Re: [Freesurfer] Use of PVC PET images (V6) : between versions compatibility and intensity normalisation

[Matthieu Vanhoutte]

Dear Douglas,

Just one more question : by default mri_gtmpvc uses pons for computing rSUV,
but is this intensity normalization done before or after partial volume
correction ? What file is used in input for intensity normalization ?

Thanks in advance !

Best regards,
Matthieu

2015-12-18 18:26 GMT+01:00 Douglas Greve :

> You'll see several files that begin with mgx:
> mgx.ctxgm.nii.gz - pvc'ed cortex gm only
> mgx.subctxgm.nii.gz - pvc'ed subcortical gm only
> mgx.gm.nii.gz - pvc'ed all gm
>
>
> On 12/18/15 6:08 AM, Matthieu Vanhoutte wrote:
>
> Hello Douglas,
>
> I have run mri_gtmpvc with static PET images using the following command :
> mri_gtmpvc --i PET.nii.gz --psf 6 --auto-mask 8 0.01 --seg gtmseg.mgz
> --reg register.dof6.lta --default-seg-merge --mgx 0.01 --o gtmpvc.output
>
> In the output directory "gtmpvc.output" where is the partial volume
> corrected PET image ?
>
> Thanks !
>
> Best regards,
> Matthieu
>
> 2015-12-15 21:07 GMT+01:00 Douglas N Greve :
>
>> Not necessarily. It needs a good segmentation, so, to the extent that v6
>> has a better segmentation then v6 is better.
>>
>> On 12/15/2015 02:57 PM, Matthieu Vanhoutte wrote:
>> >
>> > Thanks Douglas for the answer !
>> >
>> > But isn't PVC design for better working in terms of results with
>> > v6_beta than v5.3 ?
>> >
>> > Best regards,
>> >
>> > Matthieu
>> >
>> > Le 15 déc. 2015 19:02, "Douglas N Greve" < 
>> gr...@nmr.mgh.harvard.edu
>> > > a écrit :
>> >
>> > It is not subsegmented in 6.0 either:). When you run gtmseg, it will
>> > create the new segmentation that include pons and a few other things
>> >
>> > On 12/15/2015 12:56 PM, Matthieu Vanhoutte wrote:
>> > > Dear Douglas,
>> > >
>> > > Please see below :
>> > >
>> > > 2015-12-15 18:37 GMT+01:00 Douglas N Greve
>> > 
>> > > > > gr...@nmr.mgh.harvard.edu>>>:
>> > >
>> > >
>> > >
>> > > On 12/15/2015 04:46 AM, Matthieu Vanhoutte wrote:
>> > > > Dear experts,
>> > > >
>> > > > Could anyone answer to my questions below ?
>> > > >
>> > > > Thanks !
>> > > >
>> > > > Best regards,
>> > > > Matthieu
>> > > >
>> > > > 2015-12-10 10:10 GMT+01:00 Matthieu Vanhoutte
>> > > > > > 
>> > > > > >
>> > > > > 
>> > > > > > > > >
>> > > > Dear FS experts,
>> > > >
>> > > > 1) First Is it possible to use the partial volume
>> > correction
>> > > > provided in the v6 beta version of FreeSurfer despite
>> > the fact
>> > > > that recon-all have been done for all subjects with
>> > the v5.3 ?
>> > > >
>> > > Yes
>> > >
>> > >
>> > > Great ! but isn't it a problem for computing rSUV with pons as
>> > > reference structure since brainstem isn't sub-segmented in the
>> > version
>> > > 5.3 of recon-all ?
>> > >
>> > > >
>> > > >
>> > > > 2) Does this method supply an intensity normalisation
>> for
>> > > PET images ?
>> > > >
>> > > What do you mean by intensity normalization? For uptake
>> > analysis,
>> > > people
>> > > usually use SUV (standard uptake values where the whole image
>> is
>> > > scaled
>> > > by a value related to the injection mass and subject weight)
>> > or you
>> > > choose a reference structure to scale by (often called rSUV
>> for
>> > > relative). By default mri_gtmpvc uses pons, but you can
>> > choose any
>> > > structure you want with the --rescale flag
>> > >
>> > > >
>> > > >
>> > > > Best regards,
>> > > > Matthieu
>> > > >
>> > > >
>> > > >
>> > > >
>> > > > ___
>> > > > Freesurfer mailing list
>> > > > Freesurfer@nmr.mgh.harvard.edu
>> > 
>> > > > > 
>> Freesurfer@nmr.mgh.harvard.edu>>
>> > > >
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> > >
>> > > --
>> > >
>> > >
>> > > Best regards,
>> > > Matthieu
>> > >
>> > > Douglas N. Greve, Ph.D.
>> > > MGH-NMR Center
>> > > gr...@nmr.mgh.harvard.edu 
>> >   

Re: [Freesurfer] Unknown cortical parcellation in S_calcarine (lh.aparc.a2009s.annot)

[Matthieu Vanhoutte]

Hello,

Does anybody have an idea ?

Thanks in advance !

Best regards,
Matthieu

2016-01-08 16:59 GMT+01:00 Matthieu Vanhoutte :

> Dear FS's experts,
>
> Projecting volumic data onto native surface (brain mask:
> "Unknown_S_calcarine_ROI_mask.jpg"), I observed that a thin region in the
> S_calcarine was set to 0.
>
> I loaded then the inflated left surface and the l.aparc.a2009s.annot
> ("Unknown_S_calcarine_ROI_annot.jpg") and took into account that this
> region
> inside the S_calcarine was set as "unknown" in the parcellation file .
>
> So I checked the aseg at the anterior end of the calcarine and see if it
> incorrectly labeled some voxels there as ventricle. I corrected the aseg
> and rerun from there with this command :
>
>
>
> *recon-all -all -sd ${SUBJECTS_DIR} -subjid ${SUBJECT_ID}
> -nuintensitycor-3T -make all*
> However, this command exited with errors (please find attached
> recon-all_log.txt).
>
> Thanks in advance far any helping !
>
> Best regards,
> Matthieu
>
> 2016-01-08 10:14 GMT+01:00 Matthieu Vanhoutte  >:
>
>> Hi Bruce,
>>
>> I erased the false ventricle signal and re-run with -make all option.
>>
>> However, Recon-all exited with errors:
>>
>> ---
>>> #@# 1/1 Hallaert_Beatrice_M0_2010-12-15 Thu Jan  7 19:46:56 CET 2016
>>> --
>>> ---
>>> mri_surf2surf --srcsubject Hallaert_Beatrice_M0_2010-12-15 --srchemi lh
>>> --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg
>>> sphere.reg --tval
>>> ./tmp.mris_preproc.16394/Hallaert_Beatrice_M0_2010-12-15.1.mgh --sval
>>> /NAS/tupac/matthieu/FS5.3/Hallaert_Beatrice_M0_2010-12-15/surf/lh.volume
>>> --jac --sfmt curv --noreshape --no-cortex
>>> Source registration surface changed to sphere.reg
>>> Target registration surface changed to sphere.reg
>>> srcsubject = Hallaert_Beatrice_M0_2010-12-15
>>> srcval =
>>> /NAS/tupac/matthieu/FS5.3/Hallaert_Beatrice_M0_2010-12-15/surf/lh.volume
>>> srctype= curv
>>> trgsubject = fsaverage
>>> trgval =
>>> ./tmp.mris_preproc.16394/Hallaert_Beatrice_M0_2010-12-15.1.mgh
>>> trgtype=
>>> srcsurfreg = sphere.reg
>>> trgsurfreg = sphere.reg
>>> srchemi= lh
>>> trghemi= lh
>>> frame  = 0
>>> fwhm-in= 0
>>> fwhm-out   = 0
>>> label-src  = (null)
>>> label-trg  = (null)
>>> OKToRevFaceOrder  = 1
>>> Reading source surface reg
>>> /NAS/tupac/matthieu/FS5.3/Hallaert_Beatrice_M0_2010-12-15/surf/lh.sphere.reg
>>> Loading source data
>>> Reading curvature file
>>> /NAS/tupac/matthieu/FS5.3/Hallaert_Beatrice_M0_2010-12-15/surf/lh.volume
>>> ERROR: number of vertices in
>>> /NAS/tupac/matthieu/FS5.3/Hallaert_Beatrice_M0_2010-12-15/surf/lh.volume
>>> does not match surface (124822,125094)
>>> ERROR: reading curvature file
>>> Linux toto 3.13.0-24-generic #47-Ubuntu SMP Fri May 2 23:30:00 UTC 2014
>>> x86_64 x86_64 x86_64 GNU/Linux
>>>
>>> recon-all -s Hallaert_Beatrice_M0_2010-12-15 exited with ERRORS at Thu
>>> Jan  7 19:46:57 CET 2016
>>>
>>
>> Please find attached the logs.
>>
>> Moreover, I visualized aparc.a2009.annot and there's still unknown label
>> in calcarine.
>>
>> Best regards,
>> Matthieu
>>
>>
>> 2016-01-07 17:52 GMT+01:00 Matthieu Vanhoutte <
>> matthieuvanhou...@gmail.com>:
>>
>>> Hi Bruce,
>>>
>>> Thank you I erased false ventricle and rerun recon-all with option -make
>>> all.
>>>
>>> Is there any mean to prevent this problem ?
>>>
>>> Best regards,
>>> Matthieu
>>>
>>> -
>>> Matthieu Vanhoutte, MSc
>>> Research Engineer - Department of Neuroradiology
>>> Regional University Hospital, Lille, France
>>> http://www.ci2c.fr
>>>
>>> 2016-01-07 16:21 GMT+01:00 Bruce Fischl :
>>>
 it's the bit of ventricle at e.g. 150, 117, 76 in the aseg. This should
 be unknown instead. You can erase it all from the aseg.mgz, then rerun
 recon-all -make all I think

 Bruce
 On Thu, 7 Jan 2016, matthieuvanhou...@gmail.com wrote:

 Matthieu (matthieuvanhou...@gmail.com) has uploaded some files for you
> at the Martinos Center FileDrop:
>
> + T1.mgz (3.89 MiB) <
> http://gate.nmr.mgh.harvard.edu/filedrop2/?u=83wgnvpqp7q=1qg3sxihniv
> >
> + aseg.mgz (230.42 KiB) <
> http://gate.nmr.mgh.harvard.edu/filedrop2/?u=83wgnvpqp7q=41rb99vxdza
> >
> + aparc.a2009s+aseg.mgz (406.09 KiB) <
> http://gate.nmr.mgh.harvard.edu/filedrop2/?u=83wgnvpqp7q=b68kofegemp
> >
>
> Also, they left this message for you:
> Hi Bruce,
>
> I couldn't see what you've explained to me. I attached the T1 and aseg
> files, could you please give me coordinates of this phenomen ?
>
> Once problem have been seen, what is the process to follow for
> correcting aseg labels and re-run recon-all at which step ?
>
> Thanks in advance !
>
> Best regards,
> Matthieu
>
>
> Hi 

[Freesurfer] Cortical reconstruction

[Mohamed Ali Bahri]

Dear Freesurfer Experts,

I am wondering if the cortical reconstruction is possible for the 
quantitative mri images (R1, MT, PD...) obtained with the multiparameter 
sequences .
If yes which image should i use?

Many thanks in advance,

Mohamed

-- 
Dr. Mohamed Ali Bahri,
1er Logisticien de Recherche,
Cyclotron Research Centre,
University of Liège, Belgium
m.ba...@ulg.ac.be

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Re: [Freesurfer] Calculating new volumes

[Douglas Greve]

For binarization use mri_binarize. For intersecting, you can use 
mri_binarize with the --mask option. If you want to add to volumes, you 
can use fscalc, eg

fscalc vol1.mgh sum vol2.mgh -o sum.mgh
fscalc has a bunch of options. Run it with -help to see

On 1/11/16 11:30 AM, Julio Alberto González Torre wrote:



Hi Freesurfer experts.

Is there any tool to perfom volume calculations? Such binarize a 
volume, intersect two volumes, sum volumes etc?


Thanks.



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[Freesurfer] R: R: Re: FDR correction

[stdp82]

Hi list,

I have resolved my issue on the previous point 2 by downloading matlab file 
on:
https://sites.google.com/site/kittipat/mvpa-for-brain-
fmri/convert_matlab_nifti

after the command that you suggesedt:
fdrthresh = fast_fdrthresh(p,0.05);
the script produce p=0.053

Therefore, coming back to my answer I guess that no setting of the FDR 
threshold to 0.05/3 is requested in order to correct for multiple comparison 
(right and left hemispheres + subcortical). Is it correct?

On the previous point 4 my answer remains open.
I have used this command line:
mri_surfcluster --in sig.nii.gz --hemi rh --sign abs --no-adjust --fdr 0.05 --
minarea 5 --sum summaryfile --subject fsaverage  --annot aparc

but I have difficulty to undestand which is the option to visualize the map 
corrected by mri_surfcluster.
Additionally, from --help I do not understand the use of --ocn and --cst 
options.

Best regards,


Stefano 



>>Messaggio originale
>>Da: std...@virgilio.it
>>Data: 7-gen-2016 15.40
>>A: 
>>Ogg: [Freesurfer] R: Re:  FDR correction
>>
>>Thanks.
>>
>>- on question 2:
>>I have run 
>>rh = MRIread('sig.mgh');
>>but this error occur
>>Undefined function 'MRIread' for input arguments of type 'char'.
>>no help is permitted on MRIread
>>
>>-on question 3:
>>I'm using this command line to visualize the map describing the functional 
>>connectivity form seed to cortex
>>
>>tksurfer fsaverage rh inflated -aparc -overlay R_seed/my-glm.wls/group.
>>diff/sig.nii.gz -fminmax 1.3 3
>>tksurfer fsaverage lh inflated -aparc -overlay L_seed/my-glm.wls/group.
>>diff/sig.nii.gz -fminmax 1.3 3
>>
>>in this way I visualize correctly for right and left hemisphere the 
>>connectivity from ipsilateral seed.
>>If I would visualize the the connectivity from contralateral seed, how can 
I 
>>do?
>>
>>If I use 
>>tksurfer fsaverage lh inflated -aparc -overlay R_seed/my-glm.wls/group.
>>diff/sig.nii.gz -fminmax 1.3 3
>>tksurfer fsaverage rh inflated -aparc -overlay L_seed/my-glm.wls/group.
>>diff/sig.nii.gz -fminmax 1.3 3t
>>
>>-on question 4:
>>I have resolved with this command line:
>>mri_surfcluster --in sig.nii.gz --hemi rh --sign abs --no-adjust --fdr 0.05 
>--
>>minarea 5 --sum summaryfile --subject fsaverage  --annot aparc
>>
>>but I have difficulty to undestand which is the option to visualize the map 
>>corrected by mri_surfcluster.
>>Additionally, from --help I do not understand the use of --ocn and --cst 
>>options.
>>
>>Best regards,
>>
>>
>>Stefano
>>
>>
>>
>>
>>
>>>Messaggio originale
>>>Da: gr...@nmr.mgh.harvard.edu
>>>Data: 7-gen-2016 0.34
>>>A: 
>>>Ogg: Re: [Freesurfer] FDR correction
>>>
>>>
>>>
>>>On 01/06/2016 11:00 AM, std...@virgilio.it wrote:
 Hi list,

 I would like to ask you a number of questions regarding the FDR which 
 is performed following seed-based fcMRI using FS-FAST.
 1-In the previous mail you have suggested me to use mir_fdr command 
 line (version 6.0). Because I have some problem with new version 
 license (as reported in previous mail) and, overall I have run my data 
 using version 5.3, I would ask you whether FDR integrated in tksurfer 
 (version 5.3) is however reliable as the FDR included in 6.0?
>>>Yes, they call the same code.

 2-Becouse the FDR analysis was performed separately for the right and 
 left hemispheres and the subcortical structures, should I set the FDR 
 threshold to 0.05/3 in order to correct for multiple comparison? (I 
 have one group)
>>>I'm not sure. You can try to run both hemispheres in matlab, somethiing 
like
>>>lh = MRIread('sig.lh.mgh');
>>>lhp = 10^-abs(lh.vol);
>>>rh = MRIread('sig.rh.mgh');
>>>rlhp = 10^-abs(rh.vol);
>>>
>>>p = [lhp rhp];
>>>fdrthresh = fast_fdrthresh(p,fdr);
>>>

 3- Is easy for me to follow the guidelines and visualize the cortical 
 areas which are functionally connected with the omolateral seed. How 
 can I do to visualize also the the cortical areas which are 
 functionally connected with the controlateral seed? If change only the 
 rh/lh in command line the visualization of the results is wrong.
>>>I don't understand.

 4- I'd like to perform mri_surfcluster on a group to eliminate cluster 
 < 5
 voxels from sig.nii.gz after FDR correction. I'm running 
 mri_surfcluster --in
 sig.nii.gz --hemi rh --sign abs --fdr 0.05 --minarea 5 --sum 
 summaryfile --ocn
 ocnid
 but --subject ... must be included.
 How should do I do? I would like to run my analysis on group results, 
 not on a single subject.
>>>If this is from a group analysis, the subject is probablly fsaverage

 Thanks for your work.
 Regards,


 Stefano



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>>>
>>>-- 

[Freesurfer] propagating edits across in the FreeSurfer longitudinal stream

[Collins, Jessica Ann]

Dear FS Community,

I am currently using FreeSurfer 5.3 to conduct a longitudinal analysis of 
atrophy in Semantic Dementia. Because of the profound temporal pole atrophy in 
these patients, I have been making a lot of manual edits (mostly control points 
and wm edits) to the baseline scan, and these edits are often consistent across 
different time points for the same individual. I understand that with the 
longitudinal stream it is necessary to make edits to all cross-sectional scans, 
however I was wondering if there was any way to propagate manual edits made at 
one time point to future time points for the same subject? Any insight would be 
appreciated!

Best regards,
Jessica

Jessica Collins, Ph.D.
Postdoctoral Research Fellow
Department of Neurology
MGH-Harvard Medical School



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Re: [Freesurfer] Question about Intracranial Volume

[pietro de rossi]

Thanks a lot Bruce.
 Cheers

2016-01-11 14:43 GMT+01:00 Bruce Fischl :

> Hi Pietro
>
> ICV (or eTIV) is computed using Randy Buckner's method, so you can cite
> his paper. Correcting for whole brain volume is certainly a reasonable
> thing to do but note that then you are testing a somewhat different
> hypothesis (that local atrophy is faster than whole-brain atrophy, as
> opposed to whether atrophy exists at all)
>
> cheers
> Bruce
>
>
>
> On Mon, 11 Jan 2016, pietro de rossi wrote:
>
> Dear FreeSurfers,
>> I am editing a paper on subcortical volumes in deficit schizophrenia after
>> some reviewers' comments.
>> On of them suggested me to correct the volumes of subcortical structures
>> for
>> whole brain volume instead of intracranial volume. In the reviewer's
>> opinion
>> ICV  estimated by FreeSurfer 5.1 has a bad quality and is not reliable.
>> However,  neither the reviewer provides any evidence, nor I could find
>> any...
>> Is there any evidence for this?
>>
>> Thanks in advance,
>>
>> Pietro
>>
>> --
>> Pietro De Rossi, MD
>> -
>> Sapienza Università di Roma, Facoltà di Medicina e Psicologia,
>> Dipartimento
>> NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale
>> Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma
>>
>> NESMOS Department (Neurosciences, Mental Health and Sensory Functions),
>> School of Medicine and Psychology, Sapienza University, Sant’Andrea
>> Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy
>>
>> Laboratorio di Neuropsichiatria, Dipartimento di Neurologia Clinica e
>> Comportamentale, IRCCS Fondazione Santa Lucia, via Ardeatina 306 - 00179
>> Roma
>>
>> Tel. +39 (0)6 51501358
>>
>> Fax +39 (0)6 90280774
>>
>> web: http://www.neuropsichiatrialab.com
>>
>>
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> addressed. If you believe this e-mail was sent to you in error and the
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> contains patient information, please contact the Partners Compliance
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> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>


-- 
Pietro De Rossi, MD
-
Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento
NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale
Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma

NESMOS Department (Neurosciences, Mental Health and Sensory Functions),
School of Medicine and Psychology, Sapienza University, Sant’Andrea
Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy

Laboratorio di Neuropsichiatria, Dipartimento di Neurologia Clinica e
Comportamentale, IRCCS Fondazione Santa Lucia, via Ardeatina 306 - 00179
Roma

Tel. +39 (0)6 51501358

Fax +39 (0)6 90280774
web: http://www.neuropsichiatrialab.com
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Re: [Freesurfer] Question about Intracranial Volume

[Bruce Fischl]

Hi Pietro

ICV (or eTIV) is computed using Randy Buckner's method, so you can cite 
his paper. Correcting for whole brain volume is certainly a reasonable 
thing to do but note that then you are testing a somewhat different 
hypothesis (that local atrophy is faster than whole-brain atrophy, as 
opposed to whether atrophy exists at all)


cheers
Bruce


On Mon, 11 Jan 2016, pietro de rossi wrote:


Dear FreeSurfers,
I am editing a paper on subcortical volumes in deficit schizophrenia after
some reviewers' comments.
On of them suggested me to correct the volumes of subcortical structures for
whole brain volume instead of intracranial volume. In the reviewer's opinion
ICV  estimated by FreeSurfer 5.1 has a bad quality and is not reliable.
However,  neither the reviewer provides any evidence, nor I could find
any...
Is there any evidence for this?

Thanks in advance,

Pietro

--
Pietro De Rossi, MD
-
Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento
NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale
Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma

NESMOS Department (Neurosciences, Mental Health and Sensory Functions),
School of Medicine and Psychology, Sapienza University, Sant’Andrea
Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy

Laboratorio di Neuropsichiatria, Dipartimento di Neurologia Clinica e
Comportamentale, IRCCS Fondazione Santa Lucia, via Ardeatina 306 - 00179
Roma

Tel. +39 (0)6 51501358

Fax +39 (0)6 90280774

web: http://www.neuropsichiatrialab.com

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Re: [Freesurfer] Question about Intracranial Volume

[Harms, Michael]

Hi Pietro,
One additional thing to consider is that the ICV (eTIV) is entirely
dependent on the Talairach transform.  Frequently, the accuracy of
Talairach transform isn¹t explicitly checked by users, because the
surfaces, aseg, etc can be accurate even if the Talairach transform isn¹t.

cheers,
-MH

--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 1/11/16, 7:43 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Bruce Fischl"  wrote:

Hi Pietro

ICV (or eTIV) is computed using Randy Buckner's method, so you can cite
his paper. Correcting for whole brain volume is certainly a reasonable
thing to do but note that then you are testing a somewhat different
hypothesis (that local atrophy is faster than whole-brain atrophy, as
opposed to whether atrophy exists at all)

cheers
Bruce


On Mon, 11 Jan 2016, pietro de rossi wrote:

> Dear FreeSurfers,
> I am editing a paper on subcortical volumes in deficit schizophrenia
>after
> some reviewers' comments.
> On of them suggested me to correct the volumes of subcortical structures
>for
> whole brain volume instead of intracranial volume. In the reviewer's
>opinion
> ICV  estimated by FreeSurfer 5.1 has a bad quality and is not reliable.
> However,  neither the reviewer provides any evidence, nor I could find
> any...
> Is there any evidence for this?
>
> Thanks in advance,
>
> Pietro
>
> --
> Pietro De Rossi, MD
> -
> Sapienza Università di Roma, Facoltà di Medicina e Psicologia,
>Dipartimento
> NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale
> Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma
>
> NESMOS Department (Neurosciences, Mental Health and Sensory Functions),
> School of Medicine and Psychology, Sapienza University, Sant¹Andrea
> Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy
>
> Laboratorio di Neuropsichiatria, Dipartimento di Neurologia Clinica e
> Comportamentale, IRCCS Fondazione Santa Lucia, via Ardeatina 306 - 00179
> Roma
>
> Tel. +39 (0)6 51501358
>
> Fax +39 (0)6 90280774
>
> web: http://www.neuropsichiatrialab.com
>



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Re: [Freesurfer] Hippocampal Subfields (6.0) Error

[Eugenio Iglesias]

Dear Andrew, 
sorry for the late reply. 
Aren't there any error outputs for the two cases? 
If not, would you mind uploading the subjects so I can take a look? 
Cheers, 
Eugenio 


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

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


From: "Andrew Schoen"  
To: "Freesurfer support list"  
Sent: Wednesday, December 23, 2015 4:05:00 PM 
Subject: [Freesurfer] Hippocampal Subfields (6.0) Error 

Hi all, 
We are running some hippocampal subfield segmentations for two independent 
studies. They have already been processed through the standard pipeline (5.3), 
so I was just running the following command: 

recon-all -s ${subjectid} -hippocampal-subfields-T1 

For both test cases, the processing seems to have halted (no more updates to 
the log file), but the command keeps running. For one study, it trailed off 
here: 


 
Resolution level 1 iteration 2 deformation iterations 13 
Number of Meshes: 1 
Using CG optimizer 
Did one deformation step of max. 0.00037944 voxels in 14.6033 seconds 

minLogLikelihoodTimesPrior = 

2.3442e+06 

Resolution level 1 iteration 2 deformation iterations 14 
Number of Meshes: 1 
Using CG optimizer 
Did one deformation step of max. 1.3541e-06 voxels in 3.5131 seconds 

minLogLikelihoodTimesPrior = 

2.3442e+06 

Resolution level 1 iteration 2 deformation iterations 15 
Number of Meshes: 1 
Using CG optimizer 
Did one deformation step of max. 0 voxels in 30.0807 seconds 

minLogLikelihoodTimesPrior = 

2.3442e+06 

maximalDeformation is too small; stopping 
Iteration 3 of 7 
(eof) 

 


and the other here: 


 
Making Left-Accumbens-area map to reduced label 13 
-- 
Making Unknown map to reduced label 14 
Computing hyperparameters for estimation of Gaussians parameters 
Estimating typical intensities of molecular layer and alveus 
For ML in T1, we assume gray with high N 
In T2, we actually assume the same hypermean 
Smoothing mesh collection with kernel size 1.50 ...Smoothing class: 0 
Smoothing class: 1 
Smoothing class: 2 
Smoothing class: 3 
Smoothing class: 4 
Smoothing class: 5 
Smoothing class: 6 
Smoothing class: 7 
Smoothing class: 8 
Smoothing class: 9 
Smoothing class: 10 
Smoothing class: 11 
Smoothing class: 12 
Smoothing class: 13 
done 
numberOfImages = 2 
Image: 0 
Image: 2 
Iteration 1 of 7 
(eof) 

 


Interestingly, for one study, we have T2-weighted images, and when I ran with 
that (same subject as second log, above), it ran to completion fine. 

Any idea what might be happening? Let me know if any other info would be 
useful! 

Thanks! 

Andrew Schoen 
Center for Healthy Minds 
Waisman Center 
University of Wisconsin - Madison 

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[Freesurfer] Question about Intracranial Volume

[pietro de rossi]

Dear FreeSurfers,

I am editing a paper on subcortical volumes in deficit schizophrenia after
some reviewers' comments.
On of them suggested me to correct the volumes of subcortical structures
for whole brain volume instead of intracranial volume. In the reviewer's
opinion ICV  estimated by FreeSurfer 5.1 has a bad quality and is not
reliable. However,  neither the reviewer provides any evidence, nor I could
find any...
Is there any evidence for this?

Thanks in advance,

Pietro

-- 
Pietro De Rossi, MD
-
Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento
NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale
Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma

NESMOS Department (Neurosciences, Mental Health and Sensory Functions),
School of Medicine and Psychology, Sapienza University, Sant’Andrea
Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy

Laboratorio di Neuropsichiatria, Dipartimento di Neurologia Clinica e
Comportamentale, IRCCS Fondazione Santa Lucia, via Ardeatina 306 - 00179
Roma

Tel. +39 (0)6 51501358

Fax +39 (0)6 90280774
web: http://www.neuropsichiatrialab.com
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Re: [Freesurfer] Question about Intracranial Volume

[pietro de rossi]

I see.
This is very helpful.
Thanks

2016-01-11 15:15 GMT+01:00 Harms, Michael :

>
> Hi Pietro,
> One additional thing to consider is that the ICV (eTIV) is entirely
> dependent on the Talairach transform.  Frequently, the accuracy of
> Talairach transform isn¹t explicitly checked by users, because the
> surfaces, aseg, etc can be accurate even if the Talairach transform isn¹t.
>
> cheers,
> -MH
>
> --
> Michael Harms, Ph.D.
>
> ---
> Conte Center for the Neuroscience of Mental Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave.Tel: 314-747-6173
> St. Louis, MO  63110Email: mha...@wustl.edu
>
>
>
>
> On 1/11/16, 7:43 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
> Bruce Fischl"  fis...@nmr.mgh.harvard.edu> wrote:
>
> Hi Pietro
>
> ICV (or eTIV) is computed using Randy Buckner's method, so you can cite
> his paper. Correcting for whole brain volume is certainly a reasonable
> thing to do but note that then you are testing a somewhat different
> hypothesis (that local atrophy is faster than whole-brain atrophy, as
> opposed to whether atrophy exists at all)
>
> cheers
> Bruce
>
>
> On Mon, 11 Jan 2016, pietro de rossi wrote:
>
> > Dear FreeSurfers,
> > I am editing a paper on subcortical volumes in deficit schizophrenia
> >after
> > some reviewers' comments.
> > On of them suggested me to correct the volumes of subcortical structures
> >for
> > whole brain volume instead of intracranial volume. In the reviewer's
> >opinion
> > ICV  estimated by FreeSurfer 5.1 has a bad quality and is not reliable.
> > However,  neither the reviewer provides any evidence, nor I could find
> > any...
> > Is there any evidence for this?
> >
> > Thanks in advance,
> >
> > Pietro
> >
> > --
> > Pietro De Rossi, MD
> > -
> > Sapienza Università di Roma, Facoltà di Medicina e Psicologia,
> >Dipartimento
> > NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale
> > Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma
> >
> > NESMOS Department (Neurosciences, Mental Health and Sensory Functions),
> > School of Medicine and Psychology, Sapienza University, Sant¹Andrea
> > Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy
> >
> > Laboratorio di Neuropsichiatria, Dipartimento di Neurologia Clinica e
> > Comportamentale, IRCCS Fondazione Santa Lucia, via Ardeatina 306 - 00179
> > Roma
> >
> > Tel. +39 (0)6 51501358
> >
> > Fax +39 (0)6 90280774
> >
> > web: http://www.neuropsichiatrialab.com
> >
>
>
> 
> The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If you
> are not the intended recipient, be advised that any unauthorized use,
> disclosure, copying or the taking of any action in reliance on the contents
> of this information is strictly prohibited. If you have received this email
> in error, please immediately notify the sender via telephone or return mail.
>
> ___
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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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> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>


-- 
Pietro De Rossi, MD
-
Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento
NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale
Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma

NESMOS Department (Neurosciences, Mental Health and Sensory Functions),
School of Medicine and Psychology, Sapienza University, Sant’Andrea
Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy

Laboratorio di Neuropsichiatria, Dipartimento di Neurologia Clinica e
Comportamentale, IRCCS Fondazione Santa Lucia, via Ardeatina 306 - 00179
Roma

Tel. +39 (0)6 51501358

Fax +39 (0)6 90280774
web: http://www.neuropsichiatrialab.com
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Re: [Freesurfer] Cortical reconstruction

[Bruce Fischl]

Hi Mohamed

you can use mri_synthesize to create a flash image with good T1 contrast 
from quantitative maps and run it through recon-all.

cheers
Bruce
On Mon, 11 Jan 2016, 
Mohamed Ali Bahri wrote:

> Dear Freesurfer Experts,
>
> I am wondering if the cortical reconstruction is possible for the
> quantitative mri images (R1, MT, PD...) obtained with the multiparameter
> sequences .
> If yes which image should i use?
>
> Many thanks in advance,
>
> Mohamed
>
>
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Re: [Freesurfer] PET processing seg fault with mri_glmfit --mrtm1

[Douglas N Greve]

The km.hb.tac.nii.gz is not a volume. It is a single voxel of data 
stored in nii format. This format is needed to input to mri_glmfit. Try 
loading it in matlab, eg,

hb = fast_vol2mat( MRIread('km.hb.tac.nii.gz'));
plot(hb)

if that is all 0s then it will surely cause mrtm1 to fail.

doug

On 01/07/2016 11:40 PM, Jonathan DuBois wrote:
> Hi Freesurfer developers,
>
> I’m trying to perform BP analysis with mri_glmfit —mrtm1. I ran mri_gtmpvc 
> without PVC, which finished without error. However, the km.hb.tac.nii.gz 
> appears empty when I open it with fslview or tkmedit, although this may be 
> due to the nature of the file (I’m not sure what it is supposed to show). The 
> km.ref.tac.dat and km.hb.tac.dat are normal.
> Please let me know what you think.
>
> The command and error:
> mri_glmfit --y km.hb.tac.nii.gz --mrtm1 km.ref.tac.dat time.dat --o mrtm1 
> --no-est-fwhm --nii.gz
> Segmentation fault (core dumped)
>
> Where time.dat is a text file with the time (in seconds) of each frame:
> 0 30 60 90 120 150 180 240 300 360 420 540 660 780 900 1020 1140 1260 1380 
> 1620 1860 2100 2400 2700 3000 3300
>
> I’m using the linux version 6 beta downloaded on Oct. 30th
> freesurfer-Linux-centos4_x86_64-dev-20151030
>
> Best,
> Jonathan
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>
>

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] Reading values from overlays with PETcoreg

[Douglas N Greve]

If you want to use partial volume correction, then you are better off 
using mri_gtmpvc with the bbr registration, something like

1. To start, run

gtmseg --s subject

This will take a couple of hours and produces some files needed for GTM 
PVC (which is used for GTM, MG, RBV).

2. You'd then register the PET to the anatomical with bbregister
(probably with --t2 weighting). Make sure to save the output as an LTA
(--lta). I usually use the mean TAC as the input. You can do this in
parallel with #1.

3. You'd then run mri_gtmpvc, something like

mri_gtmpvc --i pet.nii.gz --psf PSF  --auto-mask PSF+2 .01 --seg gtmseg.mgz
--reg reg.lta --default-seg-merge  --o gtmpvc.output

PSF is the point-spread FWHM of the scanner; reg.lta is the
registration from #2. By default, this will scale by pons.  The output
will be gtm.stats.dat and gtm.nii.gz. They both basically have the
same information. gtm.stats.dat is an easy to read text file. Where
each row is an ROI, something like:

9   17 Left-Hippocampussubcort_gm   473 
174.0831.406   0.1216

9 = nineth row
17 = index for RO
Left-Hippocampus = name of ROI
subcort_gm = tissue class
473 = number of PET voxels in the ROI
174 = variance reduction factor for ROI (based on GLM/SGTM)
1.406 = PVC uptake of ROI relative to Pons
0.1216 = resdiual varaince across voxels in the ROI

gtm.nii.gz is a nifti file with each "voxel" being an ROI. The value
is the PVC uptake of ROI relative to Pons. These can easily be
concatenated together (mri_concat) and used as input to mri_glmfit
for group analysis.




On 01/08/2016 04:22 AM, Benjamin Spurny wrote:
> Dear Freesurfer experts!
>
> I am currently working on PET analysis using FS
>
> I coregistered my PET with the processed MR using bbregister,
> transfered it to a surface using mri_vol2surf
> and now createt an overlay in freeview with the lh.inflated and used the
> labels from the lh.aparc.a2009s.annot file.
>
> In freeview i get the corresponding BP value for each vertex now but
> is there a way to get a list of vertices with the corresponding BP value
> and the corresponding ROI this vertex belongs to?
> Or is there a better to do this analyis?
>
> Many thanks in advance!
>
> Benjamin
>
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>
>

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

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

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Re: [Freesurfer] Use of PVC PET images (V6) : between versions compatibility and intensity normalisation

[Matthieu Vanhoutte]

Dear Douglas,

If the pons intensity used to normalize has been PVC'ed, couldn't we have
an output of mri_gtmpvc with the whole brain PVC'ed ?

Because the only files on output of mri_gtmpvc are :
mgx.ctxgm.nii.gz - pvc'ed cortex gm only
mgx.subctxgm.nii.gz - pvc'ed subcortical gm only
mgx.gm.nii.gz - pvc'ed all gm

Best regards,
Matthieu

2016-01-11 18:20 GMT+01:00 Douglas N Greve :

>
> The pons intensity used to normalize has been PVC'ed. The file used is
> the input file.
>
>
> On 01/11/2016 04:04 AM, Matthieu Vanhoutte wrote:
> > Dear Douglas,
> >
> > Just one more question : by default mri_gtmpvc uses pons for computing
> > rSUV, but is this intensity normalization done before or after partial
> > volume correction ? What file is used in input for intensity
> > normalization ?
> >
> > Thanks in advance !
> >
> > Best regards,
> > Matthieu
> >
> > 2015-12-18 18:26 GMT+01:00 Douglas Greve  > >:
> >
> > You'll see several files that begin with mgx:
> > mgx.ctxgm.nii.gz - pvc'ed cortex gm only
> > mgx.subctxgm.nii.gz - pvc'ed subcortical gm only
> > mgx.gm.nii.gz - pvc'ed all gm
> >
> >
> > On 12/18/15 6:08 AM, Matthieu Vanhoutte wrote:
> >> Hello Douglas,
> >>
> >> I have run mri_gtmpvc with static PET images using the following
> >> command :
> >> mri_gtmpvc --i PET.nii.gz --psf 6 --auto-mask 8 0.01 --seg
> >> gtmseg.mgz --reg register.dof6.lta --default-seg-merge --mgx 0.01
> >> --o gtmpvc.output
> >>
> >> In the output directory "gtmpvc.output" where is the partial
> >> volume corrected PET image ?
> >>
> >> Thanks !
> >>
> >> Best regards,
> >> Matthieu
> >>
> >> 2015-12-15 21:07 GMT+01:00 Douglas N Greve
> >> >:
> >>
> >> Not necessarily. It needs a good segmentation, so, to the
> >> extent that v6
> >> has a better segmentation then v6 is better.
> >>
> >> On 12/15/2015 02:57 PM, Matthieu Vanhoutte wrote:
> >> >
> >> > Thanks Douglas for the answer !
> >> >
> >> > But isn't PVC design for better working in terms of results
> >> with
> >> > v6_beta than v5.3 ?
> >> >
> >> > Best regards,
> >> >
> >> > Matthieu
> >> >
> >> > Le 15 déc. 2015 19:02, "Douglas N Greve"
> >> 
> >> >  >> >> a écrit :
> >> >
> >> > It is not subsegmented in 6.0 either:). When you run
> >> gtmseg, it will
> >> > create the new segmentation that include pons and a few
> >> other things
> >> >
> >> > On 12/15/2015 12:56 PM, Matthieu Vanhoutte wrote:
> >> > > Dear Douglas,
> >> > >
> >> > > Please see below :
> >> > >
> >> > > 2015-12-15 18:37 GMT+01:00 Douglas N Greve
> >> >  >> 
> >>  >> >
> >> > >  >> 
> >> >  >>  >> > >
> >> > >
> >> > >
> >> > > On 12/15/2015 04:46 AM, Matthieu Vanhoutte wrote:
> >> > > > Dear experts,
> >> > > >
> >> > > > Could anyone answer to my questions below ?
> >> > > >
> >> > > > Thanks !
> >> > > >
> >> > > > Best regards,
> >> > > > Matthieu
> >> > > >
> >> > > > 2015-12-10 10:10 GMT+01:00 Matthieu Vanhoutte
> >> > > >  >> 
> >> >  >> >
> >> > >  >> 
> >> >  >> >>
> >> > >  >> 
> >> >  >> >
> >> > >  >> 
> >> >  >> :
> >> > > >
> >> > > > Dear 

Re: [Freesurfer] searchable Destrieux atlas by recon all labels?

[Douglas N Greve]

On 01/10/2016 12:20 PM, Andrea Bozoki wrote:
>   Plus, the
> minute you take an ROI created by Freesurfer to analyze a PET image (which
> cannot be surface-rendered accurately due to its inherent low resolution),
> you are forced to ³translate² the borders of ROIs from FS to a
> coordinate-based scheme anyway.

Not so fast. See for example Greve, et al, 2014. Cortical surface-based 
analysis reduces bias and variance in kinetic
modeling of brain PET data

>
> I will try implementing your Freeview solution; thanks again.
>
> Andrea B.
>
>
> On 1/9/16, 5:42 PM, "dgw"  wrote:
>
>> Hi Andrea,
>>
>> As far as I know no.
>>
>> Additionally, i don't think it makes a lot of sense to do, because the
>> two parcellations are created in fsaverage space, and while there are
>> morphings etc. that are possible these tricks will always introduce
>> errors etc. Additionally MNI space is defined in a completely different
>> way to Freesurfer space, and so translating the one two the other is
>> strange, because in FS you have locations on a surface while in MNI they
>> are 3d coordinates. Occasionally frustrating reviewers demand MNI
>> coordinates, likely not realizing that in that translation they are
>> being provided with strange data, and we have to send them something,
>> but overall, I find that picking the atlas/space which makes sense for
>> that question is the best place to start.
>>
>> hth
>> d
>>
>> On 1/9/16 12:40 PM, Andrea Bozoki wrote:
>>> Thank you. This is helpful.
>>>
>>> As to the broader question: is there truly no interactive, online atlas
>>> that uses either the Destrieux or Duvernoy parcellation scheme to
>>> examine
>>> the landmark boundaries with respect to, say, MNI space?
>>>
>>> Thanks,
>>> Andrea
>>>
>>> On 1/7/16, 4:26 PM, "dgw"  wrote:
>>>
 freeview partial solution

 If this is important to you, you could write a quick script to do this
 for you:

 1. mri_annotation2label to output all labels

 2. write a script to launch freeview and load all of the labels
 (reading the color and applying it from the FS ctab file)

 e.g. freeview -f
 surf/lh.inflated:label=label/lh.BA1.label:label_color=255,0,0 &

 3 you could then scroll through and click all of them off, and then
 click to load each one individually.

 or perhaps a new option could be added to the surface label called
 :label_opacity=0 (which would uncheck the view label option).

 hth
 d

 On Thu, Jan 7, 2016 at 3:53 PM, Bruce Fischl
 
 wrote:
> Hi Andrea
>
> I'm not sure what you mean but I'm pretty certain the answer is "no".
>
> sorry
> Bruce
>
> On Thu, 7 Jan 2016, Andrea Bozoki wrote:
>
>> Is there any interactive or searchable version of the Destrieux atlas
>> parcellations (the ones used by aparc.a2009s.annot)?
>>
>> It would be very helpful to be able to toggle back and forth between
>> individual recon-all labels and a color atlas of the relevant region
>> when
>> examining ROI-based quantitative output (output that is not visual).
>>
>>
>>
>> Thanks,
>>
>> Andrea B.
>>
>>
>>
>>
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>>>
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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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[Freesurfer] Calculating new volumes

[Julio Alberto González Torre]

Hi Freesurfer experts.

Is there any tool to perfom volume calculations? Such binarize a volume, 
intersect two volumes, sum volumes etc?

Thanks.

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[Freesurfer] Free surfer- correcting for head size

[Christina van den Brink]

Hello,

I have a question regarding volume-correction for the morphometry stats 
obtained via recon-all. I’ve noted that eTIV is derived using the atlas scaling 
factor in order to account for head size. I’m wondering whether the other 
volumes given, e.g. TotalGray or lhCorticalWhiteMatter, have also been 
corrected for head size? If not, is there a recommended method in which to do 
so so that regional volumes can be compared between participants?

Many thanks for your help!

Best,

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[Freesurfer] fMRI activation color inversion

[Hirsch, Gabriella]

Hi FreeSurfer experts,

I recently ran a simple fMRI analysis in FSL and now generating images of the 
activation in freesurfer using reg-feat2anat to register the functional 
activation to the freesurfer recon-all files, and generating the images using 
tksurfer:

tksurfer pilot_3 lh inflated -annot aparc.annot -ov 
run4578_COMB.gfeat/cope1.feat/stats/zstat1.nii.gz -ovreg 
run4_fwhm8.feat/reg/freesurfer/anat2std.register.dat -fthresh 4 -fslope 1

However I have come across a strange occurrence when I change the threshold. 
Specifically, when I set the -fthresh flag (bolded) as 4 (i.e. p=0.0001) or 
less, the activation colors comes off as they should (see 4_blue attached) in 
terms of how I set up the contrasts. But when I set my threshold to 5 or higher 
(changing nothing else), the colors of the activation invert (see 5_red 
attached).

What does this mean? How can I fix this?

Any ideas would be greatly appreciated!

Thank you!
Gabriella


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Re: [Freesurfer] Use of PVC PET images (V6) : between versions compatibility and intensity normalisation

[Douglas N Greve]

The pons intensity used to normalize has been PVC'ed. The file used is 
the input file.


On 01/11/2016 04:04 AM, Matthieu Vanhoutte wrote:
> Dear Douglas,
>
> Just one more question : by default mri_gtmpvc uses pons for computing 
> rSUV, but is this intensity normalization done before or after partial 
> volume correction ? What file is used in input for intensity 
> normalization ?
>
> Thanks in advance !
>
> Best regards,
> Matthieu
>
> 2015-12-18 18:26 GMT+01:00 Douglas Greve  >:
>
> You'll see several files that begin with mgx:
> mgx.ctxgm.nii.gz - pvc'ed cortex gm only
> mgx.subctxgm.nii.gz - pvc'ed subcortical gm only
> mgx.gm.nii.gz - pvc'ed all gm
>
>
> On 12/18/15 6:08 AM, Matthieu Vanhoutte wrote:
>> Hello Douglas,
>>
>> I have run mri_gtmpvc with static PET images using the following
>> command :
>> mri_gtmpvc --i PET.nii.gz --psf 6 --auto-mask 8 0.01 --seg
>> gtmseg.mgz --reg register.dof6.lta --default-seg-merge --mgx 0.01
>> --o gtmpvc.output
>>
>> In the output directory "gtmpvc.output" where is the partial
>> volume corrected PET image ?
>>
>> Thanks !
>>
>> Best regards,
>> Matthieu
>>
>> 2015-12-15 21:07 GMT+01:00 Douglas N Greve
>> >:
>>
>> Not necessarily. It needs a good segmentation, so, to the
>> extent that v6
>> has a better segmentation then v6 is better.
>>
>> On 12/15/2015 02:57 PM, Matthieu Vanhoutte wrote:
>> >
>> > Thanks Douglas for the answer !
>> >
>> > But isn't PVC design for better working in terms of results
>> with
>> > v6_beta than v5.3 ?
>> >
>> > Best regards,
>> >
>> > Matthieu
>> >
>> > Le 15 déc. 2015 19:02, "Douglas N Greve"
>> 
>> > > >> a écrit :
>> >
>> > It is not subsegmented in 6.0 either:). When you run
>> gtmseg, it will
>> > create the new segmentation that include pons and a few
>> other things
>> >
>> > On 12/15/2015 12:56 PM, Matthieu Vanhoutte wrote:
>> > > Dear Douglas,
>> > >
>> > > Please see below :
>> > >
>> > > 2015-12-15 18:37 GMT+01:00 Douglas N Greve
>> > > 
>> > >
>> > > > 
>> > > > > >
>> > >
>> > >
>> > > On 12/15/2015 04:46 AM, Matthieu Vanhoutte wrote:
>> > > > Dear experts,
>> > > >
>> > > > Could anyone answer to my questions below ?
>> > > >
>> > > > Thanks !
>> > > >
>> > > > Best regards,
>> > > > Matthieu
>> > > >
>> > > > 2015-12-10 10:10 GMT+01:00 Matthieu Vanhoutte
>> > > > > 
>> > > >
>> > > > 
>> > > >>
>> > > > 
>> > > >
>> > > > 
>> > > :
>> > > >
>> > > > Dear FS experts,
>> > > >
>> > > > 1) First Is it possible to use the partial
>> volume
>> > correction
>> > > > provided in the v6 beta version of
>> FreeSurfer despite
>> > the fact
>> > > > that recon-all have been done for all
>> subjects with
>> > the v5.3 ?
>> > > >
>> > > Yes
>> > >
>> > >
>> > > Great ! but isn't it a problem for computing rSUV
>> with pons as
>> > > reference structure since brainstem isn't
>> 

Re: [Freesurfer] About the pdf_gamma function in fsfast's toolbox

[Douglas N Greve]

No, it is not. Have you tried using -fslhrf option in mkanalysis-sess?

On 01/09/2016 12:13 AM, LiTuX Sol wrote:
>
> Hi,
>
> I’m working on some fMRI data processing these days. In order to 
> construct a HRF, I find this Matlab function in fsfast. But after some 
> careful comparison, it seems that the gamma pdf in this function is 
> not consistent with FSL’s version, and differs from the standard gamma 
> pdf. So perhaps it is a typo in your code?
>
> In this function, the gamma pdf is written as:
>
> > pdfx = (b.^2) .* (…);
>
> But comparing to FSL’s feat_model.cc, I think this term should be
>
> > pdfx = (b.^a) .*(…);
>
> Which will be consistent with the original gamma pdf from Wikipedia.
>
> Thanks for your nice software and thanks for your attention.
>
> Su,
>
> ---
>
> From Beijing Normal University.
>
>
>
> ___
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
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Re: [Freesurfer] error in selxavg3-sess

[Douglas N Greve]

Hi Neha, I've attached a file called load_nifti.m. Put this in 
$FREESURFER_HOME/matlab (after making a backup of what is there). Then 
re-run and let me know if that fixes the problem.

doug


On 01/09/2016 06:00 AM, neha hooda wrote:

Hii

I am using freesurfer to find the resting state connectivity. I used 
selxavg3-sess to analyze the data. But it neither terminates nor gives 
the error. Any help will be appreciated.


Regards
Neha


--
selxavg3-sess logfile is 
/home/neha/projectfolder/log/selxavg3-sess-bold-fc.lpccseed.surf.lh-160109152215.log

--
preproc-sess -s sessionid -d /home/neha/projectfolder -a 
fc.lpccseed.surf.lh -nolog

--
preproc-sess logfile is /dev/null
--
$Id: preproc-sess,v 1.45.2.3 2013/01/22 22:09:10 greve Exp $
NC_2
setenv FREESURFER_HOME /home/NC_2/shubham/freesurfer/freesurfer/
setenv SUBJECTS_DIR /home/neha/AKE01/PA0/ST0/
Linux tapan 2.6.32-573.7.1.el6.x86_64 #1 SMP Tue Sep 22 22:00:00 UTC 
2015 x86_64 x86_64 x86_64 GNU/Linux

/home/neha/projectfolder
/home/NC_2/shubham/freesurfer/freesurfer//fsfast/bin/preproc-sess
-s sessionid -d /home/neha/projectfolder -a fc.lpccseed.surf.lh -nolog
Sat Jan  9 15:22:16 IST 2016
instem   f
mc   1 f fmcpr
stc  0 fmcpr
sm   0
mask 1   brain
sessionid Template -
mktemplate-sess -s sessionid -d /home/neha/projectfolder -fsd bold 
-nolog -update


Session: /home/neha/projectfolder/sessionid 
Sat Jan  9 15:22:16 IST 2016
Detected input format at nii.gz
sessionid Update not needed
  Run: 004 
  Sat Jan  9 15:22:16 IST 2016
  sessionid 004 Update not needed
Sat Jan  9 15:22:16 IST 2016
mktemplate-sess completed
sessionid Mask 
mkbrainmask-sess -maskstem brain -fsd bold -s sessionid -d 
/home/neha/projectfolder -nolog -update


/home/neha/projectfolder/sessionid
Sat Jan  9 15:22:16 IST 2016
sessionid Update not needed for session-level mask
sessionid Update not needed for run 004 mask
sessionid Update not needed for run 004 meanval
Sat Jan  9 15:22:16 IST 2016
mkbrainmask-sess done
sessionid Registration -
register-sess -s sessionid -d /home/neha/projectfolder -fsd bold -dof 
6 -per-run -nolog -update

--
register-sess logfile is /dev/null
--
Sat Jan  9 15:22:16 IST 2016

setenv SUBJECTS_DIR /home/neha/AKE01/PA0/ST0/
cd /home/neha/projectfolder
/home/NC_2/shubham/freesurfer/freesurfer//fsfast/bin/register-sess -s 
sessionid -d /home/neha/projectfolder -fsd bold -dof 6 -per-run -nolog 
-update


freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Linux tapan 2.6.32-573.7.1.el6.x86_64 #1 SMP Tue Sep 22 22:00:00 UTC 
2015 x86_64 x86_64 x86_64 GNU/Linux


Session: /home/neha/projectfolder/sessionid 
Sat Jan  9 15:22:16 IST 2016
  Run: 004 
Sat Jan  9 15:22:16 IST 2016
Update not needed
Sat Jan  9 15:22:16 IST 2016
register-sess completed
sessionid MC -
mc-sess -fstem f -fmcstem fmcpr -s sessionid -d 
/home/neha/projectfolder -fsd bold -per-run -nolog -update

Logfile is /dev/null
---
/home/neha/projectfolder/sessionid
RunList: 004
sessionid 004 Update not needed


Sat Jan  9 15:22:16 IST 2016
mc-sess completed SUCCESSFULLY
sessionid To MNI305 -
rawfunc2tal-sess -fwhm 5 -s sessionid -d /home/neha/projectfolder -fsd 
bold -nolog -update -subcort-mask -per-run

--
1/1 sessionid
  1/1 sessionid 004 
Sat Jan  9 15:22:16 IST 2016
/home/neha/projectfolder/sessionid/bold/004/masks/brain.mni305.2mm.nii.gz 
does not need updating

sessionid 004 Update not needed

Sat Jan  9 15:22:16 IST 2016
rawfunc2tal-sess completed

Started at Sat Jan 9 15:22:16 IST 2016
Ended   at Sat Jan  9 15:22:16 IST 2016
preproc-sess done
---
/home/neha/projectfolder/sessionid
Sat Jan  9 15:22:17 IST 2016
anadir = /home/neha/projectfolder/sessionid/bold/fc.lpccseed.surf.lh
DoGLMFit = 1
DoContrasts = 1
UpdateNeeded = 1
--
--- matlab output 
MATLAB is selecting SOFTWARE OPENGL rendering.

< M A T L A B (R) >
  Copyright 1984-2014 The MathWorks, Inc.
   R2014b (8.4.0.150421) 64-bit (glnxa64)
 September 15, 2014


To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com 
.


>> >> >> >> >> >> 

Re: [Freesurfer] BA46 volume from rostral mid-frontal gyrus

[Douglas N Greve]

Use mri_vol2label to create a label file. If you want the label on the 
surface, then use mri_label2label with the --paint option

On 01/09/2016 03:11 PM, Jae Cho wrote:
> Dear FreeSurfer Experts,
>
> Could someone help me with a pipeline for creating a label from an 
> edited existing label? I have aligned the aparc+aseg and its 
> respective orig into ac-pc plane using AFNI. I then used fslmaths to 
> make an ROI of just the rh_mid-frontal-gyrus. After editing the ROI 
> using freeview, I am having trouble identifying which commands to use 
> in order to create a new label and extracting the volume.
>
> Thank you,
> Jae
>
>
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
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Re: [Freesurfer] Free surfer- correcting for head size

[Bruce Fischl]

Hi Christina

we don't correct any volumes for head size - we just provide the 
information for you to do it yourself. I think including it as a 
regressor is more common than dividing it out, but perhaps others can 
comment.


cheers
Bruce
On Mon, 11 Jan 2016, Christina van den Brink wrote:


Hello,
I have a question regarding volume-correction for the morphometry stats
obtained via recon-all. I’ve noted that eTIV is derived using the atlas
scaling factor in order to account for head size. I’m wondering whether the
other volumes given, e.g. TotalGray or lhCorticalWhiteMatter, have also been
corrected for head size? If not, is there a recommended method in which to
do so so that regional volumes can be compared between participants?

Many thanks for your help!

Best,

Christina

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Re: [Freesurfer] fMRI activation color inversion

[Douglas N Greve]

There is another parameter called -fmid. The final mapping is a 
complicated combination of all three (fthresh, fmin, fslope). I usally 
use the -fminmax option which is easier to explain. -fminmax 2 5 means 
that the threshold is set to 2 and that at 5 the color will saturate.
doug

On 01/11/2016 12:18 PM, Hirsch, Gabriella wrote:
> Hi FreeSurfer experts,
>
> I recently ran a simple fMRI analysis in FSL and now generating images 
> of the activation in freesurfer using reg-feat2anat to register the 
> functional activation to the freesurfer recon-all files, and 
> generating the images using tksurfer:
>
> /tksurfer pilot_3 lh inflated -annot aparc.annot -ov 
> run4578_COMB.gfeat/cope1.feat/stats/zstat1.nii.gz -ovreg 
> run4_fwhm8.feat/reg/freesurfer/anat2std.register.dat *-fthresh 4 
> *-fslope 1/
>
> However I have come across a strange occurrence when I change the 
> threshold. Specifically, when I set the -fthresh flag (bolded) as 4 
> (i.e. p=0.0001) or less, the activation colors comes off as they 
> should (see 4_blue attached) in terms of how I set up the contrasts. 
> But when I set my threshold to 5 or higher (changing nothing else), 
> the colors of the activation invert (see 5_red attached).
>
> What does this mean? How can I fix this?
>
> Any ideas would be greatly appreciated!
>
> Thank you!
> Gabriella
>
>
> Mass. Eye and Ear Confidentiality Notice: This e-mail and any files 
> transmitted with it are confidential and are intended solely for the 
> use of the individual(s) addressed in the message above. This 
> communication may contain sensitive or confidential information. If 
> you are not an intended recipient, dissemination, forwarding, 
> printing, or copying of this e-mail is strictly prohibited. If you 
> believe you have received this e-mail in error and the email contains 
> patient information, please contact the Mass. Eye and Ear Compliance 
> Line at 617-263-1600. If the e-mail was sent to you in error but does 
> not contain patient information, please contact the sender and delete 
> the e-mail.
>
>
> ___
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> 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

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Re: [Freesurfer] Use of PVC PET images (V6) : between versions compatibility and intensity normalisation

[Douglas N Greve]

I'm not sure exactly what you mean. I guess you could set all voxels in 
a given ROI to be the value of that ROI? This is not really a voxel-wise 
correction and probably would not do what you want. You can use the mgx 
data (corrected with muller-gartner method). There is also a --rbv 
(region-based voxel-wise, Thomas 2012) option.


On 01/11/2016 12:34 PM, Matthieu Vanhoutte wrote:
> Dear Douglas,
>
> If the pons intensity used to normalize has been PVC'ed, couldn't we 
> have an output of mri_gtmpvc with the whole brain PVC'ed ?
>
> Because the only files on output of mri_gtmpvc are :
> mgx.ctxgm.nii.gz - pvc'ed cortex gm only
> mgx.subctxgm.nii.gz - pvc'ed subcortical gm only
> mgx.gm.nii.gz - pvc'ed all gm
>
> Best regards,
> Matthieu
>
> 2016-01-11 18:20 GMT+01:00 Douglas N Greve  >:
>
>
> The pons intensity used to normalize has been PVC'ed. The file used is
> the input file.
>
>
> On 01/11/2016 04:04 AM, Matthieu Vanhoutte wrote:
> > Dear Douglas,
> >
> > Just one more question : by default mri_gtmpvc uses pons for
> computing
> > rSUV, but is this intensity normalization done before or after
> partial
> > volume correction ? What file is used in input for intensity
> > normalization ?
> >
> > Thanks in advance !
> >
> > Best regards,
> > Matthieu
> >
> > 2015-12-18 18:26 GMT+01:00 Douglas Greve
> 
> >  >>:
> >
> > You'll see several files that begin with mgx:
> > mgx.ctxgm.nii.gz - pvc'ed cortex gm only
> > mgx.subctxgm.nii.gz - pvc'ed subcortical gm only
> > mgx.gm.nii.gz - pvc'ed all gm
> >
> >
> > On 12/18/15 6:08 AM, Matthieu Vanhoutte wrote:
> >> Hello Douglas,
> >>
> >> I have run mri_gtmpvc with static PET images using the
> following
> >> command :
> >> mri_gtmpvc --i PET.nii.gz --psf 6 --auto-mask 8 0.01 --seg
> >> gtmseg.mgz --reg register.dof6.lta --default-seg-merge
> --mgx 0.01
> >> --o gtmpvc.output
> >>
> >> In the output directory "gtmpvc.output" where is the partial
> >> volume corrected PET image ?
> >>
> >> Thanks !
> >>
> >> Best regards,
> >> Matthieu
> >>
> >> 2015-12-15 21:07 GMT+01:00 Douglas N Greve
> >>  
>  >>:
> >>
> >> Not necessarily. It needs a good segmentation, so, to the
> >> extent that v6
> >> has a better segmentation then v6 is better.
> >>
> >> On 12/15/2015 02:57 PM, Matthieu Vanhoutte wrote:
> >> >
> >> > Thanks Douglas for the answer !
> >> >
> >> > But isn't PVC design for better working in terms of
> results
> >> with
> >> > v6_beta than v5.3 ?
> >> >
> >> > Best regards,
> >> >
> >> > Matthieu
> >> >
> >> > Le 15 déc. 2015 19:02, "Douglas N Greve"
> >>  
> >
> >> >  
> >>   >> >
> >> > It is not subsegmented in 6.0 either:). When you run
> >> gtmseg, it will
> >> > create the new segmentation that include pons and
> a few
> >> other things
> >> >
> >> > On 12/15/2015 12:56 PM, Matthieu Vanhoutte wrote:
> >> > > Dear Douglas,
> >> > >
> >> > > Please see below :
> >> > >
> >> > > 2015-12-15 18:37 GMT+01:00 Douglas N Greve
> >> >  
> >>  >
> >>  
> >>  >>
> >> > >  
> >>  >
> >> >  
> >>  

Re: [Freesurfer] fMRI activation color inversion

[Hirsch, Gabriella]

Thanks Doug! This is very good to know. Is there a ratio or relationship 
between the fmin and fmax that is optimal, as in, should we keep a 2 to 5 ratio?


Gabriella 

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: Monday, January 11, 2016 12:55 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] fMRI activation color inversion

There is another parameter called -fmid. The final mapping is a complicated 
combination of all three (fthresh, fmin, fslope). I usally use the -fminmax 
option which is easier to explain. -fminmax 2 5 means that the threshold is set 
to 2 and that at 5 the color will saturate.
doug

On 01/11/2016 12:18 PM, Hirsch, Gabriella wrote:
> Hi FreeSurfer experts,
>
> I recently ran a simple fMRI analysis in FSL and now generating images 
> of the activation in freesurfer using reg-feat2anat to register the 
> functional activation to the freesurfer recon-all files, and 
> generating the images using tksurfer:
>
> /tksurfer pilot_3 lh inflated -annot aparc.annot -ov 
> run4578_COMB.gfeat/cope1.feat/stats/zstat1.nii.gz -ovreg 
> run4_fwhm8.feat/reg/freesurfer/anat2std.register.dat *-fthresh 4 
> *-fslope 1/
>
> However I have come across a strange occurrence when I change the 
> threshold. Specifically, when I set the -fthresh flag (bolded) as 4 
> (i.e. p=0.0001) or less, the activation colors comes off as they 
> should (see 4_blue attached) in terms of how I set up the contrasts.
> But when I set my threshold to 5 or higher (changing nothing else), 
> the colors of the activation invert (see 5_red attached).
>
> What does this mean? How can I fix this?
>
> Any ideas would be greatly appreciated!
>
> Thank you!
> Gabriella
>
>
> Mass. Eye and Ear Confidentiality Notice: This e-mail and any files 
> transmitted with it are confidential and are intended solely for the 
> use of the individual(s) addressed in the message above. This 
> communication may contain sensitive or confidential information. If 
> you are not an intended recipient, dissemination, forwarding, 
> printing, or copying of this e-mail is strictly prohibited. If you 
> believe you have received this e-mail in error and the email contains 
> patient information, please contact the Mass. Eye and Ear Compliance 
> Line at 617-263-1600. If the e-mail was sent to you in error but does 
> not contain patient information, please contact the sender and delete 
> the e-mail.
>
>
> ___
> 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
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www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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properly dispose of the e-mail.




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Re: [Freesurfer] fMRI activation color inversion

[Hirsch, Gabriella]

OK, thanks!


Gabriella 


-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: Monday, January 11, 2016 2:31 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] fMRI activation color inversion

no, it is a matter of taste. Note that 2 is the threshold. If you are looking 
at sig maps, then the threshold may be important. The p-value threshold is 
10^-fthresh


On 01/11/2016 02:19 PM, Hirsch, Gabriella wrote:
> Thanks Doug! This is very good to know. Is there a ratio or relationship 
> between the fmin and fmax that is optimal, as in, should we keep a 2 to 5 
> ratio?
>
>
> Gabriella
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N 
> Greve
> Sent: Monday, January 11, 2016 12:55 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] fMRI activation color inversion
>
> There is another parameter called -fmid. The final mapping is a complicated 
> combination of all three (fthresh, fmin, fslope). I usally use the -fminmax 
> option which is easier to explain. -fminmax 2 5 means that the threshold is 
> set to 2 and that at 5 the color will saturate.
> doug
>
> On 01/11/2016 12:18 PM, Hirsch, Gabriella wrote:
>> Hi FreeSurfer experts,
>>
>> I recently ran a simple fMRI analysis in FSL and now generating 
>> images of the activation in freesurfer using reg-feat2anat to 
>> register the functional activation to the freesurfer recon-all files, 
>> and generating the images using tksurfer:
>>
>> /tksurfer pilot_3 lh inflated -annot aparc.annot -ov 
>> run4578_COMB.gfeat/cope1.feat/stats/zstat1.nii.gz -ovreg 
>> run4_fwhm8.feat/reg/freesurfer/anat2std.register.dat *-fthresh 4 
>> *-fslope 1/
>>
>> However I have come across a strange occurrence when I change the 
>> threshold. Specifically, when I set the -fthresh flag (bolded) as 4 
>> (i.e. p=0.0001) or less, the activation colors comes off as they 
>> should (see 4_blue attached) in terms of how I set up the contrasts.
>> But when I set my threshold to 5 or higher (changing nothing else), 
>> the colors of the activation invert (see 5_red attached).
>>
>> What does this mean? How can I fix this?
>>
>> Any ideas would be greatly appreciated!
>>
>> Thank you!
>> Gabriella
>>
>>
>> Mass. Eye and Ear Confidentiality Notice: This e-mail and any files 
>> transmitted with it are confidential and are intended solely for the 
>> use of the individual(s) addressed in the message above. This 
>> communication may contain sensitive or confidential information. If 
>> you are not an intended recipient, dissemination, forwarding, 
>> printing, or copying of this e-mail is strictly prohibited. If you 
>> believe you have received this e-mail in error and the email contains 
>> patient information, please contact the Mass. Eye and Ear Compliance 
>> Line at 617-263-1600. If the e-mail was sent to you in error but does 
>> not contain patient information, please contact the sender and delete 
>> the e-mail.
>>
>>
>> ___
>> 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.
>
>
>
>
> ___
> 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
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Re: [Freesurfer] Use of PVC PET images (V6) : between versions compatibility and intensity normalisation

[Douglas N Greve]

On 01/11/2016 02:14 PM, Matthieu Vanhoutte wrote:
> Dear Douglas,
>
> Sorry if I wasn't clear. With the PVC, voxels intensities are modified,
> right ?
Not necessarily. The GTM does not work this way. MG and RBV do. For an 
ROI analysis, the GTM is by far the preferred method.
> So, in the case of anatomical intensity normalization based on
> gray matter of cerebellum, is the mean activity of gray cerebellum taken
> from the original PET image or from the PVC'ed PET image ?
Again, not the right question for GTM
>
> Best regards,
> Matthieu
>
> Le 11/01/2016 18:52, Douglas N Greve a écrit :
>> I'm not sure exactly what you mean. I guess you could set all voxels in
>> a given ROI to be the value of that ROI? This is not really a voxel-wise
>> correction and probably would not do what you want. You can use the mgx
>> data (corrected with muller-gartner method). There is also a --rbv
>> (region-based voxel-wise, Thomas 2012) option.
>>
>>
>> On 01/11/2016 12:34 PM, Matthieu Vanhoutte wrote:
>>> Dear Douglas,
>>>
>>> If the pons intensity used to normalize has been PVC'ed, couldn't we
>>> have an output of mri_gtmpvc with the whole brain PVC'ed ?
>>>
>>> Because the only files on output of mri_gtmpvc are :
>>> mgx.ctxgm.nii.gz - pvc'ed cortex gm only
>>> mgx.subctxgm.nii.gz - pvc'ed subcortical gm only
>>> mgx.gm.nii.gz - pvc'ed all gm
>>>
>>> Best regards,
>>> Matthieu
>>>
>>> 2016-01-11 18:20 GMT+01:00 Douglas N Greve >> >:
>>>
>>>
>>>   The pons intensity used to normalize has been PVC'ed. The file used is
>>>   the input file.
>>>
>>>
>>>   On 01/11/2016 04:04 AM, Matthieu Vanhoutte wrote:
>>>   > Dear Douglas,
>>>   >
>>>   > Just one more question : by default mri_gtmpvc uses pons for
>>>   computing
>>>   > rSUV, but is this intensity normalization done before or after
>>>   partial
>>>   > volume correction ? What file is used in input for intensity
>>>   > normalization ?
>>>   >
>>>   > Thanks in advance !
>>>   >
>>>   > Best regards,
>>>   > Matthieu
>>>   >
>>>   > 2015-12-18 18:26 GMT+01:00 Douglas Greve
>>>   
>>>   > >>   >>:
>>>   >
>>>   > You'll see several files that begin with mgx:
>>>   > mgx.ctxgm.nii.gz - pvc'ed cortex gm only
>>>   > mgx.subctxgm.nii.gz - pvc'ed subcortical gm only
>>>   > mgx.gm.nii.gz - pvc'ed all gm
>>>   >
>>>   >
>>>   > On 12/18/15 6:08 AM, Matthieu Vanhoutte wrote:
>>>   >> Hello Douglas,
>>>   >>
>>>   >> I have run mri_gtmpvc with static PET images using the
>>>   following
>>>   >> command :
>>>   >> mri_gtmpvc --i PET.nii.gz --psf 6 --auto-mask 8 0.01 --seg
>>>   >> gtmseg.mgz --reg register.dof6.lta --default-seg-merge
>>>   --mgx 0.01
>>>   >> --o gtmpvc.output
>>>   >>
>>>   >> In the output directory "gtmpvc.output" where is the partial
>>>   >> volume corrected PET image ?
>>>   >>
>>>   >> Thanks !
>>>   >>
>>>   >> Best regards,
>>>   >> Matthieu
>>>   >>
>>>   >> 2015-12-15 21:07 GMT+01:00 Douglas N Greve
>>>   >> >>   
>>>   >>   >>:
>>>   >>
>>>   >> Not necessarily. It needs a good segmentation, so, to the
>>>   >> extent that v6
>>>   >> has a better segmentation then v6 is better.
>>>   >>
>>>   >> On 12/15/2015 02:57 PM, Matthieu Vanhoutte wrote:
>>>   >> >
>>>   >> > Thanks Douglas for the answer !
>>>   >> >
>>>   >> > But isn't PVC design for better working in terms of
>>>   results
>>>   >> with
>>>   >> > v6_beta than v5.3 ?
>>>   >> >
>>>   >> > Best regards,
>>>   >> >
>>>   >> > Matthieu
>>>   >> >
>>>   >> > Le 15 déc. 2015 19:02, "Douglas N Greve"
>>>   >> >>   
>>>   >
>>>   >> > >>   
>>>   >> >>   >>   >> >
>>>   >> > It is not subsegmented in 6.0 either:). When you run
>>>   >> gtmseg, it will
>>>   >> > create the new segmentation that include pons and
>>>   a few
>>>   >> other things
>>>   >> >
>>>   >> > On 

Re: [Freesurfer] Use of PVC PET images (V6) : between versions compatibility and intensity normalisation

[Douglas N Greve]

Yes with MGPVC the voxel values are rescaled by the MG formula. Note 
that MG (and RBV) use GTM as a preprocessing step. If you average the MG 
output over an ROI, then it comes close to the GTM value.

On 01/11/2016 02:39 PM, Matthieu Vanhoutte wrote:
> Le 11/01/2016 20:33, Douglas N Greve a écrit :
>> On 01/11/2016 02:14 PM, Matthieu Vanhoutte wrote:
>>> Dear Douglas,
>>>
>>> Sorry if I wasn't clear. With the PVC, voxels intensities are modified,
>>> right ?
>> Not necessarily. The GTM does not work this way. MG and RBV do. For an
>> ROI analysis, the GTM is by far the preferred method.
> I suppose I used MG method since I specified  --mgx option (I would 
> like to do an entire cortex analysis) ?
> With MG PVC, voxels intensities are the modified ?
>
> Best regards,
> Matthieu
>>> So, in the case of anatomical intensity normalization based on
>>> gray matter of cerebellum, is the mean activity of gray cerebellum taken
>>> from the original PET image or from the PVC'ed PET image ?
>> Again, not the right question for GTM
>>> Best regards,
>>> Matthieu
>>>
>>> Le 11/01/2016 18:52, Douglas N Greve a écrit :
 I'm not sure exactly what you mean. I guess you could set all voxels in
 a given ROI to be the value of that ROI? This is not really a voxel-wise
 correction and probably would not do what you want. You can use the mgx
 data (corrected with muller-gartner method). There is also a --rbv
 (region-based voxel-wise, Thomas 2012) option.


 On 01/11/2016 12:34 PM, Matthieu Vanhoutte wrote:
> Dear Douglas,
>
> If the pons intensity used to normalize has been PVC'ed, couldn't we
> have an output of mri_gtmpvc with the whole brain PVC'ed ?
>
> Because the only files on output of mri_gtmpvc are :
> mgx.ctxgm.nii.gz - pvc'ed cortex gm only
> mgx.subctxgm.nii.gz - pvc'ed subcortical gm only
> mgx.gm.nii.gz - pvc'ed all gm
>
> Best regards,
> Matthieu
>
> 2016-01-11 18:20 GMT+01:00 Douglas N Greve  >:
>
>
>The pons intensity used to normalize has been PVC'ed. The file 
> used is
>the input file.
>
>
>On 01/11/2016 04:04 AM, Matthieu Vanhoutte wrote:
>> Dear Douglas,
>>
>> Just one more question : by default mri_gtmpvc uses pons for
>computing
>> rSUV, but is this intensity normalization done before or after
>partial
>> volume correction ? What file is used in input for intensity
>> normalization ?
>>
>> Thanks in advance !
>>
>> Best regards,
>> Matthieu
>>
>> 2015-12-18 18:26 GMT+01:00 Douglas Greve
>
>> >>:
>>
>> You'll see several files that begin with mgx:
>> mgx.ctxgm.nii.gz - pvc'ed cortex gm only
>> mgx.subctxgm.nii.gz - pvc'ed subcortical gm only
>> mgx.gm.nii.gz - pvc'ed all gm
>>
>>
>> On 12/18/15 6:08 AM, Matthieu Vanhoutte wrote:
>>> Hello Douglas,
>>>
>>> I have run mri_gtmpvc with static PET images using the
>following
>>> command :
>>> mri_gtmpvc --i PET.nii.gz --psf 6 --auto-mask 8 0.01 --seg
>>> gtmseg.mgz --reg register.dof6.lta --default-seg-merge
>--mgx 0.01
>>> --o gtmpvc.output
>>>
>>> In the output directory "gtmpvc.output" where is the partial
>>> volume corrected PET image ?
>>>
>>> Thanks !
>>>
>>> Best regards,
>>> Matthieu
>>>
>>> 2015-12-15 21:07 GMT+01:00 Douglas N Greve
>>> 
>>>:
>>>
>>> Not necessarily. It needs a good segmentation, so, to 
> the
>>> extent that v6
>>> has a better segmentation then v6 is better.
>>>
>>> On 12/15/2015 02:57 PM, Matthieu Vanhoutte wrote:
>>> >
>>> > Thanks Douglas for the answer !
>>> >
>>> > But isn't PVC design for better working in terms of
>results
>>> with
>>> > v6_beta than v5.3 ?
>>> >
>>> > Best regards,
>>> >
>>> > 

Re: [Freesurfer] Use of PVC PET images (V6) : between versions compatibility and intensity normalisation

[Matthieu Vanhoutte]

Dear Douglas,

Sorry if I wasn't clear. With the PVC, voxels intensities are modified, 
right ? So, in the case of anatomical intensity normalization based on 
gray matter of cerebellum, is the mean activity of gray cerebellum taken 
from the original PET image or from the PVC'ed PET image ?

Best regards,
Matthieu

Le 11/01/2016 18:52, Douglas N Greve a écrit :
> I'm not sure exactly what you mean. I guess you could set all voxels in
> a given ROI to be the value of that ROI? This is not really a voxel-wise
> correction and probably would not do what you want. You can use the mgx
> data (corrected with muller-gartner method). There is also a --rbv
> (region-based voxel-wise, Thomas 2012) option.
>
>
> On 01/11/2016 12:34 PM, Matthieu Vanhoutte wrote:
>> Dear Douglas,
>>
>> If the pons intensity used to normalize has been PVC'ed, couldn't we
>> have an output of mri_gtmpvc with the whole brain PVC'ed ?
>>
>> Because the only files on output of mri_gtmpvc are :
>> mgx.ctxgm.nii.gz - pvc'ed cortex gm only
>> mgx.subctxgm.nii.gz - pvc'ed subcortical gm only
>> mgx.gm.nii.gz - pvc'ed all gm
>>
>> Best regards,
>> Matthieu
>>
>> 2016-01-11 18:20 GMT+01:00 Douglas N Greve > >:
>>
>>
>>  The pons intensity used to normalize has been PVC'ed. The file used is
>>  the input file.
>>
>>
>>  On 01/11/2016 04:04 AM, Matthieu Vanhoutte wrote:
>>  > Dear Douglas,
>>  >
>>  > Just one more question : by default mri_gtmpvc uses pons for
>>  computing
>>  > rSUV, but is this intensity normalization done before or after
>>  partial
>>  > volume correction ? What file is used in input for intensity
>>  > normalization ?
>>  >
>>  > Thanks in advance !
>>  >
>>  > Best regards,
>>  > Matthieu
>>  >
>>  > 2015-12-18 18:26 GMT+01:00 Douglas Greve
>>  
>>  > >  >>:
>>  >
>>  > You'll see several files that begin with mgx:
>>  > mgx.ctxgm.nii.gz - pvc'ed cortex gm only
>>  > mgx.subctxgm.nii.gz - pvc'ed subcortical gm only
>>  > mgx.gm.nii.gz - pvc'ed all gm
>>  >
>>  >
>>  > On 12/18/15 6:08 AM, Matthieu Vanhoutte wrote:
>>  >> Hello Douglas,
>>  >>
>>  >> I have run mri_gtmpvc with static PET images using the
>>  following
>>  >> command :
>>  >> mri_gtmpvc --i PET.nii.gz --psf 6 --auto-mask 8 0.01 --seg
>>  >> gtmseg.mgz --reg register.dof6.lta --default-seg-merge
>>  --mgx 0.01
>>  >> --o gtmpvc.output
>>  >>
>>  >> In the output directory "gtmpvc.output" where is the partial
>>  >> volume corrected PET image ?
>>  >>
>>  >> Thanks !
>>  >>
>>  >> Best regards,
>>  >> Matthieu
>>  >>
>>  >> 2015-12-15 21:07 GMT+01:00 Douglas N Greve
>>  >> >  
>>  >  >>:
>>  >>
>>  >> Not necessarily. It needs a good segmentation, so, to the
>>  >> extent that v6
>>  >> has a better segmentation then v6 is better.
>>  >>
>>  >> On 12/15/2015 02:57 PM, Matthieu Vanhoutte wrote:
>>  >> >
>>  >> > Thanks Douglas for the answer !
>>  >> >
>>  >> > But isn't PVC design for better working in terms of
>>  results
>>  >> with
>>  >> > v6_beta than v5.3 ?
>>  >> >
>>  >> > Best regards,
>>  >> >
>>  >> > Matthieu
>>  >> >
>>  >> > Le 15 déc. 2015 19:02, "Douglas N Greve"
>>  >> >  
>>  >
>>  >> > >  
>>  >> >  >  >> >
>>  >> > It is not subsegmented in 6.0 either:). When you run
>>  >> gtmseg, it will
>>  >> > create the new segmentation that include pons and
>>  a few
>>  >> other things
>>  >> >
>>  >> > On 12/15/2015 12:56 PM, Matthieu Vanhoutte wrote:
>>  >> > > Dear Douglas,
>>  >> > >
>>  >> > > Please see below :
>>  >> > >
>>  >> > > 2015-12-15 18:37 GMT+01:00 Douglas N Greve
>>  >> > >  
>>  >> >  

Re: [Freesurfer] fMRI activation color inversion

[Douglas N Greve]

no, it is a matter of taste. Note that 2 is the threshold. If you are 
looking at sig maps, then the threshold may be important. The p-value 
threshold is 10^-fthresh


On 01/11/2016 02:19 PM, Hirsch, Gabriella wrote:
> Thanks Doug! This is very good to know. Is there a ratio or relationship 
> between the fmin and fmax that is optimal, as in, should we keep a 2 to 5 
> ratio?
>
>
> Gabriella
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
> Sent: Monday, January 11, 2016 12:55 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] fMRI activation color inversion
>
> There is another parameter called -fmid. The final mapping is a complicated 
> combination of all three (fthresh, fmin, fslope). I usally use the -fminmax 
> option which is easier to explain. -fminmax 2 5 means that the threshold is 
> set to 2 and that at 5 the color will saturate.
> doug
>
> On 01/11/2016 12:18 PM, Hirsch, Gabriella wrote:
>> Hi FreeSurfer experts,
>>
>> I recently ran a simple fMRI analysis in FSL and now generating images
>> of the activation in freesurfer using reg-feat2anat to register the
>> functional activation to the freesurfer recon-all files, and
>> generating the images using tksurfer:
>>
>> /tksurfer pilot_3 lh inflated -annot aparc.annot -ov
>> run4578_COMB.gfeat/cope1.feat/stats/zstat1.nii.gz -ovreg
>> run4_fwhm8.feat/reg/freesurfer/anat2std.register.dat *-fthresh 4
>> *-fslope 1/
>>
>> However I have come across a strange occurrence when I change the
>> threshold. Specifically, when I set the -fthresh flag (bolded) as 4
>> (i.e. p=0.0001) or less, the activation colors comes off as they
>> should (see 4_blue attached) in terms of how I set up the contrasts.
>> But when I set my threshold to 5 or higher (changing nothing else),
>> the colors of the activation invert (see 5_red attached).
>>
>> What does this mean? How can I fix this?
>>
>> Any ideas would be greatly appreciated!
>>
>> Thank you!
>> Gabriella
>>
>>
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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
>
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>
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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

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Re: [Freesurfer] Use of PVC PET images (V6) : between versions compatibility and intensity normalisation

[Matthieu Vanhoutte]

Le 11/01/2016 20:33, Douglas N Greve a écrit :


On 01/11/2016 02:14 PM, Matthieu Vanhoutte wrote:

Dear Douglas,

Sorry if I wasn't clear. With the PVC, voxels intensities are modified,
right ?

Not necessarily. The GTM does not work this way. MG and RBV do. For an
ROI analysis, the GTM is by far the preferred method.
I suppose I used MG method since I specified --mgx option (I would like 
to do an entire cortex analysis) ?

With MG PVC, voxels intensities are the modified ?

Best regards,
Matthieu

So, in the case of anatomical intensity normalization based on
gray matter of cerebellum, is the mean activity of gray cerebellum taken
from the original PET image or from the PVC'ed PET image ?

Again, not the right question for GTM

Best regards,
Matthieu

Le 11/01/2016 18:52, Douglas N Greve a écrit :

I'm not sure exactly what you mean. I guess you could set all voxels in
a given ROI to be the value of that ROI? This is not really a voxel-wise
correction and probably would not do what you want. You can use the mgx
data (corrected with muller-gartner method). There is also a --rbv
(region-based voxel-wise, Thomas 2012) option.


On 01/11/2016 12:34 PM, Matthieu Vanhoutte wrote:

Dear Douglas,

If the pons intensity used to normalize has been PVC'ed, couldn't we
have an output of mri_gtmpvc with the whole brain PVC'ed ?

Because the only files on output of mri_gtmpvc are :
mgx.ctxgm.nii.gz - pvc'ed cortex gm only
mgx.subctxgm.nii.gz - pvc'ed subcortical gm only
mgx.gm.nii.gz - pvc'ed all gm

Best regards,
Matthieu

2016-01-11 18:20 GMT+01:00 Douglas N Greve >:


   The pons intensity used to normalize has been PVC'ed. The file used is
   the input file.


   On 01/11/2016 04:04 AM, Matthieu Vanhoutte wrote:
   > Dear Douglas,
   >
   > Just one more question : by default mri_gtmpvc uses pons for
   computing
   > rSUV, but is this intensity normalization done before or after
   partial
   > volume correction ? What file is used in input for intensity
   > normalization ?
   >
   > Thanks in advance !
   >
   > Best regards,
   > Matthieu
   >
   > 2015-12-18 18:26 GMT+01:00 Douglas Greve
   
   > >>:
   >
   > You'll see several files that begin with mgx:
   > mgx.ctxgm.nii.gz - pvc'ed cortex gm only
   > mgx.subctxgm.nii.gz - pvc'ed subcortical gm only
   > mgx.gm.nii.gz - pvc'ed all gm
   >
   >
   > On 12/18/15 6:08 AM, Matthieu Vanhoutte wrote:
   >> Hello Douglas,
   >>
   >> I have run mri_gtmpvc with static PET images using the
   following
   >> command :
   >> mri_gtmpvc --i PET.nii.gz --psf 6 --auto-mask 8 0.01 --seg
   >> gtmseg.mgz --reg register.dof6.lta --default-seg-merge
   --mgx 0.01
   >> --o gtmpvc.output
   >>
   >> In the output directory "gtmpvc.output" where is the partial
   >> volume corrected PET image ?
   >>
   >> Thanks !
   >>
   >> Best regards,
   >> Matthieu
   >>
   >> 2015-12-15 21:07 GMT+01:00 Douglas N Greve
   >> 
   >>:
   >>
   >> Not necessarily. It needs a good segmentation, so, to the
   >> extent that v6
   >> has a better segmentation then v6 is better.
   >>
   >> On 12/15/2015 02:57 PM, Matthieu Vanhoutte wrote:
   >> >
   >> > Thanks Douglas for the answer !
   >> >
   >> > But isn't PVC design for better working in terms of
   results
   >> with
   >> > v6_beta than v5.3 ?
   >> >
   >> > Best regards,
   >> >
   >> > Matthieu
   >> >
   >> > Le 15 déc. 2015 19:02, "Douglas N Greve"
   >> 
   >
   >> > 
   >> > >
   >> > It is not subsegmented in 6.0 either:). When you run
   >> gtmseg, it will
   >> > create the new segmentation that include pons and
   a few
   >> other things
   >> >
   >> > On 12/15/2015 12:56 PM, Matthieu Vanhoutte wrote:
   >> > > Dear Douglas,
   >> > >
   >>