Re: [Freesurfer] [External] Re: seg.mgz testing for FS7 beta

[Zeng, Victor (BIDMC - Keshavan - Psychiatry)]

Thank you, it works very well, and at a glance seems actually a lot more 
precise than aseg.mgz, especially with the cerebellum :)

Hope it will be implemented in some shape or form to recon-all

Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--


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

Sent: Thursday, February 27, 2020 1:01 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [External] Re: [Freesurfer] seg.mgz testing for FS7 beta

Don't use the T1.mgz (that has been heavily processed by recon-all). Use
the orig.mgz instead

On 2/25/20 8:44 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
>
> Hi Freesurfer team,
>
>
> I've run samseg for one participant, using the /mri/T1.mgz as the
> input, but the output seg.mgz is awful, w/ the ventricles being
> overestimated and the outer perimeter of the gray matter considered as
> the "Head-ExtraCerebral." I know in mind you all just want to know if
> it runs in FS7.0beta, but is this something I'm suppose to be expecting?
>
>
> best,
>
>
> Victor Zeng
> Beth Israel Deaconess Medical Center
> Keshavan Lab
> --
>
> 
>
> This message is intended for the use of the person(s) to whom it may
> be addressed. It may contain information that is privileged,
> confidential, or otherwise protected from disclosure under applicable
> law. If you are not the intended recipient, any dissemination,
> distribution, copying, or use of this information is prohibited. If
> you have received this message in error, please permanently delete it
> and immediately notify the sender. Thank you.
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwICAg&c=WknmpdNpvrlj2B5K1aWVqL1SOiF30547pqSuOmtwXTQ&r=ziAm16qmlGqGtX5PhV9Harh0DYcHWCNZ9xWh5fPQIi0&m=OVWICugoJB4I3yYSHzbgPDjr7jFo5-r4rcMYrYBcaOg&s=8C0tRFaxdL51QypDM9aYkP-l8d63tyVybhh9Ky9RyS8&e=

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwICAg&c=WknmpdNpvrlj2B5K1aWVqL1SOiF30547pqSuOmtwXTQ&r=ziAm16qmlGqGtX5PhV9Harh0DYcHWCNZ9xWh5fPQIi0&m=OVWICugoJB4I3yYSHzbgPDjr7jFo5-r4rcMYrYBcaOg&s=8C0tRFaxdL51QypDM9aYkP-l8d63tyVybhh9Ky9RyS8&e=



This message is intended for the use of the person(s) to whom it may be 
addressed. It may contain information that is privileged, confidential, or 
otherwise protected from disclosure under applicable law. If you are not the 
intended recipient, any dissemination, distribution, copying, or use of this 
information is prohibited. If you have received this message in error, please 
permanently delete it and immediately notify the sender. Thank you.

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

Re: [Freesurfer] aparcstats2table

[Douglas N. Greve]

yes

On 2/25/20 2:05 AM, Devika K wrote:
>
> External Email - Use Caution
>
> Hi,
>
> Can I use the below command to extract the cortical thickness using 
> Destrieux Atlas from longitudinally preprocessed subjects?
> aparcstats2table --hemi lh \
>--subjects 004 021 040 067 080 092 \
>--meas thickness \
>--parc aparc.a2009s \
>--tablefile lh.aparc.a2009.thickness.table
> Regards
> Devika K
>
>
>
>
> ___
> 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] seg.mgz testing for FS7 beta

[Douglas N. Greve]

Don't use the T1.mgz (that has been heavily processed by recon-all). Use 
the orig.mgz instead

On 2/25/20 8:44 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
>
> Hi Freesurfer team,
>
>
> I've run samseg for one participant, using the /mri/T1.mgz as the 
> input, but the output seg.mgz is awful, w/ the ventricles being 
> overestimated and the outer perimeter of the gray matter considered as 
> the "Head-ExtraCerebral." I know in mind you all just want to know if 
> it runs in FS7.0beta, but is this something I'm suppose to be expecting?
>
>
> best,
>
>
> Victor Zeng
> Beth Israel Deaconess Medical Center
> Keshavan Lab
> --
>
> 
>
> This message is intended for the use of the person(s) to whom it may 
> be addressed. It may contain information that is privileged, 
> confidential, or otherwise protected from disclosure under applicable 
> law. If you are not the intended recipient, any dissemination, 
> distribution, copying, or use of this information is prohibited. If 
> you have received this message in error, please permanently delete it 
> and immediately notify the sender. Thank you.
>
> ___
> 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

[Freesurfer] Job post: full-time research assistant in the lab of Dr. Emily Finn, Dartmouth College

[Emily S. Finn]

External Email - Use Caution

Dear Freesurfer users,

The laboratory of Dr. Emily Finn in the Department of Psychological and Brain 
Sciences at Dartmouth College is seeking a full-time Research Assistant for a 
targeted start date of July 2020. The research of the lab focuses on individual 
differences in brain activity and connectivity, and how these relate to 
behavior. Some key questions are: How do our intrinsic traits bias our 
perceptions and judgments, and how is this reflected in patterns of brain 
activity? Why might different people arrive at different interpretations of the 
same experience? Our research combines behavioral, neuroimaging and 
computational modeling techniques to study individual differences in cognition, 
especially under rich, dynamic, “naturalistic” stimulation such as watching 
movies or listening to stories. This position is especially well-suited for 
individuals planning to apply for a PhD in cognitive neuroscience or 
psychology. The position would be for an initial 1 year, with an ability to 
renew up to 2 additional years thereafter based on performance. Preference will 
be given to applicants who are willing to stay at least two years. Questions 
may be directed to Emily Finn (emily.s.f...@dartmouth.edu). For full 
consideration, please apply by March 13, 2020.

Position Purpose
Plays a crucial role in helping to set up the lab as well as conduct 
experiments. The Research Assistant’s role will involve administrative tasks, 
such as purchases, participant recruitment, ethics applications, organizing 
files, and setting up meetings. Conducts research, including designing 
experiments, collecting data, analyzing data, and writing papers, with the aim 
of completing an independent research project by the end of their time. The 
Research Assistant will learn techniques in programming, functional MRI brain 
scanning, and in-person and online behavioral experimentation.

Required Qualifications
- Bachelor’s degree with a major in psychology, neuroscience, cognitive 
science, computer science, biology, or a similar field
- Previous experience in one or more laboratory methods, procedures and 
techniques as well as the equipment and instruments, e.g., fMRI data 
acquisition, eye-tracking, behavioral experimentation
- Ability to work independently and apply critical thinking and sound judgment
- Excellent organizational and time management skills
- Knowledge of software for writing and presentation (e.g., Microsoft Office), 
and online scientific literature search engines

Preferred Qualifications
- Two years of relevant laboratory/ research experience during undergraduate
- General programming and computational skills for data analysis (e.g., Python, 
MATLAB, R)
- Experience with neuroimaging analysis software (e.g., AFNI, SPM, FSL) and 
experiment creation (e.g., PsychoPy, Psychtoolbox)
- Experience working with human participants

For more information or to apply: 
https://searchjobs.dartmouth.edu/postings/53845


--
Emily S. Finn, PhD
Assistant Professor, beginning July 2020
Psychological & Brain Sciences
Dartmouth College
esfinn.github.io

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

Re: [Freesurfer] Full analysis chain without Topology fix, Talairach check?

[Bruce Fischl]

Hi Dylan

I think you could probably do a recon without topology fixing although of 
course the spherical mapping will then be multi-valued. It will take a bit 
of hacking at recon-all to get it to work though as it is not a use-case 
that we explicitly support.


cheers
Bruce
 On Thu, 27 Feb 2020, 
hs...@mskcc.org wrote:




External Email - Use Caution

Dear Freesurfers,


I am attempting to run the full reconstruction in Freesurfer on several
hundred patient images with diseased areas of the brain.

Without skipping any steps of the analysis chain, I am able to complete the
full reconstruction for about 50% of said patients. When the analysis is
able to complete, the disease sites are generally not included in the white
or gray segmentation labels, which is ideal for my use case. However, when
the disease is far from the cortical surface, it generally results in a
large topological defect. (In other cases, the Talairach check fails.) I
would like to know, does it really make sense to try to analyze the images
with a "real" topological defect, and if so, how to accomplish it?


I have tried to run the reconstruction with flags "-nofix" and
"-notal-check" to accept an imperfect Talairach transform and avoid crashes
trying to fix these unfixable topological defects. Unfortunately, the step
"mris_autodet_gwstats" which comes after "mris_sphere", seems to look for a
file "surf/lh.orig.premesh" which is not found, causing a crash. From what I
can understand, that file is produced by the so-called old topology fix [1],
so it would imply that a full analysis chain is not supported if you
eschew topology-fixing. Is this a feature, or do you recommend modifying
the logic of the script to work around it? This is as far as I got, but I
suppose there may be steps later in the analysis chain that will also look
for files only produced if the topology fix runs.


For your information, I am currently using the nightly build from February
12 for CentOS7, and I am amenable to switching to an older or newer build.
Thank you for taking the time to help me.


Best regards,

Dylan Hsu, Ph.D

Memorial Sloan-Kettering Cancer Center


[1] https://github.com/freesurfer/freesurfer/blob/6044b3df08de93c15e4b44807
349f21d9e4bc794/scripts/recon-all#L3128-L3139



=

Please note that this e-mail and any files transmitted from
Memorial Sloan Kettering Cancer Center may be privileged, confidential,
and protected from disclosure under applicable law. If the reader of
this message is not the intended recipient, or an employee or agent
responsible for delivering this message to the intended recipient,
you are hereby notified that any reading, dissemination, distribution,
copying, or other use of this communication or any of its attachments
is strictly prohibited. If you have received this communication in
error, please notify the sender immediately by replying to this message
and deleting this message, any attachments, and all copies and backups
from your computer.


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

[Freesurfer] Full analysis chain without Topology fix, Talairach check?

[HsuD3]

External Email - Use Caution

Dear Freesurfers,


I am attempting to run the full reconstruction in Freesurfer on several hundred 
patient images with diseased areas of the brain.

Without skipping any steps of the analysis chain, I am able to complete the 
full reconstruction for about 50% of said patients. When the analysis is able 
to complete, the disease sites are generally not included in the white or gray 
segmentation labels, which is ideal for my use case. However, when the disease 
is far from the cortical surface, it generally results in a large topological 
defect. (In other cases, the Talairach check fails.) I would like to know, does 
it really make sense to try to analyze the images with a "real" topological 
defect, and if so, how to accomplish it?


I have tried to run the reconstruction with flags "-nofix" and "-notal-check" 
to accept an imperfect Talairach transform and avoid crashes trying to fix 
these unfixable topological defects. Unfortunately, the step 
"mris_autodet_gwstats" which comes after "mris_sphere", seems to look for a 
file "surf/lh.orig.premesh" which is not found, causing a crash. From what I 
can understand, that file is produced by the so-called old topology fix [1], so 
it would imply that a full analysis chain is not supported if you eschew 
topology-fixing. Is this a feature, or do you recommend modifying the logic of 
the script to work around it? This is as far as I got, but I suppose there may 
be steps later in the analysis chain that will also look for files only 
produced if the topology fix runs.


For your information, I am currently using the nightly build from February 12 
for CentOS7, and I am amenable to switching to an older or newer build. Thank 
you for taking the time to help me.


Best regards,

Dylan Hsu, Ph.D

Memorial Sloan-Kettering Cancer Center


[1]  
https://github.com/freesurfer/freesurfer/blob/6044b3df08de93c15e4b44807349f21d9e4bc794/scripts/recon-all#L3128-L3139



=

 Please note that this e-mail and any files transmitted from
 Memorial Sloan Kettering Cancer Center may be privileged, confidential,
 and protected from disclosure under applicable law. If the reader of
 this message is not the intended recipient, or an employee or agent
 responsible for delivering this message to the intended recipient,
 you are hereby notified that any reading, dissemination, distribution,
 copying, or other use of this communication or any of its attachments
 is strictly prohibited.  If you have received this communication in
 error, please notify the sender immediately by replying to this message
 and deleting this message, any attachments, and all copies and backups
 from your computer.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Segmentation problem

[Marina Fernández]

External Email - Use Caution

Dear Freesurfeer experts,


After running the recon-all, a part of the temporal lobe of one subject was
removed.

I used the watershed algorithm to be less agressive in the skull stripping
step:

recon-all -skullstrip -wsthresh 35 -clean-bm -no-wsgcaatlas -subjid sub_001

And the problem was solved in the brainmask.mgz volume because I can see
the temporal lobe completely, but the surfaces are still displaced. In
order to correct the surfaces I used the white matter edit tool but there
is no change after correcting WM and running the recon-all -autorecon2-wm
-autorecon3. I also used control points and but the following error was
shown in the terminal when I run the recon-all -autorecon2-cp -autorecon3:

recon-all -s sub_001 existed with errors

I detected that there are very high values in the white matter of this part
of the temporal lobe (even 132), maybe it has something to do. What can I
do to solve the problem with this subject?


Thank you very much in advance.

Best regards,

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

[Freesurfer] mri_vol2surf produces invalid surface

[Shuntaro Aoki]

External Email - Use Caution

Dear mailing list,

I was trying to convert a volume image to a freesurfer surface (as
gii) with `mri_vol2surf` for visualization, but ended up with invalid
surface data (i.e., a file not loadable by freeview).

What I did was:

---
% mri_vol2surf --version
stable5
% mri_vol2surf --src ./sample_volume.nii.gz --regheader sample-sub
--hemi lh --out ./sample_vol2surf_lh.gii
---

Here, `sample_volume.nii.gz` is a volume image (such as a statistical
map) registered to an individual reference T1w image of subject
`sample-sub`, which was the input of recon-all for the subject.
The command completed without errors:

---
srcvol = ./sample_volume.nii.gz
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
Done loading volume
Computing registration from header.
  Using /home/share/data/fmri/freesurfer/subjects/sample-sub/mri/orig.mgz
as target reference.
Reading surface
/home/share/data/fmri/freesurfer/subjects/sample-sub/surf/lh.white
Done reading source surface
Mapping Source Volume onto Source Subject Surface
 1 0 0 0
using old
Done mapping volume to surface
Number of source voxels hit = 31055
Writing to ./sample_vol2surf_lh.gii
Dim: 155685 1 1
---

Then I tried to open the resulting surface `sample_vol2surf_lh.gii`
with freeview (ver 1.0 build 2013-05-13) but it failed, saying "Failed
to load Surface".
I also got the following shell output:

---
mriseadGIFTIfile: mris is NULL! found when parsing file
/home/mu/aoki/work/surf_sphere/sample_vol2surf_lh.gii
MRISread failed
mriseadGIFTIfile: mris is NULL! found when parsing file
/home/mu/aoki/work/surf_sphere/sample_vol2surf_lh.gii
---

The output of `mris_info` is:

---
% mris_info sample_vol2surf_lh.gii
==
gifti_image struct
version= 1.0
numDA  = 1
gim->meta nvpairs struct, len = 3 :
nvpair: 'UserName' = 'aoki'
nvpair: 'Date' = 'Thu Feb 27 17:32:40 2020'
nvpair: 'gifticlib-version' = 'gifti library version 1.09, 28 June, 2010'

gim->labeltable giiLabelTable struct, len = 0 :
--
gim->darray[0] giiDataArray struct
intent  0 = NIFTI_INTENT_NONE
datatype   16 = NIFTI_TYPE_FLOAT32
ind_ord 1 = RowMajorOrder
num_dim   = 1
dims  = 155685, 0, 0, 0, 0, 0
encoding3 = GZipBase64Binary
endian  2 = LittleEndian
ext_fname =
ext_offset= 0
darray->meta nvpairs struct, len = 0 :
data   = 
nvals  = 155685
nbyper = 4
numCS  = 0
darray->ex_atrs nvpairs struct, len = 0 :
--
gifti_image struct
swapped= 0
compressed = 1
 -- darray totals: 1 MB
gim->ex_atrs nvpairs struct, len = 0 :
==
---

I checked matching between voxels in the input volume and the surface
with the output of --srchit option and found the registration was
fine.

I also tried mgh output but got another invalid file.

---
% mris_info sample_vol2surf_lh.mgh
ERROR: MRISread: file 'sample_vol2surf_lh.mgh' has 0 vertices!
Probably trying to use a scalar data file as a surface!

No such file or directory
---

I would appreciate any advice on this.

Regards,


Shuntaro


-- 

Shuntaro C. Aoki, Ph.D.

Program-specific Researcher
Neuroinformatics group
Graduate School of Informatics
Kyoto University

s_a...@i.kyoto-u.ac.jp


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