from:"Yagmur Ozdemir 19"

External Email - Use Caution

I am using mri_vol2vol --mov L_AIP_mask.nii.gz --targ 
$FSLDIR/standard/MNI152_T1_1mm_brain.nii.gz --inv --reg 
$FREESURFER_HOME/average/mni152.mni305.subfov1.dat --o L_AIP_MNI152.nii.gz 
--interp nearest

(I used mni152.mni305.subfov1.dat in my registration of T1.mgz into MNI152 
space, at the time mni152.register.dat created weird flipping problems, so I am 
using it here as well)

So when I check this in freeview it paints the whole brain and I see that the 
file is not binarized. I attached a picture, the brain under is the adjusted 
MNI152 T1 which I corrected manually.

I also tried this:
mri_label2vol --seg L_AIP_mask.nii.gz --reg 
$FREESURFER_HOME/average/mni152.mni305.subfov1.dat --invertmtx --o 
L_AIP_MNI152.nii.gz
And it created a binarized volume just like I wanted, but registration was way 
off and not possible to correct manually because the unmasked volume is so 
small. I tried to feed a template volume inside this and it didn't create 
anything.

Thank you for all the help!
Best
Idil

[X]

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
[dgr...@mgh.harvard.edu]
Sent: Tuesday, July 24, 2018 5:09 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] tkregister2 scripting- help with saving reg.dat

no idea how to help with the vol2vol problem without a command line and more 
description of the problem

On 7/24/18 6:52 AM, Yagmur Ozdemir 19 wrote:

External Email - Use Caution

By copying the matrix that comes up in the terminal, then readjusting it, if 
needed, in a different .dat file, I can fix the issue. But I would still 
appreciate any suggestions on how to use mri_vol2vol with a binarized mask, or 
what might be causing the system to fill the whole volume.

Best
Idil

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 on behalf of Yagmur Ozdemir 19 
[yozdemi...@amherst.edu<mailto:yozdemi...@amherst.edu>]
Sent: Tuesday, July 24, 2018 1:23 PM
To: Freesurfer support list 
‎[freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>]‎
Subject: [Freesurfer] tkregister2 scripting- help with saving reg.dat


External Email - Use Caution

Hello freesurfer experts,

I am editing the registration matrix between two volumes (fsaverage's T1 to fit 
MNI152 from fsl) using tkregister2, and I cannot save the registration because 
I do not have permission to change the .dat file I originally opened with 
tkregister2. I cannot change the permissions. I do not want to lose all the 
editing I have done so far, so would really appreciate if someone could give me 
advice on how to save the registration as a seperate file either in GUI or from 
terminal.

FYI, I know ideally I shouldn't need to edit the registration but for some 
reason I had weird flipping issues when using mri_vol2vol and 
mni152.register.dat with --inv option. Also the system for some reason does not 
recognize a binary volume with the --interp nearest option, so fills in the 
whole volume. I would appreciate any suggestions.

Best
Idil






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Re: [Freesurfer] How to convert label to volume

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In --temp /home/zwj/SCH_immune/A00 you seem to be missing the last bit of the 
file name, like .mgz or .nii. This option passes the template volume you want 
the output volume to match.

For the second question, you can load that annotation and the individual label 
both in freeview. When you say overlay a label, what is the file format? You 
can load it as an overlay if it ends with .mgz .nii etc, so if a volume file. I 
would suggest looking at the freeview manual.

Best
Idil

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Dongsheng Wu 
[dswu...@163.com]
Sent: Tuesday, July 24, 2018 4:15 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] How to convert label to volume


External Email - Use Caution

Dear experts,
Could you tell us how to convert label to volume? when I run this command 
"mri_label2vol --label lh.insular.label --temp /home/zwj/SCH_immune/A001 
--identity --o insular.img",  errors happened: corRead(): can't open file 
/home/zwj/SCH_immune/A001/COR-.info
ERROR: reading /home/zwj/SCH_immune/A001 header

In addtion, I am going to overlay a specific label to the template as 
following, could you tell me how to do it?
 [cid:6841681e$1$164cc6e6aa3$Coremail$dswuscu$163.com]



Thanks
Best Regards

Wu




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Re: [Freesurfer] tkregister2 scripting- help with saving reg.dat

External Email - Use Caution

By copying the matrix that comes up in the terminal, then readjusting it, if 
needed, in a different .dat file, I can fix the issue. But I would still 
appreciate any suggestions on how to use mri_vol2vol with a binarized mask, or 
what might be causing the system to fill the whole volume.

Best
Idil

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Yagmur Ozdemir 19 
[yozdemi...@amherst.edu]
Sent: Tuesday, July 24, 2018 1:23 PM
To: Freesurfer support list ‎[freesurfer@nmr.mgh.harvard.edu]‎
Subject: [Freesurfer] tkregister2 scripting- help with saving reg.dat


External Email - Use Caution

Hello freesurfer experts,

I am editing the registration matrix between two volumes (fsaverage's T1 to fit 
MNI152 from fsl) using tkregister2, and I cannot save the registration because 
I do not have permission to change the .dat file I originally opened with 
tkregister2. I cannot change the permissions. I do not want to lose all the 
editing I have done so far, so would really appreciate if someone could give me 
advice on how to save the registration as a seperate file either in GUI or from 
terminal.

FYI, I know ideally I shouldn't need to edit the registration but for some 
reason I had weird flipping issues when using mri_vol2vol and 
mni152.register.dat with --inv option. Also the system for some reason does not 
recognize a binary volume with the --interp nearest option, so fills in the 
whole volume. I would appreciate any suggestions.

Best
Idil



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[Freesurfer] tkregister2 scripting- help with saving reg.dat

External Email - Use Caution

Hello freesurfer experts,

I am editing the registration matrix between two volumes (fsaverage's T1 to fit 
MNI152 from fsl) using tkregister2, and I cannot save the registration because 
I do not have permission to change the .dat file I originally opened with 
tkregister2. I cannot change the permissions. I do not want to lose all the 
editing I have done so far, so would really appreciate if someone could give me 
advice on how to save the registration as a seperate file either in GUI or from 
terminal.

FYI, I know ideally I shouldn't need to edit the registration but for some 
reason I had weird flipping issues when using mri_vol2vol and 
mni152.register.dat with --inv option. Also the system for some reason does not 
recognize a binary volume with the --interp nearest option, so fills in the 
whole volume. I would appreciate any suggestions.

Best
Idil



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Re: [Freesurfer] loading multiple saved points

2018-07-16 Thread Yagmur Ozdemir 19

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Basically an edit.dat file with points in each row?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N. Greve 
[dgr...@mgh.harvard.edu]
Sent: Monday, July 16, 2018 5:54 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] loading multiple saved points

Not in tksurfer/tkmedit. You can create a point list to be used in freeview.

On 07/16/2018 10:50 AM, Yagmur Ozdemir 19 wrote:
>
> External Email - Use Caution
>
> Hello Freesurfer experts,
>
> I am wondering if there is any way I can load up multiple points I
> saved in tkmedit, in either viewing software at the same time. Each
> time I defined a point, I changed the edit.dat file's name so it would
> save as individual files, but when I try to load there is no option to
> choose amongst dat files, and I noticed that if there are multiple
> points saved in edit.dat when you "go to saved point" it will load the
> last point saved. I think I am able to load these into either freeview
> or tksurfer because in all GUIs the system looks for edit.dat.
>
> I think I can load the last points one by one in tksurfer, delete the
> last vertex from file and save it on tksurfer surface, but I am really
> for a more intuitive and portable way.
>
> Best
> Idil
>
>
>
>
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[Freesurfer] loading multiple saved points

2018-07-16 Thread Yagmur Ozdemir 19

External Email - Use Caution

Hello Freesurfer experts,

I am wondering if there is any way I can load up multiple points I saved in 
tkmedit, in either viewing software at the same time. Each time I defined a 
point, I changed the edit.dat file's name so it would save as individual files, 
but when I try to load there is no option to choose amongst dat files, and I 
noticed that if there are multiple points saved in edit.dat when you "go to 
saved point" it will load the last point saved. I think I am able to load these 
into either freeview or tksurfer because in all GUIs the system looks for 
edit.dat.

I think I can load the last points one by one in tksurfer, delete the last 
vertex from file and save it on tksurfer surface, but I am really for a more 
intuitive and portable way.

Best
Idil


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Re: [Freesurfer] differing display colors for 2+ labels in tksurfer

2018-06-23 Thread Yagmur Ozdemir 19

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Hello Katie,

I just checked it and it works well. Thank you for the help!

Best
Idil

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Kathryn Devaney 
[kdeva...@bu.edu]
Sent: Friday, June 22, 2018 2:02 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] differing display colors for 2+ labels in tksurfer

External Email - Use Caution

Idil,

>From the command line with tksurfer open you can use the labl_set_color 
>command - label is zero indexed based on the order that they were loaded.

See here for more details:  
https://surfer.nmr.mgh.harvard.edu/fswiki/TkSurferGuide/TkSurferScripting/TkSurferScriptingReference

Cheers,
Katie

On Tue, Jun 19, 2018 at 11:13 AM, Yagmur Ozdemir 19 
mailto:yozdemi...@amherst.edu>> wrote:

External Email - Use Caution

Hello freesurfer experts,

I am aiming to view 3 to 8 different labels on one flattened surface patch 
created in tksurfer. Even if I can manually select the color of first 
label, the next ones end up sharing the same color and I cannot seem to change 
this from the interface and I didn't come across any command line options for 
this. Any advice on how to set these different colors? I see that freeview can 
handle this, but to my knowledge it cannot open flattened patches?

Any help would be deeply appreciated.
Best
Idil

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Re: [Freesurfer] differing display colors for 2+ labels in tksurfer

2018-06-19 Thread Yagmur Ozdemir 19

External Email - Use Caution

I should also add that I cannot create an annot file as then all share multiple 
vertices.

Best 
Idil

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Yagmur Ozdemir 19 
[yozdemi...@amherst.edu]
Sent: Tuesday, June 19, 2018 9:13 PM
To: Freesurfer support list ‎[freesurfer@nmr.mgh.harvard.edu]‎
Subject: [Freesurfer] differing display colors for 2+ labels in tksurfer

External Email - Use Caution

Hello freesurfer experts,

I am aiming to view 3 to 8 different labels on one flattened surface patch 
created in tksurfer. Even if I can manually select the color of first 
label, the next ones end up sharing the same color and I cannot seem to change 
this from the interface and I didn't come across any command line options for 
this. Any advice on how to set these different colors? I see that freeview can 
handle this, but to my knowledge it cannot open flattened patches?

Any help would be deeply appreciated.
Best
Idil

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[Freesurfer] differing display colors for 2+ labels in tksurfer

2018-06-19 Thread Yagmur Ozdemir 19

External Email - Use Caution

Hello freesurfer experts,

I am aiming to view 3 to 8 different labels on one flattened surface patch 
created in tksurfer. Even if I can manually select the color of first 
label, the next ones end up sharing the same color and I cannot seem to change 
this from the interface and I didn't come across any command line options for 
this. Any advice on how to set these different colors? I see that freeview can 
handle this, but to my knowledge it cannot open flattened patches?

Any help would be deeply appreciated.
Best
Idil
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Re: [Freesurfer] averaging surface labels?

I didn't come across that script, thank you!

Best
Idil

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
[dgr...@mgh.harvard.edu]
Sent: Monday, March 19, 2018 7:00 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] averaging surface labels?

why do you need to go into the volume at all? If the labels exist on the 
surface in the format of an annotation file, then you can use annot2std

On 3/16/18 3:08 PM, Yagmur Ozdemir 19 wrote:
Hello FreeSurfer experts,

I am trying to create a group average of labels defined on inflated surface, 
and so far I tried mri_label2vol which succesfully got the labels to volume 
space and binarized for averaging, however when I sample this back to the 
inflated surface of fsaverage, using mri_label2label, the location is 
completely wrong and the label looks very distorted. I tried to use 
mri_vol2surf and mri_vol2roi instead for the latter portion and both did not 
work. Do you have any suggestions? I think mri_vol2surf can work if I have a 
register.dat file for fsaverage vol->surf but so far I didn't come across one 
and couldn't see how to create one.

Also I think if I can create overlays out of the labels, then I can do 
mri_concat to average them out and with mri_cor2label get them out as labels 
again. However I did not come across a script that creates overlays out of 
labels.

Thank you for all the thoughts and suggestions

Best
Idil

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Re: [Freesurfer] isxconcat-sess error: trgsubject

Thank you!

Best
Idil

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
[dgr...@mgh.harvard.edu]
Sent: Monday, March 19, 2018 6:25 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] isxconcat-sess error: trgsubject


isxconcat-sess assumes that you sampled all your subjects to the common surface 
(fsaverage). You will have to re-run selxavg3-sess using data on fsaverage.

On 3/19/18 12:15 PM, Yagmur Ozdemir 19 wrote:
Thank you for the help!

root@ubuntu:~/local/freesurfer/Project_bold# mri_info --dim 
Sess01/bold/rtopyTR2.lh//mask.nii.gz
128461 1 1 1
root@ubuntu:~/local/freesurfer/Project_bold# mri_info --dim 
Sess02/bold/rtopyTR2.lh//mask.nii.gz
143033 1 1 1
root@ubuntu:~/local/freesurfer/Project_bold# mri_info --dim 
Sess03/bold/rtopyTR2.lh//mask.nii.gz
163154 1 1 1
root@ubuntu:~/local/freesurfer/Project_bold# mri_info --dim 
Sess04/bold/rtopyTR2.lh//mask.nii.gz
124330 1 1 1
root@ubuntu:~/local/freesurfer/Project_bold# mri_info --dim 
Sess07/bold/rtopyTR2.lh//mask.nii.gz
120332 1 1 1
root@ubuntu:~/local/freesurfer/Project_bold# mri_info --dim 
Sess08/bold/rtopyTR2.lh//mask.nii.gz
102780 1 1 1
root@ubuntu:~/local/freesurfer/Project_bold# mri_info --dim 
Sess09/bold/rtopyTR2.lh//mask.nii.gz
130063 1 1 1
root@ubuntu:~/local/freesurfer/Project_bold# mri_info --dim 
Sess10/bold/rtopyTR2.lh//mask.nii.gz
129873 1 1 1


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 on behalf of Douglas Greve 
[dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>]
Sent: Monday, March 19, 2018 5:40 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] isxconcat-sess error: trgsubject


Can you run

mri_info --dim Sess01/bold/rtopyTR2.lh//mask.nii.gz

for each of your subjects and send us the result?

On 3/19/18 7:52 AM, Yagmur Ozdemir 19 wrote:
Hello Freesurfer developers,

I am trying to concatenate session files of different subjects using 
isxconcat-sess. I am not really sure why " INFO:trgsubject is self, this will 
fail unless all sessions are the same subject" pops up as I understand this is 
what isxconcat-sess is meant to do, and I used --subject fsaverage in some 
tries. I am not sure if there is something I am doing wrong, or the problem is 
coming from the "//" in the output lines. When I took out either Sess01 and 
Sess02 from the list to be sure it wasn't a problem specific to it, I got the 
same error.

Below is the error output.

Best
Idil

INFO: trgsubject is self, this will fail unless all sessions are the same 
subject
group/rtopyTR2.lh/log/isxconcat.log
cd /home/vm01/local/freesurfer/Project_bold
isxconcat0-sess -f sessid -m mask -o group/rtopyTR2.lh/masks.nii.gz -a 
rtopyTR2.lh

/home/vm01/local/freesurfer/Project_bold
mri_concat 
/home/vm01/local/freesurfer/Project_bold/Sess01/bold/rtopyTR2.lh//mask.nii.gz 
/home/vm01/local/freesurfer/Project_bold/Sess02/bold/rtopyTR2.lh//mask.nii.gz 
/home/vm01/local/freesurfer/Project_bold/Sess03/bold/rtopyTR2.lh//mask.nii.gz 
/home/vm01/local/freesurfer/Project_bold/Sess04/bold/rtopyTR2.lh//mask.nii.gz 
/home/vm01/local/freesurfer/Project_bold/Sess07/bold/rtopyTR2.lh//mask.nii.gz 
/home/vm01/local/freesurfer/Project_bold/Sess08/bold/rtopyTR2.lh//mask.nii.gz 
/home/vm01/local/freesurfer/Project_bold/Sess09/bold/rtopyTR2.lh//mask.nii.gz 
/home/vm01/local/freesurfer/Project_bold/Sess10/bold/rtopyTR2.lh//mask.nii.gz 
--o group/rtopyTR2.lh/masks.nii.gz
ninputs = 8
Checking inputs
ERROR: dimension mismatch between 
/home/vm01/local/freesurfer/Project_bold/Sess01/bold/rtopyTR2.lh//mask.nii.gz 
and 
/home/vm01/local/freesurfer/Project_bold/Sess02/bold/rtopyTR2.lh//mask.nii.gz




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Re: [Freesurfer] isxconcat-sess error: trgsubject

Thank you for the help!

root@ubuntu:~/local/freesurfer/Project_bold# mri_info --dim 
Sess01/bold/rtopyTR2.lh//mask.nii.gz
128461 1 1 1
root@ubuntu:~/local/freesurfer/Project_bold# mri_info --dim 
Sess02/bold/rtopyTR2.lh//mask.nii.gz
143033 1 1 1
root@ubuntu:~/local/freesurfer/Project_bold# mri_info --dim 
Sess03/bold/rtopyTR2.lh//mask.nii.gz
163154 1 1 1
root@ubuntu:~/local/freesurfer/Project_bold# mri_info --dim 
Sess04/bold/rtopyTR2.lh//mask.nii.gz
124330 1 1 1
root@ubuntu:~/local/freesurfer/Project_bold# mri_info --dim 
Sess07/bold/rtopyTR2.lh//mask.nii.gz
120332 1 1 1
root@ubuntu:~/local/freesurfer/Project_bold# mri_info --dim 
Sess08/bold/rtopyTR2.lh//mask.nii.gz
102780 1 1 1
root@ubuntu:~/local/freesurfer/Project_bold# mri_info --dim 
Sess09/bold/rtopyTR2.lh//mask.nii.gz
130063 1 1 1
root@ubuntu:~/local/freesurfer/Project_bold# mri_info --dim 
Sess10/bold/rtopyTR2.lh//mask.nii.gz
129873 1 1 1


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
[dgr...@mgh.harvard.edu]
Sent: Monday, March 19, 2018 5:40 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] isxconcat-sess error: trgsubject


Can you run

mri_info --dim Sess01/bold/rtopyTR2.lh//mask.nii.gz

for each of your subjects and send us the result?

On 3/19/18 7:52 AM, Yagmur Ozdemir 19 wrote:
Hello Freesurfer developers,

I am trying to concatenate session files of different subjects using 
isxconcat-sess. I am not really sure why " INFO:trgsubject is self, this will 
fail unless all sessions are the same subject" pops up as I understand this is 
what isxconcat-sess is meant to do, and I used --subject fsaverage in some 
tries. I am not sure if there is something I am doing wrong, or the problem is 
coming from the "//" in the output lines. When I took out either Sess01 and 
Sess02 from the list to be sure it wasn't a problem specific to it, I got the 
same error.

Below is the error output.

Best
Idil

INFO: trgsubject is self, this will fail unless all sessions are the same 
subject
group/rtopyTR2.lh/log/isxconcat.log
cd /home/vm01/local/freesurfer/Project_bold
isxconcat0-sess -f sessid -m mask -o group/rtopyTR2.lh/masks.nii.gz -a 
rtopyTR2.lh

/home/vm01/local/freesurfer/Project_bold
mri_concat 
/home/vm01/local/freesurfer/Project_bold/Sess01/bold/rtopyTR2.lh//mask.nii.gz 
/home/vm01/local/freesurfer/Project_bold/Sess02/bold/rtopyTR2.lh//mask.nii.gz 
/home/vm01/local/freesurfer/Project_bold/Sess03/bold/rtopyTR2.lh//mask.nii.gz 
/home/vm01/local/freesurfer/Project_bold/Sess04/bold/rtopyTR2.lh//mask.nii.gz 
/home/vm01/local/freesurfer/Project_bold/Sess07/bold/rtopyTR2.lh//mask.nii.gz 
/home/vm01/local/freesurfer/Project_bold/Sess08/bold/rtopyTR2.lh//mask.nii.gz 
/home/vm01/local/freesurfer/Project_bold/Sess09/bold/rtopyTR2.lh//mask.nii.gz 
/home/vm01/local/freesurfer/Project_bold/Sess10/bold/rtopyTR2.lh//mask.nii.gz 
--o group/rtopyTR2.lh/masks.nii.gz
ninputs = 8
Checking inputs
ERROR: dimension mismatch between 
/home/vm01/local/freesurfer/Project_bold/Sess01/bold/rtopyTR2.lh//mask.nii.gz 
and 
/home/vm01/local/freesurfer/Project_bold/Sess02/bold/rtopyTR2.lh//mask.nii.gz




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[Freesurfer] isxconcat-sess error: trgsubject

Hello Freesurfer developers,

I am trying to concatenate session files of different subjects using 
isxconcat-sess. I am not really sure why " INFO:trgsubject is self, this will 
fail unless all sessions are the same subject" pops up as I understand this is 
what isxconcat-sess is meant to do, and I used --subject fsaverage in some 
tries. I am not sure if there is something I am doing wrong, or the problem is 
coming from the "//" in the output lines. When I took out either Sess01 and 
Sess02 from the list to be sure it wasn't a problem specific to it, I got the 
same error.

Below is the error output.

Best
Idil

INFO: trgsubject is self, this will fail unless all sessions are the same 
subject
group/rtopyTR2.lh/log/isxconcat.log
cd /home/vm01/local/freesurfer/Project_bold
isxconcat0-sess -f sessid -m mask -o group/rtopyTR2.lh/masks.nii.gz -a 
rtopyTR2.lh

/home/vm01/local/freesurfer/Project_bold
mri_concat 
/home/vm01/local/freesurfer/Project_bold/Sess01/bold/rtopyTR2.lh//mask.nii.gz 
/home/vm01/local/freesurfer/Project_bold/Sess02/bold/rtopyTR2.lh//mask.nii.gz 
/home/vm01/local/freesurfer/Project_bold/Sess03/bold/rtopyTR2.lh//mask.nii.gz 
/home/vm01/local/freesurfer/Project_bold/Sess04/bold/rtopyTR2.lh//mask.nii.gz 
/home/vm01/local/freesurfer/Project_bold/Sess07/bold/rtopyTR2.lh//mask.nii.gz 
/home/vm01/local/freesurfer/Project_bold/Sess08/bold/rtopyTR2.lh//mask.nii.gz 
/home/vm01/local/freesurfer/Project_bold/Sess09/bold/rtopyTR2.lh//mask.nii.gz 
/home/vm01/local/freesurfer/Project_bold/Sess10/bold/rtopyTR2.lh//mask.nii.gz 
--o group/rtopyTR2.lh/masks.nii.gz
ninputs = 8
Checking inputs
ERROR: dimension mismatch between 
/home/vm01/local/freesurfer/Project_bold/Sess01/bold/rtopyTR2.lh//mask.nii.gz 
and 
/home/vm01/local/freesurfer/Project_bold/Sess02/bold/rtopyTR2.lh//mask.nii.gz

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[Freesurfer] averaging surface labels?

2018-03-16 Thread Yagmur Ozdemir 19

Hello FreeSurfer experts,

I am trying to create a group average of labels defined on inflated surface, 
and so far I tried mri_label2vol which succesfully got the labels to volume 
space and binarized for averaging, however when I sample this back to the 
inflated surface of fsaverage, using mri_label2label, the location is 
completely wrong and the label looks very distorted. I tried to use 
mri_vol2surf and mri_vol2roi instead for the latter portion and both did not 
work. Do you have any suggestions? I think mri_vol2surf can work if I have a 
register.dat file for fsaverage vol->surf but so far I didn't come across one 
and couldn't see how to create one.

Also I think if I can create overlays out of the labels, then I can do 
mri_concat to average them out and with mri_cor2label get them out as labels 
again. However I did not come across a script that creates overlays out of 
labels.

Thank you for all the thoughts and suggestions

Best
Idil
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Re: [Freesurfer] tksurfer/freeview vertex coordinates difference?

2018-03-03 Thread Yagmur Ozdemir 19

Thank you!

Best
Idil 

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Thursday, March 01, 2018 5:46 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] tksurfer/freeview vertex coordinates difference?

Hi Idil

we keep track of different kinds of RAS coordinates, which may not be the
same (surface ras, scanner ras, etc...).
cheers
Bruce

On Thu, 1 Mar 2018, Yagmur Ozdemir 19 wrote:

> Hello FS experts,
>
> I am wondering if anyone knows why the same vertices' coordinates are shown 
> slightly different when
> opened in freesurfer and tksurfer. I was checking some annotation files for 
> each subject across the
> two on inflated surface, and noticed slight coordinate differences in RAS.
> ex. freesurfer vertex 2407 [-18.23, -78.84, 27.92] - tksurfer vertex 2407 
> [-18.48, -78.82,
> 28.23]
>
> Best
> Idil
>
>
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[Freesurfer] tksurfer/freeview vertex coordinates difference?

2018-03-01 Thread Yagmur Ozdemir 19

Hello FS experts,

I am wondering if anyone knows why the same vertices' coordinates are shown 
slightly different when opened in freesurfer and tksurfer. I was checking some 
annotation files for each subject across the two on inflated surface, and 
noticed slight coordinate differences in RAS.
ex. freesurfer vertex 2407 [-18.23, -78.84, 27.92] - tksurfer vertex 2407 
[-18.48, -78.82, 28.23]

Best
Idil
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Re: [Freesurfer] fast_selxavg3.m error/analysis.info file

2018-02-06 Thread Yagmur Ozdemir 19

That works, thank you!

Best
Idil 

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Monday, February 05, 2018 9:21 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file

Try running selxavg3-sess with -monly sxa3.m

Then start matlab and run sxa3.m


On 02/05/2018 02:02 PM, Yagmur Ozdemir 19 wrote:
> Dr. Greve,
>
> I tried with root access and it still gave the same error. I am using a 
> virtual machine from our server that I connect with VCN, and it has 
> freesurfer and matlab installed and setup in its shell. The VM has Ubuntu 
> 16.04 (Xenial), Freesurfer v.6, and Matlab R2016b. I appreciate your help.
>
> Best
> Idil
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Monday, February 05, 2018 8:34 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
>
> I don't know, it is all very weird. What platform are you using?
>
>
> On 02/05/2018 01:27 PM, Yagmur Ozdemir 19 wrote:
>> Dr. Greve,
>>
>> Yes I have tried making new files. (I also gave the previous files and 
>> folders full permission with chmod which again didn't work) Mkanalysis-sess 
>> did not have any problems as expected, but mkcontrast-sess failed for the 
>> same reason of not being able to open the .config file that it should be 
>> creating under the analysis folder.
>>
>> I am not the root user of the system, but maybe getting sudo access would be 
>> helpful? I can look into this.
>>
>> Best
>> Idil
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Monday, February 05, 2018 6:53 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
>>
>> I cannot replicate this. There must be some strange permission error.
>> Can you try to make a new analysis with a different name and just see if
>> fails?
>>
>>
>> On 2/4/18 12:50 PM, Yagmur Ozdemir 19 wrote:
>>> Hello Dr. Greve,
>>>
>>> The analysis.info file is below. I should also say that, when I am trying 
>>> to create new analysis and contrast files, while creating the .config file 
>>> for contrast, th system gives the same error saying that it cannot enter 
>>> the file.
>>>
>>> # FSBUILD freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
>>> # MKAVERSION $Id: mkanalysis-sess,v 1.78 2015/12/10 22:51:30 zkaufman Exp $
>>> # MKACMD /home/vm01/local/freesurfer/fsfast/bin/mkanalysis-sess -surface 
>>> self lh -analysis rtopyTR2.lh -paradigm rtopy.par -TR 2 -nconditions 1 
>>> -event-related -fwhm 5 -per-run -fsd bold -refeventdur 10 -gammafit 2.25 
>>> 1.25 -force
>>> # DATE Tue Jan 30 07:14:05 EST 2018
>>>
>>> analysis rtopyTR2.lh
>>> mcstem fmcpr
>>> fsd bold
>>> TR 2
>>> RegDOF 6
>>> PerSession 0
>>> RawSpace surface self lh
>>> mask brain
>>> RawFWHM 5
>>> RawSTC none
>>> nSliceGroups 1
>>> UseB0DC 0
>>> ApplySubCortMask 1
>>> inorm 100
>>> acfbins 30
>>> fixacf  1
>>> acffwhm 20
>>> acfsvd  0
>>> designtype event-related
>>> nskip 0
>>> polyfit 2
>>> HPFCutoffHz 0
>>> HeteroGCor 0
>>> nconditions 1
>>> parname rtopy.par
>>> RefEventDur 10
>>> timewindow 40.000000
>>> prestim 0
>>> TER 0.05
>>> gamma 2.25 1.25 2 0
>>> stimulusdelay -1.
>>> Condition 1 Condition01
>>>
>>> Best,
>>> Idil
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
>>> [gr...@nmr.mgh.harvard.edu]
>>> Sent: Saturday, February 03, 2018 9:21 PM
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
>>>
>>> Strange. Can you send me the analysis.info file?
>>>
>>>
>>> On 1/31/18 9:26 AM, Yagmur Ozdemir 19 wrote:
>>>> Hello Dr. Greve,
>&g

Re: [Freesurfer] fast_selxavg3.m error/analysis.info file

2018-02-05 Thread Yagmur Ozdemir 19

Dr. Greve,

I tried with root access and it still gave the same error. I am using a virtual 
machine from our server that I connect with VCN, and it has freesurfer and 
matlab installed and setup in its shell. The VM has Ubuntu 16.04 (Xenial), 
Freesurfer v.6, and Matlab R2016b. I appreciate your help.

Best
Idil 

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Monday, February 05, 2018 8:34 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file

I don't know, it is all very weird. What platform are you using?


On 02/05/2018 01:27 PM, Yagmur Ozdemir 19 wrote:
> Dr. Greve,
>
> Yes I have tried making new files. (I also gave the previous files and 
> folders full permission with chmod which again didn't work) Mkanalysis-sess 
> did not have any problems as expected, but mkcontrast-sess failed for the 
> same reason of not being able to open the .config file that it should be 
> creating under the analysis folder.
>
> I am not the root user of the system, but maybe getting sudo access would be 
> helpful? I can look into this.
>
> Best
> Idil
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Monday, February 05, 2018 6:53 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
>
> I cannot replicate this. There must be some strange permission error.
> Can you try to make a new analysis with a different name and just see if
> fails?
>
>
> On 2/4/18 12:50 PM, Yagmur Ozdemir 19 wrote:
>> Hello Dr. Greve,
>>
>> The analysis.info file is below. I should also say that, when I am trying to 
>> create new analysis and contrast files, while creating the .config file for 
>> contrast, th system gives the same error saying that it cannot enter the 
>> file.
>>
>> # FSBUILD freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
>> # MKAVERSION $Id: mkanalysis-sess,v 1.78 2015/12/10 22:51:30 zkaufman Exp $
>> # MKACMD /home/vm01/local/freesurfer/fsfast/bin/mkanalysis-sess -surface 
>> self lh -analysis rtopyTR2.lh -paradigm rtopy.par -TR 2 -nconditions 1 
>> -event-related -fwhm 5 -per-run -fsd bold -refeventdur 10 -gammafit 2.25 
>> 1.25 -force
>> # DATE Tue Jan 30 07:14:05 EST 2018
>>
>> analysis rtopyTR2.lh
>> mcstem fmcpr
>> fsd bold
>> TR 2
>> RegDOF 6
>> PerSession 0
>> RawSpace surface self lh
>> mask brain
>> RawFWHM 5
>> RawSTC none
>> nSliceGroups 1
>> UseB0DC 0
>> ApplySubCortMask 1
>> inorm 100
>> acfbins 30
>> fixacf  1
>> acffwhm 20
>> acfsvd  0
>> designtype event-related
>> nskip 0
>> polyfit 2
>> HPFCutoffHz 0
>> HeteroGCor 0
>> nconditions 1
>> parname rtopy.par
>> RefEventDur 10
>> timewindow 40.00
>> prestim 0
>> TER 0.05
>> gamma 2.25 1.25 2 0
>> stimulusdelay -1.
>> Condition 1 Condition01
>>
>> Best,
>> Idil
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Saturday, February 03, 2018 9:21 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
>>
>> Strange. Can you send me the analysis.info file?
>>
>>
>> On 1/31/18 9:26 AM, Yagmur Ozdemir 19 wrote:
>>> Hello Dr. Greve,
>>>
>>> Yes it exists. The output below was with debug option.
>>>
>>> Best
>>> Idil
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
>>> [gr...@nmr.mgh.harvard.edu]
>>> Sent: Tuesday, January 30, 2018 8:40 PM
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
>>>
>>> Does the file 
>>> /home/vm01/local/freesurfer/Project_bold/rtopyTR2.rh/analysis.info exist? 
>>> If so, can you run it with -debug as the first option and send the terminal 
>>> output?
>>>
>>> On 1/30/18 8:51 AM, Yagmur Ozdemir 19 wrote:
>>>
>>>
>>> Hello FreeSurfer experts,
>>>
>>> I am getting th

Re: [Freesurfer] fast_selxavg3.m error/analysis.info file

2018-02-05 Thread Yagmur Ozdemir 19

Dr. Greve,

Yes I have tried making new files. (I also gave the previous files and folders 
full permission with chmod which again didn't work) Mkanalysis-sess did not 
have any problems as expected, but mkcontrast-sess failed for the same reason 
of not being able to open the .config file that it should be creating under the 
analysis folder. 

I am not the root user of the system, but maybe getting sudo access would be 
helpful? I can look into this. 

Best
Idil 

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Monday, February 05, 2018 6:53 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file

I cannot replicate this. There must be some strange permission error.
Can you try to make a new analysis with a different name and just see if
fails?


On 2/4/18 12:50 PM, Yagmur Ozdemir 19 wrote:
> Hello Dr. Greve,
>
> The analysis.info file is below. I should also say that, when I am trying to 
> create new analysis and contrast files, while creating the .config file for 
> contrast, th system gives the same error saying that it cannot enter the file.
>
> # FSBUILD freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
> # MKAVERSION $Id: mkanalysis-sess,v 1.78 2015/12/10 22:51:30 zkaufman Exp $
> # MKACMD /home/vm01/local/freesurfer/fsfast/bin/mkanalysis-sess -surface self 
> lh -analysis rtopyTR2.lh -paradigm rtopy.par -TR 2 -nconditions 1 
> -event-related -fwhm 5 -per-run -fsd bold -refeventdur 10 -gammafit 2.25 1.25 
> -force
> # DATE Tue Jan 30 07:14:05 EST 2018
>
> analysis rtopyTR2.lh
> mcstem fmcpr
> fsd bold
> TR 2
> RegDOF 6
> PerSession 0
> RawSpace surface self lh
> mask brain
> RawFWHM 5
> RawSTC none
> nSliceGroups 1
> UseB0DC 0
> ApplySubCortMask 1
> inorm 100
> acfbins 30
> fixacf  1
> acffwhm 20
> acfsvd  0
> designtype event-related
> nskip 0
> polyfit 2
> HPFCutoffHz 0
> HeteroGCor 0
> nconditions 1
> parname rtopy.par
> RefEventDur 10
> timewindow 40.00
> prestim 0
> TER 0.05
> gamma 2.25 1.25 2 0
> stimulusdelay -1.
> Condition 1 Condition01
>
> Best,
> Idil
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Saturday, February 03, 2018 9:21 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
>
> Strange. Can you send me the analysis.info file?
>
>
> On 1/31/18 9:26 AM, Yagmur Ozdemir 19 wrote:
>> Hello Dr. Greve,
>>
>> Yes it exists. The output below was with debug option.
>>
>> Best
>> Idil
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Tuesday, January 30, 2018 8:40 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
>>
>> Does the file 
>> /home/vm01/local/freesurfer/Project_bold/rtopyTR2.rh/analysis.info exist? If 
>> so, can you run it with -debug as the first option and send the terminal 
>> output?
>>
>> On 1/30/18 8:51 AM, Yagmur Ozdemir 19 wrote:
>>
>>
>> Hello FreeSurfer experts,
>>
>> I am getting this strange error when running selxavg3-sess. (in selxavg3 
>> command I am calling the analysis file with: -a rtopyTR2.rh) When the system 
>> enters fast_selxavg3, it cannot read analysis.info, thus produces the 
>> following output:
>>
>> #@# Sess05 ###
>> /home/vm01/local/freesurfer/Project_bold/Sess05
>> -
>> $Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $
>> -
>> outtop = /home/vm01/local/freesurfer/Project_bold
>> Extension format = nii.gz
>> ERROR: could not open rtopyTR2.rh/analysis.info
>> else
>> else
>> echo "--" | tee -a $LF
>> echo --
>> tee -a 
>> /home/vm01/local/freesurfer/Project_bold/log/selxavg3-sess-bold-rtopyTR2.rh-180130082919.log
>> --
>> rm $MLF
>> rm /tmp/selxavg3-sess-10173.m
>> if ( ! -e $okfile ) then
>> if ( ! -e /tmp/selxavg3-sess-10173.ok ) then
>> echo "ERROR: fast_selxavg3() failed\n" ;
>> echo ERROR: fast_selxa

Re: [Freesurfer] fast_selxavg3.m error/analysis.info file

2018-02-04 Thread Yagmur Ozdemir 19

Hello Dr. Greve,

The analysis.info file is below. I should also say that, when I am trying to 
create new analysis and contrast files, while creating the .config file for 
contrast, th system gives the same error saying that it cannot enter the file.

# FSBUILD freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
# MKAVERSION $Id: mkanalysis-sess,v 1.78 2015/12/10 22:51:30 zkaufman Exp $
# MKACMD /home/vm01/local/freesurfer/fsfast/bin/mkanalysis-sess -surface self 
lh -analysis rtopyTR2.lh -paradigm rtopy.par -TR 2 -nconditions 1 
-event-related -fwhm 5 -per-run -fsd bold -refeventdur 10 -gammafit 2.25 1.25 
-force
# DATE Tue Jan 30 07:14:05 EST 2018

analysis rtopyTR2.lh
mcstem fmcpr
fsd bold
TR 2
RegDOF 6
PerSession 0
RawSpace surface self lh
mask brain
RawFWHM 5
RawSTC none
nSliceGroups 1
UseB0DC 0
ApplySubCortMask 1
inorm 100
acfbins 30
fixacf  1
acffwhm 20
acfsvd  0
designtype event-related
nskip 0
polyfit 2
HPFCutoffHz 0
HeteroGCor 0
nconditions 1
parname rtopy.par
RefEventDur 10
timewindow 40.00
prestim 0
TER 0.05
gamma 2.25 1.25 2 0
stimulusdelay -1.
Condition 1 Condition01

Best,
Idil 

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Saturday, February 03, 2018 9:21 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file

Strange. Can you send me the analysis.info file?


On 1/31/18 9:26 AM, Yagmur Ozdemir 19 wrote:
> Hello Dr. Greve,
>
> Yes it exists. The output below was with debug option.
>
> Best
> Idil
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Tuesday, January 30, 2018 8:40 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
>
> Does the file 
> /home/vm01/local/freesurfer/Project_bold/rtopyTR2.rh/analysis.info exist? If 
> so, can you run it with -debug as the first option and send the terminal 
> output?
>
> On 1/30/18 8:51 AM, Yagmur Ozdemir 19 wrote:
>
>
> Hello FreeSurfer experts,
>
> I am getting this strange error when running selxavg3-sess. (in selxavg3 
> command I am calling the analysis file with: -a rtopyTR2.rh) When the system 
> enters fast_selxavg3, it cannot read analysis.info, thus produces the 
> following output:
>
> #@# Sess05 ###
> /home/vm01/local/freesurfer/Project_bold/Sess05
> -
> $Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $
> -
> outtop = /home/vm01/local/freesurfer/Project_bold
> Extension format = nii.gz
> ERROR: could not open rtopyTR2.rh/analysis.info
> else
> else
> echo "--" | tee -a $LF
> echo --
> tee -a 
> /home/vm01/local/freesurfer/Project_bold/log/selxavg3-sess-bold-rtopyTR2.rh-180130082919.log
> --
> rm $MLF
> rm /tmp/selxavg3-sess-10173.m
> if ( ! -e $okfile ) then
> if ( ! -e /tmp/selxavg3-sess-10173.ok ) then
> echo "ERROR: fast_selxavg3() failed\n" ;
> echo ERROR: fast_selxavg3() failed\n
> ERROR: fast_selxavg3() failed\n
> exit 1 ;
> exit 1
>
> The analysis folder it is referring to( rtopyTR2.rh) is in the directory from 
> which I am calling selxavg3-sess. It has the analysis.info file in which 
> doesn't have any restrictions. To troubleshoot, I moved the folder to inside 
> the session's functional directory and inside the session folder and these 
> didn't create any changes. I looked at the script and tried to debug there 
> but didn't give any results. It gave a similar error when trying to open the 
> config file of contrast in mkcontrast-sess. (I also don't have root 
> access)Any help is appreciated!
>
> Best,
> Idil
>
>
>
>
>
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>
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Re: [Freesurfer] fast_selxavg3.m error/analysis.info file

2018-01-31 Thread Yagmur Ozdemir 19

Hello Dr. Greve,

Yes it exists. The output below was with debug option. 

Best
Idil

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Tuesday, January 30, 2018 8:40 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file

Does the file 
/home/vm01/local/freesurfer/Project_bold/rtopyTR2.rh/analysis.info exist? If 
so, can you run it with -debug as the first option and send the terminal output?

On 1/30/18 8:51 AM, Yagmur Ozdemir 19 wrote:


Hello FreeSurfer experts,

I am getting this strange error when running selxavg3-sess. (in selxavg3 
command I am calling the analysis file with: -a rtopyTR2.rh) When the system 
enters fast_selxavg3, it cannot read analysis.info, thus produces the following 
output:

#@# Sess05 ###
/home/vm01/local/freesurfer/Project_bold/Sess05
-
$Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $
-
outtop = /home/vm01/local/freesurfer/Project_bold
Extension format = nii.gz
ERROR: could not open rtopyTR2.rh/analysis.info
else
else
echo "--" | tee -a $LF
echo --
tee -a 
/home/vm01/local/freesurfer/Project_bold/log/selxavg3-sess-bold-rtopyTR2.rh-180130082919.log
--
rm $MLF
rm /tmp/selxavg3-sess-10173.m
if ( ! -e $okfile ) then
if ( ! -e /tmp/selxavg3-sess-10173.ok ) then
echo "ERROR: fast_selxavg3() failed\n" ;
echo ERROR: fast_selxavg3() failed\n
ERROR: fast_selxavg3() failed\n
exit 1 ;
exit 1

The analysis folder it is referring to( rtopyTR2.rh) is in the directory from 
which I am calling selxavg3-sess. It has the analysis.info file in which 
doesn't have any restrictions. To troubleshoot, I moved the folder to inside 
the session's functional directory and inside the session folder and these 
didn't create any changes. I looked at the script and tried to debug there but 
didn't give any results. It gave a similar error when trying to open the config 
file of contrast in mkcontrast-sess. (I also don't have root access)Any help is 
appreciated!

Best,
Idil





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[Freesurfer] fast_selxavg3.m error/analysis.info file

2018-01-30 Thread Yagmur Ozdemir 19

Hello FreeSurfer experts,

I am getting this strange error when running selxavg3-sess. (in selxavg3
command I am calling the analysis file with: -a rtopyTR2.rh) When the system
enters fast_selxavg3, it cannot read analysis.info, thus produces the following
output:

#@# Sess05 ###
/home/vm01/local/freesurfer/Project_bold/Sess05
-
$Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $
-
outtop = /home/vm01/local/freesurfer/Project_bold
Extension format = nii.gz
ERROR: could not open rtopyTR2.rh/analysis.info
else
else
echo "--" | tee -a $LF
echo --
tee -a
/home/vm01/local/freesurfer/Project_bold/log/selxavg3-sess-bold-rtopyTR2.rh-180130082919.log
--
rm $MLF
rm /tmp/selxavg3-sess-10173.m
if ( ! -e $okfile ) then
if ( ! -e /tmp/selxavg3-sess-10173.ok ) then
echo "ERROR: fast_selxavg3() failed\n" ;
echo ERROR: fast_selxavg3() failed\n
ERROR: fast_selxavg3() failed\n
exit 1 ;
exit 1

The analysis folder it is referring to( rtopyTR2.rh) is in the directory from
which I am calling selxavg3-sess. It has the analysis.info file in which
doesn't have any restrictions. To troubleshoot, I moved the folder to inside
the session's functional directory and inside the session folder and these
didn't create any changes. I looked at the script and tried to debug there but
didn't give any results. It gave a similar error when trying to open the config
file of contrast in mkcontrast-sess. (I also don't have root access)Any help is
appreciated!

Best,
Idil

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Re: [Freesurfer] JRE error in fsfast/matlab

2017-12-13 Thread Yagmur Ozdemir 19

Yes it terminates prematurely.

Best
Idil

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Wednesday, December 13, 2017 5:50 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] JRE error in fsfast/matlab

By default the graphics are turned off when running selxavg-sess. I often see 
that error message, but it never ends up causing the program to terminate. Is 
your process terminating prematurely?

On 12/13/17 10:24 AM, Yagmur Ozdemir 19 wrote:
Hello FreeSurfer experts,

I have been running into a matlab-related problem that I was wondering if 
anyone came across. I am using Matlab2017b with Freesurfer 6.0. Whenever I run 
selxavg-sess<https://surfer.nmr.mgh.harvard.edu/fswiki/selxavg-sess> command, 
the matlab tries to find the OpenGL rendering, then gives a Java fatal error 
with a failure to find the Java Runtime Environment and exits. (I don't have 
the command outputs with me right now, sorry.) I have been trying to fix it 
with getting a better graphics card, OpenGL, getting Octave etc but this error 
didn't come up when I was using an earlier version of Matlab. I would 
appreciate any help.

Best
Idil

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[Freesurfer] JRE error in fsfast/matlab

2017-12-13 Thread Yagmur Ozdemir 19

Hello FreeSurfer experts,

I have been running into a matlab-related problem that I was wondering if 
anyone came across. I am using Matlab2017b with Freesurfer 6.0. Whenever I run 
selxavg-sess command, 
the matlab tries to find the OpenGL rendering, then gives a Java fatal error 
with a failure to find the Java Runtime Environment and exits. (I don't have 
the command outputs with me right now, sorry.) I have been trying to fix it 
with getting a better graphics card, OpenGL, getting Octave etc but this error 
didn't come up when I was using an earlier version of Matlab. I would 
appreciate any help.

Best
Idil
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Re: [Freesurfer] % overlap of multiple labels

2017-11-20 Thread Yagmur Ozdemir 19

Yes, that was actually what I meant.

Thank you!
Idil

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Tuesday, November 21, 2017 12:14 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] % overlap of multiple labels

I'm not sure I really understand your question.  For the annotation case it
reads the color table out of the annotation file (it is stored in the
header), then gots through every annotation in the table in order and
computes overlap

  On Mon, 20 Nov 2017,
Yagmur Ozdemir 19 wrote:

> Dr. Fischl,
>
> Thank you for the suggestion, I believe a --label-list option still does a 
> one-on-one comparison but I will think about it.
> Another question: in the annotation file option, does the script look at the 
> names of labels in the annotation file to match labels across annotation 
> files for comparison or does it proceed from the list ordering?
>
> Best
> Idil
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
> [fis...@nmr.mgh.harvard.edu]
> Sent: Saturday, November 18, 2017 5:43 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] % overlap of multiple labels
>
> Hi Idil
>
> I think you can use --label-list for multiple labels, or stuff them into
> annot files and it should do everything it finds.
>
> cheers
> Bruce
> On Fri, 17 Nov 2017,
> Yagmur Ozdemir 19 wrote:
>
>> Hello Freesurfer experts,
>>
>> I am using the mris_compute_parc_overlap command to compute the % overlap of 
>> two labels of the same
>> region. Is there a way to do this for multiple labels?
>>
>> Best
>> Idil
>>
>>
>>
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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.
>
>
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>
>
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Re: [Freesurfer] % overlap of multiple labels

2017-11-20 Thread Yagmur Ozdemir 19

Dr. Fischl,

Thank you for the suggestion, I believe a --label-list option still does a 
one-on-one comparison but I will think about it. 
Another question: in the annotation file option, does the script look at the 
names of labels in the annotation file to match labels across annotation files 
for comparison or does it proceed from the list ordering?

Best
Idil

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Saturday, November 18, 2017 5:43 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] % overlap of multiple labels

Hi Idil

I think you can use --label-list for multiple labels, or stuff them into
annot files and it should do everything it finds.

cheers
Bruce
On Fri, 17 Nov 2017,
Yagmur Ozdemir 19 wrote:

> Hello Freesurfer experts,
>
> I am using the mris_compute_parc_overlap command to compute the % overlap of 
> two labels of the same
> region. Is there a way to do this for multiple labels?
>
> Best
> Idil
>
>
>
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[Freesurfer] % overlap of multiple labels

2017-11-17 Thread Yagmur Ozdemir 19

Hello Freesurfer experts,

I am using the mris_compute_parc_overlap command to compute the % overlap of 
two labels of the same region. Is there a way to do this for multiple labels?

Best
Idil

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Re: [Freesurfer] register.dof6.dat file missing with register-sess

2017-10-16 Thread Yagmur Ozdemir 19

I am using version 6.0.0 and this is made from scratch. Just a couple of days 
ago I processed a different subject but used the special retinotopy procedure 
and didn't come across this problem. I first noticed this error in selxavg-sess 
and went back and used mkbrainmask, register-sess and preprocessed a couple of 
times again with -force and either per-run or -session to try troubleshooting.

Idil

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Monday, October 16, 2017 6:18 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] register.dof6.dat file missing with register-sess


which version of FS are you using? Is this a new analysis done from scratch or 
had you preprocessed before?

On 10/15/17 4:10 PM, Yagmur Ozdemir 19 wrote:
Hello Freesurfer experts,

After I run preproc-sess with this command (
 preproc-sess -surface self lhrh -fwhm 5 -fsd Retinotopy -per-run -s Sess01 -s 
Sess02 ), I get an error saying that the register.dof6.dat file is missing and 
I should run register-sess to create it. When I run this with the debug option 
(register-sess -s Sess01 -s Sess02 -d . -fsd bold -per-run -debug) the system 
again fails to create the register file and gives pretty much the same error 
preproc-sess spit out:

MinCost:
tkregister2_cmdl --mov bold/002/template.nii.gz --reg 
bold/002/register.dof6.dat --noedit --ltaout bold/002/register.dof6.lta
regio_read_register(): No such file or directory
Could not open bold/002/register.dof6.dat
tkregister_tcl /home/cemnl-cmap/Desktop/freesurfer/tktools/tkregister2.tcl
INFO: no target volume specified, assuming FreeSurfer orig volume.
target  volume orig
movable volume bold/002/template.nii.gz
reg file   bold/002/register.dof6.dat
LoadVol0
ZeroCRAS   0
$Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $
Diagnostic Level -1
ERROR: reading bold/002/register.dof6.dat
Cleaning up

I thought of manually creating it with bbregister command but  I am not sure 
about which scan I should use for "volume used for motion correction," and I 
would rather prefer to fix this with preproc-sess command.

Also I attached a portion from file "register.dof6.dat.log" file I could get 
for my each run. I hope these excerpts help. I would deeply appreciate any help.

Best,
Idil


COREGpreproc() done
Testing if mov and target overlap
Numerical result out of range
mri_segreg --mov bold/002/tmp.bbregister.12926/template.nii --init-reg 
bold/002/tmp.bbregister.12926/reg.init.dat --out-reg 
bold/002/tmp.bbregister.12926/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 
--tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 
--gm-gt-wm 0.5
regio_read_register(): No such file or directory
Could not open bold/002/tmp.bbregister.12926/reg.init.dat
mri_segreg --mov bold/002/tmp.bbregister.12926/template.nii --init-reg 
bold/002/tmp.bbregister.12926/bbr.pass1.dat --out-reg 
bold/002/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 
--tol1d 1e-3 --c0 0 --mincost bold/002/register.dof6.dat.mincost --dof 6 --nmax 
36 --param bold/002/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 
--cur-reg bold/002/tmp.bbregister.12926/reg.curopt.dat --gm-proj-frac 0.5 
--nsub 1 --gm-gt-wm 0.5
regio_read_register(): No such file or directory
Could not open bold/002/tmp.bbregister.12926/bbr.pass1.dat
MinCost:
tkregister2_cmdl --mov bold/002/template.nii.gz --reg 
bold/002/register.dof6.dat --noedit --ltaout bold/002/register.dof6.lta
tkregister_tcl /home/cemnl-cmap/Desktop/freesurfer/tktools/tkregister2.tcl
INFO: no target volume specified, assuming FreeSurfer orig volume.
target  volume orig
movable volume bold/002/template.nii.gz
reg file   bold/002/register.dof6.dat
LoadVol0
ZeroCRAS   0
$Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $
Diagnostic Level -1
ERROR: reading bold/002/register.dof6.dat
Cleaning up

Started at Sun Oct 15 15:32:07 EDT 2017
Ended   at Sun Oct 15 15:32:41 EDT 2017
BBR-Run-Time-Sec 34

bbregister Done
To check results, run:
tkregisterfv --mov bold/002/template.nii.gz --reg bold/002/register.dof6.lta 
--surfs



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[Freesurfer] register.dof6.dat file missing with register-sess

2017-10-15 Thread Yagmur Ozdemir 19

Hello Freesurfer experts,

After I run preproc-sess with this command (
 preproc-sess -surface self lhrh -fwhm 5 -fsd Retinotopy -per-run -s Sess01 -s 
Sess02 ), I get an error saying that the register.dof6.dat file is missing and 
I should run register-sess to create it. When I run this with the debug option 
(register-sess -s Sess01 -s Sess02 -d . -fsd bold -per-run -debug) the system 
again fails to create the register file and gives pretty much the same error 
preproc-sess spit out:

MinCost:
tkregister2_cmdl --mov bold/002/template.nii.gz --reg 
bold/002/register.dof6.dat --noedit --ltaout bold/002/register.dof6.lta
regio_read_register(): No such file or directory
Could not open bold/002/register.dof6.dat
tkregister_tcl /home/cemnl-cmap/Desktop/freesurfer/tktools/tkregister2.tcl
INFO: no target volume specified, assuming FreeSurfer orig volume.
target  volume orig
movable volume bold/002/template.nii.gz
reg file   bold/002/register.dof6.dat
LoadVol0
ZeroCRAS   0
$Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $
Diagnostic Level -1
ERROR: reading bold/002/register.dof6.dat
Cleaning up

I thought of manually creating it with bbregister command but  I am not sure 
about which scan I should use for "volume used for motion correction," and I 
would rather prefer to fix this with preproc-sess command.

Also I attached a portion from file "register.dof6.dat.log" file I could get 
for my each run. I hope these excerpts help. I would deeply appreciate any help.

Best,
Idil


COREGpreproc() done
Testing if mov and target overlap
Numerical result out of range
mri_segreg --mov bold/002/tmp.bbregister.12926/template.nii --init-reg 
bold/002/tmp.bbregister.12926/reg.init.dat --out-reg 
bold/002/tmp.bbregister.12926/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 
--tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 
--gm-gt-wm 0.5
regio_read_register(): No such file or directory
Could not open bold/002/tmp.bbregister.12926/reg.init.dat
mri_segreg --mov bold/002/tmp.bbregister.12926/template.nii --init-reg 
bold/002/tmp.bbregister.12926/bbr.pass1.dat --out-reg 
bold/002/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 
--tol1d 1e-3 --c0 0 --mincost bold/002/register.dof6.dat.mincost --dof 6 --nmax 
36 --param bold/002/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 
--cur-reg bold/002/tmp.bbregister.12926/reg.curopt.dat --gm-proj-frac 0.5 
--nsub 1 --gm-gt-wm 0.5
regio_read_register(): No such file or directory
Could not open bold/002/tmp.bbregister.12926/bbr.pass1.dat
MinCost:
tkregister2_cmdl --mov bold/002/template.nii.gz --reg 
bold/002/register.dof6.dat --noedit --ltaout bold/002/register.dof6.lta
tkregister_tcl /home/cemnl-cmap/Desktop/freesurfer/tktools/tkregister2.tcl
INFO: no target volume specified, assuming FreeSurfer orig volume.
target  volume orig
movable volume bold/002/template.nii.gz
reg file   bold/002/register.dof6.dat
LoadVol0
ZeroCRAS   0
$Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $
Diagnostic Level -1
ERROR: reading bold/002/register.dof6.dat
Cleaning up

Started at Sun Oct 15 15:32:07 EDT 2017
Ended   at Sun Oct 15 15:32:41 EDT 2017
BBR-Run-Time-Sec 34

bbregister Done
To check results, run:
tkregisterfv --mov bold/002/template.nii.gz --reg bold/002/register.dof6.lta 
--surfs
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Re: [Freesurfer] generating automatic functional label

2017-09-27 Thread Yagmur Ozdemir 19

Hello Dr. Greve,

Sorry for the late response; I thought my initial description was enough. 

As far as I understand, the fMRI version of this code would automatically 
define an ROI based on cluster-extent based tresholding of functional data that 
contains the significant regions. Then loads a selected anatomical ROI(like a 
label) for comparison with this functional area, and I am not entirely sure how 
this comparison works but at the end outputs, I guess, an estimation of this 
area and produces an anatomical+functional "label." The anatomical label it 
uses comes from Freesurfer and I found this code in a website related to 
Martinos center (https://martinos.org/mne/stable/index.html) so I wanted to 
take my chances for asking about it here. I am basically looking for a way to 
define ROIs automatically in freesurfer. 

Best,
Idil 

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Tuesday, September 26, 2017 12:53 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] generating automatic functional label

Hi Idil, I'm not going to plow through someone else's code:) If you want
to summarize what it does, I might be able to figure out if we have
something that does it.

On 09/25/2017 03:21 PM, Yagmur Ozdemir 19 wrote:
> Hello FreeSurfer developers,
>
> This is a piece of code I came across for producing a functional label
> with using time course estimates from  MEG/EEG data, for freesurfer
> use. I am wondering if something similar is available to estimate a
> functional label/region from fMRI data with similar tresholding.
>
> https://martinos.org/mne/stable/auto_examples/inverse/plot_label_from_stc.html#generate-a-functional-label-from-source-estimates
>
> Best,
> Idil
>
>
> ___
> 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/

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[Freesurfer] generating automatic functional label

2017-09-25 Thread Yagmur Ozdemir 19

Hello FreeSurfer developers,

This is a piece of code I came across for producing a functional label with 
using time course estimates from  MEG/EEG data, for freesurfer use. I am 
wondering if something similar is available to estimate a functional 
label/region from fMRI data with similar tresholding.

https://martinos.org/mne/stable/auto_examples/inverse/plot_label_from_stc.html#generate-a-functional-label-from-source-estimates

Best,
Idil
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Re: [Freesurfer] Matlab(?) failure in selxavg3-sess

2017-09-20 Thread Yagmur Ozdemir 19

Also I should add: I am running freesurfer from a Linux subsystem for Windows. 
Matlab was installed to Windows before obtaining freesurfer. 

Best,
Idil 

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Yagmur Ozdemir 19 
[yozdemi...@amherst.edu]
Sent: Thursday, September 21, 2017 12:16 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Matlab(?) failure in selxavg3-sess

It says that it's not on the path. I thought export MATLAB would fix that issue 
but apparently not.

Best,
Idil

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Wednesday, September 20, 2017 11:42 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Matlab(?) failure in selxavg3-sess

what happens if you run the getmatlab command?


If you don't have a startup.m, then create one


On 09/20/2017 04:34 PM, Yagmur Ozdemir 19 wrote:
> Hello freesurfer experts,
>
> When I run the selxavg3-sess command (for retinotopy) , the command
> exits with this
> "fast_selxavg3b('/mnt/c/Users/yagmuridil/Desktop/freesurfer/Project/Sess01/bold/rtopy.self.lh/sxa3.config.txt')
> if(~fast_fileexists('/tmp/selxavg3-sess-3166.ok')); quit; end"
> and then gives a "Matlab: Command not found" error. Can anyone help me
> troubleshoot this? I initially thought there was a problem with the
> system recognizing the Matlab in my computer, I tried to export a
> Matlab home, and tried to follow the steps here
> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg05046.html
> but my ~/matlab folder doesn't have a startup.m file.
>
> >>1/1 /mnt/c/Users/yagmuridil/Desktop/freesurfer/Project/Sess01
> Çrş Eyl 20 16:17:28 DST 2017
> anadir =
> /mnt/c/Users/yagmuridil/Desktop/freesurfer/Project/Sess01/bold/rtopy.self.lh
> DoGLMFit = 1
> DoContrasts = 1
> UpdateNeeded = 1
> Sess01 Update needed
> /mnt/c/Users/yagmuridil/Desktop/freesurfer/Project/Sess01/bold/rtopy.self.lh/sxa3.config.txt
> MLF is /tmp/selxavg3-sess-3166.m
> --
> % Çrş Eyl 20 16:17:26 DST 2017
> % /mnt/c/Users/yagmuridil/Desktop/freesurfer/Project
> %  rtopy.self.lh
> which fast_selxavg3
> which fast_ldanaflac
> which MRIread
>
>
> fast_selxavg3b('/mnt/c/Users/yagmuridil/Desktop/freesurfer/Project/Sess01/bold/rtopy.self.lh/sxa3.config.txt')
> if(~fast_fileexists('/tmp/selxavg3-sess-3166.ok')); quit; end
> %
>
>
> quit;
> --
> --
> --- matlab output 
> matlab: Command not found.
> --
> ERROR: fast_selxavg3() failed\n
>
>
> Thank you,
> Idil
>
>
>
>
>
>
>
> ___
> 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/

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contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] Matlab(?) failure in selxavg3-sess

2017-09-20 Thread Yagmur Ozdemir 19

It says that it's not on the path. I thought export MATLAB would fix that issue 
but apparently not. 

Best,
Idil 

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Wednesday, September 20, 2017 11:42 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Matlab(?) failure in selxavg3-sess

what happens if you run the getmatlab command?


If you don't have a startup.m, then create one


On 09/20/2017 04:34 PM, Yagmur Ozdemir 19 wrote:
> Hello freesurfer experts,
>
> When I run the selxavg3-sess command (for retinotopy) , the command
> exits with this
> "fast_selxavg3b('/mnt/c/Users/yagmuridil/Desktop/freesurfer/Project/Sess01/bold/rtopy.self.lh/sxa3.config.txt')
> if(~fast_fileexists('/tmp/selxavg3-sess-3166.ok')); quit; end"
> and then gives a "Matlab: Command not found" error. Can anyone help me
> troubleshoot this? I initially thought there was a problem with the
> system recognizing the Matlab in my computer, I tried to export a
> Matlab home, and tried to follow the steps here
> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg05046.html
> but my ~/matlab folder doesn't have a startup.m file.
>
> >>1/1 /mnt/c/Users/yagmuridil/Desktop/freesurfer/Project/Sess01
> Çrş Eyl 20 16:17:28 DST 2017
> anadir =
> /mnt/c/Users/yagmuridil/Desktop/freesurfer/Project/Sess01/bold/rtopy.self.lh
> DoGLMFit = 1
> DoContrasts = 1
> UpdateNeeded = 1
> Sess01 Update needed
> /mnt/c/Users/yagmuridil/Desktop/freesurfer/Project/Sess01/bold/rtopy.self.lh/sxa3.config.txt
> MLF is /tmp/selxavg3-sess-3166.m
> --
> % Çrş Eyl 20 16:17:26 DST 2017
> % /mnt/c/Users/yagmuridil/Desktop/freesurfer/Project
> %  rtopy.self.lh
> which fast_selxavg3
> which fast_ldanaflac
> which MRIread
>
>
> fast_selxavg3b('/mnt/c/Users/yagmuridil/Desktop/freesurfer/Project/Sess01/bold/rtopy.self.lh/sxa3.config.txt')
> if(~fast_fileexists('/tmp/selxavg3-sess-3166.ok')); quit; end
> %
>
>
> quit;
> --
> --
> --- matlab output 
> matlab: Command not found.
> --
> ERROR: fast_selxavg3() failed\n
>
>
> Thank you,
> Idil
>
>
>
>
>
>
>
> ___
> 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/

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The information in this e-mail is intended only for the person to whom it is
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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
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[Freesurfer] Matlab(?) failure in selxavg3-sess

2017-09-20 Thread Yagmur Ozdemir 19

Hello freesurfer experts,

When I run the selxavg3-sess command (for retinotopy) , the command exits with 
this
"fast_selxavg3b('/mnt/c/Users/yagmuridil/Desktop/freesurfer/Project/Sess01/bold/rtopy.self.lh/sxa3.config.txt')
if(~fast_fileexists('/tmp/selxavg3-sess-3166.ok')); quit; end"
and then gives a "Matlab: Command not found" error. Can anyone help me 
troubleshoot this? I initially thought there was a problem with the system 
recognizing the Matlab in my computer, I tried to export a Matlab home, and 
tried to follow the steps here 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg05046.html but 
my ~/matlab folder doesn't have a startup.m file.

>>1/1 /mnt/c/Users/yagmuridil/Desktop/freesurfer/Project/Sess01
Çrş Eyl 20 16:17:28 DST 2017
anadir = 
/mnt/c/Users/yagmuridil/Desktop/freesurfer/Project/Sess01/bold/rtopy.self.lh
DoGLMFit = 1
DoContrasts = 1
UpdateNeeded = 1
Sess01 Update needed
/mnt/c/Users/yagmuridil/Desktop/freesurfer/Project/Sess01/bold/rtopy.self.lh/sxa3.config.txt
MLF is /tmp/selxavg3-sess-3166.m
--
% Çrş Eyl 20 16:17:26 DST 2017
% /mnt/c/Users/yagmuridil/Desktop/freesurfer/Project
%  rtopy.self.lh
which fast_selxavg3
which fast_ldanaflac
which MRIread


fast_selxavg3b('/mnt/c/Users/yagmuridil/Desktop/freesurfer/Project/Sess01/bold/rtopy.self.lh/sxa3.config.txt')
if(~fast_fileexists('/tmp/selxavg3-sess-3166.ok')); quit; end
%


quit;
--
--
--- matlab output 
matlab: Command not found.
--
ERROR: fast_selxavg3() failed\n


Thank you,
Idil





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Re: [Freesurfer] mask alignment problem/mri_mask

I looked at their orientation differences using mri_info and used this command;
mri_convert --in_orientation LIA --out_orientation AIL native.template.mgh 
native.corrected.nii
But still there is an alignment problem. Looks like the  xform info differs so 
can I use the mri_mask command with specifying the xform option?

This info is for the mask volume I want to use;
  type: MGH
dimensions: 256 x 256 x 256
   voxel sizes: 1.00, 1.00, 1.00
  type: FLOAT (3)
   fov: 256.000
   dof: 0
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -128.0, zend: 128.0
TR: 1000.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 
degrees
   nframes: 1
   PhEncDir: UNKNOWN
   FieldStrength: 0.00
ras xform present
xform info: x_r =  -1., y_r =   0., z_r =  -0., c_r = 3.2153
  : x_a =   0., y_a =  -0., z_a =   1., c_a =   -10.8083
  : x_s =  -0., y_s =  -1., z_s =   0., c_s =-8.7367

talairach xfm : 
Orientation   : LIA
Primary Slice Direction: coronal

voxel to ras transform:
   -1.   0.  -0.   131.2153
0.  -0.   1.  -138.8083
   -0.  -1.   0.   119.2633
0.   0.   0. 1.

voxel-to-ras determinant -1

ras to voxel transform:
   -1.  -0.   0.   131.2153
0.   0.  -1.   119.2633
0.   1.  -0.   138.8084
   -0.  -0.  -0. 1.

This information is of the volume file I want to overlay the mask on;

Volume information for MW_IIHC_aTAL.nii
  type: nii
dimensions: 256 x 256 x 256
   voxel sizes: 1.00, 1.00, 1.00
  type: FLOAT (3)
   fov: 256.000
   dof: 0
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -128.0, zend: 128.0
TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 
degrees
   nframes: 1
   PhEncDir: UNKNOWN
   FieldStrength: 0.00
ras xform present
xform info: x_r =  -0.0553, y_r =   0.0101, z_r =  -0.9984, c_r =-3.7597
  : x_a =   0.9863, y_a =   0.1563, z_a =  -0.0530, c_a =11.9244
  : x_s =   0.1555, y_s =  -0.9877, z_s =  -0.0186, c_s =-9.5782
Orientation   : AIL
Primary Slice Direction: sagittal

voxel to ras transform:
   -0.0553   0.0101  -0.9984   129.8205
0.9863   0.1563  -0.0530  -127.5422
0.1555  -0.9877  -0.018699.3136
0.   0.   0. 1.

voxel-to-ras determinant 1

ras to voxel transform:
   -0.0553   0.9863   0.1555   117.5212
0.0101   0.1563  -0.9877   116.7140
   -0.9984  -0.0530  -0.0186   124.7003
0.   0.   0. 1.

Best,
Idil

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Yagmur Ozdemir 19 
[yozdemi...@amherst.edu]
Sent: Thursday, August 17, 2017 7:07 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] mask alignment problem/mri_mask

Yes; sorry. The mask is created by an applied docker image which produced 
volume and surface files of the template in both the brain's native and 
freesurfer origin orientation. MW_IIHC_aTAL.nii is the brain file of the same 
subject I exported from another software-I am hoping to export the template 
eventually to use in there-. native.template.mgh is the template file produced 
by the docker; it is the red/orange areas in the picture I sent. 
native.orientation.mgh is just a random name I gave to the output file.

Best,
Idil

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Thursday, August 17, 2017 7:03 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] mask alignment problem/mri_mask

Hi Idil

you need to give us much more information to be able to help you. How did
you create the mask? Why volume to you expect it to be in register with?
What are the volumes MW_IIHC_aTAL.nii native.template.mgh  and
native.orientation.mgh ?

Bruce


On Thu, 17 Aug 2017, Yagmur Ozdemir 19 wrote:

> It seems to be in the right orientation now but there is still an alignment 
> problem; the mask is too far off from the brain. Sorry to be constantly 
> asking questions; but do you have any suggestions onto how to fix this?
>
> Best,
> Idil
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
> [fis...@nmr.mgh.harvard.edu]
> Sent: Thursday, August 17, 2017 6:55 PM
> To: Freesurfer support l

Re: [Freesurfer] mask alignment problem/mri_mask

Yes; sorry. The mask is created by an applied docker image which produced 
volume and surface files of the template in both the brain's native and 
freesurfer origin orientation. MW_IIHC_aTAL.nii is the brain file of the same 
subject I exported from another software-I am hoping to export the template 
eventually to use in there-. native.template.mgh is the template file produced 
by the docker; it is the red/orange areas in the picture I sent. 
native.orientation.mgh is just a random name I gave to the output file.

Best,
Idil

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Thursday, August 17, 2017 7:03 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] mask alignment problem/mri_mask

Hi Idil

you need to give us much more information to be able to help you. How did
you create the mask? Why volume to you expect it to be in register with?
What are the volumes MW_IIHC_aTAL.nii native.template.mgh  and
native.orientation.mgh ?

Bruce


On Thu, 17 Aug 2017, Yagmur Ozdemir 19 wrote:

> It seems to be in the right orientation now but there is still an alignment 
> problem; the mask is too far off from the brain. Sorry to be constantly 
> asking questions; but do you have any suggestions onto how to fix this?
>
> Best,
> Idil
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
> [fis...@nmr.mgh.harvard.edu]
> Sent: Thursday, August 17, 2017 6:55 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] mask alignment problem/mri_mask
>
> if you want to reslice the mask to be like a template volume, use "-rl"
> instead of "-at"
>
> cheers
> Bruce
> On Thu, 17 Aug 2017, Yagmur Ozdemir 19 wrote:
>
>> I do not have a transform file I can use so I was wondering if I can simply 
>> use the volume file I am trying to adapt the mask to as the transform file 
>> in the -at option. But looks like I cannot;
>>
>> mri_convert -at MW_IIHC_aTAL.nii native.template.mgh native.orientation.mgh
>> mri_convert.bin -at MW_IIHC_aTAL.nii native.template_.mgh 
>> native.orientation.mgh
>> $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
>> reading from native.template.mgh...
>> TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
>> i_ras = (-1, 0, -9.31323e-10)
>> j_ras = (0, -1.49012e-08, -1)
>> k_ras = (-1.62981e-09, 1, 1.49012e-08)
>> INFO: Reading transformation from file MW_IIHC_aTAL.nii...
>> Reading transform with LTAreadEx()
>> INFO: This REGISTER_DAT transform is valid only for volumes between  COR 
>> types with c_(r,a,s) = 0.
>> regio_read_register(): No such file or directory
>> Error reading inplaneres from MW_IIHC_aTAL.nii
>> ltaReadRegisterDat: could not read MW_IIHC_aTAL.nii
>> No such file or directory
>> ERROR: Reading transform from file MW_IIHC_aTAL.nii
>>
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
>> [fis...@nmr.mgh.harvard.edu]
>> Sent: Thursday, August 17, 2017 6:50 PM
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] mask alignment problem/mri_mask
>>
>> sorry, I don't understand
>> Bruce
>> On Thu, 17 Aug 2017, Yagmur Ozdemir 19 wrote:
>>
>>> Thank you!
>>>
>>> Then I guess I would use the volume as the transform file to convert my 
>>> mask.
>>>
>>> Best,
>>> Idil
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
>>> [fis...@nmr.mgh.harvard.edu]
>>> Sent: Thursday, August 17, 2017 6:41 PM
>>> To: Freesurfer support list
>>> Subject: Re: [Freesurfer] mask alignment problem/mri_mask
>>>
>>> ok, but your mri_mask command line has the string "%s" in it, which is
>>> not correct. You need to specify an actual file name. I also think you
>>> are better off using mri_convert -at   to map
>>> the mask into the right coordinate system so that you can then view it in
>>> freeview to make sure it is correct
>>>
>>> cheers
>>> Bruce
>>> On Thu, 17 Aug 2017, Yagmur Ozdemir 19
>>> wrote:
>>>
>>>> The mask in volume format was created using a docker image and it works 
>>>> well both with my freesurfer origin and native volume files; the one that

Re: [Freesurfer] mask alignment problem/mri_mask

I do not have a transform file I can use so I was wondering if I can simply use 
the volume file I am trying to adapt the mask to as the transform file in the 
-at option. But looks like I cannot;

mri_convert -at MW_IIHC_aTAL.nii native.template.mgh native.orientation.mgh
mri_convert.bin -at MW_IIHC_aTAL.nii native.template_.mgh 
native.orientation.mgh 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from native.template.mgh...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, -9.31323e-10)
j_ras = (0, -1.49012e-08, -1)
k_ras = (-1.62981e-09, 1, 1.49012e-08)
INFO: Reading transformation from file MW_IIHC_aTAL.nii...
Reading transform with LTAreadEx()
INFO: This REGISTER_DAT transform is valid only for volumes between  COR types 
with c_(r,a,s) = 0.
regio_read_register(): No such file or directory
Error reading inplaneres from MW_IIHC_aTAL.nii
ltaReadRegisterDat: could not read MW_IIHC_aTAL.nii
No such file or directory
ERROR: Reading transform from file MW_IIHC_aTAL.nii


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Thursday, August 17, 2017 6:50 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] mask alignment problem/mri_mask

sorry, I don't understand
Bruce
On Thu, 17 Aug 2017, Yagmur Ozdemir 19 wrote:

> Thank you!
>
> Then I guess I would use the volume as the transform file to convert my mask.
>
> Best,
> Idil
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
> [fis...@nmr.mgh.harvard.edu]
> Sent: Thursday, August 17, 2017 6:41 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] mask alignment problem/mri_mask
>
> ok, but your mri_mask command line has the string "%s" in it, which is
> not correct. You need to specify an actual file name. I also think you
> are better off using mri_convert -at   to map
> the mask into the right coordinate system so that you can then view it in
> freeview to make sure it is correct
>
> cheers
> Bruce
> On Thu, 17 Aug 2017, Yagmur Ozdemir 19
> wrote:
>
>> The mask in volume format was created using a docker image and it works well 
>> both with my freesurfer origin and native volume files; the one that it 
>> doesn't align with is the volume file I am trying to adapt to/from a 
>> different software. The command line I used for transforming is this;
>>
>> mri_vol2vol --mov native.template_areas.mgh --targ MW_IIHC_aTAL.nii 
>> --regheader --o template.mgz --no-save-reg
>>
>> Best,
>> Idil
>>
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
>> [fis...@nmr.mgh.harvard.edu]
>> Sent: Thursday, August 17, 2017 6:14 PM
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] mask alignment problem/mri_mask
>>
>> Hi Idil
>>
>> how did you create the mask and the transform? Also, you can't specify "%s"
>> on the command line - you need an actual name of a transform file.
>>
>> cheers
>> Bruce
>>
>>
>>
>>
>> On Thu, 17 Aug 2017, Yagmur Ozdemir
>> 19 wrote:
>>
>>> Hello freesurfer experts,
>>>
>>> A volume file I want to save as a mask(the orange/red shaded areas in the
>>> picture) on top of my volume file does not align as seen in the picture. I
>>> have used mri_vol2vol to align the mask to my native volume but apparently
>>> it did not work out. I am trying to correct this by using mri_mask now;  I
>>> tried to use the option -xform %s which apparently applies the LTA transform
>>> to align mask to input volume, but now I get this error;
>>>
>>>>> lab@lab-ThinkStation-E31:~/Desktop/freesurfer/subjects/sub-01_MW/mri$
>>> mri_mask -xform %s MW_IIHC_aTAL.nii native.areas_MW_aTAL.nii
>>> MW_aTAl_masked.nii
>>> transform file name is %s
>>> WARNING: hdr.dim[4] = 0 (nframes), setting to 1
>>> niiRead(): NIFTI_UNITS_UNKNOWN, assuming mm
>>> DoAbs = 0
>>> Apply the given LTA xfrom to the mask volume
>>> Reading transform ...
>>> ltaReadFile(%s): can't open file
>>> No such file or directory
>>> mri_mask.bin: could not read transform file %s
>>> No such file or directory
>>>
>>>
>>> I would deeply appreciate if someone could help me sort out this mess.
>>>
>>> Thank you all!
>>> Best,
>>> Idil
>>>
>

Re: [Freesurfer] mask alignment problem/mri_mask

Thank you!

Then I guess I would use the volume as the transform file to convert my mask.

Best,
Idil

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Thursday, August 17, 2017 6:41 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] mask alignment problem/mri_mask

ok, but your mri_mask command line has the string "%s" in it, which is
not correct. You need to specify an actual file name. I also think you
are better off using mri_convert -at   to map
the mask into the right coordinate system so that you can then view it in
freeview to make sure it is correct

cheers
Bruce
On Thu, 17 Aug 2017, Yagmur Ozdemir 19
wrote:

> The mask in volume format was created using a docker image and it works well 
> both with my freesurfer origin and native volume files; the one that it 
> doesn't align with is the volume file I am trying to adapt to/from a 
> different software. The command line I used for transforming is this;
>
> mri_vol2vol --mov native.template_areas.mgh --targ MW_IIHC_aTAL.nii 
> --regheader --o template.mgz --no-save-reg
>
> Best,
> Idil
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
> [fis...@nmr.mgh.harvard.edu]
> Sent: Thursday, August 17, 2017 6:14 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] mask alignment problem/mri_mask
>
> Hi Idil
>
> how did you create the mask and the transform? Also, you can't specify "%s"
> on the command line - you need an actual name of a transform file.
>
> cheers
> Bruce
>
>
>
>
> On Thu, 17 Aug 2017, Yagmur Ozdemir
> 19 wrote:
>
>> Hello freesurfer experts,
>>
>> A volume file I want to save as a mask(the orange/red shaded areas in the
>> picture) on top of my volume file does not align as seen in the picture. I
>> have used mri_vol2vol to align the mask to my native volume but apparently
>> it did not work out. I am trying to correct this by using mri_mask now;  I
>> tried to use the option -xform %s which apparently applies the LTA transform
>> to align mask to input volume, but now I get this error;
>>
>>>> lab@lab-ThinkStation-E31:~/Desktop/freesurfer/subjects/sub-01_MW/mri$
>> mri_mask -xform %s MW_IIHC_aTAL.nii native.areas_MW_aTAL.nii
>> MW_aTAl_masked.nii
>> transform file name is %s
>> WARNING: hdr.dim[4] = 0 (nframes), setting to 1
>> niiRead(): NIFTI_UNITS_UNKNOWN, assuming mm
>> DoAbs = 0
>> Apply the given LTA xfrom to the mask volume
>> Reading transform ...
>> ltaReadFile(%s): can't open file
>> No such file or directory
>> mri_mask.bin: could not read transform file %s
>> No such file or directory
>>
>>
>> I would deeply appreciate if someone could help me sort out this mess.
>>
>> Thank you all!
>> Best,
>> Idil
>>
>>
>
> ___
> 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
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Re: [Freesurfer] mask alignment problem/mri_mask

The mask in volume format was created using a docker image and it works well 
both with my freesurfer origin and native volume files; the one that it doesn't 
align with is the volume file I am trying to adapt to/from a different 
software. The command line I used for transforming is this; 

mri_vol2vol --mov native.template_areas.mgh --targ MW_IIHC_aTAL.nii --regheader 
--o template.mgz --no-save-reg

Best,
Idil

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Thursday, August 17, 2017 6:14 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] mask alignment problem/mri_mask

Hi Idil

how did you create the mask and the transform? Also, you can't specify "%s"
on the command line - you need an actual name of a transform file.

cheers
Bruce

On Thu, 17 Aug 2017, Yagmur Ozdemir
19 wrote:

> Hello freesurfer experts,
>
> A volume file I want to save as a mask(the orange/red shaded areas in the
> picture) on top of my volume file does not align as seen in the picture. I
> have used mri_vol2vol to align the mask to my native volume but apparently
> it did not work out. I am trying to correct this by using mri_mask now;  I
> tried to use the option -xform %s which apparently applies the LTA transform
> to align mask to input volume, but now I get this error;
>
> >>lab@lab-ThinkStation-E31:~/Desktop/freesurfer/subjects/sub-01_MW/mri$
> mri_mask -xform %s MW_IIHC_aTAL.nii native.areas_MW_aTAL.nii
> MW_aTAl_masked.nii
> transform file name is %s
> WARNING: hdr.dim[4] = 0 (nframes), setting to 1
> niiRead(): NIFTI_UNITS_UNKNOWN, assuming mm
> DoAbs = 0
> Apply the given LTA xfrom to the mask volume
> Reading transform ...
> ltaReadFile(%s): can't open file
> No such file or directory
> mri_mask.bin: could not read transform file %s
> No such file or directory
>
>
> I would deeply appreciate if someone could help me sort out this mess.
>
> Thank you all!
> Best,
> Idil
>
>

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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] mri_binarize/mri_mask command help

2017-08-14 Thread Yagmur Ozdemir 19

I tried using it both as an input and output and the produced files both seemed 
wrong, so I was trying different combinations.

The template (a picture of it is attached in my initial email) is a mask for 
primary visual areas, and to export and use it in a different software I am 
trying to superimpose it on top of a complete skull stripped volume file like 
rawavg. I am trying to reconstruct that volume file in that other software 
hoping to visualize the mask on the software's native surface file.

Thank you for the help,
Idil 

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Monday, August 14, 2017 9:36 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_binarize/mri_mask command help

mri_binarize needs a mask or segmentation as input (eg, aparc+aseg.mgz).
can you elaborate on what you are trying to do? what do you mean by a
template?

On 08/11/2017 03:01 PM, Yagmur Ozdemir 19 wrote:
>
> Dear FreeSurfer experts,
>
> I am trying to use the following command to merge the volume file of a
> template with original T1 orientation*, with a file like rawavg to get
> the full brain volume, but the following attached image gets produced
> and I am pretty sure, as a freesurfer novice, I am using a wrong
> command line. I have tried mri_mask as well but do not think it is the
> command to go. I also checked if two volumes are in the same
> orientation using mri_orient.
>
> mri_binarize --i rawavg.mgz --o scanner.template_angle.mgz --wm+vcsf
>
> * (I have the native oriented version of this volume template as well,
> and I attached a photo of the template as well)
>
> I would deeply appreciate if someone could help me correct my command
> line. Thank you all for the time and help
>
> Idil
>
>
> ___
> Freesurfer mailing list
> 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
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] Talairach error

2017-08-10 Thread Yagmur Ozdemir 19

I would prefer to have it run with the tal registration, as I am not entirely 
sure if the registration works ok as it was made in another software, but worst 
case I will try that option. Thank you!

Idil

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Thursday, August 10, 2017 1:18 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Talairach error

It is failing the tal registration check. Does the registration look ok?
If so, then run with -no-talcheck.


On 08/09/2017 02:24 PM, Yagmur Ozdemir 19 wrote:
> Hello FreeSurfer experts,
>
> I have been running into a consistent problem of Talairach alignment
> error in my recon-all for some of my subjects, even though I was able
> to get a completed recon-all for other subjects by using the same
> procedure to obtain my nifti files. I have attached the recon-all logs
> of a successful and a Talairach failed subject respectively, and as I
> try to understand the difference, in the successful one this was tried
> the last: INFO: Trying MINC mritotal to perform Talairach align...
> then failed, then there is a "New invocation of recon-all " which
> succeeded. I do not think I made that invocation. Could someone help
> me figure out what I am missing, and how can I make recon-all continue
> as I somehow did previously?
>
> Thank you so much!
> Idil
>
>
> ___
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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
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] multi-frame input error with PAR/SEC origin file

2017-08-09 Thread Yagmur Ozdemir 19

I tried that and realized the images are very blurry so it probably will not 
run in any case. 

Thank you!
Idil 

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Wednesday, August 09, 2017 1:20 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] multi-frame input error with PAR/SEC origin file

Hi Idil
you have to figure out what the input volume has more than 1 frame (that
is, why is it 4d). It could be because you saved phase and mag, or because
there are multiple echoes, but until you understand what the additional
frames are we can't process it. YOu can start by bringing the orig.mgz up
in freeview and looking at it and seeing what the different frames look
like. If one of them looks like the T1-weighted image and the other doesn't
(maybe it's a phase map?) you would run:

cd  /home/lab/Desktop/freesurfer/subjects/sub-06-error/mri/orig/
mv 001.mgz 001.multiframe.mgz
mri_convert -nth 0 001.multiframe.mgz 001.mgz

assuming that the 0th (first) frame is the T1 weighted. If it was the next
one you would do -nth 1 instead

cheers
Bruce

On Tue, 8 Aug 2017, Yagmur Ozdemir 19 wrote:

> Hello FreeSurfer experts,
>
> I am trying to run recon-all on a nifti file converted from PAR/SEC using
> dcm2niix, and this error came up pretty soon after the script started to
> run;
>
> >> mri_convert.bin
> /home/lab/Desktop/freesurfer/subjects/sub-06_run-01_T1w.nii.gz
> /home/lab/Desktop/freesurfer/subjects/sub-06-error/mri/orig/001.mgz
> $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
> reading from
> /home/lab/Desktop/freesurfer/subjects/sub-06_run-01_T1w.nii.gz...
> TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (-1, 0, 0)
> j_ras = (-0, 0.916013, -0.401149)
> k_ras = (0, 0.401149, 0.916013)
> writing to
> /home/lab/Desktop/freesurfer/subjects/sub-06-error/mri/orig/001.mgz...
> #
> #@# MotionCor Tue Aug  8 17:42:13 EDT 2017
> Found 1 runs
> /home/lab/Desktop/freesurfer/subjects/sub-06-error/mri/orig/001.mgz
> Checking for (invalid) multi-frame inputs...
> ERROR: input(s) cannot have multiple frames!
>
> I am pretty inexperienced with FreeSurfer, but does this error mean I need
> to slice my file? I would really appreciate if someone could give me some
> ideas for commands to use.
>
> Thank you all!
> Best,
> Idil
>
>
>
>

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[Freesurfer] multi-frame input error with PAR/SEC origin file

2017-08-08 Thread Yagmur Ozdemir 19

Hello FreeSurfer experts,

I am trying to run recon-all on a nifti file converted from PAR/SEC using 
dcm2niix, and this error came up pretty soon after the script started to run;

>> mri_convert.bin 
>> /home/lab/Desktop/freesurfer/subjects/sub-06_run-01_T1w.nii.gz 
>> /home/lab/Desktop/freesurfer/subjects/sub-06-error/mri/orig/001.mgz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/lab/Desktop/freesurfer/subjects/sub-06_run-01_T1w.nii.gz...
TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (-0, 0.916013, -0.401149)
k_ras = (0, 0.401149, 0.916013)
writing to 
/home/lab/Desktop/freesurfer/subjects/sub-06-error/mri/orig/001.mgz...
#
#@# MotionCor Tue Aug  8 17:42:13 EDT 2017
Found 1 runs
/home/lab/Desktop/freesurfer/subjects/sub-06-error/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
ERROR: input(s) cannot have multiple frames!

I am pretty inexperienced with FreeSurfer, but does this error mean I need to 
slice my file? I would really appreciate if someone could give me some ideas 
for commands to use.

Thank you all!
Best,
Idil


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Re: [Freesurfer] creating mesh with specifications

2017-07-31 Thread Yagmur Ozdemir 19

That makes sense, I still wanted to see if it is possible as the other software 
I am working with is not flexible. 

Thank you!
Idil 

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Monday, July 31, 2017 6:48 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] creating mesh with specifications

Hi Idil

no, you can't specify all those things as they are defined by the topology
of the surface. You could reduce the number of vertices, but then that will
specify the edges and faces I expect. I'm not aware of any software taht
lets you set all 3, and in fact you can't do all 3 as they need to satisfy
the Euler Number relation. I guess you could in principle constrain 2 of
them and have the 3rd be computed, but I don't think we have anything that
will do that.
sorry
Bruce

On Mon, 31 Jul 2017, Yagmur Ozdemir
19 wrote:

> Hello freesurfer experts,
>
> I am trying to export an inflated surface file and its overlay made in 
> Freesurfer to a different software and it seems like the surface file needs 
> to have a
> particular number of vertices, triangles and average # of neighbors to be 
> compatible. I have used mris_decimate and mris_apply_reg to simplify the 
> files but the
> commands are not specific enough. Is there a way to use those commands in 
> such a way or simply do recon-all with these specified qualities?
>
> Thank you for the help!
> Idil
>
>
>
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[Freesurfer] creating mesh with specifications

2017-07-31 Thread Yagmur Ozdemir 19

Hello freesurfer experts,

I am trying to export an inflated surface file and its overlay made in 
Freesurfer to a different software and it seems like the surface file needs to 
have a particular number of vertices, triangles and average # of neighbors to 
be compatible. I have used mris_decimate and mris_apply_reg to simplify the 
files but the commands are not specific enough. Is there a way to use those 
commands in such a way or simply do recon-all with these specified qualities?

Thank you for the help!
Idil

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Re: [Freesurfer] Segmentation Violation problem in surface files

I just realized I needed lh.inflated in the command. I think it works now. 
Thank you for all the help!

Idil

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Tuesday, July 25, 2017 11:00 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Segmentation Violation problem in surface files

what is your command line?


On 07/25/2017 03:52 PM, Yagmur Ozdemir 19 wrote:
> When I do either of the conversions with mris_convert, the system gives 
> freadFloat: fread failed / No such file or directory then a Segmentation 
> fault error.
>
> Best,
> Idil
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
> [fis...@nmr.mgh.harvard.edu]
> Sent: Tuesday, July 25, 2017 10:21 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Segmentation Violation problem in surface files
>
> you can convert the overlays directly to nifti, but they aren't surfaces
> - they are scalar fields over the surface  (that is, they are one
> value/location with no neighborhood info). Not sure what Brainvoyager
> supports, but you could convert the surfaces to gifti
>
> cheers
> Bruce
>
>
> On
> Tue, 25 Jul 2017, Yagmur Ozdemir 19 wrote:
>
>> I am trying to export the overlays in .mgz format to Brainvoyager which 
>> recognizes nifti or its native .vmr format. However the mri_convert command 
>> gives error when I try to convert the templates. I thought if I could save 
>> the overlays directly onto the inflated surface files I could convert then 
>> visualize them in Brainvoyager, but couldn't figure that out so far. Thank 
>> you for the help!
>>
>> Idil
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
>> [fis...@nmr.mgh.harvard.edu]
>> Sent: Tuesday, July 25, 2017 7:47 PM
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] Segmentation Violation problem in surface files
>>
>> Hi Idil
>>
>> I'm not sure what you mean. If you give us a better idea of your overall
>> goal we can give you more helpful answers I expect
>> Bruce
>> On Tue, 25 Jul 2017,
>> Yagmur Ozdemir 19 wrote:
>>
>>> Bruce,
>>>
>>> Thank you so much for the help! I guess then the way to export these 
>>> overlays to other softwares is writing them on the subject's inflated 
>>> surface file.
>>>
>>> Best,
>>> Idil
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
>>> [fis...@nmr.mgh.harvard.edu]
>>> Sent: Monday, July 24, 2017 10:36 PM
>>> To: Freesurfer support list
>>> Subject: Re: [Freesurfer] Segmentation Violation problem in surface files
>>>
>>> Hi Idil,
>>>
>>> we only store surface overlays in .mgz not surfaces themselves. Try loading
>>> a surface (like lh.inflated) then load whatever you were looking at as an
>>> overlay on the surface
>>> cheers
>>> Bruce
>>>   On Mon, 24 Jul 2017, Yagmur Ozdemir 19 wrote:
>>>
>>>> Hello freesurfer experts,
>>>>
>>>> I am trying to use an occipital lobe template adapted to my data as several
>>>> surface and volume files, and there seems to be a problem with the surface
>>>> files. Whenever I try to open a surface overlay (in .mgz format) in 
>>>> freeview
>>>> this error comes up;
>>>>
>>>> freadFloat: fread failed
>>>> freadFloat: fread failed
>>>> ...
>>>> [0]PETSC ERROR:
>>>> 
>>>> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
>>>> probably memory access out of range
>>>> ...
>>>>
>>>> When I try to convert this file to nifti format a seemingly similar error
>>>> comes up;
>>>>
>>>> (...) mri_convert rh.template_areas.mgz AU_areas_template_rh.nii.gz
>>>> mri_convert.bin rh.template_areas.mgz AU_areas_template_rh.nii.gz
>>>> $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
>>>> reading from rh.template_areas.mgz...
>>>> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
>>>> i_ra

Re: [Freesurfer] Segmentation Violation problem in surface files

mris_convert -c lh.template_angle.mgz lh.template_angle.mgz 
lh.template_angle_MW.nii

Thank you for the help,
Idil

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Tuesday, July 25, 2017 11:00 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Segmentation Violation problem in surface files

what is your command line?


On 07/25/2017 03:52 PM, Yagmur Ozdemir 19 wrote:
> When I do either of the conversions with mris_convert, the system gives 
> freadFloat: fread failed / No such file or directory then a Segmentation 
> fault error.
>
> Best,
> Idil
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
> [fis...@nmr.mgh.harvard.edu]
> Sent: Tuesday, July 25, 2017 10:21 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Segmentation Violation problem in surface files
>
> you can convert the overlays directly to nifti, but they aren't surfaces
> - they are scalar fields over the surface  (that is, they are one
> value/location with no neighborhood info). Not sure what Brainvoyager
> supports, but you could convert the surfaces to gifti
>
> cheers
> Bruce
>
>
> On
> Tue, 25 Jul 2017, Yagmur Ozdemir 19 wrote:
>
>> I am trying to export the overlays in .mgz format to Brainvoyager which 
>> recognizes nifti or its native .vmr format. However the mri_convert command 
>> gives error when I try to convert the templates. I thought if I could save 
>> the overlays directly onto the inflated surface files I could convert then 
>> visualize them in Brainvoyager, but couldn't figure that out so far. Thank 
>> you for the help!
>>
>> Idil
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
>> [fis...@nmr.mgh.harvard.edu]
>> Sent: Tuesday, July 25, 2017 7:47 PM
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] Segmentation Violation problem in surface files
>>
>> Hi Idil
>>
>> I'm not sure what you mean. If you give us a better idea of your overall
>> goal we can give you more helpful answers I expect
>> Bruce
>> On Tue, 25 Jul 2017,
>> Yagmur Ozdemir 19 wrote:
>>
>>> Bruce,
>>>
>>> Thank you so much for the help! I guess then the way to export these 
>>> overlays to other softwares is writing them on the subject's inflated 
>>> surface file.
>>>
>>> Best,
>>> Idil
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
>>> [fis...@nmr.mgh.harvard.edu]
>>> Sent: Monday, July 24, 2017 10:36 PM
>>> To: Freesurfer support list
>>> Subject: Re: [Freesurfer] Segmentation Violation problem in surface files
>>>
>>> Hi Idil,
>>>
>>> we only store surface overlays in .mgz not surfaces themselves. Try loading
>>> a surface (like lh.inflated) then load whatever you were looking at as an
>>> overlay on the surface
>>> cheers
>>> Bruce
>>>   On Mon, 24 Jul 2017, Yagmur Ozdemir 19 wrote:
>>>
>>>> Hello freesurfer experts,
>>>>
>>>> I am trying to use an occipital lobe template adapted to my data as several
>>>> surface and volume files, and there seems to be a problem with the surface
>>>> files. Whenever I try to open a surface overlay (in .mgz format) in 
>>>> freeview
>>>> this error comes up;
>>>>
>>>> freadFloat: fread failed
>>>> freadFloat: fread failed
>>>> ...
>>>> [0]PETSC ERROR:
>>>> 
>>>> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
>>>> probably memory access out of range
>>>> ...
>>>>
>>>> When I try to convert this file to nifti format a seemingly similar error
>>>> comes up;
>>>>
>>>> (...) mri_convert rh.template_areas.mgz AU_areas_template_rh.nii.gz
>>>> mri_convert.bin rh.template_areas.mgz AU_areas_template_rh.nii.gz
>>>> $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
>>>> reading from rh.template_areas.mgz...
>>>> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
>>>> i_ra

Re: [Freesurfer] Segmentation Violation problem in surface files

When I do either of the conversions with mris_convert, the system gives 
freadFloat: fread failed / No such file or directory then a Segmentation fault 
error. 

Best,
Idil 

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Tuesday, July 25, 2017 10:21 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Segmentation Violation problem in surface files

you can convert the overlays directly to nifti, but they aren't surfaces
- they are scalar fields over the surface  (that is, they are one
value/location with no neighborhood info). Not sure what Brainvoyager
supports, but you could convert the surfaces to gifti

cheers
Bruce


On
Tue, 25 Jul 2017, Yagmur Ozdemir 19 wrote:

> I am trying to export the overlays in .mgz format to Brainvoyager which 
> recognizes nifti or its native .vmr format. However the mri_convert command 
> gives error when I try to convert the templates. I thought if I could save 
> the overlays directly onto the inflated surface files I could convert then 
> visualize them in Brainvoyager, but couldn't figure that out so far. Thank 
> you for the help!
>
> Idil
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
> [fis...@nmr.mgh.harvard.edu]
> Sent: Tuesday, July 25, 2017 7:47 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Segmentation Violation problem in surface files
>
> Hi Idil
>
> I'm not sure what you mean. If you give us a better idea of your overall
> goal we can give you more helpful answers I expect
> Bruce
> On Tue, 25 Jul 2017,
> Yagmur Ozdemir 19 wrote:
>
>> Bruce,
>>
>> Thank you so much for the help! I guess then the way to export these 
>> overlays to other softwares is writing them on the subject's inflated 
>> surface file.
>>
>> Best,
>> Idil
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
>> [fis...@nmr.mgh.harvard.edu]
>> Sent: Monday, July 24, 2017 10:36 PM
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] Segmentation Violation problem in surface files
>>
>> Hi Idil,
>>
>> we only store surface overlays in .mgz not surfaces themselves. Try loading
>> a surface (like lh.inflated) then load whatever you were looking at as an
>> overlay on the surface
>> cheers
>> Bruce
>>  On Mon, 24 Jul 2017, Yagmur Ozdemir 19 wrote:
>>
>>> Hello freesurfer experts,
>>>
>>> I am trying to use an occipital lobe template adapted to my data as several
>>> surface and volume files, and there seems to be a problem with the surface
>>> files. Whenever I try to open a surface overlay (in .mgz format) in freeview
>>> this error comes up;
>>>
>>> freadFloat: fread failed
>>> freadFloat: fread failed
>>> ...
>>> [0]PETSC ERROR:
>>> 
>>> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
>>> probably memory access out of range
>>> ...
>>>
>>> When I try to convert this file to nifti format a seemingly similar error
>>> comes up;
>>>
>>> (...) mri_convert rh.template_areas.mgz AU_areas_template_rh.nii.gz
>>> mri_convert.bin rh.template_areas.mgz AU_areas_template_rh.nii.gz
>>> $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
>>> reading from rh.template_areas.mgz...
>>> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
>>> i_ras = (1, 0, 0)
>>> j_ras = (0, 1, 0)
>>> k_ras = (0, 0, 1)
>>> writing to AU_areas_template_rh.nii.gz...
>>> NIFTI FORMAT ERROR: nslices 117239 in volume exceeds 32768
>>>
>>> I have tried to debug but failed so far. Has anyone come across a similar
>>> problem and do you have an opinion onto what might be causing this? The same
>>> adapted template's volume files work just fine.
>>>
>>> --I am using Ubuntu 16.04& freesurfer v.6
>>>
>>> Thank you so much!
>>> Idil
>>>
>>>
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Re: [Freesurfer] Segmentation Violation problem in surface files

I am trying to export the overlays in .mgz format to Brainvoyager which 
recognizes nifti or its native .vmr format. However the mri_convert command 
gives error when I try to convert the templates. I thought if I could save the 
overlays directly onto the inflated surface files I could convert then 
visualize them in Brainvoyager, but couldn't figure that out so far. Thank you 
for the help!

Idil 

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Tuesday, July 25, 2017 7:47 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Segmentation Violation problem in surface files

Hi Idil

I'm not sure what you mean. If you give us a better idea of your overall
goal we can give you more helpful answers I expect
Bruce
On Tue, 25 Jul 2017,
Yagmur Ozdemir 19 wrote:

> Bruce,
>
> Thank you so much for the help! I guess then the way to export these overlays 
> to other softwares is writing them on the subject's inflated surface file.
>
> Best,
> Idil
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
> [fis...@nmr.mgh.harvard.edu]
> Sent: Monday, July 24, 2017 10:36 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Segmentation Violation problem in surface files
>
> Hi Idil,
>
> we only store surface overlays in .mgz not surfaces themselves. Try loading
> a surface (like lh.inflated) then load whatever you were looking at as an
> overlay on the surface
> cheers
> Bruce
>  On Mon, 24 Jul 2017, Yagmur Ozdemir 19 wrote:
>
>> Hello freesurfer experts,
>>
>> I am trying to use an occipital lobe template adapted to my data as several
>> surface and volume files, and there seems to be a problem with the surface
>> files. Whenever I try to open a surface overlay (in .mgz format) in freeview
>> this error comes up;
>>
>> freadFloat: fread failed
>> freadFloat: fread failed
>> ...
>> [0]PETSC ERROR:
>> 
>> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
>> probably memory access out of range
>> ...
>>
>> When I try to convert this file to nifti format a seemingly similar error
>> comes up;
>>
>> (...) mri_convert rh.template_areas.mgz AU_areas_template_rh.nii.gz
>> mri_convert.bin rh.template_areas.mgz AU_areas_template_rh.nii.gz
>> $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
>> reading from rh.template_areas.mgz...
>> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
>> i_ras = (1, 0, 0)
>> j_ras = (0, 1, 0)
>> k_ras = (0, 0, 1)
>> writing to AU_areas_template_rh.nii.gz...
>> NIFTI FORMAT ERROR: nslices 117239 in volume exceeds 32768
>>
>> I have tried to debug but failed so far. Has anyone come across a similar
>> problem and do you have an opinion onto what might be causing this? The same
>> adapted template's volume files work just fine.
>>
>> --I am using Ubuntu 16.04& freesurfer v.6
>>
>> Thank you so much!
>> Idil
>>
>>
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Re: [Freesurfer] Segmentation Violation problem in surface files