e Computing (CMIC)
>
> University College London
>
> http://www.jeiglesias.com
>
> http://cmictig.cs.ucl.ac.uk/
>
>
>
>
>
> *From: *Mehul Sampat
> *Date: *Thursday, 21 June 2018 at 04:10
> *To: *Freesurfer Mailing List , "Iglesias
> Gonzalez, Eugenio"
&
External Email - Use Caution
Hi Eugenio and Bruce,
We used freesurfer-6.0.0 to segment the brain-stem into different different
structures.
I see we get two mgz files after this process:
aparc+aseg.mgz and brainstemSsLabels.v10.FSvoxelSpace.mgz
Do you have any recommendations
Hi Folks,
I have a question about the usage of the -bigventricles flag in FS 5.3.
1. Suppose i run recon-all with -bigventricles option.
2. Then i add control points and run recon-all with the -autorecon2-cp as
described in the recon-all help.
USAGE: recon-all
3. The recon-all help mentions
Hi Folks,
I am trying to run dt_recon on a Philips Achieva DTI dataset. I could not
find an example of a bvecs for this dataset so i made one in this way:
I have 850 dicom slices. mri_convert correctly splits it into 17 nifti
files (50 slices each). I took 17 dicom slices with the same
Hi Folks,
I wanted to ask which Freesurfer regions from aparc+aseg.mgz are included
in Default mode network ? Is there a relevant publication on this topic ?
Thanks
Mehul
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
--save_ribbon --save_distance subjid
I can upload the data if you would like to take a look.
Thanks
Mehul
On Fri, Aug 15, 2014 at 1:54 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:
How does the rh.aparc look?
On Aug 14, 2014, at 8:13 PM, Mehul Sampat mpsam...@gmail.com wrote:
Hi Folks,
We
, at 10:28 me PM, Mehul Sampat kmpsam...@gmail.com wrote:
Hi Bruce,
rh.aparc.stats looks good and also rh.aparc.a2009s.stats looks correct.
However, both aparc+aseg.mgz and aparc.a2009s+aseg.mgz have the issue with
missing parcellation labels in right hemisphere.
Also I suspect the issues starts
Hi Folks,
I was able to find a number of papers looking at the reliability of
cortical thickness of individual regions (ex:
https://surfer.nmr.mgh.harvard.edu/pub/articles/reliability_wonderlick.pdf)
I was wondering if there are any papers that have looked at the
reliability of the volumes of
Hi Doug,
I have a followup question on this topic. I understand the two command you
mentioned in this thread to warp a segmentation to the MNI152 space.
In the subjects dir, I see there is an average subject cvs_avg35_inMNI152
which is already in MNI space (and the volume size is 256^3). I want
Hi Folks,
I see on the tutorial websites that when voxels are added to wm.mgz or
brainmask.mgz, the new voxels are given a value of 255;
while when voxels are deleted, these locations are set to 1.
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits
Can the deleted voxels can
Hi Folks,
Once we make control points in tkmedit, they are stored in the file
control.dat
Are these control points stored in RAS co-ordinate system ?
If not what is the co-ordinate system used to store the control points
Thanks
Mehul
___
Freesurfer
On Mon, 1 Jul 2013, Mehul Sampat wrote:
Hi Folks, Once we make control points in tkmedit, they are stored in the
file control.dat
Are these control points stored in RAS co-ordinate system ?
If not what is the co-ordinate system used to store the control points
Thanks
Mehul
for
surface RAS?
Thanks
Mehul
On Mon, Jul 1, 2013 at 12:13 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote:
Hi Mehul
they can either be in real (meaning scanner) RAS or in surface RAS
cheers
Bruce
On Mon, 1 Jul 2013, Mehul Sampat wrote:
Thanks Bruce; I noticed that in the control.dat file
to surface ras
and using them that way
2. Yes.
On Mon, 1 Jul 2013, Mehul Sampat wrote:
Thanks Bruce; Okay i assume, useRealRAS should be 1 for scanner RAS;
Two questions:
1. If my control points are in scanner RAS, then can I use them directly
as
long as I set
useRealRAS to 1
Hi Folks,
I am trying to create an entorhinal cortex volume from
?h.entorhinal_exvivo.label using mri_label2vol
I cd to the subject dir ($SUBJECTS_DIR/bert) and the command I use is:
*mri_label2vol --label label/lh.entorhinal_exvivo.label --temp
mri/nu.mgz --identity --o mri/lh-new-erc.mgz *
the surfaces too and see how good it did?
doug
On 06/26/2013 06:49 PM, Mehul Sampat wrote:
Hi Folks,
I am trying to create an entorhinal cortex volume from
?h.entorhinal_exvivo.label using mri_label2vol
I cd to the subject dir ($SUBJECTS_DIR/bert) and the command I use
for it to go from 20 min to almost 5
hours! We'll investigate as that shouldn't be the case.
Bruce
On Tue, 4 Jun 2013, Mehul Sampat wrote:
In some cases, we are seeing that, for the same subject, the run time is
slower for 5.3 versus 5.2;
A quick check on recon-all-status.log shows that the CA
On 06/04/2013 01:45 PM, Mehul Sampat wrote:
Hi Zeke,
Thanks for looking into this; had a quick followup item to report.
So for the same subject recon-all -all runs through smoothly;
(it was only recon-all -autorecon1 -autorecon2 that generated the error)
I had not seen the error before
. Is
that the
error you are receiving?
http://www.mail-archive.com/**freesur...@nmr.mgh.harvard.**
edu/msg28047.htmlhttp://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28047.html
On 06/04/2013 01:45 PM, Mehul Sampat wrote:
Hi Zeke,
Thanks for looking
Hi Folks,
I am running recon-all with -autorecon1 -autorecon2, -nomotioncor
-notal-check -nonuintensitycor
(this is with fs version 5.3)
it almost runs through but toward the end, when mri_segstats is called I
get the error message:
.../mri/ribbon.mgz, -1): could not open file
any ideas why this
ps: i believe my error is the same as the one in this thread:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28047.html
Mehul
On Thu, May 30, 2013 at 12:13 AM, Mehul Sampat mpsam...@gmail.com wrote:
Hi Folks,
I am running recon-all with -autorecon1 -autorecon2, -nomotioncor
Hi Folks,
I had a question about the hippocampus subfield segmentations as described
here :
http://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation
I am planning to use this processing outline:
1. recon-all -s subject -autorecon1 -autorecon2
2. add control points
3. recon -all
Hi Folks,
I was looking at the autorecon2-cp, autorecon-pial and autorecon-wm flags
in recon-all help and also here
http://surfer.nmr.mgh.harvard.edu/fswiki/OtherUsefulFlags
My interpretation is when I use autorecon-pial, I only need the command:
recon-all --autorecon-pial -s subject
While for
subject -autorecon1 -autorecon2
2. edit brainmask.mgz (
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits)
3. recon-all -s subject *-autorecon3 (instead of -autorecon-pial)*
Thanks
Mehul
On Wed, Mar 13, 2013 at 12:31 PM, Mehul Sampat mpsam...@gmail.com wrote:
Hi Nick,
Thank you very much
Hi Folks,
Based on the tutorials, we normally run full recon-all pipeline; then add
control points if required and then
run -autorecon2-cp and -autorecon3 again.
Recently, I was looking at the process flow table:
http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable
and I have two questions:
control points
3. recon -all -s subject -autorecon2-cp -autorecon3
If Scenario B is permissible, the advantage is that, -autorecon3 is only
run once thus saving
a few hours of computation.
Thanks
Mehul
On Wed, Mar 13, 2013 at 10:35 AM, Mehul Sampat mpsam...@gmail.com wrote:
Hi Folks,
Based
-0700, Mehul Sampat wrote:
ps: just wanted to add a clarification to my question. The two
scenarios are:
Scenario A:
1. recon-all -s subject -autorecon1 -autorecon2 -autorecon3
2. add control points
3. recon -all -s subject -autorecon2-cp -autorecon3
Scenario B:
1. recon-all -s
Hi Folks,
Just wanted to share our experience with running FS 5.2-beta on Amazon Web
Services (AWS).
Basically, AWS has multiple instance types (
http://aws.amazon.com/ec2/instance-types/) and we were trying to figure out
the most cost-effective approach.
We ran two subjects through FS 5.2-beta
..
Mehul
On Fri, Feb 1, 2013 at 7:12 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote:
Hi Mehul
did you specify the # of open mp threads on the recon-all cmd line?
cheers
Bruce
On Fri, 1 Feb 2013, Mehul Sampat wrote:
Hi Folks,
Just wanted to share our experience with running FS 5.2-beta
Hi Folks,
I have a question about entorhinal cortex volume. The entorhinal cortex is
listed in ?h.aparc.stats and ?h.entorhinal_exvivo.stats. In a previous
post on the mailing list, it was mentioned that we should use the volume
measurement from ?h.entorhinal_exvivo.stats.
We would like to make
and hence we believe it is more accurate.
Not sure why you need to integrate the ex vivo one back into the
aparc+aseg, can you clarify?
cheers
Bruce
On Tue, 29 Jan 2013, Mehul Sampat wrote:
Hi Folks,
I have a question about entorhinal cortex volume. The entorhinal cortex
is listed
Hi Folks,
I just wanted to inquire about the estimated release date for Freesurfer
5.2 ?
Is there a beta version we could try out ?
Thanks
Mehul
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
Hi James,
I had the same issue. The following workaround was mentioned on the FS
mailing list:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg20335.html
It works for me.
Mehul
On Fri, Aug 3, 2012 at 10:11 AM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:
Delete that dir and run
Hi Thomas,
The following message posted by Michael Harms
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg20991.html
has some very useful options. I recently noticed that they help us with a
very similar problem...
Also, I recall that for FS v5.0 there was a flag -nuintensitycor-3T
is that
what you want?
- usually registration will be more accurate if images are skull
stripped.
Best, Martin
On Tue, 2012-01-24 at 09:39 -0800, Mehul Sampat wrote:
Hi Folks,
We have subjects with high lesion load which changes significantly
over time.
I want to use FS functions
Hi Folks,
We have subjects with high lesion load which changes significantly over
time.
I want to use FS functions to build a pipeline for comparing lesion changes
in two time-points of the same-subject.
I am thinking of using the following steps;
1) Use mri_normalize to normalize the two
Hi Clare,
I had that same error a few months ago. (I had the error in 1 out of
500+cases).
Someone on the list had suggested the following solution:
Alternatively you can try rerunning the skullstrip step, sometimes this
works as well.
recon-all -skullstrip -autorecon2 -autorecon3 -s [SubjID]
Hi Michael,
I had the same issue a few months ago. In my experience 4GB was sufficient.
If there are constraints on the memory, I think 3 GB should also work.
I also had the same issue with -gcut and FS 5.0. Back then I had tried to
figure out what was
the minimum memory required since I had
to
track down, mainly because the person who wrote this piece is long gone. If
you edit the wm to remove a defect it usually goes away
Bruce
On Mon, 31 Oct 2011, Mehul Sampat wrote:
Hi Folks
I am using Freesurfer 5.1 and I get the following error: ERROR:
_FindFacePath: could not find
Hi Folks
I am using Freesurfer 5.1 and I get the following error: ERROR:
_FindFacePath: could not find path!
Is this is a memory related issue ? The same case went through smoothly
with Freesurfer 5.0.
Also I have not seen this error over a large number of subjects and I
thought it might be
Hi Bruce and others,
My question is related to the staggering of FS jobs (see thread below).
Could you tell me by how much time you stagger the freesurfer on a cluster ?
I am using FS 5.1 on a cluster which uses sun grid engine and I have the
following error when I try to submit a large number
and not one of our's makes it harder to track down.
The delay between jobs for us is driven by how robust and rapid your
storage is. Certainly a minute or two should be enough I would think,
altough we launch much more rapidly than that typically
Bruce
On Thu, 26 May 2011, Mehul Sampat wrote
Hi Bruce,
We have two studies being conducted (one cross-sectional and one
longitudinal)
Some of the subjects in have a lot of atrophy and have large ventircles.
For the cross-sectional analysis stream are there many differences between
4.5 and the forthcoming 5.1 ? Or would it be fine to use 4.5
Hi Folks,
We used to use tkmedit to add control points and recently started using
freeview.
I have a few basic questions about saving controls points created with
freeview.
1. I noticed that in tkmedit edit controls points were saved as
control.dat in the subject_dir/tmp (e.g. bert/tmp).
When I
Hi Bruce and Nick,
I think mri_gcut seems to require a lot of memory and might be causing the
crash ?
I was running some subjects on a node (16 cpu 32 GB RAM ; thus 2GB RAM
per cpu) and some of the subjects crashed for me at the mri_gcut step. (a
few lines from recon-all.log are shown below)
Hi Folks,
In tkmedit, to toggle between the main and aux volumes, one uses ctrl-1
and ctrl-2.
I would like to change this to just 1 and 2
Is it possible to do so using tkmedit scripting ? If yes, could you tell me
which function argument I should change ?
I looked at the tkmedit scripting help
Hi Folks,
I am trying to troubleshoot an issue and I have not been able to find a
solution yet.
Here is what I am trying to do:
1. I used mri_robust_register to register a t1-weighted image to a t2-image.
mri_robust_register works very well and i also got an lta file
(t1-to-t2.lta)
2. now i
Hi Ruthger,
I use the following command to take the binary lesion mask (native space) to
the freesurfer space:
mri_convert -rl mri/brainmask.mgz -rt nearest lesion_mask_native_space.mgz
lesion_mask_fs_space.mgz
I always overlay lesion_mask_fs_space.mgz on brainmask.mgz to check that
things look
Hi Folks,
As Nick suggested 4GB per subject is best.
Here is my recent experience when memory resources may be limited and 4gb
per subject is not available. I ran FS v5.0 on a cluster on which I was
assigned a node with 16 cores and 32gb .
At a time, I am charged for all 16 cores on the node,
Hi Folks,
Currently I set the segmentation brush information from tkmedit buttons.
(For example: Set Segmentation as Use as source and also set the color)
I need to do this for a large number of subjects and I was wondering if it
was possible to do this from command line ?
thanks
Mehul
Hi Folks,
I would like to use the -nuintensitycor-3T flag as listed in the release
notes (http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes)
I had two questions about this new option:
1. Can I just use this as follows: recon-all -s bert -autorecon1 -autorecon2
-nuintensitycor-3T (then run
Hi Folks
I use mri_convert to create nifti files from the dicom images from a 3T GE
scanner.
One of the option for mri_convert is -zgez with the following description
from the mri_convert help:
-zgez, --zero_ge_z_offset set c_s=0 (appropriate for dicom files from GE
machines with isocenter
Hi Folks,
I have two MR scans per subject.
Lesions (white matter hypo-intensities) have been manually outlined for the
first time-point.
I would like to create a lesion mask for the 2nd time-point.
But instead of starting from scratch, I would like to use the lesion-mask
from the 1st time-point
Hi Folks,
I would like to create binary masks for any given structure in aseg.mgz and
aparc+aseg.mgz.
I would then also like to map the masks back to native space.
I think, I should use mri_binarize followed by mri_convert as shown in the
two examples below:
Example 1:
a. mri_binarize --i
the aseg.mgz directly to the native anatomical space. The main
difference is that it will resolve boundary voxels by voting. With your
method, you will have some voxels that will be in more than one label,
which may or may not be a problem depending on what you are doing.
doug
Mehul Sampat wrote:
Hi
Hi Folks,
I believe that I can create a binary white matter mask using
mri_wmfilter.
I was wondering if there is a way to create a probabilistic white matter
mask ?
(for each voxel, I would like to obtain the probability of it being white
matter)
I did a search on the mailing list and found the
Hi Folks,
In tkmedit, the keyboard commands to view main and aux volume are 'Ctrl+1'
and Ctrl+2'.
Is it possible for me to change them to just '1' and '2' respectively ?
(like how only 'n' is required for the navigation tool)
Thanks
Mehul
___
Hi Folks,
On the FAQ, the response to one question says that the surfaces near the
medial wall, hippocampus and amygdala are unreliable and should be excluded
from a thickness analysis. The link for this is:
Hi Folks,
We have some subjects with very large white matter (WM) lesion loads.
We noticed that the pial and main are pial surfaces are not affected by WM
lesions.
However, they seem to be affection by the juxta-cortical WM lesions (which
have dark intensity)
In the past, my colleagues have
Hi Folks,
I would like to create a binary mask volume for the Right-Thalamus (all
voxels of right-thalamus as 1 and 0 otherwise).
I looked at this help page
http://surfer.nmr.mgh.harvard.edu/fswiki/mri_vol2roi
and i think I should use the following command described on this page:
mri_vol2roi
instead. It would be something like:
mri_binarize --match 49 --i aseg.mgz --o rth.mgz
where 49 is the index for right thalamus proper (from the
FreeSurferColorLUT.txt file) and rth.mgz is the output volume
cheers,
Bruce
On Sun, 11 Apr 2010, Mehul Sampat wrote:
Hi Folks,
I would like
Hi Folks,
I was trying to help a colleague generate a wmparc for the Destrieux atlas.
That is I am trying to create wmparc.a2009s.mgz and wmparc.a2009s.stats
I used the following two commands:
mri_aparc2aseg --s subject_id --labelwm --hypo-as-wm --rip-unknown
--new-ribbon --wmparc-dmax 4 --o
Hi Martin,
Just wanted to clarify one question about edits to the longitudinal
pipeline.
Lets say there is a data-set with 200 subjects with 5 time-points each (1000
scans total).
I create the base image and i would only like to make corrections in the 200
base images (if required) and not in
Hi Folks,
I understand that control points should be used to fix errors due to bad
skull stripping or intensity normalization (are there any other scenarios
when one should use control points ?)
I followed the instructions on making corrections for issues due to
intensity normalization.
Hi Nick (and Martin)
Could you please clarify if the edits come only from the base or if they are
copied from the cross-sectionals ?
It would be great if I only had to make edit in the base .
We have 5 timepoints for each subject (each a year apart) and i want to use
the results from the
Hi Guang,
It is much faster as it does not go through the whole autorecon1, 2, 3
process.
For us, it take about 45 minutes per subject.
Regards
Mehul
On Mon, Nov 30, 2009 at 8:04 PM, Guang Zeng freesurfer...@hotmail.comwrote:
Hi, there,
I have 60 subjects which have been FS analyzed
Hi Folks,
I would like to visually check the cortical parcellation for a large number
of patients (200) using tksurfer.
Is there a script to which I could submit a list of subject id's and get it
to
launch tksurfer and display the parcellation data for each subject
sequentially ?
Thanks
Mehul
Hi Folks,
I want to create a white matter mask (a volume in which all of the white
matter voxels are 1 and 0 otherwise)
For this, I am planning to use wmparc.mgz and then set the voxels with
labels of wm-lh-? and wm-rh-? as 1.
(here wm-lh-? represents labels such wm-lh-temporalpole, wh-lh-insula
PM, Mehul Sampat mpsam...@gmail.com wrote:
Hi Folks,
I want to create a white matter mask (a volume in which all of the white
matter voxels are 1 and 0 otherwise)
For this, I am planning to use wmparc.mgz and then set the voxels with
labels of wm-lh-? and wm-rh-? as 1.
(here wm-lh
Hi Folks
In my dataset each MRI exam is 256*256*180.
I would like to convert wmparc.mgz back to 256*256*180.
Since this is the segmentation output, I think I should use set the resample
type to nearest and use a command like
mri_convert -rl mri/orig/001.mgz -rt nearest mri/wmparc.mgz
,
Bruce
On Sat, 31 Oct 2009, Mehul Sampat wrote:
Hi Folks,
If am comparing the mean thickness for certain gyri (pre-central,
post-central) in a controls versus patients.
I obtain the thickness measurements from lh.aparc.a2009s.stats and
rh.aparc.a2009s.stats
I was wondering
Hi Folks,
If am comparing the mean thickness for certain gyri (pre-central,
post-central) in a controls versus patients.
I obtain the thickness measurements from lh.aparc.a2009s.stats and
rh.aparc.a2009s.stats
I was wondering if I need to normalize these thickness measurement
with the estimated
Hi FS folks
I was trying to use the load_segstats function to read aseg.stats and
wmparc.stats
It works well will these files but I get the following error if I try to
read lh.aparc.stats or rh.aparc.stats
[segname segindex segstats] = load_segstats('lh.aparc.stats','bert');
??? Subscripted
you please suggest some good references describing the GLM theory ?
Thanks
Mehul
On Thu, Oct 29, 2009 at 10:57 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu
wrote:
Mehul Sampat wrote:
Hi FS folks,
I have a basic GLM question. I went through the tutorials online but I was
not sure
Hi FS folks,
I have a basic GLM question. I went through the tutorials online but I was
not sure and wanted to check with someone.
I am trying to compare the cortical thickness between a group of patients (n
= 166) and controls (n = 76).
For patients mean age is 49.8 +/- 9.1 and there are 55
Hi all,
I would like to segment lesions using both T1 and FLAIR images.
I think this is not possible with the current version of freesurfer. Is that
right ?
Could I somehow combine the segmentation results from aseg with the FLAIR
images ?
Regards
Mehul
Hi
I am interested in measuring the Brain Parenchymal Fraction (BPF) which is
defined as follows:
BPF = (total White Matter (WM) Volume + total Gray Matter (GM) Volume) /
(total White Matter Volume (WM) + total Gray Matter Volume (GM)+ total CSF
volume)
I think I get the White and Gray Matter
, but not sulcal CSF (which you pretty
much can't do from only a T1 volume). The ICV would give you an
approximation of the sum of it all, so yes I think what you are doing is a
reasonable approach.
cheers,
Bruce
On Thu, 19 Jul 2007, Mehul Sampat
wrote:
Hi
I am interested in measuring the Brain
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