Dear Freesurfer experts
I can not download files required for surface based inter hemispheric
registration :http://ftp.nmr.mgh.harvard.edu/fswiki/Xhemi outcome "curl: (78)
RETR response: 550"
I am currently using Mac version 5.1. Any help please?
Thanks,
Hamza
This message and any attachmen
Hi experts,
When I'm pre-processing the 4D whole brain BOLD images using "preproc-sess
-sf -mni305 -fwhm 5 -fsd bold -per-run" , the results of registration from
BOLD images to the MNI305 template are always only a small part of the
original images. I tried to use another T1_152 template instead
That was my problem Doug, thanks! I used
' sudo ln -s /Applications/MATLAB_R2011b.app/bin/matlab /usr/local/bin '
and it fixed it.
-Andrew
Message: 9
Date: Mon, 01 Jul 2013 09:46:39 -0400
From: Douglas N Greve
mailto:gr...@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Problem with FS-FAST, mkc
Hi Rebecca, have you verified that the registration to anatomical space
is correct?
doug
On 07/02/2013 08:09 AM, Lijia Wang wrote:
> Hi experts,
>
> When I'm pre-processing the 4D whole brain BOLD images using
> "preproc-sess -sf -mni305 -fwhm 5 -fsd bold -per-run" , the results of
> registrat
ok, try now
On 07/02/2013 06:53 AM, Hamza Alshuft wrote:
> Dear Freesurfer experts
>
> I can not download files required for surface based inter hemispheric
> registration :http://ftp.nmr.mgh.harvard.edu/fswiki/Xhemi outcome
> "curl: (78) RETR response: 550"
> I am currently using Mac version 5
Dear freesurfers,
Recon-all -s subject -autorecon2 returns the following error messages
*mri_segstats will not calculate Supratentorial due to missing ribbon.mgz
file*
mghRead(Path_to_subject/mri/*ribbon.mgz, -1)*: could not open file.
Prior to autorecon2, I did recon-all -s subject -autorecon1
Hi Ye, one of the programs expects that recon-all will be run all the
way through instead of in parts. You will need to download a new version
of mri_segstats from
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.centos6
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoi
Hi all,
So I am trying to reorient my sagittal scans (with messed up labels) to axial
using mri_convert (to get right label), I am able to do so but I am loosing
some data (some slices).
When I checked voxel-to-ras transform for the original and reorient image, they
were different.
How can I
what is your command line?
On 07/02/2013 11:41 AM, Ray, Siddharth wrote:
>
> Hi all,
>
> So I am trying to reorient my sagittal scans (with messed up labels)
> to axial using mri_convert (to get right label), I am able to do so
> but I am loosing some data (some slices).
>
> When I checked voxel
Hi Emily, what version of FS are you using?
doug
On 07/02/2013 11:41 AM, Emily Boeke wrote:
> Hi Doug,
>
> Sorry to be overly persistent, but I just wanted to make sure you saw this
> email!
>
> Thanks,
> Emily
>
> On Jul 1, 2013, at 9:20 AM, Emily Boeke wrote:
>
>> This was the command I ran:
Dear Douglas,
Thank you very much!
Sincerely,
Ye
On Tue, Jul 2, 2013 at 10:36 AM, Douglas N Greve
wrote:
>
> Hi Ye, one of the programs expects that recon-all will be run all the
> way through instead of in parts. You will need to download a new version
> of mri_segstats from
>
>
> ftp://surfe
Hi Doug,
Thanks for your informative replies! This is very helpful.
Cheers,
On Tuesday, July 2, 2013, Douglas N Greve wrote:
>
> We pretend the "volume" has number of columns equal to the number of
> vertices. nifti, mgh, etc, are just ways to store data
> doug
>
>
>
>
> On 07/01/2013 03:50 PM,
4.5
Emily
On Jul 2, 2013, at 11:45 AM, Douglas N Greve wrote:
>
> Hi Emily, what version of FS are you using?
> doug
>
>
> On 07/02/2013 11:41 AM, Emily Boeke wrote:
>> Hi Doug,
>>
>> Sorry to be overly persistent, but I just wanted to make sure you saw this
>> email!
>>
>> Thanks,
>> Emily
Hello,
I am currently having some difficulties with the mri_ca_normalize
command. I am attempting to create a normalized volume file using an input
brain with the following command:
mri_ca_normalize
/Volumes/Wong_Lab/CochlearImplant/UNC_NiFTI/infant-neo-mgz/mri/ -seg
/Volumes/Wong_Lab/Cochle
Hi Mark
for mri_ca_normalize all the optional arguments (prefixed with a dash)
must come before all the mandatory ones. Also, you shouldn't give it the
mri directory - give it an input volume (like nu.mgz).
cheers
Bruce
On Tue, 2 Jul 2013, Mark Plantz
wrote:
Hello,
I am currently havi
OK, in later versions it will give you the talairach coords. I would
download 5.3 and run your group analysis in that, just be careful not to
run recon-all using 5.3 (unless you want to upgrade all your subjects).
doug
On 07/02/2013 11:48 AM, Emily Boeke wrote:
> 4.5
>
> Emily
> On Jul 2, 2013,
It also looks like you have an extra forward slash at the end of seg.mgz
On 07/02/2013 12:13 PM, Bruce Fischl wrote:
> Hi Mark
>
> for mri_ca_normalize all the optional arguments (prefixed with a dash)
> must come before all the mandatory ones. Also, you shouldn't give it
> the mri directory -
Here ya go (to list)
On Tue, Jul 2, 2013 at 12:38 PM, Jonathan Holt wrote:
> Here ya go.
>
>
> On Mon, Jul 1, 2013 at 3:31 PM, Martin Reuter > wrote:
>
>> No, it's not nifti, that should work.
>>
>> Can you send me your log file and the command you issued.
>>
>> Thanks, Martin
>>
>>
>> On 07/
and the command
nohup recon-all -s 100922dt_01 -i 100922dt_nifti_revised.nii
On Tue, Jul 2, 2013 at 12:40 PM, Jonathan Holt wrote:
> Here ya go (to list)
>
>
> On Tue, Jul 2, 2013 at 12:38 PM, Jonathan Holt wrote:
>
>> Here ya go.
>>
>>
>> On Mon, Jul 1, 2013 at 3:31 PM, Martin Reuter <
>> m
Hi Peter,
After completing your Talairach and skullstrip edits have you regenerated
the brainmask.mgz? I'd recommend running the rest of recon-all
(-autorecon2 & -autorecon3) to see how the surfaces come out.
After that you can go ahead with intensity normalization (with control
points), and
It is hard to say, since 4.5 came out 3 years ago:). It is ok to do
group analysis in a different version of FS.
doug
ps. Please remember to copy the list instead of sending emails directly
to us. thanks!
On 07/02/2013 01:53 PM, Emily Boeke wrote:
> Strange, I have run simulations before in 4.
Hi Jonathan,
I changed the subject of the thread, to better reflect this problem, it
(so far) has nothing to do with longitudinal processing.
Next time, can you send the log file, it is in
/net/data4/ALSSCI/FreeSurfer201211/FreeSurfer/tpNdt/scripts/recon-all.log
not the output on the screen.
In the meantime you can check how the mri/orig/001.mgz and the
mri/orig.mgz and mri/orig_nu.mgz look.
Best, Martin
On 07/02/2013 02:16 PM, Jonathan Holt wrote:
Thanks Martin,
I have attached recon-all.log. I tried to run the process several
times, I clearly forgot to pass -all that time but
Hi Bruce,
Is -seg the correct flag to input an .mgz file instead of a .gca atlas?
After making the recommened changes, the command will not seem to work. My
input is as follows:
mri_ca_normalize -seg
/Volumes/Wong_Lab/LabMRIData/FreeSurfer/CMH-7549/mri/nu.mgz
/Volumes/Wong_Lab/CochlearImplant
Probably the script was necessary to fix this problem. Look up the
command for mri_convert, it could be that it adjusts the direction
cosines directly.
Best, Martin
On 07/02/2013 02:36 PM, Jonathan Holt wrote:
OK,
so while the structures look normal in tkmedit the orientations are
mixed up.
Dear Freesurfers,
I just realize that in the tutorial example of "geometric accuracy", *recon-all
-autorecon2-wm *is used to recreate the final surfaces; while in "lateral
ventricle", *recon-all -autorecon2-wm -autorecon3 *is used. However, the
modification steps look the same to me -- fill in the
Hi Ye
-autorecon3
should always be run after any of the autorecon2 steps. If it's not on
the tutorial, that is a mistake
cheers
Bruce
On Tue, 2 Jul 2013, ye tian wrote:
Dear Freesurfers,
I just realize that in the tutorial example of "geometric accuracy",
recon-all -autorecon2-wm is used to
Dear Bruce,
Thank you very much!
Sincerely,
Ye
On Tue, Jul 2, 2013 at 4:34 PM, Bruce Fischl wrote:
> Hi Ye
> -autorecon3
>
> should always be run after any of the autorecon2 steps. If it's not on the
> tutorial, that is a mistake
>
> cheers
> Bruce
>
> On Tue, 2 Jul 2013, ye tian wrote:
>
> D
Hi Satra - The orientation of your dwi_orig.nii.gz is LPS. What flip4fsl
will do is convert it to LAS, and perform the same conversion on the
gradient table that you provide. This of course assumes that
dwi_orig.nii.gz and your gradient table are consistent as they come out of
your custom pre
Hi Satra - What you're showing in the screenshots would be consistent with
a L-R flip of the gradient directions, which is what my comparison of your
gradients to the original Siemens gradients indicated. (Assuming the data
was acquired with the standard Siemens 60 gradient directions.)
a.y
-seg
would be the correct flag if you wanted to specify an aseg-type volume to
do the normalizaton based on instead of using a transform and the gca. You
can't give it an intensity volume though (lke the nu.mgz) - it won't know
what to do with it
Bruce
On Tue, 2 Jul 2013, Mark Plantz wrote
Hi Gari, use --targ for a target volume (not a subject) to use as the
template for the output. The target subject is actually stored in the
register.dat file, so you can just spec --fstarg (no arguments)
doug
On 7/1/13 2:45 PM, Garikoitz Lerma-Usabiaga wrote:
Hi,
I want to obtain volume s
hi ay,
so this is what i did. i flipped the gradient LR intentionally, ran
flip4fsl and then dtifit and now the eigenvec 1 looks good, but not if i
run dtifit prior to flip4fsl.
but this brings me back to my original point which is that my image and the
gradients are (i think) already in proper o
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