Re: [Freesurfer] sphere.reg file

[Douglas N. Greve]

Can you send the terminal output of mris_preproc?

On 3/6/2020 4:28 PM, Marina Fernández wrote:


External Email - Use Caution

These are the previous emails:
1 » » » » » » » » » » » »
Dear freesurfer experts,
I run the following commands to perform analysis with projected
surfaces on my average subject:


make_average_subject --out my_avg_subject --fsgd  fsgd.txt


surfreg --s s_001 --t  my_avg_subject --o my_avg_subject.sphere.reg


mris_preproc --fsgd nfsgd.txt --target my_avg_subject --meas thickness
--srcfmt curv --hemi [l/r]h --out  [l/r]h.fsgd.mgh


Theoretically, the mri_preproc function will automatically use the
my_avg_subject.sphere.reg file because I specify my_avg_subject as the
target subject. The problem is that in the output that comes out in
the terminal while this function is running, it is specified that the
file [l/r]h.sphere.reg is selected instead of
[l/r]h.my_avg_subject.sphere.reg.


Additionally, I did a test specifying the flag "--surfreg
my_avg_subject.sphere.reg" in mris_preproc and the values of the
output surface are different from the output that I have when I don't
specify the flag --surfreg in mris_preproc (so, If I don't specify it,
I think that definitely the function doesn't automatically use the
file generated in surfreg, I think the default sphere.reg is used).


What should I do? Is it better to specify the “--surfreg
my_avg_subject.sphere.reg” flag in the mris_preproc function?


Thanks in advance.
Best regards,
Marina.
2 » » » » » » » » » » » »
what version of freesurfer are you running?
3 » » » » » » » » » » » »
We are using Freesurfer v6.0
4 » » » » » » » » » » » »
can you include the previous emails?

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Re: [Freesurfer] PetSurfer reference region

[Douglas N. Greve]

I think the issue is that your input has multiple frames (6). It will 
compute the scaling from all 6 whereas the gtm.stats file is only from 
the first frame. Try running it with a single frame. Note that the 
gtm.nii.gz will have all the frames for each ROI.



On 3/6/2020 3:56 PM, Dincer, Aylin wrote:

 External Email - Use Caution

Thanks for the quick reply. I attached the terminal output to this email. We 
are running this on v6.

Best,
Aylin

___
Message: 9
Date: Fri, 6 Mar 2020 11:50:51 -0500
From: "Douglas N. Greve" 
Subject: Re: [Freesurfer] PetSurfer reference region
To: 
Message-ID: <64d6089e-f818-e30e-deff-98a812b72...@mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

I cannot replicate this in either v6 or v7beta. Can you send the
terminal output?

On 3/5/2020 1:32 PM, Dincer, Aylin wrote:

External Email - Use Caution

Hello PetSurfer experts,

We are using the cerebellum cortex as our reference region, but
noticed that the SUVR values for lh/rh cerebellum cortex do not have a
value of 1 (which is what we were expecting). The actual SUVR values
are 1.31 for the lh and 1.35 for the rh cerebellum cortex. I attached
the stats file (gtm.stats.dat) and below is the command we ran.

mri_gtmpvc --i regmean.nii.gz --reg regmean_template.reg.lta --psf
${FWHM} --seg ${MR_ID}/mri/gtmseg.mgz --default-seg-merge --auto-mask
PSF+2 .01 --mgx .01 --rescale 8 47 ?o regmean_gtmpvc_output

Let me know if you need any more details.

Thanks so much,

Aylin



_

Aylin Dincer

Senior Research Technician

NeuroImaging Laboratories

Imaging Core, Benzinger Lab

314-362-3629



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Re: [Freesurfer] sphere.reg file

[Marina Fernández]

External Email - Use Caution

These are the previous emails:



1 » » » » » » » » » » » »



Dear freesurfer experts,


I run the following commands to perform analysis with projected
surfaces on my average subject:


make_average_subject --out my_avg_subject --fsgd  fsgd.txt


surfreg --s s_001 --t  my_avg_subject --o my_avg_subject.sphere.reg


mris_preproc --fsgd nfsgd.txt --target my_avg_subject --meas thickness
--srcfmt curv --hemi [l/r]h --out  [l/r]h.fsgd.mgh


Theoretically, the mri_preproc function will automatically use the
my_avg_subject.sphere.reg file because I specify my_avg_subject as the
target subject. The problem is that in the output that comes out in
the terminal while this function is running, it is specified that the
file [l/r]h.sphere.reg is selected instead of
[l/r]h.my_avg_subject.sphere.reg.


Additionally, I did a test specifying the flag "--surfreg
my_avg_subject.sphere.reg" in mris_preproc and the values of the
output surface are different from the output that I have when I don't
specify the flag --surfreg in mris_preproc (so, If I don't specify it,
I think that definitely the function doesn't automatically use the
file generated in surfreg, I think the default sphere.reg is used).


What should I do? Is it better to specify the “--surfreg
my_avg_subject.sphere.reg” flag in the mris_preproc function?


Thanks in advance.
Best regards,
Marina.




2 » » » » » » » » » » » »


what version of freesurfer are you running?



3 » » » » » » » » » » » »


We are using Freesurfer v6.0



4 » » » » » » » » » » » »


can you include the previous emails?






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Re: [Freesurfer] PetSurfer reference region

[Dincer, Aylin]

External Email - Use Caution

Thanks for the quick reply. I attached the terminal output to this email. We 
are running this on v6.

Best,
Aylin

___
Message: 9
Date: Fri, 6 Mar 2020 11:50:51 -0500
From: "Douglas N. Greve" 
Subject: Re: [Freesurfer] PetSurfer reference region
To: 
Message-ID: <64d6089e-f818-e30e-deff-98a812b72...@mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

I cannot replicate this in either v6 or v7beta. Can you send the
terminal output?

On 3/5/2020 1:32 PM, Dincer, Aylin wrote:
>
> External Email - Use Caution
>
> Hello PetSurfer experts,
>
> We are using the cerebellum cortex as our reference region, but
> noticed that the SUVR values for lh/rh cerebellum cortex do not have a
> value of 1 (which is what we were expecting). The actual SUVR values
> are 1.31 for the lh and 1.35 for the rh cerebellum cortex. I attached
> the stats file (gtm.stats.dat) and below is the command we ran.
>
> mri_gtmpvc --i regmean.nii.gz --reg regmean_template.reg.lta --psf
> ${FWHM} --seg ${MR_ID}/mri/gtmseg.mgz --default-seg-merge --auto-mask
> PSF+2 .01 --mgx .01 --rescale 8 47 ?o regmean_gtmpvc_output
>
> Let me know if you need any more details.
>
> Thanks so much,
>
> Aylin
>
> 
>
> _
>
> Aylin Dincer
>
> Senior Research Technician
>
> NeuroImaging Laboratories
>
> Imaging Core, Benzinger Lab
>
> 314-362-3629
>
> 
>
> The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If
> you are not the intended recipient, be advised that any unauthorized
> use, disclosure, copying or the taking of any action in reliance on
> the contents of this information is strictly prohibited. If you have
> received this email in error, please immediately notify the sender via
> telephone or return mail.
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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pet_regmiddle_pvc_rerun_2020_03_06.log
Description: pet_regmiddle_pvc_rerun_2020_03_06.log
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Re: [Freesurfer] sphere.reg file

[Douglas N. Greve]

can you include the previous emails?

On 3/6/2020 1:50 PM, Marina Fernández wrote:


External Email - Use Caution

We are using Freesurfer v6.0


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Re: [Freesurfer] Tracula Inquiry

[Ledesma, Jason]

External Email - Use Caution

Hi,


Thanks for your help.


I am now seeing this error:

Admins-iMac:XXXneurology$ trac-all -prep -c XXX.24.14Configfile.rtf
Missing }.
Missing }.
}: Command not found.
Missing }.
red255green255blue255: Command not found.
}: Command not found.
Missing }.
}: Command not found.
margl1440margr1440vieww9460viewh8400viewkind0: Command not found.
pardtx720tx1440tx2160tx2880tx3600tx4320tx5040tx5760tx6480tx7200tx7920tx8640pardirnaturalpartightenfactor0:
 Command not found.
Badly placed (.
ERROR: run list is longer than subject list



Attached is my config file. Can you tell me what might be wrong?  Thanks.


Sincerely,

Jason Ledesma
Staff Research Associate
Phone: 1(424)571-7755
E-mail: jason.lede...@labiomed.org



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Paul Wighton 

Sent: Thursday, March 5, 2020 11:29:23 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Tracula Inquiry

[External Email]

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Hi Jason,

Tracula depends on FSL.  If you have FSL installed, all that should be needed 
is to define FSL_DIR before sourcing  `$FREESURFER_HOME/SetUpFreeSurfer.sh`

So using your example above, you could go

```
export FREESURFER_HOME=/Applications/freesurfer
export FSL_DIR=/location/of/fsl/binaries
source $FREESURFER_HOME/SetUpFreeSurfer.sh
```

-Paul


On Thu, Mar 5, 2020 at 12:45 PM Ledesma, Jason 
mailto:jason.lede...@lundquist.org>> wrote:

External Email - Use Caution

Hello,


I am having trouble carrying out Tracula on Freesurfer. See the following 
script (for confidentiality, patient's name has been replaced by XXX):


Admins-iMac:~ neurology$ export FREESURFER_HOME=/Applications/freesurfer

Admins-iMac:~ neurology$

Admins-iMac:~ neurology$ 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

Admins-iMac:~ neurology$ export 
SUBJECTS_DIR=/Applications/freesurfer/subjects/XXX

Admins-iMac:~ neurology$ cd /Applications/freesurfer/subjects/XXX

Admins-iMac:XXX neurology$ trac-all -prep -c XXX7.24.14Configfile

FSLDIR: Undefined variable.

Admins-iMac:XXX neurology$


My Config text file has the following info:


setenv SUBJECTS_DIR Applications/freesurfer/subjects/XXX/XXX7.24.2014/mri

set dtroot = Applications/freesurfer/subjects/XXX/XXX7.24.2014/mri

set subjlist = (XXX7.24.14)

set dcmroot = Applications/freesurfer/subjects/XXX/XXX7.24.14AXDWI

set dcmlist = ( MR0001.dcm )

set bvecfile = 
(Applications/freesurfer/subjects/XXX/20140724_132003HNSBRAINMSREVISEDs005a1001.bvec.txt)

set bvalfile = 
(Applications/freesurfer/subjects/XXX/20140724_132003HNSBRAINMSREVISEDs005a1001.bval.txt)

set doeddy = 1

set dorotbvecs = 1

set usemaskanat = 1

set threat = 0.3

set doregflt = 0

set doregbbr = 1

set doregmni = 1

set doregcvs = 0

set mnitemp = $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz

set pathlist = ( lh.cst_AS rh.cst_AS \

   lh.ilf_AS rh.ilf_AS \

   lh.unc_AS rh.unc_AS \

   fmajor_PP fminor_PP \

   lh.atr_PP rh.atr_PP \

   lh.cab_PP rh.cab_PP \

   lh.ccg_PP rh.ccg_PP \

   lh.slfp_PP rh.slfp_PP \

   lh.slft_PP rh.slft_PP )

set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5)


Please advise. Thanks.



Sincerely,

Jason Ledesma
Staff Research Associate
Phone: 1(424)571-7755
E-mail: jason.lede...@labiomed.org



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XXX7.24.14Configfile.rtf
Description: XXX7.24.14Configfile.rtf
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Re: [Freesurfer] sphere.reg file

[Marina Fernández]

External Email - Use Caution

We are using Freesurfer v6.0
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Re: [Freesurfer] mri_vol2vol

[Benjamin Ineichen]

External Email - Use Caution

the space in which the image was aqcuired.

Am Fr., 6. März 2020 um 18:31 Uhr schrieb Douglas N. Greve <
dgr...@mgh.harvard.edu>:

> what is "native space"?
>
> On 3/6/2020 12:09 PM, Benjamin Ineichen wrote:
>
> External Email - Use Caution
> example.mgz is just some example mask created on a template in native
> space. And I would need to transform it to MNI space. Thus, I ran:
> mri_vol2vol --talres 1  --interp nearest --mov example.mgz --s 001.mgz
> --targ $FREESURFER_HOME/subjects/fsaverage/mri/orig.mgz --regheader --o
> example.mni305.mgz
>
> The transformed mask (example.mni305) is located in a completely different
> brain region in the MNI template compared to the native mask in the native
> template (see screenshots). How I can I correct this? Do I need to register
> the native and MNI template first?
>
> Thanks!
>
> /Ben
>
> Am Fr., 6. März 2020 um 17:59 Uhr schrieb Douglas N. Greve <
> dgr...@mgh.harvard.edu>:
>
>> What is example.mgz?
>>
>> If you want to transfer the orig.mgz, you can do it with
>> mri_vol2vol --tal --talres 1 --interp nearest --mov orig.mgz --s subject
>> --o example.mni305.mgz
>>
>>
>>
>> On 2/20/2020 3:53 PM, Benjamin Ineichen wrote:
>>
>> External Email - Use Caution
>> Dear Freesurfer experts,
>>
>> In order to transform a segmentation mask (example.mgz) from native so
>> standard MNI space I ran:
>> mri_vol2vol --talres 1  --interp nearest --mov example.mgz --s 001.mgz
>> --targ $FREESURFER_HOME/subjects/fsaverage/mri/orig.mgz --regheader --o
>> example.mni305.mgz
>>
>> the output example.mni305.mgz did somehow transform to a different space
>> as you can see in Screenshot orig where the native mask is white and the
>> transformed mask is red. However, the masks seems to be in a
>> completely different brain region in the native MNI space (Screenshot MNI).
>> But the point of transforming my segmentation mask is that the segmented
>> mask should be in the same brain region but just transformed to the
>> standard space. How can I correct this?
>>
>> Many thanks for the support!
>>
>> /Ben
>>
>> --
>> 
>> Benjamin Victor Ineichen, MD PhD
>> Karolinska Institutet
>> Center for Molecular Medicine
>> Stockholm, Sweden
>> ineic...@protonmail.ch
>> +41 76 391 04 01
>>
>> Dr. med. et Dr. rer. nat. ETH Benjamin Victor Ineichen
>> Karolinska Institutet
>> Center for Molecular Medicine
>> Stockholm, Sweden
>> ineic...@protonmail.ch
>> +41 76 391 04 01
>>
>> ___
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>>
>>
>> ___
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> --
> 
> Benjamin Victor Ineichen, MD PhD
> Karolinska Institutet
> Center for Molecular Medicine
> Stockholm, Sweden
> ineic...@protonmail.ch
> +41 76 391 04 01
>
> Dr. med. et Dr. rer. nat. ETH Benjamin Victor Ineichen
> Karolinska Institutet
> Center for Molecular Medicine
> Stockholm, Sweden
> ineic...@protonmail.ch
> +41 76 391 04 01
>
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>
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-- 

Benjamin Victor Ineichen, MD PhD
Karolinska Institutet
Center for Molecular Medicine
Stockholm, Sweden
ineic...@protonmail.ch
+41 76 391 04 01

Dr. med. et Dr. rer. nat. ETH Benjamin Victor Ineichen
Karolinska Institutet
Center for Molecular Medicine
Stockholm, Sweden
ineic...@protonmail.ch
+41 76 391 04 01
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Re: [Freesurfer] mri_vol2vol

[Douglas N. Greve]

what is "native space"?

On 3/6/2020 12:09 PM, Benjamin Ineichen wrote:


External Email - Use Caution

example.mgz is just some example mask created on a template in native 
space. And I would need to transform it to MNI space. Thus, I ran:
mri_vol2vol --talres 1  --interp nearest --mov example.mgz --s 001.mgz 
--targ $FREESURFER_HOME/subjects/fsaverage/mri/orig.mgz --regheader 
--o example.mni305.mgz


The transformed mask (example.mni305) is located in a completely 
different brain region in the MNI template compared to the native mask 
in the native template (see screenshots). How I can I correct this? Do 
I need to register the native and MNI template first?


Thanks!

/Ben

Am Fr., 6. März 2020 um 17:59 Uhr schrieb Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>>:


What is example.mgz?

If you want to transfer the orig.mgz, you can do it with
mri_vol2vol --tal --talres 1 --interp nearest --mov orig.mgz --s
subject --o example.mni305.mgz



On 2/20/2020 3:53 PM, Benjamin Ineichen wrote:


External Email - Use Caution

Dear Freesurfer experts,

In order to transform a segmentation mask (example.mgz) from
native so standard MNI space I ran:
mri_vol2vol --talres 1  --interp nearest --mov example.mgz --s
001.mgz --targ $FREESURFER_HOME/subjects/fsaverage/mri/orig.mgz
--regheader --o example.mni305.mgz

the output example.mni305.mgz did somehow transform to a
different space as you can see in Screenshot orig where the
native mask is white and the transformed mask is red. However,
the masks seems to be in a completely different brain region in
the native MNI space (Screenshot MNI). But the point of
transforming my segmentation mask is that the segmented mask
should be in the same brain region but just transformed to the
standard space. How can I correct this?

Many thanks for the support!

/Ben

-- 


Benjamin Victor Ineichen, MD PhD
Karolinska Institutet
Center for Molecular Medicine
Stockholm, Sweden
ineic...@protonmail.ch 
+41 76 391 04 01

Dr. med. et Dr. rer. nat. ETH Benjamin Victor Ineichen
Karolinska Institutet
Center for Molecular Medicine
Stockholm, Sweden
ineic...@protonmail.ch 
+41 76 391 04 01

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--

Benjamin Victor Ineichen, MD PhD
Karolinska Institutet
Center for Molecular Medicine
Stockholm, Sweden
ineic...@protonmail.ch 
+41 76 391 04 01

Dr. med. et Dr. rer. nat. ETH Benjamin Victor Ineichen
Karolinska Institutet
Center for Molecular Medicine
Stockholm, Sweden
ineic...@protonmail.ch 
+41 76 391 04 01

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Re: [Freesurfer] samseg permissions error

[Douglas N. Greve]

what is your command line and terminal output?

On 2/24/2020 10:50 AM, Russo, Andrew William wrote:

Hello Freesurfer Developers,

I am trying to use the "samseg" function in /usr/local/freesurfer/dev 
but do not have permission to access the directory 
/usr/local/freesurfer/dev/subjects/fsaverage. Is this a restricted 
directory?


ValueError: file 
/usr/local/freesurfer/dev/subjects/fsaverage/mri/orig.mgz does not exist

ERROR: fs_time run_samseg

I did not find any related issues with samseg on the archive and I 
have had it work in the past. Before running samseg I sourced the 
freesurfer environment:

export FREESURFER_HOME=/usr/local/freesurfer/dev
source $FREESURFER_HOME/SetUpFreeSurfer.sh
(Using Freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0)

Thank you in advance,
Andrew
/
/Andrew Russo
Clinical Research Coordinator
Multiple Sclerosis Imaging Lab
Massachusetts General Hospital
149 13th Street | Boston, MA 02129
617-726-7531



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Re: [Freesurfer] Apply transformation

[Douglas N. Greve]

*Od:* freesurfer-boun...@nmr.mgh.harvard.edu 
 za uživatele Adam Rytina 


*Odesláno:* sobota 15. února 2020 19:52
*Komu:* Freesurfer support list 
*Předmět:* Re: [Freesurfer] Apply transformation

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Thanks, unfortunately, I am making some mistake but I don´t know where.

First of all I run autorecon1 on my anatomical T1 data (the orig.mgz 
image is saved in /usr/local/freesurfer/subjects/anatomical).
Then in the /usr/local/freesurfer/data I run mri_robust register 
command of the T1 and diffusion DWI data. The registration.lta file is 
saved here.
Don't use robust register for this, use bbregister (but you will have to 
run recon-all to completion)


Now I add an anatomical mask "3D_T1_brain_mask.nii" to the same folder 
/usr/local/freesurfer/data that I want to transform to the anatomical 
T1 space.

Is this in the conformed space (ie, same as orig.mgz)?


In the same /usr/local/freesurfer/data I run : "mri_vol2vol --lta 
registration.lta --mov 3D_T1_brain_mask.nii --o f-in-anat3.nii --s 
anatomical --fstarg"

If you are trying to transfer it to the DTI space, then use
mri_vol2vol --lta bbr.registration.lta --targ 3D_T1_brain_mask.nii --mov 
dti.nii  --o f-in-anat3.nii --s anatomical --interp nearest


To sum up, I am aiming to apply a transformation matrix on the T1 
anatomical brain mask and transform it to the T1 space defined by 3D 
T1 image.
The problem is this command transforms orig.mgz file (a skull stripped 
T1 image) instead of 3D_T1_brain_mask.nii.


Please, do you know where I make mistake?

Thanks a lot

*Od:* freesurfer-boun...@nmr.mgh.harvard.edu 
 za uživatele Douglas Greve 


*Odesláno:* sobota 15. února 2020 17:15
*Komu:* freesurfer@nmr.mgh.harvard.edu 
*Předmět:* Re: [Freesurfer] Apply transformation
Yes, mri_vol2vol

On 2/15/20 11:07 AM, Adam Rytina wrote:


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Hello all,

I want to apply the saved transformation (a transformation matrix 4x4 
acquired by registration of an anatomical and a diffusion image) on 
my input anatomical mask and change a final FOV by specifying a 
diffusion reference image (its voxels size). It means to apply the 
same command as the command ApplyXFM in FSL FLIRT. Does this option 
exist also in Freesurfer?


Thanks a lot
Regards
Adam



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Re: [Freesurfer] mri_vol2vol

[Douglas N. Greve]

What is example.mgz?

If you want to transfer the orig.mgz, you can do it with
mri_vol2vol --tal --talres 1 --interp nearest --mov orig.mgz --s subject 
--o example.mni305.mgz




On 2/20/2020 3:53 PM, Benjamin Ineichen wrote:


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Dear Freesurfer experts,

In order to transform a segmentation mask (example.mgz) from native so 
standard MNI space I ran:
mri_vol2vol --talres 1  --interp nearest --mov example.mgz --s 001.mgz 
--targ $FREESURFER_HOME/subjects/fsaverage/mri/orig.mgz --regheader 
--o example.mni305.mgz


the output example.mni305.mgz did somehow transform to a different 
space as you can see in Screenshot orig where the native mask is white 
and the transformed mask is red. However, the masks seems to be in a 
completely different brain region in the native MNI space (Screenshot 
MNI). But the point of transforming my segmentation mask is that the 
segmented mask should be in the same brain region but just transformed 
to the standard space. How can I correct this?


Many thanks for the support!

/Ben

--

Benjamin Victor Ineichen, MD PhD
Karolinska Institutet
Center for Molecular Medicine
Stockholm, Sweden
ineic...@protonmail.ch 
+41 76 391 04 01

Dr. med. et Dr. rer. nat. ETH Benjamin Victor Ineichen
Karolinska Institutet
Center for Molecular Medicine
Stockholm, Sweden
ineic...@protonmail.ch 
+41 76 391 04 01

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Re: [Freesurfer] within-subject contrast between runs

[Douglas N. Greve]

On 3/6/2020 11:15 AM, Milde, Christopher wrote:


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Dear Freesurfer Experts,


I have a very basic questions about creating subject-wise contrasts 
between runs


*
*

*Background*

Study with two runs per subject where each run corresponds two a 
different condition (i.e. Stimulation A (on - off) and Stimulation B 
(on - off).


I performed the preprocessing and 1st levels stats in the native 
subjects space



*Questions*

  * How can I obtain a within-subjects contrast between two runs (the
Stimulation A vs. Stimulation B )  obtained in two runs within one
session?

The easiest way is to code the conditions differently in the paradigm 
file (eg, instead of two conditions, you'd have 4, ARun1, BRun1, ARun2, 
BRun2), then just create contrasts as normal


  * Can I obtain this within-subject contrast by staying in the native
subject space?

It can be done in fsaverage or the native subject surface space, it is 
not related.


  * Do I have to concatenate both runs and create a new parradigm file?


No, see above



Thanks for your support


Sincerely

Chris




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Re: [Freesurfer] questions about vertex information

[Douglas N. Greve]

Try

mris_convert -n lh.white lh.white.norm.asc



On 3/6/2020 11:07 AM, Jedy wrote:


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Dear FreeSurfer friends,

Does anybody know how to extract vertex information of lh.white and 
lh.pial?  I would like to extract normal vector and other information 
of each vetex.


I would be very appreciated if someone can give me some suggestions.

Thank you very much!

Best

-jedy

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Re: [Freesurfer] PetSurfer reference region

[Douglas N. Greve]

I cannot replicate this in either v6 or v7beta. Can you send the 
terminal output?


On 3/5/2020 1:32 PM, Dincer, Aylin wrote:


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Hello PetSurfer experts,

We are using the cerebellum cortex as our reference region, but 
noticed that the SUVR values for lh/rh cerebellum cortex do not have a 
value of 1 (which is what we were expecting). The actual SUVR values 
are 1.31 for the lh and 1.35 for the rh cerebellum cortex. I attached 
the stats file (gtm.stats.dat) and below is the command we ran.


mri_gtmpvc --i regmean.nii.gz --reg regmean_template.reg.lta --psf 
${FWHM} --seg ${MR_ID}/mri/gtmseg.mgz --default-seg-merge --auto-mask 
PSF+2 .01 --mgx .01 --rescale 8 47 –o regmean_gtmpvc_output


Let me know if you need any more details.

Thanks so much,

Aylin



_

Aylin Dincer

Senior Research Technician

NeuroImaging Laboratories

Imaging Core, Benzinger Lab

314-362-3629



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Re: [Freesurfer] sphere.reg file

[Douglas N. Greve]

what version of freesurfer are you running?

On 3/6/2020 10:03 AM, Marina Fernández wrote:


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Dear freesurfer experts,
I run the following commands to perform analysis with projected surfaces on my 
average subject:
make_average_subject --out my_avg_subject --fsgd  fsgd.txt
surfreg --s s_001 --t  my_avg_subject --o my_avg_subject.sphere.reg
mris_preproc --fsgd nfsgd.txt --target my_avg_subject --meas thickness --srcfmt 
curv --hemi [l/r]h --out  [l/r]h.fsgd.mgh
Theoretically, the mri_preproc function will automatically use the 
my_avg_subject.sphere.reg file because I specify my_avg_subject as the target 
subject. The problem is that in the output that comes out in the terminal while 
this function is running, it is specified that the file [l/r]h.sphere.reg is 
selected instead of [l/r]h.my_avg_subject.sphere.reg.
Additionally, I did a test specifying the flag "--surfreg 
my_avg_subject.sphere.reg" in mris_preproc and the values of the output surface are 
different from the output that I have when I don't specify the flag --surfreg in 
mris_preproc (so, If I don't specify it, I think that definitely the function doesn't 
automatically use the file generated in surfreg, I think the default sphere.reg is used).
What should I do? Is it better to specify the “--surfreg 
my_avg_subject.sphere.reg” flag in the mris_preproc function?
Thanks in advance.
Best regards,
Marina.


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Re: [Freesurfer] Converting ANTs nonlinear transform to .m3z

[Douglas N. Greve]

I think Andrew H might have a way to do this, but he's on vacation until 
next week. Try back then.


On 3/5/2020 12:29 PM, Ardesch, D.J. wrote:


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Dear FreeSurfer experts,

I am working on some monkey data and trying to get an accurate 
nonlinear transform to talairach space (talairach.m3z in the -careg 
stage). The problem is that the monkey brains look so different from 
the human brain that this registration ends up being very far off, 
even with an accurate talairach.lta.


As an alternative, I did a two-stage nonlinear registration using ANTs 
(first from subject to a macaque template and then from macaque 
template to talairach), which gives an accurate nonlinear transform. 
However, I can’t seem to convert this nonlinear transform file 
correctly from .nii.gz to the .m3z format that FreeSurfer needs to 
continue down the pipeline.


How would one go about converting the nonlinear transform from ANTs to 
a correct .m3z file?


Some other things I tried:

  * I have tried a workaround in which I applied the inverse ANTs
transform to the first frame of RB_all_2016-05-10.vc700.gca to get
the talairach volume in subject space, and then ran
mri_ca_register on that volume to obtain a talairach.m3z. That
transform works but is still not accurate enough unfortunately.

  * The nonlinear transform itself seems correct because when I apply
it to the movable volume using ANTs the results are similar to:

mri_convert movable.mgz –apply_transform talairach.m3z -oc 0 0 0 
movable_in_talairach.mgz


where movable.mgz is the talairach volume in subject space and 
talairach.m3z is the transform made by mri_ca_register.


The dimensions, orientation, and voxel size of 
movable_in_talairach.mgz and my own transformed volume are identical.


Any help would be greatly appreciated!

Platform: MacOS Mojave

Version: FreeSurfer 6.0.0


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Re: [Freesurfer] Extract specific LGI and Volume values

[Douglas N. Greve]

what is your command line?

On 3/5/2020 1:50 AM, Tien Pham wrote:


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Thank you for your suggestion.
I tried to use freeview to load surface on the label I created. But 
terminal showed this error '' freadFloat: fread failed '' many times.
I tried to load label with qdec and I got the error (pic 1) I attached 
below.
I also tried to load surface with qdec and this error displayed in 
terminal (pic 2).

I am very appreciated when you helped me before.
I am looking forward to hearing from you.
Thank you very much.

On Mon, Feb 24, 2020 at 11:16 PM Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:


Try using freeview

On 2/18/2020 8:17 PM, Tien Pham wrote:


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Thank you for your email.
I tried to load the label with qdec and freeview and both were
not worked.
When i tried with qdec, It said '' load the surface first '' then
I did but It did not work and showed some errors.
The other way when I tried to load with qdec, qdec was closed
suddenly without any notification.
I am looking forward to hearing from you.

On Fri, Feb 14, 2020 at 11:44 PM Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>> wrote:

What tool are you trying to use to load the label? What
happens when you try?

On 2/7/2020 10:11 PM, Tien Pham wrote:


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Thank you for your email. I run exactly the command
mri_label2label as you suggested, and the command finished
without any problem.
But I did not know why I could not open the label.
Please help me. Thank you once again.

On Tue, Feb 4, 2020 at 2:55 AM Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>> wrote:

sorry for the delay. You will have to use
mri_label2label to map the label from the fsaverage
space to the individual space


On 1/31/2020 10:01 PM, Tien Pham wrote:


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Can you read my message?
I used longitudinal pipeline for my data set with two
time points and measured the LGI differences between them.
Then I created the label based on significant clusters
which showed in QDEC.
I tried to load the label on the subjects in cross,
base, long steps but it did not work.
I am looking forward to hearing from you. Thank you
very much.

On Sat, Feb 1, 2020 at 8:08 AM Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>> wrote:

Sorry, I do not have the previous emails, can you
repost with previous emails in the message?

On 1/28/2020 7:35 PM, Tien Pham wrote:


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Thank you for your response.
I used longitudinal pipeline for my data set with
two time points and calculated the LGI differences
between them.
Then I created the label based on significant
clusters which showed in QDEC.
I tried to load the label on subjects in cross,
base, long steps but it did not work.
I am looking forward to hearing from you. Thank
you so much.

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Re: [Freesurfer] 2 surface mri_glmfit as independent variables

[Douglas N. Greve]

Sorry, not sure what you are trying to do. From your equation it looks 
like you are not doing a voxel-wise analysis but instead using maps to 
try to predict cognition? If so, this is a multivariate analysis whereas 
mri_glmfit does voxel-wise analysis. We don't really have any tools to 
do multivariate analysis.



On 3/3/2020 7:05 PM, Adam Martersteck wrote:


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Hi FreeSurfer team,

I have a question about running mri_glmfit with 2 different surface 
modalities as the independent variable and a single value per 
participant as the dependent variable. I'm trying to examine the 
unique and shared contribution of the 2 surfaces to predict a 
cognitive measure.

E.g. Cognition ~ ?h.thickness + ?h.PET

I tried mri_glmfit with the "--table" option, giving it a column of 
scores per participant (in the aseg2stats table format), and then 
using "--pvr lh.thickness-stack.fsaverage.mgh" and a second "--pvr 
lh.PET-stack.fsaverage.mgh", using contrasts matrices as [0 0 1], [0 1 
0], and [0 1 1].


_When I run mri_glmfit it returns:_
ERROR: mri_reshape: number of elements cannot change
  nv1 = 163842, nv1 = 1

It continues to run, but all surface maps are full of zeroes. Any 
suggestions? Is there a better way to do this?


Thanks,
Adam

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Re: [Freesurfer] Registration of DIR (Double Inversion Recovery) series

[Douglas N. Greve]

yes, your command looks correct

On 3/3/2020 2:05 PM, Xiaojiang Yang wrote:


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Hi all,

I want to register DIR (Double Inversion Recovery) series to T1 series 
using Freesurfer. I used the command line similar to that used for 
FLAIR registration:


bbregister --s subject001 --mov 
dicom/subject001/20141003_MR/3_Sag_Space_DIR/2.25.97015757385982906453797720915266163627.dcm 
--lta subjects/subject001/mri/transforms/DirTest.auto.lta 
 --init-coreg --T2


where the option --T2 is still used. Since in DIR series, gray matter 
is brighter than white matter, I use --T2 as the contrast argument.


I wan's able to check how precise the results are. I will take some 
time to do check that.


But anyone can tell me: Did I do it correctly? what is the better way 
or correct way to do the above-mentioned registration?


Thank you!
Xiaojiang


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Re: [Freesurfer] petsurfer

[Douglas N. Greve]

I cannot replicate this, eg

In matlab
a = fast_vol2mat(MRIread('gtm.nii.gz'));
a(1:10)
  Columns 1 through 7
    0.7957    1.0565    1.5711    1.7842    1.8625    1.9539 1.2499
  Columns 8 through 10
    1.3188    1.4063    1.2536

From gtm,.stats.dat
  1    2 Left-Cerebral-White-Matter  wm 25583 
10872.101    0.796   0.1501
  2    7 Left-Cerebellum-White-Matter    wm 1472  691.994    
1.057   0.1843
  3    8 Left-Cerebellum-Cortex  subcort_gm 5326 
2833.077    1.571   0.1451
  4   10 Left-Thalamus-Proper    subcort_gm 643  333.888    
1.784   0.1808
  5   11 Left-Caudate    subcort_gm 353  117.232    
1.863   0.1650
  6   12 Left-Putamen    subcort_gm 576  256.726    
1.954   0.1543
  7   13 Left-Pallidum   subcort_gm 146   52.532    
1.250   0.0782
  8   16 Brain-Stem  subcort_gm 1139  
517.830    1.319   0.2061
  9   17 Left-Hippocampus    subcort_gm 477  174.082    
1.406   0.1226
 10   18 Left-Amygdala   subcort_gm 186   65.184    
1.254   0.0847


You can see that the values match




On 3/3/2020 12:39 PM, Laboratorio de Neurociencia Funcional wrote:


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Dear Freesurfer experts,
I have compared the PVC uptake values of gtm.stats with the values of
gtm.nii.gz with the function load_nii in matlab. I noted
that values in matlab are reversed, i. e., the first value in
gtm.stats matches with the last value in gtm.nii.gz and so on.

Could you confirm me that nopvc.nii.gz values are also reversed
when loaded with load_nii in matlab? I have no way to check this.
Thank you in advance.
Best, Marina

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Re: [Freesurfer] Issue with BBR and Applying CVS Warps to Diffusion Data

[Douglas N. Greve]

Try this instead
set gcam = 
$SUBJECTS_DIR/$subject/cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z
set dstreg = 
$FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri.2mm/register.lta
mri_vol2vol --gcam ${meanb0_bet} ${b0toT1mat_bet} $gcam $dstreg 0 1 
${b0_to040_2_t1w}


This (admittedly cryptic) command should put it into the mri.2mm space 
of cvs_avg35_inMNI152

0 above means don't use a B0 distortion map
1 above means to use triliinear interp


On 3/2/2020 10:35 PM, Austin Patrick wrote:


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I’d be happy to. This is the call:

mri_vol2vol --targ ${target} \

--m3z $cvsmorph \

--noDefM3zPath --reg ${b0toT1mat_bet} \

--mov ${meanb0_bet} \

--o ${b0_to040_2_t1w} \

--interp trilin

Thanks,

-Austin

*From: * on behalf of "Douglas 
N. Greve" 

*Reply-To: *Freesurfer support list 
*Date: *Monday, March 2, 2020 at 8:58 PM
*To: *"freesurfer@nmr.mgh.harvard.edu" 
*Subject: *Re: [Freesurfer] Issue with BBR and Applying CVS Warps to 
Diffusion Data


Can you send the mri_vol2vol command line?

On 2/28/2020 4:46 PM, Austin Patrick wrote:

*External Email - Use Caution *

The b0-to-anat look fine. I’m using mri_vol2vol with trilinear
interpolation to apply the CVS warps.

Thanks,

-Austin

*From: *
 on behalf of
"Douglas N. Greve" 

*Reply-To: *Freesurfer support list


*Date: *Friday, February 28, 2020 at 3:18 PM
*To: *"freesurfer@nmr.mgh.harvard.edu"



*Subject: *Re: [Freesurfer] Issue with BBR and Applying CVS Warps
to Diffusion Data

So the B0-to-Anat registration is ok? What command are you using
to map the B0s into the CVS space?

On 2/26/2020 3:50 PM, Austin Patrick wrote:

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Dear All,

I have used CVS to align around 180 scans to a single,
representative subject. I have then used BBR to align the mean
b0 image to register the diffusion data to the native space T1
and then apply CVS warps; however, the resulting aligned
images for calculated maps from the DWIs are very poor with a
great deal of heterogeneity, especially at the boundary but
also within white matter. The coefficient of variation of the
mean b0 BB registered to the T1 is around 30% globally
(excluding the edges of the brain) and 40% or greater for FA.
I have reviewed the initial rigid registration of the b0s to
the T1s for gross misalignment and found that FLIRT performed
pretty well and didn’t fail for any of my subjects and didn’t
require manual adjustment; however, the result of after
applying the CVS warps is quite poor. The data T1s are 1mm
(MPnRAGE) and the b0s are at 2mm. The DWIs were corrected for
eddy currents, Gibbs’ ringing, rician noise, and B0
distortions and look pretty great. The DWIs are 70x180x180 at
2mm isotropic and the T1s are 256x256x256 at 1mm isotropic.
Are there any suggestions for this issue? I have tried
re-aligning the DTI parameter maps to the b0s before applying
the CVS warps (although they should be in the same space) and
I have tried using both the –t2 and –dti, as well as with/out
the –fsl-init flag. Is bbregister shifting the origin for the
images at all? Any help would be appreciated.

Cheers,

-Austin

--

Austin M. Bazydlo, MS

PhD Candidate

Dept. of Medical Physics

University of Wisconsin-Madison




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Re: [Freesurfer] registrations

[Douglas N. Greve]

why not just use the aseg? it has been cleaned up with the surfaces, so 
it should represent everything inside the pial surface pretty well.

On 3/2/2020 4:52 PM, Octavian Lie wrote:
>  External Email - Use Caution
>
> Dear Bruce & All,
>
> Sure, I wanted some advice from the greats before registering pre and
> posteresection (intrasubject) scans.
> I tried both registrations on several patient data, bbregister clearly
> superior to mri_robust_register (used with orig/mgz) for both
> postresection T1 or T2 registration to FS output, even when using a
> mask for the resection volume with the latter.
> The best results were using one hemisphere option (the
> healthy/nonresected one), and the default or init-fsl for
> initialization (init-spm and init-rr failed often), smth like
> bbregister --s subj --mov T1postop.nii --lta register_hemiR.lta --o
> T1bbr_hemiR_fsl.nii --t1 --rh-only --init-fsl
>
> My last question relates to creating a binary mask from pial surfaces,
> but to include mesial temporal structures (amygdala, hippocampus). I
> tried the following, but the mris_fill process is killed (OOM) after I
> upgraded to ubuntu 18.04. Is there another, more straightforward
> solution for the mask?
> Thank you,
> Octavian
>
> mris_fill -c -r 1 surf/rh.pial mri/rh.pial.filled.mgz & \
> mris_fill -c -r 1 surf/lh.pial mri/lh.pial.filled.mgz & \
> mri_concat --combine --i mri/rh.pial.filled.mgz --i
> mri/lh.pial.filled.mgz --o mri/pial.filled.mgz
> cd ./mri ; \
> mri_binarize --i aseg.mgz --match 5 --match 9 --match 10 --match 14
> --match 17 --match 18 --match 19\
>   --match 25 --match 31 --match 44 --match 48 --match 49 --match 53
> --match 54 --match 55 --match 57\
>   --match 63 --match 86 --match 96 --match 97 --match 105 --match 106
> --match 114 --match 115\
>   --match 195 --match 199 --match 203 --match 204 --match 205 --match
> 216 --match 222 --match 225\
>   --match 507 --match 557 --match 1200 --match 1201 --match 1205
> --match 1206 --match 2200 --match 2201\
>   --match 2205 --match 2206 --o hippoamy.mask.mgz & \
> fscalc pial.filled.mgz add hippoamy.mask.mgz -o epimask.mgz
>
>
>
>
>
>
>
> On Sun, Feb 23, 2020 at 8:51 PM Bruce Fischl  
> wrote:
>> Hi Octavian
>>
>> 1. Not sure - you should try them. If you have reasonable surfaces I
>> think bbreg lets you specify masks to ignore, which should be giant help
>> in this scenario. On the other hand, mri_robust_register does this
>> automatically. They are both relatively fast so why not try and see?
>>
>> 2. Same answer as before. mri_robust_register has flags to tell it to use
>> an inter-modal similarity function, but you can also tell bbregister it is
>> a T2 and it should do a good job (and implicitly register to the T1 since
>> it is already aligned with the surface).
>>
>> 3. I'm not sure what you mean - can you explain further?
>>
>> cheers
>> Bruce
>>
>>
>>
>> On Sun,
>> 23 Feb 2020, Octavian Lie wrote:
>>
>>> External Email - Use Caution
>>>
>>> Dear All,
>>>
>>> I need to register:
>>> 1. T1.mgz to a T1 postresection volume (no contrast), with large
>>> resection. Which one should I use, mri_robust_register, or bbregister,
>>> if the latter, which is the better initiator (nmi, spm, fsl)?
>>>
>>> 2. T1.mgz to a 3D FLAIR SPACE sequence (outside of the flair space
>>> recon-all flag), which FS registration tool should I use?
>>>
>>> 3. I then need to mask the coregistered T1 postresection with a T1.mgz mask.
>>>
>>> I would appreciate commands (either names, or full command lines),
>>> please advise.
>>>
>>> Thank you,
>>> Octavian
>>>
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>>>
>>>
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Re: [Freesurfer] group analysis for same group in 2 conditions

[Douglas N. Greve]

What quantity do you want to compare across subjects/goggle condition? 
Sorry for the delay, I have not worked much with the retinotopy code in 
a while and don't have it at my fingertips



On 3/2/2020 9:08 AM, Marco Ninghetto wrote:


External Email - Use Caution

Since that each subject undergoes to both conditions and functional 
images are in 2 different folders, I modify my folder structure and 
put functional folders together. It means that now I have a main 
functional folder (pRFs_functionals) in which I have all subjects two 
times named differently (eg: SUBJ06YG and SUBJ06NG, where YG means 
with goggles condition and NG means without goggles condition). 
Something like below:

image.png
All the subjects have one structural image in a folder named 
"fs_output". Now that all functionals are together, my question is how 
to create the FSGD file. At this moment FSGD looks like this:

image.png
Each subject has his own structural data saved in a folder called 
"sub-xx", inside the main folder from "recon-all". So, my doubt is how 
to name subjects inside the FSGD in such a way that FREESURFER would 
know it has to compare the same subject two times in two different 
conditions.

Command is:

mris_preproc --fsgd RetinotopyStudy --target fsaverage --hemi
?h --out ?h.out.retinotopy

Thank you for your effort in solving this matter,
Marco

On Fri, 28 Feb 2020 at 23:17, Marco Ninghetto 
mailto:m.ninghe...@nencki.edu.pl>> wrote:


Thanks for your support. Here my "mkanalysis-sess" command:

mkanalysis-sess -a rtopy.self.?h.ng -surface self ?h
-paradigm rtopy.par -retinotopy 41 -TR 2.5 -fsd bold -fwhm
5 -per-run


I run this command for both no goggles condition
(rtopy.self.?h.ng) and for yes goggles (rtopy.self.?h.yg).
The functional data were acquired using rotating wedge 45deg
counter-clockwise and expanding ring (out) stimuli. One cycle
lasted 41sec, each stimulus had 6 cycles.


On Fri, 28 Feb 2020, 22:24 Douglas N. Greve,
mailto:dgr...@mgh.harvard.edu>> wrote:

What quantity from the retinotopy analysis do you want to
compare across subjects? Eg, the phase? Can you send your
mkanalysis-sess command?

On 2/28/2020 8:17 AM, Marco Ninghetto wrote:


External Email - Use Caution

Dear experts,
I'm performing a study on visual pathways, in which each
participant undergoes to 2 different conditions. One in
normal sight (NG, i.e.: No Goggles) and second in narrowed
sight using special goggles (YG, i.e.: Yes Goggles). I'd like
to compare the results between these two conditions
(basically, subject A, B, C in cond1 versus subject A, B, C
in cond2).

I created the FSGD file (attached as "RetinotopyStudy" file)
and the contrast matrices, organised as:

1 -1 , named "YG-NG.mtx"
-1 1,  named "NG-YG.mtx"

In this FSGD sample file, I reported only subjects from 7 to 12.
My folders are organised as follows:

main >> recon_output  >> sub-yy (X folders for X
subjects)
>> Contrasts (with contrast files)
>> FSGD (with FSGD files)
>> fsaverage (subjects template created during
recon-all -qcache)
        >> pRF_function >> analNG (inside, there are
the functionals for each subject in NG condition)
>> analYG  (inside, there are the functionals for
each subject in YG condition) 



Once I used the pipeline for the retinotopy analysis
and
I have results for each participant, and now I'd like to make
2nd lev analysis. So the idea would be, as you probably
already got it, condition Yes Goggles versus condition No
Goggles. I use the command:

mris_preproc --fsgd RetinotopyStudy --target
fsaverage --hemi ?h --out outputname.mgh


But I'm not sure it would calculate in the right way.
The question is: how would I organise the FSGD file or
folders in such a way that FREESURFER would know that it has
to compare results from the same subjects but from two
different folders (analNG vs analYG)?

Hoping that's clear, I really look forward to hear from you soon.
Thank you for your time,
Marco

-- 
---

Marco Ninghetto, PhD candidate
Laboratory of Neuroplasticity
Nencki Institute of Experimental Biology
Polish Academy of Sciences
3 Pasteur Street, 02-093 Warsaw, Poland

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[Freesurfer] within-subject contrast between runs

[Milde, Christopher]

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Dear Freesurfer Experts,


I have a very basic questions about creating subject-wise contrasts between runs



Background

Study with two runs per subject where each run corresponds two a different 
condition (i.e. Stimulation A (on - off) and Stimulation B (on - off).

I performed the preprocessing and 1st levels stats in the native subjects space


Questions

  *   How can I obtain a within-subjects contrast between two runs (the 
Stimulation A vs. Stimulation B )  obtained in two runs within one session?
  *   Can I obtain this within-subject contrast by staying in the native 
subject space?
  *   Do I have to concatenate both runs and create a new parradigm file?


Thanks for your support


Sincerely

Chris


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[Freesurfer] questions about vertex information

[Jedy]

External Email - Use Caution

Dear FreeSurfer friends,


Does anybody know how to extract vertex information of lh.white and 
lh.pial? I would like to extract normal vector and other information of 
each vetex.


I would be very appreciated if someone can give me some suggestions.


Thank you very much!


Best



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[Freesurfer] Open lab manager position in Perception & Brain Dynamics Laboratory at NYU Medical Center

[Wu, Yuan hao]

External Email - Use Caution

Sorry for spamming. The contact email in the previous mail contains a typo


The Perception & Brain Dynamics Laboratory (http://www.med.nyu.edu/helab/) at 
New York University School of Medicine is looking for a lab manager to start in 
spring/summer 2020. The Laboratory is within the Neuroscience Institute at NYU 
Langone Health(http://www.med.nyu.edu/neuroscience), affiliated with 
Departments of Neurology,  Neuroscience and Physiology, and Radiology. Our 
research focus is on understanding the neural bases of perceptual awareness 
using multimodal imaging (fMRI, MEG, EEG, ECoG) and stimulation (tDCS, TMS) 
techniques in humans, combined with computational neuroscience approaches. We 
are looking for a bright and driven candidate with a Bachelor's or Master's 
degree who is dedicated to neuroscience research. A variety of backgrounds, 
including neuroscience, biology, psychology, and computer science is possible, 
and experience with programming is highly desirable. In addition, the ideal 
candidate has high responsibility and dependability, as well as excellent 
critical thinking, organizational and leadership skills. Performing independent 
research is an important aspect of the position, in addition to lab management 
duties. A minimal commitment of 2 years is required. Interested candidates 
please send a cover letter, a CV, undergraduate and/or graduate transcript, and 
names and contacts of two to three referees, to Prof. Biyu J. He at 
biyu.jade...@gmail.com, with the subject line "Lab manager application 2020". 
The application is rolling, so please submit your materials as soon as possible.
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[Freesurfer] Open lab manager position in Perception & Brain Dynamics Laboratory at NYU Medical Center

[Wu, Yuan hao]

External Email - Use Caution

The Perception & Brain Dynamics Laboratory (http://www.med.nyu.edu/helab/) at 
New York University School of Medicine is looking for a lab manager to start in 
spring/summer 2020. The Laboratory is within the Neuroscience Institute at NYU 
Langone Health(http://www.med.nyu.edu/neuroscience), affiliated with 
Departments of Neurology,  Neuroscience and Physiology, and Radiology. Our 
research focus is on understanding the neural bases of perceptual awareness 
using multimodal imaging (fMRI, MEG, EEG, ECoG) and stimulation (tDCS, TMS) 
techniques in humans, combined with computational neuroscience approaches. We 
are looking for a bright and driven candidate with a Bachelor's or Master's 
degree who is dedicated to neuroscience research. A variety of backgrounds, 
including neuroscience, biology, psychology, and computer science is possible, 
and experience with programming is highly desirable. In addition, the ideal 
candidate has high responsibility and dependability, as well as excellent 
critical thinking, organizational and leadership skills. Performing independent 
research is an important aspect of the position, in addition to lab management 
duties. A minimal commitment of 2 years is required. Interested candidates 
please send a cover letter, a CV, undergraduate and/or graduate transcript, and 
names and contacts of two to three referees, to Prof. Biyu J. He at 
biyu.jade...@gmail.com, with the subject line "Lab manager application 2020". 
The application is rolling, so please submit your materials as soon as possible.
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[Freesurfer] sphere.reg file

[Marina Fernández]

External Email - Use Caution

Dear freesurfer experts,


I run the following commands to perform analysis with projected
surfaces on my average subject:


make_average_subject --out my_avg_subject --fsgd  fsgd.txt


surfreg --s s_001 --t  my_avg_subject --o my_avg_subject.sphere.reg


mris_preproc --fsgd nfsgd.txt --target my_avg_subject --meas thickness
--srcfmt curv --hemi [l/r]h --out  [l/r]h.fsgd.mgh


Theoretically, the mri_preproc function will automatically use the
my_avg_subject.sphere.reg file because I specify my_avg_subject as the
target subject. The problem is that in the output that comes out in
the terminal while this function is running, it is specified that the
file [l/r]h.sphere.reg is selected instead of
[l/r]h.my_avg_subject.sphere.reg.


Additionally, I did a test specifying the flag "--surfreg
my_avg_subject.sphere.reg" in mris_preproc and the values of the
output surface are different from the output that I have when I don't
specify the flag --surfreg in mris_preproc (so, If I don't specify it,
I think that definitely the function doesn't automatically use the
file generated in surfreg, I think the default sphere.reg is used).


What should I do? Is it better to specify the “--surfreg
my_avg_subject.sphere.reg” flag in the mris_preproc function?


Thanks in advance.

Best regards,

Marina.
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Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"

[Frank Chau]

External Email - Use Caution

Dear Tim,

The FOV of my T1 series is 256 x 240. Is it the FOV of the T1 series will 
affect the process Recon-all? If yes, how would it impact my output results?

Regards

Frank



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Tim Schäfer 

Sent: 05 March 2020 2:25
To: Freesurfer support list
Subject: Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"

External Email - Use Caution

Thanks for providing the image. Looks fine to me as well.

What is a bit strange is that when running `mri_info` on the file you provided, 
it shows a FOV of 256 (not 284!) for me, so I have no idea why this error is 
triggered in recon-all.

Maybe somebody else has an idea...

Tim

> On March 4, 2020 at 4:47 PM Frank Chau  wrote:
>
>
> External Email - Use Caution
>
> Dear Tim,
>
> I have checked the orig.mgz file and nothing usual was found (please see the 
> attachment image)
>
> For downloading my orig.mgz: 
> https://www.dropbox.com/s/crkndenx8ev957v/orig.mgz?dl=0
>
> Regards
>
> Frank
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Tim Schäfer 
> 
> Sent: 04 March 2020 23:27
> To: Freesurfer support list
> Subject: Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"
>
> External Email - Use Caution
>
> Dear Frank,
>
> if you search the log in your Dropbox for 'error', this comes up:
>
> 
> ERROR! FOV=284.000 > 256
> Include the flag -cw256 with recon-all!
> Inspect orig.mgz to ensure the head is fully visible.
> 
>
> Did you have a look at the orig.mgz?
>
> Best,
>
> Tim
>
>
> > On March 4, 2020 at 2:59 PM Frank Chau  wrote:
> >
> >
> > External Email - Use Caution
> >
> > Hello FreeSurfer Developers,
> >
> > I ran a recon-all on a recent batch of T1 Nifti files and all ended with 
> > "exited with ERRORS". For example: "recon-all -s Chan_Pui_Kim_42M_T1 exited 
> > with ERRORS at Sat Jan 11 01:32:55 HKT 2020".
> >
> > I've searched the email archive list and I found other researcher 
> > encountered same problem before. However, I am quite sure their root causes 
> > are not same as my case. 3 possible causes were found in the email archive 
> > which about "exited with ERRORS":
> >
> >   1.  The version of freesurfer (I have already used the latest 6.0.0 
> > version)
> >   2.  Hard disk space (My computer have enough hard disk space)
> >   3.  sharing folder between virtual machine and original platform. (I use 
> > freesurfer in Mac OS which do not have this problem)
> >
> > I uploaded the recon-all.log to my dropbox in case it's of any use.
> >
> >
> > 1) FreeSurfer version: Darwin-OSX-stable-pub-v6.0.0-2beb96c
> >
> > 2) Platform: MAC OS X 10.11.6
> >
> > 3) uname -a: Darwin PFCs-MacBook-Pro.local 15.6.0 Darwin Kernel Version 
> > 15.6.0: Thu Jun 21 20:07:40 PDT 2018; root:xnu-3248.73.11~1/RELEASE_X86_64 
> > x86_64
> >
> > 4) recon-all.log, please download at:
> >
> > https://www.dropbox.com/s/bxb2vyhz3koo83s/recon-all.log-%20Terminal%20Output%20log%2020%20Jan%202020%20.txt?dl=0
> >
> >
> >
> > Regards
> >
> > Frank
> >
> > ---
> >
> > FRANK  C Y CHAU
> >
> >
> >
> > Research assistant
> >
> > Division of Neurology
> >
> > Department of Medicine
> >
> >
> >
> > Tel: +852 6340 2553
> >
> > Fax: 2872 5828
> >
> >
> >
> > E-mail : cyfr...@hku.hk
> >
> >
> >
> >
> >
> > Rm 304, 3/F, New Clinical building, Queen Mary Hospital, 102 Pokfulam Road, 
> > Hong Kong
> >
> >
> > ___
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>
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Re: [Freesurfer] some basic questions regarding longitudinal analyses in Freesurfer

[Martin Reuter]

Hi Lara, 

if you are sure you will stick with 15fwhm, you can do either one. 
If you plan to also run analysis at different fwhm, you can first map
and then smooth at different levels. 

Either way, it should not make a big difference. 

Best, Martin

On Fri, 2020-02-21 at 15:41 +, Lara Foland-Ross wrote:
> External Email - Use Caution
> 
> Hi Martin, 
> 
> Thanks. This makes a lot of sense. I'll merge my subjects' surface
> files that have been registered to fsaverage, then follow the rest of
> the protocol listed at 
> https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels.
> 
> One quick follow up question - when I use mris_preproc to merge
> thickness files, should I merge subjects' smoothed data (e.g.,
> lh.thickness.fwhm15.fsaverage.mgh) and skip the smoothing step (run
> using mri_surf2surf)? Or should I merge unsmoothed data (e.g.,
> lh.thickness.fwhm0.fsaverage.mgh) and then smooth once merged?
> 
> Thanks again,
> Lara
> 
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Martin Reuter <
> mreu...@nmr.mgh.harvard.edu>
> Sent: Friday, February 21, 2020 1:10 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] some basic questions regarding longitudinal
> analyses  in Freesurfer
> 
> Hi Lara,
> 
> no, you should not use time point 1 as base.
> 
> You need to distinguish between the image processing part and the
> statistics post processing analysis (LME). These are two separate
> things.
> 
> For the image processing in the longitudinal pipeline, we create the
> base (=subject template). The name base can be misleading and has
> nothing to do with "baseline". That is why we try to refer to it as
> "subject_template" in most documentation now.
> Anyway, one never analyzes results of the subject template, but of
> the
> final fine-tuned time points after the -long runs.
> 
> In your case, you can simply process the images independently (cross
> sectionally) and still perform the statistical LME analysis where you
> group results from the same subject.
> 
> For measures from the stats files (aseg, aparc...) you just obtain
> those from the cross dirs with asegstats2table. For surface results
> you
> simply map everything to fsaverage (mris_preproc) and then run the
> LME.
> 
> Best, Martin
> 
> 
> On Thu, 2020-02-20 at 21:53 +, Lara Foland-Ross wrote:
> > External Email - Use Caution
> > 
> > Hi there,
> > 
> > Reposting this message (below). Would appreciate any guidance you
> > can
> > provide.
> > 
> > Thanks,
> > Lara
> > 
> > 
> > From: freesurfer-boun...@nmr.mgh.harvard.edu <
> > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Lara Foland-
> > Ross
> > 
> > Sent: Friday, February 7, 2020 12:46 PM
> > To: freesurfer@nmr.mgh.harvard.edu
> > Subject: [Freesurfer] some basic questions regarding longitudinal
> > analyses  in Freesurfer
> > 
> > External Email - Use Caution
> > 
> > Hello,
> > 
> > I'm analyzing a large dataset using an LME model to examine
> > longitudinal changes in brain structure that vary as a function of
> > group (patients vs controls). Because some participants were
> > scanned
> > several years apart in early childhood, the intra-subject
> > registration failed in the longitudinal processing stream. For this
> > reason, my data were not initially processed using the longitudinal
> > processing stream within Freesurfer. However, per this thread -
> > https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg55847.html
> >  - I still plan to use the LME model. As I understand it, this
> > model
> > assumes that the longitudinal processing stream was
> > conducted.  Therefore, I have the following questions:
> > 
> > 1. would the "base" (aka within-subject template) for each subject
> > be
> > = time point 1?
> > 2. would the "long run" for each subject be = each subject's
> > individual time points?
> > 3. assuming #1 and 2 are correct, would I need to set my directory
> > structure to match that used in the longitudinal processing stream?
> > For example, if I have 2 time points for subject 1234, and they are
> > initially labeled "1234.time1" and "1234.time2", then in order to
> > run
> > the LME model, I would create a copy of "1234.time1" and rename the
> > copy as "1234" to indicate to the software that this should be used
> > as the base. And, I would also need to rename "1234.time1" and
> > "1234.time2" as "1234.time1.long.1234" and "1234.time2.long.1234"
> > to
> > indicate that these folders should be used as the longitudinal time
> > points.
> > 
> > Does this seem appropriate?
> > 
> > Thanks in advance for your help,
> > Lara
> > 
> > Lara Foland-Ross, Ph.D.
> > Senior Research Associate and Imaging Lab Manager
> > Center for Interdisciplinary Brain Sciences Research
> > Stanford University School of Medicine
> > 401 Quarry Road, Room 1356
> > Stanford, CA