After recon-all (recon-all -all -s 479_001), which finished without
errors, the T1.mgz appears as a binary mask. I am using Freesurfer v 6.0
and Ubuntu 16.04. Please let me know if you need further files.
Thank you,
Manuel
On Thu, Mar 16, 2017 at 4:09 PM, Douglas N Greve
wrote:
> what is the
Dear FS Expert
I am doing analysis from the group_analysis_tutorial data to practice and
learn. However, I come across the error window like it shows on the
attached picture (please see the attachment) when I press the button
"Generate Stats Data Table." Please help me how can I can find the file
Hi Manuel
how do you know it is binary? Have you tried changing the window levels
in freeview when you view it? And in general when you report errors
please include the full screen output of what you ran, and in cases like
this, and image to illustrate the issue.
cheers
Bruce
On Fri, 17 Mar
Hi freesurfers,
I am using xhemi to map the right hemisphere of each subject to the left
hemisphere of the same subject. The first xhemi command works fine, but the
2nd step for mapping the label, I get this error: "Option --src-label
unknown"
Do you know how to fix this?
Marissa
___
Thanks Bruce. Please let me know your recommendations.
> On Mar 16, 2017, at 4:18 PM, Bruce Fischl wrote:
>
> Hi Padma
>
> wow, lots of things making this one hard! Low gray/white contrast, low
> bandwidth/high distortion, noisy, pathology and I'm guessing this was a
> contrast-enhanced scan
Hi Ferdi,
Sorry for the late response.
Is this a standard resolution (1mm) T1? I’m very surprised; it’s never required
more than 14GB on our data.
Cheers,
/Eugenio
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http
Hi,
Your SUBJECTS_DIR environment variable is not set for the subjects you want
to analyse,
you can either set it on the terminal or inside the fsgd file.
from terminal:->export SUBJECTS_DIR=/home/limachi/freesurfer/subjects
inside fsdg:-> SUBJECTS_DIR /home/limachi/freesurfer/subjects
please send command line
On 3/17/17 10:38 AM, Marissa Pifer wrote:
Hi freesurfers,
I am using xhemi to map the right hemisphere of each subject to the
left hemisphere of the same subject. The first xhemi command works
fine, but the 2nd step for mapping the label, I get this error:
"Option -
Marcs-MacBook-Pro:SRMC01-1 marchaut$ mris_apply_reg --src-label
label/rh.V1_exvivo.thresh.label --trg rh-on-lh.V1_exvivo.thresh.label
--streg xhemi/surf/lh.fsaverage_sym.sphere.reg
surf/lh.fsaverage_sym.sphere.reg
ERROR: Option --src-label unknown
On Fri, Mar 17, 2017 at 11:26 AM, Douglas Greve
Are you using v5.3? You will need a version 6. You can get this binary
for v6 here
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_apply_reg
On 03/17/2017 11:47 AM, Marissa Pifer wrote:
>
> Marcs-MacBook-Pro:SRMC01-1 marchaut$ mris_apply_reg --src-label
> label/rh.V1_exvivo.thresh.label
or you need to run recon-all -qcache
On 03/17/2017 11:25 AM, Dr. M. Shahid wrote:
> Hi,
>
> Your SUBJECTS_DIR environment variable is not set for the subjects you
> want to analyse,
> you can either set it on the terminal or inside the fsgd file.
>
>
> from terminal:->export SUBJECTS_DIR=/ho
Yes I am using 5.3.
Thank you!
Marissa
On Fri, Mar 17, 2017 at 12:23 PM, Douglas N Greve wrote:
> Are you using v5.3? You will need a version 6. You can get this binary
> for v6 here
>
> https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_apply_reg
>
>
> On 03/17/2017 11:47 AM, Marissa Pifer
Hi FreeSurfer Developers,
I'm having trouble using bbregister with the `--init-best` flag, a minimal
example and error message is like this:
$> bbregister --s ag00 --mov data/ag00/align/raiders/run00_ref.nii.gz
--init-best --bold --lta data/ag00/align/raiders/run00_ref_to_anat.lta
ERROR: cannot sp
It seems that a freesurfer user just submitted a pull request yesterday
that fixes this bug:
https://github.com/freesurfer/freesurfer/pull/24
Feel free to download the fixed version:
https://github.com/freesurfer/freesurfer/blob/dev/scripts/bbregister
On 03/17/2017 02:47 PM, Feilong Ma
Awesome! Thanks for your help!
Best,
Feilong
On Fri, Mar 17, 2017 at 2:57 PM, Z K wrote:
> It seems that a freesurfer user just submitted a pull request yesterday
> that fixes this bug:
>
> https://github.com/freesurfer/freesurfer/pull/24
>
> Feel free to download the fixed version:
>
> ht
Hi Feilong, you do not need to use --init-best with bbregister anymore.
It automatically uses --init-coreg (a remake of the spm coreg) which is
the best as far a I can tell
On 03/17/2017 02:47 PM, Feilong Ma wrote:
> Hi FreeSurfer Developers,
>
> I'm having trouble using bbregister with the `--
Thanks, Doug! I've run bbregister with --init-best on my data comparing
coreg, fsl, rr, and header; most of the times the choice is coreg as you
said (59 out of 88 total runs).
Best,
Feilong
On Fri, Mar 17, 2017 at 4:11 PM, Douglas N Greve
wrote:
> Hi Feilong, you do not need to use --init-bes
what happened in the ones that coreg was not the best? what is the
nature of the data?
On 3/17/17 6:39 PM, Feilong Ma wrote:
Thanks, Doug! I've run bbregister with --init-best on my data
comparing coreg, fsl, rr, and header; most of the times the choice is
coreg as you said (59 out of 88 tot
In those cases the cost of coreg is quite close to the optimal, for
example, 0.366088 vs 0.366089. I guess the final results won't differ much
if I used --init-coreg instead of --init-best.
Best,
Feilong
On Fri, Mar 17, 2017 at 10:04 PM, Douglas Greve
wrote:
> what happened in the ones that co
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