Hi Anastasia,
Here are the bvec and bval files you asked me about.
Sincerely,
Florian
>>> Anastasia Yendiki 18.08.13 22.52 Uhr >>>
Hi Florian - Can you please also attach the bvecs/bvals files from the
dmri directory?
Thanks,
a.y
On Sun, 18 Aug 2013, Borsodi Florian wrote:
> Hi Anastasi
Hi all,
I am trying to run recon-all on a structural for one of my subjects, but
freesurfer exited with errors during the last few stages (the ones covered by
autorecon-3). It appears that it is just missing some label - the problem
occurs at the following stage:
painting output onto subject M
HI all,
We had submitted a paper based on cortical thickness analysis in Qdec. The
reviewer's had couple concerns regarding the QDec analysis. We would
appreciate your help to address/resolve those issues. Here are the concerns:
(1) What was the rationale of using 10mm smoothing? The typical fMRI
Hello freesurfers,
I have an image that is in RAS orientation with the axial primary slice
direction. Is there anyway to change this to LIA orientation with the
coronal primary slice direction? I am assuming mri_convert would work, but
I'm not sure which flags to use.
Thanks in advance.
MP
__
Dear Doug,
Would you please shine some light on what quantities are being plotted in
those statistical maps of QDEC? Some linear combination of the columns of
the design matrix?
Also, what is the "default" design matrix?
Thank you very much!
Sincerely,
Ye
On Tue, Aug 13, 2013 at 11:45 PM, Dou
Hi Luzia
the lh.EC_average should be a symlink to
$FREESURFER_HOME/subjects/lh.EC_average
if it doesn't exist, create it with ln -s
cheers
Bruce
On Mon, 19 Aug 2013, Troebinger, Luzia wrote:
> Hi all,
>
> I am trying to run recon-all on a structural for one of my subjects, but
> freesurfer
Your original labels are not on fsaverage. You need to transfer them to
fsaverage using mri_label2label. That should fix your first problem. The
2nd should be fixed by having your ctab go from 0 to 58 with 0 being the
unknown label
doug
On 08/18/2013 02:51 PM, Stephen Politzer-Ahles wrote:
> H
Dear Doug,
thank you very much for your reply!Point c, is now ok.
Stefano
Messaggio originale
Da: gr...@nmr.mgh.harvard.edu
Data: 4-ago-2013 20.34
A:
Ogg: Re: [Freesurfer] Statistical concerns
On 8/1/13 7:56 AM, std...@virgilio.it
wrote:
H
try setting the orientation string to LIA
On 08/19/2013 11:15 AM, Mark Plantz wrote:
> Hello freesurfers,
>
>I have an image that is in RAS orientation with the axial primary
> slice direction. Is there anyway to change this to LIA orientation
> with the coronal primary slice direction? I am
Hello,
I received an error on several terminals running trac-all –path –c
Configuration_file.txt
55 slices processed
56 slices processed
56 slices processed
57 slices processed
57 slices processed
58 slices processed
59 slices processed
60 slices processed
61 slices processed
Queuing post proces
Dear Doug,
If I only have two groups, does the statistical test reduce to a two-tail
t-test?
Sorry, I meant to ask what the "default" contrast is, meaning what the
contrast is when I specify no nuisance factor?
Is there an official document where the QDEC setup is gone over
systematically?
Than
QDEC creates a sentence that describes each contrast. Is that sentence
not clear? I think the only other docs we have for QDEC are the tutorial.
doug
On 08/19/2013 12:19 PM, ye tian wrote:
> Dear Doug,
>
> If I only have two groups, does the statistical test reduce to a
> two-tail t-test?
>
1. Segmentation of partial brain
Dear FreeSurfers,
1. Can I expect recon-all to work on a T1W image where only part of the
brain is in FOV? The obvious answer is that I should just try, but it would
help to know in case I get unexpected results. Perhaps a more appropriate
question is: what should
On 08/19/2013 12:42 PM, Liane Hunter wrote:
>
> 1. Segmentation of partial brain
>
> Dear FreeSurfers,
>
> 1. Can I expect recon-all to work on a T1W image where only part of
> the brain is in FOV? The obvious answer is that I should just try, but
> it would help to know in case I get unexpected
From: Francesco Siciliano
Sent: Monday, August 19, 2013 12:54 PM
To: Francesco Siciliano
Subject: RE: [Tracula] error running trac-all –path –c Configuration_file.txt
I also noticed that even on those that appeared to finish, there was no dpath
folder. Any help w
On 08/16/2013 05:02 PM, Binod Thapa-Chhetry wrote:
> HI all,
>
> We had submitted a paper based on cortical thickness analysis in Qdec.
> The reviewer's had couple concerns regarding the QDec analysis. We
> would appreciate your help to address/resolve those issues. Here are
> the concerns:
>
>
I am looking at intracranial electrode recordings from some epileptic
patients. The locations of the electrodes have been determined using a
preoperative MRI and a postoperative CT scan. The locations are in RAS
coordinates. Is there some sort of function that will allow me to translate
the RAS coo
Hi
Du A.T. Brain 2007 ”Different regional patterns of cortical thinning in
AD" - used the smoothing level of 10-mm. This article can be added as
reference.
Additionally "higher smoothing levels, for ex. at 20 mm, would bring
partially inflated patterns due to excessive smoothing and due to
fa
Hi Francesco - There's a list of bedpostx output files here:
http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/fdt/fdt_bedpostx.html
The best way to determine if bedpostx finished running properly is to
check if those files were created in the dmri.bedpostX directory.
a.y
On Mon, 19 Aug 2013, Fra
Hi Sujith, look at this page and see if it answers your questions
http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
doug
On 08/19/2013 01:23 PM, sujith vijayan wrote:
> I am looking at intracranial electrode recordings from some epileptic
> patients. The locations of the electrodes hav
Hi All,
I'm trying to use funcroi-table-sess, but whenever I send this command:
funcroi-table-sess -roi l_amyg_test -analysis habit_concat.mni305
-contrast neg1Vfix -sf subjects.lst -o l_amyg_neg1Vfix.dat
I get this error:
set: Variable name must begin with a letter
So far as I can tell, all t
Hi Anastasia:
I wish to echo David's sentiments. Thanks for this great software. I was
able to process and extract data for all brains without losing any of the
brains. Thanks so much.
best,
Alan
On Fri, Aug 16, 2013 at 12:14 PM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:
>
> Ok
Hi all,
What's the difference between the curvature and folding measures outputted
in the aparc stats files (i.e. mean, gaussian, folding index, and curvature
index)? Additionally, which measures are the most reliable for individual
differences?
Thanks,
Mike
Michael Kranz
Graduate Research Assis
Sorry about that. I must have clicked 'reply' by mistake rather than
'reply all'. I wouldn't want to deprive anyone of the opportunity to help
me resolve this issue.
--The issue--
I looked at the segmentation in tkmedit and the labels for the ventricles
showed up the same as in subjects that worke
Hi Freesurfer experts,
I am trying to make an average surface from several monkey surfaces, and I
ran into a problem with make_average_subject. Specifically, I do not have
an aparc file nor a talairach.xfm. It seems that these problems have come
up on the list before (
http://www.mail-archive.com/f
Hello all,
While running recon-all for a subject, I ran into the following error
message:
*reading aseg from
/Users/IngvalsonLab/Desktop/avgseg_seg_test/mri/aseg.auto_noCCseg.mgz*
*reading norm from /Users/IngvalsonLab/Desktop/avgseg_seg_test/mri/norm.mgz*
*0 voxels in left wm, 0 in right w
Great to hear. Thanks, Alan!
On Mon, 19 Aug 2013, Alan Francis wrote:
Hi Anastasia:
I wish to echo David's sentiments. Thanks for this great software. I was able
to process and extract data for all
brains without losing any of the brains. Thanks so much.
best,
Alan
On Fri, Aug 16, 2013 a
check out these links
http://surfer.nmr.mgh.harvard.edu/fswiki/MeanCurvature
http://surfer.nmr.mgh.harvard.edu/fswiki/GaussianCurvature
On 08/19/2013 02:15 PM, Michael Kranz wrote:
> Hi all,
>
> What's the difference between the curvature and folding measures
> outputted in the aparc stats file
I've put that script here
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface.no-aparc
On 08/19/2013 02:53 PM, Caspar M. Schwiedrzik wrote:
> Hi Freesurfer experts,
> I am trying to make an average surface from several monkey surfaces,
> and I ran into a problem
Hi Doug,
that's great, thank you very much.
>From the previous posts I assume that this does not solve the issue with
the missing Talairach.xfm. Do you have a recommendation for that?
Thanks, Caspar
2013/8/19 Douglas N Greve
>
> I've put that script here
>
>
> ftp://surfer.nmr.mgh.harvard.edu/t
I would probably just try to do it by hand. Copy a file with the
identity matrix into the right folder, then run
tkregister2 --fstal --s subject
It will bring the human atlas up. I would then play with it a little bit
to get it to look ok. For surface-based applications, it will have no
effec
Is there a folder called "log" in the directly you are running it from?
If not, try creating one. If so, then
run it with -debug as the first arg and send me the terminal output.
doug
On 08/19/2013 02:07 PM, Joseph Andreano wrote:
> Hi All,
>
> I'm trying to use funcroi-table-sess, but wheneve
That looks good. Run these commands
cd AC30_1319/Bold1/001
mri_label2vol --aparc+aseg --temp template.nii.gz --reg
register.dof6.dat --o aparc+aseg.nii.gz
mri_binarize --i aparc+aseg.nii.gz --match 4 --match 5 --match 43
--match 44 --match 31 --match 63 --count countfile.dat
then send me the c
Hi Francesco - The bedpostx files are created when you run trac-all -bedp.
Then you need to run trac-all -path to reconstruct the paths under
dpath/... as the final step. Did you run this?
a.y
On Mon, 19 Aug 2013, Francesco Siciliano wrote:
Thank you!
Is it normal, however, not to have a
Is it possible to do a conjunction analysis between subjects using one
contrast? So far I've been able to do comparisons between contrasts within
subjects but not between subjects.
Thanks,
-Ronny
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
Hi Ronny, you can use mri_concat with the --conjunction option, but I
don't have a -sess command that does it
doug
On 08/19/2013 05:00 PM, preci...@nmr.mgh.harvard.edu wrote:
> Is it possible to do a conjunction analysis between subjects using one
> contrast? So far I've been able to do compari
Hi Doug,
I ran make_average_surface.no-aparc and identity matrices on my data, and I
seems to have completed the averaging without an error. However, when I try
to view the result with tksurfer, I get an error because there is no
average T1 for the average subject. How would you recommend I go abou
i have tried running the centos 4 & 6 versions of freesurfer on ubuntu
12.04, and with either i am getting a memory error when i simply run
mri_info on an mgz file (this does not happen on my osx
machine
for the same file
, and the license file is fine):
"""
znzTAGskip: tag=1667787808, failed to c
You can just copy in the T1.mgz from fsaverage (won't matter that it is
human), or you can try running make_average_volume to make a NHP
volume. Not sure that will work, but make sure to use --no-aseg
doug
On 8/19/13 8:43 PM, Caspar M. Schwiedrzik wrote:
Hi Doug,
I ran make_average_surfac
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