You can find information on using our ftp site here:
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
Thanks,
Lee
On Mar 5, 2015, 22:16, at 22:16, Pedro Rosa wrote:
>Sure. How can I do it?
>
>Sent from my iPhone
>
>> On Mar 6, 2015, at 00:01, Bruce Fischl
>wrote:
>>
>> Can you put i
Hi Doug,Thanks for your reply.This is the terminal output:
[Eran-Harels-MacBook-Pro:doors_group_51014/doors11.lh/r-vs-nr] eiran%
mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir group.glm
--nii.gz --surface fsaverage lhReading source surface
/Applications/freesurfer/subjects/fs
Sure. How can I do it?
Sent from my iPhone
> On Mar 6, 2015, at 00:01, Bruce Fischl wrote:
>
> Can you put it on our ftp site instead?
>
>
>
>> On Mar 5, 2015, at 9:37 PM, Pedro Rosa wrote:
>>
>> Hi,
>> It will upload in an hour, I guess:
>> https://www.dropbox.com/sh/n9talmyxiafdt56/AADF
Can you put it on our ftp site instead?
> On Mar 5, 2015, at 9:37 PM, Pedro Rosa wrote:
>
> Hi,
> It will upload in an hour, I guess:
> https://www.dropbox.com/sh/n9talmyxiafdt56/AADFttKFv3erLqDd48OpjQsna?dl=0
> Thanks a lot,
> Pedro.
>
>> On Mar 5, 2015, at 23:32, Bruce Fischl wrote:
>>
>
Hi,
It will upload in an hour, I guess:
https://www.dropbox.com/sh/n9talmyxiafdt56/AADFttKFv3erLqDd48OpjQsna?dl=0
Thanks a lot,
Pedro.
> On Mar 5, 2015, at 23:32, Bruce Fischl wrote:
>
> Hmmm, if you upload it we will take a look
> Bruce
>
>
>
>> On Mar 5, 2015, at 9:26 PM, Pedro Rosa - Gmai
Hmmm, if you upload it we will take a look
Bruce
> On Mar 5, 2015, at 9:26 PM, Pedro Rosa - Gmail
> wrote:
>
> That’s from a 1.5T-SPGR GE scanner with 0.86x0.86x1.5mm voxel size, echo time
> 5.2ms, repetition time 21.7ms, angle 20, FOV 22, matrix size 256x192mm.
>
> Pedro Rosa
>
>> On Thur
That’s from a 1.5T-SPGR GE scanner with 0.86x0.86x1.5mm voxel size, echo time
5.2ms, repetition time 21.7ms, angle 20, FOV 22, matrix size 256x192mm.
Pedro Rosa
On Thursday, March 5, 2015 at 11:11 PM, Bruce Fischl wrote:
> What are your acquisition parameters, voxel size etc...?
>
>
>
What are your acquisition parameters, voxel size etc...?
> On Mar 5, 2015, at 9:08 PM, Pedro Rosa - Gmail
> wrote:
>
> Hi, Bruce.
> Yes, it it the T1.mgz. Is it a large topological error? Can I correct it
> editing wm.mgz?
> Thanks,
> Pedro.
>> On Thursday, March 5, 2015 at 10:52 PM, Bruce F
Hi, Bruce.
Yes, it it the T1.mgz. Is it a large topological error? Can I correct it
editing wm.mgz?
Thanks,
Pedro.
On Thursday, March 5, 2015 at 10:52 PM, Bruce Fischl wrote:
> What is the background image? Is it the t1 that your reconned? Can you give
> us the details about it?
>
>
>
> On M
Dear Bruce,
Reading the doc for read_annotation, it suggests that label entry
values should correspond to the colortable.table(:,5) indices. I wanted to
use it on Desikan annotation atlas and find annotation scout names for
selected cortical points:
[vertices, label, colortable] = read_annotati
[SORRY IF THIS IS A DUPLICATE]
Dear Colleagues:
The Diffusion Study Group is sponsoring a novel Fiber Tractography Challenge to
stimulate an interactive discussion on diffusion reconstruction and
tractography methods at this year’s study group meeting at ISMRM 2015 in
Toronto. The Challenge w
What is the background image? Is it the t1 that your reconned? Can you give us
the details about it?
> On Mar 5, 2015, at 8:28 PM, Pedro Rosa - Gmail
> wrote:
>
> Dear FreeSurfer,
> I have found several subjects to have temporal lobe misegmentations (usually
> neocortical, as attached, but
Dear FreeSurfer,
I have found several subjects to have temporal lobe misegmentations (usually
neocortical, as attached, but sometimes mesial tempporal), and less frequently
in the insula.
I could find in the manual editing page from the Wiki a way to fix this. How
should I do it?
Thanks a lot,
yes, it does exist in that space. As long as your folding pattern atlas is
in register with fsaverage it should work ok. But of course if your
motivation is that your pediatric subjects have different folding patterns
(which I'm not sure I believe unless they are *very* young), then the whole
p
I don't think this makes sense unless you have created a new label atlas
for your individual subjects. The current label atlas exists in the
fsaverage space. Maybe Bruce can weigh in.
On 03/05/2015 04:46 PM, Jason Tourville wrote:
> Hi Doug,
> Perhaps I should back up and explain our goal. We a
Hi Doug,
Perhaps I should back up and explain our goal. We are using Freesurfer to
recon pediatric data sets and are planning to use the surface labels as
seeds for connectivity studies and for morphometric analyses. We're
concerned that using the fsaverage surface template as the target for
surfac
Did you run different subjects with different version of freesurfer (or
with different version of mri_segstats)?
On 03/05/2015 04:26 PM, Maria Kharitonova wrote:
> Hi all,
>
> I’m trying to extract aseg and aparc stats. Aparc worked fine, but
> when I’m trying to extract aseg stats, I get the f
Hi all,
I'm trying to extract aseg and aparc stats. Aparc worked fine, but when I'm
trying to extract aseg stats, I get the following warnings, then error:
Parsing the .stats files
WARN: 3696 nmeasures = 66, expecting 55
WARN: 4455 nmeasures = 66, expecting 55
Building the table..
ERROR: All sta
Great- thanks for the quick reply!
m
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
[fis...@nmr.mgh.harvard.edu]
Sent: Thursday, March 05, 2015 4:00 PM
To: Freesurfer support list
Subject: R
sorry, the answer is pretty much "no" to both questions. We have 3D-printed
surface models, but the steps for doing so aren't documented or supported.
I guess the easiest thing to do would be to combine the surfaces in matlab.
You'll have to add the # of vertices in one hemi to all the indices i
The mris_register command is what does the registration and creates a
new sphere.reg file. surfreg just implements that command mris_register
command.
I'm not sure what you mean by the labeling steps.
On 03/05/2015 03:53 PM, Jason Tourville wrote:
> Hi Doug,
> I've run the steps outlined in th
I'm having the same issue- any updates on this problem that Jason Naftulin
posted?
Thanks,
m
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Naftulin, Jason Scott
Sent: Friday, February 27, 2015 2:50 PM
To: frees
Hi Doug,
I've run the steps outlined in the SurfaceRegAndTemplates page so far. So:
make_average_subject --out newtemplate --subjects subj1 subj2 subj3 ...
foreach subject (subj1 subj2 subj3 ...)
cd $SUBJECTS_DIR/subject
mris_register -curv surf/lh.sphere \
$SUBJECTS_DIR/newtemplate/lh.r
Hi Bruce,
By template here, I mean the folding pattern .tif files. The intention is
to have a replacement for the fsaverage template for surfer
co-registration.
Cheers,
Jason
On Thu, Mar 5, 2015 at 3:18 PM, Bruce Fischl
wrote:
> Hi Jason
>
> I don't think so - you'll probably have to edit the
If you used make_average_subject to create the template, you can run
surfreg to do the registration. If/when you run mris_preproc, make sure
to spec both the target subject and the new spherical registration
On 03/05/2015 03:18 PM, Bruce Fischl wrote:
> Hi Jason
>
> I don't think so - you'll p
Hi Jason
I don't think so - you'll probably have to edit the recon-all script. And
by template do you just mean the folding pattern .tif files, or do you
meant the parcellation atlases (*.gcs)?
cheers
Bruce
On Thu, 5 Mar 2015, Jason Tourville
wrote:
> Greetings,
> I have generated custom surf
Greetings,
I have generated custom surface templates from pediatric data sets. To
apply it to the larger data set, is it sufficient to simply run the
autorecon3 steps (perhaps skipping the mris_sphere step)? If so, is there a
handy flag for running this with recon-all and/or a way to run autorecon3
Yes. You don't want to sample at the white because you'll get large
partial volume effects. The mid is better. Having said that, I don't see
large differences in fMRI at typical voxel sizes ~3mm
doug
On 03/05/2015 12:27 PM, Matthieu Vanhoutte wrote:
> Many thanks Doug !
>
> Last point of vue c
Hi Anastasia and others,
I am sorry if I just did a bad job, but I could not find information on how
information from the cortical parcellation is used in the path tracking done by
TRACULA, especially, which cortical labels are used as determinants (seed,
waypoint) for which tracts.
It would b
The icoorder is only needed if you don't have a target subject.
To do your group analysis, you can just run mri_concat, eg,
mri_concat subject1/lh.fwhm3.fsaverage.cbf.mgh
subject2/lh.fwhm3.fsaverage.cbf.mgh --o
all.subjects.lh.fwhm3.fsaverage.cbf.mgh
Then use all.subjects.lh.fwhm3.fsaverage.c
Thanks !
Why remove icoorder because it was suggested in the mri_vol2surf --help
examples ?
May I ask you a last question : I want to make a group analyse with
freesurfer tools. With these CBF projected on fsaverage and smooth (with
the last command line), could I do as if my data were previously
yes, but remove icoorder
On 03/05/2015 11:50 AM, Matthieu Vanhoutte wrote:
> Ok, thanks.
>
> Then is this command below summarise the best for project on fsaverage
> and smooth, according to our mails exchange :
>
> /mri_vol2surf --mov ///cbf.nii.gz/ --hemi lh --surf mid --o
> //lh.fwhm3.fsavera
Ok, thanks.
Then is this command below summarise the best for project on fsaverage and
smooth, according to our mails exchange :
*mri_vol2surf --mov **cbf.nii.gz --hemi lh --surf mid --o
**lh.fwhm3.fsaverage.cbf.mgh
--regheader **subj_id --surf-fwhm 3* --trgsubject fsaverage --icoorder 7
--cortex
w format is the paint format output from your vol2surf command. We tend
not to use either w or curv formats anymore
On 03/05/2015 11:19 AM, Matthieu Vanhoutte wrote:
> I don't know if we are talking about the same thing.
>
> In precedent mail you told me solution #1 was better :
>
> */# Project an
I don't know if we are talking about the same thing.
In precedent mail you told me solution #1 was better :
*# Project and smooth onto anatomical surface* (--surf mid : mean surface
between pial and white)
*mri_vol2surf --mov **cbf.nii.gz --hemi lh --surf mid --o lh.fwhm3.cbf.w
--regheader *
*s
https://surfer.nmr.mgh.harvard.edu/fswiki/TestingFreeSurfer
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Data
!!!
-Zeke
On 03/05/2015 01:35 AM, Hassan bakhshi wrote:
> Hi
>
> Where can i find data to test freesurfer
>
> I want to test recon-all command and then get volume of hippoca
Just add --trgsubject fsaverage to the mri_vol2surf command line. Run
mri_vol2surf with --help to get more info
On 03/05/2015 10:52 AM, Matthieu Vanhoutte wrote:
> Thank you Douglas but I don't understand the solution you propose.
> Could you please show me the command lines ?
>
> -
You can also get the cras from
mri_info --cras orig.mgz
On 03/04/2015 07:35 PM, Bruce Fischl wrote:
> hmmm, not sure why. If this is a problem we can certainly change it,
> just let us know
> On Thu, 5 Mar 2015, Krieger, Donald N. wrote:
>
>>
>> Hi Zack,
>>
>>
>>
>> It looks like mris_info
Thank you Douglas but I don't understand the solution you propose. Could
you please show me the command lines ?
-
Matthieu Vanhoutte, MSc
Research Engineer - Department of Neuroradiology
Regional University Hospital, Lille, France
2015-03-05 16:45 GMT+01:00 Dou
Also, you can do everything in one vol2surf command with --trgsubject
fsaverage. It is identical to doing it in two steps
On 03/05/2015 08:12 AM, Matthieu Vanhoutte wrote:
> *Update from precedent mail*
>
> Concerning projection on fsaverage, is it better, worse or equivalent
> to do (1) or (2) ?
#1 is probably better. BTW, why are you changing format from w to curv?
Why use curv at all? I'd use mgz or nifti.
On 03/05/2015 08:10 AM, Matthieu Vanhoutte wrote:
> Thank you Doug for precisely helping me on smooth detailed command.
>
> Concerning projection on fsaverage, is it better, wors
*Update from precedent mail*
Concerning projection on fsaverage, is it better, worse or equivalent to do
(1) or (2) ?
(1)
*# Project and smooth onto anatomical surface* (--surf mid : mean surface
between pial and white)
*mri_vol2surf --mov **cbf.nii.gz --hemi lh --surf mid --o lh.fwhm3.cbf.w
--
Thank you Doug for precisely helping me on smooth detailed command.
Concerning projection on fsaverage, is it better, worse or equivalent to do
(1) or (2) ?
(1)
*# Project and smooth onto anatomical surface* (--surf mid : mean surface
between pial and white)
*mri_vol2surf --mov **cbf.nii.gz --h
Glad it helped, Zack.
It’s such a pleasure to come across something I understand.
Regards,
Don
[Signature0001]
Don Krieger, Ph.D.
Department of Neurological Surgery
University of Pittsburgh
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf O
Hi Marie,
Freesurfer version is: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0;
Matlab version: 7.9.0 (R2009b).
Also when I open matlab I get warning that:
Warning: glibc 2.3.4 - Your version
glibc 2.3.6 - MATLAB built using this version
I have attached recon-all.log fi
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