[Freesurfer] Job posting: SRA at UCSD

2022-04-25 Thread Wang, Xin 
External Email - Use Caution

Imaging Researcher
University of California, San Diego.
Apply in Institution’s website 
(https://secure-web.cisco.com/1SDJQkDq6j9d8jlPgTY38dMqz5jAkszVSyrb5fr9lxdmTS2UQdtxkDv6psRu-rVLopDpJxd3C2OzndVaWjjBAWNWNoHwbdsmVrkmbosaIxM_ZWGCvQPe0IjSMG7l3jTtjO0NPUqeAiqOmPJiKHJO0taFX68-otfjv_RwThnZhIwnR36Toa9RcsKf-zc5HwogkJUJlaSIj6B02k3QfEwKgIOIa_qebnYe6MVMsWSFu6FUb8lhU9wEj6S-yjC1zYpc3orEqpmslq9hSPIUDgxJaEA6iSUOsQCc-O8NY36yhuzr3313cFFAOCTPB37o9a284/https%3A%2F%2Femployment.ucsd.edu%2Fimaging-researcher-hybrid-remote-115355%2Fjob%2F19041227)
This position will work a hybrid schedule which includes a combination of 
working both onsite and remote.
DESCRIPTION
The research project will involve multiple neuroimaging studies examining 
biomarkers of brain aging and dementia. These studies will be partially 
conducted in collaboration with the UC San Diego Shiley-Marcos Alzheimer’s 
Disease Research Center. These studies will employ structural, diffusion and 
contrast MRI, amyloid and tau PET, neuropsychological testing, and blood and/or 
CSF biomarkers, among other tools, to better understand how brain 
microstructure, vascular integrity, and neuropathology, relate to disease risk 
and cognitive decline in Alzheimer’s disease or related dementias.
Under the supervision of the project PIs (Drs. Reas and Banks), the incumbent 
will serve as a research project associate for multiple research protocols 
assessing neuroimaging biomarkers of dementia. Incumbent is responsible for 
organizing and managing brain imaging research data. Incumbent will manage 
Linux based workstations for post processing/data manipulation, and data 
analysis as well as create, maintain and update research databases. Provide 
support in project administration and publication preparation of imaging 
research. May provide assistance and have direct communication with subjects 
and families involved in research projects.
MINIMUM QUALIFICATIONS
· Bachelor's degree (psychology, neuroscience, biology, cognitive 
science, statistics, computer science or related field preferred) or equivalent 
work experience.
· Proven knowledge of human subjects research policies and procedures. 
Knowledge of the human subject consent process, and federal government 
regulations pertaining to consenting of subjects. On-line training certificate 
(acquired on job). Knowledge of IRB, and sponsored research requirements.
· Experience in a clinical trials research environment including basic 
understanding of persons with dementia, preferred experience with MRI in order 
to recruit, schedule, and test patients for clinical study subjects.
· Thorough working knowledge of medical and scientific terminology.
· Knowledge of statistical analysis of quantitative brain imaging data 
measures using SPSS, Matlab, and other statistical programs and prefer skills 
in coding.
· Strong experienced with computers (Personal computer and Macintosh). 
Skill with personal computers, word processing, spreadsheet, e-mail software, 
databases, etc. Specifically Linux OS and the Microsoft office suite (excel, 
access, powerpoint, word, etc).
· Proven ability to determine sources of clinical data, analyze the 
data and information obtained, in order to create documents and to propose 
solutions to issues and to help in developing standardized operational 
procedures.
· Proven ability in researching clinical data in preparation for grant 
applications and technical manuals, staying abreast of new research 
developments. Ability to abstract information from protocol and investigator 
brochure, which requires summarizing large quantities of data.
· Skill in assembling written narrative information using word 
processing software for documenting image analysis procedures and tracking data.
· Excellent interpersonal skills with the ability to use tact and 
diplomacy with subjects (including patients with cognitive impairment), their 
families, faculty and institutional staff, as well as when representing the 
agency in the community.
· Ability to collaborate and communicate effectively and diplomatically 
at all organizational levels, both verbally and in writing. Ability to work 
professionally and effectively with a diverse population, including the 
business community, academicians, staff and students.
· Excellent record keeping, database management, detail oriented, 
logical, methodological approach to problem solving, strong process 
orientation, strong administrative and organizational skills with demonstrated 
ability to prioritize assignments, maintain workflow, and work productively in 
meeting critical deadlines and milestones.
PREFERRED QUALIFICATIONS
· Working knowledge of UCSD Human Research Protections Program policies 
and Procedures.
SPECIAL CONDITIONS
· Employment is subject to a criminal background check and 
pre-employment physical.

Re: [Freesurfer] Cortical depth at each cortical voxel

2022-04-25 Thread Fotiadis, Panagiotis 
External Email - Use Caution

Hi Iman,

Apologies for the follow up! I had a couple questions concerning the software:


  1.  Concerning the MLI_thickness.m function: I used a binary mask of the 
cortical ribbon (= I) as its first input and L (where L = 
makeLineSegments(round(.2*size(I,1)) ) as the second input (similarly to the 
suggestion in EXAMPLE.m file). I tried different radii as well for the 
makeLineSegments function and the thickness results are highly linear to each 
other. Do those inputs seem reasonable in this case (i.e., for real 3D MRI 
scans), in your opinion?

  2.  Concerning the cortical depth calculation for each voxel: Unless I’m 
mistaken, the (cortical depth = Thickness/2 – SkeletonDistance) equation would 
give me the cortical depth of each voxel from the closest surface layer, right? 
 So for instance, if my voxel of interest were “above” the skeleton (i.e., the 
middle layer of the cortical ribbon), then the above equation would give out 
its distance from the surface layer that is also above the skeleton, whereas if 
my voxel were “below” the skeleton, then the aforementioned equation would give 
its distance from the surface layer that is also below the skeleton, right?

Would there be, however, a way to compute the cortical depth of each cortical 
voxel from the outer surface layer of the cortical ribbon? I believe that would 
be distance t1(v) mentioned in the equations and text in p. 3199 of your paper, 
but I unfortunately wasn’t able to pinpoint that variable in the scripts. Is 
that variable hard-coded in the scripts, or would you recommend that I follow a 
different approach to calculate that (for instance set up a conditional 
argument where I use cortical depth = Thickness/2 – SkeletonDistance if the 
voxel is above the skeleton layer, and cortical depth = Thickness/2 + 
SkeletonDistance if the voxel is below the skeleton layer)?

Thank you again very much for your time and help!

Best,
Panos

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Aganj, Iman 

Date: Thursday, April 21, 2022 at 1:02 PM
To: Freesurfer support list 
Subject: [External] Re: [Freesurfer] Cortical depth at each cortical voxel
Of course! Please let me know if you have any questions about the toolbox.

Best,
Iman

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Fotiadis, Panagiotis
Sent: Thursday, April 21, 2022 12:32 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Cortical depth at each cortical voxel

Hi Iman,

That is extremely helpful, thank you very much (also the paper is a great read)!

Best,
Panos


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Aganj, Iman 
mailto:iag...@mgh.harvard.edu>>
Date: Thursday, April 21, 2022 at 12:06 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [External] Re: [Freesurfer] Cortical depth at each cortical voxel
Hi Panos,

You can do such a volumetric analysis using this toolbox:

Code:  
https://secure-web.cisco.com/1aYbkYK9EB8dLkrEX21j0egOZL7nT0mvGS7CHiROVK3xraHGSG2VrtOcDKOyQ8-xb2I_JVqsnSPkCEVl9_QhdaN-riOqph5K5EH48IjtNNVbrioiUpWYX5z1pluutFoJJyhlSn2yyEjQlR7eEatlb1ltPK8DzELeQfHlFCaBXUnjH6blpyshvyerzuvEmSnLWjAJCTFU9q5ZzJtViq-04A_xpF6d8sR9qmdAzG9t_te24znRtJC_fFfC1Rlb8DEGLvMowwZuqQd3euCP7F_ZZYaSyYitM9-YZ1UugldA3PPF6_lUr78lxAM0-Q5ey8Y0E2UHZWlf2wA6tJtKmopBX1g/https%3A%2F%2Fwww.nitrc.org%2Fprojects%2Fthickness
Paper:  
https://secure-web.cisco.com/15F5CSKI6vBb-t2e4UEugAKn12N8XZD3Scziuo982hS_6tzDCG5BqIv-W5980bgLouVEKH6ds4fLPr7-KJq5F1SrU0MotzgxZ5Bn-jhwr3uEFJuQOd0W9lLmNVzTo8xi68TZGk8YegYf7YGtDePZbv1pK_-0cQefChxtoZ8uYImJbHXgxTQTc7-A6gsZRlpee5k2NhiXaOaLGlLjNY2HmrO_SrydNiWSgWgCaJZJOkZq4Gb3WUgwH0_1Yo_Dvc8wnZ8A73DFAVLHqtop4Rjh_g4K8lLVZDoLVZH-RCXsWDPkscqU4fu0u93fhrehzKkRkvUtDmckE8aarbt-dHJa4IQ/https%3A%2F%2Fonlinelibrary.wiley.com%2Fdoi%2Fepdf%2F10.1002%2Fhbm.20740

You can apply the MLI_thickness function to the gray matter (soft or binary) 
mask, which returns the layer thickness at each voxel (Thickness) and the 
distance of each voxel to the center of the layer (SkeletonDistance). Cortical 
depth would then be SkeletonDistance at the given voxel subtracted from half of 
Thickness (at the voxel, or preferably on the skeleton for better accuracy). A 
tutorial is included in the EXAMPLE file.

Best,
Iman

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Fotiadis, Panagiotis
Sent: Thursday, April 21, 2022 11:48 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Cortical depth at each cortical voxel

Hi FS experts,

I was wondering whether there was a way to assign each cortical voxel within 
the T1w (volumetric) scan an index corresponding to its “cortical depth.” I 
have essentially taken the cortical ribbon .mgz file, assigned each

Re: [Freesurfer] recon-all error

2022-04-25 Thread Rebecca Elizabeth Cooper 
External Email - Use Caution

Dear Yujing,



Thank you kindly for your support. Please see attached.



Kind regards,

Rebecca
 Downloads.zip




*From:* freesurfer-boun...@nmr.mgh.harvard.edu <
freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Huang, Yujing
*Sent:* Tuesday, 26 April 2022 8:34 AM
*To:* Freesurfer support list 
*Subject:* Re: [Freesurfer] recon-all error



Hi Rebecca,



We would like to understand why those dicom files are not recognized by
Freesurfer. If it is possible, can you provide us some of those dicom files
to debug?



Thanks.



Yujing



*From:* freesurfer-boun...@nmr.mgh.harvard.edu <
freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Huang, Yujing
*Sent:* Saturday, April 23, 2022 1:50 PM
*To:* 'Freesurfer support list' 
*Subject:* Re: [Freesurfer] recon-all error



Hi Rebecca,



Thank you for the information.



I'm wondering if you would like to try converting those dicom using
dcm2niix to .nii, and then feed .nii to recon-all pipeline.



You can download dcm2niix here:

https://secure-web.cisco.com/1Swb2oS6hDVyvEnob9HiqJ3vv48refI6wmxC3PAZbvpWnceOxMkeYxcebCPqkVaLSNgG6VxoxEz26TRJ4RxBV5jWaqFMRTq7XZhd2c0Aud7Bdss9XZxI137TQO0m2MTefk54kPhZ0opUewOFNdWPHqMvsXVewXnvr0KVTzmDNGSqfmIJ08UCbtC-gAhcyvbGqxK7FfDhAXJvsv7xPxYrFTxyoZmRG9wYZF0shHunkZOs5gUch8cDlYjiA6sS6YKaGt0hgNEsA6edCTApA_vm7_9wkT1Gis0d8FKje6z4qWWKqjtAwxjbaf-QhFvyzOVwlxWZqVgFJkIWZxVH4furhFQ/https%3A%2F%2Fgithub.com%2Frordenlab%2Fdcm2niix



I use the following command to do conversion: dcm2niix -o  -f
"%s_%p" 



Please note that  needs to be specified as last parameter.  '-f
<>' specifies output file name format - "%s_%p" will have series no +
protocol as prefix.



Hope these helps.



Best,



Yujing




--

*From:* freesurfer-boun...@nmr.mgh.harvard.edu <
freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of
coope...@student.unimelb.edu.au 
*Sent:* Saturday, April 23, 2022 2:44 AM
*To:* 'Freesurfer support list' 
*Subject:* Re: [Freesurfer] recon-all error



*External Email - Use Caution*

Hi Yujing,



I guess not. This is the output:



cooperr@marge:/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms$
mri_probedicom --i
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256



ERROR:
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256
is not a dicom file or some other problem



Entering IsDICOM
(/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256)



ERROR:
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256
is not a dicom file or some other problem



I also ran straight to the dicom files themselves, with the same response:



cooperr@marge:/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms$
mri_probedicom --i
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001



ERROR:
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001
is not a dicom file or some other problem



Entering IsDICOM
(/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001)

Opening
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001
as part10

DCM_FILEOPENFAILED

   20092 DCM failed to open file:
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001
in DCM_OpenFile

Opening as littleendian

DCM_FILEOPENFAILED

Opening as bigendian

DCM_FILEOPENFAILED

Opening as format conversion

DCM_ILLEGALOPTION

Leaving IsDICOM
(/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001)



ERROR:
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001
is not a dicom file or some other problem



Thank you,



Rebecca





*From:* freesurfer-boun...@nmr.mgh.harvard.edu <
freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Huang, Yujing
*Sent:* Friday, 22 April 2022 11:11 PM
*To:* 'Freesurfer support list' 
*Subject:* Re: [Freesurfer] recon-all error



Hi Rebecca,



I’m wondering if the dicom files are being recogniz

Re: [Freesurfer] recon-all error

2022-04-25 Thread Huang, Yujing 
Hi Rebecca,

We would like to understand why those dicom files are not recognized by 
Freesurfer. If it is possible, can you provide us some of those dicom files to 
debug?

Thanks.

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Huang, Yujing
Sent: Saturday, April 23, 2022 1:50 PM
To: 'Freesurfer support list' 
Subject: Re: [Freesurfer] recon-all error

Hi Rebecca,

Thank you for the information.

I'm wondering if you would like to try converting those dicom using dcm2niix to 
.nii, and then feed .nii to recon-all pipeline.

You can download dcm2niix here:
https://github.com/rordenlab/dcm2niix

I use the following command to do conversion: dcm2niix -o  -f 
"%s_%p" 

Please note that  needs to be specified as last parameter.  '-f <>' 
specifies output file name format - "%s_%p" will have series no + protocol as 
prefix.

Hope these helps.

Best,

Yujing



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of 
coope...@student.unimelb.edu.au 
mailto:coope...@student.unimelb.edu.au>>
Sent: Saturday, April 23, 2022 2:44 AM
To: 'Freesurfer support list' 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] recon-all error


External Email - Use Caution

Hi Yujing,



I guess not. This is the output:



cooperr@marge:/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms$ 
mri_probedicom --i 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256



ERROR: 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256
 is not a dicom file or some other problem



Entering IsDICOM 
(/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256)



ERROR: 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256
 is not a dicom file or some other problem



I also ran straight to the dicom files themselves, with the same response:



cooperr@marge:/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms$ 
mri_probedicom --i 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001



ERROR: 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001
 is not a dicom file or some other problem



Entering IsDICOM 
(/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001)

Opening 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001
 as part10

DCM_FILEOPENFAILED

   20092 DCM failed to open file: 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001
 in DCM_OpenFile

Opening as littleendian

DCM_FILEOPENFAILED

Opening as bigendian

DCM_FILEOPENFAILED

Opening as format conversion

DCM_ILLEGALOPTION

Leaving IsDICOM 
(/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001)



ERROR: 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001
 is not a dicom file or some other problem



Thank you,



Rebecca





From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Huang, Yujing
Sent: Friday, 22 April 2022 11:11 PM
To: 'Freesurfer support list' 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] recon-all error



Hi Rebecca,



I'm wondering if the dicom files are being recognized.



Can you run the following command with some dicom files in the directory?

mri_probedicom --i  --d filetype



(Replace  with full path to dicom file.)



Thanks.



Yujing



From: coope...@student.unimelb.edu.au 
mailto:coope...@student.unimelb.edu.au>>
Sent: Friday, April 22, 2022 1:34 AM
To: Huang, Yujing mailto:yhuan...@mgh.harvard.edu>>; 
'Freesurfer support list' 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: RE: [Freesurfer] recon-all error



External Email - Use Caution

Dear Yujing,



Thank you for your reply.

  1.  Confirmed I am running Freesurfer 6.0.
  2.  I am running both commands from within the individual subject directory 
(ID=1003156). The parent folder contains several folders all labelled with 
different subject IDs, and within each contains the dicom directories.
  3.  I attempted this and received the error:



/Applications/freesurfer_v6/bin/dcmunpack -src 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x

Re: [Freesurfer] Beta values (resubmitting)

2022-04-25 Thread Laura Willers de Souza 
External Email - Use Caution

Thanks so much!

I would also like to confirm that I am interpreting the beta values correctly 
for a second model.

Model 2: Two Groups, One Covariate

Contrasts (DOSS): difference between the group intercepts; covariate effect.


The fsgd file looks like this:

GroupDescriptorFile 1

Title CU_CI_CSF
MeasurementName thickness
Class CU
Class CI
Variables cortisolCSF
Input 011_S_0003_S9128 CI 2.397895273
Input 022_S_0004_S9233 CI 2.772588722
Input 011_S_0005_S9137 CU 3.044522438
Input 011_S_0008_S9196 CU 2.397895273
Input 011_S_0010_S8800 CI 2.151762203

... (n=300)

The file with the beta values contains 3 lines (image below).
[cid:image003.png@01D858C5.3392CD10]

  *   The first line would be the beta value for the intercept of the 1st 
group; the second line for the intercept of the 2nd group; and the third line 
for the slope of the covariate?
 *   Thus the glm equation for the 1st cluster would be:
 *   1st group  cortical thickness = 2.64 - 0.12X + n
 *   2nd group --- cortical thickness = 2.54 – 0.12X + n


Am I interpreting correctly?


Thank you very much for all the help!


Laura Willers de Souza

Master Student in Biochemistry

Zimmer Lab - Federal University of Rio Grande do Sul

- Porto Alegre/RS - Brazil


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Re: [Freesurfer] Does PETSurfer calculate ROI-wise values by averaging?

2022-04-25 Thread Zhener Zhang 
External Email - Use Caution

Hi Douglas,

Thanks! We ran the following for one of our subjects:
mri_gtmpvc --i sz013_BPnd.nii --reg sz013_BPnd.reg.lta --seg 
~/sz013/mri/gtmseg.mgz --default-seg-merge --no-tfe --no-rescale --o 
~/sz013/gtmpvc.output

Thanks,
ZZ
On Apr 24, 2022, 13:45 -0700, Zhener Zhang , wrote:
Hi Douglas,

Thank you for the reply!

The mri_gtmpvc outputs were expected and there was no reason for us to suspect 
that something was wrong. I was just curious as to the general process behind 
PETSurfer’s ROI-wise value calculation. Was each ROI-wise output generated by 
averaging across all voxels of an ROI?

Thanks!
Zhener Zhang


On Apr 20, 2022, 09:50 -0700, Zhener Zhang , wrote:
Hello,

I have a question regarding the way ROI-wise values are calculated using 
PETSurfer.

We ran the PETSurfer pipeline with PVC=0 and noticed that a relatively small 
ROI like Putamen has one of the highest values of regional distribution of a 
PET tracer.

Is it the case that the PETSurfer ROI-wise value outputs were averaged, or 
normalized by each ROI’s volume? And what measure was divided, GM volume, 
number of voxels, or something else?

Thank you in advance!

Best regards,
Zhener

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Re: [Freesurfer] Orthographic camera in FreeView

2022-04-25 Thread Anderson M. Winkler 
External Email - Use Caution

Hi Ruopeng,

Thank you for adding this feature! Much appreciated!

It doesn't seem to have worked quite yet, though:

*freeview: symbol lookup error:
/gpfs/gsfs6/users/EDB/opt/freesurfer/7.2.0/lib/qt/plugins/platforms/../../lib/libQt5XcbQpa.so.5:
undefined symbol: FT_Get_Font_Format*

I tried in two ways: (a) replacing freeview from 7.2.0 as per the
instructions, and also (b) running from the whole dev version. Both gave
the same error message.

Since we are at it :-) may I ask another related feature? In tksurfer, if
we had a bigger brain and a smaller brain, and opened them in separate
instances, we'd still see the bigger as bigger than the smaller. That is,
the default scaling was fixed regardless of the size of the surfaces. WIth
FreeView, it appears that by default the surfaces are scaled to cover some
fixed amount of the window (say, maybe 90% or so). It's fine as is just for
browsing, but if we call in a script and take screenshots, we have the
impression that the brains all have the same size, even when they differ
(sometimes substantially).

Thanks again!

All the best,

Anderson


On Mon, Apr 25, 2022 at 10:18 AM Wang, Ruopeng 
wrote:

> Hi Anderson,
>
> I’ve added “Orthographic view” option for the 3D viewport. It can be
> activated from right click menu in the view. You can download the latest
> build of freeview here:
>
> https://secure-web.cisco.com/1Jf501D91H-op1cklH0NEXBp4CngHCC6k-BcsMwioDfsUbaU_bffOu_8X5v2xH1F1WjtgGxCQwp3712llE8H8Qz6AOEAPuPeJo03QWo3_6tpvIkbvPETjkj-KeALjtWz71PfVBDhpY5MfBWgU4IlUdFwPw_-knEzNDs2qDWARMZgCzDbDy83KdPp2Pp-bSpB0Qzbo-fUD5VNX5j5aseiXXq6NzewV0_9fWfpWhiyJ8-e9Y5Xd0Uq4pA_dy7_uJ_5C588pMrfwckNIZ1gC4lVRadF16btGwGs9hUVgDRmhmji62KsNkNffeJPyRul0m-HnNUO4X89Epb7M4agLwMtb3A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FUpdateFreeview
>
> Best,
> Ruopeng
>
> On Apr 15, 2022, at 10:23 AM, Anderson M. Winkler 
> wrote:
>
> External Email - Use Caution
>
> Hi all,
>
> Is there a way to configure the camera in the 3D viewport in FreeView to
> use an orthographic projection instead of perspective (which currently is
> the default)?
>
> Orthographic used to be the default in tksurfer. A nice feature about it
> is that when we zoom, the effect is the same as scaling the projection (as
> opposed to introducing distortions). It makes a difference when we are
> collating screen captures for a figure, for example.
>
> I checked the help but don't seem to find any related option (in 7.2).
>
> Thanks!
>
> All the best,
>
> Anderson
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> sender of this message immediately.  Continuing

Re: [Freesurfer] Orthographic camera in FreeView

2022-04-25 Thread Wang, Ruopeng 
Hi Anderson,

I’ve added “Orthographic view” option for the 3D viewport. It can be activated 
from right click menu in the view. You can download the latest build of 
freeview here:

https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview

Best,
Ruopeng

On Apr 15, 2022, at 10:23 AM, Anderson M. Winkler 
mailto:wink...@fmrib.ox.ac.uk>> wrote:


External Email - Use Caution

Hi all,

Is there a way to configure the camera in the 3D viewport in FreeView to use an 
orthographic projection instead of perspective (which currently is the default)?

Orthographic used to be the default in tksurfer. A nice feature about it is 
that when we zoom, the effect is the same as scaling the projection (as opposed 
to introducing distortions). It makes a difference when we are collating screen 
captures for a figure, for example.

I checked the help but don't seem to find any related option (in 7.2).

Thanks!

All the best,

Anderson
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The information in this e-mail is intended only for the person to whom it is 
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[Freesurfer] FreeSurfer 7Zip archive passcode

2022-04-25 Thread Katharina Hense 
External Email - Use Caution

Hello,
 
I'm trying to expand the 7Zip archive for FreeSurfer on the VirtualBox. Can I 
get the passcode for
FS_7_2_0_Ubuntu_18_04_06.ova.7z?
 
Sincerely,
Katharina
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