Re: [Freesurfer] Zero angle for retinotopy

[Douglas Greve]

Yes, 0 is where the wedge starts.
doug


On 2/7/16 7:56 AM, Mohamed Abdelhack wrote:
Does this mean that the zero angle is the one where the wedge starts 
rotating in the experiment?
Does this apply to eccentricity experiment also (In my lab's protocol 
it doesn't start from zero)?


On Sat, Feb 6, 2016 at 2:20 AM, dgw > wrote:


Hi,

I know Doug is away, so he may correct me later, but I believe it
doesn't matter, as long as it is consistent across runs, and you know
what it is. It will just determine where the angle 0 activity goes (in
a color map etc.). The way FS-FAST does the mapping it just may mean
your colors don't line up with others.

hth
d

On Thu, Feb 4, 2016 at 11:52 PM,  > wrote:
> Dear all,
>
>
>
> I am wondering about what the zero angle for retinotopy
corresponds to in
> retinotopy analysis. I mean corresponding to the wedge being at
zero angle
> in circular coordinate map (horizontal) or vertical up?
>
>
>
> Thank you,
>
> Best,
>
>
>
>
> ___
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>
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to whom it is
> addressed. If you believe this e-mail was sent to you in error
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> e-mail
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Re: [Freesurfer] error in motion correction

[Douglas Greve]

In 4.5 I don't think there is a way to run it when different runs have 
different number of slices. Version 5+ will handle it properly. If you 
really want to use 4.5, then you'll have to put it in a different 
functional subdir (FSD, eg, bold), and create a new analysis for it, 
then combine them together after analysis. A bit of a hassle.


On 2/8/16 5:58 PM, Ji Won Bang wrote:

Dear. Freesurfer team.

As another attempt, I run the motion correction without the argument 
-targrun:


mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino

However, I get the same error message again.

Why is that?

Thanks so much for your effort and time.

I appreciate it a lot.

Best,
Ji Won


2016-02-08 17:16 GMT-05:00 Ji Won Bang >:


Dear. Freesurfer team.

I'd appreciate any advice from you.

When doing the motion correction, I'd like to align all EPI
data(bold_retino) to the first EPI of target run(bold_decode/003).
However, the number of slices for target run(33) and the number of
slices(32) for input run(bold_retino) are different.

When I type: mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino
-targrun $DATA_DIR/$SUBJECT/bold_decode/003

Freesurfer says that:
** FATAL ERROR: perhaps you could make your datasets match?
ERROR: 3dvolreg
Invalid null command.

These two kinds of run (bold_decode, bold_retino) were collected
in one scan per subject, so the head position should not be too
different...

Do you have any suggestions for fixing this error?

Should I do 3dWarp -deoblique?

Thank you so much.

Best,
Ji Won

2016-02-08 16:30 GMT-05:00 Ji Won Bang >:

Dear. Freesurfer team.

Hi.

I'm using freesurfer 4.5 version.

While doing the motion correction, an error occurred.

the command I used:
mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino -targrun
$DATA_DIR/$SUBJECT/bold_decode/003

the error I have:
/home/jbang/Projects/replay/epi/replay01/bold_retino
3dvolreg -verbose -dfile 025/fmc.mcdat -base
025/tmp.mc-afni2.32291/tempvol.nii.gz -prefix
025/tmp.mc-afni2.32291/outvol.nii.gz
025/tmp.mc-afni2.32291/invol.nii.gz
++ 3dvolreg: AFNI version=AFNI_2008_07_18_1710 (Feb 10 2009)
[64-bit]
++ Authored by: RW Cox
*+ WARNING:   If you are performing spatial transformations on
an oblique dset,
  such as 025/tmp.mc-afni2.32291/tempvol.nii.gz,
  or viewing/combining it with volumes of differing obliquity,
  you should consider running:
 3dWarp -deoblique
  on this and  other oblique datasets in the same session.
 See 3dWarp -help for details.
++ Oblique dataset:025/tmp.mc-afni2.32291/tempvol.nii.gz is
3.263868 degrees from plumb.
++ Reading in base dataset 025/tmp.mc-afni2.32291/tempvol.nii.gz
++ Oblique dataset:025/tmp.mc-afni2.32291/invol.nii.gz is
4.564286 degrees from plumb.
++ centers of base and input datasets are 9.09 mm apart
** Input ./invol.nii.gz+orig.HEAD and base
./tempvol.nii.gz+orig.HEAD don't have same dimensions!
   Input: nx=74  ny=74  nz=32
   Base:  nx=74  ny=74  nz=33
** FATAL ERROR: perhaps you could make your datasets match?
ERROR: 3dvolreg
Invalid null command.

I think it's because the volume size is different.

The volume size for bold_retino is: number of slices 32
The volume size for bold_decode: number of slices 33

What should I do to correct this error?

Thank you for taking your time.

Best,
Ji Won





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Re: [Freesurfer] Zero angle for retinotopy

[m.abouelyazid]

Thanks,

I am currently trying to figure out a way to translate the data I get out of FS 
which defaults to a single rotating wedge to my double wedge experiment. It 
seems to me that the positive and negative angles are reversed for each 
hemisphere.
Does FS do some kind of mirroring for angles for each hemisphere so that angles 
on the upper visual field are always positive?

Best,
Mohamed

From: Douglas Greve
Sent: Tuesday, February 9, 2016 1:29 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Zero angle for retinotopy

Yes, 0 is where the wedge starts.
doug

On 2/7/16 7:56 AM, Mohamed Abdelhack wrote:
Does this mean that the zero angle is the one where the wedge starts rotating 
in the experiment? 
Does this apply to eccentricity experiment also (In my lab's protocol it 
doesn't start from zero)?

On Sat, Feb 6, 2016 at 2:20 AM, dgw  wrote:
Hi,

I know Doug is away, so he may correct me later, but I believe it
doesn't matter, as long as it is consistent across runs, and you know
what it is. It will just determine where the angle 0 activity goes (in
a color map etc.). The way FS-FAST does the mapping it just may mean
your colors don't line up with others.

hth
d

On Thu, Feb 4, 2016 at 11:52 PM,   wrote:
> Dear all,
>
>
>
> I am wondering about what the zero angle for retinotopy corresponds to in
> retinotopy analysis. I mean corresponding to the wedge being at zero angle
> in circular coordinate map (horizontal) or vertical up?
>
>
>
> Thank you,
>
> Best,
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
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[Freesurfer] mri_convert Ubuntu 14.04 LTS not working (neither is freeview)

[Veronica.Popescu]

Dear all,
I have just installed FreeSurfer 5.3.0. on Ubuntu 14.04 LTS (64-bit). 
The mri_convert doesn't work with no error message. which mri_convert gives 
/usr/local/freesurfer/bin/mri_convert. Of course neither does recon-all (which 
exits with errors with no error message in the log).
I made sure all the paths are 777. I did the recommended "sudo ln -s 
libjpeg.so.8 libjpeg.so.62 sudo ln -s libtiff.so.4 libtiff.so.3" in 
x86_64-linux-gnu. 
The same problem with freeview, nothing happens. 
Thank you in advance!
Veronica



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[Freesurfer] error in motion correction

[Ji Won Bang]

Dear. Freesurfer team.

Hi.

I'm using freesurfer 4.5 version.

While doing the motion correction, an error occurred.

the command I used:
mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino -targrun
$DATA_DIR/$SUBJECT/bold_decode/003

the error I have:
/home/jbang/Projects/replay/epi/replay01/bold_retino
3dvolreg -verbose -dfile 025/fmc.mcdat -base
025/tmp.mc-afni2.32291/tempvol.nii.gz -prefix
025/tmp.mc-afni2.32291/outvol.nii.gz 025/tmp.mc-afni2.32291/invol.nii.gz
++ 3dvolreg: AFNI version=AFNI_2008_07_18_1710 (Feb 10 2009) [64-bit]
++ Authored by: RW Cox
*+ WARNING:   If you are performing spatial transformations on an oblique
dset,
  such as 025/tmp.mc-afni2.32291/tempvol.nii.gz,
  or viewing/combining it with volumes of differing obliquity,
  you should consider running:
 3dWarp -deoblique
  on this and  other oblique datasets in the same session.
 See 3dWarp -help for details.
++ Oblique dataset:025/tmp.mc-afni2.32291/tempvol.nii.gz is 3.263868
degrees from plumb.
++ Reading in base dataset 025/tmp.mc-afni2.32291/tempvol.nii.gz
++ Oblique dataset:025/tmp.mc-afni2.32291/invol.nii.gz is 4.564286 degrees
from plumb.
++ centers of base and input datasets are 9.09 mm apart
** Input ./invol.nii.gz+orig.HEAD and base ./tempvol.nii.gz+orig.HEAD don't
have same dimensions!
   Input: nx=74  ny=74  nz=32
   Base:  nx=74  ny=74  nz=33
** FATAL ERROR: perhaps you could make your datasets match?
ERROR: 3dvolreg
Invalid null command.

I think it's because the volume size is different.

The volume size for bold_retino is: number of slices 32
The volume size for bold_decode: number of slices 33

What should I do to correct this error?

Thank you for taking your time.

Best,
Ji Won
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Re: [Freesurfer] tkregister2 - horizontal and coronal inverted in the functional only

[Ilaria Sani]

Sent: Sunday, February 7, 2016 10:44 PM

On 2/5/16 12:49 PM, Ilaria Sani wrote:
Dear All,

I have a functional and a T1 registered, but they are not in anatomical 
coordinates.
Do you mean neither are in the "conformed" 256^3, 1mm^3 FreeSurfer coordinates?

Both the T1 and the functional are "conformed" 256^3, 1mm^3
I put the anatomical in the desired position by using tkregister2.
Was the T1 used to generate the FS results? If so,  why do you need to get it 
into FS coordinates? If not, then use bbregister to create the registration 
file, then use mri_vol2vol to map it into FS space.

I'm working with multimodal data. I acquired DTI data and inherited the T1 and 
the functional.
The T1 was previously used for other purposes and it came in different 
coordinates.
I used tkregister2 and mri_vol2vol to put the T1 in Talairach coordinates and 
create the registration file.
Then, I  used the reoriented T1 to get gray-white matter segmentation.
Now I would like to apply the same registration to the functional and place 
seeds in the DTI data.
When I do so, the output image has the coronal and horizontal view inverted.
How can I solve this problem?

Thanks,
Ilaria

I was hoping to use the output reg file to re-position the functional as well.
Use bbregister to register the functional to FS coordinates, then again use 
mri_vol2vol.

I got an unexpected output!
The functional looks reoriented BUT, coronal is horizontal, horizontal is 
coronal and sagittal is 90deg rotated.

How did it happen and how can I fix the problem?

Thanks,
Ilaria




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[Freesurfer] R: Re: To use a ROI.label as seed in FS-FAST

[stdp82]

Thanks.I have down a right ad left ROI on the surface.Next, I have run:
mri_label2vol --label ramgseed_rhsurf.label --temp 
$SUBJECTS_DIR/fsaverage/mri/orig.mgz --identity --subject fsaverage --hemi rh 
--o RIGHT_ROI.nii.gzmri_label2vol --label ramgseed_lhsurf.label --temp 
$SUBJECTS_DIR/fsaverage/mri/orig.mgz --identity --subject fsaverage --hemi rh 
--o LEFT_ROI.nii.gz

mri_convert RIGHT_ROI.nii.gz RIGHT_ROI.mgzmri_convert LEFT_ROI.nii.gz 
LEFT_ROI.mgz

fcseed-config -segid 1 -seg RIGHT_ROI.mgz -fsd rest -mean -cfg 
RIGHT_ROI.configfcseed-config -segid 1 -seg LEFT_ROI.mgz -fsd rest -mean -cfg 
LEFT_ROI.config

fcseed-sess -s subj1_FS -cfg RIGHT_ROI.config
fcseed-sess -s subj1_FS -cfg LEFT_ROI.config
but during fcseed-sess this error occurs:
$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $cwd cmdline 
mri_segstats --i 
/Applications/freesurfer/subjects/fMRI/subj1/rest/001/fmcpr.nii.gz --seg 
/Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/mask.nii.gz
 --id 1 --sum 
/Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/junk.sum
 --avgwfvol 
/Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/avgwf.mgh
 sysname  Darwinhostname iMac-di-Stefano.localmachine  x86_64user 
StefanoUseRobust  0Loading 
/Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/mask.nii.gzLoading
 /Applications/freesurfer/subjects/fMRI/subj1/rest/001/fmcpr.nii.gzVoxel Volume 
is 64.5752 mm^3Generating list of segmentation idsFound   1 
segmentationsComputing statistics for each segmentation  0 1
  0   0.000MRIalloc(0, 1, 1): bad parmReporting on  
 0 segmentationsComputing spatial average of each frameWriting to 
/Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/avgwf.mghSegmentation
 fault 



Messaggio originale

Da: Douglas Greve 

Data: 8-feb-2016 4.38

A: 

Ogg: Re: [Freesurfer] To use a ROI.label as seed in FS-FAST




  
  
Use mri_label2vol to convert the label into a volume in the
anatomical space and store it in $SUBJECTS_DIR/subject/mri. Make
sure to use --fill-ribbon if the label is surface-based. When
running fcseed-config, specify the volume with the -seg option and
use -segid 1



On 2/7/16 3:16 PM, std...@virgilio.it
  wrote:



  Hi list,




I would like to use as seed in FS-FAST a ROI.label which I
  have drawn on a cluster in tksurfer.
How can I do it?
Should I use mri_label2vol?


  
Thanks.



Stefano


  
  

  

  
  

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Re: [Freesurfer] error in motion correction

[Ji Won Bang]

Dear. Freesurfer team.

I'd appreciate any advice from you.

When doing the motion correction, I'd like to align all EPI
data(bold_retino) to the first EPI of target run(bold_decode/003). However,
the number of slices for target run(33) and the number of slices(32) for
input run(bold_retino) are different.

When I type: mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino -targrun
$DATA_DIR/$SUBJECT/bold_decode/003

Freesurfer says that:
** FATAL ERROR: perhaps you could make your datasets match?
ERROR: 3dvolreg
Invalid null command.

These two kinds of run (bold_decode, bold_retino) were collected in one
scan per subject, so the head position should not be too different...

Do you have any suggestions for fixing this error?

Should I do 3dWarp -deoblique?

Thank you so much.

Best,
Ji Won

2016-02-08 16:30 GMT-05:00 Ji Won Bang :

> Dear. Freesurfer team.
>
> Hi.
>
> I'm using freesurfer 4.5 version.
>
> While doing the motion correction, an error occurred.
>
> the command I used:
> mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino -targrun
> $DATA_DIR/$SUBJECT/bold_decode/003
>
> the error I have:
> /home/jbang/Projects/replay/epi/replay01/bold_retino
> 3dvolreg -verbose -dfile 025/fmc.mcdat -base
> 025/tmp.mc-afni2.32291/tempvol.nii.gz -prefix
> 025/tmp.mc-afni2.32291/outvol.nii.gz 025/tmp.mc-afni2.32291/invol.nii.gz
> ++ 3dvolreg: AFNI version=AFNI_2008_07_18_1710 (Feb 10 2009) [64-bit]
> ++ Authored by: RW Cox
> *+ WARNING:   If you are performing spatial transformations on an oblique
> dset,
>   such as 025/tmp.mc-afni2.32291/tempvol.nii.gz,
>   or viewing/combining it with volumes of differing obliquity,
>   you should consider running:
>  3dWarp -deoblique
>   on this and  other oblique datasets in the same session.
>  See 3dWarp -help for details.
> ++ Oblique dataset:025/tmp.mc-afni2.32291/tempvol.nii.gz is 3.263868
> degrees from plumb.
> ++ Reading in base dataset 025/tmp.mc-afni2.32291/tempvol.nii.gz
> ++ Oblique dataset:025/tmp.mc-afni2.32291/invol.nii.gz is 4.564286 degrees
> from plumb.
> ++ centers of base and input datasets are 9.09 mm apart
> ** Input ./invol.nii.gz+orig.HEAD and base ./tempvol.nii.gz+orig.HEAD
> don't have same dimensions!
>Input: nx=74  ny=74  nz=32
>Base:  nx=74  ny=74  nz=33
> ** FATAL ERROR: perhaps you could make your datasets match?
> ERROR: 3dvolreg
> Invalid null command.
>
> I think it's because the volume size is different.
>
> The volume size for bold_retino is: number of slices 32
> The volume size for bold_decode: number of slices 33
>
> What should I do to correct this error?
>
> Thank you for taking your time.
>
> Best,
> Ji Won
>
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Re: [Freesurfer] error in motion correction

[Ji Won Bang]

Dear. Freesurfer team.

As another attempt, I run the motion correction without the argument
-targrun:

mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino

However, I get the same error message again.

Why is that?

Thanks so much for your effort and time.

I appreciate it a lot.

Best,
Ji Won


2016-02-08 17:16 GMT-05:00 Ji Won Bang :

> Dear. Freesurfer team.
>
> I'd appreciate any advice from you.
>
> When doing the motion correction, I'd like to align all EPI
> data(bold_retino) to the first EPI of target run(bold_decode/003). However,
> the number of slices for target run(33) and the number of slices(32) for
> input run(bold_retino) are different.
>
> When I type: mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino
> -targrun $DATA_DIR/$SUBJECT/bold_decode/003
>
> Freesurfer says that:
> ** FATAL ERROR: perhaps you could make your datasets match?
> ERROR: 3dvolreg
> Invalid null command.
>
> These two kinds of run (bold_decode, bold_retino) were collected in one
> scan per subject, so the head position should not be too different...
>
> Do you have any suggestions for fixing this error?
>
> Should I do 3dWarp -deoblique?
>
> Thank you so much.
>
> Best,
> Ji Won
>
> 2016-02-08 16:30 GMT-05:00 Ji Won Bang :
>
>> Dear. Freesurfer team.
>>
>> Hi.
>>
>> I'm using freesurfer 4.5 version.
>>
>> While doing the motion correction, an error occurred.
>>
>> the command I used:
>> mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino -targrun
>> $DATA_DIR/$SUBJECT/bold_decode/003
>>
>> the error I have:
>> /home/jbang/Projects/replay/epi/replay01/bold_retino
>> 3dvolreg -verbose -dfile 025/fmc.mcdat -base
>> 025/tmp.mc-afni2.32291/tempvol.nii.gz -prefix
>> 025/tmp.mc-afni2.32291/outvol.nii.gz 025/tmp.mc-afni2.32291/invol.nii.gz
>> ++ 3dvolreg: AFNI version=AFNI_2008_07_18_1710 (Feb 10 2009) [64-bit]
>> ++ Authored by: RW Cox
>> *+ WARNING:   If you are performing spatial transformations on an oblique
>> dset,
>>   such as 025/tmp.mc-afni2.32291/tempvol.nii.gz,
>>   or viewing/combining it with volumes of differing obliquity,
>>   you should consider running:
>>  3dWarp -deoblique
>>   on this and  other oblique datasets in the same session.
>>  See 3dWarp -help for details.
>> ++ Oblique dataset:025/tmp.mc-afni2.32291/tempvol.nii.gz is 3.263868
>> degrees from plumb.
>> ++ Reading in base dataset 025/tmp.mc-afni2.32291/tempvol.nii.gz
>> ++ Oblique dataset:025/tmp.mc-afni2.32291/invol.nii.gz is 4.564286
>> degrees from plumb.
>> ++ centers of base and input datasets are 9.09 mm apart
>> ** Input ./invol.nii.gz+orig.HEAD and base ./tempvol.nii.gz+orig.HEAD
>> don't have same dimensions!
>>Input: nx=74  ny=74  nz=32
>>Base:  nx=74  ny=74  nz=33
>> ** FATAL ERROR: perhaps you could make your datasets match?
>> ERROR: 3dvolreg
>> Invalid null command.
>>
>> I think it's because the volume size is different.
>>
>> The volume size for bold_retino is: number of slices 32
>> The volume size for bold_decode: number of slices 33
>>
>> What should I do to correct this error?
>>
>> Thank you for taking your time.
>>
>> Best,
>> Ji Won
>>
>
>
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