Re: [Freesurfer] FSGD file formatting for Xhemi

[Jose Graterol]

External Email - Use Caution

Thanks for your answer. A follow up question:
How should I then specify the variable's values per hemisphere
while making the FSGD file if I want to add covariates when
running mri_glmfit?

Thanks in advance.

On Fri, Oct 25, 2019 at 12:18 AM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> If you are trying to determine whether the hemispheres are different,
> then you need to do the subtraction between the hemis (ie, the
> --paired-diff). If you want to look at the hemispheres separately, then
> don't combine them in a single file
>
> On 10/21/19 4:58 AM, Jose Graterol wrote:
> >
> > External Email - Use Caution
> >
> > Thanks for your answer.
> >
> > I want to correlate TMS values in 17 stroke patients. Following the
> > instructions provided to Anders in this link
> >
> https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subject:%22%5C%5BFreesurfer%5C%5D+flipping+surface+data%22&o=newest&f=1
> > I created the --y file that joins the affected hemispheres together
> > and the unaffected hemispheres together. I omitted the --paired-diff
> > flag. When I run mri_glmfit with --fsgd it asks for 34 inputs. I am
> > guessing those are for the 34 hemispheres of the patients in the order
> > mentioned in my first email. Would this be the right way to correlate
> > the variables?
> >
> > In short, I am trying to test if there is a difference in cortical
> > thickness, while adding covariates, between the affected and
> > unaffected hemispheres in stroke patients.
> >
> > Thanks in advance
> >
> > On Fri, Oct 18, 2019 at 3:57 PM Greve, Douglas N.,Ph.D.
> > mailto:dgr...@mgh.harvard.edu>> wrote:
> >
> > What are you trying to test? Usually you don't have lh and rh in
> > the same glm
> >
> > On 10/17/19 7:09 AM, Jose Graterol wrote:
> >>
> >> External Email - Use Caution
> >>
> >> Dear Freesurfer Community,
> >>
> >> I have a question regarding the formatting of the FSGD file while
> >> doing an analysis with Xhemi.
> >> First the --y file was created as previously explained in another
> >> discussion
> >> (
> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg63965.html
> ).
> >> That is, mris_preproc with --xhemi and no --fsgd flag.
> >>
> >> If I understood correctly, that would create a mgh file with the
> >> following order: sub01lh, sub01rh, sub02lh, sub02rh...
> >> Then the FSGD file while running mri_glmfit would be:
> >> GroupDescriptorFile 1
> >> Title xxx
> >> Class sub
> >> Variables   var1
> >> Input   sub01lh   sub   var1_lh_sub01
> >> Input   sub01rh   sub   var1_rh_sub01
> >> Input   sub02lh   sub   var1_lh_sub02
> >> Input   sub02rh   sub   var1_rh_sub02
> >>
> >> Would this be correct? If so, what would be the best case for
> >> specifying a variable like age? Just repeating the value 2 times?
> >>
> >> As always, thanks in advance
> >>
> >> Kind Regards
> >>
> >> José
> >>
> >>
> >> ___
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[Freesurfer] Thalamic subnuclei color table

[Crawford, Anna]

External Email - Use Caution

Hello,


Just a quick question. We recently installed the new thalamus segmentation 
subroutine.  It's really wonderful, and much promise to our work.

I can't find a lookup table with the numerical labels from the FS output to the 
thalamic nuclei.  The numbers around between 8103-8133 on the right, and 8203 
and 8233 on the left.  Can you point me in the right direction for this?

For other FS segmented volumes I always use the following, but it doesn't 
include these thalamic subnuclei

http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI/FreeSurferColorLUT

Thank you,
Anna


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Re: [Freesurfer] Thalamic subnuclei color table

[Lilla Zollei]

Hi Anna,

See attached.

Lilla

On Fri, 25 Oct 2019, Crawford, Anna wrote:



External Email - Use Caution

Hello,


Just a quick question. We recently installed the new thalamus segmentation 
subroutine.  It’s really wonderful, and much promise to our work.

I can’t find a lookup table with the numerical labels from the FS output to the 
thalamic nuclei.  The numbers around between 8103-8133 on the right, and 8203 
and 8233 on the left.  Can you point me in the right direction for this?
 
For other FS segmented volumes I always use the following, but it doesn’t 
include these thalamic subnuclei
 
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI/FreeSurferColorLUT
 
Thank you,
Anna



Please consider the environment before printing this e-mail

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locations. Confidentiality Note: This message is intended for use only by the 
individual or entity
to which it is addressed and may contain information that is privileged, 
confidential, and exempt from disclosure under applicable law. If the reader of 
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whether electronic or hard copy. Thank you.
#$Id: FreeSurferColorLUT.txt,v 1.105 2015/07/29 18:23:03 greve Exp $

#No. Label Name:R   G   B   A

0   Unknown 0   0   0   0
1   Left-Cerebral-Exterior  70  130 180 0
2   Left-Cerebral-White-Matter  245 245 245 0
3   Left-Cerebral-Cortex205 62  78  0
4   Left-Lateral-Ventricle  120 18  134 0
5   Left-Inf-Lat-Vent   196 58  250 0
6   Left-Cerebellum-Exterior0   148 0   0
7   Left-Cerebellum-White-Matter220 248 164 0
8   Left-Cerebellum-Cortex  230 148 34  0
9   Left-Thalamus-unused0   118 14  0
10  Left-Thalamus   0   118 14  0
11  Left-Caudate122 186 220 0
12  Left-Putamen236 13  176 0
13  Left-Pallidum   12  48  255 0
14  3rd-Ventricle   204 182 142 0
15  4th-Ventricle   42  204 164 0
16  Brain-Stem  119 159 176 0
17  Left-Hippocampus220 216 20  0
18  Left-Amygdala   103 255 255 0
19  Left-Insula 80  196 98  0
20  Left-Operculum  60  58  210 0
21  Line-1  60  58  210 0
22  Line-2  60  58  210 0
23  Line-3  60  58  210 0
24  CSF 60  60  60  0
25  Left-Lesion 255 165 0   0
26  Left-Accumbens-area 255 165 0   0
27  Left-Substancia-Nigra   0   255 127 0
28  Left-VentralDC  165 42  42  0
29  Left-undetermined   135 206 235 0
30  Left-vessel 160 32  240 0
31  Left-choroid-plexus 0   200 200 0
32  Left-F3orb  100 50  100 0
33  Left-lOg135 50  74  0
34  Left-aOg122 135 50  0
35  Left-mOg51  50  135 0
36  Left-pOg74  155 60  0
37  Left-Stellate   120 62  43  0
38  Left-Porg   74  155 60  0
39  Left-Aorg   122 135 50  0
40  Right-Cerebral-Exterior 70  130 180 0
41  Right-Cerebral-White-Matter 245 245 245 0
42  Right-Cerebral-Cortex   205 62  78  0
43  Right-Lateral-Ventricle 120 18  134 0
44  Right-Inf-Lat-Vent  196 58  250 0
45  Right-Cerebellum-Exterior   0   148 0   0
46  Right-Cerebellum-White-Matter   220 248 164 0
47  Right-Cerebellum-Cortex 230 148 34  0
48  Right-Thalamus-unused   0   118 14  0
49  Right-Thalamus  0   118 14  0
50  Right-Caudate   122 186 220 0
51  Right-Putamen   236 13  176 0
52  Right-Pallidum  13  48  255 0
53  Right-Hippocampus   220 216 20  0
54  Right-Amygdala  1

Re: [Freesurfer] [EXT] Re: Thalamic subnuclei color table

[Crawford, Anna]

External Email - Use Caution

Thank you!


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Lilla Zollei 

Sent: Friday, October 25, 2019 8:41 AM
To: Freesurfer support list
Subject: [EXT] Re: [Freesurfer] Thalamic subnuclei color table


Hi Anna,

See attached.

Lilla

On Fri, 25 Oct 2019, Crawford, Anna wrote:

>
> External Email - Use Caution
>
> Hello,
>
>
> Just a quick question. We recently installed the new thalamus segmentation 
> subroutine.  It's really wonderful, and much promise to our work.
>
> I can't find a lookup table with the numerical labels from the FS output to 
> the thalamic nuclei.  The numbers around between 8103-8133 on the right, and 
> 8203 and 8233 on the left.  Can you point me in the right direction for this?
>
> For other FS segmented volumes I always use the following, but it doesn't 
> include these thalamic subnuclei
>
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI/FreeSurferColorLUT
>
> Thank you,
> Anna
>
>
>
> Please consider the environment before printing this e-mail
>
> Cleveland Clinic is currently ranked as one of the nation's top hospitals by 
> U.S. News & World Report (2019-2020). Visit us online at 
> http://www.clevelandclinic.org for a complete 
> listing of our services, staff and locations. Confidentiality Note: This 
> message is intended for use only by the individual or entity
> to which it is addressed and may contain information that is privileged, 
> confidential, and exempt from disclosure under applicable law. If the reader 
> of this message is not the intended recipient or the employee or agent 
> responsible for delivering the message to the intended recipient, you are 
> hereby notified
> that any dissemination, distribution or copying of this communication is 
> strictly prohibited. If you have received this communication in error, please 
> contact the sender immediately and destroy the material in its entirety, 
> whether electronic or hard copy. Thank you.
>


Please consider the environment before printing this e-mail

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U.S. News & World Report (2017-2018). Visit us online at 
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and locations. Confidentiality Note: This message is intended for use only by 
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that is privileged, confidential, and exempt from disclosure under applicable 
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[Freesurfer] view labels in native space

[Nasiriavanaki, Zahra]

Hi Freesurfer experts

I have a few labels that correspond to activation clusters in fsaverage space 
for an individual subject. I used mri_label2label to transfer them to native 
space of the subject.

export SUBJECTS_DIR=/autofs/space/oprah_001/users/zn025/looming_7T/SUBJECTS_DIR
mri_label2label --srclabel  ./first_levels/$subj/label/aparc/pos/lh-0001.label  
--trglabel lh-new.label  --srcsubject fsaverage --trgsubject ${subj} 
--regmethod surface --hemi lh

When I overlay the native label on top of the fsaverage significance map 
(tksurfer fsaverage lh inflated -ov sig.nii.gz), it looks like small dots all 
over the map.
Is this because I'm viewing the native label in fsaverage space?
Is there a way to view these labels in this subject's native space instead of 
fsaverage, something like tksurfer native(instead of fsaverage) lh inflated -ov 
sig.nii.gz?

Thank you very much in advance
Mona


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129


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Re: [Freesurfer] recon-all at native resolution

[Greve, Douglas N.,Ph.D.]

There was no snapshot. Can you resend?

On 10/24/2019 7:06 PM, Alexopoulos, Dimitrios wrote:
>  External Email - Use Caution
>
> I apologize for the confusion.  Whether I use the -hires or -conf2hires flag 
> the subcortical segmentations look good.
>
> The cortical segmentations have some issues in the ventral medial area (see 
> snapshot below), which is likely caused by difficulty in FS delineating WM 
> superior to the gyrus rectus. I'm not sure how to correct this so I was 
> thinking the higher resolution data may lead to a better WM segmentation?
>
> Is my thinking correct? If so, which flag is best?
>
> Jim
>
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  On Behalf Of Greve, Douglas N.,Ph.D.
> Sent: Thursday, October 24, 2019 5:37 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] recon-all at native resolution
>
> You mean the surfaces using -hires look fine? If so, then continue to use 
> -hires
>
> On 10/24/19 6:32 PM, Alexopoulos, Dimitrios wrote:
>>   External Email - Use Caution
>>
>> The cortical parcellations in the aseg and aparc+seg have some issues in the 
>> orbital prefrontal regions and we're were hoping that the higher resolution 
>> images would help. The surfaces look fine.
>>
>> We should use the -hires flag instead in this scenario?
>>
>> Thx.
>>
>> -Original Message-
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>  On Behalf Of Greve, Douglas N.,Ph.D.
>> Sent: Thursday, October 24, 2019 5:06 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] recon-all at native resolution
>>
>> oh, sorry, yes it is. The surfaces are placed on the high res volumes,
>> but the aseg will be at 1mm. If you need the aseg at highres, then you
>> will need to use the -hires flag (but the surfaces will suffer)
>>
>> On 10/24/19 2:55 PM, Alexopoulos, Dimitrios wrote:
>>>External Email - Use Caution
>>>
>>> Doug,
>>>
>>> I copied over files and ran using the  -conf2hires flag, however, the 
>>> orig.mgz/brainmask.mgz are resampled to 1mm isotropic not the native 0.8mm.
>>>
>>> Using the -hires flag maintains the orig.mgz/brainmask.mgz at native 0.8mm 
>>> resolution.
>>>
>>> Is this expected when running -conf2hires?
>>>
>>> Jim
>>>
>>> -Original Message-
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>>  On Behalf Of Greve, Douglas 
>>> N.,Ph.D.
>>> Sent: Tuesday, October 15, 2019 11:54 AM
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] recon-all at native resolution
>>>
>>> better to use a patch I created for the HCP, see
>>> https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/hc
>>> p
>>> /readme
>>>
>>>
>>> On 10/15/19 12:13 PM, Alexopoulos, Dimitrios wrote:
External Email - Use Caution

 We have data acquired at 0.8mm isotropic and would like to maintain
 this resolution in the processing stream rather than FS resampling to 1mm.

 Is the command to do this 'recon-all -hires -all'?

 Are there any drawback to doing this?

 Jim

 
 -
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>>> 
>>> 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.
>>>
>>>
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>> The materials in this message a

Re: [Freesurfer] recon-all at native resolution

[Alexopoulos, Dimitrios]

External Email - Use Caution

Opps, here are the snapshots. The aseg subcortical look good using either the 
-hires or -conf2hires flags.

The cortical parcellation is not including some ctx in several regions 
including the region below.





[cid:image001.png@01D58B27.A63D2C70]





[cid:image002.png@01D58B27.A63D2C70]



-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Greve, Douglas N.,Ph.D.
Sent: Friday, October 25, 2019 11:17 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon-all at native resolution



There was no snapshot. Can you resend?



On 10/24/2019 7:06 PM, Alexopoulos, Dimitrios wrote:

>  External Email - Use Caution

>

> I apologize for the confusion.  Whether I use the -hires or -conf2hires flag 
> the subcortical segmentations look good.

>

> The cortical segmentations have some issues in the ventral medial area (see 
> snapshot below), which is likely caused by difficulty in FS delineating WM 
> superior to the gyrus rectus. I'm not sure how to correct this so I was 
> thinking the higher resolution data may lead to a better WM segmentation?

>

> Is my thinking correct? If so, which flag is best?

>

> Jim

>

>

> -Original Message-

> From: 
> freesurfer-boun...@nmr.mgh.harvard.edu
>  
> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
>  On Behalf Of Greve, Douglas N.,Ph.D.

> Sent: Thursday, October 24, 2019 5:37 PM

> To: freesurfer@nmr.mgh.harvard.edu

> Subject: Re: [Freesurfer] recon-all at native resolution

>

> You mean the surfaces using -hires look fine? If so, then continue to

> use -hires

>

> On 10/24/19 6:32 PM, Alexopoulos, Dimitrios wrote:

>>   External Email - Use Caution

>>

>> The cortical parcellations in the aseg and aparc+seg have some issues in the 
>> orbital prefrontal regions and we're were hoping that the higher resolution 
>> images would help. The surfaces look fine.

>>

>> We should use the -hires flag instead in this scenario?

>>

>> Thx.

>>

>> -Original Message-

>> From: 
>> freesurfer-boun...@nmr.mgh.harvard.edu
>>  
>> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
>>  On Behalf Of Greve, Douglas N.,Ph.D.

>> Sent: Thursday, October 24, 2019 5:06 PM

>> To: freesurfer@nmr.mgh.harvard.edu

>> Subject: Re: [Freesurfer] recon-all at native resolution

>>

>> oh, sorry, yes it is. The surfaces are placed on the high res

>> volumes, but the aseg will be at 1mm. If you need the aseg at

>> highres, then you will need to use the -hires flag (but the surfaces

>> will suffer)

>>

>> On 10/24/19 2:55 PM, Alexopoulos, Dimitrios wrote:

>>>External Email - Use Caution

>>>

>>> Doug,

>>>

>>> I copied over files and ran using the  -conf2hires flag, however, the 
>>> orig.mgz/brainmask.mgz are resampled to 1mm isotropic not the native 0.8mm.

>>>

>>> Using the -hires flag maintains the orig.mgz/brainmask.mgz at native 0.8mm 
>>> resolution.

>>>

>>> Is this expected when running -conf2hires?

>>>

>>> Jim

>>>

>>> -Original Message-

>>> From: 
>>> freesurfer-boun...@nmr.mgh.harvard.edu
>>>  
>>> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
>>>  On Behalf Of Greve, Douglas N.,Ph.D.

>>> Sent: Tuesday, October 15, 2019 11:54 AM

>>> To: freesurfer@nmr.mgh.harvard.edu

>>> Subject: Re: [Freesurfer] recon-all at native resolution

>>>

>>> better to use a patch I created for the HCP, see

>>> https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/h

>>> c

>>> p

>>> /readme

>>>

>>>

>>> On 10/15/19 12:13 PM, Alexopoulos, Dimitrios wrote:

External Email - Use Caution



 We have data acquired at 0.8mm isotropic and would like to maintain

 this resolution in the processing stream rather than FS resampling to 1mm.



 Is the command to do this 'recon-all -hires -all'?



 Are there any drawback to doing this?



 Jim



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 -

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 If you are not the intended recipient, be advised that any

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 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.





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[Freesurfer] Open Faculty Position in Psychology at the University of Nevada, Reno

[Stephanie Otto]

External Email - Use Caution

Greetings Freesurfer Group,

I'm not sure if it is acceptable to post open positions here, but our
department is currently seeking to fill an Assistant Professor position and
we would be grateful if you could share this information with the
Freesurfer community. Thanks in advance!

The Department of Psychology at the University of Nevada, Reno, is seeking
applications for a tenure-track Assistant/Associate Professor in Cognitive
Neuroscience.  The level will be determined by the Department and will be
commensurate with the selected candidate’s experience, knowledge, skills,
and abilities.  We are particularly interested in candidates whose research
includes advanced techniques in neuroimaging and/or computational
approaches.  The candidate’s area of research should complement the
strengths of the department in visual and multisensory processing.
Successful candidates will be expected to establish a nationally
recognized, extramurally funded research program, train graduate students,
and participate in undergraduate teaching.  Competitive startup funds are
available.

Required Qualifications
PhD in Neuroscience or related field; postdoctoral research experience.

Preferred Qualifications
A strong publication record; potential for strong teaching skills;
expertise that complements and expands the research capacity of the
department; the potential to develop a nationally-competitive research
program.

Compensation Grade
Assistant Professor -- Rank II
Associate Professor -- Rank III

Total Compensation
The total compensation package includes a negotiable competitive salary,
moving allowance (if applicable), a rich retirement plan, health insurance
options that include dental and vision, life insurance, long-term
disability, along with many other benefits. Additionally, there is a
grant-in-aid educational benefit for faculty and dependents.  For more
information, please visit: UNR Benefits

Faculty Dual Career Assistance Program
The University of Nevada, Reno recognizes the importance of addressing
dual-career couples’ professional needs. We offer a dual career assistance
program to newly hired faculty spouses/partners that provides resources and
assists them to identify career opportunities in Northern Nevada. Dual
Career Program

Department Information
The department contributes to both the undergraduate and graduate
interdisciplinary training programs in Neuroscience (approximately 440
undergraduates and 35 doctoral students).  The department has 32
tenure-ladder faculty, four teaching faculty, and a corps of administrative
staff; it is home to the Psychology major (900 students) and graduate
programs in Cognitive and Brain Sciences, Behavior Analysis, and Clinical
Psychology (120 students across three programs).  A wide array of resources
for neuroimaging is provided through the Center for Integrative
Neuroscience (an NIH COBRE award), including 3T fMRI, high-density EEG,
fNIRS, and Adaptive Optics. The Center also houses a research core
supporting applications of Virtual and Augmented Reality, and a core for
Cellular and Molecular Imaging including confocal and 2-photon microscopy.
Reno is located next to the Sierra Nevada near Lake Tahoe, and has been
rated one of the best small cities in the US for outdoor recreation and
overall quality of life.

Contact Information
Sharee Williams at (775) 682-8795 or shar...@unr.edu

Required Attachment(s)
Please attach the following documents to your application.
1) Resume/CV
2) Cover Letter
3) Contact information for five professional references
4) Statement of Research and Teaching Interests
5) Please write a brief statement (one page maximum) about how you would
contribute toward our mission of creating a culturally inclusive
environment in the role for which you are applying


Best,
Stephanie Otto
Doctoral Candidate, Cognitive and Brain Sciences Program
Department of Psychology, MSS 414/MS0296
University of Nevada, Reno
so...@nevada.unr.edu
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