[Freesurfer] reg-feat2anat error ("mri_convert ERROR: could not determine file")

[Emily Coffey]

Hello,

I am having a similar problem to that posted several times previously. I 
get an error when running reg-feat2anat to register FSL feat files to 
the freesurfer reconstruction, see:

https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-June/038437.html

because the 
subjectsfeatfolder.feat/reg/freesurfer/tmp/refvol.fslregister.nii file 
does not seem to make itself.

I'm wondering where I can find an active link to an updated 
reg-feat2anat, as all the links I find in threads are not working.

I did find a potential workaround: if I create the /mri/tmp directory 
and convert the .mgz file from the freesurfer output to .nii here, as 
explained on this website 
(http://wikis.la.utexas.edu/imagelab/book/how-convert-mgz-structural-files-nii-structural-files)
 
I can create the missing nii file and rerun the registration, however, 
I'm uncertain about the orientation parameters as although the 
orientation of the nii matches that of my original T1, the resulting 
registration in freesurer is nonsense.

Example of the command I am using to manually convert the .mgz to nii:

mri_convert --in_type mgz --out_type nii 
subjectsfreesurferfolder/mri/brainmask.mgz --out_orientation RAS 
subjectsfeatfolder.feat/reg/freesurfer/tmp/refvol.fslregister.nii


Any suggestions on either the updated file location or the workaround 
much appreciated!


Notes:

I am running this version of FreeSurfer:
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
On Linux: Ubuntu 12.04.5 LTS

Emily
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[Freesurfer] reg-feat2anat update

[Hirsch, Gabriella]

Hi FS experts,

I had a quick query I was hoping you could help with;

I am trying to load functional data analyzed in FSL in Freesurfer using 
reg-feat2anat 
(http://freesurfer.net/fswiki/FsTutorial/RegisterFeatOntoAnatomical) and seem 
to be having the same problem as the person in this thread:

https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-June/038639.html

In other words, the anat2exf.register.dat file is not being created. I tried to 
download the new version of reg-feat2anat posted by Doug in the thread but I'm 
getting an error when downloading with wget: "no such file reg-feat2anat"

Has the location of this file changed?

Thank you!

Best,
Gabriella
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Re: [Freesurfer] reg-feat2anat problem

[Mariam Sood]

Hello Doug,
sorry for the delay. But thank you for going through the log and giving me 
helpful advice. The problems I was having with registration were down to the 
fact that the anatomical (brain mask) and functional were oriented differently 
and the flirt command line options (search angle in x,y,z:-90 to +90 degrees) 
used by reg-feat2anat were insufficient for correcting that. Changing those 
parameters (searchrx, searchry and searchrz to -180 to 180) fixed my problems 
and gave me good registration.  
Many thanks,
Mariam. 



On 4 Feb 2014, at 17:15, Douglas N Greve  wrote:

> 
> From the output it looks like the func-anat registration is off, 
> probably because of the partial FoV is causing the FSL registration used 
> to init BBR to be off (often happens with a partial FoV). Were the 
> anatomical and functional acquired at the same time? If so, then you'll 
> have to bypass reg-feat2anat to create the registration.
> 
> Unless you use --overwrite-exf2std, the exf2anat will not affect the exf2std
> 
> doug
> 
> 
> On 02/02/2014 05:59 PM, Mariam Sood wrote:
>> Hello Doug,
>> Thank you for your reply. I tried to investigate it further and would be 
>> grateful for your advice. While the reg-feat2anat registration (default FSL 
>> option) looks way off, the FEAT generated registration, both 
>> functional-anatomical and functional-standard look fine. I have used 
>> brainmask.nii as the anatomical in the registration tab of FEAT (with ‘bbr’ 
>> option selected for functional-standard registration and linear 12DOF for 
>> registration to standard). This is a partial FOV image and the determinant 
>> of functional & anatomical have opposite signs. Attached, please find my 
>> reg-feat2anat log file.
>> 
>> Also from your reply, what I understood is that exf2std.reg.dat is generated 
>> by FSL routines. Won’t exf2anat registration play any part in this?
>> 
>> I also have a T1-weighted alignment scan acquired with the same orientation 
>> and slice-block centre as the functional data. Is it possible to make use of 
>> this to get better registration should other methods fail?
>> 
>> Many thanks,
>> Mariam.
>> 
>> 
>> 
>> 
>> 
>> On 30 Jan 2014, at 17:43, Douglas N Greve  wrote:
>> 
>>> The second warning you don't need to worry about. I should change that
>>> to not be a warning. reg-feat2anat is only registering the functional
>>> and anatomical. If the registration to mni152 does not look good, then
>>> that is an FSL issue
>>> doug
>>> 
>>> On 01/30/2014 11:06 AM, Mariam Sood wrote:
 Hello,
 
 I am running reg-feat2anat and facing some problems.
 
 First I ran the command in its default mode using FSL initialisation
 /reg-feat2anat --feat featdir.feat --subject s. /That gave me a bad
 registration. There is a warning coming up
 ///WARNING: //initial G-W contrast is negative, but expecting positive./
 /  If the mov data has a T1 contrast, re-run with --T1/
 
 Next I tried the command using -spm option. The within-subject
 registration (anat2exf) looks good, but the registration to the
 standard does not look that good, although not as bad as with -fsl
 option.
 
 The structural and the functional are using different conventions
 (structural is in radiological convention, whereas functional is
 neurological). I presume the determinants are associated with this and
 they have opposite signs. The orientations are also different.
 Additionally in both the log files (one with -fsl option and -spm
 option), I get another warning /WARNING:: Flipping Left/Right
 orientation (as det < 0). /Not sure whether this warning is something
 I should worry about.
 
 Much appreciate your help.
 
 Many thanks,
 Mariam.
 
 
 
 
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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
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>>> HelpLine at
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>>> error
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Re: [Freesurfer] reg-feat2anat problem

[Douglas N Greve]

 From the output it looks like the func-anat registration is off, 
probably because of the partial FoV is causing the FSL registration used 
to init BBR to be off (often happens with a partial FoV). Were the 
anatomical and functional acquired at the same time? If so, then you'll 
have to bypass reg-feat2anat to create the registration.

Unless you use --overwrite-exf2std, the exf2anat will not affect the exf2std

doug


On 02/02/2014 05:59 PM, Mariam Sood wrote:
> Hello Doug,
> Thank you for your reply. I tried to investigate it further and would be 
> grateful for your advice. While the reg-feat2anat registration (default FSL 
> option) looks way off, the FEAT generated registration, both 
> functional-anatomical and functional-standard look fine. I have used 
> brainmask.nii as the anatomical in the registration tab of FEAT (with ‘bbr’ 
> option selected for functional-standard registration and linear 12DOF for 
> registration to standard). This is a partial FOV image and the determinant of 
> functional & anatomical have opposite signs. Attached, please find my 
> reg-feat2anat log file.
>
> Also from your reply, what I understood is that exf2std.reg.dat is generated 
> by FSL routines. Won’t exf2anat registration play any part in this?
>
> I also have a T1-weighted alignment scan acquired with the same orientation 
> and slice-block centre as the functional data. Is it possible to make use of 
> this to get better registration should other methods fail?
>
> Many thanks,
> Mariam.
>
>
>
>
>
> On 30 Jan 2014, at 17:43, Douglas N Greve  wrote:
>
>> The second warning you don't need to worry about. I should change that
>> to not be a warning. reg-feat2anat is only registering the functional
>> and anatomical. If the registration to mni152 does not look good, then
>> that is an FSL issue
>> doug
>>
>> On 01/30/2014 11:06 AM, Mariam Sood wrote:
>>> Hello,
>>>
>>> I am running reg-feat2anat and facing some problems.
>>>
>>> First I ran the command in its default mode using FSL initialisation
>>> /reg-feat2anat --feat featdir.feat --subject s. /That gave me a bad
>>> registration. There is a warning coming up
>>> ///WARNING: //initial G-W contrast is negative, but expecting positive./
>>> /  If the mov data has a T1 contrast, re-run with --T1/
>>>
>>> Next I tried the command using -spm option. The within-subject
>>> registration (anat2exf) looks good, but the registration to the
>>> standard does not look that good, although not as bad as with -fsl
>>> option.
>>>
>>> The structural and the functional are using different conventions
>>> (structural is in radiological convention, whereas functional is
>>> neurological). I presume the determinants are associated with this and
>>> they have opposite signs. The orientations are also different.
>>> Additionally in both the log files (one with -fsl option and -spm
>>> option), I get another warning /WARNING:: Flipping Left/Right
>>> orientation (as det < 0). /Not sure whether this warning is something
>>> I should worry about.
>>>
>>> Much appreciate your help.
>>>
>>> Many thanks,
>>> Mariam.
>>>
>>>
>>>
>>>
>>> ___
>>> 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
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it is
>> addressed. If you believe this e-mail was sent to you in error and the e-mail
>> contains patient information, please contact the Partners Compliance 
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you in 
>> error
>> but does not contain patient information, please contact the sender and 
>> properly
>> dispose of the e-mail.
>>
>
>
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-- 
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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
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Re: [Freesurfer] reg-feat2anat problem

[Douglas N Greve]

The second warning you don't need to worry about. I should change that 
to not be a warning. reg-feat2anat is only registering the functional 
and anatomical. If the registration to mni152 does not look good, then 
that is an FSL issue
doug

On 01/30/2014 11:06 AM, Mariam Sood wrote:
> Hello,
>
> I am running reg-feat2anat and facing some problems.
>
> First I ran the command in its default mode using FSL initialisation 
> /reg-feat2anat --feat featdir.feat --subject s. /That gave me a bad 
> registration. There is a warning coming up
> ///WARNING: //initial G-W contrast is negative, but expecting positive./
> /  If the mov data has a T1 contrast, re-run with --T1/
>
> Next I tried the command using -spm option. The within-subject 
> registration (anat2exf) looks good, but the registration to the 
> standard does not look that good, although not as bad as with -fsl 
> option.
>
> The structural and the functional are using different conventions 
> (structural is in radiological convention, whereas functional is 
> neurological). I presume the determinants are associated with this and 
> they have opposite signs. The orientations are also different. 
> Additionally in both the log files (one with -fsl option and -spm 
> option), I get another warning /WARNING:: Flipping Left/Right 
> orientation (as det < 0). /Not sure whether this warning is something 
> I should worry about.
>
> Much appreciate your help.
>
> Many thanks,
> Mariam.
>
>
>
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
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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
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[Freesurfer] reg-feat2anat problem

[Mariam Sood]

Hello,

I am running reg-feat2anat and facing some problems. 

First I ran the command in its default mode using FSL initialisation 
reg-feat2anat --feat featdir.feat --subject s. That gave me a bad registration. 
There is a warning coming up 
   WARNING: initial G-W contrast is negative, but expecting positive.
  If the mov data has a T1 contrast, re-run with --T1

Next I tried the command using -spm option. The within-subject registration 
(anat2exf) looks good, but the registration to the standard does not look that 
good, although not as bad as with -fsl option. 

The structural and the functional are using different conventions (structural 
is in radiological convention, whereas functional is neurological). I presume 
the determinants are associated with this and they have opposite signs. The 
orientations are also different. Additionally in both the log files (one with 
-fsl option and -spm option), I get another warning WARNING:: Flipping 
Left/Right orientation (as det < 0). Not sure whether this warning is something 
I should worry about.  

Much appreciate your help. 

Many thanks,
Mariam.


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Re: [Freesurfer] reg-feat2anat failure..

[Douglas Greve]

Does that file exist? Do you have permissions?
doug




On 6/12/13 12:59 PM, Sudhin A. Shah wrote:

Hi,

recon-all was successful.

But when I try
reg-feat2anat --feat '/home//func/2_reg' --subject xyz

I get an error with
MRISread(/home/sudhin/Data/freesurfer_subjects//xyz/surf/lh.white): 
could not open file

Loading mov
Projecting LH Surfs
Loading lh.white surf
No such file or directory

Thanks!



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[Freesurfer] reg-feat2anat failure..

[Sudhin A. Shah]

Hi,

recon-all was successful.

But when I try
reg-feat2anat --feat '/home//func/2_reg' --subject xyz

I get an error with
MRISread(/home/sudhin/Data/freesurfer_subjects//xyz/surf/lh.white): could not 
open file
Loading mov
Projecting LH Surfs
Loading lh.white surf
No such file or directory

Thanks!

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Re: [Freesurfer] reg-feat2anat error in Ubuntu 12.04 and a workaround

[Douglas N Greve]

there might have been a change in libraries, but it is impossible to 
know without seeing your command line and terminal output

On 05/03/2012 07:36 AM, Auer, Tibor wrote:
>
> I have recently upgraded my Ubuntu system from 11.10 to 12.04.
>
> Before the upgrade I had no problem at all! After the upgrade the 
> “reg-feat2anat” stopped working: it gave an error when converting the 
> subject/mri/brainmask.mgz to 
> featdir.feat/reg/freesurfer/tmp/refvol.fslregister.nii.
>
> However, when I do the conversion manually before the “reg-feat2anat”, 
> it works without further error.
>
> Is there any explanation for this behavior?
>
> *Auer, Tibor M.D. Ph.D*.
>
> Biomedizinische NMR Forschungs GmbH
>
> am Max-Planck Institut für Biophysikalische Chemie
>
> Am Fassberg 11
>
> 37077 Göttingen
>
> Germany
>
> Phone/Work: +49-(0)551-201-1725
>
> Phone/Home: +49-(0)551-387-0076
>
> Mobile: +49-(0)176-8012-7921
>
> Mail: ta...@mpibpc.mpg.de 
>
>
>
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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
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[Freesurfer] reg-feat2anat error in Ubuntu 12.04 and a workaround

[Auer, Tibor]

I have recently upgraded my Ubuntu system from 11.10 to 12.04.

Before the upgrade I had no problem at all! After the upgrade the
"reg-feat2anat" stopped working: it gave an error when converting the
subject/mri/brainmask.mgz to
featdir.feat/reg/freesurfer/tmp/refvol.fslregister.nii. 

 

However, when I do the conversion manually before the "reg-feat2anat", it
works without further error.

 

Is there any explanation for this behavior?

 

Auer, Tibor M.D. Ph.D.

Biomedizinische NMR Forschungs GmbH

am Max-Planck Institut für Biophysikalische Chemie

Am Fassberg 11

37077 Göttingen

Germany

Phone/Work: +49-(0)551-201-1725

Phone/Home: +49-(0)551-387-0076

Mobile: +49-(0)176-8012-7921

Mail: ta...@mpibpc.mpg.de

 

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Re: [Freesurfer] reg-feat2anat --feat --manxfm func2std

[Douglas N Greve]

It will replace it.
doug

On 04/14/2012 09:52 AM, Michelle Umali wrote:
> Hi Freesurfers,
> I ran reg-feat2anat and am now checking registration.  For some
> subjects I had to edit the registration of feat to standard space.
> So, do I have to replace the example_func2standard.mat fsl's
> example_func2standard.mat in the reg folder or is this done
> automatically?
>
> Is this the only file that has to be copied over?
>
> Thanks.
> Michelle
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>
>

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

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[Freesurfer] reg-feat2anat --feat --manxfm func2std

[Michelle Umali]

Hi Freesurfers,
I ran reg-feat2anat and am now checking registration.  For some
subjects I had to edit the registration of feat to standard space.
So, do I have to replace the example_func2standard.mat fsl's
example_func2standard.mat in the reg folder or is this done
automatically?

Is this the only file that has to be copied over?

Thanks.
Michelle
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Re: [Freesurfer] reg-feat2anat

[Douglas N Greve]

you can just copy it
doug

Michelle Umali wrote:
> Dear Freesurfers,
> I've previoiusly run reg-feat2anat on some fsl feat data, but now my 
> advisor things i should re-preprocess my fsl data with a larger kernel 
> size.
>
> Since it's the same dataset , do I have to re-run reg-feat2anat on 
> this or can I just copy the registration folder from the old analysis?
>
> Thanks.
> Michelle
> 
>
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

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[Freesurfer] reg-feat2anat

[Michelle Umali]

Dear Freesurfers,
I've previoiusly run reg-feat2anat on some fsl feat data, but now my
advisor things i should re-preprocess my fsl data with a larger kernel size.

Since it's the same dataset , do I have to re-run reg-feat2anat on this or
can I just copy the registration folder from the old analysis?

Thanks.
Michelle
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Re: [Freesurfer] reg-feat2anat failure

[Douglas N Greve]

This file is created when you run reg-feat2anat and should be the one 
that gets changed with --manxfm func2anat. You can handle this 
differently if you

1. Manually edit the anat2exf.register.dat so that it is relatively 
close (no need to be perfect)
cd feat/reg/freesurfer
tkregister2 --mov ../../example_func.nii.gz --reg anat2exf.register.dat 
--surfs

2. Run bbregister:
cp anat2exf.register.dat backup.anat2exf.register.dat # Make a backup
bbregister --mov ../../example_func.nii.gz --init-reg 
anat2exf.register.dat --reg anat2exf.register.dat --bold

this second step will fine-tune your hand-edited version. Then go back 
and run aparc2feat, etc.

doug



Michelle Umali wrote:
> Hi Doug,
> The file that changed was exf2std.register.dat.   How do I specify 
> that I wanted that anat2exf.register.dat is supposed to be edited? At 
> what point in the processing stream does this occur?
>
> Did editing exf2std.register.dat do anything?
>
> Thanks.
> Michelle
>
>
>
> On Tue, Oct 18, 2011 at 2:17 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> The registration that should be used for all of these is
> anat2exf.register.dat found in feat/reg/freesurfer. Can you verify
> that that was the one that you manually changed? Look at the time
> stamp as compared to the other files in that folder.
> doug
>
> Michelle Umali wrote:
>
> Hi Doug,
> I am using reg-feat2anat  on the feat directory of each run.
> reg-feat2anat --feat feadir.feat --subject XX
> Then I checked and adjusted the registration with:
> reg-feat2anat --feat featdir.feat --manual
> Next I checked and adjusted the registration to the standard with:
> reg-feat2anat --feat featdir.feat --manxfm func2std
>
> To generate cortical binary masks I used:
> aparc2feat --feat featdir.feat --annot BA
> fslmaths featdir.feat/reg/freesurfer/lh.BA.nii.gz -thr 10
> -uthr 10 featdir.feat/reg/freesurfer/V1_l.nii.gz
>
> To generate subcortical binary masks I did:
> aseg2feat --feat featdir.feat --aseg aparc+aseg
> fslmaths featdir.feat/reg/freesurfer/aparc+aseg.nii.gz
> -thr 54 -uthr 54 featdir.feat/reg/freesurfer/amygdala_r.nii.gz
>
> When I looked at the masks in FSLview and checked the masks
> against the other atlases, everything was off even after
> painstakingly editing the registrations.
> Is there something I am doing wrong?
>
> Thanks.
> Michelle
>
>On Mon, Oct 17, 2011 at 1:36 PM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>
>  >> wrote:
>
>How are you generating the masks?
>doug
>
>Michelle Umali wrote:
>
>Hi Freesurfers,
>I've run reg-feat2anat on several subjects in order to
>generate binary masks to use in an FSL ppi.
>For 3 subjects, this completely failed.
>
>When I looked at the fsl's own registration of fsl feat 2
>standard (via tkregister2), the registration is fine, but
>after running reg-feat2anat, the registration of the
> feat to
>the freesurfer anatomical and the feat to standard are
>completely off.
>
>I manually fixed and saved the registration edits via
>reg-feat2anat --manual, but when I generated the masks
> again,
>they were totally wrong still.
>When looking at freesurfer's feat to standard
> registration, it
>looks like all the brains weren't tall enough in the
> saggital
>view.  Am I supposed to stretch the feat brain to fit?
>
>How can I fix this so that the masks are accurate?
>
>Thanks.
>Michelle
>  
>  
> 
>
>___
>Freesurfer mailing list
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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
> 

Re: [Freesurfer] reg-feat2anat failure

[Douglas N Greve]

The registration that should be used for all of these is 
anat2exf.register.dat found in feat/reg/freesurfer. Can you verify that 
that was the one that you manually changed? Look at the time stamp as 
compared to the other files in that folder.
doug

Michelle Umali wrote:
> Hi Doug,
> I am using reg-feat2anat  on the feat directory of each run.
>  reg-feat2anat --feat feadir.feat --subject XX
> Then I checked and adjusted the registration with:
>  reg-feat2anat --feat featdir.feat --manual
> Next I checked and adjusted the registration to the standard with:
>  reg-feat2anat --feat featdir.feat --manxfm func2std
>
> To generate cortical binary masks I used:
>  aparc2feat --feat featdir.feat --annot BA
>  fslmaths featdir.feat/reg/freesurfer/lh.BA.nii.gz -thr 10 -uthr 
> 10 featdir.feat/reg/freesurfer/V1_l.nii.gz
>
> To generate subcortical binary masks I did:
>  aseg2feat --feat featdir.feat --aseg aparc+aseg
>  fslmaths featdir.feat/reg/freesurfer/aparc+aseg.nii.gz -thr 54 
> -uthr 54 featdir.feat/reg/freesurfer/amygdala_r.nii.gz
>
> When I looked at the masks in FSLview and checked the masks against 
> the other atlases, everything was off even after painstakingly editing 
> the registrations. 
>
> Is there something I am doing wrong?
>
> Thanks.
> Michelle
>
> 
> On Mon, Oct 17, 2011 at 1:36 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> How are you generating the masks?
> doug
>
> Michelle Umali wrote:
>
> Hi Freesurfers,
> I've run reg-feat2anat on several subjects in order to
> generate binary masks to use in an FSL ppi.
> For 3 subjects, this completely failed.
>
> When I looked at the fsl's own registration of fsl feat 2
> standard (via tkregister2), the registration is fine, but
> after running reg-feat2anat, the registration of the feat to
> the freesurfer anatomical and the feat to standard are
> completely off.
>
> I manually fixed and saved the registration edits via
> reg-feat2anat --manual, but when I generated the masks again,
> they were totally wrong still.
> When looking at freesurfer's feat to standard registration, it
> looks like all the brains weren't tall enough in the saggital
> view.  Am I supposed to stretch the feat brain to fit?
>
> How can I fix this so that the masks are accurate?
>
> Thanks.
> Michelle
> 
> 
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
> Phone Number: 617-724-2358  Fax: 617-726-7422
> 
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
>
>
>
> 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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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

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Re: [Freesurfer] reg-feat2anat failure

[Michelle Umali]

Hi Doug,
I am using reg-feat2anat  on the feat directory of each run.
 reg-feat2anat --feat feadir.feat --subject XX
Then I checked and adjusted the registration with:
 reg-feat2anat --feat featdir.feat --manual
Next I checked and adjusted the registration to the standard with:
 reg-feat2anat --feat featdir.feat --manxfm func2std

To generate cortical binary masks I used:
 aparc2feat --feat featdir.feat --annot BA
 fslmaths featdir.feat/reg/freesurfer/lh.BA.nii.gz -thr 10 -uthr 10
featdir.feat/reg/freesurfer/V1_l.nii.gz

To generate subcortical binary masks I did:
 aseg2feat --feat featdir.feat --aseg aparc+aseg
 fslmaths featdir.feat/reg/freesurfer/aparc+aseg.nii.gz -thr 54 -uthr 54
featdir.feat/reg/freesurfer/amygdala_r.nii.gz

When I looked at the masks in FSLview and checked the masks against the
other atlases, everything was off even after painstakingly editing the
registrations.

Is there something I am doing wrong?

Thanks.
Michelle


On Mon, Oct 17, 2011 at 1:36 PM, Douglas N Greve
wrote:

> How are you generating the masks?
> doug
>
> Michelle Umali wrote:
>
>> Hi Freesurfers,
>> I've run reg-feat2anat on several subjects in order to generate binary
>> masks to use in an FSL ppi.
>> For 3 subjects, this completely failed.
>>
>> When I looked at the fsl's own registration of fsl feat 2 standard (via
>> tkregister2), the registration is fine, but after running reg-feat2anat, the
>> registration of the feat to the freesurfer anatomical and the feat to
>> standard are completely off.
>>
>> I manually fixed and saved the registration edits via reg-feat2anat
>> --manual, but when I generated the masks again, they were totally wrong
>> still.
>> When looking at freesurfer's feat to standard registration, it looks like
>> all the brains weren't tall enough in the saggital view.  Am I supposed to
>> stretch the feat brain to fit?
>>
>> How can I fix this so that the masks are accurate?
>>
>> Thanks.
>> Michelle
>> --**--**
>> 
>>
>> __**_
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer
>>
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358 Fax: 617-726-7422
>
> Bugs: 
> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting
> FileDrop: 
> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html
>
>
>
> 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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Re: [Freesurfer] reg-feat2anat failure

[Douglas N Greve]

How are you generating the masks?
doug

Michelle Umali wrote:
> Hi Freesurfers,
> I've run reg-feat2anat on several subjects in order to generate binary 
> masks to use in an FSL ppi.
> For 3 subjects, this completely failed.
>
> When I looked at the fsl's own registration of fsl feat 2 standard 
> (via tkregister2), the registration is fine, but after running 
> reg-feat2anat, the registration of the feat to the freesurfer 
> anatomical and the feat to standard are completely off.
>
> I manually fixed and saved the registration edits via reg-feat2anat 
> --manual, but when I generated the masks again, they were totally 
> wrong still.
> When looking at freesurfer's feat to standard registration, it looks 
> like all the brains weren't tall enough in the saggital view.  Am I 
> supposed to stretch the feat brain to fit?
>
> How can I fix this so that the masks are accurate?
>
> Thanks.
> Michelle
> 
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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[Freesurfer] reg-feat2anat failure

[Michelle Umali]

Hi Freesurfers,
I've run reg-feat2anat on several subjects in order to generate binary masks
to use in an FSL ppi.
For 3 subjects, this completely failed.

When I looked at the fsl's own registration of fsl feat 2 standard (via
tkregister2), the registration is fine, but after running reg-feat2anat, the
registration of the feat to the freesurfer anatomical and the feat to
standard are completely off.

I manually fixed and saved the registration edits via reg-feat2anat
--manual, but when I generated the masks again, they were totally wrong
still.
When looking at freesurfer's feat to standard registration, it looks like
all the brains weren't tall enough in the saggital view.  Am I supposed to
stretch the feat brain to fit?

How can I fix this so that the masks are accurate?

Thanks.
Michelle
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[Freesurfer] Using Freesurfer reg-feat2anat registration to replace original FEAT

[Michelle Umali]

Dear Freesurfers,
I've analyzed a run of functional data in FEAT and then used reg-feat2anat
to register the FEAT results to the Freesurfer anatomicals.  It turns out
the original FLIRT registration was bad.  When I looked at the reg-feat2anat
results, images were flipped 90 degrees.  I made edits manually in
reg-feat2anat to fix this.

How do I feed this corrected registration back into FSL so it can be used
instead of the original FLIRT registration in later FEAT analyses?

Thanks.
Michelle
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[Freesurfer] reg-feat2anat: major failure

[Michelle Umali]

Hi Freesurfers,
I've run reg-feat2anat to register my FSL FEAT data to the freesurfer
anatomical data.
And for most subjects the registration needs a little manual editing (which
sometimes includes stretching).
But for a few subjects, registration is terrible, e.g. coronal is switched
with horizontal or orig surfaces are completely off the FEAT brain.

So I looked into my original FEAT directory and FSL's registration between
example_func to standard looked fine, but example_func to highres failed.

Is there a way to use Freesurfer to register example_func to high res for
use in a FEAT analysis so that later reg-feat2anat works?

Thanks.
Michelle
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[Freesurfer] reg-feat2anat: correct anat2exf.register.dat only or also func2std?

[Agnieszka Burzynska]

Dear experts,
I am using reg-feat2anat  to register my functional data from FSL to
anatomical and starndard space in Freesurfer.

For some subjects the registration is bad.

I can easily fix anat2exf.register.dat. However, as specified in
reg-feat2anat ‹help, I know that the registration failed as the func2std is
incorrect, too.

Is it enough to correct anat2exf.register.dat to correctly transfer
functional data from feat to the surface space or do I also need to correct
func2std? It seems to me that in the next steps I am using, such as sampling
the functional data to fsaverage and further calculations in the fsaverage
space do not rely on func2std. Is this correct?

Cheers,
Aga


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Re: [Freesurfer] reg-feat2anat problem

[Douglas N Greve]

That would be the same as specifying highres.nii.gz as the intermediate 
registration (--int to bbregister). Is this what you tried?
doug

Cris Lanting wrote:
> Dear all,
> dear Doug,
>
>   
>> If you have a partial FOV, then it
>> will  probably fail. You can test this by running bbregister outside of the
>> reg-feat2anat. You can look in the reg-feat2anat for a command line, but it
>> should be something like:
>>
>> bbregister --s subject --mov example_func.nii.gz --bold --init-fsl --reg
>> register.dat
>>
>> If this fails, you have a couple of options. If the functional and
>> anatomical were acquired in the same session, then you can use --init-header
>> instead of --init-fsl. If they are not but you have a full-brain of anything
>> acquired during the same session as the functional, you can pass that as an
>> intermediate volume to bbregister (--int).
>>
>> doug
>>
>>
>> 
>
> I've tried the --init-fsl option and the --init-header but they both
> seem to fail. I noticed that there is a --init-reg option;
> Is it not an idea to normalise the T1 (mprage) file called
> highress.nii.gz (output registerT1.dat) and then in a second step
> apply this to a previously registered file
> (example_func2highres.nii.gz) using the --init-reg option?
>
> so, in short, would this approach work?
> example_func.nii.gz -> example_func2highres.nii.gz (using flirt or
> anything that works)
> bbregister --s subject --mov highres.nii.gz --T1 --init-fsl --reg 
> registerT1.dat
> bbregister --s subject --mov example_func2highres.nii.gz --bold
> --init-reg registerT1.dat --reg registerfunc.dat
> (ps, I haven't tried this yet...)
>
> Or are there other options
>
> Kind regards,
> Cris
>
>
>   

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

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Re: [Freesurfer] reg-feat2anat problem

[Douglas N Greve]

Which version of freesurfer are you running? At one point, reg-feat2anat 
was dependent on the feat registration, but "now" it is not. I don't 
know whether you fall into the "now" category. If you have a partial 
FOV, then it will  probably fail. You can test this by running 
bbregister outside of the reg-feat2anat. You can look in the 
reg-feat2anat for a command line, but it should be something like:

bbregister --s subject --mov example_func.nii.gz --bold --init-fsl --reg 
register.dat

If this fails, you have a couple of options. If the functional and 
anatomical were acquired in the same session, then you can use 
--init-header instead of --init-fsl. If they are not but you have a 
full-brain of anything acquired during the same session as the 
functional, you can pass that as an intermediate volume to bbregister 
(--int).

doug



Cris Lanting wrote:
> Dear all,
>
> I'm having a slight problem with reg-feat2anat to transform functional
> data (FSL) to anatomical (Freesurfer) in that the resulting
> transformation seems completely wrong.
> What I've done so far is the following:
>
> 1) run FEAT including the normal FEAT registration (which I know fails
> due to a lack of FOV in the functional data)
> 2) re-run the Flirt for a proper registration (i.e. by using the
> -usesqform option to obtain better registration)
> 3) overwrite the example_func2highres.mat, highres2standard.mat and
> example_func2standard.mat file with the newly obtained registration
> files.
> (The resulting files are now properly registered when viewing in e.g. fslview)
> 4) Run updatefeatreg 
> 5) Start FEAT and change the mode to run Post-stats only. Select the
> FEAT output directory as input. Go into the registration tab and turn
> off all registration. Press GO.
> (steps 3-5 following the FSL FAQ on custom registration into a FEAT analysis)
>
> 6) run a complete freesurfer segmentation and all the rest using recon-all etc
> 7) reg-feat2anat --feat featdir.feat --subject subjectid
>
> When I now check the registration, it seems completely wrong...
> My guess would be that it has to do with the re-registration in steps
> 2-5 but as far as I can tell the files are registered properly to the
> anatomy scan (and to the template (or standard), the
> MNI152_T1_1mm_brain file)
>
> Any ideas?
> (Not sure whether it is appreciated if I send a screenshot as
> attachment, so I'll leave it for now)
>
> Cheers,
> Cris
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>   

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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[Freesurfer] reg-feat2anat problem

[Cris Lanting]

Dear all,

I'm having a slight problem with reg-feat2anat to transform functional
data (FSL) to anatomical (Freesurfer) in that the resulting
transformation seems completely wrong.
What I've done so far is the following:

1) run FEAT including the normal FEAT registration (which I know fails
due to a lack of FOV in the functional data)
2) re-run the Flirt for a proper registration (i.e. by using the
-usesqform option to obtain better registration)
3) overwrite the example_func2highres.mat, highres2standard.mat and
example_func2standard.mat file with the newly obtained registration
files.
(The resulting files are now properly registered when viewing in e.g. fslview)
4) Run updatefeatreg 
5) Start FEAT and change the mode to run Post-stats only. Select the
FEAT output directory as input. Go into the registration tab and turn
off all registration. Press GO.
(steps 3-5 following the FSL FAQ on custom registration into a FEAT analysis)

6) run a complete freesurfer segmentation and all the rest using recon-all etc
7) reg-feat2anat --feat featdir.feat --subject subjectid

When I now check the registration, it seems completely wrong...
My guess would be that it has to do with the re-registration in steps
2-5 but as far as I can tell the files are registered properly to the
anatomy scan (and to the template (or standard), the
MNI152_T1_1mm_brain file)

Any ideas?
(Not sure whether it is appreciated if I send a screenshot as
attachment, so I'll leave it for now)

Cheers,
Cris

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Re: [Freesurfer] reg-feat2anat: a problem!

[Burzynska, Aga]

Good point, I will do that! But so far when I looked, the L-R flip did not 
happen.

Thank you!
Aga

Aga Burzynska
Max Planck Institute for Human Development
Neurocognition of Decision Making
Lentzeallee 94
14195 Berlin
Ph: + 49 30 82406 335



-Ursprüngliche Nachricht-
Von: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
Gesendet: Mi 2011-02-09 17:11
An: Burzynska, Aga
Cc: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: AW: [Freesurfer] reg-feat2anat: a problem!
 
Yea, though I might just go to 179 to make sure there's not a flip.
doug

Burzynska, Aga wrote:
>
> Dear Doug,
> The determinant sign is negative for both example_func and orig.mgz 
> (-73.6 and -1, respecitively).
>
> The files differed also in their format, type, vox2ras-fsl and 
> orientation, but I guess it is ok.
>
> My feeling was that flirt is unable to fit the brain given the maximum 
> angle of rotation 90, so I doubled this using:
> re-feat2anat --dof 6 --maxangle 180 --feat run1.feat --subject xx
>
> I tried this on several subjects and the registration looks very good: 
> I would not make it better manually.
>
> Can I assume it works now?
>
> Cheers,
> Aga
>
>
>
>
>
> -Ursprüngliche Nachricht-
> Von: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
> Gesendet: Mo 2011-02-07 19:36
> An: Burzynska, Aga
> Cc: 'freesurfer@nmr.mgh.harvard.edu'
> Betreff: Re: [Freesurfer] reg-feat2anat: a problem!
>
> That is not a problem. By "anatomical" I meant the FreeSurfer anatomical
> (eg, orig.mgz)
> doug
>
> Agnieszka Burzynska wrote:
> > Dear Doug,
> > Thank you a lot!
> > Our feat data is always nifti, but anatomical FSL data is sometimes 
> in the
> > analyze format. Is this already a problem?
> >
> > I will now check the rest.
> >
> > Thank you, cheers,
> > Aga
> >
> >
> > On 2/7/11 4:35 PM, "Douglas N Greve"  wrote:
> >
> >  
> >> Hi Aga, are you using nifti? If analyze, that could be the problem. Do
> >> your functionals and anatomicals have a different sign to their
> >> determinants (you can check with mri_info). In principle, reg-feat2anat
> >> should handle this but in some cases it does not. The 5.1 version will
> >> handle it properly. If they do have the same sign, then look 
> through the
> >> log file and find the flirt command. Run that command by itself 
> (you may
> >> need to run reg-feat2anat with --nocleanup to keep it from deleting the
> >> files). If that fails, then contact the FSL people
> >>
> >> doug
> >>
> >> Agnieszka Burzynska wrote:
> >>
> >>> Dear all,
> >>> I am using the command reg-feat2anat to transform functional data
> >>> pre-processed in FSL to the anatomical image in Freesurfer.
> >>>
> >>> As suggested, I check the registration with reg-feat2anat --feat
> >>> run2.feat  >>>
> >>> I have 3 runs of functional data for each subject. Surprisingly, some
> >>> runs are registered well but others not (even of the same subject, so
> >>> using the same reference anatomical images: see the attached image.
> >>> Upper row: bad registration of one run and lower row: good
> >>> registration of another run).
> >>>
> >>> I have no problem to manually correct the registrations, it works
> >>> well, but as I have many subjects, I wonder if there may be a way to
> >>> change some options of reg-feat2anat to make it work better? Can you
> >>> see from the attached image what is the problem with my images? (I
> >>> viewed the functional and anatomical data of a few subjects, some woth
> >>> good and some with bad registration and see no difference or flip)
> >>>
> >>> Thanks a lot for your help!
> >>> Aga
> >>>
> >>> 
> 
> >>>
> >>> 
> 
> >>>
> >>> ___
> >>> Freesurfer mailing list
> >>> Freesurfer@nmr.mgh.harvard.edu
> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>>  
> >
> >
> >
> >  
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: www.nmr.mgh.harvard.edu/facility/

Re: [Freesurfer] reg-feat2anat: a problem!

[Douglas N Greve]

Yea, though I might just go to 179 to make sure there's not a flip.
doug

Burzynska, Aga wrote:
>
> Dear Doug,
> The determinant sign is negative for both example_func and orig.mgz 
> (-73.6 and -1, respecitively).
>
> The files differed also in their format, type, vox2ras-fsl and 
> orientation, but I guess it is ok.
>
> My feeling was that flirt is unable to fit the brain given the maximum 
> angle of rotation 90, so I doubled this using:
> re-feat2anat --dof 6 --maxangle 180 --feat run1.feat --subject xx
>
> I tried this on several subjects and the registration looks very good: 
> I would not make it better manually.
>
> Can I assume it works now?
>
> Cheers,
> Aga
>
>
>
>
>
> -Ursprüngliche Nachricht-
> Von: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
> Gesendet: Mo 2011-02-07 19:36
> An: Burzynska, Aga
> Cc: 'freesurfer@nmr.mgh.harvard.edu'
> Betreff: Re: [Freesurfer] reg-feat2anat: a problem!
>
> That is not a problem. By "anatomical" I meant the FreeSurfer anatomical
> (eg, orig.mgz)
> doug
>
> Agnieszka Burzynska wrote:
> > Dear Doug,
> > Thank you a lot!
> > Our feat data is always nifti, but anatomical FSL data is sometimes 
> in the
> > analyze format. Is this already a problem?
> >
> > I will now check the rest.
> >
> > Thank you, cheers,
> > Aga
> >
> >
> > On 2/7/11 4:35 PM, "Douglas N Greve"  wrote:
> >
> >  
> >> Hi Aga, are you using nifti? If analyze, that could be the problem. Do
> >> your functionals and anatomicals have a different sign to their
> >> determinants (you can check with mri_info). In principle, reg-feat2anat
> >> should handle this but in some cases it does not. The 5.1 version will
> >> handle it properly. If they do have the same sign, then look 
> through the
> >> log file and find the flirt command. Run that command by itself 
> (you may
> >> need to run reg-feat2anat with --nocleanup to keep it from deleting the
> >> files). If that fails, then contact the FSL people
> >>
> >> doug
> >>
> >> Agnieszka Burzynska wrote:
> >>
> >>> Dear all,
> >>> I am using the command reg-feat2anat to transform functional data
> >>> pre-processed in FSL to the anatomical image in Freesurfer.
> >>>
> >>> As suggested, I check the registration with reg-feat2anat --feat
> >>> run2.feat  >>>
> >>> I have 3 runs of functional data for each subject. Surprisingly, some
> >>> runs are registered well but others not (even of the same subject, so
> >>> using the same reference anatomical images: see the attached image.
> >>> Upper row: bad registration of one run and lower row: good
> >>> registration of another run).
> >>>
> >>> I have no problem to manually correct the registrations, it works
> >>> well, but as I have many subjects, I wonder if there may be a way to
> >>> change some options of reg-feat2anat to make it work better? Can you
> >>> see from the attached image what is the problem with my images? (I
> >>> viewed the functional and anatomical data of a few subjects, some woth
> >>> good and some with bad registration and see no difference or flip)
> >>>
> >>> Thanks a lot for your help!
> >>> Aga
> >>>
> >>> 
> 
> >>>
> >>> 
> 
> >>>
> >>> ___
> >>> Freesurfer mailing list
> >>> Freesurfer@nmr.mgh.harvard.edu
> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>>  
> >
> >
> >
> >  
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
>
>
> 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.
>
>

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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

Re: [Freesurfer] reg-feat2anat: a problem!

[Burzynska, Aga]

Dear Doug,
The determinant sign is negative for both example_func and orig.mgz (-73.6 and 
-1, respecitively). 

The files differed also in their format, type, vox2ras-fsl and orientation, but 
I guess it is ok.

My feeling was that flirt is unable to fit the brain given the maximum angle of 
rotation 90, so I doubled this using:
re-feat2anat --dof 6 --maxangle 180 --feat run1.feat --subject xx

I tried this on several subjects and the registration looks very good: I would 
not make it better manually.

Can I assume it works now?

Cheers,
Aga





-Ursprüngliche Nachricht-
Von: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
Gesendet: Mo 2011-02-07 19:36
An: Burzynska, Aga
Cc: 'freesurfer@nmr.mgh.harvard.edu'
Betreff: Re: [Freesurfer] reg-feat2anat: a problem!
 
That is not a problem. By "anatomical" I meant the FreeSurfer anatomical 
(eg, orig.mgz)
doug

Agnieszka Burzynska wrote:
> Dear Doug,
> Thank you a lot!
> Our feat data is always nifti, but anatomical FSL data is sometimes in the
> analyze format. Is this already a problem?
>
> I will now check the rest.
>
> Thank you, cheers,
> Aga
>
>
> On 2/7/11 4:35 PM, "Douglas N Greve"  wrote:
>
>   
>> Hi Aga, are you using nifti? If analyze, that could be the problem. Do
>> your functionals and anatomicals have a different sign to their
>> determinants (you can check with mri_info). In principle, reg-feat2anat
>> should handle this but in some cases it does not. The 5.1 version will
>> handle it properly. If they do have the same sign, then look through the
>> log file and find the flirt command. Run that command by itself (you may
>> need to run reg-feat2anat with --nocleanup to keep it from deleting the
>> files). If that fails, then contact the FSL people
>>
>> doug
>>
>> Agnieszka Burzynska wrote:
>> 
>>> Dear all,
>>> I am using the command reg-feat2anat to transform functional data
>>> pre-processed in FSL to the anatomical image in Freesurfer.
>>>
>>> As suggested, I check the registration with reg-feat2anat --feat
>>> run2.feat >>
>>> I have 3 runs of functional data for each subject. Surprisingly, some
>>> runs are registered well but others not (even of the same subject, so
>>> using the same reference anatomical images: see the attached image.
>>> Upper row: bad registration of one run and lower row: good
>>> registration of another run).
>>>
>>> I have no problem to manually correct the registrations, it works
>>> well, but as I have many subjects, I wonder if there may be a way to
>>> change some options of reg-feat2anat to make it work better? Can you
>>> see from the attached image what is the problem with my images? (I
>>> viewed the functional and anatomical data of a few subjects, some woth
>>> good and some with bad registration and see no difference or flip)
>>>
>>> Thanks a lot for your help!
>>> Aga
>>>
>>> 
>>>
>>> 
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>   
>
>
>
>   

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html



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
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] reg-feat2anat: a problem!

[Douglas N Greve]

That is not a problem. By "anatomical" I meant the FreeSurfer anatomical 
(eg, orig.mgz)
doug

Agnieszka Burzynska wrote:
> Dear Doug,
> Thank you a lot!
> Our feat data is always nifti, but anatomical FSL data is sometimes in the
> analyze format. Is this already a problem?
>
> I will now check the rest.
>
> Thank you, cheers,
> Aga
>
>
> On 2/7/11 4:35 PM, "Douglas N Greve"  wrote:
>
>   
>> Hi Aga, are you using nifti? If analyze, that could be the problem. Do
>> your functionals and anatomicals have a different sign to their
>> determinants (you can check with mri_info). In principle, reg-feat2anat
>> should handle this but in some cases it does not. The 5.1 version will
>> handle it properly. If they do have the same sign, then look through the
>> log file and find the flirt command. Run that command by itself (you may
>> need to run reg-feat2anat with --nocleanup to keep it from deleting the
>> files). If that fails, then contact the FSL people
>>
>> doug
>>
>> Agnieszka Burzynska wrote:
>> 
>>> Dear all,
>>> I am using the command reg-feat2anat to transform functional data
>>> pre-processed in FSL to the anatomical image in Freesurfer.
>>>
>>> As suggested, I check the registration with reg-feat2anat --feat
>>> run2.feat ‹manual.
>>>
>>> I have 3 runs of functional data for each subject. Surprisingly, some
>>> runs are registered well but others not (even of the same subject, so
>>> using the same reference anatomical images: see the attached image.
>>> Upper row: bad registration of one run and lower row: good
>>> registration of another run).
>>>
>>> I have no problem to manually correct the registrations, it works
>>> well, but as I have many subjects, I wonder if there may be a way to
>>> change some options of reg-feat2anat to make it work better? Can you
>>> see from the attached image what is the problem with my images? (I
>>> viewed the functional and anatomical data of a few subjects, some woth
>>> good and some with bad registration and see no difference or flip)
>>>
>>> Thanks a lot for your help!
>>> Aga
>>>
>>> 
>>>
>>> 
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>   
>
>
>
>   

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

___
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] reg-feat2anat: a problem!

[Agnieszka Burzynska]

Dear Doug,
Thank you a lot!
Our feat data is always nifti, but anatomical FSL data is sometimes in the
analyze format. Is this already a problem?

I will now check the rest.

Thank you, cheers,
Aga


On 2/7/11 4:35 PM, "Douglas N Greve"  wrote:

> Hi Aga, are you using nifti? If analyze, that could be the problem. Do
> your functionals and anatomicals have a different sign to their
> determinants (you can check with mri_info). In principle, reg-feat2anat
> should handle this but in some cases it does not. The 5.1 version will
> handle it properly. If they do have the same sign, then look through the
> log file and find the flirt command. Run that command by itself (you may
> need to run reg-feat2anat with --nocleanup to keep it from deleting the
> files). If that fails, then contact the FSL people
> 
> doug
> 
> Agnieszka Burzynska wrote:
>> Dear all,
>> I am using the command reg-feat2anat to transform functional data
>> pre-processed in FSL to the anatomical image in Freesurfer.
>> 
>> As suggested, I check the registration with reg-feat2anat --feat
>> run2.feat ‹manual.
>> 
>> I have 3 runs of functional data for each subject. Surprisingly, some
>> runs are registered well but others not (even of the same subject, so
>> using the same reference anatomical images: see the attached image.
>> Upper row: bad registration of one run and lower row: good
>> registration of another run).
>> 
>> I have no problem to manually correct the registrations, it works
>> well, but as I have many subjects, I wonder if there may be a way to
>> change some options of reg-feat2anat to make it work better? Can you
>> see from the attached image what is the problem with my images? (I
>> viewed the functional and anatomical data of a few subjects, some woth
>> good and some with bad registration and see no difference or flip)
>> 
>> Thanks a lot for your help!
>> Aga
>> 
>> 
>> 
>> 
>> 
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] reg-feat2anat: a problem!

[Douglas N Greve]

Hi Aga, are you using nifti? If analyze, that could be the problem. Do 
your functionals and anatomicals have a different sign to their 
determinants (you can check with mri_info). In principle, reg-feat2anat 
should handle this but in some cases it does not. The 5.1 version will 
handle it properly. If they do have the same sign, then look through the 
log file and find the flirt command. Run that command by itself (you may 
need to run reg-feat2anat with --nocleanup to keep it from deleting the 
files). If that fails, then contact the FSL people

doug

Agnieszka Burzynska wrote:
> Dear all,
> I am using the command reg-feat2anat to transform functional data 
> pre-processed in FSL to the anatomical image in Freesurfer.
>
> As suggested, I check the registration with reg-feat2anat --feat 
> run2.feat —manual.
>
> I have 3 runs of functional data for each subject. Surprisingly, some 
> runs are registered well but others not (even of the same subject, so 
> using the same reference anatomical images: see the attached image. 
> Upper row: bad registration of one run and lower row: good 
> registration of another run).
>
> I have no problem to manually correct the registrations, it works 
> well, but as I have many subjects, I wonder if there may be a way to 
> change some options of reg-feat2anat to make it work better? Can you 
> see from the attached image what is the problem with my images? (I 
> viewed the functional and anatomical data of a few subjects, some woth 
> good and some with bad registration and see no difference or flip)
>
> Thanks a lot for your help!
> Aga
>
> 
>
> 
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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[Freesurfer] reg-feat2anat basics

[Georg Homola]

Hi Doug!

May be a very basic question for better understanding, but how much does
reg-feat2anat care about the FSL preprocessing e.g. dewarping? And
especially important for me, does it make a difference if you FNIRT or FLIRT
on first level? Is it a good idea to process non-linearly registered
subjects with reg-feat2anat? In other words: is anat2exf.register.dat
actually affected by FEAT preprocessing output (warp field and
transformation matrices), or not at all? 

Many thanks in advance
Georg


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RE: [Freesurfer] reg-feat2anat failed

[Wang, Xin]

Hello, Dr. Greve,
I followed the steps in the tkregister2 --help: converted both example_func and 
orig.mgz to .img of ANALYZE format and ran the tkregister2 use -- fsl 
example_func2highres.mat of fsl/FEAT. The two brains are in the different views 
(i.e., axial view of example_func overlay on the coronal view of orig). I am 
still struggle with same questions as before. I appreciate any suggestion.
 
Thank you,
 
Xin Wang  



From: Wang, Xin
Sent: Tue 1/13/2009 4:36 PM
To: Douglas N Greve
Cc: freesurfer
Subject: RE: [Freesurfer] reg-feat2anat failed


Sorry for the confusion. Let me rephase my questions.
 
question 1: I want to use the example_func2highres.mat created by fsl/FEAT 
registration to register example_func and orig.mgz. Can the flag --fslregout or 
--fsl do it?
 
Question 2: These numbers appear in the terminal whenever I click a point in 
tkregister2? What do these numbers mean?  
Screen:  256 257 (113,113,113), inorm = 1, mov_frame = 0
 Anat:(128 126 127)   (   0.0   -1.02.0)   25.  32.7
 Func:( 31  32  21)   (   4.23.11.4)  756.  112.5
 
question 3: I can only see the middle portion of the brain in tkregister2 when 
I zoomed in. How can I see other parts of the target and movable pictures?
 
Thank you,
 
Xin Wang
  


 


From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
Sent: Tue 1/13/2009 4:19 PM
To: Wang, Xin
Subject: Re: [Freesurfer] reg-feat2anat failed




1) I don't know what you mean. The fslmatout is for creating an fsl mat
file from a freesurfer register.dat

2. I don't know what you mean.

3. What do you mean by "moving the two images together"?


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RE: [Freesurfer] reg-feat2anat failed

[Wang, Xin]

Sorry for the confusion. Let me rephase my questions.
 
question 1: I want to use the example_func2highres.mat created by fsl/FEAT 
registration to register example_func and orig.mgz. Can the flag --fslregout or 
--fsl do it?
 
Question 2: These numbers appear in the terminal whenever I click a point in 
tkregister2? What do these numbers mean?  
Screen:  256 257 (113,113,113), inorm = 1, mov_frame = 0
 Anat:(128 126 127)   (   0.0   -1.02.0)   25.  32.7
 Func:( 31  32  21)   (   4.23.11.4)  756.  112.5
 
question 3: I can only see the middle portion of the brain in tkregister2 when 
I zoomed in. How can I see other parts of the target and movable pictures?
 
Thank you,
 
Xin Wang
  


 


From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
Sent: Tue 1/13/2009 4:19 PM
To: Wang, Xin
Subject: Re: [Freesurfer] reg-feat2anat failed




1) I don't know what you mean. The fslmatout is for creating an fsl mat
file from a freesurfer register.dat

2. I don't know what you mean.

3. What do you mean by "moving the two images together"?


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Re: [Freesurfer] reg-feat2anat failed

[Douglas N Greve]

no, that's right. Does the example_func have a positive determinant?

Wang, Xin wrote:


Hello, Dr. Greve,
I used brain.mgz of freesurfer after mri_converted it to nii.gz as 
highres in feat registration with the thinking that the brain.mgz is 
the final product of freesurfer pre-processing. Using scalp-striped 
brain.mgz should be more comparable between fsl and FS than using 
T1.mgz or orig.mgz as I guess. Correct me if I am wrong.


Xin 



-Original Message-
From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
Sent: Tue 1/13/2009 11:27 AM
To: Wang, Xin
Cc: analysis-b...@nmr.mgh.harvard.edu; freesurfer
Subject: Re: [Freesurfer] reg-feat2anat failed


what did you use as the highres volume in feat? If you want that reg to
work, it has to be a "freesurfer anatomical volume", meaning 256^3, 1mm3

doug

Wang, Xin wrote:
>
> Hello, Freesurfer group,
> I registered the example_func.nii.gz to brain.mgz in tkregister2 using
> FS/anat2exf.register.dat, and --fslregout
> fsl.feat/reg/example_func2highres.mat. I have a couple of questions.
>
> 1) could anybody confirm that using--fslregout does apply .mat file
> for registration based on the following information on the screen?
> surfname set to orig
> target  volume PT01/mri/brain.mgz
> movable volume
> Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/example_func.nii.gz
> reg file  
> 
Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/reg/freesurfer/anat2exf.register.dat

> LoadVol1
> ZeroCRAS   0
> $Id: tkregister2.c,v 1.86.2.2 2008/03/10 14:02:35 nicks Exp $
> Diagnostic Level -1
>  Input registration matrix 
>  0.995  -0.028   0.093   4.032;
> -0.091   0.069   0.994   1.194;
> -0.035  -0.997   0.066   0.264;
>  0.000   0.000   0.000   1.000;
> float2int = 0
> ---
> INFO: loading target PT01/mri/brain.mgz
> INFO: changing target type to float
> 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
> Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/example_func.nii.gz
> Tmov: 
> -3.438   0.000   0.000   110.000;
>  0.000   0.000   3.000  -60.000;
>  0.000  -3.438   0.000   110.000;
>  0.000   0.000   0.000   1.000;
> mkheaderreg = 0, float2int = 0
>  Input registration matrix 
>  0.995  -0.028   0.093   4.032;
> -0.091   0.069   0.994   1.194;
> -0.035  -0.997   0.066   0.264;
>  0.000   0.000   0.000   1.000;
> subject = PT01
> Reading lh surface orig
> Done reading surface
> Reading rh surface orig
> Done reading surface
> Zoom Factor = 2
> FOV = 256
> Opening window PT01
> NVIDIA: could not open the device file /dev/nvidiactl (Permission 
denied).

> NVIDIA: Direct rendering failed; attempting indirect rendering.
> Setting scale
> Tagging mov volume
> tkregister2: interface: 
/net/dysthymia/freesurfer/lib/tcl/tkregister2.tcl

> tkregister.tcl: startup done
> tkregister.tcl: default macro interface (to change: macro,mini,micro)
> tkregister.tcl: or: setenv tkregisterinterface {macro,mini,micro}
> %
>
> 2) The results are quite the same (and good) in the tkregister2 with a
> slightly difference as shown below.
> Could anyone please tell me what these numbers mean?
>
> with .bat file
> Screen:  256 257 (113,113,113), inorm = 1, mov_frame = 0
>   Anat:(128 126 127)   (   0.0   -1.02.0)   25.32.7
>   Func:( 31  32  21)   (   4.23.11.4)  756.   112.5
>
> with .mat file
> Screen:  257 257 (175,175,175), inorm = 1, mov_frame = 0
>   Anat:(128 126 127)   (   0.0   -1.02.0)   25.28.3
>   Func:( 31  32  21)   (   4.23.11.4)  756.   106.2
>
> Thanks,
>
> Xin
>
>
> -Original Message-
> From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
> Sent: Mon 1/12/2009 4:02 PM
> To: Wang, Xin
> Cc: analysis-b...@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] reg-feat2anat failed
>
>
>  reg-feat2anat calls fslregister, so they should produce the same
> result. There is no need for an "intermediate" volume since you are
> registering from the subject's EPI to the subject's structure. Does the
> registration not look good?
>
>
> Wang, Xin wrote:
> > Thank you, Dr. Greve. It seems work ok. what is the difference between
> > reg-feat2anat and fslregister? although both commands are working for
> > me, I don't think either of them serve my propose. Freesurfer does not
> > use initial_highres to improve the reg of example_func to highres, but
> > FSL/FEAT uses this inter-mediate step. I try to use registration.mat
> >

Re: [Freesurfer] reg-feat2anat failed

[Douglas N Greve]

yes, though you might have to click on the iamge window

Wang, Xin wrote:


an additional question about tkregister2: can I move both targ and mov 
together when I zoomed in to a magnified view?

Thanks,

Xin


-Original Message-
From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
Sent: Tue 1/13/2009 11:27 AM
To: Wang, Xin
Cc: analysis-b...@nmr.mgh.harvard.edu; freesurfer
Subject: Re: [Freesurfer] reg-feat2anat failed


what did you use as the highres volume in feat? If you want that reg to
work, it has to be a "freesurfer anatomical volume", meaning 256^3, 1mm3

doug

Wang, Xin wrote:
>
> Hello, Freesurfer group,
> I registered the example_func.nii.gz to brain.mgz in tkregister2 using
> FS/anat2exf.register.dat, and --fslregout
> fsl.feat/reg/example_func2highres.mat. I have a couple of questions.
>
> 1) could anybody confirm that using--fslregout does apply .mat file
> for registration based on the following information on the screen?
> surfname set to orig
> target  volume PT01/mri/brain.mgz
> movable volume
> Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/example_func.nii.gz
> reg file  
> 
Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/reg/freesurfer/anat2exf.register.dat

> LoadVol1
> ZeroCRAS   0
> $Id: tkregister2.c,v 1.86.2.2 2008/03/10 14:02:35 nicks Exp $
> Diagnostic Level -1
>  Input registration matrix 
>  0.995  -0.028   0.093   4.032;
> -0.091   0.069   0.994   1.194;
> -0.035  -0.997   0.066   0.264;
>  0.000   0.000   0.000   1.000;
> float2int = 0
> ---
> INFO: loading target PT01/mri/brain.mgz
> INFO: changing target type to float
> 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
> Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/example_func.nii.gz
> Tmov: 
> -3.438   0.000   0.000   110.000;
>  0.000   0.000   3.000  -60.000;
>  0.000  -3.438   0.000   110.000;
>  0.000   0.000   0.000   1.000;
> mkheaderreg = 0, float2int = 0
>  Input registration matrix 
>  0.995  -0.028   0.093   4.032;
> -0.091   0.069   0.994   1.194;
> -0.035  -0.997   0.066   0.264;
>  0.000   0.000   0.000   1.000;
> subject = PT01
> Reading lh surface orig
> Done reading surface
> Reading rh surface orig
> Done reading surface
> Zoom Factor = 2
> FOV = 256
> Opening window PT01
> NVIDIA: could not open the device file /dev/nvidiactl (Permission 
denied).

> NVIDIA: Direct rendering failed; attempting indirect rendering.
> Setting scale
> Tagging mov volume
> tkregister2: interface: 
/net/dysthymia/freesurfer/lib/tcl/tkregister2.tcl

> tkregister.tcl: startup done
> tkregister.tcl: default macro interface (to change: macro,mini,micro)
> tkregister.tcl: or: setenv tkregisterinterface {macro,mini,micro}
> %
>
> 2) The results are quite the same (and good) in the tkregister2 with a
> slightly difference as shown below.
> Could anyone please tell me what these numbers mean?
>
> with .bat file
> Screen:  256 257 (113,113,113), inorm = 1, mov_frame = 0
>   Anat:(128 126 127)   (   0.0   -1.02.0)   25.32.7
>   Func:( 31  32  21)   (   4.23.11.4)  756.   112.5
>
> with .mat file
> Screen:  257 257 (175,175,175), inorm = 1, mov_frame = 0
>   Anat:(128 126 127)   (   0.0   -1.02.0)   25.28.3
>   Func:( 31  32  21)   (   4.23.1    1.4)  756.0000   106.2
>
> Thanks,
>
> Xin
>
>
> -Original Message-
> From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
> Sent: Mon 1/12/2009 4:02 PM
> To: Wang, Xin
> Cc: analysis-b...@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] reg-feat2anat failed
>
>
>  reg-feat2anat calls fslregister, so they should produce the same
> result. There is no need for an "intermediate" volume since you are
> registering from the subject's EPI to the subject's structure. Does the
> registration not look good?
>
>
> Wang, Xin wrote:
> > Thank you, Dr. Greve. It seems work ok. what is the difference between
> > reg-feat2anat and fslregister? although both commands are working for
> > me, I don't think either of them serve my propose. Freesurfer does not
> > use initial_highres to improve the reg of example_func to highres, but
> > FSL/FEAT uses this inter-mediate step. I try to use registration.mat
> > files of FSL/FEAT step-wise registrations to improve the
> > reg.   I think flag --fsl allow me to use a fsl.mat file as reg
> > file. How to make it work in the way I need?
> >
> > Thank you again,
> >
> > Xin

Re: [Freesurfer] reg-feat2anat failed

[Douglas N Greve]

what did you use as the highres volume in feat? If you want that reg to 
work, it has to be a "freesurfer anatomical volume", meaning 256^3, 1mm3


doug

Wang, Xin wrote:


Hello, Freesurfer group,
I registered the example_func.nii.gz to brain.mgz in tkregister2 using 
FS/anat2exf.register.dat, and --fslregout 
fsl.feat/reg/example_func2highres.mat. I have a couple of questions.


1) could anybody confirm that using--fslregout does apply .mat file 
for registration based on the following information on the screen?

surfname set to orig
target  volume PT01/mri/brain.mgz
movable volume 
Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/example_func.nii.gz
reg file   
Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/reg/freesurfer/anat2exf.register.dat

LoadVol1
ZeroCRAS   0
$Id: tkregister2.c,v 1.86.2.2 2008/03/10 14:02:35 nicks Exp $
Diagnostic Level -1
 Input registration matrix 
 0.995  -0.028   0.093   4.032;
-0.091   0.069   0.994   1.194;
-0.035  -0.997   0.066   0.264;
 0.000   0.000   0.000   1.000;
float2int = 0
---
INFO: loading target PT01/mri/brain.mgz
INFO: changing target type to float
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 
Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/example_func.nii.gz

Tmov: 
-3.438   0.000   0.000   110.000;
 0.000   0.000   3.000  -60.000;
 0.000  -3.438   0.000   110.000;
 0.000   0.000   0.000   1.000;
mkheaderreg = 0, float2int = 0
 Input registration matrix 
 0.995  -0.028   0.093   4.032;
-0.091   0.069   0.994   1.194;
-0.035  -0.997   0.066   0.264;
 0.000   0.000   0.000   1.000;
subject = PT01
Reading lh surface orig
Done reading surface
Reading rh surface orig
Done reading surface
Zoom Factor = 2
FOV = 256
Opening window PT01
NVIDIA: could not open the device file /dev/nvidiactl (Permission denied).
NVIDIA: Direct rendering failed; attempting indirect rendering.
Setting scale
Tagging mov volume
tkregister2: interface: /net/dysthymia/freesurfer/lib/tcl/tkregister2.tcl
tkregister.tcl: startup done
tkregister.tcl: default macro interface (to change: macro,mini,micro)
tkregister.tcl: or: setenv tkregisterinterface {macro,mini,micro}
%

2) The results are quite the same (and good) in the tkregister2 with a 
slightly difference as shown below.

Could anyone please tell me what these numbers mean?

with .bat file
Screen:  256 257 (113,113,113), inorm = 1, mov_frame = 0
  Anat:(128 126 127)   (   0.0   -1.02.0)   25.32.7
  Func:( 31  32  21)   (   4.23.11.4)  756.   112.5

with .mat file
Screen:  257 257 (175,175,175), inorm = 1, mov_frame = 0
  Anat:(128 126 127)   (   0.0   -1.02.0)   25.28.3
  Func:( 31  32  21)   (   4.23.11.4)  756.   106.2

Thanks,

Xin


-Original Message-
From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
Sent: Mon 1/12/2009 4:02 PM
To: Wang, Xin
Cc: analysis-b...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] reg-feat2anat failed


 reg-feat2anat calls fslregister, so they should produce the same
result. There is no need for an "intermediate" volume since you are
registering from the subject's EPI to the subject's structure. Does the
registration not look good?


Wang, Xin wrote:
> Thank you, Dr. Greve. It seems work ok. what is the difference between
> reg-feat2anat and fslregister? although both commands are working for
> me, I don't think either of them serve my propose. Freesurfer does not
> use initial_highres to improve the reg of example_func to highres, but
> FSL/FEAT uses this inter-mediate step. I try to use registration.mat
> files of FSL/FEAT step-wise registrations to improve the
> reg.   I think flag --fsl allow me to use a fsl.mat file as reg
> file. How to make it work in the way I need?
> 
> Thank you again,
> 
> Xin 
>

> 
> *From:* Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
> *Sent:* Mon 1/12/2009 3:29 PM
> *To:* Wang, Xin
> *Cc:* analysis-b...@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] reg-feat2anat failed
>
> when you say everything looked ok, do you mean that the orientation was
> correct? If so, try running this:
>
> fslregister --s subject --mov example_func.nii.gz --reg newreg.dat
>
> then
>
> tkregister2 --mov example_func.nii.gz --reg newreg.dat --surfs
>
>
>
>
> Wang, Xin wrote:
> > Sorry, Dr. Greve. I copied addtional parts after I killed the
> > tkmedit. The following is on the screen when I saw the image.
> >
> > []$ tkmedit -f
> > Recall/SM5DF1212/PT01_Recall_SM5DF1212.feat/example_func.nii.gz
> > Reading /net/dysthymia/freesurfer/lib/tcl/tkm_common.tc

Re: [Freesurfer] reg-feat2anat failed

[Doug Greve]

Hi Xin, I'm not sure what's going wrong here, I think I need more info. 
Can you follow the steps in surfer.nmr.mgh.harvard.edu/fswiki/BugReporting?


doug


Wang, Xin wrote:


hello, Freesurfer group,

I try to use registration.mat files of FSL/FEAT routines, instead of 
anat2example_func.bat, to register the orig.mgz and 
example_func.nii.gz with the thinking that using initial_highres in 
FEAT may improve the reg. However, tkregister2 catastrophically failed 
to register two brains when I use --fsl flag. Modifying header of 
example_func with mri_convert does not solve the problem. I will 
appreciate any suggestion on using .mat file for registration.


second question: what is the best registration of example_func and 
orig.mgz? In another word, what should I check besides things in the 
FS tutorial when I check/modify the registration in tkregister2? Is 
there golden reference points I can use?


Thank you in advance for any suggestion.

Xin wang



-Original Message-
From: Doug Greve [mailto:gr...@nmr.mgh.harvard.edu]
Sent: Mon 12/15/2008 1:26 PM
To: Wang, Xin
Cc: freesurfer
Subject: Re: [Freesurfer] reg-feat2anat failed

There is a flag in the nifti header saying whether the qform or sform
are valid, and it looks like your scripts do not set this flag. You can
use mri_convert (the freesurfer program). This will create valid files
that can be read into any program.

doug

Wang, Xin wrote:

> Thank you very much for your quick reply, Dr. Greve. I asked our
> institutional MRI center for correct information on qform and sform
> since the header of nifti files are created by their scripts. But I do
> not know what they can do to fix this problem. I will appreciate if
> you have any further suggestion on how to do the registration without
> the information on qform and sform in case I can not get them. Does
> convert to ANALYZE format or manually correct in tkregister2 work?
>
> Thank you again,
>
> Xin
>
>
> -Original Message-
> From: Doug Greve [mailto:gr...@nmr.mgh.harvard.edu]
> Sent: Mon 12/15/2008 1:09 PM
> To: Wang, Xin
> Cc: freesurfer
> Subject: Re: [Freesurfer] reg-feat2anat failed
>
> Hi Xin, the problem is that neither the sform nor the qform are valid.
> Did the message below not appear when you ran tkmedit?
>
> WARNING: neither NIfTI-1 qform or sform are valid
> WARNING: your volume will probably be incorrectly oriented
>
> Fix that, and everything will work fine.
>
> doug
>
>
> Wang, Xin wrote:
>
> > Hello, Freesurfer group,
> > I am registering the fMRI results to surface using reg-feat2anat (v
> > 1.26.2.1 2007/08/15) and tkregister2. The automatic registration
> > catastrophically failed in the subject space, but worked fine in the
> > standard space. The orientations of example_func.nii.gz in the subject
> > space are flipped in any view. I use the tkmedit to view the
> > example_func, and found the orientation is wrong. It seems Freesurfer
> > can not read nifti header correctly. I attach the reg-feat2anat log
> > file and an example_func.nii.gz.
> > I found the following message from Freesurfer email list.
> > 
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg05573.html

> > Does Freesurfer have a solution for this type of problems by now?
> >
> > Thank you in advance,
> >
> > Xin
> >
> 
>

> >
> >___
> >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
>
> In order to help us help you, please follow the steps in:
> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
>
>

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

In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting





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


In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


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RE: [Freesurfer] reg-feat2anat failed

[Wang, Xin]

hello, Freesurfer group,

I try to use registration.mat files of FSL/FEAT routines, instead of 
anat2example_func.bat, to register the orig.mgz and example_func.nii.gz with 
the thinking that using initial_highres in FEAT may improve the reg. However, 
tkregister2 catastrophically failed to register two brains when I use --fsl 
flag. Modifying header of example_func with mri_convert does not solve the 
problem. I will appreciate any suggestion on using .mat file for registration. 

second question: what is the best registration of example_func and orig.mgz? In 
another word, what should I check besides things in the FS tutorial when I 
check/modify the registration in tkregister2? Is there golden reference points 
I can use?

Thank you in advance for any suggestion.

Xin wang 


-Original Message-
From: Doug Greve [mailto:gr...@nmr.mgh.harvard.edu]
Sent: Mon 12/15/2008 1:26 PM
To: Wang, Xin
Cc: freesurfer
Subject: Re: [Freesurfer] reg-feat2anat failed
 
There is a flag in the nifti header saying whether the qform or sform 
are valid, and it looks like your scripts do not set this flag. You can 
use mri_convert (the freesurfer program). This will create valid files 
that can be read into any program.

doug

Wang, Xin wrote:

> Thank you very much for your quick reply, Dr. Greve. I asked our 
> institutional MRI center for correct information on qform and sform 
> since the header of nifti files are created by their scripts. But I do 
> not know what they can do to fix this problem. I will appreciate if 
> you have any further suggestion on how to do the registration without 
> the information on qform and sform in case I can not get them. Does 
> convert to ANALYZE format or manually correct in tkregister2 work?
>
> Thank you again,
>
> Xin 
>
>
> -Original Message-
> From: Doug Greve [mailto:gr...@nmr.mgh.harvard.edu]
> Sent: Mon 12/15/2008 1:09 PM
> To: Wang, Xin
> Cc: freesurfer
> Subject: Re: [Freesurfer] reg-feat2anat failed
>
> Hi Xin, the problem is that neither the sform nor the qform are valid.
> Did the message below not appear when you ran tkmedit?
>
> WARNING: neither NIfTI-1 qform or sform are valid
> WARNING: your volume will probably be incorrectly oriented
>
> Fix that, and everything will work fine.
>
> doug
>
>
> Wang, Xin wrote:
>
> > Hello, Freesurfer group,
> > I am registering the fMRI results to surface using reg-feat2anat (v
> > 1.26.2.1 2007/08/15) and tkregister2. The automatic registration
> > catastrophically failed in the subject space, but worked fine in the
> > standard space. The orientations of example_func.nii.gz in the subject
> > space are flipped in any view. I use the tkmedit to view the
> > example_func, and found the orientation is wrong. It seems Freesurfer
> > can not read nifti header correctly. I attach the reg-feat2anat log
> > file and an example_func.nii.gz. 
> > I found the following message from Freesurfer email list.
> > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg05573.html
> > Does Freesurfer have a solution for this type of problems by now?
> >
> > Thank you in advance,
> >
> > Xin
> >
> >
> >
> >___
> >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
>
> In order to help us help you, please follow the steps in:
> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
>
>

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

In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting



___
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Re: [Freesurfer] reg-feat2anat failed

[Doug Greve]

There is a flag in the nifti header saying whether the qform or sform 
are valid, and it looks like your scripts do not set this flag. You can 
use mri_convert (the freesurfer program). This will create valid files 
that can be read into any program.


doug

Wang, Xin wrote:

Thank you very much for your quick reply, Dr. Greve. I asked our 
institutional MRI center for correct information on qform and sform 
since the header of nifti files are created by their scripts. But I do 
not know what they can do to fix this problem. I will appreciate if 
you have any further suggestion on how to do the registration without 
the information on qform and sform in case I can not get them. Does 
convert to ANALYZE format or manually correct in tkregister2 work?


Thank you again,

Xin 



-Original Message-
From: Doug Greve [mailto:gr...@nmr.mgh.harvard.edu]
Sent: Mon 12/15/2008 1:09 PM
To: Wang, Xin
Cc: freesurfer
Subject: Re: [Freesurfer] reg-feat2anat failed

Hi Xin, the problem is that neither the sform nor the qform are valid.
Did the message below not appear when you ran tkmedit?

WARNING: neither NIfTI-1 qform or sform are valid
WARNING: your volume will probably be incorrectly oriented

Fix that, and everything will work fine.

doug


Wang, Xin wrote:

> Hello, Freesurfer group,
> I am registering the fMRI results to surface using reg-feat2anat (v
> 1.26.2.1 2007/08/15) and tkregister2. The automatic registration
> catastrophically failed in the subject space, but worked fine in the
> standard space. The orientations of example_func.nii.gz in the subject
> space are flipped in any view. I use the tkmedit to view the
> example_func, and found the orientation is wrong. It seems Freesurfer
> can not read nifti header correctly. I attach the reg-feat2anat log
> file and an example_func.nii.gz. 
> I found the following message from Freesurfer email list.

> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg05573.html
> Does Freesurfer have a solution for this type of problems by now?
>
> Thank you in advance,
>
> Xin
>
>
>
>___
>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

In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting





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


In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


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

RE: [Freesurfer] reg-feat2anat failed

[Wang, Xin]

Thank you very much for your quick reply, Dr. Greve. I asked our institutional 
MRI center for correct information on qform and sform since the header of nifti 
files are created by their scripts. But I do not know what they can do to fix 
this problem. I will appreciate if you have any further suggestion on how to do 
the registration without the information on qform and sform in case I can not 
get them. Does convert to ANALYZE format or manually correct in tkregister2 
work?

Thank you again,

Xin  


-Original Message-
From: Doug Greve [mailto:gr...@nmr.mgh.harvard.edu]
Sent: Mon 12/15/2008 1:09 PM
To: Wang, Xin
Cc: freesurfer
Subject: Re: [Freesurfer] reg-feat2anat failed
 
Hi Xin, the problem is that neither the sform nor the qform are valid. 
Did the message below not appear when you ran tkmedit?

WARNING: neither NIfTI-1 qform or sform are valid
WARNING: your volume will probably be incorrectly oriented

Fix that, and everything will work fine.

doug


Wang, Xin wrote:

> Hello, Freesurfer group,
> I am registering the fMRI results to surface using reg-feat2anat (v 
> 1.26.2.1 2007/08/15) and tkregister2. The automatic registration 
> catastrophically failed in the subject space, but worked fine in the 
> standard space. The orientations of example_func.nii.gz in the subject 
> space are flipped in any view. I use the tkmedit to view the 
> example_func, and found the orientation is wrong. It seems Freesurfer 
> can not read nifti header correctly. I attach the reg-feat2anat log 
> file and an example_func.nii.gz.  
> I found the following message from Freesurfer email list.
> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg05573.html
> Does Freesurfer have a solution for this type of problems by now?
>
> Thank you in advance,
>
> Xin
>
>
>
>___
>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

In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting



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

Re: [Freesurfer] reg-feat2anat failed

[Doug Greve]

Hi Xin, the problem is that neither the sform nor the qform are valid. 
Did the message below not appear when you ran tkmedit?


WARNING: neither NIfTI-1 qform or sform are valid
WARNING: your volume will probably be incorrectly oriented

Fix that, and everything will work fine.

doug


Wang, Xin wrote:


Hello, Freesurfer group,
I am registering the fMRI results to surface using reg-feat2anat (v 
1.26.2.1 2007/08/15) and tkregister2. The automatic registration 
catastrophically failed in the subject space, but worked fine in the 
standard space. The orientations of example_func.nii.gz in the subject 
space are flipped in any view. I use the tkmedit to view the 
example_func, and found the orientation is wrong. It seems Freesurfer 
can not read nifti header correctly. I attach the reg-feat2anat log 
file and an example_func.nii.gz.  
I found the following message from Freesurfer email list.

http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg05573.html
Does Freesurfer have a solution for this type of problems by now?

Thank you in advance,

Xin



___
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


In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


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

[Freesurfer] reg-feat2anat misregistration (potentially resolved?)

[Fred Dick]

Dear Doug et al.,

a while back there was a post on peculiar registration problems using  
reg-feat2anat, e.g., the registration using reg-feat2anat was quite  
off (seriously rotated or similar), whereas barebones flirt on the  
same volumes did better. I didn't spot a resolution on the message  
boards, but I have found that the EPIs end up being rotated  
incorrectly (around A-P axis) when I run flirt with the initial  
registration (from tkregister2-cmdl), but not with the same command  
minus -init.  I didn't see any hidden option flags in reg-feat2anat  
for blowing off -init (although did spot one in fslregister), so am  
guessing that other people haven't found this to be a problem.


I should mention that I'm using reg-feat2anat on a partial volume scan  
- there may not be the same issue with whole-head EPIs...


Apologies if I missed a previously posted solution,

best,
Fred
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Re: [Freesurfer] reg -feat2anat error reg -feat2anat error

[Doug Greve]

I don't know what's going wrong. It looks like you cannot even run a 
tcsh script. Do you have a sys admin that you can show this to?


doug

Furlong, Carolyn wrote:


Freesurfer RedHat 9 version

on SUSE Linux 9.3

Cheers
Carolyn


-Original Message-
From: Doug Greve [mailto:[EMAIL PROTECTED]
Sent: Mon 04/06/2007 16:36
To: Furlong, Carolyn
Cc: Freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] reg -feat2anat error   reg -feat2anat error

what platform are you running on?

Furlong, Carolyn wrote:

> Hi Doug
>
> This is what happened when I ran it with --debug
>
> Kate/Flatmap1> reg-feat2anat --feat
> /disc2/Kate/Data_FSL/Pre_AM/AM_preAM_BET.feat --subject AMoore --debug
> 'nknown option: `-
> Usage: tcsh [ -bcdefilmnqstvVxX ] [ argument ... ].
>
> After I replaced the binaries that you suggested in previous emails,
> the other processes would now no longer run...
>
> Healthy_Volunteers/Colton_Structural> mri_convert -i Colton.nii.gz
> -subjid Colton -autorecon1
> mri_convert: error while loading shared libraries: libstdc++.so.6:
> cannot open shared object file: No such file or directory
>
> Flatmap1/Healthy_Volunteers> tkregister2 --mgz --s Colton -fstal
> tkregister2: error while loading shared libraries: libtix8.1.8.4.so:
> cannot open shared object file: No such file or directory
>
> I changed mri_convert and tkregister2 back to their original version
> and they worked fine again.  When I run the old version of
> reg-feat2anat I still get the original error:
>
> ERROR: could not read
> /disc2/Kate/Data_FSL/Pre_AM/AM_preAM_BET.feat/example_func.nii.gz as 24
>
> Not sure what is going on?
>
> Best wishes
> Carolyn
>
>
>
>
>
>
> -Original Message-
> From: Doug Greve [mailto:[EMAIL PROTECTED]
> Sent: Mon 04/06/2007 15:07
> To: Furlong, Carolyn
> Cc: Freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] reg -feat2anat error   reg -feat2anat error
>
> wow, not sure what's going on there. Can you add --debug to the cmd
> line, caputre the terminal output, and send it to me?
>
> Furlong, Carolyn wrote:
>
> > Hi Doug
> >
> > we tried adding the binaries Doug sent us (MRI_convert, reg2anat and
> > tkregister2, make average subject, make average surface anfd make
> > avergae volume), but now we get a different error:reg-feat2anat --feat
> > ./disc2/Kate/Data_FSL/Pre_AM/AM_preAM_BET.feat/reg/ --subject AMoore
> >
> > 'nknown option: `-
> > Usage: tcsh [ -bcdefilmnqstvVxX ] [ argument ... ].
> >
> > What should I do?
> >
> > Best wishes
> > Carolyn
> >
> > -Original Message-
> > From: Doug Greve [mailto:[EMAIL PROTECTED]
> > Sent: Mon 21/05/2007 17:16
> > To: Furlong, Carolyn
> > Cc: Freesurfer@nmr.mgh.harvard.edu
> > Subject: Re: [Freesurfer] reg -feat2anat error
> >
> > Did you see my email from last week? It looks like the problem was 
fixed

> > with new versions of a few programs.
> >
> > doug
> >
> > Furlong, Carolyn wrote:
> >
> > >
> > > Hi Doug
> > >
> > > Please find attached the logfile that you requested, sorry for the
> > > delay, I am only able to work on this one day a week.
> > >
> > > Best wishes
> > > Carolyn
> > >
> > >
> > >
> > >
> > >
> > > Actually, I wanted the log file found in
> > > featdir/reg/freesurfer/reg-feat2anat.log.
> > >
> > > doug
> > >
> > > Furlong, Carolyn wrote:
> > >
> > > > Hi
> > > >
> > > >
> > > > niiRead(): unsupported timing pattern in
> > > Pre_DB/DB_Prelip_BET.feat/example_func.nii.gz
> > > >
> > > > sorry for the delay,
> > > >
> > > > Best wishes
> > > >
> > > > Carolyn
> > > >
> > > > can you send the log file?
> > > >
> > > > Furlong, Carolyn wrote:
> > > >
> > > >> Hi,
> > > >>
> > > >> When I try to register my functional data to anatomical data 
using

> > > >>
> > > >> reg-feat2anat --feat feat_directory --subject subject_name
> > > >>
> > > >> I get the following error message
> > > >>
> > > >> ERROR: could not read ///example_func.nii.gz as 24
> > > >>
> > > >> What does this mean? And how can I fix this?
> > > >>
> > > >> Best wishes
> > > >> Carolyn
> > > >>
> > > >>

RE: [Freesurfer] reg -feat2anat error reg -feat2anat error

[Furlong, Carolyn]

Freesurfer RedHat 9 version 

on SUSE Linux 9.3

Cheers
Carolyn


-Original Message-
From: Doug Greve [mailto:[EMAIL PROTECTED]
Sent: Mon 04/06/2007 16:36
To: Furlong, Carolyn
Cc: Freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] reg -feat2anat error   reg -feat2anat error
 
what platform are you running on?

Furlong, Carolyn wrote:

> Hi Doug
>
> This is what happened when I ran it with --debug
>
> Kate/Flatmap1> reg-feat2anat --feat 
> /disc2/Kate/Data_FSL/Pre_AM/AM_preAM_BET.feat --subject AMoore --debug
> 'nknown option: `-
> Usage: tcsh [ -bcdefilmnqstvVxX ] [ argument ... ].
>
> After I replaced the binaries that you suggested in previous emails, 
> the other processes would now no longer run...
>
> Healthy_Volunteers/Colton_Structural> mri_convert -i Colton.nii.gz 
> -subjid Colton -autorecon1
> mri_convert: error while loading shared libraries: libstdc++.so.6: 
> cannot open shared object file: No such file or directory
>
> Flatmap1/Healthy_Volunteers> tkregister2 --mgz --s Colton -fstal
> tkregister2: error while loading shared libraries: libtix8.1.8.4.so: 
> cannot open shared object file: No such file or directory
>
> I changed mri_convert and tkregister2 back to their original version 
> and they worked fine again.  When I run the old version of 
> reg-feat2anat I still get the original error:
>
> ERROR: could not read 
> /disc2/Kate/Data_FSL/Pre_AM/AM_preAM_BET.feat/example_func.nii.gz as 24
>
> Not sure what is going on?
>
> Best wishes
> Carolyn
>
>
>
>
>
>
> -Original Message-
> From: Doug Greve [mailto:[EMAIL PROTECTED]
> Sent: Mon 04/06/2007 15:07
> To: Furlong, Carolyn
> Cc: Freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] reg -feat2anat error   reg -feat2anat error
>
> wow, not sure what's going on there. Can you add --debug to the cmd
> line, caputre the terminal output, and send it to me?
>
> Furlong, Carolyn wrote:
>
> > Hi Doug
> >
> > we tried adding the binaries Doug sent us (MRI_convert, reg2anat and
> > tkregister2, make average subject, make average surface anfd make
> > avergae volume), but now we get a different error:reg-feat2anat --feat
> > ./disc2/Kate/Data_FSL/Pre_AM/AM_preAM_BET.feat/reg/ --subject AMoore
> >
> > 'nknown option: `-
> > Usage: tcsh [ -bcdefilmnqstvVxX ] [ argument ... ].
> >
> > What should I do?
> >
> > Best wishes
> > Carolyn
> >
> > -Original Message-
> > From: Doug Greve [mailto:[EMAIL PROTECTED]
> > Sent: Mon 21/05/2007 17:16
> > To: Furlong, Carolyn
> > Cc: Freesurfer@nmr.mgh.harvard.edu
> > Subject: Re: [Freesurfer] reg -feat2anat error
> >
> > Did you see my email from last week? It looks like the problem was fixed
> > with new versions of a few programs.
> >
> > doug
> >
> > Furlong, Carolyn wrote:
> >
> > >
> > > Hi Doug
> > >
> > > Please find attached the logfile that you requested, sorry for the
> > > delay, I am only able to work on this one day a week.
> > >
> > > Best wishes
> > > Carolyn
> > >
> > >
> > >
> > >
> > >
> > > Actually, I wanted the log file found in
> > > featdir/reg/freesurfer/reg-feat2anat.log.
> > >
> > > doug
> > >
> > > Furlong, Carolyn wrote:
> > >
> > > > Hi
> > > >
> > > >
> > > > niiRead(): unsupported timing pattern in
> > > Pre_DB/DB_Prelip_BET.feat/example_func.nii.gz
> > > >
> > > > sorry for the delay,
> > > >
> > > > Best wishes
> > > >
> > > > Carolyn
> > > >
> > > > can you send the log file?
> > > >
> > > > Furlong, Carolyn wrote:
> > > >
> > > >> Hi,
> > > >>
> > > >> When I try to register my functional data to anatomical data using
> > > >>
> > > >> reg-feat2anat --feat feat_directory --subject subject_name
> > > >>
> > > >> I get the following error message
> > > >>
> > > >> ERROR: could not read ///example_func.nii.gz as 24
> > > >>
> > > >> What does this mean? And how can I fix this?
> > > >>
> > > >> Best wishes
> > > >> Carolyn
> > > >>
> > > >>
> > > >>___
> > > >>Freesurfer mailing list
> > > >>Freesurfer@nmr.mgh.harvard.edu
&

Re: [Freesurfer] reg- feat2anat error-problem

[Doug Greve]

How did you check it? Can you check it with

reg-feat2anat --feat  Akkaya_Zuhre_1_9++.feat/ --subject akkaya --manxfm 
func2std


doug

uzay emir wrote:


Hi doug
the example_func to standard space registration  is correct.
 
I do not know what to do.
 
Uzay
 



Doug Greve <[EMAIL PROTECTED]> wrote:

It sounds like something has to be fixed. Is the example_func to
standard space registration correct? If not, then you will need to
fix it. That registration is purely FSL.

doug

uzay emir wrote:


Hi,
Orientation problem is outlined below.
1-When the target in coronal view, movable(example_func) is sagital.
2- When the target is in sagital view, movable is  coronal.
3- axial view is teh same both movable and target but The problem
in this situation is that there is an angle between movable and
target.


I followed all the steps. Right now should I expect that
reg-feat2anat solves the big problems or should i have to
register manually with tkregister2?

 


Regards

Uzay


Doug Greve <[EMAIL PROTECTED]> wrote:

What do you mean there was an orientation problem? If you use
analyze files, then it relies on the FSL reg to std space
being correct. Is it?

uzay emir wrote:


Thank you,it is working now. However, I have anorientation
problem with automatic registration results. This problem
has been mentioned before but i could not find any reply.  I
think this is something related following lines where I
found it in the reg- feat2anat log file.
Regards

Uzay

- INFO: could not 
find /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file for 
direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse 
unflipped (default). INFO: if not valid, please provide the information in 
/home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file   
- INFO: using NIfTI-1 
sform- INFO: 
could not find /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat 
file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 0, 
transverse unflipped (default). INFO: if not valid, please provide the information in
/home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file 
- 
- INFO: could not 
find /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file 
for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 0, 
transverse unflipped (default). INFO: if not valid, please provide the information 
in /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file


__
Do You Yahoo!?
Tired of spam? Yahoo! Mail has the best spam protection around
http://mail.yahoo.com


 Fri May 18 11:13:12 EEST 2007  
/home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/orig  
/home/uzay/freesurfer_3/freesurfer/bin//reg-feat2anat  --feat
Akkaya_Zuhre_1_9++.feat/ --subject akkaya  Linux localhost.localdomain 
2.6.12-1.1381_FC3 #1 Fri Oct 21 03:46:55 EDT 2005 i686 i686 i386 GNU/Linux  
mri_convert 
/home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz 
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/tmp/anat.nii.gz  mri_convert 
/home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz 
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/tmp/anat.nii.gz   $Id: mri_convert.c,v 
1.141 2007/04/26 05:31:21 greve Exp $  reading from   
/home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz...  
TR=11.00, TE=4.92, TI=4.92, flip angle=15.00  i_ras = (-1, 2.56273e-11, 
6.83856e-10)  j_ras = (-1.17877e-09, -2.94451e-16, -1)  k_ras = (3.0538e-12, 1, 
-9.84868e-13)  writing to 
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/tmp/anat.nii.gz...  example_func 
ras_good_flag   ---  
Initializing exf2anat from crude std2anat  tkregister2 --targ
/home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz --mov 
/home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.img --reg 
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/anat2std.register.dat --fslregout 
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/std2anat.fsl.mat --regheader --noedit  
target  volume 
/home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz  movable 
volume /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.img  
reg file Akkaya_Zuhre_1_9++.feat//reg/freesurfer/anat2std.register.dat  
LoadVol0  $Id: 

Re: [Freesurfer] reg- feat2anat error-problem

[uzay emir]

Hi doug
  the example_func to standard space registration  is correct. 
   
  I do not know what to do.
   
  Uzay
   
  

Doug Greve <[EMAIL PROTECTED]> wrote:
  It sounds like something has to be fixed. Is the example_func to standard 
space registration correct? If not, then you will need to fix it. That 
registration is purely FSL.

doug

uzay emir wrote:   Hi,
Orientation problem is outlined below.
1-When the target in coronal view, movable(example_func) is sagital.
2- When the target is in sagital view, movable is  coronal.
3- axial view is teh same both movable and target but The problem in this 
situation is that there is an angle between movable and target.


I followed all the steps. Right now should I expect that reg-feat2anat solves 
the big problems or should i have to register manually with tkregister2?

 

Regards

Uzay


Doug Greve <[EMAIL PROTECTED]> wrote:   What do you mean there was an 
orientation problem? If you use analyze files, then it relies on the FSL reg to 
std space being correct. Is it?

uzay emir wrote:   Thank you,it is working now. However, I have anorientation 
problem with automatic registration results. This problem has been mentioned 
before but i could not find any reply.  I think this is something related 
following lines where I found it in the reg- feat2anat log file. 
Regards

Uzay
  
- INFO: could 
not find /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat 
file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 
0, transverse unflipped (default). INFO: if not valid, please provide the 
information in 
/home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file   
- INFO: using 
NIfTI-1 sform
- INFO: could 
not find /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat 
file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 
0, transverse unflipped (default). INFO: if not valid, please provide the 
information in 
/home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file 
-
 - INFO: could 
not find /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat 
file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 
0, transverse unflipped (default). INFO: if not valid, please provide the 
information in 
/home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file

  __
Do You Yahoo!?
Tired of spam? Yahoo! Mail has the best spam protection around 
http://mail.yahoo.com 


-
  Fri May 18 11:13:12 EEST 2007  
/home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/orig  
/home/uzay/freesurfer_3/freesurfer/bin//reg-feat2anat  --feat 
Akkaya_Zuhre_1_9++.feat/ --subject akkaya  Linux localhost.localdomain 
2.6.12-1.1381_FC3 #1 Fri Oct 21 03:46:55 EDT 2005 i686 i686 i386 GNU/Linux  
mri_convert 
/home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz 
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/tmp/anat.nii.gz  mri_convert 
/home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz 
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/tmp/anat.nii.gz   $Id: mri_convert.c,v 
1.141 2007/04/26 05:31:21 greve Exp $  reading from   
/home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz...  
TR=11.00, TE=4.92, TI=4.92, flip angle=15.00  i_ras = (-1, 2.56273e-11, 
6.83856e-10)  j_ras = (-1.17877e-09, -2.94451e-16, -1)  k_ras = (3.0538e-12, 1, 
-9.84868e-13)  writing to 
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/tmp/anat.nii.gz...  example_func
 ras_good_flag   ---  
Initializing exf2anat from crude std2anat  tkregister2 --targ 
/home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz --mov 
/home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.img --reg 
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/anat2std.register.dat --fslregout 
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/std2anat.fsl.mat --regheader --noedit  
target  volume 
/home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz  movable 
volume /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.img  
reg file Akkaya_Zuhre_1_9++.feat//reg/freesurfer/anat2std.register.dat  
LoadVol0  $Id: tkregister2.c,v 1.80 2007/05/11 18:39:00 greve Exp $  
Diagnostic Level -1  INFO: loading target 
/home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.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 

Re: [Freesurfer] reg -feat2anat error reg -feat2anat error

[Doug Greve]

what platform are you running on?

Furlong, Carolyn wrote:


Hi Doug

This is what happened when I ran it with --debug

Kate/Flatmap1> reg-feat2anat --feat 
/disc2/Kate/Data_FSL/Pre_AM/AM_preAM_BET.feat --subject AMoore --debug

'nknown option: `-
Usage: tcsh [ -bcdefilmnqstvVxX ] [ argument ... ].

After I replaced the binaries that you suggested in previous emails, 
the other processes would now no longer run...


Healthy_Volunteers/Colton_Structural> mri_convert -i Colton.nii.gz 
-subjid Colton -autorecon1
mri_convert: error while loading shared libraries: libstdc++.so.6: 
cannot open shared object file: No such file or directory


Flatmap1/Healthy_Volunteers> tkregister2 --mgz --s Colton -fstal
tkregister2: error while loading shared libraries: libtix8.1.8.4.so: 
cannot open shared object file: No such file or directory


I changed mri_convert and tkregister2 back to their original version 
and they worked fine again.  When I run the old version of 
reg-feat2anat I still get the original error:


ERROR: could not read 
/disc2/Kate/Data_FSL/Pre_AM/AM_preAM_BET.feat/example_func.nii.gz as 24


Not sure what is going on?

Best wishes
Carolyn






-Original Message-
From: Doug Greve [mailto:[EMAIL PROTECTED]
Sent: Mon 04/06/2007 15:07
To: Furlong, Carolyn
Cc: Freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] reg -feat2anat error   reg -feat2anat error

wow, not sure what's going on there. Can you add --debug to the cmd
line, caputre the terminal output, and send it to me?

Furlong, Carolyn wrote:

> Hi Doug
>
> we tried adding the binaries Doug sent us (MRI_convert, reg2anat and
> tkregister2, make average subject, make average surface anfd make
> avergae volume), but now we get a different error:reg-feat2anat --feat
> ./disc2/Kate/Data_FSL/Pre_AM/AM_preAM_BET.feat/reg/ --subject AMoore
>
> 'nknown option: `-
> Usage: tcsh [ -bcdefilmnqstvVxX ] [ argument ... ].
>
> What should I do?
>
> Best wishes
> Carolyn
>
> -Original Message-
> From: Doug Greve [mailto:[EMAIL PROTECTED]
> Sent: Mon 21/05/2007 17:16
> To: Furlong, Carolyn
> Cc: Freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] reg -feat2anat error
>
> Did you see my email from last week? It looks like the problem was fixed
> with new versions of a few programs.
>
> doug
>
> Furlong, Carolyn wrote:
>
> >
> > Hi Doug
> >
> > Please find attached the logfile that you requested, sorry for the
> > delay, I am only able to work on this one day a week.
> >
> > Best wishes
> > Carolyn
> >
> >
> >
> >
> >
> > Actually, I wanted the log file found in
> > featdir/reg/freesurfer/reg-feat2anat.log.
> >
> > doug
> >
> > Furlong, Carolyn wrote:
> >
> > > Hi
> > >
> > >
> > > niiRead(): unsupported timing pattern in
> > Pre_DB/DB_Prelip_BET.feat/example_func.nii.gz
> > >
> > > sorry for the delay,
> > >
> > > Best wishes
> > >
> > > Carolyn
> > >
> > > can you send the log file?
> > >
> > > Furlong, Carolyn wrote:
> > >
> > >> Hi,
> > >>
> > >> When I try to register my functional data to anatomical data using
> > >>
> > >> reg-feat2anat --feat feat_directory --subject subject_name
> > >>
> > >> I get the following error message
> > >>
> > >> ERROR: could not read ///example_func.nii.gz as 24
> > >>
> > >> What does this mean? And how can I fix this?
> > >>
> > >> Best wishes
> > >> Carolyn
> > >>
> > >>
> > >>___
> > >>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
> > >[EMAIL PROTECTED]
> > >Phone Number: 617-724-2358
> > >Fax: 617-726-7422
> > >
> > >In order to help us help you, please follow the steps in:
> > >surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > >
> > >
> > >
> > >___
> > >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
> > [EMAIL PROTECTED]
> > Phone Number: 617-724-2358
> > Fax: 617-726-7422
> >
> > In order to

RE: [Freesurfer] reg -feat2anat error reg -feat2anat error

[Furlong, Carolyn]

Hi Doug

This is what happened when I ran it with --debug

Kate/Flatmap1> reg-feat2anat --feat 
/disc2/Kate/Data_FSL/Pre_AM/AM_preAM_BET.feat --subject AMoore --debug
'nknown option: `-
Usage: tcsh [ -bcdefilmnqstvVxX ] [ argument ... ].

After I replaced the binaries that you suggested in previous emails, the other 
processes would now no longer run...

Healthy_Volunteers/Colton_Structural> mri_convert -i Colton.nii.gz -subjid 
Colton -autorecon1
mri_convert: error while loading shared libraries: libstdc++.so.6: cannot open 
shared object file: No such file or directory

Flatmap1/Healthy_Volunteers> tkregister2 --mgz --s Colton -fstal
tkregister2: error while loading shared libraries: libtix8.1.8.4.so: cannot 
open shared object file: No such file or directory

I changed mri_convert and tkregister2 back to their original version and they 
worked fine again.  When I run the old version of reg-feat2anat I still get the 
original error: 

ERROR: could not read 
/disc2/Kate/Data_FSL/Pre_AM/AM_preAM_BET.feat/example_func.nii.gz as 24

Not sure what is going on?

Best wishes
Carolyn 


 



-Original Message-
From: Doug Greve [mailto:[EMAIL PROTECTED]
Sent: Mon 04/06/2007 15:07
To: Furlong, Carolyn
Cc: Freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] reg -feat2anat error   reg -feat2anat error
 
wow, not sure what's going on there. Can you add --debug to the cmd 
line, caputre the terminal output, and send it to me?

Furlong, Carolyn wrote:

> Hi Doug
>
> we tried adding the binaries Doug sent us (MRI_convert, reg2anat and 
> tkregister2, make average subject, make average surface anfd make 
> avergae volume), but now we get a different error:reg-feat2anat --feat 
> ./disc2/Kate/Data_FSL/Pre_AM/AM_preAM_BET.feat/reg/ --subject AMoore
>
> 'nknown option: `-
> Usage: tcsh [ -bcdefilmnqstvVxX ] [ argument ... ].
>
> What should I do?
>
> Best wishes
> Carolyn
>
> -Original Message-
> From: Doug Greve [mailto:[EMAIL PROTECTED]
> Sent: Mon 21/05/2007 17:16
> To: Furlong, Carolyn
> Cc: Freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] reg -feat2anat error
>
> Did you see my email from last week? It looks like the problem was fixed
> with new versions of a few programs.
>
> doug
>
> Furlong, Carolyn wrote:
>
> >
> > Hi Doug
> >
> > Please find attached the logfile that you requested, sorry for the
> > delay, I am only able to work on this one day a week.
> >
> > Best wishes
> > Carolyn
> >
> >
> >
> >
> >
> > Actually, I wanted the log file found in
> > featdir/reg/freesurfer/reg-feat2anat.log.
> >
> > doug
> >
> > Furlong, Carolyn wrote:
> >
> > > Hi
> > >
> > >
> > > niiRead(): unsupported timing pattern in
> > Pre_DB/DB_Prelip_BET.feat/example_func.nii.gz
> > >
> > > sorry for the delay,
> > >
> > > Best wishes
> > >
> > > Carolyn
> > >
> > > can you send the log file?
> > >
> > > Furlong, Carolyn wrote:
> > >
> > >> Hi,
> > >>
> > >> When I try to register my functional data to anatomical data using
> > >>
> > >> reg-feat2anat --feat feat_directory --subject subject_name
> > >>
> > >> I get the following error message
> > >>
> > >> ERROR: could not read ///example_func.nii.gz as 24
> > >>
> > >> What does this mean? And how can I fix this?
> > >>
> > >> Best wishes
> > >> Carolyn
> > >>
> > >>
> > >>___
> > >>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
> > >[EMAIL PROTECTED]
> > >Phone Number: 617-724-2358
> > >Fax: 617-726-7422
> > >
> > >In order to help us help you, please follow the steps in:
> > >surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > >
> > >
> > >
> > >___
> > >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
> > [EMAIL PROTECTED]
> > Phone Number: 617-724-2358
> > Fax: 617-726-7422
> >
> > In order to help us help you, please follow the steps in:
> > surfer

Re: [Freesurfer] reg -feat2anat error reg -feat2anat error

[Doug Greve]

wow, not sure what's going on there. Can you add --debug to the cmd 
line, caputre the terminal output, and send it to me?


Furlong, Carolyn wrote:


Hi Doug

we tried adding the binaries Doug sent us (MRI_convert, reg2anat and 
tkregister2, make average subject, make average surface anfd make 
avergae volume), but now we get a different error:reg-feat2anat --feat 
./disc2/Kate/Data_FSL/Pre_AM/AM_preAM_BET.feat/reg/ --subject AMoore


'nknown option: `-
Usage: tcsh [ -bcdefilmnqstvVxX ] [ argument ... ].

What should I do?

Best wishes
Carolyn

-Original Message-
From: Doug Greve [mailto:[EMAIL PROTECTED]
Sent: Mon 21/05/2007 17:16
To: Furlong, Carolyn
Cc: Freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] reg -feat2anat error

Did you see my email from last week? It looks like the problem was fixed
with new versions of a few programs.

doug

Furlong, Carolyn wrote:

>
> Hi Doug
>
> Please find attached the logfile that you requested, sorry for the
> delay, I am only able to work on this one day a week.
>
> Best wishes
> Carolyn
>
>
>
>
>
> Actually, I wanted the log file found in
> featdir/reg/freesurfer/reg-feat2anat.log.
>
> doug
>
> Furlong, Carolyn wrote:
>
> > Hi
> >
> >
> > niiRead(): unsupported timing pattern in
> Pre_DB/DB_Prelip_BET.feat/example_func.nii.gz
> >
> > sorry for the delay,
> >
> > Best wishes
> >
> > Carolyn
> >
> > can you send the log file?
> >
> > Furlong, Carolyn wrote:
> >
> >> Hi,
> >>
> >> When I try to register my functional data to anatomical data using
> >>
> >> reg-feat2anat --feat feat_directory --subject subject_name
> >>
> >> I get the following error message
> >>
> >> ERROR: could not read ///example_func.nii.gz as 24
> >>
> >> What does this mean? And how can I fix this?
> >>
> >> Best wishes
> >> Carolyn
> >>
> >>
> >>___
> >>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
> >[EMAIL PROTECTED]
> >Phone Number: 617-724-2358
> >Fax: 617-726-7422
> >
> >In order to help us help you, please follow the steps in:
> >surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> >
> >
> >
> >___
> >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
> [EMAIL PROTECTED]
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> In order to help us help you, please follow the steps in:
> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
>
>
>
>Mon May 21 10:38:18 BST 2007
>/disc2/Kate/Flatmap1
>/home/progs/freesurfer/bin//reg-feat2anat
>--feat /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat --subject AMoore
>Linux dh108101 2.6.11.4-20a-smp #1 SMP Wed Mar 23 21:52:37 UTC 2005 
i686 i686 i386 GNU/Linux
>mri_convert /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz 
/disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii.gz
>mri_convert /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz 
/disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii.gz

>reading from /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz...
>TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
>i_ras = (-1, 0, 0)
>j_ras = (0, 0, -1)
>k_ras = (0, 1, 0)
>writing to 
/disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii.gz...

>example_func ras_good_flag
>---
>Initializing exf2anat from crude std2anat
>tkregister2 --targ /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz --mov 
/home/progs/fsl/etc/standard/avg152T1_brain.img --reg 
/disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/anat2std.register.dat 
--fslregout 
/disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/std2anat.fsl.mat 
--regheader --noedit

>target  volume /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz
>movable volume /home/progs/fsl/etc/standard/avg152T1_brain.img
>reg file   
/disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/anat2std.register.dat

>LoadVol0
>$Id: tkregister2.c,v 1.49.2.4 2006/03/27 21:48:16 greve Exp $
>Diagnostic Level -1
>INFO: loading target /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz
>Ttarg: 
>-1.000  

[Freesurfer] reg -feat2anat error reg -feat2anat error

[Furlong, Carolyn]

Hi Doug

we tried adding the binaries Doug sent us (MRI_convert, reg2anat and 
tkregister2, make average subject, make average surface anfd make avergae 
volume), but now we get a different error:reg-feat2anat --feat 
./disc2/Kate/Data_FSL/Pre_AM/AM_preAM_BET.feat/reg/ --subject AMoore

'nknown option: `-
Usage: tcsh [ -bcdefilmnqstvVxX ] [ argument ... ]. 

What should I do?

Best wishes
Carolyn

-Original Message-
From: Doug Greve [mailto:[EMAIL PROTECTED]
Sent: Mon 21/05/2007 17:16
To: Furlong, Carolyn
Cc: Freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] reg -feat2anat error
 
Did you see my email from last week? It looks like the problem was fixed 
with new versions of a few programs.

doug

Furlong, Carolyn wrote:

>
> Hi Doug
>
> Please find attached the logfile that you requested, sorry for the 
> delay, I am only able to work on this one day a week.
>
> Best wishes
> Carolyn
>
>
>
>
>
> Actually, I wanted the log file found in 
> featdir/reg/freesurfer/reg-feat2anat.log.
>
> doug
>
> Furlong, Carolyn wrote:
>
> > Hi
> > 
> > 
> > niiRead(): unsupported timing pattern in 
> Pre_DB/DB_Prelip_BET.feat/example_func.nii.gz
> >
> > sorry for the delay,
> >
> > Best wishes
> >
> > Carolyn
> > 
> > can you send the log file?
> >
> > Furlong, Carolyn wrote:
> >
> >> Hi,
> >>
> >> When I try to register my functional data to anatomical data using
> >>
> >> reg-feat2anat --feat feat_directory --subject subject_name
> >>
> >> I get the following error message
> >>
> >> ERROR: could not read ///example_func.nii.gz as 24
> >>
> >> What does this mean? And how can I fix this?
> >>
> >> Best wishes
> >> Carolyn
> >>
> >>
> >>___
> >>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
> >[EMAIL PROTECTED]
> >Phone Number: 617-724-2358
> >Fax: 617-726-7422
> >
> >In order to help us help you, please follow the steps in:
> >surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> >
> >
> >
> >___
> >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
> [EMAIL PROTECTED]
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> In order to help us help you, please follow the steps in:
> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
>
>
>
>Mon May 21 10:38:18 BST 2007
>/disc2/Kate/Flatmap1
>/home/progs/freesurfer/bin//reg-feat2anat
>--feat /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat --subject AMoore
>Linux dh108101 2.6.11.4-20a-smp #1 SMP Wed Mar 23 21:52:37 UTC 2005 i686 i686 
>i386 GNU/Linux
>mri_convert /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz 
>/disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii.gz
>mri_convert /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz 
>/disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii.gz 
>reading from /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz...
>TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
>i_ras = (-1, 0, 0)
>j_ras = (0, 0, -1)
>k_ras = (0, 1, 0)
>writing to 
>/disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii.gz...
>example_func ras_good_flag 
>---
>Initializing exf2anat from crude std2anat
>tkregister2 --targ /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz --mov 
>/home/progs/fsl/etc/standard/avg152T1_brain.img --reg 
>/disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/anat2std.register.dat
> --fslregout 
>/disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/std2anat.fsl.mat 
>--regheader --noedit
>target  volume /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz
>movable volume /home/progs/fsl/etc/standard/avg152T1_brain.img
>reg file   
>/disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/anat2std.register.dat
>LoadVol0
>$Id: tkregister2.c,v 1.49.2.4 2006/03/27 21:48:16 greve Exp $
>Diagnostic Level -1
>INFO: loading target /disc2/Kate/Flatmap1/AMoore/mri/brain.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

Re: [Freesurfer] reg- feat2anat error-problem

[Doug Greve]

It sounds like something has to be fixed. Is the example_func to 
standard space registration correct? If not, then you will need to fix 
it. That registration is purely FSL.


doug

uzay emir wrote:


Hi,
Orientation problem is outlined below.
1-When the target in coronal view, movable(example_func) is sagital.
2- When the target is in sagital view, movable is  coronal.
3- axial view is teh same both movable and target but The problem in 
this situation is that there is an angle between movable and target.



I followed all the steps. Right now should I expect that reg-feat2anat 
solves the big problems or should i have to register manually with 
tkregister2?


 


Regards

Uzay


Doug Greve <[EMAIL PROTECTED]> wrote:

What do you mean there was an orientation problem? If you use
analyze files, then it relies on the FSL reg to std space being
correct. Is it?

uzay emir wrote:


Thank you,it is working now. However, I have anorientation
problem with automatic registration results. This problem has
been mentioned before but i could not find any reply.  I think
this is something related following lines where I found it in the
reg- feat2anat log file.
Regards

Uzay

- INFO: could not 
find /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file 
for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 0, 
transverse unflipped (default). INFO: if not valid, please provide the information 
in /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file
- INFO: using NIfTI-1 sform 
- INFO: could not find /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file - - INFO: could not find /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file



__
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Tired of spam? Yahoo! Mail has the best spam protection around
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Fri May 18 11:13:12 EEST 2007
/home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/orig
/home/uzay/freesurfer_3/freesurfer/bin//reg-feat2anat
--feat Akkaya_Zuhre_1_9++.feat/ --subject akkaya
Linux localhost.localdomain 2.6.12-1.1381_FC3 #1 Fri Oct 21 03:46:55 EDT 2005 
i686 i686 i386 GNU/Linux
mri_convert 
/home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz 
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/tmp/anat.nii.gz
mri_convert /home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz Akkaya_Zuhre_1_9++.feat//reg/freesurfer/tmp/anat.nii.gz 
$Id: mri_convert.c,v 1.141 2007/04/26 05:31:21 greve Exp $

reading from
/home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz...
TR=11.00, TE=4.92, TI=4.92, flip angle=15.00
i_ras = (-1, 2.56273e-11, 6.83856e-10)
j_ras = (-1.17877e-09, -2.94451e-16, -1)
k_ras = (3.0538e-12, 1, -9.84868e-13)
writing to Akkaya_Zuhre_1_9++.feat//reg/freesurfer/tmp/anat.nii.gz...
example_func ras_good_flag 
---

Initializing exf2anat from crude std2anat
tkregister2 --targ 
/home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz --mov 
/home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.img --reg 
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/anat2std.register.dat --fslregout 
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/std2anat.fsl.mat --regheader --noedit
target  volume 
/home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz
movable volume 
/home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.img
reg file  
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/anat2std.register.dat

LoadVol0
$Id: tkregister2.c,v 1.80 2007/05/11 18:39:00 greve Exp $
Diagnostic Level -1
INFO: loading target 
/home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.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 
/home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.img
Tmov: 
-2.000   0.000   0.000   91.000;
0.000  

Re: [Freesurfer] reg- feat2anat error-problem

[uzay emir]

Hi,
 Orientation problem is outlined below.
 1-When the target in coronal view, movable(example_func) is sagital.
 2- When the target is in sagital view, movable is  coronal.
 3- axial view is teh same both movable and target but The problem in this 
situation is that there is an angle between movable and target.
 
 
 I followed all the steps. Right now should I expect that reg-feat2anat solves 
the big problems or should i have to register manually with tkregister2?
 
  
 
 Regards
 
 Uzay
 

Doug Greve <[EMAIL PROTECTED]> wrote:   What do you mean there was an 
orientation problem? If you use analyze files, then it relies on the FSL reg to 
std space being correct. Is it?
 
 uzay emir wrote: Thank you,it is working now. However, I have anorientation 
problem with automatic registration results. This problem has been mentioned 
before but i could not find any reply.  I think this is something related 
following lines where I found it in the reg- feat2anat log file. 
 Regards
   
 Uzay
 
- INFO: could 
not find /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat 
file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 
0, transverse unflipped (default). INFO: if not valid, please provide the 
information in 
/home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file 
- INFO: using 
NIfTI-1 sform 
 - INFO: could 
not find /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat 
file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 
0, transverse unflipped (default). INFO: if not valid, please provide the 
information in 
/home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file 
- 
- INFO: could 
not find /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat 
file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 
0, transverse unflipped (default). INFO: if not valid, please provide the 
information in 
/home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file
   
__
 Do You Yahoo!?
 Tired of spam? Yahoo! Mail has the best spam protection around 
 http://mail.yahoo.com 
   

-

Fri May 18 11:13:12 EEST 2007
/home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/orig
/home/uzay/freesurfer_3/freesurfer/bin//reg-feat2anat
--feat Akkaya_Zuhre_1_9++.feat/ --subject akkaya
Linux localhost.localdomain 2.6.12-1.1381_FC3 #1 Fri Oct 21 03:46:55 EDT 2005 
i686 i686 i386 GNU/Linux
mri_convert 
/home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz 
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/tmp/anat.nii.gz
mri_convert 
/home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz 
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/tmp/anat.nii.gz 
$Id: mri_convert.c,v 1.141 2007/04/26 05:31:21 greve Exp $
reading from 
/home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz...
TR=11.00, TE=4.92, TI=4.92, flip angle=15.00
i_ras = (-1, 2.56273e-11, 6.83856e-10)
j_ras = (-1.17877e-09, -2.94451e-16, -1)
k_ras = (3.0538e-12, 1, -9.84868e-13)
writing to Akkaya_Zuhre_1_9++.feat//reg/freesurfer/tmp/anat.nii.gz...
example_func ras_good_flag 
---
Initializing exf2anat from crude std2anat
tkregister2 --targ 
/home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz --mov 
/home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.img --reg 
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/anat2std.register.dat --fslregout 
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/std2anat.fsl.mat --regheader --noedit
target  volume 
/home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz
movable volume 
/home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.img
reg file   Akkaya_Zuhre_1_9++.feat//reg/freesurfer/anat2std.register.dat
LoadVol0
$Id: tkregister2.c,v 1.80 2007/05/11 18:39:00 greve Exp $
Diagnostic Level -1
INFO: loading target 
/home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.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 
/home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.img
Tmov: 
-2.000   0.000   0.000   91.000;
 0.000   0.000   2.000  -91.000;
 0.000  -2.000   0.000   109.000;
 0.000   0.000   0.000   1.000;
mkheaderreg = 1, float2int = 0
Computing reg from header (and possibly input matrix)
 Input registration matrix (computed) 
 

Re: [Freesurfer] reg -feat2anat error

[Doug Greve]

Did you see my email from last week? It looks like the problem was fixed 
with new versions of a few programs.


doug

Furlong, Carolyn wrote:



Hi Doug

Please find attached the logfile that you requested, sorry for the 
delay, I am only able to work on this one day a week.


Best wishes
Carolyn





Actually, I wanted the log file found in 
featdir/reg/freesurfer/reg-feat2anat.log.


doug

Furlong, Carolyn wrote:

> Hi
> 
> 
> niiRead(): unsupported timing pattern in 
Pre_DB/DB_Prelip_BET.feat/example_func.nii.gz

>
> sorry for the delay,
>
> Best wishes
>
> Carolyn
> 
> can you send the log file?

>
> Furlong, Carolyn wrote:
>
>> Hi,
>>
>> When I try to register my functional data to anatomical data using
>>
>> reg-feat2anat --feat feat_directory --subject subject_name
>>
>> I get the following error message
>>
>> ERROR: could not read ///example_func.nii.gz as 24
>>
>> What does this mean? And how can I fix this?
>>
>> Best wishes
>> Carolyn
>>
>>
>>___
>>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
>[EMAIL PROTECTED]
>Phone Number: 617-724-2358
>Fax: 617-726-7422
>
>In order to help us help you, please follow the steps in:
>surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
>
>
>___
>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
[EMAIL PROTECTED]
Phone Number: 617-724-2358
Fax: 617-726-7422

In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting




Mon May 21 10:38:18 BST 2007
/disc2/Kate/Flatmap1
/home/progs/freesurfer/bin//reg-feat2anat
--feat /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat --subject AMoore
Linux dh108101 2.6.11.4-20a-smp #1 SMP Wed Mar 23 21:52:37 UTC 2005 i686 i686 
i386 GNU/Linux
mri_convert /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz 
/disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii.gz
mri_convert /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii.gz 
reading from /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz...

TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to 
/disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii.gz...
example_func ras_good_flag 
---

Initializing exf2anat from crude std2anat
tkregister2 --targ /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz --mov 
/home/progs/fsl/etc/standard/avg152T1_brain.img --reg 
/disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/anat2std.register.dat
 --fslregout 
/disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/std2anat.fsl.mat 
--regheader --noedit
target  volume /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz
movable volume /home/progs/fsl/etc/standard/avg152T1_brain.img
reg file   
/disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/anat2std.register.dat
LoadVol0
$Id: tkregister2.c,v 1.49.2.4 2006/03/27 21:48:16 greve Exp $
Diagnostic Level -1
INFO: loading target /disc2/Kate/Flatmap1/AMoore/mri/brain.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 /home/progs/fsl/etc/standard/avg152T1_brain.img
Tmov: 
-2.000   0.000   0.000   91.000;
0.000   0.000   2.000  -91.000;
0.000  -2.000   0.000   109.000;
0.000   0.000   0.000   1.000;
mkheaderreg = 1, float2int = 0
 Input registration matrix (computed) 
1.000   0.000   0.000   0.000;
0.000   0.000   1.000   30.861;
0.000  -1.000   0.000  -52.627;
0.000   0.000   0.000   1.000;
---
 Input registration matrix 
1.000   0.000   0.000   0.000;
0.000   0.000   1.000   30.861;
0.000  -1.000   0.000  -52.627;
0.000   0.000   0.000   1.000;
subject = subject-unknown
RegMat ---
1.000   0.000   0.000   0.000;
0.000   0.000   1.000   30.861;
0.000  -1.000   0.000  -52.627;
0.000   0.000   0.000   1.000;
register: file 
/disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/anat2std.register.dat
 written
FSLOUTPUTTYPE NIFTI_GZ 
tkreg2FSL: mov det = -8, ref det = -1

mri_matrix_multiply -fsl -bin -iim 
/disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/example_func2standard.mat 
-iim 
/disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/std2anat.fsl.mat 
-om 
/disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/exf2anat.init.fsl.mat
betfunc /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/example_func 
/disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg

[Freesurfer] reg -feat2anat error

[Furlong, Carolyn]

Hi Doug 

Please find attached the logfile that you requested, sorry for the delay, I am 
only able to work on this one day a week.

Best wishes
Carolyn





Actually, I wanted the log file found in 
featdir/reg/freesurfer/reg-feat2anat.log.

doug

Furlong, Carolyn wrote:

> Hi
>  
>  
> niiRead(): unsupported timing pattern in 
> Pre_DB/DB_Prelip_BET.feat/example_func.nii.gz
>
> sorry for the delay,
>
> Best wishes
>
> Carolyn
>  
> can you send the log file?
>
> Furlong, Carolyn wrote:
>
>> Hi,
>>
>> When I try to register my functional data to anatomical data using
>>
>> reg-feat2anat --feat feat_directory --subject subject_name
>>
>> I get the following error message
>>
>> ERROR: could not read ///example_func.nii.gz as 24
>>
>> What does this mean? And how can I fix this?
>>
>> Best wishes
>> Carolyn
>>
>>
>>___
>>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
>[EMAIL PROTECTED]
>Phone Number: 617-724-2358 
>Fax: 617-726-7422
>
>In order to help us help you, please follow the steps in:
>surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
>
>
>___
>Freesurfer mailing list
>Freesurfer@nmr.mgh.harvard.edu
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>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358 
Fax: 617-726-7422

In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


Mon May 21 10:38:18 BST 2007
/disc2/Kate/Flatmap1
/home/progs/freesurfer/bin//reg-feat2anat
--feat /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat --subject AMoore
Linux dh108101 2.6.11.4-20a-smp #1 SMP Wed Mar 23 21:52:37 UTC 2005 i686 i686 i386 GNU/Linux
mri_convert /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii.gz
mri_convert /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii.gz 
reading from /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii.gz...
example_func ras_good_flag 
---
Initializing exf2anat from crude std2anat
tkregister2 --targ /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz --mov /home/progs/fsl/etc/standard/avg152T1_brain.img --reg /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/anat2std.register.dat --fslregout /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/std2anat.fsl.mat --regheader --noedit
target  volume /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz
movable volume /home/progs/fsl/etc/standard/avg152T1_brain.img
reg file   /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/anat2std.register.dat
LoadVol0
$Id: tkregister2.c,v 1.49.2.4 2006/03/27 21:48:16 greve Exp $
Diagnostic Level -1
INFO: loading target /disc2/Kate/Flatmap1/AMoore/mri/brain.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 /home/progs/fsl/etc/standard/avg152T1_brain.img
Tmov: 
-2.000   0.000   0.000   91.000;
 0.000   0.000   2.000  -91.000;
 0.000  -2.000   0.000   109.000;
 0.000   0.000   0.000   1.000;
mkheaderreg = 1, float2int = 0
 Input registration matrix (computed) 
 1.000   0.000   0.000   0.000;
 0.000   0.000   1.000   30.861;
 0.000  -1.000   0.000  -52.627;
 0.000   0.000   0.000   1.000;
---
 Input registration matrix 
 1.000   0.000   0.000   0.000;
 0.000   0.000   1.000   30.861;
 0.000  -1.000   0.000  -52.627;
 0.000   0.000   0.000   1.000;
subject = subject-unknown
RegMat ---
 1.000   0.000   0.000   0.000;
 0.000   0.000   1.000   30.861;
 0.000  -1.000   0.000  -52.627;
 0.000   0.000   0.000   1.000;
register: file /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/anat2std.register.dat written
FSLOUTPUTTYPE NIFTI_GZ 
tkreg2FSL: mov det = -8, ref det = -1
mri_matrix_multiply -fsl -bin -iim /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/example_func2standard.mat -iim /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/std2anat.fsl.mat -om /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/exf2anat.init.fsl.mat
betfunc /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/example_func /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/exfbet
Mon May 21 10:38:32 BST 2007
flirt -ref /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii.gz -in /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/exfb

Re: [Freesurfer] reg- feat2anat error-problem

[Doug Greve]

What do you mean there was an orientation problem? If you use analyze 
files, then it relies on the FSL reg to std space being correct. Is it?


uzay emir wrote:

Thank you,it is working now. However, I have anorientation problem 
with automatic registration results. This problem has been mentioned 
before but i could not find any reply.  I think this is something 
related following lines where I found it in the reg- feat2anat log file.

Regards

Uzay

- INFO: could not find /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file - INFO: using NIfTI-1 sform 
- INFO: could not find /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file - - INFO: could not find /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file



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Fri May 18 11:13:12 EEST 2007
/home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/orig
/home/uzay/freesurfer_3/freesurfer/bin//reg-feat2anat
--feat Akkaya_Zuhre_1_9++.feat/ --subject akkaya
Linux localhost.localdomain 2.6.12-1.1381_FC3 #1 Fri Oct 21 03:46:55 EDT 2005 
i686 i686 i386 GNU/Linux
mri_convert 
/home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz 
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/tmp/anat.nii.gz
mri_convert /home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz Akkaya_Zuhre_1_9++.feat//reg/freesurfer/tmp/anat.nii.gz 
$Id: mri_convert.c,v 1.141 2007/04/26 05:31:21 greve Exp $

reading from 
/home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz...
TR=11.00, TE=4.92, TI=4.92, flip angle=15.00
i_ras = (-1, 2.56273e-11, 6.83856e-10)
j_ras = (-1.17877e-09, -2.94451e-16, -1)
k_ras = (3.0538e-12, 1, -9.84868e-13)
writing to Akkaya_Zuhre_1_9++.feat//reg/freesurfer/tmp/anat.nii.gz...
example_func ras_good_flag 
---

Initializing exf2anat from crude std2anat
tkregister2 --targ 
/home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz --mov 
/home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.img --reg 
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/anat2std.register.dat --fslregout 
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/std2anat.fsl.mat --regheader --noedit
target  volume 
/home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz
movable volume 
/home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.img
reg file   Akkaya_Zuhre_1_9++.feat//reg/freesurfer/anat2std.register.dat
LoadVol0
$Id: tkregister2.c,v 1.80 2007/05/11 18:39:00 greve Exp $
Diagnostic Level -1
INFO: loading target 
/home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.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 
/home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.img
Tmov: 
-2.000   0.000   0.000   91.000;
0.000   0.000   2.000  -91.000;
0.000  -2.000   0.000   109.000;
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   1.414;
-0.000  -0.000   1.000  -30.612;
0.000  -1.000  -0.000  -44.496;
0.000   0.000   0.000   1.000;
---
 Input registration matrix 
1.000   0.000   0.000   1.414;
-0.000  -0.000   1.000  -30.612;
0.000  -1.000  -0.000  -44.496;
0.000   0.000   0.000   1.000;
subject = subject-unknown
RegMat ---
1.000   0.000   0.000   1.414;
-0.000  -0.000   1.000  -30.612;
0.000  -1.000  -0.000  -44.496;
0.000   0.000   0.000   1.000;
register: file Akkaya_Zuhre_1_9++.feat//re

Re: [Freesurfer] reg- feat2anat error-problem

[uzay emir]

Thank you,it is working now. However, I have anorientation problem with 
automatic registration results. This problem has been mentioned before but i 
could not find any reply.  I think this is something related following lines 
where I found it in the reg- feat2anat log file. 
 Regards
 
 Uzay
   
- INFO: could 
not find /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat 
file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 
0, transverse unflipped (default). INFO: if not valid, please provide the 
information in 
/home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file 
- INFO: using 
NIfTI-1 sform  
- INFO: could 
not find /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat 
file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 
0, transverse unflipped (default). INFO: if not valid, please provide the 
information in 
/home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file 
-
 - INFO: could 
not find /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat 
file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 
0, transverse unflipped (default). INFO: if not valid, please provide the 
information in 
/home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file


 __
Do You Yahoo!?
Tired of spam?  Yahoo! Mail has the best spam protection around 
http://mail.yahoo.com Fri May 18 11:13:12 EEST 2007
/home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/orig
/home/uzay/freesurfer_3/freesurfer/bin//reg-feat2anat
--feat Akkaya_Zuhre_1_9++.feat/ --subject akkaya
Linux localhost.localdomain 2.6.12-1.1381_FC3 #1 Fri Oct 21 03:46:55 EDT 2005 i686 i686 i386 GNU/Linux
mri_convert /home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz Akkaya_Zuhre_1_9++.feat//reg/freesurfer/tmp/anat.nii.gz
mri_convert /home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz Akkaya_Zuhre_1_9++.feat//reg/freesurfer/tmp/anat.nii.gz 
$Id: mri_convert.c,v 1.141 2007/04/26 05:31:21 greve Exp $
reading from /home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz...
TR=11.00, TE=4.92, TI=4.92, flip angle=15.00
i_ras = (-1, 2.56273e-11, 6.83856e-10)
j_ras = (-1.17877e-09, -2.94451e-16, -1)
k_ras = (3.0538e-12, 1, -9.84868e-13)
writing to Akkaya_Zuhre_1_9++.feat//reg/freesurfer/tmp/anat.nii.gz...
example_func ras_good_flag 
---
Initializing exf2anat from crude std2anat
tkregister2 --targ /home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz --mov /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.img --reg Akkaya_Zuhre_1_9++.feat//reg/freesurfer/anat2std.register.dat --fslregout Akkaya_Zuhre_1_9++.feat//reg/freesurfer/std2anat.fsl.mat --regheader --noedit
target  volume /home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz
movable volume /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.img
reg file   Akkaya_Zuhre_1_9++.feat//reg/freesurfer/anat2std.register.dat
LoadVol0
$Id: tkregister2.c,v 1.80 2007/05/11 18:39:00 greve Exp $
Diagnostic Level -1
INFO: loading target /home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.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 /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.img
Tmov: 
-2.000   0.000   0.000   91.000;
 0.000   0.000   2.000  -91.000;
 0.000  -2.000   0.000   109.000;
 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   1.414;
-0.000  -0.000   1.000  -30.612;
 0.000  -1.000  -0.000  -44.496;
 0.000   0.000   0.000   1.000;
---
 Input registration matrix 
 1.000   0.000   0.000   1.414;
-0.000  -0.000   1.000  -30.612;
 0.000  -1.000  -0.000  -44.496;
 0.000   0.000   0.000   1.000;
subject = subject-unknown
RegMat ---
 1.000   0.000   0.000   1.414;
-0.000  -0.000   1.000  -30.612;
 0.000  -1.000  -0.000  -44.496;
 0.000   0.000   0.000   1.000;
register: file Akkaya_Zuhre_1_9++.feat//reg/freesurfer/anat2std.register.dat written
FSLOUTPUTTYPE NIFTI_GZ 
tkreg2FSL: mov det = -8, ref det = -1
mri_matrix_multiply -fsl -bin -iim Akkaya_Zuhre_1_9++.feat//reg/example_func2standard.mat -iim Akkay

Re: [Freesurfer] reg- feat2anat error

[Doug Greve]

I think this may have been a problem with our nifti reader that I fixed 
a few months ago. I see from the log file that you are using a 
freesurfer version that is about a year old. So, can you try using the 
versions of reg-feat2anat, mri_convert, and tkregister2 that I put in 
tp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve? The last 
two are binaries compiled for Linux.


doug

uzay emir wrote:


Hi,

Actually I have the same problem. Here is my log file,

Regards

Uzay

Doug Greve <[EMAIL PROTECTED]> wrote:


Actually, I wanted the log file found in
featdir/reg/freesurfer/reg-feat2anat.log.

doug

Furlong, Carolyn wrote:


Hi
 
 
niiRead(): unsupported timing pattern in

Pre_DB/DB_Prelip_BET.feat/example_func.nii.gz
sorry for the delay,
Best wishes
Carolyn
 
can you send the log file?


Furlong, Carolyn wrote:


Hi,

When I try to register my functional data to anatomical data using

reg-feat2anat --feat feat_directory --subject subject_name

I get the following error message

ERROR: could not read ///example_func.nii.gz as 24

What does this mean? And how can I fix this?

Best wishes
Carolyn



___
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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
[EMAIL PROTECTED]
Phone Number:
617-724-2358 
Fax: 617-726-7422


In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting




___
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
[EMAIL PROTECTED]
Phone Number: 617-724-2358 
Fax: 617-726-7422


In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

   


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



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Thu May 17 10:05:02 EEST 2007
/home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/orig
/home/uzay/freesurfer_3/freesurfer/bin//reg-feat2anat
--feat Akkaya_Zuhre_1_9++.feat/ --subject akkaya
Linux localhost.localdomain 2.6.12-1.1381_FC3 #1 Fri Oct 21 03:46:55 EDT 2005 
i686 i686 i386 GNU/Linux
mri_convert /home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brain.mgz 
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/tmp/anat.nii.gz
mri_convert /home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brain.mgz Akkaya_Zuhre_1_9++.feat//reg/freesurfer/tmp/anat.nii.gz 
reading from /home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brain.mgz...

TR=11.00, TE=4.92, TI=4.92, flip angle=15.00
i_ras = (-1, 2.56273e-11, 6.83856e-10)
j_ras = (-1.17877e-09, -2.94451e-16, -1)
k_ras = (3.0538e-12, 1, -9.84868e-13)
writing to Akkaya_Zuhre_1_9++.feat//reg/freesurfer/tmp/anat.nii.gz...
example_func ras_good_flag 
---

Initializing exf2anat from crude std2anat
tkregister2 --targ 
/home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brain.mgz --mov 
/usr/local/fsl/etc/standard/avg152T1_brain.img --reg 
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/anat2std.register.dat --fslregout 
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/std2anat.fsl.mat --regheader --noedit
target  volume /home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brain.mgz
movable volume /usr/local/fsl/etc/standard/avg152T1_brain.img
reg file   Akkaya_Zuhre_1_9++.feat//reg/freesurfer/anat2std.register.dat
LoadVol0
$Id: tkregister2.c,v 1.49.2.4 2006/03/27 21:48:16 greve Exp $
Diagnostic Level -1
INFO: loading target 
/home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brain.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 /usr/local/fsl/etc/standard/avg152T1_brain.img
Tmov: 
-2.000   0.000   0.000   91.000;
0.000   0.000   2.000  -91.000;
0.000  -2.000   0.000   109.000;
0.000   0.000   0.000   1.000;
mkheaderreg = 1, float2int = 0
 Input registration matrix (computed) 
1.000   0.000   0.000   1.414;
-0.000  -0.000   1.000  -30.612;
0.000  -1.000  -0.000  -44.496;
0.000  

Re: [Freesurfer] reg- feat2anat error

[uzay emir]

Hi,
 
 Actually I have the same problem. Here is my log file,

 Regards
 
 Uzay

Doug Greve <[EMAIL PROTECTED]> wrote:   
 Actually, I wanted the log file found in 
featdir/reg/freesurfer/reg-feat2anat.log. 
 
 doug
 
 Furlong, Carolyn wrote:  Hi


   niiRead(): unsupported timing pattern in 
Pre_DB/DB_Prelip_BET.feat/example_func.nii.gz 
   
   sorry for the delay, 
   Best wishes 
   Carolyn

   can you send the log file?
   
 Furlong, Carolyn wrote: 
Hi,
 
 When I try to register my functional data to anatomical data using
 
 reg-feat2anat --feat feat_directory --subject subject_name
 
 I get the following error message
 
 ERROR: could not read ///example_func.nii.gz as 24
 
 What does this mean? And how can I fix this?
 
 Best wishes
 Carolyn
 
 

-

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MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358 
Fax: 617-726-7422

In order to help us help you, please follow the steps in:
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MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358 
Fax: 617-726-7422

In order to help us help you, please follow the steps in:
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-
We won't tell. Get more on shows you hate to love
(and love to hate): Yahoo! TV's Guilty Pleasures list.Thu May 17 10:05:02 EEST 2007
/home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/orig
/home/uzay/freesurfer_3/freesurfer/bin//reg-feat2anat
--feat Akkaya_Zuhre_1_9++.feat/ --subject akkaya
Linux localhost.localdomain 2.6.12-1.1381_FC3 #1 Fri Oct 21 03:46:55 EDT 2005 i686 i686 i386 GNU/Linux
mri_convert /home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brain.mgz Akkaya_Zuhre_1_9++.feat//reg/freesurfer/tmp/anat.nii.gz
mri_convert /home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brain.mgz Akkaya_Zuhre_1_9++.feat//reg/freesurfer/tmp/anat.nii.gz 
reading from /home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brain.mgz...
TR=11.00, TE=4.92, TI=4.92, flip angle=15.00
i_ras = (-1, 2.56273e-11, 6.83856e-10)
j_ras = (-1.17877e-09, -2.94451e-16, -1)
k_ras = (3.0538e-12, 1, -9.84868e-13)
writing to Akkaya_Zuhre_1_9++.feat//reg/freesurfer/tmp/anat.nii.gz...
example_func ras_good_flag 
---
Initializing exf2anat from crude std2anat
tkregister2 --targ /home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brain.mgz --mov /usr/local/fsl/etc/standard/avg152T1_brain.img --reg Akkaya_Zuhre_1_9++.feat//reg/freesurfer/anat2std.register.dat --fslregout Akkaya_Zuhre_1_9++.feat//reg/freesurfer/std2anat.fsl.mat --regheader --noedit
target  volume /home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brain.mgz
movable volume /usr/local/fsl/etc/standard/avg152T1_brain.img
reg file   Akkaya_Zuhre_1_9++.feat//reg/freesurfer/anat2std.register.dat
LoadVol0
$Id: tkregister2.c,v 1.49.2.4 2006/03/27 21:48:16 greve Exp $
Diagnostic Level -1
INFO: loading target /home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brain.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 /usr/local/fsl/etc/standard/avg152T1_brain.img
Tmov: 
-2.000   0.000   0.000   91.000;
 0.000   0.000   2.000  -91.000;
 0.000  -2.000   0.000   109.000;
 0.000   0.000   0.000   1.000;
mkheaderreg = 1, float2int = 0
 Input registration matrix (computed) 
 1.000   0.000   0.000   1.414;
-0.000  -0.000   1.000  -30.612;
 0.000  -1.000  -0.000  -44.496;
 0.000   0.000   0.000   1.000;
---
 Input registration matrix 
 1.000   0.000   0.000   1.414;
-0.000  -0.000   1.000  -30.612;
 0.000  -1.000  -0.000  -44.496;
 0.000   0.000   0.000   1.000;
subject = subject-unknown
RegMat ---
 1.000   0.000   0.000   1.414;
-0.000  -0.000   1.000  -30.612;
 0.000  -1.000  -0.000  -44.496;
 0.000   0.000   0.000   1.000;
register: file Akkaya_Zuhre_1_9++.feat//reg/freesurfer/anat2std.register.dat written
FSLOUTPUTTYPE NIFTI_GZ 
tkreg2FSL: mov det = -8, ref det = -1
mri_matrix_multiply -fsl -bin -iim Akkaya_Zuhre_1_9++.feat//reg/example_func2standard.mat -iim Akkaya_Zuhre_1_9++.feat//reg/freesurfer/std2anat.fsl.mat -om Ak

Re: [Freesurfer] reg- feat2anat error

[Doug Greve]

Actually, I wanted the log file found in 
featdir/reg/freesurfer/reg-feat2anat.log.


doug

Furlong, Carolyn wrote:


Hi
 
 
niiRead(): unsupported timing pattern in 
Pre_DB/DB_Prelip_BET.feat/example_func.nii.gz


sorry for the delay,

Best wishes

Carolyn

 
can you send the log file?


Furlong, Carolyn wrote:


Hi,

When I try to register my functional data to anatomical data using

reg-feat2anat --feat feat_directory --subject subject_name

I get the following error message

ERROR: could not read ///example_func.nii.gz as 24

What does this mean? And how can I fix this?

Best wishes
Carolyn



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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358 
Fax: 617-726-7422


In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting




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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358 
Fax: 617-726-7422


In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


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Re: [Freesurfer] reg- feat2anat error

[Furlong, Carolyn]

Hi
 
 
niiRead(): unsupported timing pattern in 
Pre_DB/DB_Prelip_BET.feat/example_func.nii.gz 


sorry for the delay, 

Best wishes 

Carolyn

 
can you send the log file?

Furlong, Carolyn wrote: 

Hi,

When I try to register my functional data to anatomical data using

reg-feat2anat --feat feat_directory --subject subject_name

I get the following error message

ERROR: could not read ///example_func.nii.gz as 24

What does this mean? And how can I fix this?

Best wishes
Carolyn






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

 


-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358 
Fax: 617-726-7422

In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


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Re: [Freesurfer] reg-feat2anat regsitration problems

[Doug Greve]

can you send the information described in 
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting?


doug

[EMAIL PROTECTED] wrote:


Hi Doug & others,
 
I am trying to use reg-feat2anat as it is described on the FSL web page:

http://www.fmrib.ox.ac.uk/fsl/freesurfer/index.html
 
However, I always seem t get a very bad registration. I tried 
using different values for  --maxangle --cost mutualinfo --bins, but 
maintained --dof always at 6 for rigid body registration of the T1 and 
EPI, but didn't gt any good results.
Initially I thought it might be because reg-fea2anat does not use a 
skull-stripped T1, but  when I run Feat using the T1.mgz (converted to 
.nii.gz) as the main structural image for Registration (and the MNI 
brain as standard space), both with 'Full Search' option and dof = 6, 
the registration (with FEAT)  works well.
Is there anything else I can try to make it work with reg-feat2anat. 
Why wouldn't the registration work on my data with reg-feat2anat given 
that it works with Feat?
 
Any comments or suggestions would be very appreciated.
 
best,


Sandy


Be a better Heartthrob. Get better relationship answers 
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someone who knows.

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Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358 
Fax: 617-726-7422


In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


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[Freesurfer] reg-feat2anat regsitration problems

[[EMAIL PROTECTED]]

Hi Doug & others,
   
  I am trying to use reg-feat2anat as it is described on the FSL web page:
  http://www.fmrib.ox.ac.uk/fsl/freesurfer/index.html
   
  However, I always seem t get a very bad registration. I tried using different 
values for  --maxangle --cost mutualinfo --bins, but maintained --dof always at 
6 for rigid body registration of the T1 and EPI, but didn't gt any good results.
  Initially I thought it might be because reg-fea2anat does not use a 
skull-stripped T1, but  when I run Feat using the T1.mgz (converted to .nii.gz) 
as the main structural image for Registration (and the MNI brain as standard 
space), both with 'Full Search' option and dof = 6, the registration (with 
FEAT)  works well. 
  Is there anything else I can try to make it work with reg-feat2anat. Why 
wouldn't the registration work on my data with reg-feat2anat given that it 
works with Feat?
   
  Any comments or suggestions would be very appreciated.
   
  best,
  
Sandy

   
-
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Re: [Freesurfer] reg- feat2anat error

[Doug Greve]

can you send the log file?

Furlong, Carolyn wrote:


Hi,

When I try to register my functional data to anatomical data using

reg-feat2anat --feat feat_directory --subject subject_name

I get the following error message

ERROR: could not read ///example_func.nii.gz as 24

What does this mean? And how can I fix this?

Best wishes
Carolyn



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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358 
Fax: 617-726-7422


In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


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[Freesurfer] reg- feat2anat error

[Furlong, Carolyn]

Hi, 

When I try to register my functional data to anatomical data using 

reg-feat2anat --feat feat_directory --subject subject_name

I get the following error message 

ERROR: could not read ///example_func.nii.gz as 24

What does this mean? And how can I fix this?

Best wishes
Carolyn
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[Freesurfer] reg-feat2anat problem

[Elaine Leung]

Hello,

I'm trying to display some FEAT statistics on a surface I created
using Freesurfer using instructions from
http://www.fmrib.ox.ac.uk/fsl/freesurfer/index.html.  The automatic
registration function reg-feat2anat seems to have failed and I'm not
sure what I should do to re-orient the slices better.  I've attached a
picture, hopefully it will convey my problem.

Also, looking at the log files, I noticed the line

INFO: could not find
/home/eleung1/freesurfer/fsl/etc/standard/avg152T1_brain.mat file for
direction cosine info.
INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default).
INFO: if not valid, please provide the information in
/home/eleung1/freesurfer/fsl/etc/standard/avg152T1_brain.mat file

Where do I get the file avg152T1_brain.mat?

Thanks for your help,
Elaine
<>
Tue Feb 20 11:42:45 EST 2007
/home/eleung1/freesurfer/subjects
/home/eleung1/freesurfer/bin//reg-feat2anat
--feat /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat --subject n002
Linux brodmann.bu.edu 2.6.9-22.0.1.ELsmp #1 SMP Thu Oct 27 13:14:25 CDT 2005 i686 i686 i386 GNU/Linux
mri_convert /home/eleung1/freesurfer/subjects/n002/mri/brain.mgz /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/tmp/anat.nii.gz
mri_convert /home/eleung1/freesurfer/subjects/n002/mri/brain.mgz /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/tmp/anat.nii.gz 
reading from /home/eleung1/freesurfer/subjects/n002/mri/brain.mgz...
TR=2530.00, TE=3.39, TI=1100.00, flip angle=7.00
i_ras = (-1, -8.15313e-11, 3.35233e-10)
j_ras = (3.14573e-09, -4.86297e-10, -1)
k_ras = (9.86348e-10, 1, 1.31955e-09)
writing to /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/tmp/anat.nii.gz...
example_func ras_good_flag 1
---
Initializing exf2anat with header
tkregister2 --targ /home/eleung1/freesurfer/subjects/n002/mri/brain.mgz --mov /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/example_func.nii.gz --reg /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/anat2exf.register.dat.init --fslregout /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/exf2anat.init.fsl.mat --regheader --noedit
target  volume /home/eleung1/freesurfer/subjects/n002/mri/brain.mgz
movable volume /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/example_func.nii.gz
reg file   /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/anat2exf.register.dat.init
LoadVol0
$Id: tkregister2.c,v 1.49.2.4 2006/03/27 21:48:16 greve Exp $
Diagnostic Level -1
INFO: using NIfTI-1 sform 
INFO: loading target /home/eleung1/freesurfer/subjects/n002/mri/brain.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 /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/example_func.nii.gz
INFO: using NIfTI-1 sform 
Tmov: 
-3.125   0.000   0.000   100.000;
 0.000   0.000   2.200  -60.500;
 0.000  -3.125   0.000   100.000;
 0.000   0.000   0.000   1.000;
mkheaderreg = 1, float2int = 0
 Input registration matrix (computed) 
 1.000   0.000  -0.000   7.451;
-0.000   0.000   1.000  -20.153;
-0.000  -1.000  -0.000  -59.694;
 0.000   0.000   0.000   1.000;
---
 Input registration matrix 
 1.000   0.000  -0.000   7.451;
-0.000   0.000   1.000  -20.153;
-0.000  -1.000  -0.000  -59.694;
 0.000   0.000   0.000   1.000;
subject = subject-unknown
RegMat ---
 1.000   0.000  -0.000   7.451;
-0.000   0.000   1.000  -20.153;
-0.000  -1.000  -0.000  -59.694;
 0.000   0.000   0.000   1.000;
register: file /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/anat2exf.register.dat.init written
FSLOUTPUTTYPE NIFTI_GZ 
tkreg2FSL: mov det = -21.4844, ref det = -1
betfunc /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/example_func /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/tmp/exfbet
Tue Feb 20 11:42:55 EST 2007
flirt -ref /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/tmp/anat.nii.gz -in /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/tmp/exfbet.nii.gz -init /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfe