Re: [Freesurfer] improving white/grey segmentation in recon -all for better volume estmation

[Dr. Benson]

It does look better.  Can you send me some more images--in axial and
coronal planes?

On Wed, Mar 30, 2016 at 4:26 PM, Ramtilak Gattu 
wrote:

>
> Thank you for recommending the expert options. I have run this on two
> subjects (rows) and you can see the post analysis results on the right
> (column) in the attached  image  . As you have mentioned it didnt work well
> in the cerebellum any other ways to improve in the inferior regions?
>
> Thanks
>
> Regards
> Tilak
> 
> From: Ramtilak Gattu
> Sent: Monday, March 28, 2016 5:12 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] improving white/grey segmentation in recon -all
> for better volume estmation
>
> Thank you,
>
> Attached is the scripts folder for one subject .
>
> Thanks
>
> Regards
> Tilak
> 
> From: Ramtilak Gattu
> Sent: Monday, March 28, 2016 4:11 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] improving white/grey segmentation in recon -all
> for better volume estmation
>
> Sorry, Actually just found out that the receiving coil is the 12 channel
> head coil and the transmitting coil is the body coil. I am attaching a
> snapshot showing the sag orientation of the three cases that I previously
> mentioned and uploaded for your review.
>
> >From these figures do you really think there is not enough contrast, just
> wondering
>
> 1) why it worked in the bottom image and it failed in the upper two
> (T1_sag_comparison.jpg)
> 2) it failed in the left image and did good in the right image
> (T1_sag_comparison_2.jpg).
>
> We have similar data in 25 of the subjects. Is there a way to salvage the
> existing data and improve our results we will certainly follow your input
> in changing the existing protocol and collect some data and run the
> analysis to see if it improves the results.
>
> One more thought is if is there any other way around to increase the
> contrast by taking help from T2 image and run recon-all. Do you think it
> will help?
>
> Thanks for you help .
>
> Regards
> Tilak
>
> 
> From: Bruce Fischl 
> Sent: Monday, March 28, 2016 11:22 AM
> To: Ramtilak Gattu
> Subject: Re: [Freesurfer] improving white/grey segmentation in recon -all
> for better volume estmation
>
> what was the transmit coil? I think I would either reduce the voxel sizes a
> bit or not use grappa. Probably go to 1.2 mm or so, which would be a 70%
> increase in SNR. That won't help the transmit bias field though if you have
> one. The 8 channel can also sometimes be a problem. The 32 channel coils
> work much better
>
> On Mon, 28 Mar 2016, Ramtilak Gattu wrote:
>
> > Hey Bruce,
> >
> > The scans are done on 3T Siemens TRIO and 8 coil head channel with a
> GRAPPA of 2.
> >
> > Here is the screen shot of protocol used.
> >
> >
> https://waynestateprod-my.sharepoint.com/personal/ao3080_wayne_edu/_layouts/15/guestaccess.aspx?guestaccesstoken=VJ0QiLxUz9fI6GCUofGHq7IAQY6k4uG50U0ic0zBkHE%3d=034b186e0a218401590414fc271f3cf5f
> >
> > Thanks
> >
> > Regards
> > Tilak
> >
> >
> >
> > 
> > From: Ramtilak Gattu
> > Sent: Sunday, March 27, 2016 3:23 PM
> > To: Bruce Fischl
> > Subject: Re: [Freesurfer] improving white/grey segmentation in recon
> -all for better volume estmation
> >
> > Hey Bruce,
> >
> > I have uploaded the files in
> >
> >
> https://waynestateprod-my.sharepoint.com/personal/ao3080_wayne_edu/_layouts/15/guestaccess.aspx?guestaccesstoken=0MdoYLvWY2ZYOdi983YqZtMFGMns%2b5WB6dNeC3osudU%3d=000b5dcba90f2419e9bdf4ce77dfd7a5e
> >
> > I have also included the 001.mgz in there.
> >
> > Thanks
> >
> > Regards
> > Tilak
> >
> > 
> > From: Bruce Fischl 
> > Sent: Saturday, March 26, 2016 8:35 PM
> > To: Ramtilak Gattu
> > Subject: Re: [Freesurfer] improving white/grey segmentation in recon
> -all for better volume estmation
> >
> > can you send me the rawavg.mgz from the subjects's mri file instead of
> > these dicoms (which I can't read)
> > On Sat, 26 Mar 2016, Ramtilak Gattu wrote:
> >
> >>
> >> Hey Bruce,
> >>
> >>
> >> Thanks for the quick reply.
> >>
> >>
> >> I have uploaded the cases in
> >>
> >>
> >>
> https://waynestateprod-my.sharepoint.com/personal/ao3080_wayne_edu/_layouts/15/guestaccess.aspx?guestaccesstoken=%2bkyhy0gR4k7Q3AechqG%2bjqb89ALB94
> >> xWlpwBQnNAhG8%3d=0a72431d82b4d4b9b924cccbdfb7f34f8
> >>
> >>
> >> The voxel dimensions are 1x1x1 mm.
> >>
> >>
> >>
> >> Thanks
> >>
> >>
> >> Regards
> >>
> >> Tilak
> >>
> >>
> >>
> >>
> 
> >> From: Ramtilak Gattu
> >> Sent: Friday, March 25, 2016 9:59 PM
> >> To: freesurfer@nmr.mgh.harvard.edu
> >> Cc: tilakga...@hotmail.com
> >> Subject: improving white/grey 

[Freesurfer] Longitudinal TRACULA - Error in path reconstruction

[Emad Ahmadi]

Hi Anastasia,

I hope you’re enjoying your evening!

I’m doing longitudinal TRACULA analysis on two subjects, each having two time 
points. I have already taken the steps of longitudinal recon-all and trac-all 
-prep & -bedp.

Now I’m trying to do trac-all -path, but it gives me an error that I cannot 
recognize. I would greatly appreciate your help. I’ve attached the log files 
and the config file.

Thank you so much,
Emad


Emad Ahmadi, MD
---
Research Fellow in Radiology
Massachusetts General Hospital
Harvard Medical School

25 New Chardon Street, Suite 400
Boston, MA 02114
Tel: 617 726 5237
Email: e...@nmr.mgh.harvard.edu


trc_.e11258806
Description: application/applefile


trc_.o11258806
Description: Binary data


trc_0001.e11258808
Description: application/applefile


trc_0001.o11258808
Description: Binary data
# FreeSurfer SUBJECTS_DIR
# T1 images and FreeSurfer segmentations are expected to be found here
#_
setenv SUBJECTS_DIR /cluster/guptagp/Emad/3LT/subjDir
setenv RAW_DATA /cluster/guptagp/Emad/3LT/rawData
#_

# Output directory where trac-all results will be saved
# Default: Same as SUBJECTS_DIR
#
#set dtroot = /path/to/tracts/of/ducks

# Subject IDs (one per time point per subject)
#_
set subjlist = ( 2a \
 2b \
 3a \
 3b )
#_

# Longitudinal base template subject IDs (one for each time point above)
#_
set baselist = ( 2tem \
 2tem \
 3tem \
 3tem )
#_

# In case you want to analyze only Huey and Louie
# Default: Run analysis on all time points and subjects
#
#set runlist = (1 2 5 6)

# Input diffusion DICOMs (file names relative to dcmroot)
# If original DICOMs don't exist, these can be in other image format
# but then the gradient table and b-value table must be specified (see below)
#_
set dcmroot = $RAW_DATA
set dcmlist = ( 2a/Diffusion/IM-0001-0001.dcm \
2b/Diffusion/IM-0001-0001.dcm \
3a/Diffusion/IM-0001-0001.dcm \
3b/Diffusion/IM-0003-0001.dcm )
#_

# Diffusion gradient tables (if there is a different one for each scan)
# Must be specified if inputs are not MGH DICOMs
# The tables must have either three columns, where each row is a gradient vector
# or three rows, where each column is a gradient vector
# There must be as many gradient vectors as volumes in the diffusion data set
# Default: Read from DICOM header
#_
set bveclist = (/cluster/guptagp/Emad/3LT/subjDir/codes/bvecXinv.txt \
/cluster/guptagp/Emad/3LT/subjDir/codes/bvecXinv.txt \
/cluster/guptagp/Emad/3LT/subjDir/codes/bvecXinv.txt \
/cluster/guptagp/Emad/3LT/subjDir/codes/bvecXinv.txt)
#_

# Diffusion gradient table (if using the same one for all scans)
# Must be specified if inputs are not MGH DICOMs
# The table must have either three columns, where each row is a gradient vector
# or three rows, where each column is a gradient vector
# There must be as many gradient vectors as volumes in the diffusion data set
# Default: Read from DICOM header
#_
#set bvecfile = /cluster/guptagp/Emad/3LT/subjDir/codes/bvecXinv.txt
#_

# Diffusion b-value table
# Must be specified if inputs are not MGH DICOMs
# There must be as many b-values as volumes in the diffusion data set
# Default: Read from DICOM header
#_
set bvalfile = /cluster/guptagp/Emad/3LT/subjDir/codes/bval.txt
#_

# Perform registration-based B0-inhomogeneity compensation?
# Default: 0 (no)
#
#set dob0 = 1

# Input B0 field map magnitude DICOMs (file names relative to dcmroot)
# Only used if dob0 = 1
# Default: None
#
#set b0mlist = ( huey/year1/fmag/XXX-1.dcm \
huey/year2/fmag/XXX-1.dcm \
dewey/year1/fmag/XXX-1.dcm \
dewey/year2/fmag/XXX-1.dcm \
louie/year1/fmag/XXX-1.dcm \
louie/year2/fmag/XXX-1.dcm )

# Input B0 field map phase DICOMs (file names relative to dcmroot)
# Only used if dob0 = 1
# Default: None
#
#set b0plist = ( huey/year1/fphas/XXX-1.dcm \
huey/year2/fphas/XXX-1.dcm \
dewey/year1/fphas/XXX-1.dcm \
dewey/year2/fphas/XXX-1.dcm \
louie/year1/fphas/XXX-1.dcm \
   

Re: [Freesurfer] DODS vs DOSS for correlation analysis

[Cassandra Wannan]

Hi Doug,

I'm using version 5.3. I had read about the bug but the release notes for
5.3 didn't mention not using DOSS in Qdec, so I thought the issue must have
been resolved. If not, I'll let my colleagues know as I believe some of
them are still using DOSS in Qdec.

Cheers,

Cassie
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Re: [Freesurfer] bbregister problems with PET data

[Martin Reuter]

Hi Adam,

not sure robust_register robent will work on this type of stuff (never 
tested it). I would recommend to keep the radius small (2,or 3), but 
switch on --entcorrection.


You can also try robust_register with normalized mutual information 
(NMI) or simple MI to see how that works.


You will probably be able to tell if a registration is completely off, 
but if you get something that looks similar to FLIRT it will be hard to 
judge which one is better.


Good luck, Martin


On 03/30/2016 03:41 PM, Adam Martersteck wrote:

Hi Freesurfer team,

I’m encountering a problem using bbregister on PET data:

-- When I attempt to register a PET volume to T1-space the asymmetric 
tracer uptake of the PET throws off proper registration. (Treating the 
PET as a T1 because of the non-specific white matter uptake > grey 
matter signal).


-- You can really see the bbregister mis-registration in this gif 
here: https://goo.gl/iM6yrT


-- It (expectedly) attempts to find the best match between signal 
intensities on both the left and right surfaces, but is inherently 
biased by the asymmetric uptake shifts the entire volume to the right.


-- Are there any suggestions for dealing with asymmetric scans like 
this? Stick with just a simple FLIRT? It doesn't seem to do that great 
a job for everyone.


Cutting left and right hemispheres apart and register separately?

Using Martin’s new robust register for multi-modal data? Any 
suggestions on the parameters of ROBENT?


Thanks,
Adam


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--
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web  : http://reuter.mit.edu

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Re: [Freesurfer] longitudinal pipeline surface error

[Martin Reuter]

Hi Mihaela,

does the cross sectional run of that time point, and the base look OK? 
Also check if this time point is aligned correctly to the base (e.g. 
open norm.mgz from the long and the base, they should be aligned).  If 
all this is OK, then I would recommend to re-run this long run again, 
but make sure you are removing the longitudinal directory first so that 
it re-runs from scratch. If that does not fix it, we would need to get 
the data for debugging.


Thanks, Martin

On 03/30/2016 03:19 PM, Mihaela Stefan wrote:

Dear FreeSurfers,

We are doing a longitudinal analysis with three time points (MRI1, 
MRI2, MRI3). All the subjects were processed well except for one. The 
MRI3.long of that subject has very bad surfaces (see attachment - I am 
also attaching the log file). The cross, the template and the first 
two long runs were reconned well, though. We can't figure out why this 
third run is so bad.


As a note, we processed all the cross runs on an Ubuntu machine but we 
ran the longitudinal pipeline on a computer cluster (both with 
freesurfer v5.3). We ran the long twice for that subject thinking that 
the pipeline crashed somehow the first time. However, the results were 
the same.


Any help would be appreciated.

Thanks!
Mihaela


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--
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web  : http://reuter.mit.edu

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[Freesurfer] bbregister problems with PET data

[Adam Martersteck]

 Hi Freesurfer team,

I’m encountering a problem using bbregister on PET data:

-- When I attempt to register a PET volume to T1-space the asymmetric
tracer uptake of the PET throws off proper registration. (Treating the PET
as a T1 because of the non-specific white matter uptake > grey matter
signal).

-- You can really see the bbregister mis-registration in this gif here:
https://goo.gl/iM6yrT

-- It (expectedly) attempts to find the best match between signal
intensities on both the left and right surfaces, but is inherently biased
by the asymmetric uptake shifts the entire volume to the right.

-- Are there any suggestions for dealing with asymmetric scans like this?
Stick with just a simple FLIRT? It doesn't seem to do that great a job for
everyone.

Cutting left and right hemispheres apart and register separately?

Using Martin’s new robust register for multi-modal data? Any suggestions on
the parameters of ROBENT?

Thanks,
Adam
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Re: [Freesurfer] whole brain is yellow

[Miracle Ozzoude]

Hello doug,
What threshold seems plausible? Thanks
Miracle

Sent from my BlackBerry 10 smartphone.
  Original Message
From: Douglas N Greve
Sent: Monday, March 28, 2016 4:18 PM
To: freesurfer@nmr.mgh.harvard.edu
Reply To: Freesurfer support list
Subject: Re: [Freesurfer] whole brain is yellow


Try changing the threshold. I think the threshold is set to 0 by default
so you are seeing all the 0-valued voxels and it looks like the whole
brain is active

On 03/28/2016 02:14 PM, Miracle Ozzoude wrote:
> This were the conversations leading up to it
> "Hello Bruce and Douglas,
> This is what my design looks like.
> GroupDescriptorFile 1
> Class Group1
> Class Group2
> Variables Age Firstsessionscore
> Input subj1 Group1 72 0.76
> Input subj2 Group1 67 0.43
> Input subj3 Group2 80 1.23
> The contrast matrix i used was [0 0 0 0 0.5 0.5]. I am writing to investigate 
> if thickness correlates with the score removing the effects of group and age. 
> The uncorrected map had blue and red colors in some areas of the brain. The 
> blue color (thickness decreases withe score) seems unlike because i was 
> expecting all red color(thickness increases with score). After I correcting 
> for multiple comparison using 3 pos --cwpvalthresh 0.05, I tried to view the 
> corrected map however, my entire left hemisphere was yellow with no clusters. 
> how do i fix this?Thanks
> Miracle
> -what was your mri_glmfit-sim command line?
> doug
> -mri_glmfit-sim --glmdir lh.firstsessionscore1.glmdir --cache 3 pos  
> --cwpvalthresh  0.05 --2spaces
> miracle
> -not sure what is happening. Can you tar up the glmfit folder and send it to 
> me at our file drop? doug
> I just sent it. miracle
> -What command did you use to visualize? There are no significant clusters
> so the brain should have been totally blank. doug
> - this was the command i used "Freeview -f $ SUBJECTS_DIR / fsaverage / surf 
> / lh.inflated -viewport 3d
> Once I opened freesurfer, I viewed  lh.secondsessionscore1.glmdir--> 
> cache.the30.pos.sig.cluster.mgh using the overlay icon ; and 
> lh.secondsessioncore1.glmdir ---> cache.the30.pos.sig.ocn.annot using the 
> annotation icon"
> Thanks
> miracle
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Douglas N Greve 
> 
> Sent: March 28, 2016 6:04 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] whole brain is yellow
>
> please also include all previous correspondence. We get a lot of emails
> here and we can't keep track of each person's case, so we have to look
> at the previous email chain. thanks!
> doug
>
> On 03/28/2016 02:00 PM, Miracle Ozzoude wrote:
>> Hello Douglas,
>>
>> this was the command i used "Freeview -f $ SUBJECTS_DIR / fsaverage /
>> surf / lh.inflated -viewport 3d
>> Once I opened freesurfer, I viewed lh.secondsessionscore1.glmdir-->
>> cache.the30.pos.sig.cluster.mgh using the overlay icon ; and
>> lh.secondsessioncore1.glmdir ---> cache.the30.pos.sig.ocn.annot using
>> the annotation icon"
>>
>> Thanks
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
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>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine 
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in 
> error
> but does not contain patient information, please contact the sender and 
> properly
> dispose of the e-mail.
>
>
> ___
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>
>

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] stacked iteration in brainstem segmentation

[Eugenio Iglesias]

Hi Claudia,
Sorry for the late response. 
I am aware of this bug and I'm exploring possible solutions. How often does it 
happen in your data (i.e., how many subjects out of how many)?
Cheers,
Eugenio

Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer

- Original Message -
From: "Claudia Testa" 
To: "Freesurfer support list" 
Sent: Friday, March 25, 2016 1:03:42 PM
Subject: [Freesurfer] stacked iteration in brainstem segmentation

Dear all,

I wrote few weeks ago for a problem regarding Freesurfer 6.0 and the 
-brainstem-structures option.
The bug was solved downloading the new available version but I still have some 
problems.
The recon-all -s subject -brainstem-structures
stacks at a certain point (always the same one: "Iteration 2 of 7")  for some 
subjects and for others it succeedes.
In attach there is the log file for one successful segmentation 
(brainstem-structures_ok.log) and one for a failed segmentation 
(brainstem-structures.log).
Can you help me?

Thanks a lot

Claudia

5x1000 AI GIOVANI RICERCATORI
DELL'UNIVERSITÀ DI BOLOGNA
Codice Fiscale: 80007010376

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[Freesurfer] Increase VBOX disksize

[shi yao wang]

Dear Sir/Madam
I am using freesurfer to proceeding brain MRI data.
I have 30 cases. However, the space for home is no enough.
I am wondering how can I increase disk space to computing my data.
I use Vbox unbentu system.

thanks
Lawrence
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Re: [Freesurfer] Regarding: oblique view

[Bruce Fischl]

Hi Sampada

could you include our previous corresponance in your emails so I can keep 
track of what we were talking about? If your slice thickness is really 
6.5mm (or slice thickness + gap) then that is probably the source of your 
problems. You need something much closer to isotropic


cheers
Bruce
On Wed, 30 Mar 2016, 
Dr Sampada Sinha wrote:



Hello Bruce,

Thanks for following it up. ​Sorry for tardy response. I am at the mercy of
power supply and Internet connectivity here. ​The details of scans are
enclosed as a snapshots. Peculiar thing is that we have processed about
23-24 participants' sMRI having similar scanning parameters and their
surface reconstruction is okay. One thing I would like to ask, if I may (?)
is that:​
why am I seeing this problem in this particular participant and why not in
other ones that have been processed?​ All participants so far pre-processed
with recon-all have similar sMRI image protocol.​

Appreciate all your help!

Thanks and kind regards,

Sampada




--
Sampada
Pre-doctoral student
Department of Geriatric Mental Health (DGMH)
King George Medical University
Lucknow-226003
India









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