Re: [Freesurfer] xhemi label

[Marissa Pifer]

Hi Doug,

I'm not sure how to use this binary. Do I need to install it?

Marissa

On Fri, Mar 17, 2017 at 12:23 PM, Douglas N Greve  wrote:

> Are you using v5.3? You will need a version 6. You can get this binary
> for v6 here
>
> https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_apply_reg
>
>
> On 03/17/2017 11:47 AM, Marissa Pifer wrote:
> >
> > Marcs-MacBook-Pro:SRMC01-1 marchaut$ mris_apply_reg --src-label
> > label/rh.V1_exvivo.thresh.label --trg rh-on-lh.V1_exvivo.thresh.label
> > --streg xhemi/surf/lh.fsaverage_sym.sphere.reg
> > surf/lh.fsaverage_sym.sphere.reg
> >
> > ERROR: Option --src-label unknown
> >
> >
> >
> > On Fri, Mar 17, 2017 at 11:26 AM, Douglas Greve
> > mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >
> > please send command line
> >
> >
> > On 3/17/17 10:38 AM, Marissa Pifer wrote:
> >> Hi freesurfers,
> >>
> >> I am using xhemi to map the right hemisphere of each subject to
> >> the left hemisphere of the same subject. The first xhemi command
> >> works fine, but the 2nd step for mapping the label, I get this
> >> error: "Option --src-label unknown"
> >>
> >> Do you know how to fix this?
> >>
> >> Marissa
> >>
> >>
> >> ___
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> >> 
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >> 
> > ___ Freesurfer mailing
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> >  The
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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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[Freesurfer] Running recon-all with FLAIR / MRISread(../surf/lh.white.preaparc): could not open file

[Veronica Munoz]

Dear all,

I'm trying to add FLAIR data to a subject. I did the first ("classic") 
recon-all on a platform so I get the following warnings:


INFO: FreeSurfer build stamps do not match
Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

INFO: current FREESURFER_HOME does not match that of previous processing.
Current: /home/munoz/Documents/freesurfer
Previous: 
/tmp/wrk/DIRAC_piXnbapilot/50587390/recon-all.sh-445574845579047/freesurfer


Then recon all exits with the following error:

#@# Jacobian white lh Tue Mar 21 12:25:24 CET 2017
/media/sf_C_DRIVE/Users/munoz/Documents/Stage_FLI/results/FLAIRtest/AC_005/scripts

 mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg 
../surf/lh.jacobian_white


reading surface from ../surf/lh.white.preaparc...
MRISread(../surf/lh.white.preaparc): could not open file
No such file or directory
mris_jacobian: could not read surface file ../surf/lh.white.preaparc
No such file or directory
Linux iu-dv-464-vm.creatis.insa-lyon.fr 4.9.7-201.fc25.x86_64 #1 SMP Thu 
Feb 2 23:32:42 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux


Does this have something to do with my current Freesurfer version ? I 
don't really know what information does "preaparc" contain.


Thank you for your help.

Best regards,

Veronica
veronica.mu...@creatis.insa-lyon.fr 


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[Freesurfer] White matter volume in each lobe

[Ahearn, T]

Hello
I need separate grey and white volumes for the frontal and temporal lobes. I 
have values for grey volume from

mri_annotation2label --subject 01 --hemi lh --lobesStrict lobar_annotation
mris_anatomical_statson the  lh.lobar_annotation.annot file to generate a 
text file.


I've also run similar to the following and now have a text file 
wmparc.a2009.stats.

mri_aparc2aseg --s subject --labelwm --hypo-as-wm --rip-unknown
--volmask --o mri/wmparc.a2009s.mgz --a2009s --ctxseg aparc.a2009s+aseg.mgz

  mri_segstats --seg mri/wmparc.a2009s.mgz --sum
stats/wmparc.a2009s.stats --pv mri/norm.mgz --excludeid 0
--brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz
--in-intensity-name norm --in-intensity-units MR --subject subject
--surf-wm-vol
--ctab $FREESURFER_HOME/WMParcStatsLUT.txt --etiv


Is there a standard list of labels in this file that are used to create the 
frontal and temporal lobes?


Thanks




The University of Aberdeen is a charity registered in Scotland, No SC013683.
Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. 
SC013683.
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[Freesurfer] white matter volumes for frontal and temporal lobes

[Ahearn, T]

Hello
I need separate grey and white volumes for the frontal and temporal lobes. I 
have values for grey volume from the following...

mri_annotation2label --subject 01 --hemi lh --lobesStrict lobar_annotation
mris_anatomical_statson the  lh.lobar_annotation.annot file to generate a 
text file.


I've also run similar to the below  and now have a text file wmparc.a2009.stats.

mri_aparc2aseg --s subject --labelwm --hypo-as-wm --rip-unknown
--volmask --o mri/wmparc.a2009s.mgz --a2009s --ctxseg aparc.a2009s+aseg.mgz

  mri_segstats --seg mri/wmparc.a2009s.mgz --sum
stats/wmparc.a2009s.stats --pv mri/norm.mgz --excludeid 0
--brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz
--in-intensity-name norm --in-intensity-units MR --subject subject
--surf-wm-vol
--ctab $FREESURFER_HOME/WMParcStatsLUT.txt --etiv


Is there a standard list of labels in this file that are used to create the 
frontal and temporal lobes?


Thanks
Trev



The University of Aberdeen is a charity registered in Scotland, No SC013683.
Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. 
SC013683.
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Re: [Freesurfer] Running recon-all with FLAIR / MRISread(../surf/lh.white.preaparc): could not open file

[Bruce Fischl]

Hi Veronica

it's because you are mixing versions. Can you rerun your subject with 
6.0 from scratch?


cheers
Bruce
On Tue, 21 Mar 2017, Veronica Munoz wrote:


Dear all,

I'm trying to add FLAIR data to a subject. I did the first ("classic")
recon-all on a platform so I get the following warnings:

INFO: FreeSurfer build stamps do not match
Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

INFO: current FREESURFER_HOME does not match that of previous processing.
    Current: /home/munoz/Documents/freesurfer
    
Previous:/tmp/wrk/DIRAC_piXnbapilot/50587390/recon-all.sh-445574845579047/freesurfer


Then recon all exits with the following error:

#@# Jacobian white lh Tue Mar 21 12:25:24 CET 2017
/media/sf_C_DRIVE/Users/munoz/Documents/Stage_FLI/results/FLAIRtest/AC_005/
scripts

 mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg
../surf/lh.jacobian_white

reading surface from ../surf/lh.white.preaparc...
MRISread(../surf/lh.white.preaparc): could not open file
No such file or directory
mris_jacobian: could not read surface file ../surf/lh.white.preaparc
No such file or directory
Linux iu-dv-464-vm.creatis.insa-lyon.fr 4.9.7-201.fc25.x86_64 #1 SMP Thu Feb
2 23:32:42 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux

Does this have something to do with my current Freesurfer version ? I don't
really know what information does "preaparc" contain.

Thank you for your help.

Best regards,

Veronica
veronica.mu...@creatis.insa-lyon.fr



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Re: [Freesurfer] display SPM results on inflated surface?

[Schoot, Lotte]

Hi Doug and others,

A while ago, I got this reply to my question below (thanks!). I tried to look 
in to it, but I am a bit confused (probably because I am very new to 
Freesurfer).
My results are on the MNI 152, but I don't understand what you mean with 'run 
the mni152 through freesurfer'. Is this the process to get the register.dat 
file that is required in mri_vol2surf?
What would you recommend to get the register.dat file? Is it possible to use 
bbregister for that? I have tried this, but I don't know whether it is correct:

bbregister --s fsaverage --mov con_0001.nii --init-spm --reg register.dat --bold


Thanks!
Lotte


>If your results are on the MNI152, you can run the mni152 through
>freesurfer, then use mri_vol2surf to map the data to the surface then
>view it with freeview (or tksurfer). You should not confuse this with
>doing the fMRI analysis on the surface. You will not have the benefits
>of surface-based analysis


On 02/15/2017 03:37 PM, Schoot, Lotte wrote:
> Hi all,
>
> I was wondering if you knew of a way to display SPM results onto the
> inflated surface in Freesurfer.
>
> I have tried using SurfRend but there seem to be problems which might
> be due to the fact the results are obtained with SPM12 and SurfRend
> was designed to work with SPM5.
>
> Thanks,
> Lotte
>
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve at 
nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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[Freesurfer] Custom brain segmentation to equal sized regions

[david . kamson]

Freesurfers,

Is there a way to segment each hemisphere to an identical number of equal
sized regions which are as close in size and location as possible to their
contralateral homotopic regions.
Eg. I’d like to segment the left hemisphere to regions with a 2 cm2
surface and do the same for the right in order to compare asymmetries in
these small regions. Anybody had done this before?

David

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Re: [Freesurfer] Custom brain segmentation to equal sized regions

[Bruce Fischl]

Hi David

mris_make_face_parcellation can do what you want for the cortex. If you use 
the sphere used for cross-hemisphere registration as input I think 
(Hopefully Doug  can tell us what it is called)

cheers
Bruce




On 
Tue, 21 Mar 2017, david.kam...@pet.wayne.edu wrote:

> Freesurfers,
>
> Is there a way to segment each hemisphere to an identical number of equal
> sized regions which are as close in size and location as possible to their
> contralateral homotopic regions.
> Eg. I?d like to segment the left hemisphere to regions with a 2 cm2
> surface and do the same for the right in order to compare asymmetries in
> these small regions. Anybody had done this before?
>
> David
>
> ___
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>
>
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[Freesurfer] [FSL] Re Orient image from AP to PA axis

[Dev vasu]

Dear all,

I would like to if there is any procedure to reorient the image ( flip )
from AP axis to PA , I have around 50 scans all of which are scanned in A/P
axis and i would like to reorient them , kindly please let me know if there
is any procedure.

I tried mri_convert and orient_mri is freesurfer but i could not see any
changes


Thanks
Vasudev
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[Freesurfer] Hippocampal Subfields Posterior Probability

[Bharadwaj, Pradyumna - (prad)]

Hello Dr. Iglesias,


I'm currently examining the distributions of the posterior probabilities of the 
different hippocampal subfields, and I'm interested in obtaining the 
probability distribution images for the subfields that correspond to the 
volumes output in the subjects text file.


While I can use mri_binarize on ?h.hippoSfLabels-T1.v10.mgz to obtain the 
subfield masks and use them to obtain the posterior probabilities distribution 
after soft segmentation,

is there some other straighforward way to obtain these posterior probabilities 
for the volumes stated in the output text file ?


A follow up question - It appears that the soft segmentation approach 
approximates thresholding the posteriors by a value around 0.5 ? In your 
opinion, is this value acceptable and have you found similar values in your 
testing ?


Thanks!

-Prad


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Re: [Freesurfer] Hippocampal Subfields Posterior Probability

[Iglesias Gonzalez, Eugenio]

Dear Prad,
There is a “secret” way of getting the posteriors. You need to set the 
environment variable WRITE_POSTERIORS to 1 before you call recon-all.
In (t)csh:
setenv WRITE_POSTERIORS 1
In bash:
export WRITE_POSTERIORS=1
And then call recon-all -hippocampal-subfields-T1(T2) as usual.

The discrete segmentation picks, for each voxel, the most likely label. The 
posterior of this label might or might not be above 0.5. For instance, if a 
voxel has p=0.4 of being CA1, p=0.3 of being background, and p=0.3 of being 
fimbria, it will be labeled as CA1 (even though p<0.5 for such subfield). Some 
people seem to prefer a 2-stage approach, in which a hippocampal mask is first 
created by selecting the voxels for which p(background)<0.5, and then each 
voxel within that mask is colored with the most likely subfield at that 
location.

I hope this helps!

Cheers,

/Eugenio



Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 21 Mar 2017, at 20:09, Bharadwaj, Pradyumna - (prad) 
mailto:p...@email.arizona.edu>> wrote:

Hello Dr. Iglesias,

I'm currently examining the distributions of the posterior probabilities of the 
different hippocampal subfields, and I'm interested in obtaining the 
probability distribution images for the subfields that correspond to the 
volumes output in the subjects text file.

While I can use mri_binarize on ?h.hippoSfLabels-T1.v10.mgz to obtain the 
subfield masks and use them to obtain the posterior probabilities distribution 
after soft segmentation,
is there some other straighforward way to obtain these posterior probabilities 
for the volumes stated in the output text file ?

A follow up question - It appears that the soft segmentation approach 
approximates thresholding the posteriors by a value around 0.5 ? In your 
opinion, is this value acceptable and have you found similar values in your 
testing ?

Thanks!
-Prad


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[Freesurfer] PETsurfer surface based analysis

[miracle ozzoude]

Hello,
I am working through the PETsurfer surface based analysis and i have couple
of question
a) Since the procedure is the same as surface based analysis for cortical
thickness except mri_vol2surf, Can I use the procedure for thickness?
b) What is the difference between mris_preproc and mri_concat. If I use
mris_preproc, do I also need to use mri_concat? Also, can I use
mris_preproc instead of mri_concat?
c) Can I use mri_surf2surf in place of mris_fwhm? If no, why?
d) While researching PETsurfer surface based analysis in the forum, I came
across multiple trends that used the "--projfrac" flag in both mri_vol2surf
command and mris_preproc command. At what stage should I include this flag
and why?
e) If I want to perform a multimodal analysis using thickness&PET or
Surface area&PET, Can anyone confirm if this is the correct steps.

   - Perform surface base analysis for cortical thickness from step 1
   (mris_preproc) to correction for multiple comparison
   - Perform PET surface based analysis from step 1 (gtmseg) to step 5.
   While conducting mri_glmfit, include the smoothed thickness map
   (?h.thickness.10B.mgh) as pvr (per vertex regressor)
   - e.g. mri_glmfit --y lh.pet.10.mgh --fsgd your.fsgd dods --pvr
   lh.thickness.10B.mgh --C contrast.mtx --surf fsaverage lh --cortex --glmdir
   pvr.lh.pet.thickness.glmdir
   - Lastly, build a new monte carlo correction for multiple comparison.

Thank you
Best,
Paul
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[Freesurfer] [FSL or FREESURFER] SIEMENS FIELDMAP B0 UNWARPING FOR DTI

[VA Research]

Hello FSL and FS pros,

I am trying to pre process DW images but am not sure how to unwarp images.

We are using Siemens Skyra 3T and output fieldmaps;

2 files output from the scanner;
the first file contains two magnitude files in one
the second file contains the single phase difference image

---
FSL
---


through FSL we have run
eddy correct, bet the magnitude file, and run fsl prepare fieldmap
(example code below)

I am not sure how to use the prelude and FUGUE command and am unclear on
their inputs/outputs

Does anyone in FSL land have a clear tutorial of how to utilize these tools?

for example, given my type of fieldmaps do i need to use prelude?

later through FSL stream we would like to complete
bet preprocessed DW images, dtifit, bedpostx


FREESURFERS

I have read over the TRACULA requirements and how to edit the configuration
files.

There is mention of eddy current correction that is available through
tracula but nothing mentioned for dealing with the warping issue.

Does anyone in freesurfer land have any suggestions on how to tackle this
as a part of the tracula data stream?


Any input will be appreciated,
Thanks so much

Joseph Veliz
Brentwood Biomedical Research
VA Hospital West Los Angeles



example

#Eddy correction
eddy_correct ${name}_dti.nii.gz
/Users/seahorse/Studies/NN/DTI/${name}/${name}DTI_eddy.nii.gz 0

#BET fieldmap mag super tight; exclude all non brain voxels
bet 10001_dtiFMmag1mag2.nii.gz
/Users/seahorse/Studies/NN/DTI/10001/10001dtimags_brain.nii.gz -F -m -f 0.85

#generate fieldmap in rad/s for FEAT or FUGUE
fsl_prepare_fieldmap SIEMENS 10001_dtiFMphase.nii.gz
10001dtimags_brain.nii.gz fmap_rads 2.46

#Prelude
prelude -c data --unwrap=result
prelude --complex=data -u result

#FUGUE Utility for Geometrically Unwarping EPIs; performs unwarping of an
EPI image based on fieldmap data
fugue -i epi -p unwrappedphase --dwell=dwelltime --asym=asymtime -s
0.5 -u result
fugue -i epi --dwell=dwelltime --loadfmap=fieldmap -u result
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[Freesurfer] question about "mean curvatura"

[李慧]

Dear FreeSurfer Group,


Sorry for interrupting.


I am Hui Li, a researcher fron Beijing, China, interesting in sMRI of mind 
disorder. Recently, I am working on some data about schizophrenia. I compared 
the patients and healthy controls, and found that the main difference between 
these two groups is the index of "meancurv". So I searched online for the 
papers described "meancurv" of using FreeSurfer package, however, most of the 
papers reported an index---gyrificaiton, some of the gyrificaiton was 
calculated from "absoult mean curvatura", for example articles from Dr. Luders 
(A curvature-based approach to estimate local gyrification on the cortical 
surface, NeuroImage, 2006, 29, 1224). Then I looked for how to calculate 
"meancurv" in FreeSurfer, I found that "The curvature in general is measured as 
1/r, where r is the radius of an inscribed circle. Since mean curvature is the 
average of the two principal curvatures it has the units of 1/mm. The Gaussian 
curvature is the product of them, so it is 1/mm^2". I am confused about these 
two concepts of "mean curvatura", could you help me to understand the "mean 
curvatura" in FreeSurfer? What is the biological meaning of this index, does it 
share the same anatomical meaning with Dr. Luders'? Could I use "mean 
curvatura" from FreeSurfer represent Gyrification Index?


Thanks all of you so much.


Hui Li

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