Dear all,
I am wondering about what the zero angle for retinotopy corresponds to in
retinotopy analysis. I mean corresponding to the wedge being at zero angle in
circular coordinate map (horizontal) or vertical up?
Thank you,
Best,
___
Freesurfer mai
Hi Doug,
Thank you for taking the time to answer, I really appreciate it! I have
completed this step for all subjects, and created the lh.wm.mgh and rh.wm.mgh
files. What should be the next step for creating those maps? Unsure on how to
overlay the mgh files.
Thanks,
Sabrina
> On Feb 4, 20
I used tksurfer…
I found the error actually it was due to the order by which I load the data
into freeview. It has to be loading the ROI first and then loading the volume
along with the associated registry. When this order is violated all sorts of
problems happen.
On the other hand, I am unable
how were the labels made?
On Fri, 5 Feb 2016, m.abouelya...@gmail.com wrote:
Dear all,
I am wondering about the template that I should use for use to convert custom
made labels to
volumes. I have used the template.nii.gz file that gets generated in the fMRI
analysis folder
corresponding t
Dear all,
I am wondering about the template that I should use for use to convert custom
made labels to volumes. I have used the template.nii.gz file that gets
generated in the fMRI analysis folder corresponding to the same subject along
with the register.dat file located in the same location.
Thank you!
Best,
Ji Won
> On Feb 4, 2016, at 7:01 PM, Douglas Greve wrote:
>
> that is not generated when unpacking. It is generated when you run
> preproc-sess
>
>
>> On 2/4/16 6:09 PM, Ji Won Bang wrote:
>> Hi, again.
>>
>> I tried dcmunpack:
>> dcmunpack -src $DATA_DIR/$SUBJECT/DICOM/d
Maybe Christophe can answer?
On Thu, 4 Feb 2016, Adam David Felton wrote:
> Hello,
> I checked the listserv history, but couldn't find an answer to my question:
>
> With the 2009 parcellation scheme, 1) does the planum temporale parcellation
> include the
> posterior ascending ramus (which Destr
Hello,
I checked the listserv history, but couldn't find an answer to my question:
With the 2009 parcellation scheme, 1) does the planum temporale
parcellation include the posterior ascending ramus (which Destrieux et al.
2010 seems to imply) and 2) does the planum temporale include the posterior
that is not generated when unpacking. It is generated when you run
preproc-sess
On 2/4/16 6:09 PM, Ji Won Bang wrote:
Hi, again.
I tried dcmunpack:
dcmunpack -src $DATA_DIR/$SUBJECT/DICOM/day1 -targ $DATA_DIR/$SUBJECT/
-fsfast -run 3 bold nii f.nii
It worked.
Inside $DATA_DIR/$SUBJECT/bol
Hi Sabrina, sorry, I was working on a grant, and now I'm out of town
until Monday. I can try to push you forward on this now, but I have to
be brief. Those images where made from data created with the pctsurfcon
scriopt. If you run it with --help, you will get some docs on it. This
is already r
Hi, again.
I tried dcmunpack:
dcmunpack -src $DATA_DIR/$SUBJECT/DICOM/day1 -targ $DATA_DIR/$SUBJECT/
-fsfast -run 3 bold nii f.nii
It worked.
Inside $DATA_DIR/$SUBJECT/bold/003/, I see only 2 files: f.nii
f-infodump.dat
On the instruction page (
http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFu
Hi,
I am having trouble to generate .mgz file from DICOM. However, I was able to
run the same code with NIFTI file. What did I do wrong? Thanks for your help.
Kan
NUA502608:300T1 kding$ ls
3010-0.dcm 3010-27.dcm
3010-1.dcm 3010-28.dcm
3010-10.dcm 3010-29.dcm
301
Dear Freesurfer experts,
I am working on brain stem segmentation analysis using the new module included
in FS6.
The analysis ran properly for 38/40 subjects. I have an issue with two subjects.
I sent my jobs to the cluster as always using the following command line:
pbsubmit -c " recon-all -su
Hi sorry, haven't heard back yet from Freesurfers. Just following up on how to
generate gray matter & white matter intensity maps overlaid onto brain like in
Salat paper.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2750073/#R57
Figure 1 (c). The mean maps of signal intensity.
Thanks!
Hi.
When I tried dcmunpack:
dcmunpack -src $DATA_DIR/$SUBJECT/DICOM/day1 -targ
$DATA_DIR/$SUBJECT/bold_decode -fsfast -seqcfg $LOG_DIR/$UNPACK
I had error:
ERROR: Flag -seqcfg unrecognized.
-src /home/jbang/Projects/replay/epi//replay01/DICOM/day1 -targ
/home/jbang/Projects/replay/epi//replay01/b
I'm not sure what the difference is. Compute the mean of the 2nd column,
then subtract that number from the values in the 2nd column.
doug
On 2/2/16 7:30 AM, Nabin Koirala wrote:
Thank you for your response . Sorry but for my understanding, should i
substract the mean from the data (demean) or
Hi Ji Won, can you try dcmunpack? Should take the same arguments
On 2/4/16 10:28 AM, Ji Won Bang wrote:
Dear. Freesurfer team.
Hi. Our lab tried to unpack DICOM files using both freesurfer v4.5.0
and v5.3.0.
The command line is:
unpacksdcmdir -src $DATA_DIR/$SUBJECT/DICOM/day1 -targ
$DATA_
Thanks a lot for your prompt reply and suggestion!
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve
Sent: donderdag 4 februari 2016 17:01
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer]
Hi Anna, don't use --projfrac-avg as that will average the values over
the ribbon (and so give non-integer results). Just use --projfrac
On 2/4/16 9:07 AM, Gardumi Anna (PSYCHOLOGY) wrote:
> Dear all,
>
> I have checked the result of projecting a map from volume to surface with
> nearest neighbo
Can you view it in tkmedit? Are there any voxels that are super bright
relative to the rest of them? One really bright voxel may cause the
screen to appear black. If you click on points in the middle, are the
values in the control non-zero?
On 2/4/16 8:08 AM, Worker, Amanda wrote:
Hi,
Chan
Hi Deniz - It seems that it finds the folders of the 2 time points, but
not the folder of the longitudinal base template. This is the template
that longitudinal recon-all creates in its 2nd processing step. In your
case, it would be
/data_august/Deniz/DTI_long/subjects/med_AhJa94
Doe
Hi Peter - Have you defined "bvecfile" in your configuration file? I
suspect it doesn't know where to find the gradient table.
a.y
On Thu, 4 Feb 2016, Parzer, Peter wrote:
> Hi,
>
> trying to do my first steps with tracula I got stuck early in the
> preprocessing step. The DICOM import and pr
Dear. Freesurfer team.
Hi. Our lab tried to unpack DICOM files using both freesurfer v4.5.0 and
v5.3.0.
The command line is:
unpacksdcmdir -src $DATA_DIR/$SUBJECT/DICOM/day1 -targ
$DATA_DIR/$SUBJECT/bold_decode -fsfast -seqcfg $LOG_DIR/$UNPACK
And I get the error message:
$Id: unpacksdcmdir,v
if you move the mouse around do you seen any non-zero values in the
"mouse" side of the info windows at the bottom? Are the voxel coords
reasonable?
If you upload the volume we'll take a look.
On Thu, 4 Feb 2016, Worker,
Amanda wrote:
Hi,
Changing the min and max fields doesn't make it
Hi Amanda
sometimes freeview doesn't do a good job setting the window levels. Try
changing them manually, or draw a box with shift-middle mouse (it will
show in green)
cheers
Bruce
On Thu, 4 Feb 2016, Worker, Amanda wrote:
Hi All,
I was hoping someone could help with an issue that I'm h
Hi Will
I expect that means that the talairach.xfm is off by a ton (i.e. by a 90
deg rotation or more). You are probably better off starting with the
identity matrix.
cheers
Bruce
On Thu, 4 Feb 2016, will brown wrote:
Message: 3
Date: Tue, 2 Feb 2016 14:17:02 -0500
From: Bruce Fis
Dear all,
I have checked the result of projecting a map from volume to surface with
nearest neighbor "interpolation" with the following command:
mri_vol2surf --mov DiscreteMap.nii --reg $REGMAT --hemi lh --projfrac-avg 0 1
0.2 --interp nearest --o DiscreteMap_InFS_projAvg02_SurfLh.mgh
and the
Hi,
Changing the min and max fields doesn't make it visible, however changing the
color map to Lookup Table makes the volume all red. But I can't seem to do much
else.
Amanda
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of dgw
Sent: 04 February
Amanda,
Is there a progress bar still running? Have you tried changing the window min
max fields?
hth
d
Sent from my Phone
> On Feb 4, 2016, at 06:46, Worker, Amanda wrote:
>
> Hi All,
>
>
> I was hoping someone could help with an issue that I'm having that I'm sure
> has a simple explana
Hi all,
I am currently working on retinotopy data and I managed to get the maps but I
don’t really understand the angle meanings in the polar case. Like is zero
angle meaning horizontal or vertical stimulus.
The reason it is puzzling me is that I seem to get response over the whole 360
degree
Hi All,
I was hoping someone could help with an issue that I'm having that I'm sure has
a simple explanation. I have a proton density map in nifti format that I am
trying to convert to mgz using mri_convert.
However, when I load the original nifti file into freeview, I get a blank
screen an
Hi,
trying to do my first steps with tracula I got stuck early in the preprocessing
step. The DICOM import and preparation for FSL seem to work (mri_convert,
mri_probedicom, flip4fsl, fslswapdim, fslorient). But then trac-preproc wants
to move a file named dwi_orig_flip.mghdti.bvecs that does n
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