Hi experts,
A quick question: I installed FS 5.1 a month ago, should I replace with this
recon-all file and run it with flag -clean-tal in the future? why the steps
have to be switched?
Thanks!
2012-04-19
Chunhui Chen
_
State Key Laboratory of Cognitive Neuroscience and
Dear Freesurfers,
I analyzed a dataset with FS 5.1 but upon loading the data in tksurfer I get
the following error:
mrisReadTriangleFile(/.../surf/lh.sphere.reg): surface doesn't match
/.../surf/lh.inflated
The same error occurs when I run mris_preproc as a step before GLM analyses
Hello FS experts,
A quick question for you all. Does the FS stream produce any values for the
Prefrontal Cortex specifically?
Thanks,
Fatima
E-pos vrywaringsklousule
Hierdie e-pos mag vertroulike inligting bevat en mag regtens geprivilegeerd
wees en is
Hi Efrat,
Could you send me the recon-all-status.log file for one of your v4.5
subjects that have completed recon-all without errors? You would find
this file in the scripts sub-directory of the subject.
-Louis
On Mon, 16 Apr 2012, Efrat Kliper wrote:
Dear FreeSurfer expert,
I am trying to
Hi Cat,
You'll need to rerun those subjects with 5.1 to be able to use the
longitudinal analysis in 5.1.
You can also find a detailed explanation on how to go about edits here:
https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits
Allison
On Wed, 18 Apr 2012, Cat Chong wrote:
Dear
Hi all,
I would like to make a fine-grained surface parcellation from aparc -
let's say 500 labels, and I would like the labels to be more or less
isometric. When subdividing the parcellation with
mris_divide_parcellation, the labels become very stretched instead of
isometric. Is there a way to
Hi Linda
I think that's one too many constraints. Do you need it to be based on the
original parcellattion? If not and a uniform parcellation will do you can
use mris_make_face_parcellation.
cheers
Bruce
On Thu, 19 Apr 2012, Linda Douw wrote:
Hi all,
I would like to make a fine-grained
Hi Cat,
you can run 5.1 base and longitudinal on top of 5.0 cross sectional runs. Since
you have not edited anything yet, I would however recommend to re-run the cross
scectional runs with 5.1
For edits, please look at the wiki page
http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits
Hi Kourosh,
you can ask the freesurfer list for these kind of questions. I believe that
the ras coordinates are not changed, so reslicing everyhting as the original
inputs will be sufficient (no transform, only based on the header
information)
e.g.
mri_convert -rt nearest -rl
Hi all,
I've been following an e-mail on this list-serve from Joshua Lee
regarding poor hippocampal segmentations in Freesurfer 5.1. He
mentions using -use-mritotal in the recon-all command to overcome
tal-check failures to help fix the segmentation and make them more
like those produced by
Hi,
I'm new to Freesurfer, so this may be a silly question.
I would like to run mri_cvs_register, but I decided to run mri_cvs_check
first to make sure I have all the files. This is the message I received:
FreeSurfer:/mridata/fs_analysis mri_cvs_check --mov sub26 --template sub47
The following
Hi Jackie,
You will not need that file any more, so if that is the only file missing
you can go ahead with the registration. I will update the mri_cvs_check
script to reflect that.
Lilla
On Thu, 19 Apr 2012, Jackie Leung wrote:
Hi,
I'm new to Freesurfer, so this may be a silly question.
hi,
I'm trying to run mri_cvs_register and I'm getting a strange error
message.
MRISread(CVS_test_26to47_1/lh.resample.white): could not open file
No such file or directory
Error reading surface CVS_test_26to47_1/lh.resample.white
I've checked the directory and the file definitely exists.
It
Hi,
I have a question regarding how the clusters are labeled after the results of
a Monte-Carlo Simulation. Similar regions from 2 different patient populations
seem to be labeled differently. On one of my results, the cluster has been
labeled as in the precentral region and a similar region
Hi Jackie,
Could you attach the log file?
Thanks, Lilla
On Thu, 19 Apr 2012, Jackie Leung wrote:
hi,
I'm trying to run mri_cvs_register and I'm getting a strange error message.
MRISread(CVS_test_26to47_1/lh.resample.white): could not open file
No such file or directory
Error reading
ok... please see attached.
note: The directory name is different in this log file, but the error is
the same. I've been testing this problem with many different directories.
thanks,
jackie
On Thu, Apr 19, 2012 at 5:37 PM, Lilla Zollei
lzol...@nmr.mgh.harvard.eduwrote:
Hi Jackie,
Could you
Hi all,
I had a question when convert a surface to volume space.
First, I converted a volume nifti data to fsaverage:
mris_preproc --target fsaverage --hemi lh --iv data.nii bb_register.dat
--out data.lh.mgh
Then, I want to convert the data.lh.mgh to volume space, I tried
mri_surf2vol,
Hi Steven,
It has been recommended to me that in case of Tal-check failures, the
use of the -use-mritotal flag will overcome this issue. However, this
substitutes Freesurfer's registration algorithms with a function from
MNI, I believe. In general, I have heard it said that mritotal does a
poorer
Nick,
Thank you. This recon-all script resolved my problems. I really
appreciate this post.
-
Josh
-
Joshua Lee
UC Davis
On Tue, Apr 17, 2012 at 7:51 AM, Nick Schmansky
ni...@nmr.mgh.harvard.edu wrote:
Ed,
email probably trounced it. recon-all is a text file. attached is a
gzipped
Hi Fabricio - You can only use the formats supported by mri_convert:
http://surfer.nmr.mgh.harvard.edu/fswiki/mri_convert
Dicom or nifti is recommended.
Hope this helps,
Anastasia.
On Thu, 19 Apr 2012, fabricio feltrin wrote:
Hi Anastatia.
Is it possible to use REC/PAR images from philips
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