Re: [Freesurfer] Queries on Freeview and opening files of 'stat' and 'surf' folders

[Koustav Chatterjee]

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Thanks Ruopeng.
Can you please answer *why I won't be able to open files in 'stat','surf'
folder.* It seems an application is required to open it. Can you tell
please?
Thank you,
KC

On Fri, Oct 2, 2020 at 8:25 PM Wang, Ruopeng  wrote:

> Hi KC,
>
> Freeview is a comprehensive volume and surface viewer and editor. You can
> load mri, surf and label files in it. Regarding your last question, if you
> meant going through slices, you can use up/down arrow keys. If you meant
> going through different volume images, you can use Alt+C key to cycle
> through them.
>
> Best,
> Ruopeng
>
> On Oct 2, 2020, at 2:44 AM, Koustav Chatterjee <
> chatterjeekous...@gmail.com> wrote:
>
> External Email - Use Caution
>
>
> Dear Sir,
>
> I have stuck with two basic steps while installing FreesUrfer in my new
> system. May I request you to help me resolving the problem.
>
> 1. After successful completion of  'recon-all' command , a folder named as
> 'samplept1' has been formed under /usr/local/freesurfer/subjects.
> Subjectpt1 consists of different folders including 'label', 'mri', 'stat',
> 'surf' etc. Now, I was trying to acquire data from 'surf' and 'stat'
> folders. However, I am unable to open them. It seems to me a specific
> application is required. Please advise.
>
> 2. Could you please explain what is the purpose of having 'freeview'. Is
> it only only to check manually whether all the preprocessing steps such as
> skull stripping has been done correctly by recon-all or not?
>
> 3. I am unable to surf images  one by one using  "P age up and down keys
> in keyboard". How should I surf the images one by one?
>
> Your help is appreciated.
>
> Thank you very much.
> KC
>
>
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>
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Re: [Freesurfer] Seed ROI FC

[Douglas N. Greve]

Do you have a /scratch folder?
Also, please send the full terminal output

On 10/2/2020 5:44 AM, Lorenzo Pini wrote:


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Dear expert

I'm trying to perform FC seed ROI analysis through FSfast pipeline
After preprocessing I run:
selxavg3-sess -s subject1 -a fsrest.surf.lh -no-con-ok -svres

but I got the following error:
ERROR: /bin/bash: 
/scratch/tp9f57a7bb_2ea1_450b_b0e8_8cdd47a2eb8b.load_nifti.m.nii: No 
such file or directory
ERROR: loading 
/home/user/Desktop/test/subjects/subject1/fsrest/001/fmcpr.sm5.self.lh.nii.gz 
as analyze
ERROR: attempting to read 
/home/user/Desktop/test/subjects/subject1/fsrest/001/fmcpr.sm5.self.lh

--
ERROR: fast_selxavg3() failed\n

Moreover, I'm a bit confused how to compute whole brain seed-ROI 
surface map, using a pre-specified seed ROI created in orig.mgz space 
(sphere 5mm)


Thanks in advance,
Lorenzo

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Re: [Freesurfer] QDEC command not found

[Douglas N. Greve]

We are no longer distributing or supporting qdec

On 10/2/2020 6:17 AM, Enrico Collantoni wrote:


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Dear freesurfer experts,
I installed the 7.1.1 version of freesurfer in iOS enviroment (10.15.4). I could run the 
recon-all without any problems. However, trying to open qdec I obtain "command not 
found". I've never had this problem with previous versions.
Could you help me?
Many thanks
Enrico Collantoni

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Re: [Freesurfer] Use ICV measures from freesurfer v7.1.0 to correct cortical volumes extracted from freesurfer v6.0

[Douglas N. Greve]

I think it is probably ok, but why not use the ICV from v7?


On 10/2/2020 5:37 AM, Jayachandra Raghava wrote:


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Hello Freesurfer Developers,

I have extracted ICV measures using samseg from freesurfer v7.1.0. I 
would like to use this measure to correct the cortical volumes that i 
have extracted from the same subjects using freesurfer v6.0.


1) Is it advisable to use ICV measures from another freesurfer version 
to correct the cortical volumes that i have extracted from the same 
subjects using freesurfer v6.0?


OR

2) Do you advice that i should re-calculate the cortical volumes using 
freesurfer 7.1.0 in order to correct them using the ICV 
measures extracted from samseg?


Nice weekend!
Jay

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Re: [Freesurfer] Queries on Freeview and opening files of 'stat' and 'surf' folders

[Wang, Ruopeng]

Hi KC,

Freeview is a comprehensive volume and surface viewer and editor. You can load 
mri, surf and label files in it. Regarding your last question, if you meant 
going through slices, you can use up/down arrow keys. If you meant going 
through different volume images, you can use Alt+C key to cycle through them.

Best,
Ruopeng

On Oct 2, 2020, at 2:44 AM, Koustav Chatterjee 
mailto:chatterjeekous...@gmail.com>> wrote:


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Dear Sir,

I have stuck with two basic steps while installing FreesUrfer in my new system. 
May I request you to help me resolving the problem.

1. After successful completion of  'recon-all' command , a folder named as 
'samplept1' has been formed under /usr/local/freesurfer/subjects. Subjectpt1 
consists of different folders including 'label', 'mri', 'stat', 'surf' etc. 
Now, I was trying to acquire data from 'surf' and 'stat' folders. However, I am 
unable to open them. It seems to me a specific application is required. Please 
advise.

2. Could you please explain what is the purpose of having 'freeview'. Is it 
only only to check manually whether all the preprocessing steps such as skull 
stripping has been done correctly by recon-all or not?

3. I am unable to surf images  one by one using  "P age up and down keys in 
keyboard". How should I surf the images one by one?

Your help is appreciated.

Thank you very much.
KC


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Re: [Freesurfer] How to draw streamlines and their corresponding ROIs using freeview {Disarmed} {Disarmed}

[Wang, Ruopeng]

Hi Zhiyuan,

You can load the file as volume and select Lookup Table as the color map to 
show labels.

Best,
Ruopeng

On Oct 1, 2020, at 6:01 PM, Zhiyuan Yu 
mailto:z...@my.fsu.edu>> wrote:

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Hi Ruopeng,

I am trying to load ROI file in freeview to display the ROIs. But I do not know 
what kind of ROI file I need. I try to use destrieux_dilated_labels.nii.gz but 
freeview cannot open this label file. Could you please tell me?


Best,
Zhiyuan Yu



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Wang, Ruopeng 
mailto:rwa...@mgh.harvard.edu>>
Sent: Tuesday, September 29, 2020 11:20 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] How to draw streamlines and their corresponding ROIs 
using freeview {Disarmed}

Hi Zhiyuan,

You can load .trk file from “Load Tract” menu in freeview. Mat format is not 
supported unfortunately.

Best,
Ruopeng

On Sep 28, 2020, at 10:21 PM, Zhiyuan Yu 
mailto:z...@my.fsu.edu>> wrote:

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Hi Ruopeng,

Thanks for your answer! My streamlines are in mat and trk file formats and I 
cannot load the fiber tracts as way points in Freeview. Could you please tell 
me why?


Best,
Zhiyuan Yu




From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Wang, Ruopeng 
mailto:rwa...@mgh.harvard.edu>>
Sent: Monday, September 28, 2020 9:17 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] How to draw streamlines and their corresponding ROIs 
using freeview

Hi Zhiyuan,

You can draw streamlines in freeview as way points and turn on the spline 
display. ROIs can be drawn as labels.

Best,
Ruopeng

On Sep 26, 2020, at 2:46 PM, Zhiyuan Yu 
mailto:z...@my.fsu.edu>> wrote:

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Hi,

I have extracted fibers and the corresponding ROIs. I would like to know how 
can I draw them together using freeview.

Thank you,
Zhiyuan


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Re: [Freesurfer] grey matter thickness map and SNR

[Douglas N. Greve]

Only that the parametric assumptions are better met and so mcz controls 
the FPR better


On 9/30/2020 2:29 PM, miracle ozzoude wrote:


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Hello Doug,

Any advantages of surface-based smoothing of the gm thickness maps 
beside increasing signal to noise ratio? I read the paper and based on 
the results and conclusion, mcz with higher threshold and fwhm should 
be fine (though permutation is recommended) for thickness.


best,
paul


On Wed, Sep 30, 2020 at 10:37 AM miracle ozzoude > wrote:


Thank you very much Doug. I appreciate it. I guess we will have to
redo our analyses based using permutation and hope the results are
the same


On Wed, Sep 30, 2020 at 10:22 AM Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>> wrote:


For statistical analysis, the reviewer is right, see
https://pubmed.ncbi.nlm.nih.gov/29288131
We are recommending permutation analysis, see


https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm
or
https://surfer.nmr.mgh.harvard.edu/fswiki/FsPalm

On 9/30/2020 9:23 AM, miracle ozzoude wrote:


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Hello Experts,

I have a question regarding grey matter thickness map and
signal to noise ratio. Does smoothing of the map increase
signal to noise during surface based cortical thickness
analyses? if yes or no, why? This question was asked by a
reviewer in one of our manuscript because he/she thinks that
one of the reasons to perform smoothing is to comply with
random field theory hypotheses, when controlling for multiple
testing.

We did apply multiple comparison corrections using monte
carlo simulation with cluster threshold of 2, 5000
iterations, and bonferroni.

Thanks alot.

best,
Paul

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[Freesurfer] QDEC command not found

[Enrico Collantoni]

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Dear freesurfer experts,
I installed the 7.1.1 version of freesurfer in iOS enviroment
(10.15.4). I could run the recon-all without any problems. However,
trying to open qdec I obtain "command not found". I've never had this
problem with previous versions.

Could you help me?

Many thanks


Enrico Collantoni
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[Freesurfer] Seed ROI FC

[Lorenzo Pini]

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Dear expert

I'm trying to perform FC seed ROI analysis through FSfast pipeline
After preprocessing I run:
selxavg3-sess -s subject1 -a fsrest.surf.lh -no-con-ok -svres

but I got the following error:
ERROR: /bin/bash:
/scratch/tp9f57a7bb_2ea1_450b_b0e8_8cdd47a2eb8b.load_nifti.m.nii: No such
file or directory
ERROR: loading
/home/user/Desktop/test/subjects/subject1/fsrest/001/fmcpr.sm5.self.lh.nii.gz
as analyze
ERROR: attempting to read
/home/user/Desktop/test/subjects/subject1/fsrest/001/fmcpr.sm5.self.lh
--
ERROR: fast_selxavg3() failed\n

Moreover, I'm a bit confused how to compute whole brain seed-ROI surface
map, using a pre-specified seed ROI created in orig.mgz space (sphere 5mm)

Thanks in advance,
Lorenzo
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[Freesurfer] Use ICV measures from freesurfer v7.1.0 to correct cortical volumes extracted from freesurfer v6.0

[Jayachandra Raghava]

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Hello Freesurfer Developers,

I have extracted ICV measures using samseg from freesurfer v7.1.0. I would
like to use this measure to correct the cortical volumes that i have
extracted from the same subjects using freesurfer v6.0.

1) Is it advisable to use ICV measures from another freesurfer version to
correct the cortical volumes that i have extracted from the same subjects
using freesurfer v6.0?

OR

2) Do you advice that i should re-calculate the cortical volumes using
freesurfer 7.1.0 in order to correct them using the ICV measures extracted
from samseg?

Nice weekend!
Jay
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[Freesurfer] Infant FreeSurfer issues

[k3ops]

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Hi FreeSurfer team,

I’ve been using the Infant FreeSurfer pipeline on 3DT1 sequences for few weeks 
now on infants from 0.4 to 5.4 years-old.

I know Infant FreeSurfer is recommended for 0-2 years old infant but standard 
FreeSurfer was failing due to many lacunar infarcts in the white matter.
So I tried Infant FreeSurfer with an age of 2 years old even for 2 to 5.4 
years-old subjects and results look good.
I know standard FreeSurfer has been tested on infant from 4.2 years-old, so 
what would be your recommendation for subjects from 2 to 4.2 years old?
Have you already run Infant FreeSurfer on subjects older than 2 years-old?
Do you recommend it?

I also have some processing issues with my actual data:
  1. Pixels with 0 value => probably out of the brainmask so the pixels are set 
to 0 after masking
 So, sometimes lateral ventricles are miss-segmented 
(https://ibb.co/JpWG9st)
  2. Thalamus region is missing from the aseg stat export (always equal to 0 
mm3), do you have a fix? Should I fix a LUT file?
  3. Would it be possible to get the non-skullstripped N3 corrected 3D T1 in 
the MNI space (3D iso)? I was not able to find the registered 3DT1 to re-apply 
the N3 correction, I only found the input 3DT1 (mprage.nii.gz) in its native 
space.
  4. Do you have any workaround for large ventricles segmentation issue 
(https://ibb.co/nnbZcYs)?
 Standard FreeSurfer has a -bigventricle option, do you have a similar 
approach?

And some additional questions:
• brainstem seems to be split into multiple sub-regions, is it possible get the 
entire brainstem volume in the aseg stat export?
• I saw that corpus callosum is not present in the “aseg” segmentation, so is 
this region out of the Infant FreeSurfer atlases?
• Is it possible to get the mean cortical thickness for the labels you are 
providing?

Many thanks as I know there are plenty of questions here :)
Best,
Florent

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