Re: [Freesurfer] Freeview CLI feature request

2020-03-25 Thread VINCENT KOPPELMANS 
External Email - Use Caution

Thank you for your quick and positive reply.

Best,
Vincent

From:  on behalf of Ruopeng Wang 

Reply-To: Freesurfer support list 
Date: Wednesday, 25 March 2020 at 16:41
To: Freesurfer support list 
Subject: Re: [Freesurfer] Freeview CLI feature request

Sure. We’ll add those in.

Best,
Ruopeng


On Mar 25, 2020, at 6:28 PM, VINCENT KOPPELMANS 
mailto:vincent.koppelm...@utah.edu>> wrote:

External Email - Use Caution

Dear FreeSurfer team,

I am currently using FreeView v3.0, Darwin Build Mar 25 2020 00:009:39

Would it be possible to add the following features as command line flags to 
FreeView?

1) Set opacity for a surface
It is currently only possible via CLI to set opacity for volumes, surface 
overlays, and labels, but not for the surface itself.

2) Set smoothing iterations for isosurfaces
This can only be done in the GUI, not yet via the CLI.

Thank you for your consideration.

- Vincent
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Re: [Freesurfer] Freeview CLI feature request

2020-03-25 Thread Ruopeng Wang 
Sure. We’ll add those in.

Best,
Ruopeng

> On Mar 25, 2020, at 6:28 PM, VINCENT KOPPELMANS  
> wrote:
> 
> External Email - Use Caution
> 
> 
> Dear FreeSurfer team,
>  
> I am currently using FreeView v3.0, Darwin Build Mar 25 2020 00:009:39
>  
> Would it be possible to add the following features as command line flags to 
> FreeView?
>  
> 1) Set opacity for a surface
> It is currently only possible via CLI to set opacity for volumes, surface 
> overlays, and labels, but not for the surface itself.
>  
> 2) Set smoothing iterations for isosurfaces
> This can only be done in the GUI, not yet via the CLI.
>  
> Thank you for your consideration.
>  
> - Vincent
> ___
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> Freesurfer@nmr.mgh.harvard.edu 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
> 
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[Freesurfer] Freeview CLI feature request

2020-03-25 Thread VINCENT KOPPELMANS 
External Email - Use Caution

Dear FreeSurfer team,

I am currently using FreeView v3.0, Darwin Build Mar 25 2020 00:009:39

Would it be possible to add the following features as command line flags to 
FreeView?

1) Set opacity for a surface
It is currently only possible via CLI to set opacity for volumes, surface 
overlays, and labels, but not for the surface itself.

2) Set smoothing iterations for isosurfaces
This can only be done in the GUI, not yet via the CLI.

Thank you for your consideration.

- Vincent
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[Freesurfer] Registration file types confusion

2020-03-25 Thread Xiaojiang Yang 
External Email - Use Caution

Hi everyone,

I am confused by the two types of registration files: .lta and .dat.

.dat file is simpler and easier to understand. But for the .lta files,
there seems to be no detailed explanation regarding it. Can anyone point
out to me where can I find the detail explanation of the file? And, what's
the relationship between .lta and .dat file?

Also, .lta files seem to cause some compatibility issues. For example, if I
use the tkregister2 utility to make some changes to the registration file
of type .lta (generated by bbregister), like below

tkregister2 --mov $someSeries --reg
$SUBJECTS_DIR/$subjectid/mri/transforms/FLAIR.auto.lta --surf pial

and save it from the GUI, then many errors occur in the console window,
like below:
..
MatrixAsciiReadFrom: could not scanf parms
ERROR: TransformLTA2RegDat(): type = 2011264000, must be 1 or 0 or 14
Segmentation fault (core dumped)

Actually that is because the registration file has been saved in the format
of .dat, although the file extension is still .lta, and the tkregister2
program finally cracks when reading the newly saved .lta file.

Anyone can solve my confusion? Thank you!
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Re: [Freesurfer] mri_deface download link not found

2020-03-25 Thread Hoopes, Andrew 
Ah thanks Tim, I misread. The links on that wiki page are fixed now. Sorry for 
the confusion.
Andrew

On 3/25/20, 3:32 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Tim 
Schäfer"  
wrote:

External Email - Use Caution

I think the problem is not with running the version he downloaded, but the 
fact that he could not download it, because all download links on the website 
at https://surfer.nmr.mgh.harvard.edu/fswiki/mri_deface are dead.

I downloaded mri_deface from that website about a month ago, back then the 
links were still okay. It seems something went wrong on the server in the 
meantime.

Best,

Tim

> On March 24, 2020 at 6:39 PM "Hoopes, Andrew"  
wrote:
> 
> 
> Hi Hailey,
> 
> Can you provide some more info about your issue, like what version you 
downloaded and a copy/paste of the command line you ran with the error message.
> 
> Thanks
> Andrew
> 
> From:  on behalf of "D'Silva, 
Hailey" 
> Reply-To: FS Help 
> Date: Tuesday, March 24, 2020 at 7:24 AM
> To: FS Help 
> Subject: [Freesurfer] mri_deface download link not found
> 
> 
> External Email - Use Caution
> Hello Freesurfer Experts!
> I'm trying to anonymize a number of T1s by using mri_deface, but am 
getting a "Not Found" error when I try to download the tools for it.
> 
> Thanks for your help,
> Hailey
> 
> 
> 
> 
> 
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Re: [Freesurfer] VM_setup

2020-03-25 Thread fsbuild 
External Email - Use Caution

Hello Pierpaolo,

Just sent it to your email.  You can email me back directly if you need 
something.

- R.On Mar 25, 2020, at 14:34, Pierpaolo Croce 
 
wrote:External Email - Use 
CautionDear List, I have 
followed the virtual machine setup for virtual box freesurfer installation... 
Starting ubuntu, ask me developers account informations. Which is the 
password?-- Ing. Pierpaolo Croce, PhD.Institute for Advanced Biomedical 
Technologies - ITABandDepartment of Neuroscience and ImagingUniversity of 
Chieti "G. D'Annunzio"Via dei Vestini, 3366013 Chieti, 
Italy___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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[Freesurfer] VM_setup

2020-03-25 Thread Pierpaolo Croce 
External Email - Use Caution

Dear List,
I have followed the virtual machine setup for virtual box freesurfer
installation.. Starting ubuntu, ask me developers account informations.
Which is the password?
-- 

Ing. Pierpaolo Croce, PhD.
Institute for Advanced Biomedical Technologies - ITAB
and
Department of Neuroscience and Imaging
University of Chieti "G. D'Annunzio"
Via dei Vestini, 33
66013 Chieti, Italy
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Re: [Freesurfer] Misalignment of boundaries and T1 (Freesurfer/SamSrf)

2020-03-25 Thread Bruce Fischl 

Hi Mason

I can't tell from those images except that it looks reasonable
cheers
Bruce
On Wed, 25 
Mar 2020, Mason Wells wrote:


   External Email - Use Caution 


Hi again Bruce,

I have now installed the relevant libpng packages and have freeview open. The 
segmentation doesn’t look brilliant in some areas. What do you think?

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: wells...@cardiff.ac.uk
Tel: 02920 879628
Web: Cardiff University webpage 

Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: wells...@caerdydd.ac.uk
Ffôn: 02920 879628


On 25/03/2020, 16:28, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Mason 
Wells"  
wrote:

   External Email - Use Caution

   Hi Bruce,

   I get the following error message when I try to load freeview

   Setting up environment for FreeSurfer/FS-FAST (and FSL)
   FREESURFER_HOME   /usr/local/freesurfer
   FSFAST_HOME   /usr/local/freesurfer/fsfast
   FSF_OUTPUT_FORMAT nii.gz
   SUBJECTS_DIR  /usr/local/freesurfer/subjects
   MNI_DIR   /usr/local/freesurfer/mni
   FSL_DIR   /usr/local/fsl
   masontwells@masontwells-VIG800S:~$ freeview
   freeview.bin: error while loading shared libraries: libpng12.so.0: cannot 
open shared object file: No such file or directory

   Mason T Wells, MSc
   PhD student
   School of Optometry and Vision Sciences
   & Cardiff University Brain Research
   Imaging Centre (CUBRIC), School of Psychology
   Cardiff University
   Cardiff
   CF24 4HQ
   UK

   Email: wells...@cardiff.ac.uk
   Tel: 02920 879628
   Web: Cardiff University webpage 

   Mason T Wells, MSc
   Myfyriwr PhD
   Yr Ysgol Optometreg a Gwyddorau’r Golwg
   & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
   Prifysgol Caerdydd
   Heol Maindy
   Caerdydd
   CF24 4HQ
   DU

   E-bost: wells...@caerdydd.ac.uk
   Ffôn: 02920 879628


   On 25/03/2020, 16:19, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce 
Fischl"  wrote:

   something like

   freeview -v $SUBJECTS_DIR//mri/norm.mgz \
 -f $SUBJECTS_DIR//surf/?h.white

   cheers
   Bruce


   On Wed, 25 Mar 2020, Mason Wells wrote:

   >External Email - Use Caution
   >
   > Hi Bruce,
   >
   > Thanks for getting back to me. Sorry, but I am not sure I follow what 
you mean here.
   > Could you please explain how I would check this?
   >
   > Thanks again for your help.
   > Mason
   >
   > Mason T Wells, MSc
   > PhD student
   > School of Optometry and Vision Sciences
   > & Cardiff University Brain Research
   > Imaging Centre (CUBRIC), School of Psychology
   > Cardiff University
   > Cardiff
   > CF24 4HQ
   > UK
   >
   > Email: wells...@cardiff.ac.uk
   > Tel: 02920 879628
   > Web: Cardiff University webpage 

   > Mason T Wells, MSc
   > Myfyriwr PhD
   > Yr Ysgol Optometreg a Gwyddorau’r Golwg
   > & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr 
Ysgol Seicoleg
   > Prifysgol Caerdydd
   > Heol Maindy
   > Caerdydd
   > CF24 4HQ
   > DU
   >
   > E-bost: wells...@caerdydd.ac.uk
   > Ffôn: 02920 879628
   >
   >
   > On 25/03/2020, 16:11, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce 
Fischl"  wrote:
   >
   >Hi Mason
   >
   >can you confirm that things look ok within FreeSurfer if you look 
at the
   >surface over the volume in freeview?
   >
   >cheers
   >Bruce
   >On Wed, 25 Mar 2020, Mason Wells wrote:
   >
   >>
   >> External Email - Use Caution
   >>
   >> Hello Freesurfer developers,
   >>
   >>
   >>
   >> I am using Freesurfer and SamSrf for prf mapping. I have ran the 
recon-all
   >> command which finished without errors. However, the white/grey 
matter
   >> boundaries are significantly misaligned with the subjects T1 
(images
   >> attached).  Below are the steps I have taken to reach this point 
in the
   >> analysis:
   >>
   >>
   >>
   >>  1. Run fsl_anat to get a bias corrected T1 and T1_biascor_brain.
   >>  2. Ran Feat
   >>
   >> · Distortion correction of the EPI
   >>
   >> · Motion correction
   >>
   >> ·

Re: [Freesurfer] Misalignment of boundaries and T1 (Freesurfer/SamSrf)

2020-03-25 Thread Mason Wells 
External Email - Use Caution

Hi Bruce,

I get the following error message when I try to load freeview

Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer
FSFAST_HOME   /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /usr/local/freesurfer/subjects
MNI_DIR   /usr/local/freesurfer/mni
FSL_DIR   /usr/local/fsl
masontwells@masontwells-VIG800S:~$ freeview
freeview.bin: error while loading shared libraries: libpng12.so.0: cannot open 
shared object file: No such file or directory

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff   
CF24 4HQ
UK
 
Email: wells...@cardiff.ac.uk
Tel: 02920 879628
Web: Cardiff University webpage 

Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd   
CF24 4HQ 
DU
 
E-bost: wells...@caerdydd.ac.uk
Ffôn: 02920 879628
 

On 25/03/2020, 16:19, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Bruce Fischl"  wrote:

something like

freeview -v $SUBJECTS_DIR//mri/norm.mgz \
  -f $SUBJECTS_DIR//surf/?h.white

cheers
Bruce


On Wed, 25 Mar 2020, Mason Wells wrote:

>External Email - Use Caution
>
> Hi Bruce,
>
> Thanks for getting back to me. Sorry, but I am not sure I follow what you 
mean here.
> Could you please explain how I would check this?
>
> Thanks again for your help.
> Mason
>
> Mason T Wells, MSc
> PhD student
> School of Optometry and Vision Sciences
> & Cardiff University Brain Research
> Imaging Centre (CUBRIC), School of Psychology
> Cardiff University
> Cardiff
> CF24 4HQ
> UK
>
> Email: wells...@cardiff.ac.uk
> Tel: 02920 879628
> Web: Cardiff University webpage 

> Mason T Wells, MSc
> Myfyriwr PhD
> Yr Ysgol Optometreg a Gwyddorau’r Golwg
> & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr 
Ysgol Seicoleg
> Prifysgol Caerdydd
> Heol Maindy
> Caerdydd
> CF24 4HQ
> DU
>
> E-bost: wells...@caerdydd.ac.uk
> Ffôn: 02920 879628
>
>
> On 25/03/2020, 16:11, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf 
of Bruce Fischl"  wrote:
>
>Hi Mason
>
>can you confirm that things look ok within FreeSurfer if you look at 
the
>surface over the volume in freeview?
>
>cheers
>Bruce
>On Wed, 25 Mar 2020, Mason Wells wrote:
>
>>
>> External Email - Use Caution
>>
>> Hello Freesurfer developers,
>>
>>
>>
>> I am using Freesurfer and SamSrf for prf mapping. I have ran the 
recon-all
>> command which finished without errors. However, the white/grey matter
>> boundaries are significantly misaligned with the subjects T1 (images
>> attached).  Below are the steps I have taken to reach this point in 
the
>> analysis:
>>
>>
>>
>>  1. Run fsl_anat to get a bias corrected T1 and T1_biascor_brain.
>>  2. Ran Feat
>>
>> · Distortion correction of the EPI
>>
>> · Motion correction
>>
>> · No smoothing
>>
>> · Highpass filter
>>
>> · No registration to whole brain
>>
>> · Register to T1_biascorr_brain
>>
>> · Register to standard space
>>
>>  3. Ran recon-all on T1_biascorr
>>  4. Convert T1/T1_brain/orig(001) from mgz to nii
>>  5. Check registration (using the SurfaceProjection command from the 
SamSrf
>> package) which leads to the attached images named S1 and S1.
>>
>>
>>
>> Freesurfer version:
>> freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
>>
>> Platform: Linux 5.3.0-40-generic x86_64
>>
>> Uname: Linux masontwells-VIG800S 5.3.0-40-generic #32~18.04.1-Ubuntu 
SMP Mon
>> Feb 3 14:05:59 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
>>
>>
>>
>> As you can see, the registration is significantly misaligned.
>>
>> Can anyone offer any advice on this/suggest a way to rectify it?
>>
>>
>>
>>
>>
>> Thanks in advance,
>>
>> Mason
>>
>>
>>
>> Mason T Wells, MSc
>>
>> PhD student
>>
>> School of Optometry and V

Re: [Freesurfer] Misalignment of boundaries and T1 (Freesurfer/SamSrf)

2020-03-25 Thread Bruce Fischl 

something like

freeview -v $SUBJECTS_DIR//mri/norm.mgz \
 -f $SUBJECTS_DIR//surf/?h.white

cheers
Bruce


On Wed, 25 Mar 2020, Mason Wells wrote:


   External Email - Use Caution

Hi Bruce,

Thanks for getting back to me. Sorry, but I am not sure I follow what you mean 
here.
Could you please explain how I would check this?

Thanks again for your help.
Mason

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: wells...@cardiff.ac.uk
Tel: 02920 879628
Web: Cardiff University webpage 

Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: wells...@caerdydd.ac.uk
Ffôn: 02920 879628


On 25/03/2020, 16:11, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce 
Fischl"  wrote:

   Hi Mason

   can you confirm that things look ok within FreeSurfer if you look at the
   surface over the volume in freeview?

   cheers
   Bruce
   On Wed, 25 Mar 2020, Mason Wells wrote:

   >
   > External Email - Use Caution
   >
   > Hello Freesurfer developers,
   >
   >
   >
   > I am using Freesurfer and SamSrf for prf mapping. I have ran the recon-all
   > command which finished without errors. However, the white/grey matter
   > boundaries are significantly misaligned with the subjects T1 (images
   > attached).  Below are the steps I have taken to reach this point in the
   > analysis:
   >
   >
   >
   >  1. Run fsl_anat to get a bias corrected T1 and T1_biascor_brain.
   >  2. Ran Feat
   >
   > · Distortion correction of the EPI
   >
   > · Motion correction
   >
   > · No smoothing
   >
   > · Highpass filter
   >
   > · No registration to whole brain
   >
   > · Register to T1_biascorr_brain
   >
   > · Register to standard space
   >
   >  3. Ran recon-all on T1_biascorr
   >  4. Convert T1/T1_brain/orig(001) from mgz to nii
   >  5. Check registration (using the SurfaceProjection command from the SamSrf
   > package) which leads to the attached images named S1 and S1.
   >
   >
   >
   > Freesurfer version:
   > freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
   >
   > Platform: Linux 5.3.0-40-generic x86_64
   >
   > Uname: Linux masontwells-VIG800S 5.3.0-40-generic #32~18.04.1-Ubuntu SMP 
Mon
   > Feb 3 14:05:59 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
   >
   >
   >
   > As you can see, the registration is significantly misaligned.
   >
   > Can anyone offer any advice on this/suggest a way to rectify it?
   >
   >
   >
   >
   >
   > Thanks in advance,
   >
   > Mason
   >
   >
   >
   > Mason T Wells, MSc
   >
   > PhD student
   >
   > School of Optometry and Vision Sciences
   >
   > & Cardiff University Brain Research
   >
   > Imaging Centre (CUBRIC), School of Psychology
   >
   > Cardiff University
   >
   > Cardiff
   >
   > CF24 4HQ
   >
   > UK
   >
   >
   >
   > Email: wells...@cardiff.ac.uk
   >
   > Tel: 02920 879628
   >
   > Web: Cardiff University webpage
   >
   > Mason T Wells, MSc
   >
   > Myfyriwr PhD
   >
   > Yr Ysgol Optometreg a Gwyddorau’r Golwg
   >
   > & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr 
Ysgol
   > Seicoleg
   >
   > Prifysgol Caerdydd
   >
   > Heol Maindy
   >
   > Caerdydd
   >
   > CF24 4HQ
   >
   > DU
   >
   >
   >
   > E-bost: wells...@caerdydd.ac.uk
   >
   > Ffôn: 02920 879628
   >
   >
   >
   >
   >


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[Freesurfer] PhD student opportunity: Caen, France

2020-03-25 Thread briend 
External Email - Use Caution

PhD position at the University of Caen (in the Cyceron platform for the 
MRI part and in the INSERM 1075-COMETE, Caen, France)
"Can orthostatic intolerance be predicted by an anatomical indicator?"

All the information for the application are here:
https://recrutement.cnes.fr/en/annonce/898759-94-can-orthostatic-intolerance-be-predicted-by-an-anatomical-indicator-14000-caen

To apply, we invite you to contact the PhD/research supervisor at COMETE 
herve.norm...@unicaen.fr and fill, with him/her, the co-financing part 
of the online application form by April 15, 2020.

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Re: [Freesurfer] Misalignment of boundaries and T1 (Freesurfer/SamSrf)

2020-03-25 Thread Mason Wells 
External Email - Use Caution

Hi Bruce,

Thanks for getting back to me. Sorry, but I am not sure I follow what you mean 
here. 
Could you please explain how I would check this?

Thanks again for your help.
Mason

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff   
CF24 4HQ
UK
 
Email: wells...@cardiff.ac.uk
Tel: 02920 879628
Web: Cardiff University webpage 

Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd   
CF24 4HQ 
DU
 
E-bost: wells...@caerdydd.ac.uk
Ffôn: 02920 879628
 

On 25/03/2020, 16:11, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Bruce Fischl"  wrote:

Hi Mason

can you confirm that things look ok within FreeSurfer if you look at the 
surface over the volume in freeview?

cheers
Bruce
On Wed, 25 Mar 2020, Mason Wells wrote:

> 
> External Email - Use Caution
> 
> Hello Freesurfer developers,
> 
>  
> 
> I am using Freesurfer and SamSrf for prf mapping. I have ran the recon-all
> command which finished without errors. However, the white/grey matter
> boundaries are significantly misaligned with the subjects T1 (images
> attached).  Below are the steps I have taken to reach this point in the
> analysis:
> 
>  
>
>  1. Run fsl_anat to get a bias corrected T1 and T1_biascor_brain.
>  2. Ran Feat
> 
> · Distortion correction of the EPI
> 
> · Motion correction
> 
> · No smoothing
> 
> · Highpass filter
> 
> · No registration to whole brain
> 
> · Register to T1_biascorr_brain
> 
> · Register to standard space
>
>  3. Ran recon-all on T1_biascorr
>  4. Convert T1/T1_brain/orig(001) from mgz to nii
>  5. Check registration (using the SurfaceProjection command from the 
SamSrf
> package) which leads to the attached images named S1 and S1.
> 
>  
> 
> Freesurfer version:
> freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
> 
> Platform: Linux 5.3.0-40-generic x86_64
> 
> Uname: Linux masontwells-VIG800S 5.3.0-40-generic #32~18.04.1-Ubuntu SMP 
Mon
> Feb 3 14:05:59 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
> 
>  
> 
> As you can see, the registration is significantly misaligned.
> 
> Can anyone offer any advice on this/suggest a way to rectify it?
> 
>  
> 
>  
> 
> Thanks in advance,
> 
> Mason
> 
>  
> 
> Mason T Wells, MSc
> 
> PhD student
> 
> School of Optometry and Vision Sciences
> 
> & Cardiff University Brain Research
> 
> Imaging Centre (CUBRIC), School of Psychology
> 
> Cardiff University
> 
> Cardiff   
> 
> CF24 4HQ
> 
> UK
> 
>  
> 
> Email: wells...@cardiff.ac.uk
> 
> Tel: 02920 879628
> 
> Web: Cardiff University webpage
> 
> Mason T Wells, MSc
> 
> Myfyriwr PhD
> 
> Yr Ysgol Optometreg a Gwyddorau’r Golwg
> 
> & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr 
Ysgol
> Seicoleg
> 
> Prifysgol Caerdydd
> 
> Heol Maindy
> 
> Caerdydd   
> 
> CF24 4HQ 
> 
> DU
> 
>  
> 
> E-bost: wells...@caerdydd.ac.uk
> 
> Ffôn: 02920 879628
> 
>  
> 
> 
>


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[Freesurfer] Using mri_glmfit to regress out wm and ventricle signal

2020-03-25 Thread Mcnorgan, Christopher 
External Email - Use Caution

I’ve been using mri_glmfit to regress out motion correction parameters and 
linear trends and saving residuals in surface space by first generating a QA 
matrix for the volume:

 mri_glmfit --y ${source_dir}/${r}/${filepat}.${surf}.${hemi}.nii.gz \
--glmdir ${source_dir}/${r}/{hemi}.detrend \
--qa \
--surf ${SURFTOUSE} lh
Then merging the QA and MC matrices into a single matrix of nuisance regressors:

paste ${source_dir}/${r}/lh.detrend/Xg.dat mcprextreg > nuisance

And finally, regressing out the nuisance values and saving the residuals
 mri_glmfit --y ${source_dir}/${r}/${filepat}.${surf}.${hemi}.nii.gz \
--glmdir ${source_dir}/${r}/${hemi}.detrend \
--X nuisance \
--no-contrasts-ok --save-yhat --eres-save \
--surf ${SURFTOUSE} ${hemi}

Is there a straightforward way of obtaining mean white matter and csf signal in 
my nuisance regressor matrix? I was unable to find any preprocessing step or 
application of mri_glmfit that will provide these values or regress out these 
values automatically.

(Also note: the —qa flag is not documented in the mri_glmfit help; I must’ve 
learned of it from a previous email to this list)

Thanks

/**
* Chris McNorgan
* Assistant Professor
* Department of Psychology
* University at Buffalo,
* The State University of New York
* http://ccnlab.buffalo.edu/
* Office: 716.645.0236
* Lab: 716.645.0222
**/

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Re: [Freesurfer] Misalignment of boundaries and T1 (Freesurfer/SamSrf)

2020-03-25 Thread Bruce Fischl 

Hi Mason

can you confirm that things look ok within FreeSurfer if you look at the 
surface over the volume in freeview?


cheers
Bruce
On Wed, 25 Mar 2020, Mason Wells wrote:



External Email - Use Caution

Hello Freesurfer developers,

 

I am using Freesurfer and SamSrf for prf mapping. I have ran the recon-all
command which finished without errors. However, the white/grey matter
boundaries are significantly misaligned with the subjects T1 (images
attached).  Below are the steps I have taken to reach this point in the
analysis:

 

 1. Run fsl_anat to get a bias corrected T1 and T1_biascor_brain.
 2. Ran Feat

· Distortion correction of the EPI

· Motion correction

· No smoothing

· Highpass filter

· No registration to whole brain

· Register to T1_biascorr_brain

· Register to standard space

 3. Ran recon-all on T1_biascorr
 4. Convert T1/T1_brain/orig(001) from mgz to nii
 5. Check registration (using the SurfaceProjection command from the SamSrf
package) which leads to the attached images named S1 and S1.

 

Freesurfer version:
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

Platform: Linux 5.3.0-40-generic x86_64

Uname: Linux masontwells-VIG800S 5.3.0-40-generic #32~18.04.1-Ubuntu SMP Mon
Feb 3 14:05:59 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux

 

As you can see, the registration is significantly misaligned.

Can anyone offer any advice on this/suggest a way to rectify it?

 

 

Thanks in advance,

Mason

 

Mason T Wells, MSc

PhD student

School of Optometry and Vision Sciences

& Cardiff University Brain Research

Imaging Centre (CUBRIC), School of Psychology

Cardiff University

Cardiff   

CF24 4HQ

UK

 

Email: wells...@cardiff.ac.uk

Tel: 02920 879628

Web: Cardiff University webpage

Mason T Wells, MSc

Myfyriwr PhD

Yr Ysgol Optometreg a Gwyddorau’r Golwg

& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol
Seicoleg

Prifysgol Caerdydd

Heol Maindy

Caerdydd   

CF24 4HQ 

DU

 

E-bost: wells...@caerdydd.ac.uk

Ffôn: 02920 879628

 


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Re: [Freesurfer] training set

2020-03-25 Thread Bruce Fischl 

Hi Javier

no, that's not correct, depending on which training set you mean. For the 
Bayesian segmentation (aseg) we used 40 datasets distributed in age and 
pathology (10 each for young, middle age, elderly and AD).


cheers
Bruce
On Wed, 25 Mar 
2020, javier quilis wrote:




External Email - Use Caution

Thanks for the answer. 

I can not open the power point for some reason. Is there any paper where I
can check this? I think the dataset used by freesurfer is in the MNI Average
Brain (305 MRI) Stereotaxic Model and this dataset only use MRIs from young
people, is this correct?

Thanks again.
Bests, 
Javier






De: freesurfer-boun...@nmr.mgh.harvard.edu
 en nombre de Douglas N. Greve

Enviado: viernes, 20 de marzo de 2020 15:39
Para: freesurfer@nmr.mgh.harvard.edu 
Asunto: Re: [Freesurfer] training set  
Try the tutorial slides
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI
It does not go into a lot of detail, but it will give you the relevant
lectures


On 3/17/2020 8:54 AM, javier quilis wrote:

  External Email - Use Caution

  Hello everyone, 

I'm trying to do a study of a comparison between the automated methods
to analyze structural MRI from FSL and Freesurfer. I am interested in
the training set used by Freesurfer to do the brain segmentation and I
can not find a detailed description of it. Is there any source where
this set is described?

Thanks in advance.
Bests, 
Javier Quilis

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Re: [Freesurfer] ERROR - build stamps do not match

2020-03-25 Thread Danielian, Laura (NIH/NINDS) [E] 
External Email - Use Caution

Thanks Andrew!  I’ll look into these options.

Take care,
Laura


From: "Hoopes, Andrew" 
Reply-To: Freesurfer support list 
Date: Tuesday, March 24, 2020 at 4:07 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] ERROR - build stamps do not match

Hi Laura,

The error in the last few lines tells you what you need to know. Your install 
is missing a freesurfer license, which you must copy into $FREESURFER_HOME. I 
assume you already have one since you’ve run recons before, but if you need to 
re-register, you can do this at 
http://surfer.nmr.mgh.harvard.edu/registration.html

And when you combine results from different operating systems, your analysis is 
no longer consistent across subjects. While we try to minimize cross-platform 
discrepancies as much as we can, there is a possibility that low-level 
differences will skew (and invalidate) the results of your study. If you’re 
stuck running things on a macbook for now, I recommend installing a VM or 
docker container that matches the OS and version previously used in your 
analysis, and running your recons on that.

best
Andrew

From:  on behalf of "Danielian, Laura 
(NIH/NINDS) [E]" 
Reply-To: FS Help 
Date: Tuesday, March 24, 2020 at 1:55 PM
To: FS Help 
Subject: Re: [Freesurfer] ERROR - build stamps do not match


External Email - Use Caution

Hi Andrew,



Here is the entirety of the terminal after the recon-all -wm command (with 
personal info removed).  Can you tell from this what is causing it to die?  I’m 
still getting everything set up so I may have an incomplete setup/download.





INFO: FreeSurfer build stamps do not match

Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c

INFO: SUBJECTS_DIR is /Volumes/###

Actual FREESURFER_HOME /Applications/freesurfer

-rwx--+ 1 ###  ###\Domain Users  1689971 Mar 20 15:50 
/Volumes/###/scripts/recon-all.log

Darwin ### 18.7.0 Darwin Kernel Version 18.7.0: Thu Jan 23 06:52:12 PST 2020; 
root:xnu-4903.278.25~1/RELEASE_X86_64 x86_64

#

#@# Mask BFS Mon Mar 23 11:55:31 EDT 2020

/Volumes/###/mri

\n mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz \n

threshold mask volume at 5

--

ERROR: FreeSurfer license file /Applications/freesurfer/license.txt not found.

  If you are outside the NMR-Martinos Center,

  go to http://surfer.nmr.mgh.harvard.edu/registration.html to

  get a valid license file (it's free).

  If you are inside the NMR-Martinos Center,

  make sure to source the standard environment.

--

Darwin ### 18.7.0 Darwin Kernel Version 18.7.0: Thu Jan 23 06:52:12 PST 2020; 
root:xnu-4903.278.25~1/RELEASE_X86_64 x86_64



recon-all -s ### exited with ERRORS at Mon Mar 23 11:55:35 EDT 2020





Unfortunately, I may not have a choice about using 2 different OS to do the 
analysis, due to the total shutdown of our offices and additional time 
constraints.  Is there any other way to work around this other than starting 
from scratch?  If I combine the data later for analyses, what are the potential 
problems I could face?



Thanks for your help!



Laura


From: "Hoopes, Andrew" 
Reply-To: Freesurfer support list 
Date: Tuesday, March 24, 2020 at 1:38 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] ERROR - build stamps do not match

Hi Laura,

For any study, it is essential that you process all of your subjects on the 
same operating system. Even though the same FS version is used, there will be 
underlying system-level differences that may lead to small inconsistencies 
across your linux and mac results.

Also, are your recons dying after printing “build stamps do not match”? That 
message should just be a warning and not force a recon-all exit unless 
REQUIRE_FS_MATCH is enabled (it’s not by default).

Best
Andrew


From:  on behalf of "Danielian, Laura 
(NIH/NINDS) [E]" 
Reply-To: FS Help 
Date: Tuesday, March 24, 2020 at 10:05 AM
To: FS Help 
Subject: [Freesurfer] ERROR - build stamps do not match


External Email - Use Caution
Hi,

I have been processing datasets on my Linux on v6.0 but have recently been made 
to work from home where I only have access to a Mac.  I’m getting the following 
error message when continuing the editing on datasets that were already started 
on my Linux:

INFO: FreeSurfer build stamps do not match
Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c

A few questions:

Is it feasible to override this error message for subjects that I have already 
started processing since they are both using v6.0?

I have about half of my data set already fully processed using a Linux – if I 
start processing the second half from sc

[Freesurfer] Problem with version of mri_surfcluster provided with fspalm

2020-03-25 Thread Syam Gadde 
External Email - Use Caution

Hi,

We have a user trying to use fspalm.  I followed all the directions to install, 
but are getting an error with the new mri_surfcluster that we were asked to 
download with fspalm.  Here is the dummy command I ran to replicate the error:

mri_surfcluster --thmin 0 --subject fsaverage --hemi lh --in 
/usr/local/packages/freesurfer_v6.0.0/subjects/fsaverage/surf/lh.white

and the end of its output:

<...>
subjectsdir= /usr/local/packages/freesurfer_v6.0.0/subjects
FixMNI = 1
- XFM matrix (RAS2RAS) ---
/usr/local/packages/freesurfer_v6.0.0/subjects/fsaverage/mri/transforms/talairach.xfm
 1.0   0.0   0.0   0.0;
 0.0   1.0   0.0   0.0;
 0.0   0.0   1.0   0.0;
 0.0   0.0   0.0   1.0;

Reading source surface 
/usr/local/packages/freesurfer_v6.0.0/subjects/fsaverage/surf/lh.white
MRISread(x�https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=subject:%22%5C%5BFreesurfer%5C%5D+mri_surfcluster+ERROR%22&o=newest

but the error message is misleading.  The problem is not in reading the surface 
file, but in trying to read a file name made up of non-ascii (or presumably 
unicode) characters.  As shown by strace:

...
read(3, "", 8192)   = 0
open("/proc/sys/crypto/fips_enabled", O_RDONLY) = 4
read(4, "0\n", 31)  = 2
close(4)= 0
close(3)= 0
munmap(0x7f8413571000, 8192)= 0
open("\310\215\26\f\376\177", O_RDONLY) = -1 ENOENT (No such file or directory)
write(2, "MRISread(\310\215\26\f\376\177): could not open"..., 
37MRISread(ȍ^V^L^?): c
ould not open file) = 37
...

Any thoughts on how to proceed?  Thanks,

-syam


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Re: [Freesurfer] training set

2020-03-25 Thread javier quilis 
External Email - Use Caution

Thanks for the answer.

I can not open the power point for some reason. Is there any paper where I can 
check this? I think the dataset used by freesurfer is in the MNI Average Brain 
(305 MRI) Stereotaxic Model and this dataset only use MRIs from young people, 
is this correct?

Thanks again.
Bests,
Javier






De: freesurfer-boun...@nmr.mgh.harvard.edu 
 en nombre de Douglas N. Greve 

Enviado: viernes, 20 de marzo de 2020 15:39
Para: freesurfer@nmr.mgh.harvard.edu 
Asunto: Re: [Freesurfer] training set

Try the tutorial slides
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI
It does not go into a lot of detail, but it will give you the relevant lectures


On 3/17/2020 8:54 AM, javier quilis wrote:

External Email - Use Caution

Hello everyone,

I'm trying to do a study of a comparison between the automated methods to 
analyze structural MRI from FSL and Freesurfer. I am interested in the training 
set used by Freesurfer to do the brain segmentation and I can not find a 
detailed description of it. Is there any source where this set is described?

Thanks in advance.
Bests,
Javier Quilis



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Re: [Freesurfer] mri_deface download link not found

2020-03-25 Thread Tim Schäfer 
External Email - Use Caution

I think the problem is not with running the version he downloaded, but the fact 
that he could not download it, because all download links on the website at 
https://surfer.nmr.mgh.harvard.edu/fswiki/mri_deface are dead.

I downloaded mri_deface from that website about a month ago, back then the 
links were still okay. It seems something went wrong on the server in the 
meantime.

Best,

Tim

> On March 24, 2020 at 6:39 PM "Hoopes, Andrew"  wrote:
> 
> 
> Hi Hailey,
> 
> Can you provide some more info about your issue, like what version you 
> downloaded and a copy/paste of the command line you ran with the error 
> message.
> 
> Thanks
> Andrew
> 
> From:  on behalf of "D'Silva, Hailey" 
> 
> Reply-To: FS Help 
> Date: Tuesday, March 24, 2020 at 7:24 AM
> To: FS Help 
> Subject: [Freesurfer] mri_deface download link not found
> 
> 
> External Email - Use Caution
> Hello Freesurfer Experts!
> I'm trying to anonymize a number of T1s by using mri_deface, but am getting a 
> "Not Found" error when I try to download the tools for it.
> 
> Thanks for your help,
> Hailey
> 
> 
> 
> 
> 
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