[Freesurfer] problem with hard coded directory (/scratch)

[Fengji Geng]

Dear all,
I am currently using freesurfer 6.0 (development version) to run hippocampal 
subfields segmentation and encountered a 'mkdir' error, which is attached 
below. Our troubleshooting found that some scripts in the 
...freesurfer/dev/sys/bin directory with things like:

  if(-e /scratch)   set tmpdir = /scratch/tmpdir.bbmask.$$
  if(! -e /scratch) set tmpdir = $outdir/tmpdir.bbmask.$$

However, /scratch is a directory that is not writable in our server. So, we 
made changes to all of the scripts that testing the existence of /scratch. 
However, there are several places where they incorrectly test for the /scratch 
directory using -e instead of -dw, the /scratch is hard coded in there so it 
can't be changed.

Looking forward to hearing suggestions and comments.

Fengji
---

Here begins the error message:

hippocampus:/<2>hippocampus/HMN/data/FG_Temp: 
#
#@# Hippocampal Subfields processing (T1 only) left Wed Nov 18 21:57:45 EST 2015
--
Setting up environment variables
---
LD_LIBRARY_PATH is 
.:/cell_root/software/freesurfer/dev/sys/MCRv80/runtime/glnxa64:/cell_root/software/freesurfer/dev/sys/MCRv80/bin/glnxa64:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/os/glnxa64:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:/cell_root/software/gsl/current/sys/lib:/cell_root/software/fastx/current/lib/fastx_server/lib
Warning: application is running on a locale different from the original 
platform locale.
Error using mkdir
Read-only file system

Error in segmentSubjectT1_autoEstimateAlveusML (line 113)



MATLAB:MKDIR:OSError
#
#@# Hippocampal Subfields processing (T1 only) right Wed Nov 18 21:57:50 EST 
2015
--
Setting up environment variables
---
LD_LIBRARY_PATH is 
.:/cell_root/software/freesurfer/dev/sys/MCRv80/runtime/glnxa64:/cell_root/software/freesurfer/dev/sys/MCRv80/bin/glnxa64:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/os/glnxa64:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:/cell_root/software/gsl/current/sys/lib:/cell_root/software/fastx/current/lib/fastx_server/lib
Warning: application is running on a locale different from the original 
platform locale.
Error using mkdir
Read-only file system

Error in segmentSubjectT1_autoEstimateAlveusML (line 113)



MATLAB:MKDIR:OSError

End of error message.

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Re: [Freesurfer] Using custom segmentations with recon-all

[Bruce Fischl]

Hi James

what kind of segmentation? If gray/white you could replace the wm.mgz and 
go from there, otherwise you would replace the aseg.mgz. In either case, 
make sure you use our conventions (the FreeSurferColorLUT.txt for the 
aseg, or set every wm voxel to the brain.mgz intensity if it is in the 
white matter, and zero otherwise)


cheers
Bruce
On Thu, 3 Dec 2015, james pardon wrote:


Dear All,
I was wondering whether there is a simple way to pass T1 segmentations I have 
from another software
to Freesurfer, in order to do the remaining  recon-all steps?

Thank you in advance,
James

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[Freesurfer] Using custom segmentations with recon-all

[james pardon]

Dear All,

I was wondering whether there is a simple way to pass T1 segmentations I
have from another software to Freesurfer, in order to do the remaining
 recon-all steps?

Thank you in advance,
James
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Re: [Freesurfer] Freesurfer Version mismatch between Subject and Control Stamp in autorecon2 and autorecon3

[Bruce Fischl]

Hi Amy

looks like you processed them on different machines that use different 
version of freesurfer. One is centos4 with FS 5.0 and one is centos 6 with 
5.3. You definitely don't want to mix these.

Bruce


On Thu, 3 Dec 2015, Amy L wrote:

> Hi all,
> 
> I'm sorry if this is a silly question, but what might cause the version of 
> Freesurfer to be
> different in the Subject and Current Stamps of the output following 
> autorecon2 and autorecon3? And
> is this a problem? The relevant lines of output are as follows:
> 
> INFO: FreeSurfer build stamps do not match
> Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
> Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0
> 
> Thanks very much for any insight!
> 
>
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Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure (mris_euler_number) using high res (0.5mm isotropic) T1 image

[Bruce Fischl]

Hi Ajay

I have found the problem that messed up the surfaces and fixed it. We can 
get you an updated mris_fix_topology that will not generate corrupted 
surfaces. However, the underlying problem is huge topological defects 
caused by low gray/white contrast in this data. For example in the left 
hemi, there is on in the insula (e.g. voxels around 362, 213, 200 and 364, 
229, 207 and in the temporal lobe (351, 286, 282, 283, 309, 258).



Basically the gray/white contrast isn't high enough for us to accurately 
segment the wm with our default procedures. Control points may help a bit, 
but you may also need to manually edit the wm.mgz to remove the largest 
defects. The easiest way to do this is to visualize them on the 
lh.inflated.nofix surface with the lh.defect_labels overlaid to show you 
where the defects are, then go into the volume in the wm.mgz and either add 
control points or erase wm to fix things.


Let us know if you want a new mris_fix_topology. I'm not sure it is worth 
the trouble since while it will now generate topologically correct surfaces 
for this dataset, they will not be geometrically acccurate in the vicinity 
of the huge (>200,000 vertices!) defects.


cheers
Bruce


On Wed, 2 Dec 2015, Ajay Kurani wrote:


Hi Bruce,

  The template is the ICBM 2009b nonlinear template (0.5mm isotropic) which I 
downloaded from the
McGills site (http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009).  
The template has a
range of values from 0-100.  Then I combined the csf/wm/gm masks (derived from 
the 2009c template
which is 1mm isotropic) and resampled to 0.5 mm to mask the brain.  
Subsequently I rescaled the
data to have a range of 0-255 and used this output as my input T1 for 
Freesurfer.  Thank you very
much for looking into this matter, it is much appreciated!  I will look at the 
file as you
suggested.

Sincerely,
Ajay

On Tue, Dec 1, 2015 at 7:55 AM, Bruce Fischl  wrote:
  Hi Ajay

  can you explain your entire processing stream, including the details of 
the
  acquisition? What sequence/coil/scanner was used? You could fix your 
problem by looking
  at the defects on the inflated.nofix, overlaying
  lh.defect_labels on it to see where they are, then figuring out what 
caused them in the
  volume. However, there is a bug in mris_fix_topology that only comes up 
when it
  encounters a large enough defect (with nvertices>200,000). The code tries 
to avoid
  running it's normal genetic algorithm as it would take days (or weeks) to 
finish, since
  it scales with the square of the number of vertices. I haven't figured 
out what is
  going wrong yet, but hopefully will have a code fix soon.

  cheers
  Bruce


  On Tue, 1 Dec 2015, Ajay Kurani wrote:

Hi Bruce,  When looking at my top slices in brain ask I noticed 
that the
gray/white matter shows but the darker areas surrounding it are not 
present
(this usually goes to the edge of the brain).  Could the large 
defects be a
result of having masked this out on the input file?  I multiplied 
the
template with the GM/WM/CSF masks they provided to get the brain 
extracted
so I only see this missing in the very top few slices of the brain.

Thanks,
Ajay

On Tuesday, December 1, 2015, Bruce Fischl 

wrote:
      Hi Falk

      I don't think you need to rerun the qsphere. I'm pretty sure
      this is a bug in mris_fix_topology for giant defects, but
      haven't finished tracking it down yet

      cheers
      Bruce


      On Tue, 1 Dec 2015, Falk Lüsebrink wrote:


            Hi Ajay,

             

            you should

             

            cp ?h.orig.nofix ?h.orig

            cp ?h.inflated.nofix ?h.inflated

             

            with ? being l or r depending your hemisphere.
            After the fixing stage the
            surfaces got damaged somehow, therefore you have to
            recreate it them. I’m
            not entirely sure about the qsphere. Probably you
            have to run the -qsphere
            stage again also.

             

            Best,

            Falk

             

             

            Von: Ajay Kurani [mailto:dr.ajay.kur...@gmail.com]
            Gesendet: Montag, 30. November 2015 21:50
            An: Falk Lüsebrink
            Cc: Freesurfer support list; Bruce Fischl
            Betreff: Re: [Freesurfer] Freesurfer 6.0 -
            Autorecon2 failure
  

Re: [Freesurfer] problem with hard coded directory (/scratch)

[Bruce Fischl]

thanks Fengji

sounds like something we should fix.

cheers
Bruce
On Thu, 3 Dec 2015, Fengji Geng wrote:


Dear all, 
I am currently using freesurfer 6.0 (development version) to run hippocampal 
subfields segmentation
and encountered a 'mkdir' error, which is attached below. Our troubleshooting 
found that some
scripts in the ...freesurfer/dev/sys/bin directory with things like:

  if(-e /scratch)   set tmpdir = /scratch/tmpdir.bbmask.$$
  if(! -e /scratch) set tmpdir = $outdir/tmpdir.bbmask.$$
However, /scratch is a directory that is not writable in our server. So, we 
made changes to all of
the scripts that testing the existence of /scratch. However, there are several 
places where they
incorrectly test for the /scratch directory using -e instead of -dw, the 
/scratch is hard coded in
there so it can't be changed. 

Looking forward to hearing suggestions and comments.

Fengji

--
-


Here begins the error message:

 

hippocampus:/<2>hippocampus/HMN/data/FG_Temp: 
#

#@# Hippocampal Subfields processing (T1 only) left Wed Nov 18 21:57:45 EST 2015

--

Setting up environment variables

---

LD_LIBRARY_PATH 
is.:/cell_root/software/freesurfer/dev/sys/MCRv80/runtime/glnxa64:/cell_root/software/freesurfer/dev
/sys/MCRv80/bin/glnxa64:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/os/glnxa64:/cell_root/so
ftware/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/cell_root/soft
ware/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/cell_root/software/frees
urfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/cell_root/software/freesurfer/dev/
sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:/cell_root/software/gsl/current/sys/lib:/cell_root/s
oftware/fastx/current/lib/fastx_server/lib

Warning: application is running on a locale different from the original 
platform locale.

Error using mkdir

Read-only file system

 

Error in segmentSubjectT1_autoEstimateAlveusML (line 113)

 

 

 

MATLAB:MKDIR:OSError

#

#@# Hippocampal Subfields processing (T1 only) right Wed Nov 18 21:57:50 EST 
2015

--

Setting up environment variables

---

LD_LIBRARY_PATH 
is.:/cell_root/software/freesurfer/dev/sys/MCRv80/runtime/glnxa64:/cell_root/software/freesurfer/dev
/sys/MCRv80/bin/glnxa64:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/os/glnxa64:/cell_root/so
ftware/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/cell_root/soft
ware/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/cell_root/software/frees
urfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/cell_root/software/freesurfer/dev/
sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:/cell_root/software/gsl/current/sys/lib:/cell_root/s
oftware/fastx/current/lib/fastx_server/lib

Warning: application is running on a locale different from the original 
platform locale.

Error using mkdir

Read-only file system

 

Error in segmentSubjectT1_autoEstimateAlveusML (line 113)

 

 

 

MATLAB:MKDIR:OSError

 

End of error message.

 


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Re: [Freesurfer] converting labels to MNI space

[Francesca Strappini]

Thank you!

I run the recon-all on the MNI brain and now the first step, label2label,
produced a label which is perfectly mapped on the surface of the MNI
template.
I tried to run the second step, mapping the new label to the volume, but I
still got the shift downward.

mri_label2vol --label lh.V1dorsalLG_MNI.label --temp
/usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz --o
lh.V1dorsalLG_MNI.nii.gz --identity

Best
Francesca



2015-12-01 20:26 GMT+02:00 Douglas N Greve :

> Try adding --invertmtx to the mri_label2vol command. I don't think the
> label2label command does anything, does it? Also, you might have better
> alignment if you run recon-all on the mni152 brain, then use
> mri_label2label to map the label from the individual into the 152 space
> using the surface transform, then convert that to the volume.
>
> On 11/30/2015 10:13 AM, Francesca Strappini wrote:
> > Dear FreeSurfer experts,
> >
> > I'm trying to convert some retinotopic labels I created on the surface
> > of each individual subject to MNI305 space for FSL.
> >
> > I run the following commands, but the output is not registered
> > correctly. It seems to be shifted downward.
> >
> > mni152reg --s LG
> >
> > mri_label2label --srclabel lh.V1dorsalLG.label  --s LG --regmethod
> > surface --trglabel lh.V1dorsalLG_new.label --hemi lh
> >
> > mri_label2vol --label lh.V1dorsalLG_new.label --reg
> > /usr/local/freesurfer/subjects/LG/mri/mni152.orig.mgz.reg --temp
> > /usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz --o
> > lh.V1dorsalLG_new_MNI.nii.gz
> >
> > Thanks for your help,
> > Francesca
> >
> > --
> > Francesca Strappini, Ph.D.
> > Neurobiology Department
> > Weizmann Institute of Science
> > 234 Herzl Street, Rehovot 7610001 Israel
> > Tel.: +972 58 444 2584
> > E-mail: francesca.strapp...@weizmann.ac.il
> > 
> >
> >
> > ___
> > 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.
>
>


-- 
Francesca Strappini, Ph.D.
Neurobiology Department
Weizmann Institute of Science
234 Herzl Street, Rehovot 7610001 Israel
Tel.: +972 58 444 2584
E-mail: francesca.strapp...@weizmann.ac.il
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Re: [Freesurfer] converting labels to MNI space

[Douglas Greve]

Use --regheader /usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz 
instead of --identity



On 12/3/15 8:46 AM, Francesca Strappini wrote:

Thank you!

I run the recon-all on the MNI brain and now the first step, 
label2label, produced a label which is perfectly mapped on the surface 
of the MNI template.
I tried to run the second step, mapping the new label to the volume, 
but I still got the shift downward.


mri_label2vol --label lh.V1dorsalLG_MNI.label --temp 
/usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz --o 
lh.V1dorsalLG_MNI.nii.gz --identity


Best
Francesca



2015-12-01 20:26 GMT+02:00 Douglas N Greve >:


Try adding --invertmtx to the mri_label2vol command. I don't think the
label2label command does anything, does it? Also, you might have
better
alignment if you run recon-all on the mni152 brain, then use
mri_label2label to map the label from the individual into the 152
space
using the surface transform, then convert that to the volume.

On 11/30/2015 10:13 AM, Francesca Strappini wrote:
> Dear FreeSurfer experts,
>
> I'm trying to convert some retinotopic labels I created on the
surface
> of each individual subject to MNI305 space for FSL.
>
> I run the following commands, but the output is not registered
> correctly. It seems to be shifted downward.
>
> mni152reg --s LG
>
> mri_label2label --srclabel lh.V1dorsalLG.label  --s LG --regmethod
> surface --trglabel lh.V1dorsalLG_new.label --hemi lh
>
> mri_label2vol --label lh.V1dorsalLG_new.label --reg
> /usr/local/freesurfer/subjects/LG/mri/mni152.orig.mgz.reg --temp
> /usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz --o
> lh.V1dorsalLG_new_MNI.nii.gz
>
> Thanks for your help,
> Francesca
>
> --
> Francesca Strappini, Ph.D.
> Neurobiology Department
> Weizmann Institute of Science
> 234 Herzl Street, Rehovot 7610001 Israel
> Tel.: +972 58 444 2584
> E-mail: francesca.strapp...@weizmann.ac.il

> >
>
>
> ___
> 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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--
Francesca Strappini, Ph.D.
Neurobiology Department
Weizmann Institute of Science
234 Herzl Street, Rehovot 7610001 Israel
Tel.: +972 58 444 2584
E-mail: francesca.strapp...@weizmann.ac.il 




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[Freesurfer] Recon-all -bigventricles option : general use or not in Alzheimer cases ?

[Matthieu Vanhoutte]

Dear FreeSurfer experts,

My question is in the title. I'm working on Alzheimer case where most of
the cases have large ventricles. Is it better in general use to apply
-bigventricles option on all subjects (for homogeneous calculus or
something like that...) or to distinct subtle cases of patients with not so
big ventricles ?

Thanks in advance for helping !

Best regards,

Matthie
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[Freesurfer] g-w.pct vs. g-w. ratio

[Andrews, Derek]

Dear FreeSurfer Support team and Community

I am wondering if someone can give me an explanation of the difference between 
g-w.pct and g:w ratio (as calculated by; fscalc lh.gm.mgh div lh.wm.mgh -o 
lh.ratio.mgh)

Will both these measures essentially measure the relationship between grey and 
white matter signal intensity but in a different way?


Best, Derek




Derek Sayre Andrews, MSc
PhD Candidate

The Sackler Institute for Translational Neurodevelopment

Department of Forensic and Neurodevelopmental Sciences

Institute of Psychiatry, Psychology & Neuroscience, King's College London

Telephone: +44 (0)20 7848 5701
Email: derek.andr...@kcl.ac.uk

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[Freesurfer] nu_correct error (FS 6 beta)

[COX Simon]

Dear all,

I'd be very grateful for a bit of help with the following problem.

I'm running FreeSurfer 6.0 (I read a suggestion that there had been some 
compatibility issues running the current stable FS release with newer versions 
of openSUSE) on a cluster. However, nu_correct seems to be hitting an issue:

ncopen: filename "./tmp.mri_nu_correct.mni.9548/0/nu1_est.mnc.temp": No such 
file or directory
miopen: MINC package entry point
nu_estimate_np_and_em: crashed while running mincmath (termination status=768)
nu_correct: crashed while running nu_estimate_np_and_em (termination status=768)
ERROR: nu_correct

The directory exists, and there are several other files written here 
("nu0.mnc", "nu1_corr.mnc", "nu1_mask.mnc", "nu1_residue.mnc" and 
"nu1_temp.mnc") so it doesn't appear to be having an issue with write access to 
this location.

Many thanks in advance for your help,

Simon

Simon R. Cox
Centre for Cognitive Ageing and Cognitive Epidemiology
University of Edinburgh
7 George Square
Edinburgh EH8 9JZ
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
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Re: [Freesurfer] Recon-all -bigventricles option : general use or not in Alzheimer cases ?

[Bruce Fischl]

Hi Matthie

do you find that it doesn't work well without bigventricles? You just 
want to be sure that you process your data in the same way so there is no 
bias in the results. We have found that most early AD cases work fine 
without needing special flags. It's more for late stage AD or hydrocephalus 
and such.

cheers
Bruce



On Thu, 3 Dec 2015, Matthieu 
Vanhoutte wrote:

> Dear FreeSurfer experts,
> 
> My question is in the title. I'm working on Alzheimer case where most of the 
> cases have large
> ventricles. Is it better in general use to apply -bigventricles option on all 
> subjects (for
> homogeneous calculus or something like that...) or to distinct subtle cases 
> of patients with not so
> big ventricles ?
> 
> Thanks in advance for helping !
> 
> Best regards,
> 
> Matthie
> 
>
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[Freesurfer] obtain volumetric data with qdec

[Clara Kühn]

Dear FreeSurfer Experts,

I'm trying to follow the steps described in the univeriate LME for longitudinal 
data (https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels). 
Could you explain how you did this step:
"The qdec.table.dat file was then used to collect volumetric data for all 
subjects within the Freesurfer's Qdec interface. This resulted in a new Qdec 
table which had the previous columns plus three new columns."

I followed the instructions with mri_preproc and mri_surf2surf but when I then 
open qdec to obtain the volumetric data for (in my case) BA45 it always gives 
out the error "Error in Analyze: Coudln't open 
/path_to_subject_base/lh.thickness.fwhm0.templatename.mgz or .mgh file"
I understand that it can't find that file because it isn't there. 

Which steps do I additionally need to perfom to be able to be able to obtain 
said volumetric data. Is there an extra turorial or walkthrough for that?

Cheers, Clara

-- 
Clara Kühn, Phd Student
 
Max-Planck-Institute for Human Cognitive and Brain Science
Department of Neuropsychology
Stephanstrasse 1A
04103 Leipzig, Germany

Phone: +49 341 - 9940 2271
Fax: +49 341 - 9940 2260
Web: www.cbs.mpg.de
E-Mail: cku...@cbs.mpg.de

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Re: [Freesurfer] g-w.pct vs. g-w. ratio

[Douglas N Greve]

g-w.pct is computed as

pct = 100*(w-g)/((w+g)/2)

in the pctsurfcon script


On 12/03/2015 12:18 PM, Andrews, Derek wrote:
> Dear FreeSurfer Support team and Community
>
> I am wondering if someone can give me an explanation of the difference 
> between g-w.pct and g:w ratio (as calculated by; fscalc lh.gm.mgh div 
> lh.wm.mgh -o lh.ratio.mgh)
> Will both these measures essentially measure the relationship between 
> grey and white matter signal intensity but in a different way?
>
>
> Best, Derek
>
>
> 
>
> *Derek Sayre Andrews, MSc*
> PhD Candidate
>
> The Sackler Institute for Translational Neurodevelopment
>
> Department of Forensic and Neurodevelopmental Sciences
>
> Institute of Psychiatry, Psychology & Neuroscience, King's College London
>
> Telephone: +44 (0)20 7848 5701
> Email: derek.andr...@kcl.ac.uk
>
>
>
>
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] Grey matter， white matter and CSF volumes

[Douglas N Greve]

looks mostly right. For CSF there is a "CSF" label that should be 
included. For WM, you may or may not want to include brainstem.

On 12/03/2015 12:20 PM, Jinsong Tang wrote:
> Hello,
>
> I want to calculate the Grey matter, white matter and  CSF  volumes.
>
> The total gray matter volume is already in the ASEG file.
>
> Then
> I add up following volumes for ventricular CSF: Left Lateral Ventricle 
> + Left Inferior Lateral Ventricle + Right lateral Ventricle  + Right 
> Inf Lateral Ventricle + 3rd Ventricle + 4th Ventricle + 5th Ventricle 
>  + Right choroids plexus + left choroids plexus.
>
> also,
>
>  I add up following volumes for white matter volume: 
>  CorticalWhiteMatterVol +Left-Cerebellum-White-Matter + 
> Right-Cerebellum-White-Matter.
>
> Are these right?
>
> Thanks,
>
> Jinsong
>
>
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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
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Re: [Freesurfer] converting labels to MNI space

[Bruce Fischl]

Hi Francesca

your output is a volume not an ROI, so you need to load it as a volume in 
freeview to check it


cheers
Bruce

On Thu, 3 Dec 2015, Francesca Strappini wrote:


Thanks!
I run this command:

mri_label2vol --label lh.V1dorsalLG_MNI.label --temp
/usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz --regheader
/usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz --o lh.V1dorsalLG_MNI.nii.gz

but unfortunately, it gave me the same big downward shift (I checked it with 
fslview).

But if  I try to open the ROI with freeview it gives me this error:
freeview.bin: empty label
LabelRead failed
freeview.bin: empty label

2015-12-03 16:57 GMT+02:00 Douglas Greve :
  Use --regheader /usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz instead 
of --identity


  On 12/3/15 8:46 AM, Francesca Strappini wrote:
  Thank you!
I run the recon-all on the MNI brain and now the first step, label2label, 
produced a
label which is perfectly mapped on the surface of the MNI template. 
I tried to run the second step, mapping the new label to the volume, but I 
still got
the shift downward. 

mri_label2vol --label lh.V1dorsalLG_MNI.label --temp
/usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz --o lh.V1dorsalLG_MNI.nii.gz
--identity

Best
Francesca



2015-12-01 20:26 GMT+02:00 Douglas N Greve :
  Try adding --invertmtx to the mri_label2vol command. I don't think the
  label2label command does anything, does it? Also, you might have better
  alignment if you run recon-all on the mni152 brain, then use
  mri_label2label to map the label from the individual into the 152 space
  using the surface transform, then convert that to the volume.

  On 11/30/2015 10:13 AM, Francesca Strappini wrote:
  > Dear FreeSurfer experts,
  >
  > I'm trying to convert some retinotopic labels I created on the surface
  > of each individual subject to MNI305 space for FSL.
  >
  > I run the following commands, but the output is not registered
  > correctly. It seems to be shifted downward.
  >
  > mni152reg --s LG
  >
  > mri_label2label --srclabel lh.V1dorsalLG.label  --s LG --regmethod
  > surface --trglabel lh.V1dorsalLG_new.label --hemi lh
  >
  > mri_label2vol --label lh.V1dorsalLG_new.label --reg
  > /usr/local/freesurfer/subjects/LG/mri/mni152.orig.mgz.reg --temp
  > /usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz --o
  > lh.V1dorsalLG_new_MNI.nii.gz
  >
  > Thanks for your help,
  > Francesca
  >
  > --
  > Francesca Strappini, Ph.D.
  > Neurobiology Department
  > Weizmann Institute of Science
  > 234 Herzl Street, Rehovot 7610001 Israel
  > Tel.: +972 58 444 2584
  > E-mail: francesca.strapp...@weizmann.ac.il
> 
>
>
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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
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--
Francesca Strappini, Ph.D.
Neurobiology Department
Weizmann Institute of Science
234 Herzl Street, Rehovot 7610001 Israel
Tel.: +972 58 444 2584
E-mail: francesca.strapp...@weizmann.ac.il


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--
Francesca Strappini, Ph.D.
Neurobiology Department
Weizmann 

Re: [Freesurfer] converting labels to MNI space

[Francesca Strappini]

Thanks!

I run this command:

mri_label2vol --label lh.V1dorsalLG_MNI.label --temp
/usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz --regheader
/usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz --o
lh.V1dorsalLG_MNI.nii.gz

but unfortunately, it gave me the same big downward shift (I checked it
with fslview).

But if  I try to open the ROI with freeview it gives me this error:
freeview.bin: empty label
LabelRead failed
freeview.bin: empty label

2015-12-03 16:57 GMT+02:00 Douglas Greve :

> Use --regheader /usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz instead
> of --identity
>
>
>
> On 12/3/15 8:46 AM, Francesca Strappini wrote:
>
> Thank you!
>
> I run the recon-all on the MNI brain and now the first step, label2label,
> produced a label which is perfectly mapped on the surface of the MNI
> template.
> I tried to run the second step, mapping the new label to the volume, but I
> still got the shift downward.
>
> mri_label2vol --label lh.V1dorsalLG_MNI.label --temp
> /usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz --o
> lh.V1dorsalLG_MNI.nii.gz --identity
>
> Best
> Francesca
>
>
>
> 2015-12-01 20:26 GMT+02:00 Douglas N Greve :
>
>> Try adding --invertmtx to the mri_label2vol command. I don't think the
>> label2label command does anything, does it? Also, you might have better
>> alignment if you run recon-all on the mni152 brain, then use
>> mri_label2label to map the label from the individual into the 152 space
>> using the surface transform, then convert that to the volume.
>>
>> On 11/30/2015 10:13 AM, Francesca Strappini wrote:
>> > Dear FreeSurfer experts,
>> >
>> > I'm trying to convert some retinotopic labels I created on the surface
>> > of each individual subject to MNI305 space for FSL.
>> >
>> > I run the following commands, but the output is not registered
>> > correctly. It seems to be shifted downward.
>> >
>> > mni152reg --s LG
>> >
>> > mri_label2label --srclabel lh.V1dorsalLG.label  --s LG --regmethod
>> > surface --trglabel lh.V1dorsalLG_new.label --hemi lh
>> >
>> > mri_label2vol --label lh.V1dorsalLG_new.label --reg
>> > /usr/local/freesurfer/subjects/LG/mri/mni152.orig.mgz.reg --temp
>> > /usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz --o
>> > lh.V1dorsalLG_new_MNI.nii.gz
>> >
>> > Thanks for your help,
>> > Francesca
>> >
>> > --
>> > Francesca Strappini, Ph.D.
>> > Neurobiology Department
>> > Weizmann Institute of Science
>> > 234 Herzl Street, Rehovot 7610001 Israel
>> > Tel.: +972 58 444 2584
>> > E-mail: francesca.strapp...@weizmann.ac.il
>> > 
>> >
>> >
>> > ___
>> > 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/
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> 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.
>>
>>
>
>
> --
> Francesca Strappini, Ph.D.
> Neurobiology Department
> Weizmann Institute of Science
> 234 Herzl Street, Rehovot 7610001 Israel
> Tel.: +972 58 444 2584
> E-mail: francesca.strapp...@weizmann.ac.il
>
>
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> 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
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-- 
Francesca Strappini, Ph.D.
Neurobiology Department
Weizmann Institute of Science
234 Herzl Street, Rehovot 7610001 Israel
Tel.: +972 58 444 

[Freesurfer] Freesurfer 6.0 - Autorecon2 failure (mris_euler_number) using high res (0.5mm isotropic) T1 image

[Ajay Kurani]

Hi Bruce,
   If it isn't too much trouble could you send the program update?  I have
another set of images (2009c template) which I can contrast enhance for
GM/WM regions so I can try this set of images to process along with the
images I sent you.

Thanks,
Ajay

On Thursday, December 3, 2015, Bruce Fischl > wrote:

> Hi Ajay
>
> I have found the problem that messed up the surfaces and fixed it. We can
> get you an updated mris_fix_topology that will not generate corrupted
> surfaces. However, the underlying problem is huge topological defects
> caused by low gray/white contrast in this data. For example in the left
> hemi, there is on in the insula (e.g. voxels around 362, 213, 200 and 364,
> 229, 207 and in the temporal lobe (351, 286, 282, 283, 309, 258).
>
>
> Basically the gray/white contrast isn't high enough for us to accurately
> segment the wm with our default procedures. Control points may help a bit,
> but you may also need to manually edit the wm.mgz to remove the largest
> defects. The easiest way to do this is to visualize them on the
> lh.inflated.nofix surface with the lh.defect_labels overlaid to show you
> where the defects are, then go into the volume in the wm.mgz and either add
> control points or erase wm to fix things.
>
> Let us know if you want a new mris_fix_topology. I'm not sure it is worth
> the trouble since while it will now generate topologically correct surfaces
> for this dataset, they will not be geometrically acccurate in the vicinity
> of the huge (>200,000 vertices!) defects.
>
> cheers
> Bruce
>
>
> On Wed, 2 Dec 2015, Ajay Kurani wrote:
>
> Hi Bruce,
>>
>>   The template is the ICBM 2009b nonlinear template (0.5mm isotropic)
>> which I downloaded from the
>> McGills site (
>> http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009).  The
>> template has a
>> range of values from 0-100.  Then I combined the csf/wm/gm masks (derived
>> from the 2009c template
>> which is 1mm isotropic) and resampled to 0.5 mm to mask the brain.
>> Subsequently I rescaled the
>> data to have a range of 0-255 and used this output as my input T1 for
>> Freesurfer.  Thank you very
>> much for looking into this matter, it is much appreciated!  I will look
>> at the file as you
>> suggested.
>>
>> Sincerely,
>> Ajay
>>
>> On Tue, Dec 1, 2015 at 7:55 AM, Bruce Fischl 
>> wrote:
>>   Hi Ajay
>>
>>   can you explain your entire processing stream, including the
>> details of the
>>   acquisition? What sequence/coil/scanner was used? You could fix
>> your problem by looking
>>   at the defects on the inflated.nofix, overlaying
>>   lh.defect_labels on it to see where they are, then figuring out
>> what caused them in the
>>   volume. However, there is a bug in mris_fix_topology that only
>> comes up when it
>>   encounters a large enough defect (with nvertices>200,000). The code
>> tries to avoid
>>   running it's normal genetic algorithm as it would take days (or
>> weeks) to finish, since
>>   it scales with the square of the number of vertices. I haven't
>> figured out what is
>>   going wrong yet, but hopefully will have a code fix soon.
>>
>>   cheers
>>   Bruce
>>
>>
>>   On Tue, 1 Dec 2015, Ajay Kurani wrote:
>>
>> Hi Bruce,  When looking at my top slices in brain ask I
>> noticed that the
>> gray/white matter shows but the darker areas surrounding it
>> are not present
>> (this usually goes to the edge of the brain).  Could the
>> large defects be a
>> result of having masked this out on the input file?  I
>> multiplied the
>> template with the GM/WM/CSF masks they provided to get the
>> brain extracted
>> so I only see this missing in the very top few slices of the
>> brain.
>>
>> Thanks,
>> Ajay
>>
>> On Tuesday, December 1, 2015, Bruce Fischl <
>> fis...@nmr.mgh.harvard.edu>
>> wrote:
>>   Hi Falk
>>
>>   I don't think you need to rerun the qsphere. I'm pretty
>> sure
>>   this is a bug in mris_fix_topology for giant defects,
>> but
>>   haven't finished tracking it down yet
>>
>>   cheers
>>   Bruce
>>
>>
>>   On Tue, 1 Dec 2015, Falk Lüsebrink wrote:
>>
>>
>> Hi Ajay,
>>
>>
>>
>> you should
>>
>>
>>
>> cp ?h.orig.nofix ?h.orig
>>
>> cp ?h.inflated.nofix ?h.inflated
>>
>>
>>
>> with ? being l or r depending your hemisphere.
>> After the fixing stage the
>> surfaces got damaged somehow, therefore you have
>> to
>> recreate it them. I’m
>> not entirely sure about the qsphere. 

Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure (mris_euler_number) using high res (0.5mm isotropic) T1 image

[Bruce Fischl]

sure Zeke can get it to you if you tell himn your hardware/software env, 
but as I said if you have defects that are that big they are unlikelly to 
be corrected to produce geometrically accurate surfaces.


cheers
Bruce
On Thu, 3 Dec 2015, 
Ajay Kurani wrote:



Hi Bruce,   If it isn't too much trouble could you send the program update?  I 
have another set of
images (2009c template) which I can contrast enhance for GM/WM regions so I can 
try this set of
images to process along with the images I sent you.

Thanks,
Ajay

On Thursday, December 3, 2015, Bruce Fischl  wrote:
  Hi Ajay

  I have found the problem that messed up the surfaces and fixed it. We can 
get you an
  updated mris_fix_topology that will not generate corrupted surfaces. 
However, the
  underlying problem is huge topological defects caused by low gray/white 
contrast in
  this data. For example in the left hemi, there is on in the insula (e.g. 
voxels around
  362, 213, 200 and 364, 229, 207 and in the temporal lobe (351, 286, 282, 
283, 309,
  258).


  Basically the gray/white contrast isn't high enough for us to accurately 
segment the wm
  with our default procedures. Control points may help a bit, but you may 
also need to
  manually edit the wm.mgz to remove the largest defects. The easiest way 
to do this is
  to visualize them on the lh.inflated.nofix surface with the 
lh.defect_labels overlaid
  to show you where the defects are, then go into the volume in the wm.mgz 
and either add
  control points or erase wm to fix things.

  Let us know if you want a new mris_fix_topology. I'm not sure it is worth 
the trouble
  since while it will now generate topologically correct surfaces for this 
dataset, they
  will not be geometrically acccurate in the vicinity of the huge (>200,000 
vertices!)
  defects.

  cheers
  Bruce


  On Wed, 2 Dec 2015, Ajay Kurani wrote:

Hi Bruce,

  The template is the ICBM 2009b nonlinear template (0.5mm 
isotropic) which
I downloaded from the
McGills site
(http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009).  The
template has a
range of values from 0-100.  Then I combined the csf/wm/gm masks 
(derived
from the 2009c template
which is 1mm isotropic) and resampled to 0.5 mm to mask the brain. 
Subsequently I rescaled the
data to have a range of 0-255 and used this output as my input T1 
for
Freesurfer.  Thank you very
much for looking into this matter, it is much appreciated!  I will 
look at
the file as you
suggested.

Sincerely,
Ajay

On Tue, Dec 1, 2015 at 7:55 AM, Bruce Fischl 

wrote:
      Hi Ajay

      can you explain your entire processing stream, including the 
details
of the
      acquisition? What sequence/coil/scanner was used? You could 
fix your
problem by looking
      at the defects on the inflated.nofix, overlaying
      lh.defect_labels on it to see where they are, then figuring 
out what
caused them in the
      volume. However, there is a bug in mris_fix_topology that 
only comes
up when it
      encounters a large enough defect (with nvertices>200,000). 
The code
tries to avoid
      running it's normal genetic algorithm as it would take days 
(or
weeks) to finish, since
      it scales with the square of the number of vertices. I haven't
figured out what is
      going wrong yet, but hopefully will have a code fix soon.

      cheers
      Bruce


      On Tue, 1 Dec 2015, Ajay Kurani wrote:

            Hi Bruce,  When looking at my top slices in brain ask I 
noticed
that the
            gray/white matter shows but the darker areas 
surrounding it are
not present
            (this usually goes to the edge of the brain).  Could 
the large
defects be a
            result of having masked this out on the input file?  I
multiplied the
            template with the GM/WM/CSF masks they provided to get 
the
brain extracted
            so I only see this missing in the very top few slices 
of the
brain.

            Thanks,
            Ajay

            On Tuesday, December 1, 2015, Bruce Fischl

            wrote:
                  Hi Falk

                  I don't think you need to rerun the qsphere. I'm 
pretty
sure
   

Re: [Freesurfer] converting labels to MNI space

[Douglas N Greve]

oops, gave you the wrong option, it should be

--regheader $SUBJECTS_DIR/mni152-recon/mri/orig.mgz



On 12/03/2015 10:22 AM, Francesca Strappini wrote:
> Thanks!
>
> I run this command:
>
> mri_label2vol --label lh.V1dorsalLG_MNI.label --temp 
> /usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz --regheader 
> /usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz --o 
> lh.V1dorsalLG_MNI.nii.gz
>
> but unfortunately, it gave me the same big downward shift (I checked 
> it with fslview).
>
> But if  I try to open the ROI with freeview it gives me this error:
> freeview.bin: empty label
> LabelRead failed
> freeview.bin: empty label
>
> 2015-12-03 16:57 GMT+02:00 Douglas Greve  >:
>
> Use --regheader /usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz
> instead of --identity
>
>
>
> On 12/3/15 8:46 AM, Francesca Strappini wrote:
>> Thank you!
>>
>> I run the recon-all on the MNI brain and now the first step,
>> label2label, produced a label which is perfectly mapped on the
>> surface of the MNI template.
>> I tried to run the second step, mapping the new label to the
>> volume, but I still got the shift downward.
>>
>> mri_label2vol --label lh.V1dorsalLG_MNI.label --temp
>> /usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz --o
>> lh.V1dorsalLG_MNI.nii.gz --identity
>>
>> Best
>> Francesca
>>
>>
>>
>> 2015-12-01 20:26 GMT+02:00 Douglas N Greve
>> >:
>>
>> Try adding --invertmtx to the mri_label2vol command. I don't
>> think the
>> label2label command does anything, does it? Also, you might
>> have better
>> alignment if you run recon-all on the mni152 brain, then use
>> mri_label2label to map the label from the individual into the
>> 152 space
>> using the surface transform, then convert that to the volume.
>>
>> On 11/30/2015 10:13 AM, Francesca Strappini wrote:
>> > Dear FreeSurfer experts,
>> >
>> > I'm trying to convert some retinotopic labels I created on
>> the surface
>> > of each individual subject to MNI305 space for FSL.
>> >
>> > I run the following commands, but the output is not registered
>> > correctly. It seems to be shifted downward.
>> >
>> > mni152reg --s LG
>> >
>> > mri_label2label --srclabel lh.V1dorsalLG.label  --s LG
>> --regmethod
>> > surface --trglabel lh.V1dorsalLG_new.label --hemi lh
>> >
>> > mri_label2vol --label lh.V1dorsalLG_new.label --reg
>> > /usr/local/freesurfer/subjects/LG/mri/mni152.orig.mgz.reg
>> --temp
>> > /usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz --o
>> > lh.V1dorsalLG_new_MNI.nii.gz
>> >
>> > Thanks for your help,
>> > Francesca
>> >
>> > --
>> > Francesca Strappini, Ph.D.
>> > Neurobiology Department
>> > Weizmann Institute of Science
>> > 234 Herzl Street, Rehovot 7610001 Israel
>> > Tel.: +972 58 444 2584 
>> > E-mail: francesca.strapp...@weizmann.ac.il
>> 
>> > > >
>> >
>> >
>> > ___
>> > 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/
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> 
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> 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
>> 

[Freesurfer] brainstemSsLabels.v10.mgz sub-labels (e.g., brainstem, pons, etc.) not included in mri_convert

[Jonathan Plasencia]

Hello Everyone,

I've run the Freesurfer 6.0 and created the sub-brainstem structures (e.g.,
pons, midbrain, etc.). I would like to convert the
brainstemSsLabels.v10.mgz results to a .nii file. However, unlike when I
use mri_convert for aseg.mgz, I only get an image of the brainstem itself
as a single intensity (or label) and not subparts (or labels for pons,
midbrain, etc.). Is there a way to get the labels for all sub-brainstem
parts included in the nii writeout, using mri_convert or another function
in freesurfer?

Best,

Jon
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[Freesurfer] Left and right white matter intensity ratio

[Sabrina Yu]

Hi there,

Would it be possible to use pctsurfcon to calculate the ratio of white matter 
signal intensity between left and right hemispheres?

Thank you
Sabrina
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dispose of the e-mail.

Re: [Freesurfer] Left and right white matter intensity ratio

[Douglas N Greve]

see if this tool is what you need. It allows you to map to the homolgous 
vertex on the contralateral hemisphere
http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi

On 12/03/2015 05:25 PM, Sabrina Yu wrote:
>
> Hi there,
>
>
> Would it be possible to use pctsurfcon to calculate the ratio of white 
> matter signal intensity between left and right hemispheres?
>
> Thank you
> Sabrina
>
>
> ___
> 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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] segmentation labels

[Lim, Lena]

Dear Experts,

I tried to run the following to get the segmentation volumes but encountered 
the errors below...  How can I get the volumes of the insula and thalamus and 
also the inferior prefrontal cortex please?

[spjwker@nanlnx2 FSL]1% asegstats2table --subjects PAC01... PAC70 --segno 9 48 
19 55 --tablefile aseg.vol.table
SUBJECTS_DIR : /home/spjwker_PAC/Lena/CT_SA/FSL
Parsing the .stats files
Building the table..
ERROR: cannot find the corresponding segmentation for the id:19 you provided
in any of the .stats files parsed

Many thanks,

Lena

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Re: [Freesurfer] Left and right white matter intensity ratio

[Sabrina Yu]

Hi Doug, 

Thanks for the quick reply. Is Xhemi only for measuring volumes for both 
hemispheres? 

https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg35097.html
You mentioned editing pctsurfcon to set white matter and gray matter in this 
email thread here. Can this be used to measure of white matter intensity for lh 
only, and then rh only? This email thread sounded promising for what I need, 
but am also unsure of how to input set wm and gm commands.

Thanks, 
Sabrina


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N Greve 

Sent: Thursday, December 3, 2015 2:31 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Left and right white matter intensity ratio

see if this tool is what you need. It allows you to map to the homolgous
vertex on the contralateral hemisphere
http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi

On 12/03/2015 05:25 PM, Sabrina Yu wrote:
>
> Hi there,
>
>
> Would it be possible to use pctsurfcon to calculate the ratio of white
> matter signal intensity between left and right hemispheres?
>
> Thank you
> Sabrina
>
>
> ___
> 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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Re: [Freesurfer] converting labels to MNI space

[Francesca Strappini]

Thank you Doug and Bruce now everything works and the region is
perfectly aligned!

Best
Francesca

2015-12-03 18:03 GMT+02:00 Douglas N Greve :

> oops, gave you the wrong option, it should be
>
> --regheader $SUBJECTS_DIR/mni152-recon/mri/orig.mgz
>
>
>
> On 12/03/2015 10:22 AM, Francesca Strappini wrote:
> > Thanks!
> >
> > I run this command:
> >
> > mri_label2vol --label lh.V1dorsalLG_MNI.label --temp
> > /usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz --regheader
> > /usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz --o
> > lh.V1dorsalLG_MNI.nii.gz
> >
> > but unfortunately, it gave me the same big downward shift (I checked
> > it with fslview).
> >
> > But if  I try to open the ROI with freeview it gives me this error:
> > freeview.bin: empty label
> > LabelRead failed
> > freeview.bin: empty label
> >
> > 2015-12-03 16:57 GMT+02:00 Douglas Greve  > >:
> >
> > Use --regheader /usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz
> > instead of --identity
> >
> >
> >
> > On 12/3/15 8:46 AM, Francesca Strappini wrote:
> >> Thank you!
> >>
> >> I run the recon-all on the MNI brain and now the first step,
> >> label2label, produced a label which is perfectly mapped on the
> >> surface of the MNI template.
> >> I tried to run the second step, mapping the new label to the
> >> volume, but I still got the shift downward.
> >>
> >> mri_label2vol --label lh.V1dorsalLG_MNI.label --temp
> >> /usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz --o
> >> lh.V1dorsalLG_MNI.nii.gz --identity
> >>
> >> Best
> >> Francesca
> >>
> >>
> >>
> >> 2015-12-01 20:26 GMT+02:00 Douglas N Greve
> >> >:
> >>
> >> Try adding --invertmtx to the mri_label2vol command. I don't
> >> think the
> >> label2label command does anything, does it? Also, you might
> >> have better
> >> alignment if you run recon-all on the mni152 brain, then use
> >> mri_label2label to map the label from the individual into the
> >> 152 space
> >> using the surface transform, then convert that to the volume.
> >>
> >> On 11/30/2015 10:13 AM, Francesca Strappini wrote:
> >> > Dear FreeSurfer experts,
> >> >
> >> > I'm trying to convert some retinotopic labels I created on
> >> the surface
> >> > of each individual subject to MNI305 space for FSL.
> >> >
> >> > I run the following commands, but the output is not registered
> >> > correctly. It seems to be shifted downward.
> >> >
> >> > mni152reg --s LG
> >> >
> >> > mri_label2label --srclabel lh.V1dorsalLG.label  --s LG
> >> --regmethod
> >> > surface --trglabel lh.V1dorsalLG_new.label --hemi lh
> >> >
> >> > mri_label2vol --label lh.V1dorsalLG_new.label --reg
> >> > /usr/local/freesurfer/subjects/LG/mri/mni152.orig.mgz.reg
> >> --temp
> >> > /usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz --o
> >> > lh.V1dorsalLG_new_MNI.nii.gz
> >> >
> >> > Thanks for your help,
> >> > Francesca
> >> >
> >> > --
> >> > Francesca Strappini, Ph.D.
> >> > Neurobiology Department
> >> > Weizmann Institute of Science
> >> > 234 Herzl Street, Rehovot 7610001 Israel
> >> > Tel.: +972 58 444 2584 
> >> > E-mail: francesca.strapp...@weizmann.ac.il
> >> 
> >> >  >> >
> >> >
> >> >
> >> > ___
> >> > 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/
> >>
> >> ___
> >> Freesurfer mailing list
> >> Freesurfer@nmr.mgh.harvard.edu
> >> 

Re: [Freesurfer] converting labels to MNI space

[Bruce Fischl]

glad it worked out
Bruce
On Thu, 3 Dec 2015, Francesca Strappini wrote:


Thank you Doug and Bruce now everything works and the region is perfectly 
aligned! 
Best
Francesca

2015-12-03 18:03 GMT+02:00 Douglas N Greve :
  oops, gave you the wrong option, it should be

  --regheader $SUBJECTS_DIR/mni152-recon/mri/orig.mgz



  On 12/03/2015 10:22 AM, Francesca Strappini wrote:
  > Thanks!
  >
  > I run this command:
  >
  > mri_label2vol --label lh.V1dorsalLG_MNI.label --temp
  > /usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz --regheader
  > /usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz --o
  > lh.V1dorsalLG_MNI.nii.gz
  >
  > but unfortunately, it gave me the same big downward shift (I checked
  > it with fslview).
  >
  > But if  I try to open the ROI with freeview it gives me this error:
  > freeview.bin: empty label
  > LabelRead failed
  > freeview.bin: empty label
  >
  > 2015-12-03 16:57 GMT+02:00 Douglas Greve  >:
  >
  >     Use --regheader /usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz
  >     instead of --identity
  >
  >
  >
  >     On 12/3/15 8:46 AM, Francesca Strappini wrote:
  >>     Thank you!
  >>
  >>     I run the recon-all on the MNI brain and now the first step,
  >>     label2label, produced a label which is perfectly mapped on the
  >>     surface of the MNI template.
  >>     I tried to run the second step, mapping the new label to the
  >>     volume, but I still got the shift downward.
  >>
  >>     mri_label2vol --label lh.V1dorsalLG_MNI.label --temp
  >>     /usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz --o
  >>     lh.V1dorsalLG_MNI.nii.gz --identity
  >>
  >>     Best
  >>     Francesca
  >>
  >>
  >>
  >>     2015-12-01 20:26 GMT+02:00 Douglas N Greve
  >>     >:
  >>
  >>         Try adding --invertmtx to the mri_label2vol command. I don't
  >>         think the
  >>         label2label command does anything, does it? Also, you might
  >>         have better
  >>         alignment if you run recon-all on the mni152 brain, then use
  >>         mri_label2label to map the label from the individual into the
  >>         152 space
  >>         using the surface transform, then convert that to the volume.
  >>
  >>         On 11/30/2015 10:13 AM, Francesca Strappini wrote:
  >>         > Dear FreeSurfer experts,
  >>         >
  >>         > I'm trying to convert some retinotopic labels I created on
  >>         the surface
  >>         > of each individual subject to MNI305 space for FSL.
  >>         >
  >>         > I run the following commands, but the output is not 
registered
  >>         > correctly. It seems to be shifted downward.
  >>         >
  >>         > mni152reg --s LG
  >>         >
  >>         > mri_label2label --srclabel lh.V1dorsalLG.label  --s LG
  >>         --regmethod
  >>         > surface --trglabel lh.V1dorsalLG_new.label --hemi lh
  >>         >
  >>         > mri_label2vol --label lh.V1dorsalLG_new.label --reg
  >>         > /usr/local/freesurfer/subjects/LG/mri/mni152.orig.mgz.reg
  >>         --temp
  >>         > /usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz --o
  >>         > lh.V1dorsalLG_new_MNI.nii.gz
  >>         >
  >>         > Thanks for your help,
  >>         > Francesca
  >>         >
  >>         > --
  >>         > Francesca Strappini, Ph.D.
  >>         > Neurobiology Department
  >>         > Weizmann Institute of Science
  >>         > 234 Herzl Street, Rehovot 7610001 Israel
>>         > Tel.: +972 58 444 2584 
>>         > E-mail: francesca.strapp...@weizmann.ac.il
>>         
>>         > >         >
>>         >
>>         >
>>         > ___
>>         > 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
>>         

Re: [Freesurfer] Left and right white matter intensity ratio

[Douglas Greve]

I guess I'm not sure what you are trying to do. Can you elaborate?

On 12/3/15 6:24 PM, Sabrina Yu wrote:
> Hi Doug,
>
> Thanks for the quick reply. Is Xhemi only for measuring volumes for both 
> hemispheres?
>
> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg35097.html
> You mentioned editing pctsurfcon to set white matter and gray matter in this 
> email thread here. Can this be used to measure of white matter intensity for 
> lh only, and then rh only? This email thread sounded promising for what I 
> need, but am also unsure of how to input set wm and gm commands.
>
> Thanks,
> Sabrina
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Douglas N Greve 
> 
> Sent: Thursday, December 3, 2015 2:31 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Left and right white matter intensity ratio
>
> see if this tool is what you need. It allows you to map to the homolgous
> vertex on the contralateral hemisphere
> http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
>
> On 12/03/2015 05:25 PM, Sabrina Yu wrote:
>> Hi there,
>>
>>
>> Would it be possible to use pctsurfcon to calculate the ratio of white
>> matter signal intensity between left and right hemispheres?
>>
>> Thank you
>> Sabrina
>>
>>
>> ___
>> 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/
>
> ___
> Freesurfer mailing list
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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 
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Re: [Freesurfer] Grey matter， white matter and CSF volumes

[Jinsong Tang]

Hello Doug,

Thank you so much for your help.

Best,

Jinsong

On Fri, Dec 4, 2015 at 1:28 AM, Douglas N Greve 
wrote:

> looks mostly right. For CSF there is a "CSF" label that should be
> included. For WM, you may or may not want to include brainstem.
>
> On 12/03/2015 12:20 PM, Jinsong Tang wrote:
> > Hello,
> >
> > I want to calculate the Grey matter, white matter and  CSF  volumes.
> >
> > The total gray matter volume is already in the ASEG file.
> >
> > Then
> > I add up following volumes for ventricular CSF: Left Lateral Ventricle
> > + Left Inferior Lateral Ventricle + Right lateral Ventricle  + Right
> > Inf Lateral Ventricle + 3rd Ventricle + 4th Ventricle + 5th Ventricle
> >  + Right choroids plexus + left choroids plexus.
> >
> > also,
> >
> >  I add up following volumes for white matter volume:
> >  CorticalWhiteMatterVol +Left-Cerebellum-White-Matter +
> > Right-Cerebellum-White-Matter.
> >
> > Are these right?
> >
> > Thanks,
> >
> > Jinsong
> >
> >
> > ___
> > 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
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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
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