Hi,
After loading, for example, flattened patch I would like to go back to a
standard, inflated brain without patch while I preserve all my overlays. Is
it possible?
Thanks,
Vadim
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Hi Vadim
yes, click the "clear cuts" button (or menu item, I can't remember)
Bruce
On Thu,
2 Dec 2010, Vadim Axel wrote:
> Hi,
>
> After loading, for example, flattened patch I would like to go back to a
> standard, inflated brain without patch while I preserve all my overlays. Is
> it possible?
Thanks, Bruce.
Though "clear cuts" button indeed works fine with 3d patches, the procedure
results in complete mess with flattened patches...
On Thu, Dec 2, 2010 at 3:00 PM, Bruce Fischl wrote:
> Hi Vadim
>
> yes, click the "clear cuts" button (or menu item, I can't remember)
> Bruce
>
> On Thu,
Try clicking the inflated surface button afterwards
On Dec 2, 2010, at 8:16 AM, Vadim Axel wrote:
> Thanks, Bruce.
> Though "clear cuts" button indeed works fine with 3d patches, the procedure
> results in complete mess with flattened patches...
>
> On Thu, Dec 2, 2010 at 3:00 PM, Bruce F
Hello,
I have uploaded the subject/mri/orig/001.mgz file for the participant
with the error described here:
https://www.nmr.mgh.harvard.edu/facility/filedrop/showgroup/22563/1/7580a7afd98a5fbbc1519ff23f3a37ff
Thanks,
Jennifer
On Mon, Nov 29, 2010 at 7:55 AM, Bruce Fischl
wrote:
> Hi Jennifer,
OK, this is a bug in 4.5 in which it ignores the nskip option. This is
fixed in version 5.0. If you need to continue with 4.5, you can use a
tpexclude file to remove the 1st two time points, something like:
echo "0 2" > 100524AK_infIPS/bold/007/tpexclude.dat
echo "0 2" > 100524AK_infIPS/bold/014
Hello,
Is there a way to individually save slices within a nifti file in the nifti
format
using the mri_convert command?
Thank you.
Best,
Lisa
__
Lisa F. Akiyama
Research Study Assistant
Institute for Learning & Brain Sciences (I-LABS)
University of Washington
E-mai
Hi,
I have been given data that I need to put in a specific format so that
it's useable to me. I know how to use mri_convert to convert between
analyze and nifti. However, I need one file per run, whereas this
data comes such that every frame is a separate analyze file. How do I
combine them?
Th
Try
mri_concat *.img --o f.nii
doug
Rita Loiotile wrote:
> Hi,
> I have been given data that I need to put in a specific format so that
> it's useable to me. I know how to use mri_convert to convert between
> analyze and nifti. However, I need one file per run, whereas this
> data comes such t
Try the --slice-crop option
doug
Lisa F. Akiyama wrote:
> Hello,
>
> Is there a way to individually save slices within a nifti file in the
> nifti format
> using the mri_convert command?
>
> Thank you.
>
>
> Best,
> Lisa
> __
> Lisa F. Akiyama
> Research Study Assist
Hi all,
I was running an event-related analysis where the number of targets change,
and I would really like to find an area that tracks their behavioral
performance so that it would increase as set size increases, but then level
off when performance does.
Basically I have 5 set sizes, 1,2,3,4,6 i
Hi All,
I've just installed freesurfer onto a linux node, and immediately
encountered a problem when trying to run my first scan. After executing the
recon-all command, the terminal spits out a string of errors saying:
[freesurfer home path]/mri_convert: Exec format error. Binary file not
execu
what version did you download?
Nathan Dankner wrote:
> Hi All,
>
> I've just installed freesurfer onto a linux node, and immediately
> encountered a problem when trying to run my first scan. After
> executing the recon-all command, the terminal spits out a string of
> errors saying:
>
> [frees
I downloaded version 5, and installed it into my home directory, as opposed
to user/local... I don't know if that's an issue or not
On Thu, Dec 2, 2010 at 4:43 PM, Douglas N Greve
wrote:
> what version did you download?
>
> Nathan Dankner wrote:
>
>> Hi All,
>>
>> I've just installed freesurfer
Can you be more specific? Which file in particular? We have different
distributions for different platforms. If you downloaded one that does
not match your platform then it will generate that error.
doug
Nathan Dankner wrote:
> I downloaded version 5, and installed it into my home directory, as
Oh sorry. I downloaded the CentOS 64-bit linux file, which should match my
platform...
On Thu, Dec 2, 2010 at 5:06 PM, Douglas N Greve
wrote:
> Can you be more specific? Which file in particular? We have different
> distributions for different platforms. If you downloaded one that does not
> mat
Can you send the result of
cat $FREESURFER_HOME/build-stamp.txt
Nathan Dankner wrote:
> Oh sorry. I downloaded the CentOS 64-bit linux file, which should
> match my platform...
>
> On Thu, Dec 2, 2010 at 5:06 PM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> Can you be m
Hi Doug,
Thanks for the tip.
I ran the following command, but no output was created:
todd: mri_convert -i $SUBJECTS_DIR/mni305_minc/average_305_test.nii
--slice-crop 0 154 -o $SUBJECTS_DIR/mni305_minc/average_305_test_slice0.nii
mri_convert -i
/usr/local/freesurfer/subjects/mni305_minc/average_30
does average_305_test_slice0.nii not exist? Do you have write perms to
that dir? I just tried it here, and it works
doug
Lisa F. Akiyama wrote:
> Hi Doug,
>
> Thanks for the tip.
> I ran the following command, but no output was created:
>
> todd: mri_convert -i
> $SUBJECTS_DIR/mni305_min
Hi Doug,
Thanks for the tips.
It is working now.
Best,
Lisa
__
Lisa F. Akiyama
Research Study Assistant
Institute for Learning & Brain Sciences (I-LABS)
University of Washington
Portage Bay Building, BOX 357988
Seattle, WA 98195-7988 U.S.A.
E-mail: lris...@uw.edu
P
Hi All,
I'm using : freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0
I'd like to plot HDR for each condition for each subject.
With FreeSurfer v4.5.0, I did so with func2roi-sess and roisummary-sess.
With v5.0, those commands do not seem to work.
I could get a table with:
> funcroi-config -anal
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