[Freesurfer] What is "...S_central" in Destrieux atlas?

[Christophe Destrieux]

External Email - Use Caution

Right

See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2937159/ 
 , table 1
Best


> 
> Christophe Destrieux
> Laboratoire d'anatomie - Faculte de Medecine
> 10, bd Tonnelle - 37032 Tours
> 02 47 36 61 36
> 
> 
> 
> 
>> Le 15 nov. 2018 à 01:49, Bruce Fischl  a écrit :
>> 
>> S_ is for sulcus and G_ is for gyrus, so S_central is the central sulcus. I 
>> think Christophe included a table in his paper (right Christophe?)
>> 
>> cheers
>> Bruce
>>> On Wed, 14 Nov 2018, Colin Birkenbihl wrote:
>>> 
>>>External Email - Use Caution
>>> Dear all,
>>> I am currently working with MRI features calculated with the Destrieux 
>>> atlas.
>>> As an output I have features named like:
>>> Vol_Right_S_Central
>>> Vol_Left_G_precentral
>>> or
>>> Vol_Left_S_orbital-H_Shaped
>>> I wanted to ask you, what these features stand for and if there is some 
>>> mapping of those feature
>>> names to brain region names which are clearly interpretable.
>>> If not, it would be great if you could tell me what the above mentioned 
>>> features refer to.
>>> It would be great if you could help me.
>>> Best wishes,
>>> Colin

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[Freesurfer] 'lh_G_Ins_lg_cent_ins_volume' and 'lh_G_insular_short_volume'

[Christophe Destrieux]

External Email - Use Caution

Hi Rujing
Sorry for the late answer. These 2 labels correspond to the insula

The insula is divided by the central sulcus of the insula (S_cent_ins_) into 
long insular gyri (G_Ins_lg) and short insular gyri (G_insular_short). 

Since the cortex lining the central sulcus of the insula was quite small, it 
has been grouped together with the the long insular gyri ( 
'lh_G_Ins_lg_cent_ins_volume’)

If you are interested in the volume of the whole insula you need to add the 
volumes of these two anatomical classes.

For a complete list of anatomical classes and explanations on their anatomical 
meaning see : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2937159/

Best

Christophe Destrieux, 
Unité iBrain UMRS INSERM U1253, Université de Tours 
https://ibrain.univ-tours.fr/ 

Service de Neurochirurgie 
et Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé - 37032 Tours 
- France 
tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07 






> Le 21 nov. 2018 à 17:12, Bruce Fischl  a écrit :
> 
> you are getting very popular!
> 
> 
> -- Forwarded message --
> Date: Wed, 21 Nov 2018 14:30:13 +0800
> From: charujing123 
> Reply-To: Freesurfer support list 
> To: "freesurfer@nmr.mgh.harvard.edu" 
> Subject: [Freesurfer] 'lh_G_Ins_lg_cent_ins_volume' and
>'lh_G_insular_short_volume'
> 
> 
> External Email - Use Caution
> 
> Hi, what is difference between and 'lh_G_insular_short_volume'. Are
> these both insula?
> Thanks.
> Rujing
>  
> 2018-11-21
> 
> 
> charujing123
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Re: [Freesurfer] How to automate recon-all command for multiple subjects

[Vivek Sharma]

External Email - Use Caution

Thanks!

On Tue, Nov 20, 2018 at 8:57 PM Bruce Fischl 
wrote:

>
> in csh it would be something like
>
> setenv SUBJECTS_DIR 
> foreach fname ($dir/*.nii)
> set fonly=${f:t}
> set fnoext=${f:r}
> recon-all -i $fname -s $fnoext -all
> end
>
>
> On Tue, 20 Nov 2018, Vivek Sharma wrote:
>
> >
> > External Email - Use Caution
> >
> > I have a folder, lets name xyz which contains .nii file. Now I want to
> run recon-all for all the
> > files in that folder. Please let me know how I can do that.
> >
> > On Tue, Nov 20, 2018 at 11:40 AM Vivek Sharma <
> vivek.sharma1...@gmail.com> wrote:
> >   I'm trying to run this code but it's not working. What should be
> $i in the code?
> >   On Mon, Nov 19, 2018 at 9:15 PM Bruce Fischl <
> fis...@nmr.mgh.harvard.edu> wrote:
> >   or you could do that all on a single line:
> >
> >   recon-all -i $SUBJECTS_DIR/$i/ -s $i -all
> >
> >   cheers
> >   Bruce
> >
> >   On Mon, 19 Nov 2018,
> >   Alex Hanganu
> >   wrote:
> >
> >   >
> >   > External Email - Use Caution
> >   >
> >   > HI Vivek,
> >   > you probably need 2 steps, first registration, second recon-all.
> Something
> >   > like:
> >   >
> >   > ...
> >   > do
> >   >recon-all -i $SUBJECTS_DIR/$i/ -s $i
> >   >recon-all -all -subjid $i
> >   >
> >   >
> >   > I didn't check if the scrips runs. That's the general structure.
> >   >
> >   > Best,
> >   > Alex
> >   >
> >   > Le lun. 19 nov. 2018, à 06 h 26, Vivek Sharma <
> vivek.sharma1...@gmail.com> a
> >   > écrit :
> >   >
> >   >   External Email - Use Caution
> >   >
> >   >   Hi,
> >   > I'm using freesurfer to generate head surfaces using MRI file.
> >   > I want to execute recon-all command for number of subjects, but
> unable
> >   > to run it.
> >   > The script I'm using is:
> >   >
> >   > for i in `cat *subs.txt*`
> >   > do
> >   > recon-all -s $i -all -qcache
> >   > done
> >   >
> >   > subs.txt contains the name of folder that contains .nii file.
> >   > The scripts ends with the following error:
> >   >
> >   > ERROR: no run data found in
> >   > /cblhome/vivek/freesurfer/subjects/sub-CC110033_T1w/mri. Make
> sure to
> >   > have a volume called 001.mgz in
> >   > /cblhome/vivek/freesurfer/subjects/sub-CC110033_T1w/mri/orig.
> >   > If you have a second run of data call it 002.mgz, etc.
> >   > See also:
> >   > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion
> >   > Linux cblhost 4.4.0-83-generic #106~14.04.1-Ubuntu SMP Mon Jun 26
> >   > 18:10:19 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
> >   >
> >   > Please let me know how I can run recon-all for multiple subjects.
> >   > Thank you.
> >   >
> >   > --
> >   > Vivek Sharma
> >   > Mobile: +919953582034
> >   > Skype: vivek.sharma1015
> >   > ___
> >   > Freesurfer mailing list
> >   > Freesurfer@nmr.mgh.harvard.edu
> >   > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >   >
> >   >
> >   >___
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> >   Freesurfer@nmr.mgh.harvard.edu
> >   https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >
> > --
> > Vivek Sharma
> > Mobile: +919953582034
> > Skype: vivek.sharma1015
> >
> >
> >
> > --
> > Vivek Sharma
> > Mobile: +919953582034
> > Skype: vivek.sharma1015
> >
> >___
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-- 
Vivek Sharma
Mobile: +919953582034
Skype: vivek.sharma1015
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Re: [Freesurfer] Corrupted T1 file (?) but segmentation look fine

[Bruce Fischl]

Hi Anneliis

freeview tries to guess the right window levels to display a volume, but 
sometimes fails. Try changing the min/max or window/level with the T1.mgz 
highlighted and see if it looks better. Alternatively, load the norm.mgz, 
which will probably look better with freeview's default algorithm


cheers
Bruce
On Wed, 21 
Nov 2018, Anneliis Sartin-tarm wrote:




External Email - Use Caution

Hello all,


I have been running into a curious problem with a couple brains (8 out of 150 
seem to have this
problem) running through the recon-all pipeline. Upon loading brainmask.mgz, 
T1.mgz, and
corresponding white matter and pial surfaces in Freeview, my colleague and I 
received an error that
T1.mgz failed to load. Segmentation and parcellation seemed to run smoothly and 
accurately, however,
the size of the T1.mgz file was 0. Assuming the file had been corrupted somehow 
(our server through
which we run recon-all and store our data has tons of available memory), we 
reran the
brains affected. Upon loading up the same re-run surfaces, T1.mgz loaded into 
the GUI as white,
washed out voxels, displaying no brain at all. The size of this file is large, 
as well as all other
surface and volume files. Curiously, the brainmask file seems 
normalized/stripped fine and surfaces
displayed over the T1 look accurately segmented. I attached a screenshot 
displaying the T1.mgz file
and surfaces that I'm referring to. 


I have a few concerns and questions. Because T1.mgz doesn't seem to be 
necessary for downstream
manual editing and processing, can we proceed as normal, only displaying and 
using the brainmask
file to make edits? Will our surface and volume metrics export properly without 
a usable T1 file?
Lastly, any clues to how this might have occurred are welcomed. It seems like 
the mri_normalize step
is the culprit, although the nu.mgz files corresponding to these brains seem 
normally sized.


Best,

Anneliis Sartin-Tarm

Associate Research Specialist
Neurocircuitry of Trauma and PTSD Study
UW-Madison Dept. Psychiatry
608-262-6375


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Re: [Freesurfer] freeview showing results in a strange manner

[姜时泽]

External Email - Use Caution

Hi Ruopeng,
my freeview command for this result is 'freeview -v lh.subj1.mgz'.
I tried 'freeview -f lh.subj1.mgz' also, the message with in terminal said 
'freadFloat: fread failed'
Thank you

Shize







At 2018-11-22 06:38:29, "Ruopeng Wang"  wrote:
What is your freeview command? Is there any message shown in the terminal?


Ruopeng



On Nov 21, 2018, at 5:07 PM, 姜时泽  wrote:


|
|
Dear freesurfer experts,
I am using freesurfer to analyze my PET data according to the tutorial online. 
It works pretty well and I write the values of the results of each region to 
the template with Matlab (file attached here entitled "lh.subj1.mgz"). However, 
when I try to open it with freeview, the image looks quite strange 
('Picture_1') but it works with tksurfer (Picture_2). Does any one know what is 
wrong with this? Did I plot the result in a wrong way?


Thanks very much
Shize





--


Shize Jiang
Fudan University,
Department of neurosurgery, Huashan Hospital, Shanghai Medical College
Shanghai,200032,P.R.China
Mobile: (86)18317079839
E-Mail: sjian...@fudan.edu.cn












|
|
| |



 

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Re: [Freesurfer] freeview showing results in a strange manner

[Ruopeng Wang]

What is your freeview command? Is there any message shown in the terminal?

Ruopeng

> On Nov 21, 2018, at 5:07 PM, 姜时泽  wrote:
> 
> Dear freesurfer experts,
> I am using freesurfer to analyze my PET data according to the tutorial 
> online. It works pretty well and I write the values of the results of each 
> region to the template with Matlab (file attached here entitled 
> "lh.subj1.mgz"). However, when I try to open it with freeview, the image 
> looks quite strange ('Picture_1') but it works with tksurfer (Picture_2). 
> Does any one know what is wrong with this? Did I plot the result in a wrong 
> way?
> 
> Thanks very much
> Shize
> 
> 
> 
> 
> --
> Shize Jiang
> Fudan University,
> Department of neurosurgery, Huashan Hospital, Shanghai Medical College
> Shanghai,200032,P.R.China
> Mobile: (86)18317079839
> E-Mail: sjian...@fudan.edu.cn 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
>  
> ___
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Re: [Freesurfer] Paired Analysis Contrasts

[srishti goel]

External Email - Use Caution

Hi Douglas,

Thank you so much for your response. We just want to be extra careful about
the way we are doing this and so below I have outlined the exact pattern of
the group descriptor files we are using along with the contrast. Please let
me know if you think this is correct or not. The questions we are asking
with this analysis are the same as I outlined in the previous email.

*This is our first group descriptor file:*

GroupDescriptorFile 1
Title BEIP 8 vs. 16 compare CAU (0) And FCG (1)
Class Main
Input005_16.long.005Main
Input005_8.long.005Main
Input006_16.long.006Main
Input006_8.long.006Main

*This is our second group descriptor file:*

GroupDescriptorFile 1
Title BEIP longitudinal Compare CAU (0) And FCG (1)
Class cau
Class fc
Input005_long_pair fc
Input006_long_pair cau

The contrast to understand group differences in thickness between 8 and 16
yr old data sets are:
1 -1

*Question1:* Is this correct?
*Question 2:* If we use the below mentioned way to set up our second group
descriptor file, will the above contrasts still work? Or can we use 0 1
contrast with the file below to get at the same thing? We actually ran it
both ways and the results weren't similar but I specifically ask this
question because we are a little worried about the above 'second group
descriptor file' not having a column that says 'Main' and we are trying to
understand the right way to do our analyses.

*Example group descriptor file 2:*
GroupDescriptorFile 1
Title BEIP longitudinal Compare CAU (0) And FCG (1)
Class Main
Variables group
Input005_long_pair Main 1
Input006_long_pair Main 0

Thank you so much! I appreciate all your help with this!

Best,
Srishti
Social/Clinical Research Specialist
Child Imaging Research and Life Experiences Lab
University of North Carolina at Chapel Hill
email (W): srish...@email.unc.edu
skype: srishti.goel12



On Wed, Nov 14, 2018 at 2:50 PM srishti goel <23srishtig...@gmail.com>
wrote:

> Hi Douglas,
>
> Thank you so much for your response. We just want to be extra careful
> about the way we are doing this and so below I have outlined the exact
> pattern of the group descriptor files we are using along with the contrast.
> Please let me know if you think this is correct or not. The questions we
> are asking with this analysis are the same as I outlined in the previous
> email.
>
> *This is our first group descriptor file:*
>
> GroupDescriptorFile 1
> Title BEIP 8 vs. 16 compare CAU (0) And FCG (1)
> Class Main
> Input005_16.long.005Main
> Input005_8.long.005Main
> Input006_16.long.006Main
> Input006_8.long.006Main
>
> *This is our second group descriptor file:*
>
> GroupDescriptorFile 1
> Title BEIP longitudinal Compare CAU (0) And FCG (1)
> Class cau
> Class fc
> Input005_long_pair fc
> Input006_long_pair cau
>
> The contrast to understand group differences in thickness between 8 and 16
> yr old data sets are:
> 1 -1
>
> *Question1:* Is this correct?
> *Question 2:* If we use the below mentioned way to set up our second
> group descriptor file, will the above contrasts still work? Or can we use 0
> 1 contrast with the file below to get at the same thing? We actually ran it
> both ways and the results weren't similar but I specifically ask this
> question because we are a little worried about the above 'second group
> descriptor file' not having a column that says 'Main' and we are trying to
> understand the right way to do our analyses.
>
> *Example group descriptor file 2:*
> GroupDescriptorFile 1
> Title BEIP longitudinal Compare CAU (0) And FCG (1)
> Class Main
> Variables group
> Input005_long_pair Main 1
> Input006_long_pair Main 0
>
> Thank you so much! I appreciate all your help with this!
>
> Best,
> Srishti
> Social/Clinical Research Specialist
> Child Imaging Research and Life Experiences Lab
> University of North Carolina at Chapel Hill
> email (W): srish...@email.unc.edu
> skype: srishti.goel12
>
>
>
> On Wed, Nov 7, 2018 at 9:24 AM Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> wrote:
>
>>
>>
>> On 10/24/2018 09:45 PM, srishti goel wrote:
>> >
>> > External Email - Use Caution
>> >
>> > Hello,
>> >
>> > I am trying to perform a paired analysis for a data set that has
>> > subjects' who belong to either group1 or group2 and have data at time
>> > point1 (tp1) and time point2 (tp2). I am following all the steps on
>> > the wiki but I want to clarify if the contrasts I plan to use for my
>> > analyses are appropriate.
>> >
>> > For my analyses, I only have two groups and no covariates. I am
>> > interested to know if the decrease in cortical thickness of subjects
>> > in group 1 across tp1 and tp2 is more than the decrease in cortical
>> > thickness of subjects in group 2 across tp1 and tp2. The contrast I
>> > think should be used for this is: 1 -1. Is that correct?
>> Yes, if you first take the difference between tp1 and tp2.

[Freesurfer] Corrupted T1 file (?) but segmentation look fine

[Anneliis Sartin-tarm]

External Email - Use Caution

Hello all,


I have been running into a curious problem with a couple brains (8 out of 150 
seem to have this problem) running through the recon-all pipeline. Upon loading 
brainmask.mgz, T1.mgz, and corresponding white matter and pial surfaces in 
Freeview, my colleague and I received an error that T1.mgz failed to load. 
Segmentation and parcellation seemed to run smoothly and accurately, however, 
the size of the T1.mgz file was 0. Assuming the file had been corrupted somehow 
(our server through which we run recon-all and store our data has tons of 
available memory), we reran the brains affected. Upon loading up the same 
re-run surfaces, T1.mgz loaded into the GUI as white, washed out voxels, 
displaying no brain at all. The size of this file is large, as well as all 
other surface and volume files. Curiously, the brainmask file seems 
normalized/stripped fine and surfaces displayed over the T1 look accurately 
segmented. I attached a screenshot displaying the T1.mgz file and surfaces that 
I'm referring to.


I have a few concerns and questions. Because T1.mgz doesn't seem to be 
necessary for downstream manual editing and processing, can we proceed as 
normal, only displaying and using the brainmask file to make edits? Will our 
surface and volume metrics export properly without a usable T1 file? Lastly, 
any clues to how this might have occurred are welcomed. It seems like the 
mri_normalize step is the culprit, although the nu.mgz files corresponding to 
these brains seem normally sized.


Best,

Anneliis Sartin-Tarm

Associate Research Specialist
Neurocircuitry of Trauma and PTSD Study
UW-Madison Dept. Psychiatry
608-262-6375
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Re: [Freesurfer] Recon-all - mghRead could not read rawavg.mgz

[Batuhan Erkat]

External Email - Use Caution

Hi Bram,

I uploaded all the files, including my input image and recon-all scripts.
As you can see, there are no errors for mri_convert, but there is for
mghRead(). If you inspect the 001.mgz and rawavg.mgz files, you'll realize
that they are corrupted and probably that's why mghRead fails to read
rawavg.mgz.

Can you see the files, did I do the file transmission correctly?

Best,
Batuhan

On Wed, Nov 21, 2018 at 7:32 PM Diamond, Bram Ryder <
brdiam...@mgh.harvard.edu> wrote:

> Hi Batuhan,
>
> Can you please upload the BE2 subject data using our ftp file exchange and
> let me know the exact command and terminal output when you ran
>  mri_convert?
>
> Info on our ftp file exchange:
> https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
>
> Thanks,
> Bram
>
>
> *Bram R. Diamond, BSc*
> Research Technician II
> Laboratory for Computational Neuroimaging
> Martinos Center for Biomedical Imaging
> Massachusetts General Hospital
> 149 13th Street
> Charlestown, MA 02129
> (p): 617-726-6598
>
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-- 

MSc Candidate

Neuroscience Graduate Program
National Magnetic Resonance Research Center (UMRAM) &
Aysel Sabuncu Brain Research Center

Bilkent University
Ankara, 06800
Turkey
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[Freesurfer] Recon-all - mghRead could not read rawavg.mgz

[Diamond, Bram Ryder]

Hi Batuhan,

Can you please upload the BE2 subject data using our ftp file exchange and let 
me know the exact command and terminal output when you ran mri_convert?

Info on our ftp file exchange: 
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange

Thanks,
Bram


Bram R. Diamond, BSc
Research Technician II
Laboratory for Computational Neuroimaging
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street
Charlestown, MA 02129
(p): 617-726-6598

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[Freesurfer] ?????? ?????? ?????? Recon-all run error

[1013364183]

External Email - Use Caution

Dear Bruce,
  I am sorry to let you wait so long, I have some troubles in transferring the 
data set, but it has been solved. Now I have sent the data set to ftp. I hope 
you can take the time to help us deal with the data set. We have already 
Running this data set for a long time but did not get results, the name of the 
data set is data_Yujunjie.zip,. The run command and the expert file are in the 
attachment.


Express your heartfelt thanks again??


yours yujunjie


--  --
??: "Bruce Fischl";
: 2018??11??18??(??) 11:15
??: "Freesurfer support list";

: Re: [Freesurfer] ??  ??  Recon-all run error



Instructions on how you can upload tarred and gzipped files here:

https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange

On Sun, 18 Nov 
2018, 
1013364183 wrote:

> 
> External Email - Use Caution
> 
> Dear Bruce,
>   I am very sorry to bother you. We are currently experimenting with 
> freesurfer, but I have
> encountered a lot of problems during the experiment. We have three 
> resolutions of data, the skull of
> medium-resolution data can't be removed (neck can't be removed), and with 
> high-resolution data, it
> will report memory transfer errors. You said before that we can submit data 
> sets to you, how should
> we provide you with data sets?
> 
> Thanks in advance
> yours yujunjie
> 
> --  --
> ??: "Bruce Fischl";
> : 2018??11??7??(??) 2:42
> ??: "Freesurfer support list";
> : Re: [Freesurfer] ?? Recon-all run error
> 
> does it occur if you run it outside of recon-all? Do you have enough free
> ram? If so, you can filedrop us the dataset and we can try to replicate and
> fit ix.
> 
> On Tue, 6 Nov 2018, 1013364183 wrote:
> 
> >
> > External Email - Use Caution   
> >
> > Dear Bruce,
> >   I found the error location in the recon-all.log folder. Here is the place 
> > where it went wrong??I
> > don't think it's the reason for insufficient memory..
> >   ''mri_convert.bin: putget.c:322: fill_NC_var: Assertion `chunksz % 4 == 
> > 0' failed.''
> >   This data is ok when we run with versions prior to freesurfer 6.0. But 
> > after we run the 6.0
> > version and set the expert file, this error will occur.Do I need to step 
> > through the instructions
> to
> > see the problem? How should this error be solved?
> >
> > Thanks in advance
> >
> > yours yujunjie
> >
> > --  --
> > ??: "Bruce Fischl";
> > : 2018??11??6??(??) 9:40
> > ??: "Freesurfer support list";
> > : Re: [Freesurfer] Recon-all run error
> >
> > that certainly looks like something is running out of ram. Can you run
> > the command that failed directly on the command line and see if it works?
> > Was anything else running on the machine at the time? We do report total
> > and free memory at the start of the recon in the recon-all.log file
> >
> > cheers
> > Bruce
> > On Tue,
> > 6 Nov 2018, 1013364183 wrote:
> >
> > >
> > > External Email - Use Caution   
> > >
> > > Dear FS,
> > > When we run ??recon-all?? with a 5GB high-resolution image, core dumped 
> > > appears when the
> > mri_convert
> > > command is executed. The specific errors are as follows:
> > > /opt/el7/pkgs/freesurfer/freesurfer_6.0/bin/mri_convert: line 3: 29235 
> > > Aborted (core dumped)
> > > mri_convert.bin "$@"
> > > ERROR: converting to minc
> > > We want to know if our high resolution image is too large for freesurfer 
> > > to handle, or our
> > computer
> > > memory (64GB running memory) is limited.
> > >
> > > Thanks a lot in advance!
> > > yours sincerely,
> > > yu junjie
> > >
> > >
> > >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
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expert.opts
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recon-all.txt
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