[Freesurfer] Download link for infantFS

[Mahmoud]

External Email - Use Caution

Hello Freesurfer developers,

I am interested to download and use the infantFS. I followed the
instructions on the wiki and filled out the form on this page
https://martinos.org/lab/lcn/resources/infant_fs_download

I received a confirmation email saying that "Thank you, your submission has
been received. Please, allow us 48hrs to respond." but I did not receive
anything after 4 days. I called Dr. Zollei's office and left a message but
no response yet.

Could anyone please let me know what am I supposed to do? Did I miss
something?

I appreciate your help.

Best,
Mahmoud
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Re: [Freesurfer] Trouble Installing FreeSurfer {Disarmed}

[fsbuild]

External Email - Use Caution

… Correction - with the v switch “tar -xzvf” it is going to list every fileit 
expands and then return to the “$” prompt.
- R.

On , at 18:11 1/28/2019, fsbuild fsbu...@contbay.com 
wrote:External Email - Use 
CautionHello Rodrigo,Did you 
download the tar file freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz 
from this page, and attempt to follow the steps below 
?https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstallIf you do not have 
permission to untar (write files) into /usr/local, you could try using another 
path.But usually if the tar command has a problem it will echo some 
error/text to the terminal, e.g., "Permission denied", or say there was an 
error.If the command simply returns to the prompt than it should have 
succeeded, e.g., success with "$" bash shell prompt.$ tar -C /usr/local -xzvf 
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz$Please try and point 
out the step that does not work for you.- R.On , at 17:47 1/28/2019, 
Rodrigo Montenegro rmontenegr...@gmail.com 
wrote:External Email - Use 
CautionDear FreeSurfer 
Team,I’m a Medicine student at Oxford University and I have just 
registered to FreeSurfer. I just went through the registration process so I'm 
very new to FreeSurfer but have only run to problems so far and would like to 
ask for your help:1.I have 
register with FreeSurferWiki but can’t login: it gives me one of the following 
errors:i.“Error
 403 Login/Edit allowed only on https/SSL connections Login/Edit allowed only 
on https/SSL connections Guru Meditation: XID: 1153030795 Varnish cache 
serve”.ii.Or
 that it is an “Invalid username or password” (not sure 
if2.More importantly I 
have also tried to install FreeSurfer in Virtual Box (4096 MB Memory; 32 MD 
Video Memory; Ubuntu 64 Bits) without any success. The Ubuntu system works fine 
and I have the “freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz” to 
install FreeSurfer but the being totally new to Linux I have not had success to 
install 
it:i.I’m
 not sure if at all the files are unzipped from the .gz 
file.ii.And
 I have been unable to create the Bash files to define the environment for 
it.3.Finally, I notice 
that you do have an installation for Virtual Disk Image but the download for it 
(ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Virtualbox-linux-x86-stable-pub-v5.3-full.vdi.gz)
 is a gz file not a .vdi file as it should be (see picture 
below):image002.jpgSo either way I wasn’t able to get 
through with the installation and any help is appreciated.Could you 
please provide some advice?Many thanks,Rodrigo 
Montenegro+44(0)7503070807___Freesurfer
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Re: [Freesurfer] Trouble Installing FreeSurfer

[fsbuild]

External Email - Use Caution

Hello Rodrigo,
Did you download the tar file 
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz from this page, and 
attempt to follow the steps below ?
https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
If you do not have permission to untar (write files) into /usr/local, you could 
try using another path. 

But usually if the tar command has a problem it will echo some error/text to 
the terminal, e.g., "Permission denied", or say there was an error.

If the command simply returns to the prompt than it should have succeeded, 
e.g., success with "$" bash shell prompt.

$ tar -C /usr/local -xzvf 
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz$
Please try and point out the step that does not work for you.

- R.

On , at 17:47 1/28/2019, Rodrigo Montenegro 
rmontenegr...@gmail.com 
wrote:External Email - Use 
CautionDear FreeSurfer 
Team,I’m a Medicine student at Oxford University and I have just 
registered to FreeSurfer. I just went through the registration process so I'm 
very new to FreeSurfer but have only run to problems so far and would like to 
ask for your help:1.I have 
register with FreeSurferWiki but can’t login: it gives me one of the following 
errors:i.“Error
 403 Login/Edit allowed only on https/SSL connections Login/Edit allowed only 
on https/SSL connections Guru Meditation: XID: 1153030795 Varnish cache 
serve”.ii.Or
 that it is an “Invalid username or password” (not sure 
if2.More importantly I 
have also tried to install FreeSurfer in Virtual Box (4096 MB Memory; 32 MD 
Video Memory; Ubuntu 64 Bits) without any success. The Ubuntu system works fine 
and I have the “freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz” to 
install FreeSurfer but the being totally new to Linux I have not had success to 
install 
it:i.I’m
 not sure if at all the files are unzipped from the .gz 
file.ii.And
 I have been unable to create the Bash files to define the environment for 
it.3.Finally, I notice 
that you do have an installation for Virtual Disk Image but the download for it 
(ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Virtualbox-linux-x86-stable-pub-v5.3-full.vdi..gz)
 is a gz file not a .vdi file as it should be (see picture 
below):image002.jpgSo either way I wasn’t able to get 
through with the installation and any help is appreciated.Could you 
please provide some advice?Many thanks,Rodrigo 
Montenegro+44(0)7503070807___Freesurfer
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[Freesurfer] Trouble Installing FreeSurfer

[Rodrigo Montenegro]

External Email - Use Caution

Dear FreeSurfer Team,

 

I'm a Medicine student at Oxford University and I have just registered to
FreeSurfer. I just went through the registration process so I'm very new to
FreeSurfer but have only run to problems so far and would like to ask for
your help:

 

1.   I have register with FreeSurferWiki but can't login: it gives me
one of the following errors:

i.  "Error 403 Login/Edit allowed only on https/SSL
connections Login/Edit allowed only on https/SSL connections Guru
Meditation: XID: 1153030795 Varnish cache serve".

ii.   Or that it is an "Invalid username or password" (not
sure if 

 

2.   More importantly I have also tried to install FreeSurfer in Virtual
Box (4096 MB Memory; 32 MD Video Memory; Ubuntu 64 Bits) without any
success. The Ubuntu system works fine and I have the
"freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz" to install
FreeSurfer but the being totally new to Linux I have not had success to
install it:

i. I'm not sure if at all the files are unzipped from
the .gz file.

ii.   And I have been unable to create the Bash files to
define the environment for it.

 

3.Finally, I notice that you do have an installation for Virtual
Disk Image but the download for it
(ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Virtu
albox-linux-x86-stable-pub-v5.3-full.vdi.gz) is a gz file not a .vdi file as
it should be (see picture below):

 



 

So either way I wasn't able to get through with the installation and any
help is appreciated.

 

Could you please provide some advice?

 

Many thanks,

 

Rodrigo Montenegro

+44(0)7503070807

 

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Re: [Freesurfer] mri_vol2vol

[Nasiriavanaki, Zahra]

Thank you very much


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129




From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Greve, Douglas N.,Ph.D. 

Sent: Monday, January 28, 2019 3:17:36 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_vol2vol

that should work

On 1/28/19 2:44 PM, Nasiriavanaki, Zahra wrote:

Dear Freesurfers


Hi

I am trying to project a subcortical volume , that I manually made, from 
fsaverage to individual subject's space.

I was wondering if it's ok if I use mri_vol2vol for this purpose. I copied my 
command below:


mri_vol2vol --mov ./${ROI}/ROI4.mgz  --targ 
$SUBJECTS_DIR/fsaverage/mri/orig.mgz --o $SUBJECTS_DIR/${subj}/mri/${ROI}.mgz 
--talres 2 --interp nearest --regheader


Thanks

Mona


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129





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Re: [Freesurfer] cortical thickness calculation based on hammersmith segmentation

[Boris Rauchmann]

External Email - Use Caution

Hi Bruce,

thank you for your quick answer. I managed it now to create cannot files based 
on the atlas volumetric segmentations.

I first created:

mri_vol2surf —src  .../Hammers_mith_atlas_n30r83_SPM5.nii --out 
.../Hammers_AVG.nii --out_type mgh --hemi lh --mni152reg

then applied:

mris_apply_reg --src .../hammers_lh_avg_surf.mgh --trg 
.../hammers_lh_INDI_0021.mgh --streg $SUBJECTS_DIR/fsaverage/surf/lh.sphere.reg 
 .../0021/surf/lh.sphere 

and:

mris_seg2annot --seg /.../hammers_lh_INDI_0021.mgh   --s 0021 --h lh --ctab 
/.../ExploreDTI_Pcode/Source/Misc/My_FS_LUT.txt  --o 
.../lh.hammersmithINDI.annot

My question now is how can I create a suitable LUT with the correct labels for 
the cortical parcellations? I have only a .csv file with the labels for the 
volumetric atlas? 

My goal is to use 

mris_anatomical_stats -a .../0021/label/lh.hammersmithINDI.annot -b 0021 lh

to get the cortical thickness values of each segment in the annot for every 
participant file.

Thanks again, 
Boris




> Am 27.01.2019 um 23:58 schrieb Bruce Fischl :
> 
> Hi Boris
> 
> vol2surf samples a scalar overlay in the volume to be a scalar overlay on the 
> surface. This is NOT the same as a surface itself - it contains no geometry 
> or topology information. Try giving freeview a surface (which I guess you 
> have for subject 0021). Something like
> 
> freeview -f \
> 0021/surf/lh.inflated:overlay=lhHammers_mith_atlas_n30r83_SPM5surf.mgh
> 
> cheers
> Bruce
> 
> 
> On Sun, 27 Jan 2019, Boris Rauchmann wrote:
> 
>> External Email - Use Caution
>> Hi,
>> I used the following commands:
>>  mri_vol2surf —src  .../Hammers_mith_atlas_n30r83_SPM5.nii  --out 
>> lhHammers_mith_atlas_n30r83_SPM5surf.mgh
>> --out_type mgh --hemi lh --regheader 0021
>> srcvol = .../Hammers_mith_atlas_n30r83_SPM5.nii
>> srcreg unspecified
>> srcregold = 0
>> srcwarp unspecified
>> surf = white
>> hemi = lh
>> reshape = 0
>> interp = nearest
>> float2int = round
>> GetProjMax = 0
>> INFO: float2int code = 0
>> Done loading volume
>> Computing registration from header.
>>   Using .../0021/mri/orig.mgz as target reference.
>> Reading surface .../0021/surf/lh.white
>> Done reading source surface
>> Mapping Source Volume onto Source Subject Surface
>>  1 0 0 0
>> using old
>> Done mapping volume to surface
>> Number of source voxels hit = 76207
>> Writing to lhHammers_mith_atlas_n30r83_SPM5surf.mgh
>> Dim: 125545 1 1
>> it creates the .mgh file but when I try to open in in Freeview or tksurfer 
>> to check the surface file I get the
>> following error message:
>> my_computer$ freeview
>> ERROR: MRISread: file ‚/.../lhHammers_mith_atlas_n30r83_SPM5surf.mgh' has 0 
>> vertices!
>> Probably trying to use a scalar data file as a surface!
>> nquads=65537,  nvertices=0
>> ERROR: MRISread: file , /…/lhHammers_mith_atlas_n30r83_SPM5surf.mgh' has 
>> many more faces than vertices!
>> Probably trying to use a scalar data file as a surface!
>> [0]PETSC ERROR: 
>> 
>> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, 
>> probably memory access out of range
>> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
>> [0]PETSC ERROR: or see 
>> http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
>> ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to 
>> find memory corruption errors
>> [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and 
>> run 
>> [0]PETSC ERROR: to get more information on the crash.
>> [0]PETSC ERROR: - Error Message 
>> 
>> [0]PETSC ERROR: Signal received!
>> [0]PETSC ERROR: 
>> 
>> [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 
>> CDT 2008 HG revision:
>> 4466c6289a0922df26e20626fd4a0b4dd03c8124
>> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
>> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
>> [0]PETSC ERROR: See docs/index.html for manual pages.
>> [0]PETSC ERROR: 
>> 
>> [0]PETSC ERROR: Unknown Name on a darwin12. named my_computer.local by boris 
>> Sun Jan 27 23:12:45 2019
>> [0]PETSC ERROR: Libraries linked from
>> /usr/pubsw/packages/petsc/2.3.3-p13-64b/src/petsc-2.3.3-p13/lib/darwin12.2.0-c-opt
>> [0]PETSC ERROR: Configure run at Mon Dec 17 15:29:35 2012
>> [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc 
>> --with-fc=0 --download-f-blas-lapack=0
>> --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 
>> --with-shared=0 COPTFLAGS=-O3
>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
>> [0]PETSC ERROR: 
>> 
>> [0]PETSC ERROR: User 

Re: [Freesurfer] mri_vol2vol

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

that should work

On 1/28/19 2:44 PM, Nasiriavanaki, Zahra wrote:

Dear Freesurfers


Hi

I am trying to project a subcortical volume , that I manually made, from 
fsaverage to individual subject's space.

I was wondering if it's ok if I use mri_vol2vol for this purpose. I copied my 
command below:


mri_vol2vol --mov ./${ROI}/ROI4.mgz  --targ 
$SUBJECTS_DIR/fsaverage/mri/orig.mgz --o $SUBJECTS_DIR/${subj}/mri/${ROI}.mgz 
--talres 2 --interp nearest --regheader


Thanks

Mona


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129





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[Freesurfer] mri_vol2vol

[Nasiriavanaki, Zahra]

Dear Freesurfers


Hi

I am trying to project a subcortical volume , that I manually made, from 
fsaverage to individual subject's space.

I was wondering if it's ok if I use mri_vol2vol for this purpose. I copied my 
command below:


mri_vol2vol --mov ./${ROI}/ROI4.mgz  --targ 
$SUBJECTS_DIR/fsaverage/mri/orig.mgz --o $SUBJECTS_DIR/${subj}/mri/${ROI}.mgz 
--talres 2 --interp nearest --regheader


Thanks

Mona


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129


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Re: [Freesurfer] Cortical & subcortical cluster size

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

Can you be more specific?

On 1/28/19 2:12 PM, Jahan, Bushra wrote:

Hi,


I'm wondering which column in the FreeSurfer summary file represents the 
cluster size for the cortical and subcortical clusters.



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[Freesurfer] Cortical & subcortical cluster size

[Jahan, Bushra]

Hi,


I'm wondering which column in the FreeSurfer summary file represents the 
cluster size for the cortical and subcortical clusters.
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[Freesurfer] Cannot create template when running longitudinal freesurfer 6.0.0

[Kilian Pohl]

External Email - Use Caution

Hi ,

The following command worked fine under 5.3.0

recon-all -openmp 88 -sd 
LAB_S00308/standard/20161209_2776_12092016/structural/longitudinal/freesurfer 
-base template_baseline_1  -tp baseline -tp 1 -all

but now it produces there error

ERROR: It appears that the -base templateID that you passed:
    -base template_baseline_1
    is an existing regular (cross sectional) run!
    Please make sure you pass a new name (not one of
    the time points) for the template with -base.
    For example, if you are trying to create a -base:

    \' -base BertTemplate -tp Bert1 -tp Bert2 ... \'

There is no existing regular (cross sectional) run.


Do you know what the issue is ?

The only dirs in 
LAB_S00308/standard/20161209_2776_12092016/structural/longitudinal/freesurfer 
are

lrwxrwxrwx 1 djk root 100 Jan 28 10:29 1 -> 
../../../../20161209_2776_12092016/structural/freesurfer6/LAB_S00308_standard_20161209_2776_12092016
lrwxrwxrwx 1 djk root 100 Jan 28 10:29 baseline -> 
../../../../20080725_3594_07252008/structural/freesurfer6/LAB_S00308_standard_20080725_3594_07252008
drwxr-xr-x 3 djk root  23 Jan 28 10:29 template_baseline_1


Thanks

Kilian





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[Freesurfer] R: Question regarding white substance with Freesurfer

[Erika Portera]

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the problem is that also adding voxel to fix the defect, when I re-process the 
subject, the changes are not visible.



Da: freesurfer-boun...@nmr.mgh.harvard.edu 
 per conto di Greve, Douglas N.,Ph.D. 

Inviato: lunedì 28 gennaio 2019 16:46
A: freesurfer@nmr.mgh.harvard.edu
Oggetto: Re: [Freesurfer] Question regarding white substance with Freesurfer

This is probably an incorrectly fixed defect. Look at the tutorial for fixing 
defects. Basically, you need to look at the wm.mgz volume in that area and 
manually fix the segmentation errors that caused the defect.

On 1/28/19 11:25 AM, Erika Portera wrote:

External Email - Use Caution

Good evening,
I write you to resolve a problem with the program of freesurfer.
Also following the tutorial for the corrections, I don't succeed in integrating 
parts of white substance.
The problem concerns the underlying images ( error temporal gyrus sx)
I thank you for your help.

Erika Portera





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Re: [Freesurfer] Question regarding white substance with Freesurfer

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

This is probably an incorrectly fixed defect. Look at the tutorial for fixing 
defects. Basically, you need to look at the wm.mgz volume in that area and 
manually fix the segmentation errors that caused the defect.

On 1/28/19 11:25 AM, Erika Portera wrote:

External Email - Use Caution

Good evening,
I write you to resolve a problem with the program of freesurfer.
Also following the tutorial for the corrections, I don't succeed in integrating 
parts of white substance.
The problem concerns the underlying images ( error temporal gyrus sx)
I thank you for your help.

Erika Portera





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Re: [Freesurfer] [PETSurfer] Intensity normalization of PET images without PVE correction

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

If you intend to use one of the aseg structures, then they are the same.

On 1/28/19 10:14 AM, Matthieu Vanhoutte wrote:

External Email - Use Caution

Hi Douglas,


Le 25 janv. 2019 à 18:01, Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> a écrit :



On 1/25/19 7:57 AM, Matthieu Vanhoutte wrote:

External Email - Use Caution

Dear Douglas,

Could you precise me:
1) Is the intensity rescaling of PET image included in the mri_gtmpvc command 
based on reference region in gtmseg.mgz file rather than aseg.mgz ?
It depends. If you are using pons, then that is not part of the aseg and is 
generated as part of the creation of gtmseg. But most of the rest of gtmseg is 
derived from the aseg and surfaces.

Is it better to use gtmseg.mgz or aseg.mgz to extract reference region’s mean 
intensity ?


2) Is this rescaling applied before PVE correction or after (i.e. based on PVE 
corrected reference region’s mean intensity) ?
After

Many thanks in advance for helping.

Best,
Matthieu

Le 7 janv. 2019 à 17:26, Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> a écrit :



On 1/7/19 11:18 AM, Matthieu Vanhoutte wrote:

External Email - Use Caution

I used the following command to obtain only rescaled voxel-wise PET image (with 
no PVC):
mri_gtmpvc --i PET.nii.gz --reg Pet2T1.register.dof6.lta --psf 0 --no-tfe --seg 
gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --rbv --o  nopvc

If I omitted --rbv or --mgx option I didn't get the rescaled voxel-wise PET 
image (without PVC). Could I obtain the rescaled voxel-wise PET image (without 
PVC) just by dividing each voxel of the native PET image by the mean of the 
reference region ?
Yes

Best,
Matt

Le lun. 7 janv. 2019 à 16:01, Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> a écrit :
I'm not sure what you mean. If you are turning off PVC, why are you computing 
RBV and MGX? What is your command line? What do you mean that these options 
don't seem to work?

On 12/21/18 2:22 PM, Matthieu Vanhoutte wrote:

External Email - Use Caution

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. 
mailto:dgr...@mgh.harvard.edu>> 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:

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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] Intensity normalization of PET images without PVE correction

[Matthieu Vanhoutte]

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Hi Douglas,


> Le 25 janv. 2019 à 18:01, Greve, Douglas N.,Ph.D.  a 
> écrit :
> 
> 
> 
> On 1/25/19 7:57 AM, Matthieu Vanhoutte wrote:
>> External Email - Use Caution
>> 
>> Dear Douglas,
>> 
>> Could you precise me:
>> 1) Is the intensity rescaling of PET image included in the mri_gtmpvc 
>> command based on reference region in gtmseg.mgz file rather than aseg.mgz ?
> It depends. If you are using pons, then that is not part of the aseg and is 
> generated as part of the creation of gtmseg. But most of the rest of gtmseg 
> is derived from the aseg and surfaces.

Is it better to use gtmseg.mgz or aseg.mgz to extract reference region’s mean 
intensity ?


>> 2) Is this rescaling applied before PVE correction or after (i.e. based on 
>> PVE corrected reference region’s mean intensity) ?
> After
>> 
>> Many thanks in advance for helping.
>> 
>> Best,
>> Matthieu
>> 
>>> Le 7 janv. 2019 à 17:26, Greve, Douglas N.,Ph.D. >> > a écrit :
>>> 
>>> 
>>> 
>>> On 1/7/19 11:18 AM, Matthieu Vanhoutte wrote:
 External Email - Use Caution
 
 
 I used the following command to obtain only rescaled voxel-wise PET image 
 (with no PVC):
 mri_gtmpvc --i PET.nii.gz --reg Pet2T1.register.dof6.lta --psf 0 --no-tfe 
 --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --rbv --o  nopvc
 
 If I omitted --rbv or --mgx option I didn't get the rescaled voxel-wise 
 PET image (without PVC). Could I obtain the rescaled voxel-wise PET image 
 (without PVC) just by dividing each voxel of the native PET image by the 
 mean of the reference region ?
>>> Yes
 
 Best,
 Matt
 
 Le lun. 7 janv. 2019 à 16:01, Greve, Douglas N.,Ph.D. 
 mailto:dgr...@mgh.harvard.edu>> a écrit :
 I'm not sure what you mean. If you are turning off PVC, why are you 
 computing RBV and MGX? What is your command line? What do you mean that 
 these options don't seem to work?
 
 On 12/21/18 2:22 PM, Matthieu Vanhoutte wrote:
> External Email - Use Caution
> 
> 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. 
> mailto:dgr...@mgh.harvard.edu>> 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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[Freesurfer] Italian Summer School: Interdisciplinary Research on Brain Network Dynamics

[Jovicich, Jorge]

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Dear all,

we are organizing an international summer school on interdisciplinary 
research oriented to the study of brain network dynamics (June 24-28, 
2019). More information: https://event.unitn.it/brandyschool2019/

Feel free to disseminate to relevant groups.

Regards,

     Jorge

-- 
Jorge Jovicich, Ph.D.

MR Lab Head
Center for Mind/Brain Sciences
University of Trento,
Via delle Regole, 101
38100 Mattarello (TN)
Italy

Telephone: +39-0461-28 3064
Fax: +39-0461-28-3066
Email: jorge.jovic...@unitn.it
MRI Methods Group: http://r.unitn.it/en/cimec/mri
CIMEC: http://www.cimec.unitn.it/


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