do those files exist in that path?
cheers
Bruce
On Sat, 2 Aug 2014, Isaiah C. Smith
wrote:
Hello Bruce,
I am trying to check the output of the mri data that I processed I start
using MNE. I placed the file in a folder called Practice in my documents,
and I am using the following command:
tcs
Hello Bruce,
I am trying to check the output of the mri data that I processed I start using
MNE. I placed the file in a folder called Practice in my documents, and I am
using the following command:
tcsh
source your_freesurfer_dir/SetUpFreeSurfer.csh
setenv SUBJECTS_DIR $TUTORIAL_DATA/buckner_da
Thanks
Sent from my iPhone
> On Jul 31, 2014, at 10:47 AM, "Bruce Fischl"
> wrote:
>
> Hi Isaiah
>
> you should go through the tutorials on our website - they detail all this
> information
>
> cheers
> Bruce
>
>
>> On Thu, 31 Jul 2014, Isaiah C. Smith wrote:
>>
>> Yes, how do i view the
Hi Isaiah
you should go through the tutorials on our website - they detail all this
information
cheers
Bruce
On Thu, 31 Jul 2014, Isaiah C. Smith wrote:
> Yes, how do i view the files and where can I find where every has been placed
>
>> On Jul 31, 2014, at 8:26 AM, "Bruce Fischl"
>> wrote:
Yes, how do i view the files and where can I find where every has been placed
> On Jul 31, 2014, at 8:26 AM, "Bruce Fischl"
> wrote:
>
> there are many, many files in many different formats (e.g. volumes in
> .mgz format, surfaces in our internal format, labels, parcellations,
> etc...)
>> On
there are many, many files in many different formats (e.g. volumes in
.mgz format, surfaces in our internal format, labels, parcellations,
etc...)
On Thu, 31 Jul 2014, Isaiah C. Smith wrote:
> The files after recon-all
>> On Jul 31, 2014, at 7:10 AM, "Bruce Fischl"
>> wrote:
>>
>> the format o
The files after recon-all
> On Jul 31, 2014, at 7:10 AM, "Bruce Fischl"
> wrote:
>
> the format of what?
>> On Thu, 31 Jul 2014, Isaiah C. Smith wrote:
>>
>> Thank you,
>> I will go there now. But regarding the output of freesurfer, the format will
>> be .ccd?
>>
>>> On Jul 30, 2014, at 7:23
the format of what?
On Thu, 31 Jul 2014, Isaiah C. Smith wrote:
> Thank you,
> I will go there now. But regarding the output of freesurfer, the format will
> be .ccd?
>
> On Jul 30, 2014, at 7:23 PM, Bruce Fischl wrote:
>
>> Hi Isaiah
>>
>> you might check out MNE from Matti Hamalainen (ccd). It
Hello Bruce,
The I am a little confused with the results of the recon-all command? Does the
recon-all -help explain the file placement?
Isaiah
> On Jul 30, 2014, at 6:21 AM, "Bruce Fischl"
> wrote:
>
> Hi Isaiah
>
> remove the space. It should be:
>
> recon-all
>
> cheers
> Bruce
>> On We
Thank you,
I will go there now. But regarding the output of freesurfer, the format will be
.ccd?
On Jul 30, 2014, at 7:23 PM, Bruce Fischl wrote:
> Hi Isaiah
>
> you might check out MNE from Matti Hamalainen (ccd). It does all this and
> more (using FreeSurfer surfaces and segmentations)
>
Hi Isaiah
you might check out MNE from Matti Hamalainen (ccd). It does all this and
more (using FreeSurfer surfaces and segmentations)
cheers
Bruce
On Thu, 31 Jul 2014, Isaiah C. Smith wrote:
Thank you so much, Bruce. I think that I got it. Overall, I am trying to
create a source volume co
Thank you so much, Bruce.
I think that I got it. Overall, I am trying to create a source volume
conduction model, calculate the lead field matrix, and then create a source
model. My instructor said that it might be possible to do this in Freesurfer.
Sorry, I am kind of new to using the terminal
you need a "-" before each option, so it should be
recon-all -help
On Wed, 30 Jul 2014,
Isaiah C. Smith wrote:
The recon-all option is no longer working and neither is the other one. I am
getting an error.
Isaiahs-MacBook-Pro:~ IsaiahSmith$ recon-all help
ERROR: Flag help unrecognized.
help
Hi Isaiah
remove the space. It should be:
recon-all
cheers
Bruce
On Wed, 30 Jul 2014, Isaiah C.
Smith wrote:
The command is not found.
Last login: Tue Jul 29 17:42:52 on ttys001
freesurfer-Darwin-lion-stable-pub-v5.3.0
Setting up environment for FreeSurfer/FS-FAST (and FS
The recon-all option is no longer working and neither is the other one. I am
getting an error.
Isaiahs-MacBook-Pro:~ IsaiahSmith$ recon-all help
ERROR: Flag help unrecognized.
help
Darwin Isaiahs-MacBook-Pro.local 13.3.0 Darwin Kernel Version 13.3.0: Tue Jun
3 21:27:35 PDT 2014; root:xnu-2422.1
The command is not found.
Last login: Tue Jul 29 17:42:52 on ttys001
freesurfer-Darwin-lion-stable-pub-v5.3.0
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /Applications/freesurfer
FSFAST_HOME /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii
does that file exist? You don't want angle brackets <> around the name
(the angle brackets typically mean "replace this with an actual name"
cheers
Bruce
On
Wed, 30 Jul 2014, Isaiah C. Smith wrote:
Hello and thanks again, Bruce,
I am not sure what is going wrong here. I tried what you said
Hello and thanks again, Bruce,
I am not sure what is going wrong here. I tried what you said and I am getting
this.
Isaiahs-MacBook-Pro:~ IsaiahSmith$ recon- all -i -s
-sd
-all
-bash: os005a1001.nii: No such file or directory
On Jul 22, 2014, at 4:44 PM, Bruce Fischl
mailto:fis...@nmr.m
Hi Isaiah
recon-all -i -s -sd in> -all
should do the trick. should be a *single* file in the right
dicom series, or a .nii file. Don't use analyze
Bruce
On Tue, 22 Jul 2014, Isaiah C. Smith wrote:
Hello Bruce,
Thanks for the response; I tried the inputs from the check freesurfer page
Hello Bruce,
Thanks for the response; I tried the inputs from the check freesurfer page. I
just tried to do the run recon-all and got the list of possible commands. The
input images are unix executable files separately, but I can convert them to
.hdr/.img or .nii using mricron. They are MRI ima
Hi Isaiah
what are the input images that you have? What format and what imaging
sequence? You should be able to just run recon-all on them (check out
recon-all -help)
cheers
Bruce
On Tue, 22 Jul 2014, Isaiah C. Smith wrote:
> Hello All,
>
> I was testing to see if the freesurfer program works
Hello All,
I was testing to see if the freesurfer program works and it does seem to work
for anything besides the free viewer program. I do not know what is wrong with
the others; do you have any ideas? Also I am trying to use the inhomogeneity
correction, convert the images that I have to 1x1x
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