Hi Sara
sure, you can look up the thalamus labels in FreeSurferColorLUT.txt (10
and 49 for lh and rh), then use either mri_extract_labels or mri_binarize
to pull our ROIs.
cheers
Bruce
On Mon, 7 Aug 2017, sarai...@alumni.ubc.ca wrote:
> Hi Freesurfer team,
> Is it possible to extract Thalamus a
Hi Juhyoung
can you just cut and paste the text into the email instead of a screen
shot?
thanks
Bruce
On Mon, 7 Aug 2017, Juhyoung Ryu wrote:
Sure, screenshot image is below with commands.
On Aug 7, 2017, at 11:14 AM, Bruce Fischl wrote:
can you send us the entire screeen output of t
try SetUpFreeSurfer.sh (note the capital letters)
On 8/5/17 11:04 PM, 水墨丹青 wrote:
TO: freesurfer@nmr.mgh.harvard.edu
FROM: fsu...@worlduniversity.edu
SUBJECT: installation error error: there is no setupfreesurfer.sh file
Hello FreeSurfer Developers,
I'm attempting to install freesufer on m
Dear team,
I have completed cross-sectional pipeline on my pediatric case with a baseline
and 4 follow up time points between 4-7 years of age. However, I was not able
to run longitudinal pipeline on it as the base template creation failed with
some topological errors. I assume this failure is
Hello FreeSurfer experts,
I have many FS5.1 edited-subjects that I want to use in an application that
only takes FS5.3 formatted statistics. I ran 20 subjects in FS51 and FS53. I
took the FS51 subjects and reran recon-all -segstats (in FS53) and it updated
aseg.stats closer to the values for FS
Hi Doug and Freesurfer Experts,
I am trying to see whether cortical thinning gets progressively less severe as
we move further away from a seed/voxel (e.g. precuneus). Is it possible to
perform correlations between the (a) distance between a given vertex to
specific point on fsaverage, and the
Hi Sneha
can you send us the commad you ran and the full screen output inluding
the error and also the recon-all.log?
cheers
Bruce
On Mon, 7
Aug 2017, Sneha Pandya wrote:
>
> Dear team,
>
>
> I have completed cross-sectional pipeline on my pediatric case with a
> baseline and 4 follow up
Hi John
I think the FSL group has some nice tools to fix these distortions either
with or without field maps (topup for example)
cheers
Bruce
On Mon, 7 Aug 2017, John
Anderson wrote:
Dear Freesurfer experts,
I want to inquire if there are any tools or any methods to improve T1 images which
it should, although you may need to configure it differently since the
distortion is in a different direction. We have used it to correct FLASH
readouts
cheers
Bruce
On Mon, 7 Aug 2017, John Anderson
wrote:
Dear Dr Bruce,
Thank you very much for the quick response.
Topup works for DTI and
Hi Bruce,
Here is what I did. For each subject:
a) used the original (non-skull stripped) brain for the 001.mgz file as
input - located in the Subnum/mri directory
b) used mri_convert to get the afni skull-stripped brains and renamed them
"brainmask.mgz" , located in the Subnum/mri directory.
c) T
Hi Sneha
can you include the output as text instead of an image?
thanks
Bruce
On Mon, 7 Aug 2017,
Sneha Pandya wrote:
Hi Bruce,
Please find attached recon-all.log file and I used following command to run the
base:
recon-all -base ped1_base -tp ped1_0 -tp ped1_1 -tp ped1_2 -tp ped1_3 -t
Dear Dr Bruce,
Thank you very much for the quick response.
Topup works for DTI and I am wondering if it works for the T1 images.
Thanks again!
John
> Original Message
> Subject: Re: [Freesurfer] susceptibility-induced distortions
> Local Time: August 7, 2017 1:54 PM
> UTC Time: A
Hi Bruce,
Sure, please see highlighted below part of screen output showing the error.
Since I ran the command within a screen sesison I have saved executed screen
session to a log file. Find attached log file with output of entire run. Please
let me know if any other files are required and if
Hi Ariel – Have you run freesurfer on the structural images of your subjects?
Are those freesurfer recons found in what you have defined as SUBJECTS_DIR in
your configuration file?
Best,
a.y
From:
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of "Lin, Yizhi" mailto:l...@union.edu
Dear Freesurfer team,
In the mri_glmfit-sim summary output file, I get a number of output variables,
and I'm not sure what some of them are. Could you explain the ones in bold to
me?
# ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZCWP CWPLow
CWPH NVtxsWghtVtx Annot
Dear Bruce and Doug,
Thank u for your replay saying that it is possible to manually draw the
pineal gland using freeview and extract stats for it.
Can u please refer me to a link on wiki that explain how to do it?
I'm not familiar with this procedure and although Doug explain it in brief
I feel
see here
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisClusterSummary
On 08/07/2017 02:40 PM, Van Der Deijl, Rosanne wrote:
> Dear Freesurfer team,
>
> In the mri_glmfit-sim summary output file, I get a number of output
> variables, and I'm not sure what some of them are. Co
Please, see attached or below for details.
Lilla
Postdoctoral Research Fellow Position in Infant Brain MRI analysis at the
A.A. Martinos Center, MGH and Harvard Medical School under Dr. Lilla
Zöllei
A postdoctoral fellow is recruited for an NIH funded project for
developing Freesurfer-compa
Hi,
After checking the images in the viewer, it appears that 001.mgz and
brainmask.mgz are in the correct orientation, but brain.mgz (created by
freesurfer) is rotated 90 degrees. The dimensions of the images don't match
either.
001.mgz and brainmask.mgz are:
dim1 219
dim2 268
I can't remember all the differences:), but there might have been a
change in how the estimated ICV is computed, and the partial volume
correction may have changed. I general, I think it should be fine
On 08/07/2017 01:23 PM, Hatton, Sean wrote:
> Hello FreeSurfer experts,
>
> I have many FS5.1
Thank you for your reply, that is all I am seeing :D
Have a great week!
Sean Hatton, PhD
Postdoctoral Scholar, Department of Psychiatry
UCSD
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Dear Anastasia,
I used dicom images to run my subjects, and yes, those freesurfer recons
were found in SUBJECTS_DIR in my configuration file. Thanks.
best,
Ariel
On Mon, Aug 7, 2017 at 2:39 PM, Yendiki, Anastasia wrote:
> Hi Ariel – Have you run freesurfer on the structural images of your
> su
I am running tracula pre-processing step, and the computer showed an error
message:
Location of aparc+aseg's relative to base: dlabel/mni/aparc+aseg.nii.gz
Brain mask for output subject: Segmentation fault (core dumped)
Linux Brain 4.2.0-27-generic #32~14.04.1-Ubuntu SMP Fri Jan 22 15:32:26 UTC
201
Hi Rotem, can you repost with previous correspondence?
On 08/07/2017 02:59 PM, Rotem Saar wrote:
> Dear Bruce and Doug,
>
> Thank u for your replay saying that it is possible to manually draw
> the pineal gland using freeview and extract stats for it.
>
> Can u please refer me to a link on wiki
what was your mri_convert command line? It should be something like
mri_convert -rl orig.mgz afni_stripped_volume.brik brainmask.mgz
cheers
Bruce
On Mon,
7 Aug 2017, Michelle VanTieghem wrote:
Hi Bruce,
Here is what I did. For each subject:
a) used the original (non-skull stripped) brain
what viewer did you check in? If not freeview, look at it in freeview
On
Mon, 7 Aug 2017, Michelle VanTieghem wrote:
Hi,
After checking the images in the viewer, it appears that 001.mgz and
brainmask.mgz are in the correct orientation, but brain.mgz (created by
freesurfer) is rotated 90 degre
thanks Sneha
you'll probably need to wait until tomorrow for Martin to read his email :)
cheers
Bruce
On Mon, 7 Aug 2017, Sneha Pandya wrote:
Hi Bruce,
Sure, please see highlighted below part of screen output showing the error.
Since I ran the command within a screen sesison I have saved e
Hi freesurfer team
I'm just wondering if there is any way to extract left and right pial from
manually parecllated file apar+aseg .mgh
I need to view them with the new parecellation file
Thanks in advance
Fatima
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Freesurfe
===
server2:20170214_JEL JuhyoungRyu$ recon-all -subject JEL_v6 -i T1_bfc.nii
-T2 T2_bfc.nii -T2pial -all -hires
INFO: hi-res volumes are conformed to the min voxel size
Subject Stamp: freesurfer-Darwin-
Thank you so much. That was really helpful.
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
[fis...@nmr.mgh.harvard.edu]
Sent: Monday, August 07, 2017 7:15 AM
To: Freesurfer support list
Subje
What do you see when you run:
ls /media/brain/brains/TN_retro/Tracula/AN01/mri
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Lin, Yizhi
[l...@union.edu]
Sent: Monday, August 07, 2017 3:22 PM
To: Freesurfer supp
Hi Ariel – Have you run freesurfer on the structural images of your subjects?
Are those freesurfer recons found in what you have defined as SUBJECTS_DIR in
your configuration file?
Best,
a.y
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.
Can anyone provide me the link of freesurfer version 5.3 vdi file? I was trying
to install it in windows 10 using virtual box, but its not working.
Thanks
Ruchira
From: Tabassum, Ruchira
Sent: Saturday, August 5, 2017 1:22 PM
To: 'freesurfer@nmr.mgh.harvard.edu'
Subject: Need Urgent Help!! Rega
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