Re: [Freesurfer] Preprocessing functional MRI

[Martin Juneja]

Hi Zeke,

Thank you so much !
It's working really well now. I have one more question- is there any way I
can display labels (name of the areas) as well on the maps I see (using
tksurfer command you suggested).

Thanks Zeke once again.

On Tue, Apr 26, 2016 at 4:44 PM, Z K  wrote:

> The "freadFloat: fread failed" is a warning, not an error, and can be
> ignored.
>
> The ces.nii.gz, cesvar.nii.gz, sig.nii.gz files are surface overlays
> stored in a "volume" format, so they have to be viewed on the surface.
> You can do with this with something like:
>
>$> tksurferfv fsaverage lh inflated -ov sig.nii.gz -fminmax 2 3
>
> -Zeke
>
>
> On 04/26/2016 04:07 PM, Martin Juneja wrote:
> > Hello again,
> >
> > Somehow I figured out the error I had related to *.config. Now I am able
> > to run successfully all the 8 steps for 1 subject. I can see all the
> > files generated in a new folder i.e. ces.nii.gz, cesvar.nii.gz,
> > sig.nii.gz etc.
> > But when I try to display any of these files using FreeView (after
> > overlaying over inflated surface), it doesn't display anything and gives
> > me error "freadFloat: fread failed".
> >
> > I would really appreciate any suggestions how can I display functional
> > connectivity maps?
> >
> > Thanks,
> > MJ
> >
> > On Tue, Apr 26, 2016 at 10:53 AM, Martin Juneja  > > wrote:
> >
> > Hello everyone,
> >
> > I am following this page to process fMRI data:
> >
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough
> >
> > I am able to run until step-3 but at step 4, I am not sure what
> > should be directory to run this command. If I run the command in
> > SUBJECTS_DIR directory, it runs for a second and creates a
> > mean*.config file. But next step 5 requires *.config file to run,
> > not the mean*.config
> >
> > Just a quick background:
> > I preprocessed all subjects structural data using recon-all and the
> > processed folders are in my FreeSurfer SUBJECTS_DIR path and the
> > folder after preprocessing functional data (after running step-3) is
> > also in SUBJECTS_DIR path.
> >
> > Any help would be greatly appreciated.
> >
> > MJ
> >
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
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>
>
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Re: [Freesurfer] Preprocessing functional MRI

[Z K]

The "freadFloat: fread failed" is a warning, not an error, and can be 
ignored.

The ces.nii.gz, cesvar.nii.gz, sig.nii.gz files are surface overlays 
stored in a "volume" format, so they have to be viewed on the surface. 
You can do with this with something like:

   $> tksurferfv fsaverage lh inflated -ov sig.nii.gz -fminmax 2 3

-Zeke


On 04/26/2016 04:07 PM, Martin Juneja wrote:
> Hello again,
>
> Somehow I figured out the error I had related to *.config. Now I am able
> to run successfully all the 8 steps for 1 subject. I can see all the
> files generated in a new folder i.e. ces.nii.gz, cesvar.nii.gz,
> sig.nii.gz etc.
> But when I try to display any of these files using FreeView (after
> overlaying over inflated surface), it doesn't display anything and gives
> me error "freadFloat: fread failed".
>
> I would really appreciate any suggestions how can I display functional
> connectivity maps?
>
> Thanks,
> MJ
>
> On Tue, Apr 26, 2016 at 10:53 AM, Martin Juneja  > wrote:
>
> Hello everyone,
>
> I am following this page to process fMRI data:
> 
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough
>
> I am able to run until step-3 but at step 4, I am not sure what
> should be directory to run this command. If I run the command in
> SUBJECTS_DIR directory, it runs for a second and creates a
> mean*.config file. But next step 5 requires *.config file to run,
> not the mean*.config
>
> Just a quick background:
> I preprocessed all subjects structural data using recon-all and the
> processed folders are in my FreeSurfer SUBJECTS_DIR path and the
> folder after preprocessing functional data (after running step-3) is
> also in SUBJECTS_DIR path.
>
> Any help would be greatly appreciated.
>
> MJ
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
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Re: [Freesurfer] labels

[Trisanna Sprung-Much]

thanks Dr. Fischl - it seems to match well so I will continue to use this
method. It would be great if Ruopeng could eventually edit Freesurfer to
allow for thresholding .labels too.

On another note, is there a way to edit labels in Freeview in a similar
manner to doing so in tksurfer?* From what I can tell, one can only edit
volume segmentations in Freeview.*

best

Trisanna



--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Mon, Apr 25, 2016 at 8:43 PM, Bruce Fischl 
wrote:

> yes, that sounds right. Does it look correct? That is, are areas 1/4 etc..
> in the central sulcus and such?
> On Mon, 25 Apr 2016, Trisanna Sprung-Much wrote:
>
> Not a problem, Dr. Fischl!
>> In the meantime, could you please confirm that I am opening up a
>> cytoarchitectonic probability map I have as .mnc
>> correctly?
>>
>> I basically change it to a surface overlay.mgz using mri_vol2surf and
>> then open it as an overlay with a surface in
>> Freeview. I can then change the thresholds using "configure overlay".
>>
>> best
>>
>> Trisanna
>>
>> --
>> Ph.D. CandidateMcGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Mon, Apr 25, 2016 at 6:53 PM, Bruce Fischl 
>> wrote:
>>   Hi Trisanna
>>
>>   yes, but Ruopeng is on vacation to it will be a while
>>
>>   Bruce
>>   On Mon, 25 Apr 2016, Trisanna Sprung-Much wrote:
>>
>> Hi there
>>
>> With regards to this email from March, I cannot seem to be
>> able to change
>> thresholds of .labels in Freeview. Could this be added as an
>> option?
>>
>> best wishes
>>
>> Trisanna
>>
>> --
>> Ph.D. CandidateMcGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Sun, Mar 13, 2016 at 1:45 PM, Bruce Fischl <
>> fis...@nmr.mgh.harvard.edu>
>> wrote:
>>   Hi Trisanna
>>
>>   1. the .thresh labels have been thresholded with a
>> p-value
>>   threshold that is "best" on our training set of
>>   manually/architectonically defined labels.
>>
>>   2. Hmmm, not sure, but we have stopped development on
>> tksurfer.
>>   Can you try this on freeview? I can't remember if
>> freeview
>>   allows changing thresholds in labels, but if not
>> Ruopeng can add
>>   it to his list of feature requests
>>
>>   cheers
>>   Bruce
>>
>>
>>
>>   On Sat, 12 Mar 2016, Trisanna Sprung-Much wrote:
>>
>> Hi there
>> I have two questions regarding using the labels
>> with
>> tksurfer:
>>
>> 1. What exactly has been done to change the .label
>> (e.g. lh BA44.label) to
>> .thresh.label (e.g. lh BA44.thresh.label?
>>
>> 2. The instructions on this page
>>
>>
>> https://surfer.nmr.mgh.harvard.edu/fswiki/BrodmannAreaMaps
>>
>> to overlay the labels and set the Min and Max do
>> not
>> seem to work for me - I
>> cannot seem to alter the Min from 2 and the Max
>> from
>> 5. Any thoughts as to
>> why?
>>
>> thanks very much!
>>
>> Trisanna
>>
>>
>> --
>> Ph.D. CandidateMcGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>>
>>
>>   ___
>>   Freesurfer mailing list
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>>
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>   The information in this e-mail is intended only for the
>> person
>>   to whom it is
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>> in error
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>>   contains patient information, please contact the
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>>   Compliance HelpLine at
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>>   to you in error
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Re: [Freesurfer] Preprocessing functional MRI

[dgw]

Martin,

You need to provide more details for us to help you. What version of
FreeSurfer? What exactly did you type in the command line as both your
analysis and your call to freeview?

If I were to take a wild guess, I would say you have the wrong surface
loaded. That tutorial does the analysis on the fsaverage inflated
surface.

hth
d

On Tue, Apr 26, 2016 at 4:07 PM, Martin Juneja  wrote:
> Hello again,
>
> Somehow I figured out the error I had related to *.config. Now I am able to
> run successfully all the 8 steps for 1 subject. I can see all the files
> generated in a new folder i.e. ces.nii.gz, cesvar.nii.gz, sig.nii.gz etc.
> But when I try to display any of these files using FreeView (after
> overlaying over inflated surface), it doesn't display anything and gives me
> error "freadFloat: fread failed".
>
> I would really appreciate any suggestions how can I display functional
> connectivity maps?
>
> Thanks,
> MJ
>
> On Tue, Apr 26, 2016 at 10:53 AM, Martin Juneja  wrote:
>>
>> Hello everyone,
>>
>> I am following this page to process fMRI data:
>>
>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough
>>
>> I am able to run until step-3 but at step 4, I am not sure what should be
>> directory to run this command. If I run the command in SUBJECTS_DIR
>> directory, it runs for a second and creates a mean*.config file. But next
>> step 5 requires *.config file to run, not the mean*.config
>>
>> Just a quick background:
>> I preprocessed all subjects structural data using recon-all and the
>> processed folders are in my FreeSurfer SUBJECTS_DIR path and the folder
>> after preprocessing functional data (after running step-3) is also in
>> SUBJECTS_DIR path.
>>
>> Any help would be greatly appreciated.
>>
>> MJ
>
>
>
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>
>
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> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
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> properly
> dispose of the e-mail.
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Re: [Freesurfer] Preprocessing functional MRI

[Martin Juneja]

Hello again,

Somehow I figured out the error I had related to *.config. Now I am able to
run successfully all the 8 steps for 1 subject. I can see all the files
generated in a new folder i.e. ces.nii.gz, cesvar.nii.gz, sig.nii.gz etc.
But when I try to display any of these files using FreeView (after
overlaying over inflated surface), it doesn't display anything and gives me
error "freadFloat: fread failed".

I would really appreciate any suggestions how can I display functional
connectivity maps?

Thanks,
MJ

On Tue, Apr 26, 2016 at 10:53 AM, Martin Juneja  wrote:

> Hello everyone,
>
> I am following this page to process fMRI data:
>
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough
>
> I am able to run until step-3 but at step 4, I am not sure what should be
> directory to run this command. If I run the command in SUBJECTS_DIR
> directory, it runs for a second and creates a mean*.config file. But next
> step 5 requires *.config file to run, not the mean*.config
>
> Just a quick background:
> I preprocessed all subjects structural data using recon-all and the
> processed folders are in my FreeSurfer SUBJECTS_DIR path and the folder
> after preprocessing functional data (after running step-3) is also in
> SUBJECTS_DIR path.
>
> Any help would be greatly appreciated.
>
> MJ
>
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Re: [Freesurfer] white surf area

[Bruce Fischl]

Hi Hassan

we have answered you every time! Is is the total surface area of the white 
matter surface. It is just a single number per hemisphere so there is 
nothing to visualize
Bruce


On Tue, 26 Apr 2016, Hassan bakhshi wrote:

> 
> Hello Bruce,
> Sorry I'm in a hurry and its 3rd time I emailed.
> What is exactly the feature white surface area and how can I visualize it?
> Kind regards,
> 
> 
>
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Re: [Freesurfer] white surf area

[Hassan bakhshi]

Hello Bruce,
Sorry I'm in a hurry and its 3rd time I emailed.
What is exactly the feature white surface area and how can I visualize it?
Kind regards,
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[Freesurfer] Preprocessing functional MRI

[Martin Juneja]

Hello everyone,

I am following this page to process fMRI data:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough

I am able to run until step-3 but at step 4, I am not sure what should be
directory to run this command. If I run the command in SUBJECTS_DIR
directory, it runs for a second and creates a mean*.config file. But next
step 5 requires *.config file to run, not the mean*.config

Just a quick background:
I preprocessed all subjects structural data using recon-all and the
processed folders are in my FreeSurfer SUBJECTS_DIR path and the folder
after preprocessing functional data (after running step-3) is also in
SUBJECTS_DIR path.

Any help would be greatly appreciated.

MJ
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dispose of the e-mail.

Re: [Freesurfer] hippocampal subfield analysis - registered two scans prior to analysis

[Lara Foland-Ross]

My apologies - there was a typo in my last message. The error reads that the 
program could not find mri/001.mgz:

cibsr-i27-410:inProgress6.0b kel32$ pwd
/Volumes/Xspace/Freesurfer/inProgress6.0b
cibsr-i27-410:inProgress6.0b kel32$ ls
18512_T1_v5.3_hipp_v6.0 18512_hipp  fsaverage
cibsr-i27-410:inProgress6.0b kel32$ recon-all -all -s 18512_T1_v5.3_hipp_v6.0 
-hippocampal-subfields-T2 
/Volumes/Xspace/Freesurfer/Liraglutide6.0b/rawdata/18512_hipp/MR.1.2.840.113619.2.283.4120.7575399.16012.1376585566.598.dcm
 T2hipp_in_long
INFO: FreeSurfer build stamps do not match
Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
Current Stamp: freesurfer-Darwin-OSX-dev-20160326
INFO: SUBJECTS_DIR is /Volumes/Xspace/Freesurfer/inProgress6.0b
Actual FREESURFER_HOME /Volumes/ToolsMac/freesurfer6.0b
-rw-rw-r--  1 kel32  staff  1368492 Apr 26 08:33 
/Volumes/Xspace/Freesurfer/inProgress6.0b/18512_T1_v5.3_hipp_v6.0/scripts/recon-all.log
Darwin cibsr-i27-410.stanford.edu 12.6.0 Darwin Kernel Version 12.6.0: Wed Mar 
18 16:23:48 PDT 2015; root:xnu-2050.48.19~1/RELEASE_X86_64 x86_64
dyld: DYLD_ environment variables being ignored because main executable 
(/usr/bin/top) is setuid or setgid
INFO: current FREESURFER_HOME does not match that of previous processing.
Current: /Volumes/ToolsMac/freesurfer6.0b
Previous: /Volumes/ToolsMac/freesurfer5.3
#
#@# MotionCor Tue Apr 26 08:41:07 PDT 2016
ERROR: no run data found in 
/Volumes/Xspace/Freesurfer/inProgress6.0b/18512_T1_v5.3_hipp_v6.0/mri. Make 
sure to
have a volume called 001.mgz in  
/Volumes/Xspace/Freesurfer/inProgress6.0b/18512_T1_v5.3_hipp_v6.0/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
Darwin cibsr-i27-410.stanford.edu 12.6.0 Darwin Kernel Version 12.6.0: Wed Mar 
18 16:23:48 PDT 2015; root:xnu-2050.48.19~1/RELEASE_X86_64 x86_64

recon-all -s 18512_T1_v5.3_hipp_v6.0 exited with ERRORS at Tue Apr 26 08:41:08 
PDT 2016

For more details, see the log file 
/Volumes/Xspace/Freesurfer/inProgress6.0b/18512_T1_v5.3_hipp_v6.0/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


Can you please advise on how best to proceed?

May thanks!
Lara

Lara Foland-Ross, Ph.D.
Research Associate
Center for Interdisciplinary Brain Sciences Research
Stanford University School of Medicine
401 Quarry Road, Room 1356
Stanford, CA 94305-5795


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

Sent: Tuesday, April 26, 2016 6:06 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] hippocampal subfield analysis - registered two scans 
prior to analysis

Hi Lara,

mri/orig.mgz should be there also in the longitudinal directories. If it
is missing, more might be wrong. I would recommend rerunning those long
runs from scratch.

Best, Martin

On 04/25/2016 07:07 PM, Lara Foland-Ross wrote:
> Thank you Eugenio! This worked like a charm.
>
> Wondering now if you could help me troubleshoot running this command on 2 
> scans from a single subject (time 1 and time 2) that were processed using the 
> longitudinal pipeline in version 5.3.
>
> I ran the following:
>
> recon-all -all -s 18512_T1_v5.3_hipp_v6.0 -hippocampal-subfields-T2 
> 18512_hipp/MR.1.2.840.113619.2.283.4120.7575399.16012.1376585566.598.dcm 
> T2hipp
>
> and got the error that Freesurfer could not find mri/orig file... It is 
> indeed not there, presumably because it isn't produced after the creation and 
> editing of the long.base timepoints. I read elsewhere on the list that the 
> hippocampal subfield analysis could be run on the individual longitudinal 
> timepoints but can't seem to get this to work. Can you advise?
>
> Many thanks in advance for your continued help!
> Lara
>
>
> Lara Foland-Ross, Ph.D.
> Research Associate
> Center for Interdisciplinary Brain Sciences Research
> Stanford University School of Medicine
> 401 Quarry Road, Room 1356
> Stanford, CA 94305-5795
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Eugenio Iglesias 
> 
> Sent: Tuesday, April 5, 2016 3:59 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] hippocampal subfield analysis - registered two 
> scans prior to analysis
>
> Almost correct!
> recon-all -all -s subj1_T1 -i subj1_T1/I0001.dcm -hippocampal-subfields-T1T2 
> subj1_hipp/I0001.dcm T2hipp
> Also, this is assuming that you have defined the environment variable 
> SUBJECTS_DIR. Otherwise, you'd need to add the flag -sd .
> Cheers,
> /Eugenio
>
>
> Juan Eugenio Iglesias
> Postdoctoral researcher BCBL
> www.jeiglesias.com
> www.bcbl.eu
>
> Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
>
> - Original 

Re: [Freesurfer] hippocampal subfield analysis - registered two scans prior to analysis

[Martin Reuter]

Hi Lara,

mri/orig.mgz should be there also in the longitudinal directories. If it 
is missing, more might be wrong. I would recommend rerunning those long 
runs from scratch.

Best, Martin

On 04/25/2016 07:07 PM, Lara Foland-Ross wrote:
> Thank you Eugenio! This worked like a charm.
>
> Wondering now if you could help me troubleshoot running this command on 2 
> scans from a single subject (time 1 and time 2) that were processed using the 
> longitudinal pipeline in version 5.3.
>
> I ran the following:
>
> recon-all -all -s 18512_T1_v5.3_hipp_v6.0 -hippocampal-subfields-T2 
> 18512_hipp/MR.1.2.840.113619.2.283.4120.7575399.16012.1376585566.598.dcm 
> T2hipp
>
> and got the error that Freesurfer could not find mri/orig file... It is 
> indeed not there, presumably because it isn't produced after the creation and 
> editing of the long.base timepoints. I read elsewhere on the list that the 
> hippocampal subfield analysis could be run on the individual longitudinal 
> timepoints but can't seem to get this to work. Can you advise?
>
> Many thanks in advance for your continued help!
> Lara
>
>
> Lara Foland-Ross, Ph.D.
> Research Associate
> Center for Interdisciplinary Brain Sciences Research
> Stanford University School of Medicine
> 401 Quarry Road, Room 1356
> Stanford, CA 94305-5795
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Eugenio Iglesias 
> 
> Sent: Tuesday, April 5, 2016 3:59 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] hippocampal subfield analysis - registered two 
> scans prior to analysis
>
> Almost correct!
> recon-all -all -s subj1_T1 -i subj1_T1/I0001.dcm -hippocampal-subfields-T1T2 
> subj1_hipp/I0001.dcm T2hipp
> Also, this is assuming that you have defined the environment variable 
> SUBJECTS_DIR. Otherwise, you'd need to add the flag -sd .
> Cheers,
> /Eugenio
>
>
> Juan Eugenio Iglesias
> Postdoctoral researcher BCBL
> www.jeiglesias.com
> www.bcbl.eu
>
> Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
>
> - Original Message -
> From: "Lara Foland-Ross" 
> To: "Freesurfer support list" 
> Sent: Wednesday, April 6, 2016 12:29:09 AM
> Subject: Re: [Freesurfer] hippocampal subfield analysis - registered two 
> scans prior to analysis
>
> Hi Eugenio,
>
> Thank you so much for the quick and helpful reply.  I checked the images in 
> Freeview and they actually line up quite nicely!
>
> Can you provide further guidance on how to run recon-all once with both the 
> -all and the hippocampal-subfields-T1T2 flags?
>
> For example, in my rawdata directory, I have two folders: subj1_T1 and 
> subj1_hipp. I cd'd into the rawdata folder and ran the following with no 
> success:
>
> recon-all -all -s subj1_T1 -i subj1_T1/I0001.dcm -hippocampal-subfields-T1T2 
> subj1_hipp T2hipp
>
> Is this directory setup correct? And can you please point out the errors in 
> the above recon-all command?
>
> Many thanks again for your help!
> Lara
>
> Lara Foland-Ross, Ph.D.
> Research Associate
> Center for Interdisciplinary Brain Sciences Research
> Stanford University School of Medicine
> 401 Quarry Road, Room 1356
> Stanford, CA 94305-5795
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Eugenio Iglesias 
> 
> Sent: Tuesday, April 5, 2016 2:32 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] hippocampal subfield analysis - registered two 
> scans prior to analysis
>
> Dear Lara,
> Two things:
> 1. You don't need to recon the T2 scan. The recon-all stream only works for 
> T1 data anyway.
> 2. The registration between the T1 and T2 scans happens internally (with a 
> mri_register command similar to the one you wrote) during the hippocampal 
> subfield segmentation. You only need to coarsely align the T1 and T2 scans 
> manually if the initial alignment between the two is terrible. What happens 
> when you open them both in Freeview?
> 3. If the alignment is decent, just run recon-all once, with both the -all 
> and the -hippocampal-subfields-T1T2 flags.
> Feel free to send me the T1 and T2 scans if you are not sure whether they are 
> sufficiently well aligned or not.
> Cheers,
> /Eugenio
>
> Juan Eugenio Iglesias
> Postdoctoral researcher BCBL
> www.jeiglesias.com
> www.bcbl.eu
>
> Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
>
> - Original Message -
> From: "Lara Foland-Ross" 
> To: "Freesurfer support list" 
> Sent: Tuesday, April 5, 2016 11:14:39 PM
> Subject: [Freesurfer] hippocampal subfield analysis - registered two scans 
> prior to analysis
>
> Hello,
>
> I'm beginning a hippocampal subfield analysis in the beta version of 
> Freesurfer 6.0. I have a whole brain 

Re: [Freesurfer] improving white/grey segmentation in recon -all for better volume estmation

[Bruce Fischl]

Hi Tilak

I think you need to improve your data if that is an option. I couldn't 
see the gray/white boundary in either occipital or perirolandic cortex, 
so no parameters are going to help there


cheers
Bruce
On Mon, 25 Apr 2016, Ramtilak Gattu 
wrote:



Hey Bruce,
Following up with the question can I find any documentation to improve the
segmentation like what are the parameters that needs to be tweaked. Can we
use any seed points to classify and improve the segmentation? How to decide
the thresholds in choosing the parameters to improve the segmentation?

Thanks

Regards
Tilak

On Mon, Apr 25, 2016 at 12:17 PM, Ramtilak Gattu
 wrote:
  Hey Bruce,
These scans are done on 3T Siemens Trio.

Will send you CNR for some of the cases . Are you looking for any
specific structures in particular.

Thanks

Regards
Tilak

On Mon, Apr 25, 2016 at 12:01 PM, Ramtilak Gattu
 wrote:
  Hello Bruce,
Thanks for the response. I previously mentioned the parameters
in the earlier discussion  for the same topic and you have
suggested to decrease the TE and increase the voxelsize to 1.2mm
 for better SNR. For the recollection I am again mentioning the
complete parameters here- 

The parameter in the  sequence are TE=4.92 ms, TR=19 ms, Flip angle =20 degr
ees, voxel size 1x1x1, receiving coil is the 12 channel

head coil and the transmitting coil is the body coil and GRAPPA of 2. We are
 using  Freesurfer version 5.3.

I am including all the recon result files for one case for your review.

https://waynestateprod-my.sharepoint.com/personal/ao3080_wayne_edu/_layouts/
15/guestaccess.aspx?guestaccesstoken=etz0FRv0sU01dbi%2fRsmwZmSlq5pNMZA5%2fXh
u5hDy10Q%3d=1bd7f60d2dc074a12ae531ebbdcb3829b

Thanks

Regards

Tilak

On Sun, Apr 24, 2016 at 1:52 PM, Ramtilak Gattu
 wrote:
  Hello Bruce,
Attached are the files for two subjects with brain.mgz and
lh.white.
 
The values of WM in those regions in brain.mgz are above
90.

Thanks

Regards
Tilak


On Sun, Apr 24, 2016 at 1:49 PM, Ramtilak Gattu
 wrote:


On Sat, Apr 23, 2016 at 7:47 PM, Ramtilak Gattu
 wrote:
  Hello Bruce,

  Thanks a lot for your earlier expert
  option suggestion in improving the
  segmentation during the recon process. I
  am attaching a snap shot where yellow is
  with expert options and red is with
  default options. My concern is where I
  have indicated with blue arrows . Could
  you please suggest why is it still
  failing to pick up those areas. Is it
  because of 

a) misregistration with the atlas
         (i)  if so where can I find the
results after the non linear registration and 
         (ii) would it be possible to improve
with any more expert options during  the
registration and the segmentation
subsequently.

b) or is it should be just changing the lower
limit values for the WM and higher limit
values for the GM. I am not sure which way to
tune the values should I go low on WM values
and go high on GM values. These are the actual
values 

mri_segment -wlo 87.7  -ghi 103.3
mris_make_surfaces -min_gray_at_white_border
79.4  -max_border_white 109.3
 -min_border_white 90  -max_csf 68.7
 -max_gray 98.7 -max_gray_at_csf_border 84.7
 -min_gray_at_csf_border 58.1

For example Should these be changed to 

mri_segment -wlo 80  -ghi 110

Thanks for your help in advance.

Regards
Tilak


Thanks

Regards
Tilak


From: Ramtilak Gattu
Sent: Wednesday, March 30, 2016 4:26 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] improving white/grey
segmentation in recon -all for better volume
estmation

Thank you for recommending the expert options.
I have run this on two subjects (rows) and you
can see the post analysis results on the right
(column) in the attached  image  . As you have
mentioned it didnt work well in the cerebellum
any other ways to improve in the inferior
regions?

Thanks

Regards
Tilak

From: Ramtilak Gattu
Sent: Monday, March 28, 2016 5:12 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] improving white/grey
segmentation in recon -all for better volume
estmation

Thank you,

Attached is the scripts folder for one subject
.

Thanks

Regards
Tilak

From: Ramtilak Gattu
Sent: Monday, March 28, 2016 4:11 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] improving white/grey
segmentation in recon -all for better volume
estmation

Sorry, Actually just found out that the
receiving coil is the 12 channel head coil and
the transmitting coil is the body coil. I am
attaching a snapshot showing the sag
orientation of the three cases that I
previously mentioned and uploaded for your
review.

>From these figures do you really think there
is not enough contrast, just wondering

1) why it worked in the bottom 

Re: [Freesurfer] coordinates to values

[Bruce Fischl]

if you put them into a label file you can use mri_label_vals for this

cheers
Bruce
On 
Mon, 25 Apr 2016, prasser wrote:




Hi,

Could you please let me know the command that takes say, ras coordinates (or
a list of them) and a .mgz as input, and outputs the corresponding voxel
values from the .mgz?

Thanks.

 

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