Dear Anastasia and Christopher,
I could run the new version and greaty appreciate your advices.
Thank you for everything!
Anri
**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里
*
you can create a label in fsaverage space (or some other space) and then
use mri_label2label to transfer it to an individual
doug
On 12/15/14 12:11 PM, pietro de rossi wrote:
Dear Freesurfers,
we are trying to determine the thickness values for the medial
prefrontal cortex as defined by the a
You can try this version of recon-all (make sure to make a backup of the
one that exists)
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/recon-all.53.patch
You can then run it with -bbr-init-header
doug
On 12/14/14 11:39 PM, Benjamin Baird wrote:
Hello,
We are having the sa
Thank you Bruce,
I try this out.
On Dec 16, 2014 7:58 AM, "Bruce Fischl" wrote:
> I'm not sure what to tell you then. You need to save it in a format that
> preserves the direction cosine information. This shouldn't be that hard to
> do (e.g in matlab)
> Bruce
>
>
> On Tue, 16 Dec 2014, Gunjan G
I'm not sure what to tell you then. You need to save it in a format that
preserves the direction cosine information. This shouldn't be that hard to
do (e.g in matlab)
Bruce
On Tue, 16 Dec 2014, Gunjan
Gautam wrote:
I think that won't resolve my issue because I need to deal with a specific
I think that won't resolve my issue because I need to deal with a specific
set of noise removal algorithms and nonuniformity correction algorithms.
On Dec 16, 2014 7:50 AM, "Bruce Fischl" wrote:
> have you tried just giving the original volume to recon-all? We typically
> deal with this kind of t
have you tried just giving the original volume to recon-all? We typically
deal with this kind of thing internally (and in 3D, not on a
slice-by-slice basis)
cheers
Bruce
On Tue, 16 Dec 2014, Gunjan Gautam wrote:
Sure,
My data(3D volume) is having different ranges of noise and nonuniformity
Sure,
My data(3D volume) is having different ranges of noise and nonuniformity so
I want to apply different algorithms to get rid of these and analyze the
extent.
On Dec 16, 2014 7:40 AM, "Bruce Fischl" wrote:
> Hi Gunjan
> can you elaborate? What kind of modifications would you want to make to
Hi Gunjan
can you elaborate? What kind of modifications would you want to make to
each slice?
Bruce
On Tue, 16 Dec 2014, Gunjan Gautam wrote:
Yes Bruce, minc is a volume but I want to perform some experiments and see
the aftereffects.
This is how I come from 3D to 2D to make changes in each
Yes Bruce, minc is a volume but I want to perform some experiments and see
the aftereffects.
This is how I come from 3D to 2D to make changes in each slice and again I
rejoin these slices (2D to 3D). I don't know if anything other than NIfTi
gives this much flexibility or it could be dealt without
It looks like the ln -s command is failing either because dwi.nii.gz does not
exist or data.nii.gz does exist.
I think you've ruled out that you don't have write permission to the directory
by trying to execute it as root.
ln -sf /media/Sokol/Subj/041/dmri/dwi.nii.gz
/media/Sokol/Subj/041/dmri/
isn't the minc a volume? It certainly supports holding an entire volume
in a single file
On Tue, 16 Dec 2014, Gunjan Gautam wrote:
Ok , I try this out.
I converted it to nii because after processing 2D slices of the volume, I
can easily switch to 3D space(ie stacking) in order to apply brain
Ok , I try this out.
I converted it to nii because after processing 2D slices of the volume, I
can easily switch to 3D space(ie stacking) in order to apply brain
extraction tools as NIfTi provides some of the useful utilities.
On Dec 16, 2014 6:59 AM, "Bruce Fischl" wrote:
> why do you need to c
I think certain filesystems don't support sym linking (e.g. FAT32). So that
might be it.
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Katherine Damme
[katherine.da...@gmail.com]
Sent: Monday, December
p.s and make sure that the anatomical directions that freeview shows
reflect the actual orientation of the brain
On Tue, 16 Dec 2014, Gunjan
Gautam wrote:
Hi Bruce,
Originally, data was in MINC format.
On Dec 16, 2014 1:54 AM, "Bruce Fischl" wrote:
Hi Gunjan
what was the origi
why do you need to convert it to nifti? Can you process the minc directly?
See if freeview can display it:
freeview -v file.mnc
On
Tue, 16 Dec 2014, Gunjan Gautam wrote:
Hi Bruce,
Originally, data was in MINC format.
On Dec 16, 2014 1:54 AM, "Bruce Fischl" wrote:
Hi Gunjan
Pradeep,
Our lab will be getting a Haswell-based system soon and will evaluate
any speed gains. The system is a Dell PowerEdge R730 with an Intel®
Xeon® E5‐2643 v3 3.4GHz processor.
N.
On Mon, 2014-12-15 at 13:43 +0530, pradeep mahato wrote:
> Hello everyone,
>
>
> Have anyone used Broadw
Hi Douglas,
I uploaded my glmdir to you on the 3/12/14 (named
site-gender-group-prothaplotype.area.lh.glmdir.zip). Can you see what
the problem is?
Kind regards,
Bronwyn Overs
Research Assistant
Neuroscience Research Australia
Neuroscience Research Australia
Margarete Ainsworth Building
Ba
Hi Bruce,
Originally, data was in MINC format.
On Dec 16, 2014 1:54 AM, "Bruce Fischl" wrote:
> Hi Gunjan
>
> what was the original data format that you had? Once you have converted it
> to nifti in your current stream you can no longer use the data, so you have
> to start further upstream
>
> c
I've been interested in these 2 questions, since I have similar issues:
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg38213.html
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg39282.html
What does it mean if I find a valid-appearing tract with reinit=0, but then
los
Hi Ben,
You should be able to map it back with mri_surf2vol. I haven't done
this, but the wiki page looks fairly detailed:
http://surfer.nmr.mgh.harvard.edu/fswiki/mri_surf2vol
HTH
D
On Mon, Dec 15, 2014 at 3:43 PM, Benjamin Zimmerman
wrote:
> Hi all,
>
> FsFast has an excellent individual reti
Hi Amirhossein,
you would need to do the following steps:
- make sure your ROI label is in the longitudinal directories (the
.long.baseid)
- in your longitudinal directories use the command mris_anatomical_stats
to compute the statistics on the label, this will create a stats text
file as outp
It's hard to tell what's causing the error without seeing the entire
trac-all.log. However, by glancing at your config file you seem to still
have B0 inhomogeneity correction turned on (dob0 = 1) but without
specifying any field map dicoms. I'd turn it off and see if that fixes it.
On Mon, 1
Where would I be specifying a directory as an input/output?
I used the following cmd: /usr/local/freesurfer/bin/trac-all -prep -c
dmri.fy
On Sun, Dec 14, 2014 at 7:12 PM, Bruce Fischl
wrote:
>
> Hi Katerine
>
> the COR-* format is an old one that we don't use anymore. If you specify a
> director
Hi all,
FsFast has an excellent individual retinotopy analysis that allows me to
see phase data on the inflated surface of the brain. Is there a way to view
the results of the retinotopy analysis in the subject's original volumetric
space rather than on the subject's surface space?
Thank you for
Hi Gunjan
what was the original data format that you had? Once you have converted
it to nifti in your current stream you can no longer use the data, so you
have to start further upstream
cheers
Bruce
On Tue, 16 Dec 2014, Gunjan Gautam wrote:
I don't have dicom for this subject but it can
I don't have dicom for this subject but it can easily be converted to from
.nii to .dcm.
I try this out and get back to you if I stuck at some point.
Thanks,
Gunjan
On Dec 16, 2014 12:49 AM, "Bruce Fischl"
wrote:
> do you have the dicom data for this subject? If so, it will be separated
> into
do you have the dicom data for this subject? If so, it will be separated
into different "series" each corresponding to one acquisition (e.g. a
T1-weighted one such as mprage or FLASH). Typically that series will have
more than 150 slices (since that's what it takes to cover the brain at
close t
We are planning to generate a surface template from edited reconstructions
of pediatric cortical surfaces (ages 3-11). We plan use this template for
surface coregistration of a large pediatric dataset that we're accruing of
roughly the same age range. I.e., we aren't simply trying to generate a
tem
Hi Bruce,
I am sorry to say that I did not get you properly.
Could you please say a bit more about "a *single* slice in the correct
series ". I want to try this option.
On Dec 16, 2014 12:13 AM, "Bruce Fischl" wrote:
> Hi Gunjan
>
> freesurfer will handle the dicom slices just find. Just give r
Hi Gunjan
freesurfer will handle the dicom slices just find. Just give recon-all a
*single* slice in the correct series with the -i command and it should
work. I don't know medcon, but it is not propagating the direction cosine
info into the nifti, which means that the nifti files are effectiv
Thanks Bruce,
I used "medcon" command (Ubuntu) for the stacking of 2D slices in order to
convert it in a volume. These slices were obtained from a volume itself and
after making some intensity changes, a volume is formed (using medcon)
again. Then I fed this volume as input to FS in order to extra
Yes, download the update, unzip it, and copy the new files over the old
files in the $FREESURFER_HOME/bin directory. Until you do that you'll be
using the old version.
On Mon, 15 Dec 2014, Anri WATANABE wrote:
Yes, I guess I'm running the old version.
Is this right that I should overwrite s
Hi Gunjan
the problem is that the nifti volume doesn't contain the direction cosine
information that we need to figure out what directions are A/P, I/S and
L/R. mri_convert warns of this:
mri_convert m000-stacks-m000-t1_icbm_normal_1mm_pn0_rf0-1.nii.gz test.mgz
mri_convert m000-stacks-m00
Dear Freesurfers,
we are trying to determine the thickness values for the medial prefrontal
cortex as defined by the anatomic boundaries shown in the *attached picture
(area in purple)*.
We would like to sum different areas or maybe label the area on the single
scans and then extract thickness val
It is not possible to know whether this is a good idea or not. If you
want to do it, here are the instructions
doug
# Create an average subject (Creates $SUBJECTS_DIR/newtemplate)
make_average_subject --out newtemplate --subjects subj1 subj2 subj3 ...
# Register each subject to the new template
Hi Pradeep
we haven't found much difference in terms of how well we process, but
there hasn't been a lot of work done (a bit in Asian vs. Caucasian).
We do estimate total intracranial volume (eTIV), which is in the stats file
and can be used as a regressor
cheers
Bruce
On Mon, 15 Dec 2014, pr
We are seeking an enthusiastic and motivated candidate for a PhD project
beginning in the first half of 2015. The project is a joint initiative of the
Melbourne Neuropsychiatry Centre (Department of Psychiatry) and the Melbourne
School of Psychological Sciences, The University of Melbourne, and
Hi Bruce,
Thank you for your help, I will also post this in the MNE group.
best
Peng
On Fri, Dec 12, 2014 at 3:20 PM, Bruce Fischl
wrote:
> Hi Peng
>
> yes, for sure. This is what Matti Hamalainen's excellent MNE package is
> designed for. I'll cc Matti so he can chime in
>
> cheers
> Bruce
Hi Doug
Thanks a lot
Cheers
Jürgen
Von: Douglas Greve
Antworten an: Freesurfer Mailinglist
Datum: Donnerstag, 27. November 2014 03:31
An: Freesurfer Mailinglist
Betreff: Re: [Freesurfer] mri_glmfit-sim
Specify the cluster-wise p-value to be 1 (ie, --cwpvalthresh 1)
doug
Hello Experts,
There is a significant differences between a African, Asian or a Caucasian
brain size.
How does FreeSurfer recon-all performs for these different types of brain.
I am doing brain MRI analysis for Asian brain, will the default brain atlas
will be ok?
If not how do I load another brai
Hello everyone,
Have anyone used Broadwell or Haswell process for Brain MRI image
processing.
If used can you please mention the system configuration you are using.
How long does it take to run recon-all process for one brain MRI image.
Thanking you
Pradeep Kumar Mahato
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