Re: [Freesurfer] mri_cvs_register quit for mris_resample: Command not found

[Cong]

Hi Z K 
The contents of build-stamp.txt are 
freesurfer-Darwin-lion-stable-pub-v5.3.0.

Best Wishes
Cong Chen

> Date: Tue, 18 Oct 2016 11:09:20 -0400
> From: Z K 
> 
> 
> Hello,
> 
> Can you provide me with the contents of your 
> /Applications/freesurfer/build-stamp.txt file?
> 
> 
> 
> On 10/18/2016 10:13 AM, Cong wrote:
>> Dear freesufer experts
>>I?m learning DTI image process according to steps in  FsTutorial/
>> Diffusion_DtiIntegration. In Spatial Normalization I need create a
>> .m3z morph file
>> through mir_cvs_register. I used command mri_cvs_register --mov
>> subjectname --template cvs_avg35. But it always stop for mris_resample:
>> Command not found. I run freesurfer v5.3.0 in a MacBook Pro. Two log
>> file in cvs folder are attached. Could you give me some advice? Thanks
>> very much.
>> 
>> Best Wishes
>> Cong Chen



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Re: [Freesurfer] Optimal combination of MRI-sequences

[Bruce Fischl]

Hi Erik

if you mean what sequences should you acquire, Andre van der Kouwe has a 
website with recommendations for different platforms. Typicall we like a 
multi-echo MPRAGE and a T2-SPACE FLAIR scan as well if you have time


cheers
Bruce
On Tue, 
18 Oct 2016, Erik Lindberg wrote:




Dear Freesufer experts,

 

We are in the process of starting a large MRI project on normal aging and 
dementia.

 

There has been a lot of discussions about what sequences to use.

 

We are now thinking about combining several sequences. Is there an optimal 
combination of MRI sequences
for Freesufer?

 


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Re: [Freesurfer] Cortical Thickness Zero Values

[Bruce Fischl]

Hi Taha

none that I can think of. The medial wall is pretty substantial region 
though - I am more concerned about your subject with only 53 vertices in 
it. You can visualize it by loading the ?h.cortex.label onto the inflated 
surface. Everything not in the label should be set to 0


cheers
Bruce


On Tue, 18 
Oct 2016, Taha Abdullah wrote:



I see now, thanks for the answer. If I may, is there any particular reason why 
such a disparity between
two subjects, is this due to anatomical variability between individuals? I was 
surprised by the 9,000
values that was missing. 

On Fri, Oct 14, 2016 at 10:40 AM, Douglas Greve  
wrote:

  The entire medial wall has thickness values of 0 because there is no 
cortex there. There
  needs to be a surface in that area because we need a closed surface.


  On 10/12/16 8:10 PM, Taha Abdullah wrote:
  Hello All,
Quick question, I ran recon-all with the qcache option and after converting the
?.thickness.fsaverage.mgh to an ascii text file via mri_convert I am noticing 
some vertices
have 0mm thickness and it varies, for example, one subject had 53 vertices 
labeled as zeros
while another had over 9,000 vertices. Is there a method I can use to have a 
thickness value
for each of the 163000+ vertices? I am not sure if this is a possible 
registration issue to
mni305. 

Thanks in advance,
Taha 
--
Taha Abdullah
Department of Physiology,
Northwestern University Feinberg School of Medicine
MS in Physiology and Biophysics, Georgetown University 2015
Work Cell: (312)-451-8468


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--
Taha Abdullah
Department of Physiology,
Northwestern University Feinberg School of Medicine
MS in Physiology and Biophysics, Georgetown University 2015
Work Cell: (312)-451-8468

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Re: [Freesurfer] Training Tracula to add more pathways

[Kristafor Farrant]

Bump


On Thu, Sep 29, 2016 at 4:02 PM, Kristafor Farrant  wrote:

> Hi there,
>
> As a complete newbie to the Tracula tool, I have a questions about using
> it. Is it possible to train tracula to track additional pathways other than
> the 18 thats are already included? I was to track several pathways that are
> not included with Tracula.
>
> Best,
>
> Kris
>
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Re: [Freesurfer] Optimal combination of MRI-sequences

[Matt Glasser]

What do you mean by ³combining² sequences?

Peace,

Matt.

From:   on behalf of Erik Lindberg

Reply-To:  Freesurfer support list 
Date:  Tuesday, October 18, 2016 at 2:52 PM
To:  
Subject:  [Freesurfer] Optimal combination of MRI-sequences

Dear Freesufer experts,
 
We are in the process of starting a large MRI project on normal aging and
dementia.
 
There has been a lot of discussions about what sequences to use.
 
We are now thinking about combining several sequences. Is there an optimal
combination of MRI sequences for Freesufer?
 
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Re: [Freesurfer] Cortical Thickness Zero Values

[Taha Abdullah]

I see now, thanks for the answer. If I may, is there any particular reason
why such a disparity between two subjects, is this due to anatomical
variability between individuals? I was surprised by the 9,000 values that
was missing.

On Fri, Oct 14, 2016 at 10:40 AM, Douglas Greve 
wrote:

> The entire medial wall has thickness values of 0 because there is no
> cortex there. There needs to be a surface in that area because we need a
> closed surface.
>
> On 10/12/16 8:10 PM, Taha Abdullah wrote:
>
> Hello All,
>
> Quick question, I ran recon-all with the qcache option and after
> converting the ?.thickness.fsaverage.mgh to an ascii text file via
> mri_convert I am noticing some vertices have 0mm thickness and it varies,
> for example, one subject had 53 vertices labeled as zeros while another
> had over 9,000 vertices. Is there a method I can use to have a thickness
> value for each of the 163000+ vertices? I am not sure if this is a possible
> registration issue to mni305.
>
> Thanks in advance,
> Taha
> --
> *Taha Abdullah*
> *Department of Physiology,*
>
> *Northwestern University Feinberg School of Medicine *
> *MS in Physiology and Biophysics, Georgetown University 2015*
> *Work Cell: (312)-451-8468 <%28312%29-451-8468>*
>
>
> ___
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>
>
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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.
>
>


-- 
*Taha Abdullah*
*Department of Physiology,*

*Northwestern University Feinberg School of Medicine*
*MS in Physiology and Biophysics, Georgetown University 2015*
*Work Cell: (312)-451-8468*
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Re: [Freesurfer] Using "for" to run multiple subjects

[Douglas N Greve]

The * is what makes the script useful as that allows it to process all 
the subjects without you having to specify every subject. That script 
only works if you have already set up your subject's folders in the 
directory structure freesurfer expects. Is this the case? Or are you 
working from dicom files?


On 10/15/2016 02:52 PM, Farzaneh keyvanfard wrote:
> /Dear expert,/
> /
> /
> /I want to run recon-all for 100 subject /simultaneously. I found the 
> following link about it, but as I'm a beginner in this field, I don't 
> understand how to use it. Would you please kindly give an example with 
> a subject names, directory , etc. what should be written instead of * 
> , or how could I define the number of subjects, ...? Thank you very much.
> https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/Scripts/Two
> Best Regards
>
>
> F.Keyvanfard
> 
>
>
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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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[Freesurfer] Optimal combination of MRI-sequences

[Erik Lindberg]

Dear Freesufer experts,



We are in the process of starting a large MRI project on normal aging and
dementia.



There has been a lot of discussions about what sequences to use.



We are now thinking about combining several sequences. Is there an optimal
combination of MRI sequences for Freesufer?
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Re: [Freesurfer] 2 beginner questions

[Paul Wighton]

Hi Brad,

I don't have any experience with your first issue, but with regards to your
second issue: are you running Windows10 as the host OS and Ubuntu as the
guest OS?  Ubuntu requires root (or admin) access to install packages.  If
you installed Ubuntu yourself, it should have prompted you to create a
username and password.  That password should have root privileges.  If you
obtained the VM from someone else, I'd ask them what the root password is.

-Paul

On Tue, Oct 4, 2016 at 9:20 AM, Brad Matushewski  wrote:

>
>
> I am running Freesurfer on a Virtual machine on Windows 10.
>
>
>
> 1)  I am having difficulty creating a shared drive between Windows
> and Freesufer / Linux.  Has anyone had success with this?
>
> 2)  I tried to install gedit.  I went to the Ubuntu software centre
> and downloaded it.  I then asked me for a password for authentication
> before I could install it.  I never set up any such password…Where is this
> coming from and how do I proceed?
>
> 3)
>
>
>
> [image: Logo]
>
> Brad J. Matushewski, M.Sc., R.Kin., CSEP-CEP.
>
> Laboratory for Brain & Heart Health
> School of Kinesiology
> Western University
> Room 402, Arthur & Sonia Labatt Health Sciences Building
> London, ON, Canada, N6A 5B9
> Tel: (519) 661-2111 x 89066
> Fax: (519) 850-2447
>
>
>
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Re: [Freesurfer] recon-all -s bert exited with errors

[Qinggang Yu]

Hi Zeke,

Thanks for your reply! The issue has been resolved - it was the temp folder
on the system running out of space. But thank you very much for your
suggestions!

Best,
Qinggang

On Tue, Oct 18, 2016 at 10:07 AM, Z K  wrote:

> What version of perl are you using?
>
>$> perl --version
>
> If its perl 5.20 (or maybe 5.22) than the error you are encountering is
> because because that version of perl is incompatible with the MNI tools
> shipped with the version of freesurfer you are using.
>
> The easiest way to remedy the situation is to download and install the
> development version of freesurfer which fixes this issue and will be
> included in the upcoming 6.0 release (see "Development Version"):
>
>https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
>
> -Zeke
>
> On 10/17/2016 12:32 PM, Qinggang Yu wrote:
> > Hello FreeSurfer Developers,
> >
> > I was trying to run recon-all -all, and it failed roughly 30s after it
> > started running, with the error message being: recon-all -s bert exited
> > with errors.
> >
> > Freesurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
> > Platform: Red Hat Enterprise Linux Client Release 5.2
> > uname -a: Linux schizo.psych.med.umich.edu
> >  2.6.18-92.1.13.el5 #1 SMP Wed Sep 24
> > 19:32:05 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux
> > recon-all.log: see attached
> >
> > Please let me know how I can fix this. Thank you very much!
> >
> > Best,
> > Qinggang
> >
> >
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Re: [Freesurfer] GLM on cortical and subcortical volume

[Douglas Greve]

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI

this does not have the mri_glmfit command, but that is the same doing 
the voxel-wise stats with the change in --y. This does not include 
correction for ICV



On 10/18/16 10:53 AM, miracle ozzoude wrote:

hello doug,
Thanks for the response. Please can you send me the link. Also, does 
GLM correct for total intracranial volume or do I need to create fsgd 
file with total intracranial volume as covariate? Thanks


On Tue, Oct 18, 2016 at 10:48 AM, Douglas Greve 
> wrote:


do you mean volumes of ROIs? Yes, there is a tutorial on this in
our wiki, but basically you need to run aparcstats2table and/or
asegstats2table to create a table of volumes for each subject and
ROI. Then use mrI_glmfit with the --table option instead of --y


On 10/18/16 10:18 AM, miracle ozzoude wrote:

Hello Expert,
Is there are way to perform glm analysis on cortical and
subcortical volumes. Thanks
Best,.
Paul


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Re: [Freesurfer] mri_cvs_register quit for mris_resample: Command not found

[Z K]

Hello,

Can you provide me with the contents of your 
/Applications/freesurfer/build-stamp.txt file?



On 10/18/2016 10:13 AM, Cong wrote:
> Dear freesufer experts
> I’m learning DTI image process according to steps in  FsTutorial/
> Diffusion_DtiIntegration. In Spatial Normalization I need create a
> .m3z morph file
> through mir_cvs_register. I used command mri_cvs_register --mov
> subjectname --template cvs_avg35. But it always stop for mris_resample:
> Command not found. I run freesurfer v5.3.0 in a MacBook Pro. Two log
> file in cvs folder are attached. Could you give me some advice? Thanks
> very much.
>
> Best Wishes
> Cong Chen
>
>
>
>
>
>
>
>
>
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Re: [Freesurfer] GLM on cortical and subcortical volume

[miracle ozzoude]

hello doug,
Thanks for the response. Please can you send me the link. Also, does GLM
correct for total intracranial volume or do I need to create fsgd file with
total intracranial volume as covariate? Thanks

On Tue, Oct 18, 2016 at 10:48 AM, Douglas Greve 
wrote:

> do you mean volumes of ROIs? Yes, there is a tutorial on this in our wiki,
> but basically you need to run aparcstats2table and/or asegstats2table to
> create a table of volumes for each subject and ROI. Then use mrI_glmfit
> with the --table option instead of --y
>
> On 10/18/16 10:18 AM, miracle ozzoude wrote:
>
> Hello Expert,
> Is there are way to perform glm analysis on cortical and subcortical
> volumes. Thanks
> Best,.
> Paul
>
>
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Re: [Freesurfer] GLM on cortical and subcortical volume

[Douglas Greve]

do you mean volumes of ROIs? Yes, there is a tutorial on this in our 
wiki, but basically you need to run aparcstats2table and/or 
asegstats2table to create a table of volumes for each subject and ROI. 
Then use mrI_glmfit with the --table option instead of --y



On 10/18/16 10:18 AM, miracle ozzoude wrote:

Hello Expert,
Is there are way to perform glm analysis on cortical and subcortical 
volumes. Thanks

Best,.
Paul


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[Freesurfer] GLM on cortical and subcortical volume

[miracle ozzoude]

Hello Expert,
Is there are way to perform glm analysis on cortical and subcortical
volumes. Thanks
Best,.
Paul
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Re: [Freesurfer] recon-all -s bert exited with errors

[Z K]

What version of perl are you using?

   $> perl --version

If its perl 5.20 (or maybe 5.22) than the error you are encountering is 
because because that version of perl is incompatible with the MNI tools 
shipped with the version of freesurfer you are using.

The easiest way to remedy the situation is to download and install the 
development version of freesurfer which fixes this issue and will be 
included in the upcoming 6.0 release (see "Development Version"):

   https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall

-Zeke

On 10/17/2016 12:32 PM, Qinggang Yu wrote:
> Hello FreeSurfer Developers,
>
> I was trying to run recon-all -all, and it failed roughly 30s after it
> started running, with the error message being: recon-all -s bert exited
> with errors.
>
> Freesurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
> Platform: Red Hat Enterprise Linux Client Release 5.2
> uname -a: Linux schizo.psych.med.umich.edu
>  2.6.18-92.1.13.el5 #1 SMP Wed Sep 24
> 19:32:05 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux
> recon-all.log: see attached
>
> Please let me know how I can fix this. Thank you very much!
>
> Best,
> Qinggang
>
>
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[Freesurfer] mri_cvs_register quit for mris_resample: Command not found

[Cong]

Dear freesufer experts    I’m learning DTI image process according to steps in  FsTutorial/ Diffusion_DtiIntegration. In Spatial Normalization I need create a .m3z morph file through mir_cvs_register. I used command mri_cvs_register --mov subjectname --template cvs_avg35. But it always stop for mris_resample: Command not found. I run freesurfer v5.3.0 in a MacBook Pro. Two log file in cvs folder are attached. Could you give me some advice? Thanks very much.Best WishesCong Chen

con002_to_cvs_avg35.mri_cvs_register.1610182007.log
Description: Binary data


summary.con002_to_cvs_avg35.mri_cvs_register.1610182007.log
Description: Binary data
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Re: [Freesurfer] mri_nu_correct crash

[Z K]

Oops, I meant to write "Ubuntu 16 comes with a version of perl that is 
*incompatible* with the MNI tools..."


On 10/18/2016 10:03 AM, Z K wrote:
> Ubuntu 16 comes with a version of perl that is compatible with the MNI
> tools shipped with the version of freesurfer you are using.
>
> The easiest way to remedy the situation is to download and install the
> development version of freesurfer which fixes this issue and will be
> included in the upcoming 6.0 release (see "Development Version"):
>
>https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
>
> -Zeke
>
> On 10/17/2016 09:28 AM, Burkhard Maess wrote:
>> hello Freesurfer developers,
>>
>> during the recon-all (autorecon1) processing, it seems that the 
>> mne_nu_correct procedure does not always manage to finish successfully. I 
>> have searched the net, found a question in the mailing list, which seemed to 
>> be similar, but no answer 
>> (http://www.bic.mni.mcgill.ca/pipermail/minc-users/2015-November/004205.html).
>>
>> Our status file shows, that we had sometimes runs which were completed 
>> without errors. Maybe, we should not have started the recon-all a second 
>> time. It would be very great if you could help with further hints. For 
>> instance, could we remove a file or several files to roll back to the 
>> situation when it worked?
>>
>> all the best,
>> Burkhard
>>
>> .
>>
>> FREESURFER_VERSION:  freesurfer-x86_64-unknown-linux-gnu-stable5-20130513
>> Platform: ubuntu 16.04  (xfce)
>>> uname -a
>> Linux ren 4.4.0-38-generic #57-Ubuntu SMP Tue Sep 6 15:42:33 UTC 2016 x86_64 
>> x86_64 x86_64 GNU/Linux
>>
>> Command:
>> freesurfer=5.3.0_maess@ren:/scr/eber2/intstats > recon-all -autorecon1 
>> -nuintensitycor-3T -subjid is09
>>
>>
>>
>>
>> --
>> Dr. Burkhard Maess
>> Max Planck Institute for Human Cognitive and Brain Sciences
>> Stephanstr. 1a, P.O. Box 500355, D-04303 Leipzig
>> Aussenstelle Bennewitz, phone/fax: +49(3425)8875-2526/-2511   mail: maess 
>> 'at' cbs.mpg.de,   http://www.cbs.mpg.de
>>
>>
>>
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>>
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Re: [Freesurfer] mri_nu_correct crash

[Z K]

Ubuntu 16 comes with a version of perl that is compatible with the MNI 
tools shipped with the version of freesurfer you are using.

The easiest way to remedy the situation is to download and install the 
development version of freesurfer which fixes this issue and will be 
included in the upcoming 6.0 release (see "Development Version"):

   https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall

-Zeke

On 10/17/2016 09:28 AM, Burkhard Maess wrote:
> hello Freesurfer developers,
>
> during the recon-all (autorecon1) processing, it seems that the 
> mne_nu_correct procedure does not always manage to finish successfully. I 
> have searched the net, found a question in the mailing list, which seemed to 
> be similar, but no answer 
> (http://www.bic.mni.mcgill.ca/pipermail/minc-users/2015-November/004205.html).
>
> Our status file shows, that we had sometimes runs which were completed 
> without errors. Maybe, we should not have started the recon-all a second 
> time. It would be very great if you could help with further hints. For 
> instance, could we remove a file or several files to roll back to the 
> situation when it worked?
>
> all the best,
> Burkhard
>
> .
>
> FREESURFER_VERSION:  freesurfer-x86_64-unknown-linux-gnu-stable5-20130513
> Platform: ubuntu 16.04  (xfce)
>> uname -a
> Linux ren 4.4.0-38-generic #57-Ubuntu SMP Tue Sep 6 15:42:33 UTC 2016 x86_64 
> x86_64 x86_64 GNU/Linux
>
> Command:
> freesurfer=5.3.0_maess@ren:/scr/eber2/intstats > recon-all -autorecon1 
> -nuintensitycor-3T -subjid is09
>
>
>
>
> --
> Dr. Burkhard Maess
> Max Planck Institute for Human Cognitive and Brain Sciences
> Stephanstr. 1a, P.O. Box 500355, D-04303 Leipzig
> Aussenstelle Bennewitz, phone/fax: +49(3425)8875-2526/-2511   mail: maess 
> 'at' cbs.mpg.de,   http://www.cbs.mpg.de
>
>
>
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