[Freesurfer] Volume are different in asegstats vs matlab

[Lee Subin Kristine]

Hi,



I have a question about volume info from freesurfer vs matlab.

I am looking at, say, the left hippocampus volume from asegstats, which was 
3778.2 mm^3.
When I try to get the same volume by loading aseg.nii on matlab, however, I get 
a different number, 3945.

For matlab, I used the following command, which counts the number of voxels 
equal to the left hippocampus segment id:
length(find(aseg.img==17))

This was done after I converted the original aseg.mgz file into native space, 
using 2 different methods:
(1) mri_convert -rl rawavg.mgz -rt nearest -i aseg.mgz -o bert_aseg.nii

(2) mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o bert_aseg.nii 
--regheader aseg.mgz
In both cases, the output was 3945.

The rawavg.mgz used here is also 1mm isovoxel, so I don't think it is due to 
the difference in voxel dimensions.



What could be the cause of the difference in volume?

Thanks,

Kristine






Sent from Mail for Windows 10

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Re: [Freesurfer] Hippocampal Subfields Module, output error

[Iglesias Gonzalez, Eugenio]

Thanks, Aura.
What exact version of FreeSurfer are you using? I’m assuming it’s a development 
version, but from when? The results are indeed weird…



--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From:  on behalf of "Hurtado, Aura 
Maria" 
Reply-To: Freesurfer support list 
Date: Friday, 23 March 2018 at 05:28
To: Freesurfer support list 
Subject: Re: [Freesurfer] Hippocampal Subfields Module, output error

Hi Eugenio,

Thank you for replying so quickly to my lengthy message. I correct some of my 
statements,

1. Matlab 8.4 was used (not 8.2)
2. When I ran the cross-sectional subfield command, I did not get exit errors 
as I did with the longitudinal command (kvlGetOptimizer). I got output errors 
and warnings of non convergence in the log file.

-I see your point. I mean the built-in hippocampal module (v10) worked when 
reconall was run with fs60 (hippoSf). When run independently, the hippocampal 
module (v21) exited with errors when using segmentHA_T1_long.sh, and the output 
was off when using segmentHA_T1.sh (this is better seen in pic 3). I hope this 
clarifies a bit. Please tell me if it doesn’t.

These are screenshots of the images output by jobs that exited without 
processing errors:
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[Freesurfer] Positions available in Dr. Zeynep Saygin's lab at OSU

[Saygin, Zeynep M.]

TECHNICAL ASSISTANT, The Ohio State University, Dept. of Psychology – Dr. 
Zeynep Saygin’s Lab, to assist with neuroscience research on the functional and 
structural architecture of the human brain in adults and children.  The Z-lab 
studies the functional differentiation of the human brain across early 
development and adulthood, and the plasticity of the brain in response to 
disorders and injury (see zeynepsaygin.com for recent 
publications). The primary responsibilities will include programming, running, 
and analyzing behavioral and brain-imaging experiments using functional 
magnetic resonance imaging (fMRI), diffusion weighted imaging (DWI), functional 
connectivity, and behavioral evaluations of infants, children, and adults.  
This position is an excellent opportunity for individuals considering future 
graduate studies. We are seeking an aspiring, self-motivated researcher with 
strong coding/programming skills who is excited about the developing brain, 
cognitive neuroscience, and/or clinical disorders and demonstrates evidence of 
a serious interest in a career in the field.
Required: strong mathematical, statistical, and coding skills (e.g., MATLAB, 
Python, shell scripting); strong interpersonal skills for interacting with a 
diverse group of people including children and parents; a bachelor's degree in 
psychology, neuroscience, cognitive science, computer science, data science, 
engineering, physics, or math; and strong organizational skills.
Interested individuals should contact saygi...@osu.edu 
with a CV and names of 2-3 references.

POSTDOCTORAL FELLOW, The Ohio State University, Dept. of Psychology – Dr. 
Zeynep Saygin’s Lab.  We seek an outstanding scientist with a recent Ph.D. in 
cognitive neuroscience, developmental psychology, or related area, who has 
experience with neuroimaging methods (MRI, fMRI, DWI, and/or functional 
connectivity) and who is interested in any or all of the following: 
understanding the functional and structural architecture of the brain, how it 
develops in healthy individuals, and how it changes with disorders and brain 
injury in both adults and children.  See 
zeynepsaygin.com for recent publications.  The fellow 
will be involved in conducting and planning behavioral and neuroimaging 
research studies in neonates, infants, children, and adults. Proficiency in 
programming is necessary.   This position is fully funded.  Initial hire is for 
one year with additional years contingent on fit and progress.
OSU is located in Columbus, Ohio and is home to a vibrant community of 
cognitive neuroscientists, computational modelers, and vision scientists in the 
Psychology Department and Center for Cognitive and Brain Sciences.  Fellows 
will have access to state-of-the-art MRI and EEG facilities located inside the 
Psychology building.
Interested individuals should contact saygi...@osu.edu 
with a CV, names of 3 references, and a statement of research interests.
---
Zeynep M. Saygin, Ph.D.
Assistant Professor of Psychology
The Ohio State University
205 Psychology Bldg. 1835 Neil Ave
Columbus, OH 43210
614-292-3059
zlab

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Re: [Freesurfer] Volume are different in asegstats vs matlab

[Bruce Fischl]

Hi Kristine

the aseg.stats volume uses partial volume correction to get subvoxel 
accuracy.


cheers
Bruce
On Fri, 23 Mar 2018, Lee Subin Kristine wrote:



Hi,

 

I have a question about volume info from freesurfer vs matlab.


I am looking at, say, the left hippocampus volume from asegstats, which was 
3778.2 mm^3.
When I try to get the same volume by loading aseg.nii on matlab, however, I get 
a different number,
3945.

For matlab, I used the following command, which counts the number of voxels 
equal to the left
hippocampus segment id:
length(find(aseg.img==17))

This was done after I converted the original aseg.mgz file into native space, 
using 2 different
methods:
(1) mri_convert -rl rawavg.mgz -rt nearest -i aseg.mgz -o bert_aseg.nii

(2) mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o bert_aseg.nii 
--regheader aseg.mgz
In both cases, the output was 3945.

The rawavg.mgz used here is also 1mm isovoxel, so I don't think it is due to 
the difference in voxel
dimensions.

 

What could be the cause of the difference in volume?

Thanks,

Kristine

 

 

 

 

Sent from Mail for Windows 10

 


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[Freesurfer] using T2 for hippo subfields

[Alexopoulos, Dimitrios]

Hi. We are acquiring sequences on a pediatric cohort that include a T1-mprage 
(0.8mm isotropic) and a T2-space (1mm isotropic), and I'd like to run the 
hippocampal subfields module on the subjects using FS 6.0.

Is it recommended/useful to run the multispectral segmentation mode with the 
additional lower resolution T2 sequence?
I read that you really only benefit if the T2 is of similar or better 
resolution than the T1.

If that's the case, would it be best to just run with the single T1 but with 
the hi-res flag in the recon-all command?

Thanks.
Jim






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Re: [Freesurfer] using T2 for hippo subfields

[Iglesias Gonzalez, Eugenio]

Hi Jim,
In the end it’s an empirical question, but my gut feeling is that the T1 with 
hi-res flag will be best.
Cheers,
/E

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From:  on behalf of "Alexopoulos, 
Dimitrios" 
Reply-To: Freesurfer support list 
Date: Friday, 23 March 2018 at 16:00
To: Freesurfer support list 
Subject: [Freesurfer] using T2 for hippo subfields

Hi. We are acquiring sequences on a pediatric cohort that include a T1-mprage 
(0.8mm isotropic) and a T2-space (1mm isotropic), and I’d like to run the 
hippocampal subfields module on the subjects using FS 6.0.

Is it recommended/useful to run the multispectral segmentation mode with the 
additional lower resolution T2 sequence?
I read that you really only benefit if the T2 is of similar or better 
resolution than the T1.

If that’s the case, would it be best to just run with the single T1 but with 
the hi-res flag in the recon-all command?

Thanks.
Jim






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Re: [Freesurfer] Different DWI protocols

[Cano Catala, Marta]

Hi,

Have you been able to read my follow-up question?

Thanks,

M. Cano

De: Cano Catala, Marta
Enviado: lunes, 19 de marzo de 2018 13:33
Para: Freesurfer support list
Asunto: Re: [Freesurfer] Different DWI protocols

Thank you for your reply. I see that it is not a good idea to mix within 
subjects DWI acquisition protocols. Regarding between subjects DWI acquisiton 
protocols, I only have one sample and my aim is to evaluate within subjects 
changes after a treatment (I'm not going to evaluate between subjects). In this 
case, could I use different acquisition protocols between subjects? And if I 
finally used different acquisition protocols should I correct for that in a 
second level?

Thanks,

M. Cano

De: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] en nombre de Yendiki, Anastasia 
[ayend...@mgh.harvard.edu]
Enviado: lunes, 19 de marzo de 2018 12:39
Para: Freesurfer support list
Asunto: Re: [Freesurfer] Different DWI protocols

Probably not a good idea, depending on how the data are balanced across 
acquisition protocols. If you find differences between time points of subjects 
or between subjects, you want to be ensure that those differences are not 
because of acquisition differences. If, for example time point is always 
collected with one protocol and time point 2 is always collected with another, 
you won’t be able to tell.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Cano Catala, Marta" 
mailto:mcanocat...@mgh.harvard.edu>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Monday, March 19, 2018 at 11:20 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Different DWI protocols

Dear TRACULA experts,

I'm running a longitudinal trac-all analysis and I'm wondering whether or not I 
could include different DWI acquisition protocols both between subjects and 
within subjects in the same analysis.

Thank you,

M. Cano


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Re: [Freesurfer] Different DWI protocols

[Yendiki, Anastasia]

It's possible that the differences between time points are different for each 
of the acquisition protocols. In that case, by adding a different acquisition 
protocol, you may be increasing the variability of your effect across subjects, 
in which case you'd need a bigger effect size to be able to detect it. You can 
include the protocol as a linear regressor, but it's unlikely that this is a 
perfect solution. If you have a choice, it's best to stick to the same protocol.


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Cano Catala, Marta 

Sent: Monday, March 19, 2018 1:33:15 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Different DWI protocols

Thank you for your reply. I see that it is not a good idea to mix within 
subjects DWI acquisition protocols. Regarding between subjects DWI acquisiton 
protocols, I only have one sample and my aim is to evaluate within subjects 
changes after a treatment (I'm not going to evaluate between subjects). In this 
case, could I use different acquisition protocols between subjects? And if I 
finally used different acquisition protocols should I correct for that in a 
second level?

Thanks,

M. Cano

De: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] en nombre de Yendiki, Anastasia 
[ayend...@mgh.harvard.edu]
Enviado: lunes, 19 de marzo de 2018 12:39
Para: Freesurfer support list
Asunto: Re: [Freesurfer] Different DWI protocols

Probably not a good idea, depending on how the data are balanced across 
acquisition protocols. If you find differences between time points of subjects 
or between subjects, you want to be ensure that those differences are not 
because of acquisition differences. If, for example time point is always 
collected with one protocol and time point 2 is always collected with another, 
you won’t be able to tell.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Cano Catala, Marta" 
mailto:mcanocat...@mgh.harvard.edu>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Monday, March 19, 2018 at 11:20 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Different DWI protocols

Dear TRACULA experts,

I'm running a longitudinal trac-all analysis and I'm wondering whether or not I 
could include different DWI acquisition protocols both between subjects and 
within subjects in the same analysis.

Thank you,

M. Cano


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Re: [Freesurfer] Functional Overlap Map

[nm644]

Thank you very much!

> On Mar 22, 2018, at 2:31 PM, Douglas Greve  wrote:
> 
> you can view it with
> tksurferfv fsaverage lh inflated -aparc -overlay conjunction.nii.gz -fminmax 
> 2 5
> tksurferfv is a front-end for freeview. You can change the thresholds in 
> freeview
> 
> On 3/22/18 12:27 PM, nm644 wrote:
>> Thank you for the quick reply.
>> 
>> As you may be able to tell I'm a bit new at this so am still unsure about 
>> some things but yes a conjunction analysis is exactly what I want to do. 
>> Just a little more background, all the tasks are exactly the same in that 
>> they all have a null condition (set to 0 in all the paradigm files) with the 
>> same duration and the ON of all tasks also has the same duration across all 
>> tasks. I've also set the ON blocks in the 3 different paradigm files to be 
>> 1,2,3 instead of all being 1.
>> 
>> Thus far I've done:
>> 
>> 1)
>> mkanalysis-sess \
>>   -fsd bold -stc up -surface fsaverage lh -fwhm 5 \
>>   -event-related -paradigm para.tsv -nconditions 3 \
>>   -spmhrf 0 -TR 0.984 -refeventdur 24 -nskip 2 -polyfit 2 \
>>   -analysis conjunction_analysis.lh  -per-run -force
>> 
>> 2) Create all the contrasts
>> mkcontrast-sess -analysis conjunction_analysis.lh -contrast task-1 -a 1
>> mkcontrast-sess -analysis conjunction_analysis.lh -contrast task-2 -a 2
>> mkcontrast-sess -analysis conjunction_analysis.lh -contrast task-3 -a 3
>> 
>> 3) Run the analysis with
>> selxavg3-sess -s subj01 -analysis conjunction_analysis.lh \
>> -c task-1 \
>> -c task-2 \
>> -c task-3
>> 
>> Then cd into subj01/bold/conjunction_analysis.lh
>>  
>> and finally
>> 
>> 4) mri_concat
>> mri_concat lang-cond-1/sig.nii.gz lang-cond-2/sig.nii.gz 
>> lang-cond-3/sig.nii.gz --conjunct 
>> --o conjunction.nii.gz
>> 
>> Does this look right? Also, what would be the proper command to view the 
>> conjunction after running this? Sorry this is very long winded, I just want 
>> to make sure I'm doing everything properly.
>> 
>> Thank you again!
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>  on behalf of Douglas N. Greve 
>> 
>> Sent: Tuesday, March 20, 2018 7:25:31 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Functional Overlap Map
>>  
>> I'm not entirely sure what you are doing. It sounds like you have 3 
>> different conditions and want to find out where the activation for all 
>> conditions overlaps. But what you have done is to combine all conditions 
>> into a single condition, so you are seeing where the average activation 
>> is, which is different than the overlap (and why it looks to have to 
>> much of an extent). To do what you want to do, you should model each 
>> condition as a separate condition in mkanalysis (ie, -nconditions 3 and 
>> change your paradigm file), set up 3 contrasts (one for each condition, 
>> ie, -a 1, -a 2, -a 3), then you will need to do a conjunction analysis 
>> (mri_concat con1/sig.nii.gz con2/sig.nii.gz con3/sig.nii.gz --conjunct 
>> --o conjunction.nii.gz). You can then view the conjunction with freeview 
>> (or tksurfer/tkmedit)
>> 
>> 
>> On 03/20/2018 06:30 PM, nm644 wrote:
>> >
>> > Hello Freesurfer experts,
>> >
>> > My question may have already been solved in a previous thread. I have 
>> > three runs of block-design bold scans. All three are quite similar. 
>> > They all have only 2 blocks, one for rest and one for task. I’m trying 
>> > to create a functional map that displays where the functional 
>> > activation of these three runs overlap. I used the code below with no 
>> > errors:
>> >
>> > preproc-sess -s subj01 -fsd bold -stc up -surface fsaverage lhrh 
>> > -mni305 -fwhm 5 -per-run
>> >
>> > mkanalysis-sess \
>> >
>> >   -fsd bold -stc up -surface fsaverage lh -fwhm 5 \
>> >
>> > -event-related -paradigm para.tsv -nconditions 1 \
>> >
>> >   -spmhrf 0 -TR 0.984 -refeventdur 24 -nskip 2 -polyfit 2 \
>> >
>> >   -analysis TaskOverlap.lh  -per-run -force
>> >
>> > mkcontrast-sess -analysis TaskOverlap.lh -contrast con1 -a 1
>> >
>> > selxavg3-sess -s subj01 -analysis TaskOverlap.lh
>> >
>> > And to display:
>> >
>> > tksurfer-sess -s subj01 \
>> >
>> > -analysis TaskOverlap.lh \
>> >
>> > -c con1
>> >
>> > Or
>> >
>> > tksurfer-sess -s subj01 \
>> >
>> > -analysis TaskOverlap.lh \
>> >
>> > -c con1 -map fsig
>> >
>> > The problem is that when I view the output it seems that there’s far 
>> > more activation than there should be when trying to find mutual 
>> > overlap between the three tasks. If anyone has any suggestions it 
>> > would be much appreciated.
>> >
>> > Have a great day!
>> >
>> >
>> >
>> > ___
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>> 
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>> 
>> 
>> The information in this e-mail is inte

Re: [Freesurfer] Hippocampal Subfields Module, output error

[Hurtado, Aura Maria]

Thanks, Eugenio. We used the stable 6 version for reconall:
reconall -all back in 06 13 2017,
this is the build-stamp.txt: 
freesurfer-Linux-centos6_x86_64-stable-v6-20170215-dc3d7a6
reconall -long back in 02 27 2018,
this is the build-stamp.txt: 
freesurfer-Linux-centos7_x86_64-stable-v6-20161229-80ac5eb

I did use a development version for the hippocampal analyses on 02/28, 03/01 
and 03/02. I can’t find any specific references to those…

Aura M.






On Mar 23, 2018, at 5:43 AM, Iglesias Gonzalez, Eugenio 
mailto:e.igles...@ucl.ac.uk>> wrote:

Thanks, Aura.
What exact version of FreeSurfer are you using? I’m assuming it’s a development 
version, but from when? The results are indeed weird…

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Hurtado, Aura Maria" 
mailto:ahurt...@mgh.harvard.edu>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Friday, 23 March 2018 at 05:28
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Hippocampal Subfields Module, output error

Hi Eugenio,

Thank you for replying so quickly to my lengthy message. I correct some of my 
statements,

1. Matlab 8.4 was used (not 8.2)
2. When I ran the cross-sectional subfield command, I did not get exit errors 
as I did with the longitudinal command (kvlGetOptimizer). I got output errors 
and warnings of non convergence in the log file.

-I see your point. I mean the built-in hippocampal module (v10) worked when 
reconall was run with fs60 (hippoSf). When run independently, the hippocampal 
module (v21) exited with errors when using segmentHA_T1_long.sh, and the output 
was off when using segmentHA_T1.sh (this is better seen in pic 3). I hope this 
clarifies a bit. Please tell me if it doesn’t.

These are screenshots of the images output by jobs that exited without 
processing errors:

Pic 1 is an overlay of:
rh.hippoAmygLabels-T1 and lh.hippoAmygLabels-T1 output by segmentHA_T1_long.sh 
SUBJ1_timepoint1.long.SUBJ1_basetemplate
aseg and T1 output by fs60 reconall -long
(I am now noticing these *.long.* directories contain hippoSfVolumes text 
files, but not hippoSfLabels mgz files...)



Pic 2 is an overlay of:
rh.hippoAmygLabels-T1 and lh.hippoAmygLabels-T1 output by segmentHA_T1.sh 
SUBJ1_timepoint1.long.SUBJ1_basetemplate
aseg and T1 output by fs60 reconall




Pic 3 is an overlay of:
rh.hippoAmygLabels-T1 output by segmentHA_T1.sh SUBJ1_timepoint1
aseg, T1 and lh.hippoSfLabels-T1.v10 output by fs60 reconall



Thanks again

Aura M.






On Mar 21, 2018, at 6:33 PM, Iglesias Gonzalez, Eugenio 
mailto:e.igles...@ucl.ac.uk>> wrote:

Hi Aura,

1. What do you mean by “loading Matlab 8.2”? It should be Matlab 8.4 (2014b).
2. “Some still did”: what error did you get?

- Also, I’m confused by what you wrote, that subfields worked but hippocampal 
module didn’t (aren’t they the same thing?)
- Finally: can you please send us a screenshot of one of those abruptly cut 
hippocampi, so I better understand what might be going on?

Cheers,

/Eugenio


--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Hurtado, Aura Maria" 
mailto:ahurt...@mgh.harvard.edu>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Wednesday, 21 March 2018 at 22:24
To: "freesurfer@nmr.mgh.harvard.edu" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Hippocampal Subfields Module, output error

Hi,

I am attempting to use the longitudinal pipeline of the "hippocampal subfields 
and nuclei of amygdala”, but keep getting a flawed output.

My dataset consists of images from a longitudinal study with some dropouts. 
First, I ran the reconall longitudinal pipeline in fs60 for all subjects. I got 
no errors. Then, I tried

1. Running the longitudinal pipeline of the hippocampal module, loading Matlab 
8.2 to run
segmentHA_T1_long.sh SUBJ1_basetemplate
segmentHA_T1_long.sh SUBJ2_basetemplate
etc

I got an error in most of these jobs (mostly for templates of subjects with 
multiple visits) that read

"ERROR: MatlabObjectArray(0x7fd7ce84cea0): Trying to access non-existing object 
(25)

Error in kvlGetOptimizer (line 11)

Error in SegmentSubfieldsT1Longitudinal (line 1155)”

2. I then tried running the cross sectional pipeline for each one of the 
timepoints in subjects already processed by the reconall longitudinal pipeline 
(i. e. segmentations in the  .long. directories)
segmentHA_T1.sh SUBJ1_timepoint1.long.SUBJ1_basetemplate
segmentHA_T1.sh SUBJ1_timepoint2.long.SUBJ1_basetemplate
segmentHA_T1.sh SUBJ2_timep