Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could not establish read access to rh.area

2024-03-12 Thread Ariko, Taylor 
External Email - Use Caution

That would be wonderful, thank you.

Best,
Taylor

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

Date: Thursday, March 7, 2024 at 9:05 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could 
not establish read access to rh.area
Yujing, you can just send Taylor a binary that can be put in the local version 
of $FREESURFER/bin
On 3/6/2024 11:45 AM, Huang, Yujing wrote:
Hi Taylor,

Thanks for sharing the data.

I see the problem now.  The first 14336 bytes of your rh.area fit SIGNA_FILE 
criteria. So, it is read as SIGNA_FILE instead of MRI_CURV_FILE.

We will have a fix in dev version. But I’m not sure how to get around this in 
FS 7.2.

Best,

Yujing

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 On Behalf Of Ariko, Taylor
Sent: Wednesday, March 6, 2024 9:47 AM
To: Freesurfer support list 

Subject: Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could 
not establish read access to rh.area


External Email - Use Caution
Hello Yujing,


If I rerun this command:

mris_place_surface --area-map ../surf/rh.white ../surf/rh.area

It says it is writing curvature file in the command line output:

writing curvature file ../surf/rh.area

Though the problem persists (mri_info says same thing as before). I have 
attached rh.white and rh.area for your review.


Many thanks,
Taylor



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>>
Date: Wednesday, March 6, 2024 at 8:37 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could 
not establish read access to rh.area
It doesn’t look like rh.area is recognized correctly. ‘mri_info rh.area’ should 
show it is a ‘curv’ file with nvertices x 1 x 1 dimensions.

I’m not sure where exactly the area values are calculated. What happen if you 
re-run this step?
mris_place_surface --area-map ../surf/rh.white ../surf/rh.area

Can you share the ?h.white and ?h.area?

Best,

Yujing







From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Ariko, Taylor
Sent: Tuesday, March 5, 2024 7:24 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could 
not establish read access to rh.area


External Email - Use Caution
Hello Yujing,


Thank you for your quick response!


When I run:

mris_calc -o rh.area.mid /path/to/subject/surf/rh.area add 
/path/to/subject/surf/rh.area.pial

I get the following error:

error: No such file or directory
error: read_signa(/Volumes/Beta/Carmen/t1/p03_8/p03_8/surf/I.001): could not 
open file
error: No such file or directory
error:
mris_calc: could not establish read access to 
'/Volumes/Beta/Carmen/t1/p03_8/p03_8/surf/rh.area'.


But when I run:

mri_info rh.area

I get the following output:

Volume information for rh.area
  type: unknown
dimensions: 831 x 10015 x 25953
   voxel sizes: -0.00, -0.00,nan
  type: SHORT (4)
   fov: 1016.473
   dof: 1
xstart: 0.0, xend: 990983162970892849632569550308376576.0
ystart: -0.0, yend: 3079152361728581627851833344.0
zstart: -0.0, zend: -3815443229699337177012458129513775104.0
TR: 0.00 msec, TE: -0.00 msec, TI: 0.00 msec, flip angle: 0.00 
degrees
   nframes: 1
   PhEncDir: UNKNOWN
   FieldStrength: 0.00
ras xform present
xform info: x_r =  -1., y_r =   0., z_r =   0., c_r = 
-18770011487391973376.
  : x_a =   0., y_a =   0., z_a =   1., c_a =nan
  : x_s =   0., y_s =  -1., z_s =   0., c_s =-0.
Orientation   : LIA
Primary Slice Direction: coronal

voxel to ras transform:
0.  -0.  nannan
   -0.  -0.  nannan
   -0.   0.  nannan
0.   0.   0. 1.

voxel-to-ras determinant nan

ras to voxel transform:
error: mat = NULL!


It appears that this is where the issue is coming from. Any ideas on why this 
is occurring? The brain is normal and has good rh.white and rh.pial surfaces.


Many thanks,
Taylor


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>>
Date: Tuesday, March 5, 2024 at 4:25 PM
To: Freesurfer support list 
mail

[Freesurfer] Thalamic segmentation with FGATIR not running

2024-03-12 Thread Amrita Pal 
External Email - Use Caution

Hi

While doing thalamic segmentation with FGATIR additional volume, I am
getting an error that
"BIAS field corrected version of additional volume found; no need to recompute
error: No such file or directory
error: WARNING: 419053 NaNs found in volume tempT1.mgz..
and I get a blank ThalamicNucleiv.12.FGATIR.mgz

Can you please help spot the error?

Thanks and regards

-- 
Amrita


Virus-free.http://secure-web.cisco.com/1KBgLFDHeUPow5GUMM81SK3Q8c-uFtm-1aqcDLFxskgRpWljrFRDiBRAtmhNWswyufnXsotW3nc4eGTo1DB3Kz3kcTwdGcWQFw2TWRIc0bOwdYl2pouygaCWpwjczO133YqKpQOMasU7fN-keWYGa7tNR-Co8h_qQQbLjm-b4nMKHxm77yF0KhalniYsXPX5vfEdo82jlh_tJkpmd3okupj8sucKCEt6Xhecau0v1EaDuZlGrddpsWhw6X_aeV-1EiQHfuH1wJzYT36bodgBjBSXF1l8usWQ4K1e8mMudeYQ_hb8KwLyNlUi6U0wlmadKPW8DGSBjH3olwA7uzVGfuA/http%3A%2F%2Fwww.avg.com

<#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could not establish read access to rh.area

2024-03-12 Thread Huang, Yujing 
[​Folder icon] 
https://partnershealthcare-my.sharepoint.com/:f:/g/personal/yhuang43_mgh_harvard_edu/EpPzvvFe_jJFvpRs1gHUEwcB_z1zoKX_V0KktTrtGvHklw?email=taylor.ariko%40miami.edu&e=nQS1oZ

I uploaded those two binaries to OneDrive. Let me know if you can access them.


From: Huang, Yujing
Sent: Tuesday, March 12, 2024 2:55 PM
To: 'Freesurfer support list' 
Subject: RE: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could 
not establish read access to rh.area

Hi Taylor,

Attached are mri_info and mris_calc from our dev version for Darwin-x86-64. 
Make a copy of your current binaries, and copy them into your 
$FREESURFER_HOME/bin. Make sure they have the execute permission.

Let me know how they work for you!

Best,

Yujing

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Ariko, Taylor
Sent: Tuesday, March 12, 2024 9:53 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could 
not establish read access to rh.area


External Email - Use Caution
That would be wonderful, thank you.

Best,
Taylor

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>>
Date: Thursday, March 7, 2024 at 9:05 AM
To: freesurfer@nmr.mgh.harvard.edu 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could 
not establish read access to rh.area
Yujing, you can just send Taylor a binary that can be put in the local version 
of $FREESURFER/bin
On 3/6/2024 11:45 AM, Huang, Yujing wrote:
Hi Taylor,

Thanks for sharing the data.

I see the problem now.  The first 14336 bytes of your rh.area fit SIGNA_FILE 
criteria. So, it is read as SIGNA_FILE instead of MRI_CURV_FILE.

We will have a fix in dev version. But I’m not sure how to get around this in 
FS 7.2.

Best,

Yujing

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 On Behalf Of Ariko, Taylor
Sent: Wednesday, March 6, 2024 9:47 AM
To: Freesurfer support list 

Subject: Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could 
not establish read access to rh.area


External Email - Use Caution
Hello Yujing,


If I rerun this command:

mris_place_surface --area-map ../surf/rh.white ../surf/rh.area

It says it is writing curvature file in the command line output:

writing curvature file ../surf/rh.area

Though the problem persists (mri_info says same thing as before). I have 
attached rh.white and rh.area for your review.


Many thanks,
Taylor



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>>
Date: Wednesday, March 6, 2024 at 8:37 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could 
not establish read access to rh.area
It doesn’t look like rh.area is recognized correctly. ‘mri_info rh.area’ should 
show it is a ‘curv’ file with nvertices x 1 x 1 dimensions.

I’m not sure where exactly the area values are calculated. What happen if you 
re-run this step?
mris_place_surface --area-map ../surf/rh.white ../surf/rh.area

Can you share the ?h.white and ?h.area?

Best,

Yujing







From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Ariko, Taylor
Sent: Tuesday, March 5, 2024 7:24 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could 
not establish read access to rh.area


External Email - Use Caution
Hello Yujing,


Thank you for your quick response!


When I run:

mris_calc -o rh.area.mid /path/to/subject/surf/rh.area add 
/path/to/subject/surf/rh.area.pial

I get the following error:

error: No such file or directory
error: read_signa(/Volumes/Beta/Carmen/t1/p03_8/p03_8/surf/I.001): could not 
open file
error: No such file or directory
error:
mris_calc: could not establish read access to 
'/Volumes/Beta/Carmen/t1/p03_8/p03_8/surf/rh.area'.


But when I run:

mri_info rh.area

I get the following output:

Volume information for rh.area
  type: unknown
dimensions: 831 x 10015 x 25953
   voxel sizes: -0.00, -0.00,nan
  type: SHORT (4)
   fov: 1016.473
   dof: 1
xstart: 0.0, xend: 990983162970892849632569550308376576.0
ystart: -0.0, yend: 3079152361728581

[Freesurfer] Postdoctoral Position on PET and structural MRI/DTI at Brown University

2024-03-12 Thread Topper, Mackenzie 
External Email - Use Caution

Position: Postdoctoral Position in Neuroimaging Research on Brain
Aging and Alzheimer’s disease

Area: Brain Aging and Alzheimer’s disease

Department: Department of Psychiatry and Human Behavior

Institution: Brown University

We are seeking a highly motivated postdoctoral researcher to lead an
NIH-funded project in the Laboratory for Cognitive and Translational
Neuroscience (Director: Dr. Hwamee Oh) at Brown University. The
project is to use amyloid and tau PET and structural MRI/DTI to study
the impact of Alzheimer’s disease pathologies on structural and
functional networks among cognitively normal older adults and patients
with cognitive impairment.

Applicants with a Ph.D. degree in cognitive neuroscience,
computational neuroscience, biomedical engineering, or a relevant field
are encouraged to apply. Prior experience with human neuroimaging in
PET and/or structural MRI, and familiarity with programming in relevant
languages (e.g., Python, MATLAB) are required. Applicants with
experience with amyloid and tau PET or diffusion weighted imaging are
especially encouraged to apply. The successful candidate is expected
to demonstrate communication skills, motivation and interest in the
area of neuroscience of cognitive and brain aging and Alzheimer’s
disease, and the ability to independently develop research questions
and work in collaboration with other team members.

A preferred start date is Summer 2024, although it can be flexible. The
position is primarily affiliated with the Department of Psychiatry and
Human Behavior at Brown University.

Interested applicants should email a brief description of research
background and career goals, and CV with a list of 3 references to Dr.
Hwamee Oh at hwamee...@brown.edu.

Contact Website:
https://secure-web.cisco.com/1NHAukz0oR4V4SHC4tbhOyQXDoh4Si5BlldXlY0aCBWiubpOMY2to5yYIo0d6UEi48mvV2wgCOZpdDEg8ePITHjLjVhAb_XmnoNURctSuJ8ps_2WyzAJdpVlJOpXkbzXS0-BCmd3fGOjmak_yqsB1VNj0KnKd9sv4XgigsPM5W2c9VTwW6OUs5u4YZSe-mxWfR4NOA0UCYoG5fWXqOi4Jf2YQH9JQ593xXtg656chX_SXrEoaycEt_ANePhKQDNggSxWW66Ege-T_olcWt_sU6nlhrteq2ItTwlfk9ktCGnnT93mdhkc27CuUW1K5HGHeM_q2vB2GLGAwuTBUTxGH-g/https%3A%2F%2Fsites.brown.edu%2Foh-ctnlab%2Favailable-positions%2F

-- 
Mackenzie Topper
Research Assistant & Lab Manager
Oh Lab
Brown University
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 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
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