[Freesurfer] Brain to skull distance

[yusif Al-kheder]

Hello,
Is it possible to use freesurfer to determine the distance between the skull 
and brain?

Youssif
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Re: [Freesurfer] Can we use fressurfer 6 with the Human connectome project's pipeline ?

[Matt Glasser]

Hi Bruce,

I don¹t think the hires T1w and T2w stuff are as accurate as 5.3 in the
HCP 0.7mm data that I have looked at (and as I recall at least one other
user had some similar issues, as did one of my collaborators), but that
was all I meant to refer to.  Sorry if my reply came across more general
than that, as of course we want to move to using FreeSurfer V6+ in the
future.  It is the highres T1w and T2w stuff that my pipelines are
designed to exploit, however.  Also there are some changes I have to make
to the HCP Pipelines for FreeSurfer V6+ because of differing file names,
etc.

Best,

Matt.

On 3/13/17, 9:40 PM, "Bruce Fischl"
 wrote:

>Hi Matt
>
>To state without qualification that "6.0 has some regressions as far as
>surface placement" is incorrect. We quantified its test-retest
>reliability, 
>accuracy and power to detect disease effects and all were improved
>relative 
>to 5.3. We tested V6 on hundreds of datasets across an array of
>pathologies 
>and different MR sequences, field strengths and scanners. We visually
>inspected dozens of brains multiple times in the process of improving
>accuracy and robustness. I can believe that on Wash U HCP data there
>could 
>be some specific issues, but to imply that V6 is generally less accurate
>is 
>simply incorrect.
>
>cheers
>Bruce
>
>
>On Mon, 13 Mar 2017, Matt Glasser wrote:
>
>> Not yet.  We are hoping FreeSurfer 6.1 will work nicely with the HCP
>> Pipelines.  For now version 6.0 has some regressions as far as surface
>> placement goes and there are also some adaptations we need to make to
>>the
>> pipelines.  
>> 
>> Peace,
>> 
>> Matt.
>> 
>> From:  on behalf of CAGNA
>>Bastien
>> 
>> Reply-To: Freesurfer support list 
>> Date: Monday, March 13, 2017 at 7:21 AM
>> To: "freesurfer@nmr.mgh.harvard.edu" 
>> Subject: [Freesurfer] Can we use fressurfer 6 with the Human connectome
>> project's pipeline ?
>> 
>> Dear freesurfer experts,
>> 
>> 
>> I'm wondering if it's possible to run the human connetome project's
>>minimal
>> processing pipeline using freesurfer 6 ?
>> 
>> 
>> Does it require some update of the pipeline or is there anybody that
>>have
>> already enjoyed the new freesurfer version with this pipeline ?
>> 
>> 
>> Thank you for your attention and your help,
>> 
>> Bastien Cagna
>> 
>> 
>> 
>> ___ Freesurfer mailing list
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>>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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>is
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>contains patient information, please contact the Partners Compliance
>HelpLine at
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>error
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>properly
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Re: [Freesurfer] Can we use fressurfer 6 with the Human connectome project's pipeline ?

[Bruce Fischl]

Hi Matt

To state without qualification that "6.0 has some regressions as far as 
surface placement" is incorrect. We quantified its test-retest reliability, 
accuracy and power to detect disease effects and all were improved relative 
to 5.3. We tested V6 on hundreds of datasets across an array of pathologies 
and different MR sequences, field strengths and scanners. We visually 
inspected dozens of brains multiple times in the process of improving
accuracy and robustness. I can believe that on Wash U HCP data there could 
be some specific issues, but to imply that V6 is generally less accurate is 
simply incorrect.


cheers
Bruce


On Mon, 13 Mar 2017, Matt Glasser wrote:


Not yet.  We are hoping FreeSurfer 6.1 will work nicely with the HCP
Pipelines.  For now version 6.0 has some regressions as far as surface
placement goes and there are also some adaptations we need to make to the
pipelines.  

Peace,

Matt.

From:  on behalf of CAGNA Bastien

Reply-To: Freesurfer support list 
Date: Monday, March 13, 2017 at 7:21 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Can we use fressurfer 6 with the Human connectome
project's pipeline ?

Dear freesurfer experts,


I'm wondering if it's possible to run the human connetome project's minimal
processing pipeline using freesurfer 6 ?


Does it require some update of the pipeline or is there anybody that have
already enjoyed the new freesurfer version with this pipeline ?


Thank you for your attention and your help,

Bastien Cagna



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Re: [Freesurfer] Can we use fressurfer 6 with the Human connectome project's pipeline ?

[Douglas Greve]

To augment Matt's comment, the v6.0 T1-only stream is more accurate and 
sensitive to than 5.3 according to our tests (both cortically and 
subcortically). I think Matt has found some examples where the T1+T2 
stream has some inaccurate placement. Matt, weren't you going to send me 
examples?


doug



On 3/13/17 5:09 PM, Matt Glasser wrote:
Not yet.  We are hoping FreeSurfer 6.1 will work nicely with the HCP 
Pipelines.  For now version 6.0 has some regressions as far as surface 
placement goes and there are also some adaptations we need to make to 
the pipelines.


Peace,

Matt.

From: > on behalf of CAGNA 
Bastien >
Reply-To: Freesurfer support list >

Date: Monday, March 13, 2017 at 7:21 AM
To: "freesurfer@nmr.mgh.harvard.edu 
" 
>
Subject: [Freesurfer] Can we use fressurfer 6 with the Human 
connectome project's pipeline ?


Dear freesurfer experts,


I'm wondering if it's possible to run the human connetome project's 
minimal processing pipeline using freesurfer 6 ?



Does it require some update of the pipeline or is there anybody that 
have already enjoyed the new freesurfer version with this pipeline ?



Thank you for your attention and your help,

Bastien Cagna



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Re: [Freesurfer] Error viewing corrected results

[Sahil Bajaj]

Hi Antonin,

This makes a good sense now. Now, my results are making more sense
with clustere_tstat_fwep.mgz,
where the cluster is very close to higher PCC values.

Thank you so very much Antonin all your help, patience and time in figuring
out all these issues :).

Thanks,
Sahil

On Fri, Mar 10, 2017 at 4:09 PM, Antonin Skoch  wrote:

> Dear Sahil,
>
> -approx tail and -twotail are completely different things:
>
> -approx tail switch on the tail approximation which speeds up the
> permutations.
>
> -twotail switch on two-sided hypothesis, without -twotail the hypothesis
> is only one-sided.
>
> It is reassuring that you see some clusters in _tstat_fwep.mgz now. I
> think that this starts to make sense: Since without -twotail there was no
> value in clustere_tstat_fwep.mgz, I think that your setup without -twotail
> was testing the opposite one-sided hypothesis.
>
> You have to decide which hypothesis you want to test. If you want to test
> one-sided hypothesis of negative correlation and use cluster forming
> threshold 0.05 (~ 1.3 in FreeSurfer -log10(p) convention), then I think you
> should invert sign of your contrast vector in Contrast.csv.
>
> With one-sided hypothesis you can modify your cluster-forming threshold to
> qnorm(1-10^-1.3)=1.643704 to be consistent with the mri_glmfit-sim
> behaviour.
>
> If you are testing two-sided hypothesis, your command line is I think
> almost OK, with following recommendations
>
> When not using -approx tail, I would increase number of permutations at
> least to 5000.
> Or add -approx tail and then you are running with tail approximation. Then
> you can retain -n 500 as Anderson recommended and your execution time would
> be much shorter.
>
> To report on cluster by use mri_surfcluster, you can use the code snippet
> I send in some of my earlier mails. You can also get cluster-wise p-value
> by loading the *clustere_tstat_fwep.mgz into freeview and clicking on the
> cluster. You can get cluster area by clicking on particular cluster in
> clustere_tstat.mgz.
>
> For visualization purposes Anderson mentioned that it is better to use
> -log10(p) (use the option -logp). Then you can interactively threshold your
> clusters according to the cluster-wise p-values (put 1.3 to min to hide
> clusters not significant at cluster-wise p=0.05).
> Do not forget to apply Bonferroni correction on your p-values when you
> analyze both hemispheres.
>
> To get *cope.mgz for the comparison, you should add -saveglm.
>
> As for comparison of F.mgh and dpv_tstat.mgh: F should be (approximately?)
> square of _tstat at the same vertex, if your contrast vector has one row.
> The correspondence should be (almost?) exact in orthogonal design (as I
> wrote previously, I got exact correspondence in my testing orthogonal
> design). I am not sure for non-orthogonal but I think that this should
> approximately also correspond, so -2 in dpv_tstat.mgh and 12 in F.mgh in
> the same vertex is maybe OK, but I am not sure.
>
> Antonin
>
>
>
> Hi Antonin,
>
> Just quick updates and few more points:
>
> (A) Earlier, I was using "-approx tail" in my PALM command and I was not
> getting any thing close to that big cluster but I noticed that you
> mentioned '-twotail' in your last email. So I replaced "-approx tail"
> with ''-twotail''
> so the command I am running now is:
>
> palm -i *.10.mgh -s fsaverage/surf/lh.white
> fsaverage/surf/lh.white.avg.area.mgh
> -d Xg.csv -t Contrast.csv -m mask.mgh -o Left_Hemi_results -C 1.95
> -twotail
> -n 500 -nouncorrected
>
> and I found that I can see a cluster when I view *_culstere_tstat_fwep or
> _dpv_tstat_fwep (both positive magnitude), which are very identical to
> sig.mgh (negative magnitude) from mri_glmfit and big cluster of very high
> negative PCC which I sent earlier.
>
> Here, I am sending you a screen of *_culstere_tstat_fwep, *_dpv_tstat_fwep
> and sig.mgh.
>
> Could you please confirm if thats correct? If so, I have few more
> questions:
> - When reporting about this cluster for publication, how can I find the
> size, annotation etc. of this cluster?
> - What 'min' and 'max' range of color bar would you recommend when
> reporting *_culstere_tstat_fwep results for the best view possible (at p <
> 0.05)?
>
> (B). Even though you said the matchings are valid for orthogonal design
> only, still I just check quickly and found that:
>
> 1. Here, I could not find any file with name: *cope.mgh
> 2. Here, clusters between F.mgh and *dpv_tstat.mgh are very similar but
> magnitude of dpv_tstat.mgh is very small and negative (~ -2) and of F.mgh
> is very high and positive (~ +12)
> 3. Here, magnitude of sig.mgh is roughly same as *dpv_tstat_uncp.mgh: both
> negative and similar big cluster (I am assuming that *dpv_tstat_uncp.mgh
> represents uncorrected p here and is same as *dpv_tstat.mgh, somehow I do
> not see *_uncp.mgh in my outputs).
>
> Thanks a lot for Antonin,
> Sahil
>
>
> On Fri, Mar 10, 2017 at 1:58 AM, Antonin Skoch  wrote:

Re: [Freesurfer] incorrect surfaces and aseg labeling in subject with large occipital horns of lateral ventricle

[Douglas N Greve]

Hi Antonin, where did you upload them to?


On 03/13/2017 05:51 PM, Antonin Skoch wrote:
> Dear experts,
>
> in my longitudinal study with 2 timepoints I encountered issue with 
> aseg.presurf labeling and white/pial surface estimation of one subject 
> in region of occipital horns of lateral ventricle. The voxels in horns 
> are mislabeled as either white or gray matter or contain zero values.
> I am still in the stage 1 of longitudinal stream, so this is classical 
> cross-sectional recon-all stream.
>
> I tried to reprocess this subject by using recon-all -s subj 
> -bigventricles -FLAIRpial (despite the fact that the subject does not 
> have generally enlarged ventricles I thought that this could help 
> nonlinear registration by mri_ca_register ). In case of timepoint 2 
> this helped to correctly label left occipital horn and corrected error 
> with surfaces, but right occipital horn remained labeled as white matter.
>
> In contrast, in case of timepoint 1 the -bigventricles did not help to 
> label left occipital horn and additionally new massive error with 
> white surface placement appeared in the region of occipital horn of 
> left lateral ventricle. See the attached screenshots to ilustrate this 
> issue:
>
> tp1_nobigventricles_surface_OK
> tp1_bigventricles_surface_error
> tp2_nobigventricles_surface_error
> tp2_bigventricles_surface_OK
>
> I have uploaded file 
> occipital_horn_ventricle_aseg_and_surf_error.tar.gz containing 4 
> recons (timepoint 1 and 2 with and withoug -bigventricles) to your server.
>
> I suppose that the root of the problem is incorrect nonlinear 
> registration. Could you please advise how to diagnose and solve the error?
>
> I am using development version from beginning of february 2017.
>
> Regards,
>
> Antonin Skoch
>
>
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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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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[Freesurfer] incorrect surfaces and aseg labeling in subject with large occipital horns of lateral ventricle

[Antonin Skoch]

Dear experts,

in my longitudinal study with 2 timepoints I encountered issue with 
aseg.presurf labeling and white/pial surface estimation of one subject in 
region of occipital horns of lateral ventricle. The voxels in horns are 
mislabeled as either white or gray matter or contain zero values.
I am still in the stage 1 of longitudinal stream, so this is classical 
cross-sectional recon-all stream.

I tried to reprocess this subject by using recon-all -s subj -bigventricles 
-FLAIRpial (despite the fact that the subject does not have generally enlarged 
ventricles I thought that this could help nonlinear registration by 
mri_ca_register ). In case of timepoint 2 this helped to correctly label left 
occipital horn and corrected error with surfaces, but right occipital horn 
remained labeled as white matter.

In contrast, in case of timepoint 1 the -bigventricles did not help to label 
left occipital horn and additionally new massive error with white surface 
placement appeared in the region of occipital horn of left lateral ventricle. 
See the attached screenshots to ilustrate this issue:

tp1_nobigventricles_surface_OK
tp1_bigventricles_surface_error
tp2_nobigventricles_surface_error
tp2_bigventricles_surface_OK

I have uploaded file occipital_horn_ventricle_aseg_and_surf_error.tar.gz 
containing 4 recons (timepoint 1 and 2 with and withoug -bigventricles) to your 
server.

I suppose that the root of the problem is incorrect nonlinear registration. 
Could you please advise how to diagnose and solve the error?

I am using development version from beginning of february 2017.

Regards,

Antonin Skoch
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Re: [Freesurfer] mri_vol2surf

[Douglas N Greve]

The file you created is not a label so don't try to load it with -label. 
Instead use -overlay file.mgh -fminmax .5 1



On 03/13/2017 05:40 PM, Redwan Maatoug wrote:
> Hi Douglas,
>
> Sorry to bother you, again.
> Actually, my command was t1 and not t2 but even with t1 nothing works.
> So if my command line is exact, do you think it is a problem with my 
> files ?
>
> Thank you,
>
> Redwan Maatoug
> Resident in psychiatry
> Stanford University
> Amit Etkin lab
>
> On 13 March 2017 at 13:41, Douglas N Greve  > wrote:
>
> Use --t1 (I assume the --tw was supposed to be --t2, which is
> wrong for
> that mni152 volume)
>
>
> On 03/09/2017 08:58 PM, Redwan Maatoug wrote:
> > Hi Douglas,
> >
> > Indeed you have already helped me !
> > Thank you for your help and for your time.
> >
> > I have tried  to do, as you said.
> > I have used  the brain image for the registration and then I have
> > tried to convert my ROI nifti volumetric file into a surface file
> > using this registration file.
> >
> > I do not know what is wrong with my command line and I tried
> many many
> > things.
> >
> > I have attached two files
> > (MNI152_T1_2mm_brain.nii is the brain file,
> > multdemand_MCC_SMA_thr50.nii.gz is the ROI file).
> >
> > I have tried the following commands :
> > 1) *bbregister --s fsaverage --mov MNI152_T1_2mm_brain.nii --reg
> > MNI152.dat --tw --init-coreg*
> >
> > 2) *mri_vol2surf --mov multdemand_MCC_SMA_thr50.nii.gz --reg
> > MNI152.dat --hemi lh --o ./multidem.mgh*
> >
> > I do not know if the output format .mgh is correct.
> > Anyway when I launch it with :
> > *tksurfer fsaverage lh inflated -label multidem.mgh*
> >
> > the multidem.mgh file does not appear.
> >
> > Thank you by advance for your advice,
> > Best,
> > Redwan
> >
> > On 9 March 2017 at 09:09, Douglas N Greve
> 
> >  >> wrote:
> >
> > didn't I respond to this earlier this week? the images
> appear to be
> > binarized regions of interest and not whole (or ever partial)
> > brain. To
> > run the registration, you will need an actual brain. If you
> > created the
> > ROI from a brain image, then use that image to create the reg,
> > then run
> > vol2surf using that reg with the ROI as input
> >
> >
> > On 03/07/2017 03:02 PM, Redwan Maatoug wrote:
> > > Hi experts,
> > >
> > > I try to convert my volumetric nifti file to surface files.
> > >
> > > My nifti volumetric file looks like : 1. screenshot
> > > I have first registered the volumetric file using bbregister
> > with this
> > > command line :
> > > *bbregister --s fsaverage --mov segment_7.nii --reg
> > segment_7.dat --t1
> > > --init-coreg*
> > >
> > > then I have used the following command line and the file
> looks like
> > > screenshot 1 attached :
> > > *tkregister2 --mov segment_7.nii --reg register7.dat --surf*
> > >
> > > And after that, I have tried to convert my volumetric file to
> > surface
> > > file with this command line :
> > >
> > > *mri_vol2surf --src segment_7.nii --srcreg register7.dat
> --hemi
> > lh --o
> > > ./segment_7-lh.nii --float2int round*
> > >
> > > But with this command when I load the file with freeview
> it does not
> > > work and with tkregister the file is empty.
> > >
> > > Or this one :
> > >
> > > *mri_vol2surf --src segment_7.nii --srcreg register7.dat
> --hemi
> > lh --o
> > > ./segment_7-lh.w --out_type paint --float2int tkregister*
> > >
> > > But with this command I have this warning :
> > > Warning: all vertex values are zero
> > >
> > > Could you please help me to convert my volumetric files
> because I am
> > > probably doing someting wrong. All my files come from an
> Atlas and I
> > > just need to convert them to surfaces files.
> > >
> > > Thank you for your help,
> > > Redwan
> > >
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> 
> >  >
> > >
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 

Re: [Freesurfer] mri_vol2surf

[Redwan Maatoug]

Hi Douglas,

Sorry to bother you, again.
Actually, my command was t1 and not t2 but even with t1 nothing works.
So if my command line is exact, do you think it is a problem with my files ?

Thank you,

Redwan Maatoug
Resident in psychiatry
Stanford University
Amit Etkin lab

On 13 March 2017 at 13:41, Douglas N Greve 
wrote:

> Use --t1 (I assume the --tw was supposed to be --t2, which is wrong for
> that mni152 volume)
>
>
> On 03/09/2017 08:58 PM, Redwan Maatoug wrote:
> > Hi Douglas,
> >
> > Indeed you have already helped me !
> > Thank you for your help and for your time.
> >
> > I have tried  to do, as you said.
> > I have used  the brain image for the registration and then I have
> > tried to convert my ROI nifti volumetric file into a surface file
> > using this registration file.
> >
> > I do not know what is wrong with my command line and I tried many many
> > things.
> >
> > I have attached two files
> > (MNI152_T1_2mm_brain.nii is the brain file,
> > multdemand_MCC_SMA_thr50.nii.gz is the ROI file).
> >
> > I have tried the following commands :
> > 1) *bbregister --s fsaverage --mov MNI152_T1_2mm_brain.nii --reg
> > MNI152.dat --tw --init-coreg*
> >
> > 2) *mri_vol2surf --mov multdemand_MCC_SMA_thr50.nii.gz --reg
> > MNI152.dat --hemi lh --o ./multidem.mgh*
> >
> > I do not know if the output format .mgh is correct.
> > Anyway when I launch it with :
> > *tksurfer fsaverage lh inflated -label multidem.mgh*
> >
> > the multidem.mgh file does not appear.
> >
> > Thank you by advance for your advice,
> > Best,
> > Redwan
> >
> > On 9 March 2017 at 09:09, Douglas N Greve  > > wrote:
> >
> > didn't I respond to this earlier this week? the images appear to be
> > binarized regions of interest and not whole (or ever partial)
> > brain. To
> > run the registration, you will need an actual brain. If you
> > created the
> > ROI from a brain image, then use that image to create the reg,
> > then run
> > vol2surf using that reg with the ROI as input
> >
> >
> > On 03/07/2017 03:02 PM, Redwan Maatoug wrote:
> > > Hi experts,
> > >
> > > I try to convert my volumetric nifti file to surface files.
> > >
> > > My nifti volumetric file looks like : 1. screenshot
> > > I have first registered the volumetric file using bbregister
> > with this
> > > command line :
> > > *bbregister --s fsaverage --mov segment_7.nii --reg
> > segment_7.dat --t1
> > > --init-coreg*
> > >
> > > then I have used the following command line and the file looks like
> > > screenshot 1 attached :
> > > *tkregister2 --mov segment_7.nii --reg register7.dat --surf*
> > >
> > > And after that, I have tried to convert my volumetric file to
> > surface
> > > file with this command line :
> > >
> > > *mri_vol2surf --src segment_7.nii --srcreg register7.dat --hemi
> > lh --o
> > > ./segment_7-lh.nii --float2int round*
> > >
> > > But with this command when I load the file with freeview it does
> not
> > > work and with tkregister the file is empty.
> > >
> > > Or this one :
> > >
> > > *mri_vol2surf --src segment_7.nii --srcreg register7.dat --hemi
> > lh --o
> > > ./segment_7-lh.w --out_type paint --float2int tkregister*
> > >
> > > But with this command I have this warning :
> > > Warning: all vertex values are zero
> > >
> > > Could you please help me to convert my volumetric files because I
> am
> > > probably doing someting wrong. All my files come from an Atlas and
> I
> > > just need to convert them to surfaces files.
> > >
> > > Thank you for your help,
> > > Redwan
> > >
> > >
> > >
> > > ___
> > > 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
> > 

Re: [Freesurfer] mri_surfcluster to obtain ROI (label) centroid MNI coordinates

[Douglas N Greve]

It turns out that setting --min to 0 causes a problem. Try setting it to 
something close to 0, eg 1e-6


On 03/09/2017 03:10 AM, Ladan Shahshahani wrote:
> Hi,
>
> Following previous discussions on the mailing list, I am using 
> mri_surfcluster to extract MNI (or Talairach) coordinates of a label 
> using:
>
> mri_surfcluster --in $SUBJECTS_DIR/fsaverage/surf/lh.area --clabel 
> lh.G_cingulate-Isthmus.label --sum ~/Desktop/pract3 --centroid --thmin 
> 0 --hemi lh --subject fsaverage --nofixmni
> I tried different labels, but for all of them I get the following 
> coordinates (for left hemisphere):
> -29.4  -22.0   17.4
>
> I see that others are having the same problem, like the one in the 
> following link:
> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2015-November/042446.html
>
> Am I missing something here?
> What can I do to solve this problem?
>
> Bests,
> Ladan
>
>
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Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] BUG: bbregister --init-best needs to unset InitCoreg

[Douglas N Greve]

just use mri_coreg -- that is the best!


On 03/13/2017 04:27 PM, Christopher Markiewicz wrote:
> Hi all,
>
> bbregister --init-best always produces "ERROR: cannot spec an init 
> method with --init-best", because InitCoreg is defined as 1 by 
> default, and never set to 0 by --init-best. (Setting something else 
> that unsets InitCoreg will trigger the same error.)
>
> Example, given SUBJ and EPI:
>
> $ bbregister --init-best --s $SUBJ --mov $EPI --o 
> ${EPI%.nii.gz}_bbr.nii.gz --reg ${EPI%.nii.gz}_bbr.dat
> ERROR: cannot spec an init method with --init-best
>
> Using FreeSurfer 6.0 release installed on an Ubuntu 16.04 machine.
>
> Thanks,
> Chris
>
>
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> Freesurfer@nmr.mgh.harvard.edu
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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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
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Re: [Freesurfer] Can we use fressurfer 6 with the Human connectome project's pipeline ?

[Matt Glasser]

Not yet.  We are hoping FreeSurfer 6.1 will work nicely with the HCP
Pipelines.  For now version 6.0 has some regressions as far as surface
placement goes and there are also some adaptations we need to make to the
pipelines.  

Peace,

Matt.

From:   on behalf of CAGNA Bastien

Reply-To:  Freesurfer support list 
Date:  Monday, March 13, 2017 at 7:21 AM
To:  "freesurfer@nmr.mgh.harvard.edu" 
Subject:  [Freesurfer] Can we use fressurfer 6 with the Human connectome
project's pipeline ?

Dear freesurfer experts,



I'm wondering if it's possible to run the human connetome project's minimal
processing pipeline using freesurfer 6 ?



Does it require some update of the pipeline or is there anybody that have
already enjoyed the new freesurfer version with this pipeline ?



Thank you for your attention and your help,

Bastien Cagna




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Re: [Freesurfer] mri_vol2surf

[Douglas N Greve]

Use --t1 (I assume the --tw was supposed to be --t2, which is wrong for 
that mni152 volume)


On 03/09/2017 08:58 PM, Redwan Maatoug wrote:
> Hi Douglas,
>
> Indeed you have already helped me !
> Thank you for your help and for your time.
>
> I have tried  to do, as you said.
> I have used  the brain image for the registration and then I have 
> tried to convert my ROI nifti volumetric file into a surface file 
> using this registration file.
>
> I do not know what is wrong with my command line and I tried many many 
> things.
>
> I have attached two files
> (MNI152_T1_2mm_brain.nii is the brain file, 
> multdemand_MCC_SMA_thr50.nii.gz is the ROI file).
>
> I have tried the following commands :
> 1) *bbregister --s fsaverage --mov MNI152_T1_2mm_brain.nii --reg 
> MNI152.dat --tw --init-coreg*
>
> 2) *mri_vol2surf --mov multdemand_MCC_SMA_thr50.nii.gz --reg 
> MNI152.dat --hemi lh --o ./multidem.mgh*
>
> I do not know if the output format .mgh is correct.
> Anyway when I launch it with :
> *tksurfer fsaverage lh inflated -label multidem.mgh*
>
> the multidem.mgh file does not appear.
>
> Thank you by advance for your advice,
> Best,
> Redwan
>
> On 9 March 2017 at 09:09, Douglas N Greve  > wrote:
>
> didn't I respond to this earlier this week? the images appear to be
> binarized regions of interest and not whole (or ever partial)
> brain. To
> run the registration, you will need an actual brain. If you
> created the
> ROI from a brain image, then use that image to create the reg,
> then run
> vol2surf using that reg with the ROI as input
>
>
> On 03/07/2017 03:02 PM, Redwan Maatoug wrote:
> > Hi experts,
> >
> > I try to convert my volumetric nifti file to surface files.
> >
> > My nifti volumetric file looks like : 1. screenshot
> > I have first registered the volumetric file using bbregister
> with this
> > command line :
> > *bbregister --s fsaverage --mov segment_7.nii --reg
> segment_7.dat --t1
> > --init-coreg*
> >
> > then I have used the following command line and the file looks like
> > screenshot 1 attached :
> > *tkregister2 --mov segment_7.nii --reg register7.dat --surf*
> >
> > And after that, I have tried to convert my volumetric file to
> surface
> > file with this command line :
> >
> > *mri_vol2surf --src segment_7.nii --srcreg register7.dat --hemi
> lh --o
> > ./segment_7-lh.nii --float2int round*
> >
> > But with this command when I load the file with freeview it does not
> > work and with tkregister the file is empty.
> >
> > Or this one :
> >
> > *mri_vol2surf --src segment_7.nii --srcreg register7.dat --hemi
> lh --o
> > ./segment_7-lh.w --out_type paint --float2int tkregister*
> >
> > But with this command I have this warning :
> > Warning: all vertex values are zero
> >
> > Could you please help me to convert my volumetric files because I am
> > probably doing someting wrong. All my files come from an Atlas and I
> > just need to convert them to surfaces files.
> >
> > Thank you for your help,
> > Redwan
> >
> >
> >
> > ___
> > 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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>  . If the e-mail was sent
> to you in 

[Freesurfer] BUG: bbregister --init-best needs to unset InitCoreg

[Christopher Markiewicz]

Hi all,

bbregister --init-best always produces "ERROR: cannot spec an init method
with --init-best", because InitCoreg is defined as 1 by default, and never
set to 0 by --init-best. (Setting something else that unsets InitCoreg will
trigger the same error.)

Example, given SUBJ and EPI:

$ bbregister --init-best --s $SUBJ --mov $EPI --o ${EPI%.nii.gz}_bbr.nii.gz
--reg ${EPI%.nii.gz}_bbr.dat
ERROR: cannot spec an init method with --init-best

Using FreeSurfer 6.0 release installed on an Ubuntu 16.04 machine.

Thanks,
Chris
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Re: [Freesurfer] Qdec effect sizes, correlation coefficient

[Douglas N Greve]

if you use the version 6 of mri_glmfit, it will automatically output the 
pcc.mgh file. If you want a cohen's D, then you can

cd glmdir/contrast

fscalc gamma.mgh div ../rstd.mgh -o cohensd.mgh



On 03/13/2017 01:45 PM, Juan Baldermann wrote:
> Dear all,
>
> I did a correlation analysis in qdec and now I want to report effect 
> sizes of my significant clustes. How can I extract a correlation 
> coefficient for this type of analyis? Or any other effect size? I saw 
> that i can derive them from the pcc.mgh file, but this somehow didn't 
> work in matlab...does the gamma.mgh file also have effect sizes per 
> cluster?
>
> Kind regards
> Carlos
>
>
> 
> Dr. med. Juan Carlos Baldermann
> Wissenschaftlicher Mitarbeiter, Assistenzarzt
> AG Neurobiologie und Neuromodulation psychischer Erkrankungen
> Klinik für Psychiatrie und Psychotherapie
> Universitätsklinikum Köln
> Kerpener Str. 62
> D - 50937 Köln
> Telefon: 0221- 478 86211
> Email: juan.balderm...@uk-koeln.de
> __
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Re: [Freesurfer] Report indicating aseg edits

[Douglas N Greve]

It does not, but you could make one easily enough, eg,

cd $SUBJCTS_DIR/subject/mri

fscalc aseg.auto.mgz sub aseg.manual.mgz -o aseg.diff.mgz

mri_binarize --i aseg.diff.mgz --min 0.5 --o aseg.diff.bin.mgz

mri_segstats --i aseg.diff.bin.mgz --accumulate --seg aseg.mgz 
--ctab-default --sum aseg.diffs.dat

The "mean" column will have the number of edits for that region has. For 
aseg.mgz you can pass it either the auto or the manual



On 03/13/2017 10:52 AM, Tamara Tavares wrote:
> Hello,
>
> I am currently checking and editing the aseg outputs in my 
> longitudinal data. I was wondering whether Freesurfer offers a report 
> indicating the edits I have made to aseg output.
>
> Thank you,
> Tamara
>
>
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Re: [Freesurfer] Extract the cortical thickness

[Douglas N Greve]

You can use aparcstats2table to report the thickness, surface area, and 
volume as a table from a group of subjects. Is that what you want?


On 03/13/2017 02:01 AM, Duy Nguyen wrote:
> Dear FreeSurfer expert
>
> I wonder that whether I can use the command aparc2statstable to get 
> the cortical thickness or is it better to get the cortical thickness 
> of a volume defined ROI or is there the easy way to get the most 
> accurate cortical thickness from ROI
>
> I am following the pipeline "VolumeRoiCorticalThickness" but I do not 
> understand how I can get ROI mask called ROI5.nii and TT_avg152T1.nii.
>
> Sorry if this question is too obvious for me to overlook something.
> Any help is appreciated since I am newbie on FreeSurfer.
> Best regards,
> *--v-- Peace --v--*
> *Duy Nguyễn *
> *Biomedical Engineering Department- IU HCMC*
> *Cell: (+84)90056*
> *Email: duy.nguyen...@gmail.com *
>
>
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Re: [Freesurfer] recon_all error on MacOS 10.12.13 Sierra: during mris_smooth. dyld: lazy symbol binding

[Daniela]

Hello,

Sorry for the late reply. I did try re-running it and it did work this
time! Thank you.


Daniela

On Mon, Mar 6, 2017 at 12:15 AM,   wrote:
> Hello Daniela,
>
> Ive been looking into this error, and although I am unable to replicate it
> on my Mac, I do have what might be a potential solution. Could you please
> source freesurfer, then run the following command.
>
>   $> sudo -E fs_update
>
> Then retry the subject with the parallel flag. Please let me know how it
> goes if you end up trying again. Thanks.
>
> -Zeke
>
>> I second the problem found in this thread:
>>
>> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51917.html
>>
>> I recently downloaded FreeSurfer v. 6 on a macOS 10.12. To work around the
>> System Integrity Protection issue, I installed my freesurfer folder in a
>> local "Documents" folder instead of in Applications and that seemed to
>> allow me to keep System Integrity Protection enabled while running
>> FreeSurfer commands.
>>
>> Last night I ran recon-all on the same subject simultaneously, one using
>> the -parallel tag and the other without it. This morning I see that only
>> the one with the -parallel tag exited with errors and it seems to be this
>> same "lazy symbol" error (see attached for recon-all error log).
>>
>> dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
>>   Referenced from:
>> /Users/Ajay/Documents/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
>>   Expected in: /usr/lib/libSystem.B.dylib
>>
>> I can try running with System Integrity Protection off to see if that will
>> make the -parallel tag work... any other thoughts?
>>
>>
>> Thanks,
>> Daniela
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[Freesurfer] Qdec effect sizes, correlation coefficient

[Juan Baldermann]

Dear all,

I did a correlation analysis in qdec and now I want to report effect sizes of 
my significant clustes. How can I extract a correlation coefficient for this 
type of analyis? Or any other effect size? I saw that i can derive them from 
the pcc.mgh file, but this somehow didn't work in matlab...does the gamma.mgh 
file also have effect sizes per cluster?

Kind regards
Carlos



Dr. med. Juan Carlos Baldermann
Wissenschaftlicher Mitarbeiter, Assistenzarzt
AG Neurobiologie und Neuromodulation psychischer Erkrankungen

Klinik für Psychiatrie und Psychotherapie
Universitätsklinikum Köln
Kerpener Str. 62
D - 50937 Köln
Telefon: 0221- 478 86211
Email: juan.balderm...@uk-koeln.de
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Re: [Freesurfer] How to cite freeview

[Bruce Fischl]

I guess just cite the "FreeSurfer" paper
On Mon, 13 Mar 2017, Luigi Antelmi 
wrote:

> Hello,
> what is the correct way to cite freeview in a papar for a manual rois 
> segmentation task?
> Thanks,
> Luigi.
> 
>
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Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 Cross and Long Streams

[David Semanek]

Thanks, I have uploaded the cross and long stream processing from one subject 
which requires numerous white matter edits to correct defects in the white 
matter surfaces; the file is on the ftp server as dsemanek.zip.

Both of the cross subject folders, s02_t1 and s02_t2 have had edits done to 
both the brainmask as well as the wm files, and autorecon2-wm and autorecon-3 
have been run on them, as well as the long folder for the first time point, 
s02_t1.long.s02_base.

It was in working with the rerun results of s02_t1.long.s02_base that I noticed 
the white matter surfaces after being regenerated with the edited wm.mgz did 
not reflect any of the edits. The easiest way to see this is to load the wm.mgz 
with the white matter surfaces and scroll through the slices, there are 
numerous areas where the contours of the white matter surfaces do not follow 
the voxels of the wm.mgz volume, mostly near what should be identified as 
hyperintense gray matter. I’m fairly certain the white matter surfaces didn’t 
change at all after running autorecon2-wm with the wm.mgz edits.

Thanks for taking a look at our data.

Best,

David P. Semanek, HCISPP
Research Technician, Posner Lab
Division of Child and Adolescent Psychiatry
Columbia University Medical Center
New York State Psychiatric Institute
1051 Riverside Drive, Pardes Bldg. Rm. 2424
New York, NY 10032
PH: (646) 774-5885
 
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On 3/12/17, 4:13 PM, "Bruce Fischl"  wrote:

Hi David

if you upload a subject to our ftp site and give us enough detail to
replicate what you tried we will take a look

cheers
Bruce
On Fri, 10 Mar 2017, David
Semanek wrote:

>
> Hello, I have worked quite a bit in the past with fs 5.3 on datasets which
> required a fair number of manual edits to the white matter volume in order
> to correct defects in the white matter surface. Typically, these edits 
take
> the form of removing voxels in the wm.mgz volume that have been 
incorrectly
> identified as white matter, usually near the pial surface caused by
> intensity artifacts resulting from motion. My experience in the past is 
that
> generating the white matter surface after edits to the wm.mgz volume will
> reliably change the geometry of the resulting surfaces.
>
>  
>
> However, on my current dataset, 1.5T adolescent brains with pervasive 
motion
> artifacts that do not meet the threshold for unusable data, absolutely no
> intervention I have done on the wm.mgz volume has any impact at all on the
> generation of the white matter surfaces. I am really very puzzled by this.
> All of the files that result from wm.mgz reflect the edits, however the 
aseg
> does not.
>
>  
>
> The resulting white matter surfaces always follow the aseg white matter
> definitions and never the wm.mgz edits. I feel as if there might be
> something I am missing but this protocol has reliably been used to do 
white
> matter edits in the past. I thought it may be an issue with fs 6 or the 
long
> stream, but I have tried the same edits in 5.3, 6, long and cross streams
> and nothing at all has worked.
>
>  
>
> Does anyone have any suggestions, or perhaps a hint that I am overlooking
> something common?
>
>  
>
> Thanks,
>
>  
>
> David P. Semanek, HCISPP
>
> Research Technician, Posner Lab
>
> Division of Child and Adolescent Psychiatry
>
> Columbia University Medical Center
>
> New York State Psychiatric Institute
>
> 1051 Riverside Drive, Pardes Bldg. Rm. 2424
>
> New York, NY 10032
>
> PH: (646) 774-5885
>
>  
>
> IMPORTANT NOTICE:  This e-mail is meant only for the use of the intended
> recipient.  It may contain confidential information which is legally
> privileged or otherwise protected by law.  If you received this e-mail in
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[Freesurfer] Report indicating aseg edits

[Tamara Tavares]

Hello,

I am currently checking and editing the aseg outputs in my longitudinal
data. I was wondering whether Freesurfer offers a report indicating the
edits I have made to aseg output.

Thank you,
Tamara
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Re: [Freesurfer] Intensity normalization in longitudinal processing

[Jaiashre Sridhar]

Bruce,

We had previously addressed an issue with creating the bases from 5 timepoints 
in v5.1 where mri_robust_register failed. We were advised by Dr. Martin Reuter 
to either replace mri_robust_register & mri_robust_template binary with the 
ones from v5.3 or to run all the bases and longs in v5.3. We chose to run the 
longitudinal stream in v6.0 as it was released by then.
If it is not safe to mix versions (cross in v5.1; base-long in v6.0), could you 
clarify if it is alright to just use the binaries from v5.3/v6.0?

Thank you very much,
Jaiashre.
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Re: [Freesurfer] WM/pial edits

[Octavian Lie]

Dear All,


Please advise. Some of the dural enclosure defects involve both wm and pia
surfaces (wm/pia extending to dura), so in those cases, correcting pia will
also touch the wm. Editing wm in wm.mgz and running recon-all
-autorecon2-wm -autorecon3 ameliorates but does not solve the wm defect
issue (some wm in some places still extending (albeit less) outside to
encompass some dural segments). At this point, to options I see are:
- to edit brainmask.mgz for pial surface, but because wm will be touched by
this correction, to run the whole -autorecon2 -autorecon 3
- to edit brain.finalsurfs.mgz for pial, then run -autorecon -pial, but I
do not know what this does to wm since wm is upstream.

Thank you,

Octavian









On Fri, Mar 10, 2017 at 9:51 AM, Bruce Fischl 
wrote:

> Hi Octavian
>
> if you want to regenerate the pial surface you have to run autorecon3 also.
>
> And I don't think you want to edit the wm.mgz for wm edits. Probably you
> should edit brain.finalsurfs.mgz for both wm and pial. Can someone who has
> done more recent recons than I have confirm this?
>
> cheers
> Bruce
>
>
>
> On Thu, 9 Mar 2017, Octavian Lie wrote:
>
> Dear All,
>>
>> A simple issue of precedence. In the recon-all pipeline, wm edits take
>> precedence to pial edits.
>> If there are both wm and pial defects, should one apply edits
>> sequentially,
>> say on brainmask.mgz (first wm edits, rerun recon-all say recon-all
>> -autorecon2 -wm, then do pial edits, rerun recon-all say recon-all
>> -autorecon2 -pial) or to some extent pial edits influence the final
>> surface
>> generation in conjunction to wm edits (understood that the latter may
>> influence more the final form than the former -pial- edits), in that case
>> one may do both edits, then run -autorecon2 -wm only.
>>
>> Please advise,
>> Octavian
>>
>>
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Re: [Freesurfer] Error recon-all program quits at mri_nu_correct

[Z K]

Freesurfer v5.3 will fail at the mri_nu_correct.mni command on newer Linux 
distributions (that come with perl version 5.22 and higher) due to an 
incompatibility with the mni tools shipped with FreeSurfer and newer versions 
of perl. The issue has been fixed in the latest release of freesurfer. 

> On Mar 13, 2017, at 7:01 AM, David WALTER  wrote:
> 
> Hello FreeSurfer Developers,
>  
> I’m trying with an engineer to launch a recon-all command but it seems to 
> fail and I don’t find any verbose logs to help me to understand what is the 
> problem.
> 
> Please find in attachment all the logs I have and we are on CentOS 6.8
>  
> Thanks for your help
>  
> --
> David WALTER
> The computer guy
> david.wal...@ens.fr
> 01/44/32/27/94
>  
> INSERM U960
> Laboratoire de Neurosciences Cognitives
> Ecole Normale Supérieure
> 29, rue d'Ulm
> 75005 Paris
>  
> 
> 
> 
> 
> 
> 
> 
> 
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[Freesurfer] How to cite freeview

[Luigi Antelmi]

Hello,
what is the correct way to cite freeview in a papar for a manual rois
segmentation task?
Thanks,
Luigi.
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[Freesurfer] Can we use fressurfer 6 with the Human connectome project's pipeline ?

[CAGNA Bastien]

Dear freesurfer experts,


I'm wondering if it's possible to run the human connetome project's minimal 
processing pipeline using freesurfer 6 ?


Does it require some update of the pipeline or is there anybody that have 
already enjoyed the new freesurfer version with this pipeline ?


Thank you for your attention and your help,

Bastien Cagna


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[Freesurfer] Extract the cortical thickness

[Duy Nguyen]

Dear FreeSurfer expert

I wonder that whether I can use the command aparc2statstable to get the
cortical thickness or is it better to get the cortical thickness of a
volume defined ROI or is there the easy way to get the most accurate
cortical thickness from ROI

I am following the pipeline "VolumeRoiCorticalThickness" but I do not
understand how I can get ROI mask called ROI5.nii and TT_avg152T1.nii.

Sorry if this question is too obvious for me to overlook something.
Any help is appreciated since I am newbie on FreeSurfer.
Best regards,
*--v-- Peace --v--*
*Duy Nguyễn *
*Biomedical Engineering Department- IU HCMC*
*Cell: (+84)90056*
*Email: duy.nguyen...@gmail.com *
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