Re: [Freesurfer] Longitudinal Hippocampal Subfields - error during segmentation {Disarmed}

[Iglesias Gonzalez, Eugenio]

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Hi Rachel
This is very weird. What exact version are you using? 6.0 or dev?
Cheers
Eugenio

Juan Eugenio Iglesias

ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London

Research staff
Martinos Center for Biomedical Imaging
Massachusetts General Hospital and Harvard Medical School

Research Affiliate
Computer Science and Artificial Intelligence Laboratory (CSAIL)
Massachusetts Institute of Technology


www.jeiglesias.comwww.jeiglesias.com>




From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Rachel Phillips 

Sent: Friday, January 4, 2019 7:43:45 PM
To: freesurfer@nmr.mgh.harvard.edu
Cc: Courtney Haswell
Subject: [Freesurfer] Longitudinal Hippocampal Subfields - error during 
segmentation


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Hello,


I have run a longitudinal sample (up to 4 timepoints per subject) through the 
Freesurfer 6.0 longitudinal processing pipeline, and currently I am attempting 
to produce the longitudinal hippocampal subfield segmentation with the 
following command: longHippoSubfieldsT1.sh  [SubjectsDirectory]. I am 
receiving the following error: "Error using SegmentSubfeldsT1Longitudinal (line 
441) The vector of prior probabilities in the mesh nodes must always sum to one 
over all classes".


Below is an example of the output that precedes this error:


[> In SegmentSubfieldsT1Longitudinal at 418]
Reading contexts of file 
/usr/local/packages/freesurfer_v6.0.0/average/HippoSF/atlas/compressionLookupTable.txt
--
Making Lateral-nucleus map to reduced label 1
Making Paralaminar-nucleus map to reduced label 1
Making Basal-nucleus map to reduced label 1
Making Accessory-Basal-nucleus map to reduced label 1
Making Corticoamygdaloid-transitio map to reduced label 1
Making Central-nucleus map to reduced label 1
Making Cortical-nucleus map to reduced label 1
Making Medial-nucleus map to reduced label 1
Making Anterior-amygdaloid-area-AAA map to reduced label 1
--
Making alveus map to reduced label 2
Making Hippocampal_tail map to reduced label 2
Making HATA map to reduced label 2
Making fimbria map to reduced label 2
Making parasubiculum map to reduced label 2
Making hippocampal-fissure map to reduced label 2
--
Making Left-Cerebral-Cortex map to reduced label 3
--
Making Left-Cerebral-White-Matter map to reduced label 4
--
Making Left-Lateral-Ventricle map to reduced label 5
--
Making Left-choroid-plexus map to reduced label 6
--
Making Unknown map to reduced label 7
--
Making Left-VentralDC map to reduced label 8
--
Making Left-Putamen map to reduced label 9
--
Making Left-Pallidum map to reduced label 10
--
Making Left-Thalamus-Proper map to reduced label 11
--
Making Left-Accumbens-area map to reduced label 12
--
Making Left-Caudate map to reduced label 13
Error using SegmentSubfieldsT1Longitudinal (line 441)
The vector of prior probabilities in the mesh nodes must always sum to one over 
all classes

Any guidance on this error would be greatly appreciated.

Thanks,
Rachel
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Re: [Freesurfer] Setting the origin in native space

[Bruce Fischl]

try using the switch:

mri_convert -rt nearest ...

to use nearest neighbor interpolation (which is what you need to resample a 
segmentation volume)


cheers
Bruce


On Sun, 6 Jan 2019, Nillo, Ryan Michael R wrote:



External Email - Use Caution

Thanks for your help, Bruce. This worked like a charm! How would I register the 
output segmentation
back to the subject's T1.mgz? When I use mri_convert, the ROIs have a weird 
border around them.


thanks again,

Ryan 

__
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of
Bruce Fischl 
Sent: Wednesday, December 19, 2018 11:43:03 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Setting the origin in native space  
Hi Ryan

I think mri_convert -at   

should do the trick.

cheers
Bruce


On Wed, 19 Dec
2018, Nillo, Ryan Michael R wrote:

>    External Email - Use Caution
>
> Hello FreeSurfer users,
>
> I want to use the suit software to segment the cerebellum, however the 
software requires the origin
be set at the anterior composure. I know the Talairach image’s origin is set at 
the anterior commisure
and that there is a Talairach transformation in mri/transforms. Is there a way 
to use this information
to set the origin to the anterior commisure in the native space image?
>
> Thanks in advance,
> Ryan Nillo
> Staff Research Associate
> UCSF Department of Radiology and Biomedical Imaging
>
>
> ___
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To see the collection of prior postings to the list, visit the Freesurfer 
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archive which includes
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>
>
>

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Re: [Freesurfer] Setting the origin in native space

[Nillo, Ryan Michael R]

External Email - Use Caution

Thanks for your help, Bruce. This worked like a charm! How would I register the 
output segmentation back to the subject's T1.mgz? When I use mri_convert, the 
ROIs have a weird border around them.


thanks again,

Ryan


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Bruce Fischl 

Sent: Wednesday, December 19, 2018 11:43:03 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Setting the origin in native space

Hi Ryan

I think mri_convert -at   

should do the trick.

cheers
Bruce


On Wed, 19 Dec
2018, Nillo, Ryan Michael R wrote:

>External Email - Use Caution
>
> Hello FreeSurfer users,
>
> I want to use the suit software to segment the cerebellum, however the 
> software requires the origin be set at the anterior composure. I know the 
> Talairach image’s origin is set at the anterior commisure and that there is a 
> Talairach transformation in mri/transforms. Is there a way to use this 
> information to set the origin to the anterior commisure in the native space 
> image?
>
> Thanks in advance,
> Ryan Nillo
> Staff Research Associate
> UCSF Department of Radiology and Biomedical Imaging
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer Info Page - Harvard 
University
mail.nmr.mgh.harvard.edu
To see the collection of prior postings to the list, visit the Freesurfer 
Archives.. A searchable archive which of messages PRIOR to March 2004 is at 
this site A searchable archive which includes messages AFTER March 2004 is at 
this site. Using Freesurfer



>
>
>
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Re: [Freesurfer] FSGD file

[Raffaele Dubbioso]

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Thanks, but I got the following error message:

RROR: matrix is ill-conditioned or badly scaled, condno = 1e+08

Possible problem with experimental design:
Check for duplicate entries and/or lack of range of
continuous variables within a class.
If you seek help with this problem, make sure to send:
  1. Your command line:
mri_glmfit.bin --y rh.t1t2ratio_30_fmed_3sm_decurv.fsavg.mgh --fsgd
age_gender.fsgd --pvr rh.thickness_30.fsavg.mgh --C group.diff.mtx --surf
fsaverage rh --cortex --glmdir
rh_allbrain_t1t2_group_thickness_age_gender.glmdir
  2. The FSGD file (if using one)
  3. And the design matrix above
Attempting to diagnose further
SumSq: Min=0.00 (col 5), Max=146.140350 (col 3)
 The scale is much different between columns 5 and 3, you may want to
 normalize by subtracting the mean and dividing by the standard deviation.
Column 5,  all values are 0
Column 6,  all values are 0
Columns 5 and 6 are the same


Il giorno dom 6 gen 2019 alle ore 20:18 Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> ha scritto:

> yes, that is the right contrast
>
> On 1/5/19 7:30 AM, Raffaele Dubbioso wrote:
>
> External Email - Use Caution
> Thanks a lot.
> Sorry if I bother you again:
> If I want to remove thickness, age and gender as nuisance variables;
> My FSGD file should be:
>
> GroupDescriptorFile 1
> Title Func
> Class HC
> Class CMT
> Variables  Age gender
> Input fs_VF HC  46 Female
> Input fs_RF HC 24 Female
> ...
>
> My group.diff.mtx should be:
> 1 -1 0 0 0 0 0
>
> Is it ok?
>
> Thanks a lot
> Raffaele
>
> Il giorno gio 3 gen 2019 alle ore 20:11 Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> ha scritto:
>
>> The contrast is not correct for your design. Your design matrix will
>> have 3 columns, one for HC, one for CMT, and one for
>> rh.thickness_30.fsavg.mgh. Ie, it automatcailly interprets PVRs in a
>> DOSS kind of way. If you want to test for a difference in
>> thickness-meylin slopes between the two groups, you will need to have
>> two PVRs, one where the value is the thickness for HC subjects and 0 for
>> CMT subjects, the other the reverse, then set your contrast to 0 0 1 -1.
>> If you just want to remove thickness as a nuisance, then you can stick
>> with what you have and just use a contrast of 1 -1 0
>>
>> On 12/25/18 5:05 AM, Raffaele Dubbioso wrote:
>> >
>> > External Email - Use Caution
>> >
>> > Dear Freesurfer team,
>> >
>> > I'm running a group analysis where I'd like to compare myelination
>> > between two groups regressing out cortical thickness.
>> > Unfortunately I get always the same error message:
>> > dimension mismatch between X and contrast group.diff.mtx   X has 3
>> > cols, C has 4 cols. Is my group.mtx correct?
>> >
>> > My command line is:
>> > mri_glmfit --y rh.t1t2ratio_30_fmed_3sm_decurv.fsavg.mgh --fsgd
>> > thickness.fsgd --pvr rh.thickness_30.fsavg.mgh --C group.diff.mtx --C
>> > group-x-thick --Cg1g2.intercept.mts --C g1g2.thick.mtx --surf
>> > fsaverage rh --cortex --glmdir rh_allbrain_t1t2_group_thickness.glmdir
>> >
>> > My group_diff.mtx: 1 -1 0 0
>> >
>> > This is my FSGD FILE:
>> > GroupDescriptorFile 1
>> > Title Myelin
>> > Class HC
>> > Class CMT
>> > Inputfs_VFHC
>> > 
>> >
>> >
>> >  Thank you very much for your help
>> >
>> > Best regards,
>> > Raffaele
>> >
>> > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> ___
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>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> --
>
> ___
> Raffaele Dubbioso, MD, PhD
> University Federico II of Naples
> Department of Neurosciences, Reproductive Sciences
> and Odontostomatology.
> Via Sergio Pansini, 5
> 80131 Napoli, ITALY
> phone: +39-0817464579
> fax: +39-0817462667
>
> ___
> Freesurfer mailing 
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>
>
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-- 

___
Raffaele Dubbioso, MD, PhD
University Federico II of Naples
Department of Neurosciences, Reproductive Sciences
and Odontostomatology.
Via Sergio Pansini, 5
80131 Napoli, ITALY
phone: +39-0817464579
fax: +39-0817462667
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Re: [Freesurfer] Robust PET signal projection

[Matthieu Vanhoutte]

External Email - Use Caution

Hi Douglas,

Could you answer to my previous request ?

Best,
Matt

> Le 21 déc. 2018 à 20:31, Matthieu Vanhoutte  a 
> écrit :
> 
> Thanks Douglas.
> 
> Is there a way to compute a weighted average in one command with fscalc ?
> 
> Best,
> Matthieu
> 
> 
> Le mar. 18 déc. 2018 à 18:03, Greve, Douglas N.,Ph.D.  > a écrit :
> you can use mri_vol2surf to sample at different depths. If you want a simple 
> average across cortex, then you can use --projfrac-avg .35 .65 .05
> If you want to do more sophisticated weighting, then you will have to sample 
> at each layer and then combine the files (eg, fscalc). Unless you have very 
> small voxels, it probably will not make a difference. 
> 
> On 12/18/18 4:50 AM, Matthieu Vanhoutte wrote:
>> External Email - Use Caution
>> 
>> Dear experts,
>> 
>> Is there any advice on this point ?
>> 
>> Best,
>> Matthieu
>> 
>> 
>> Le mer. 12 déc. 2018 à 10:47, Matthieu Vanhoutte 
>> mailto:matthieuvanhou...@gmail.com>> a écrit :
>> Dear Freesurfer's experts,
>> 
>> In order to have a robust PET signal projection, is it possible compute the 
>> projected PET signal as a weighted average of the PET signal intersecting 
>> with the surfaces ranging from 35 to 65% of the cortical tickness with a 
>> step t=5% ?
>> 
>> More weight would be given to the surfaces located near the mid distance 
>> between the pial and white surfaces as they have a higher probability to be 
>> well located within the cortex (using a normal distribution for example).
>> 
>> Thank you for helping.
>> 
>> Best,
>> Matthieu
>> 
>> 
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Re: [Freesurfer] [PETSurfer] Intensity normalization of PET images without PVE correction

[Matthieu Vanhoutte]

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Hi Douglas,

Could you answer to my previous request ?

Best,
Matt

> Le 21 déc. 2018 à 20:22, Matthieu Vanhoutte  a 
> écrit :
> 
> Hi Douglas,
> 
> Thanks for helping.
> 
> To have an only rescaled voxel-wise PET image, these options seem to work 
> only when -rbv method is used and not -mgx.
> 
> Do you know why ?
> 
> Best,
> Matthieu 
> 
> 
> Le mar. 18 déc. 2018 à 17:58, Greve, Douglas N.,Ph.D.  > a écrit :
> You will need to set --psf 0 and --no-tfe to fully turn off PVC. 
> 
> On 12/18/18 4:50 AM, Matthieu Vanhoutte wrote:
>> External Email - Use Caution
>> 
>> Hi Douglas,
>> 
>> Could you help me on this point ?
>> 
>> Best,
>> Matthieu
>> 
>> 
>> Le mer. 12 déc. 2018 à 10:50, Matthieu Vanhoutte 
>> mailto:matthieuvanhou...@gmail.com>> a écrit :
>> Dear Douglas,
>> 
>> Is it possible to use mri_gtmpvc command in order to intensity normalize PET 
>> images without applying PVE correction by setting --psf to 0 ?
>> 
>> Best,
>> Matthieu
>> 
>> 
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Re: [Freesurfer] [PETsurfer] Use of MGX and RBV partial volume correction

[Matthieu Vanhoutte]

External Email - Use Caution

Hi Douglas,

Could you answer to my previous request ?

Best,
Matt

> Le 21 déc. 2018 à 20:29, Matthieu Vanhoutte  a 
> écrit :
> 
> Hi Douglas,
> 
> Thanks for these clarifications. I have however one misunderstanding.
> 
> When sampling PVC corrected PET image onto surface:
> - I use bbpet2anat.lta when MGX was used as specified un tutorial
> - I use rbv2anat.lta when RBV was used
> 
> But why not to use template.reg.lta computed by mri_coreg ? What are the 
> differences between those different files ?
> 
> Best,
> Matthieu
> 
> Le mar. 18 déc. 2018 à 18:13, Greve, Douglas N.,Ph.D.  > a écrit :
> 
> 
> On 12/7/18 9:29 AM, Matthieu Vanhoutte wrote:
> >  External Email - Use Caution
> >
> > Hi Douglas,
> >
> > Thanks for these clarifications. I added some others questions inline below.
> >
> > Best,
> > Matthieu
> >
> >> Le 6 déc. 2018 à 17:25, Greve, Douglas N.,Ph.D.  >> > a écrit :
> >>
> >>
> >>
> >> On 11/30/2018 07:15 AM, Matthieu Vanhoutte wrote:
> >>>  External Email - Use Caution
> >>>
> >>> Hi Douglas,
> >>>
> >>> Thank you for answering. Please find below new questions.
> >>> Bien cordialement,
> >>>
> >>>
> >>> Le ven. 30 nov. 2018 à 00:00, Greve, Douglas N.,Ph.D.
> >>> mailto:dgr...@mgh.harvard.edu> 
> >>> >> a écrit :
> >>>
> >>> Hi Matthieu, sorry for the delay
> >>>
> >>> On 11/29/2018 12:50 PM, Matthieu Vanhoutte wrote:
> External Email - Use Caution
> 
>  Dear Freesurfer's experts,
> 
>  I tried to use PETSurfer to correct partial volume effect on my
> >>> FDG PET images, testing both Muller-Gartner and RBV corrections.
>  I ran the commands specified in PETSurfer website and used the
> >>> two following commands for both MGX and RBV corrections respectively:
>  mri_gtmpvc --i PET.nii.gz --reg register.dof6.lta --psf-col 5.51
> >>> --psf-row 5.51 --psf-slice 5.9 --seg gtmseg.mgz
> >>> --default-seg-merge --auto-mask PSF .01 --mgx .01 --o ./gtmpvc.output
>  mri_gtmpvc --i PET.nii.gz --reg register.dof6.lta --psf-col 5.51
> >>> --psf-row 5.51 --psf-slice 5.9 --seg gtmseg.mgz
> >>> --default-seg-merge --auto-mask PSF .01 --rbv --o rbv.output.orig
>  1) However, I found that cortical output mgx.ctxgm.nii.gz of MGX
> >>> correction encompass more than just GM and values at the
> >>> boundaries of mgx.ctxgm.nii.gz seem to me very high or aberrant.
> >>> This is expected. The MG method gives you a value every place that
> >>> there
> >>> is GM signal *in the PET volume after partial volume effects*. So
> >>> basically, if you were to take the cortical ribbon and smooth it
> >>> by your
> >>> PSF, every non-zero voxel has some GM in it (which is why the
> >>> edges are
> >>> so high). When you run it with --mgx .01, it will exclude voxels that
> >>> have less than 1% GM after smoothing. If you you are disturbed by the
> >>> wide ribbon, just make the threshold higher. In theory, every point
> >>> along the surface normal gives you a valid answer, but the further
> >>> from
> >>> the center of the ribbon, the noisier it is going to be, so we
> >>> generally
> >>> only sample it at the center (--projfrac 0.5 to mri_vol2surf).
> >>>
> >>>
> >>> Basically, please find below the mgx.ctxgm with threshold set at 0.01:
> >>> image.png
> >>>
> >>> Then threshold set at 0.1:
> >>> image.png
> >>>
> >>> Values at some parts of the cortex (olfactory, visual) are not the
> >>> same between the two thresholds. In the first one in these parts of
> >>> the brain, values are higher than the second and seem kind of
> >>> aberrant. Is there no reason to prefer a threshold at 0.1 than 0.01 ?
> >>> For example, in (Douglas et al., 2016, NeuroImage) a threshold of 0.3
> >>> has been found to be optimal: how determine visually or quantitatively
> >>> this optimal threshold ?
> >> So when you click on the same voxel in both images, you get different
> >> values? Or is it just that the color scale is changing? The threshold
> >> should not change the values, just what is in or out of the final mask.
> >> The threshold of 0.3 was chosen mainly because it worked for the ROI
> >> analysis. In general, you should use GTM instead of MG for ROI analysis.
> >> For surface-based analysis, the threshold is not critical because the GM
> >> PVF is generally pretty high in cortex. It will make more of a
> >> difference in subcortical analysis.
> > Yes, thresholding at 0.01 and 0.1 gave me different values in the same 
> > voxel in both images. Whereas when thresholding between 0.1 and 0.3 gave me 
> > same values. What could it be due to ?
> I don't know. Are the differences widespread or just a voxel near the edge?
> >
> > GTM is always computed in the *.stat file whatever the method specified in 
> > mr

Re: [Freesurfer] FSGD file

[Greve, Douglas N.,Ph.D.]

yes, that is the right contrast

On 1/5/19 7:30 AM, Raffaele Dubbioso wrote:

External Email - Use Caution

Thanks a lot.
Sorry if I bother you again:
If I want to remove thickness, age and gender as nuisance variables;
My FSGD file should be:

GroupDescriptorFile 1
Title Func
Class HC
Class CMT
Variables  Age gender
Input fs_VF HC  46 Female
Input fs_RF HC 24 Female
...

My group.diff.mtx should be:
1 -1 0 0 0 0 0

Is it ok?

Thanks a lot
Raffaele

Il giorno gio 3 gen 2019 alle ore 20:11 Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> ha scritto:
The contrast is not correct for your design. Your design matrix will
have 3 columns, one for HC, one for CMT, and one for
rh.thickness_30.fsavg.mgh. Ie, it automatcailly interprets PVRs in a
DOSS kind of way. If you want to test for a difference in
thickness-meylin slopes between the two groups, you will need to have
two PVRs, one where the value is the thickness for HC subjects and 0 for
CMT subjects, the other the reverse, then set your contrast to 0 0 1 -1.
If you just want to remove thickness as a nuisance, then you can stick
with what you have and just use a contrast of 1 -1 0

On 12/25/18 5:05 AM, Raffaele Dubbioso wrote:
>
> External Email - Use Caution
>
> Dear Freesurfer team,
>
> I'm running a group analysis where I'd like to compare myelination
> between two groups regressing out cortical thickness.
> Unfortunately I get always the same error message:
> dimension mismatch between X and contrast group.diff.mtx   X has 3
> cols, C has 4 cols. Is my group.mtx correct?
>
> My command line is:
> mri_glmfit --y rh.t1t2ratio_30_fmed_3sm_decurv.fsavg.mgh --fsgd
> thickness.fsgd --pvr rh.thickness_30.fsavg.mgh --C group.diff.mtx --C
> group-x-thick --Cg1g2.intercept.mts --C g1g2.thick.mtx --surf
> fsaverage rh --cortex --glmdir rh_allbrain_t1t2_group_thickness.glmdir
>
> My group_diff.mtx: 1 -1 0 0
>
> This is my FSGD FILE:
> GroupDescriptorFile 1
> Title Myelin
> Class HC
> Class CMT
> Inputfs_VFHC
> 
>
>
>  Thank you very much for your help
>
> Best regards,
> Raffaele
>
> ___
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--

___
Raffaele Dubbioso, MD, PhD
University Federico II of Naples
Department of Neurosciences, Reproductive Sciences
and Odontostomatology.
Via Sergio Pansini, 5
80131 Napoli, ITALY
phone: +39-0817464579
fax: +39-0817462667



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