date:20130807


Hi Yunxin

can you explain a bit more about what you are trying to achieve? We 
already provide a tesselated representation of the pial surface. I 
don't think it will be possible to discretize it into a volume and 
retesseelate with a fast marching algorithm without giving up lots of 
accuracy


cheers
Bruce


On Wed, 7 Aug 2013, Yunxin Wang wrote:


Hi Bruce,
Thanks very much for the explanation. According to your suggestion, I think 
maybe I should try to figure it out with a 2D fast
marching process. I could extract it to a 2 dimension matrix by matlab with 
FreeSurfer package, right?

Best,
Yunxin 


2013/8/6 Bruce Fischl fis...@nmr.mgh.harvard.edu
  Hi Yunxin

  could you cc the list so that others can answer? I don't think you will 
be able to get a reasonable surface out of a
  discretized 256*3 volume for the pial surface. There are many, many 
places where the pial surface comes within a
  fraction of a mm of itself that you will not be able to represent.

  cheers
  Bruce

  On Tue, 6 Aug 2013, Yunxin Wang wrote:

Hi Bruce,
Thanks for your response. Actually I want to use the fast marching 
toolbox
to further analyze the pial surface that FreeSurfer has 
reconstructed
automatically, but according to the procedure only the pial surface 
will be
used for fast marching process and I found out the input file of 
fast
marching is a 256*256*256 matlab file which I could just load in 
matlab but
couldn't see any detail. Do you think I can use the 
freesurfer_read_surf
function in matlab to transfer the surface? 

Best,
Yunxin


2013/8/5 Bruce Fischl fis...@nmr.mgh.harvard.edu
      Hi Yunxin

      the surface lives in a continuum and is 2D. Do you mean 
filling
      the space between the ?h.white and ?h.pial surfaces? We do 
that
      as part of recon-all and create ribbon volumes in the mri dir
      cheers
      Bruce


      On Mon, 5 Aug 2013, Yunxin Wang wrote:

            Hi dear all,
            I'm new here and I've a simple question that how
            could I transfer the reconstructed pial surface
            file(like lh.pial) into a
            256*256*256 matlab matrix used in later fast
            marching process?

            Any suggestion will be appreciated!
            Thank guys.

            Best,
            Yunxin Wang






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[Freesurfer] set message

Hi folks,

When issuing a recon-all command, I'm seeing the following message:

set: Variable name must contain alphanumeric characters

recon-all stalls and doesn't move forward (doesn't even create the subject
directory).

I'm using Freesurfer 5.3.0
(freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0) on Ubuntu 12.04.2. In
fact, we just upgraded to this version of Ubuntu from an older version of
Mandriva and to this latest version of Freesurfer. recon-all did not
produce this message before these two upgrades. Any help you can offer
would be most appreciated! Thanks in advance.

Best,

Heather

-- 
Heather L. Urry, Ph.D.
Department of Psychology
Tufts University
490 Boston Avenue
Medford, MA 02155

email: heather.u...@tufts.edu
phone:  617-627-3733
fax: 617-627-3181

http://ase.tufts.edu/psychology/ebbl
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[Freesurfer] mri_cvs_register for EPI

2013-08-07 Thread Marcel Falkiewicz

Hello,
 I'm trying to use mri_cvs_register (whose registration accuracy is, by the
way, jaw-dropping) for EPI images. However, the descriptions which I've
found on the web do not make the task easier. My goal is to get functional
images in cvs_avg35_inMNI152 space, resampled to 3mm isotropic resoluton
(for subsequent ICA analysis). I'm taking following steps:

1. recon-all on anatomical data (obvious)

2. mri_cvs_register (mri_cvs_register --targ cvs_avg35_inMNI152 --mov
subject)

I do not understand what the files stored in cvs folder are needed for. As
far as I understand the normalization process, I need a file which stores
the subject - template warp. Which file is it? Do I need to use the
--nocleanup option in mri_cvs_register to get the aforementioned file?

In the wiki page a following command line is recommended to reconstruct
this warp when the --nocleanup options was not used:

createMorph --out fullCVSmorph.tm3d --template template.mgz \

   - --subject movingvol.mgz --in gcam nlalign-afteraseg-norm.m3z \ morph
   el_reg_toTEMPLATE.tm3d

However, there is no single *.tm3d file in my cvs directory... Here are the
files that are present:

el_reg_tocvs_avg35_inMNI152.affine.mgz
el_reg_tocvs_avg35_inMNI152_aseg.mgz
el_reg_tocvs_avg35_inMNI152.mgz
final_CVSmorphed_tocvs_avg35_inMNI152_aseg.mgz
final_CVSmorphed_tocvs_avg35_inMNI152_norm.mgz
final_CVSmorph_tocvs_avg35_inMNI152.m3z
lh.dbg_surf.pial
lh.dbg_surf.white
lh.resample.aparc.annot
lh.resample.pial
lh.resample.white
nlalign-afteraseg-norm.mgz
nlalign-aseg.mgz
rh.dbg_surf.pial
rh.dbg_surf.white
rh.resample.aparc.annot
rh.resample.pial
rh.resample.white
step1_CVSmorphed_tocvs_avg35_inMNI152_aseg.mgz
step1_CVSmorphed_tocvs_avg35_inMNI152_norm.mgz
summary.AC1004_to_cvs_avg35_inMNI152.mri_cvs_register.1308031447.log
transform.txt

In my particular case, which images should be entered as arguments to
--template and --subject ?


3. standard EPI pre-processing, which results in motion-correction
parameters and realigned images

4. coregistration of EPI to anatomical data with BBR. The transformation is
stored as register.dof6.dat, which contain the mapping EPI - anatomical

I understand that the next step is combining the registrations from step
(2) and (4) in order to get EPI images in cvs_MNI space. This can be
accomplished with mri_vol2vol. However, I do not understand which files
should be used for this registration.


Sorry for the lenghty post, but I'm quite new to freesurfer and I'm a bit
confused:)


Best regards,
 Marcel
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Re: [Freesurfer] Longitudinal correction of volumes - eTIV


Hi Alex, use the eTIV from the longitudinal subject. In theory, the size 
of the skull is not changing, and the longitudinal analysis gives you 
the best estimate of this unchanging number.
doug

On 08/06/2013 06:00 PM, Alex Hanganu wrote:
 Hello,

 I am measuring the changes of subcortical volumes in a longitudinal 
 study, so I took the volumes from longitudinal subjects 
 (/name.long.base/). Now we need to perform the correction using the 
 eTIV parameter, but the eTIV for longitudinal subjects for all time 
 points is the same (/i//.e. eTIV for subject-time1.long.base = eTIV 
 for subject-time2.long.base/)

 Is it correct to perform the correction using the eTIV values from the 
 longitudinal subjects, or we should use these measures from the 
 cross-sectional corresponding subjects ?

 Thanks,

 Alex.


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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] set message

what is your command line?




On 08/07/2013 10:19 AM, Heather L. Urry wrote:
 Hi folks,

 When issuing a recon-all command, I'm seeing the following message:

 set: Variable name must contain alphanumeric characters

 recon-all stalls and doesn't move forward (doesn't even create the 
 subject directory).

 I'm using Freesurfer 5.3.0 
 (freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0) on Ubuntu 12.04.2. 
 In fact, we just upgraded to this version of Ubuntu from an older 
 version of Mandriva and to this latest version of Freesurfer. 
 recon-all did not produce this message before these two upgrades. Any 
 help you can offer would be most appreciated! Thanks in advance.

 Best,

 Heather

 -- 
 Heather L. Urry, Ph.D.
 Department of Psychology
 Tufts University
 490 Boston Avenue
 Medford, MA 02155

 email: heather.u...@tufts.edu mailto:heather.u...@tufts.edu
 phone:  617-627-3733
 fax: 617-627-3181

 http://ase.tufts.edu/psychology/ebbl


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

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] Longitudinal correction of volumes - eTIV

2013-08-07 Thread Alex Hanganu

Thank you Doug !



Le 7/8 11:44, Douglas N Greve a écrit :
 Hi Alex, use the eTIV from the longitudinal subject. In theory, the size
 of the skull is not changing, and the longitudinal analysis gives you
 the best estimate of this unchanging number.
 doug

 On 08/06/2013 06:00 PM, Alex Hanganu wrote:
 Hello,

 I am measuring the changes of subcortical volumes in a longitudinal
 study, so I took the volumes from longitudinal subjects
 (/name.long.base/). Now we need to perform the correction using the
 eTIV parameter, but the eTIV for longitudinal subjects for all time
 points is the same (/i//.e. eTIV for subject-time1.long.base = eTIV
 for subject-time2.long.base/)

 Is it correct to perform the correction using the eTIV values from the
 longitudinal subjects, or we should use these measures from the
 cross-sectional corresponding subjects ?

 Thanks,

 Alex.


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

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[Freesurfer] Tracula question

2013-08-07 Thread Alan Francis

Hi Anastasia:

For one brain I got this error message :

csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons]
: trac-all -prep -c
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc-107

Too many ('s.
ERROR: must specify as many DWI dicoms as subjects

I tried specifying the exact number of DWI dicoms but it is not working.
Should I send you my dmrirc for this brain?

thanks,

Alan
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Re: [Freesurfer] trac-all inquiry



Hi David - Every time you run trac-all, the results get appended to this 
file, so you need to look for error messages only in the more recent 
invocation of trac-all. The first error there seems to be:


Error: bvecs and bvals don't have the same number of entries

Do you have the same number of b-values and gradient vectors and volumes 
in your DWI series?


a.y

On Tue, 6 Aug 2013, Soto, David wrote:


hi

I upgraded to FS 5.3 but still encountering issues with
trac-all prep.

The log is attached, things I noted after inspecting it

1)  INFO: FreeSurfer build stamps do not match
Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0

2) Error: input image /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb 
not valid
3) Image Exception : #22 :: ERROR: Could not open image 
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb_brain
4) Image Exception : #22 :: ERROR: Could not open image
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/diff/White-Matter++.
5) ERROR: Could not read 
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/dtifit_FA.nii.gz
but despite all this it says:
trac-preproc finished without error at Tue Aug  6 21:27:30 BST 2013

thanks for your help

cheers
ds

http://www1.imperial.ac.uk/medicine/people/d.soto/





From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu]
Sent: 06 August 2013 19:30
To: Soto, David
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer]  trac-all inquiry

I see, you're using the old version of tracula (from freesurfer 5.1). In
that version, you had to define the number of low-b images in the
configuration file. I strongly recommend updating to freesurfer 5.3. A lot
of things have improved in tracula since then.

Also, in the future please attach any log files as separate attachments
instead of pasting them into the body of your email - this causes the body
of the email to exceed the limit allowable on the list.

Thanks,
a.y


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Re: [Freesurfer] Tracula question


Yes, please attach the dmrirc and trac-all.log. Thanks!

a.y

On Wed, 7 Aug 2013, Alan Francis wrote:

 Hi Anastasia:
 
 For one brain I got this error message :
 
 csh::alanf@cerebro 
 [/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons]
  : trac-all -prep
 -c 
 /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc-107
 
 Too many ('s.
 ERROR: must specify as many DWI dicoms as subjects
 
 I tried specifying the exact number of DWI dicoms but it is not working. 
 Should I send you my dmrirc for this brain?
 
 thanks,
 
 Alan
 

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Re: [Freesurfer] Validation of results

2013-08-07 Thread Sinead Kelly

Hi Doug,

I can't visualize the maps on the linux server I'm using but I have the
cluster summary files below for DODS and DOSS. As you can see they are
quite different. What do you think might be driving the DODS result? I want
to look at the difference in surface area between the two genotype groups
while regressing out the effects of age and gender. Is this a non result?
Thank you for your help!

Sinead

DODS
ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWPCWPLow
CWPHi NVtxs Annot
1 -3.298 36614541.01-26.0 -53.1 62.2 0.77340 0.76580
0.78100 1177 superiorparietal
22.9189004 1642.43 -8.59.7 65.2 0.01020 0.00840
0.01200 2790 superiorfrontal
32.626 126211363.55-30.3 -65.2 40.5 0.98580 0.98360
0.98800 817 inferiorparietal
42.4416490313.02-30.5 -35.1 58.4 0.99660 0.99560
0.99760 693 postcentral
52.375 107140 1095.56-10.9 -57.2 44.7 0.09720 0.09180
0.10260 2308 precuneus
62.347 132687414.79-38.62.1 24.8 0.95300 0.94920
0.95680 974 precentral
72.284 97632 1510.86-41.4 -50.0 -14.4 0.01820 0.01580
0.02060 2446 fusiform
82.122 111909365.94-49.2 -29.5 -3.0 0.98480 0.98260
0.98700 837 superiortemporal
92.070 74111444.95-54.7 -42.06.3 0.92120 0.91620
0.92600 998 bankssts
101.809 85712281.07-57.0 -30.8 21.7 0.99860 0.99800
0.99920 598 supramarginal
111.796 121724312.87-10.0 64.36.5 0.99660 0.99560
0.99760 485 superiorfrontal

DOSS
ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZCWPCWPLow
CWPHi NVtxs Annot
1 -2.520 76782605.90-27.75.0 51.5 0.66030
0.65420 0.66640 1055 caudalmiddlefrontal
22.125 116630316.10-36.3 -83.8 -15.4 0.99640
0.99560 0.99720 415 lateraloccipital
3 -2.076 80150568.86-40.26.5 20.9 0.73090
0.72520 0.73660 1240 parsopercularis

On 5 August 2013 05:05, Douglas Greve gr...@nmr.mgh.harvard.edu wrote:

Hi Sinead, that all looks good. The only thing I would do differently
would be to test whether there is a difference in age-area slopes between
TT and TG (contrast 0 0 0 0 -.5 -.5 .5 .5). If there is, then that makes
the difference of the intercepts between the areas of the groups. If no
difference that survives multiple comparisons, then you can re-run your
group difference using the DOSS model, ie, add doss after the fsgd file
on the mri_glmfit command line, and use a contrast of [-.5 -.5 .5 .5 0].
The DOSS model forces the slopes to be the same which assures that the
difference in intercept is interpretable.

Finally, if you are using version 5.1 or lower, you will need to get a
patch and rerun mris_preproc.

For a description of the method used for correction, you can use the text
from Greve, et al,
A Surface-based Analysis of Language Lateralization and Cortical
Asymmetry.http://www.researchgate.net/publication/236906359_A_Surface-based_Analysis_of_Language_Lateralization_and_Cortical_AsymmetryJournal
of Cog Neurosci. 2013.

doug

On 7/30/13 7:53 AM, Sinead Kelly wrote:

Dear freesurfer users,

I would really appreciate if anybody could confirm that I have preformed
my analysis correctly as I have very little experience with freesurfer and
I want to make sure that my result is a true finding. Firstly, I am looking
at the effect of a schizophrenia risk variant on cortical surface area in a
large sample of healthy controls.

a. I performed preprocessing on all of my subjects using *recon-all.*
b. I then qcached my data (resampling it to the average subject -*fsaverage
*)
c. An FSGD file was then created for statistical analysis to look at
differences between TT carriers and TG carriers with age and gender as
covariates of no interest. Here is an example of the file I created:

GroupDescriptorFile 1
Title MIR137
Class TTMale
Class TTFemale
Class TGMale
Class TGFemale

Variables Age
Input CON3140 TGFemale 37
Input CON3891 TTFemale 33
Input CON4664 TTFemale 40
Input CON5591 TTMale 41
Input CON7009 TGMale 21
Input CON7024 TTMale 59
Input CON7038 TTMale 56
Input CON7050 TTMale 30
Input CON7054 TTMale 43
Input CON7055 TTMale 43
Input CON7072 TTFemale 41

d. I applied the following contrast:

-0.5 -0.5 0.5 0.5 0 0 0 0

e. I followed the online tutorial by firstly running the
*mris_preproc*script with
*area.fwhm10.fsaverage* as my input file. Is this correct? (I ran this
separately for the left and right hemisphere).
f. I then ran the *mri_glmfi*t script followed by the *mri_glmfit-sim*script:
*mri_glmfit-sim --glmdir rh.MIR137_area.glmdir --sim mc-z 5000 1.3
mc-z.abs --sim-sign abs --cwpvalthresh .999 --overwrite* (I ran this
separately for each hemisphere)

Does this look correct?

When this ran I then checked the

Re: [Freesurfer] set message

Here it is:

recon-all -i /home/hurry01/r/resdep_mri_data/resdep014/265000-10-1.dcm -s
resdep214 -all 

(sorry for not thinking to include it originally)

Heather


On Wed, Aug 7, 2013 at 11:48 AM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:

 what is your command line?




 On 08/07/2013 10:19 AM, Heather L. Urry wrote:
  Hi folks,
 
  When issuing a recon-all command, I'm seeing the following message:
 
  set: Variable name must contain alphanumeric characters
 
  recon-all stalls and doesn't move forward (doesn't even create the
  subject directory).
 
  I'm using Freesurfer 5.3.0
  (freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0) on Ubuntu 12.04.2.
  In fact, we just upgraded to this version of Ubuntu from an older
  version of Mandriva and to this latest version of Freesurfer.
  recon-all did not produce this message before these two upgrades. Any
  help you can offer would be most appreciated! Thanks in advance.
 
  Best,
 
  Heather
 
  --
  Heather L. Urry, Ph.D.
  Department of Psychology
  Tufts University
  490 Boston Avenue
  Medford, MA 02155
 
  email: heather.u...@tufts.edu mailto:heather.u...@tufts.edu
  phone:  617-627-3733
  fax: 617-627-3181
 
  http://ase.tufts.edu/psychology/ebbl
 
 
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 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Department of Psychology
Tufts University
490 Boston Avenue
Medford, MA 02155

email: heather.u...@tufts.edu
phone:  617-627-3733
fax: 617-627-3181

http://ase.tufts.edu/psychology/ebbl
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Re: [Freesurfer] set message

and what shell are you using
On Wed, 7 Aug 2013, Douglas N Greve wrote:

 what is your command line?




 On 08/07/2013 10:19 AM, Heather L. Urry wrote:
 Hi folks,

 When issuing a recon-all command, I'm seeing the following message:

 set: Variable name must contain alphanumeric characters

 recon-all stalls and doesn't move forward (doesn't even create the
 subject directory).

 I'm using Freesurfer 5.3.0
 (freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0) on Ubuntu 12.04.2.
 In fact, we just upgraded to this version of Ubuntu from an older
 version of Mandriva and to this latest version of Freesurfer.
 recon-all did not produce this message before these two upgrades. Any
 help you can offer would be most appreciated! Thanks in advance.

 Best,

 Heather

 --
 Heather L. Urry, Ph.D.
 Department of Psychology
 Tufts University
 490 Boston Avenue
 Medford, MA 02155

 email: heather.u...@tufts.edu mailto:heather.u...@tufts.edu
 phone:  617-627-3733
 fax: 617-627-3181

 http://ase.tufts.edu/psychology/ebbl


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Re: [Freesurfer] set message

Ah, sorry-- that too:   tcsh 6.18.01.

(The command, which I just sent in a previous message, was as follows:

recon-all -i /home/hurry01/r/resdep_mri_data/resdep014/265000-10-1.dcm -s
resdep214 -all 

)

Heather


On Wed, Aug 7, 2013 at 12:42 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote:

 and what shell are you using
 On Wed, 7 Aug 2013, Douglas N Greve wrote:

  what is your command line?
 
 
 
 
  On 08/07/2013 10:19 AM, Heather L. Urry wrote:
  Hi folks,
 
  When issuing a recon-all command, I'm seeing the following message:
 
  set: Variable name must contain alphanumeric characters
 
  recon-all stalls and doesn't move forward (doesn't even create the
  subject directory).
 
  I'm using Freesurfer 5.3.0
  (freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0) on Ubuntu 12.04.2.
  In fact, we just upgraded to this version of Ubuntu from an older
  version of Mandriva and to this latest version of Freesurfer.
  recon-all did not produce this message before these two upgrades. Any
  help you can offer would be most appreciated! Thanks in advance.
 
  Best,
 
  Heather
 
  --
  Heather L. Urry, Ph.D.
  Department of Psychology
  Tufts University
  490 Boston Avenue
  Medford, MA 02155
 
  email: heather.u...@tufts.edu mailto:heather.u...@tufts.edu
  phone:  617-627-3733
  fax: 617-627-3181
 
  http://ase.tufts.edu/psychology/ebbl
 
 
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  Freesurfer@nmr.mgh.harvard.edu
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 
 
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 e-mail
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-- 
Heather L. Urry, Ph.D.
Department of Psychology
Tufts University
490 Boston Avenue
Medford, MA 02155

email: heather.u...@tufts.edu
phone:  617-627-3733
fax: 617-627-3181

http://ase.tufts.edu/psychology/ebbl
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[Freesurfer] mri_ca_train UCHAR/FLOAT

2013-08-07 Thread Mark Plantz

Hello freesurfers,

   I am currently attempting to run mri_ca_train to create a .GCA atlas
based of off a series of subjects. I am receiving the following error:

***
processing subject CMH-3074, 1 of 10...
mri_ca_train: segmentation file
/Volumes/Wong_Lab/LabMRIData/FreeSurfer/CMH-3074/mri/seg_edited.mgz is not
type UCHAR or FLOAT



Is there an easy way to convert the file to UCHAR or FLOAT in FreeSurfer?
Will this change the data/labels?

Thank you!

-MP
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Re: [Freesurfer] mri_ca_train UCHAR/FLOAT


yes, mri_convert -odt float will do it. What format is it in?

On Wed, 7 Aug 2013, Mark 
Plantz wrote:



Hello freesurfers,
   I am currently attempting to run mri_ca_train to create a .GCA atlas based 
of off a series of subjects. I am receiving the
following error:

***
processing subject CMH-3074, 1 of 10...
mri_ca_train: segmentation file 
/Volumes/Wong_Lab/LabMRIData/FreeSurfer/CMH-3074/mri/seg_edited.mgz is not type 
UCHAR or FLOAT



Is there an easy way to convert the file to UCHAR or FLOAT in FreeSurfer? Will 
this change the data/labels?

Thank you!

-MP

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Re: [Freesurfer] mri_ca_train UCHAR/FLOAT

2013-08-07 Thread Mark Plantz

It is currently in INT format. Thank you.

MP


On Wed, Aug 7, 2013 at 11:51 AM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote:

 yes, mri_convert -odt float will do it. What format is it in?


 On Wed, 7 Aug 2013, Mark Plantz wrote:

  Hello freesurfers,
I am currently attempting to run mri_ca_train to create a .GCA atlas
 based of off a series of subjects. I am receiving the
 following error:

 
 ***
 processing subject CMH-3074, 1 of 10...
 mri_ca_train: segmentation file /Volumes/Wong_Lab/LabMRIData/**
 FreeSurfer/CMH-3074/mri/seg_**edited.mgz is not type UCHAR or FLOAT



 Is there an easy way to convert the file to UCHAR or FLOAT in FreeSurfer?
 Will this change the data/labels?

 Thank you!

 -MP




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 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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  If the e-mail was sent to you in error
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[Freesurfer] 5.3.0 patch

2013-08-07 Thread Moran Cohn

Dear Freesurfer experts,
I recently installed the stable 5.3.0 version of Freesurfer (CentOS 4, 64-bit) 
and encountered the known problem with the missing ribbon.mgz file when running 
-autorecon1 -autorecon2. I wonder how I can obtain the patch mentioned for this 
problem in the release notes, and would be very thankful for your help.
Kind regards,
Moran Cohn





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u niet de geadresseerde(n) bent, wordt u verzocht de verzender hiervan op de 
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Re: [Freesurfer] Tracula question

2013-08-07 Thread Alan Francis

Thank you Anastasia. Another brain had a different problem: Here is the
trac-all log:

mri_concat --i
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_frame.nii.gz
--mean --o
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/lowb.nii.gz
niiRead(): error opening file
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_frame.nii.gz
ninputs = 1
Checking inputs
ERROR: reading
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_frame.nii.gz
Linux cerebro 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013
x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Wed Aug 7 13:01:21 EDT 2013

thanks so much,

Alan

On Wed, Aug 7, 2013 at 1:11 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:

Hi Alan - Try removing the \ character from the end of the dcmlist
definition. That's a change of line character.

a.y

On Wed, 7 Aug 2013, Alan Francis wrote:

Hi Anastasia:

Here is the trac-all log. Please find attached the dmrirc file.

csh::alanf@cerebro [/autofs/space/dali_003/users/**
BW_project_DTI/FreeSurfer_5.3_**Data/diffusion_recons] : trac-all -prep
-c /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_**
Data/diffusion_recons/dmrirc-**107

Too many ('s.
ERROR: must specify as many DWI dicoms as subjects

Thank you so much.

Alan

On Wed, Aug 7, 2013 at 12:32 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:

Yes, please attach the dmrirc and trac-all.log. Thanks!

a.y

On Wed, 7 Aug 2013, Alan Francis wrote:

Hi Anastasia:

For one brain I got this error message :

csh::alanf@cerebro
[/autofs/space/dali_003/users/**
BW_project_DTI/FreeSurfer_5.3_**Data/diffusion_recons] : trac-all
-prep
-c /autofs/space/dali_003/users/**
BW_project_DTI/FreeSurfer_5.3_**Data/diffusion_recons/dmrirc-**107

Too many ('s.
ERROR: must specify as many DWI dicoms as subjects

I tried specifying the exact number of DWI dicoms but it is
not working. Should I send you my
dmrirc for this brain?

thanks,

Alan

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[Freesurfer] Different results in surface and volume analyses

2013-08-07 Thread Emily Boeke

Hello everyone,

I am looking at a visual stimulus vs fixation contrast in my individual 
subjects' data to make sure we are seeing normal activation there. If I look at 
the surface data in tksurfer, I see activation in the occipital cortex, but in 
the mni305 analysis, there is no activation in this region.

These are the preprocess , mkanalysis, and selxavg commands I used for the 
surface vs. mni305:

preproc-sess -s amur_dss -df sesspar -per-run -fwhm 5 -sliceorder down -surface 
fsaverage lhrh -mni305-2mm -fsd cond

mkanalysis-sess -fsd cond -surface fsaverage lh -fwhm 5 -paradigm 
Fear_Gen_Cond.par -event-related -TR 3 -nconditions 3 -polyfit 4 -spmhrf 0 
-refeventdur 6 -analysis cond.sm05.lh -per-run -nskip 4 -stc down

mkanalysis-sess -fsd cond -surface fsaverage rh -fwhm 5 -paradigm 
Fear_Gen_Cond.par -event-related -TR 3 -nconditions 3 -polyfit 4 -spmhrf 0 
-refeventdur 6 -analysis cond.sm05.rh -per-run -nskip 4 -stc down

mkanalysis-sess -fsd cond -mni305 2 -fwhm 5 -paradigm Fear_Gen_Cond.par 
-event-related -TR 3 -nconditions 3 -polyfit 4 -spmhrf 0 -refeventdur 6 
-analysis cond.sm05.mni305 -per-run -nskip 4 -stc down

selxavg3-sess -s amur_dss -df sesspar -analysis cond.sm.lh
selxavg3-sess -s amur_dss -df sesspar -analysis cond.sm.rh
selxavg3-sess -s amur_dss -df sesspar -analysis cond.sm.mni305

Why might we be seeing this activation on the surface map but not the volume 
one?

Thanks!
Emily
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Re: [Freesurfer] Tracula question

Please attach the file trac-all.log. I can't tell what's going on just by
looking at the end of it.

On Wed, 7 Aug 2013, Alan Francis wrote:

Thank you Anastasia. Another brain had a different problem: Here is the
trac-all log:

trac-preproc exited with ERRORS at Wed Aug 7 13:01:21 EDT 2013

thanks so much,

Alan

On Wed, Aug 7, 2013 at 1:11 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:

Hi Alan - Try removing the \ character from the end of the dcmlist
definition. That's a change of line
character.

a.y

On Wed, 7 Aug 2013, Alan Francis wrote:

Hi Anastasia:

Here is the trac-all log. Please find attached the dmrirc file.

csh::alanf@cerebro

[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons]
: trac-all
-prep
-c
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc-107

Too many ('s.
ERROR: must specify as many DWI dicoms as subjects

Thank you so much.

Alan

On Wed, Aug 7, 2013 at 12:32 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:

Yes, please attach the dmrirc and trac-all.log. Thanks!

a.y

On Wed, 7 Aug 2013, Alan Francis wrote:

Hi Anastasia:

For one brain I got this error message :

csh::alanf@cerebro
[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons]
: trac-all
-prep
-c

/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc-107

Too many ('s.
ERROR: must specify as many DWI dicoms as subjects

I tried specifying the exact number of DWI dicoms but
it is not working. Should I
send you my
dmrirc for this brain?

thanks,

Alan

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Re: [Freesurfer] 5.3.0 patch


get mri_segstats from here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats
then
cp mri_segstats $FREESURFER_HOME/bin

doug



On 08/07/2013 01:09 PM, Moran Cohn wrote:

 Dear Freesurfer experts,

 I recently installed the stable 5.3.0 version of Freesurfer (CentOS 4, 
 64-bit) and encountered the known problem with the missing ribbon.mgz 
 file when running –autorecon1 –autorecon2. I wonder how I can obtain 
 the patch mentioned for this problem in the release notes, and would 
 be very thankful for your help.

 Kind regards,

 Moran Cohn


 
 Dit e-mailbericht is alleen bestemd voor de geadresseerde(n). Het kan 
 informatie bevatten die persoonlijk is en niet openbaar mag worden 
 gemaakt krachtens wet- of regelgeving. Gebruik door anderen is niet 
 toegestaan. Indien u niet de geadresseerde(n) bent, wordt u verzocht 
 de verzender hiervan op de hoogte te stellen en het bericht te verwijderen


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

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] set message

Ah! That was helpful, Doug. While eliminating the  at the end didn't do
anything, running the debug version of the command shows the following at
the end of log.txt (attached):

set subjdir = $SUBJECTS_DIR/$subjid
set subjdir = /home/hurry01/.gvfs/ebblvm$ on
callunavm.psy.tufts.edu/projects/resdep/data/mri/resdep214

This is where the set message gets spit out. It's - for obvious reasons -
not happy with that path. I'll work with IT over on this end as it likely
has something to do with the way we're mounting the Windows shares on which
data are stored and processed.

Best,

Heather

On Wed, Aug 7, 2013 at 1:13 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:

 Hmm, not sure what is going on.

 First, run it without the ampersand on the end.

 If that still crashes, then run this and send me log.txt

 recon-all  -debug  -i
 /home/hurry01/r/resdep_mri_data/resdep014/265000-10-1.dcm -s resdep214
 -all | tee log.txt

 doug


 On 08/07/2013 12:47 PM, Heather L. Urry wrote:
 
  Ah, sorry-- that too:   tcsh 6.18.01.
 
  (The command, which I just sent in a previous message, was as follows:
 
  recon-all -i /home/hurry01/r/resdep_mri_data/resdep014/265000-10-1.dcm
  -s resdep214 -all 
 
  )
 
  Heather
 
 
  On Wed, Aug 7, 2013 at 12:42 PM, Bruce Fischl
  fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu wrote:
 
  and what shell are you using
  On Wed, 7 Aug 2013, Douglas N Greve wrote:
 
   what is your command line?
  
  
  
  
   On 08/07/2013 10:19 AM, Heather L. Urry wrote:
   Hi folks,
  
   When issuing a recon-all command, I'm seeing the following
 message:
  
   set: Variable name must contain alphanumeric characters
  
   recon-all stalls and doesn't move forward (doesn't even create the
   subject directory).
  
   I'm using Freesurfer 5.3.0
   (freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0) on Ubuntu
  12.04.2.
   In fact, we just upgraded to this version of Ubuntu from an older
   version of Mandriva and to this latest version of Freesurfer.
   recon-all did not produce this message before these two
  upgrades. Any
   help you can offer would be most appreciated! Thanks in advance.
  
   Best,
  
   Heather
  
   --
   Heather L. Urry, Ph.D.
   Department of Psychology
   Tufts University
   490 Boston Avenue
   Medford, MA 02155
  
   email: heather.u...@tufts.edu mailto:heather.u...@tufts.edu
  mailto:heather.u...@tufts.edu mailto:heather.u...@tufts.edu
   phone: 617-627-3733 tel:617-627-3733
   fax: 617-627-3181 tel:617-627-3181
  
   http://ase.tufts.edu/psychology/ebbl
  
  
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 Freesurfer@nmr.mgh.harvard.edu
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 
 
  The information in this e-mail is intended only for the person to
  whom it is
  addressed. If you believe this e-mail was sent to you in error and
  the e-mail
  contains patient information, please contact the Partners
  Compliance HelpLine at
  http://www.partners.org/complianceline . If the e-mail was sent to
  you in error
  but does not contain patient information, please contact the
  sender and properly
  dispose of the e-mail.
 
 
 
 
  --
  Heather L. Urry, Ph.D.
  Department of Psychology
  Tufts University
  490 Boston Avenue
  Medford, MA 02155
 
  email: heather.u...@tufts.edu mailto:heather.u...@tufts.edu
  phone:  617-627-3733
  fax: 617-627-3181
 
  http://ase.tufts.edu/psychology/ebbl
 
 
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 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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-- 
Heather L. Urry, Ph.D.
Department of Psychology
Tufts University
490 Boston Avenue
Medford, MA 02155

email: heather.u...@tufts.edu
phone:  617-627-3733
fax: 617-627-3181

http://ase.tufts.edu/psychology/ebbl
set echo = 1 ;
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 5 != 0 )

set flag = $argv[1] ; shift ;

Re: [Freesurfer] hippo_subfields atlas

2013-08-07 Thread Rajapillai Pillai

Hi again!

I have another question about the hippocampal subfields atlas--might be a
silly one. Is there a way to extract volumes from the mesh collection?

Thanks a lot,
Raja

On Wed, Jul 31, 2013 at 5:06 PM, Juan Eugenio Iglesias
igles...@nmr.mgh.harvard.edu wrote:

Sounds good, but please email the list, rather than only me ;-)
/E

On 07/31/2013 05:03 PM, Rajapillai Pillai wrote:

Thanks a lot. I'll let you know if I have any more issues.

Best regards,
Raja

On Wed, Jul 31, 2013 at 4:44 PM, Juan Eugenio Iglesias
igles...@nmr.mgh.harvard.edu wrote:

Did you run recon-all -subjid bert -hippo-subfields? If so, there should
be a log file with the output from the hippo-subfield code in
$SUBJECTS_DIR/bert/scripts/hippo-subfields.log. You can take a look at it
to get an idea of what happened.
Kind regards,
/Eugenio

On 07/31/2013 04:38 PM, Rajapillai Pillai wrote:

Thanks very much for the prompt response. The command I ran was

$ kvlQuantifyPosteriorProbabilityImages
/Applications/freesurfer/data/GEMS/compressionLookupTable.txt
posterior_right_* posterior_Right-Hippocampus.mgz

in $SUBJECTS_DIR/bert/mri

And yeah, it's not in the mri directory. Any idea what might have gone
wrong and how I can try and fix it?

Thanks,
Raja

On Wed, Jul 31, 2013 at 4:29 PM, Juan Eugenio Iglesias
igles...@nmr.mgh.harvard.edu wrote:

Hi Raja,

I'm have a question regarding the GEMS hippocampal segmentation. I saw
on the wiki how to run -hippo_subfields, but how do I access the atlas
itself? What file is it under.

That would be $FREESURFER_HOME/data/GEMS/CurrentMeshCollection30.gz

Also, I'm not sure if I'm missing some files: whenever I try to do one
of the individual commands using, for example,
posterior_Right_Hippocampus.mgz, it gives the following error:

volumeInVoxels:
terminate called after throwing an instance of 'itk::ExceptionObject'
what(): itkMGHImageIO.cxx:216:
itk::ERROR: MGHImageIO(0x56b5c0): Can't find/open file:
posterior_Right-Hippocampus.mgz
Abort trap

What command is this? In any case, it's pretty clear that the file is
missing

Also, upon searching through my freesurfer directory, I cannot find
any posterior_Right-Hippocamus.mgz or posterior_Left-Hippocampus.mgz files.

It should be under the mri directory. If it isn't, there was some
problem running the algorithms.

Cheers,

/Eugenio

Thanks very much for your time,
Raja

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-
Juan Eugenio Iglesias,
PhDhttp://www.jeiglesias.comigles...@nmr.mgh.harvard.edu
Athinoula A. Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, Massachusetts 2129
U.S.A.

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Re: [Freesurfer] Tracula question

2013-08-07 Thread Alan Francis

Hi Anastasia:

Here is the trac-all log. Thanks so much:


csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/106/Diffusion_Recons]
: trac-all -prep -c
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc-106
INFO: SUBJECTS_DIR is
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons
INFO: Diffusion root is
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/
Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable5_3_0
trac-preproc -c
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/scripts/dmrirc.local
-log
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/scripts/trac-all.log
-cmd
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/scripts/trac-all.cmd
#-
/usr/local/freesurfer/stable5_3_0//bin/trac-preproc
#-
#@# Image corrections Wed Aug  7 13:16:17 EDT 2013
mri_convert
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/Diffusion_Recons/20080928_121245216000-21-01DIFFUSIONHighResValeraBI106s021a001.nii
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig.nii.gz
mri_convert
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/Diffusion_Recons/20080928_121245216000-21-01DIFFUSIONHighResValeraBI106s021a001.nii
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig.nii.gz

$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/Diffusion_Recons/20080928_121245216000-21-01DIFFUSIONHighResValeraBI106s021a001.nii...
TR=7570.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 1.63925e-05, 3.62902e-06)
j_ras = (1.67894e-05, 0.976296, 0.21644)
k_ras = (0, -0.21644, 0.976296)
writing to
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig.nii.gz...
cp
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/106/Diffusion_Recons/bvecs
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig.mghdti.bvecs
cp
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/106/Diffusion_Recons/bvecs
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig.mghdti.bvals
flip4fsl
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig.nii.gz
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig_flip.nii.gz
INFO: input image orientation is LAS
INFO: input image determinant is -6.8719
fslswapdim
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig.nii.gz
x y z
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig_flip.nii.gz
fslorient -forceradiological
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig_flip.nii.gz
INFO: found
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig.mghdti.bvals,
converting to FSL format
INFO: found
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig.mghdti.bvecs,
converting to FSL format
mv -f
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig_flip.mghdti.bvecs
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/bvecs
mv -f
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig_flip.mghdti.bvals
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/bvals
eddy_correct
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig_flip.nii.gz
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi.nii.gz
0
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0001
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0002
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0003
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0004
processing

Re: [Freesurfer] Tracula question



It looks like there may be something wrong with the bval file. Are you 
using a different one for this particular subject?


On Wed, 7 Aug 2013, Alan Francis wrote:


Hi Anastasia:

Here is the trac-all log. Thanks so much:


csh::alanf@cerebro
[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/106/Diffusion_Recons]
 : trac-all
-prep -c 
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc-106
INFO: SUBJECTS_DIR is 
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons
INFO: Diffusion root is 
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/
Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable5_3_0
trac-preproc -c
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/scripts/dmrirc.local
 -log
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/scripts/trac-all.log
 -cmd
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/scripts/trac-all.cmd
#-
/usr/local/freesurfer/stable5_3_0//bin/trac-preproc
#-
#@# Image corrections Wed Aug  7 13:16:17 EDT 2013
mri_convert/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/Diffusion_Recons/20080928_12124
5216000-21-01DIFFUSIONHighResValeraBI106s021a001.nii
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig.nii.gz
mri_convert/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/Diffusion_Recons/20080928_12124
5216000-21-01DIFFUSIONHighResValeraBI106s021a001.nii
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig.nii.gz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading 
from/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/Diffusion_Recons/20080928_12124
5216000-21-01DIFFUSIONHighResValeraBI106s021a001.nii...
TR=7570.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 1.63925e-05, 3.62902e-06)
j_ras = (1.67894e-05, 0.976296, 0.21644)
k_ras = (0, -0.21644, 0.976296)
writing to
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig.nii.gz...
cp 
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/106/Diffusion_Recons/bvecs
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig.mghdti.bvecs
cp 
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/106/Diffusion_Recons/bvecs
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig.mghdti.bvals
flip4fsl 
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig.nii.gz
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig_flip.nii.gz
INFO: input image orientation is LAS
INFO: input image determinant is -6.8719
fslswapdim 
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig.nii.gz
x y z 
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig_flip.nii.gz
fslorient -forceradiological
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig_flip.nii.gz
INFO: found
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig.mghdti.bvals,
converting to FSL format
INFO: found
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig.mghdti.bvecs,
converting to FSL format
mv 
-f/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig_flip.mghdti.bvecs
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/bvecs
mv 
-f/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig_flip.mghdti.bvals
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/bvals
eddy_correct
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig_flip.nii.gz
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi.nii.gz
 0
processing 
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp
processing 
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0001
processing 
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0002
processing 
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0003
processing

[Freesurfer] preferred method for generating appropriate bvecs for tracula

2013-08-07 Thread Salil Soman

Hi,

I have dicoms that I turn to nifti using dcm2nii (with the default settings
plus anonymization option turned on [-a y]). The bvec files it generates by
default are 3 rows by n columns (where n is b0 number + directions). I am
under the impression tracula requires this to be converted to a n row by 3
column file. 1) is this correct, 2) is there a preferred way to perform
this transformation on linux systems?

Thanks you,

-Sal
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[Freesurfer] Group analysis

2013-08-07 Thread Marcos Martins da Silva

Hi, FreeSurfers.
Is it possible to use FreeSurfer's group analysis tools to investigate
surface deformation instead of thickness? I guess it would be
interesting for subcortical structures like putamen, amygdala or
hippocampus. Let's say you get the putamen data from 15 subjects and
compare it to putamen data from fsaverage, After correct registration, I
guess we can detect regions of contraction and expansion leading to
changes in the putamen contour. I imagined it could be done if we
calculate the signed Euclidean distances between the corresponding
points of for each subject's putamen and fsaverage, with positive and
negative values indicating, for example, the presence of an outward or
inward surface deformation. After all calculation I guess we can get a
similar result to the pictures we can see at
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis  but
showing only a putamen and the colors meaning surface deformation
instead of thickness. This way, you can notice morphological differences
among subjects even if they have the same volume.
Thanks in advance,
Marcos 
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[Freesurfer] flip hemisphere of manual label

2013-08-07 Thread Jonathan DuBois

Hi,

Is there a way to transpose a manual surface label in fsaverage space onto
the contralateral hemisphere? With tksurfer it opens in the opposite
hemisphere but it does not correspond to the contralateral region.
Thanks in advance.

Best,
Jonathan
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[Freesurfer] Curvature, cortical thickness, LGI and artifacts

2013-08-07 Thread Erin Browning

Hello--

Our dataset has 130ish scans with a bad temporal lobe artifact and a minor
parietal lobe artifact. This artifact has affected the normalization and
thus the white matter/gray matter selection, which we've manually fixed.
However, the temporal lobe artifact is bad enough that chunks of data are
missing in the surfaces. How will this affect curvature and LGI? We saw we
can constrain our cortical thickness analyses to an ROI using mri_glmfit.
Can we do this with curvature and LGI, and will having chunks of data
missing affect readings elsewhere in the brain?

Thank you,
Erin Browning
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Re: [Freesurfer] preferred method for generating appropriate bvecs for tracula


set x = `cat bvecs | awk '{if (NR==1) print}'`
set y = `cat bvecs | awk '{if (NR==2) print}'`
set z = `cat bvecs | awk '{if (NR==3) print}'`

@ k = 1
while ( $k = `head -1 bvecs|wc -w` )
   echo $x[$k] $y[$k] $z[$k]
   @ k = $k + 1
end

I'd make sure though dcm2nii doesn't L-R flip the gradient vectors, I 
think there was a thread recently that suggested it might.

On Wed, 7 Aug 2013, Salil Soman wrote:

 Hi,
 I have dicoms that I turn to nifti using dcm2nii (with the default settings 
 plus anonymization option turned on [-a
 y]). The bvec files it generates by default are 3 rows by n columns (where n 
 is b0 number + directions). I am under
 the impression tracula requires this to be converted to a n row by 3 column 
 file. 1) is this correct, 2) is there a
 preferred way to perform this transformation on linux systems?
 
 Thanks you,
 
 -Sal
 

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[Freesurfer] error when using selxavg3-sess in retinotopy analysis

2013-08-07 Thread Sepide Movaghati

Hi,

I followed the steps for doing the retinotopy analysis. At the end I made my 
analysis as follows:

mkanalysis-sess -a Retinotopy_ZY -surface self lh -TR 2 -retinotopy 36 
-paradigm rtopy.par -fsd bold -fwhm 5

and then execute selxavg3-sess:
selxavg3-sess –a Retinotopy_ZY –s session1

then I got this error which I do not how to solve it:

outtop = /export01/data/sepid/subjects/ZY
Extension format = nii.gz
Error using fscanf
Invalid file identifier.  Use fopen to generate a valid file identifier.

Error in flac_customize (line 47)
  flacnew.sourcesubject = fscanf(fp,'%s',1);

Error in fast_selxavg3 (line 65)
flac0 = flac_customize(flac0);

 --
ERROR: fast_selxavg3() failed\n


I would appreciate if you help me through this.
Regards,
Sepide

-

I


I

-





a
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Re: [Freesurfer] preferred method for generating appropriate bvecs for tracula

2013-08-07 Thread Salil Soman

Thank you for the email.

I saw a warning to check for flipping L-R from the dcm2nii site:
http://www.mccauslandcenter.sc.edu/mricro/mricron/dcm2nii.html

Is the problem you mentioned vendor specific (I have all GE data). Is there
a different tool you would recommend for generating the bvec files? I would
prefer to run tracula right off the original dicom images but transferring
them to the cluster and anonymizing them would be prohibitively difficult.

I could not find the freesurfer archive message you referred to. Any
pointers would be greatly appreciated.

Best wishes,

Sal


On Wed, Aug 7, 2013 at 1:12 PM, Anastasia Yendiki 
ayend...@nmr.mgh.harvard.edu wrote:


 set x = `cat bvecs | awk '{if (NR==1) print}'`
 set y = `cat bvecs | awk '{if (NR==2) print}'`
 set z = `cat bvecs | awk '{if (NR==3) print}'`

 @ k = 1
 while ( $k = `head -1 bvecs|wc -w` )
   echo $x[$k] $y[$k] $z[$k]
   @ k = $k + 1
 end

 I'd make sure though dcm2nii doesn't L-R flip the gradient vectors, I
 think there was a thread recently that suggested it might.


 On Wed, 7 Aug 2013, Salil Soman wrote:

  Hi,
 I have dicoms that I turn to nifti using dcm2nii (with the default
 settings plus anonymization option turned on [-a
 y]). The bvec files it generates by default are 3 rows by n columns
 (where n is b0 number + directions). I am under
 the impression tracula requires this to be converted to a n row by 3
 column file. 1) is this correct, 2) is there a
 preferred way to perform this transformation on linux systems?

 Thanks you,

 -Sal




 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/**compliancelinehttp://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.




-- 
Salil Soman, MD, MS
Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory
Fellow - Palo Alto War Related Illness and Injury Study Center
WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System
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Re: [Freesurfer] hippo_subfields atlas

2013-08-07 Thread Juan Eugenio Iglesias

Shame on me; there's a way of doing this. You need a reference volume; 
for the hippocampal subfield atlas:

$FREESURFER_HOME/data/GEMS/CurrentMeshCollection30.gz
the reference volume would be:
$FREESURFER_HOME/data/GEMS/imageDump.mgz

The command would be:

kvlRasterizeAtlasMesh CurrentMeshCollection30.gz imageDump.mgz 
[labelNumber] [meshNumber]


meshNumber is the index of the mesh to extract in the collection; use 
-1 for the reference position.
labelNumber is the label whose probability map you want to rasterize ( 0 
= white matter, 1 = gray matter, 2 = CSF, 9 = CA1, etc; see 
$FREESURFER_HOME/data/GEMS/compressionLookupTable.txt).


From the volumetric rasterized prior probability map, you can easily 
compute volumes, if you want.


Cheers, and sorry again for the original wrong answer,

/Eugenio




On 08/07/2013 01:30 PM, Rajapillai Pillai wrote:

Hi again!

I have another question about the hippocampal subfields atlas--might 
be a silly one. Is there a way to extract volumes from the mesh 
collection?


Thanks a lot,
Raja


On Wed, Jul 31, 2013 at 5:06 PM, Juan Eugenio Iglesias 
igles...@nmr.mgh.harvard.edu mailto:igles...@nmr.mgh.harvard.edu 
wrote:


Sounds good, but please email the list, rather than only me ;-)
/E


On 07/31/2013 05:03 PM, Rajapillai Pillai wrote:

Thanks a lot. I'll let you know if I have any more issues.

Best regards,
Raja


On Wed, Jul 31, 2013 at 4:44 PM, Juan Eugenio Iglesias
igles...@nmr.mgh.harvard.edu
mailto:igles...@nmr.mgh.harvard.edu wrote:

Did you run recon-all -subjid bert -hippo-subfields? If so,
there should be a log file with the output from the
hippo-subfield code in
$SUBJECTS_DIR/bert/scripts/hippo-subfields.log. You can take
a look at it to get an idea of what happened.
Kind regards,
/Eugenio


On 07/31/2013 04:38 PM, Rajapillai Pillai wrote:

Thanks very much for the prompt response. The command I ran was

$ kvlQuantifyPosteriorProbabilityImages
/Applications/freesurfer/data/GEMS/compressionLookupTable.txt 
posterior_right_*
posterior_Right-Hippocampus.mgz

in $SUBJECTS_DIR/bert/mri

And yeah, it's not in the mri directory. Any idea what might
have gone wrong and how I can try and fix it?

Thanks,
Raja


On Wed, Jul 31, 2013 at 4:29 PM, Juan Eugenio Iglesias
igles...@nmr.mgh.harvard.edu
mailto:igles...@nmr.mgh.harvard.edu wrote:

Hi Raja,




I'm have a question regarding the GEMS hippocampal
segmentation. I saw on the wiki how to run
-hippo_subfields, but how do I access the atlas itself?
What file is it under.


That would be
$FREESURFER_HOME/data/GEMS/CurrentMeshCollection30.gz




Also, I'm not sure if I'm missing some files: whenever
I try to do one of the individual commands using, for
example, posterior_Right_Hippocampus.mgz, it gives the
following error:

volumeInVoxels:
terminate called after throwing an instance of
'itk::ExceptionObject'
what():  itkMGHImageIO.cxx:216:
itk::ERROR: MGHImageIO(0x56b5c0): Can't find/open file:
posterior_Right-Hippocampus.mgz
Abort trap



What command is this? In any case, it's pretty clear
that the file is missing



Also, upon searching through my freesurfer directory, I
cannot find any posterior_Right-Hippocamus.mgz or
posterior_Left-Hippocampus.mgz files.

It should be under the mri directory. If it isn't,
there was some problem running the algorithms.

Cheers,

/Eugenio






Thanks very much for your time,
Raja


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-- 
-

Juan Eugenio Iglesias, PhD
http://www.jeiglesias.com
igles...@nmr.mgh.harvard.edu  mailto:igles...@nmr.mgh.harvard.edu
Athinoula A. Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, Massachusetts 2129
U.S.A.

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Re: [Freesurfer] hippo_subfields atlas

2013-08-07 Thread Rajapillai Pillai

Thanks very much!

On Wed, Aug 7, 2013 at 4:23 PM, Juan Eugenio Iglesias
igles...@nmr.mgh.harvard.edu wrote:

Shame on me; there's a way of doing this. You need a reference volume;
for the hippocampal subfield atlas:
$FREESURFER_HOME/data/GEMS/CurrentMeshCollection30.gz
the reference volume would be:
$FREESURFER_HOME/data/GEMS/imageDump.mgz

The command would be:

kvlRasterizeAtlasMesh CurrentMeshCollection30.gz imageDump.mgz
[labelNumber] [meshNumber]

meshNumber is the index of the mesh to extract in the collection; use -1
for the reference position.
labelNumber is the label whose probability map you want to rasterize ( 0 =
white matter, 1 = gray matter, 2 = CSF, 9 = CA1, etc; see
$FREESURFER_HOME/data/GEMS/compressionLookupTable.txt).

From the volumetric rasterized prior probability map, you can easily
compute volumes, if you want.

Cheers, and sorry again for the original wrong answer,

/Eugenio

On 08/07/2013 01:30 PM, Rajapillai Pillai wrote:

Hi again!

I have another question about the hippocampal subfields atlas--might be
a silly one. Is there a way to extract volumes from the mesh collection?

Thanks a lot,
Raja

On Wed, Jul 31, 2013 at 5:06 PM, Juan Eugenio Iglesias
igles...@nmr.mgh.harvard.edu wrote:

Sounds good, but please email the list, rather than only me ;-)
/E

On 07/31/2013 05:03 PM, Rajapillai Pillai wrote:

Thanks a lot. I'll let you know if I have any more issues.

Best regards,
Raja

On Wed, Jul 31, 2013 at 4:44 PM, Juan Eugenio Iglesias
igles...@nmr.mgh.harvard.edu wrote:

Did you run recon-all -subjid bert -hippo-subfields? If so, there
should be a log file with the output from the hippo-subfield code in
$SUBJECTS_DIR/bert/scripts/hippo-subfields.log. You can take a look at it
to get an idea of what happened.
Kind regards,
/Eugenio

On 07/31/2013 04:38 PM, Rajapillai Pillai wrote:

Thanks very much for the prompt response. The command I ran was

$ kvlQuantifyPosteriorProbabilityImages
/Applications/freesurfer/data/GEMS/compressionLookupTable.txt
posterior_right_* posterior_Right-Hippocampus.mgz

in $SUBJECTS_DIR/bert/mri

And yeah, it's not in the mri directory. Any idea what might have gone
wrong and how I can try and fix it?

Thanks,
Raja

On Wed, Jul 31, 2013 at 4:29 PM, Juan Eugenio Iglesias
igles...@nmr.mgh.harvard.edu wrote:

Hi Raja,

I'm have a question regarding the GEMS hippocampal segmentation. I saw
on the wiki how to run -hippo_subfields, but how do I access the atlas
itself? What file is it under.

That would be $FREESURFER_HOME/data/GEMS/CurrentMeshCollection30.gz

Also, I'm not sure if I'm missing some files: whenever I try to do
one of the individual commands using, for example,
posterior_Right_Hippocampus.mgz, it gives the following error:

What command is this? In any case, it's pretty clear that the file is
missing

Also, upon searching through my freesurfer directory, I cannot find
any posterior_Right-Hippocamus.mgz or posterior_Left-Hippocampus.mgz files.

It should be under the mri directory. If it isn't, there was some
problem running the algorithms.

Cheers,

/Eugenio

Thanks very much for your time,
Raja

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e-mail
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Re: [Freesurfer] preferred method for generating appropriate bvecs for tracula



Hi Sal - Right now you'd just have to try it on one data set and look at 
the eigenvectors of the tensor (display dmri/dtifit_V1.nii.gz as lines) to 
make sure they're pointing in the right way.


I'm hoping for the next freesurfer release to finally get mri_convert to 
read gradient vectors off the dicom header in a way that ends this 
gradient flipping madness once and for all. But for now you just have to 
check before you proceed, sorry!


a.y

On Wed, 7 Aug 2013, Salil Soman wrote:


Thank you for the email.
I saw a warning to check for flipping L-R from the dcm2nii site:
http://www.mccauslandcenter.sc.edu/mricro/mricron/dcm2nii.html

Is the problem you mentioned vendor specific (I have all GE data). Is there a 
different tool you would recommend for
generating the bvec files? I would prefer to run tracula right off the original 
dicom images but transferring them to
the cluster and anonymizing them would be prohibitively difficult.

I could not find the freesurfer archive message you referred to. Any pointers 
would be greatly appreciated.

Best wishes,

Sal


On Wed, Aug 7, 2013 at 1:12 PM, Anastasia Yendiki 
ayend...@nmr.mgh.harvard.edu wrote:

  set x = `cat bvecs | awk '{if (NR==1) print}'`
  set y = `cat bvecs | awk '{if (NR==2) print}'`
  set z = `cat bvecs | awk '{if (NR==3) print}'`

  @ k = 1
  while ( $k = `head -1 bvecs|wc -w` )
    echo $x[$k] $y[$k] $z[$k]
    @ k = $k + 1
  end

  I'd make sure though dcm2nii doesn't L-R flip the gradient vectors, I 
think there was a thread recently
  that suggested it might.

  On Wed, 7 Aug 2013, Salil Soman wrote:

Hi,
I have dicoms that I turn to nifti using dcm2nii (with the default 
settings plus anonymization
option turned on [-a
y]). The bvec files it generates by default are 3 rows by n columns 
(where n is b0 number +
directions). I am under
the impression tracula requires this to be converted to a n row by 
3 column file. 1) is this
correct, 2) is there a
preferred way to perform this transformation on linux systems?

Thanks you,

-Sal




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.




--
Salil Soman, MD, MS
Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory
Fellow - Palo Alto War Related Illness and Injury Study Center
WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System

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Re: [Freesurfer] preferred method for generating appropriate bvecs for tracula

2013-08-07 Thread Salil Soman

Thank you for your response. Is there a best way to review the eigenvectors
(tkmedit, freeview, other program?).

Thank you.


-S
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Re: [Freesurfer] preferred method for generating appropriate bvecs for tracula



Freeview can do this in principle, but the current version of freeview has 
a known bug with displaying eigenvectors as lines (see known issues in 
http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes), so for now you can 
use fslview.


On Wed, 7 Aug 2013, Salil Soman wrote:


Thank you for your response. Is there a best way to review the eigenvectors 
(tkmedit, freeview, other program?). 
Thank you.


-S

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Re: [Freesurfer] hippo_subfields atlas

2013-08-07 Thread Rajapillai Pillai

Final question regarding this: what combinations of labels and meshes
should I use? Should I do all combinations between labels and positions,
matching labels/positions only, etc? How can I tell which meshes correspond
to what labels/areas?

Thanks for your time,
Raja

On Wed, Aug 7, 2013 at 4:26 PM, Rajapillai Pillai
raja.i.pil...@gmail.comwrote:

Thanks very much!

On Wed, Aug 7, 2013 at 4:23 PM, Juan Eugenio Iglesias
igles...@nmr.mgh.harvard.edu wrote:

The command would be:

kvlRasterizeAtlasMesh CurrentMeshCollection30.gz imageDump.mgz
[labelNumber] [meshNumber]

meshNumber is the index of the mesh to extract in the collection; use
-1 for the reference position.
labelNumber is the label whose probability map you want to rasterize ( 0
= white matter, 1 = gray matter, 2 = CSF, 9 = CA1, etc; see
$FREESURFER_HOME/data/GEMS/compressionLookupTable.txt).

From the volumetric rasterized prior probability map, you can easily
compute volumes, if you want.

Cheers, and sorry again for the original wrong answer,

/Eugenio

On 08/07/2013 01:30 PM, Rajapillai Pillai wrote:

Hi again!

I have another question about the hippocampal subfields atlas--might be
a silly one. Is there a way to extract volumes from the mesh collection?

Thanks a lot,
Raja

On Wed, Jul 31, 2013 at 5:06 PM, Juan Eugenio Iglesias
igles...@nmr.mgh.harvard.edu wrote:

Sounds good, but please email the list, rather than only me ;-)
/E

On 07/31/2013 05:03 PM, Rajapillai Pillai wrote:

Thanks a lot. I'll let you know if I have any more issues.

Best regards,
Raja

On Wed, Jul 31, 2013 at 4:44 PM, Juan Eugenio Iglesias
igles...@nmr.mgh.harvard.edu wrote:

Did you run recon-all -subjid bert -hippo-subfields? If so, there
should be a log file with the output from the hippo-subfield code in
$SUBJECTS_DIR/bert/scripts/hippo-subfields.log. You can take a look at it
to get an idea of what happened.
Kind regards,
/Eugenio

On 07/31/2013 04:38 PM, Rajapillai Pillai wrote:

Thanks very much for the prompt response. The command I ran was

$ kvlQuantifyPosteriorProbabilityImages
/Applications/freesurfer/data/GEMS/compressionLookupTable.txt
posterior_right_* posterior_Right-Hippocampus.mgz

in $SUBJECTS_DIR/bert/mri

And yeah, it's not in the mri directory. Any idea what might have
gone wrong and how I can try and fix it?

Thanks,
Raja

On Wed, Jul 31, 2013 at 4:29 PM, Juan Eugenio Iglesias
igles...@nmr.mgh.harvard.edu wrote:

Hi Raja,

I'm have a question regarding the GEMS hippocampal segmentation. I
saw on the wiki how to run -hippo_subfields, but how do I access the atlas
itself? What file is it under.

That would be $FREESURFER_HOME/data/GEMS/CurrentMeshCollection30.gz

Also, I'm not sure if I'm missing some files: whenever I try to do
one of the individual commands using, for example,
posterior_Right_Hippocampus.mgz, it gives the following error:

What command is this? In any case, it's pretty clear that the file is
missing

Also, upon searching through my freesurfer directory, I cannot find
any posterior_Right-Hippocamus.mgz or posterior_Left-Hippocampus.mgz
files.

It should be under the mri directory. If it isn't, there was some
problem running the algorithms.

Cheers,

/Eugenio

Thanks very much for your time,
Raja

___
Freesurfer mailing
listfreesur...@nmr.mgh.harvard.eduhttps://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.

--
-
Juan Eugenio Iglesias,
PhDhttp://www.jeiglesias.comigles...@nmr.mgh.harvard.edu
Athinoula A. Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301

[Freesurfer] (no subject)

2013-08-07 Thread aqureshi

Hi Dr. Fischl,

I had a couple subjects that failed recon-all. Although the error log said
recon-all failed at mri_watershed it looks like the root problem is a
couple steps earlier, because the nu.mgz looks too dark. This was
discussed in a previous thread from 2008.

http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07293.html.

You wrote, p.s. are the 001.mgz and 002.mgz dark? The orig.mgz? Sometimes
nu_correct can create very dark images, and there are some switches you
can loo through to correct them. Alternatively if it is the 001.mgz,
mri_convert has a scale option you can use.

On my subject 001.mgz looks good (there was no 002.mgz file). It is only
nu.mgz that looks too dark. It looks like the solution you gave then was
for a problematic 001.mgz file, but from your response it looks as if the
problem was nu.mgz the solution would be different. What are the switches
you can loop through to correct the nu.mgz.

Thanks,
Abid

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Re: [Freesurfer] error when using selxavg3-sess in retinotopy analysis

It is having problems reading the subjectname file in the session 
folder. Look in there to see if there is something obviously wrong. Did 
you create it on a windows computer?
doug


On 08/07/2013 04:16 PM, Sepide Movaghati wrote:
 Hi,

 I followed the steps for doing the retinotopy analysis. At the end I 
 made my analysis as follows:

 mkanalysis-sess -a Retinotopy_ZY -surface self lh -TR 2 -retinotopy 
 36-paradigm rtopy.par -fsd bold -fwhm 5

 and then execute selxavg3-sess:
 selxavg3-sess –a Retinotopy_ZY –s session1

 then I got this error which I do not how to solve it:

 outtop = /export01/data/sepid/subjects/ZY
 Extension format = nii.gz
 Error using fscanf
 Invalid file identifier. Use fopen to generate a valid file identifier.

 Error in flac_customize (line 47)
 flacnew.sourcesubject = fscanf(fp,'%s',1);

 Error in fast_selxavg3 (line 65)
 flac0 = flac_customize(flac0);

  --
 ERROR: fast_selxavg3() failed\n


 I would appreciate if you help me through this.
 Regards,
 Sepide

 -

 I


 I

 -





 a



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Re: [Freesurfer] (no subject)

Hi Abid

what version of FS are you using?
Bruce
On Wed, 7 Aug 2013, 
aqure...@nmr.mgh.harvard.edu wrote:

 Hi Dr. Fischl,

 I had a couple subjects that failed recon-all. Although the error log said
 recon-all failed at mri_watershed it looks like the root problem is a
 couple steps earlier, because the nu.mgz looks too dark. This was
 discussed in a previous thread from 2008.

 http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07293.html.

 You wrote, p.s. are the 001.mgz and 002.mgz dark? The orig.mgz? Sometimes
 nu_correct can create very dark images, and there are some switches you
 can loo through to correct them. Alternatively if it is the 001.mgz,
 mri_convert has a scale option you can use.

 On my subject 001.mgz looks good (there was no 002.mgz file). It is only
 nu.mgz that looks too dark. It looks like the solution you gave then was
 for a problematic 001.mgz file, but from your response it looks as if the
 problem was nu.mgz the solution would be different. What are the switches
 you can loop through to correct the nu.mgz.

 Thanks,
 Abid

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Re: [Freesurfer] Different results in surface and volume analyses

Hi Emily, the processing stream is designed to mask out cortical regions 
from the volume analysis. The volume analysis is used for subcortical 
structures. To make sure that the same voxels are not analyzed twice, 
the cortical surface is masked out of the mni305 analysis.
doug

ps. If you really want to see the full volume analysis, then there are 
some flags that will do this.




On 08/07/2013 01:15 PM, Emily Boeke wrote:
 Hello everyone,

 I am looking at a visual stimulus vs fixation contrast in my individual 
 subjects' data to make sure we are seeing normal activation there. If I look 
 at the surface data in tksurfer, I see activation in the occipital cortex, 
 but in the mni305 analysis, there is no activation in this region.

 These are the preprocess , mkanalysis, and selxavg commands I used for the 
 surface vs. mni305:

 preproc-sess -s amur_dss -df sesspar -per-run -fwhm 5 -sliceorder down 
 -surface fsaverage lhrh -mni305-2mm -fsd cond

 mkanalysis-sess -fsd cond -surface fsaverage lh -fwhm 5 -paradigm 
 Fear_Gen_Cond.par -event-related -TR 3 -nconditions 3 -polyfit 4 -spmhrf 0 
 -refeventdur 6 -analysis cond.sm05.lh -per-run -nskip 4 -stc down

 mkanalysis-sess -fsd cond -surface fsaverage rh -fwhm 5 -paradigm 
 Fear_Gen_Cond.par -event-related -TR 3 -nconditions 3 -polyfit 4 -spmhrf 0 
 -refeventdur 6 -analysis cond.sm05.rh -per-run -nskip 4 -stc down

 mkanalysis-sess -fsd cond -mni305 2 -fwhm 5 -paradigm Fear_Gen_Cond.par 
 -event-related -TR 3 -nconditions 3 -polyfit 4 -spmhrf 0 -refeventdur 6 
 -analysis cond.sm05.mni305 -per-run -nskip 4 -stc down

 selxavg3-sess -s amur_dss -df sesspar -analysis cond.sm.lh
 selxavg3-sess -s amur_dss -df sesspar -analysis cond.sm.rh
 selxavg3-sess -s amur_dss -df sesspar -analysis cond.sm.mni305

 Why might we be seeing this activation on the surface map but not the volume 
 one?

 Thanks!
 Emily
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
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Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] Group analysis