Re: [Freesurfer] LGI ERROR

[郑凤莲]

Hi Greve,


Thanks for your help. It is that I only use FWMH = 5 to do my study, it is 
decided by  my data. Can I think  it so?


Sincerely,
Zheng






At 2017-12-14 00:06:39, "Douglas Greve"  wrote:


The FWHM used in the MC simulation is computed from the data itself. The final 
FWHM is a mixture of the applied FWHM and smoothness inherent in the data. LGI 
has a lot of inherent smoothness, so the final FWHM is very large. The MC sim 
table only goes up to 30mm, after that it generates an error




On 12/13/17 2:19 AM, 郑凤莲 wrote:

Hi professors,

I am using Freesurfer 6.0 for calculating LGI. I have done 'recon-all' for 
it. When I ran Monte Carlo in qdec (FWHM=10), it has errors:
However, when FWHM=5, It was ok. What led to this result? I don't know why.


Thanks in advance !
Zheng









 






 




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Re: [Freesurfer] mri_surf2surf on edited subjects

[Defenderfer, Matthew K]

The number of vertices match between the lh.sphere.reg and lh.pial. All of the 
timestamps are the same as well. I just tried this with v5.3 as well and the 
problem is the same. Thank you for helping with this!


-Matt Defenderfer


Matthew K. Defenderfer B.S. | Graduate Research Assistant

Graduate Biomedical Sciences | Neuroscience

UAB | The University of Alabama at Birmingham

Laboratory of Kristina Visscher, PhD

Department of Neurobiology

CIRC 111 | C: (865) 805-6389



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Bruce Fischl 

Sent: Wednesday, December 13, 2017 4:16:03 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] mri_surf2surf on edited subjects

Hi Matt

can you run mris_euler_number on that subject's lh.sphere.reg and see if it
has the same number of vertices as the lh.pial for example? Or check
timestamps. If it was not recreated after your editing you will need to
rerun part of recon-all

cheers
Bruce


On
Wed, 13 Dec 2017, Defenderfer, Matthew K wrote:

>
> Hi all,
>
>
> I am trying to transfer a surface file from fsaverage_sym space to a recently 
> edited individual
> subject's hemisphere. I previously ran recon-all on the subject and then 
> edited the wm, brainmask, etc.
> to fix some defects I had found. Before the edits, I could transfer the 
> surface and load it on the
> subject's hemisphere as an overlay perfectly fine. After editing and 
> rerunning the subject through
> recon-all and the xhemi pipeline, I tried to transfer and load the overlay 
> again using the following
> command, same as originally:
>
>
> mri_surf2surf --srcsubject fsaverage_sym --srcsurfreg sphere.reg --trgsubject 
> subj001 --trgsurfreg
> fsaverage_sym.sphere.reg --hemi lh --sval template.sym.mgh --tval 
> subj001/surf/template.sym.mgh
>
>
> The command completes, but the resulting overlay does not have the same 
> number of vertices as the
> surface. It does however, have the same number of vertices as the original 
> surface from before
> rerunning the recon-all command. So it seems like it's still transferring the 
> overlay to original
> surface. My SUBJECTS_DIR does not have the subjects' original recon-all data 
> in it either, just the
> data from the edited recon-all. Any help on this would be appreciated. Thank 
> you!
>
>
> -Matt Defenderfer
>
>
> Matthew K. Defenderfer B.S. | Graduate Research Assistant
>
> Graduate Biomedical Sciences | Neuroscience
>
> UAB | The University of Alabama at Birmingham
>
> Laboratory of Kristina Visscher, PhD
>
> Department of Neurobiology
>
> CIRC 111 | C: (865) 805-6389
>
>
>
>
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Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst

[Diamond, Bram Ryder]

Hi Martin,


We've taken a look at the scans you uploaded, and unfortunately it won't be 
possible to run the standard recon-all on your subject.  Recon-all is not 
designed to work on scans with such large lesions.  If you are interested, 
there may be a way to generate a reasonable model of the right hemisphere.


Best,

Bram


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Loeffler, Martin 

Sent: Tuesday, December 12, 2017 11:57:36 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst

Dear Bruce,
I have uploaded the respective files. If there is something missing let me know.
Cheers,
Martin


-Ursprüngliche Nachricht-
Von: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl
Gesendet: Dienstag, 12. Dezember 2017 16:35
An: Freesurfer support list
Betreff: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst

Hi Martin

we are happy to take a look, but can't really tell much from a screenshot.
Feel free to upload the subject to our ftp site if you want us to help

cheers
Bruce

On Tue, 12 Dec 2017, Loeffler, Martin wrote:

> Dear Bruce,
>
> thanks for the quick reply! You are right, of course. I do find errors in 
> lh.inflated.nofix.
> I have attached a screenshot of the biggest errors I found..
> Can you maybe guide me a little how to fix the issue? Do I just cancel the 
> running recon-all process, and set control points and run again? Investing 
> some time in manual editing would be fine as it's a case study...
>
> Thanks for your help,
> Martin
>
>
> 
> Von: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] im Auftrag von
> Bruce Fischl [fis...@nmr.mgh.harvard.edu]
> Gesendet: Montag, 11. Dezember 2017 22:47
> An: Freesurfer support list
> Betreff: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst
>
> Hi Martin
>
> a defect that large means that something big went wrong (skull or dura
> attached, etc...). Try looking at the ?h.orig.nofix and/or the
> ?h.inflated.nofix surfaces with the ?h.defect_labels overlayed to find
> defect 9
>
> cheers
> Bruce
>
>
> On Mon, 11 Dec 2017, Loeffler, Martin wrote:
>
>>
>> Dear FreeSurfer team,
>>
>>
>>
>> For a case report I'm running recon-all on a patient with a giant
>> arachnoid cyst in the left hemisphere. It gets stuck at this point (last 
>> message):
>>
>> CORRECTING DEFECT 9 (vertices=21935, convex hull=1992, v0=31849)
>>
>> XL defect detected...
>>
>> It is stuck here since a whole day now, so I'm not expecting it to
>> advance.
>>
>> Following this post:
>> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg48891.html I 
>> looked at the wm.mgz, but did not find huge errors.
>>
>> Do you have any ideas what the problem might be or what I can do to work 
>> around it?
>>
>>
>>
>> Thanks,
>>
>> Martin
>>
>>
>>
>>
>>
>>
>>

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Re: [Freesurfer] mri_surf2surf on edited subjects

[Bruce Fischl]

Hi Matt

can you run mris_euler_number on that subject's lh.sphere.reg and see if it 
has the same number of vertices as the lh.pial for example? Or check 
timestamps. If it was not recreated after your editing you will need to 
rerun part of recon-all


cheers
Bruce


On 
Wed, 13 Dec 2017, Defenderfer, Matthew K wrote:




Hi all,


I am trying to transfer a surface file from fsaverage_sym space to a recently 
edited individual
subject's hemisphere. I previously ran recon-all on the subject and then edited 
the wm, brainmask, etc.
to fix some defects I had found. Before the edits, I could transfer the surface 
and load it on the
subject's hemisphere as an overlay perfectly fine. After editing and rerunning 
the subject through
recon-all and the xhemi pipeline, I tried to transfer and load the overlay 
again using the following
command, same as originally:


mri_surf2surf --srcsubject fsaverage_sym --srcsurfreg sphere.reg --trgsubject 
subj001 --trgsurfreg
fsaverage_sym.sphere.reg --hemi lh --sval template.sym.mgh --tval 
subj001/surf/template.sym.mgh


The command completes, but the resulting overlay does not have the same number 
of vertices as the
surface. It does however, have the same number of vertices as the original 
surface from before
rerunning the recon-all command. So it seems like it's still transferring the 
overlay to original
surface. My SUBJECTS_DIR does not have the subjects' original recon-all data in 
it either, just the
data from the edited recon-all. Any help on this would be appreciated. Thank 
you!


-Matt Defenderfer


Matthew K. Defenderfer B.S. | Graduate Research Assistant

Graduate Biomedical Sciences | Neuroscience

UAB | The University of Alabama at Birmingham

Laboratory of Kristina Visscher, PhD

Department of Neurobiology

CIRC 111 | C: (865) 805-6389



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[Freesurfer] mri_surf2surf on edited subjects

[Defenderfer, Matthew K]

Hi all,


I am trying to transfer a surface file from fsaverage_sym space to a recently 
edited individual subject's hemisphere. I previously ran recon-all on the 
subject and then edited the wm, brainmask, etc. to fix some defects I had 
found. Before the edits, I could transfer the surface and load it on the 
subject's hemisphere as an overlay perfectly fine. After editing and rerunning 
the subject through recon-all and the xhemi pipeline, I tried to transfer and 
load the overlay again using the following command, same as originally:


mri_surf2surf --srcsubject fsaverage_sym --srcsurfreg sphere.reg --trgsubject 
subj001 --trgsurfreg fsaverage_sym.sphere.reg --hemi lh --sval template.sym.mgh 
--tval subj001/surf/template.sym.mgh


The command completes, but the resulting overlay does not have the same number 
of vertices as the surface. It does however, have the same number of vertices 
as the original surface from before rerunning the recon-all command. So it 
seems like it's still transferring the overlay to original surface. My 
SUBJECTS_DIR does not have the subjects' original recon-all data in it either, 
just the data from the edited recon-all. Any help on this would be appreciated. 
Thank you!


-Matt Defenderfer


Matthew K. Defenderfer B.S. | Graduate Research Assistant

Graduate Biomedical Sciences | Neuroscience

UAB | The University of Alabama at Birmingham

Laboratory of Kristina Visscher, PhD

Department of Neurobiology

CIRC 111 | C: (865) 805-6389

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Re: [Freesurfer] Dura classified as GM in brainmask

[FSL Analysis]

Hi Bruce,


Thank you for your reply. I am using 5.3.0 version. Do I still only
correct misclassified GM voxels in the brainmask?


For the subjects with brain classified as cerebral cortex in the aseg
file which is outside of the pial surface (but present in the
brainmask) how do I correct this:

1. If it should be GM how do I edit the pial surface?

2. If it is non-brain matter how do I remove it from the aseg file- do
I erase these voxels from the brainmask even though they are not in
the pial surface mask?



Thanks,


Ciara



Hi Ciara

what version are you running? I think you only need to correct voxels that
cause the white and/or pial surfaces to be incorrect, as we correct the
aseg with them (at least I think we do in v6)

cheers
Bruce


On Wed, Dec 13, 2017 at 12:11 PM, FSL Analysis 
wrote:

> Hi again,
>
> I realize my last question about the brainmask did not make sense. I meant
> to ask if I have to either manually delete all non-brain voxels around the
> eye area which is very time consuming per subject or just delete those
> misclassified as GM? ( I check this through the command: tkmedit
> subj_output brainmask.mgz -aux T1.mgz -surfs)
>
> Also for some subjects:
> 1. When I open freeview and look at the aseg file there is area around the
> eye misclassified as cerebral cortex for some subjects.
> 2. When I load the pial surface the aseg file shows cerebral cortex in the
> temporal poles and frontal lobes near the eye region outside of the pial
> surface outline. How do I edit this?
>
>
>
> I look forward to your response.
>
>
>
>
> Thanks
>
> On Tue, Dec 12, 2017 at 4:21 PM, FSL Analysis 
> wrote:
>
>> Hi all,
>>
>> I have processed data using freesurfer and the output for most of my
>> subjects did not remove all of the eye and dura around it during skull
>> stripping. When I check the brainmask there is dura (or blood vessel) in
>> the frontal lobe that is classified as GM.
>>
>> I am wondering if I have to manually edit the skullstrip and rerun
>> recon-all or do I just edit the brainmask file by deleting non-brain
>> voxels? Or do I have to do both?
>>
>> If I only edit the brainmask file does this skip any other important
>> processing steps that may affect my results?
>>
>> I am planning on looking at brain volumes and cortical thickness and how
>> they relate to behavioral measures.
>>
>>
>>
>>
>> Kind Regards,
>>
>> Ciara
>>
>
>
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Re: [Freesurfer] ?h.DKTatlas100.gcs to annot

[Bruce Fischl]

they would be in $FREESURFER_HOME/subjects/fsaverage/label

On Wed, 13 Dec 
2017, tony han wrote:




Hi Bruce,


Thanks. If there is one available, could you point me to the location of the 
files? I check
$FREESURFER_HOME/average and can't find annot files for DKTatlas. 


If I'm going to make one with one of the fsaverage subjects, there won't be any 
difference of the
resultant annot file no matter which fsaverage subject {fsaverage, 
fsaverage3,...,fsaverage6} I use,
right?


Best,

Tony


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of
Bruce Fischl 
Sent: Wednesday, December 13, 2017 12:06:18 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] ?h.DKTatlas100.gcs to annot  
Hi Tony

I think we distribute one, but if not you should just be able to run
mris_ca_label on the fsaverage subject to generate one.

cheers
Bruce
On Wed, 13 Dec 2017,
tony han wrote:

>
> Hi,
>
>
> Is it possible to get an annot file for ?h.DKTatlas100.gcs, not for 
individuals, but for fsaverage
atlas? I want to plot the 'standard' parcellation, instead of individual ones, 
on the surface so
> that I can use as a general reference. Thanks!
>
>
> Tony
>
>
>

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Re: [Freesurfer] JRE error in fsfast/matlab

[Yagmur Ozdemir 19]

Yes it terminates prematurely.

Best
Idil

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Wednesday, December 13, 2017 5:50 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] JRE error in fsfast/matlab

By default the graphics are turned off when running selxavg-sess. I often see 
that error message, but it never ends up causing the program to terminate. Is 
your process terminating prematurely?

On 12/13/17 10:24 AM, Yagmur Ozdemir 19 wrote:
Hello FreeSurfer experts,

I have been running into a matlab-related problem that I was wondering if 
anyone came across. I am using Matlab2017b with Freesurfer 6.0. Whenever I run 
selxavg-sess command, 
the matlab tries to find the OpenGL rendering, then gives a Java fatal error 
with a failure to find the Java Runtime Environment and exits. (I don't have 
the command outputs with me right now, sorry.) I have been trying to fix it 
with getting a better graphics card, OpenGL, getting Octave etc but this error 
didn't come up when I was using an earlier version of Matlab. I would 
appreciate any help.

Best
Idil



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[Freesurfer] Transforming invasive electrodes coordinates to a template brain

[Peled, Noam]

Dear freesurfer experts,

I would like to present invasive electrodes from different subjects in the same 
template brain.

I thought about doing a volumetric registration (all the electrodes are depth) 
using mri_cvs_register:

mri_cvs_register --mov {subject} --template {template} --outdir 
$SUBJECTS_DIR/{template}/mri_cvs_register --step3

And then using mri_vol2vol that'll use the resulting m3z transformation file.

Can I do it for a list of coordinates?


Thanks,

Noam
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Re: [Freesurfer] ?h.DKTatlas100.gcs to annot

[tony han]

Hi Bruce,


Thanks. If there is one available, could you point me to the location of the 
files? I check $FREESURFER_HOME/average and can't find annot files for DKTatlas.


If I'm going to make one with one of the fsaverage subjects, there won't be any 
difference of the resultant annot file no matter which fsaverage subject 
{fsaverage, fsaverage3,...,fsaverage6} I use, right?


Best,

Tony


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Bruce Fischl 

Sent: Wednesday, December 13, 2017 12:06:18 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] ?h.DKTatlas100.gcs to annot

Hi Tony

I think we distribute one, but if not you should just be able to run
mris_ca_label on the fsaverage subject to generate one.

cheers
Bruce
On Wed, 13 Dec 2017,
tony han wrote:

>
> Hi,
>
>
> Is it possible to get an annot file for ?h.DKTatlas100.gcs, not for 
> individuals, but for fsaverage atlas? I want to plot the 'standard' 
> parcellation, instead of individual ones, on the surface so
> that I can use as a general reference. Thanks!
>
>
> Tony
>
>
>
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[Freesurfer] Voxel time-series within a specific functional ROI

[Ashley Cole]

I am working on an fMRI-adaptation experiment and was wondering how to
extract voxel time-series within a specific functional ROI.

I have created a functional ROI mask. This mask has only one time-point.

According to this thread
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-October/040811.html
I need to I use the funcroi-table-sess command multiple times. Is this
correct? So if I have 270 TRs. I have to run the command 270 times?



Thanks,

AC
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Re: [Freesurfer] free surfer v5 & 6

[Lilla Zollei]

Hi Gianluca,

> I am working with data coming from two different versions of Freesurfer, v5.1 
> and v6.
> As measurements looks different (an excerpt below from aseg.stats files), I 
> am trying to see if  that difference is statistically relevant.
> Could you anticipate something with this respect?

We do not advise you to include data processed with different versions in 
the same study as there are differences between our releases.

> One more question is about voxel counting and their volume. aseg.stats prints 
> out that # VoxelVolume_mm3 1
> but volumes from v.6 seems to be  sometimes greater sometimes lower than the 
> voxel number,
> while in v. 5.1 they correspond.
> Could you give me some clarification?

I do not understand your question. Are you asking about the volume 
differences between the two versions?

Lilla

>
> v.6
>
> # ColHeaders  Index SegId NVoxels Volume_mm3 StructName normMean normStdDev 
> normMin normMax normRange
>  1   4  5424 5779.6  Left-Lateral-Ventricle22.1768
> 15.6303 0.81.81.
>  2   5   198  225.9  Left-Inf-Lat-Vent 43.8838
> 14.0865 6.77.71.
>  3   7 1744418248.8  Left-Cerebellum-White-Matter  80.5691 
> 8.732220.   133.   113.
>  4   8 6925869340.7  Left-Cerebellum-Cortex49.2701
> 12.9332 0.   128.   128.
>  5  10  8758 8432.7  Left-Thalamus-Proper  81.4639
> 10.850037.   123.86.
>
> v. 5.1
>
> # ColHeaders  Index SegId NVoxels Volume_mm3 StructName normMean normStdDev 
> normMin normMax normRange
>  1   4  5013 5013.0  Left-Lateral-Ventricle16.7825
> 16.6860 0.82.82.
>  2   5   161  161.0  Left-Inf-Lat-Vent 39.9084
> 12.2446 7.73.66.
>  3   7 1925019250.0  Left-Cerebellum-White-Matter  83.1263 
> 8.164041.   110.69.
>  4   8 6024660246.0  Left-Cerebellum-Cortex50.8222
> 10.7915 5.93.88.
>  5  10  7911 7911.0  Left-Thalamus-Proper  88.1600
> 10.422643.   134.91.
>
>
>
>
>
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Re: [Freesurfer] PET partial volume correction:mri_gtmpvc error

[Herranz Muelas, Elena]

Hi Doug,


Thanks for your response. Actually, we do modify the aseg.mgz (Sorry, I didn't 
realized and I shouldn't have considered this a 'standard FS pipeline').


We work with Multiple Sclerosis patients and because of the size and number of 
lesions in some of them, the pial and WM surfaces that we obtain after a first 
run of “recon-all -all ” are not accurate. FreeSurfer pipeline for healthy 
subjects or small lesions requires to edit wm.mgz -- but these edits don't fix 
our issue of WM & GM surface getting pulled in by lesions. Given the size and 
number of lesions in some of our MS patients, using control points make the 
entire recon worse. So after repeated testing, the solution we arrived at was 
to insert manually drawn lesion masks into segmentation volumes as 
"WM-hypointensities". We label manually drawn lesion masks as 
"WM-hypointensities" on aseg.mgz, and wm.mgz. We then do a second run of 
recon-all and check the surfaces again. Once they are ok we run “recon-all 
-autorecon3” and check the final output.


In principle, we only change voxels in aseg.mgz to "WM-hypointensities", so I 
don't know why these unexpected values appear. Just to check, I renamed the 
'aseg.auto.mgz' as 'aseg.mgz' and re-run again the steps for PVC:


1. Segmentation for GTM:

gtmseg --s $subj"_recon" --xcerseg


In this step I get the following warnings:


WARNING: segid   59 Right-Substancia-Nigra tissue type is not set
WARNING: segid   61 Right-undetermined tissue type is not set
WARNING: segid   64 Right-F3orb tissue type is not set
WARNING: segid   73 Left-Interior tissue type is not set
WARNING: segid   81 Left-non-WM-hypointensities tissue type is not set
WARNING: segid   86 Left_future_WMSA tissue type is not set


2. Registration:

mri_coreg --s $subj"_recon" --mov $path_to_suvr/SUVR.nii.gz --reg 
$path_to_suvr/SUVR.reg.lta

3. PVC:

mri_gtmpvc --i $path_to_suvr/SUVR.nii.gz --reg $path_to_suvr/SUVR.reg.lta --psf 
6 --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx .01 --o 
$path_to_recon/$subj"_recon"/gtmpvc.output.


And still get the same error (below) (maybe because there are other files that 
are based in the previous aseg.mgz? )


Checking tissue type
ERROR: CheckSegTissueType() tissue type for seg 64 Right-F3orb not set
Failed tissue type check


Any help with this would be very much appreciate it!


Thanks!


Elena



From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Thursday, December 07, 2017 12:19 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] PET partial volume correction:mri_gtmpvc error

Hi  Elena, it looks like the aseg.mgz has several unexpected segments in
it. The aseg.auto.mgz looks ok, so I think FS is working properly. It
looks like you made some changes to the aseg. What did you do?


On 12/06/2017 03:51 PM, Douglas N Greve wrote:
> Did you run this through the standard FS pipeline? If so, can you send
> me the FS analysis for this subject? You can upload it here
>
> https://gate.nmr.mgh.harvard.edu/filedrop2
FileDrop v2.0 - Martinos Center for Biomedical 
Imaging
gate.nmr.mgh.harvard.edu
Filedrop is for sending files work-related files up to 2GiB; For files over 
2GiB, please use the Accellion File Transfer from Partners; Filedrop is not a 
secure ...


>
>
> On 12/06/2017 09:46 AM, Herranz Muelas, Elena wrote:
>> Dear Freesurfers,
>>
>>
>> I am trying to apply partial volume correction to my PET images,
>> following  the steps explained in the PetSurfer wiki.
>>
>>
>> When I run the mri_gtmpvc command, it works fine for most of the
>> subjects but for some of them I get the following error message:
>>
>>
>> /autofs/space/alicudi_002/users/mscat/users/caterina/MR-PET/MSPET06/PET/PET-space
>> Loading input
>> /autofs/space/alicudi_002/users/mscat/users/caterina/MR-PET/MSPET06/PET/PET-space/SUVR.nii.gz
>>done loading input 1 frames
>> $Id: mri_gtmpvc.c,v 1.69.2.1 2016/07/08 19:50:25 zkaufman Exp $
>> setenv SUBJECTS_DIR
>> /autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3
>> cd /autofs/space/alicudi_002/users/mscat/users/elena/scripts/PVC
>> mri_gtmpvc --i
>> /autofs/space/alicudi_002/users/mscat/users/caterina/MR-PET/MSPET06/PET/PET-space/SUVR.nii.gz
>> --reg
>> /autofs/space/alicudi_002/users/mscat/users/caterina/MR-PET/MSPET06/PET/PET-space/SUVR.reg.lta
>> --psf 6 --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx
>> .01 --o
>> /autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3/MSPET06_recon/gtmpvc.output
>> sysname  Linux
>> hostname alicudi.nmr.mgh.harvard.edu
>> machine  x86_64
>> user ehmuelas
>> vgthresh   0.001000
>> nReplace   18
>> 0. 0. 0. 0. 0. 0.
>> 40 avail.processors, using 1
>> Creating output directory
>> 

Re: [Freesurfer] Dura classified as GM in brainmask

[Bruce Fischl]

Hi Ciara

what version are you running? I think you only need to correct voxels that 
cause the white and/or pial surfaces to be incorrect, as we correct the 
aseg with them (at least I think we do in v6)


cheers
Bruce


On Wed, 13 Dec 2017, FSL Analysis wrote:


Hi again,
I realize my last question about the brainmask did not make sense. I meant to 
ask if I have to either manually delete all non-brain voxels around the eye 
area which is very time consuming per subject
or just delete those misclassified as GM? ( I check this through this command: 
tkmedit subj_output brainmask.mgz -aux T1.mgz -surfs)

Also for some subjects:
1. When I open freeview and look at the aseg file there is area around the eye 
misclassified as cerebral cortex for some subjects. 
2. When I load the pial surface the aseg file shows cerebral cortex in the 
temporal poles and frontal lobes near the eye region outside of the pial 
surface outline. How do I edit this? 



I look forward to your response.




Thanks.

On Tue, Dec 12, 2017 at 4:21 PM, FSL Analysis  wrote:
  Hi all,
I have processed data using freesurfer and the output for most of my subjects 
did not remove all of the eye and dura around it during skull stripping. When I 
check the brainmask there is dura
(or blood vessel) in the frontal lobe that is classified as GM.

I am wondering if I have to manually edit the skullstrip and rerun recon-all or 
do I just edit the brainmask file by deleting non-brain voxels? Or do I have to 
do both? 

If I only edit the brainmask file does this skip any other important processing 
steps that may affect my results?

I am planning on looking at brain volumes and cortical thickness and how they 
relate to behavioral measures.




Kind Regards,

Ciara



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Re: [Freesurfer] ?h.DKTatlas100.gcs to annot

[Bruce Fischl]

Hi Tony

I think we distribute one, but if not you should just be able to run 
mris_ca_label on the fsaverage subject to generate one.


cheers
Bruce
On Wed, 13 Dec 2017, 
tony han wrote:




Hi,


Is it possible to get an annot file for ?h.DKTatlas100.gcs, not for 
individuals, but for fsaverage atlas? I want to plot the 'standard' 
parcellation, instead of individual ones, on the surface so
that I can use as a general reference. Thanks!


Tony


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Re: [Freesurfer] Hippocampal Subfield and Amyg Nuclei ICV Correction

[Maksimovskiy, Arkadiy]

Hi Eugenio,

Thank you so much for the helpful information!

Best,
Arkadiy
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Re: [Freesurfer] Dura classified as GM in brainmask

[FSL Analysis]

Hi again,

I realize my last question about the brainmask did not make sense. I meant
to ask if I have to either manually delete all non-brain voxels around the
eye area which is very time consuming per subject or just delete those
misclassified as GM? ( I check this through the command: tkmedit
subj_output brainmask.mgz -aux T1.mgz -surfs)

Also for some subjects:
1. When I open freeview and look at the aseg file there is area around the
eye misclassified as cerebral cortex for some subjects.
2. When I load the pial surface the aseg file shows cerebral cortex in the
temporal poles and frontal lobes near the eye region outside of the pial
surface outline. How do I edit this?



I look forward to your response.




Thanks

On Tue, Dec 12, 2017 at 4:21 PM, FSL Analysis  wrote:

> Hi all,
>
> I have processed data using freesurfer and the output for most of my
> subjects did not remove all of the eye and dura around it during skull
> stripping. When I check the brainmask there is dura (or blood vessel) in
> the frontal lobe that is classified as GM.
>
> I am wondering if I have to manually edit the skullstrip and rerun
> recon-all or do I just edit the brainmask file by deleting non-brain
> voxels? Or do I have to do both?
>
> If I only edit the brainmask file does this skip any other important
> processing steps that may affect my results?
>
> I am planning on looking at brain volumes and cortical thickness and how
> they relate to behavioral measures.
>
>
>
>
> Kind Regards,
>
> Ciara
>
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Re: [Freesurfer] Hippocampal Subfield and Amyg Nuclei ICV Correction

[Iglesias Gonzalez, Eugenio]

Hi Arkadiy
1. Yes
2. If you’re correcting the subfields by hippocampal volume: a) the question is 
a different one (“which fraction of the hippo volume is attributed to each 
subfield”); and b) I wouldn’t correct by ICV, because the values are already 
fractions / normalized (see point a).
Cheers,
/Eugenio

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


From:  on behalf of "Maksimovskiy, 
Arkadiy" 
Reply-To: Freesurfer support list 
Date: Wednesday, 13 December 2017 at 16:08
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Hippocampal Subfield and Amyg Nuclei ICV Correction

Dear Experts,

I have seen this question pop up a few times in the forum, but have not seen a 
clear response, so I was wondering if someone might be able to clarify or offer 
their opinion.


  1.  Do the hippocampal subfields and amygdala nuclei need to be corrected for 
ICV (either by including ICV as a covariate or taking the ration if each 
subfield to the ICV)?
  2.  If so, might it make more sense to correct them (perhaps take the ratio 
of each subfield to the hippocampus) for the volume of the hippocampus (after 
the hipp. itself has been corrected for the ICV)? If the correction is 
recommended, I am wondering about whether the second option might be better, 
because the ICV correction might be introducing too much variability for such a 
small sub-structure, whereas, correcting for just the hippocampus volume might 
be a bit more accurate.

I found two ways of dealing with this in the relevant papers for the hipp. 
Subfield and amyg nuclei, respectively, quoted below:

“Then, we correct these estimates for age and intracranial volume (ICV) by 
regressing them out with a general linear model. This step is important because 
the subregion volumes are strongly correlated with these two variables, which 
can easily confound the analysis – subjects with large ICV and/or of younger 
age are expected to have larger hippocampi; see for instance (Mueller, Schuff, 
Yaffe, Madison, Miller, & Weiner, 2010). Moreover, such correction was used in 
(Mueller, et al., 2013), so we used this correction as well in order to 
directly compare the results” (Iglesias, 2015)

“ICV was added as a covariate to all ANOVAs” (Saygin, 2017)

I would love to hear any advice/perspective.

Thank you in advance.
Arkadiy
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Re: [Freesurfer] Creating functional ROI

[Ashley Cole]

I was wondering if there is other way than using matlab to do this.

On Mon, Dec 11, 2017 at 9:07 PM, Ashley Cole  wrote:

> Thank you, Doug. This worked.
>
> Now I have two questions:
>
> 1- Is it possible for a given threshold in funcroi-config to have let say
> 15 voxels on the surface but zero voxels in the volume? When I load the
> .sig map, I can see activation for a given threshold on the volume but when
> I run the funcroi-config and funcroi-sess, I get zero voxels. However, it
> returns non zero voxels for the surface.
>
>
> 2- Now that I have configured my functional ROIs on my localizer data, how
> can I find the percent change signal within that ROI for my experiment data
> (non-localizer session)?
>
> Sorry for my naiive questions.
>
> Best,
> Ashley
>
> On Wed, Dec 6, 2017 at 3:02 PM, Douglas N Greve  > wrote:
>
>> Try using a seg instead of an annot, eg, -seg aparc+aseg.mgz 1007 for
>> left fusiform
>>
>>
>> On 12/06/2017 12:13 PM, Ashley Cole wrote:
>> > Hi,
>> >
>> > I was wondering if anyone could kindly help me on this matter.
>> >
>> > Thank you,
>> >
>> > Ashley
>> >
>> > On Wed, Nov 29, 2017 at 11:46 AM, Ashley Cole > > > wrote:
>> >
>> > Hi Doug,
>> >
>> >
>> > I ran the funcroi-config command the same way the tutorial
>> > suggested: *"funcroi-config -annot aparc fusiform -analysis
>> > eba-fba.native.rh -contrast faces-vs-objects -thresh 2 -sign pos
>> > -roi rh.fus.test.roicfg -force"*
>> >
>> > However, I got this error:
>> > *"annotations can only be used with surface-based analyses"*
>> > I have done my mkanalysis-sess in the _native space_, i.e.:
>> > *"**mkanalysis-sess -fsd bold -stc odd -surface self rh -fwhm 5
>> > -event-related -paradigm ..."*
>> >
>> > Do you think this is the problem? Meaning, the surface here should
>> > be fsaverage instead of self? And if yes, what if I need
>> > everything in the native space?
>> > Thank you,
>> >
>> > Ashley
>> >
>> >
>> >
>> > On Mon, Nov 13, 2017 at 10:21 AM, Douglas N Greve
>> > >
>> > wrote:
>> >
>> > Start with funcroi-config. Run it with -help to get
>> > documentation
>> > including several examples. Let me know if you still have
>> > questions
>> >
>> >
>> > On 11/11/2017 11:56 AM, Ashley Cole wrote:
>> > > Dear Doug/Bruce,
>> > > I appreciate any insights on this.
>> > > Thank you,
>> > > Ashely
>> > >
>> > > 
>> > >
>> > >
>> > > I am new to FreeSurfer and I apologize in advance if my
>> > questions are
>> > > too naiive.
>> > >
>> > > My main goal is to keep everything in the native space.
>> > Also, I am
>> > > looking for percent signal change in selected ROIs.
>> > >
>> > >
>> > > First, I ran recon-all command. Then, I preprocessed the
>> > functional
>> > > data in native space. The command that I ran was:
>> > >
>> > > preproc-sess -s sess01 -fsd bold -stc odd -surface self
>> > lhrh -mni305
>> > > -fwhm 5 -per-session -force
>> > >
>> > >
>> > >
>> > > Then, I configured my analyses and contrasts in each
>> > hemisphere, as
>> > > well as the volume.
>> > >
>> > > Finally, I ran the analyses for each hemispheres and the
>> > volume. I ran
>> > > this command:
>> > >
>> > >
>> > > selxavg3-sess -s sess01 -analysis ffa.native.rh
>> > >
>> > >
>> > >
>> > > Lastly, I visualized the results by running these
>> commands:
>> > >
>> > > tksurfer-sess -s sess01 -hemi rh -analysis ffa.native.rh
>> -c
>> > > faces-vs-bodies -self
>> > >
>> > >
>> > >
>> > > tkmedit-sess -s sess01 -analysis ffa.native.mni -c
>> > faces-vs-bodies -self
>> > >
>> > >
>> > >
>> > > So far, I think I have done everything correctly. I am
>> > seeing the
>> > > activation ROIs where I am supposed to.
>> > >
>> > >
>> > >
>> > > Now, I would like to be able to select these
>> > ROIs/clusters, take their
>> > > voxel coordinates/numbers and create a mask. (These are
>> > my localizer
>> > > nii files.) Then, use this mask on the main experiment
>> > 

Re: [Freesurfer] Dura classified as GM in brainmask

[FSL Analysis]

Hi again,

I realize my last question about the brainmask did not make sense. I meant
to ask if I have to either manually delete all non-brain voxels around the
eye area which is very time consuming per subject or just delete those
misclassified as GM? ( I check this through this command: tkmedit
subj_output brainmask.mgz -aux T1.mgz -surfs)

Also for some subjects:
1. When I open freeview and look at the aseg file there is area around the
eye misclassified as cerebral cortex for some subjects.
2. When I load the pial surface the aseg file shows cerebral cortex in the
temporal poles and frontal lobes near the eye region outside of the pial
surface outline. How do I edit this?



I look forward to your response.




Thanks.

On Tue, Dec 12, 2017 at 4:21 PM, FSL Analysis  wrote:

> Hi all,
>
> I have processed data using freesurfer and the output for most of my
> subjects did not remove all of the eye and dura around it during skull
> stripping. When I check the brainmask there is dura (or blood vessel) in
> the frontal lobe that is classified as GM.
>
> I am wondering if I have to manually edit the skullstrip and rerun
> recon-all or do I just edit the brainmask file by deleting non-brain
> voxels? Or do I have to do both?
>
> If I only edit the brainmask file does this skip any other important
> processing steps that may affect my results?
>
> I am planning on looking at brain volumes and cortical thickness and how
> they relate to behavioral measures.
>
>
>
>
> Kind Regards,
>
> Ciara
>
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[Freesurfer] ?h.DKTatlas100.gcs to annot

[tony han]

Hi,


Is it possible to get an annot file for ?h.DKTatlas100.gcs, not for 
individuals, but for fsaverage atlas? I want to plot the 'standard' 
parcellation, instead of individual ones, on the surface so that I can use as a 
general reference. Thanks!


Tony
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[Freesurfer] Hippocampal Subfield and Amyg Nuclei ICV Correction

[Maksimovskiy, Arkadiy]

Dear Experts,

I have seen this question pop up a few times in the forum, but have not seen a 
clear response, so I was wondering if someone might be able to clarify or offer 
their opinion.


  1.  Do the hippocampal subfields and amygdala nuclei need to be corrected for 
ICV (either by including ICV as a covariate or taking the ration if each 
subfield to the ICV)?
  2.  If so, might it make more sense to correct them (perhaps take the ratio 
of each subfield to the hippocampus) for the volume of the hippocampus (after 
the hipp. itself has been corrected for the ICV)? If the correction is 
recommended, I am wondering about whether the second option might be better, 
because the ICV correction might be introducing too much variability for such a 
small sub-structure, whereas, correcting for just the hippocampus volume might 
be a bit more accurate.

I found two ways of dealing with this in the relevant papers for the hipp. 
Subfield and amyg nuclei, respectively, quoted below:

“Then, we correct these estimates for age and intracranial volume (ICV) by 
regressing them out with a general linear model. This step is important because 
the subregion volumes are strongly correlated with these two variables, which 
can easily confound the analysis – subjects with large ICV and/or of younger 
age are expected to have larger hippocampi; see for instance (Mueller, Schuff, 
Yaffe, Madison, Miller, & Weiner, 2010). Moreover, such correction was used in 
(Mueller, et al., 2013), so we used this correction as well in order to 
directly compare the results” (Iglesias, 2015)

“ICV was added as a covariate to all ANOVAs” (Saygin, 2017)

I would love to hear any advice/perspective.

Thank you in advance.
Arkadiy
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Re: [Freesurfer] LGI ERROR

[Douglas Greve]

The FWHM used in the MC simulation is computed from the data itself. The 
final FWHM is a mixture of the applied FWHM and smoothness inherent in 
the data. LGI has a lot of inherent smoothness, so the final FWHM is 
very large. The MC sim table only goes up to 30mm, after that it 
generates an error



On 12/13/17 2:19 AM, 郑凤莲 wrote:

Hi professors,
    I am using Freesurfer 6.0 for calculating LGI. I have done 
'recon-all' for it. When I ran Monte Carlo in qdec (FWHM=10), it has 
errors:
However, when FWHM=5, It was ok. What led to this result? I don't know 
why.


Thanks in advance !
Zheng










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Re: [Freesurfer] cortical thickness smoothing

[Douglas Greve]

On 12/13/17 8:03 AM, John Anderson wrote:

Dear Dr Greve thank you so much for the advice.

Kindly, I have one addition question and I highly appreciate your 
feedback!
Smoothing on surface is very interesting and it is really more 
accurate than applying the Gaussian smoothing directly on volumetric 
images. I don't see any aggressive shifts in the signal when I smooth 
on surface! In this context, I want to know if the following procedure 
is legitimate:


To  smooth PET volumetric images. I am thinking of using 
"mri_vol2surf" to sample and smooth the PET images on surface. Can I 
then use "mri_surf2vol" to move the smoothed images on surface to 
volume. How about the subcortical regions- is the smoothing on surface 
applicable for the whole brain, or just for the regions between 
pial/white?
You can, but this is usually only done for display purposes (eg, you 
want to show the surface data in the volume along with the subcortical 
data). Usually, we do three separate analyses: left hemi, right hemi, 
and subcortical, smoothing each one in the appropriate way.




You have to sample the volumetric PET data onto the surface

(mri_vol2surf) and then smooth it there (mri_surf2surf or mris_fwhm).



On 12/12/2017 11:23 AM, John Anderson wrote:

> Dear Dr Bruce, I highly appreciate the response.

> I want to smooth PET volumetric images, when I use "fslmaths", it

> shifts the signal from the cortex to the underlying structures. I

> think (depending on wiki) that Freesurfer handles this issue by

> smoothing on sphere. Which is the recommendded stream in PETsurfer.

>

> I am wondering if there are any commands within Freesurfer that can be

> used to smooth volumtric PET images without taking the average signal

> of the neighboring voxels (like in Gaussian smoothing).

>

> Also, I have question about mri_fwhm:

> what is the difference between the flags (--smooth-only; --fwhm). I am

> aware that "mri_fwhm" is very well explained in FS wiki, but I was

> unable to exactly understand the difference. For instance when I use

> the flag --smooth-only the output image is somehow similar to the

> input image. Is Gaussian in this cases ~1

mri_fwhm (and mris_fwhm) where initially developed to measure the FWHM

but I extended it to be able to apply smoothing (--fwhm) as well as

measure the smoothness. The --smooth-only says to not do the FWHM

estimate (just smooth it).

>

> Thanks in advance!

> J

>

>

>

>

>

>

>>  Original Message 

>> Subject: Re: [Freesurfer] cortical thickness smoothing

>> Local Time: December 12, 2017 10:38 AM

>> UTC Time: December 12, 2017 3:38 PM

>> From: fis...@nmr.mgh.harvard.edu 

>> To: John Anderson >, Freesurfer support


>> list >


>>

>> Hi John

>>

>> I don't think fslmaths takes a surface topology so they won't be 
the same


>> (mri_surf2surf smooths within the surface and fslmaths smooths in the

>> volume I believe)

>>

>> cheers

>> Bruce

>>

>>

>> On Tue, 12 Dec 2017, John Anderson wrote:

>>

>>Dear Freesurfer experts,

>>I ran recon-all with the flag -qcache to generate smoothed

>>cortical thickness maps.

>>In order to check how the flag "-qcache" is smoothing the

>>cortical thickness data. I looked into the

>>file $subj_dir/scripts/recon-all.log" which showed that the

>>following command was applied:

>>mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 5--sval

>>lh.sulc.fsaverage.mgh --tval

>>lh.sulc.fwhm5.fsaverage.mgh --cortex

>>Please I want to know whether the flag "--fwhm" applies similar

>>smoothing method to the smoothing

>>output of the command "fslmaths":

>>fslmaths  -kernel gauss 2.213 -fmean

>> -odt float

>>I want to smooth two different modality-images using the cortical

>>thickness smoothing method.

>>Thank you for any advice!

>>John

>>

>>

>>

>> The information in this e-mail is intended only for the person to

>> whom it is

>> addressed. If you believe this e-mail was sent to you in error and

>> the e-mail

>> contains patient information, please contact the Partners Compliance

>> HelpLine at

>> http://www.partners.org/complianceline . If the e-mail was sent to

>> you in error

>> but does not contain patient information, please contact the sender

>> and properly

>> dispose of the e-mail.

>

>

>

> ___

> Freesurfer mailing list

> Freesurfer@nmr.mgh.harvard.edu 

> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


--

Douglas N. Greve, Ph.D.

MGH-NMR Center

gr...@nmr.mgh.harvard.edu 

Phone Number: 617-724-2358

Fax: 617-726-7422


Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting 



FileDrop: 

Re: [Freesurfer] JRE error in fsfast/matlab

[Douglas Greve]

By default the graphics are turned off when running selxavg-sess. I 
often see that error message, but it never ends up causing the program 
to terminate. Is your process terminating prematurely?



On 12/13/17 10:24 AM, Yagmur Ozdemir 19 wrote:

Hello FreeSurfer experts,

I have been running into a matlab-related problem that I was wondering 
if anyone came across. I am using Matlab2017b with Freesurfer 6.0. 
Whenever I run selxavg-sess 
 command, the 
matlab tries to find the OpenGL rendering, then gives a Java fatal 
error with a failure to find the Java Runtime Environment and exits. 
(I don't have the command outputs with me right now, sorry.) I have 
been trying to fix it with getting a better graphics card, OpenGL, 
getting Octave etc but this error didn't come up when I was using an 
earlier version of Matlab. I would appreciate any help.


Best
Idil


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[Freesurfer] JRE error in fsfast/matlab

[Yagmur Ozdemir 19]

Hello FreeSurfer experts,

I have been running into a matlab-related problem that I was wondering if 
anyone came across. I am using Matlab2017b with Freesurfer 6.0. Whenever I run 
selxavg-sess command, 
the matlab tries to find the OpenGL rendering, then gives a Java fatal error 
with a failure to find the Java Runtime Environment and exits. (I don't have 
the command outputs with me right now, sorry.) I have been trying to fix it 
with getting a better graphics card, OpenGL, getting Octave etc but this error 
didn't come up when I was using an earlier version of Matlab. I would 
appreciate any help.

Best
Idil
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Re: [Freesurfer] cortical thickness smoothing

[John Anderson]

Dear Dr Greve thank you so much for the advice.

Kindly, I have one addition question and I highly appreciate your feedback!
Smoothing on surface is very interesting and it is really more accurate than 
applying the Gaussian smoothing directly on volumetric images. I don't see any 
aggressive shifts in the signal when I smooth on surface! In this context, I 
want to know if the following procedure is legitimate:

To  smooth PET volumetric images. I am thinking of using "mri_vol2surf" to 
sample and smooth the PET images on surface. Can I then use "mri_surf2vol" to 
move the smoothed images on surface to volume. How about the subcortical 
regions- is the smoothing on surface applicable for the whole brain, or just 
for the regions between pial/white?

You have to sample the volumetric PET data onto the surface

(mri_vol2surf) and then smooth it there (mri_surf2surf or mris_fwhm).

On 12/12/2017 11:23 AM, John Anderson wrote:

> Dear Dr Bruce, I highly appreciate the response.

> I want to smooth PET volumetric images, when I use "fslmaths", it

> shifts the signal from the cortex to the underlying structures. I

> think (depending on wiki) that Freesurfer handles this issue by

> smoothing on sphere. Which is the recommendded stream in PETsurfer.

>

> I am wondering if there are any commands within Freesurfer that can be

> used to smooth volumtric PET images without taking the average signal

> of the neighboring voxels (like in Gaussian smoothing).

>

> Also, I have question about mri_fwhm:

> what is the difference between the flags (--smooth-only; --fwhm). I am

> aware that "mri_fwhm" is very well explained in FS wiki, but I was

> unable to exactly understand the difference. For instance when I use

> the flag --smooth-only the output image is somehow similar to the

> input image. Is Gaussian in this cases ~1

mri_fwhm (and mris_fwhm) where initially developed to measure the FWHM

but I extended it to be able to apply smoothing (--fwhm) as well as

measure the smoothness. The --smooth-only says to not do the FWHM

estimate (just smooth it).

>

> Thanks in advance!

> J

>

>

>

>

>

>

>>  Original Message 

>> Subject: Re: [Freesurfer] cortical thickness smoothing

>> Local Time: December 12, 2017 10:38 AM

>> UTC Time: December 12, 2017 3:38 PM

>> From: fis...@nmr.mgh.harvard.edu

>> To: John Anderson , Freesurfer support

>> list 

>>

>> Hi John

>>

>> I don't think fslmaths takes a surface topology so they won't be the same

>> (mri_surf2surf smooths within the surface and fslmaths smooths in the

>> volume I believe)

>>

>> cheers

>> Bruce

>>

>>

>> On Tue, 12 Dec 2017, John Anderson wrote:

>>

>> Dear Freesurfer experts,

>> I ran recon-all with the flag -qcache to generate smoothed

>> cortical thickness maps.

>> In order to check how the flag "-qcache" is smoothing the

>> cortical thickness data. I looked into the

>> file $subj_dir/scripts/recon-all.log" which showed that the

>> following command was applied:

>> mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 5--sval

>> lh.sulc.fsaverage.mgh --tval

>> lh.sulc.fwhm5.fsaverage.mgh --cortex

>> Please I want to know whether the flag "--fwhm" applies similar

>> smoothing method to the smoothing

>> output of the command "fslmaths":

>> fslmaths  -kernel gauss 2.213 -fmean

>>  -odt float

>> I want to smooth two different modality-images using the cortical

>> thickness smoothing method.

>> Thank you for any advice!

>> John

>>

>>

>>

>> The information in this e-mail is intended only for the person to

>> whom it is

>> addressed. If you believe this e-mail was sent to you in error and

>> the e-mail

>> contains patient information, please contact the Partners Compliance

>> HelpLine at

>> http://www.partners.org/complianceline . If the e-mail was sent to

>> you in error

>> but does not contain patient information, please contact the sender

>> and properly

>> dispose of the e-mail.

>

>

>

> ___

> Freesurfer mailing list

> Freesurfer@nmr.mgh.harvard.edu

> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--

Douglas N. Greve, Ph.D.

MGH-NMR Center

gr...@nmr.mgh.harvard.edu

Phone Number: 617-724-2358

Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2

www.nmr.mgh.harvard.edu/facility/filedrop/index.html

Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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The information in 

[Freesurfer] extract surface area for singe vertex

[Clara Kühn]

Dear Freesurfer experts,

I've run a longitudinal two stage model of 2 time points to look at the rate of 
change in surface area and whether my two groups change differently. I find a 
superior parietal cluster in the right hemisphere. So far I've already run the 
mri_glmfit-sim to get the values of rate of change in this cluster for each 
subject. Now I would like to extract the peak vertex that I get the coordinates 
of from mri_glmfit-sim for each subject from each time point.

I have tried to use mri_convert

mris_convert -c 
$SUBJECTS_DIR/WL8K_1.long.WL8K.base/surf/lh.thickness.fwhm10.81kids_template.mgh
 $SUBJECTS_DIR/001/WL8K_1.long.WL8K.base/lh.orig 
$SUBJECTS_DIR/WL8K_1.long.WL8K.base/lh.thickness.fwhm10.81kids_template.vertices.asc

however, I get this error message:

ERROR: number of vertices in 
/nobackup/etsch2/kids/prepost-61kids/WL8K_1.long.WL8K.base/surf/lh.thickness.fwhm10.81kids_template.mgh
 does not match surface (97361,109356)

I've read in other threads that I'm supposed to use mri_surf2surf to map it to 
my template (81kids_template). I thought I had already done that before the 
analysis when running long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas 
thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label 
--time years --qcache 81kids_template


Could you tell me what I need to do to extract the values of the peak vertex in 
my significant cluster for each subject and each time point?
Thank you so much!
Clara

-- 
Clara Kühn, Phd Candidate
 
Max-Planck-Institute for Human Cognitive and Brain Science
Department of Neuropsychology
Stephanstrasse 1A
04103 Leipzig, Germany

Phone: +49 341 - 9940 2271
Fax: +49 341 - 9940 2260
Web: www.cbs.mpg.de
E-Mail: cku...@cbs.mpg.de

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[Freesurfer] [Re] medial wall label in Freesurfer 6

[M del Mar Velasco]

Hi Andrew,


Thanks very much! I have tried the new version of make_average_surface and it 
works fine. I am very gratefull.


Best,


M del Mar
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[Freesurfer] Research engineer in Neuroimaging wanted

[Olivier Coulon]

Dear Freesurfer list,
the 'Institut de Neuroscience de la Timone ' 
(INT), Marseille, France, is  looking for a research engineer for a 
duration of one year. The candidate will bring a scientific support to 
MR neuroimaging research. If satisfactory, the contract will lead to a 
permanent position as an Aix-Marseille University research engineer at INT.


Do not hesitate to pass this annoucement to anybody interested.

Full details are available following this link 
.

contact: olivier.cou...@univ-amu.fr

--
Olivier Coulon,
CNRS Research Director
Aix-Marseille University,
Institut de Neurosciences de la Timone
Faculté de Médecine,
27 Bd Jean Moulin
13005 Marseille -  France
MeCA Research Group
http://www.meca-brain.org

https://sites.google.com/site/oliviercoulon

olivier.cou...@univ-amu.fr 
Tel: +33 (0)4 91 32 40 59

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