Dear doug,
Thanks for your precious prompt, I will try.
All the best.
2013-11-20
Rujing Zha
发件人：Douglas N Greve
发送时间：2013-11-20 00:20
主题：Re: [Freesurfer] how to obtain subjects cortical thickness and then analyze
unpair t-test
收件人："freesurfer"
抄送：
Look at our tutorial on group analysis o
Hi,
I need to reinstall an older version of Freesurfer, but the only link I found:
Old releases are here. seems to require a login and password. How can I
access this?___
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Hi Nathaniel
yes, there is a dcmdrle utility you can use (thanks to Thomas Witzel for
pointing this out to me)
cheers
Bruce
On Tue, 19 Nov 2013, Nathaniel Reynolds wrote:
>
> Hi,
>
>
> I'm working with some clinical DICOMs which appear to have their image data
> compressed with a RLE lossles
Hi,
I'm working with some clinical DICOMs which appear to have their image data
compressed with a RLE lossless algorithm. I need to decompress these images.
When I run into jpeg compression, I can use the "dcmdjpeg" function. The
"dcmdjpeg" function doesn't work on the RLE-compressed files, nat
looks ok. you should not need --outdir
you can use mri_aparc2aseg to create a nifti file. This is what is used
to create aparc+aseg.mgz from the aparc annotation and aseg.mgz. Look in
the recon-all.log file for an example command line (just change the
output name so you don't overwrite). The as
Devin,
The VirtualBox install of freesurfer is an unsupported version that has
been provided as a convenience to Windows users or other users that wish
to use the freesurfer software but do not have immediate access to Mac
or Linux platform. The Virtual box installation is literally just an
Xu
Thanks a lot for the very quick reply!
does this look OK?
mri_annotation2label --subject P2 --hemi rh --outdir
freeSurfer_Results/P2/moj_labels/ --lobesStrict
freeSurfer_Results/P2/moj_labels/freeSurfer_lobes
how can I convert the annotation file to nii.gz?!
also, could please explain a bit
Can you send the aseg2feat log file? Also, please remember to post to
the list instead of to me personally. thanks!
doug
On 11/19/2013 03:17 PM, Sudhin A. Shah wrote:
> yes, it looks fine..
>
> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
> Sent: Tu
Those are some big segs. Have you checked the registration?
On 11/19/2013 02:41 PM, Sudhin A. Shah wrote:
> yes :) For example in this 1 subject segs (
> 200520082010 201120132021 20232025
> 2029 100510081011 10131021) are
there were probably some small segmentations that were lost. Is this
causing a problem?
On 11/19/2013 02:22 PM, Sudhin A. Shah wrote:
> Hello,
>
> This is regarding the registration of functional data to freesurfer
> parcellations
> (http://freesurfer.net/fswiki/FsTutorial/MapSegmentationsToFunc
Hello,
This is regarding the registration of functional data to freesurfer
parcellations
(http://freesurfer.net/fswiki/FsTutorial/MapSegmentationsToFunctionalSpace).
The rsfMRI is sampled at 2x2x2.
After running reg-feat2anat and aseg2feat
>> a = MRIread('aparc+aseg'); %Original aparc+aseg ou
Christiane,
The log you sent me doesn't correspond to the error you first wrote in your
email. The error reads as follow in your log:
---
>> reading filled volume...
closing volume...
{??? Undefined function or method 'fspecial' for input arguments of type
'char'.
Error in ==>
Hi Pietro,
I think you should try redoing the control points from scratch, but with
fewer control points and sparser placement. Currently you have 198
control points tightly packed in only a couple regions. Furthermore,
there is one control point at 128, 128, 128 which is right in the thalamu
The problem is with the mat file, not the input. The matrix should be an
ascii text file.
doug
On 11/18/2013 12:09 PM, Laura M. Tully wrote:
> Hello freesurfers,
>
> I'm trying to run mri_glmfit between groups analysis (patients vs.
> controls) with gender, age, medication (continuous), and dur
The label will be totally off because it was not created in the
conformed anatomical space of fsaverage. Does the mask look ok? If you
want to view the label, use something like
tkmedit -f $SUBJECTS_DIR/fsaverage/mri.2mm/orig.mgz -ov sig.mgh -seg
$SUBJECTS_DIR/fsaverage/mri.2mm/aseg.mgz
doug
Try running mri_annotation2label with the --lobesStrict option
doug
On 11/19/2013 11:15 AM, Mojdeh Zamyadi wrote:
> Hi all,
>
> I'm interested in getting a lobar segmentation of the cortex and I've
> already ran recon-all on my subjects. I'm now confused by the outputs
> and was wondering if som
Look at our tutorial on group analysis on the wiki. Briefly, you need to
run mris_preproc (transforms all subjects' thickness maps to surface
atlas space), mri_surf2surf to smooth the thickness maps, then create an
FSGD file and run mri_glmfit to perform the t tests
doug
On 11/19/2013 08:07
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Hi all,
I'm interested in getting a lobar segmentation of the cortex and I've
already ran recon-all on my subjects. I'm now confused by the outputs
and was wondering if someone could tell me which output file contains
segmentation that can be merged to get a 4 lobe parcellation similar to:
htt
Hi,we have finished cross sectional scanworkups in Freesurfer 5.1 and gone
through qa. Can we use these scanworkups for further processing in the
longitudinal stream in Freesurfer 5.3?
Knut J___
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Hi Rujing,
If you are looking for the cortical thickness measures of a subject, you
can find it in that subject's freesurfer directory in the 'stats' folder.
In there, you will find a file called ?h.aparc.stats - one for each
hemisphere. Within the stats file, you'll see the Average thickness f
The entire hippocampus is currently labeled by default in the recon-all
stream. You can see it in the aseg.mgz (in the mri directory) and
find volume information in stats/aseg.stats.
To get the hippocampal subfields you have to run recon-all with an
additional flag. This is documented here:
Hello,
I didn't see hippocampus listed in the Desikan-Killiany, Destrieux, or
DKTatlas40 atlases. Is there an existing atlas that contains the hippocampal
subfields? If not, what options exist for getting the hippocampus into an
atlas?
Thank you,
Brian
___
Dear all,
Ater recon-all,which image can I select to group t-test? And do they need
process in advance?
Thanks very much.
All the best.
2013-11-19
Rujing Zha___
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