[Freesurfer] make_average_surface with unique surface

[Gabrielle-Ann Torre]

External Email - Use Caution

Hello developers,

I'm attempting to compute a group average of a surface generated using
mris_vol2surf. The generated surface is a ratio of T1-T2, as described in
Glasser and Van Essen, 2011. Such a surface exists as a symbolic link in
each subjects' /surf folder.

When I apply make_average_surface to a set of subjects, I get the following
error:

$Id: make_average_surface,v 1.62 2016/02/16 17:17:20 zkaufman Exp $

Wed Jan 29 19:14:37 EST 2020

/projectnb/perlab/projects/DNAP/brains/alex4

output ddir is /projectnb/perlab/projects/DNAP/brains

uid=323856(gat) gid=275709(perpwm) groups=275709(perpwm),275954(perlab)



make_average_surface



Wed Jan 29 19:14:37 EST 2020

/projectnb/perlab/projects/DNAP/brains/alex4

/share/pkg.7/freesurfer/6.0/install/bin/make_average_surface

--out alex4 --subjects p0110 p0246 --surf-reg surf.t1t2.ratio

input subjects: p0110 p0246

output subject: alex4

mri_add_xform_to_header -c auto
/projectnb/perlab/projects/DNAP/brains/alex4/mri/mni305.cor.mgz
/projectnb/perlab/projects/DNAP/brains/alex4/mri/mni305.cor.mgz

INFO: extension is mgz


#@# Making lh registration template -

/projectnb/perlab/projects/DNAP/brains/alex4

mris_make_template -norot -annot aparc lh surf.t1t2.ratio p0110 p0246
lh.reg.template.tif

not aligning hemispheres before averaging.

zeroing medial wall in aparc

creating new parameterization...


processing subject p0110 (1 of 2)

reading spherical surface
/projectnb/perlab/projects/DNAP/brains/p0110/surf/lh.surf.t1t2.ratio...

MRISread(/projectnb/perlab/projects/DNAP/brains/p0110/surf/lh.surf.t1t2.ratio):
could not open file

No such file or directory

mris_make_template: could not read surface file
/projectnb/perlab/projects/DNAP/brains/p0110/surf/lh.surf.t1t2.ratio

No such file or directory

I have tried this using both "lh.surf.t1t2.ratio" and "surf.t1t2.ratio" as
the name of the surface but neither works. I have also tried it with and
without the .mgz file extension.

Not sure what the error is or why my surface is unreadable. Does
mris_vol2surf not generate surfaces that can be used as alternate surfaces
using the --surf-reg flag?

Any help would be appreciated!

Best,
Gabrielle

-- 
Gabrielle-Ann Torre, Ph.D.

Center for the Study of Learning
Georgetown University Medical Center
Building D, Suite 150
W: *202-687-2823*
C:

*520-393-9252 *
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Cannot load overlay through GUI

[Fengdan Ye]

External Email - Use Caution

Dear FreeSurfer experts:

I encountered a weird problem when trying to load overlay through the Freeview 
GUI. I opened a surface file through terminal command “freeview -f lh.pial”, 
and then in the GUI I clicked Overlay -> load generic -> Select overlay file. 
After I selected the overlay file Freeview stopped responding. The following 
messages showed up in terminal:

2020-01-29 16:13:31.469 Freeview[1067:24667] warning:  determined it was necessary to 
configure <_NSFunctionRowPanel: 0x7fee49fe2c70> to support remote view vibrancy
2020-01-29 16:13:31.491 Freeview[1067:24667] warning:  determined it was necessary to 
configure <_NSFunctionRowPanel: 0x7fee49fe2c70> to support remote view vibrancy

The first message showed up when I clicked on the folder icon to select overlay 
file, and the second message showed up when I clicked “Open” after I selected 
overlay file.

However, if I just ran “freeview -f rh.pial:overlay=”, the 
viewer could open the overlay file without problem. 

Is there any fix for this GUI problem? I am on macOS Catalina Version 10.15.2.

Thank you,
Fengdan

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Job opening: MRI Senior Research Specialist at OHIO STATE UNIVERSITY

[Xiangrui Li]

External Email - Use Caution

MRI Senior Research Specialist

OHIO STATE UNIVERSITY



The Center for Cognitive and Behavioral Brain Imaging
 (CCBBI), in the College of Arts and Sciences,
seeks an MRI (Magnetic Resonance Imagining) Senior Research Specialist to
join our team. The College of Arts and Sciences is the largest college and
the academic heart of the university. The College hosts 81 majors. With 38
departments, 20+ world-class research centers, and more than 2,000 faculty
and staff members, students have the unique opportunity to study with the
best artists, scholars, and scientists in their field.  The College values
diversity and offers a supportive, open, and inclusive community.



The CCBBI, directed by Dr. Ruchika Prakash, is a state-of-the art imaging
center, housing a research- dedicated 3T Siemens Prisma scanner and
supporting principal investigators across the university conducting
scientific investigations related to human and animal imaging. The MRI
Senior Research Specialist remains informed of the latest technical
developments in the field of functional MRI, and communicates these
developments to users of the facility, both in-person and through research
seminars; meets frequently with center users to learn about current and
future needs as pertaining to sequences or fMRI techniques; and actively
engages in the development and use of novel fMRI techniques to improve the
technical caliber of the center; provides technical support to current and
new pilot and funded research projects at the center; assists center users
to optimize MRI, fMRI, and DTI sequences for different experimental needs;
works with users to develop custom-tailored sequences; participates in the
teaching mission of the center and educates users in image acquisition,
processing, and data analysis through comprehensible presentations in
research seminars and user workshops; participates with other CCBBI staff
in teaching the annual Introduction to fMRI course every spring; maintains
proper functioning of the Siemens Prisma MRI system, including quality
checks, and related hardware in the facility, and debugs any hardware
problem(s), and interfaces with representatives of various hardware vendors
to find solutions to problem(s); works with the CCBBI team to maintain and
monitor the safety of the participants and the fMRI facility; position
available for one year with the possibility of extension based on
satisfactory performance and availability of funds.



Successful candidates must have earned a Doctoral degree in MR physics,
biomedical engineering, electrical engineering or related field; research
experience in a technical field closely related to MRI, fMRI, and DTI;
experience in managing MRI system(s).



If you are interested in being considered for the position, review the full
job description and qualifications and apply online at
https://www.jobsatosu.com, under job listing #457097 and submit a cover
letter detailing background and experiences, a CV, the expected date of
availability, and the names and contact of three references.



If you have questions about the position or the center, please contact Dr.
Ruchika Prakash at prakash...@osu.edu



CCBBI Website: https://ccbbi.osu.edu/



*To build a diverse workforce, The Ohio State University encourages
applications from all individuals. Ohio State is an Equal
Opportunity/Affirmative Action Employer. All qualified applicants will
receive consideration for employment without regard to age, race, color,
religion, sex, sexual orientation, gender identity, national origin,
disability status, or protected veteran status.*
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] format bvalues bvectors tracula

[Renew Andrade]

External Email - Use Caution

Dear FreeSurfer experts:I have tried to run tracula -prep but I cannot get to 
no where for the moment. I keep receiving this error. I assumed numbers had to 
be aligned in rows and columns. But none either that or one space in between 
seems to work. I don't know what format means with respect to bvalues o 
bvectors. It is not clear enough to me in the tutorial how do I have to fix the 
issue. 

Sincerely, 
Andrade. 


root@andraderenew:/home/andraderenew# trac-all -prep -c 
'/media/andraderenew/backup/image_databases/processed_data/freesurfer_preprocessed/dmrirc.IXI'
 
Too many ('s.
INFO: SUBJECTS_DIR is 
/media/andraderenew/backup/image_databases/processed_data/freesurfer_preprocessed
INFO: Diffusion root is 
/media/andraderenew/backup/image_databases/processed_data/freesurfer_preprocessed
Actual FREESURFER_HOME /usr/local/freesurfer
INFO: FreeSurfer build stamps do not match
Subject Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
INFO: current FREESURFER_HOME does not match that of previous processing.
    Current: /usr/local/freesurfer
    Previous: /Applications/freesurfer
trac-preproc -c 
/media/andraderenew/backup/image_databases/processed_data/freesurfer_preprocessed/IXI_25_Guys_T1/scripts/dmrirc.local
 -log 
/media/andraderenew/backup/image_databases/processed_data/freesurfer_preprocessed/IXI_25_Guys_T1/scripts/trac-all.log
 -cmd 
/media/andraderenew/backup/image_databases/processed_data/freesurfer_preprocessed/IXI_25_Guys_T1/scripts/trac-all.cmd
#-
/usr/local/freesurfer/bin/trac-preproc 
#-
#@# Image corrections mié ene 29 17:42:22 CET 2020
mri_convert --bvec-voxel 
/media/andraderenew/backup/image_databases/IXI_dataset/guest-20191220_131017/25_Guys/DTI/NIfTI/IXI025-Guys-0852-DTI-00.nii.gz
 
/media/andraderenew/backup/image_databases/processed_data/freesurfer_preprocessed/IXI_25_Guys_T1/dmri/dwi_orig.nii.gz
mri_convert.bin --bvec-voxel 
/media/andraderenew/backup/image_databases/IXI_dataset/guest-20191220_131017/25_Guys/DTI/NIfTI/IXI025-Guys-0852-DTI-00.nii.gz
 
/media/andraderenew/backup/image_databases/processed_data/freesurfer_preprocessed/IXI_25_Guys_T1/dmri/dwi_orig.nii.gz
 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from 
/media/andraderenew/backup/image_databases/IXI_dataset/guest-20191220_131017/25_Guys/DTI/NIfTI/IXI025-Guys-0852-DTI-00.nii.gz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998725, -0.0503472, 0.00377193)
j_ras = (-0.0504772, 0.994141, -0.0955763)
k_ras = (-0.00106217, 0.0956448, 0.995415)
writing to 
/media/andraderenew/backup/image_databases/processed_data/freesurfer_preprocessed/IXI_25_Guys_T1/dmri/dwi_orig.nii.gz...
cp 
/media/andraderenew/backup/image_databases/IXI_dataset/guest-20191220_131017/25_Guys/DTI/bvec/gradients.txt
 
/media/andraderenew/backup/image_databases/processed_data/freesurfer_preprocessed/IXI_25_Guys_T1/dmri/dwi_orig.bvecs
ERROR: Must specify input table of b-values
Linux andraderenew 5.0.0-37-generic #40~18.04.1-Ubuntu SMP Thu Nov 14 12:06:39 
UTC 2019 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at mié ene 29 17:42:22 CET 2020









dmrirc.IXI
Description: Binary data
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] TRACULA Preprocessing Error

[Yendiki, Anastasia]

Thanks, Ameen. We'll look into this and let you know.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Al Qadi, Ameen 

Sent: Wednesday, January 29, 2020 11:04:46 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] TRACULA Preprocessing Error


External Email - Use Caution

Hi Anastasia,

There wasn't a directory called "elmo.2005" in diffusion_recons, only a 
directory called "Diff001". I had to copy the elmo.2005 directory from 
diffusion_tutorial to diffusion_recons to get tract-all to run.

Best,
Ameen

On Tue, Jan 28, 2020 at 8:48 PM Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:
Hi Ameen - diffusion_recons/elmo.2005 should have the freesurfer recon of the 
T1 data and diffusion_tutorial/elmo.2005 should have the diffusion data. Can 
you confirm if this was in what you downloaded?

Thanks!
a.y

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Al Qadi, Ameen 
mailto:ameen.alq...@icahn.mssm.edu>>
Sent: Tuesday, January 28, 2020 5:38 PM
To: freesurfer@nmr.mgh.harvard.edu 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] TRACULA Preprocessing Error


External Email - Use Caution

Hi Freesurfer Developers,

I downloaded the Freesurfer tutorial data to run the TRACULA tutorial, and 
encountered a number of issues:

1. When running trac-all, I get the following error:

trac-all -prep -c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial
INFO: SUBJECTS_DIR is 
/zstore/data/aalqadi/aalqadi/tutorial_data/diffusion_recons
INFO: Diffusion root is 
/zstore/data/aalqadi/aalqadi/tutorial_data/diffusion_tutorial
Actual FREESURFER_HOME /usr/local/freesurfer
ERROR: cannot find 
/zstore/data/aalqadi/aalqadi/tutorial_data/diffusion_recons/elmo.2005

I found the elmo.2005 directory in diffusion_tutorial, and not 
diffusion_recons. Unsure why this happened, I copied all the data from 
diffusion_tutorial to diffusion_recons.

2. After re-running trac-all, the following error appeared:

mri_convert --bvec-voxel 
/zstore/data/aalqadi/aalqadi/tutorial_data/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm
 
/zstore/data/aalqadi/aalqadi/tutorial_data/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz
mri_convert.bin --bvec-voxel 
/zstore/data/aalqadi/aalqadi/tutorial_data/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm
 
/zstore/data/aalqadi/aalqadi/tutorial_data/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz
ERROR: file 
/zstore/data/aalqadi/aalqadi/tutorial_data/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm
 does not exist
trac-preproc exited with ERRORS at Tue 28 Jan 2020 10:21:41 PM UTC

The issues with mri_convert stemmed from the failure to locate the 
dwi_orig.nii.gz file in diffusion_tutorial/elmo.2005/dmri/. The dmri 
subdirectory did not have the .gz file, so I was wondering if there was an 
issue with the tutorial data? (Couldn't find the .gz file anywhere else, 
re-downloaded the data and the same error showed up).

Any guidance would be much appreciated. The log file for error #2 is attached.

Best,
Ameen
--
Ameen Al Qadi
MSBS Candidate
Icahn School Of Medicine at Mount Sinai '20
+1-646-500-1521
ameen.alq...@icahn.mssm.edu
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


--
Ameen Al Qadi
MSBS Candidate
Icahn School Of Medicine at Mount Sinai '20
+1-646-500-1521
ameen.alq...@icahn.mssm.edu
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] TRACULA Preprocessing Error

[Al Qadi, Ameen]

External Email - Use Caution

Hi Anastasia,

There wasn't a directory called "elmo.2005" in diffusion_recons, only a
directory called "Diff001". I had to copy the elmo.2005 directory from
diffusion_tutorial to diffusion_recons to get tract-all to run.

Best,
Ameen

On Tue, Jan 28, 2020 at 8:48 PM Yendiki, Anastasia 
wrote:

> Hi Ameen - diffusion_recons/elmo.2005 should have the freesurfer recon of
> the T1 data and diffusion_tutorial/elmo.2005 should have the diffusion
> data. Can you confirm if this was in what you downloaded?
>
> Thanks!
> a.y
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Al Qadi, Ameen <
> ameen.alq...@icahn.mssm.edu>
> *Sent:* Tuesday, January 28, 2020 5:38 PM
> *To:* freesurfer@nmr.mgh.harvard.edu 
> *Subject:* [Freesurfer] TRACULA Preprocessing Error
>
>
> External Email - Use Caution
>
> Hi Freesurfer Developers,
>
> I downloaded the Freesurfer tutorial data to run the TRACULA tutorial, and
> encountered a number of issues:
>
> 1. When running trac-all, I get the following error:
>
> trac-all -prep -c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial
> INFO: SUBJECTS_DIR is
> /zstore/data/aalqadi/aalqadi/tutorial_data/diffusion_recons
> INFO: Diffusion root is
> /zstore/data/aalqadi/aalqadi/tutorial_data/diffusion_tutorial
> Actual FREESURFER_HOME /usr/local/freesurfer
> ERROR: cannot find
> /zstore/data/aalqadi/aalqadi/tutorial_data/diffusion_recons/elmo.2005
>
> I found the elmo.2005 directory in *diffusion_tutorial*, and not
> *diffusion_recons*. Unsure why this happened, I copied all the data
> from diffusion_tutorial to diffusion_recons.
>
> 2. After re-running trac-all, the following error appeared:
>
> mri_convert --bvec-voxel
> /zstore/data/aalqadi/aalqadi/tutorial_data/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm
> /zstore/data/aalqadi/aalqadi/tutorial_data/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz
> mri_convert.bin --bvec-voxel
> /zstore/data/aalqadi/aalqadi/tutorial_data/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm
> /zstore/data/aalqadi/aalqadi/tutorial_data/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz
>
> ERROR: file
> /zstore/data/aalqadi/aalqadi/tutorial_data/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm
> does not exist
> trac-preproc exited with ERRORS at Tue 28 Jan 2020 10:21:41 PM UTC
>
> The issues with mri_convert stemmed from the failure to locate the
> * dwi_orig.nii.gz* file in diffusion_tutorial/elmo.2005/dmri/. The dmri
> subdirectory did not have the .gz file, so I was wondering if there was an
> issue with the tutorial data? (Couldn't find the .gz file anywhere else,
> re-downloaded the data and the same error showed up).
>
> Any guidance would be much appreciated. The log file for error #2 is
> attached.
>
> Best,
> Ameen
> --
> Ameen Al Qadi
> MSBS Candidate
> Icahn School Of Medicine at Mount Sinai '20
> +1-646-500-1521
> ameen.alq...@icahn.mssm.edu
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



-- 
Ameen Al Qadi
MSBS Candidate
Icahn School Of Medicine at Mount Sinai '20
+1-646-500-1521
ameen.alq...@icahn.mssm.edu
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] mri_glmfit with flag -pvr

[Vicky Shi]

External Email - Use Caution

Hi Doug,

Thank you so much for your respond. Greatly appreciate it!!

I have one more question. If I run glm with FSGD and contrast file
mentioned in my previous email, it should be DOSS, correct? However, when I
tried to run it using the same FSGD, contrast and command mentioned in my
previous email, the screen prints are telling me it is DODS as below:
INFO: gd2mtx_method is dods

I just want to confirm that I am using DOSS in this condition. And, if I
want to use DODS, I will have to make two thickness file as -pvr inputs for
each group, is this correct?

Thank you so much for your time.
Vicky



On Fri, Jan 10, 2020 at 11:22 AM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> Your FSGD and command look correct. As for whether it is a good idea or
> not, I'm not sure (you're probably the best person to decide that). One
> thing to keep in mind is that if there are true thickness differences you
> might see some differences due to partial voluming. I would also remove the
> mean of the thickness. You can so this with
> mri_glmfit --surf fsaverage lh --osgm --y lh.thickness.sm10.mgz --o
> glm.osgm.lh --eres-save :
> Then use glm.osgm.lh/eres.mgh as the PVR
>
> On 1/8/2020 9:45 PM, Vicky Shi wrote:
>
> External Email - Use Caution
> Dear Freesurfer team,
>
> I am running the glm analysis on CBF maps. I have two class and I want to
> see the group difference regressing out the cortex thickness. I know that I
> can add the average cortical thickness as one covariable in FSDG file.
> However, I think it might worth trying to do this with GLM by using a per
> vertex regressor (thickness).
>
> My fsgd file is like below:
>
> Class Patient
> Class CTL
> INPUT subj1 Patient
> INPUT subj2 CTL
> 
>
> My command is below:
> mri_glmfit --y lh.fsaverage.cbf.sm10.mgz --fsgd fsgd.txt --C contrast.mtx
> --glmdir lh.output.glmdir --surf fsaverage lh --pvr lh.thickness.sm10.mgz
>
> My contrast matrix is -1 1 0.
>
> I am wondering if what I do is correct or not. Does it make sense or I
> should use the mean thickness as regressor?
>
> Thank you for your time!
>
> Best regards,
> Vicky
>
>
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Anatomicuts usage

[Yendiki, Anastasia]

Hi Nayan - The second link is if you want to download the source code for the 
dev version and compile it yourself. The first link is if you want to download 
it already compiled so you can just run it (which I'm guessing is what you 
probably want).

a.y

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of nayan wadhwani 

Sent: Wednesday, January 29, 2020 2:37 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Anatomicuts usage


External Email - Use Caution

Hi Anastasia,
Thanks for your reply, i have no experience on how to use dev version of 
freesurfer. But from the tutorial are you referring me to 
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/this page to use 
dev version or this  https://surfer.nmr.mgh.harvard.edu/fswiki/DevelopersGuide 
please help me to select appropriate method and if it is second method than 
please help me how to use that.

Thanks and Regards
Nayan Wadhwani


On Wed, Jan 29, 2020 at 5:40 PM Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:
Hi Nayan - The plan is to make it available with the next release but it needs 
to undergo more testing. At the moment you can use it from the dev version and, 
as with anything in the dev version, keep in mind that things may change by the 
time they're in the official release. We appreciate any feedback you have. 
Thanks!

Anastasia.

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of nayan wadhwani mailto:nayanw...@gmail.com>>
Sent: Wednesday, January 29, 2020 4:56 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Anatomicuts usage


External Email - Use Caution

Hello FS users,
I am trying to use Anatomicuts tool of freesurfer for macOS. Since I was not 
using ./dev version of freesufer so I am unable to set the environment for the 
tool
and is it available for use or will be available with the new release itself.

Thanks and Regards
Nayan Wadhwani
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Xl defect in Freesurfer

[Bruce Fischl]

Hi Devika

the very large defects can take a very long time to fix, and probably 
won't produce good results. They are typically caused by something 
significant going wrong - large portions of the skull left behind and 
connected to the surface, an incorrect aseg, that kind of thing. You should 
take a look at the orig.nofix and inflated.nofix over the wm.mgz for that 
hemisphere to diagnose what is going on.


Let us know how it goes.

cheers
Bruce


 On Wed, 29 
Jan 2020, Devika K wrote:




External Email - Use Caution

Hi Freesurfer Team,

I am running recon-all command in parallel. one of my subject's
(recon-all.log file) is showing Xl defect and it has been in this step
overnight and there is no further progress.  PFA of recon-all.log file and
recon-all-status.log file of the above-mentioned subject. The recon-all
process for this subject is not terminated with an error, it's still
running.

Could you please help me to resolve this issue?










Regards
Devika K
Research Scholar, Dept of EEE
e: k_dev...@cb.students.amrita.edu
Amrita Vishwa Vidyapeetham
Coimbatore, India

[49ac6b9ec558bb2a131355dfeedf4fbc75a30fea.png?u=4623946]

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Anatomicuts usage

[nayan wadhwani]

External Email - Use Caution

Hi Anastasia,
Thanks for your reply, i have no experience on how to use dev version of
freesurfer. But from the tutorial are you referring me to
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/this page to
use dev version or this
https://surfer.nmr.mgh.harvard.edu/fswiki/DevelopersGuide please help me to
select appropriate method and if it is second method than please help me
how to use that.

Thanks and Regards
Nayan Wadhwani


On Wed, Jan 29, 2020 at 5:40 PM Yendiki, Anastasia 
wrote:

> Hi Nayan - The plan is to make it available with the next release but it
> needs to undergo more testing. At the moment you can use it from the dev
> version and, as with anything in the dev version, keep in mind that things
> may change by the time they're in the official release. We appreciate any
> feedback you have. Thanks!
>
> Anastasia.
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of nayan wadhwani <
> nayanw...@gmail.com>
> *Sent:* Wednesday, January 29, 2020 4:56 AM
> *To:* Freesurfer support list 
> *Subject:* [Freesurfer] Anatomicuts usage
>
>
> External Email - Use Caution
>
> Hello FS users,
> I am trying to use Anatomicuts tool of freesurfer for macOS. Since I was
> not using ./dev version of freesufer so I am unable to set the environment
> for the tool
> and is it available for use or will be available with the new release
> itself.
>
> Thanks and Regards
> Nayan Wadhwani
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Anatomicuts usage

[Yendiki, Anastasia]

Hi Nayan - The plan is to make it available with the next release but it needs 
to undergo more testing. At the moment you can use it from the dev version and, 
as with anything in the dev version, keep in mind that things may change by the 
time they're in the official release. We appreciate any feedback you have. 
Thanks!

Anastasia.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of nayan wadhwani 

Sent: Wednesday, January 29, 2020 4:56 AM
To: Freesurfer support list 
Subject: [Freesurfer] Anatomicuts usage


External Email - Use Caution

Hello FS users,
I am trying to use Anatomicuts tool of freesurfer for macOS. Since I was not 
using ./dev version of freesufer so I am unable to set the environment for the 
tool
and is it available for use or will be available with the new release itself.

Thanks and Regards
Nayan Wadhwani
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Anatomicuts usage

[nayan wadhwani]

External Email - Use Caution

Hello FS users,
I am trying to use Anatomicuts tool of freesurfer for macOS. Since I was
not using ./dev version of freesufer so I am unable to set the environment
for the tool
and is it available for use or will be available with the new release
itself.

Thanks and Regards
Nayan Wadhwani
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer