Re: [Freesurfer] Extract specific LGI and Volume values

[Tien Pham]

External Email - Use Caution

Thank you for your suggestion.
I tried to use freeview to load surface on the label I created. But
terminal showed this error '' freadFloat: fread failed '' many times.
I tried to load label with qdec and I got the error (pic 1) I attached
below.
I also tried to load surface with qdec and this error displayed in terminal
(pic 2).
I am very appreciated when you helped me before.
I am looking forward to hearing from you.
Thank you very much.

On Mon, Feb 24, 2020 at 11:16 PM Douglas N. Greve 
wrote:

> Try using freeview
>
> On 2/18/2020 8:17 PM, Tien Pham wrote:
>
> External Email - Use Caution
> Thank you for your email.
> I tried to load the label with qdec and freeview and both were not worked.
> When i tried with qdec, It said '' load the surface first '' then I did
> but It did not work and showed some errors.
> The other way when I tried to load with qdec, qdec was closed suddenly
> without any notification.
> I am looking forward to hearing from you.
>
> On Fri, Feb 14, 2020 at 11:44 PM Douglas N. Greve 
> wrote:
>
>> What tool are you trying to use to load the label? What happens when you
>> try?
>>
>> On 2/7/2020 10:11 PM, Tien Pham wrote:
>>
>> External Email - Use Caution
>> Thank you for your email. I run exactly the command mri_label2label as
>> you suggested, and the command finished without any problem.
>> But I did not know why I could not open the label.
>> Please help me. Thank you once again.
>>
>> On Tue, Feb 4, 2020 at 2:55 AM Douglas N. Greve 
>> wrote:
>>
>>> sorry for the delay. You will have to use mri_label2label to map the
>>> label from the fsaverage space to the individual space
>>>
>>>
>>> On 1/31/2020 10:01 PM, Tien Pham wrote:
>>>
>>> External Email - Use Caution
>>> Can you read my message?
>>> I used longitudinal pipeline for my data set with two time points and
>>> measured the LGI differences between them.
>>> Then I created the label based on significant clusters which showed in
>>> QDEC.
>>> I tried to load the label on the subjects in cross, base, long steps
>>> but it did not work.
>>> I am looking forward to hearing from you. Thank you very much.
>>>
>>> On Sat, Feb 1, 2020 at 8:08 AM Douglas N. Greve 
>>> wrote:
>>>
 Sorry, I do not have the previous emails, can you repost with previous
 emails in the message?

 On 1/28/2020 7:35 PM, Tien Pham wrote:

 External Email - Use Caution
 Thank you for your response.

 I used longitudinal pipeline for my data set with two time points and
 calculated the LGI differences between them.
 Then I created the label based on significant clusters which showed in
 QDEC.
 I tried to load the label on subjects in cross, base, long steps but it
 did not work.
 I am looking forward to hearing from you. Thank you so much.

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Re: [Freesurfer] ubuntu: run freesurfer in two terminal

[Bruce Fischl]

sure, as long as you have more than one core. You can run them in the same
terminal as long as you put & at the end of the line

On Thu, 5 Mar 2020, ZhangBo wrote:



External Email - Use Caution

Hello FreeSurfer Developers,

My computer doesn't support cuda. To speed up data processing, could I open
two terminal, and in each of them, I first runing:

$> export FREESURFER_HOME=/usr/local/freesurfer
$> export FREESURFER_HOME=/SetUpFreeSurfer.sh
$> export SUBJECTS_DIR=/usr/local/freesurfer/subjects/

then running:
recon-all -s sub-01 -i sub-01_T1w.nii.gz -all (for terminal 1)
recon-all -s sub-02 -i sub-02_T1w.nii.gz -all (for terminal 2)

Thanks.




 



 


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[Freesurfer] ubuntu: run freesurfer in two terminal

[ZhangBo]

External Email - Use Caution

Hello FreeSurfer Developers,


My computer doesn't support cuda. To speed up data processing, could I open two 
terminal, and in each of them, I first runing:


$> export FREESURFER_HOME=/usr/local/freesurfer
$> export FREESURFER_HOME=/SetUpFreeSurfer.sh
$> export SUBJECTS_DIR=/usr/local/freesurfer/subjects/


then running:
recon-all -s sub-01 -i sub-01_T1w.nii.gz -all (for terminal 1)
recon-all -s sub-02 -i sub-02_T1w.nii.gz -all (for terminal 2)


Thanks.








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Re: [Freesurfer] (no subject)

[Douglas N. Greve]

It is is really bright there, try putting a few control points in WM 
(make sure they are in WM)

On 3/3/20 12:30 PM, Laboratorio de Neurociencia Funcional wrote:
>
> External Email - Use Caution
>
> Dear Freesurfeer experts,
> After running the recon-all in one of my subjets, part of the temporal lobe 
> was partially excluded. Then, I tried to use the watershed algorithm to be 
> less agressive in the skull stripping
> as follows:
>
> recon-all -skullstrip -wsthresh 35 -clean-bm -no-wsgcaatlas -subjid sub_001
>
> The problem was solved in the brainmask.mgz but not in the cortical surfaces. 
> To
> handle this issue, I edited the white matter and run the recon-all 
> -autorecon2-wm
> -autorecon3 without success. I also placed control points but the following 
> error appeared after running
> the recon-all -autorecon2-cp -autorecon3:
>
> recon-all -s sub_001 existed with errors
>
> I noted that white matter of this part of the temporal lobe has high values 
> (up to 132). What can I
> do to solve the problem with this subject?
>
> Thank you in advance.
>
> Best regards,
> Marina
>
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Re: [Freesurfer] CBF data for mri_glmfit processing

[Douglas N. Greve]

Try the MultiModal integration Part 2 on this page
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial
There is a lecture and a tutorial


On 3/3/20 3:03 AM, Beata Brzeska wrote:
>
> External Email - Use Caution
>
>
> Hello everyone,
>
> I am using Freesurfer 6.0 on linux cluster.
>
> We are analyzing CBF data (ASL derived) coupled with fMRI task in 
> longitudinal design. The fMRI data was analyzed in FS-FAST (with 
> paired-diff) and now we want to repeat the group analyses on CBF maps. 
> So far I registered the ASL data to individual anatomy and 
> successfully transformed into fsaverage surface space (and smoothed 
> afterwards). The data looks good so far - I can overlay it on inflated 
> fsaverage surface.
>
> My question is: how to stack the data for further mri_glmfit 
> processing? I suppose I should use mris_preproc for this purpose, but 
> I am at loss with which flags are appropriate and hoe to use CBF maps 
> as an input here.
>
>
> So far I did as follows for all the subjects, timepoints and hemispheres:
>
> bbregister --s Sub01_I --mov Sub01_I_CBF.nii.gz --t2 --reg 
> Sub01_I_reg.dat ;
>
> mri_vol2surf --src Sub01_I_CBF.nii.gz --trgsubject fsaverage --out 
> Sub01_I_CBF_to_surf_lh.nii.gz --srcreg Sub01_I_reg.dat --hemi lh
>
> mris_fwhm --s fsaverage --hemi lh --fwhm 5 --smooth-only --i 
> Sub01_I_CBF_to_surf_lh.nii.gz --o Sub01_I_CBF_to_surf_lh_smooth.nii.gz;
>
>
> I would really appreciate your help.
>
> Thanks,
>
> Beata
>
>
>
>
> --
> Beata Brzeska
> Medical University of Gdansk, Poland
> Radiology Department
> -- 
> Beata Brzeska
> Zakład Radiologii
> Uniwersyteckie Centrum Kliniczne w Gdańsku
>
>
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Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"

[Tim Schäfer]

External Email - Use Caution

Thanks for providing the image. Looks fine to me as well. 

What is a bit strange is that when running `mri_info` on the file you provided, 
it shows a FOV of 256 (not 284!) for me, so I have no idea why this error is 
triggered in recon-all. 

Maybe somebody else has an idea...

Tim

> On March 4, 2020 at 4:47 PM Frank Chau  wrote:
> 
> 
> External Email - Use Caution
> 
> Dear Tim,
> 
> I have checked the orig.mgz file and nothing usual was found (please see the 
> attachment image)
> 
> For downloading my orig.mgz: 
> https://www.dropbox.com/s/crkndenx8ev957v/orig.mgz?dl=0
> 
> Regards
> 
> Frank
> 
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Tim Schäfer 
> 
> Sent: 04 March 2020 23:27
> To: Freesurfer support list
> Subject: Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"
> 
> External Email - Use Caution
> 
> Dear Frank,
> 
> if you search the log in your Dropbox for 'error', this comes up:
> 
> 
> ERROR! FOV=284.000 > 256
> Include the flag -cw256 with recon-all!
> Inspect orig.mgz to ensure the head is fully visible.
> 
> 
> Did you have a look at the orig.mgz?
> 
> Best,
> 
> Tim
> 
> 
> > On March 4, 2020 at 2:59 PM Frank Chau  wrote:
> >
> >
> > External Email - Use Caution
> >
> > Hello FreeSurfer Developers,
> >
> > I ran a recon-all on a recent batch of T1 Nifti files and all ended with 
> > "exited with ERRORS". For example: "recon-all -s Chan_Pui_Kim_42M_T1 exited 
> > with ERRORS at Sat Jan 11 01:32:55 HKT 2020".
> >
> > I've searched the email archive list and I found other researcher 
> > encountered same problem before. However, I am quite sure their root causes 
> > are not same as my case. 3 possible causes were found in the email archive 
> > which about "exited with ERRORS":
> >
> >   1.  The version of freesurfer (I have already used the latest 6.0.0 
> > version)
> >   2.  Hard disk space (My computer have enough hard disk space)
> >   3.  sharing folder between virtual machine and original platform. (I use 
> > freesurfer in Mac OS which do not have this problem)
> >
> > I uploaded the recon-all.log to my dropbox in case it's of any use.
> >
> >
> > 1) FreeSurfer version: Darwin-OSX-stable-pub-v6.0.0-2beb96c
> >
> > 2) Platform: MAC OS X 10.11.6
> >
> > 3) uname -a: Darwin PFCs-MacBook-Pro.local 15.6.0 Darwin Kernel Version 
> > 15.6.0: Thu Jun 21 20:07:40 PDT 2018; root:xnu-3248.73.11~1/RELEASE_X86_64 
> > x86_64
> >
> > 4) recon-all.log, please download at:
> >
> > https://www.dropbox.com/s/bxb2vyhz3koo83s/recon-all.log-%20Terminal%20Output%20log%2020%20Jan%202020%20.txt?dl=0
> >
> >
> >
> > Regards
> >
> > Frank
> >
> > ---
> >
> > FRANK  C Y CHAU
> >
> >
> >
> > Research assistant
> >
> > Division of Neurology
> >
> > Department of Medicine
> >
> >
> >
> > Tel: +852 6340 2553
> >
> > Fax: 2872 5828
> >
> >
> >
> > E-mail : cyfr...@hku.hk
> >
> >
> >
> >
> >
> > Rm 304, 3/F, New Clinical building, Queen Mary Hospital, 102 Pokfulam Road, 
> > Hong Kong
> >
> >
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Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"

[Tim Schäfer]

External Email - Use Caution

Dear Frank,

if you search the log in your Dropbox for 'error', this comes up:


ERROR! FOV=284.000 > 256
Include the flag -cw256 with recon-all!
Inspect orig.mgz to ensure the head is fully visible.


Did you have a look at the orig.mgz?

Best,

Tim


> On March 4, 2020 at 2:59 PM Frank Chau  wrote:
> 
> 
> External Email - Use Caution
> 
> Hello FreeSurfer Developers,
> 
> I ran a recon-all on a recent batch of T1 Nifti files and all ended with 
> "exited with ERRORS". For example: "recon-all -s Chan_Pui_Kim_42M_T1 exited 
> with ERRORS at Sat Jan 11 01:32:55 HKT 2020".
> 
> I've searched the email archive list and I found other researcher encountered 
> same problem before. However, I am quite sure their root causes are not same 
> as my case. 3 possible causes were found in the email archive which about 
> "exited with ERRORS":
> 
>   1.  The version of freesurfer (I have already used the latest 6.0.0 version)
>   2.  Hard disk space (My computer have enough hard disk space)
>   3.  sharing folder between virtual machine and original platform. (I use 
> freesurfer in Mac OS which do not have this problem)
> 
> I uploaded the recon-all.log to my dropbox in case it's of any use.
> 
> 
> 1) FreeSurfer version: Darwin-OSX-stable-pub-v6.0.0-2beb96c
> 
> 2) Platform: MAC OS X 10.11.6
> 
> 3) uname -a: Darwin PFCs-MacBook-Pro.local 15.6.0 Darwin Kernel Version 
> 15.6.0: Thu Jun 21 20:07:40 PDT 2018; root:xnu-3248.73.11~1/RELEASE_X86_64 
> x86_64
> 
> 4) recon-all.log, please download at:
> 
> https://www.dropbox.com/s/bxb2vyhz3koo83s/recon-all.log-%20Terminal%20Output%20log%2020%20Jan%202020%20.txt?dl=0
> 
> 
> 
> Regards
> 
> Frank
> 
> ---
> 
> FRANK  C Y CHAU
> 
> 
> 
> Research assistant
> 
> Division of Neurology
> 
> Department of Medicine
> 
> 
> 
> Tel: +852 6340 2553
> 
> Fax: 2872 5828
> 
> 
> 
> E-mail : cyfr...@hku.hk
> 
> 
> 
> 
> 
> Rm 304, 3/F, New Clinical building, Queen Mary Hospital, 102 Pokfulam Road, 
> Hong Kong
> 
> 
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[Freesurfer] freesurfer- recon-all "exited with ERRORS"

[Frank Chau]

External Email - Use Caution

Hello FreeSurfer Developers,

I ran a recon-all on a recent batch of T1 Nifti files and all ended with 
"exited with ERRORS". For example: "recon-all -s Chan_Pui_Kim_42M_T1 exited 
with ERRORS at Sat Jan 11 01:32:55 HKT 2020".

I've searched the email archive list and I found other researcher encountered 
same problem before. However, I am quite sure their root causes are not same as 
my case. 3 possible causes were found in the email archive which about "exited 
with ERRORS":

  1.  The version of freesurfer (I have already used the latest 6.0.0 version)
  2.  Hard disk space (My computer have enough hard disk space)
  3.  sharing folder between virtual machine and original platform. (I use 
freesurfer in Mac OS which do not have this problem)

I uploaded the recon-all.log to my dropbox in case it's of any use.


1) FreeSurfer version: Darwin-OSX-stable-pub-v6.0.0-2beb96c

2) Platform: MAC OS X 10.11.6

3) uname -a: Darwin PFCs-MacBook-Pro.local 15.6.0 Darwin Kernel Version 15.6.0: 
Thu Jun 21 20:07:40 PDT 2018; root:xnu-3248.73.11~1/RELEASE_X86_64 x86_64

4) recon-all.log, please download at:

https://www.dropbox.com/s/bxb2vyhz3koo83s/recon-all.log-%20Terminal%20Output%20log%2020%20Jan%202020%20.txt?dl=0



Regards

Frank

---

FRANK  C Y CHAU



Research assistant

Division of Neurology

Department of Medicine



Tel: +852 6340 2553

Fax: 2872 5828



E-mail : cyfr...@hku.hk





Rm 304, 3/F, New Clinical building, Queen Mary Hospital, 102 Pokfulam Road, 
Hong Kong


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