I did type the same line es mentioned in your Email and I did not put the 1.3
in quotes.
However, it is still not working:-( Any other ideas???
Thanks.
DH
> Subject: Re: [Freesurfer] Extracting thickness, area and folding values from
> Qdec
> From: dgwake...@gmail.com
> Date: Thu, 1
Hi Jeff
if you send us the .csv file we will see if we can replicate and fix
cheers
Bruce
On Thu,
13 Mar 2014, Jeff Stevenson wrote:
> hi freesurfer folks, just had a nasty bug crash my whole mac workstation.
> yikes! i loaded lh and rh pial surfaces into freeview and went to assign
> annotati
Hi Koushik,
there is a way to add time points without recreating the base:
recon-all -long -addtp -all
This is what the recon-all help says about that:
"If a new timepoint needs to be added to a longitudinal run where a base
subject
has already been created (from prior timepoints), then th
Could anyone help me deal with error in integrating Freesurfer with Surfstat ?
Because "MNI object" data was not available not like as written in the web
documentation (http://www.math.mcgill.ca/keith/surfstat/), I used my own
patient's MRI data with Freesurfer software.
(CIVET software is
Run it with --debug as the first option and send me the terminal output
doug
On 3/14/14 3:44 AM, Dusan Hirjak wrote:
I did type the same line es mentioned in your Email and I did not put
the 1.3 in quotes.
However, it is still not working:-( Any other ideas???
Thanks.
DH
> Subject: Re: [Fr
Dear Experts,
I have read the previous posts in the list regarding restricted ROI
analysis. So I generated my label from tksurfer and used that for group
difference analysis by adding --label to mri_glmfit, but the result
(sig.mgh) seems just a masked version of the analysis including whole brain
(
Thanks Martin, I will try it out.
K
From: Martin Reuter [mailto:mreu...@nmr.mgh.harvard.edu]
Sent: Friday, March 14, 2014 9:31 AM
To: Govindarajan, Koushik Athreya; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] adding time points to longitudinal base template
Hi Koushik,
there is a
lh.thickness is not a surface file, it is a surface overlay. Try reading
in lh.white as a surface
doug
On 03/14/2014 10:34 AM, 조규호 wrote:
>
> Could anyone help me deal with error in integrating Freesurfer with
> Surfstat ?
>
> Because "MNI object" data was not available not like as written in
you are doing it the right way. There is no difference in the
uncorrected analysis. There will be a difference when you correct for
multiple comparisons
doug
On 03/14/2014 11:15 AM, amirhossein manzouri wrote:
> Dear Experts,
> I have read the previous posts in the list regarding restricted RO
Hi Doug -Using the overlay threshold flags, I see that the .mgh (yes, the .mg was a cut/paste typo) is in the occipital region and should be frontal, temporal and parietal regions. So, I must be doing something wrong in the mri_vol2surf command:> mri_vol2surf --src $SUBJECTS_DIR/[subj]/label/LECN_
oh, sorry, I had not seen that the LECN...nii file was already in
subject space. In that case use --regheader subjectname instead of --srcreg
doug
On 03/13/2014 05:53 PM, Barbara Weiland wrote:
> Hi Doug -
>
> Using the overlay threshold flags, I see that the .mgh (yes, the .mg
> was a cut/pas
This actually happens on any random non-annotation file. I'll fix it.
Ruopeng
On 03/14/2014 08:25 AM, Bruce Fischl wrote:
> Hi Jeff
>
> if you send us the .csv file we will see if we can replicate and fix
>
> cheers
> Bruce
> On Thu,
> 13 Mar 2014, Jeff Stevenson wrote:
>
>> hi freesurfer folks,
ok, thanks
On Fri, 14 Mar 2014, Ruopeng Wang wrote:
> This actually happens on any random non-annotation file. I'll fix it.
>
> Ruopeng
>
> On 03/14/2014 08:25 AM, Bruce Fischl wrote:
>> Hi Jeff
>>
>> if you send us the .csv file we will see if we can replicate and fix
>>
>> cheers
>> Bruce
>> O
does the brightness/contrast window you display not work?
On 03/14/2014 12:59 PM, Borzello, Mia wrote:
> Hi Freesurfers,
>
> I recently coregisered a patient and am trying to visualize the
> electrodes in tkmedit now, but I'm unable to see them very clearly.
> The CT has 1mm slices, so I don't th
sure. It's under view->configure->brightness/contrast I believe
On Fri, 14
Mar 2014, Borzello, Mia wrote:
Hi Freesurfers,
I recently coregisered a patient and am trying to visualize the electrodes
in tkmedit now, but I'm unable to see them very clearly. The CT has 1mm
slices, so I don't think
no it doesn't help at all.
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Friday, March 14, 2014 1:11 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [
Hi Doug -OK - Now I am able to move the ROIs to subject space and verify them with tksurfer:
[subj]/surf/LECN_M87191258_lh_surf.mghThen I am having the same error I encountered before when I try to convert these to a label using:The output file label has -1 in the first column rather
Use the --surf option
On 03/14/2014 01:18 PM, Barbara Weiland wrote:
> Hi Doug -
>
> OK - Now I am able to move the ROIs to subject space and verify them
> with tksurfer:
> [subj]/surf/LECN_M87191258_lh_surf.mgh
> Then I am having the same error I encountered before when I try to
> convert
Hi list,
in Wakana et al., 2007, the SLF was divided in parietal and temporal
components. As I understand it, the same subdivision has been made in Yendiki
et al, 2011. In details, SLFp should correspond to SLF III and SLFt to arcuate
fascicle.Tractography studies showed that the anatomy of the
Hi Stefano - Our SLFt was indeed labeled as defined in Wakana et al, so it
is frontotemporal.
a.y
On Fri, 14 Mar 2014, std...@virgilio.it wrote:
Hi list,
in Wakana et al., 2007, the SLF was divided in parietal and temporal
components. As I understand it, the same subdivision has been made
Dear FreeSurfer experts,
I've been using FreeSurfer for 2 months now, and I have a question on how
to proceed to do the following thing:
My goal is to obtain the CRS coordinates of the corpus callossum.
Here is what I was thinking to do, based on what I read:
1. Annotation to segmentation:
m
Hi Thomas
you are probably better off getting it right out of the aseg.mgz. The cc
labels in it are:
#define CC_Posterior 251
#define CC_Mid_Posterior 252
#define CC_Central253
#define CC_Mid_Anterior 254
#define CC_Anterior 255
so you should just be able to run mri_extr
Great - thanks for your help - got it all working now!
___
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The information in this e-mail is intended only for the person to whom it i
Hi All,
Although the question of flipping hemispheres has come up before, I
still struggling with it.
I'm working on a longitudinal study with stroke subjects (half with lh
lesions, half with rh lesions). We want to compare only the
non-lesioned, healthy, hemispheres at 2 timepoints (pre- and
You have uncovered a bug. I don't think anyone has tried to run xhemi on
a longitudinal data set before. There is a work-around. First run
xhemireg --s subject --no-tal
Then run
surfreg --s subj1_Tp1.long.subj1_base --t fsaverage_sym --rh --xhemi
I think this should work
doug
On 03/14/2014
Actually, I don't think this will work. What version of FS are you running?
I've created a patch of the 5.3 recon-all here
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/recon-all.53.patch
Copy this to $FREESURFER_HOME/bin/recon-all (after making a backup!)
then re-run
doug
O
Thanks -- (I thought I might not have understood the processing pipeline
properly.)
I'm running 5.3, I'll try the patch and let you know how it works.
Peggy
On 3/14/14, 16:07 , Douglas N Greve wrote:
> Actually, I don't think this will work. What version of FS are you running?
>
> I've created
Hi,
I've been using dmri_motion to quantify motion in our DTI data. Can you give
any guidance on selecting values for the -D and -T flags? I didn't see
anything in the wiki or in your related papers and it can have a substantial
effect on the outputs.
Thanks.
Hi Ruth - These parameters are described in Benner 2011 (cited in our
paper). The -T threshold is mostly what you might need to change,
depending on your scanner. You should look at the low-b images and find a
rough lower threshold for the image intensities of brain voxels. It
doesn't have to
Thanks Anastasia,
I'd looked at the Benner article which didn't give a rationale for the
selection of thresholds. I've been testing different T values and am settling
on something much higher than the default (~700). With the default value
nearly all of our scans wind up with floor values (0 a
I am trying to preproc-sess my data (fwhm 1.5, per-run, native space) with
this command
preproc-sess -fwhm 1.5 -fsd bold -per-run
I expect it to generate fmcpr.sm1.5.nii.gz for each run of my dataset.
Although preproc-sess finishes without any error, it only generates
fmcpr.nii.gz and when I run
Hi Ruth - Indeed, setting the intensity threshold too low compared to the
intensities in your low-b images will lead to underestimating the amount
of signal drop-out due to motion.
a.y
On Fri, 14 Mar 2014, Ruth Carper wrote:
Thanks Anastasia,
I'd looked at the Benner article which didn't g
Hi doug and other FS experts,
Thanks very much doug.
rh.ttest.thickness.10.mgh is created from the mris_preproc to merge all the
subjects' thickness into one file. Then group t-test can be done.
I try tksurfer -t rh.ttest.thickness.10.mgh, but the command window echoes its
usage.
Just as you told
Hi doug and other FS experts,
Thanks doug.
I have 2 new questions:
1,What you told me is generate a hemisphere. So there is only one hemisphere I
can see in the AFNI?
2,After typing this code:
"mri_surf2vol --surfval rh.36sb.10.mgh --hemi rh --fillribbon --subject
fsaverage --template
/mnt/sdb1/
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