[Freesurfer] editing and converting

[Jenny Mercolini]

Hi Freesurfers,

I am new to this software and i am trying to learn how to use it.

I have two questions:

1) if I do recon-all on a group of 20 subject, and I am primarily
interested in a few regions (In my case - amygdala, insula and anterior
cingulate cortex), do I have to edit all the datasets in tkmedit to make
sure that these ROIs are "where they ar supposed to be"?

2) What is the easiest way to convert recon'ed data from FreeSurfer space
to original subject space ( and mgz files to nifti files)?

Thank you so much for your help!

Kind regards, Jenny
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Re: [Freesurfer] recon-all: too many levels of symbolic links

[Bruce Fischl]

Looks like you don't have 
> /home/virtualuser/freesurfer/subjects/lh.EC_average

You will need to download it
Cheers
Bruce

On Dec 20, 2012, at 12:32 AM, Linda Zhang  wrote:

> Hi Bruce,
> 
> This is what I get:
> 
> FreeSurfer:~/freesurfer/lindadata> ls -l
> drwxr-sr-x 42 virtualuser virtualuser 4096 2012-11-17 07:38 subjects
> FreeSurfer:~/freesurfer/lindadata> ls /subjects/lh.EC_average/surf
> ls: cannot access /subjects/lh.EC_average/surf: No such file or directory
> FreeSurfer:~/freesurfer/lindadata> ls -l /subjects/lh.EC_average 
> lrwxrwxrwx 1 virtualuser virtualuser 51 2012-11-17 07:38 
> /home/virtualuser/freesurfer/lindadata/subjects/lh.EC_average -> 
> /home/virtualuser/freesurfer/subjects/lh.EC_average
> FreeSurfer:~/freesurfer/lindadata> ls /home/virtualuser/freesurfer/subjects/
> cvs_avg35  fsaverage  fsaverage3  fsaverage4  fsaverage5  fsaverage6  README  
> V1_average
> 
> 
> 
> 
> On 19 December 2012 21:43, Bruce Fischl  wrote:
>  ls -1 $FREESURFER_HOME/subjects
> cvs_avg35/
> cvs_avg35_inMNI152/
> fsaverage/
> fsaverage3/
> fsaverage4/
> fsaverage5/
> fsaverage6/
> fsaverage_sym/
> lh.EC_average/
> README
> rh.EC_average/
> sample-001.mgz
> sample-002.mgz
> surfer.log
> V1_average/
> 
> not sure why it thinks it doesn't exist. What are the permissions on
> 
> /home/virtualuser/freesurfer/lindadata/subjects/lh.EC_average
> 
> can you do an ls on
> 
> /home/virtualuser/freesurfer/lindadata/subjects/lh.EC_average/surf
> 
> and post the results? Also do:
> 
> ls -l /home/virtualuser/freesurfer/lindadata/subjects/lh.EC_average
> 
> 
> On Wed, 19 Dec 2012, Linda Zhang wrote:
> 
> Dear all,
> 
> I've run into the same error with recon-all -autorecon3.  It could be that 
> when I moved my data into the new SUBJECTS_DIR, I
> missed something out.  What files should be in the $FREESURFER_HOME/subjects 
> directory?
> 
> The error reads as follows:
> 
> #@# Ex-vivo Entorhinal Cortex Label lh Fri Dec 14 19:07:03 HKT 2012
> INFO: lh.EC_average subject does not exist in SUBJECTS_DIR
> INFO: Creating symlink to lh.EC_average subject...
> 
>  cd /home/virtualuser/freesurfer/lindadata/subjects; ln -s 
> /home/virtualuser/freesurfer/subjects/lh.EC_average; cd -
> 
> ln: creating symbolic link `./lh.EC_average': File exists
> 
>  mris_spherical_average -erode 1 -orig white -t 0.4 -o ncpoCCW label 
> lh.entorhinal lh sphere.reg lh.EC_average
> lh.entorhinal_exvivo.label
> 
> painting output onto subject ncpoCCW.
> processing subject lh.EC_average...
> MRISread(/home/virtualuser/freesurfer/lindadata/subjects/lh.EC_average/surf/lh.sphere.reg):
>  could not open file
> eroding label 1 times before writing
> thresholding label stat at 0.400 before writing
> No such file or directory
> mris_spherical_average: could not read surface file
> /home/virtualuser/freesurfer/lindadata/subjects/lh.EC_average/surf/lh.sphere.reg
> No such file or directory
> Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC 
> 2011 i686 GNU/Linux
> 
> recon-all -s ncpoCCW exited with ERRORS at Fri Dec 14 19:07:07 HKT 2012
> 
> For more details, see the log file 
> /home/virtualuser/freesurfer/lindadata/subjects/ncpoCCW/scripts/recon-all.log
> To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 
> 
> Cheers,
> Linda
> 
> 
> 
> On 14 November 2012 22:29, Linda Zhang  wrote:
> 
>   Thanks Bruce.  It has 6gb assigned to the virtualbox, I'm running 
> another process alongside it.  I'll stop the other
>   one and try again.
> 
>   On 14 Nov 2012 22:14, "Bruce Fischl"  wrote:
> sounds like you are running out of memory. How much ram is in 
> that machine? Are other processes running
> at the same time?
> On Wed, 14 Nov 2012, Linda Zhang wrote:
> 
>   Dear all,
>   After moving my data to a different folder, I've come 
> across a different error when running
>   recon-all (autorecon2 and 3).  The
>   last few lines are as follows:
> 
>   0117: dt=32.368000, rms=0.713 (0.122%), neg=0, invalid=766
>   0118: dt=32.368000, rms=0.713 (0.033%), neg=0, invalid=766
>   0119: dt=32.368000, rms=0.712 (0.059%), neg=0, invalid=766
>   0120: dt=32.368000, rms=0.712 (0.081%), neg=0, invalid=766
>   0121: dt=16.184000, rms=0.712 (0.009%), neg=0, invalid=766
>   Killed
>   ERROR: mri_ca_register with non-zero status 137
>   but continuing despite the error
>   #--
>   #@# CA Reg Inv Wed Nov 14 15:47:37 HKT 2012
>   /home/virtualuser/freesurfer/lindadata/subjects/ncvoCYJ/mri
> 
>mri_ca_register -invert-and-save transforms/talairach.m3z 
> 
>   Loading, Inverting, Saving, Exiting ...
>   Reading transforms/talairach.m3z 
>   ER

Re: [Freesurfer] recon-all: too many levels of symbolic links

[Linda Zhang]

Thanks Bruce, from where? Should I download the other directories I seem to
be missing as well?
On 20 Dec 2012 21:26, "Bruce Fischl"  wrote:

> Looks like you don't have
>
> /home/virtualuser/freesurfer/subjects/lh.EC_average
>
>
> You will need to download it
> Cheers
> Bruce
>
> On Dec 20, 2012, at 12:32 AM, Linda Zhang  wrote:
>
> Hi Bruce,
>
> This is what I get:
>
> FreeSurfer:~/freesurfer/lindadata> ls -l
> drwxr-sr-x 42 virtualuser virtualuser 4096 2012-11-17 07:38 subjects
> FreeSurfer:~/freesurfer/lindadata> ls /subjects/lh.EC_average/surf
> ls: cannot access /subjects/lh.EC_average/surf: No such file or directory
> FreeSurfer:~/freesurfer/lindadata> ls -l /subjects/lh.EC_average
> lrwxrwxrwx 1 virtualuser virtualuser 51 2012-11-17 07:38
> /home/virtualuser/freesurfer/lindadata/subjects/lh.EC_average ->
> /home/virtualuser/freesurfer/subjects/lh.EC_average
> FreeSurfer:~/freesurfer/lindadata> ls
> /home/virtualuser/freesurfer/subjects/
> cvs_avg35  fsaverage  fsaverage3  fsaverage4  fsaverage5  fsaverage6
> README  V1_average
>
>
>
>
> On 19 December 2012 21:43, Bruce Fischl wrote:
>
>>  ls -1 $FREESURFER_HOME/subjects
>> cvs_avg35/
>> cvs_avg35_inMNI152/
>> fsaverage/
>> fsaverage3/
>> fsaverage4/
>> fsaverage5/
>> fsaverage6/
>> fsaverage_sym/
>> lh.EC_average/
>> README
>> rh.EC_average/
>> sample-001.mgz
>> sample-002.mgz
>> surfer.log
>> V1_average/
>>
>> not sure why it thinks it doesn't exist. What are the permissions on
>>
>> /home/virtualuser/freesurfer/**lindadata/subjects/lh.EC_**average
>>
>> can you do an ls on
>>
>> /home/virtualuser/freesurfer/**lindadata/subjects/lh.EC_**average/surf
>>
>> and post the results? Also do:
>>
>> ls -l /home/virtualuser/freesurfer/**lindadata/subjects/lh.EC_**average
>>
>>
>> On Wed, 19 Dec 2012, Linda Zhang wrote:
>>
>>  Dear all,
>>>
>>> I've run into the same error with recon-all -autorecon3.  It could be
>>> that when I moved my data into the new SUBJECTS_DIR, I
>>> missed something out.  What files should be in the
>>> $FREESURFER_HOME/subjects directory?
>>>
>>> The error reads as follows:
>>>
>>> #@# Ex-vivo Entorhinal Cortex Label lh Fri Dec 14 19:07:03 HKT 2012
>>> INFO: lh.EC_average subject does not exist in SUBJECTS_DIR
>>> INFO: Creating symlink to lh.EC_average subject...
>>>
>>>  cd /home/virtualuser/freesurfer/**lindadata/subjects; ln -s
>>> /home/virtualuser/freesurfer/**subjects/lh.EC_average; cd -
>>>
>>> ln: creating symbolic link `./lh.EC_average': File exists
>>>
>>>  mris_spherical_average -erode 1 -orig white -t 0.4 -o ncpoCCW label
>>> lh.entorhinal lh sphere.reg lh.EC_average
>>> lh.entorhinal_exvivo.label
>>>
>>> painting output onto subject ncpoCCW.
>>> processing subject lh.EC_average...
>>> MRISread(/home/virtualuser/**freesurfer/lindadata/subjects/**
>>> lh.EC_average/surf/lh.sphere.**reg): could not open file
>>> eroding label 1 times before writing
>>> thresholding label stat at 0.400 before writing
>>> No such file or directory
>>> mris_spherical_average: could not read surface file
>>> /home/virtualuser/freesurfer/**lindadata/subjects/lh.EC_**
>>> average/surf/lh.sphere.reg
>>> No such file or directory
>>> Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39
>>> UTC 2011 i686 GNU/Linux
>>>
>>> recon-all -s ncpoCCW exited with ERRORS at Fri Dec 14 19:07:07 HKT 2012
>>>
>>> For more details, see the log file /home/virtualuser/freesurfer/**
>>> lindadata/subjects/ncpoCCW/**scripts/recon-all.log
>>> To report a problem, see http://surfer.nmr.mgh.harvard.**
>>> edu/fswiki/BugReporting
>>>
>>>
>>> Cheers,
>>> Linda
>>>
>>>
>>>
>>> On 14 November 2012 22:29, Linda Zhang  wrote:
>>>
>>>   Thanks Bruce.  It has 6gb assigned to the virtualbox, I'm running
>>> another process alongside it.  I'll stop the other
>>>   one and try again.
>>>
>>>   On 14 Nov 2012 22:14, "Bruce Fischl" 
>>> wrote:
>>> sounds like you are running out of memory. How much ram is
>>> in that machine? Are other processes running
>>> at the same time?
>>> On Wed, 14 Nov 2012, Linda Zhang wrote:
>>>
>>>   Dear all,
>>>   After moving my data to a different folder, I've come
>>> across a different error when running
>>>   recon-all (autorecon2 and 3).  The
>>>   last few lines are as follows:
>>>
>>>   0117: dt=32.368000, rms=0.713 (0.122%), neg=0,
>>> invalid=766
>>>   0118: dt=32.368000, rms=0.713 (0.033%), neg=0,
>>> invalid=766
>>>   0119: dt=32.368000, rms=0.712 (0.059%), neg=0,
>>> invalid=766
>>>   0120: dt=32.368000, rms=0.712 (0.081%), neg=0,
>>> invalid=766
>>>   0121: dt=16.184000, rms=0.712 (0.009%), neg=0,
>>> invalid=766
>>>   Killed
>>>   ERROR: mri_ca_register with non-zero status 137
>>>   but continuing despite the error
>>> 

Re: [Freesurfer] editing and converting

[Bruce Fischl]

Hi Jenny
1) yes, they are usually fine, but you *always* should look at the regions you 
are hoping to make biological statements about.


2) mri_convert -rl rawavg.mgz -rt nearest aseg.mgz aseg.rawavg.nii

Wold convert the aseg. Not that they are already in the original RAS space, 
just a different voxel space
Cheers
Bruce

On Dec 20, 2012, at 6:48 AM, Jenny Mercolini  wrote:

> Hi Freesurfers,
> 
> I am new to this software and i am trying to learn how to use it.
> 
> I have two questions:
> 
> 1) if I do recon-all on a group of 20 subject, and I am primarily interested 
> in a few regions (In my case - amygdala, insula and anterior cingulate 
> cortex), do I have to edit all the datasets in tkmedit to make sure that 
> these ROIs are "where they ar supposed to be"?  
> 
> 2) What is the easiest way to convert recon'ed data from FreeSurfer space to 
> original subject space ( and mgz files to nifti files)?
> 
> Thank you so much for your help!
> 
> Kind regards, Jenny
> ___
> 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
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] recon-all: too many levels of symbolic links

[Bruce Fischl]

Which other ones? Grab a whole new distribution, unpack it somewhere and either 
use it or move the dirs you need where you want them. Or wait a few weeks for 
5.2
Bruce


On Dec 20, 2012, at 8:29 AM, Linda Zhang  wrote:

> Thanks Bruce, from where? Should I download the other directories I seem to 
> be missing as well?
> 
> On 20 Dec 2012 21:26, "Bruce Fischl"  wrote:
> Looks like you don't have 
>> /home/virtualuser/freesurfer/subjects/lh.EC_average
> 
> You will need to download it
> Cheers
> Bruce
> 
> On Dec 20, 2012, at 12:32 AM, Linda Zhang  wrote:
> 
>> Hi Bruce,
>> 
>> This is what I get:
>> 
>> FreeSurfer:~/freesurfer/lindadata> ls -l
>> drwxr-sr-x 42 virtualuser virtualuser 4096 2012-11-17 07:38 subjects
>> FreeSurfer:~/freesurfer/lindadata> ls /subjects/lh.EC_average/surf
>> ls: cannot access /subjects/lh.EC_average/surf: No such file or directory
>> FreeSurfer:~/freesurfer/lindadata> ls -l /subjects/lh.EC_average 
>> lrwxrwxrwx 1 virtualuser virtualuser 51 2012-11-17 07:38 
>> /home/virtualuser/freesurfer/lindadata/subjects/lh.EC_average -> 
>> /home/virtualuser/freesurfer/subjects/lh.EC_average
>> FreeSurfer:~/freesurfer/lindadata> ls /home/virtualuser/freesurfer/subjects/
>> cvs_avg35  fsaverage  fsaverage3  fsaverage4  fsaverage5  fsaverage6  README 
>>  V1_average
>> 
>> 
>> 
>> 
>> On 19 December 2012 21:43, Bruce Fischl  wrote:
>>  ls -1 $FREESURFER_HOME/subjects
>> cvs_avg35/
>> cvs_avg35_inMNI152/
>> fsaverage/
>> fsaverage3/
>> fsaverage4/
>> fsaverage5/
>> fsaverage6/
>> fsaverage_sym/
>> lh.EC_average/
>> README
>> rh.EC_average/
>> sample-001.mgz
>> sample-002.mgz
>> surfer.log
>> V1_average/
>> 
>> not sure why it thinks it doesn't exist. What are the permissions on
>> 
>> /home/virtualuser/freesurfer/lindadata/subjects/lh.EC_average
>> 
>> can you do an ls on
>> 
>> /home/virtualuser/freesurfer/lindadata/subjects/lh.EC_average/surf
>> 
>> and post the results? Also do:
>> 
>> ls -l /home/virtualuser/freesurfer/lindadata/subjects/lh.EC_average
>> 
>> 
>> On Wed, 19 Dec 2012, Linda Zhang wrote:
>> 
>> Dear all,
>> 
>> I've run into the same error with recon-all -autorecon3.  It could be that 
>> when I moved my data into the new SUBJECTS_DIR, I
>> missed something out.  What files should be in the $FREESURFER_HOME/subjects 
>> directory?
>> 
>> The error reads as follows:
>> 
>> #@# Ex-vivo Entorhinal Cortex Label lh Fri Dec 14 19:07:03 HKT 2012
>> INFO: lh.EC_average subject does not exist in SUBJECTS_DIR
>> INFO: Creating symlink to lh.EC_average subject...
>> 
>>  cd /home/virtualuser/freesurfer/lindadata/subjects; ln -s 
>> /home/virtualuser/freesurfer/subjects/lh.EC_average; cd -
>> 
>> ln: creating symbolic link `./lh.EC_average': File exists
>> 
>>  mris_spherical_average -erode 1 -orig white -t 0.4 -o ncpoCCW label 
>> lh.entorhinal lh sphere.reg lh.EC_average
>> lh.entorhinal_exvivo.label
>> 
>> painting output onto subject ncpoCCW.
>> processing subject lh.EC_average...
>> MRISread(/home/virtualuser/freesurfer/lindadata/subjects/lh.EC_average/surf/lh.sphere.reg):
>>  could not open file
>> eroding label 1 times before writing
>> thresholding label stat at 0.400 before writing
>> No such file or directory
>> mris_spherical_average: could not read surface file
>> /home/virtualuser/freesurfer/lindadata/subjects/lh.EC_average/surf/lh.sphere.reg
>> No such file or directory
>> Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC 
>> 2011 i686 GNU/Linux
>> 
>> recon-all -s ncpoCCW exited with ERRORS at Fri Dec 14 19:07:07 HKT 2012
>> 
>> For more details, see the log file 
>> /home/virtualuser/freesurfer/lindadata/subjects/ncpoCCW/scripts/recon-all.log
>> To report a problem, see 
>> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> 
>> 
>> Cheers,
>> Linda
>> 
>> 
>> 
>> On 14 November 2012 22:29, Linda Zhang  wrote:
>> 
>>   Thanks Bruce.  It has 6gb assigned to the virtualbox, I'm running 
>> another process alongside it.  I'll stop the other
>>   one and try again.
>> 
>>   On 14 Nov 2012 22:14, "Bruce Fischl"  
>> wrote:
>> sounds like you are running out of memory. How much ram is in 
>> that machine? Are other processes running
>> at the same time?
>> On Wed, 14 Nov 2012, Linda Zhang wrote:
>> 
>>   Dear all,
>>   After moving my data to a different folder, I've come 
>> across a different error when running
>>   recon-all (autorecon2 and 3).  The
>>   last few lines are as follows:
>> 
>>   0117: dt=32.368000, rms=0.713 (0.122%), neg=0, invalid=766
>>   0118: dt=32.368000, rms=0.713 (0.033%), neg=0, invalid=766
>>   0119: dt=32.368000, rms=0.712 (0.059%), neg=0, invalid=766
>>   0120: dt=32.368000, rms=0.712 (0.081%), neg=0, invalid=766
>>   0121: dt=16.184000, rms=0.712 (0.009%), neg=0, invalid=766
>>   Killed
>>   ERROR

Re: [Freesurfer] new atlas

[Bruce Fischl]

Hi Gabriel
Colin27 I believe has been reconned, and if not you can just run it and use our 
standard tools for mapping. The others you can use the talairach.xfm for, but 
it won't be terribly accurate. You can't use our training and labeling unless 
you have the original datasets that went into the atlas.
Cheers
Bruce



On Dec 19, 2012, at 8:05 AM, Gabriel Gonzalez Escamilla  wrote:

> Dear Freesurfers,
> 
> Sorry for so many and basic questions lately.
> 
> I'm working with my set of subjects (T1), and I'm looking for a different WM 
> parcellation than the aseg.mgz, I have an atlas (JHU atlas in MNI space, Mori 
> et al 1999, and some other in Colin27 space).
> 
> I'm guessing I will have to use the FSaverage subject as target space. Since 
> FS has many algorithms to make registrations, and the mris_ca_train requieres 
> the predefined labels into an anootation file. I'm wondering about the best 
> way to translate all the WM labeling from this atlas into FS space. 
> 
> 
> Many thanks in advanced,
> Gabriel
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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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
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] space of T1.mgz

[Bruce Fischl]

Hi Mojdeh
Have you checked out Koen van Leemput's hippocampal fled segmentation that you 
can run through recon-all? It might do what you want automatically.
Cheers
Bruce



On Dec 19, 2012, at 4:07 PM, Mojdeh Zamyadi  wrote:

> Hi there,
> 
> Sorry, if my question is confusing. This is what I want to do, I have
> two groups of controls and patients and I've already run recon-all on
> them. I now want to know the head/body/tail volumes. What I did was:
> 1. used "mri_binarize" to get the right and left hippocampal masks from
> the cortical segmentation (using label numbers 17, 53)
> 2. used "mri_convert" to convert left_hippo.mgz, right_hippo.mgz and
> T1.mgz into .nii files.
> 3. use itk SNAP to manually segment the total hippocampus (the
> freesurfer mask) into head, body and tail.
> 
> now, my questions is regarding the last step. If the individual
> segmentations are in the native space, I can't be sure that the
> landmarks I'm using for head/body/tail separation is always the same
> (since some of the subjects might be in an oblique space). So would you
> recommend that I first register the T1 and segmentations all into a
> common space? Also, I was wondering if the segmentation is going to
> effect the actual volume (since the brain is going to be stretched and
> transformed while doing the registration). I hope I made my question
> clear and I would greatly appreciate your advice.
> 
> Thanks,
> -Mojdeh
> 
> On 12/18/2012 12:58 PM, Bruce Fischl wrote:
>> Hi Mojdeh
>> 
>> they are not in atlas space and the volumes are for that subject, so
>> you shouldn't have to do anything if I understand you correctly
>> 
>> cheers
>> Bruce
>> 
>> On Tue, 18 Dec 2012, Mojdeh Zamyadi wrote:
>> 
>>> Hi Doug,
>>> 
>>> Thanks for the quick reply. I actually saw this link before first
>>> posting my question but it doesn't quite answer my question. What I want
>>> to know is whether the T1.mgz&  aseg.mgz files are in an atlas space? if
>>> that's the case, it means the segmentation for all my subjects are in
>>> the same space and I don't need to convert anything if I want to compare
>>> their hippocampal volumes. I'm not quite sure if any sort of
>>> registration to an atlas is done in any steps of recon-all or not. I
>>> would appreciate if could clarify this for me.
>>> 
>>> Thanks,
>>> -Mojdeh
>>> 
>>> On 12/18/2012 12:18 PM, Douglas N Greve wrote:
 Hi Mojdeh, try looking at this doc
 http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
 doug
 
 On 12/18/2012 11:09 AM, Mojdeh Zamyadi wrote:
> Hi all,
> 
> I want to segment the hippocampus into head/body/tail in itk SNAP
> using
> the hippocampus mask that I create from the result of recon-all
> segmentation. My question is, are the T1.mgz and aseg.mgz files in the
> native space of the image or in the atlas space? I know the voxel size
> is different (1x1x1 mm) from the original voxel size (0.49x0.49x0.45),
> but I want to know if the original images are registered to a common
> atlas space or just resampled to a different voxel size. The reason
> I'm
> asking this, is because I'm doing a group study and I want to make
> sure
> all my subjects are in the same space so that the segmentation I do is
> accurate for all.
> 
> Thanks for your help,
> 
> Mojdeh Zamyadi, MSc
> Clinical Research Project Assistant
> The Hospital for Sick Children
> 555 University Avenue
> Toronto ON M5G 1X8
> 
> 
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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
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Re: [Freesurfer] putamen seg

[Bruce Fischl]

Hi Greg
What version are you using and what acquisition? There are some expert options 
you could try like editing one volume and using it as an example for all 
further intensity estimations
Cheers
Bruce 



On Dec 18, 2012, at 5:40 PM, Gregory Kirk  wrote:

> 
> Hi,
> 
> tried to use control points to improve the segmentation of the putamen in the
> difficult area between putamen,claustrum & insula. adding some white matter 
> control points does not seem to insluence the aseg segmentation. control 
> points are set to 110 after reprocessing 
> with recon-all -autorecon2-cp -autorecon3 -subjid 008 ( v5.1), but these same 
> points are still labeled as putamen?
> 
> also i do see that some white matter filaments have leaked into the putamen, 
> so the mailing list
> comments that control points would mess it up seems it would be correct ( if 
> it was affecting
> the putamen seg, which it does not seem to have done at all).
> 
> so options are manual editing, here ask opinions, the extra tissue added 
> between the putamen&insula it is doing consistently, so taking the unedited 
> volumes, after checking there are no odd other things added or missing
> might be more unbiased estimate, that volumes after several human raters had 
> selectively removed a few voxels here and there ?
> 
> any opinions ?
> 
> thanks
> 
> greg
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Re: [Freesurfer] Error with fs-fast selxavg3-sess

[Yuval Harpaz]

> Dear FreeSurfer group
> I am new to free surfer and have dificulties running fs-fast analysis for
> the first time
> I use freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 on ubuntu but ran
> the same commands for the same data on a NMR computer (nmr-stable5.0-env)
> which gave the same error
> the data was acquired using GE machine
>
> I have 1 subject 2 conditions and used the below commands to process my
> data
> running  selxavg3-sess gave errors for gammafit and FIR. here is the
> script and error for gammafit.
>
> mkanalysis-sess -analysis vg.sm5.lh -surface self lh -event-related
> -paradigm VG.par -polyfit 2 -nskip 0 -nconditions 2 -TR 4 -mcextreg -fsd
> bold -gammafit 2.25 1.25 -fwhm 5 -refeventdur 3
> mkcontrast-sess -analysis vg.sm5.lh -contrast VG-vs-OE -a 2 -c 1
> selxavg3-sess -s vgoe -analysis vg.sm5.lh
> ...
> Output argument "partype" (and maybe others) not assigned during call to
>
> "/usr/local/freesurfer/stable5_0_0/fsfast/toolbox/fast_ldpar4.m>fast_ldpar4".
>
> Error in flac_customize (line 123)
> [par partype] = fast_ldpar4(parpath);
>
> Error in fast_selxavg3 (line 67)
> flac0 = flac_customize(flac0);
>
>
> for FIR the error was
>
> ERROR: creating FIR design matrix for Condition01
> ??? Attempt to reference field of non-structure array.
>
> Error in ==> flac_customize at 357
> if(~isempty(flacnew.TFmtx))
>
> Error in ==> fast_selxavg3 at 65
> flac0 = flac_customize(flac0);
>
> do you have any idea what it might be?
> at some point I got complaints about NaNs in my data which are not allowed
> for SVD but I cannot replicate the error
> thanks
> --
> Yuval
>
>
>
>
> Dr .Harpaz
>
> BIU MEG lab 
>
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[Freesurfer] downloading GradientUnwarping

[John Drozd]

Hello,

I would like to download and install the software described at

http://surfer.nmr.mgh.harvard.edu/fswiki/GradientUnwarping

Your email address is listed on this website.

I cannot find a download link.

We would like to use this with Freesurfer.

Do you know where I can download this software from?

Thank you,

John

John J. Drozd, M.Sc., Ph.D.
Post-Doctoral Fellow
Robarts Research Institute
Western University
London, Ontario, Canada
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Re: [Freesurfer] downloading GradientUnwarping

[dgw]

Is it not included in your freesurfer installation?

To check:
After sourcing Freesurfer type

which grad_unwarp

HTH
Dan

On Thu, Dec 20, 2012 at 9:42 AM, John Drozd  wrote:
> Hello,
>
> I would like to download and install the software described at
>
> http://surfer.nmr.mgh.harvard.edu/fswiki/GradientUnwarping
>
> Your email address is listed on this website.
>
> I cannot find a download link.
>
> We would like to use this with Freesurfer.
>
> Do you know where I can download this software from?
>
> Thank you,
>
> John
>
> John J. Drozd, M.Sc., Ph.D.
> Post-Doctoral Fellow
> Robarts Research Institute
> Western University
> London, Ontario, Canada
>
>
>
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[Freesurfer] Running SPM8

[Staples, Lindsay Katharine]

Hi-

Our Unix system was recently updated and I am now unable to use SPM 8 from 
/autofs/space/grover_001 or from /autofs/space/bert_002. I get the following 
message:

Initialising SPM...Error using fileparts
Too many output arguments.

Error in cfg_util>local_initapps (line 1217)
[p n e v] = fileparts(appcfgs{k});

Error in cfg_util (line 587)
local_initapps;

Error in spm_jobman (line 149)
cfg_util('initcfg'); % This must be the first call to cfg_util

Error in spm (line 344)
spm_jobman('initcfg');

Any words of wisdom?

Thanks!
Lindsay


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Re: [Freesurfer] Error with fs-fast selxavg3-sess

[Sebastian Moeller]

Hi Yuval,

while I have no real clue about your specific issues, it reminds e of an issue 
we had in the past. We had used some condition names that start with a number 
instead of a letter (e.g. "90degree") and the parsing code choked on that, as 
it uses the first character of a field and tries to see whether that is a 
number (as compared to taking the whole field) and that fails. (This 
complication only arrises as the code tries to allow 3, 4 and 5? column formats 
for the paradigm files, where the condition name lives in different columns or 
so). Alas at that time we grudgingly changed our condition naming and moved on, 
instead of properly fixing this and feeding the changes back to Doug (sorry for 
that). So on the off-chance that this is the issue check your condition naming 
inside the parameter file for numeric prefixes…

best
Sebastian



On Dec 20, 2012, at 06:00 , Yuval Harpaz wrote:

> 
> Dear FreeSurfer group
> I am new to free surfer and have dificulties running fs-fast analysis for the 
> first time
> I use freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 on ubuntu but ran the 
> same commands for the same data on a NMR computer (nmr-stable5.0-env) which 
> gave the same error
> the data was acquired using GE machine
> 
> I have 1 subject 2 conditions and used the below commands to process my data
> running  selxavg3-sess gave errors for gammafit and FIR. here is the script 
> and error for gammafit.
> 
> mkanalysis-sess -analysis vg.sm5.lh -surface self lh -event-related -paradigm 
> VG.par -polyfit 2 -nskip 0 -nconditions 2 -TR 4 -mcextreg -fsd bold -gammafit 
> 2.25 1.25 -fwhm 5 -refeventdur 3
> mkcontrast-sess -analysis vg.sm5.lh -contrast VG-vs-OE -a 2 -c 1
> selxavg3-sess -s vgoe -analysis vg.sm5.lh
> ...
> Output argument "partype" (and maybe others) not assigned during call to
> "/usr/local/freesurfer/stable5_0_0/fsfast/toolbox/fast_ldpar4.m>fast_ldpar4".
> 
> Error in flac_customize (line 123)
> [par partype] = fast_ldpar4(parpath);
> 
> Error in fast_selxavg3 (line 67)
> flac0 = flac_customize(flac0);
> 
> 
> for FIR the error was 
> 
> ERROR: creating FIR design matrix for Condition01
> ??? Attempt to reference field of non-structure array.
> 
> Error in ==> flac_customize at 357
> if(~isempty(flacnew.TFmtx))
> 
> Error in ==> fast_selxavg3 at 65
> flac0 = flac_customize(flac0);
> 
> do you have any idea what it might be?
> at some point I got complaints about NaNs in my data which are not allowed 
> for SVD but I cannot replicate the error
> thanks
> -- 
> Yuval
> 
> 
> 
> 
> Dr .Harpaz
> 
> BIU MEG lab
> 
> 
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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
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> at
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> properly
> dispose of the e-mail.

-- 
Sebastian Moeller

telephone: +1-626-325-8598 /+1-626-395-6523 / +1-626-395-6616
fax: 626-395-8826
German GSM:  +49 - 15 77 - 1 90 31 41
mobile: +1-626-325-8598
+1-626-807-5242
US CDMA: +1-626-807-5242
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Division of Biology
MC 114-96
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USA


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Re: [Freesurfer] downloading GradientUnwarping

[John Drozd]

Thanks Dan.

It is already installed with Freesurfer as you say:

[jdrozd@trumpet bin]$ pwd
/trumpet/downloads/FreeSurfer/freesurfer/bin
[jdrozd@trumpet bin]$ ./grad_unwarp

USAGE: grad_unwarp

   -i infile   : dcmdir or dcmfile or mghfile
   -s seriesno : dicom series - needed only if invoking -i dcmdir
   -unwarp: gradient unwarping
: Optional type is the gradient unwarping displacements
: map to use - supply either scanner gradient model (sonata,
: allegra, brm, crm) or map filename.  (BRM is GE like
: UCSD's 1.5T; CRM is GE like MGH Bay 1, BWH-GE, Duke-GE.)
: If unwarping an mgh volume, user _must_ supply a type.
   -nojac   : don't do jacobian correction when unwarping
   -corfov  : resample to cor FOV (bug: recenters volume on (0,0,0))
   -cor : save as COR format instead of mgh (you should use -corfov as well)
   -interp  : method (,linear,nearest,spline)
   -o outfile  : MGH formatted by default (unless -cor is specified)
   -matlab matlab_binary  : default is
/space/lyon/6/pubsw/common/matlab/6.5/bin/matlab
  : grad_unwarp needs at least version 6.5 to
handle the long.
  : filenames.  And this installation has
crucial dicom patches.
   -version : print version string
   -help: print help text



On 12/20/12, dgw  wrote:
> Is it not included in your freesurfer installation?
>
> To check:
> After sourcing Freesurfer type
>
> which grad_unwarp
>
> HTH
> Dan
>
> On Thu, Dec 20, 2012 at 9:42 AM, John Drozd  wrote:
>> Hello,
>>
>> I would like to download and install the software described at
>>
>> http://surfer.nmr.mgh.harvard.edu/fswiki/GradientUnwarping
>>
>> Your email address is listed on this website.
>>
>> I cannot find a download link.
>>
>> We would like to use this with Freesurfer.
>>
>> Do you know where I can download this software from?
>>
>> Thank you,
>>
>> John
>>
>> John J. Drozd, M.Sc., Ph.D.
>> Post-Doctoral Fellow
>> Robarts Research Institute
>> Western University
>> London, Ontario, Canada
>>
>>
>>
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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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[Freesurfer] Monte Carlo

[Susan Alice McLaughlin]

Hi Doug,

I am trying to run a Monte Carlo simulation on functional data constrained to a 
label. Looking at a previous post - 
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-November/016290.html
 - I see that your advice is to 1) constrain when running mri_glmfit, then 2) 
use mri_glmfit-sim rather than running mri_glmfit with the simulation options. 
I have done step 1, however when I try to mri_glmfit-sim, I receive a "command 
not found" message. 

I confess that I am running an old version of Freesurfer (v 1.133.2.5). Is this 
my problem? If so, will it be a problem if I run mri_glmfit with the simulation 
options?

Thank you and happy holidays,

Susan McLaughlin
Doctoral Candidate
SPACE Lab (Stimulus-Parametric Imaging of Auditory Cortex)
Dept. of Speech and Hearing Sciences
University of Washington

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Re: [Freesurfer] Fwd: tracula problem:poor forceps major tract

[Anastasia Yendiki]

Hi Bryon - I was able to reconstruct the forceps major in your subject 
after tweaking some of the 7 control points for the initialization. I'm 
attaching the text file with the corrected control points - just drop it 
in dlabel/diff and rerun the path reconstruction (don't use reinit, 
though!)


I'd definitely not go below 7 control points for this subject b/c of how 
convoluted the shape of the forceps major is (due to enlarged ventricles & 
thin corpus callosum). You might've even gotten it to work automatically 
if you'd gone to more than 7 control points but I haven't tried.


I'll try to incorporate some of this logic into the program in the next 
version but if you need to do this edit on more cases in the meantime:


1. Fit a spline to your control points:
   dmri_spline --cpts dlabel/diff/fmajor_PP_avg33_mni_bbr_cpts_7.txt \
   --mask dmri/dtifit_FA.nii.gz \
   --out  dlabel/diff/fmajor_PP_avg33_mni_bbr_cpts_7.nii.gz

2. Display dlabel/diff/fmajor_PP_avg33_mni_bbr_cpts_7.nii.gz on top of
   dmri/dtifit_FA.nii.gz and see where the spline strays off the white
   matter.

3. Edit dlabel/diff/fmajor_PP_avg33_mni_bbr_cpts_7.txt by changing one of
   the control points that are near the part that's off the white matter.

4. Repeat.

Sorry, this is so not user friendly but we're working on improvements!

Hope this helps a bit,
a.y

On Thu, 29 Nov 2012, bryon mueller wrote:


After processing dozens of subjects through tracula I have found some subjects 
with tracts
that are one voxel along the entire tract, for example the forceps major. After 
reviewing the
data I believe the bvecs files are pointing the correct direction, I believe 
the registration
between the T1/freesurfer segmentation and DTI is reasonably good (registration 
was performed
with bbr), at least the anat_brain_mask-vent.bbr and dtifit_FA are reasonable 
and cortex.bbr
and lowb_brain seem reasonably well registered. The brain extraction does look 
poor in that a
large chunk of posterior skull remains in the anat_brain_mask-vent.bbr image 
but the as the
registrations, segmentations and parcellations look OK I believe this isn't the 
cause of my
problems.

I do see one issue: the registration between the dtifit_FA.bbr and
fmajor_PP_avg33_mni_bbr_logprior_0 images. Sections of the logprior volume are 
entirely in
the lateral ventricles of the DTI data. Please see attached jpg. This subject  
large lateral
ventricles and I am wondering if such subjects can be run successfully in 
tracula. Much
thanks for any suggestions.


65.0599  24.5455  29.0648
73.4687  33.3766  22.4575
71.6753  39.7266  24.7112
61.7057  49.7273  27.5844
49.4377  36.6735  27.1492
52.892  30.3552  22.741
57.4436  24.4573  31.4298
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Re: [Freesurfer] TRACULA tract path failure

[Anastasia Yendiki]

Hi Arman - I changed one of your 5 controls points for the forceps major 
to make sure that the initial path is well within the white matter, 
following the approach I described to Bryon in my previous email. I'm 
attaching the edited text file, please save it in the dlabel/diff/ 
directory of your subject and rerun the path reconstruction, making sure 
that reinit is not set to 1. You can rerun only the fmajor by editing the 
pathlist variable in your configuration file.


Hope this helps,
a.y

On Mon, 3 Dec 2012, Arman Eshaghi wrote:


Dear Anastasia, 
Thanks for the suggestions. The new control point didn't help. Therefore I 
uploaded remaining
images. It would be great if you could have a look again. 

All the best,
Arman


On Sat, Dec 1, 2012 at 1:45 AM, Anastasia Yendiki 
 wrote:

  Hi Arman - One more thing. Do you mind sending me the original (non-skull
  stripped) T1 as well? We'd like to test a different registration method 
on it.
  Thanks!

  a.y

  On Fri, 30 Nov 2012, Arman Eshaghi wrote:

Dear Anastasia,
Thanks for your response. I have sent a subject that the problem in
forceps minor persists. 
What I have done so far was to re-run the pipeline with "reinit=1",
check the eigenvectors, increase control
points, switch off brain anatomical mask in dmric. It made the 
tracts
look better for many subjects but this one
still has problems in forceps minor.

Thanks,
Arman


On Fri, Nov 30, 2012 at 11:08 AM, Arman Eshaghi
 wrote:
      Dear Anastasia,
      Thanks for your response. I have sent a subject that the
problem in forceps minor persists. 
What I have done so far was to re-run the pipeline with "reinit=1",
check the eigenvectors, increase control
points, switch off brain anatomical mask in dmric. It made the 
tracts
look better for many subjects but this
one still has problems in forceps minor.

Thanks,
Arman


On Wed, Nov 28, 2012 at 7:34 PM, Anastasia Yendiki
 wrote:

      Hi Arman - Have you ruled out any issues with the gradient
directions? In situations where the
      problem is wide-spread, this seems to be the usual suspect. If
you've checked the eigenvectors
      and they're ok, can you send an example case where the problem
persists? You can use this page to
      upload a tar ball of all the tracula-related directories of 
the
subject:
             
https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html

      Thanks!
      a.y

      On Mon, 26 Nov 2012, Arman Eshaghi wrote:

            Dear all,
            I have difficulty sorting out the problem with some
tracts in several subjects,
            tracts are incomplete or
            missing. As it has come up quite a few times on the 
list,
for this sort of problem I
            have first set
            "reinit=1" and then increased control points to 7, and
re-ran trac-all with "-prior"
            flag. This has worked
            for some tracts in several subjects, however there are a
few subjects that still have
            this problem. 

            It would be great if someone could let me know what else
I might be able to do in
            order to correct
            missing/faulty tracts in my subjects. (The problem is 
not
limited to a specific
            tract, it varies in
            different subjects)

            All the best,
            -Arman




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Re: [Freesurfer] clarifications about running bedpost instead of tracl-all step 2

[Anastasia Yendiki]

Hi Prerona - As I've mentioned to others, you can ignore the "Degenerate 
spline segment" message.


I can't tell what you mean by "only traced a part of the trac". Can you 
see the rest of it when you play with the threshold? Are you 
reconstructing only the ILF? If not, do the other pathways look ok? Can 
you send a screenshot of what you see when you run the "freeview -tv ..." 
command from the tutorial?


Thanks,
a.y

On Mon, 17 Dec 2012, s0675204 wrote:


Hello

I have been running trac-paths, and thought it finishes with a message
saying no errors,
I get an error saying ERROR: Degenerate spline segment in the
intermediate message logs

Also I looked at the result using this command:
freeview -v $TUTORIAL_DATA/diffusion_tutorial/Diff001/dmri/dtifit_FA.nii.gz \
   
$TUTORIAL_DATA/diffusion_tutorial/Diff001/dpath/lh.ilf_AS_avg32_mni_flt/path.pd.nii.gz:colormap=jet:isosurface=0,0:color='Red'
\
   
$TUTORIAL_DATA/diffusion_tutorial/Diff001/dpath/rh.ilf_AS_avg32_mni_flt/path.pd.nii.gz:colormap=jet:isosurface=0,0:color='Red'
&

but it had only traced a part of the trac on one side and nothing on
the other side

Can you help me understand what went wrong and how to fix it?

Thank you so much for your help!

best wishes,

Prerona



On 12 December 2012 11:57, Anastasia Yendiki
 wrote:



1) Can't hurt to delete.
2) Yes.
3) Yes.


On Wed, 12 Dec 2012, s0675204 wrote:


Hello,

thank you for your help with the first steps of running Tracula.

I was trying to run trac-all step 3 (paths), but was getting an error
with the  mergedph1samples file. I saw on the mailbase that you have
suggested to run bedpost directly to fix this

I have 3 questions about this:

1) do I need to delete any of the (temporary?) files or folders
created by trac-all step 2 before running bedpost

2) should I run bedpost INSTEAD of trac-all step 2 for the remaining
subjects?

3) you have suggested on the list to run bedpost as:
bedpostx /usr/local/freesurfer/subjects/C001/dmri
is this the same dmri folder as created by tracula step 1 (for each
subject)

Thank you so much for your help with this - I really appreciate it

best wishes

Prerona


On 10 December 2012 19:54, Anastasia Yendiki
 wrote:




I'm guessing that this shows up in the scripts/trac-all.log of a
particular
subject? Then it applies to that subject.


On Mon, 10 Dec 2012, s0675204 wrote:


Hello

My trac- preproc has completed. However, I am confused about the
status message. It says:

#-
trac-preproc finished without error at Mon Dec 10 16:32:20 EST 2012
ERROR: cannot find /home/canlilab/SBU/data/recon_output/00387

Does this mean it was completed succesfully for everyone or everyone
but that 00387 person?

Is there any way I can verify this?

thank you so much for your help

best wishes,

Prerona


On 8 December 2012 13:38, Anastasia Yendiki
 wrote:





In your dmrirc, you define multiple subjects, but only one bvecfile
and
one
bvalfile that are used for all subjects.


On Sat, 8 Dec 2012, s0675204 wrote:


the values are the same but each subject has an individual bvec &
bval
file. so it depends on how the script will read it?

On 8 December 2012 00:03, Anastasia Yendiki
 wrote:






Are the bvecs/bvals not the same for all subjects?


On Fri, 7 Dec 2012, s0675204 wrote:


oh! i thought this was how these were meant to be! i will do that.
sadly i left the lab and came home for the day but i will try it
as
soon as i am back and let you know!
thank you so much! do we have to do this for each subject or just
one
time?



On 7 December 2012 23:51, Anastasia Yendiki
 wrote:







I see. Can you try formatting them in columns (1 column for the
bvals
and
3
columns for the bvecs)?


On Fri, 7 Dec 2012, s0675204 wrote:


yes! these are the original files

well these are the files i pointed to in my config file. and i
think
the script copies them over to the dmrirc folder?

best wishes,

Prerona


On 7 December 2012 23:38, Anastasia Yendiki
 wrote:








Yes, I can see that each of the bvecs/bvals files is one long
line.
Was
that
the case for the original files that you specified in the
dmrirc?


On Fri, 7 Dec 2012, s0675204 wrote:


Hi Anastasia

I had attached the files, but maybe they did not go through to
the
mailing list? So I am sending them to your email id. Hope this
is
okay

best wishes,

Prerona



-- Forwarded message --
From: s0675204 
Date: 7 December 2012 19:44
Subject: Re: [Freesurfer] Running Tracula: trac-preproc exited
with
ERRORS
To: freesurfer@nmr.mgh.harvard.edu


Hello

I think I spoke to soon!

It ended with errors again.

I get the error message: "bvecs and bvals don't have the same
number
of
entries"

I saw on some older messages on the mail-base you said that we
need
to
check that the number of entries in the bvals is same as and
bvecs
is
3 times as much as the number of volumes. I have checked that
this
is
the case

I am wondering if it is some formatting problem? there are no
spac

Re: [Freesurfer] trouble with tracula preprocessing step

[Anastasia Yendiki]

Hi Prerona - I think this is explained in the archives on the same thread 
as the bedpostx upgrade issue. If you run bedpostx outside of trac-all, 
you should create dmri/data.nii.gz as a symbolic link to dmri/dwi.nii.gz 
and dmri/nodif_brain_mask.nii.gz as a symbolic link to whichever brain 
mask you're using, usually the aparc+aseg_mask which is under dlabel/diff.


a.y

On Mon, 17 Dec 2012, s0675204 wrote:


Hello

I have one more problem. Some of the subjects completed step 1
(preprocessing) successfully according to the logs & there are no
error messages.
However, when I try to run the bedpost step on these subjects, I get
an error message saying there is no data.nii.gz file in the dmrirc
There is however a dwi.nii.gz file present

Can you help me understand what happened here? Has something gone
wrong? How can I fix it?

Thank you so much for your help!

best wishes,

Prerona


On 17 December 2012 12:48, s0675204  wrote:

Hello

I have been running trac-paths, and thought it finishes with a message
saying no errors,
I get an error saying ERROR: Degenerate spline segment in the
intermediate message logs

Also I looked at the result using this command:
freeview -v $TUTORIAL_DATA/diffusion_tutorial/Diff001/dmri/dtifit_FA.nii.gz \

$TUTORIAL_DATA/diffusion_tutorial/Diff001/dpath/lh.ilf_AS_avg32_mni_flt/path.pd.nii.gz:colormap=jet:isosurface=0,0:color='Red'
\

$TUTORIAL_DATA/diffusion_tutorial/Diff001/dpath/rh.ilf_AS_avg32_mni_flt/path.pd.nii.gz:colormap=jet:isosurface=0,0:color='Red'
&

but it had only traced a part of the trac on one side and nothing on
the other side

Can you help me understand what went wrong and how to fix it?

Thank you so much for your help!

best wishes,

Prerona



On 12 December 2012 11:57, Anastasia Yendiki
 wrote:



1) Can't hurt to delete.
2) Yes.
3) Yes.


On Wed, 12 Dec 2012, s0675204 wrote:


Hello,

thank you for your help with the first steps of running Tracula.

I was trying to run trac-all step 3 (paths), but was getting an error
with the  mergedph1samples file. I saw on the mailbase that you have
suggested to run bedpost directly to fix this

I have 3 questions about this:

1) do I need to delete any of the (temporary?) files or folders
created by trac-all step 2 before running bedpost

2) should I run bedpost INSTEAD of trac-all step 2 for the remaining
subjects?

3) you have suggested on the list to run bedpost as:
bedpostx /usr/local/freesurfer/subjects/C001/dmri
is this the same dmri folder as created by tracula step 1 (for each
subject)

Thank you so much for your help with this - I really appreciate it

best wishes

Prerona


On 10 December 2012 19:54, Anastasia Yendiki
 wrote:




I'm guessing that this shows up in the scripts/trac-all.log of a
particular
subject? Then it applies to that subject.


On Mon, 10 Dec 2012, s0675204 wrote:


Hello

My trac- preproc has completed. However, I am confused about the
status message. It says:

#-
trac-preproc finished without error at Mon Dec 10 16:32:20 EST 2012
ERROR: cannot find /home/canlilab/SBU/data/recon_output/00387

Does this mean it was completed succesfully for everyone or everyone
but that 00387 person?

Is there any way I can verify this?

thank you so much for your help

best wishes,

Prerona


On 8 December 2012 13:38, Anastasia Yendiki
 wrote:





In your dmrirc, you define multiple subjects, but only one bvecfile
and
one
bvalfile that are used for all subjects.


On Sat, 8 Dec 2012, s0675204 wrote:


the values are the same but each subject has an individual bvec &
bval
file. so it depends on how the script will read it?

On 8 December 2012 00:03, Anastasia Yendiki
 wrote:






Are the bvecs/bvals not the same for all subjects?


On Fri, 7 Dec 2012, s0675204 wrote:


oh! i thought this was how these were meant to be! i will do that.
sadly i left the lab and came home for the day but i will try it
as
soon as i am back and let you know!
thank you so much! do we have to do this for each subject or just
one
time?



On 7 December 2012 23:51, Anastasia Yendiki
 wrote:







I see. Can you try formatting them in columns (1 column for the
bvals
and
3
columns for the bvecs)?


On Fri, 7 Dec 2012, s0675204 wrote:


yes! these are the original files

well these are the files i pointed to in my config file. and i
think
the script copies them over to the dmrirc folder?

best wishes,

Prerona


On 7 December 2012 23:38, Anastasia Yendiki
 wrote:








Yes, I can see that each of the bvecs/bvals files is one long
line.
Was
that
the case for the original files that you specified in the
dmrirc?


On Fri, 7 Dec 2012, s0675204 wrote:


Hi Anastasia

I had attached the files, but maybe they did not go through to
the
mailing list? So I am sending them to your email id. Hope this
is
okay

best wishes,

Prerona



-- Forwarded message --
From: s0675204 
Date: 7 December 2012 19:44
Subject: Re: [Freesurfer] Running Tracula: trac-preproc exited
w

Re: [Freesurfer] Diffusion Tensor Imaging

[Anastasia Yendiki]

Hi Yaniv - What results did you anticipate and what results did you get?

a.y

On Thu, 20 Dec 2012, Yaniv Kaufman wrote:

> Dear Freesurfers,
>
> I am not very experienced with Freesurfer and would like to construct a 
> Diffusion Tensor Image. I have the .bvecs, .bvals and .img files which I 
> believe should suffice. I am aware that the format is slightly old but I 
> believe it should still be fine. I attempted to use dt_recon and 
> freeview but could not quite get the results I anticipated. I would 
> really appreciate any help.
>
> Many thanks in advance,
> Yaniv
> ___
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>
>
>
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] Interpretation of voxel values in TRACULA "path.pd" images

[Anastasia Yendiki]

Hi Ping - The total number of paths that were sampled doesn't enter the 
picture. Of these sampled paths, some get rejected and some get accepted. 
The latter are added up to get an estimate of the posterior probability 
distribution of the path (that's path.pd.nii.gz). You can normalize to a 
total sum of 1 by diving that volume with its total sum.

The default threshold is 20% of the maximum value, to get rid of the tails 
of the distribution (which would need more total samples to converge than 
the center of the distribution anyway). You can of course find your own 
averages at a different threshold from path.pd.nii.gz if you wish.

Hope this helps,
a.y

On Fri, 14 Dec 2012, Ping-Hong Yeh wrote:

> Hi Anastasia,
> Just follow up on this thread..
> If 5000 samples were used for each voxel, how can I normalize the
> intensity of path.pd volumes to a sum of 1 ?
> Also what thresholding value was chosen to calculate the tract volume,
> shown in the pathstats.overall.txt ?
>
> Thanks.
> ping
>
>
>
> On Fri, Nov 9, 2012 at 10:56 AM, Anastasia Yendiki
>  wrote:
>>
>> Hi Jon - The path.pd volumes are indeed the posterior probability
>> distributions of each pathway. They are not normalized to a sum of 1
>> though b/c they're estimated by a sampling algorithm (drawing sample paths
>> from this unknown distribution and adding up the sample paths, instead of
>> estimating the distribution directly).
>>
>> Hope this helps,
>> a.y
>>
>> On Fri, 9 Nov 2012, Jon Clayden wrote:
>>
>>> Dear all,
>>> I understand that the various "path.pd" image files that are created by 
>>> TRACULA represent a posterior
>>> distribution over the corresponding tract location, but I was wondering if 
>>> someone could explain to me
>>> exactly what the values in these images mean. I assume that they are not 
>>> probabilities as such, since they
>>> have values ranging up to several hundreds.
>>>
>>> Thanks in advance,
>>> Jon
>>>
>>>
>> ___
>> Freesurfer mailing list
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it is
>> addressed. If you believe this e-mail was sent to you in error and the e-mail
>> contains patient information, please contact the Partners Compliance 
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you in 
>> error
>> but does not contain patient information, please contact the sender and 
>> properly
>> dispose of the e-mail.
>>
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>
>
>
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Re: [Freesurfer] Deterministic global tractography

[Anastasia Yendiki]

Hi Maia - It would still be probabilistic global tracrography, you'd just 
run it without anatomical priors since you don't have any prior knowledge 
of what areas your pathway goes through.

For each subject you'd need to define the two end ROIs of the pathway and 
(this is the trickier part) an initial guess for the pathway (a few 
control points on an imaginary curve that connects the two end ROIs). Is 
that easy to get for each subject? You could possibly pick the control 
points in MNI space and then map them back to each individual, if they 
align well.

You'd then run the dmri_paths command. Run it without any arguments and 
ignore anything other than the "basic inputs" section of the help. It's 
not particularly well-documented, since typically it's run through 
trac-all.

Hopefully this can get you started, let me know if you more questions.

a.y

On Mon, 17 Dec 2012, Maia Kipman wrote:

> Good Morning,
> I would like to run deterministic global tracktography on 2 tracts for
> which tract tracing techniques in animals have established white
> matter connections. However, these tracts are not part of the 18
> segmented in TRACULA. Because of crossing fibers, deterministic global
> tractography is more appropriate for the analysis I am running than
> local tracktography or probabilistic tractography. If I have run
> freesurfer segmentation for this cohort is there a mechanism I can use
> to run deterministic global tractography in the subjects native DWI
> space between two regions segmented by freesurfer?
>
> Thanks!
>
> Maia
>
> 
> Maia Kipman
> Study Coordinator
> Clinical Research Assistant
> Center for Depression, Anxiety and Stress Research
> McLean Hospital - Mail Stop #334
> 115 Mill Street
> Belmont, MA 02478
> tel:(617)855-2239
> mkip...@mclean.harvard.edu
>
>
>
> ___
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>
>
>
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[Freesurfer] eating disorders, starvation, morphometry

[Jenny Mercolini]

Hi everyone,

does anyone on the FS mailing list have any good recommendations for
litterature  on anorexia nervosa / eating disorders / starvation and brain
morphometry ?

I am especially interested in any study using FreeSurfer software.

Thank you very much in advance,

- Jenny Mercolini
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] TRACULA tract path failure

[Arman Eshaghi]

Thank you for correcting this. This in fact works. Alternatively after
re-running the pipeline with reinit=1 for so many times, as it tried
different initialization each time I managed to get the tract.

All the best,
-Arman


On Fri, Dec 21, 2012 at 12:56 AM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:

>
> Hi Arman - I changed one of your 5 controls points for the forceps major
> to make sure that the initial path is well within the white matter,
> following the approach I described to Bryon in my previous email. I'm
> attaching the edited text file, please save it in the dlabel/diff/
> directory of your subject and rerun the path reconstruction, making sure
> that reinit is not set to 1. You can rerun only the fmajor by editing the
> pathlist variable in your configuration file.
>
> Hope this helps,
> a.y
>
>
> On Mon, 3 Dec 2012, Arman Eshaghi wrote:
>
>  Dear Anastasia,
>> Thanks for the suggestions. The new control point didn't help. Therefore
>> I uploaded remaining
>> images. It would be great if you could have a look again.
>>
>> All the best,
>> Arman
>>
>>
>> On Sat, Dec 1, 2012 at 1:45 AM, Anastasia Yendiki <
>> ayend...@nmr.mgh.harvard.edu> wrote:
>>
>>   Hi Arman - One more thing. Do you mind sending me the original
>> (non-skull
>>   stripped) T1 as well? We'd like to test a different registration
>> method on it.
>>   Thanks!
>>
>>   a.y
>>
>>   On Fri, 30 Nov 2012, Arman Eshaghi wrote:
>>
>> Dear Anastasia,
>> Thanks for your response. I have sent a subject that the
>> problem in
>> forceps minor persists.
>> What I have done so far was to re-run the pipeline with
>> "reinit=1",
>> check the eigenvectors, increase control
>> points, switch off brain anatomical mask in dmric. It made
>> the tracts
>> look better for many subjects but this one
>> still has problems in forceps minor.
>>
>> Thanks,
>> Arman
>>
>>
>> On Fri, Nov 30, 2012 at 11:08 AM, Arman Eshaghi
>>  wrote:
>>   Dear Anastasia,
>>   Thanks for your response. I have sent a subject that the
>> problem in forceps minor persists.
>> What I have done so far was to re-run the pipeline with
>> "reinit=1",
>> check the eigenvectors, increase control
>> points, switch off brain anatomical mask in dmric. It made
>> the tracts
>> look better for many subjects but this
>> one still has problems in forceps minor.
>>
>> Thanks,
>> Arman
>>
>>
>> On Wed, Nov 28, 2012 at 7:34 PM, Anastasia Yendiki
>>  wrote:
>>
>>   Hi Arman - Have you ruled out any issues with the
>> gradient
>> directions? In situations where the
>>   problem is wide-spread, this seems to be the usual
>> suspect. If
>> you've checked the eigenvectors
>>   and they're ok, can you send an example case where the
>> problem
>> persists? You can use this page to
>>   upload a tar ball of all the tracula-related
>> directories of the
>> subject:
>>
>> https://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**
>> html 
>>
>>   Thanks!
>>   a.y
>>
>>   On Mon, 26 Nov 2012, Arman Eshaghi wrote:
>>
>> Dear all,
>> I have difficulty sorting out the problem with
>> some
>> tracts in several subjects,
>> tracts are incomplete or
>> missing. As it has come up quite a few times on
>> the list,
>> for this sort of problem I
>> have first set
>> "reinit=1" and then increased control points to
>> 7, and
>> re-ran trac-all with "-prior"
>> flag. This has worked
>> for some tracts in several subjects, however
>> there are a
>> few subjects that still have
>> this problem.
>>
>> It would be great if someone could let me know
>> what else
>> I might be able to do in
>> order to correct
>> missing/faulty tracts in my subjects. (The
>> problem is not
>> limited to a specific
>> tract, it varies in
>> different subjects)
>>
>> All the best,
>> -Arman
>>
>>
>>
>>
>> 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
>> con