[Freesurfer] Permutation with Non-Ortohgonal Matrices

2020-03-26 Thread Hua, Jessica 
External Email - Use Caution

Hi FreeSurfer Experts,

I am trying to correct for multiple comparisons by running a permutation for a 
non-orthogonal design. Based on reading through the blog, I came up with the 
follow script:


mri_glmfit-sim --glmdir rh.volume.AgeSex.10.glmdir --sim perm-resid 1000 3.0 
--sim-sign abs --cwp 0.05 --2spaces

I am getting the following error message:


ERROR: Flag abs unrecognized.

And when I tried to put the "abs" after "1000 3.0," I got the error message 
saying that I needed to specify the --sim-sign.

Could you please let me know how I need to edit my script? I have already run 
mris_preproc and mri_glmfit. Thanks!

---

Jessica Hua, M.A.
Cognitive and Emotional Control Lab
Doctoral Candidate Clinical Psychology
University of Missouri
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Re: [Freesurfer] Convert cespct.nii to subject's own anatomy space (for ROI analysis)

2020-03-26 Thread Douglas N. Greve 
Why are you converting it to the volume? You can load the surf-based 
file in matlab with

ces = MRIread('ces.nii.gz');
You can load the label with labe_read.m (or read_label.m, can't remember)


On 3/22/2020 12:15 PM, Star Xi wrote:


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Hi FS experts,

I’m processing the task related fMRI data and want to extract the 100 
most strongly activated voxels with in each of the visual areas (like 
V1-V3, V3A, MT etc.). It seems to I need to do the ROI analysis using 
matlab.
I meet some problems when convert files from surface space to volume 
space.


Here’s my procedures:
1. For each individual, convert cespct.nii  to volume space 
(individual space)
mri_vol2vol —mov ces.nii.gz --reg sub/bold/register.lta --fstarg 
--interp nearest --o cespct.anat.nii (dimension 256*256*256)
However, when I use MRIread to import the file, I find the values in 
cespct.anat.nii are all 0.


2. convert label  to volume space (individual space)
I want to convert label to the individual space (mri_label2label 
--outmask) and then convert it to volume space (mri_vol2vol).
mri_label2label --srclabel lh.V3A.label --srcsubject fsaverage 
--trglabel lh.v3a.sub.label --trgsubject sub --regmethod surface 
--hemi lh --outmask lh.v3a.sub.nii

mri_info lh.v3a.sub.nii (dimension is 144775x1x1, not 163842x1x1)
I’m wondering how can I have a mask in subject’s anatomy space using a 
label ?

Is there anything wrong during the transformation?
Any suggestions will be appreciated !
THANK YOU!
Star

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Re: [Freesurfer] Is it possible to "fill in" the region delimited by an ROI label?

2020-03-26 Thread Douglas N. Greve 
Sorry, I missed that you were in the volume. Try using mri_label2vol, 
something like

mri_label2vol
  --label lh.entorhinal.label
  --temp orig.mgz
  --identity
  --fillthresh .01
  --subject subjectname
  --fill-ribbon
  --o lh.ento.mgz



On 3/20/2020 11:08 PM, Mohammad Rashid wrote:


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Hello Dr. Greve,

Thank you for the response. I have extensively searched through the 
options available to me in freeview, but I could not find any sort of 
checkbox that turns off outline mode. Here is what I see, having 
selected the label file: https://i.imgur.com/Rk57Qyh.png . I've gone 
through the menus along the top as well, but to no avail. Could you 
direct me to the checkbox you mentioned?


I am using freesurfer 6.0 and freeview 2.0.

Thank you,
Mohammad



*From:* Mohammad Rashid <17m...@queensu.ca>
*Sent:* Thursday, March 19, 2020 1:11 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Is it possible to "fill in" the region delimited by an ROI 
label?

Hi all,

I'm able to load in a yellow outline for the entorhinal region by 
loading a file named ?h.entorhinal_exvivo.label as a volume. (I first 
load in a brain image such as brain.mgz, and then display the outline 
on top of it.) Is it possible to get a solid highlight of the 
entorhinal region in this manner, as opposed to just an outline of the 
region?


(Strangely enough, if I load ?h.entorhinal_exvivo.label as a label on 
an surface file, such as ?h.inflated, then the entorhinal region is 
seen filled in with a yellow color on the 3D surface. This is the 
effect I want, except on a 2D volume.)


Any help is greatly appreciated,
Mohammad

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Re: [Freesurfer] Hippocampal Volume Extraction

2020-03-26 Thread Bruce Fischl 

Hi Devika

the volumes should be in the stats/aseg.stats file for each subject.

cheers
Bruce
On Thu, 
26 Mar 2020, Devika K wrote:




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Hi,

I want to extract hippocampal volume from longitudinal samples. I am less
aware of it. I ran recon-all-all with longitudinal pipeline for all those
samples.

How I need to process further (Commands that I need to follow).
Would you please help me out?



Thanks and Regards
Devika K


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Re: [Freesurfer] Misalignment of boundaries and T1 (Freesurfer/SamSrf)

2020-03-26 Thread Bruce Fischl 

Hi Mason

not sure we can help if everything looks good in freeview. Doesn't that 
make it a SamSrf issue? Or an interface between the two packages? Have you 
checked with their support?


cheers
Bruce


On Thu, 26 Mar 2020, Mason Wells wrote:


   External Email - Use Caution

In the event that Bruce might not be able to help. I ask if anyone else on the 
list has experience with the problem described in this thread? Any help would 
be greatly appreciated.

Best wishes,
Mason

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: wells...@cardiff.ac.uk
Tel: 02920 879628
Web: Cardiff University webpage 

Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: wells...@caerdydd.ac.uk
Ffôn: 02920 879628


On 25/03/2020, 18:38, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Mason 
Wells"  
wrote:

   External Email - Use Caution

   HI Bruce,

   Ok, great. I just thought some sections of white matter had not been traced 
in their entirety (see red crosshair in attached image). If you think this all 
looks reasonable, please can you advise on the misaligned as outlined in the 
original post?

   Best wishes,
   Mason

   Mason T Wells, MSc
   PhD student
   School of Optometry and Vision Sciences
   & Cardiff University Brain Research
   Imaging Centre (CUBRIC), School of Psychology
   Cardiff University
   Cardiff
   CF24 4HQ
   UK

   Email: wells...@cardiff.ac.uk
   Tel: 02920 879628
   Web: Cardiff University webpage 

   Mason T Wells, MSc
   Myfyriwr PhD
   Yr Ysgol Optometreg a Gwyddorau’r Golwg
   & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
   Prifysgol Caerdydd
   Heol Maindy
   Caerdydd
   CF24 4HQ
   DU

   E-bost: wells...@caerdydd.ac.uk
   Ffôn: 02920 879628


   On 25/03/2020, 17:29, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce 
Fischl"  wrote:

   Hi Mason

   I can't tell from those images except that it looks reasonable
   cheers
   Bruce
   On Wed, 25
   Mar 2020, Mason Wells wrote:

   >External Email - Use Caution
   >
   > Hi again Bruce,
   >
   > I have now installed the relevant libpng packages and have freeview 
open. The segmentation doesn’t look brilliant in some areas. What do you think?
   >
   > Mason T Wells, MSc
   > PhD student
   > School of Optometry and Vision Sciences
   > & Cardiff University Brain Research
   > Imaging Centre (CUBRIC), School of Psychology
   > Cardiff University
   > Cardiff
   > CF24 4HQ
   > UK
   >
   > Email: wells...@cardiff.ac.uk
   > Tel: 02920 879628
   > Web: Cardiff University webpage 

   > Mason T Wells, MSc
   > Myfyriwr PhD
   > Yr Ysgol Optometreg a Gwyddorau’r Golwg
   > & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr 
Ysgol Seicoleg
   > Prifysgol Caerdydd
   > Heol Maindy
   > Caerdydd
   > CF24 4HQ
   > DU
   >
   > E-bost: wells...@caerdydd.ac.uk
   > Ffôn: 02920 879628
   >
   >
   > On 25/03/2020, 16:28, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Mason 
Wells"  
wrote:
   >
   >External Email - Use Caution
   >
   >Hi Bruce,
   >
   >I get the following error message when I try to load freeview
   >
   >Setting up environment for FreeSurfer/FS-FAST (and FSL)
   >FREESURFER_HOME   /usr/local/freesurfer
   >FSFAST_HOME   /usr/local/freesurfer/fsfast
   >FSF_OUTPUT_FORMAT nii.gz
   >SUBJECTS_DIR  /usr/local/freesurfer/subjects
   >MNI_DIR   /usr/local/freesurfer/mni
   >FSL_DIR   /usr/local/fsl
   >masontwells@masontwells-VIG800S:~$ freeview
   >freeview.bin: error while loading shared libraries: libpng12.so.0: 
cannot open shared object file: No such file or directory
   >
   >Mason T Wells, MSc
   >PhD student
   >School of Optometry and Vision Sciences
   >& Cardiff University Brain Research
   >Imaging Centre (CUBRIC), School of Psychology
   >Cardiff University
   >Cardiff
   >CF24 4HQ
   >UK
   >
   >Email: wells...@cardiff.ac.uk
   >Tel: 02920 879628
   >Web: Cardiff University webpage 

   >Mason T Wells, MSc
   >Myfyriwr PhD
   >

Re: [Freesurfer] training set

2020-03-26 Thread Bruce Fischl 
Have you checked the original aseg paper? If not, then it will be in 
Rahul's cortical parcellation one as it is the same data


cheers
Bruce

On Thu, 26 Mar 2020, javier quilis wrote:



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Hi Bruce, 

thanks for the answer. Is there any paper where this is explained? I want to
detail this in my paper and I would like to refer to the source. 

Thanks again, 
Javier


De: freesurfer-boun...@nmr.mgh.harvard.edu
 en nombre de Bruce Fischl

Enviado: miércoles, 25 de marzo de 2020 14:40
Para: Freesurfer support list 
Asunto: Re: [Freesurfer] training set  
Hi Javier

no, that's not correct, depending on which training set you mean. For the
Bayesian segmentation (aseg) we used 40 datasets distributed in age and
pathology (10 each for young, middle age, elderly and AD).

cheers
Bruce
On Wed, 25 Mar
2020, javier quilis wrote:

>
> External Email - Use Caution
>
> Thanks for the answer. 
>
> I can not open the power point for some reason. Is there any paper where I
> can check this? I think the dataset used by freesurfer is in the MNI
Average
> Brain (305 MRI) Stereotaxic Model and this dataset only use MRIs from
young
> people, is this correct?
>
> Thanks again.
> Bests, 
> Javier
>
>
>
>
>
>___
_
> De: freesurfer-boun...@nmr.mgh.harvard.edu
>  en nombre de Douglas N. Greve
> 
> Enviado: viernes, 20 de marzo de 2020 15:39
> Para: freesurfer@nmr.mgh.harvard.edu 
> Asunto: Re: [Freesurfer] training set  
> Try the tutorial slides
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI
> It does not go into a lot of detail, but it will give you the relevant
> lectures
>
>
> On 3/17/2020 8:54 AM, javier quilis wrote:
>
>   External Email - Use Caution
>
>   Hello everyone, 
>
> I'm trying to do a study of a comparison between the automated methods
> to analyze structural MRI from FSL and Freesurfer. I am interested in
> the training set used by Freesurfer to do the brain segmentation and I
> can not find a detailed description of it. Is there any source where
> this set is described?
>
> Thanks in advance.
> Bests, 
> Javier Quilis
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
>

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Re: [Freesurfer] Hippocampal Volume Extraction

2020-03-26 Thread Devika K 
External Email - Use Caution

Hi,

I want to extract hippocampal volume from longitudinal samples. I am less
aware of it. I ran recon-all-all with longitudinal pipeline for all those
samples.

How I need to process further (Commands that I need to follow).
Would you please help me out?



Thanks and Regards
Devika K
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Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] Misalignment of boundaries and T1 (Freesurfer/SamSrf)

2020-03-26 Thread Mason Wells 
External Email - Use Caution

In the event that Bruce might not be able to help. I ask if anyone else on the 
list has experience with the problem described in this thread? Any help would 
be greatly appreciated.

Best wishes,
Mason 

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff   
CF24 4HQ
UK
 
Email: wells...@cardiff.ac.uk
Tel: 02920 879628
Web: Cardiff University webpage 

Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd   
CF24 4HQ 
DU
 
E-bost: wells...@caerdydd.ac.uk
Ffôn: 02920 879628
 

On 25/03/2020, 18:38, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Mason Wells"  wrote:

External Email - Use Caution

HI Bruce,

Ok, great. I just thought some sections of white matter had not been traced 
in their entirety (see red crosshair in attached image). If you think this all 
looks reasonable, please can you advise on the misaligned as outlined in the 
original post?

Best wishes,
Mason 

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff   
CF24 4HQ
UK
 
Email: wells...@cardiff.ac.uk
Tel: 02920 879628
Web: Cardiff University webpage 

Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr 
Ysgol Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd   
CF24 4HQ 
DU
 
E-bost: wells...@caerdydd.ac.uk
Ffôn: 02920 879628
 

On 25/03/2020, 17:29, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Bruce Fischl"  wrote:

Hi Mason

I can't tell from those images except that it looks reasonable
cheers
Bruce
On Wed, 25 
Mar 2020, Mason Wells wrote:

>External Email - Use Caution 
>
> Hi again Bruce,
>
> I have now installed the relevant libpng packages and have freeview 
open. The segmentation doesn’t look brilliant in some areas. What do you think?
>
> Mason T Wells, MSc
> PhD student
> School of Optometry and Vision Sciences
> & Cardiff University Brain Research
> Imaging Centre (CUBRIC), School of Psychology
> Cardiff University
> Cardiff
> CF24 4HQ
> UK
>
> Email: wells...@cardiff.ac.uk
> Tel: 02920 879628
> Web: Cardiff University webpage 

> Mason T Wells, MSc
> Myfyriwr PhD
> Yr Ysgol Optometreg a Gwyddorau’r Golwg
> & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), 
Yr Ysgol Seicoleg
> Prifysgol Caerdydd
> Heol Maindy
> Caerdydd
> CF24 4HQ
> DU
>
> E-bost: wells...@caerdydd.ac.uk
> Ffôn: 02920 879628
>
>
> On 25/03/2020, 16:28, "freesurfer-boun...@nmr.mgh.harvard.edu on 
behalf of Mason Wells"  wrote:
>
>External Email - Use Caution
>
>Hi Bruce,
>
>I get the following error message when I try to load freeview
>
>Setting up environment for FreeSurfer/FS-FAST (and FSL)
>FREESURFER_HOME   /usr/local/freesurfer
>FSFAST_HOME   /usr/local/freesurfer/fsfast
>FSF_OUTPUT_FORMAT nii.gz
>SUBJECTS_DIR  /usr/local/freesurfer/subjects
>MNI_DIR   /usr/local/freesurfer/mni
>FSL_DIR   /usr/local/fsl
>masontwells@masontwells-VIG800S:~$ freeview
>freeview.bin: error while loading shared libraries: libpng12.so.0: 
cannot open shared object file: No such file or directory
>
>Mason T Wells, MSc
>PhD student
>School of Optometry and Vision Sciences
>& Cardiff University Brain Research
>Imaging Centre (CUBRIC), School of Psychology
>Cardiff University
>Cardiff
>CF24 4HQ
>UK
>
>Email: wells...@cardiff.ac.uk
>Tel: 02920 879628
>Web: Cardiff University webpage 

>Mason T Wells, MSc
>Myfyriwr PhD
>Yr Ysgol Optometreg a Gwyddorau’r Golwg
>

Re: [Freesurfer] training set

2020-03-26 Thread javier quilis 
External Email - Use Caution

Hi Bruce,

thanks for the answer. Is there any paper where this is explained? I want to 
detail this in my paper and I would like to refer to the source.

Thanks again,
Javier


De: freesurfer-boun...@nmr.mgh.harvard.edu 
 en nombre de Bruce Fischl 

Enviado: miércoles, 25 de marzo de 2020 14:40
Para: Freesurfer support list 
Asunto: Re: [Freesurfer] training set

Hi Javier

no, that's not correct, depending on which training set you mean. For the
Bayesian segmentation (aseg) we used 40 datasets distributed in age and
pathology (10 each for young, middle age, elderly and AD).

cheers
Bruce
On Wed, 25 Mar
2020, javier quilis wrote:

>
> External Email - Use Caution
>
> Thanks for the answer.
>
> I can not open the power point for some reason. Is there any paper where I
> can check this? I think the dataset used by freesurfer is in the MNI Average
> Brain (305 MRI) Stereotaxic Model and this dataset only use MRIs from young
> people, is this correct?
>
> Thanks again.
> Bests,
> Javier
>
>
>
>
>
> 
> De: freesurfer-boun...@nmr.mgh.harvard.edu
>  en nombre de Douglas N. Greve
> 
> Enviado: viernes, 20 de marzo de 2020 15:39
> Para: freesurfer@nmr.mgh.harvard.edu 
> Asunto: Re: [Freesurfer] training set
> Try the tutorial slides
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI
> It does not go into a lot of detail, but it will give you the relevant
> lectures
>
>
> On 3/17/2020 8:54 AM, javier quilis wrote:
>
>   External Email - Use Caution
>
>   Hello everyone,
>
> I'm trying to do a study of a comparison between the automated methods
> to analyze structural MRI from FSL and Freesurfer. I am interested in
> the training set used by Freesurfer to do the brain segmentation and I
> can not find a detailed description of it. Is there any source where
> this set is described?
>
> Thanks in advance.
> Bests,
> Javier Quilis
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
>
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