Re: [Freesurfer] Cluster-wise correction for multiple comparisons

[Douglas N. Greve]

See if this tutorial will help
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm


On 2/14/2020 3:28 PM, Kim, Gwang-Won wrote:


Dear Douglas N. Greve,

Thank you very much for your email.

I ran mri_glmfit without --wis. Then I tried to ran mri_glmfit-sim as 
following: mri_glmfit-sim –glmdir g2v3.wls –2spaces –perm 1000 1.3 abs.


But there is an error message “ERROR: design matrix is not orthogonal, 
cannot be use with permutation. If this something you really want to 
do, run with –perm-force”.


How can I do if I want to solve this problems?

Thanks,

Gwang-Won

---

Message: 6

Date: Fri, 14 Feb 2020 09:42:28 -0500

From: "Douglas N. Greve" 

Subject: Re: [Freesurfer] Cluster-wise correction for multiple

comparisons

To: 

Message-ID: 

Content-Type: text/plain; charset="utf-8"

You don't need to specify a mask when you run mri-glmfigt-sim. When you

 ran mri_glmfit, you already specified the mask and that gets stored in

 the glmdir and then read by mri_glmfit-sim. Your mri_glmfit-sim command

 line look right (but you don't need the --bg 1 unless you really want to

 background the process, but using only one process will not speed it up).

the other thing I want to point out is that (pseudo) weighted-least

 squares will not be taken into account by the permutation. I would rerun

 mri_glmfit without --wls and then run mri_glmfit-sim

On 2/7/2020 3:01 PM, Kim, Gwang-Won wrote:

>

> Hi there,

>

> First, I ran "mri_glmfit" using mask including 4 ROIs(file name:

 > 4_ROI.label) as follows: mri_glmfit --glmdir g2v3.wls --y ces.nii.gz

 > --wis cesvar.nii.gz --fsgd 2group.fsgd --C group.diff.mtx --lable

 > 4_ROI.label? --surface fsaverage lh - --fwhm 5 ?eres-save.

>

> Second, I'm going to process "mri_glmfit-sim" to perform a

 > cluster-wise correction for multiple comparisons.

>

> Please let me know how to process "mri_glmfit-sim" using masks (file

 > name: 4_ROI.label) .

>

> Is it right? ?mri_glmfit-sim --glmdir g2v3.wls --perm 1000 3 abs

 > --2spaces --bg 1?

>

> Thank you,

>

> Gwang-Won

>


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Re: [Freesurfer] Cluster-wise correction for multiple comparisons

[Kim, Gwang-Won]

Dear Douglas N. Greve,

Thank you very much for your email.

I ran mri_glmfit without --wis. Then I tried to ran mri_glmfit-sim as 
following: mri_glmfit-sim -glmdir g2v3.wls -2spaces -perm 1000 1.3 abs.
But there is an error message “ERROR: design matrix is not orthogonal, cannot 
be use with permutation. If this something you really want to do, run with 
-perm-force”.
How can I do if I want to solve this problems?

Thanks,
Gwang-Won

---
Message: 6
Date: Fri, 14 Feb 2020 09:42:28 -0500
From: "Douglas N. Greve" 
Subject: Re: [Freesurfer] Cluster-wise correction for multiple
comparisons
To: 
Message-ID: 
Content-Type: text/plain; charset="utf-8"

You don't need to specify a mask when you run mri-glmfigt-sim. When you
 ran mri_glmfit, you already specified the mask and that gets stored in
 the glmdir and then read by mri_glmfit-sim. Your mri_glmfit-sim command
 line look right (but you don't need the --bg 1 unless you really want to
 background the process, but using only one process will not speed it up).

the other thing I want to point out is that (pseudo) weighted-least
 squares will not be taken into account by the permutation. I would rerun
 mri_glmfit without --wls and then run mri_glmfit-sim

On 2/7/2020 3:01 PM, Kim, Gwang-Won wrote:
>
> Hi there,
>
> First, I ran "mri_glmfit" using mask including 4 ROIs(file name:
 > 4_ROI.label) as follows: mri_glmfit --glmdir g2v3.wls --y ces.nii.gz
 > --wis cesvar.nii.gz --fsgd 2group.fsgd --C group.diff.mtx --lable
 > 4_ROI.label? --surface fsaverage lh - --fwhm 5 ?eres-save.
>
> Second, I'm going to process "mri_glmfit-sim" to perform a
 > cluster-wise correction for multiple comparisons.
>
> Please let me know how to process "mri_glmfit-sim" using masks (file
 > name: 4_ROI.label) .
>
> Is it right? ?mri_glmfit-sim --glmdir g2v3.wls --perm 1000 3 abs
 > --2spaces --bg 1?
>
> Thank you,
>
> Gwang-Won
>
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Re: [Freesurfer] Pial surface not including parts of cortex

[Monica Bondy]

External Email - Use Caution

Hi, I just wanted to check in on the progress of this thread. Could you let
me know if you had the chance to take a look at the scan I sent? I'm
unfortunately having the same problem with multiple scans so if I could get
some help, I'd really appreciate it. If I somehow failed to send the files
please let me know as well.
Thank you!
Monica

On Fri, Jan 31, 2020 at 11:37 AM Monica Bondy  wrote:

> Thank you so much! I just sent the gzipped subject directory
> *subjectdir.gz. *
> My main concern is that a lot of the lateral gray matter isn't included.
> Here are some Talairach coordinates that illustrate the areas I'm concerned
> about: (-67 -27 -9) (-65 -33 22).
>
> Let me know if it didn't send properly or if I can do anything else.
>
> Thanks again,
> Monica
>
> On Fri, Jan 31, 2020 at 10:34 AM Bruce Fischl 
> wrote:
>
>> Hi Monica
>>
>> sure, if you tar and gzip the entire subject dir and ftp it to us, then
>> send us a description that includes the voxel coords of where you think
>> things should be more accurate we will take a look
>>
>> cheers
>> Bruce
>> On Fri, 31 Jan 2020,
>> Monica Bondy wrote:
>>
>> >
>> > External Email - Use Caution
>> >
>> > Dear Freesurfer experts,
>> > I was wondering if I could get some help with a problem that I keep
>> > experiencing. For some of the patients, their gray matter is not
>> properly
>> > included in the pial surface. I have tried tkmregister and using control
>> > points but neither have been successful.
>> > I have read on a separate thread that editing the wm.mgz may be helpful
>> but
>> > could I have some guidance on this please? Also, I know it can be
>> difficult
>> > to tell the problem based on the description so please let me know if I
>> can
>> > send something over to help. I'm still very much learning how to work
>> > freesurfer so I really appreciate your help.
>> > (Note: I am using version 5.3)
>> >
>> > Thank you,
>> > Monica
>> >
>> >___
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>
>
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Re: [Freesurfer] make average subject/ highres fMRI data

[Nasiriavanaki, Zahra]

Hi

I would like to follow up on this question and would appreciate if you could 
reply.

Thanks!
Mona


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129




From: Nasiriavanaki, Zahra
Sent: Monday, February 10, 2020 12:11 PM
To: Freesurfer support list 
Subject: make average subject/ highres fMRI data

Dear Freesurfer experts

Hi

I got an error when I was trying to make an average subject. I attached the log 
file.
I appreciate if you could please let me know what the problem is.
make_average_subject --out avgsubject --subjects subj1 subj2 subj 3

labeling Slice
relabeling unlikely voxels in interior of white matter
mri/norm.mgz: could not load norm volume from

Linux bee.nmr.mgh.harvard.edu 3.10.0-1062.4.3.el7.x86_64 #1 SMP Wed Nov 13 
23:58:53 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s avgsubject exited with ERRORS at Mon Feb 10 10:43:37 EST 2020

For more details, see the log file 
/autofs/space/oprah_001/users/zn025/looming_7T/SUBJECTS_DIR/avgsubject/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


Thanks
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] Request for access to the freesurfer mailing list

[Douglas N. Greve]

yes, please do

On 2/14/2020 11:17 AM, Varun Chandran wrote:


External Email - Use Caution

Dear Freesurfer committee,

I would like to use the freesurfer mailing list to post my doubts 
about the cortical thickness analysis pipeline. Therefore, could you 
please provide me the access to post my doubts on the same?


    thanks,

kind regards,
Varun Arunachalam Chandran
PhD in Neurosciences,
School of Psychology and Language Sciences,
University of Reading,
Berkshire, UK

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Re: [Freesurfer] Flip left-right orientation command

[Miguel Ángel Rivas Fernández]

External Email - Use Caution

Yes, it works!.

Thank you so much.

El vie., 14 feb. 2020 a las 17:22, Douglas N. Greve ()
escribió:

> You can try,
> mri_convert --in_orientation PIR t1_flip.nii t1_flip_flip.nii
> but I'm not promising anything
>
> On 2/14/2020 11:03 AM, Miguel Ángel Rivas Fernández wrote:
>
> External Email - Use Caution
> Dear Douglas,
>
> My image is in the correct orientation. The reason is that am using a
> software to detect brain lesions that only works in left hemisphere and my
> subject have the lesion in the right hemisphere. I tried it with the
> following command and it works
>
> mri_convert --in_orientation PIL t1.nii t1_flip.nii
>
> Now I would like to come back to the original orientation, which command
> should I use?
>
> Thanks in advance.
>
> Best regards,
>
> El vie., 14 feb. 2020 a las 16:01, Douglas N. Greve (<
> dgr...@mgh.harvard.edu>) escribió:
>
>> Is the image in the wrong orientation (ie, is it not truly in PIR) or do
>> you want to change the orientation? doing a left-right swap is more than
>> changing the orientation
>>
>> On 2/11/2020 4:06 PM, Miguel Ángel Rivas Fernández wrote:
>>
>> External Email - Use Caution
>> Dear Freesurfer experts,
>>
>> Which command should I use to flip the left-right orientation of a T1
>> image?. Actually my image is in PIR orientation, I used the following
>> command
>>
>> mri_info --orientation '/home/rmn/Desktop/study/E03/3d/coanat_E03.nii'
>>
>> *PIR*
>>
>>
>> Thanks in advance,
>>
>> Best regards,
>>
>> --
>> *Miguel Ángel Rivas Fernández*
>>
>> ___
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>>
>>
>> ___
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> --
> *Miguel Ángel Rivas Fernández*
>
> ___
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>
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-- 
*Miguel Ángel Rivas Fernández*
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Re: [Freesurfer] Flip left-right orientation command

[Douglas N. Greve]

You can try,
mri_convert --in_orientation PIR t1_flip.nii t1_flip_flip.nii
but I'm not promising anything

On 2/14/2020 11:03 AM, Miguel Ángel Rivas Fernández wrote:


External Email - Use Caution

Dear Douglas,

My image is in the correct orientation. The reason is that am using a 
software to detect brain lesions that only works in left hemisphere 
and my subject have the lesion in the right hemisphere. I tried it 
with the following command and it works


mri_convert --in_orientation PIL t1.nii t1_flip.nii

Now I would like to come back to the original orientation, which 
command should I use?


Thanks in advance.

Best regards,

El vie., 14 feb. 2020 a las 16:01, Douglas N. Greve 
(mailto:dgr...@mgh.harvard.edu>>) escribió:


Is the image in the wrong orientation (ie, is it not truly in PIR)
or do you want to change the orientation? doing a left-right swap
is more than changing the orientation

On 2/11/2020 4:06 PM, Miguel Ángel Rivas Fernández wrote:


External Email - Use Caution

Dear Freesurfer experts,

Which command should I use to flip the left-right orientation of
a T1 image?. Actually my image is in PIR orientation, I used the
following command

mri_info --orientation
'/home/rmn/Desktop/study/E03/3d/coanat_E03.nii'

*PIR*


Thanks in advance,

Best regards,

-- 
*Miguel Ángel Rivas Fernández*


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--
*Miguel Ángel Rivas Fernández*

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[Freesurfer] Request for access to the freesurfer mailing list

[Varun Chandran]

External Email - Use Caution

Dear Freesurfer committee,

I would like to use the freesurfer mailing list to post my doubts about the
cortical thickness analysis pipeline. Therefore, could you please provide
me the access to post my doubts on the same?


  thanks,

kind regards,
Varun Arunachalam Chandran
PhD in Neurosciences,
School of Psychology and Language Sciences,
University of Reading,
Berkshire, UK
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Re: [Freesurfer] Flip left-right orientation command

[Miguel Ángel Rivas Fernández]

External Email - Use Caution

Dear Douglas,

My image is in the correct orientation. The reason is that am using a
software to detect brain lesions that only works in left hemisphere and my
subject have the lesion in the right hemisphere. I tried it with the
following command and it works

mri_convert --in_orientation PIL t1.nii t1_flip.nii

Now I would like to come back to the original orientation, which command
should I use?

Thanks in advance.

Best regards,

El vie., 14 feb. 2020 a las 16:01, Douglas N. Greve ()
escribió:

> Is the image in the wrong orientation (ie, is it not truly in PIR) or do
> you want to change the orientation? doing a left-right swap is more than
> changing the orientation
>
> On 2/11/2020 4:06 PM, Miguel Ángel Rivas Fernández wrote:
>
> External Email - Use Caution
> Dear Freesurfer experts,
>
> Which command should I use to flip the left-right orientation of a T1
> image?. Actually my image is in PIR orientation, I used the following
> command
>
> mri_info --orientation '/home/rmn/Desktop/study/E03/3d/coanat_E03.nii'
>
> *PIR*
>
>
> Thanks in advance,
>
> Best regards,
>
> --
> *Miguel Ángel Rivas Fernández*
>
> ___
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>
>
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-- 
*Miguel Ángel Rivas Fernández*
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Re: [Freesurfer] watershed, saving issue

[Bruce Fischl]

Hi Kirill

I think this is a question for Matti (now ccd)

cheers
Bruce
On Fri, 14 Feb 2020, Kirill 
Elin wrote:




External Email - Use Caution

Hallo everybody,
I am not entirely sure whether this is FreeSurfer error actually.
I am doing first recon all which completes without errors. Then I need to
create BEM surfaces using the FreeSurfer watershed algorithm for MEG data
analysis using MNE-Python.
So the next command in the terminal is: mne watershed_bem --subject
subjectname
And it runs e.g. till:
mri_watershed ru_nivcsw   12490
mri_watershed done
and quits with errors like:
File"/work/modules/Ubuntu/14.04/amd64/common/anaconda3/latest/envs/neuroimaging
/lib/python3.6/site-packages/mne/utils/check.py", line 143, in _check_fname
    raise IOError('Destination file exists. Please use option '
OSError: Destination file exists. Please use option "overwrite=True" to
force overwriting.

Now, it is unclear what file destination file is meant. This happens on
several machines for all participants.
--overwrite option does not help.
The correct outcome should include bem folder with resulting files and also
watershed subfolder with resulting files. Here and the files in bem folder
are missing and there are files only in watershed subfolder.
FreeSurfer 6.0.0., Ubuntu
Thank you in advance.

Sincerely yours,
Kirill



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Re: [Freesurfer] Systematically Navigating .sphere vertices

[Tim Schäfer]

External Email - Use Caution

@Chris:

I recently needed exactly what you want in Matlab, feel free to use it:

https://github.com/dfsp-spirit/comp_neuro_science/blob/master/matlab_utility_functions/mesh_neighborhood.m

A usage example is included (see script). It's not terribly efficient, but it 
works. To get the direct neighbors (in distance 1) of vertex 500:

[verts, faces] = read_surf("path/to/lh.white");
mesh_neighborhood(faces, [500], 1);

Hint: beware of indexing differences (1-based in Matlab, 0-based in 
C/FreeSurfer) when using it.


Tim

--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany


> On February 14, 2020 at 4:15 PM "Douglas N. Greve"  
> wrote:
> 
> 
> You'll have to use read_surf.m to read in the fsaverage surface. The 
> surface will neighbor info
> 
> On 2/13/2020 1:51 PM, Mcnorgan, Christopher wrote:
> >
> > External Email - Use Caution
> >
> > I’m interested in working with data mapped to the .sphere 
> > icosohedrons. I understand from a response from Doug back in 2017 that:
> > waveforms = fast_vol2mat(MRIread('waveform.nii.gz'));
> > will give me a v x time matrix of values from my functional values.
> > In the case of fsaverage, I believe I can expect somewhere around 160K 
> > rows, 1 per vertex, for each hemisphere.
> > I was wondering how I might be able to determine the neighbors (i.e., 
> > vertices connected by an edge) for any vertex v?
> >
> > Thanks,
> > Chris
> >
> > /**
> > * Chris McNorgan
> > * Assistant Professor
> > * Department of Psychology
> > * University at Buffalo,
> > * The State University of New York
> > * http://ccnlab.buffalo.edu/
> > * Office: 716.645.0236
> > * Lab: 716.645.0222
> > **/
> >
> >
> > ___
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Re: [Freesurfer] Systematically Navigating .sphere vertices

[Douglas N. Greve]

You'll have to use read_surf.m to read in the fsaverage surface. The 
surface will neighbor info


On 2/13/2020 1:51 PM, Mcnorgan, Christopher wrote:


External Email - Use Caution

I’m interested in working with data mapped to the .sphere 
icosohedrons. I understand from a response from Doug back in 2017 that:

waveforms = fast_vol2mat(MRIread('waveform.nii.gz'));
will give me a v x time matrix of values from my functional values.
In the case of fsaverage, I believe I can expect somewhere around 160K 
rows, 1 per vertex, for each hemisphere.
I was wondering how I might be able to determine the neighbors (i.e., 
vertices connected by an edge) for any vertex v?


Thanks,
Chris

/**
* Chris McNorgan
* Assistant Professor
* Department of Psychology
* University at Buffalo,
* The State University of New York
* http://ccnlab.buffalo.edu/
* Office: 716.645.0236
* Lab: 716.645.0222
**/


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Re: [Freesurfer] ROI Analysis in a given label with Functional Constraint in FSFAST

[Douglas N. Greve]

Is the hV5+MT label already a binary volume in the FS conformed 1mm 
space (ie, same space as orig.mgz)? And what do you mean by "constrained"?


On 2/13/2020 11:04 AM, Star Xi wrote:


External Email - Use Caution

FS experts,
Commonly, I can use mri_vol2vol -> mri_segstats to extract anatomical 
ROI from aparc or aseg template.


However, now I want to extract the average percent signal change in 
the hV5+/MT by constrained  positive functional activation. The 
anatomical label is from other template.


My question is, after using mri_vol2vol, which command can extract 
signals from a given label with constrained activation ?


Thanks,

Star


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Re: [Freesurfer] study design flair T1

[Douglas N. Greve]

Any software package will do the inference on images with different 
characteristics, the question is whether the inference is valid. If you 
use different types of images, you will get different results (all 
software packages). If you try to compare two groups each with image 
types, you will have a confound with your image type and your groups and 
the inference will not be valid. Having said that, if you want to 
analyze some of your subject with T1 and some with T1+T2 and some with 
T1+FLAIR, then can certainly do so.



On 2/13/2020 8:13 AM, Renew Andrade wrote:
>  External Email - Use Caution
>
> Dear FreeSurfer experts:
>
> I am dealing with a crossectional retrospective case control  study where I 
> don't have all subjects with the same inaging protocols. I do have T1 for all 
> of them although some have T2 others FLAIR others T2+FLAIR (besides T1 for 
> all of them). My question is regarding VBM can I do inference on images with 
> different characteristics? Or should them all have T1 + T2 or T1 + FLAIR. I 
> guess this is the case that is all subjects should be processed with the same 
> protocols.  This is in Multiple Sclerosis by the way just in case it matters.
>
> Sincerely,
> Andrade.
>
> Sent from my iPhone
>
>
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Re: [Freesurfer] FSAVERAGE and LabelROI

[Douglas N. Greve]

On 2/12/2020 2:46 PM, Faizan Anwar wrote:


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Hello,

My name is Faizan Anwar. I am currently a undergraduate student at 
UCLA. I had two questions regarding freesurfer:


  * Is FSAVERAGE file a universal template that could be used with any
set of subject data, or is it a specific file created during recon
all. If yes, how can I recreate fsaverage file with a freesurfer
processed dataset (i.e. recon all was already done on this dataset
and I have moved the FS data to a different computer without the
FSAVERAGE file

fsaverage is general. When it shows up in your SUBJECTS_DIR, it is 
actually a symbolic link to $FREESURFER_HOME/subjects/fsaverage. You 
cannot create new exact fsaverage


  * Also, I wanted to ask if there is a way to extract LabelROI of
multiple subject at the same time alike aseg2stats command? and If
there is a way to do a group analysis  and visualize the
difference within that specific region?


I don't understand what you are trying to do. Can you elaborate?
Any assistance in these two questions would be extremely helpful. 
Looking forward to your reply



Thank you,

Sincerely,
Faizan Anwar

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Re: [Freesurfer] converting mgh to gii

[Douglas N. Greve]

Hi Lara, I think that is right, but I don't use gii much
doug

On 2/12/2020 2:05 PM, Lara Foland-Ross wrote:
>  External Email - Use Caution
>
> Hello Freesurfer experts,
>
> I'd like to convert my subjects' thickness mgh files to gii format for use in 
> an analysis with a separate software package. Could you please confirm 
> whether the following command is appropriate? Will this provide thickness 
> maps that are in alignment?
>
> mris_convert -c lh.thickness.fwhm15.fsaverage.mgh fsaverage/surf/lh.white 
> lh.thickness.fwhm15.fsaverage.gii
>
> Many thanks,
> Lara
>
> Lara Foland-Ross, Ph.D.
> Senior Research Associate and Imaging Lab Manager
> Center for Interdisciplinary Brain Sciences Research
> Stanford University School of Medicine
> 401 Quarry Road, Room 1356
> Stanford, CA 94305-5795
>
>
>
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Re: [Freesurfer] Volume to 5th order icosahedron tesselation Surface (with PET images)

[Douglas N. Greve]

You could do it, but  I would just use fsaverage. I don't understand 
what the relationship would be between the number of vertices on the 
surface and the number of voxels in the PET volume or the rational for 
using the 5th order ico


On 2/12/2020 8:03 AM, Marina Fernández wrote:


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Hi experts,

This is a question related to PetSurfer steps.

I would like to know if it is correct to sample the mgx volume onto 
the surface of the average subject of my dataset (created with 5th 
ordericosahedron tesselation) instead of the fsaverage (created with 
7th ordericosahedron tesselation) or if there is any problem in the 
next steps following this procedure.
We would like to do that because the volume PET resolution is more 
proportional to this number of vertex (10242). Do you think it is correct?


Best wishes,
Marina.


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Re: [Freesurfer] Problem with registration (PetSurfer)

[Douglas N. Greve]

Sorry, can you include  the previous emails, otherwise I don't know what 
the context is


On 2/12/2020 3:06 AM, Marina Fernández wrote:


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The error was shown after running tkregisterfv.



Marina.

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Re: [Freesurfer] Flip left-right orientation command

[Douglas N. Greve]

Is the image in the wrong orientation (ie, is it not truly in PIR) or do 
you want to change the orientation? doing a left-right swap is more than 
changing the orientation


On 2/11/2020 4:06 PM, Miguel Ángel Rivas Fernández wrote:


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Dear Freesurfer experts,

Which command should I use to flip the left-right orientation of a T1 
image?. Actually my image is in PIR orientation, I used the following 
command


mri_info --orientation '/home/rmn/Desktop/study/E03/3d/coanat_E03.nii'

*PIR*


Thanks in advance,

Best regards,

--
*Miguel Ángel Rivas Fernández*

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Re: [Freesurfer] Question re: hippocampal/amygdala subfields

[Douglas N. Greve]

See this page
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala


On 2/11/2020 2:54 PM, Tegan Hargreaves wrote:


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Hi all,

I am fairly new to FreeSurfer and am implanting the 
hippocampal/amygdala subfields script in our participants. As there 
are two versions of the hippocampal script (i.e., version 10 that is 
only hippocampus and version 21 which is both), I wanted to confirm 
that I should be using FS v6.0 (stable) for recon-all, and then 
running only the hippocampal/amygdala (v21) script through the dev 
version of FS. I don’t believe that I should be running the 
exclusively hippocampal script anymore, as the guide states it is now 
obsolete, but I just wanted to confirm.


Thank you so much!

Best,

Tegan

*Tegan Hargreaves, MSc*

Research Assistant

Peter Boris Centre for Addictions Research | St. Joseph’s Healthcare 
Hamilton


100 West 5^th Street, Hamilton, ON L8P 3P2

*P: *905-522-1155 ext. 36368 | *E:* tharg...@stjoes.ca 




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Re: [Freesurfer] Thickness group normalization

[Douglas N. Greve]

You need to register your subjects to the new average subject with
surfreg --s subject --t 0_1


On 2/11/2020 12:36 PM, Vyacheslav Yarkin wrote:


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I got the idea but faced an issue with mris_preproc, the command is:


mris_preproc --target 0_1 --s avg_subject_91_noexpopts --hemi lh 
--meas thickness --out avg_91_to_lh.mgh



where 0_1 is target patient to map thickness, from 
avg_subject_91_noexpopts, optained from make_average_subject.



i get the error running mris_preproc:

Reading source surface reg

  /input/HCP_T1_fs6/avg_subject_91_noexpopts/surf/lh.0_1.sphere.reg

  No such file or directory

  mri_surf2surf: could not read surface

  /input/HCP_T1_fs6/avg_subject_91_noexpopts/surf/lh.0_1.sphere.reg

  No such file or directory


Why there should be lh.0_1.sphere.reg? Have i missed some intermediate 
steps?​



​



*От:* freesurfer-boun...@nmr.mgh.harvard.edu 
 от имени Vyacheslav Yarkin 


*Отправлено:* 5 февраля 2020 г. 11:47
*Кому:* Freesurfer support list
*Тема:* Re: [Freesurfer] Thickness group normalization

External Email - Use Caution

I got the idea but faced an issue with mris_preproc, the command is:


mris_preproc --target 0_1 --s avg_subject_91_noexpopts --hemi lh 
--meas thickness --out avg_91_to_lh.mgh



where 0_1 is target patient to map thickness, from 
avg_subject_91_noexpopts, optained from make_average_subject.



i get the error running mris_preproc:

Reading source surface reg

  /input/HCP_T1_fs6/avg_subject_91_noexpopts/surf/lh.0_1.sphere.reg

  No such file or directory

  mri_surf2surf: could not read surface

  /input/HCP_T1_fs6/avg_subject_91_noexpopts/surf/lh.0_1.sphere.reg

  No such file or directory


Why there should be lh.0_1.sphere.reg? Have i missed some intermediate 
steps?​







*От:* freesurfer-boun...@nmr.mgh.harvard.edu 
 от имени Douglas N. Greve 


*Отправлено:* 3 февраля 2020 г. 20:51
*Кому:* freesurfer@nmr.mgh.harvard.edu
*Тема:* Re: [Freesurfer] Thickness group normalization

Do you have a group of subjects that you want to use as an average? If 
so, you can just map all their thickness maps to your patient subject 
with

mris_preproc --target patientsubjectname [then usual arguments]
Compute the mean with
mri_concat outputofmris_preproc.mgz --mean --o groupmean.mgz
You can then compare groupmean.mgz to your patient on a 
vertex-by-vertex baiss



On 2/3/2020 12:16 PM, Vyacheslav Yarkin wrote:


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Hello Freesurfer Team,


Would you be so kind to provide freesurfer steps to implement warping 
fsaverage mean thickness data on individual subject inflated brains ?




I am using expert opts to disable cortical thickness restriction, and 
set mris_thickness -max 20 as I want to find fcd to cortical 
surfaces. The reason i need normalization is that there is zones like 
sulci orbitales have bigger thickness accross subjects group ( 
control ) and have red LUTs on inflated thickness map. So i would 
like to normalize thickness over control group, to use it on patients 
to exclude "normal" thickness excedings to include only increased FCD 
zones. The main issue I faced is how to warp fsaverage mean thickness 
data on individual subject's inflated brain as they have vertices 
number missmatch.


Steps I tried:

1) make_average_subject

2) mri_concat --mean to create mean thicknesses over group​


Thank you


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Re: [Freesurfer] recon-all -make all

[Douglas N. Greve]

On 2/11/2020 9:26 AM, Benjamin Ineichen wrote:


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Dear Freesurfer experts,

I ran recon-all on 100 subjects. Around 20 of them needed manual 
corrections of the pial surface on the brainmask.mgz.
1.) Can I run the command: "recon-all -make all- s " on all 
100 subjects and it will only recon-all the manually edited ones or do 
I need to run it individually for the 20 subjects?
It might work, but the "make" function has always been a little 
unreliable (and probably won't be in the next version)
2.) Do I need to add the flags which I used for the original recon-all 
command to the "recon-all -make all- s , e.g. -qcache -T3 
-hippocampal subfields etc?

Yes


Many thanks!

/Ben

--

Benjamin Victor Ineichen, MD PhD
Karolinska Institutet
Center for Molecular Medicine
Stockholm, Sweden
ineic...@protonmail.ch 
+41 76 391 04 01

Dr. med. et Dr. rer. nat. ETH Benjamin Victor Ineichen
Karolinska Institutet
Center for Molecular Medicine
Stockholm, Sweden
ineic...@protonmail.ch 
+41 76 391 04 01

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Re: [Freesurfer] Three qdec analyses, different results

[Douglas N. Greve]

Even if you use the same subjects, you are performing three different 
analyses, so it is not surprising that you are getting different 
results. As to why they are wildly different, I don't know. I suspect 
that you need to demean your continuous variables.


On 2/10/2020 11:26 AM, Wang, Lily wrote:

Hi Freesurfer Team,

I made a qdec table with columns fsid, disease status (control and 
diseased), age, df, db, dtotal (which are three continuous 
psychological test scores). I performed one analysis in qdec with 
disease status as the discrete factor and each of the three test 
scores as the continuous factor with no nuisance factor chosen, for a 
total of three analyses. All three analyses ran successfully but when 
I choose "Does the average thickness differ between Control and 
Diseased?", which should ignore the test scores (right?), and applied 
an FDR = 0.05, I get wildly different results among the three analyses 
even though I believe I should get the same results since it is the 
same pool of subjects in all three analyses. Did I do something wrong?


Thank you,
Lily

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Re: [Freesurfer] Conversion between lta file type

[Douglas N. Greve]

On 2/10/2020 11:20 AM, Christian O'Reilly, Dr wrote:


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Hi,

How can I convert a LTA file type 0 (LINEAR_VOX_TO_VOX) to a type 1 
(LINEAR_RAS_TO_RAS)?

Use lta_convert


Also, given a volume x.nii.gz and a file y.lta, how do I obtaijn 
z.nii.gz as the original volume x.nii.gz transformed according to 
y.lta? I tried with mri_vol2vol but somehow I could not figure a way 
to make it work properly.
Should be mri_vol2vol --mov x.nii.gz --reg y.lta --target y.nii.gz --o 
x-in-y.nii.gz


Also, given a volume containing a full head and a second volume 
containing a stripped skull, what is the best approach with FreeSurfer 
to transform the brain so that it is properly registered with the full 
head (using an affine transform)? I tried many different ways to get 
it done with mri_robust_register and also with bbregister, but somehow 
I could not get a satisfactory result (i.e., I could always get a much 
better fit by hand using freeview)
Need more info about the nature of the data. where did it come from? are 
they two different scans? differnt sesssions?


Thank you!

Christian


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Re: [Freesurfer] PetSurfer questions

[Douglas N. Greve]

On 2/9/2020 10:19 PM, Soo-Jong Kim wrote:


External Email - Use Caution

Thank you, Dr. Greve

I checked all about your comment.

I have questions more.
1. I found that volumes or counts in gtm.stats.dat are for native PET 
space.
If co-registered PET onto corresponding MRI(i.e. MRI space) is 
available using rbv.nii.gz from mri_gtmpvc,


Or if you recommend it by gtm.stats.dat, I can use gtm.stats.dat 
--rescale (reference regions) for SUVR in PET space.

What do you prefer or recommend?

I'm not sure what you are trying to get. voxel volume or SUVR?


2. I used mri_vol2vol --mov rbv.nii.gz --targ original_PET.nii --o 
test.nii --regheader

because rbv.nii.gz is in different space.
but when overlaid with them, registration is not correct.  (WHY)
rbv.nii.gz is in different space, even not in T1.mgz space. (DKT space)
I just wanted to use the pv-corrected image for image processing.
and you also said, smoothing is required after PVC. (Surface or volume 
based smoothing (resonable).
The RBV is in anatomical space, if you want to map it back to pet space, 
you need the registration file in the aux folder (not --regheader).


Best regards,
Soo

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Re: [Freesurfer] Extract specific LGI and Volume values

[Douglas N. Greve]

What tool are you trying to use to load the label? What happens when you 
try?


On 2/7/2020 10:11 PM, Tien Pham wrote:


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Thank you for your email. I run exactly the command mri_label2label as 
you suggested, and the command finished without any problem.

But I did not know why I could not open the label.
Please help me. Thank you once again.

On Tue, Feb 4, 2020 at 2:55 AM Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:


sorry for the delay. You will have to use mri_label2label to map
the label from the fsaverage space to the individual space


On 1/31/2020 10:01 PM, Tien Pham wrote:


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Can you read my message?
I used longitudinal pipeline for my data set with two time points
and measured the LGI differences between them.
Then I created the label based on significant clusters which
showed in QDEC.
I tried to load the label on the subjects in cross, base, long
steps but it did not work.
I am looking forward to hearing from you. Thank you very much.

On Sat, Feb 1, 2020 at 8:08 AM Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>> wrote:

Sorry, I do not have the previous emails, can you repost with
previous emails in the message?

On 1/28/2020 7:35 PM, Tien Pham wrote:


External Email - Use Caution

Thank you for your response.
I used longitudinal pipeline for my data set with two time
points and calculated the LGI differences between them.
Then I created the label based on significant clusters which
showed in QDEC.
I tried to load the label on subjects in cross, base, long
steps but it did not work.
I am looking forward to hearing from you. Thank you so much.

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Re: [Freesurfer] mri_glmfit-sim error

[Douglas N. Greve]

See this page
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm

On 2/7/2020 9:52 PM, Kim, Gwang-Won wrote:


Hi there,

I ran “mri_glmfit-sim –glmdir g2v3.wls –2spaces –perm 1000 1.3 abs”.

But, there was error message as follow: “design matrix is not 
orthogonal, cannot be used with permutation. If this something you 
really want to do, run with –perm-force”


Please let me know how to process mri_glmfit-sim.

Thank you,

Gwang-Won


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Re: [Freesurfer] Cluster-wise correction for multiple comparisons

[Douglas N. Greve]

You don't need to specify a mask when you run mri-glmfigt-sim. When you 
ran mri_glmfit, you already specified the mask and that gets stored in 
the glmdir and then read by mri_glmfit-sim. Your mri_glmfit-sim command 
line look right (but you don't need the --bg 1 unless you really want to 
background the process, but using only one process will not speed it up).


the other thing I want to point out is that (pseudo) weighted-least 
squares will not be taken into account by the permutation. I would rerun 
mri_glmfit without --wls and then run mri_glmfit-sim


On 2/7/2020 3:01 PM, Kim, Gwang-Won wrote:


Hi there,

First, I ran "mri_glmfit" using mask including 4 ROIs(file name: 
4_ROI.label) as follows: mri_glmfit --glmdir g2v3.wls --y ces.nii.gz 
--wis cesvar.nii.gz --fsgd 2group.fsgd --C group.diff.mtx --lable 
4_ROI.label  --surface fsaverage lh - --fwhm 5 –eres-save.


Second, I'm going to process "mri_glmfit-sim" to perform a 
cluster-wise correction for multiple comparisons.


Please let me know how to process "mri_glmfit-sim" using masks (file 
name: 4_ROI.label) .


Is it right? “mri_glmfit-sim --glmdir g2v3.wls --perm 1000 3 abs 
--2spaces --bg 1”


Thank you,

Gwang-Won


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Re: [Freesurfer] New release plans?

[Douglas N. Greve]

We are planning on releasing a beta version 7 next week with a final 
version 7 in the middle of March



On 2/7/2020 12:30 PM, Dan Fitch wrote:


External Email - Use Caution

Hi folks! I checked the wiki and github, but couldn't find anything 
about milestones or plans for the next major release of Freesurfer.


Are there any loose dates or targets? (We're near the start of a 
5-year imaging study, and trying to plan for training and pipeline 
changes...)


Thanks for any hints you can drop!
Dan Fitch
Research Software Engineer
University of Wisconsin-Madison Center for Healthy Minds


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Re: [Freesurfer] CorticalParcellation for mask

[Douglas N. Greve]

Your can run
mni152reg --s subject
This will create a file calledsubject/ mri/transforms/reg.mni152.2mm.lta
Then use mri_label2vol to map the aparc+aseg.mgz into the mni152 space 
using the --aparc+aseg flag and specifying the mni brain as the 
--template and the reg.mni152.2mm.lta as the --reg


On 2/7/2020 5:34 AM, sang ho shin wrote:


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Dear freesurfer experts,

I am trying to make mask for '1027ctx-lh-rostralmiddlefrontal, 
2027ctx-rh-rostralmiddlefrontal ' on MNI standard image 
(MNI152_T1_2mm_brain.nii) (FreeSurferColorLUT 
)
I can get the mask of native participant's image after completing 
'recon-all'
(mri_binarize--inor86_ahj_fs/mri/aparc+aseg.mgz--match 1027--o 
nor86_ahj_dlpfc/nor86_ahj_rostalmiddlefrontal.nii.gz)

But I now want to get the mask on MNI standard image, not native image.
I wonder if you can help me.

Best regards,
Sangho
ᐧ

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Re: [Freesurfer] uploading PALS12 + overlay

[Douglas N. Greve]

Hi Valeria, I've never used PALS12 before and could not open your 
attachements (unknown file type).

doug

On 2/6/2020 1:31 PM, Barletta, Valeria wrote:

Dear Freesurfers,
Is there a way to visualized the PALS12 atlas in the same view with 
this overlay (attachments) on tksurfer or freeview?


Thanks,
Valeria

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Re: [Freesurfer] Troubles using optseq

[Douglas N. Greve]

Try running it as a single line (ie, without the backslashes and the >)

On 2/6/2020 6:26 AM, FRILEUX Solene wrote:


External Email - Use Caution


Good morning,

I am writing to you in order to ask you some help about optseq.

I am struggling using the command cmx .

I need to save the paradigms as matlab files (90 paradigms)

However, the terminal tells me it is not able to find this function.

Optseq id is $Id: optseq2.c,v 2.22 2011/04/21 19:48:51 greve Exp $

Computer is iMac retina 5K 27 pouces, 2019. 3 .1GHz Intel Core

Here is the text terminal send me :

/Applications/freesurfer/bin/optseq2 \

> --ntp 720 --tr 1.25 \

> --psdwin 016.25 \

> --ev foodCHoice1 3.5 25 \

> --ev foodCHoice2 3.5 25 \

> --ev foodCHoice3 3.5 25 \

> --ev foodCHoice4 3.5 25 \

> --tnullmin 4\

> --nkeep 90 \

> --o subcontrolfood \

> --mtx firdesign

-bash: --mtx: command not found

Thanks a lot,

Solène Frileux


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Re: [Freesurfer] Mismatch between glmfit results and mris_anatomical data in one hemisphere

[Douglas N. Greve]

You should try the analysis but with the data in the something.y.ocn.dat 
output by mri_glmfit-sim. This data contains a nsubjects x nclusters 
table of the input data (y) to the glm. If that does not show up as 
significant, then something is wrong.

doug

On 2/5/2020 11:30 AM, Hooren, Roy van (Alumni) wrote:


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Dear FreeSurfer experts,

In FreeSurfer (Darwin-OSX-stable-v6-beta-20151015 build, operating on 
Yosemite 10.10.5) I’m running into an issue that I would like to 
request your expertise on.


*The procedure I used:*

I have a dataset of 77 participants, which have been processed through 
the standard recon-all and qcache pipeline. Subsequently I’ve used 
mris_preproc to prepare the data for group anaylysis, using FSGD files 
with the DeMeanFlag 1 and ReScaleFlag 1 options. After that, 
MRI_glmfit was run with the appropriate contrasts. Finally, 
mri_glmfit-sim was used to apply cluster correction. The only (minor?) 
issue until this point is that mri_glmfit-sim often runs into a 
“Segmentation fault” error, which can be bypassed by simply rerunning 
mri_glmfit-sim until it does work. Having done this, there seem to be 
no further issues and the clusters resulting from the glm analysis, 
also after cluster correction, look nice in both hemispheres.


To further interpret the resulting clusters, I extracted individual 
labels from the annotation files resulting from the glm analyses, 
using mri_annotation2label. These labels were checked and looked 
correct. Next, these fsaverage-based labels were then warped back to 
the individual level, using mri_label2label, with each subject as the 
–trgsubject. The registration between individual labels and their 
respective inflated brain was checked and looked good on every 
hemisphere. At this point mris_anatomical_stats was used to extract 
average cortical thickness data for each cluster in each participant. 
Finally, using aparcstats2table, these values were placed in a table 
to be imported in R statistics software for visualization purposes.


*What the main problem is:*

The main issue I would like to ask your advice on appeared when the 
data was analyzed in R. In R, the same regression models were 
reconstructed as the ones that were used in mri-glmfit, in order to 
parse and visualize the contribution of each predictor in the model to 
the cortical thickness measure in each cluster. In the right 
hemisphere, the results were as expected for every cluster, showing 
highly significant effects of the variables of interest (p<0.001). 
However, when the same was repeated for the clusters in the left 
hemisphere, none of the expected effects were seen, with p values 
easily rising above 0.90. As the clusters in the left hemisphere 
survived mri_glmfit-sim cluster correction, and the outcome measure is 
average cortical thickness extracted from these clusters, there should 
be no way that this is correct data.


The fact that the data looks incorrect specifically in the left 
hemisphere, while they are as expected for the right hemisphere, leads 
me to believe left and right hemisphere may have been mixed up in one 
of the scripts. However, I have checked the used scripts meticulously 
for any point at which left and right hemisphere may have accidentally 
been mixed up, but after repeated checks I have not found any issues. 
The procedures from mri_label2label and onwards were also repeated 
with separate scripts for left and right hemispheres as a sanity 
check, and the resulting thickness values did not change. As mentioned 
before, the label overlays look good for both hemispheres at the 
individual level, so I do not believe anything went wrong at this point.


I would like to ask if you have any suggestions as to where you 
suspect the problem might lie and would greatly appreciate any 
pointers you might have.


If any more information is needed, please let me know.

Kindest regards,

Roy


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Re: [Freesurfer] Desikan and Killiany atlas

[Valentina Mancini]

External Email - Use Caution

Ok, thank you!

I'll try in this way and let you know if it works.


Best,


Valentina


Da: freesurfer-boun...@nmr.mgh.harvard.edu 
 per conto di Tim Schäfer 

Inviato: venerdì 14 febbraio 2020 13:15:29
A: Freesurfer support list
Oggetto: Re: [Freesurfer] Desikan and Killiany atlas

External Email - Use Caution

I think one way to do this would be to split the atlas into a set of label 
files using `mri_annotation2label`. I would do it for the fsaverage subject. 
This will give you one label file per atlas region. Something like this:

  cd /path/to/freesurfer/subjects/
  mri_annotation2label --subject fsaverage --hemi lh --outdir 
fsaverage/label/aparc_labels --annotation aparc
  # repeat for rh

Then you could first load the fsaverage surfaces (e.g., lh.white and rh.white) 
into freeview, and then add only the labels of the regions you want to show.

Maybe someone else knows an easier way?

Tim

--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany


> On February 14, 2020 at 12:29 PM Valentina Mancini 
>  wrote:
>
>
> External Email - Use Caution
>
> Hi Tim,
>
>
> yes, exactly something like subfigure B but if possible without the colorcode 
> (i.e. some regions yellow and some others in red) having just one value.
>
>
> This is because it would not be super correct to use a "summary measure" that 
> doesn't take into account the time and the different frequency bands.
>
>
> Thank you very much for your help.
>
>
> Best,
>
>
> Valentina
>
> 
> Da: freesurfer-boun...@nmr.mgh.harvard.edu 
>  per conto di Tim Schäfer 
> 
> Inviato: venerdì 14 febbraio 2020 12:10:32
> A: Freesurfer support list
> Oggetto: Re: [Freesurfer] Desikan and Killiany atlas
>
> External Email - Use Caution
>
> Hi Valentina,
>
> Just to be sure I get what you are asking: do you want a visualization like 
> subfigure B in this image?
>
>
> https://raw.githubusercontent.com/dfsp-spirit/fsbrain/master/web/fsbrain_vis_overview.jpg

[https://raw.githubusercontent.com/dfsp-spirit/fsbrain/master/web/fsbrain_vis_overview.jpg]

>
> So you have one value per Desikan atlas region that you want to show?
>
> Best,
>
> Tim
>
> > On February 14, 2020 at 11:49 AM Valentina Mancini 
> >  wrote:
> >
> >
> > External Email - Use Caution
> >
> > Dear Freesurfer experts,
> >
> >
> > we used the Desikan and Killiany atlas to build individual head models in 
> > order to project surface EEG data in the inverse space.
> >
> >
> > We would like to plot on the cortical surface the regions of the D atlas 
> > where we find a different functional activation.
> >
> > As I understand, there is a way to plot statistically significant results 
> > with tksurfer, but in our case we cannot show our statistical values 
> > because we should take into account also epochs and frequency and we can do 
> > that only with a time-frequency plot.
> >
> >
> > Is there a simple way to get a figure of the cortical surface with a set of 
> > predetermined regions of the D atlas highlighted only for visualization 
> > purpose?
> >
> >
> >
> > Best regards,
> >
> >
> >
> > Valentina Mancini
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
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[Freesurfer] watershed, saving issue

[Kirill Elin]

External Email - Use Caution

Hallo everybody,
I am not entirely sure whether this is FreeSurfer error actually.
I am doing first recon all which completes without errors. Then I need to
create BEM surfaces using the FreeSurfer watershed algorithm for MEG data
analysis using MNE-Python.
So the next command in the terminal is: mne watershed_bem --subject
subjectname
And it runs e.g. till:
mri_watershed ru_nivcsw   12490
mri_watershed done
and quits with errors like:
File
"/work/modules/Ubuntu/14.04/amd64/common/anaconda3/latest/envs/neuroimaging/lib/python3.6/site-packages/mne/utils/check.py",
line 143, in _check_fname
raise IOError('Destination file exists. Please use option '
OSError: Destination file exists. Please use option "overwrite=True" to
force overwriting.

Now, it is unclear what file destination file is meant. This happens on
several machines for all participants.
--overwrite option does not help.
The correct outcome should include bem folder with resulting files and also
watershed subfolder with resulting files. Here and the files in bem folder
are missing and there are files only in watershed subfolder.
FreeSurfer 6.0.0., Ubuntu
Thank you in advance.

Sincerely yours,
Kirill
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Re: [Freesurfer] Desikan and Killiany atlas

[Tim Schäfer]

External Email - Use Caution

I think one way to do this would be to split the atlas into a set of label 
files using `mri_annotation2label`. I would do it for the fsaverage subject. 
This will give you one label file per atlas region. Something like this:

  cd /path/to/freesurfer/subjects/
  mri_annotation2label --subject fsaverage --hemi lh --outdir 
fsaverage/label/aparc_labels --annotation aparc
  # repeat for rh

Then you could first load the fsaverage surfaces (e.g., lh.white and rh.white) 
into freeview, and then add only the labels of the regions you want to show.

Maybe someone else knows an easier way?

Tim

--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany


> On February 14, 2020 at 12:29 PM Valentina Mancini 
>  wrote:
> 
> 
> External Email - Use Caution
> 
> Hi Tim,
> 
> 
> yes, exactly something like subfigure B but if possible without the colorcode 
> (i.e. some regions yellow and some others in red) having just one value.
> 
> 
> This is because it would not be super correct to use a "summary measure" that 
> doesn't take into account the time and the different frequency bands.
> 
> 
> Thank you very much for your help.
> 
> 
> Best,
> 
> 
> Valentina
> 
> 
> Da: freesurfer-boun...@nmr.mgh.harvard.edu 
>  per conto di Tim Schäfer 
> 
> Inviato: venerdì 14 febbraio 2020 12:10:32
> A: Freesurfer support list
> Oggetto: Re: [Freesurfer] Desikan and Killiany atlas
> 
> External Email - Use Caution
> 
> Hi Valentina,
> 
> Just to be sure I get what you are asking: do you want a visualization like 
> subfigure B in this image?
> 
>
> https://raw.githubusercontent.com/dfsp-spirit/fsbrain/master/web/fsbrain_vis_overview.jpg
> 
> So you have one value per Desikan atlas region that you want to show?
> 
> Best,
> 
> Tim
> 
> > On February 14, 2020 at 11:49 AM Valentina Mancini 
> >  wrote:
> >
> >
> > External Email - Use Caution
> >
> > Dear Freesurfer experts,
> >
> >
> > we used the Desikan and Killiany atlas to build individual head models in 
> > order to project surface EEG data in the inverse space.
> >
> >
> > We would like to plot on the cortical surface the regions of the D atlas 
> > where we find a different functional activation.
> >
> > As I understand, there is a way to plot statistically significant results 
> > with tksurfer, but in our case we cannot show our statistical values 
> > because we should take into account also epochs and frequency and we can do 
> > that only with a time-frequency plot.
> >
> >
> > Is there a simple way to get a figure of the cortical surface with a set of 
> > predetermined regions of the D atlas highlighted only for visualization 
> > purpose?
> >
> >
> >
> > Best regards,
> >
> >
> >
> > Valentina Mancini
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> ___
> Freesurfer mailing list
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> ___
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Desikan and Killiany atlas

[Valentina Mancini]

External Email - Use Caution

Hi Tim,


yes, exactly something like subfigure B but if possible without the colorcode 
(i.e. some regions yellow and some others in red) having just one value.


This is because it would not be super correct to use a "summary measure" that 
doesn't take into account the time and the different frequency bands.


Thank you very much for your help.


Best,


Valentina


Da: freesurfer-boun...@nmr.mgh.harvard.edu 
 per conto di Tim Schäfer 

Inviato: venerdì 14 febbraio 2020 12:10:32
A: Freesurfer support list
Oggetto: Re: [Freesurfer] Desikan and Killiany atlas

External Email - Use Caution

Hi Valentina,

Just to be sure I get what you are asking: do you want a visualization like 
subfigure B in this image?

   
https://raw.githubusercontent.com/dfsp-spirit/fsbrain/master/web/fsbrain_vis_overview.jpg

So you have one value per Desikan atlas region that you want to show?

Best,

Tim

> On February 14, 2020 at 11:49 AM Valentina Mancini 
>  wrote:
>
>
> External Email - Use Caution
>
> Dear Freesurfer experts,
>
>
> we used the Desikan and Killiany atlas to build individual head models in 
> order to project surface EEG data in the inverse space.
>
>
> We would like to plot on the cortical surface the regions of the D atlas 
> where we find a different functional activation.
>
> As I understand, there is a way to plot statistically significant results 
> with tksurfer, but in our case we cannot show our statistical values because 
> we should take into account also epochs and frequency and we can do that only 
> with a time-frequency plot.
>
>
> Is there a simple way to get a figure of the cortical surface with a set of 
> predetermined regions of the D atlas highlighted only for visualization 
> purpose?
>
>
>
> Best regards,
>
>
>
> Valentina Mancini
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Desikan and Killiany atlas

[Tim Schäfer]

External Email - Use Caution

Hi Valentina,

Just to be sure I get what you are asking: do you want a visualization like 
subfigure B in this image? 

   
https://raw.githubusercontent.com/dfsp-spirit/fsbrain/master/web/fsbrain_vis_overview.jpg

So you have one value per Desikan atlas region that you want to show?

Best,

Tim

> On February 14, 2020 at 11:49 AM Valentina Mancini 
>  wrote:
> 
> 
> External Email - Use Caution
> 
> Dear Freesurfer experts,
> 
> 
> we used the Desikan and Killiany atlas to build individual head models in 
> order to project surface EEG data in the inverse space.
> 
> 
> We would like to plot on the cortical surface the regions of the D atlas 
> where we find a different functional activation.
> 
> As I understand, there is a way to plot statistically significant results 
> with tksurfer, but in our case we cannot show our statistical values because 
> we should take into account also epochs and frequency and we can do that only 
> with a time-frequency plot.
> 
> 
> Is there a simple way to get a figure of the cortical surface with a set of 
> predetermined regions of the D atlas highlighted only for visualization 
> purpose?
> 
> 
> 
> Best regards,
> 
> 
> 
> Valentina Mancini
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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[Freesurfer] Desikan and Killiany atlas

[Valentina Mancini]

External Email - Use Caution

Dear Freesurfer experts,


we used the Desikan and Killiany atlas to build individual head models in order 
to project surface EEG data in the inverse space.


We would like to plot on the cortical surface the regions of the D atlas 
where we find a different functional activation.

As I understand, there is a way to plot statistically significant results with 
tksurfer, but in our case we cannot show our statistical values because we 
should take into account also epochs and frequency and we can do that only with 
a time-frequency plot.


Is there a simple way to get a figure of the cortical surface with a set of 
predetermined regions of the D atlas highlighted only for visualization 
purpose?



Best regards,



Valentina Mancini
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[Freesurfer] Error in long_mris_slopes

[Guillaume Carey]

External Email - Use Caution

Hello everyone,

I’m currently working on a longitudinal FreeSurfer pipeline in order to compare 
cortical thickness changes across the time. I’m using FreeSurfer version 6.0.0 
(OS: Scientific Linux 7.3). I already processed the recon-all, -base and -long 
processing steps.

Now I’m trying to run the “long_mris_slopes“ processing in order to prepare the 
data for a two stage model analyze. But there is an error. 

The command:

long_mris_slopes --qdec ./qdec.dat --meas thickness --hemi lh  --do-spc 
--do-label --time month --qcache fsaverage --sd $SUBJECTDIR


At first everything seems to work well for the 1st subject and then:

 ==

SUBJECT CBTPD-001/template_CBTPD-001  mapping label to QCache

(…)

Writing label file 
/data/guillaume/ParkAnx3/freesurfer/results/CBTPD-001/template_CBTPD-001/label/lh.long.cortex.fsaverage.label
 167889

mri_label2label: Done


Traceback (most recent call last):

  File "/opt/mumc/apps/freesurfer-6.0.0/bin/long_mris_slopes", line 868, in 


dirname = tempfile.mkdtemp('',prefix,'')

  File "/usr/lib64/python2.7/tempfile.py", line 329, in mkdtemp

_os.mkdir(file, 0700)

OSError: [Errno 2] No such file or directory: 
'./tmp-CBTPD-001/template_CBTPD-001_lh_thickness_wuK7ZI'



It seems like the output “lh.long.cortex.fsaverage.label” has been created for 
this subject. But then there is a missing “tmp” folder.

I haven’t find this error in the archives. Does anyone have an idea of how to 
fix it ?



Best,

Guillaume ___
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