[Freesurfer] missing brain

2012-12-03 Thread Catherine Bois
Hi,

I am currently in the process of reconstructing my brains after edits.
However, the brains keep being reconstructed with large portions of brain
missing/cerebellum missing; ie they are much worse than before I edited
them. However, I am sure that I have only put control points in white
matter areas; ie not partial volume, so I am very confused as to why this
is happening; in one brain for example I had not put any cotnrol points
(only made a very small white matter edit). Has this happened to anyone
else before? Am i somehow running the wrong command somewhere? Could the
watershed be wrong in the script, ie accidentally changed?

Grateful for help,

Regards Cathy
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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
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] aseg.stats

2012-12-03 Thread charles laidi
Dear freesurfers.

I'm using freesurfer for two weeks. I'm currently trying to make a script
to get asegstats resultats for >100 patients.

I did this script in tcsh :

foreach filename (t1_)
asegstats2table --subjects ${filename} \
  --segno 12 18 14\
  --tablefile asegstats.txt
end

The problem is that at each loop, the n+1 subject replace the n subject, so
at the end I only have the asegstats for the last subject.

When I am replacing t1_ (it's a wild card) by t1_63537193
t1_18394856 the result is fine

so the question is : how to make a loop without over writing the n result
by the n+1 result

Thanks very much for you help

Sincerely yours,

Charles Laidi
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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
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.


Re: [Freesurfer] freeview

2012-12-03 Thread Andreas Berger
On Sunday, December 02, 2012 23:56:38 Yaniv Kaufman wrote:
> Dear Freesurfer experts,
> 
> I am trying to display DTI using freeview, however, every time I attempt to
> run freeview from the command line (I am using Ubuntu 12.4), I receive the
> following error:
> 
>   "freeview.bin: error while loading shared libraries: libjpeg.so.62: 
> cannot
> open shared object file: No such file or directory"
> 
> libjpeg.sp.62 is present in /home/freesurfer, when I attempt to open it
> directly, it gives the following error:
> 
>   "The link cannot be used, because its target 'libjepg.so.8' doesn't 
> exist"
> 
> libjepg.so.8 does in fact exist but in /usr/lib.
> 
> I am not quite sure how to direct libjpeg.so.62 to libjepg.so.8 or whether
> that would solve the problem at all. I am able to use tkmedit, tksurfer
> and do all the pre processing for MRI and DTI.
> 
> Thank you in advance.
> 
> Yaniv Kaufman
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> 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 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.

ubuntu seems to be missing a few libraries out of the box.
try 'apt-get install libjpeg62'
i'm on debian here, but i assume the package has the same name in ubuntu.

regards,
andreas
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


Re: [Freesurfer] aseg.stats

2012-12-03 Thread Andreas Berger
On Monday, December 03, 2012 13:46:11 charles laidi wrote:
> Dear freesurfers.
> 
> I'm using freesurfer for two weeks. I'm currently trying to make a script
> to get asegstats resultats for >100 patients.
> 
> I did this script in tcsh :
> 
> foreach filename (t1_)
> asegstats2table --subjects ${filename} \
>   --segno 12 18 14\
>   --tablefile asegstats.txt
> end
> 
> The problem is that at each loop, the n+1 subject replace the n subject, so
> at the end I only have the asegstats for the last subject.
> 
> When I am replacing t1_ (it's a wild card) by t1_63537193
> t1_18394856 the result is fine
> 
> so the question is : how to make a loop without over writing the n result
> by the n+1 result
> 
> Thanks very much for you help
> 
> Sincerely yours,
> 
> Charles Laidi

try just 
'asegstats2table --subjects t1_ --etcetera'

regards,
andreas
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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
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] Calculatin​g the mean intensity ratio in one specific region

2012-12-03 Thread Kong, Li
Hello everyone,


I got grey matter/ white matter intensity ratio at each vertex across the 
cortex. I would like to know the mean intensity ratio in one region (ex, 
superior temporal gyrus).


Anyone knows how to get it?


Thanks in advance!

Li
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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
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.


Re: [Freesurfer] missing brain

2012-12-03 Thread Bruce Fischl
Hi Cathy
What version are you running? If 5.1 you will need Nick's updated recon-all
Cheers
Bruce 



On Dec 3, 2012, at 5:33 AM, Catherine Bois  wrote:

> Hi,
> 
> I am currently in the process of reconstructing my brains after edits. 
> However, the brains keep being reconstructed with large portions of brain 
> missing/cerebellum missing; ie they are much worse than before I edited them. 
> However, I am sure that I have only put control points in white matter areas; 
> ie not partial volume, so I am very confused as to why this is happening; in 
> one brain for example I had not put any cotnrol points (only made a very 
> small white matter edit). Has this happened to anyone else before? Am i 
> somehow running the wrong command somewhere? Could the watershed be wrong in 
> the script, ie accidentally changed?
> 
> Grateful for help,
> 
> Regards Cathy
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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
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.



Re: [Freesurfer] VOI

2012-12-03 Thread Bruce Fischl

Hi Octavian

it's hard to say. I would think you could get a bunch of it automatically 
by looking for places that are significantly different between the two 
timpoints, but that will depend on how well they register. You can 
certainly do it manually in freeview.


cheers
Bruce
On Sun, 2 Dec 2012, octavian lie 
wrote:



Dear All,
I have 2 coregistered MR volume (pre and postresective MRI) sets for several
epilepsy patients. I need to extract the resection volume (VOI= pre -
postresection volume) as a set of voxel coordinates. Can I do this in
freesurfer? Ideally I would avoid manual delineation slice by slice as in
MRImicro and if possible I would do it automatically by thresholding, for
example. If not, manual is fine if it can be done in FS.
Please advise.
Thank you,
Octavian.

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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
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.


Re: [Freesurfer] recon-all unable to make pial and white surfaces

2012-12-03 Thread Bruce Fischl

Hi Negar

perhaps Nick or PPJ can comment on how much a virtual box needs? In any 
case, try increasing the ram and see what happens as the error message is 
pretty clear. Also, if you can run "top" or something similar 
(/usr/bin/free) to see how memory is actually available on the system that 
would help


cheers
Bruce

On Sat, 1 Dec 2012, Negar Memarian wrote:


Thank you for your reply, Bruce. I'm running FreeSurfer using a VMWare
virtual machine on Windows 7. I've set the settings of the VM to use 2 CPUs
and 6GB ram. Here is the specifications of my computer hardware:
OS: Windows 7 professional
Processor: Intel Core i7-3770 CPU @ 3.40 GHz
RAM: 8 GB
System type: 64 bit

Please let me know if you need any other info. Many thanks for your help.
-Negar
 

On Sat, Dec 1, 2012 at 11:52 AM, Bruce Fischl 
wrote:
  can you check to see how much you actually have free? You are
  definitely running out of memory, so something else is using it.
  What is your hardware/software environment?

  On Sat, 1 Dec 2012, Negar Memarian wrote:

No, I tried running just one recon and I only have
one xterm window open.
Anything I can do to fix this? 



On Sat, Dec 1, 2012 at 11:11 AM, Bruce Fischl

wrote:
      6G should be plenty. Do you have anything else
running? Maybe
      another recon at the same time?
      On Fri, 30 Nov 2012, Negar Memarian wrote:

            Hi Bruce,
            I have 8 GB ram and have assigned 6GB of
it to
            FreeSurfer. Shall I increase
            it to 8? Would that be enough or still
too low?

            Thank you,
            Negar


            On Fri, Nov 30, 2012 at 7:31 PM, Bruce
Fischl
            
            wrote:
                  Look like it is running out of
memory. How
            much ram do you have
                  on that machine?
                  Bruce



                  On Nov 30, 2012, at 9:29 PM, Negar
Memarian
                  
wrote:

                  > Hello,
                  >
                  > I ran recon-all -all on my
subject. The
            process ended after
                  several minutes with this message
at the end:
                  > recon-all -s 350_FS exited with
ERRORS at
            Fri Nov 30 17:57:59
                  PST 2012
                  >
                  > I tried loading the pial and
white surfaces
            for editing using
                  this command:
                  > tkmedit 350_FS brainmask.mgz
rh.white
            -aux-surface lh.white
                  >
                  > but looks like these surfaces do
not exist
            (since the
                  recon-all exited prematurely).
When I check
            the recon-all.log
                  file I do not see any errors
except a few
            MCSRCH errors. So I
                  cannot understand what exactly
went wrong in
            the recon-all. I've
                  attached the recon-all log file.
Can someone
            please tell me what
                  the problem is and how I can fix
it?
                  >
                  > Many thanks,
                  > Negar
                  > p.s. I tried on more than one
subject and I
            still face the
                  same issue.
                  >
                  >
                  > Negar Memarian, MASc, PhD
                  > NSERC Postdoctoral Fellow
                  > Department of Neurology
                  > David Geffen School of Medicine
at UCLA
                  >
                  > 
                  >
           
___
                  > Freesurfer mailing list
                  > Freesurfer@nmr.mgh.harvard.edu
                  >
           
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


                  The information in this e-mail is
intended
            o

Re: [Freesurfer] Calculatin​g the mean intensity ratio in one specific region

2012-12-03 Thread Bruce Fischl

Hi Li


save it as a .mgz volume and use mris_anatomical_stats with the 
parcellation you want.


cheers
Bruce
On Mon, 3 Dec 2012, Kong, Li wrote:



Hello everyone,

 

 

I got grey matter/ white matter intensity ratio at each vertex across the
cortex. I would like to know the mean intensity ratio in one region (ex,
superior temporal gyrus).

 

 

Anyone knows how to get it?

 

 

Thanks in advance!

 

Li


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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
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.


Re: [Freesurfer] TRACULA tract path failure

2012-12-03 Thread Arman Eshaghi
Dear Anastasia,

Thanks for the suggestions. The new control point didn't help. Therefore I
uploaded remaining images. It would be great if you could have a look
again.

All the best,
Arman


On Sat, Dec 1, 2012 at 1:45 AM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:

>
> Hi Arman - One more thing. Do you mind sending me the original (non-skull
> stripped) T1 as well? We'd like to test a different registration method on
> it. Thanks!
>
> a.y
>
>
> On Fri, 30 Nov 2012, Arman Eshaghi wrote:
>
>  Dear Anastasia,
>> Thanks for your response. I have sent a subject that the problem in
>> forceps minor persists.
>> What I have done so far was to re-run the pipeline with "reinit=1", check
>> the eigenvectors, increase control
>> points, switch off brain anatomical mask in dmric. It made the tracts
>> look better for many subjects but this one
>> still has problems in forceps minor.
>>
>> Thanks,
>> Arman
>>
>>
>> On Fri, Nov 30, 2012 at 11:08 AM, Arman Eshaghi 
>> wrote:
>>   Dear Anastasia,
>>   Thanks for your response. I have sent a subject that the problem in
>> forceps minor persists.
>> What I have done so far was to re-run the pipeline with "reinit=1", check
>> the eigenvectors, increase control
>> points, switch off brain anatomical mask in dmric. It made the tracts
>> look better for many subjects but this
>> one still has problems in forceps minor.
>>
>> Thanks,
>> Arman
>>
>>
>> On Wed, Nov 28, 2012 at 7:34 PM, Anastasia Yendiki <
>> ayend...@nmr.mgh.harvard.edu> wrote:
>>
>>   Hi Arman - Have you ruled out any issues with the gradient
>> directions? In situations where the
>>   problem is wide-spread, this seems to be the usual suspect. If
>> you've checked the eigenvectors
>>   and they're ok, can you send an example case where the problem
>> persists? You can use this page to
>>   upload a tar ball of all the tracula-related directories of the
>> subject:
>>   https://www.nmr.mgh.harvard.**edu/facility/filedrop/index.*
>> *html 
>>
>>   Thanks!
>>   a.y
>>
>>   On Mon, 26 Nov 2012, Arman Eshaghi wrote:
>>
>> Dear all,
>> I have difficulty sorting out the problem with some tracts in
>> several subjects,
>> tracts are incomplete or
>> missing. As it has come up quite a few times on the list, for
>> this sort of problem I
>> have first set
>> "reinit=1" and then increased control points to 7, and re-ran
>> trac-all with "-prior"
>> flag. This has worked
>> for some tracts in several subjects, however there are a few
>> subjects that still have
>> this problem.
>>
>> It would be great if someone could let me know what else I
>> might be able to do in
>> order to correct
>> missing/faulty tracts in my subjects. (The problem is not
>> limited to a specific
>> tract, it varies in
>> different subjects)
>>
>> All the best,
>> -Arman
>>
>>
>>
>>
>> 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


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.


Re: [Freesurfer] Calculatin​g the mean intensity ratio in one specific region

2012-12-03 Thread Kong, Li
Hi Bruce,

Thanks for your answer!

I tried mris_anatomical_stats command, but I met problems:
(1) I would like to get the mean intensity ratio of the superior temporal, so I 
need a label of this region.
 I first used mri_annotation2label to get lh.superiortemporal.label file.

(2) Then I used mris_anatomical_stats command as following (I saved GM/WM 
intensity ratio as lh.gm_wm.mgh):
mris_anatomical_stats -l label/lh.superiortemporal.label -t 
subj1/surf/lh.gm_wm.mgh -b -f ./lh.intensity.stats subj1 lh

 I didn't get intensity results, rather than mean thickness, area and curvature 
in this region. I got the same results in above command using "-t lh.thickness" 
instead of "-t subj1/surf/lh.gm_wm.mgh".

It looks like it didn't read the information of "lh.gm_wm.mgh", even I used "-t 
subj1/surf/lh.gm_wm.mgh".

I didn't find other appropriate flags which could instead of "-t".

Do you know how to fix this problem?

Thanks for your help!

Regards

Li





From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Monday, December 03, 2012 2:51 PM
To: Kong, Li
Cc: Freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Calculatin​g the mean intensity ratio in one specific 
region

Hi Li


save it as a .mgz volume and use mris_anatomical_stats with the
parcellation you want.

cheers
Bruce
On Mon, 3 Dec 2012, Kong, Li wrote:

>
> Hello everyone,
>
>
>
>
>
> I got grey matter/ white matter intensity ratio at each vertex across the
> cortex. I would like to know the mean intensity ratio in one region (ex,
> superior temporal gyrus).
>
>
>
>
>
> Anyone knows how to get it?
>
>
>
>
>
> Thanks in advance!
>
>
>
> Li
>
>
>


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

[Freesurfer] Insula missing

2012-12-03 Thread José Ángel Pineda
Dear experts,

I am registering cortical labels from Talairach coordinates to my native
T1. For doing this, I have run the next script lines:


tkregister --targ brainmask.mgz --mov highres_brain.nii.gz --reg
T1FS2Highres.dat --regheader --noedit

mri_label2vol --annot rh.aparc.annot --temp highres_brain.nii.gz --reg
T1FS2Highres.dat --o rh_aparc.nii.gz --hemi rh --subject FS --proj frac 0 1
.1 --fillthresh .3

and the same for the left hemi.

However I am finding two problems at the result. First Insula is missing
for both hemispheres, and second the cortical ROIs have the shape of the
figure attached, e.g. there are many voxels empty

[image: Imágenes integradas 1]

I found in previous topics, that the mri_label2vol, was updated as it left
last volume from the list out of the conversion. I tried to download it,
but it is just compiled for linux, and since Im working with mac I am not
able to run it. Could you please give me any comments to solve the problem
with the missing voxels.
About the problem with the insula, the other option is to just extract it
with mri_annotation2label, but if I could get the mri_label2vol working
correctly it would be better.

Thanks a lot

Jose

-- 

José Angel Pineda Pardo

Center of Biomedical Technology (CTB)

Parque Científico y Tecnológico de la UPM

Campus de Montegancedo

28223 Pozuelo de Alarcón, Madrid, ES
<>___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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
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] hippocampal subfield segmentation

2012-12-03 Thread Antonella Kis
Dear FS team,

I would like to know if there is any options to get the 

hippocampal subfield segmentation so I can get the volume for each segmentation 
if I

was running only recon-all for all my subjects or I need to re-run recon-all 
but with a 
hippocampal subfield segmentation option this time?


Many thanks,
Antonella
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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
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.


Re: [Freesurfer] hippocampal subfield segmentation

2012-12-03 Thread Juan Eugenio Iglesias
Hi Antonella,
Just run recon-all with the flag "-hippo-subfields" but without the flag
"-all" (otherwise you'll be rerunning a lot of stuff you do not need to
rerun):
DO: recon-all -s bert -hippo-subfields
DON'T DO: recon-all -s bert -all -hippo-subfields
Kind regards,
/Eugenio


On Mon, 2012-12-03 at 08:39 -0800, Antonella Kis wrote:
> Dear FS team,
> 
> 
> I would like to know if there is any options to get the 
> hippocampal subfield segmentation so I can get the volume for each 
> segmentation if I
> 
> was running only recon-all for all my subjects or I need to re-run recon-all 
> but with a 
>  hippocampal subfield segmentation option this time?
> 
> 
> Many thanks,
> Antonella 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
-
Juan Eugenio Iglesias, PhD
http://www.jeiglesias.com
igles...@nmr.mgh.harvard.edu
Athinoula A. Martinos Center for Biomedical Imaging
Department of Radiology, MGH, Harvard Medical School
149 Thirteenth Street, Suite 2301
Charlestown, Massachusetts 2129
U.S.A.


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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
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] Reducing pial and main surfaces

2012-12-03 Thread Jonathan Holt
I have not seen a lot of documentation on how to do this. I've attached two images of specific areas where I'd like to have the pial and main surfaces follow the actual surface of the brain. The aux volume OK in both of these cases. The empty space is segmented as white matter. In the past I have tried deleting the segmentation values and saving the segmentation, then running recon-all -autorecon2 -autorecon3 -s . Unfortunately it just resegmented the same areas as white matter and the issue was never resolved. I know about freeview but I do not know how to manually edit surfaces...What should I be doing here? jon___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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
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.


Re: [Freesurfer] Insula missing

2012-12-03 Thread Douglas Greve

  
  
For the missing insula problem, try using a newer version of
mri_label2vol
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2vol

The 2nd problem is not so easy to fix. You might be better off using
aparc+aseg.mgz as input to mri_label2vol instead of the surface
annotation.
doug


On 12/3/12 10:35 AM, José Ángel Pineda
  wrote:

Dear experts,
  
  I am registering cortical labels from Talairach coordinates to my
  native T1. For doing this, I have run the next script lines:
  
  
  tkregister --targ brainmask.mgz --mov highres_brain.nii.gz --reg
  T1FS2Highres.dat --regheader --noedit    
  
  mri_label2vol --annot rh.aparc.annot --temp highres_brain.nii.gz
  --reg T1FS2Highres.dat --o rh_aparc.nii.gz --hemi rh --subject FS
  --proj frac 0 1 .1 --fillthresh .3
  
  and the same for the left hemi.
  
  However I am finding two problems at the result. First Insula is
  missing for both hemispheres, and second the cortical ROIs have
  the shape of the figure attached, e.g. there are many voxels empty
  
  
  
  I found in previous topics, that the mri_label2vol, was updated as
  it left last volume from the list out of the conversion. I tried
  to download it, but it is just compiled for linux, and since Im
  working with mac I am not able to run it. Could you please give me
  any comments to solve the problem with the missing voxels. 
  About the problem with the insula, the other option is to just
  extract it with mri_annotation2label, but if I could get the
  mri_label2vol working correctly it would be better.
  
  Thanks a lot
  
  Jose
  
  -- 
  
José Angel
Pineda Pardo
Center of
Biomedical Technology (CTB)
Parque
Científico y Tecnológico de la UPM
Campus
de Montegancedo
28223
Pozuelo de Alarcón, Madrid, ES
  
  
  
  
  
  ___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


  

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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
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.


Re: [Freesurfer] Reducing pial and main surfaces

2012-12-03 Thread Bruce Fischl
Hi Jon

those are probably due to topological defects, the fixing of which forces 
the surfaces to enclose those spaces. See if you can find the source of 
the defect - I think fixing it will remove these problems. You can verify 
they are defects by looking at the filled.mgz. If the spaces aren't filling 
in it then it is a defect.


cheers
Bruce
On Mon, 3 Dec 
2012, Jonathan Holt wrote:

> I have not seen a lot of documentation on how to do this. I've attached two 
> images of specific areas where I'd like to have the pial and main surfaces 
> follow the actual surface of the brain. The aux volume OK in both of these 
> cases. The empty space is segmented as white matter. In the past I have tried 
> deleting the segmentation values and saving the segmentation, then running 
> recon-all -autorecon2 -autorecon3 -s . Unfortunately it just 
> resegmented the same areas as white matter and the issue was never resolved.
>
> I know about freeview but I do not know how to manually edit surfaces...
>
> What should I be doing here?
>
> jon
>
>
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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
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.



Re: [Freesurfer] Calculatin​g the mean intensity ratio in one specific region

2012-12-03 Thread Douglas Greve

Hi Li, they should not have been identical. The data under the 
"ThickAvg" column should be the value you want. This and other columns 
are mislabeled when thickness is not the actual input (eg, GrayVol is 
meaningless). You might prefer to use mri_segstats, something like

mri_segstats --slabel subject lh lh.superiortemporal.label --i 
lh.gm_wm.mgh --o gm_wm.sum.dat --excludeid 0

doug



On 12/3/12 10:12 AM, Kong, Li wrote:
> Hi Bruce,
>
> Thanks for your answer!
>
> I tried mris_anatomical_stats command, but I met problems:
> (1) I would like to get the mean intensity ratio of the superior temporal, so 
> I need a label of this region.
>   I first used mri_annotation2label to get lh.superiortemporal.label file.
>
> (2) Then I used mris_anatomical_stats command as following (I saved GM/WM 
> intensity ratio as lh.gm_wm.mgh):
>  mris_anatomical_stats -l label/lh.superiortemporal.label -t 
> subj1/surf/lh.gm_wm.mgh -b -f ./lh.intensity.stats subj1 lh
>
>   I didn't get intensity results, rather than mean thickness, area and 
> curvature in this region. I got the same results in above command using "-t 
> lh.thickness" instead of "-t subj1/surf/lh.gm_wm.mgh".
>
> It looks like it didn't read the information of "lh.gm_wm.mgh", even I used 
> "-t subj1/surf/lh.gm_wm.mgh".
>
> I didn't find other appropriate flags which could instead of "-t".
>
> Do you know how to fix this problem?
>
> Thanks for your help!
>
> Regards
>
> Li
>
>
>
>
> 
> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
> Sent: Monday, December 03, 2012 2:51 PM
> To: Kong, Li
> Cc: Freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Calculatin​g the mean intensity ratio in one 
> specific region
>
> Hi Li
>
>
> save it as a .mgz volume and use mris_anatomical_stats with the
> parcellation you want.
>
> cheers
> Bruce
> On Mon, 3 Dec 2012, Kong, Li wrote:
>
>> Hello everyone,
>>
>>
>>
>>
>>
>> I got grey matter/ white matter intensity ratio at each vertex across the
>> cortex. I would like to know the mean intensity ratio in one region (ex,
>> superior temporal gyrus).
>>
>>
>>
>>
>>
>> Anyone knows how to get it?
>>
>>
>>
>>
>>
>> Thanks in advance!
>>
>>
>>
>> Li
>>
>>
>>
>
> 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
>
>

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] wmparc 2 wmsurf

2012-12-03 Thread Juranek, Jenifer
I'm running FSv5.1.0 on RHEL6.

1)  My goal is to run a glm-fit on White Matter aparc regions for a 
"between group" surf-based analysis and evaluate spatial maps of significant 
differences.

2)  I noticed that fsaverage does not have a wmparc.mgz file, so I'm 
currently working with bert as my subject.

3)  I'd like to visualize each segid in the wmparc.mgz (volume-based) file 
on the white matter surface in the same subject (e.g. bert).

4)  I have been able to breakdown bert's wmparc.mgz file into separate 
masks (e.g. *.mgz) and labels (e.g. *.label) based on segid using mri_cor2label 
and mri_vol2surf. To get the vertices written into the label file, I have 
loaded each label and re-saved each label in tksurfer.
Q: Is there a better method for getting this (wmparc units moved from vol to 
surf) done (maybe using a matlab function?) Or is surf-based analysis of white 
matter not such a good idea.
Many Thanks for any assistance you can provide.
Cheers,
Jenifer
~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~
Jenifer Juranek, PhD
University of Texas at Houston
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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
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.