Thank you so much Bruce, it now works like a charm!
Best,
Muriel
On Jul 12, 2012, at 2:30 AM, Bruce Fischl wrote:
> Hi Muriel
>
> not sure what your second frame is, but you should be able to do this:
>
> cd $SUBJECTS_DIR//mri/orig
> mv 001.mgz multiframe.mgz
> mri_convert -nth 0 multiframe.m
you can run freeview on the 001.mgz and see what is in it. If it has more
than one frame freeview will include a slider that lets you change from one
to the other. Or you can email it to me and I'll take a look.
On Wed, 11 Jul 2012, Muriel Bruchhage wrote:
> Hi Bruce,
>
> To be quite honest, I
Hi Bruce,
To be quite honest, I am not sure, but I used the same data on a fsl
segmentation task (using a nifti format though) and I never got any error
messages back there.
Best,
Muriel
On Jul 11, 2012, at 11:26 PM, Bruce Fischl wrote:
> Hi Muriel
>
> what was the scan that you are trying t
Hi Muriel
what was the scan that you are trying to run FreeSurfer on? Did it have
more than one echo?
Bruce
On Wed, 11
Jul 2012, Muriel Bruchhage wrote:
>
> On Jul 11, 2012, at 11:23 PM, Muriel Bruchhage wrote:
>
>> I added the -all at the end and skipped the -i flag, but I still get an
>>
On Jul 11, 2012, at 11:23 PM, Muriel Bruchhage wrote:
> I added the -all at the end and skipped the -i flag, but I still get an error
> message:
>
> Checking for (invalid) multi-frame inputs...
> ERROR: input(s) cannot have multiple frames!
> /Applications/freesurfer/subjects/MRI_04_2012/GID02/
oh, you need to specify what you want it to do. Add -all at the end of
the command line and it will do everything. Note that if you are rerunning,
you can leave out the -i
cheers
Bruce
On Wed, 11 Jul 2012, Muriel
Bruchhage wrote:
> Hei,
>
> Thanks you very much again for your help!
>
> Neve
Hei,
Thanks you very much again for your help!
Nevertheless, even though I got the message that the recon-all has been done
without any errors, no talaraich transform, skull stripping or segmentation has
been done. I placed my fsaverage folder in the same folder where all my
participant-folde
sure, glad it worked out
Bruce
On Wed, 11 Jul 2012, Muriel Bruchhage wrote:
>
> It worked!
>
> Thank you so so much!
>
> Best,
> Muriel
>
> On Jul 11, 2012, at 6:34 PM, Muriel Bruchhage wrote:
>
>> Hi Bruce,
>>
>> Thank you very much for your fast response.
>>
>> Unfortunately though, I still get
It worked!
Thank you so so much!
Best,
Muriel
On Jul 11, 2012, at 6:34 PM, Muriel Bruchhage wrote:
> Hi Bruce,
>
> Thank you very much for your fast response.
>
> Unfortunately though, I still get an error response when typing in "recon-all
> -i /Applications/freesurfer/subjects/MRI_04_2012
Hi Muriel
the -s switch should be followed by a subject identifier (e.g.
subject0001), not the 001.mgz file. Note that you don't need to convert
your dicom to mgz either, just point recon-all at one slice in the correct
(T1-weighted) dicom series with -i . And one
acquisition is usually suffi
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