying to map from CRS in the CT to tkrRAS in the anatomical, I
believe. I'm a little unclear as to what exactly anat space means, but I
know that I'm trying to get it from CRS in the CT to the space in which the
surface is plotted in MATLAB, which I believe is
I don't think this is aproblem either. tkmedit/freeview will be showing
it in the acquisition RAS space (not the image coordinate space). I
don't think there is anything wrong with the actual data. If the volumes
from other packages do not show up this way in tkmedit/fv then it may
mean that t
I have T1 data that has been run through freesurfer and I want to apply the
subcortical parcellations from that analysis to some QSM data. The mailing list
and website refer to using reg-feat2anat but this require an existing feat
directory. If I make a "pseudo" feat directory with my QSM data s
Thanks Doug. I don't see an error message in xhemireg.?h.log files. Please
see attached for the files.
On Mon, Apr 28, 2014 at 4:22 PM, Douglas N Greve
wrote:
>
> Then something went wrong along the way. Check the xhemi/xhemireg.?h.log
> to see if there is an error. If not, send the log file to
Hi Doug,
I just read from the .log files that the lh.thickness/area/pial/... files
in subject/xhemi/surf are copied from subject/surf at the end of the
command. Thus it seems that I can just copy lh.volume, too?
Thanks,
Cherry
On Mon, Apr 28, 2014 at 6:25 PM, Yizhou Ma wrote:
> Thanks Doug. I
This is a basic question about the process for manual edits and the
autorecon commands. I am going to follow the recommended reconstruction
page (on fs wiki) to make manual edits on my data. The page says that you
can make all the manual edits at once. But my question is, how do you go
about runnin
Hello I have only recently started the fmri data analysis and I downloaded
freesurfer point by point from martinos site and incorporated the license
file as well into the Applications/freesurfer directory. I have run into
the first problem and that is of data conversion. My file is in dcm format
an
You can convert Dicom using MRICroN with the dcm2nii utility
shantanu
On Mon, April 28, 2014 6:55 pm, Dr Sampada Sinha wrote:
> Hello I have only recently started the fmri data analysis and I downloaded
> freesurfer point by point from martinos site and incorporated the license
> file as well in
Hello Shantanu,
Thanks for your reply.I tried using that as well. And it says that the file
is only 'read' file. I used chmod on unix but still its not working with
dcm2nii. Interstingly, when I used mriconvert software for this,it
converted all the dcm files to .img/.hdr files. This process resul
Hi Sampada,
Please cc the freesurfer list when answering/asking questions so others
can answer too. And also people with similar issues will benefit from the
discussion.
see inline for my responses.
Hth,
shantanu
On Mon, April 28, 2014 8:27 pm, Dr Sampada Sinha wrote:
> Hello Shantanu,
>
> Than
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