Re: [Freesurfer] PETSurfer questions part III

[Douglas N. Greve]

On 7/24/2020 10:27 AM, Ferraro, Pilar wrote:
>  External Email - Use Caution
>
> Hi Douglas,
>
> All the analyses have been run with FS version 6 indeed.
> If you confirm the commands below are correct, I therefore assume I should 
> rerun all the analyses using FS 7.1.
>
> I just have few remaining questions:
>
> 1. Are there any other ROIs more than the pons that you have changed from WM 
> to GM in FS 7.1?
Ventral Diencephalon (VentralDC) is now GM.
>
> 2. Is the same problem of WM/GM classification affecting MZ corrected uptake 
> estimation? I suppose WM/GM classification should affect only MG since it’s a 
> 3 compartment model, but I’m not sure.
It should not
>
> Many thanks,
>
> Pilar
>
>
>
> Commands:
> 1) With Muller-Gartner (MG):
> mri_gtmpvc --i ../Subj_PET_image --reg Subj_template.reg.lta --psf 6 --seg 
> Subj_gtmseg.mgz --default-seg-merge --mgx .01 --o gtm_MG.output
>
> Then:
> mri_segstats --i gtm_MG.output/mgx.ctxgm.nii.gz --seg 
> gtm_MG.output/aux/seg.nii.gz --ctab gtm_MG.output/aux/seg.ctab — sum 
> MG_ROI.txt
>
> 2) With Meltzer (MZ):
>
> mri_gtmpvc --i ../Subj_PET_image --reg Subj_template.reg.lta --psf 6 --seg 
> Subj_gtmseg.mgz --default-seg-merge --Meltzer .1 .1 1 —o gtm_MZ.output
>
> Then:
> mri_segstats --i gtm_MZ.output/meltzer.nii.gz --seg 
> gtm_MZ.output/aux/seg.nii.gz --ctab gtm_MZ.output/aux/seg.ctab --sum 
> MZ_ROI.txt
>
>> On 7/20/2020 2:56 AM, Ferraro, Pilar wrote:
>>> External Email - Use Caution
>>>
>>> Many thanks for the reply,
>>>
>>> Yep, unfortunately MG values are always much higher than SGTM ones (in
>>> all the ROIs).
>>> I wonder whether this might be related (for MG and MZ) to the absence
>>> of a normalization using the pons as a reference.
>>>
>>> Indeed, when I look at the file with mean values extracted for each
>>> modality, I see that the pons has always 1000 as mean uptake value for
>>> no PVC and SGTM, while for MG and MZ values in the pons range from
>>> -0.02 to -0.65 (for MG) and from 0.94 to 0.99 (for MZ).
>> Pons should be 1.000 in the SGM and NoPVC. Which version of FS are you
>> using? In version 6, pons was considered white matter, but I changed it
>> to gray matter in version 7. The bottom line on this is that you cannot
>> compute uptake in WM in MG. So, if pons (or any other ROI) is WM, then
>> its value is bogus.
>>> Below are the commands I?ve used to obtain the MG and MZ values:
>>>
>>> 1) With Muller-Gartner (MG):
>>>
>>> mri_gtmpvc --i ../Subj_PET_image --reg Subj_template.reg.lta --psf 6
>>> --seg Subj_gtmseg.mgz --default-seg-merge --mgx .01 --o gtm_MG.output
>>>
>>> ?Then:
>>>
>>> mri_segstats --i gtm_MG.output/mgx.ctxgm.nii.gz --seg
>>> gtm_MG.output/aux/seg.nii.gz --ctab gtm_MG.output/aux/seg.ctab --sum
>>> MG_ROI.txt
>>>
>>> 2) With Meltzer (MZ):
>>>
>>> mri_gtmpvc --i ../Subj_PET_image --reg Subj_template.reg.lta --psf 6
>>> --seg Subj_gtmseg.mgz --default-seg-merge --Meltzer .1 .1 1 --o
>>> gtm_MZ.output
>>>
>>> Then:
>>>
>>> mri_segstats --i gtm_MZ.output/meltzer.nii.gz --seg
>>> gtm_MZ.output/aux/seg.nii.gz --ctab gtm_MZ.output/aux/seg.ctab --sum
>>> MZ_ROI.txt
>>>
>>>
>>> Do you recognize any errors in the commands?
>>>
>>>
>>> Many thanks,
>>>
>>> Pilar
>>>
>>>
>>>
>>>
>>>
 Message: 13
 Date: Thu, 16 Jul 2020 10:19:32 -0400
 From: "Douglas N. Greve" >>> >
 Subject: Re: [Freesurfer] PETSurfer analysis question
 To: >>> >
 Message-ID: >>> >
 Content-Type: text/plain; charset="utf-8"


 The NoPVC and SGTM values are reasonable. The MG value is pretty crazy.
 I don't put stock in MZ. Is the MG value much higher than SGTM in other
 ROIs? What is your mri_gtmpvc command?


 On 7/16/2020 4:38 AM, Ferraro, Pilar wrote:
> External Email - Use Caution
>
> Hi Freesurfer experts,
>
> I?ve run a PETSurfer analysis in order to compare mean?uptake values
> of ROIs obtained with different methods: No PVC, SGTM, MG and MZ.
> However, I?ve now extracted the mean values and they are extremely
> heterogeneous.
> As an example, the same ROI (lh banks of the superior temporal sulcus)
> has the following uptake values:
>
> No PVC= 1.709
> SGTM= 2.495
> MG= 23.847
> MZ= 15.564
>
> I?m particularly worried for the huge difference between noPVC - SGTM
> values and MG-MZ values.
>
> Any advice? I wonder whether this finding is normal or there is
> something I?ve missed.
>
> Many thanks,
>
> Pilar
>
>
>
>
>
>
>
>
>> Il giorno 15 lug 2020, alle ore 6:00 PM,
>> freesurfer-requ...@nmr.mgh.harvard.edu
>> 
>>  ha scritto:
>>
>> Send Freesurfer mailing list submissions to
>> 

[Freesurfer] PETSurfer questions part III

[Ferraro, Pilar]

External Email - Use Caution

Hi Douglas,

All the analyses have been run with FS version 6 indeed. 
If you confirm the commands below are correct, I therefore assume I should 
rerun all the analyses using FS 7.1.

I just have few remaining questions:

1. Are there any other ROIs more than the pons that you have changed from WM to 
GM in FS 7.1?

2. Is the same problem of WM/GM classification affecting MZ corrected uptake 
estimation? I suppose WM/GM classification should affect only MG since it’s a 3 
compartment model, but I’m not sure.

Many thanks,

Pilar



Commands:
1) With Muller-Gartner (MG):
mri_gtmpvc --i ../Subj_PET_image --reg Subj_template.reg.lta --psf 6 --seg 
Subj_gtmseg.mgz --default-seg-merge --mgx .01 --o gtm_MG.output

Then:
mri_segstats --i gtm_MG.output/mgx.ctxgm.nii.gz --seg 
gtm_MG.output/aux/seg.nii.gz --ctab gtm_MG.output/aux/seg.ctab — sum MG_ROI.txt

2) With Meltzer (MZ):

mri_gtmpvc --i ../Subj_PET_image --reg Subj_template.reg.lta --psf 6 --seg 
Subj_gtmseg.mgz --default-seg-merge --Meltzer .1 .1 1 —o gtm_MZ.output

Then:
mri_segstats --i gtm_MZ.output/meltzer.nii.gz --seg 
gtm_MZ.output/aux/seg.nii.gz --ctab gtm_MZ.output/aux/seg.ctab --sum MZ_ROI.txt

> 
> On 7/20/2020 2:56 AM, Ferraro, Pilar wrote:
>> 
>> External Email - Use Caution
>> 
>> Many thanks for the reply,
>> 
>> Yep, unfortunately MG values are always much higher than SGTM ones (in 
>> all the ROIs).
>> I wonder whether this might be related (for MG and MZ) to the absence 
>> of a normalization using the pons as a reference.
>> 
>> Indeed, when I look at the file with mean values extracted for each 
>> modality, I see that the pons has always 1000 as mean uptake value for 
>> no PVC and SGTM, while for MG and MZ values in the pons range from 
>> -0.02 to -0.65 (for MG) and from 0.94 to 0.99 (for MZ).
> Pons should be 1.000 in the SGM and NoPVC. Which version of FS are you 
> using? In version 6, pons was considered white matter, but I changed it 
> to gray matter in version 7. The bottom line on this is that you cannot 
> compute uptake in WM in MG. So, if pons (or any other ROI) is WM, then 
> its value is bogus.
>> 
>> Below are the commands I?ve used to obtain the MG and MZ values:
>> 
>> 1) With Muller-Gartner (MG):
>> 
>> mri_gtmpvc --i ../Subj_PET_image --reg Subj_template.reg.lta --psf 6 
>> --seg Subj_gtmseg.mgz --default-seg-merge --mgx .01 --o gtm_MG.output
>> 
>> ?Then:
>> 
>> mri_segstats --i gtm_MG.output/mgx.ctxgm.nii.gz --seg 
>> gtm_MG.output/aux/seg.nii.gz --ctab gtm_MG.output/aux/seg.ctab --sum 
>> MG_ROI.txt
>> 
>> 2) With Meltzer (MZ):
>> 
>> mri_gtmpvc --i ../Subj_PET_image --reg Subj_template.reg.lta --psf 6 
>> --seg Subj_gtmseg.mgz --default-seg-merge --Meltzer .1 .1 1 --o 
>> gtm_MZ.output
>> 
>> Then:
>> 
>> mri_segstats --i gtm_MZ.output/meltzer.nii.gz --seg 
>> gtm_MZ.output/aux/seg.nii.gz --ctab gtm_MZ.output/aux/seg.ctab --sum 
>> MZ_ROI.txt
>> 
>> 
>> Do you recognize any errors in the commands?
>> 
>> 
>> Many thanks,
>> 
>> Pilar
>> 
>> 
>> 
>> 
>> 
>>> 
>>> Message: 13
>>> Date: Thu, 16 Jul 2020 10:19:32 -0400
>>> From: "Douglas N. Greve" >> >
>>> Subject: Re: [Freesurfer] PETSurfer analysis question
>>> To: >> >
>>> Message-ID: >> >
>>> Content-Type: text/plain; charset="utf-8"
>>> 
>>> 
>>> The NoPVC and SGTM values are reasonable. The MG value is pretty crazy.
>>> I don't put stock in MZ. Is the MG value much higher than SGTM in other
>>> ROIs? What is your mri_gtmpvc command?
>>> 
>>> 
>>> On 7/16/2020 4:38 AM, Ferraro, Pilar wrote:
 
 External Email - Use Caution
 
 Hi Freesurfer experts,
 
 I?ve run a PETSurfer analysis in order to compare mean?uptake values
 of ROIs obtained with different methods: No PVC, SGTM, MG and MZ.
 However, I?ve now extracted the mean values and they are extremely
 heterogeneous.
 As an example, the same ROI (lh banks of the superior temporal sulcus)
 has the following uptake values:
 
 No PVC= 1.709
 SGTM= 2.495
 MG= 23.847
 MZ= 15.564
 
 I?m particularly worried for the huge difference between noPVC - SGTM
 values and MG-MZ values.
 
 Any advice? I wonder whether this finding is normal or there is
 something I?ve missed.
 
 Many thanks,
 
 Pilar
 
 
 
 
 
 
 
 
> Il giorno 15 lug 2020, alle ore 6:00 PM,
> freesurfer-requ...@nmr.mgh.harvard.edu 
> 
>  ha scritto:
> 
> Send Freesurfer mailing list submissions to
> freesurfer@nmr.mgh.harvard.edu 
>  
> 
> 
> To subscribe or unsubscribe via the World Wide Web, visit
> 

Re: [Freesurfer] PETSurfer questions - Part II

[Douglas N. Greve]

On 7/20/2020 2:56 AM, Ferraro, Pilar wrote:


External Email - Use Caution

Many thanks for the reply,

Yep, unfortunately MG values are always much higher than SGTM ones (in 
all the ROIs).
I wonder whether this might be related (for MG and MZ) to the absence 
of a normalization using the pons as a reference.


Indeed, when I look at the file with mean values extracted for each 
modality, I see that the pons has always 1000 as mean uptake value for 
no PVC and SGTM, while for MG and MZ values in the pons range from 
-0.02 to -0.65 (for MG) and from 0.94 to 0.99 (for MZ).
Pons should be 1.000 in the SGM and NoPVC. Which version of FS are you 
using? In version 6, pons was considered white matter, but I changed it 
to gray matter in version 7. The bottom line on this is that you cannot 
compute uptake in WM in MG. So, if pons (or any other ROI) is WM, then 
its value is bogus.


Below are the commands I’ve used to obtain the MG and MZ values:

1) With Muller-Gartner (MG):

mri_gtmpvc --i ../Subj_PET_image --reg Subj_template.reg.lta --psf 6 
--seg Subj_gtmseg.mgz --default-seg-merge --mgx .01 --o gtm_MG.output


 Then:

mri_segstats --i gtm_MG.output/mgx.ctxgm.nii.gz --seg 
gtm_MG.output/aux/seg.nii.gz --ctab gtm_MG.output/aux/seg.ctab --sum 
MG_ROI.txt


2) With Meltzer (MZ):

mri_gtmpvc --i ../Subj_PET_image --reg Subj_template.reg.lta --psf 6 
--seg Subj_gtmseg.mgz --default-seg-merge --Meltzer .1 .1 1 --o 
gtm_MZ.output


Then:

mri_segstats --i gtm_MZ.output/meltzer.nii.gz --seg 
gtm_MZ.output/aux/seg.nii.gz --ctab gtm_MZ.output/aux/seg.ctab --sum 
MZ_ROI.txt



Do you recognize any errors in the commands?


Many thanks,

Pilar







Message: 13
Date: Thu, 16 Jul 2020 10:19:32 -0400
From: "Douglas N. Greve" >

Subject: Re: [Freesurfer] PETSurfer analysis question
To: >
Message-ID: >

Content-Type: text/plain; charset="utf-8"


The NoPVC and SGTM values are reasonable. The MG value is pretty crazy.
I don't put stock in MZ. Is the MG value much higher than SGTM in other
ROIs? What is your mri_gtmpvc command?


On 7/16/2020 4:38 AM, Ferraro, Pilar wrote:


External Email - Use Caution

Hi Freesurfer experts,

I?ve run a PETSurfer analysis in order to compare mean?uptake values
of ROIs obtained with different methods: No PVC, SGTM, MG and MZ.
However, I?ve now extracted the mean values and they are extremely
heterogeneous.
As an example, the same ROI (lh banks of the superior temporal sulcus)
has the following uptake values:

No PVC= 1.709
SGTM= 2.495
MG= 23.847
MZ= 15.564

I?m particularly worried for the huge difference between noPVC - SGTM
values and MG-MZ values.

Any advice? I wonder whether this finding is normal or there is
something I?ve missed.

Many thanks,

Pilar









Il giorno 15 lug 2020, alle ore 6:00 PM,
freesurfer-requ...@nmr.mgh.harvard.edu 


 ha scritto:

Send Freesurfer mailing list submissions to
freesurfer@nmr.mgh.harvard.edu 
 



To subscribe or unsubscribe via the World Wide Web, visit
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
or, via email, send a message with subject or body 'help' to
freesurfer-requ...@nmr.mgh.harvard.edu

You can reach the person managing the list at
freesurfer-ow...@nmr.mgh.harvard.edu

When replying, please edit your Subject line so it is more specific
than "Re: Contents of Freesurfer digest..."


Today's Topics:

??1. Re: recon all Freesurfer 7.1 on Mac High Sierra fails to run
?for some subjects (Douglas N. Greve)
??2. Re: mri_fieldsign error (Douglas N. Greve)
??3. Extracting PET Binding Values from Inflated Surface (O'Dell, Ryan)


--

Message: 1
Date: Wed, 15 Jul 2020 11:12:21 -0400
From: "Douglas N. Greve" 
Subject: Re: [Freesurfer] recon all Freesurfer 7.1 on Mac High Sierra
fails to run for some subjects
To: 
Message-ID: 
Content-Type: text/plain; charset="windows-1252"

Can you send the recon-all.log file for some of the failures?

On 7/15/2020 10:52 AM, Annelies Vant Westeinde wrote:


External Email - Use Caution

Dear list,

As described by others on this list, recon-all with Freesurfer 7.1 on
a Mac operating system seems to fail for around 10% of the subjects.

The following solution was offered:

sudo curl
https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/rca-long-tp-init
?-o rca-long-tp-init
sudo chmod +x rca-long-tp-init
However, this did not solve the problem for me.

I re-ran recon-all for the same subjects, but it still failed, some of
them at the following step:

"###
GCADIR /Applications/freesurfer/average
GCA RB_all_2020-01-02.gca
GCASkull 

[Freesurfer] PETSurfer questions - Part II

[Ferraro, Pilar]

External Email - Use Caution

Many thanks for the reply,

Yep, unfortunately MG values are always much higher than SGTM ones (in all the 
ROIs).
I wonder whether this might be related (for MG and MZ) to the absence of a 
normalization using the pons as a reference.

Indeed, when I look at the file with mean values extracted for each modality, I 
see that the pons has always 1000 as mean uptake value for no PVC and SGTM, 
while for MG and MZ values in the pons range from -0.02 to -0.65 (for MG) and 
from 0.94 to 0.99 (for MZ).

Below are the commands I’ve used to obtain the MG and MZ values:
1) With Muller-Gartner (MG):
mri_gtmpvc --i ../Subj_PET_image --reg Subj_template.reg.lta --psf 6 --seg 
Subj_gtmseg.mgz --default-seg-merge --mgx .01 --o gtm_MG.output
 Then:
mri_segstats --i gtm_MG.output/mgx.ctxgm.nii.gz --seg 
gtm_MG.output/aux/seg.nii.gz --ctab gtm_MG.output/aux/seg.ctab --sum MG_ROI.txt
2) With Meltzer (MZ):
mri_gtmpvc --i ../Subj_PET_image --reg Subj_template.reg.lta --psf 6 --seg 
Subj_gtmseg.mgz --default-seg-merge --Meltzer .1 .1 1 --o gtm_MZ.output
Then:
mri_segstats --i gtm_MZ.output/meltzer.nii.gz --seg 
gtm_MZ.output/aux/seg.nii.gz --ctab gtm_MZ.output/aux/seg.ctab --sum MZ_ROI.txt

Do you recognize any errors in the commands?

Many thanks,

Pilar






Message: 13
Date: Thu, 16 Jul 2020 10:19:32 -0400
From: "Douglas N. Greve" mailto:dgr...@mgh.harvard.edu>>
Subject: Re: [Freesurfer] PETSurfer analysis question
To: mailto:freesurfer@nmr.mgh.harvard.edu>>
Message-ID: 
mailto:d56acc7d-3273-4f40-ed17-570a893b2...@mgh.harvard.edu>>
Content-Type: text/plain; charset="utf-8"


The NoPVC and SGTM values are reasonable. The MG value is pretty crazy.
I don't put stock in MZ. Is the MG value much higher than SGTM in other
ROIs? What is your mri_gtmpvc command?


On 7/16/2020 4:38 AM, Ferraro, Pilar wrote:

External Email - Use Caution

Hi Freesurfer experts,

I?ve run a PETSurfer analysis in order to compare mean?uptake values
of ROIs obtained with different methods: No PVC, SGTM, MG and MZ.
However, I?ve now extracted the mean values and they are extremely
heterogeneous.
As an example, the same ROI (lh banks of the superior temporal sulcus)
has the following uptake values:

No PVC= 1.709
SGTM= 2.495
MG= 23.847
MZ= 15.564

I?m particularly worried for the huge difference between noPVC - SGTM
values and MG-MZ values.

Any advice? I wonder whether this finding is normal or there is
something I?ve missed.

Many thanks,

Pilar








Il giorno 15 lug 2020, alle ore 6:00 PM,
freesurfer-requ...@nmr.mgh.harvard.edu
 ha scritto:

Send Freesurfer mailing list submissions to
freesurfer@nmr.mgh.harvard.edu 


To subscribe or unsubscribe via the World Wide Web, visit
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
or, via email, send a message with subject or body 'help' to
freesurfer-requ...@nmr.mgh.harvard.edu

You can reach the person managing the list at
freesurfer-ow...@nmr.mgh.harvard.edu

When replying, please edit your Subject line so it is more specific
than "Re: Contents of Freesurfer digest..."


Today's Topics:

??1. Re: recon all Freesurfer 7.1 on Mac High Sierra fails to run
?for some subjects (Douglas N. Greve)
??2. Re: mri_fieldsign error (Douglas N. Greve)
??3. Extracting PET Binding Values from Inflated Surface (O'Dell, Ryan)


--

Message: 1
Date: Wed, 15 Jul 2020 11:12:21 -0400
From: "Douglas N. Greve" 
Subject: Re: [Freesurfer] recon all Freesurfer 7.1 on Mac High Sierra
fails to run for some subjects
To: 
Message-ID: 
Content-Type: text/plain; charset="windows-1252"

Can you send the recon-all.log file for some of the failures?

On 7/15/2020 10:52 AM, Annelies Vant Westeinde wrote:

External Email - Use Caution

Dear list,

As described by others on this list, recon-all with Freesurfer 7.1 on
a Mac operating system seems to fail for around 10% of the subjects.

The following solution was offered:

sudo curl
https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/rca-long-tp-init
?-o rca-long-tp-init
sudo chmod +x rca-long-tp-init
However, this did not solve the problem for me.

I re-ran recon-all for the same subjects, but it still failed, some of
them at the following step:

"###
GCADIR /Applications/freesurfer/average
GCA RB_all_2020-01-02.gca
GCASkull RB_all_withskull_2020_01_02.gca
AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif
GCSDIR /Applications/freesurfer/average
GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
###"

It simply stopped running there.

Others did finish running, but instead got a segmentation fault error.

What could I do? I have Mac High Sierra.


Annelies

Annelies van't Westeinde?| 

Re: [Freesurfer] PETSurfer / Questions

[Douglas N. Greve]

On 4/14/2020 5:40 AM, Ferraro, Pilar wrote:


External Email - Use Caution

Dear Freesurfer experts,

We are conducting a PETSurfer analysis, and have some questions on the 
best way to proceed.  Briefly, this is what we have done:


After running the standard Freesurfer analysis an all the T1 images, 
we have generated the segmentation for the GTM.
Afterwards, we have registered the PET images with the anatomicals, 
obtaining the template.reg.lta.
To check the preliminary results without any PVC, we have used the 
template.reg.lta to sample the PET volume onto the surface, with the 
following command:

 mri_vol2surf --mov subject_PET.nii \
 --reg subject_template.reg.lta \
 --projfrac 0.5 --interp nearest \
 --hemi lh --o lh.sig.mgh

We therefore obtained the lh.sig.mgh

First question. Is this procedure correct?
Yes (though you should always check the reg.lta with tkregisterfv). 
Also, why are you calling the output lh.sig.mgh? My question is about 
"sig"; it is not wrong to call it this, but "sig" is usually reserved 
for significance files and I wanted to make sure you were not confused 
by it.

Second question. Is the format of the of the output (.mgh) correct?

Any format (mgh, mgz, nifti) is ok.


In the wiki it is reported that: “If you are not using PVC, you can 
use the template.reg.lta to sample the PET volume onto the surface 
using mri_vol2surf, then apply standard surface-based analysis”.


Third question. At this point should we directly run the mri_glmfit 
with the previously obtained lh.sig.mgh?
This is probably not right. You  will need to run the mri_vol2surf 
command above for each subject to generate an output (and using 
--trgsubject fsaverage to put them into the same space), then 
concatenate all into one file (mri_concat lh.subj1.mgh lh.subj2.mgh ... 
--o lh.all.mgh), then possibly smooth (mris_fwhm), then feed that output 
as input to mri_glmfit.

Like in this way:

 mri_glmfit \
 --y lh.sig.mgh \
 --fsgd fsgd file dods\
 --C cor.mtx file \
--surf fsaverage lh \
--cortex \
--glmdir glmdir

Many thanks for any information you’ll be able to provide,

 Best,

Pilar Maria Ferraro


Il giorno 7 apr 2020, alle ore 6:00 PM, 
freesurfer-requ...@nmr.mgh.harvard.edu 
 ha scritto:


Send Freesurfer mailing list submissions to
freesurfer@nmr.mgh.harvard.edu 

To subscribe or unsubscribe via the World Wide Web, visit
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
or, via email, send a message with subject or body 'help' to
freesurfer-requ...@nmr.mgh.harvard.edu

You can reach the person managing the list at
freesurfer-ow...@nmr.mgh.harvard.edu

When replying, please edit your Subject line so it is more specific
than "Re: Contents of Freesurfer digest..."


Today's Topics:

  1. vertex number to MNI coordinates (Marina Fern?ndez)
  2. Install Freesurfer on Ubuntu (Stephan)
  3. Re: vertex number to MNI coordinates (Douglas N. Greve)
  4. Re: Install Freesurfer on Ubuntu (Peer Herholz)
  5. Re: Install Freesurfer on Ubuntu (fsbuild)
  6. Permutation with Non-Orthogonal Matrices (Hua, Jessica)
  7. Re: Permutation with Non-Orthogonal Matrices (Douglas N. Greve)
  8. Error in Tracula-all -prep (Salah Showiheen)
  9. hippocampus subfield segmentation using Siemen and GEscans
 (Kate Marvel)
 10. Chorid-plexus in Freesurfer reconall (Lijun An)
 11. Re: Chorid-plexus in Freesurfer reconall (Bruce Fischl)
 12. whether freesurfer version 7 still support GPU (Frank Robert)
 13. Re: hippocampus subfield segmentation using Siemen and GE
 scans (Iglesias Gonzalez, Juan E.)
 14. Re: whether freesurfer version 7 still support GPU
 (Hoopes, Andrew)
 15. Re: hippocampus subfield segmentation using Siemen and GE
 scans (Kate Marvel)
 16. Re: whether freesurfer version 7 still support GPU (Frank Robert)
 17. Re: whether freesurfer version 7 still support GPU
 (Hoopes, Andrew)


--

Message: 1
Date: Mon, 6 Apr 2020 22:06:24 +0200
From: Marina Fern?ndez 
Subject: [Freesurfer] vertex number to MNI coordinates
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:

Content-Type: text/plain; charset="utf-8"

   External Email - Use Caution

Dear Freesurfer experts,

I hope you can help me with the following questions:

1. What is the best way to know the MNI coordinates to which a vertex 
of a

surface corresponds?

2. I have projected the surfaces of the subjects onto the average subject
from this dataset.
Can I know the MNI coordinates corresponding to a vertex of the average
subject of my dataset?
Or do I need to project it onto the fsaverage to know the 
correspondence to

de MNI space?

3. I know that the average surface is constructed by computing the MNI305
coordinate at each vertex,
But how can I obtain the MNI152 coordinates (instead of MNI305) to 
which a

vertex corresponds? (if it is possible).


Thank you very 

Re: [Freesurfer] PETSurfer / Questions

[Ferraro, Pilar]

External Email - Use Caution

Dear Freesurfer experts,

We are conducting a PETSurfer analysis, and have some questions on the best way 
to proceed.  Briefly, this is what we have done:

After running the standard Freesurfer analysis an all the T1 images, we have 
generated the segmentation for the GTM.
Afterwards, we have registered the PET images with the anatomicals, obtaining 
the template.reg.lta.
To check the preliminary results without any PVC, we have used the 
template.reg.lta to sample the PET volume onto the surface, with the following 
command:
 mri_vol2surf --mov subject_PET.nii \
 --reg subject_template.reg.lta \
 --projfrac 0.5 --interp nearest \
 --hemi lh --o lh.sig.mgh

We therefore obtained the lh.sig.mgh

First question. Is this procedure correct?
Second question. Is the format of the of the output (.mgh) correct?

In the wiki it is reported that: “If you are not using PVC, you can use the 
template.reg.lta to sample the PET volume onto the surface using mri_vol2surf, 
then apply standard surface-based analysis”.

Third question. At this point should we directly run the mri_glmfit with the 
previously obtained lh.sig.mgh?
Like in this way:

 mri_glmfit \
 --y lh.sig.mgh \
 --fsgd fsgd file dods\
 --C cor.mtx file \
--surf fsaverage lh \
--cortex \
--glmdir glmdir

Many thanks for any information you’ll be able to provide,

 Best,

Pilar Maria Ferraro


Il giorno 7 apr 2020, alle ore 6:00 PM, 
freesurfer-requ...@nmr.mgh.harvard.edu
 ha scritto:

Send Freesurfer mailing list submissions to
freesurfer@nmr.mgh.harvard.edu

To subscribe or unsubscribe via the World Wide Web, visit
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
or, via email, send a message with subject or body 'help' to
freesurfer-requ...@nmr.mgh.harvard.edu

You can reach the person managing the list at
freesurfer-ow...@nmr.mgh.harvard.edu

When replying, please edit your Subject line so it is more specific
than "Re: Contents of Freesurfer digest..."


Today's Topics:

  1. vertex number to MNI coordinates (Marina Fern?ndez)
  2. Install Freesurfer on Ubuntu (Stephan)
  3. Re: vertex number to MNI coordinates (Douglas N. Greve)
  4. Re: Install Freesurfer on Ubuntu (Peer Herholz)
  5. Re: Install Freesurfer on Ubuntu (fsbuild)
  6. Permutation with Non-Orthogonal Matrices (Hua, Jessica)
  7. Re: Permutation with Non-Orthogonal Matrices (Douglas N. Greve)
  8. Error in Tracula-all -prep (Salah Showiheen)
  9. hippocampus subfield segmentation using Siemen and GE scans
 (Kate Marvel)
 10. Chorid-plexus in Freesurfer reconall (Lijun An)
 11. Re: Chorid-plexus in Freesurfer reconall (Bruce Fischl)
 12. whether freesurfer version 7 still support GPU (Frank Robert)
 13. Re: hippocampus subfield segmentation using Siemen and GE
 scans (Iglesias Gonzalez, Juan E.)
 14. Re: whether freesurfer version 7 still support GPU
 (Hoopes, Andrew)
 15. Re: hippocampus subfield segmentation using Siemen and GE
 scans (Kate Marvel)
 16. Re: whether freesurfer version 7 still support GPU (Frank Robert)
 17. Re: whether freesurfer version 7 still support GPU
 (Hoopes, Andrew)


--

Message: 1
Date: Mon, 6 Apr 2020 22:06:24 +0200
From: Marina Fern?ndez 
Subject: [Freesurfer] vertex number to MNI coordinates
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:

Content-Type: text/plain; charset="utf-8"

   External Email - Use Caution

Dear Freesurfer experts,

I hope you can help me with the following questions:

1. What is the best way to know the MNI coordinates to which a vertex of a
surface corresponds?

2. I have projected the surfaces of the subjects onto the average subject
from this dataset.
Can I know the MNI coordinates corresponding to a vertex of the average
subject of my dataset?
Or do I need to project it onto the fsaverage to know the correspondence to
de MNI space?

3. I know that the average surface is constructed by computing the MNI305
coordinate at each vertex,
But how can I obtain the MNI152 coordinates (instead of MNI305) to which a
vertex corresponds? (if it is possible).


Thank you very much in advance.

Best regards,
Marina
-- next part --
An HTML attachment was scrubbed...
URL: 
http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200406/48bae2d3/attachment-0001.html

--

Message: 2
Date: Mon, 6 Apr 2020 22:50:15 +0200
From: Stephan 
Subject: [Freesurfer] Install Freesurfer on Ubuntu
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:

Content-Type: text/plain; charset="utf-8"

   External Email - Use Caution

Hi,

ist there an official guideline how to install Freesurfer on Ubuntu?

Best,
Stephan
-- next part --
An HTML attachment was scrubbed...
URL: 

Re: [Freesurfer] PetSurfer questions

[Soo-Jong Kim]

External Email - Use Caution

Thank you  Dr.Greve.

I applied to rbv.nii.gz volume to anatomical space.

You said, bbpet2anat.lta. using mri_vol2vol

but I tested. registration using bbpet2anat.lta was not correct on native
T1 space.
So I tested rbv2anat.lta for registration. that was okay.

What is difference between SPM coregistration rbv onto orig.mgz and
registration using rbv2anat.lta??

Best regards
Soo
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] PetSurfer questions

[Soo-Jong Kim]

External Email - Use Caution

*Thank you Dr. Greve for your answer*


I checked all about your comment.

I have questions more.

1. I found that volumes or counts in gtm.stats.dat are for native PET
space. If co-registered PET onto corresponding MRI(i.e. MRI space) is available
using rbv.nii.gz from mri_gtmpvc,

Or if you recommend it by gtm.stats.dat, I can use gtm.stats.dat --rescale
(reference regions) for SUVR in PET space.

What do you prefer or recommend?

I'm not sure what you are trying to get. voxel volume or SUVR?


*-> Yes. Voxel volume for SUVR analysis.*

*I compared gtm.stats.dat from both GTM and RBV method.*

*They were all same SUVR. I think region masks for gtm and rbv are
same as pvc-masks, arent they?*


2. I used mri_vol2vol --mov rbv.nii.gz --targ original_PET.nii --o test.nii
--regheader

because rbv.nii.gz is in different space.
but when overlaid with them, registration is not correct.  (WHY)
rbv.nii.gz is in different space, even not in T1.mgz space. (DKT space)
I just wanted to use the pv-corrected image for image processing.

and you also said, smoothing is required after PVC. (Surface or volume based
smoothing (resonable).

The RBV is in anatomical space, if you want to map it back to pet space, you
need the registration file in the aux folder (not --regheader).

*-> RBV has 0.5mm for voxelsize. even though I put image for input which
has 1mm isotropic volume. *
*You said that 'use in lta file in aux folder'. There are many lta files.
So let me know what it is. *

*- anat2bbpet.lta*
*- anat2rbv.lta*
*- bbpet2anat.lta*
*- bbpet2pet.lta*
*- pet2bbpet.lta*
*- rbv2anat.lta*

*my purpose is this.  I want to map rbv.nii.gz to original T1MR space.
Could you tell me how to do ?*

*Thank you so much, Dr.Greve*
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] PetSurfer questions

[Douglas N. Greve]

On 2/9/2020 10:19 PM, Soo-Jong Kim wrote:


External Email - Use Caution

Thank you, Dr. Greve

I checked all about your comment.

I have questions more.
1. I found that volumes or counts in gtm.stats.dat are for native PET 
space.
If co-registered PET onto corresponding MRI(i.e. MRI space) is 
available using rbv.nii.gz from mri_gtmpvc,


Or if you recommend it by gtm.stats.dat, I can use gtm.stats.dat 
--rescale (reference regions) for SUVR in PET space.

What do you prefer or recommend?

I'm not sure what you are trying to get. voxel volume or SUVR?


2. I used mri_vol2vol --mov rbv.nii.gz --targ original_PET.nii --o 
test.nii --regheader

because rbv.nii.gz is in different space.
but when overlaid with them, registration is not correct.  (WHY)
rbv.nii.gz is in different space, even not in T1.mgz space. (DKT space)
I just wanted to use the pv-corrected image for image processing.
and you also said, smoothing is required after PVC. (Surface or volume 
based smoothing (resonable).
The RBV is in anatomical space, if you want to map it back to pet space, 
you need the registration file in the aux folder (not --regheader).


Best regards,
Soo

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] PetSurfer questions

[Soo-Jong Kim]

External Email - Use Caution

Thank you, Dr. Greve

I checked all about your comment.

I have questions more.
1. I found that volumes or counts in gtm.stats.dat are for native PET space.
If co-registered PET onto corresponding MRI(i.e. MRI space) is available
using rbv.nii.gz from mri_gtmpvc,

Or if you recommend it by gtm.stats.dat, I can use gtm.stats.dat --rescale
(reference regions) for SUVR in PET space.
What do you prefer or recommend?

2. I used mri_vol2vol --mov rbv.nii.gz --targ original_PET.nii --o test.nii
--regheader
because rbv.nii.gz is in different space.
but when overlaid with them, registration is not correct.  (WHY)
rbv.nii.gz is in different space, even not in T1.mgz space. (DKT space)
I just wanted to use the pv-corrected image for image processing.
and you also said, smoothing is required after PVC.  (Surface or volume
based smoothing (resonable).

Best regards,
Soo
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] PetSurfer questions

[Soo-Jong Kim]

External Email - Use Caution

Thank you, Dr. Greve

I checked all about your comment.

I have questions more.
1. I found that volumes or counts in gtm.stats.dat are for native PET space.
If co-registered PET onto corresponding MRI(i.e. MRI space) is available
using rbv.nii.gz from mri_gtmpvc,

Or if you recommend it by gtm.stats.dat, I can use gtm.stats.dat --rescale
(reference regions) for SUVR in PET space.
What do you prefer or recommend?

2. I used mri_vol2vol --mov rbv.nii.gz --targ original_PET.nii --o test.nii
--regheader
because rbv.nii.gz is in different space.
but when overlaid with them, registration is not correct.  (WHY)
rbv.nii.gz is in different space, even not in T1.mgz space. (DKT space)
I just wanted to use the pv-corrected image for image processing.
and you also said, smoothing is required after PVC.  (Surface or volume
based smoothing (resonable).

Best regards,
Soo
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] PetSurfer questions

[Douglas N. Greve]

On 2/3/2020 11:56 PM, Soo-Jong Kim wrote:


External Email - Use Caution

Thank you, Dr. Greve

I checked all about your comment.

I have questions more.
1. I found that volumes or counts in gtm.stats.dat are for native PET 
space.
If co-registered PET onto corresponding MRI(i.e. MRI space) is 
available using rbv.nii.gz from mri_gtmpvc,


Or if you recommend it by gtm.stats.dat, I can use gtm.stats.dat 
--rescale (reference regions) for SUVR in PET space.

What do you prefer or recommend?
I'm not sure why you would use the ROI volume from the PET analysis at 
all. Why not just use the data in the aseg.stats or the ?h.aparc.stats?


2. I used mri_vol2vol --mov rbv.nii.gz --targ original_PET.nii --o 
test.nii --regheader

because rbv.nii.gz is in different space.
but when overlaid with them, registration is not correct.  (WHY)
rbv.nii.gz is in different space, even not in T1.mgz space. (DKT space)
I just checked, and the RBV is in the anatomical space and so 
--regheader is not appropriate. if you really want to map it back to the 
pet space, you will need to supply a registration file, but there is 
probably no reason to do this.

I just wanted to use the pv-corrected image for image processing.
and you also said, smoothing is required after PVC. (Surface or volume 
based smoothing (resonable).


Best regards,
S

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] PetSurfer questions

[Soo-Jong Kim]

External Email - Use Caution

Thank you, Dr. Greve

I checked all about your comment.

I have questions more.
1. I found that volumes or counts in gtm.stats.dat are for native PET space.
If co-registered PET onto corresponding MRI(i.e. MRI space) is available
using rbv.nii.gz from mri_gtmpvc,

Or if you recommend it by gtm.stats.dat, I can use gtm.stats.dat --rescale
(reference regions) for SUVR in PET space.
What do you prefer or recommend?

2. I used mri_vol2vol --mov rbv.nii.gz --targ original_PET.nii --o test.nii
--regheader
because rbv.nii.gz is in different space.
but when overlaid with them, registration is not correct.  (WHY)
rbv.nii.gz is in different space, even not in T1.mgz space. (DKT space)
I just wanted to use the pv-corrected image for image processing.
and you also said, smoothing is required after PVC.  (Surface or volume
based smoothing (resonable).

Best regards,
S
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] PetSurfer questions

[Douglas N. Greve]

On 1/30/2020 3:39 AM, Soo-Jong Kim wrote:


External Email - Use Caution

I ran gtmseg for my partial volume correction

1. but I have a question. What regions are for the detail??
in this option.

mri_gtmpvc --default-seg-merge.

I searched mri_gtmpvc --help
but it is default schema for merging ROIs.
So I wanna know what regions you use as default. for example, in 
FreeSurferLUT. 1000, 1010, etc..


Can you tell me what regions freesurfer uses.
Look  in aux/seg.replace.list. The first column is the id of the segment 
being replaced, the 2nd is the new id
2. In general, After PVC (i.e.MG  or RBV),  Does some 
smoothing kernel apply to pv-corrected images from rbv as rbv.nii.gz?
In general, yes, but if you are going to smooth you have to do it the 
right way, otherwise you are just re-imposing PVEs. for cortex, you 
should map it to the surface and smooth on the surface; for the volume I 
would mask out all except subcortical gray and then smooth within 
subcortical gray. These are described on the PETsurfer page.


If then, how large smoothing kernel?

This is an empirical question


Best,
Soo


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] PetSurfer questions

[Soo-Jong Kim]

External Email - Use Caution

I ran gtmseg for my partial volume correction

1. but I have a question. What regions are for the detail??
in this option.

mri_gtmpvc --default-seg-merge.

I searched mri_gtmpvc --help
but it is default schema for merging ROIs.
So I wanna know what regions you use as default. for example, in
FreeSurferLUT. 1000, 1010, etc..

Can you tell me what regions freesurfer uses.

2. In general, After PVC (i.e.MG or RBV),  Does some smoothing kernel apply
to pv-corrected images from rbv as rbv.nii.gz?

If then, how large smoothing kernel?

Best,
Soo
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] PetSurfer questions

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

what ligand are you using? Do you expect it to be higher in GM and in WM? What 
are the values in the gtm.stats file relative to when you run it without PVC? 
How did you choose 5 as the --psf?

On 11/26/2019 2:53 AM, Soo-Jong Kim wrote:

External Email - Use Caution

Dear FreeSurfer experts,

Originally, I want to use RBV method for pvcorrected PET for SUVR analysis.

After generating gtmseg and coregistration to make lta file, I followed this 
code and changed some.

mri_gtmpvc --i PET.nii --reg subj1.reg.lta --psf 5 --seg gtmseg.mgz
--default-seg-merge --auto-mask PSF .01 --no-rescale --no-reduce-fov --rbv --o 
output_pvc

After this, rbv.nii.gz file was generated. and SUVR analysis was performed as 
reference region (cerebellar cortex).  But Compared to original un-pvc PET, 
Cortex SUVR was reduced.

In ideal pv-corrected PET, cortex SUVR was higher than un-pvc PET.

Is is okay if I use the output file as rbv.nii.gz ?

in Thomas et al, 2011,
He used aparc+aseg.mgz file from FreeSurfer. and he merged some regions.
Frontal, Temporal, Occipital and so on. (Only gray matter to correct PET using 
RBV method)

In that case, What are the regions to make rbv.nii.gz method in PetSurfer?  all 
regions in FreeSurfer LUT?

Can I use the rbv.nii.gz as partial volume corrected PET from RBV method?

If not, let me know what is the correct command of mri_gtmpvc.
I need only partial volume corrected PET using RBV method.

Sincerely,

Soo-Jong Kim



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] PetSurfer questions

[Soo-Jong Kim]

External Email - Use Caution

Dear FreeSurfer experts,

Originally, I want to use RBV method for pvcorrected PET for SUVR analysis.

After generating gtmseg and coregistration to make lta file, I followed
this code and changed some.

*mri_gtmpvc --i PET.nii --reg subj1.reg.lta --psf 5 --seg gtmseg.mgz *
*--default-seg-merge --auto-mask PSF .01 --no-rescale --no-reduce-fov --rbv
--o output_pvc*

After this, rbv.nii.gz file was generated. and SUVR analysis was performed
as reference region (cerebellar cortex).  But Compared to original un-pvc
PET, Cortex SUVR was reduced.

In ideal pv-corrected PET, cortex SUVR was higher than un-pvc PET.

Is is okay if I use the output file as rbv.nii.gz ?

in Thomas et al, 2011,
He used aparc+aseg.mgz file from FreeSurfer. and he merged some regions.
Frontal, Temporal, Occipital and so on. (Only gray matter to correct PET
using RBV method)

In that case, What are the regions to make rbv.nii.gz method in PetSurfer?
all regions in FreeSurfer LUT?

Can I use the rbv.nii.gz as partial volume corrected PET from RBV method?

If not, let me know what is the correct command of mri_gtmpvc.
I need only partial volume corrected PET using RBV method.

Sincerely,

Soo-Jong Kim
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer