[Freesurfer] paradigm file

[Thục Trinh]

Hello,
I'm working on fMRI analysis on flattening brain by using FSFAST tool. In
our data, subjects play game: Matrix reasoning. How can I set up the
paradigm file if the duration stimulus depends on the Time response of each
subject following each trial.

Thanks !!
Trinh
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[Freesurfer] R: Re: R: R: Re: Import mask from FSL to FS for performing seed-based FS-FAST functional connectivity

[stdp82]

My concern is whether this command line is correctfcseed-config -segid 1 -seg 
ROI_MASK. -fsd rest -mean -cfg mean.ROI_MASK.configfcseed-sess -s SessXXX -cfg 
mean.ROI_MASK.configThank youStefano


Messaggio originale
Da: gr...@nmr.mgh.harvard.edu
Data: 20-lug-2015 19.17
A: 
Ogg: Re: [Freesurfer] R: R: Re: Import mask from FSL to FS for performing 
seed-based FS-FAST functional connectivity



On 07/20/2015 02:10 AM, std...@virgilio.it wrote:
> Hi list,
>
> in the previous mail you have suggested to run fcseed-config and 
> specify -seg ROI_MASK.mgz and -segid 1 (assuming my ROI_MASK is in 
> $SUBJECTS_DIR/subject/mri).
> I have two question please.
> A- my mask is on vmPFC, thus it include the both hemispheres. Should I 
> divide it in right and left? If yes, how can I do?
You do not need to, just specify the appropriate index value. If they 
were divided between lh and rh and you wanted to merge them, you would 
just list the lh and rh indices.
> B- I have difficulties to run the fcseed-conf command:
what do you mean by "difficulties"?

> fcseed-config -segid 1 -seg ROI_MASK. -fsd rest -mean -cfg 
> mean.ROI_MASK.config
> fcseed-sess -s SessXXX -cfg mean.ROI_MASK.config
> Is these command lines corrected?
>
> Thanks,
>
>
> Stefano
>
> Messaggio originale
> Da: std...@virgilio.it
> Data: 13-lug-2015 10.16
> A: 
> Ogg: [Freesurfer] R: Re: Import mask from FSL to FS for performing 
> seed-based FS-FAST functional connectivity
>
> Hi list,
>
> When I use tkmedit the overlap between orig and ROI_MASK.nii.gz seem 
> to correspond. However, when I added the ROI_MASK.nii.gz, the orig is 
> vanished, and is remained the ROI_MASK in correct position (and in 
> white) and around all black. My concern is the correct binarization of 
> ROI_MASK which it seem correct when I use fslview.
>
> fslview orig.nii.gz ROI_MASK.nii.gz produce perfect outputs.
>
>
>
> After
> mri_label2vol --seg $SUBJECTS_DIR/ROI_MASK.nii.gz --reg 
> $FUNCTIONAL_DATA/Sess102/rest/001/register.dof6.dat --temp 
> $FUNCTIONAL_DATA/Sess102/rest/001/template.nii.gz --fillthresh 0.5 --o 
> func.vmPFC_MASK.nii
>
> The func.vmPFC_MASK.nii (344MB) seem to be empty when I open it with 
> tkmedit and too big (a red bar which cover the whole) when I use fslview.
> With MRIcron, is screen is irregularly divided in half in black and white.
>
> Which should be the advised folder for  func.vmPFC_MASK.nii?
>
>
> Thank you very much
>
>
> Stefano
>
>
> Messaggio originale
> Da: gr...@nmr.mgh.harvard.edu
> Data: 30-giu-2015 0.36
> A: 
> Ogg: Re: [Freesurfer] Import mask from FSL to FS for performing 
> seed-based FS-FAST functional connectivity
>
> Hi Stefano, sorry for the delay, I was traveling. It sounds like you
> just need to run fcseed-config and specify -seg ROI_MASK.mgz and -segid
> 1 (assuming your ROI_MASK is in $SUBJECTS_DIR/subject/mri). If the mask
> is in the orig.mgz space, then everything should work ok, but you can
> look at it with
>
> tkmedit -f orig.mgz -aux ROI_MASK.mgz
>
> You can also run
>
> mri_label2vol --seg $SUBJECTS_DIR/subject/mri/ROI_MASK.mgz --reg
> register.dof6.dat --temp template.nii.gz --fillthresh 0.5 --o
> func.ROI_MASK.nii
>
> where template.nii.gz  and register.dof6.dat are in the functional run
> folder
> doug
>
>
> On 06/12/2015 04:39 PM, std...@virgilio.it wrote:
> > Hi list,
> > I working on the combination of MRS and FS-FAST analysis.
> > I have extracted the grey matter within voxel (I will call it
> > "ROI_MASK") by using FSL tools and now it is in the same space of
> > orig.mgz (the roi mask is perfectly overlapped on orig.nii.gz when I
> > use fslview).
> >
> > I'd like to import it to FS for performing seed-based FS-FAST
> > functional connectivity.
> > The seed should the ROI MASK (GM within voxel).
> >
> > I know that the FSL and FS operate in different space and orientation.
> > I think to have resolved the problem of different space by using
> > orig.nii.gz to create ROI mask by FSL.
> > However, I'm strongly worried for orientation issues.
> > I have read the guidelines in FSL and FS sites, but I'm quite confused.
> > In detail, I'd like to ask whether I should use "mri_cor2label" to
> > transform ROI mask created by FSL to label.
> >
> > Furthmore, I'd like to be sure of the position of the ROI. How can I
> > visualize it to be sure that the seed of my FS-FAST analysis is
> > effectively the my ROI_MASK?
> >
> > I hope in your help.
> >
> > Thanks in advanced.
> >
> >
> > Stefano
> >
> >
> > ___
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> > 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.mg

[Freesurfer] mri_convert command line did not provide output file

[stdp82]

Hi list,mri_convert command line did not provide output file.This error was 
produced during the first computations of trac-all -prep command line.
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[Freesurfer] Question about pial surface correction through Freesurfer

[Tripathy, Kalyan]

Hi,



I am trying to manually correct some segmentation errors through Freesurfer. In particular, I have noticed a number of areas where the pial surface appears to miscalculated and is excluding chunks of grey matter. I tried using control points to push the
 pial surface out, and this helped reduce the grey matter exclusion, but now there are many places where the white matter surface has been reconstructed too far out, such that it includes a bunch of true grey matter within the white matter territory.

Is there a way that I can combine the original white matter surfaces with the corrected pial surfaces? When I tried to combine them in this manner and run recon-all, I received an error suggesting that the surfaces needed to match. Did I interpret that right,
 and is there a way around this?



Also, do you have any recommendations as to how I can extend the pial surface to correct grey matter omissions without incurring new errors as a result of the correction method?



Thank you for your time and help.



Kalyan








 



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Re: [Freesurfer] if: Expression Syntax

[Douglas Greve]

what environment are you running in? ie, dev or stable?

On 7/21/15 2:12 PM, Morenikeji Adebayo wrote:

Hi there,

*When running selxavg for the following session:*

nmasa_031_130412
*
*
*The following error message was generated:*
*
*
Error using MRIread (line 76)
ERROR: cannot determine format of
/autofs/cluster/iaslab/NMASA/mri/func/encoding/nmasa_031_130412/bold/015/masks/brain.mni305.2mm
(MRIread)

Error in fast_selxavg3 (line 146)
 runmask = MRIread(flac.maskfspec);
*
*
*I did some investigating and discovered that all the bold runs for 
this participant are missing the following files:*

*
*
.../func/encoding/nmasa_031_130412/bold/015/masks/brain.mni305.2mm
.../func/encoding/nmasa_031_130412/bold/015/masks/brain.fsaverage.lh.nii.gz
.../func/encoding/nmasa_031_130412/bold/015/masks/brain.fsaverage.rh.nii.gz
*
*
*
So I ran:

preproc-sess -s nmasa_031_130412 -fsd bold -stc up -surface fsaverage 
lhrh -min305 -fwhm 5 -per


*
*
*
*Which generated the following error message:*

if: Expression Syntax

**Do you have any idea what might be going wrong with this subject or 
what this error message (**if: Expression Syntax) **means?**

*
*
*
*
Thanks,
Keji
---
Morenikeji Adebayo
Clinical Research Coordinator
Department of Psychiatric Neuroscience
Massachusetts General Hospital
(p) 617.643.6347
k...@nmr.mgh.harvard.edu 



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Re: [Freesurfer] About reference to zgees_ and ztrsen_

[Z K]

I was able to get around that issue by installing the following packages:

lapack-devel.x86_64
liblapack-devel.x86_64

For more information, see the following page:

http://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page

-Zeke




On 07/21/2015 04:50 PM, Matthew, L. Wong wrote:
> Hi,
>
> I actually come across this problem twice both when trying to compile on
> a armv7 machine and an ordinary Centos 6.6 intel machine. The error
> shows up when compiling the package mri-robust-register:MyMatrix.cpp:54
>
> I understand the error comes from the zgees_ and ztrsen_ functions
> implementations were no where to be found.
>
> I tried both the developer release and the stable release, both source
> code gets this error.
>
> Does anyone encounter the same problem when compiling from source?
>
> Thanks!
> Matthew
>
>
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[Freesurfer] About reference to zgees_ and ztrsen_

[Matthew, L. Wong]

Hi,

I actually come across this problem twice both when trying to compile on a
armv7 machine and an ordinary Centos 6.6 intel machine. The error shows up
when compiling the package mri-robust-register:MyMatrix.cpp:54

I understand the error comes from the zgees_ and ztrsen_ functions
implementations were no where to be found.

I tried both the developer release and the stable release, both source code
gets this error.

Does anyone encounter the same problem when compiling from source?

Thanks!
Matthew
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Re: [Freesurfer] help on mris_preproc

[David C. Zhu]

Hi Doug,

Thanks.

I was able to resolve this issue now.

David

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: Monday, July 20, 2015 3:38 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] help on mris_preproc

I think you have a non-standard directory structure. FS is expecting something 
like
$SUBJECTS_DIR/subject1 but it looks like you have the FS results in 
$SUBJECTS_DIR/subject1/freesurfer You have to use the FS structure or else it 
will generate an error doug

On 07/20/2015 03:14 PM, David C. Zhu wrote:
> Dear Doug,
>
> I was away a while and missed your email.
>
> I have not resolved this issue yet.
>
> Could you please help?
>
> Thanks.
>
> David
>
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N 
> Greve
> Sent: Monday, June 29, 2015 6:38 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] help on mris_preproc
>
> Hi David, did you resolve this?
> doug
>
> On 06/12/2015 04:56 PM, David C. Zhu wrote:
>> Hi Doug,
>>
>> Thanks.
>>
>> I can see that the "mris_preproc" command reads the header 
>> information in "register.dat".
>>
>> I set the "." as the $SUBJECTS_DIR, and thus it seems that 
>> "mris_preproc" cannot locate the path. Is there a way to fix this?
>>
>> David
>>
>> Here is the (part of) output:
>>
>> --
>>
>> end
>>
>> while ( $#argv != 0 )
>>
>> while ( 27 != 0 )
>>
>> set flag = $argv[1] ; shift ;
>>
>> set flag = --iv
>>
>> shift
>>
>> switch ( $flag )
>>
>> switch ( --iv )
>>
>> case "--ivp":
>>
>> case --ivp:
>>
>> if ( $#argv < 2 ) goto arg2err ;
>>
>> if ( 26 < 2 ) goto arg2err
>>
>> set ivp = $argv[1] ; shift ;
>>
>> set ivp = S02520110927_Free/sum_all_norm_IRF_EA.nii
>>
>> shift
>>
>> if ( ! -e $ivp ) then
>>
>> if ( ! -e S02520110927_Free/sum_all_norm_IRF_EA.nii ) then
>>
>> set irp = $argv[1] ; shift ;
>>
>> set irp = S02520110927_Free/register.dat
>>
>> shift
>>
>> if ( ! -e "$irp" ) then
>>
>> if ( ! -e S02520110927_Free/register.dat ) then
>>
>> set ivplist = ( $ivplist $ivp ) ;
>>
>> set ivplist = ( S00720110927_Free/sum_all_norm_IRF_EA.nii
>> S01420110908_Free/sum_all_norm_IRF_EA.nii
>> S01520110811_Free/sum_all_norm_IRF_EA.nii
>> S02520110927_Free/sum_all_norm_IRF_EA.nii )
>>
>> set irplist = ( $irplist $irp ) ;
>>
>> set irplist = ( S00720110927_Free/register.dat 
>> S01420110908_Free/register.dat S01520110811_Free/register.dat 
>> S02520110927_Free/register.dat )
>>
>> set subj = `head -1 $irp` ;
>>
>> set subj = `head -1 $irp`
>>
>> head -1 S02520110927_Free/register.dat
>>
>> set subjlist = ( $subjlist $subj ) ;
>>
>> set subjlist = ( freesurfer freesurfer freesurfer freesurfer )
>>
>> set srcvol = 1 ;
>>
>> set srcvol = 1
>>
>> breaksw
>>
>> breaksw
>>
>> end
>>
>> end
>>
>> ...
>>
>> ...
>>
>> ...
>>
>> if ( 0 == 0 && 1 == 0 && 0 == 0 ) then if ( $srcsurf && $srcvol ) 
>> then if ( 0 && 1 ) then if ( $srcsurf && $#projfrac != 0 ) then if ( 
>> 0 && 0 != 0 ) then if ( $catmean && $catstd ) then if ( 0 && 0 ) then 
>> if ( $#meas && $#isplist ) then if ( 0 && 0 ) then if ( $MeasIn && 
>> $CacheIn
>> ) then if ( 0 && 0 ) then if ( $#ivplist != 0 ) then if ( 12 != 0 ) 
>> then if ( $#ivplist != $#subjlist ) then if ( 12 != 12 ) then endif 
>> endif if ( $#isplist != 0 ) then if ( 0 != 0 ) then if ( $paireddiff 
>> && ! $DoXHemi ) then if ( 0 && ! 0 ) then
>>
>> if ( ! -e $SUBJECTS_DIR ) then
>> if ( ! -e . ) then
>>
>>
>> if ( $DoXHemi ) then
>> if ( 0 ) then
>>
>> echo "nsubjects = $#subjlist" ;
>> echo nsubjects = 12
>> nsubjects = 12
>> @ nthsubj = 1 ;
>> @ nthsubj = 1
>> foreach subj ( $subjlist )
>> foreach subj ( freesurfer freesurfer freesurfer freesurfer freesurfer 
>> freesurfer freesurfer freesurfer freesurfer freesurfer freesurfer 
>> freesurfer ) set subjpath = $SUBJECTS_DIR/$subj set subjpath = 
>> ./freesurfer if ( ! -e $subjpath ) then if ( ! -e ./freesurfer ) then 
>> echo "ERROR: cannot find $subjpath"
>> echo ERROR: cannot find ./freesurfer
>> ERROR: cannot find ./freesurfer
>> exit 1 ;
>> exit 1
>>
>> *From:*freesurfer-boun...@nmr.mgh.harvard.edu
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of 
>> *Douglas Greve
>> *Sent:* Friday, June 12, 2015 3:51 PM
>> *To:* freesurfer@nmr.mgh.harvard.edu
>> *Subject:* Re: [Freesurfer] help on mris_preproc
>>
>> Can you run the 2nd command with --debug as the first option and send 
>> the terminal output?
>> doug
>>
>> On 6/12/15 12:09 PM, David C. Zhu wrote:
>>
>>  Dear FreeSurfer experts:
>>
>>  I have been using FreeSurfer for segmentation and for volumetric
>>  analyses. I want to give a try to use it for surface-based fMRI
>>  analyses.
>>
>>  I encountered some issues with mris_preproc to assemble IRF
>>  results to the fsaverage surface. Please advise on how to resolve
>>  these issues.
>>
>>  Here is what I did:
>>

[Freesurfer] QA measures mgz

[zalewk]

Excellent, thank you for sharing! I have one more question.
When running the mri_cnr function I tried using a number of different .mgz 
files with varying results, which would you recommend for the most accurate 
gm/wm and gm/csf CNR?

Best,
KZ

--

Message: 1
Date: Fri, 17 Jul 2015 18:24:28 +0200
From: "Jacek Manko" 
Subject: Re: [Freesurfer] QA measures
To: Freesurfer support list 
Cc: freesurfer@nmr.mgh.harvard.edu
Message-ID: <55a92c3ce71501.52368...@wp.pl>
Content-Type: text/plain; charset=iso-8859-2

You may find this paper useful:

http://www.biomedcentral.com/1471-2342/12/27

Authors describe there some measures such as "Euler number" and “Contrast 
to Noise ratio (CNR)". Actually, they dont belong to QA package, but they are 
definitely worth looking at.

Best,
Jacek Manko

Dnia 17-07-2015 o godz. 0:03 zal...@u.washington.edu napisa?(a):
Dear Freesurfer Team,

We would like to have a Q/A measure (or two) that would give us
indication of how well your software worked on each of our data
sets.   Obviously some image sets will be noisier than others for a
variety of reasons.  Could you point us towards what
options we may have for extracting such a measure from your processing
pipeline?  We were playing around with QAtools but
wanted to understand if there is a systematic computation of say a
handful of variables that would give us a global
representation of how well things worked for each case we run? Something
that we could compare across our patients and even
across data sets?

Best,
KZ


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--



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[Freesurfer] if: Expression Syntax

[Morenikeji Adebayo]

Hi there,

When running selxavg for the following session:

nmasa_031_130412

The following error message was generated:

Error using MRIread (line 76)
ERROR: cannot determine format of
/autofs/cluster/iaslab/NMASA/mri/func/encoding/nmasa_031_130412/bold/015/masks/brain.mni305.2mm
(MRIread)

Error in fast_selxavg3 (line 146)
  runmask = MRIread(flac.maskfspec);

I did some investigating and discovered that all the bold runs for this 
participant are missing the following files:

.../func/encoding/nmasa_031_130412/bold/015/masks/brain.mni305.2mm 
.../func/encoding/nmasa_031_130412/bold/015/masks/brain.fsaverage.lh.nii.gz
.../func/encoding/nmasa_031_130412/bold/015/masks/brain.fsaverage.rh.nii.gz

So I ran:

preproc-sess -s nmasa_031_130412 -fsd bold -stc up -surface fsaverage lhrh 
-min305 -fwhm 5 -per


Which generated the following error message:

if: Expression Syntax

Do you have any idea what might be going wrong with this subject or what this 
error message (if: Expression Syntax) means?


Thanks,
Keji
---
Morenikeji Adebayo
Clinical Research Coordinator
Department of Psychiatric Neuroscience
Massachusetts General Hospital
(p) 617.643.6347
k...@nmr.mgh.harvard.edu

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Re: [Freesurfer] How to deal with labels and structural data

[Bruce Fischl]

Hi Silas

what do you want to do with the labels? As for whether to do it on 
fsaverage or individuals, you could start with fsaverage and map it to 
your other subjects and see how accurate it looks

cheers
Bruce
On Tue, 21 Jul 2015, Silas 
wrote:

> Dear Freesurfer team,
> I've created my own labels using tksurfer and common anatomical guidelines -
> and my next step is to apply these labels to my subjects and analyze (ROI)
> cortical thickness or volume (first of all), functional data and myelination
> data.
> 1 - Do you suggest drawing a label on the surface of fsaverage and applying
> this label to the other subjects (e.g. using mri_label2label) - or drawing a
> label on each subjects surface?
> 2 - What is my next step? Do i have to run recon-all again with my new label
> in the labels folder - or should i experiment with mri_label2vol and
> mri_label2annot?
> 3 - Do you have an existing guide in this kind of analysis?
> 
> Thanks! Best, Silas
> 
>
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Re: [Freesurfer] mri_watershed mask and skull surfaces

[Bruce Fischl]

Hi Sam

if you want us to help you, you need to provide us with the full 
command line and screen output (at least!)


cheers
Bruce
On Tue, 21 Jul 2015, Sam Zorowitz 
wrote:



Hi all,
I am using mri_watershed to create skull surfaces for a cohort of subjects
for whom we were unable to collect a FLASH sequence. To improve the
estimation of the inner skull layer, I would like to use edited brainmasks.
However whenever I supply the -mask flag, and only when I supply -mask flag
to mri_watershed, the code does not run; it only brings up the help screen. 

So two questions:
(1) Is the -mask flag in mri_watershed doing what I think it is doing? Is it
masking the T1 image to only the brain so that the inner skull layer will be
estimated from the brainmask?
(2) Am I using the -mask flag correctly? I get the same result if I use
mri_watershed -mask and mri_watershed -mask . Should I be
doing something differently?

All the best,
Sam

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Re: [Freesurfer] How to deal with labels and structural data

[Douglas Greve]

On 7/21/15 10:04 AM, Silas wrote:

Dear Freesurfer team,

I've created my own labels using tksurfer and common anatomical 
guidelines - and my next step is to apply these labels to my subjects 
and analyze (ROI) cortical thickness or volume (first of all), 
functional data and myelination data.
1 - Do you suggest drawing a label on the surface of fsaverage and 
applying this label to the other subjects (e.g. using mri_label2label) 
- or drawing a label on each subjects surface?
It depends on how accurately you think you can make it and how much 
accuracy you need. Drawing it on fsaverage will be much easier than 
doing it on each subject, though the accuracy may suffer a little bit 
when mapping it to the individual. I would do it this way and see if the 
output labels meet your expectations and then make edits to the 
individual if not. Use mri_label2label to map the label from fsaverage 
to an individual. Run with --help for examples.
2 - What is my next step? Do i have to run recon-all again with my new 
label in the labels folder - or should i experiment with mri_label2vol 
and mri_label2annot?
You do not need to run recon-all again. You can run 
mris_anatomical_stats to get thickness, surface area, and volume 
estimates for this label (like the .stats files). When using it with 
functional data, you can run mri_label2vol  to map the label into the 
functional space. Run with --help for examples.

3 - Do you have an existing guide in this kind of analysis?
I'm not sure of one to do specifically these steps, though look at the 
multimodal integration tutorials and the ROI tuturials.

doug



Thanks! Best, Silas


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Re: [Freesurfer] How to deal with the distortions of EPI images when applying the parcellated results of T1 images?

[Douglas Greve]

If you did collect field maps, you can use epidewarp.fsl to create a 
voxel shift map (the only output of epidewarp.fsl that you need; you'll 
need to FSL to run that program), then use bbregister with the --vsm 
option to register your func to the struct, then use mri_vol2vol with 
the --vsm option to map your functional time courses to the anatomical 
space, then use mri_segstats with the --avgwf (or --avgwfvol) option to 
get the average time courses for each ROI (or you can do this in matlab 
easily enough too)

doug

On 7/21/15 9:29 AM, Bruce Fischl wrote:
> Hi Bingjiang
>
> did you acquire any field maps? If so, you can them to undistort the EPIs
>
> cheers
> Bruce
>
>
> On Tue, 21 Jul 2015, Bingjiang Lyu wrote:
>
>> Dear all,
>> I've got the automaticlly parcellated 'aparc.a2009s+aseg.nii' file for
>> individual T1 image, and I want to calculate functional connectivity between
>> each pair of the brain regions. I normalized both the T1 and EPI images to
>> standard MNI space using SPM12, however, the normalized structural and
>> functional images didn't match very well due to the distortion of
>> susceptibility artifacts, especially for the inferior temporal and orbital
>> frontal cortex (Please see the attached pictures). Could anyone give some
>> suggestions on better co-registration of the normalized structural and
>> functional images? Thanks a lot in advance.
>>
>> Best regards,
>> Bingjiang
>>
>> --
>> Bingjiang LyuPhD student
>> Center for MRI Research
>> Peking University
>> Beijing, China
>>
>>
>>
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>
>

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[Freesurfer] How to deal with labels and structural data

[Silas]

Dear Freesurfer team,
I've created my own labels using tksurfer and common anatomical guidelines - 
and my next step is to apply these labels to my subjects and analyze (ROI) 
cortical thickness or volume (first of all), functional data and myelination 
data.1 - Do you suggest drawing a label on the surface of fsaverage and 
applying this label to the other subjects (e.g. using mri_label2label) - or 
drawing a label on each subjects surface?2 - What is my next step? Do i have to 
run recon-all again with my new label in the labels folder - or should i 
experiment with mri_label2vol and mri_label2annot?3 - Do you have an existing 
guide in this kind of analysis?
Thanks! Best, Silas   ___
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[Freesurfer] mri_watershed mask and skull surfaces

[Sam Zorowitz]

Hi all,

I am using mri_watershed to create skull surfaces for a cohort of subjects
for whom we were unable to collect a FLASH sequence. To improve the
estimation of the inner skull layer, I would like to use edited brainmasks.
However whenever I supply the -mask flag, and only when I supply -mask flag
to mri_watershed, the code does not run; it only brings up the help screen.

So two questions:
(1) Is the -mask flag in mri_watershed doing what I think it is doing? Is
it masking the T1 image to only the brain so that the inner skull layer
will be estimated from the brainmask?
(2) Am I using the -mask flag correctly? I get the same result if I use
mri_watershed -mask and mri_watershed -mask . Should I be
doing something differently?

All the best,
Sam
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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
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] How to deal with the distortions of EPI images when applying the parcellated results of T1 images?

[Bruce Fischl]

Hi Bingjiang

did you acquire any field maps? If so, you can them to undistort the EPIs

cheers
Bruce


On Tue, 21 Jul 2015, Bingjiang Lyu wrote:

> Dear all,
> I've got the automaticlly parcellated 'aparc.a2009s+aseg.nii' file for
> individual T1 image, and I want to calculate functional connectivity between
> each pair of the brain regions. I normalized both the T1 and EPI images to
> standard MNI space using SPM12, however, the normalized structural and
> functional images didn't match very well due to the distortion of
> susceptibility artifacts, especially for the inferior temporal and orbital
> frontal cortex (Please see the attached pictures). Could anyone give some
> suggestions on better co-registration of the normalized structural and
> functional images? Thanks a lot in advance.
> 
> Best regards,
> Bingjiang
> 
> --
> Bingjiang LyuPhD student
> Center for MRI Research
> Peking University
> Beijing, China
> 
> 
>
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