[Freesurfer] zero values when run recon-all with T2pial flag (V6.0)

2019-02-01 Thread Morgan Botdorf 
External Email - Use Caution

Dear all,

I recently ran recon-all on data using the T2pial flag to improve the pial
surface (using version 6.0). The T2 images seemed to improve the pial
surfaces; however, when I extract stats using the Destrieux atlas, I get
zero values for several regions and for BrainSegVolNotVent and eTIV. If I
run recon-all without the T2 image, I get data for these
regions, BrainSegVolNotVent, and eTIV. Has anyone run into similar issues
using the T2pial flag or have an idea of what may be causing this problem?

Thank you in advance for your help!

Morgan
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[Freesurfer] Postdoctoral position in Eating Disorders at UCSD

2019-02-01 Thread Grethe, Amanda 
External Email - Use Caution

Research Postdoctoral Fellowship at UC San Diego’s Eating Disorders Center for 
Treatment and Research

The University of California, San Diego Eating Disorders Center for Treatment 
and Research is an international leader in research on the neurobiology of 
eating disorders and related problems. We have IOP and day treatment programs 
for adults, adolescents, and children with eating disorders, as well as a 
medical stabilization unit in conjunction with Rady Children’s Hospital. UCSD 
EDC’s programs are growing quickly, and we are currently accepting applications 
for postdoctoral fellows.

Current eating disorder treatments are of limited efficacy. New insight into 
neurobiological mechanisms that contribute to symptoms is supporting 
development of more effective interventions.  The UCSD program is unique in 
that it has faculty and staff who focus on combining research into neurobiology 
with treatment development.  This is an exciting opportunity for individuals to 
learn about brain and behavior and apply this knowledge to new treatment 
approaches. We also encourage applications from candidates who come from 
backgrounds outside of eating disorders, particularly anxiety, substance use, 
trauma, or pediatrics, and we have a strong preference for candidates who have 
experience or interest in functional neuroimaging.  Many of our postdocs stay 
on in permanent staff or faculty positions.

Research Postdoctoral Position

Research postdoctoral fellow: to specialize in studying mechanisms underlying 
eating disorder symptoms and psychopathology (e.g., incentive processing, 
reinforcement learning, interoception). Experience and interest in neuroimaging 
(functional MRI, structural MRI) and neurocognitive assessment is preferred, as 
we have a strong neuroimaging program conducting research on the neurobiology 
of ED. The position will entail immersion in MR image analysis using one or 
more software tools, including AFNI, FSL, SPM, FreeSurfer, and R.  Imaging 
sessions will take place at UCSD’s Center for Functional MRI, which is equipped 
with two research-dedicated GE 3T short-bore scanners.  Experience with other 
experimental methodologies is also welcome.  The ideal candidate would be a 
research-oriented person with a goal of an independent research career focused 
on cognition, brain functioning, and treatment development to translate 
research findings to improved clinical care of individuals with an eating 
disorder. Many of our research postdocs write training grants and transition to 
permanent staff or faculty positions. Appointment length is up to 2 years and 
is based upon the UC post-doctoral scholar salary scale.  The position is 
available the summer of 2019, and applications will be accepted until the 
position is filled.

Required qualifications

•   PhD in Clinical Psychology or related area

•   Experience in neurocognitive assessment preferred

•   Experience in neuroimaging or similar methods preferred

•   Preference for strong background and training in cognitive neuroscience 
and statistics

•   Established track record of publications

To apply for this position, please email a cover letter, CV, and three 
references to Christina Wierenga, PhD 
(cwiere...@ucsd.edu) and Amanda Bischoff-Grethe, PhD 
(agre...@ucsd.edu).


Amanda Bischoff-Grethe
Associate Adjunct Professor
University of California, San Diego
9500 Gilman Drive MC 0738
La Jolla, CA 92093-0738
Tel: 858-246-0604
Fax: 858-246-0556








UCSD EDTRP Research postdoc.pdf
Description: UCSD EDTRP Research postdoc.pdf
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Re: [Freesurfer] [WARNING: UNSCANNABLE EXTRACTION FAILED]RE: Freesurfer Recon-all error

2019-02-01 Thread Jones, Kevin 
External Email - Use Caution

Hi Bruce 

Sorry about that, I am not a code writer. I fixed that and got this response 
instead. 

Kevins-MacBook-Pro:~ kevin$ recon-all -all -i 758251.dcm -s Subj14
ERROR: cannot find 758251.dcm
Darwin Kevins-MacBook-Pro.local 18.2.0 Darwin Kernel Version 18.2.0: Mon Nov 12 
20:24:46 PST 2018; root:xnu-4903.231.4~2/RELEASE_X86_64 x86_64

recon-all -s  exited with ERRORS at Fri Feb  1 12:39:54 EST 2019

For more details, see the log file 
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Kevins-MacBook-Pro:~ kevin$

Thanks  again Kevin ___
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: February 1, 2019 12:27 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] [WARNING: UNSCANNABLE EXTRACTION FAILED]RE: 
Freesurfer Recon-all error

Hi Kevin,

it looks like your second command line has "-1", which should be "-i"

cheers
Bruce


On Fri, 1 Feb 2019, Jones, Kevin wrote:

>
> External Email - Use Caution
>
> Hi Falk
> Thanks for your suggestion. I tried that again without success.
>
> Last login: Fri Feb  1 07:00:13 on ttys000
>
> Kevins-MacBook-Pro:~ kevin$ export FREESURFER_HOME=/Applications/freesurfer
>
> Kevins-MacBook-Pro:~ kevin$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
>
>  freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 
>
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
>
> FREESURFER_HOME   /Applications/freesurfer
>
> FSFAST_HOME   /Applications/freesurfer/fsfast
>
> FSF_OUTPUT_FORMAT nii.gz
>
> SUBJECTS_DIR  /Applications/freesurfer/subjects
>
> MNI_DIR   /Applications/freesurfer/mni
>
> Kevins-MacBook-Pro:~ kevin$ export Case14=Applications/freesurfer/Case14
>
> Kevins-MacBook-Pro:~ kevin$ export SUBJECTS_DIR=$Case14/7581/7583
>
> Kevins-MacBook-Pro:~ kevin$ cd $Subjects_DIR
>
> Kevins-MacBook-Pro:~ kevin$ echo $SUBJECTS_DIR
>
> Applications/freesurfer/Case14/7581/7583
>
> Kevins-MacBook-Pro:~ kevin$ recon-all -all -i 758251.dcm -s Subj14
>
> ERROR: cannot find 758251.dcm
>
> Darwin Kevins-MacBook-Pro.local 18.2.0 Darwin Kernel Version 18.2.0: Mon Nov 
> 12 20:24:46 PST 2018;
> root:xnu-4903.231.4~2/RELEASE_X86_64 x86_64
>
>
> recon-all -s  exited with ERRORS at Fri Feb  1 11:34:00 EST 2019
>
>
> For more details, see the log file
>
> To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
>
> Kevins-MacBook-Pro:~ kevin$ recon-all -all -1 758251.dcm -s Subj14
>
> ERROR: Flag -1 unrecognized.
>
> -all -1 758251.dcm -s Subj14
>
> Darwin Kevins-MacBook-Pro.local 18.2.0 Darwin Kernel Version 18.2.0: Mon Nov 
> 12 20:24:46 PST 2018;
> root:xnu-4903.231.4~2/RELEASE_X86_64 x86_64
>
>
> recon-all -s  exited with ERRORS at Fri Feb  1 11:35:10 EST 2019
>
>
> For more details, see the log file
>
> To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
>
> Kevins-MacBook-Pro:~ kevin$
>
>
> I have attached a T1 MRI file with and without the .dcm added. Could this be 
> a file issue or just code writing
> mistakes.
>
>
> Thanks so  much for advice, Kevin
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of
> falk.luesebr...@med.ovgu.de [falk.luesebr...@med.ovgu.de]
> Sent: February 1, 2019 10:33 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Freesurfer Recon-all error
>
> External Email - Use Caution
>
> Hi Kevin,
>
>
>
> just an educated guess, but did you copy the line “recon-all –all –i 
> 758251.dcm –s Subj14” from somewhere (e.g.
> word)? Because it seems the dash in front of each flag is an emphasized dash, 
> probably resulting in the error. Try
> the following: “recon-all -all -i 758251.dcm -s Subj14”
>
>
>
> Best,
>
> Falk
>
>
>
> Von: freesurfer-boun...@nmr.mgh.harvard.edu 
>  Im Auftrag von Jones, Kevin
> Gesendet: Freitag, 1. Februar 2019 13:00
> An: freesurfer@nmr.mgh.harvard.edu
> Betreff: [Freesurfer] Freesurfer Recon-all error
>
>
>
> External Email - Use Caution
>
> Dear Freesurfer team
>
>
>
> Thanks for you help. I am new to freesurfer, using a mac and getting an error 
> with recon all when using my MRI
> data.
>
>
>
> I ran your tutorial recon all and the tutorial data worked fine. My burned CD 
> T1 MRI files did not have the .dcm
> added so after renaming all the files with .dcm,  the recon function still 
> gives an error message as below.
>
>
>
> Last login: Fri Feb  1 06:51:44 on ttys000
>
> Kevins-MacBook-Pro:~ kevin$ export FREESURFER_HOME=/Applications/freesurfer
>
> Kevins-MacBook-Pro:~ kevin$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
>
>  freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 
>
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
>
> FREESURFER_HOME   /Applications/freesurfer
>
> FSFAST_HOME   /Applications/freesurfer/fsfast
>
>

Re: [Freesurfer] [WARNING: UNSCANNABLE EXTRACTION FAILED]RE: Freesurfer Recon-all error

2019-02-01 Thread Bruce Fischl 

Hi Kevin

you need to specify the full path to the file 758251.dcm

cheers
Bruce

On Fri, 1 Feb 2019, Jones, Kevin wrote:


   External Email - Use Caution

Hi Bruce

Sorry about that, I am not a code writer. I fixed that and got this response 
instead.

Kevins-MacBook-Pro:~ kevin$ recon-all -all -i 758251.dcm -s Subj14
ERROR: cannot find 758251.dcm
Darwin Kevins-MacBook-Pro.local 18.2.0 Darwin Kernel Version 18.2.0: Mon Nov 12 
20:24:46 PST 2018; root:xnu-4903.231.4~2/RELEASE_X86_64 x86_64

recon-all -s  exited with ERRORS at Fri Feb  1 12:39:54 EST 2019

For more details, see the log file
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Kevins-MacBook-Pro:~ kevin$

Thanks  again Kevin ___
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: February 1, 2019 12:27 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] [WARNING: UNSCANNABLE EXTRACTION FAILED]RE: 
Freesurfer Recon-all error

Hi Kevin,

it looks like your second command line has "-1", which should be "-i"

cheers
Bruce


On Fri, 1 Feb 2019, Jones, Kevin wrote:



External Email - Use Caution

Hi Falk
Thanks for your suggestion. I tried that again without success.

Last login: Fri Feb  1 07:00:13 on ttys000

Kevins-MacBook-Pro:~ kevin$ export FREESURFER_HOME=/Applications/freesurfer

Kevins-MacBook-Pro:~ kevin$ source $FREESURFER_HOME/SetUpFreeSurfer.sh

 freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 

Setting up environment for FreeSurfer/FS-FAST (and FSL)

FREESURFER_HOME   /Applications/freesurfer

FSFAST_HOME   /Applications/freesurfer/fsfast

FSF_OUTPUT_FORMAT nii.gz

SUBJECTS_DIR  /Applications/freesurfer/subjects

MNI_DIR   /Applications/freesurfer/mni

Kevins-MacBook-Pro:~ kevin$ export Case14=Applications/freesurfer/Case14

Kevins-MacBook-Pro:~ kevin$ export SUBJECTS_DIR=$Case14/7581/7583

Kevins-MacBook-Pro:~ kevin$ cd $Subjects_DIR

Kevins-MacBook-Pro:~ kevin$ echo $SUBJECTS_DIR

Applications/freesurfer/Case14/7581/7583

Kevins-MacBook-Pro:~ kevin$ recon-all -all -i 758251.dcm -s Subj14

ERROR: cannot find 758251.dcm

Darwin Kevins-MacBook-Pro.local 18.2.0 Darwin Kernel Version 18.2.0: Mon Nov 12 
20:24:46 PST 2018;
root:xnu-4903.231.4~2/RELEASE_X86_64 x86_64


recon-all -s  exited with ERRORS at Fri Feb  1 11:34:00 EST 2019


For more details, see the log file

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


Kevins-MacBook-Pro:~ kevin$ recon-all -all -1 758251.dcm -s Subj14

ERROR: Flag -1 unrecognized.

-all -1 758251.dcm -s Subj14

Darwin Kevins-MacBook-Pro.local 18.2.0 Darwin Kernel Version 18.2.0: Mon Nov 12 
20:24:46 PST 2018;
root:xnu-4903.231.4~2/RELEASE_X86_64 x86_64


recon-all -s  exited with ERRORS at Fri Feb  1 11:35:10 EST 2019


For more details, see the log file

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


Kevins-MacBook-Pro:~ kevin$


I have attached a T1 MRI file with and without the .dcm added. Could this be a 
file issue or just code writing
mistakes.


Thanks so  much for advice, Kevin

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of
falk.luesebr...@med.ovgu.de [falk.luesebr...@med.ovgu.de]
Sent: February 1, 2019 10:33 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Freesurfer Recon-all error

External Email - Use Caution

Hi Kevin,



just an educated guess, but did you copy the line “recon-all –all –i 758251.dcm 
–s Subj14” from somewhere (e.g.
word)? Because it seems the dash in front of each flag is an emphasized dash, 
probably resulting in the error. Try
the following: “recon-all -all -i 758251.dcm -s Subj14”



Best,

Falk



Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 Im Auftrag von Jones, Kevin
Gesendet: Freitag, 1. Februar 2019 13:00
An: freesurfer@nmr.mgh.harvard.edu
Betreff: [Freesurfer] Freesurfer Recon-all error



External Email - Use Caution

Dear Freesurfer team



Thanks for you help. I am new to freesurfer, using a mac and getting an error 
with recon all when using my MRI
data.



I ran your tutorial recon all and the tutorial data worked fine. My burned CD 
T1 MRI files did not have the .dcm
added so after renaming all the files with .dcm,  the recon function still 
gives an error message as below.



Last login: Fri Feb  1 06:51:44 on ttys000

Kevins-MacBook-Pro:~ kevin$ export FREESURFER_HOME=/Applications/freesurfer

Kevins-MacBook-Pro:~ kevin$ source $FREESURFER_HOME/SetUpFreeSurfer.sh

 freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 

Setting up environment for FreeSurfer/FS-FAST (and FSL)

FREESURFER_HOME   /Applications/freesurfer

FSFAST_HOME   /Applications/freesurfer/fsfast

FSF_OUTPUT_FORMAT nii.gz

SUBJECTS_DIR  /Applications/freesurfer/subjects

MNI_DIR   /Applications/freesurfer/mni

Re: [Freesurfer] [WARNING: UNSCANNABLE EXTRACTION FAILED]RE: Freesurfer Recon-all error

2019-02-01 Thread Bruce Fischl 

Hi Kevin,

it looks like your second command line has "-1", which should be "-i"

cheers
Bruce


On Fri, 1 Feb 2019, Jones, Kevin wrote:



External Email - Use Caution

Hi Falk 
Thanks for your suggestion. I tried that again without success. 

Last login: Fri Feb  1 07:00:13 on ttys000

Kevins-MacBook-Pro:~ kevin$ export FREESURFER_HOME=/Applications/freesurfer

Kevins-MacBook-Pro:~ kevin$ source $FREESURFER_HOME/SetUpFreeSurfer.sh

 freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 

Setting up environment for FreeSurfer/FS-FAST (and FSL)

FREESURFER_HOME   /Applications/freesurfer

FSFAST_HOME       /Applications/freesurfer/fsfast

FSF_OUTPUT_FORMAT nii.gz

SUBJECTS_DIR      /Applications/freesurfer/subjects

MNI_DIR           /Applications/freesurfer/mni

Kevins-MacBook-Pro:~ kevin$ export Case14=Applications/freesurfer/Case14

Kevins-MacBook-Pro:~ kevin$ export SUBJECTS_DIR=$Case14/7581/7583

Kevins-MacBook-Pro:~ kevin$ cd $Subjects_DIR

Kevins-MacBook-Pro:~ kevin$ echo $SUBJECTS_DIR

Applications/freesurfer/Case14/7581/7583

Kevins-MacBook-Pro:~ kevin$ recon-all -all -i 758251.dcm -s Subj14

ERROR: cannot find 758251.dcm

Darwin Kevins-MacBook-Pro.local 18.2.0 Darwin Kernel Version 18.2.0: Mon Nov 12 
20:24:46 PST 2018;
root:xnu-4903.231.4~2/RELEASE_X86_64 x86_64


recon-all -s  exited with ERRORS at Fri Feb  1 11:34:00 EST 2019


For more details, see the log file 

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


Kevins-MacBook-Pro:~ kevin$ recon-all -all -1 758251.dcm -s Subj14

ERROR: Flag -1 unrecognized.

-all -1 758251.dcm -s Subj14

Darwin Kevins-MacBook-Pro.local 18.2.0 Darwin Kernel Version 18.2.0: Mon Nov 12 
20:24:46 PST 2018;
root:xnu-4903.231.4~2/RELEASE_X86_64 x86_64


recon-all -s  exited with ERRORS at Fri Feb  1 11:35:10 EST 2019


For more details, see the log file 

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


Kevins-MacBook-Pro:~ kevin$ 


I have attached a T1 MRI file with and without the .dcm added. Could this be a 
file issue or just code writing
mistakes. 


Thanks so  much for advice, Kevin  

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of
falk.luesebr...@med.ovgu.de [falk.luesebr...@med.ovgu.de]
Sent: February 1, 2019 10:33 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Freesurfer Recon-all error

External Email - Use Caution

Hi Kevin,

 

just an educated guess, but did you copy the line “recon-all –all –i 758251.dcm 
–s Subj14” from somewhere (e.g.
word)? Because it seems the dash in front of each flag is an emphasized dash, 
probably resulting in the error. Try
the following: “recon-all -all -i 758251.dcm -s Subj14”

 

Best,

Falk

 

Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 Im Auftrag von Jones, Kevin
Gesendet: Freitag, 1. Februar 2019 13:00
An: freesurfer@nmr.mgh.harvard.edu
Betreff: [Freesurfer] Freesurfer Recon-all error

 

External Email - Use Caution

Dear Freesurfer team 

 

Thanks for you help. I am new to freesurfer, using a mac and getting an error 
with recon all when using my MRI
data. 

 

I ran your tutorial recon all and the tutorial data worked fine. My burned CD 
T1 MRI files did not have the .dcm
added so after renaming all the files with .dcm,  the recon function still 
gives an error message as below.

 

Last login: Fri Feb  1 06:51:44 on ttys000

Kevins-MacBook-Pro:~ kevin$ export FREESURFER_HOME=/Applications/freesurfer

Kevins-MacBook-Pro:~ kevin$ source $FREESURFER_HOME/SetUpFreeSurfer.sh

 freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 

Setting up environment for FreeSurfer/FS-FAST (and FSL)

FREESURFER_HOME   /Applications/freesurfer

FSFAST_HOME       /Applications/freesurfer/fsfast

FSF_OUTPUT_FORMAT nii.gz

SUBJECTS_DIR      /Applications/freesurfer/subjects

MNI_DIR           /Applications/freesurfer/mni

Kevins-MacBook-Pro:~ kevin$ export Case14=Applications/freesurfer/Case14

Kevins-MacBook-Pro:~ kevin$ export SUBJECTS_DIR=$Case14/7581/7583

Kevins-MacBook-Pro:~ kevin$ cd $Subjects_DIR

Kevins-MacBook-Pro:~ kevin$ echo $SUBJECTS_DIR

Applications/freesurfer/Case14/7581/7583

Kevins-MacBook-Pro:~ kevin$ 

Kevins-MacBook-Pro:~ kevin$ recon-all –all –i 758251.dcm –s Subj14

ERROR: Flag all unrecognized.

all i 758251.dcm s Subj14

Darwin Kevins-MacBook-Pro.local 18.2.0 Darwin Kernel Version 18.2.0: Mon Nov 12 
20:24:46 PST 2018;
root:xnu-4903.231.4~2/RELEASE_X86_64 x86_64

 

recon-all -s  exited with ERRORS at Fri Feb  1 06:55:38 EST 2019

 

For more details, see the log file 

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

 

Kevins-MacBook-Pro:~ kevin$

 

Your suggestions are most appreciated. 

 

Thanks Kevin 


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

2019-02-01 Thread Matthieu Vanhoutte 
External Email - Use Caution

Hi Douglas,

Could you answer to my previous question ?

Best,
Matthieu

> Le 30 janv. 2019 à 14:48, Matthieu Vanhoutte  a 
> écrit :
> 
> Hi Douglas,
> 
> In order to apply intensity normalization to non-PVC PET images based on mean 
> intensity from reference region in gtmseg.mgz, is it better to realign & 
> reslice PET image onto gtmseg space or the reverse way ? How is it done when 
> dealing with PVC images using gtmpvc command ?
> 
> I would like to avoid too many reslicing operations before volume to surface 
> projection, how would you deal with it ?
> 
> Best,
> Matthieu
> 
>> Le 28 janv. 2019 à 17:41, Greve, Douglas N.,Ph.D. > > a écrit :
>> 
>> 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. >>> > 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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Re: [Freesurfer] Freesurfer Recon-all error

2019-02-01 Thread falk.luesebr...@med.ovgu.de 
External Email - Use Caution

Hi Kevin,

just an educated guess, but did you copy the line "recon-all -all -i 758251.dcm 
-s Subj14" from somewhere (e.g. word)? Because it seems the dash in front of 
each flag is an emphasized dash, probably resulting in the error. Try the 
following: "recon-all -all -i 758251.dcm -s Subj14"

Best,
Falk

Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 Im Auftrag von Jones, Kevin
Gesendet: Freitag, 1. Februar 2019 13:00
An: freesurfer@nmr.mgh.harvard.edu
Betreff: [Freesurfer] Freesurfer Recon-all error


External Email - Use Caution
Dear Freesurfer team

Thanks for you help. I am new to freesurfer, using a mac and getting an error 
with recon all when using my MRI data.

I ran your tutorial recon all and the tutorial data worked fine. My burned CD 
T1 MRI files did not have the .dcm added so after renaming all the files with 
.dcm,  the recon function still gives an error message as below.


Last login: Fri Feb  1 06:51:44 on ttys000

Kevins-MacBook-Pro:~ kevin$ export FREESURFER_HOME=/Applications/freesurfer

Kevins-MacBook-Pro:~ kevin$ source $FREESURFER_HOME/SetUpFreeSurfer.sh

 freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 

Setting up environment for FreeSurfer/FS-FAST (and FSL)

FREESURFER_HOME   /Applications/freesurfer

FSFAST_HOME   /Applications/freesurfer/fsfast

FSF_OUTPUT_FORMAT nii.gz

SUBJECTS_DIR  /Applications/freesurfer/subjects

MNI_DIR   /Applications/freesurfer/mni

Kevins-MacBook-Pro:~ kevin$ export Case14=Applications/freesurfer/Case14

Kevins-MacBook-Pro:~ kevin$ export SUBJECTS_DIR=$Case14/7581/7583

Kevins-MacBook-Pro:~ kevin$ cd $Subjects_DIR

Kevins-MacBook-Pro:~ kevin$ echo $SUBJECTS_DIR

Applications/freesurfer/Case14/7581/7583

Kevins-MacBook-Pro:~ kevin$

Kevins-MacBook-Pro:~ kevin$ recon-all -all -i 758251.dcm -s Subj14

ERROR: Flag all unrecognized.

all i 758251.dcm s Subj14

Darwin Kevins-MacBook-Pro.local 18.2.0 Darwin Kernel Version 18.2.0: Mon Nov 12 
20:24:46 PST 2018; root:xnu-4903.231.4~2/RELEASE_X86_64 x86_64



recon-all -s  exited with ERRORS at Fri Feb  1 06:55:38 EST 2019



For more details, see the log file

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting



Kevins-MacBook-Pro:~ kevin$

Your suggestions are most appreciated.

Thanks Kevin
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[Freesurfer] fcseedcor_multiple runs

2019-02-01 Thread Nasiriavanaki, Zahra 
Dear Freesurfers


Hi


I have been doing seed to seed connectivity analysis using fcseedcor.

I have multiple runs for each subject, and based on the fcseedcor help, I am 
supposed to average runs before comparing across subjects.

So, does it mean I should average all seed.dat files and the regressors 
(including vscf,wm,global waveform, mcprextreg) across runs?

I appreciate your time and consideration.


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] Freesurfer Recon-all error

2019-02-01 Thread Jones, Kevin 


External Email - Use Caution
Dear Freesurfer team 


Thanks for you help. I am new to freesurfer, using a mac and getting an error with recon all when using my MRI data. 


I ran your tutorial recon all and the tutorial data worked fine. My burned CD T1 MRI files did not have the .dcm added so after renaming all the files with .dcm,  the recon function still gives an error message as below.



Last login: Fri Feb 
1 06:51:44 on ttys000
Kevins-MacBook-Pro:~ kevin$ export FREESURFER_HOME=/Applications/freesurfer
Kevins-MacBook-Pro:~ kevin$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
 freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME 
  /Applications/freesurfer
FSFAST_HOME      
/Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR     
/Applications/freesurfer/subjects
MNI_DIR          
/Applications/freesurfer/mni
Kevins-MacBook-Pro:~ kevin$ export Case14=Applications/freesurfer/Case14
Kevins-MacBook-Pro:~ kevin$ export SUBJECTS_DIR=$Case14/7581/7583
Kevins-MacBook-Pro:~ kevin$ cd $Subjects_DIR
Kevins-MacBook-Pro:~ kevin$ echo $SUBJECTS_DIR
Applications/freesurfer/Case14/7581/7583
Kevins-MacBook-Pro:~ kevin$ 
Kevins-MacBook-Pro:~ kevin$ recon-all –all –i 758251.dcm –s Subj14
ERROR: Flag all unrecognized.
all i 758251.dcm s Subj14
Darwin Kevins-MacBook-Pro.local 18.2.0 Darwin Kernel Version 18.2.0: Mon Nov 12 20:24:46 PST 2018; root:xnu-4903.231.4~2/RELEASE_X86_64 x86_64


recon-all -s  
exited with ERRORS at Fri Feb  1 06:55:38 EST 2019


For more details, see the log file 
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


Kevins-MacBook-Pro:~ kevin$



Your suggestions are most appreciated. 


Thanks Kevin 




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