Re: [Freesurfer] memory allocation errors on Snow Leopard running dmri_train (fwd)

[zkauf...@nmr.mgh.harvard.edu]

Ping,

Yes, I see. We are looking into it now and will try and replicate the 
issue.

-Zeke

On 03/27/2013 05:21 PM, Ping-Hong Yeh wrote:
> Hi Zeke,
>
>   That specific subject had v5.1 recon-all run by Leopard with FS v5.1
> (another computer), but v5.2 trac-all run by Snow Leopard with FS v5.2
> . If you scroll down the log file, you will see  the
> "/Application/freesurfer", which is the v5.2 where it crashed.
>
> Anyhow I have attached the log file of another subject run by FS 5.2,
> both recon-all and trac-all.
>
> Thanks.
> ping
>
> On Wed, Mar 27, 2013 at 4:00 PM, zkauf...@nmr.mgh.harvard.edu
>  wrote:
>> Ping,
>>
>> According to line 9 of the log file you sent to Anastasia, are running
>> freesurfer version v5.1. Not version 5.2.
>>
>>
>> -Zeke
>>
>>
>>  Original Message 
>> Subject: Re: [Freesurfer] memory allocation errors on Snow Leopard running
>> dmri_train (fwd)
>> Date: Wed, 27 Mar 2013 15:17:34 -0400 (EDT)
>> From: Anastasia Yendiki 
>> To: Zeke Kaufman 
>>
>>
>>
>> -- Forwarded message --
>> Date: Wed, 27 Mar 2013 13:44:56 -0400
>> From: Ping-Hong Yeh 
>> To: Anastasia Yendiki 
>> Cc: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] memory allocation errors on Snow Leopard running
>>   dmri_train
>>
>> Hi Anastasia,
>>
>>See the attached.
>>
>> Thank you.
>> ping
>>
>>
>> On Wed, Mar 27, 2013 at 1:38 PM, Anastasia Yendiki
>>  wrote:
>>>
>>>
>>> Hi Ping - Can you send us your entire trac-all.log? There's some info in
>>> there about your system and the freesurfer build you're using that we'll
>>> need to try to replicate the problem.
>>>
>>> Thanks,
>>>
>>> a.y
>>>
>>> On Tue, 26 Mar 2013, Ping-Hong Yeh wrote:
>>>
 Hi Anastasia,

 It had the same issue before, but worked fine after installing the
 fixed dmri patch for Snow Leopard.

 Thanks.
 ping

 On Tue, Mar 26, 2013 at 5:09 PM, Anastasia Yendiki
  wrote:
>
>
>
> Hi Ping - Are you running this on the same system where you were running
> the
> 5.1 snow leopard build without a problem?
>
> a.y
>
>
> On Tue, 26 Mar 2013, Ping-Hong Yeh wrote:
>
>> Hi FS users,
>>
>> I've tested the newer Tracula FS 5.2 on Snow Leopard and ran into
>> errors. The 5.2 recon-all of T1 was finished ok.
>>
>> Here is the final part of log file.
>>
>> #@# Priors Tue Mar 26 14:39:36 EDT 2013
>> /apps/freesurfer/bin/dmri_train --outdir
>> /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/mni --out
>> lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt
>> lh.ilf_AS_avg33_mni_flt rh.ilf_AS_avg33_mni_flt
>> lh.unc_AS_avg33_mni_flt rh.unc_AS_avg33_mni_flt
>> fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt
>> lh.atr_PP_avg33_mni_flt rh.atr_PP_avg33_mni_flt
>> lh.cab_PP_avg33_mni_flt rh.cab_PP_avg33_mni_flt
>> lh.ccg_PP_avg33_mni_flt rh.ccg_PP_avg33_mni_flt
>> lh.slfp_PP_avg33_mni_flt rh.slfp_PP_avg33_mni_flt
>> lh.slft_PP_avg33_mni_flt rh.slft_PP_avg33_mni_flt --slist
>> /tmp/subj33.NCNC2348.61836.txt --trk dlabel/mni/lh.cst_AS.flt.trk
>> dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk
>> dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk
>> dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk
>> dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk
>> dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk
>> dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk
>> dlabel/mni/rh.ccg_PP.flt.trk dlabel/mni/lh.slfp_PP.flt.trk
>> dlabel/mni/rh.slfp_PP.flt.trk dlabel/mni/lh.slft_PP.flt.trk
>> dlabel/mni/rh.slft_PP.flt.trk --seg dlabel/mni/aparc+aseg.nii.gz
>> --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0
>> 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.flt.nii.gz
>> dlabel/mni/lh.cst_AS_roi2.flt.nii.gz
>> dlabel/mni/rh.cst_AS_roi1.flt.nii.gz
>> dlabel/mni/rh.cst_AS_roi2.flt.nii.gz
>> dlabel/mni/lh.ilf_AS_roi1.flt.nii.gz
>> dlabel/mni/lh.ilf_AS_roi2.flt.nii.gz
>> dlabel/mni/rh.ilf_AS_roi1.flt.nii.gz
>> dlabel/mni/rh.ilf_AS_roi2.flt.nii.gz
>> dlabel/mni/lh.unc_AS_roi1.flt.nii.gz
>> dlabel/mni/lh.unc_AS_roi2.flt.nii.gz
>> dlabel/mni/rh.unc_AS_roi1.flt.nii.gz
>> dlabel/mni/rh.unc_AS_roi2.flt.nii.gz
>> dlabel/mni/fmajor_PP_roi1.flt.nii.gz
>> dlabel/mni/fmajor_PP_roi2.flt.nii.gz
>> dlabel/mni/fminor_PP_roi1.flt.nii.gz
>> dlabel/mni/fminor_PP_roi2.flt.nii.gz
>> dlabel/mni/lh.atr_PP_roi1.flt.nii.gz
>> dlabel/mni/lh.atr_PP_roi2.flt.nii.gz
>> dlabel/mni/rh.atr_PP_roi1.flt.nii.gz
>> dlabel/mni/rh.atr_PP_roi2.flt.nii.gz
>> dlabel/mni/lh.cab_PP_roi1.flt.nii.gz
>> dlabel/mni/lh.cab_PP_roi2.flt.nii.gz
>> dlabel/mni/rh.cab_PP_roi1.flt.nii.gz
>> dlabel/mni/rh.cab_PP_roi2.flt.nii.gz
>> dlabel/mni/lh.ccg_PP_roi1.flt.nii.gz
>> dlabel/mni/lh.ccg_PP_roi2.flt.nii.gz
>> dlabel/mn

Re: [Freesurfer] error during trac-all -prep

[Jon Wieser]

attached is the dmrirc config file

- Original Message -
From: "Jon Wieser" 
To: "freesurfer" 
Sent: Wednesday, March 27, 2013 3:33:03 PM
Subject: [Freesurfer] error during trac-all -prep

i ran 
trac-all -prep -c dmrirc_single_subject
 and got the error : 

fslmaths 
/BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1223/freesurfer/dlabel/anatorig/anat_brain_mask.nii.gz
 -mul 
/BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1223/freesurfer/dlabel/anatorig/notventricles.nii.gz
 
/BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1223/freesurfer/dlabel/anatorig/anat_brain_mask-vent.nii.gz
Image Exception : #3 :: Attempted to multiply images/ROIs of different sizes
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Abort 


I have attached the trac-all .log and trac-all.error  files

I don't know how to fix this error


Thanks
Jon
-- 
Jon Wieser
Research Specialist
UW-Milwaukee
Psychology Department, Pearse Hall Rm 366
2441 East Hartford Ave
Milwaukee, WI 53211
Phone: 414-229-7145
Fax: 414-229-5219
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-- 
Jon Wieser
Research Specialist
UW-Milwaukee
Psychology Department, Pearse Hall Rm 366
2441 East Hartford Ave
Milwaukee, WI 53211
Phone: 414-229-7145
Fax: 414-229-5219


dmrirc_single_subject
Description: Binary data
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Re: [Freesurfer] Admin: Please unsubscribe this email address

[Lilla Zollei]

Hi Maish,

You can just go to

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

and unsubscribe your email address.

Lilla

On Wed, 27 Mar 2013, Dalwani, Manish wrote:

> Hello Admin,
> 
> Please unsubscribe this email address.
> 
> Regards,
> Manish
>
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[Freesurfer] Admin: Please unsubscribe this email address

[Dalwani, Manish]

Hello Admin,

Please unsubscribe this email address.

Regards,
Manish
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Re: [Freesurfer] specifying random effects in LME (Linear Mixed Effects models)

[jorge luis]

Hi Francois
 
If you want to test the model with
three random effects including intercept, time, and time*time as the
random effects then you should use [1 2 3] (these are the columns
corresponding to those covariates in X). Actually, for the example in
the wiki page we first tested [1 2 3] but the model [1 2] was the
best at most vertices.  In general, you need more than 4 repeated
measures to think of including three random effects in the model for
the covariance. Otherwise two random effects are usually enough (you
can still include time*time in the model for the mean as in the wiki
). Also, computation time increases quickly with the number of random
effects.

There is an oncoming paper that will
expand more on our longitudinal mass-univariate analyses with lme
(hopefully soon).

Best
-Jorge






>
> De: "Lalonde, Francois (NIH/NIMH) [E]" 
>Para: "freesurfer@nmr.mgh.harvard.edu"  
>Enviado: Miércoles 27 de marzo de 2013 15:20
>Asunto: [Freesurfer] specifying random effects in LME (Linear Mixed Effects 
>models)
> 
>I am following the wiki page for LME analysis and I have a quick question.  
>The Mass-univariate example near the bottom of the page proposes an initial 
>model that contains intercept, linear and quadratic terms as random effects.  
>However, the examples just below for lme_mass_fit_EM_init(),  
>lme_mass_fit_EM_Rgw() only have [1 2] as selected random effects.  Should the 
>vector Zcols contain [1 2 3] as selected random effects in order to test the 
>proposed model?
>
>Thanks,
>Francois
>
>François Lalonde, Ph.D.
>Child Psychiatry Branch
>NIMH / NIH
>10 Center Drive, Room 3N202
>Bethesda, MD  20892
>
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>
>The information in this e-mail is intended only for the person to whom it is
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>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.
>
>
>
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[Freesurfer] Fwd: Re: memory allocation errors on Snow Leopard running dmri_train (fwd)

[zkauf...@nmr.mgh.harvard.edu]

Ping,

According to line 9 of the log file you sent to Anastasia, are running 
freesurfer version v5.1. Not version 5.2.

-Zeke


 Original Message 
Subject: Re: [Freesurfer] memory allocation errors on Snow Leopard 
running dmri_train (fwd)
Date: Wed, 27 Mar 2013 15:17:34 -0400 (EDT)
From: Anastasia Yendiki 
To: Zeke Kaufman 



-- Forwarded message --
Date: Wed, 27 Mar 2013 13:44:56 -0400
From: Ping-Hong Yeh 
To: Anastasia Yendiki 
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] memory allocation errors on Snow Leopard running
  dmri_train

Hi Anastasia,

   See the attached.

Thank you.
ping


On Wed, Mar 27, 2013 at 1:38 PM, Anastasia Yendiki
 wrote:
>
> Hi Ping - Can you send us your entire trac-all.log? There's some info in
> there about your system and the freesurfer build you're using that we'll
> need to try to replicate the problem.
>
> Thanks,
>
> a.y
>
> On Tue, 26 Mar 2013, Ping-Hong Yeh wrote:
>
>> Hi Anastasia,
>>
>> It had the same issue before, but worked fine after installing the
>> fixed dmri patch for Snow Leopard.
>>
>> Thanks.
>> ping
>>
>> On Tue, Mar 26, 2013 at 5:09 PM, Anastasia Yendiki
>>  wrote:
>>>
>>>
>>> Hi Ping - Are you running this on the same system where you were running
>>> the
>>> 5.1 snow leopard build without a problem?
>>>
>>> a.y
>>>
>>>
>>> On Tue, 26 Mar 2013, Ping-Hong Yeh wrote:
>>>
 Hi FS users,

 I've tested the newer Tracula FS 5.2 on Snow Leopard and ran into
 errors. The 5.2 recon-all of T1 was finished ok.

 Here is the final part of log file.

 #@# Priors Tue Mar 26 14:39:36 EDT 2013
 /apps/freesurfer/bin/dmri_train --outdir
 /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/mni --out
 lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt
 lh.ilf_AS_avg33_mni_flt rh.ilf_AS_avg33_mni_flt
 lh.unc_AS_avg33_mni_flt rh.unc_AS_avg33_mni_flt
 fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt
 lh.atr_PP_avg33_mni_flt rh.atr_PP_avg33_mni_flt
 lh.cab_PP_avg33_mni_flt rh.cab_PP_avg33_mni_flt
 lh.ccg_PP_avg33_mni_flt rh.ccg_PP_avg33_mni_flt
 lh.slfp_PP_avg33_mni_flt rh.slfp_PP_avg33_mni_flt
 lh.slft_PP_avg33_mni_flt rh.slft_PP_avg33_mni_flt --slist
 /tmp/subj33.NCNC2348.61836.txt --trk dlabel/mni/lh.cst_AS.flt.trk
 dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk
 dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk
 dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk
 dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk
 dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk
 dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk
 dlabel/mni/rh.ccg_PP.flt.trk dlabel/mni/lh.slfp_PP.flt.trk
 dlabel/mni/rh.slfp_PP.flt.trk dlabel/mni/lh.slft_PP.flt.trk
 dlabel/mni/rh.slft_PP.flt.trk --seg dlabel/mni/aparc+aseg.nii.gz
 --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0
 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.flt.nii.gz
 dlabel/mni/lh.cst_AS_roi2.flt.nii.gz
 dlabel/mni/rh.cst_AS_roi1.flt.nii.gz
 dlabel/mni/rh.cst_AS_roi2.flt.nii.gz
 dlabel/mni/lh.ilf_AS_roi1.flt.nii.gz
 dlabel/mni/lh.ilf_AS_roi2.flt.nii.gz
 dlabel/mni/rh.ilf_AS_roi1.flt.nii.gz
 dlabel/mni/rh.ilf_AS_roi2.flt.nii.gz
 dlabel/mni/lh.unc_AS_roi1.flt.nii.gz
 dlabel/mni/lh.unc_AS_roi2.flt.nii.gz
 dlabel/mni/rh.unc_AS_roi1.flt.nii.gz
 dlabel/mni/rh.unc_AS_roi2.flt.nii.gz
 dlabel/mni/fmajor_PP_roi1.flt.nii.gz
 dlabel/mni/fmajor_PP_roi2.flt.nii.gz
 dlabel/mni/fminor_PP_roi1.flt.nii.gz
 dlabel/mni/fminor_PP_roi2.flt.nii.gz
 dlabel/mni/lh.atr_PP_roi1.flt.nii.gz
 dlabel/mni/lh.atr_PP_roi2.flt.nii.gz
 dlabel/mni/rh.atr_PP_roi1.flt.nii.gz
 dlabel/mni/rh.atr_PP_roi2.flt.nii.gz
 dlabel/mni/lh.cab_PP_roi1.flt.nii.gz
 dlabel/mni/lh.cab_PP_roi2.flt.nii.gz
 dlabel/mni/rh.cab_PP_roi1.flt.nii.gz
 dlabel/mni/rh.cab_PP_roi2.flt.nii.gz
 dlabel/mni/lh.ccg_PP_roi1.flt.nii.gz
 dlabel/mni/lh.ccg_PP_roi2.flt.nii.gz
 dlabel/mni/rh.ccg_PP_roi1.flt.nii.gz
 dlabel/mni/rh.ccg_PP_roi2.flt.nii.gz
 dlabel/mni/lh.slfp_PP_roi1.flt.nii.gz
 dlabel/mni/lh.slfp_PP_roi2.flt.nii.gz
 dlabel/mni/rh.slfp_PP_roi1.flt.nii.gz
 dlabel/mni/rh.slfp_PP_roi2.flt.nii.gz
 dlabel/mni/lh.slft_PP_roi1.flt.nii.gz
 dlabel/mni/lh.slft_PP_roi2.flt.nii.gz
 dlabel/mni/rh.slft_PP_roi1.flt.nii.gz
 dlabel/mni/rh.slft_PP_roi2.flt.nii.gz --bmask


 /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/mni/aparc+aseg_mask.nii.gz
 --fa
 /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dmri/dtifit_FA.nii.gz
 --cptdir /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/diff
 --reg

 /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dmri/xfms/mni2diff.flt.mat
 --ncpts 10 --trunc


 cwd /Users/twbrkmp2
 cmdline /apps/freesurfer/bin/dmri_train --outdir
 /Vo

[Freesurfer] Use a SPM roi to extract thickness measurements

[McMains, Stephanie]

Hi all,

I have been trying to take an SPM volume and extract FS thickness measurements.

I think I successfully took my spm volume from mni152 to fsaverage space 
(mni305) via the command line:

mri_vol2vol --mov $FREESURFER_HOME/subjects/fsaverage/mri.2mm/mni305.cor.mgz 
--targ RTPJ_9mm_001_10_64_-54_16.img --reg 
$FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --inv --o  
$SUBJECTS_DIR/2506/mri/RTPJ_mni305_9mm_001_10_64_-54_16.nii.gz

Then I turned it into an ROI:

mri_binarize --i $SUBJECTS_DIR/2506/mri/RTPJ_mni305_9mm_001_10_64_-54_16.nii.gz 
--o $SUBJECTS_DIR/2506/mri/RTPJ_mni305_roi_9mm_001_10_64_-54_16.nii.gz --min 
.01

> From here I figured I could map it to the fsaverage surface (mri_vol2surf) 
> and extract thickness measurements (mri_segstats using 
> rh.thickness.fsaverage.mgh) as suggested in the volume roi cortical thickness 
> workflow. However, some of my ROIs don't show up after I transform them.  
> From what I can tell, this is because they don't intersect with the fsaverage 
> surface.  

My thinking was that it might be better to stay within the individual subject 
space.  So I would:

1. transform ROI to subject space
2. extract thickness values from rh.thickness  

However, I am struggling to get the roi into single subject space.  I feel like 
this transform (or the inverse of it) should exist because I put all my 
subjects into fsaverage space via the -qcache flag, but i couldn't tell what to 
use.

So I tried:

fslregister --s 2506 --mov $SUBJECTS_DIR/fsaverage/mri/brainmask.mgz --reg 
$SUBJECTS_DIR/2506/fsaverage_to_indiv.dat

But the registration doesn't look all that good.  I am not sure if this is 
because the fsaverage is 'smoothed' or what.

And then I am at a loss for how to put my roi into individual space and then 
extract thickness, or even if this is the right approach.

Thanks,
Stephanie


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Re: [Freesurfer] view retinotopy results in version 5

[Y.V. Jiang]

Hi Doug,

It worked very well, thank you so much!

For future references, these are the commands I put in with this new
version of rtview (under the folder bold):

Polar angle:
rtview --lh --polar --real rtopy.self.lh/polar/real.nii.gz --imag
rtopy.self.lh/polar/imag.nii.gz --fsig rtopy.self.lh/polar/fsig.nii.gz --s
MySubjectNameInAnatomicalFolder --flat

Eccentricity:
rtview --lh --eccen --real rtopy.self.lh/eccen/real.nii.gz --imag
rtopy.self.lh/eccen/imag.nii.gz --fsig rtopy.self.lh/eccen/fsig.nii.gz --s
MySubjectNameInAnatomicalFolder --flat

I compared the results from Version 5's rtview (see above) and Version 4's
surf-sess from the same participant. The resulting maps were highly
consistent. The only difference is that the colors were more scattered in
Version 4, making it harder to identify the borders between regions.

-Yuhong

On Wed, Mar 27, 2013 at 2:35 PM, Douglas N Greve
wrote:

> Hi Yuhong, I put a new version that has a --flat and --patch option here:
>
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/rtview
>
> I have not tested it because I don't have any retinotopy handy. Can you
> test it and let me know whether it works?
>
> doug
>
>
> On 03/26/2013 03:00 PM, Y.V. Jiang wrote:
> > Hi,
> >
> > I was able to view retinotopic mapping results using rtview in version
> > 5. However, the display was on the inflated surface. Is there a way to
> > view the results on the flattened occipital map, similar to version
> > 4's surf-sess -flat?
> >
> > Thanks!
> >
> > -Yuhong
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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>
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>
>
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> addressed. If you believe this e-mail was sent to you in error and the
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Re: [Freesurfer] surf2vol

[Douglas N Greve]

it sounds like the problem is in label2surf. Where did that come from?

On 03/27/2013 12:09 PM, Daniel Lumsden wrote:
> Doug
>
> When I try to overlay the .gii files on the orig volume I get the 
> following message:
>
> "Either this surface does not contain valid volume geometry 
> information, or freeview failed to read the information. This surface 
> may not align with volumes and other surfaces"
>
>
> I presume this means there is a problem with how I've generated the 
> .gi files? I'm happy the lh.anatomicalregion.label files are working 
> fine because I can generate volumetric masks from them.
>
>
> To get the .gii files I've taken the rh.white and lh.white from the 
> surf folder and copied them into the folder I'm running the terminal 
> in. I'm then using the command:
>
>
> mris_convert rh.white rh.white.asc
>
>
> Then:
>
>
> echo lh.frontallobe.label > left_frontal_lobe.txt
>
>
> (which checking gives me a text file of that name with one line, 
> lh.frontallobe.label)
>
>
> Then:
>
>
> label2surf -s lh.white.asc -l left_frontal_lobe.txt -o 
> left_frontal_lobe.gii
>
>
> All of the named files are in the same folder.
>
>
>
> Thank you again. Confusingly, it does seem like probtrackx is doing 
> something with the .gii files!
>
>
> Dan
>
>
> Sorry, I meant does the left_frontal_lobe.gii overlay properly on the orig
> volume?
> doug
> On 03/27/2013 04:41 AM, Daniel Lumsden wrote:
> > Doug
> >
> > The .nii.gz file is completely empty and doesn't come up on any viewer
> > (fslview, tkmedit, freeview, mricron etc). The .gi files I've
> > generated appear to be tracking in probtrackx (though slowly on my
> > laptop - probably not expected given the sizes of the surfaces). I can
> > also generate binary volumetric masks from the labels using
> > mri_binarize (though they are a little bit "speckled" - with scattered
> > blank voxels).
> >
> > On my installation I'm having some intermittent difficulties with
> > tkmedit and tksurfer (not consistently opening, sometimes coming up
> > with "bus error"). Freeview is opening consistently though. I'm not
> > sure if this could be having an affect but I was planning on
> > reinstalling freesurfer today to see if that fixed it.
> >
> > Thank you again for your help
> >
> > Dan
> >
> > Does leftfrontallobe.nii.gz overlay properly in tkmedit? eg,
> > tkmedit subject orig.mgz -surfs -overlay leftfrontallobe.nii.gz -fminmax
> > .5 1
> > doug
> > On 03/26/2013 07:20 AM, Daniel Lumsden wrote:
> > > Bruce
> > >
> > > Many thanks - that's given me a lot more guidance. Following the help,
> > > i've put together the command below:
> > >
> > > mri_surf2vol --hemi lh --template /orig.mgz --outvol  > > where I want the file>/leftfrontallobe.nii.gz --surfval  > > to>/left_frontal_lobe.gii --fillribbon --volregidentity mov07
> > >
> > > Where mov07 is my subjid and left_frontal_lobe.gii is the surface I've
> > > generated from the label files to run in probtrakx. This command runs,
> > > but produces and empty nifti file. I've changed the output to .mgz
> > > with similar effect. I've substituted the rawavg.mgz file for the
> > > orig.mgz file, and tried both .nii.gz and .mgz versions of both files
> > > and still get an empty output file.  The subject is in my $SUBJECTS_DIR.
> > >
> > > Is there a way to check the .gii files? I generated them using
> > > label2surf, having used mris_convert to convert the lh.white and
> > > rh.white files from the surf folder for my subject to lh.white.asc and
> > > rh.white.asc.
> > >
> > > Thank you again for your help.
> > >
> > > Dan
> > >
> > >
> > > > Date: Mon, 25 Mar 2013 14:59:28 -0400
> > > > From: fis...@nmr.mgh.harvard.edu
> > > > To: doclums...@hotmail.com
> > > > CC: freesurfer@nmr.mgh.harvard.edu
> > > > Subject: Re: [Freesurfer] surf2vol
> > > >
> > > > Hi Dan
> > > >
> > > > try using mri_surf2vol instead (it has a much bigger help, thanks to
> > > > Doug0
> > > > Bruce
> > > > On Mon, 25 Mar 2013, Daniel Lumsden wrote:
> > > >
> > > > > Dear All
> > > > >
> > > > > Apologies for what I'm sure is a very basic question. I'm new to
> > > using freesurfer, and would like to generate cortical
> > > > > parcellations for running in probtrakx. I have followed the
> > > instructions from various sources and have managed to generate the
> > > > > parcellations from recon-all, extract the label files from the
> > > parcellation, then use mri_mergelabels and label2surf to generate
> > > > > the  the .gii files needed for probtrakx. I'd like to be able to
> > > display the surface files for illustrative purposes, but I'm
> > > > > struggling to apply the surf2vol command.
> > > > >
> > > > > From the terminal window I can see that the commands required are:
> > > > >
> > > > > surf2vol
> > > > >
> > > > > I presume that  is the .gii file I'm trying to visualise,
> > > and  is to specify the name of the output volume the
> > > > > command will generate, but what should I be using as the ?
> > > I would be very grateful for any guid

Re: [Freesurfer] Xhemi stat questions

[Douglas N Greve]

If you use

thick = fast_vol2mat(MRIread('file.mgh'));
thick will be a matrix of nsubjects-by-nvertices.

Note that the vertex indices from labels are 0-based whereas matlab 
expects 1-based.

doug


On 03/27/2013 09:08 AM, Gabriel Gonzalez Escamilla wrote:
> That makes much more sense than the thing I was looking for.
>
> Now I have a problem reading the lh.lh-rh.thickness.mgh with the 
> load_mgh.m function, as I have no idea of how to read it to get the 
> vertex by vertex thickness value of each subject.
>
> I tryed as [thick, ~,~,~]=load_mgh('file.mgh',[],[1:nSubjs])
> then reading: subjIDthick=thick(vtxID,1,1,subjID);
> where vtxID es the vertex of the .label file I want, and subjID is the 
> number of the subject.
> is that correct?
>
> All this is because I will use it as a covariate in the statistical 
> analysis as suggested in
> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg27129.html
>
>
> Regards,
> Gabriel.
>
>
>
> El 26/03/13, *Douglas N Greve *  escribió:
>> Unless you specifically need them for an individual, you should get them
>> from lh.lh-rh.thickness.mgh because that data is sampled onto the
>> symmetric template and so should be unbiased (ie, it will not
>> systematically favor lh or rh).
>> doug
>>
>>
>> On 03/26/2013 12:40 PM, Gabriel Gonzalez Escamilla wrote:
>> > Dear Doug,
>> >
>> > I meant of a given subject,
>> >
>> > But, As I'm thinking about this, I'm wondering if it has sense to have
>> > left and right cortical thickness of my every individual subjects, or
>> > if I should obtain the lh-rh thickness differences for the individuals?
>> >
>> > I suppose that I should read the lh.lh-rh.thickness.mgh created by
>> > mris_preproc to get the average differences in lh-rh hemispheres.
>> >
>> >
>> >
>> > Regards,
>> > Gabriel
>> >
>> >
>> >
>> >
>> > El 25/03/13, *Douglas N Greve *  escribió:
>> >>
>> >> Do you mean you want the right hemi thicknesses on the left hemisphere
>> >> of a given subject or on the fsaverage_sym?
>> >> doug
>> >>
>> >>
>> >> On 03/25/2013 11:25 AM, Gabriel Gonzalez Escamilla wrote:
>> >> > Thank you, so I'm keeping the one I had.
>> >> >
>> >> > Sorry for my bad explanation. When I do a normal cortical thickness
>> >> > study, I know the average thickness for a label, e.g. cortex, 
>> and the
>> >> > values at each vertex of each hemisphere are stored in
>> >> > $subject/surf/?l.thickness. I would like to know if it is 
>> possible to
>> >> > obtain the same cortical thickness measure from the lh-rh registered
>> >> > hemispheres of each subject.
>> >> >
>> >> >
>> >> > Regards,
>> >> > Gabriel
>> >> >
>> >> >
>> >> > El 25/03/13, *Douglas N Greve *  
>> escribió:
>> >> >>
>> >> >> On 03/25/2013 10:52 AM, Gabriel Gonzalez Escamilla wrote:
>> >> >> >Thanks a lot for your answer,
>> >> >> >
>> >> >> >I'm sending you attached the diff of the two mris_preproc.
>> >> >> Those differences are just added features and won't change your
>> >> results.
>> >> >> >
>> >> >> >When I wrote CT, I was meaning cortical thickness, as normally 
>> this
>> >> >> values are in surf/?h.thickness, But how do I know the
>> >> >> Xhemi-registered thickness values of each subject for lh-rh, or 
>> area
>> >> >> or any of those indices?
>> >> >> I'm not sure what you mean. When you run mris_preproc, you specify
>> >> >> whether you want thickness, etc.
>> >> >> doug
>> >> >> >
>> >> >> >Regards,
>> >> >> >Gabriel
>> >> >> >
>> >> >> >
>> >> >> >El 25/03/13, *Douglas N Greve *  
>> escribió:
>> >> >> >>
>> >> >> >>On 03/22/2013 06:45 AM, Gabriel Gonzalez Escamilla wrote:
>> >> >> >>> Dear Doug,
>> >> >> >>>
>> >> >> >>> I've seen that you restore the files to download, for the Xhemi
>> >> >> >>> registration. While I'm checking for the statistical 
>> process, I've
>> >> >> >>> seen that the one I have is: Date: 2012/12/06 16:06:52, 
>> Revision:
>> >> >> >>> 1.59.2.4, and the one that is on your ftp server is Date:
>> >> 2012/12/06
>> >> >> >>> 16:06:17, Revision: 1.66, So mine is a lower version but
>> >> recent hour,
>> >> >> >>> and the actual is newer version but seems that was created
>> >> before the
>> >> >> >>> one I have. My question is, Which one should I keep?
>> >> >> >>Can you send me a diff of the two files?
>> >> >> >>>
>> >> >> >>>  If I change the mris_precproc version. Shall I re-run this 
>> step
>> >> >> >>> before statistical analyses, to create a new
>> >> >> lh.lh-rh.thickness.sm00.mgh?
>> >> >> >>>
>> >> >> >>> On the other hand I have some doubts about the statistical
>> >> procedure.
>> >> >> >>> It's supposed that if I apply the Xhemi registration, as
>> >> result the
>> >> >> >>> left and right hemispheres are equals to each other on every
>> >> >> subject, so:
>> >> >> >>>
>> >> >> >>> A) Where can I get the CT values after the Xhemi 
>> registration to
>> >> >> >>> FSaverage_sym for the left and right hemispheres?
>> >> >> >>what are CT values?
>> >> >> >>>
>> >> >> >>>
>> >> >> >>> B) Given that I have two groups, Patients and Contr

Re: [Freesurfer] Correlation with cortical thickness

[MCLAREN, Donald]

Here is a link describing the difference in the methods:
http://onlinelibrary.wiley.com/store/10.1046/j.1365-2656.2002.00618.x/asset/j.1365-2656.2002.00618.x.pdf?v=1&t=heswinwb&s=dce1a222e16e861d105340fd919c65fb43dc39ac

Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=
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On Wed, Mar 27, 2013 at 3:39 PM, Douglas N Greve
wrote:

>
> In the 2nd option, age and weight (and other variables) are
> simultaneously fit to the data. Most people refer to this as "regressing
> out" the effect of one variable when looking at the other. But it is not
> regressing out age and then looking at the correlation of age with the
> residual.
> doug
>
>
> On 03/27/2013 07:02 AM, Martijn Steenwijk wrote:
> > Dear all,
> >
> > I've a question regarding computing correlations with cortical
> > thicknesses on the surface; Suppose I have two variables for each
> > subject: (age and weight) and I want to compute the correlation
> > between cortical thickness and weight, corrected for age.
> >
> > Option 1:
> > Fsgd contains: Variables weight
> > Contrast file contains: 0 1
> >
> > Option 2:
> > Fsgd contains: Variables age weight
> > Contrast file contains: 0 0 1
> >
> > Is it true that the effect of age is regressed out in the second
> > option; and it computes the correlation between CT and weight after
> > correcting for age?
> >
> > Best,
> > Martijn
> >
> >
> >
> > ___
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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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
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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
> 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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Re: [Freesurfer] Correlation with cortical thickness

[Douglas N Greve]

In the 2nd option, age and weight (and other variables) are 
simultaneously fit to the data. Most people refer to this as "regressing 
out" the effect of one variable when looking at the other. But it is not 
regressing out age and then looking at the correlation of age with the 
residual.
doug


On 03/27/2013 07:02 AM, Martijn Steenwijk wrote:
> Dear all,
>
> I've a question regarding computing correlations with cortical 
> thicknesses on the surface; Suppose I have two variables for each 
> subject: (age and weight) and I want to compute the correlation 
> between cortical thickness and weight, corrected for age.
>
> Option 1:
> Fsgd contains: Variables weight
> Contrast file contains: 0 1
>
> Option 2:
> Fsgd contains: Variables age weight
> Contrast file contains: 0 0 1
>
> Is it true that the effect of age is regressed out in the second 
> option; and it computes the correlation between CT and weight after 
> correcting for age?
>
> Best,
> Martijn
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] Fwd: Cortical thickness in average space

[Douglas N Greve]

what is the size of the 4D matrix?

On 03/27/2013 05:41 AM, Rafa X wrote:
> Thanks Bruce for your answer, as you asked I'm forwarding this
> question to the list in case any other can answer this.
>
> We already have the surface generated by mri_preproc, now we are
> trying to read it using the matlab function read_mgh. It returns a 4-D
> matrix, how can we interpret this data to get the cortical thickness
> values at each vertex of every subject?
>
> Rafa & Gabi
>
> 2013/3/26 Bruce Fischl :
>> Hi Rafa and Gabi
>>
>> yes, that's pretty much what the -qcache flag does in recon-all. Or you can
>> use mri_surf2surf to do it.
>>
>> cheers
>> Bruce
>>
>> On Tue, 26 Mar 2013, Rafa X wrote:
>>
>>> Hi Freesurfers,
>>> We would need to obtain the cortical thickness of each subject in the
>>> space of the average subject (built from our subject population), Does
>>> it exists?
>>> If so, Can I use the label files produced by mri_surfcluster to
>>> directly extract the mean cortical thickness of each ROI in each
>>> subject? We want to avoid to trasform each cluster to every subject.
>>>
>>> Thank you all in advance,
>>> Rafa & Gabi.
>>> ___
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>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>>
>>
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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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MGH-NMR Center
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Re: [Freesurfer] view retinotopy results in version 5

[Douglas N Greve]

Hi Yuhong, I put a new version that has a --flat and --patch option here:

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

I have not tested it because I don't have any retinotopy handy. Can you 
test it and let me know whether it works?

doug


On 03/26/2013 03:00 PM, Y.V. Jiang wrote:
> Hi,
>
> I was able to view retinotopic mapping results using rtview in version 
> 5. However, the display was on the inflated surface. Is there a way to 
> view the results on the flattened occipital map, similar to version 
> 4's surf-sess -flat?
>
> Thanks!
>
> -Yuhong
>
>
> ___
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] bbregister error with hardi data

[Douglas N Greve]

Hi Corinna, are you sure that the mri-in-hardi.nii.reg registration is 
accurate? the following should look in register:

tkregister2 --reg mri-in-hardi.nii.reg --mov mri-in-hardi.nii --surfs

doug


On 03/25/2013 06:09 PM, Corinna Bauer wrote:
> I am trying to get the V1 label to map onto my HARDI data, however, 
> the mri_label2vol registration is off. The label ends up in the 
> brainstem rather than V1. the V1 labels are in the proper location 
> when I use orig.mgz, but when I used the output from mri_vol2vol as 
> the mri-in-hardi or the hardi itself as the temp image, the location 
> of the label is off.
>
> mri_label2vol --label label/rh.V1.label --label label/lh.V1.label 
> --temp mri-in-hardi.nii --reg mri-in-hardi.nii.reg --o lindsay_v1.nii
>
>
> On Mon, Mar 25, 2013 at 4:05 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> yep, looks right
>
> On 03/25/2013 03:12 PM, Corinna Bauer wrote:
>
> Also, I now want to apply the inverse transform to move the T1
> into the HARDI space. Did I do this correctly? It looks good
> in tkregister.
>
> mri_vol2vol --mov hardi/ffiltered_func_data_01.nii.gz --targ
> mri/orig.mgz --reg register.dat --inv --o mri-in-hardi.nii
>
>
> On Mon, Mar 25, 2013 at 1:47 PM, Corinna Bauer
> mailto:corinna...@gmail.com>
> >>
> wrote:
>
> ahhh, yes, that's it. sorry my oversight.
>
> On Mon, Mar 25, 2013 at 1:45 PM, Douglas N Greve
>  
>  >> wrote:
>
> Are you sure you made the right edit? It should be
> "--fsvol
> $fsvol.mgz" It looks like you might have changed it to
> "--fsvol.mgz $fsvol"
>
>
>
> On 03/25/2013 01:30 PM, Corinna Bauer wrote:
>
> Ok I adjusted the bbregister file to say fsvol.mgz
> in the
> location you specified and got this error a bit
> later on
> in the bbregister output:
>
> setenv SUBJECTS_DIR
> /usr/local/freesurfer/subjects/symmetry
> cd /usr/local/freesurfer/subjects/symmetry/lindsay
> /usr/local/freesurfer/bin/bbregister --s lindsay --mov
> hardi/ffiltered_func_data_01.nii.gz --dti
> --init-fsl --reg
> register.dat
>
> $Id: bbregister,v 1.49.2.2 2013/02/23 01:32:22
> mreuter Exp $
> Linux lotfi 3.2.0-38-generic #61-Ubuntu SMP Tue Feb 19
> 12:18:21 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
> FREESURFER_HOME /usr/local/freesurfer
> mri_convert hardi/ffiltered_func_data_01.nii.gz
> ./tmp.bbregister.15807/template.nii
> mri_convert hardi/ffiltered_func_data_01.nii.gz
> ./tmp.bbregister.15807/template.nii
> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16
> mreuter
> Exp $
> reading from hardi/ffiltered_func_data_01.nii.gz...
> TR=17843.91, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (-0.991204, -0.025762, 0.129811)
> j_ras = (-0.0259819, 0.999662, 0)
> k_ras = (0.129768, 0.00337275, 0.991539)
> writing to ./tmp.bbregister.15807/template.nii...
> fslregister --s lindsay --mov
> ./tmp.bbregister.15807/template.nii --reg
> ./tmp.bbregister.15807/reg.init.dat --niters 1
> --maxangle
> 90 --nobetmov --tmp ./tmp.bbregister.15807/fslregister
> --dof 6 --fsvol.mgz brainmask
> ERROR: Flag --fsvol.mgz unrecognized.
> --s lindsay --mov ./tmp.bbregister.15807/template.nii
> --reg ./tmp.bbregister.15807/reg.init.dat --niters 1
> --maxangle 90 --nobetmov --tmp
> ./tmp.bbregister.15807/fslregister --dof 6 --fsvol.mgz
> brainmask
> mri_segreg --mov ./tmp.bbregister.15807/template.nii
> --init-reg ./tmp.bbregister.15807/reg.init.dat
> --out-reg
> ./tmp.bbregister.15807/bbr.pass1.dat
> --subsamp-brute 100
> --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4
> --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5
> regio_read_register(): No such file or directory
> Could not open ./tmp.bbregister.15807/reg.init.dat
> mri_segreg --mov ./tmp.bbregister.15807/template.nii
> 

Re: [Freesurfer] tractstats@table output oddity

[Jon Wieser]

if i do the 7 subjects individually, 1 by 1  with the tractstats2table for each 
subject, the data in the table are ok,

it's just when I process them all with 1 tractsstat2table command, that the 
data is the same in each row of the output

Jon

- Original Message -
From: "Jon Wieser" 
To: "freesurfer" 
Sent: Wednesday, March 27, 2013 12:17:40 PM
Subject: [Freesurfer] tractstats@table output   oddity

I ran tractstats2table   to make a table of my dti tract stats for the 
fmajor_PP tract

see the attached script file @tractstats2table   and the file list  
"fmajor_file_list.txt"
it produced the output file "fmajor_table.txt"  (attached)
in the output table   all the values for the variables are the same for the 7 
rows. 
the values are from last file in the list 
DTItracts/1276/fmajor_PP_avg23_mni_flt/pathstats.overall.txt

 why is this?  input files have different values for the various variable
Jon


-- 
Jon Wieser
Research Specialist
UW-Milwaukee
Psychology Department, Pearse Hall Rm 366
2441 East Hartford Ave
Milwaukee, WI 53211
Phone: 414-229-7145
Fax: 414-229-5219
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-- 
Jon Wieser
Research Specialist
UW-Milwaukee
Psychology Department, Pearse Hall Rm 366
2441 East Hartford Ave
Milwaukee, WI 53211
Phone: 414-229-7145
Fax: 414-229-5219
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[Freesurfer] specifying random effects in LME (Linear Mixed Effects models)

[Lalonde, Francois (NIH/NIMH) [E]]

I am following the wiki page for LME analysis and I have a quick question.  The 
Mass-univariate example near the bottom of the page proposes an initial model 
that contains intercept, linear and quadratic terms as random effects.  
However, the examples just below for lme_mass_fit_EM_init(),  
lme_mass_fit_EM_Rgw() only have [1 2] as selected random effects.  Should the 
vector Zcols contain [1 2 3] as selected random effects in order to test the 
proposed model?

Thanks,
Francois

François Lalonde, Ph.D.
Child Psychiatry Branch
NIMH / NIH
10 Center Drive, Room 3N202
Bethesda, MD  20892

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Re: [Freesurfer] question regarding creating Brodmann area

[Bruce Fischl]

you will need to upgrade to a newer version - the BA labeling  didn't exist 
in 4.5


On Wed, 27 Mar 2013, Ji Won Bang wrote:

> Dear. freesurfer users.
> I'm trying to make a label for Brodmann area 44.
> 
> According to the freesurfer manual, I've run,
> 
> recon-all -s subjid -ba-labels
> 
> However, it says Flag -ba-labels unrecognized.
> 
> I'm using freesurfer version 4.5.0.
> 
> 
> By default, recon-all is supposed to create Brodmann areas under label 
> directory.
> 
> However, inside the lable directory, I see only
> 
> aparc.annot.a2009s.ctab
> aparc.annot.ctab
> lh.aparc.a2009s.annot
> lh.aparc.annot
> lh.cortex.label
> rh.aparc.a2009s.annot
> rh.aparc.annot
> rh.cortex.label
> 
> Please leave me any comment!!
> 
> I appreciate it a lot!
> 
> Best regards,
> Ji Won Bang
> 
>
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[Freesurfer] question regarding creating Brodmann area

[Ji Won Bang]

Dear. freesurfer users.

I'm trying to make a label for Brodmann area 44.

According to the freesurfer manual, I've run,

recon-all -s subjid -ba-labels

However, it says Flag -ba-labels unrecognized.

I'm using freesurfer version 4.5.0.


By default, recon-all is supposed to create Brodmann areas under label
directory.

However, inside the lable directory, I see only

aparc.annot.a2009s.ctab
aparc.annot.ctab
lh.aparc.a2009s.annot
lh.aparc.annot
lh.cortex.label
rh.aparc.a2009s.annot
rh.aparc.annot
rh.cortex.label

Please leave me any comment!!

I appreciate it a lot!

Best regards,
Ji Won Bang
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Re: [Freesurfer] memory allocation errors on Snow Leopard running dmri_train

[Anastasia Yendiki]

Hi Ping - Can you send us your entire trac-all.log? There's some info in 
there about your system and the freesurfer build you're using that we'll 
need to try to replicate the problem.

Thanks,
a.y

On Tue, 26 Mar 2013, Ping-Hong Yeh wrote:

> Hi Anastasia,
>
> It had the same issue before, but worked fine after installing the
> fixed dmri patch for Snow Leopard.
>
> Thanks.
> ping
>
> On Tue, Mar 26, 2013 at 5:09 PM, Anastasia Yendiki
>  wrote:
>>
>> Hi Ping - Are you running this on the same system where you were running the
>> 5.1 snow leopard build without a problem?
>>
>> a.y
>>
>>
>> On Tue, 26 Mar 2013, Ping-Hong Yeh wrote:
>>
>>> Hi FS users,
>>>
>>> I've tested the newer Tracula FS 5.2 on Snow Leopard and ran into
>>> errors. The 5.2 recon-all of T1 was finished ok.
>>>
>>> Here is the final part of log file.
>>>
>>> #@# Priors Tue Mar 26 14:39:36 EDT 2013
>>> /apps/freesurfer/bin/dmri_train --outdir
>>> /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/mni --out
>>> lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt
>>> lh.ilf_AS_avg33_mni_flt rh.ilf_AS_avg33_mni_flt
>>> lh.unc_AS_avg33_mni_flt rh.unc_AS_avg33_mni_flt
>>> fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt
>>> lh.atr_PP_avg33_mni_flt rh.atr_PP_avg33_mni_flt
>>> lh.cab_PP_avg33_mni_flt rh.cab_PP_avg33_mni_flt
>>> lh.ccg_PP_avg33_mni_flt rh.ccg_PP_avg33_mni_flt
>>> lh.slfp_PP_avg33_mni_flt rh.slfp_PP_avg33_mni_flt
>>> lh.slft_PP_avg33_mni_flt rh.slft_PP_avg33_mni_flt --slist
>>> /tmp/subj33.NCNC2348.61836.txt --trk dlabel/mni/lh.cst_AS.flt.trk
>>> dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk
>>> dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk
>>> dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk
>>> dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk
>>> dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk
>>> dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk
>>> dlabel/mni/rh.ccg_PP.flt.trk dlabel/mni/lh.slfp_PP.flt.trk
>>> dlabel/mni/rh.slfp_PP.flt.trk dlabel/mni/lh.slft_PP.flt.trk
>>> dlabel/mni/rh.slft_PP.flt.trk --seg dlabel/mni/aparc+aseg.nii.gz
>>> --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0
>>> 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.flt.nii.gz
>>> dlabel/mni/lh.cst_AS_roi2.flt.nii.gz
>>> dlabel/mni/rh.cst_AS_roi1.flt.nii.gz
>>> dlabel/mni/rh.cst_AS_roi2.flt.nii.gz
>>> dlabel/mni/lh.ilf_AS_roi1.flt.nii.gz
>>> dlabel/mni/lh.ilf_AS_roi2.flt.nii.gz
>>> dlabel/mni/rh.ilf_AS_roi1.flt.nii.gz
>>> dlabel/mni/rh.ilf_AS_roi2.flt.nii.gz
>>> dlabel/mni/lh.unc_AS_roi1.flt.nii.gz
>>> dlabel/mni/lh.unc_AS_roi2.flt.nii.gz
>>> dlabel/mni/rh.unc_AS_roi1.flt.nii.gz
>>> dlabel/mni/rh.unc_AS_roi2.flt.nii.gz
>>> dlabel/mni/fmajor_PP_roi1.flt.nii.gz
>>> dlabel/mni/fmajor_PP_roi2.flt.nii.gz
>>> dlabel/mni/fminor_PP_roi1.flt.nii.gz
>>> dlabel/mni/fminor_PP_roi2.flt.nii.gz
>>> dlabel/mni/lh.atr_PP_roi1.flt.nii.gz
>>> dlabel/mni/lh.atr_PP_roi2.flt.nii.gz
>>> dlabel/mni/rh.atr_PP_roi1.flt.nii.gz
>>> dlabel/mni/rh.atr_PP_roi2.flt.nii.gz
>>> dlabel/mni/lh.cab_PP_roi1.flt.nii.gz
>>> dlabel/mni/lh.cab_PP_roi2.flt.nii.gz
>>> dlabel/mni/rh.cab_PP_roi1.flt.nii.gz
>>> dlabel/mni/rh.cab_PP_roi2.flt.nii.gz
>>> dlabel/mni/lh.ccg_PP_roi1.flt.nii.gz
>>> dlabel/mni/lh.ccg_PP_roi2.flt.nii.gz
>>> dlabel/mni/rh.ccg_PP_roi1.flt.nii.gz
>>> dlabel/mni/rh.ccg_PP_roi2.flt.nii.gz
>>> dlabel/mni/lh.slfp_PP_roi1.flt.nii.gz
>>> dlabel/mni/lh.slfp_PP_roi2.flt.nii.gz
>>> dlabel/mni/rh.slfp_PP_roi1.flt.nii.gz
>>> dlabel/mni/rh.slfp_PP_roi2.flt.nii.gz
>>> dlabel/mni/lh.slft_PP_roi1.flt.nii.gz
>>> dlabel/mni/lh.slft_PP_roi2.flt.nii.gz
>>> dlabel/mni/rh.slft_PP_roi1.flt.nii.gz
>>> dlabel/mni/rh.slft_PP_roi2.flt.nii.gz --bmask
>>>
>>> /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/mni/aparc+aseg_mask.nii.gz
>>> --fa
>>> /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dmri/dtifit_FA.nii.gz
>>> --cptdir /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/diff
>>> --reg
>>> /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dmri/xfms/mni2diff.flt.mat
>>> --ncpts 10 --trunc
>>>
>>>
>>> cwd /Users/twbrkmp2
>>> cmdline /apps/freesurfer/bin/dmri_train --outdir
>>> /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/mni --out
>>> lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt
>>> lh.ilf_AS_avg33_mni_flt rh.ilf_AS_avg33_mni_flt
>>> lh.unc_AS_avg33_mni_flt rh.unc_AS_avg33_mni_flt
>>> fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt
>>> lh.atr_PP_avg33_mni_flt rh.atr_PP_avg33_mni_flt
>>> lh.cab_PP_avg33_mni_flt rh.cab_PP_avg33_mni_flt
>>> lh.ccg_PP_avg33_mni_flt rh.ccg_PP_avg33_mni_flt
>>> lh.slfp_PP_avg33_mni_flt rh.slfp_PP_avg33_mni_flt
>>> lh.slft_PP_avg33_mni_flt rh.slft_PP_avg33_mni_flt --slist
>>> /tmp/subj33.NCNC2348.61836.txt --trk dlabel/mni/lh.cst_AS.flt.trk
>>> dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk
>>> dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk
>>> dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk
>>> dlabel/mni/fminor_PP.flt.trk dlabel/mni/l

Re: [Freesurfer] Problems with recon-all--won't generate wm or surf files

[Bruce Fischl]

Hi Hayley

I think the problem is that the nu.mgz I gave you has a voxel type of 
float (3) instead of uchar (0). You will need to figure out which volumes 
are float with mri_info, and convert each of them to uchar with:


mri_convert -odt uchar -ns 1 float.mgz uchar.mgz

where the -ns 1 flag tells it not to scale the intensities. Sorry, I 
should have thought of this before sending  you the updated nu.mgz. Make 
sure all the uchar volumes are named as we expect them 
Bruce



On Wed, 27 Mar 2013, Hayley Dorfman wrote:


Hello,

I've been having problems with recon-all for only 1 of my 50 subjects. 
Recon-all is failing somehow before white matter or
surf files are generated. The T1 and nu.mgz files look fine. Below are the 
files that my subject is missing in the 'mri'
subdirectory (they are also missing the entire surfs directory):

filled.mgz

lh.ribbon.mgz
rh.ribbon.mgz
ribbon.mgz
wm.asegedit.mgz
wm.mgz
wmparc.mgz

Below is the last few lines of output from my recon-all log file:

"#@# WM Segmentation Tue Mar 26 18:09:32 EDT 2013

mri_segment brain.mgz wm.seg.mgz

doing initial intensity segmentation...
using local statistics to label ambiguous voxels...
computing class statistics for intensity windows...
WM (104.0): 104.6 +- 4.9 [80.0 --> 125.0]
GM (72.0) : 69.4 +- 10.8 [30.0 --> 96.0]
setting bottom of white matter range to 80.2
setting top of gray matter range to 91.0
doing initial intensity segmentation...
using local statistics to label ambiguous voxels...
using local geometry to label remaining ambiguous voxels...

reclassifying voxels using Gaussian border classifier...

removing voxels with positive offset direction...
smoothing T1 volume with sigma = 0.250
removing 1-dimensional structures...
5962 sparsely connected voxels removed...
thickening thin strands
20 segments, 3294 filled
117 bright non-wm voxels segmented.
4879 diagonally connected voxels added...
white matter segmentation took 3.4 minutes
writing output to wm.seg.mgz...
changing input type from 3 to UCHAR

mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz

preserving editing changes in input volume...
mri_edit_wm_with_aseg: volume brain.mgz must be MRI_UCHAR
reading wm segmentation from wm.seg.mgz...
Linux ncfc21.rc.fas.harvard.edu 2.6.18-274.18.1.el5 #1 SMP Thu Feb 9 12:45:44 
EST 2012 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s M87190691 exited with ERRORS at Tue Mar 26 18:12:57 EDT 2013

For more details, see the log file
/ncf/jwb/studies/PrisonReward/Active/Analyses/fsrecon_n49_01252013_qdec/M87190691/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

make: *** 
[/ncf/jwb/studies/PrisonReward/Active/Analyses/fsrecon_n49_01252013_qdec/M87190691/mri/wm.mgz]
 Error 1"


Any ideas as to what might be failing?


Thanks for your help!

Hayley

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[Freesurfer] Problems with recon-all--won't generate wm or surf files

[Hayley Dorfman]

Hello,

I've been having problems with recon-all for only 1 of my 50 subjects.
Recon-all is failing somehow before white matter or surf files are
generated. The T1 and nu.mgz files look fine. Below are the files that my
subject is missing in the 'mri' subdirectory (they are also missing the
entire surfs directory):

filled.mgz

lh.ribbon.mgz
rh.ribbon.mgz
ribbon.mgz
wm.asegedit.mgz
wm.mgz
wmparc.mgz

Below is the last few lines of output from my recon-all log file:

"#@# WM Segmentation Tue Mar 26 18:09:32 EDT 2013

mri_segment brain.mgz wm.seg.mgz

doing initial intensity segmentation...
using local statistics to label ambiguous voxels...
computing class statistics for intensity windows...
WM (104.0): 104.6 +- 4.9 [80.0 --> 125.0]
GM (72.0) : 69.4 +- 10.8 [30.0 --> 96.0]
setting bottom of white matter range to 80.2
setting top of gray matter range to 91.0
doing initial intensity segmentation...
using local statistics to label ambiguous voxels...
using local geometry to label remaining ambiguous voxels...

reclassifying voxels using Gaussian border classifier...

removing voxels with positive offset direction...
smoothing T1 volume with sigma = 0.250
removing 1-dimensional structures...
5962 sparsely connected voxels removed...
thickening thin strands
20 segments, 3294 filled
117 bright non-wm voxels segmented.
4879 diagonally connected voxels added...
white matter segmentation took 3.4 minutes
writing output to wm.seg.mgz...
changing input type from 3 to UCHAR

mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz

preserving editing changes in input volume...
mri_edit_wm_with_aseg: volume brain.mgz must be MRI_UCHAR
reading wm segmentation from wm.seg.mgz...
Linux ncfc21.rc.fas.harvard.edu 2.6.18-274.18.1.el5 #1 SMP Thu Feb 9
12:45:44 EST 2012 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s M87190691 exited with ERRORS at Tue Mar 26 18:12:57 EDT 2013

For more details, see the log file
/ncf/jwb/studies/PrisonReward/Active/Analyses/fsrecon_n49_01252013_qdec/M87190691/scripts/recon-all.log
To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

make: ***
[/ncf/jwb/studies/PrisonReward/Active/Analyses/fsrecon_n49_01252013_qdec/M87190691/mri/wm.mgz]
Error 1"


Any ideas as to what might be failing?


Thanks for your help!

Hayley
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Re: [Freesurfer] CT as covariate

[Douglas N Greve]

I don't think it would make a difference, but I would use the individual 
space.
doug

On 03/27/2013 01:12 PM, Rafa X wrote:
> Dear Freesurfers
>
>
> I will introduce the mean cortial thickness as covariate into my
> statistical model, but I'm wonderind which way will be the best.
>
> To get the cortical thickness in individual space, or in AVG space?
>
>
> Thank you all in advanced,
> Rafa.
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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[Freesurfer] tractstats@table output oddity

[Jon Wieser]

I ran tractstats2table   to make a table of my dti tract stats for the 
fmajor_PP tract

see the attached script file @tractstats2table   and the file list  
"fmajor_file_list.txt"
it produced the output file "fmajor_table.txt"  (attached)
in the output table   all the values for the variables are the same for the 7 
rows. 
the values are from last file in the list 
DTItracts/1276/fmajor_PP_avg23_mni_flt/pathstats.overall.txt

 why is this?  input files have different values for the various variable
Jon


-- 
Jon Wieser
Research Specialist
UW-Milwaukee
Psychology Department, Pearse Hall Rm 366
2441 East Hartford Ave
Milwaukee, WI 53211
Phone: 414-229-7145
Fax: 414-229-5219

@tractstats2table
Description: Binary data
DTItracts/1069/fmajor_PP_avg23_mni_flt/pathstats.overall.txt 
DTItracts/1167/fmajor_PP_avg23_mni_flt/pathstats.overall.txt 
DTItracts/1191/fmajor_PP_avg23_mni_flt/pathstats.overall.txt 
DTItracts/1248/fmajor_PP_avg23_mni_flt/pathstats.overall.txt 
DTItracts/1252/fmajor_PP_avg23_mni_flt/pathstats.overall.txt 
DTItracts/1267/fmajor_PP_avg23_mni_flt/pathstats.overall.txt 
DTItracts/1276/fmajor_PP_avg23_mni_flt/pathstats.overall.txt 


fmajor  Count   Volume  Len_Min Len_Max Len_Avg Len_Center  AD_Avg  
AD_Avg_Weight   AD_Avg_Center   RD_Avg  RD_Avg_Weight   RD_Avg_Center   MD_Avg  
MD_Avg_Weight   MD_Avg_Center   FA_Avg  FA_Avg_Weight   FA_Avg_Center
freesurfer  1000.0  144.0   29.050.036.896  34.00.00133574  
0.00136416  0.00126968  0.000659806 0.000681595 0.000547329 
0.000885118 0.000909116 0.000788114 0.4350630.433158
0.486111
freesurfer  1000.0  144.0   29.050.036.896  34.00.00133574  
0.00136416  0.00126968  0.000659806 0.000681595 0.000547329 
0.000885118 0.000909116 0.000788114 0.4350630.433158
0.486111
freesurfer  1000.0  144.0   29.050.036.896  34.00.00133574  
0.00136416  0.00126968  0.000659806 0.000681595 0.000547329 
0.000885118 0.000909116 0.000788114 0.4350630.433158
0.486111
freesurfer  1000.0  144.0   29.050.036.896  34.00.00133574  
0.00136416  0.00126968  0.000659806 0.000681595 0.000547329 
0.000885118 0.000909116 0.000788114 0.4350630.433158
0.486111
freesurfer  1000.0  144.0   29.050.036.896  34.00.00133574  
0.00136416  0.00126968  0.000659806 0.000681595 0.000547329 
0.000885118 0.000909116 0.000788114 0.4350630.433158
0.486111
freesurfer  1000.0  144.0   29.050.036.896  34.00.00133574  
0.00136416  0.00126968  0.000659806 0.000681595 0.000547329 
0.000885118 0.000909116 0.000788114 0.4350630.433158
0.486111
freesurfer  1000.0  144.0   29.050.036.896  34.00.00133574  
0.00136416  0.00126968  0.000659806 0.000681595 0.000547329 
0.000885118 0.000909116 0.000788114 0.4350630.433158
0.486111
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[Freesurfer] CT as covariate

[Rafa X]

Dear Freesurfers


I will introduce the mean cortial thickness as covariate into my
statistical model, but I'm wonderind which way will be the best.

To get the cortical thickness in individual space, or in AVG space?


Thank you all in advanced,
Rafa.
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[Freesurfer] June course on structural and functional connectivity at the Martinos Center

[Anastasia Yendiki]

Dear Freesurfistas - This new course, offered at the Martinos Center right 
before the OHBM meeting, may be of interest to some of you. There are some 
open spots left.


For info on how to register and a tentative schedule, see the web page at 
the end of the announcement.


a.y

---

STRUCTURAL AND FUNCTIONAL BRAIN CONNECTIVITY AS REVEALED BY MRI

Dates: June 3-7, 2013
Themes:   Resting State Functional Connectivity and DTI/DSI/Tractography
Location: Martinos Center for Biomedical Imaging of the Massachusetts General
Hospital; Boston/Charlestown Massachusetts
Program Director: Robert L. Savoy

   In December 2012 the Martinos Center for Biomedical Imaging introduced a 
new, 5-day
program on functional and structural connectivity using MRI.  The next edition 
of this
program will be held June 3-7 (two weeks prior to the Organization for Human 
Brain
Mapping annual meeting).  There is likely to be an additional program in 2013, 
to be
held near the end of October or early November, 2013.  

   Issues associated with connectivity in the human brain are of increasing
importance, as reflected in the large number of abstracts, research articles, 
and even
entire journals devoted to this area, as well as the increased emphasis on 
lesions
within the white matter as being a source of many neuro-psychiatric disorders.  
MRI
has proven to be a valuable tool for examining connectivity both in terms of the
coordinated activities of neural networks (using BOLD-based fMRI data collected 
during
rest and during tasks) and also in terms of the structural anatomy of white 
matter
pathways of the brain (using Diffusion Tensor Imaging (DTI), Diffusion Spectrum
Imaging (DSI), and tractography programs to analyze and visualize the resulting 
data).
 Participants will learn about the technical challenges in acquisition, data
processing and visualization of brain networks via the data from fMRI during the
so-called resting state, but also available during experimenter-initiated 
cognitive
tasks.  Participants will also receive a firm grounding in the power and 
limitations
associated with using diffusion-sensitive MRI to detect and organize the 
anatomical
structure of white matter tracts in the living human brain.

   The primary goal of this program is to give researchers and clinicians a 
good start
for their investigations using these tools.  In that sense, it serves a purpose
analogous to that of the Functional MRI Visiting Fellowship Program (fMRIVFP) 
also
offered at the Martinos Center, except that the domain will be structural and
functional connectivity of myelinated fiber tracts within the living human 
brain.  The
active component of the program will be the use of software tools to promote 
quality
assurance in the data, detect outliers and other problematic attributes of the 
data,
optimize data acquisition, and flexibly visualize the data in the service of 
asking
and answering specific questions.  Participants will be expected (though not 
required)
to bring a suitable laptop computer for engaging in the hands-on exercises of 
the
program.  There will also be a section on the Connectome MRI Machine that uses
exceptionally strong gradients to enhance data acquisition of strutural and 
functional
images.

   The core faculty is drawn from the staff of the Athinoula A. Martinos Center 
(of
the Massachusetts General Hospital and Massachusetts Institute of Technology) 
and
affiliated faculty from Harvard University, McLean Hospital and other local
institutions.  Guest lecturers (at the Dec, 2012 program) included faculty from 
the
Child Mind Institute of New York, NIH, Stanford University, The Donders 
Institute, the
University of Cambridge and others.

For questions, e-mail:  fmri...@nmr.mgh.harvard.edu

For more information and registration, see:
 http://martinos.org/ConnectivityCourse___
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Incomplete and poorly formed tracts

[Susan Kuo]

Hi Anastasia,
  I saved out some of the completed trac-all.cmds following each TRACULA
'step', and I see where aparc+aseg is mapped to diffusion space. Thank you
again for all your help - my project is starting to look a lot better!


Sincerely,
Susie Kuo
NIH

On Wed, Mar 27, 2013 at 12:02 PM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:

>
> Actually the brain mask used on the diffusion data *is* the aparc+aseg
> mapped to diffusion space, so the reason you see that extra non-brain stuff
> in the FA map is because the aparc+aseg was not aligned well to it.
>
> So you just need to switch on bbregister and switch off flirt in your
> configuration file, and then rerun trac-all. If the DWI-to-T1 registration
> is good, then the masking issue will be solved too.
>
> Good luck!
>
> a.y
>
> On Wed, 27 Mar 2013, Susan Kuo wrote:
>
>  Hi Anastasia,   Thank you! I can see that the aparc+aseg spilled over
>> badly. I am
>> going to try bbregister, and then re-betting (Brain Extraction Tool-ing)
>> the original
>> image, since the dtifit_FA looks to include non-brain near the frontal
>> lobe. I'll keep
>> you and the FS community updated on the results, in case anybody is
>> curious.
>>
>>
>> Sincerely,
>> Susie Kuo
>> NIH
>>
>>
>> On Wed, Mar 27, 2013 at 10:41 AM, Anastasia Yendiki <
>> ayend...@nmr.mgh.harvard.edu>
>> wrote:
>>
>>   Hi Susie - The -tv (tract volume) option of freeview is designed
>>   specifically to display the merged*.mgz output files of tracula.
>> For a
>>   regular volume, use -v or no option at all. For best displaying the
>>   aparc+aseg, select it in freeview and choose "Lookup Table" from
>> the Color
>>   map menu.
>>
>>   Hope this helps,
>>   a.y
>>
>>   On Wed, 27 Mar 2013, Susan Kuo wrote:
>>
>> Hi Anastasia,   I'm attaching the graphic I arrived at with
>> the command:
>>
>> > freeview -tv /dlabel/diff/aparc+**
>> aseg.flt.nii.gz
>> -v
>> /dmri/dtifit_FA.**nii.gz
>>
>> Here, I used the subject I send you (Sa69845.5) for the
>> subjectID. I could not detect
>> spill over in these images, mostly because the frontal lobe is
>> a little cut off. Did
>> you perhaps use a different viewer? I'm hoping to be able to
>> detect these
>> mis-registrations better for myself in the future. Thanks for
>> all your help!
>>
>> Sincerely,
>> Susie Kuo
>> NIH
>>
>> On Wed, Mar 27, 2013 at 1:32 AM, Anastasia Yendiki
>> 
>> wrote:
>>
>>   Hi Susie - Everything under dlabel/diff is mapped to DWI
>> space (either
>>   with flirt or with bbregister, whichever you use). The
>> one in my
>>   screenshot was dlabel/diff/aparc+aseg.flt.**nii.gz.
>>
>>   a.y
>>
>>   On Wed, 27 Mar 2013, Susan Kuo wrote:
>>
>> Hi Anastasia,
>>   I see what you mean. I had previously used the
>> dtifit_FA.nii.gz image and
>> overlaid that with the aparc+aseg+2mm.nii.gz image
>> in
>> /dlabel/diff, using
>> freeview. I didn't end up with the same images as
>> you,
>> however. Can you tell
>> me which images you used to obtain this overlay?
>>
>>   I am going to run bbregister tonight, and I'll
>> let you know
>> how it goes --
>> I'm hopeful!
>>
>> Thank you again!
>>
>> Susie Kuo
>> NIH
>>
>> On Tue, Mar 26, 2013 at 5:35 PM, Anastasia Yendiki
>>  wrote:
>>
>>   Hi Susie - I'm attaching a snapshot from
>> your subject,
>> showing
>>   the aparc+aseg overlaid on the FA map. The
>> registration
>> has
>>   failed. The frontal lobe has spilled out of
>> the brain,
>> the white
>>   matter has spilled into the ventricles.
>>
>>   I strongly recommend using bbregister for
>> the
>> intra-subject
>>   registration, which is the default in the
>> latest version
>> of
>>   trac-all.
>>
>>   Hope this helps,
>>   a.y
>>
>>   On Tue, 26 Mar 2013, Susan Kuo wrote:
>>
>> Hi A

Re: [Freesurfer] surf2vol

[Daniel Lumsden]

Doug 

When I try to overlay the .gii files on the orig volume I get the following 
message:



"Either this surface does not contain valid volume geometry information, or 
freeview failed to read the information. This surface may not align with 
volumes and other surfaces"
I presume this means there is a problem with how I've generated the .gi files? 
I'm happy the lh.anatomicalregion.label files are working fine because I can 
generate volumetric masks from them.
To get the .gii files I've taken the rh.white and lh.white from the surf folder 
and copied them into the folder I'm running the terminal in. I'm then using the 
command:
mris_convert rh.white rh.white.asc
Then:
echo lh.frontallobe.label > left_frontal_lobe.txt
(which checking gives me a text file of that name with one line, 
lh.frontallobe.label)

Then:
label2surf -s lh.white.asc  -l left_frontal_lobe.txt -o left_frontal_lobe.gii
All of the named files are in the same folder.

Thank you again. Confusingly, it does seem like probtrackx is doing something 
with the .gii files!

Dan
Sorry, I meant does the left_frontal_lobe.gii overlay properly on the orig 
volume?
dougOn 03/27/2013 04:41 AM, Daniel Lumsden wrote:
> Doug
>
> The .nii.gz file is completely empty and doesn't come up on any viewer 
> (fslview, tkmedit, freeview, mricron etc). The .gi files I've 
> generated appear to be tracking in probtrackx (though slowly on my 
> laptop - probably not expected given the sizes of the surfaces). I can 
> also generate binary volumetric masks from the labels using 
> mri_binarize (though they are a little bit "speckled" - with scattered 
> blank voxels).
>
> On my installation I'm having some intermittent difficulties with 
> tkmedit and tksurfer (not consistently opening, sometimes coming up 
> with "bus error"). Freeview is opening consistently though. I'm not 
> sure if this could be having an affect but I was planning on 
> reinstalling freesurfer today to see if that fixed it.
>
> Thank you again for your help
>
> Dan
>
> Does leftfrontallobe.nii.gz overlay properly in tkmedit? eg,
> tkmedit subject orig.mgz -surfs -overlay leftfrontallobe.nii.gz -fminmax
> .5 1
> doug
> On 03/26/2013 07:20 AM, Daniel Lumsden wrote:
> > Bruce
> >
> > Many thanks - that's given me a lot more guidance. Following the help,
> > i've put together the command below:
> >
> > mri_surf2vol --hemi lh --template /orig.mgz --outvol  > where I want the file>/leftfrontallobe.nii.gz --surfval  > to>/left_frontal_lobe.gii --fillribbon --volregidentity mov07
> >
> > Where mov07 is my subjid and left_frontal_lobe.gii is the surface I've
> > generated from the label files to run in probtrakx. This command runs,
> > but produces and empty nifti file. I've changed the output to .mgz
> > with similar effect. I've substituted the rawavg.mgz file for the
> > orig.mgz file, and tried both .nii.gz and .mgz versions of both files
> > and still get an empty output file.  The subject is in my $SUBJECTS_DIR.
> >
> > Is there a way to check the .gii files? I generated them using
> > label2surf, having used mris_convert to convert the lh.white and
> > rh.white files from the surf folder for my subject to lh.white.asc and
> > rh.white.asc.
> >
> > Thank you again for your help.
> >
> > Dan
> >
> >
> > > Date: Mon, 25 Mar 2013 14:59:28 -0400
> > > From: fis...@nmr.mgh.harvard.edu
> > > To: doclums...@hotmail.com
> > > CC: freesurfer@nmr.mgh.harvard.edu
> > > Subject: Re: [Freesurfer] surf2vol
> > >
> > > Hi Dan
> > >
> > > try using mri_surf2vol instead (it has a much bigger help, thanks to
> > > Doug0
> > > Bruce
> > > On Mon, 25 Mar 2013, Daniel Lumsden wrote:
> > >
> > > > Dear All
> > > >
> > > > Apologies for what I'm sure is a very basic question. I'm new to
> > using freesurfer, and would like to generate cortical
> > > > parcellations for running in probtrakx. I have followed the
> > instructions from various sources and have managed to generate the
> > > > parcellations from recon-all, extract the label files from the
> > parcellation, then use mri_mergelabels and label2surf to generate
> > > > the  the .gii files needed for probtrakx. I'd like to be able to
> > display the surface files for illustrative purposes, but I'm
> > > > struggling to apply the surf2vol command.
> > > >
> > > > From the terminal window I can see that the commands required are:
> > > >
> > > > surf2vol
> > > >
> > > > I presume that  is the .gii file I'm trying to visualise,
> > and  is to specify the name of the output volume the
> > > > command will generate, but what should I be using as the ?
> > I would be very grateful for any guidance. Please accept my
> > > > apologies if I've missed a very obvious online explanation for
> > this and thank you in advance.
> > > >
> > > > Dan Lumsden
> > > > Clinical Research Fellow
> > > >
> > > >
> > >
> > >
> > > 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

Re: [Freesurfer] Incomplete and poorly formed tracts

[Anastasia Yendiki]

Actually the brain mask used on the diffusion data *is* the aparc+aseg 
mapped to diffusion space, so the reason you see that extra non-brain 
stuff in the FA map is because the aparc+aseg was not aligned well to it.


So you just need to switch on bbregister and switch off flirt in your 
configuration file, and then rerun trac-all. If the DWI-to-T1 registration 
is good, then the masking issue will be solved too.


Good luck!
a.y

On Wed, 27 Mar 2013, Susan Kuo wrote:


Hi Anastasia,   Thank you! I can see that the aparc+aseg spilled over badly. I 
am
going to try bbregister, and then re-betting (Brain Extraction Tool-ing) the 
original
image, since the dtifit_FA looks to include non-brain near the frontal lobe. 
I'll keep
you and the FS community updated on the results, in case anybody is curious. 


Sincerely, 
Susie Kuo
NIH


On Wed, Mar 27, 2013 at 10:41 AM, Anastasia Yendiki 

wrote:

  Hi Susie - The -tv (tract volume) option of freeview is designed
  specifically to display the merged*.mgz output files of tracula. For a
  regular volume, use -v or no option at all. For best displaying the
  aparc+aseg, select it in freeview and choose "Lookup Table" from the Color
  map menu.

  Hope this helps,
  a.y

  On Wed, 27 Mar 2013, Susan Kuo wrote:

Hi Anastasia,   I'm attaching the graphic I arrived at with
the command: 

> freeview -tv /dlabel/diff/aparc+aseg.flt.nii.gz
-v
/dmri/dtifit_FA.nii.gz

Here, I used the subject I send you (Sa69845.5) for the
subjectID. I could not detect
spill over in these images, mostly because the frontal lobe is
a little cut off. Did
you perhaps use a different viewer? I'm hoping to be able to
detect these
mis-registrations better for myself in the future. Thanks for
all your help!

Sincerely, 
Susie Kuo
NIH

On Wed, Mar 27, 2013 at 1:32 AM, Anastasia Yendiki

wrote:

      Hi Susie - Everything under dlabel/diff is mapped to DWI
space (either
      with flirt or with bbregister, whichever you use). The
one in my
      screenshot was dlabel/diff/aparc+aseg.flt.nii.gz.

      a.y

      On Wed, 27 Mar 2013, Susan Kuo wrote:

            Hi Anastasia, 
              I see what you mean. I had previously used the
            dtifit_FA.nii.gz image and
            overlaid that with the aparc+aseg+2mm.nii.gz image
in
            /dlabel/diff, using
            freeview. I didn't end up with the same images as
you,
            however. Can you tell
            me which images you used to obtain this overlay? 

              I am going to run bbregister tonight, and I'll
let you know
            how it goes --
            I'm hopeful! 

            Thank you again!

            Susie Kuo
            NIH

            On Tue, Mar 26, 2013 at 5:35 PM, Anastasia Yendiki
             wrote:

                  Hi Susie - I'm attaching a snapshot from
your subject,
            showing
                  the aparc+aseg overlaid on the FA map. The
registration
            has
                  failed. The frontal lobe has spilled out of
the brain,
            the white
                  matter has spilled into the ventricles.

                  I strongly recommend using bbregister for
the
            intra-subject
                  registration, which is the default in the
latest version
            of
                  trac-all.

                  Hope this helps,
                  a.y

                  On Tue, 26 Mar 2013, Susan Kuo wrote:

                        Hi Anastasia,   I did as you
recommended and
            checked
                        the diffusion-to-anatomical
                        registration, and the overlay of
aparc+aseg_mask
            on
                        FA, and these views seem to be
                        good. Upon closer inspection, what I
find is that
                        there are incipient 'bits' of all
                        the tracts, but they seem to not have
'grown',
                        though they are in the proper space
                        (comparin

Re: [Freesurfer] Incomplete and poorly formed tracts

[Susan Kuo]

Hi Anastasia,
  Thank you! I can see that the aparc+aseg spilled over badly. I am going
to try bbregister, and then re-betting (Brain Extraction Tool-ing) the
original image, since the dtifit_FA looks to include non-brain near the
frontal lobe. I'll keep you and the FS community updated on the results, in
case anybody is curious.


Sincerely,
Susie Kuo
NIH


On Wed, Mar 27, 2013 at 10:41 AM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:

>
> Hi Susie - The -tv (tract volume) option of freeview is designed
> specifically to display the merged*.mgz output files of tracula. For a
> regular volume, use -v or no option at all. For best displaying the
> aparc+aseg, select it in freeview and choose "Lookup Table" from the Color
> map menu.
>
> Hope this helps,
> a.y
>
> On Wed, 27 Mar 2013, Susan Kuo wrote:
>
>  Hi Anastasia,   I'm attaching the graphic I arrived at with the command:
>>
>> > freeview -tv /dlabel/diff/aparc+**aseg.flt.nii.gz -v
>> /dmri/dtifit_FA.**nii.gz
>>
>> Here, I used the subject I send you (Sa69845.5) for the subjectID. I
>> could not detect
>> spill over in these images, mostly because the frontal lobe is a little
>> cut off. Did
>> you perhaps use a different viewer? I'm hoping to be able to detect these
>> mis-registrations better for myself in the future. Thanks for all your
>> help!
>>
>> Sincerely,
>> Susie Kuo
>> NIH
>>
>> On Wed, Mar 27, 2013 at 1:32 AM, Anastasia Yendiki <
>> ayend...@nmr.mgh.harvard.edu>
>> wrote:
>>
>>   Hi Susie - Everything under dlabel/diff is mapped to DWI space
>> (either
>>   with flirt or with bbregister, whichever you use). The one in my
>>   screenshot was dlabel/diff/aparc+aseg.flt.**nii.gz.
>>
>>   a.y
>>
>>   On Wed, 27 Mar 2013, Susan Kuo wrote:
>>
>> Hi Anastasia,
>>   I see what you mean. I had previously used the
>> dtifit_FA.nii.gz image and
>> overlaid that with the aparc+aseg+2mm.nii.gz image in
>> /dlabel/diff, using
>> freeview. I didn't end up with the same images as you,
>> however. Can you tell
>> me which images you used to obtain this overlay?
>>
>>   I am going to run bbregister tonight, and I'll let you know
>> how it goes --
>> I'm hopeful!
>>
>> Thank you again!
>>
>> Susie Kuo
>> NIH
>>
>> On Tue, Mar 26, 2013 at 5:35 PM, Anastasia Yendiki
>>  wrote:
>>
>>   Hi Susie - I'm attaching a snapshot from your subject,
>> showing
>>   the aparc+aseg overlaid on the FA map. The registration
>> has
>>   failed. The frontal lobe has spilled out of the brain,
>> the white
>>   matter has spilled into the ventricles.
>>
>>   I strongly recommend using bbregister for the
>> intra-subject
>>   registration, which is the default in the latest version
>> of
>>   trac-all.
>>
>>   Hope this helps,
>>   a.y
>>
>>   On Tue, 26 Mar 2013, Susan Kuo wrote:
>>
>> Hi Anastasia,   I did as you recommended and
>> checked
>> the diffusion-to-anatomical
>> registration, and the overlay of aparc+aseg_mask
>> on
>> FA, and these views seem to be
>> good. Upon closer inspection, what I find is that
>> there are incipient 'bits' of all
>> the tracts, but they seem to not have 'grown',
>> though they are in the proper space
>> (comparing them to good brains that yielded the
>> full
>> complement of tracts). Is there a
>> configuration in your TRACULA that controls the
>> growing of the tracts specifically?
>> Perhaps I should look into that.
>>
>>   Thank you, btw, for your very prompt reply
>> yesterday- it was much appreciated!
>>
>>
>> Sincerely,
>> Susie Kuo
>> NIH
>>
>> On Mon, Mar 25, 2013 at 4:58 PM, Anastasia Yendiki
>> 
>> wrote:
>>
>>   Hi Susan - Good to hear that you get good
>> results for most of your
>>   subjects. Have you checked the aparc+aseg
>> and
>> the diffusion-to-anatomical
>>   registration for the subjects that are
>> failing? I'd check the
>>   aparc+aseg_mask (in the dlabel/diff
>

Re: [Freesurfer] Question regarding the subject directory

[Douglas N Greve]

Hi Luke, people generally use a different SUBJECTS_DIR than the default 
FS folder. You can create symbolic links to subjects in the default FS 
folder, but recon-all will do this for you.
doug

On 03/27/2013 07:53 AM, lukas.sch...@ukb.uni-bonn.de wrote:
>
> Hi folks!
>
> I would like to use a different subject dirctory (setenv SUBJECTS_DIR 
> ). Does freesurfer still finds the folders 
> which are located in the default subjects directory of the FS 
> installation? Or are they simply not needed for the recon-all process 
> ? I refer to cvs_avg35 etc. not to the test data sets.
>
> Please excuse if this question is stupid ... but considering the 
> processsing time ...
>
> Many thanks in advance,
>
> Luke
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
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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
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] surf2vol

[Douglas N Greve]

Sorry, I meant does the left_frontal_lobe.gii overlay properly on the orig 
volume?
doug

On 03/27/2013 04:41 AM, Daniel Lumsden wrote:
> Doug
>
> The .nii.gz file is completely empty and doesn't come up on any viewer 
> (fslview, tkmedit, freeview, mricron etc). The .gi files I've 
> generated appear to be tracking in probtrackx (though slowly on my 
> laptop - probably not expected given the sizes of the surfaces). I can 
> also generate binary volumetric masks from the labels using 
> mri_binarize (though they are a little bit "speckled" - with scattered 
> blank voxels).
>
> On my installation I'm having some intermittent difficulties with 
> tkmedit and tksurfer (not consistently opening, sometimes coming up 
> with "bus error"). Freeview is opening consistently though. I'm not 
> sure if this could be having an affect but I was planning on 
> reinstalling freesurfer today to see if that fixed it.
>
> Thank you again for your help
>
> Dan
>
> Does leftfrontallobe.nii.gz overlay properly in tkmedit? eg,
> tkmedit subject orig.mgz -surfs -overlay leftfrontallobe.nii.gz -fminmax
> .5 1
> doug
> On 03/26/2013 07:20 AM, Daniel Lumsden wrote:
> > Bruce
> >
> > Many thanks - that's given me a lot more guidance. Following the help,
> > i've put together the command below:
> >
> > mri_surf2vol --hemi lh --template /orig.mgz --outvol  > where I want the file>/leftfrontallobe.nii.gz --surfval  > to>/left_frontal_lobe.gii --fillribbon --volregidentity mov07
> >
> > Where mov07 is my subjid and left_frontal_lobe.gii is the surface I've
> > generated from the label files to run in probtrakx. This command runs,
> > but produces and empty nifti file. I've changed the output to .mgz
> > with similar effect. I've substituted the rawavg.mgz file for the
> > orig.mgz file, and tried both .nii.gz and .mgz versions of both files
> > and still get an empty output file.  The subject is in my $SUBJECTS_DIR.
> >
> > Is there a way to check the .gii files? I generated them using
> > label2surf, having used mris_convert to convert the lh.white and
> > rh.white files from the surf folder for my subject to lh.white.asc and
> > rh.white.asc.
> >
> > Thank you again for your help.
> >
> > Dan
> >
> >
> > > Date: Mon, 25 Mar 2013 14:59:28 -0400
> > > From: fis...@nmr.mgh.harvard.edu
> > > To: doclums...@hotmail.com
> > > CC: freesurfer@nmr.mgh.harvard.edu
> > > Subject: Re: [Freesurfer] surf2vol
> > >
> > > Hi Dan
> > >
> > > try using mri_surf2vol instead (it has a much bigger help, thanks to
> > > Doug0
> > > Bruce
> > > On Mon, 25 Mar 2013, Daniel Lumsden wrote:
> > >
> > > > Dear All
> > > >
> > > > Apologies for what I'm sure is a very basic question. I'm new to
> > using freesurfer, and would like to generate cortical
> > > > parcellations for running in probtrakx. I have followed the
> > instructions from various sources and have managed to generate the
> > > > parcellations from recon-all, extract the label files from the
> > parcellation, then use mri_mergelabels and label2surf to generate
> > > > the  the .gii files needed for probtrakx. I'd like to be able to
> > display the surface files for illustrative purposes, but I'm
> > > > struggling to apply the surf2vol command.
> > > >
> > > > From the terminal window I can see that the commands required are:
> > > >
> > > > surf2vol
> > > >
> > > > I presume that  is the .gii file I'm trying to visualise,
> > and  is to specify the name of the output volume the
> > > > command will generate, but what should I be using as the ?
> > I would be very grateful for any guidance. Please accept my
> > > > apologies if I've missed a very obvious online explanation for
> > this and thank you in advance.
> > > >
> > > > Dan Lumsden
> > > > Clinical Research Fellow
> > > >
> > > >
> > >
> > >
> > > The information in this e-mail is intended only for the person to
> > whom it is
> > > addressed. If you believe this e-mail was sent to you in error and
> > the e-mail
> > > contains patient information, please contact the Partners Compliance
> > HelpLine at
> > >http://www.partners.org/complianceline  . If the e-mail was sent to
> > you in error
> > > but does not contain patient information, please contact the sender
> > and properly
> > > dispose of the e-mail.
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> ___

Re: [Freesurfer] Incomplete and poorly formed tracts

[Anastasia Yendiki]

Hi Susie - The -tv (tract volume) option of freeview is designed 
specifically to display the merged*.mgz output files of tracula. For a 
regular volume, use -v or no option at all. For best displaying the 
aparc+aseg, select it in freeview and choose "Lookup Table" from the Color 
map menu.


Hope this helps,
a.y

On Wed, 27 Mar 2013, Susan Kuo wrote:


Hi Anastasia,   I'm attaching the graphic I arrived at with the command: 

> freeview -tv /dlabel/diff/aparc+aseg.flt.nii.gz -v
/dmri/dtifit_FA.nii.gz

Here, I used the subject I send you (Sa69845.5) for the subjectID. I could not 
detect
spill over in these images, mostly because the frontal lobe is a little cut 
off. Did
you perhaps use a different viewer? I'm hoping to be able to detect these
mis-registrations better for myself in the future. Thanks for all your help!

Sincerely, 
Susie Kuo
NIH

On Wed, Mar 27, 2013 at 1:32 AM, Anastasia Yendiki 

wrote:

  Hi Susie - Everything under dlabel/diff is mapped to DWI space (either
  with flirt or with bbregister, whichever you use). The one in my
  screenshot was dlabel/diff/aparc+aseg.flt.nii.gz.

  a.y

  On Wed, 27 Mar 2013, Susan Kuo wrote:

Hi Anastasia, 
  I see what you mean. I had previously used the
dtifit_FA.nii.gz image and
overlaid that with the aparc+aseg+2mm.nii.gz image in
/dlabel/diff, using
freeview. I didn't end up with the same images as you,
however. Can you tell
me which images you used to obtain this overlay? 

  I am going to run bbregister tonight, and I'll let you know
how it goes --
I'm hopeful! 

Thank you again!

Susie Kuo
NIH

On Tue, Mar 26, 2013 at 5:35 PM, Anastasia Yendiki
 wrote:

      Hi Susie - I'm attaching a snapshot from your subject,
showing
      the aparc+aseg overlaid on the FA map. The registration
has
      failed. The frontal lobe has spilled out of the brain,
the white
      matter has spilled into the ventricles.

      I strongly recommend using bbregister for the
intra-subject
      registration, which is the default in the latest version
of
      trac-all.

      Hope this helps,
      a.y

      On Tue, 26 Mar 2013, Susan Kuo wrote:

            Hi Anastasia,   I did as you recommended and
checked
            the diffusion-to-anatomical
            registration, and the overlay of aparc+aseg_mask
on
            FA, and these views seem to be
            good. Upon closer inspection, what I find is that
            there are incipient 'bits' of all
            the tracts, but they seem to not have 'grown',
            though they are in the proper space
            (comparing them to good brains that yielded the
full
            complement of tracts). Is there a
            configuration in your TRACULA that controls the
            growing of the tracts specifically?
            Perhaps I should look into that. 

              Thank you, btw, for your very prompt reply
            yesterday- it was much appreciated!


            Sincerely, 
            Susie Kuo
            NIH

            On Mon, Mar 25, 2013 at 4:58 PM, Anastasia Yendiki
            
            wrote:

                  Hi Susan - Good to hear that you get good
            results for most of your
                  subjects. Have you checked the aparc+aseg
and
            the diffusion-to-anatomical
                  registration for the subjects that are
            failing? I'd check the
                  aparc+aseg_mask (in the dlabel/diff
directory)
            over the FA map to see if
                  there are any holes or misregistration.

                  a.y

                  On Mon, 25 Mar 2013, Susan Kuo wrote:

                        Hi FreeSurfers and Anastasia,  
TRACULA
            is working great for
                        me, generating tracts for a sample of
20
            subject
                        brains I'm working with. However, for
3
            of the brains, I'm
                        receiving incomplete and poorly formed
            tracts.
                        I've re-run trac-

Re: [Freesurfer] Incomplete and poorly formed tracts

[Susan Kuo]

Hi Anastasia,
  I'm attaching the graphic I arrived at with the command:

> freeview -tv /dlabel/diff/aparc+aseg.flt.nii.gz -v
/dmri/dtifit_FA.nii.gz

Here, I used the subject I send you (Sa69845.5) for the subjectID. I could
not detect spill over in these images, mostly because the frontal lobe is a
little cut off. Did you perhaps use a different viewer? I'm hoping to be
able to detect these mis-registrations better for myself in the future.
Thanks for all your help!

Sincerely,
Susie Kuo
NIH

On Wed, Mar 27, 2013 at 1:32 AM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:

>
> Hi Susie - Everything under dlabel/diff is mapped to DWI space (either
> with flirt or with bbregister, whichever you use). The one in my screenshot
> was dlabel/diff/aparc+aseg.flt.**nii.gz.
>
> a.y
>
>
> On Wed, 27 Mar 2013, Susan Kuo wrote:
>
>  Hi Anastasia,
>>   I see what you mean. I had previously used the dtifit_FA.nii.gz image
>> and
>> overlaid that with the aparc+aseg+2mm.nii.gz image in /dlabel/diff, using
>> freeview. I didn't end up with the same images as you, however. Can you
>> tell
>> me which images you used to obtain this overlay?
>>
>>   I am going to run bbregister tonight, and I'll let you know how it goes
>> --
>> I'm hopeful!
>>
>> Thank you again!
>>
>> Susie Kuo
>> NIH
>>
>> On Tue, Mar 26, 2013 at 5:35 PM, Anastasia Yendiki
>>  wrote:
>>
>>   Hi Susie - I'm attaching a snapshot from your subject, showing
>>   the aparc+aseg overlaid on the FA map. The registration has
>>   failed. The frontal lobe has spilled out of the brain, the white
>>   matter has spilled into the ventricles.
>>
>>   I strongly recommend using bbregister for the intra-subject
>>   registration, which is the default in the latest version of
>>   trac-all.
>>
>>   Hope this helps,
>>   a.y
>>
>>   On Tue, 26 Mar 2013, Susan Kuo wrote:
>>
>> Hi Anastasia,   I did as you recommended and checked
>> the diffusion-to-anatomical
>> registration, and the overlay of aparc+aseg_mask on
>> FA, and these views seem to be
>> good. Upon closer inspection, what I find is that
>> there are incipient 'bits' of all
>> the tracts, but they seem to not have 'grown',
>> though they are in the proper space
>> (comparing them to good brains that yielded the full
>> complement of tracts). Is there a
>> configuration in your TRACULA that controls the
>> growing of the tracts specifically?
>> Perhaps I should look into that.
>>
>>   Thank you, btw, for your very prompt reply
>> yesterday- it was much appreciated!
>>
>>
>> Sincerely,
>> Susie Kuo
>> NIH
>>
>> On Mon, Mar 25, 2013 at 4:58 PM, Anastasia Yendiki
>> 
>> wrote:
>>
>>   Hi Susan - Good to hear that you get good
>> results for most of your
>>   subjects. Have you checked the aparc+aseg and
>> the diffusion-to-anatomical
>>   registration for the subjects that are
>> failing? I'd check the
>>   aparc+aseg_mask (in the dlabel/diff directory)
>> over the FA map to see if
>>   there are any holes or misregistration.
>>
>>   a.y
>>
>>   On Mon, 25 Mar 2013, Susan Kuo wrote:
>>
>> Hi FreeSurfers and Anastasia,   TRACULA
>> is working great for
>> me, generating tracts for a sample of 20
>> subject
>> brains I'm working with. However, for 3
>> of the brains, I'm
>> receiving incomplete and poorly formed
>> tracts.
>> I've re-run trac-all at least 2x on each
>> subject in case there
>> was a mistake in my original
>> configuration.
>> However, I am reproducing the same
>> results. Does anybody have
>> an idea why I would see these "spotty"
>> tracts?
>>
>>
>> Thank you for all your help!
>>
>> --
>> Susie Kuo
>> NIH
>>
>>
>>
>>
>> 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
>>   

Re: [Freesurfer] Xhemi stat questions

[Gabriel Gonzalez Escamilla]

That makes much more sense than the thing I was looking for.Now I have a problem reading the lh.lh-rh.thickness.mgh with the load_mgh.m function, as I have no idea of how to read it to get the vertex by vertex thickness value of each subject.I tryed as [thick, ~,~,~]=load_mgh('file.mgh',[],[1:nSubjs])then reading: subjIDthick=thick(vtxID,1,1,subjID);where vtxID es the vertex of the .label file I want, and subjID is the number of the subject.is that correct?All this is because I will use it as a covariate in the statistical analysis as suggested in http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg27129.htmlRegards,Gabriel.El 26/03/13, Douglas N Greve   escribió:Unless you specifically need them for an individual, you should get them from lh.lh-rh.thickness.mgh because that data is sampled onto the symmetric template and so should be unbiased (ie, it will not systematically favor lh or rh).dougOn 03/26/2013 12:40 PM, Gabriel Gonzalez Escamilla wrote:> Dear Doug,>> I meant of a given subject,>> But, As I'm thinking about this, I'm wondering if it has sense to have > left and right cortical thickness of my every individual subjects, or > if I should obtain the lh-rh thickness differences for the individuals?>> I suppose that I should read the lh.lh-rh.thickness.mgh created by > mris_preproc to get the average differences in lh-rh hemispheres. Regards,> Gabriel> El 25/03/13, *Douglas N Greve *  escribió: Do you mean you want the right hemi thicknesses on the left hemisphere>> of a given subject or on the fsaverage_sym?>> doug>> On 03/25/2013 11:25 AM, Gabriel Gonzalez Escamilla wrote:>> > Thank you, so I'm keeping the one I had.>> >>> > Sorry for my bad explanation. When I do a normal cortical thickness>> > study, I know the average thickness for a label, e.g. cortex, and the>> > values at each vertex of each hemisphere are stored in>> > $subject/surf/?l.thickness. I would like to know if it is possible to>> > obtain the same cortical thickness measure from the lh-rh registered>> > hemispheres of each subject.>> >>> >>> > Regards,>> > Gabriel>> >>> >>> > El 25/03/13, *Douglas N Greve *  escribió:>>  >> On 03/25/2013 10:52 AM, Gabriel Gonzalez Escamilla wrote:>> >> >Thanks a lot for your answer,>> >> >>> >> >I'm sending you attached the diff of the two mris_preproc.>> >> Those differences are just added features and won't change your >> results.>> >> >>> >> >When I wrote CT, I was meaning cortical thickness, as normally this>> >> values are in surf/?h.thickness, But how do I know the>> >> Xhemi-registered thickness values of each subject for lh-rh, or area>> >> or any of those indices?>> >> I'm not sure what you mean. When you run mris_preproc, you specify>> >> whether you want thickness, etc.>> >> doug>> >> >>> >> >Regards,>> >> >Gabriel>> >> >>> >> >>> >> >El 25/03/13, *Douglas N Greve *  escribió:>> >>  >> >>On 03/22/2013 06:45 AM, Gabriel Gonzalez Escamilla wrote:>> >> >>> Dear Doug,>> >> > >> >>> I've seen that you restore the files to download, for the Xhemi>> >> >>> registration. While I'm checking for the statistical process, I've>> >> >>> seen that the one I have is: Date: 2012/12/06 16:06:52, Revision:>> >> >>> 1.59.2.4, and the one that is on your ftp server is Date: >> 2012/12/06>> >> >>> 16:06:17, Revision: 1.66, So mine is a lower version but >> recent hour,>> >> >>> and the actual is newer version but seems that was created >> before the>> >> >>> one I have. My question is, Which one should I keep?>> >> >>Can you send me a diff of the two files?>> >> > >> >>>  If I change the mris_precproc version. Shall I re-run this step>> >> >>> before statistical analyses, to create a new>> >> lh.lh-rh.thickness.sm00.mgh?>> >> > >> >>> On the other hand I have some doubts about the statistical >> procedure.>> >> >>> It's supposed that if I apply the Xhemi registration, as >> result the>> >> >>> left and right hemispheres are equals to each other on every>> >> subject, so:>> >> > >> >>> A) Where can I get the CT values after the Xhemi registration to>> >> >>> FSaverage_sym for the left and right hemispheres?>> >> >>what are CT values?>> >> > >> > >> >>> B) Given that I have two groups, Patients and Control, with two>> >> levels>> >> >>> each, i.e male-female (Gp1male Gp1female Gp2male Gp2female>> >> >>> Gp1maleVar1 Gp1femaleVar1 Grp2maleVar1 Grp2femaleVar1), and that>> >> I can>> >> >>> set the contrasts and fsgd files as with a normal CT analisis, but>> >> >>> only on my lh.lh-rh.thickness.smXX.mgh, wich is suppose to>> >> contain the>> >> >>> left-right differences across subjects, right?>> >> > >> >>> Wich would be the right interpretation? of:>> >> >>The interpretation does not really change because it is a xhemi>> >> analysis>> >> > >> >>> 1) 5 .5 -.5 -.5 0 0 0 0>> >> >>Is the L-R difference between Grp1 and Grp2 different than 0>> >> (regressing>> >> >>out Var1 and gender)>> >> > >> >>> 2) 5 -.5 .5 -.5 0 0 0 0>> >> >>Is the L-R diffe

Re: [Freesurfer] getting started with ROI & labels

[Bruce Fischl]

Hi Fred

the first thing to do is run recon-all on a good T1-weighted anatomical 
from each of your subjects. You can then use mri_label2label to map the 
labels from one subject onto another.


good luck
Bruce
On Wed, 27 Mar 2013, Fred Lado wrote:


Dear Freesurfers,I'm interested in using FS identified labels, such as Brodman 
areas in the anatomical volume, to measure
a feature, say mean intensity in V1, in a second volume registered to the 
first.  I'm new to the use of labels, so some
advice on where to start would be appreciated. Thanks,

Fred Lado, MD PhD
Director, Neurology Service - Moses & North Divisions
Director, EEG Laboratory
Associate Clinical Professor of Neurology
Montefiore Medical Center 
718-920-8499 office
718-324-3730 fax
email: fl...@montefiore.org

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Re: [Freesurfer] How to get surface-based AAL template

[ZhiLiangLong]

Dear Br:
   Thanks for your help. I have downloaded Colin 27 subject, and the Surfrend 
toolbox. But I still have some questions about the process.
   1. You said I need transform the Colin 27 to the latest FS version (v.5.2). 
But i don't know how to do this. It is helpful if you can provide some 
information.
  2. How does the Colin 27 space differs from fsaverage MNI305 space? The group 
analysis of cortical thickness is conducted in fsaverage space, after importing 
AAL ROI into Colin 27 space, should i  transform the obtained ROI into 
fsaverage space?
 3. i don't understand what is the register.dat between COlin 27 and SPM-s 
single subject t1.nii used for? I have tried the Surfrend, and found there was 
no entry for input of register file during the processing.

Looking forward to your reply.
Best wishes.

zhiliang




At 2013-03-27 13:29:01,"Garikoitz Lerma-Usabiaga"  wrote:

Hi, 
In my case transformation to fsaverage did not work very well. What I did was:
-  from Surfrend page download Colin 27 subject and transform it to the latest 
version (now 5.2)
- with bbregister obtain register.dat between this Colin 27 subject and SPM-s 
single subject t1.nii, which is the 2mm version of Colin 27. AAL-s are defined 
in Colin 27. As they are the same subject, the registering is very good.
- now you can import every AAL ROI (in .nii form) to an annotation or in the 
form of individual labels to your FS Colin 27, using the newly created 
registering file.
- now you can use surf2surf or label2label to go to your subjects and obtain 
stats.


Br!

On 27/03/2013, at 05:35, ZhiLiangLong  wrote:


Hi all;
  I need a suface-based aal template which is compatible with FS surface 
file. Is there a way i can get the surface-based aal template? I have an idea, 
that is to just transform the AAL template (.nii file) in MNI space onto the 
surface template (e.g. fsaverage template) in FS. Is it correct? if in this 
case, how can i do the transformation?
 
Any suggestions appreciated.
Besh wishes.



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[Freesurfer] iSurf BrainView now available for Windows 8 {Disarmed}

[Pedro Paulo de Magalhães Oliveira Junior]

Today Microsoft approved iSurf BrainView version for Windows 8 Tablets and
computers. It's a free App.

http://apps.microsoft.com/windows/en-us/app/brainview/be2623f5-c5e3-4295-a28e-d3f64dc19266

BrainView is a Brain MRI tutor based on the MRI automatic segmentation
produced by FreeSurfer.

FreeSurfer is a software package developed by investigators at the
Athinoula A. Martinos Center for Biomedical Imaging.

This App uses its automatic segmentation to produce an automatic atlas of
neuroimaging based on T1 MRI Images. It also displays 3D accurate models of
brain cortex with automatic structure labeling.

A great tool for teaching brain MRI and for learning neuroanatomy.

For more reference on the educational use of iSurf BrainView:
Oliveira Jr, PPM; Fischl, Bruce; Amaro, Edson "Teaching neuroanatomy using
Iphone and IPad. In: Human Brain Mapping, 2011, Quebec, CA. Proc. Human
Brain Mapping 2011, 2011."

-
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com 
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[Freesurfer] Question regarding the subject directory

[Lukas . Scheef]

Hi folks!

I would like to use a different subject dirctory (setenv SUBJECTS_DIR ). Does freesurfer still finds the folders which are
located in the default subjects directory of the FS installation? Or are
they simply not needed for the recon-all process ? I refer to cvs_avg35
etc. not to the test data sets.

Please excuse if this question is stupid ... but considering the
processsing time ...

Many thanks in advance,

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[Freesurfer] Correlation with cortical thickness

[Martijn Steenwijk]

Dear all,

I've a question regarding computing correlations with cortical thicknesses
on the surface; Suppose I have two variables for each subject: (age and
weight) and I want to compute the correlation between cortical thickness
and weight, corrected for age.

Option 1:
Fsgd contains: Variables weight
Contrast file contains: 0 1

Option 2:
Fsgd contains: Variables age weight
Contrast file contains: 0 0 1

Is it true that the effect of age is regressed out in the second option;
and it computes the correlation between CT and weight after correcting for
age?

Best,
Martijn
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[Freesurfer] Fwd: Cortical thickness in average space

[Rafa X]

Thanks Bruce for your answer, as you asked I'm forwarding this
question to the list in case any other can answer this.

We already have the surface generated by mri_preproc, now we are
trying to read it using the matlab function read_mgh. It returns a 4-D
matrix, how can we interpret this data to get the cortical thickness
values at each vertex of every subject?

Rafa & Gabi

2013/3/26 Bruce Fischl :
> Hi Rafa and Gabi
>
> yes, that's pretty much what the -qcache flag does in recon-all. Or you can
> use mri_surf2surf to do it.
>
> cheers
> Bruce
>
> On Tue, 26 Mar 2013, Rafa X wrote:
>
>> Hi Freesurfers,
>> We would need to obtain the cortical thickness of each subject in the
>> space of the average subject (built from our subject population), Does
>> it exists?
>> If so, Can I use the label files produced by mri_surfcluster to
>> directly extract the mean cortical thickness of each ROI in each
>> subject? We want to avoid to trasform each cluster to every subject.
>>
>> Thank you all in advance,
>> Rafa & Gabi.
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>>
>>
>
>
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Re: [Freesurfer] surf2vol

[Daniel Lumsden]

Doug

The .nii.gz file is completely empty and doesn't come up on any viewer 
(fslview, tkmedit, freeview, mricron etc). The .gi files I've generated appear 
to be tracking in probtrackx (though slowly on my laptop - probably not 
expected given the sizes of the surfaces). I can also generate binary 
volumetric masks from the labels using mri_binarize (though they are a little 
bit "speckled" - with scattered blank voxels).

On my installation I'm having some intermittent difficulties with tkmedit and 
tksurfer (not consistently opening, sometimes coming up with "bus error"). 
Freeview is opening consistently though. I'm not sure if this could be having 
an affect but I was planning on reinstalling freesurfer today to see if that 
fixed it.

Thank you again for your help

Dan

Does leftfrontallobe.nii.gz overlay properly in tkmedit? eg,
tkmedit subject orig.mgz -surfs -overlay leftfrontallobe.nii.gz -fminmax 
.5 1
dougOn 03/26/2013 07:20 AM, Daniel Lumsden wrote:
> Bruce
>
> Many thanks - that's given me a lot more guidance. Following the help, 
> i've put together the command below:
>
> mri_surf2vol --hemi lh --template /orig.mgz --outvol  where I want the file>/leftfrontallobe.nii.gz --surfval  to>/left_frontal_lobe.gii --fillribbon --volregidentity mov07
>
> Where mov07 is my subjid and left_frontal_lobe.gii is the surface I've 
> generated from the label files to run in probtrakx. This command runs, 
> but produces and empty nifti file. I've changed the output to .mgz 
> with similar effect. I've substituted the rawavg.mgz file for the 
> orig.mgz file, and tried both .nii.gz and .mgz versions of both files 
> and still get an empty output file.  The subject is in my $SUBJECTS_DIR.
>
> Is there a way to check the .gii files? I generated them using 
> label2surf, having used mris_convert to convert the lh.white and 
> rh.white files from the surf folder for my subject to lh.white.asc and 
> rh.white.asc.
>
> Thank you again for your help.
>
> Dan
>
>
> > Date: Mon, 25 Mar 2013 14:59:28 -0400
> > From: fis...@nmr.mgh.harvard.edu
> > To: doclums...@hotmail.com
> > CC: freesurfer@nmr.mgh.harvard.edu
> > Subject: Re: [Freesurfer] surf2vol
> >
> > Hi Dan
> >
> > try using mri_surf2vol instead (it has a much bigger help, thanks to
> > Doug0
> > Bruce
> > On Mon, 25 Mar 2013, Daniel Lumsden wrote:
> >
> > > Dear All
> > >
> > > Apologies for what I'm sure is a very basic question. I'm new to 
> using freesurfer, and would like to generate cortical
> > > parcellations for running in probtrakx. I have followed the 
> instructions from various sources and have managed to generate the
> > > parcellations from recon-all, extract the label files from the 
> parcellation, then use mri_mergelabels and label2surf to generate
> > > the  the .gii files needed for probtrakx. I'd like to be able to 
> display the surface files for illustrative purposes, but I'm
> > > struggling to apply the surf2vol command.
> > >
> > > From the terminal window I can see that the commands required are:
> > >
> > > surf2vol
> > >
> > > I presume that  is the .gii file I'm trying to visualise, 
> and  is to specify the name of the output volume the
> > > command will generate, but what should I be using as the ? 
> I would be very grateful for any guidance. Please accept my
> > > apologies if I've missed a very obvious online explanation for 
> this and thank you in advance.
> > >
> > > Dan Lumsden
> > > Clinical Research Fellow
> > >
> > >
> >
> >
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