[Freesurfer] Coregistration to MNI

[Camargo, Aldo]

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Hi Freesurfer experts,

I want to coregister a PET image to the MNI space, can I use mri_cvs_register ?

Thanks a lot,

Aldo Camargo
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Re: [Freesurfer] FW: mri_fieldsign error

[Douglas N. Greve]

A few more questions

1. How much memory do you have on your system? You can find it from the 
first line of

/proc/meminfo
It should be something like "MemTotal:   131781468 kB"

2. What environmental limits do you have? Send the result of the "limit" 
unix command


3. I put a new version of mri_fieldsign here 
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_fieldsign. Can you 
run this version and send me the terminal output? Also, if you can run 
it outside of your bash script, it would be better.





On 7/24/2020 9:44 AM, Xiaomin Yue wrote:


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Hi Doug,

Here is output of uname -a: Linux thalamos.nimh.nih.gov  
3.10.0-1127.13.1.e17.x96-64 #1 SMP 2020 x86-64 x86-64 GNU/Linux.  For 
the second command: Centos Linux release 7.8.2003 (Core).


My system has the newest AFNI installed, do you think that could be 
the cause of the problem?


Thanks for your help!

Xiaomin

*From: *Douglas N. Greve 
*Sent: *Thursday, July 23, 2020 11:00 AM
*To: *Xiaomin Yue 
*Subject: *Re: FW: [Freesurfer] mri_fieldsign error

No, sorry, When I run it on my system it works. If I can't replicate 
the problem, I can't fix it. I don't know why you get it and I don't. 
Can you send me your system specs, ie,

- run uname -a
- the contents of /etc/redhat-release (if it exists)




On 7/23/2020 9:42 AM, Xiaomin Yue wrote:

*External Email - Use Caution *

Any ideas?

Thanks,

Xiaomin

*From: *Xiaomin Yue 
*Sent: *Tuesday, July 21, 2020 12:36 PM
*To: *Freesurfer support list 
*Subject: *Re: [Freesurfer] mri_fieldsign error

*External Email - Use Caution *

I tried on our Linux: Centos Linux 7 (core), ID_like = ‘rhel 
fedora’ with the same “segmentation fault (core dumped)” error.

Thanks,

Xiaomin

*From: *Xiaomin Yue 
*Sent: *Friday, July 17, 2020 6:07 PM
*To: *Freesurfer support list 
*Subject: *Re: [Freesurfer] mri_fieldsign error

*External Email - Use Caution *

Yes.  I will try it on a real Linux box and let you know.

Thanks,

Xiaomin

*From: *Douglas N. Greve 
*Sent: *Friday, July 17, 2020 5:32 PM
*To: *Xiaomin Yue ; Freesurfer support
list 
*Subject: *Re: [Freesurfer] mri_fieldsign error

No, it does not. The only other problem I can think of is that it
has something to do with WSL. Do you have a real linux box you can
try it on?

On 7/17/2020 5:24 PM, Xiaomin Yue wrote:

*External Email - Use Caution *

HI Doug,

Sorry for the slow response.  I got the same “segmentation
fault (core dumped)” error when running the left hemi. I
tested it multiple times.   Does this function create a
detailed log I can send to you?

Thanks,

Xiaomin

*From: *Douglas N. Greve 
*Sent: *Friday, July 17, 2020 1:07 PM
*To: *freesurfer@nmr.mgh.harvard.edu

*Subject: *Re: [Freesurfer] mri_fieldsign error

I was not able to replicate this on my CentOS7 linux box. You
sent me left hemi data, so I ran the command below

mri_fieldsign --fs fieldsign.71.nii.gz --polar
LOO.wedge.polar.lh.real.nii.gz LOO.wedge.polar.lh.imag.nii.gz
--eccen LOO.ring.eccen.lh.real.nii.gz
LOO.ring.eccen.lh.imag.nii.gz --s LOO --hemi lh --sphere

But I also noticed that the command that you gave below is for
the right hemi. Do you know if the left hemi works?


On 7/11/2020 1:43 PM, Xiaomin Yue wrote:

*External Email - Use Caution *

Hi Doug,

I used FS 7.1 under WSL to analyze retinotopy data.  Since
the ring and wedge were presented at a different
frequency, the data had to be analyzed separately for each
condition.  To get the field sign, I had to use the
mri_fieldsign function to combine polar and eccen data.  
However, an error happened with running mri_fieldsign:
“Segmentation fault  (core dumped)”.  The following is
the command-line output.

Thanks for your help!

Xiaomin

cwd /mnt/d/xyLinuxStaff/projects/wedge_amygdala

cmdline mri_fieldsign --fs
LOO_xy/bold/rtopy.wedge.self.rh/fieldsign/fieldsign.nii.gz
--polar LOO_xy/bold/rtopy.wedge.self.rh/polar/real.nii.gz
LOO_xy/bold/rtopy.wedge.self.rh/polar/imag.nii.gz --eccen
../ring_amygdala/LOO_xy/bold/rtopy.ring.self.rh/eccen/real.nii.gz
../ring_amygdala/LOO_xy/bold/rtopy.ri

Re: [Freesurfer] Question for Multiple Sclerosis

[Douglas N. Greve]

Yes, just copy aseg.mgz and edit the copy. Then run mri_segstats. Look 
in recon-all.log for the mri_segstats command that is used to create the 
aseg.stats file. Adapt that command. The output will have an entry for 
the lesion (make sure to use code 99 for the label id).


On 7/24/2020 1:43 PM, Manuel, Morganne wrote:


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Hey Freesurfer,

I am new to Freesurfer. I wanting to use Freesurfer for measuring grey 
and white matter volumes in Multiple sclerosis. However I am wondering 
if there is a way to manually make a lesion mask for each individual 
and then use the mask to subtract the lesion volume from the white 
matter volume. We run recon we break it apart. So is there a certain 
recon set I can use to add the lesion mask to tell Freesurfer to 
subtract this volume from the white matter?


Many thanks,

Morganne


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Re: [Freesurfer] FS 7.1 update

[Douglas N. Greve]

I don't know what you mean. Do you want to install 7.1 on top of 6.0? 
That's probably not a good idea. They can exist on the same computer. 
Not sure what you mean by remotely

On 7/24/2020 10:36 AM, Ferraro, Pilar wrote:
>  External Email - Use Caution
>
> Hi Freesurfer experts,
>
> I'ld like to know whether it's possible to update a FS version (from 6.0 to 
> 7.1) also remotely.
>
> Many thanks,
>
> Pilar
>
>
>
>> Il giorno 24 lug 2020, alle ore 4:27 PM, Ferraro, Pilar 
>>  ha scritto:
>>
>> 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.
>

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@nmr.mgh.

Re: [Freesurfer] The input for Petsurfer

[Douglas N. Greve]

It is not really possible. It is designed assuming you have MRIs.

On 7/24/2020 10:06 AM, Hengameh Marzbani wrote:


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Hello Freesurfer developers,
I have PET images for brain and I want to analyze them with Petsurfer. 
But I don't have T1-weighted MRI of each subject.

What should I do? Is it possible?
Thank you in advance, Best regards, Hengameh



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Re: [Freesurfer] Fwd: Re: Segmentation with FreeSurfer 7.1

[Douglas N. Greve]

Here is the page on topo defects
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefectV6.0

I can't answer your other questions because the previous emails are not 
in this one. If you repost with previous correspondance, then I can answer.


On 7/24/2020 8:12 AM, Sara PONTICORVO wrote:


External Email - Use Caution

Subject: Re: Re: [Freesurfer] Segmentation with FreeSurfer 7.1
Message-ID >



Hi, thanks a lot.
What do you mean for topological default?
We have checked our data, and there aren't any visible artifacts (if 
you were referring to this kind of things). Actually we have seen 
these problems in about 50% of the already acquired data.
If it can be useful for you we can also send you the raw DICOM images 
to check yourself.
It is possible that there are some default settings in the 7.1 
recon-all pipeline that we can adjust?


Thanks again,
Sara


--
Sara Ponticorvo
PhD Student
Departement of Medicine Surgery and Dentistry, University of Salerno

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Re: [Freesurfer] mesh referential

[Douglas N. Greve]

The surface coordinates are in what we call "tkRegister space". Check 
out this page (and slide deck on this page)

https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems


On 7/24/2020 4:53 AM, TACONNE Marion (INTERN) wrote:


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Hello,

I would like to know in which referential is the meshes ( lh.smoothwm 
for example). Is it RAS ? If not, how can we change the mesh 
referential in this referential.


Thank you in advance for your time and answer.

Best regards,

Marion Taconné

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[Freesurfer] Question for Multiple Sclerosis

[Manuel, Morganne]

External Email - Use Caution

Hey Freesurfer,

I am new to Freesurfer. I wanting to use Freesurfer for measuring grey and 
white matter volumes in Multiple sclerosis. However I am wondering if there is 
a way to manually make a lesion mask for each individual and then use the mask 
to subtract the lesion volume from the white matter volume. We run recon we 
break it apart. So is there a certain recon set I can use to add the lesion 
mask to tell Freesurfer to subtract this volume from the white matter?

Many thanks,

Morganne
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Re: [Freesurfer] FreeSurfer 7.1.0 VirtualBox Installation password

[fsbuild]

External Email - Use Caution

Hello Nuri,
I am sending the password directly to your email.
-R.

On Jul 24, 2020, at 09:30, Choi, Nuri  
wrote:External Email - Use 
CautionHi,I followed the given 
instructions on this page (https://surfer.nmr.mgh.harvard.edu/fswiki/VM_67) but 
could not find the README file to find the password to log in to the developer 
account. I've seen that other users in the archive received the password 
privately via email - may I request the password as well? Sorry if this is 
quite redundant on your end...Thank you very 
much,-Nuri___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard..edu/mailman/listinfo/freesurfer​
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Re: [Freesurfer] Extract the cerebellum

[Douglas N. Greve]

Try
mri_binarize --i aseg.mgz --match 7 8 46 47 --o cerebellum.nii.gz
Those numbers come from $FREESURFER_HOME/FreeSurferColorLUT.txt

On 7/23/2020 9:47 PM, Camargo, Aldo wrote:


External Email - Use Caution

Hi Freesurfer experts,

I am trying to extract only the cerebellum and then save it to nii 
file. How can I do it with freesurfer ?


Thanks a lot and have a nice day,

Aldo


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Re: [Freesurfer] FS 7.1 update

[Ferraro, Pilar]

External Email - Use Caution

Hi Freesurfer experts,

I'ld like to know whether it's possible to update a FS version (from 6.0 to 
7.1) also remotely.

Many thanks,

Pilar



> Il giorno 24 lug 2020, alle ore 4:27 PM, Ferraro, Pilar 
>  ha scritto:
> 
> 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

[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
> https://mail.nmr.mgh.

[Freesurfer] The input for Petsurfer

[Hengameh Marzbani]

External Email - Use Caution

Hello Freesurfer developers,


I have PET images for brain and I want to analyze them with Petsurfer.
But I don't have T1-weighted MRI of each subject.

What should I do? Is it possible?


Thank you in advance,
Best regards,
Hengameh
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[Freesurfer] Working with cortical surface area - parcellation size?

[Yash Patel]

External Email - Use Caution

Hi Freesurfer colleagues,

I want to analyze regional profiles of differences in cortical surface area 
(SA). However, SA and its group differences in SA depend on parcellation size. 
In order to mitigate this effect, should I create a parcellation that has 
roughly equal area per ROI in FSaverage space, or equal number of vtx per ROI 
in FSaverage space.
Looking at smaller ROIs than the DK atlas - so I will be making the 
parcellation in any case.

Thanks - any advice would be much appreciated
Yash
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[Freesurfer] FreeSurfer 7.1.0 VirtualBox Installation password

[Choi, Nuri]

External Email - Use Caution

Hi,

I followed the given instructions on this page 
(https://surfer.nmr.mgh.harvard.edu/fswiki/VM_67) but could not find the README 
file to find the password to log in to the developer account. I've seen that 
other users in the archive received the password privately via email - may I 
request the password as well? Sorry if this is quite redundant on your end...

Thank you very much,
-Nuri
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[Freesurfer] Fwd: Re: Segmentation with FreeSurfer 7.1

[Sara PONTICORVO]

External Email - Use Caution

Subject: Re: Re: [Freesurfer] Segmentation with FreeSurfer 7.1
Message-ID 


Hi, thanks a lot.
What do you mean for topological default?
We have checked our data, and there aren't any visible artifacts (if you
were referring to this kind of things). Actually we have seen these
problems in about 50% of the already acquired data.
If it can be useful for you we can also send you the raw DICOM images to
check yourself.
It is possible that there are some default settings in the 7.1 recon-all
pipeline that we can adjust?

Thanks again,
Sara


-- 
Sara Ponticorvo
PhD Student
Departement of Medicine Surgery and Dentistry, University of Salerno
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[Freesurfer] FreeSurfer 7.1.0 tkmedit not opening - please help

[Nils Böer]

External Email - Use Caution

Hello everyone,

I'm having a problem with tkmedit on the pre-installed Freesurfer 7.1.0
version for as Ubuntu guest on a Windows 10 host (via Oracle VM).

I did work with the 6.0 version before but changed to Freesurfer 7.1 and
used the .vdi for Oracle VM where Freesurfer is pre-installed. I did run
recon-all for all my data and now wanted to start to check the surfaces
with tkmedit. When I try running tkmedit (tkmedit P_01 brainmask.mgz -aux
T1.mgz -surfs) it shows me, that it Converted the surfaces but no window is
opening. When I'm closing the console it shows me, that there is a process
running in the background but the tkmedit window is missing.

I hope someone knows how to solve the problem.

Best regards,

Nils
-- 

Nils Böer
Research Assistant with Bachelor Degree (WHB)
*Psychology and Movement*
University of Paderborn
Department of Sports and Health
Warburger Str. 100
33098 Paderborn
Room: Sp 1.401

Email: nils.tobia...@gmail.com / nbo...@mail.uni-paderborn.de

Web: https://sug.uni-paderborn.de/en/sport/sportpsychologie/team/
 https://sug.uni-paderborn.de/department/it/



Virenfrei.
www.avast.com

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[Freesurfer] mesh referential

[TACONNE Marion (INTERN)]

External Email - Use Caution

Hello,
I would like to know in which referential is the meshes ( lh.smoothwm for 
example). Is it RAS ? If not, how can we change the mesh referential in this 
referential.
Thank you in advance for your time and answer.
Best regards,

Marion Taconné


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