date:20160914

Re: [Freesurfer] Fwd: Tkregister2 error, moveable not present just white screen

2016-09-14 Thread A Nunes

Hi Dough,

Thanks for your help. I was using the preprocessed thinking that after
motion correction it would be more accurate and --init-header because they
where acquired in the same session. I changed to a raw moveable and the
results did not change for the following:

With -init-fsl the moveable is now showing, but about 40% of the subjects
the registration has fail, in many cases the moveable is rotated with
respect to the target. I tried to use -init-spm but then the moveable and
target don't even overlay.

I also tried to use a successful registration .dat from another subject
using the command  --init-reg $SUBJECTS_DIR/subj2/mri/register.dat  but the
registration is not accurate.

In many cases there is the WARNING: initial G-W contrast was negative, but
expected positive. If the mov data has a T1 contrast, re-run with --T1. if
I run the same command changing --bold to --T1 the results aren't good, as
well as if I try -int $SUBJECTS_DIR/subj//T1.mgz.

Is there anything else to try rather than manual registration? I just have
the T1 and the fmri.  Would you recommend another registration method?

Thanks
Adonay


On Mon, Sep 12, 2016 at 12:37 PM, Douglas N Greve  wrote:

> I think the problem is the initialization. I noticed you used
> --init-header. This should only be used if the two volumes were acquired
> during the same session and the direction cosines (ie, geometry) info is
> accurate for both. Is this the case? I noticed that the input has
> "preproc" in the name, so I'm a bit suspicious. You can try --init-fsl
> instead
>
>
> On 09/12/2016 01:36 PM, A Nunes wrote:
> > Hi Doug
> >
> > I can't see any errors in the log file, and with other datasets I did
> > not have this issue. My register.dat is:
> >
> > 50664
> > 3.00
> > 4.50
> > 0.15
> > 9.996076822280884e-01 -2.117119915783405e-02 -1.833262108266354e-02
> > 3.139470825195312e+02
> > 1.872027479112148e-02 1.825972087681293e-02 9.996579289436340e-01
> > 2.150849456787109e+02
> > -2.082921005785465e-02 -9.996089935302734e-01 1.864889077842236e-02
> > 4.339286499023438e+02
> > 0 0 0 1
> > round
> >
> > and my register.dat.log is:
> >
> > setenv SUBJECTS_DIR /Users/adonay/Desktop/data/freesurfer/5
> > cd /Users/adonay/Desktop/data/prepo_cpac
> > /Applications/freesurfer/bin/bbregister --s 50664 --mov
> > 50664_preprocessed.nii.gz --init-header --reg
> > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/register.dat --bold
> >
> > $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $
> > Darwin sc-155014 15.6.0 Darwin Kernel Version 15.6.0: Mon Aug 29
> > 20:21:34 PDT 2016; root:xnu-3248.60.11~1/RELEASE_X86_64 x86_64
> > FREESURFER_HOME /Applications/freesurfer
> > mri_convert 50664_preprocessed.nii.gz
> > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.
> bbregister.14726/template.nii
> > mri_convert 50664_preprocessed.nii.gz
> > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.
> bbregister.14726/template.nii
> >
> > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> > reading from 50664_preprocessed.nii.gz...
> > TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
> > i_ras = (-1, -0, 0)
> > j_ras = (-0, 1, 0)
> > k_ras = (-0, -0, 1)
> > writing to
> > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.
> bbregister.14726/template.nii...
> > tkregister2_cmdl --s 50664 --mov
> > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.
> bbregister.14726/template.nii
> > --regheader --reg
> > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.
> bbregister.14726/reg.init.dat
> > --noedit
> > tkregister_tcl /Applications/freesurfer/tktools/tkregister2.tcl
> > INFO: no target volume specified, assuming FreeSurfer orig volume.
> > target  volume orig
> > movable volume
> > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.
> bbregister.14726/template.nii
> > reg file
> > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.
> bbregister.14726/reg.init.dat
> > LoadVol0
> > ZeroCRAS   0
> > $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $
> > Diagnostic Level -1
> > INFO: loading target
> > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/orig.mgz
> > Ttarg: 
> > -1.000   0.000   0.000   128.000;
> >  0.000   0.000   1.000  -128.000;
> >  0.000  -1.000   0.000   128.000;
> >  0.000   0.000   0.000   1.000;
> > INFO: loading movable
> > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.
> bbregister.14726/template.nii
> > Tmov: 
> > -3.000   0.000   0.000   96.000;
> >  0.000   0.000   4.500  -63.000;
> >  0.000  -3.000   0.000   96.000;
> >  0.000   0.000   0.000   1.000;
> > mkheaderreg = 1, float2int = 0
> > Computing reg from header (and possibly input matrix)
> >  Input registration matrix (computed) 
> >  1.000   0.000   0.000   307.685;
> >  0.000   0.000   1.000   216.216;
> >  0.000  -1.000   0.000   435.341;
> >  0.000   0.000   0.000   1.000;
> >

Re: [Freesurfer] Getting combined bvals/bvecs

2016-09-14 Thread Anastasia Yendiki



Hi Marissa - You have to specify as many b-values and gradient vectors as 
there are volumes in your DWI data file. This means that, if you combine 
the AP and PA volumes, you also have to concatenate the bvals from the two 
into one file, and do the same with the bvecs. Make sure that the order in 
which the AP and PA volumes are combined is the same as the order in which 
the corresponding bvals and bvecs are combined.


Hope this helps,

a.y

On Wed, 14 Sep 2016, Marissa Pifer wrote:


Hello freesurfer experts,
I am trying to run tracula on subjects that have separate AP/PA direction DTI 
files. We combined the data
into one using topup, and would now like to run tracula on the subject. The 
problem is, the combined file
doesn't have a bvals/bvecs file. When I try to use the original bval/bvec 
files, I get the error that the
bvals and bvecs don't match up. I have tried combining the files into one, and 
then running a dicom to
nifty conversion to get a combined bvals/bvecs output, but that results again 
in two separate bvals/bvecs
files as well. I then tried just have two specified bvals and bvecs. This did 
not give us an error
message, but trac-prep took only a few seconds and did not complete the steps 
it was supposed to to create
the directories for trac-bedp to complete. I have attached our dmrirc.example 
file and the log for the
trac-prep step for your reference. 

The questions then are; is there a way to get one bvals/bvecs file that has the 
correct parameters for the
AP and PA combined file. Or, if not, is there a way to run tracula with two 
sets of bvals and bvecs (one
for the AP and one for the PA direction)? 

In case you need this information, the process is being run with freesurfer 
5.3, on a macbook pro OS X
version 10.9.5. 

Thank you in advance, 

Marissa 

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[Freesurfer] (no subject)

2016-09-14 Thread Rodriguez-Thompson, Anais

Hi FreeSurfer experts,

I'm running a task-based analysis on mni305 space, running a regression of 
load-dependent activation on RBC folate values, regressing out the effects of 
age and gender.

The analysis runs fine, but when I visualize the sig.mgh map in tkmedit there 
is a border of functional values that are ridiculously high (100 and 
-100). I've attached an image of one of the slices to this email as 
well as the mri_glmfit log, the fsgd file, and the contrast matrix. 

My glmfit command is 

mri_glmfit 
--y 
cluster/roffman/users/Stable5_PerRun/Analyses_GDD/GDD_Adults/136_GDD_2vFix_RBC_Folate/SIRP_LoadRegression_Stable5.3_012616_sm5_mni305/Cond2vFix/ces.nii.gz
--fsgd 
/cluster/roffman/users/fsgd/GDD/136_GDD_2vFix_Covary_RBC_Folate_linear.fsgd 
--no-prune
--fwhm 6
--C /cluster/roffman/users/fsgd/OneGroupOneCovariateRegressOut2Covariates.mtx
--glmdir 
/cluster/roffman/users/Stable5_PerRun/Analyses_GDD/GDD_Adults/136_GDD_2vFix_RBC_Folate/SIRP_LoadRegression_Stable5.3_012616_sm5_mni305/Cond2vFix/Tal2vFix_Covary_RBCFolate_Nuis_Gender_Age_noprune

Do you know why my command is creating these artificially high values and how 
to fix it? Any guidance would be greatly appreciated. 

Thanks,

Anais Rodriguez-Thompson
Clinical Research Coordinator
Brain Genomics Laboratory
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Phone: (617) 643-3215

136_GDD_2vFix_Covary_RBC_Folate_linear.fsgd
Description: 136_GDD_2vFix_Covary_RBC_Folate_linear.fsgd

$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
cwd /autofs/cluster/roffman/users/Stable5_PerRun/Analyses_GDD/GDD_Adults/151_GDD_2vFix_Serum_Folate/SIRP_LoadRegression_Stable5.3_012616_sm5_mni305/Cond2vFix/Tal_2vFix_Covary_SerumFolate_Nuis_Gender_Age_noprune/OneGroupOneCovariateRegressOut2Covariates
cmdline mri_glmfit --y /cluster/roffman/users/Stable5_PerRun/Analyses_GDD/GDD_Adults/136_GDD_2vFix_RBC_Folate/SIRP_LoadRegression_Stable5.3_012616_sm5_mni305/Cond2vFix/ces.nii.gz --fsgd /cluster/roffman/users/fsgd/GDD/136_GDD_2vFix_Covary_RBC_Folate_linear.fsgd --no-prune --fwhm 6 --glmdir /cluster/roffman/users/Stable5_PerRun/Analyses_GDD/GDD_Adults/136_GDD_2vFix_RBC_Folate/SIRP_LoadRegression_Stable5.3_012616_sm5_mni305/Cond2vFix/Tal2vFix_Covary_RBCFolate_Nuis_Gender_Age_noprune --C /cluster/roffman/users/fsgd/OneGroupOneCovariateRegressOut2Covariates.mtx 
sysname  Linux
hostname dauntless
machine  x86_64
user arodthom
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
fwhm 6.00
OneSampleGroupMean 0
y/autofs/cluster/roffman/users/Stable5_PerRun/Analyses_GDD/GDD_Adults/136_GDD_2vFix_RBC_Folate/SIRP_LoadRegression_Stable5.3_012616_sm5_mni305/Cond2vFix/ces.nii.gz
logyflag 0
usedti  0
FSGD /cluster/roffman/users/fsgd/GDD/136_GDD_2vFix_Covary_RBC_Folate_linear.fsgd
glmdir /cluster/roffman/users/Stable5_PerRun/Analyses_GDD/GDD_Adults/136_GDD_2vFix_RBC_Folate/SIRP_LoadRegression_Stable5.3_012616_sm5_mni305/Cond2vFix/Tal2vFix_Covary_RBCFolate_Nuis_Gender_Age_noprune
IllCondOK 0
ReScaleX 1
DoFFx 0


OneGroupOneCovariateRegressOut2Covariates.mtx
Description: OneGroupOneCovariateRegressOut2Covariates.mtx
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Re: [Freesurfer] "Talairach Transform: transforms/talairach.xfm FAILED"

2016-09-14 Thread Uquillas, Federico D'Oleire

Hi Bruce,
Thanks so much.

So, how would I check if it actually failed or not?

How would I turn off the checking?

How would I manually correct it? 

Would running without it be essentially the same as turning off the checking 
(procedurally)?

Best,

Fred

> On Sep 14, 2016, at 15:59, Bruce Fischl  wrote:
> 
> Hi Fred
> 
> have you checked the transform to see if it actually failed? If not, you 
> can just turn off the checking. If it did, you can manually correct it 
> (or run without it)
> 
> cheers
> Bruce
> 
>> On Wed, 14 Sep 2016, Uquillas, Federico D'Oleire wrote:
>> 
>> Dear fellow FreeSurfer users,
>> 
>> I can't get a subject to recon-all all the way through without crashing, 
>> regardless of the FS version used (deleted and started from scratch several 
>> times).
>> 
>> It always fails with a Talairach transform fail error.
>> 
>> Wondering if anybody else has experienced this issue before and if there's a 
>> way to solve it.
>> 
>> Thank you very much.
>> 
>> All the best,
>> 
>> Fred
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>> 
>> 
>> 
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Re: [Freesurfer] "Talairach Transform: transforms/talairach.xfm FAILED"

2016-09-14 Thread Bruce Fischl

Hi Fred

have you checked the transform to see if it actually failed? If not, you 
can just turn off the checking. If it did, you can manually correct it 
(or run without it)

cheers
Bruce

On Wed, 14 Sep 2016, Uquillas, Federico D'Oleire wrote:

> Dear fellow FreeSurfer users,
>
> I can't get a subject to recon-all all the way through without crashing, 
> regardless of the FS version used (deleted and started from scratch several 
> times).
>
> It always fails with a Talairach transform fail error.
>
> Wondering if anybody else has experienced this issue before and if there's a 
> way to solve it.
>
> Thank you very much.
>
> All the best,
>
> Fred
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>
>
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[Freesurfer] Convert 4D volume time-series into surface time-series

2016-09-14 Thread Prokopis Prokopiou

Hello freesurfer experts,

 

I am trying to register a functional volumetric image (.nii) into a surface
(.gii) to produce a functional surface image (.gii), where each node of the
image will contain a time-series. My purpose for doing this is to use
freeview to visualize the time-series of each node. I've tried to do this
using bbregister to obtain a registration matrix of the functional image
into a structural image, mri_vol2surf to resample the functional volume, and
finally mris_convert to convert the resampled functional volume into a (4d)
functional surface. The details of how I used these commands are as follow:

bbregister --s AL_subject/AL \

   --mov
/home/osboxes/Desktop/Windows-Share/EEG_fMRI_Data_CUBRIC/AL/eyesshut_mc_bet.
feat/filtered_func_data.nii \

   --reg /home/osboxes/Desktop/AL_registrations/AL.mat \

--init-fsl --t2

 

mri_vol2surf --mov
/home/osboxes/Desktop/Windows-Share/EEG_fMRI_Data_CUBRIC/AL/eyesshut_mc_bet.
feat/filtered_func_data.nii --reg
/home/osboxes/Desktop/AL_registrations/AL.mat --projfrac 0.5 --hemi lh --o
/home/osboxes/Desktop/AL_registrations/AL_surface_time_series_lh.mgh
--projfrac 0.5 --interp nearest

 

mris_convert -f
/home/osboxes/Desktop/AL_registrations/AL_surface_time_series_lh.mgh \

 
/home/osboxes/Desktop/Windows-Share/EEG_fMRI_Data_CUBRIC/EEG_fMRI_FreeSurfer
_anatomies/AL_subject/AL/surf/lh.white \

  /home/osboxes/Desktop/AL_registrations/AL_surface_time_series_lh.gii

 

Although these commands run without any error, the result
(AL_surface_time_series_lh.gii) cannot be opened in freeview, presumably
because the produced 4d functional surface does not have the necessary
surface information (vertices, faces) needed by freeview in order to open
it. More specifically, when I try to open it I get MRISread failed

mriseadGIFTIfile: mris is NULL! found when parsing file
/home/osboxes/Desktop/AL_registrations/AL_surface_time_series_lh.gii in the
terminal.

I am new user of freesurfer and I would appreciate if someone could help me
with this.

Thanks,
Prokopis

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[Freesurfer] Cortical thickness to volume

2016-09-14 Thread neuroimage analyst

Hi, Freesurfer Users.

I tried searching for this question on the mailing list but couldn't get an
answer. Hence, I am posting this here again.

I ran the freesurfer analysis and got cortical thickness map for my group.
I want to build an adjacency matrix by finding the correlation between the
cortical thickness of various ROIs on an atlas (Either the
default freesurfer atlas or AAL atlas).
1) How can I map the cortical thickness map to freesurfer template volume
so that I can average the cortical thickness in the ROI to build the
connectivity matrix?
2) Instead of mapping to freesurfer template, if I have to use AAL atlas
can I simply map the cortical thickness map to MNI template and use AAL
atlas in MNI template to carry out step (1). If yes, how should I go about
doing that?

I would appreciate any response.

Thanks

Regards!
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[Freesurfer] "Talairach Transform: transforms/talairach.xfm FAILED"

2016-09-14 Thread Uquillas, Federico D'Oleire

Dear fellow FreeSurfer users,

I can't get a subject to recon-all all the way through without crashing, 
regardless of the FS version used (deleted and started from scratch several 
times).

It always fails with a Talairach transform fail error.

Wondering if anybody else has experienced this issue before and if there's a 
way to solve it.

Thank you very much.

All the best,

Fred
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Re: [Freesurfer] QA tools

2016-09-14 Thread Lee Tirrell



Hi John,

Do tkmedit and tksurfer work by themselves? You can try this by running the 
following commands (assuming your SUBJECTS_DIR is set to the location 
containinng your subject ALS-0038):


tkmedit ALS-0038 norm.mgz
tksurfer ALS-0038 rh pial

Best,
Lee


On Tue, 13 Sep 2016, John Anderson wrote:



Hello, FS experts,
I am trying to use QA tool: 
I ran the following command 
recon_checker -snaps-only -s-file subjects.txt
 
The script output the following:
X11 connection rejected because of wrong authentication.
GLUT: Fatal Error in tkmedit.bin: could not open display: localhost:12.0
X11 connection rejected because of wrong authentication.
GLUT: Fatal Error in tksurfer.bin: could not open display: localhost:12.0
X11 connection rejected because of wrong authentication.
GLUT: Fatal Error in tksurfer.bin: could not open display: localhost:12.0
     Taking snapshots for subject ALS-0038
X11 connection rejected because of wrong authentication.
GLUT: Fatal Error in tkmedit.bin: could not open display: localhost:12.0
X11 connection rejected because of wrong authentication.
GLUT: Fatal Error in tksurfer.bin: could not open display: localhost:12.0
X11 connection rejected because of wrong authentication.
GLUT: Fatal Error in tksurfer.bin: could not open display: localhost:12.0
 
 
At the end it said that he process finshed. I checked the AQ folder and the 
snaps where not there 
 
Any suggestions!
 
Bests,
John 

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Re: [Freesurfer] convert FSFAST files to gifti format

2016-09-14 Thread Douglas Greve

not sure, maybe one of the HCP folks could weigh in. You might try 
converting the lh.nii.gz to mgh file first. Should not make a 
difference, but it might

On 9/14/16 10:24 AM, Sabin Khadka wrote:

Doug- I did try
mris_convert -o $SUBJECTS_DIR/FSsub/surf/lh.white 
$SUBJECTS_DIR/sub/REST/bold/001/fmcpr.odd.sm5.fsaverage.lh.nii.gz 
fmcpr.lh.gifit-file.gii

I still get freadFloat: frear failed error.

On separate note: Is is possible to convert these FSFAST generated 
files (fmcpr.odd.sm5.fsaverage.?h.nii.gz and 
 fmcpr.odd.sm5.mni305.2mm.nii.gz) into CIFTI format?

-Sabin

On Tue, Sep 13, 2016 at 3:09 PM Sabin Khadka > wrote:

Hi Doug- I did try
mris_convert -o $SUBJECTS_DIR/FSsub/surf/lh.white
$SUBJECTS_DIR/sub/REST/bold/001/fmcpr.odd.sm5.fsaverage.lh.nii.gz
fmcpr.lh.gifit-file.gii

I still get freadFloat: frear failed error.

Cheers,
Sabin Khadka

On Tue, Sep 13, 2016 at 2:53 PM, Douglas N Greve
> wrote:

what is your mris_convert command line? You need to include vertex
position information (eg, -o lh.white)

On 09/12/2016 03:32 PM, Sabin Khadka wrote:
> Hi all,
>
> Is there a way to convert FSFAST files
> (fmcpr.odd.sm5.fsaverage.?h.nii.gz) files to convert into gifti
> format? I've tried mris_convert but it does not work.
>
> Thanks for help.
>
> Cheers,
> Sabin Khadka
>
>
> ___
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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 

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Re: [Freesurfer] convert FSFAST files to gifti format

2016-09-14 Thread Sabin Khadka

Doug- I did try
mris_convert -o $SUBJECTS_DIR/FSsub/surf/lh.white
$SUBJECTS_DIR/sub/REST/bold/001/fmcpr.odd.sm5.fsaverage.lh.nii.gz
fmcpr.lh.gifit-file.gii

I still get freadFloat: frear failed error.

On separate note: Is is possible to convert these FSFAST generated files
(fmcpr.odd.sm5.fsaverage.?h.nii.gz and  fmcpr.odd.sm5.mni305.2mm.nii.gz)
into CIFTI format?

-Sabin

On Tue, Sep 13, 2016 at 3:09 PM Sabin Khadka 
wrote:

> Hi Doug- I did try
> mris_convert -o $SUBJECTS_DIR/FSsub/surf/lh.white
> $SUBJECTS_DIR/sub/REST/bold/001/fmcpr.odd.sm5.fsaverage.lh.nii.gz
> fmcpr.lh.gifit-file.gii
>
> I still get freadFloat: frear failed error.
>
> Cheers,
> Sabin Khadka
>
> On Tue, Sep 13, 2016 at 2:53 PM, Douglas N Greve <
> gr...@nmr.mgh.harvard.edu> wrote:
>
>> what is your mris_convert command line? You need to include vertex
>> position information (eg, -o lh.white)
>>
>>
>> On 09/12/2016 03:32 PM, Sabin Khadka wrote:
>> > Hi all,
>> >
>> > Is there a way to convert FSFAST files
>> > (fmcpr.odd.sm5.fsaverage.?h.nii.gz) files to convert into gifti
>> > format? I've tried mris_convert but it does not work.
>> >
>> > Thanks for help.
>> >
>> > Cheers,
>> > Sabin Khadka
>> >
>> >
>> > ___
>> > 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: 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/
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
>
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contains patient information, please contact the Partners Compliance HelpLine at
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