Hi guys,
I just wanted to make sure I am understanding everything correct.
I have done recon -all -all on all my subjects. Can I now just use the
numbers in the .stats files to compare these with my other measures?
It seems to be very (almost too) simple, so I that's why I am checking to
see whet
Aha, Ok, I will try to get my hands on that data and give it a go.
Thanks for the help!
Heidi
On 6/1/16, 4:01 AM, "Anastasia Yendiki"
wrote:
>
>The input needs to be the diffusion-weighted images, not the FA, MD, etc.
>There should be as many volumes in this input nifti as there are b-values
>in
The input needs to be the diffusion-weighted images, not the FA, MD, etc.
There should be as many volumes in this input nifti as there are b-values
in bval file and gradient vectors in the bvec file. The image
registration, tractography, etc etc is performed on the diffusion-weighted
images,
Dear Freesurfer experts,
Sorry for resending this post.
mri_cc does not seem to be working properly to parcellate corpus callosum.
As per one of the previous posts, there is a bug in the current release of
mri_cc. However, the link provided in the same thread for an updated
version of mri_cc is n
Hi Bruce,
Our main concern is that we will be incorporating additional sources of
error by doing so! But it seems there is no way to get around it.
Thanks for the prompt response!
Maryam
On Tue, May 31, 2016 at 7:07 PM, Bruce Fischl
wrote:
> Hi Maryam
>
> why don't you want to use tracula? Th
Hi Maryam
why don't you want to use tracula? That is what it is designed for
cheers
Bruce
On Tue,
31 May 2016, Syeda Wajiha Maryam wrote:
> Hello Freesurfer experts,
>
> I am looking to extract certain white matter pathways (for instance, the
> superior longitudinal fasciculus, uncinate fascic
Hello Freesurfer experts,
I am looking to extract certain white matter pathways (for instance, the
superior longitudinal fasciculus, uncinate fasciculus) with freesurfer
which I believe are affected by Alzheimer's Disease. But it seems that
these can only be obtained by performing tractography usi
I see. Can you tell us a bit about the input data? It looks pretty blurry.
I suspect that you have topological defects that are incorrectly fixed in
those regions, probably because a bunch of the white matter was missed. Is
the white matter significantly darker than 110 there? You could try some
Yes, each nifti contains one volume. I have different nifti’s for the
different metrics (FA, MD,..)
Is there a way I can use the trac-all on these files?
On 5/31/16, 9:26 PM, "Anastasia Yendiki"
wrote:
>
>Some of the errors make me suspect that your input DWI files contain only
>one volume. Coul
We precluded the use of mris_anatomical_stats with fsaverage because by
default it will not compute the area appropriately. You can use
mri_segstats with --annot fsaverage lh yourparc --i
$SUBJECTS_DIR/fsaverage/surf/lh.white.avg.area.mgh --accumulate --sum
summary.stats
On 05/31/2016 04:31
yes, typically it is a mistake that we want to catch
cheers
Bruce
On Tue, 31 May 2016,
Satrajit Ghosh wrote:
> thank you doug, martin, and bruce.
> martin: i believe she was doing this for motion correction
>
> i've attached the error this person observed below. so it does seem that
> mri_robus
Hi folks,
I'm trying to split a cluster from mri_glmfit-sim into two separate
regions. (Ginormous blob of activation across multiple structures of
interest...)
I've gotten to the point of generating a new annotation with the
separate labels for my separate regions, but am stuck getting a
"cluster
thank you doug, martin, and bruce.
martin: i believe she was doing this for motion correction
i've attached the error this person observed below. so it does seem that
mri_robust_template at present doesn't do any resampling.
bruce: we can definitely see ways in which this could be done outside
r
Hi Shyam
it's hard to give you an answer unless I understand what the source of
your inaccuracy is. Perhaps you can point an image that is zoomed in on a
region with arrows to indicate where you think things need improving? I
don't really understand your image. If the green circles are control
Yes the green circles are control points. The control points shown in the
picture show surfaces we feel are not accurate.
Additionally, how are we supposed to use the control points, do we place
them on the inner most boundary of the WM?
Also, going back to the original questions: How do you reco
Hi Shyam
can you add arrows to show where you don't think the surfaces are
accurate?
And are the green circles meant to be control points? If so, I'm
surprised that didn't break everything since they need to be added to the
interior of the WM.
cheers
Bruce
On Tue, 31 May 2016, Limachia,
Some of the errors make me suspect that your input DWI files contain only
one volume. Could this be the case?
On Tue, 31 May 2016, Jacobs H (NP) wrote:
Hmm, weird, as I put a # in front of it. Putting the eddy current to 0
gives the same error. Enclosed is the config file.
Thank you so much
Hi Satra
it will probably reject this by default, which you can get around be
reslicing one of them to be like the other. Or "conforming" both of them.
cheers
Bruce
On
Tue, 31 May 2016, Satrajit Ghosh wrote:
> hi folks,
> does recon-all work if the input T1s for the same participant have diffe
Thanks a lot!
Cico
Francesco Cardinale, MD
Neurosurgeon
"Claudio Munari" Centre for Epilepsy and Parkinson Surgery - Ospedale Niguarda
"Ca' Granda"
Piazza dell'Ospedale Maggiore, 3 - 20162 - Milano - Italia
phone 0039 02 64442917
fax 0039 02 64442868
e-mail francesco.cardin...@ospedaleniguarda.
Hmm, weird, as I put a # in front of it. Putting the eddy current to 0
gives the same error. Enclosed is the config file.
Thank you so much
Heidi
On 5/31/16, 8:13 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Anastasia Yendiki" wrote:
>
>Hi Heidi - It knows where to find the freesurf
Hi Heidi - It knows where to find the freesurfer recons of the T1's from
SUBJECTS_DIR (see example config file). Based on your log file, it looks
like you haven't turned off the eddy current compensation, because it's
trying to run it. If you attach your config file, I'll take a look.
Best,
a
Thanks! I tried to adapt the configuration file and it got a bit further,
but then crashes again. Not sure why? I have added the log file, so that
maybe you could have a look at what is happening?
Also, how does the trac-all command knows where to find the T1 data?
Thanks
Heidi
On 5/31/16, 5:07 PM
You can use mri_convert, like
mri_convert lh.thickness --ascii lh.thickness.txt
this will create a text file with a single column, one row for each
vertex. You can also use
mri_convert lh.thickness --ascii+crsf lh.thickness.txt
This will create 5 columns, the first being the column number, th
I see. Could be we specifically test for that and stop processing. It is
a bad idea to average from different resolutions. Probably averaging is
not even helpful at all, especially with newer images.
Anyway, if someone points me at some data, I can take a look.
Best, Martin
On 05/31/2016 01:
It expects both polar and eccen. You can "fake" an eccentricity run by
just copying one of the polar runs and calling it eccen
On 05/31/2016 07:35 AM, Steinmann, Iris wrote:
>
> Dear freesurfers,
>
> I try to run a retinotopy analysis following the instruction on
>
> https://surfer.nmr.mgh.harvar
I tried this recently and it failed. I did not pursue it any further
On 05/31/2016 01:32 PM, Martin Reuter wrote:
> Do you mean several inputs for motion correction (averaging), or for a
> longitudinal study?
>
> I haven't tested it, but for averaging, we use mri_robust_template and
> I see no r
Sorry, not sure what you are asking. It sounds like you have exactly the
situation in that web page except you have diagnosis as a factor instead
of handedness.
On 05/30/2016 09:39 AM, Hao wen wrote:
>
> Hello, FS experts:
>
> I am now doing the group analysis with covariates(age, gender), I am
Do you mean several inputs for motion correction (averaging), or for a
longitudinal study?
I haven't tested it, but for averaging, we use mri_robust_template and I
see no reason why it should not work. It probably reslices at the
resolution of the first input to create rawavg and then conforms
No, I don't think it does
On 05/31/2016 10:13 AM, Satrajit Ghosh wrote:
> hi folks,
>
> does recon-all work if the input T1s for the same participant have
> different resolutions? (i don't have a dataset to test, but trying to
> debug some issues another group has been having).
>
> cheers,
>
> s
No, that just allows you to run selxavg3-sess without having specified
any contrasts with mkcontrast-sess
On 05/31/2016 08:05 AM, Leila Reddy wrote:
> Sorry I meant to ask if the weight for the baseline/fixation is set to
> -1 (not 0).
>
> Thanks,
> Leila
>
>
> On Tuesday, May 31, 2016 1:44 PM,
have you seen our worked-out examples?
http://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples
On 05/31/2016 03:39 AM, Clara Kühn wrote:
> Dear FreeSurfer experts,
>
> I would like to correlate my thickness data with behavioral measures. Can I
> do that with glmfit? If so, could you explain how to
It did not find any voxels in the ROI. This can happen for several
reasons. First, check your registratoin (tkregister-sess). Second, it
can happen because the size of the ROI is too small and does not occupy
enough space in a voxel. Try changing the -fillthresh to something
smaller than the de
Sorry for the delay. This is because sphere.reg only applies to
fsaverage. Previously, the specification of a different target would
only influence smoothing done as part of mris_preproc; the registration
would still be done to fsaverage. This is probably not the intent of
people who are specif
Hi Bruce,
Is there any new timeline regarding the release of the v6 beta? Because I'm
currently waiting on that version for my project's work because of the new
hipppocampal module and knowing that will help me a lot.
Thanks,
Tyson
On Tue, May 3, 2016 at 5:51 AM, Bruce Fischl
wrote:
> Hi Tyson
Dear list members,
please find below a link to a postdoc position annoucement that might be
of interest, in the field of cortical morphometry for developmental
studies and autism.
http://www.meca-brain.org/2016/05/31/we-are-looking-for-a-post-doc/
O. Coulon
--
Olivier Coulon,
Aix-Marseille U
No, it should be pointed to the DWI data, which can be corrected niftis
instead of the original dicoms. I would recommend turning off all the
corrections in the configuration file, and then running everything without
skipping steps. This will create all the files that are expected to be
there
Dear Freesurfers,
I wonder if you could please help me with this issue, it may be similar
to this post?
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg40092.html
Ran it just fine a while back, but now it is failing with this error.
Thank you very much,
Best wishes,
Barbara
Dear Anastasia,
Thanks for the feedback. So, does this mean that the dcm root should be
pointed towards the T1¹s? I have the FreeSurfer recon-all output in a
different folder.
Enclosed is the log file (of one subject) and the configuration file. You
will see that I tried the inter and intra option
hi folks,
does recon-all work if the input T1s for the same participant have
different resolutions? (i don't have a dataset to test, but trying to debug
some issues another group has been having).
cheers,
satra
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Hi Heidi - The intra-subject registration step that you're trying to run
registers your subject's DWI and T1 images. It expects to find those
images. It doesn't use the FA, MD, etc in any way.
Did the log file get created in scripts/trac-all.log? If so, can you
please send that file and your
Hi Anri - Can you also send your log file (scripts/trac-all.log)? I'll
need to see what exactly was running when the error occurred. Thanks!
a.y
On Sat, 28 May 2016, Anri WATANABE wrote:
Hello Anastasia,sorry for few information and let me tell you command and error
log.
Command: trac-all
Sorry I meant to ask if the weight for the baseline/fixation is set to -1 (not
0).
Thanks,Leila
On Tuesday, May 31, 2016 1:44 PM, Leila Reddy wrote:
Hi,I was just wondering what exactly the -no-con-ok option does in
selxavg3-sess. Is it the same as setting the weights for all condition
Hi,I was just wondering what exactly the -no-con-ok option does in
selxavg3-sess. Is it the same as setting the weights for all conditions to 1
and give the baseline/fixation (i.e., 0s in the para files) a weight of 0?
Thanks,
Leila
___
Freesurfer maili
Dear FreeSurfer experts,
I would like to correlate my thickness data with behavioral measures. Can I do
that with glmfit? If so, could you explain how to specify the contrast for that?
My fsgd file looks like this:
GroupDescriptorFile 1
Class 1male plus blue
Class 1female plus red
Class 2male
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