Hi doug,
I apologize for the delay. I've verified that the registration to the native
anatomical space is correct. I read the processing log. It seems that the
registration of volume is implemented from functional to anatomical, then
anatomical to mni305 spaces. So I also test the registration
Dear Bruce, Thanks again for the response. I have FLAIR images for each
subject acquired with MPRAGE/T1. I wonder in which way I can use FLAIR
images in the analyses of cortical thickness to be able to edit (subtract)
only the part of the brain which is missegmented (segmented as gray matter
where
yes, that would be fine. Or autorecon2-wm and autorecon3 will be faster
Bruce
On Sat, 13 Jul 2013, ye tian wrote:
Dear Freesurfers,
It turns out that I should edit both brainmask.mgz and wm.mgz for a subject.
In this case, may I recompile with recon-all -autorecon2 -autorecon3 to save
time?
Hi,
I am trying to figure out how to load thickness data into python such that
I would be able to identify the thickness at a given mesh node and also
identify surrounding nodes. I searched the mailinglist and found this
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07307.html but
if the FLAIR is reasonably high resolution (no voxel dimension greater
than around 1.5mm) then you can use the -flairpial switch to recon-all
cheers
Bruce
On Mon,
15 Jul 2013, amirhossein manzouri wrote:
Dear Bruce, Thanks again for the response. I have FLAIR images for each
subject
hi sebastian,
please take a look at pysurfer (https://github.com/nipy/pysurfer) and
nibabel (https://github.com/nipy/nibabel).
the relevant code is here:
https://github.com/nipy/nibabel/blob/master/nibabel/freesurfer/io.py
cheers,
satra
On Mon, Jul 15, 2013 at 9:11 AM, Sebastian Urchs
Dear all,
I attended the Seattle course a couple of weeks ago. Actually I m using mice
data in my analysis, and I was wondering if I can use freesurfer for that as
well ?I understand there is not so much sulci and gyria problem in mice data as
in human, however a flattened surface registration
Dear Sir，
I have found two files in the surf folder.One is 'lh.curv',the other is
'lh.inflated.h'.I have found some one said that the 'lh.curv' can be used to
quantify the curvature. but int the wiki, the command 'mris_curvature' can
ouput the file 'lh.inflated.h' which is MeanCurvature. So I
Dear Experts,
I am running trac-all -prep -c dmrirc on my DWI data. After flip4fsl step I
get the attached bval and bvec file which the bvec one is wrong so the
process exits with error in dtifit. I have also attached original bvec and
bval.
--
Best regards,
Amirhossein Manzouri
bvals
OK, I've fixed this one. Let me know if you want an updated binary.
doug
On 07/12/2013 10:47 PM, Joseph Dien wrote:
In the annot files generated by mri_glmfit-sim in 5.2.0 (e.g.,
cache.th20.pos.sig.ocn.annot), the names of the clusters take the form:
cluster0
cluster-001
cluster-002
…
Hi FS Community,
I was wondering which command(s) is(are) being used in the Motion Correction
part of the recon-all process, to merge the mri/orig/XXX.mgz files and correct
for any motion.
Thank you for your time!
Best,
Panos
___
Freesurfer mailing
Hi Gerit - Can you please send the entire trac-all.log for this subject?
There could be some clues in the info that's printed out from the earlier
steps, even if there's no outright error in those steps.
Thanks,
a.y
On Fri, 5 Jul 2013, Gerit Pfuhl wrote:
Dear Freesurfer experts,
for
Hi Matt - For how to tell tracula to use CVS registration, see Specify
the inter-subject registration method here:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula
Does this answer your question?
a.y
On Mon, 8 Jul 2013, Hoptman, Matthew wrote:
Hi all,
I see how to
Dear Freesurfer experts,
I have been using Freesurfer in combination with rtview.sh to visualize my
retinotopic mapping results (rotating wedge) and to define masks for individual
visual areas. The command that I use for this is something like:
rtview.sh --s *subj_id* --lh --polar --real
Hello freesurfers,
I am currently attempting to create a normalized .mgz file from an
input brain using mri_ca_normalize. Ultimately, I will use the norm.mgz
file to create a .gca atlas for infant MRI's.
Currently, I have three of the four required arguments. I am lacking the
Hi Andrew - My guess is that it's something about the file
dmri/dwi_orig.mghdti.bvals that's causing the error. Could you please send
along that file?
Also, how did you fix your previous configuration file problem? Letting
the list know about the resolution of the issue would help other
Hi Anastasia,
I noticed that my pathstats.byvoxel.txt files are missing the last four
values (AD_Avg RD_Avg MD_Avg FA_Avg) even though I'm certain I ran
trac-all -path -c dmrircFile correctly. Do you have any idea why this
might be? e.g. a configuration file change?
Thank you!
--
Susie Kuo
lh.curv is the spatially smoothed mean curvature of the lh.white surface.
lh.inflated.H is the mean curvatureof the inflated surface.
cheers
Bruce
On Mon, 15 Jul
2013, ??? wrote:
Dear Sir? I have found two files in the surf folder.One is 'lh.curv',the other
is 'lh.inflated.h'.I have found
Hi Anastasia,
I believe the issue I had with the pathstats.byvoxel.txt not displaying
the last four values (AD_Avg RD_Avg MD_Avg FA_Avg
) is owing to the fact that trac-all was run with FREESURFER 5.1. I believe
that FREESURFER 5.2 may be needed to generate path.pd.trk, and from that,
the above
Hi Mark
do you have a segmentaton for the brain?
Bruce
On Mon, 15 Jul 2013, Mark Plantz
wrote:
Hello freesurfers,
I am currently attempting to create a normalized .mgz file from an input
brain using mri_ca_normalize.
Ultimately, I will use the norm.mgz file to create a .gca atlas for
Hi Panos,
The motion correction itself is carried out using the mri_robust_template
binary. The motion correction step also includes an mri_convert command to
conform the volume and mri_add_xform_to_header.
example taken from recon-all dev table:
Dear Freesurfers,
I used Qdec to do two-group comparison on cortical thickness. Demeaned age
was used as the covariate. The question I¹m looking at is that ³Does the
thickness-age correlation differ between C1 and C3?²
When FWHM=15mm was chosen, I got confused results: When I used threshold
if the edits are aimed at only correcting the pial surface you don't need
to run autorecon2-wm. Sometimes the pial is incorrect because the white is
also wrong, then you need to run them both
cheers
Bruce
On Mon, 15 Jul 2013, ye tian wrote:
Dear Bruce and freesurfers,
I still don't fully
Freesurfer et al.,
I'd like to try out some simple cortical thickness regression analysis in
mri_glmfit. These would be analyses of one continuous score (e.g.,
Temperament) and several continuous nuisance variables (e.g., Age, IQ,
Site, etc). However, before getting started I wanted to run my
Dear Bruce,
Thank you very much!
In my experience, autorecon-pial does seem to alter white matter
assignment, which seems to contradict the statement that autorecon-pial
regenerates all final surfaces.
Sincerely,
Ye
On Mon, Jul 15, 2013 at 12:09 PM, Bruce Fischl
Hi Susie - The initial placement of the control points plays a much bigger
role than the end ROIs. The path being initialized in a bad location would
be more of a problem than the end ROIs being too generous. So I'd check
rh.unc_AS_avg32_mni_bbr_cpts_5.nii.gz before editing the end ROIs. Does
it does recreate the white and pial surfaces, but not all steps, and not
the segmentation step that creates the wm.mgz and hence the lh.orig and
rh.orig files. Erasing dura for example shouldn't require rerunning
autorecon2-wm (since the wm.mgz isn't expected to change)
cheers
Bruce
On Mon,
Hi Benjamin, BBR does not need higher resolution. Do you mean motion in
the anatomical or motion in the DTI? BBR should be pretty robust in
either case. It is hard to know what might be going on without more
details of why you think it is getting worse.
doug
On 07/14/2013 08:01 AM,
Hi Amirhossein - Are your original bvecs/bvals in 3-row format instead of
3-column format?
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula
Thanks,
a.y
On Mon, 15 Jul 2013, amirhossein manzouri wrote:
Dear Experts,
I am running trac-all -prep -c dmrirc on my DWI data. After
Hi Wayne, this is the problem with these types of corrections. As you
change the parameters, the null distribution for cluster sizes change.
At a threshold of .01 you may get a cluster that is smaller than at .05,
but it may be more significant because the shape of the null
distribution
Hi Avram, it basically looks ok, but I'm confused about the scanner
regressor. If these are two different MRI scanners, one at 1T and one at
3T, you should probably make different classes for them. Perhaps the
same thing for the Console variable.
doug
On 07/15/2013 01:19 PM, Avram Holmes
Mark, you can run
recon-all -s subject -motioncor -talairach
And it will run it upto the creation of the talairach matrix. If you
only have one run, then you don't need -motioncor
doug
On 07/15/2013 12:35 PM, Mark Plantz wrote:
Hello freesurfers,
I am currently attempting to create
Doug,
Thanks for the quick response. Scanner refers to site (e.g., Harvard,
McLean, MGH Bay4, MGH Bay6, etc.) console refers to the console software
version (e.g., B13, B15, B17. etc.). Any advice on how many conditions a
class can have before I should code it numerically?
Avram
On Mon, Jul
Hi Frederic, we don't have anything that will look as nice as that. But
it is possible to create a single vertex label then dilate the label to
create a circle.
doug
On 07/14/2013 01:28 PM, Frédéric Briend wrote:
Dear FreeSurfer team,
Firstall, thanks a lot to your great contribution in the
Hi Qasim, we don't really support non-human applications. Some people
have made modification to do monkey, but I've never seen anyone attempt
mouse or rat. Once you get to a point where you have surfaces, then
doing the surface registration would not be hard.
doug
On 07/15/2013 10:54 AM,
Hi Satra,
thank you very much - this has been tremendously helpful. I have now
identfied neighbouring verteces within a certain distance using networkx
and all_pairs_dijkstra_path_length.
I would now like to create my own curvature overlay (similar to the
thickness file) by assigning non-zero
Hi Matt - The CVS morph under xfms/cvs/ maps the individual anatomical to
the CVS template. To map from individual diffusion to the CVS template,
you'd have to first use diffusion-to-anatomical affine transform file
under xfms/.
Hope this helps,
a.y
On Mon, 15 Jul 2013, Hoptman, Matthew
That is exactly right! Those were added after 5.1.
On Mon, 15 Jul 2013, Susan Kuo wrote:
Hi Anastasia, I believe the issue I had with the pathstats.byvoxel.txt not
displaying the last four values (AD_Avg RD_Avg MD_Avg FA_Avg ) is owing to the
fact
that trac-all was run with FREESURFER
Hi Anastasia,
Yes, that was my problem. I think I need to use
mri_vol2vol --targ ../../../cvs_avg35_inMNI152/mri/norm.mgz --m3z
../../cvs/cvs_avg35_inMNI152/final_CVSmorph_tocvs_avg35_inMNI152.m3z
--noDefM3zPath --reg diff2anat.bbr.mat --mov ../dtifit_FA.nii.gz --o
diffvol2CVS.nii.gz
I should add that there several other reasons to be using the newer
version of tracula (from 5.2 or 5.3), including speed and other
improvements listed here:
http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates
Also note that using 5.2 or 5.3 won't make a difference in terms of
Hi Matt - The --reg option expects a .dat file. There should be one
produced by bbregister in the xfms/ directory?
a.y
On Mon, 15 Jul 2013, Hoptman, Matthew wrote:
Hi Anastasia,
Yes, that was my problem. I think I need to use
mri_vol2vol --targ ../../../cvs_avg35_inMNI152/mri/norm.mgz
This interface is a little complicated and not intuitive. The map you
see is an angle map thresholded at p.01. This thresholding is done
internally and has nothing to do with the Min/Max/Slope.
If you want to correct for multiple comparisons, then you will need to
run selxavg3-sess with -fwhm
Hi again,
I was wondering whether my previous message was received, since it had
rather large attachments. I look forward to receiving a reply with regards
to my questions!
Thank you,
Tudor
On 12 July 2013 16:03, Tudor Popescu tud...@gmail.com wrote:
Thanks Bruce. So the massive chunks that
Got it. Can you send me a listing of the contents of the xfms/ directory?
Conversions b/w formats can be done with tkregister2, but the .dat file
should normally be there since it's the default format for bbregister.
On Mon, 15 Jul 2013, Hoptman, Matthew wrote:
Right, that's been my
Hi all,
Small question related to the number of structural runs required for optimal
results: I was wondering whether someone tested the assumption that using two
scans rather than one improves the segmentation process and the cortical
surface reconstruction / thickness estimation? I've not
Hi Marie, I have not seen a publication on it. I've played around with
it a bit and could not convince myself that there was a huge win in
using 2, but it also depends a bit on your acquisition. If you have a
lot of acceleration or really small voxels, then maybe it makes a bigger
difference.
Hi Matt - Try anatorig2diff.bbr.dat.
a.y
On Mon, 15 Jul 2013, Hoptman, Matthew wrote:
Hi Anastasia,
Here it is:
anat2anatorig.dat anatorig2diff.bbr.dat anatorig2diff.bbr.dat.sum
diff2mni.bbr.mat
anat2anatorig.dat~ anatorig2diff.bbr.dat~ anatorig2diff.bbr.mat
I only have anecdotal evidence on this. (using version 5.1)
I found that if both scans had a little motion, then using both
improved reconstruction.
If one scan was pretty bad, and the other was pretty good, then using
the pretty good one on its own was better than using both.
If both were
Hi folks,
I am wondering if anyone has run into this problem before, and has a solution.
We are trying to post-hoc anonymize FreeSurfer reconstructions. It's a simple
matter to move the reconstruction directory, as well as to replace any
instances of the old subject ID in text files (e.g.
Hi Doug,
Thanks for the quick reply. A few more details:
What do you mean by position (AC/PC)? Do you mean the col, row,
slice? We don't find the actual AC or PC.
Yes: 3D coordinates in any identified coordinate systems. For now, we
are asking our users to mark those points manually. It would
Hi Andy, there is nothing in the current distribution that does this,
but I just added something that does. If you're running locally, you can
use the devenvironment and run
mris_convert --delete-cmds lh.pial lh.pial.new
The resulting surface is the same without the command lines, eg,
I attached the file above.
For the configuration problem, I actually just installed freesurfer onto one of
our newer macs and it seemed to work fine. I was running it on an older linux
version of freesurfer. Still couldnt figure the issue on the linux though for
the config file.
Thanks, Anastasia,
That worked. Sorry I missed it!!
--Mat
-Original Message-
From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
Sent: Monday, July 15, 2013 3:17 PM
To: Hoptman, Matthew
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] application of mri_cvs_register
Hi Jonathan, FreeSurfer folks:
Did you have success in combining 4 echoes of MEMPRAGE images into one? I
went through the archives and it appears to me that you would use:
mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh only after the
scan has been through the recon all process. My
Hi Andrew
I think if you read them in matlab and write them back out it will strip
that stuff.
cheers
Bruce
On Mon, 15 Jul 2013, Andrew Ward wrote:
Hi folks,
I am wondering if anyone has run into this problem before, and has a
solution.
We are trying to post-hoc anonymize FreeSurfer
Hi Alan
to use the 4 echoes you want to compute the rms. I think something like
mri_average -noconform -sqr mprage_echo?.mgz mprage_rms.mgz
should do the trick (then use mprage_rms.mgz as the input to recon-all)
cheers
Bruce
On
Mon, 15 Jul 2013, Alan Francis wrote:
Hi Jonathan,
Thanks Bruce.
On Mon, Jul 15, 2013 at 4:52 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote:
Hi Alan
to use the 4 echoes you want to compute the rms. I think something like
mri_average -noconform -sqr mprage_echo?.mgz mprage_rms.mgz
should do the trick (then use mprage_rms.mgz as the
By that I mean that I only have a normal MPRAGE anatomical scan. By
inflated I mean that I ran recon-all on this anatomical so that I can
display the inflated surface for example. So when I said I inflated the
anatomical I meant I ran recon-all. Sorry for the confusing terminology.
On Mon, Jul
Dear Bruce,
Thank you very much!
Sincerely,
Ye
On Mon, Jul 15, 2013 at 12:37 PM, Bruce Fischl
fis...@nmr.mgh.harvard.eduwrote:
it does recreate the white and pial surfaces, but not all steps, and not
the segmentation step that creates the wm.mgz and hence the lh.orig and
rh.orig files.
Dear FreeSurfer Expert,
I would like to draw the specific ROI of the DK atlas (not specific individual,
but this ROI in general). I'm wondering how this ROI can be extracted/created
as a mask so that I can draw it on the brain using some software?
Could you please advise?
Thanks a lot,
Daniel
Hi Daniel
sorry, can you clarify? The DK atlas is estimated on every brain that you
run recon-all on and stored in the label directory. Is that what you want?
cheers
Bruce
On Mon, 15 Jul 2013,
Yang, Daniel wrote:
Dear FreeSurfer Expert,
I would like to draw the specific ROI of the DK
Hello,I have successfully installed freeon my mac pro server.but when i try to
run the tkmedit it is giving the following error message, although I have
copied the license information in freesurfer home directory.[Geodesics:~] EGI%
tkmedit bert
you need a license file, you can get one from the FS site. Save it into
/Applications/freesurfer/license (not .license).
doug
On 7/15/13 10:37 PM, Muhammad Naveed Iqbal Qureshi wrote:
Hello,
I have successfully installed freeon my mac pro server.
but when i try to run the tkmedit it is giving
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