[Freesurfer] Adding tracts to Tracula!

[Seán Froudist Walsh]

Hi FreeSurfing Gurus,

I would like to add some new tracts to the Tracula pipeline using my own
regions of interest. What would be the best way to do this?

All the best and many thanks in advance,

Seán
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[Freesurfer] mri_label2label problem

[Righart, Ruthger Dr.]

Dear Freesurfers,

I am using mri_label2label in Fs v5.0.0 to map a label between subjects. I have 
some problems in that the target label shows little holes while the location of 
the target label seems to correspond rather well with the source label. 
Checking these holes backward to the source subject using the function 
tools/send to subject in tksurfer ... brings the saved point in the source 
label.

I think this problem has been reported in the list before (see copy below) but 
unfortunately I do not find a solution that removes the holes. In my case I see 
this now and then both for ROIs that I drew myself in tksurfer but also 
pre-defined ROIs that were already there (e.g., 
rh.G_and_S_cingul-Mid-Ant.label). What might go wrong here? I am using 
--regmethod surface and trgsurf white. 

I wondered further how one may check how well mri_label2label worked for each 
subject. Is there a way to test that source and target labels have the same 
location in terms of for example gyri and sulci? Are there cases that 
mri_label2label cannot work?

Thank you very much for your help, any suggestions appreciated!

Ruthger Righart (PhD)

Institute for Stroke and Dementia Research (ISD)
Klinikum der Universität München
Max-Lebsche-Platz 30
81377 Munich | Germany

ruthger.righ...@med.uni-muenchen.de




http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15125.html

Re: [Freesurfer] Mri_label2label problem?
Douglas N Greve
Tue, 21 Sep 2010 06:47:09 -0700
what does the original label look like? Can you convert one of the 
predefined labels (eg, lh.V1.label) to see if the same thing happens?

doug

Pye, Brandon (NIH/NIMH) [F] wrote:
> Hey guys,
>
> We are using mri_label2label to convert a label created from a cluster (using 
> mri_surfcluster) from an average subject to each individual subject.  We have 
> 6 individual labels that we are converting.  All of the analysis is done 
> using surface data.  I use the command in the generalized form listed below:
>
> Mri_label2label -srcsubject fsaverage -srclabel cluster1.label -trg subject 
> Subject -trglabel Subject_cluster1.label -regmethod surface -hemi lh
>
> 5 of the 6 labels transfer well, but a 6th label translated to the correct 
> anatomical location, but the number of labeled vertices is greatly reduced 
> after the translation.  This problem persists across all subjects.  There 
> doesn't appear to be much interior to the label, just a lot of the outline of 
> the label (i.e. If the outline of the label is yellow and the interior is 
> blue, I see a lot of yellow and not much blue, as if there are a bunch of 
> small "islands").  The region on them most inferior part of the lateral 
> surface approximately where the temporal and occipital lobes meet.
>
> Any ideas what might be going on?
>
> Thanks,
> -
> Brandon Pye
> Post-Baccalaureate IRTA
> Laboratory of Brain and Cognition, NIMH/NIH/DHHS
> Building 10, Room 4C214
> 10 Center Dr MSC 1366
> Bethesda, MD 20892
> Phone: (301) 402-3893
> Fax: (301) 402-0921
> brandon@nih.gov
>
>

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Re: [Freesurfer] Tracula - error in pre-proc

[rspriti]

Hi Phoebe,

The fslroi part extracts all the low-b images from the 4D diffusion data
and creates an average low-b mask.

fslroi

 is the number of 3D low-b volumes to be extracted from the 4D
diffusion volume. For some reason tracula is unable to read the no. of
low-b images from your dicom header (Is this an MGH acquisition?). If you
know the number of low-b volumes you can specify that in the configuration
file using the following command:

set nb0 = *No. of low-b images*

Once you set that value it should not throw that error. From what you ran
in the commandline, I assume that in your dti acquisition 0 through 25 are
low-b volumes.

Creating the low-b image mask is the last step in the first stepwise
directive of tracula (-corr). You can go through the rest of the steps by
specifying any or all of the stepwise directives:

Ex: trac-all -intra -inter -masks -tensor -prior -c
./scripts/dmrirc_single_subject

Please let us know if you have any questions or problems running the same.

Thanks,
Priti

> Hi,
>
> I do the pre-processing with the following command:
>
> trac-all -prep -c ./scripts/dmrirc_single_subject
>
> THe process exits with error when it comes to fslroi (attached pls find
> the log file).  I try to re-run the fslroi command as follow:
>
> fslroi
> /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/dwi.nii.
> gz
> /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/lowb.nii.gz
>
> 0 25
>
> It works and the lowb.nii.gz looks normal.  In case if I have the same
> problem with another dataset, how can I incorporate the number of frames
> (25) in the trac-all command for the fslroi?  Can I continue the remaining
> procedures of trac-all from this point?
>
> Thank you.
>
> Phoebe.
> --
> ___
> Phoebe Suk-tak Chan, Ph.D.
> Athinoula A. Martinos Center for Biomedical Imaging
> Massachusetts General Hospital
> Bldg. 149, 13th St., mailcode 149-2301
> Charlestown, MA 02129
> pho...@nmr.mgh.harvard.edu
>
>
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Re: [Freesurfer] mri_label2label problem

[Douglas N Greve]

Can you send me the label?
doug

Righart, Ruthger Dr. wrote:
> Dear Freesurfers,
>
> I am using mri_label2label in Fs v5.0.0 to map a label between subjects. I 
> have some problems in that the target label shows little holes while the 
> location of the target label seems to correspond rather well with the source 
> label. Checking these holes backward to the source subject using the function 
> tools/send to subject in tksurfer ... brings the saved point in the source 
> label.
>
> I think this problem has been reported in the list before (see copy below) 
> but unfortunately I do not find a solution that removes the holes. In my case 
> I see this now and then both for ROIs that I drew myself in tksurfer but also 
> pre-defined ROIs that were already there (e.g., 
> rh.G_and_S_cingul-Mid-Ant.label). What might go wrong here? I am using 
> --regmethod surface and trgsurf white. 
>
> I wondered further how one may check how well mri_label2label worked for each 
> subject. Is there a way to test that source and target labels have the same 
> location in terms of for example gyri and sulci? Are there cases that 
> mri_label2label cannot work?
>
> Thank you very much for your help, any suggestions appreciated!
>
> Ruthger Righart (PhD)
>
> Institute for Stroke and Dementia Research (ISD)
> Klinikum der Universität München
> Max-Lebsche-Platz 30
> 81377 Munich | Germany
>
> ruthger.righ...@med.uni-muenchen.de
>
>
>
>
> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15125.html
>
> Re: [Freesurfer] Mri_label2label problem?
> Douglas N Greve
Tue, 21 Sep 2010 06:47:09 -0700
> what does the original label look like? Can you convert one of the 
> predefined labels (eg, lh.V1.label) to see if the same thing happens?
>
> doug
>
> Pye, Brandon (NIH/NIMH) [F] wrote:
>   
>> Hey guys,
>>
>> We are using mri_label2label to convert a label created from a cluster 
>> (using 
>> mri_surfcluster) from an average subject to each individual subject.  We 
>> have 
>> 6 individual labels that we are converting.  All of the analysis is done 
>> using surface data.  I use the command in the generalized form listed below:
>>
>> Mri_label2label -srcsubject fsaverage -srclabel cluster1.label -trg subject 
>> Subject -trglabel Subject_cluster1.label -regmethod surface -hemi lh
>>
>> 5 of the 6 labels transfer well, but a 6th label translated to the correct 
>> anatomical location, but the number of labeled vertices is greatly reduced 
>> after the translation.  This problem persists across all subjects.  There 
>> doesn't appear to be much interior to the label, just a lot of the outline 
>> of 
>> the label (i.e. If the outline of the label is yellow and the interior is 
>> blue, I see a lot of yellow and not much blue, as if there are a bunch of 
>> small "islands").  The region on them most inferior part of the lateral 
>> surface approximately where the temporal and occipital lobes meet.
>>
>> Any ideas what might be going on?
>>
>> Thanks,
>> -
>> Brandon Pye
>> Post-Baccalaureate IRTA
>> Laboratory of Brain and Cognition, NIMH/NIH/DHHS
>> Building 10, Room 4C214
>> 10 Center Dr MSC 1366
>> Bethesda, MD 20892
>> Phone: (301) 402-3893
>> Fax: (301) 402-0921
>> brandon@nih.gov
>>
>>
>> 
>
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>
>
>   

-- 
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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
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Re: [Freesurfer] Adding tracts to Tracula!

[Anastasia Yendiki]

Hi Seán - Which tracts do you want to add? Our existing tracts have been 
labeled on 33 healthy subjects. It's certainly possible to include new 
tracts in the atlas but someone has to do the labeling on the same or a 
similar set of subjects.


a.y

On Wed, 15 Jun 2011, Seán Froudist Walsh wrote:


Hi FreeSurfing Gurus,

I would like to add some new tracts to the Tracula pipeline using my own
regions of interest. What would be the best way to do this?

All the best and many thanks in advance,

Seán

 

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Re: [Freesurfer] Adding tracts to Tracula!

[Seán Froudist Walsh]

Hi Anastasia,

Thanks for getting back to me and well done on making a very nice program.
The first tracts I would like to have are the optic radiations, but there
are others that would be nice to include: a three part arcuate fasiculus (a
la Catani et al., 2005) rather than a 2 part one, Fornix, anterior
commissure.

If I were to manually do the dissections for the 33 subjects, what would be
the most Tracula compatible way of doing it? I normally use TrackVis but I
figure making all of the file conversions might be a nightmare. Which
program was used in the original virtual dissections?

Any further suggestions? Perhaps some of these tracts are included but I've
missed them.

Sean



On 15 June 2011 08:37, Anastasia Yendiki wrote:

>
> Hi Seán - Which tracts do you want to add? Our existing tracts have been
> labeled on 33 healthy subjects. It's certainly possible to include new
> tracts in the atlas but someone has to do the labeling on the same or a
> similar set of subjects.
>
> a.y
>
>
> On Wed, 15 Jun 2011, Seán Froudist Walsh wrote:
>
>  Hi FreeSurfing Gurus,
>>
>> I would like to add some new tracts to the Tracula pipeline using my own
>> regions of interest. What would be the best way to do this?
>>
>> All the best and many thanks in advance,
>>
>> Seán
>>
>>
>>
>>
>>
>
> 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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Re: [Freesurfer] Adding tracts to Tracula!

[Anthony Dick]

Hello all,

Is there any atlas to which these tracs are referenced? For cortical 
anatomical boundaries there is broad consensus and a published 
referenced atlas, which makes Freesurfer's automatic parcellation of 
cortical regions an excellent tool. But there is not (as is often 
assumed) as broad a consensus on white matter tracts (e.g., there is no 
middle longitudinal fasciculus in the recent Oishi et al. white matter 
atlas and many would argue it doesn't exist; the existence of separate 
inferior longitudinal fasciculus and inferior occipitofrontal fasciculus 
is disputed; Catani's arcuate fasciculus is based on one paper etc.). Is 
it such a good idea to go automatically identifying white matter tracts 
without saying how they are identified?


Anthony

On 6/15/11 12:07 PM, Seán Froudist Walsh wrote:

Hi Anastasia,

Thanks for getting back to me and well done on making a very nice 
program. The first tracts I would like to have are the optic 
radiations, but there are others that would be nice to include: a 
three part arcuate fasiculus (a la Catani et al., 2005) rather than a 
2 part one, Fornix, anterior commissure.


If I were to manually do the dissections for the 33 subjects, what 
would be the most Tracula compatible way of doing it? I normally use 
TrackVis but I figure making all of the file conversions might be a 
nightmare. Which program was used in the original virtual dissections?


Any further suggestions? Perhaps some of these tracts are included but 
I've missed them.


Sean



On 15 June 2011 08:37, Anastasia Yendiki > wrote:



Hi Seán - Which tracts do you want to add? Our existing tracts
have been labeled on 33 healthy subjects. It's certainly possible
to include new tracts in the atlas but someone has to do the
labeling on the same or a similar set of subjects.

a.y


On Wed, 15 Jun 2011, Seán Froudist Walsh wrote:

Hi FreeSurfing Gurus,

I would like to add some new tracts to the Tracula pipeline
using my own
regions of interest. What would be the best way to do this?

All the best and many thanks in advance,

Seán






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whom it is
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the e-mail
contains patient information, please contact the Partners
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--
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Assistant Professor
Department of Psychology
Florida International University
Modesto A. Maidique Campus DM 296B
11200 S.W. 8th Street
Miami, FL 33199
Phone: 305-348-4202 (try this first)
Lab Phone: 305-348-9057 or 305-348-9055
Fax: 305-348-3879
Email: ad...@fiu.edu
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Re: [Freesurfer] Adding tracts to Tracula!

[Anastasia Yendiki]

Hi Anthony - The labeling was done based on Wakana et al 2007. We did not 
include the IFOF exactly b/c of the controversy surrounding it.


a.y

On Wed, 15 Jun 2011, Anthony Dick wrote:


Hello all,

Is there any atlas to which these tracs are referenced? For cortical
anatomical boundaries there is broad consensus and a published referenced
atlas, which makes Freesurfer's automatic parcellation of cortical regions
an excellent tool. But there is not (as is often assumed) as broad a
consensus on white matter tracts (e.g., there is no middle longitudinal
fasciculus in the recent Oishi et al. white matter atlas and many would
argue it doesn't exist; the existence of separate inferior longitudinal
fasciculus and inferior occipitofrontal fasciculus is disputed; Catani's
arcuate fasciculus is based on one paper etc.). Is it such a good idea to go
automatically identifying white matter tracts without saying how they are
identified?  

Anthony

On 6/15/11 12:07 PM, Seán Froudist Walsh wrote:
  Hi Anastasia,

  Thanks for getting back to me and well done on making a very
  nice program. The first tracts I would like to have are the
  optic radiations, but there are others that would be nice to
  include: a three part arcuate fasiculus (a la Catani et al.,
  2005) rather than a 2 part one, Fornix, anterior commissure.

  If I were to manually do the dissections for the 33 subjects,
  what would be the most Tracula compatible way of doing it? I
  normally use TrackVis but I figure making all of the file
  conversions might be a nightmare. Which program was used in the
  original virtual dissections?

  Any further suggestions? Perhaps some of these tracts are
  included but I've missed them.

  Sean



  On 15 June 2011 08:37, Anastasia Yendiki
   wrote:

Hi Seán - Which tracts do you want to add? Our
existing tracts have been labeled on 33 healthy
subjects. It's certainly possible to include new
tracts in the atlas but someone has to do the
labeling on the same or a similar set of subjects.

a.y

On Wed, 15 Jun 2011, Seán Froudist Walsh wrote:

  Hi FreeSurfing Gurus,

  I would like to add some new tracts to
  the Tracula pipeline using my own
  regions of interest. What would be the
  best way to do this?

  All the best and many thanks in advance,

  Seán

   




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l
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Re: [Freesurfer] Adding tracts to Tracula!

[Anthony Dick]

Hello Anastasia,

This just reinforces my point. Tracts #7 and #8 of that paper are the 
inferior longitudinal fasciculus and the inferior occipitofrontal 
fasciculus, respectively. But you have chosen to leave one out 
(incidentally, both appear in the Oishi atlas). Note that in this paper, 
the authors recommend manual intervention for certain tracts.

When a tool like this is developed, it gets referenced in papers which 
gives it a kind of legitimacy. What we want to avoid here is giving 
legitimacy to fiber pathways that may not actually exist, or missing 
ones that do because the tool left them out. So what is the rule for how 
pathways are added or removed from this tool? It seems that simply 
requesting that they be added can potentially result in such an 
addition, or that deciding not to include a tract for whatever reason 
can result in its disappearance. This gives any pathway identified by 
this tool a legitimacy it might not otherwise have.

I am not necessarily against the tool (I think it is better for 
exploratory analysis), but I am against the idea, from the Wiki, that 
Tracula "obviates the need for manual intervention for tract solutions 
and thus facilitates the application of tractography to large datasets". 
This seems to me to be a horrible idea. Tractography is not at this 
point a completely data driven procedure.

Anthony

On 6/15/11 12:44 PM, Anastasia Yendiki wrote:
>
> Hi Anthony - The labeling was done based on Wakana et al 2007. We did 
> not include the IFOF exactly b/c of the controversy surrounding it.
>
> a.y
>
> On Wed, 15 Jun 2011, Anthony Dick wrote:
>
>> Hello all,
>>
>> Is there any atlas to which these tracs are referenced? For cortical
>> anatomical boundaries there is broad consensus and a published 
>> referenced
>> atlas, which makes Freesurfer's automatic parcellation of cortical 
>> regions
>> an excellent tool. But there is not (as is often assumed) as broad a
>> consensus on white matter tracts (e.g., there is no middle longitudinal
>> fasciculus in the recent Oishi et al. white matter atlas and many would
>> argue it doesn't exist; the existence of separate inferior longitudinal
>> fasciculus and inferior occipitofrontal fasciculus is disputed; Catani's
>> arcuate fasciculus is based on one paper etc.). Is it such a good 
>> idea to go
>> automatically identifying white matter tracts without saying how they 
>> are
>> identified?
>>
>> Anthony
>>
>> On 6/15/11 12:07 PM, Seán Froudist Walsh wrote:
>>   Hi Anastasia,
>>
>>   Thanks for getting back to me and well done on making a very
>>   nice program. The first tracts I would like to have are the
>>   optic radiations, but there are others that would be nice to
>>   include: a three part arcuate fasiculus (a la Catani et al.,
>>   2005) rather than a 2 part one, Fornix, anterior commissure.
>>
>>   If I were to manually do the dissections for the 33 subjects,
>>   what would be the most Tracula compatible way of doing it? I
>>   normally use TrackVis but I figure making all of the file
>>   conversions might be a nightmare. Which program was used in the
>>   original virtual dissections?
>>
>>   Any further suggestions? Perhaps some of these tracts are
>>   included but I've missed them.
>>
>>   Sean
>>
>>
>>
>>   On 15 June 2011 08:37, Anastasia Yendiki
>>  wrote:
>>
>> Hi Seán - Which tracts do you want to add? Our
>> existing tracts have been labeled on 33 healthy
>> subjects. It's certainly possible to include new
>> tracts in the atlas but someone has to do the
>> labeling on the same or a similar set of subjects.
>>
>> a.y
>>
>> On Wed, 15 Jun 2011, Seán Froudist Walsh wrote:
>>
>>   Hi FreeSurfing Gurus,
>>
>>   I would like to add some new tracts to
>>   the Tracula pipeline using my own
>>   regions of interest. What would be the
>>   best way to do this?
>>
>>   All the best and many thanks in advance,
>>
>>   Seán
>>
>>
>>
>>
>>
>>
>> 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.
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to 
>> whom it is
>> addressed. If you believe this e-mail was sent to you in error and 
>> the e-mai
>> l
>> contain

Re: [Freesurfer] Adding tracts to Tracula!

[Bruce Fischl]

Hi Anthony

we included the tracts that we found that we could segment reliably, under 
the guidance of a trained neuroanatomist. Certainly we can only do as well 
as the information contained in the diffusion data, but we have found that 
we can automated what someone with neuroanatomical expertise could obtain 
by following the Wakana protocol. I don't think we make any claims beyond 
that, but in and of itself it seemed like a worthy goal, opening up the 
field of tractography to a bigger potential user pool. Certainly that comes 
with potential problems, as it does in fMRI. I don't see it being 
significantly different than people guessing Brodmann areal identity based 
on visual inspection of folding patterns and presumed homology with the 
macaque. It's a useful tool, but like all tools you can overintepret the 
results if you are not cautious.


cheers
Bruce




On Wed, 15 Jun 2011, Anthony Dick wrote:


Hello Anastasia,

This just reinforces my point. Tracts #7 and #8 of that paper are the
inferior longitudinal fasciculus and the inferior occipitofrontal
fasciculus, respectively. But you have chosen to leave one out
(incidentally, both appear in the Oishi atlas). Note that in this paper,
the authors recommend manual intervention for certain tracts.

When a tool like this is developed, it gets referenced in papers which
gives it a kind of legitimacy. What we want to avoid here is giving
legitimacy to fiber pathways that may not actually exist, or missing
ones that do because the tool left them out. So what is the rule for how
pathways are added or removed from this tool? It seems that simply
requesting that they be added can potentially result in such an
addition, or that deciding not to include a tract for whatever reason
can result in its disappearance. This gives any pathway identified by
this tool a legitimacy it might not otherwise have.

I am not necessarily against the tool (I think it is better for
exploratory analysis), but I am against the idea, from the Wiki, that
Tracula "obviates the need for manual intervention for tract solutions
and thus facilitates the application of tractography to large datasets".
This seems to me to be a horrible idea. Tractography is not at this
point a completely data driven procedure.

Anthony

On 6/15/11 12:44 PM, Anastasia Yendiki wrote:


Hi Anthony - The labeling was done based on Wakana et al 2007. We did
not include the IFOF exactly b/c of the controversy surrounding it.

a.y

On Wed, 15 Jun 2011, Anthony Dick wrote:


Hello all,

Is there any atlas to which these tracs are referenced? For cortical
anatomical boundaries there is broad consensus and a published
referenced
atlas, which makes Freesurfer's automatic parcellation of cortical
regions
an excellent tool. But there is not (as is often assumed) as broad a
consensus on white matter tracts (e.g., there is no middle longitudinal
fasciculus in the recent Oishi et al. white matter atlas and many would
argue it doesn't exist; the existence of separate inferior longitudinal
fasciculus and inferior occipitofrontal fasciculus is disputed; Catani's
arcuate fasciculus is based on one paper etc.). Is it such a good
idea to go
automatically identifying white matter tracts without saying how they
are
identified?

Anthony

On 6/15/11 12:07 PM, Seán Froudist Walsh wrote:
  Hi Anastasia,

  Thanks for getting back to me and well done on making a very
  nice program. The first tracts I would like to have are the
  optic radiations, but there are others that would be nice to
  include: a three part arcuate fasiculus (a la Catani et al.,
  2005) rather than a 2 part one, Fornix, anterior commissure.

  If I were to manually do the dissections for the 33 subjects,
  what would be the most Tracula compatible way of doing it? I
  normally use TrackVis but I figure making all of the file
  conversions might be a nightmare. Which program was used in the
  original virtual dissections?

  Any further suggestions? Perhaps some of these tracts are
  included but I've missed them.

  Sean



  On 15 June 2011 08:37, Anastasia Yendiki
 wrote:

Hi Seán - Which tracts do you want to add? Our
existing tracts have been labeled on 33 healthy
subjects. It's certainly possible to include new
tracts in the atlas but someone has to do the
labeling on the same or a similar set of subjects.

a.y

On Wed, 15 Jun 2011, Seán Froudist Walsh wrote:

  Hi FreeSurfing Gurus,

  I would like to add some new tracts to
  the Tracula pipeline using my own
  regions of interest. What would be the
  best way to do this?

  All the best and many thanks in advance,

  Seán






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

Re: [Freesurfer] Adding tracts to Tracula!

[Anthony Dick]

Good points Bruce. I guess I am more worried about the people using it, 
who will not be as cautious for large datasets. Also--one thing that was 
a huge benefit for the cortical parcellation was a quantification of the 
manual vs. automated parcellation differences, but this does not appear 
to be published yet (unless I missed it). Any added pathways should have 
to meet the same standards.

Anthony

On 6/15/11 1:07 PM, Bruce Fischl wrote:
> Hi Anthony
>
> we included the tracts that we found that we could segment reliably, 
> under the guidance of a trained neuroanatomist. Certainly we can only 
> do as well as the information contained in the diffusion data, but we 
> have found that we can automated what someone with neuroanatomical 
> expertise could obtain by following the Wakana protocol. I don't think 
> we make any claims beyond that, but in and of itself it seemed like a 
> worthy goal, opening up the field of tractography to a bigger 
> potential user pool. Certainly that comes with potential problems, as 
> it does in fMRI. I don't see it being significantly different than 
> people guessing Brodmann areal identity based on visual inspection of 
> folding patterns and presumed homology with the macaque. It's a useful 
> tool, but like all tools you can overintepret the results if you are 
> not cautious.
>
> cheers
> Bruce
>
>
>
>
> On Wed, 15 Jun 2011, Anthony Dick wrote:
>
>> Hello Anastasia,
>>
>> This just reinforces my point. Tracts #7 and #8 of that paper are the
>> inferior longitudinal fasciculus and the inferior occipitofrontal
>> fasciculus, respectively. But you have chosen to leave one out
>> (incidentally, both appear in the Oishi atlas). Note that in this paper,
>> the authors recommend manual intervention for certain tracts.
>>
>> When a tool like this is developed, it gets referenced in papers which
>> gives it a kind of legitimacy. What we want to avoid here is giving
>> legitimacy to fiber pathways that may not actually exist, or missing
>> ones that do because the tool left them out. So what is the rule for how
>> pathways are added or removed from this tool? It seems that simply
>> requesting that they be added can potentially result in such an
>> addition, or that deciding not to include a tract for whatever reason
>> can result in its disappearance. This gives any pathway identified by
>> this tool a legitimacy it might not otherwise have.
>>
>> I am not necessarily against the tool (I think it is better for
>> exploratory analysis), but I am against the idea, from the Wiki, that
>> Tracula "obviates the need for manual intervention for tract solutions
>> and thus facilitates the application of tractography to large datasets".
>> This seems to me to be a horrible idea. Tractography is not at this
>> point a completely data driven procedure.
>>
>> Anthony
>>
>> On 6/15/11 12:44 PM, Anastasia Yendiki wrote:
>>>
>>> Hi Anthony - The labeling was done based on Wakana et al 2007. We did
>>> not include the IFOF exactly b/c of the controversy surrounding it.
>>>
>>> a.y
>>>
>>> On Wed, 15 Jun 2011, Anthony Dick wrote:
>>>
 Hello all,

 Is there any atlas to which these tracs are referenced? For cortical
 anatomical boundaries there is broad consensus and a published
 referenced
 atlas, which makes Freesurfer's automatic parcellation of cortical
 regions
 an excellent tool. But there is not (as is often assumed) as broad a
 consensus on white matter tracts (e.g., there is no middle 
 longitudinal
 fasciculus in the recent Oishi et al. white matter atlas and many 
 would
 argue it doesn't exist; the existence of separate inferior 
 longitudinal
 fasciculus and inferior occipitofrontal fasciculus is disputed; 
 Catani's
 arcuate fasciculus is based on one paper etc.). Is it such a good
 idea to go
 automatically identifying white matter tracts without saying how they
 are
 identified?

 Anthony

 On 6/15/11 12:07 PM, Seán Froudist Walsh wrote:
   Hi Anastasia,

   Thanks for getting back to me and well done on making a very
   nice program. The first tracts I would like to have are the
   optic radiations, but there are others that would be nice to
   include: a three part arcuate fasiculus (a la Catani et al.,
   2005) rather than a 2 part one, Fornix, anterior commissure.

   If I were to manually do the dissections for the 33 subjects,
   what would be the most Tracula compatible way of doing it? I
   normally use TrackVis but I figure making all of the file
   conversions might be a nightmare. Which program was used in the
   original virtual dissections?

   Any further suggestions? Perhaps some of these tracts are
   included but I've missed them.

   Sean



   On 15 June 2011 08:37, Anastasia Yendiki
  wrote:

   

Re: [Freesurfer] Adding tracts to Tracula!

[Bruce Fischl]

Hi Anthony

we are trying to get that piece of it published :) Hopefully soon!

Bruce
On Wed, 15 Jun 2011, 
Anthony Dick wrote:


Good points Bruce. I guess I am more worried about the people using it, who 
will not be as cautious for large datasets. Also--one thing that was a huge 
benefit for the cortical parcellation was a quantification of the manual vs. 
automated parcellation differences, but this does not appear to be published 
yet (unless I missed it). Any added pathways should have to meet the same 
standards.


Anthony

On 6/15/11 1:07 PM, Bruce Fischl wrote:

Hi Anthony

we included the tracts that we found that we could segment reliably, under 
the guidance of a trained neuroanatomist. Certainly we can only do as well 
as the information contained in the diffusion data, but we have found that 
we can automated what someone with neuroanatomical expertise could obtain 
by following the Wakana protocol. I don't think we make any claims beyond 
that, but in and of itself it seemed like a worthy goal, opening up the 
field of tractography to a bigger potential user pool. Certainly that comes 
with potential problems, as it does in fMRI. I don't see it being 
significantly different than people guessing Brodmann areal identity based 
on visual inspection of folding patterns and presumed homology with the 
macaque. It's a useful tool, but like all tools you can overintepret the 
results if you are not cautious.


cheers
Bruce




On Wed, 15 Jun 2011, Anthony Dick wrote:


Hello Anastasia,

This just reinforces my point. Tracts #7 and #8 of that paper are the
inferior longitudinal fasciculus and the inferior occipitofrontal
fasciculus, respectively. But you have chosen to leave one out
(incidentally, both appear in the Oishi atlas). Note that in this paper,
the authors recommend manual intervention for certain tracts.

When a tool like this is developed, it gets referenced in papers which
gives it a kind of legitimacy. What we want to avoid here is giving
legitimacy to fiber pathways that may not actually exist, or missing
ones that do because the tool left them out. So what is the rule for how
pathways are added or removed from this tool? It seems that simply
requesting that they be added can potentially result in such an
addition, or that deciding not to include a tract for whatever reason
can result in its disappearance. This gives any pathway identified by
this tool a legitimacy it might not otherwise have.

I am not necessarily against the tool (I think it is better for
exploratory analysis), but I am against the idea, from the Wiki, that
Tracula "obviates the need for manual intervention for tract solutions
and thus facilitates the application of tractography to large datasets".
This seems to me to be a horrible idea. Tractography is not at this
point a completely data driven procedure.

Anthony

On 6/15/11 12:44 PM, Anastasia Yendiki wrote:


Hi Anthony - The labeling was done based on Wakana et al 2007. We did
not include the IFOF exactly b/c of the controversy surrounding it.

a.y

On Wed, 15 Jun 2011, Anthony Dick wrote:


Hello all,

Is there any atlas to which these tracs are referenced? For cortical
anatomical boundaries there is broad consensus and a published
referenced
atlas, which makes Freesurfer's automatic parcellation of cortical
regions
an excellent tool. But there is not (as is often assumed) as broad a
consensus on white matter tracts (e.g., there is no middle longitudinal
fasciculus in the recent Oishi et al. white matter atlas and many would
argue it doesn't exist; the existence of separate inferior longitudinal
fasciculus and inferior occipitofrontal fasciculus is disputed; Catani's
arcuate fasciculus is based on one paper etc.). Is it such a good
idea to go
automatically identifying white matter tracts without saying how they
are
identified?

Anthony

On 6/15/11 12:07 PM, Seán Froudist Walsh wrote:
  Hi Anastasia,

  Thanks for getting back to me and well done on making a very
  nice program. The first tracts I would like to have are the
  optic radiations, but there are others that would be nice to
  include: a three part arcuate fasiculus (a la Catani et al.,
  2005) rather than a 2 part one, Fornix, anterior commissure.

  If I were to manually do the dissections for the 33 subjects,
  what would be the most Tracula compatible way of doing it? I
  normally use TrackVis but I figure making all of the file
  conversions might be a nightmare. Which program was used in the
  original virtual dissections?

  Any further suggestions? Perhaps some of these tracts are
  included but I've missed them.

  Sean



  On 15 June 2011 08:37, Anastasia Yendiki
 wrote:

Hi Seán - Which tracts do you want to add? Our
existing tracts have been labeled on 33 healthy
subjects. It's certainly possible to include new
tracts in the atlas but someone has to do the
labeling on

Re: [Freesurfer] Whole brain parcellation contd..

[Sudhin A. Shah]

Hi,

Is there anyway to know all the label #s that are in aparc+aseg-inhighres.mgz. 

Thank you,

S

On 06/13/11, "Sudhin A. Shah"   wrote:
> 
> 
> Hi Sorry for bothering you again, but I am not sure I understand.
> 
> I was running whole brain correlation analysis (voxel by voxel). BUT for 
> comparison purposes, I want to compute region by region correlation matrix.
> So, I want to divide up the brain into freesurfer parcellated regions - i.e. 
> with no overlap, but with full coverage of whole brain.
> 
> I have looked at FreeSurferColorLUT.txt and am confused because there are 
> several sets and overlap (eg. 19 and 55 vs 2035..)
> 
> If I use the following, can I ensure no overlap and full coverage?
> 1)Subcortical: 9-13, 16-19, 48-55, 58 - 59, 85,86
> 2)Cortex: 1002- 1034, 2002- 2034
> 
> I am asking if there is an established list of whole brain parcellations 
> before I rely on label names to choose the ROIS
> 
> On 06/13/11, Douglas N Greve   wrote:
> > 
> > Anything that is non-0 will cover the whole brain.
> > doug
> > 
> > Sudhin A. Shah wrote:
> > > Hi, thank you. Is there a range in the labels that will ensure that I am 
> > > including the whole brain? I.e. I see labels for Cx, but not subcortical..
> > > If I take labels 1001 to 2001 ( for eg ) will that cover whole brain?
> > >
> > > Thank you,
> > > S
> > >
> > >
> > >
> > > On Jun 13, 2011, at 10:59 AM, Douglas N Greve  
> > > wrote:
> > >
> > >   
> > >> That is fine, or you can use mri_binarize with the --match option. The 
> > >> numbers that correspond to each label can be found in  
> > >> $FREESURFER_HOME/FreeSurferColorLUT.txt. You can also get at them visual 
> > >> as I described in my previous email with tkmedit:
> > >>
> > >> tkmedit subject orig.mgz -aux aseg.mgz -aseg
> > >>
> > >> doug
> > >>
> > >>
> > >> Sudhin A. Shah wrote:
> > >> 
> > >>> I mean that I am using FSL to create binary masks from freesurfer 
> > >>> parcellated regions. Unless there is a better way :)
> > >>>
> > >>> S
> > >>>
> > >>>
> > >>>
> > >>> On Jun 10, 2011, at 7:13 PM, Douglas N Greve 
> > >>>  wrote:
> > >>>
> > >>>  
> > >>>   
> >  What do you mean you are doing it with FEAT?
> > 
> >  Sudhin A. Shah wrote:
> >     
> >  
> > > Hello,
> > >
> > > I am a beginner so please bear with me. I want to obtain binary masks 
> > > for every region (Cortical + subcortical). I am using FSL(feat) to do 
> > > this BUT am not sure what the labels would be.
> > >
> > > I have looked at FreeSurferColorLUT.txt for aparc+aseg-in-highres.mgz 
> > > BUT do not know which labels to use to avoid overlap and ensure full 
> > > coverage.
> > >
> > > Thank you,
> > >
> > > S
> > >
> > >
> > > 
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
> > > (https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer)
> > >  
> > >   
> >  -- 
> >  Douglas N. Greve, Ph.D.
> >  MGH-NMR Center
> >  gr...@nmr.mgh.harvard.edu
> >  Phone Number: 617-724-2358 Fax: 617-726-7422
> > 
> >  Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> >  FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > 
> >  ___
> >  Freesurfer mailing list
> >  Freesurfer@nmr.mgh.harvard.edu
> >  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
> >  (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 
> >  (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.
> > 
> >     
> >  
> > >>>  
> > >>>   
> > >> -- 
> > >> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > >>
> > >> 
> > >
> > >
> > >   
> > 
> > -- 
> > 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: www.nmr.mgh.harvard.edu/facility/

Re: [Freesurfer] Adding tracts to Tracula!

[Anastasia Yendiki]

It's under review! In short, this is not a purely data driven approach. 
It's data + prior info on the anatomy of the tracts derived from a 
manually labeled set of subjects. The prior info is the anatomical 
segmentation labels that surround the tract. So the knowledge that the 
neuroanatomist would apply manually is now included in the algorithm. This 
is what the wiki statement about not needing manual intervention refers 
to.


Hope this helps,
a.y

On Wed, 15 Jun 2011, Anthony Dick wrote:

Good points Bruce. I guess I am more worried about the people using it, who 
will not be as cautious for large datasets. Also--one thing that was a huge 
benefit for the cortical parcellation was a quantification of the manual vs. 
automated parcellation differences, but this does not appear to be published 
yet (unless I missed it). Any added pathways should have to meet the same 
standards.


Anthony

On 6/15/11 1:07 PM, Bruce Fischl wrote:

 Hi Anthony

 we included the tracts that we found that we could segment reliably, under
 the guidance of a trained neuroanatomist. Certainly we can only do as well
 as the information contained in the diffusion data, but we have found that
 we can automated what someone with neuroanatomical expertise could obtain
 by following the Wakana protocol. I don't think we make any claims beyond
 that, but in and of itself it seemed like a worthy goal, opening up the
 field of tractography to a bigger potential user pool. Certainly that
 comes with potential problems, as it does in fMRI. I don't see it being
 significantly different than people guessing Brodmann areal identity based
 on visual inspection of folding patterns and presumed homology with the
 macaque. It's a useful tool, but like all tools you can overintepret the
 results if you are not cautious.

 cheers
 Bruce




 On Wed, 15 Jun 2011, Anthony Dick wrote:

>  Hello Anastasia,
> 
>  This just reinforces my point. Tracts #7 and #8 of that paper are the

>  inferior longitudinal fasciculus and the inferior occipitofrontal
>  fasciculus, respectively. But you have chosen to leave one out
>  (incidentally, both appear in the Oishi atlas). Note that in this paper,
>  the authors recommend manual intervention for certain tracts.
> 
>  When a tool like this is developed, it gets referenced in papers which

>  gives it a kind of legitimacy. What we want to avoid here is giving
>  legitimacy to fiber pathways that may not actually exist, or missing
>  ones that do because the tool left them out. So what is the rule for how
>  pathways are added or removed from this tool? It seems that simply
>  requesting that they be added can potentially result in such an
>  addition, or that deciding not to include a tract for whatever reason
>  can result in its disappearance. This gives any pathway identified by
>  this tool a legitimacy it might not otherwise have.
> 
>  I am not necessarily against the tool (I think it is better for

>  exploratory analysis), but I am against the idea, from the Wiki, that
>  Tracula "obviates the need for manual intervention for tract solutions
>  and thus facilitates the application of tractography to large datasets".
>  This seems to me to be a horrible idea. Tractography is not at this
>  point a completely data driven procedure.
> 
>  Anthony
> 
>  On 6/15/11 12:44 PM, Anastasia Yendiki wrote:
> > 
> >  Hi Anthony - The labeling was done based on Wakana et al 2007. We did

> >  not include the IFOF exactly b/c of the controversy surrounding it.
> > 
> >  a.y
> > 
> >  On Wed, 15 Jun 2011, Anthony Dick wrote:
> > 
> > >  Hello all,
> > > 
> > >  Is there any atlas to which these tracs are referenced? For cortical

> > >  anatomical boundaries there is broad consensus and a published
> > >  referenced
> > >  atlas, which makes Freesurfer's automatic parcellation of cortical
> > >  regions
> > >  an excellent tool. But there is not (as is often assumed) as broad a
> > >  consensus on white matter tracts (e.g., there is no middle 
> > >  longitudinal
> > >  fasciculus in the recent Oishi et al. white matter atlas and many 
> > >  would
> > >  argue it doesn't exist; the existence of separate inferior 
> > >  longitudinal
> > >  fasciculus and inferior occipitofrontal fasciculus is disputed; 
> > >  Catani's

> > >  arcuate fasciculus is based on one paper etc.). Is it such a good
> > >  idea to go
> > >  automatically identifying white matter tracts without saying how 
> > >  they

> > >  are
> > >  identified?
> > > 
> > >  Anthony
> > > 
> > >  On 6/15/11 12:07 PM, Seán Froudist Walsh wrote:

> > >Hi Anastasia,
> > > 
> > >Thanks for getting back to me and well done on making a very

> > >nice program. The first tracts I would like to have are the
> > >optic radiations, but there are others that would be nice to
> > >include: a three part arcuate fasiculus (a la Catani et al.,
> > >2005) rather than a 2 part one, Fornix, anterior commissure.
> > > 
> > >

[Freesurfer] fsaverage in stable5

[Rebecca Dautoff]

Hi all
we are having trouble accessing stable5/subjects/fsaverage and are
wondering whether this is permanent and we should move out symbolic links
to stabel5_1_0

thanks,
becca
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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.

[Freesurfer] cvs template missing in 5.1

[Martin Kavec]

Hi,

I did a fresh download and install of the FS-5.1.0 for CentOS_x86_64
and I am not finding the cvs_avg35 template in
$FREESURFER_HOME/subjects. Plus the cvs settings text file is not
there either. In contrast Mac distribution has it. Is there any
problem with cvs on CentOS_x86_64 platform?

Thanks,

Martin
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Whole brain parcellation contd..

[Douglas N Greve]

You are guaranteed not to have overlap regardless of what you do as 
there is only one label at each voxel. For Cortex, what you have is 
fine. For subcortical, you can use what is in 
$FREESURFER_HOME/ASegStatsLUT.txt. This has {Left,Right}-Cerebral-Cortex 
which can be ignored.

doug

Sudhin A. Shah wrote:
> Hi,
>
> Is there anyway to know all the label #s that are in 
> aparc+aseg-inhighres.mgz.
>
> Thank you,
>
> S
>
> On 06/13/11, *"Sudhin A. Shah" *  wrote:
>> Hi Sorry for bothering you again, but I am not sure I understand.
>>
>> I was running whole brain correlation analysis (voxel by voxel). BUT 
>> for comparison purposes, I want to compute region by region 
>> correlation matrix.
>> So, I want to divide up the brain into freesurfer parcellated regions 
>> - i.e. with no overlap, but with full coverage of whole brain.
>>
>> I have looked at FreeSurferColorLUT.txt and am confused because there 
>> are several sets and overlap (eg. 19 and 55 vs 2035..)
>>
>> If I use the following, can I ensure no overlap and full coverage?
>> 1)Subcortical: 9-13, 16-19, 48-55, 58 - 59, 85,86
>> 2)Cortex: 1002- 1034, 2002- 2034
>>
>> I am asking if there is an established list of whole brain 
>> parcellations before I rely on label names to choose the ROIS
>>
>> On 06/13/11, *Douglas N Greve *  wrote:
>>> Anything that is non-0 will cover the whole brain.
>>> doug
>>>
>>> Sudhin A. Shah wrote:
>>> > Hi, thank you. Is there a range in the labels that will ensure 
>>> that I am including the whole brain? I.e. I see labels for Cx, but 
>>> not subcortical..
>>> > If I take labels 1001 to 2001 ( for eg ) will that cover whole brain?
>>> >
>>> > Thank you,
>>> > S
>>> >
>>> >
>>> >
>>> > On Jun 13, 2011, at 10:59 AM, Douglas N Greve 
>>>  wrote:
>>> >
>>> >  
>>> >> That is fine, or you can use mri_binarize with the --match 
>>> option. The numbers that correspond to each label can be found in  
>>> $FREESURFER_HOME/FreeSurferColorLUT.txt. You can also get at them 
>>> visual as I described in my previous email with tkmedit:
>>> >>
>>> >> tkmedit subject orig.mgz -aux aseg.mgz -aseg
>>> >>
>>> >> doug
>>> >>
>>> >>
>>> >> Sudhin A. Shah wrote:
>>> >>
>>> >>> I mean that I am using FSL to create binary masks from 
>>> freesurfer parcellated regions. Unless there is a better way :)
>>> >>>
>>> >>> S
>>> >>>
>>> >>>
>>> >>>
>>> >>> On Jun 10, 2011, at 7:13 PM, Douglas N Greve 
>>>  wrote:
>>> >>>
>>> >>> 
>>> >>>  
>>>  What do you mean you are doing it with FEAT?
>>> 
>>>  Sudhin A. Shah wrote:
>>>    
>>> 
>>> > Hello,
>>> >
>>> > I am a beginner so please bear with me. I want to obtain 
>>> binary masks for every region (Cortical + subcortical). I am using 
>>> FSL(feat) to do this BUT am not sure what the labels would be.
>>> >
>>> > I have looked at FreeSurferColorLUT.txt for 
>>> aparc+aseg-in-highres.mgz BUT do not know which labels to use to 
>>> avoid overlap and ensure full coverage.
>>> >
>>> > Thank you,
>>> >
>>> > S
>>> >
>>> >
>>> > 
>>> 
>>> >
>>> > ___
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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
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>>> 
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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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>> >>
>>> >>
>>> >
>>> >
>>> >  
>>>
>>> -- 
>>> 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/B

Re: [Freesurfer] fsaverage in stable5

[Nick Schmansky]

becca,

it should be fixed now.  for some reason the world-readable bits were
cleared on that directory.

you can email me directly (or krish) if you encounter any other read
permission problems with the nmr center installation.

n.


On Wed, 2011-06-15 at 13:33 -0400, Rebecca Dautoff wrote:
> Hi all
> we are having trouble accessing stable5/subjects/fsaverage and are
> wondering whether this is permanent and we should move out symbolic links
> to stabel5_1_0
> 
> thanks,
> becca
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[Freesurfer] display amygdala only in tkmedit?

[Ariel Brown]

Hi There,
I'm trying to come up with an image of the amygdala to display on a  
single subject's brainmask.mgz.  Can I display the aseg labels  
individually in tkmedit?

Thanks so much,
Ariel
---
Ariel Brown, PhD

Research Fellow
Department of Psychiatry
Mass General Hospital & Harvard Medical School

Visiting Scientist
Department of Brain & Cognitive Sciences
Massachusetts Institute of Technology

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[Freesurfer] Custom color table overlay for ROI analysis

[Shashwath Meda]

Hello Freesurfers - I just finished up with some group ROI analyses on
thickness and surface area measures derived from Freesurfer. Basically ran
the recon-all command, extracted individual ROI measures from the aparc and
aseg files and did my between-group analyses in SPSS. Now, i'd like to
display the significant ROIs on the brain with its corresponding p/F value.
What would be the easiest and most straightforward way to do this?


Thanks,
Shashwath
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[Freesurfer] mri_annotation2labels

[Sudhin A. Shah]

Hi,

I am trying to use this for the aparc+aseg-in-highres.mgz file instead of the 
default aparc

mri_annotation2label --subject AY --hemi lh --outdir $fsfolder/AY/labels  this 
works

But how do I specify aparc+aseg-in-highres.mgz

I tried --aparc+aseg-in-highres but it was not recognised..

Thank you,
S





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Re: [Freesurfer] Custom color table overlay for ROI analysis

[Alan Francis]

Hi Shashwath:

The QDEC model in FS will allow you to do this. The website has all the
details.

best,

Alan

On Wed, Jun 15, 2011 at 5:02 PM, Shashwath Meda wrote:

> Hello Freesurfers - I just finished up with some group ROI analyses on
> thickness and surface area measures derived from Freesurfer. Basically ran
> the recon-all command, extracted individual ROI measures from the aparc and
> aseg files and did my between-group analyses in SPSS. Now, i'd like to
> display the significant ROIs on the brain with its corresponding p/F value.
> What would be the easiest and most straightforward way to do this?
>
>
> Thanks,
> Shashwath
>
>
>
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> properly
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[Freesurfer] hippocampal subfields

[Wayne Su]

One quick question: how to convert hippocampal subfields back to FS space?
Wayne
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[Freesurfer] pre-bedposted data in tracula

[Scott Sorg]

Hello,

If I already ran bedpostx on my diffusion data, how can I skip this step in 
tracula and still get it to run smoothly.

Thank you,

Scott
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Re: [Freesurfer] display amygdala only in tkmedit?

[Bruce Fischl]

Hi Ariel
You can use mri_binarize to extract just the label you want and visualize is 
(or mri_extract_label)
Cheers
Bruce



On Jun 15, 2011, at 4:48 PM, Ariel Brown  wrote:

> Hi There,
> I'm trying to come up with an image of the amygdala to display on a  
> single subject's brainmask.mgz.  Can I display the aseg labels  
> individually in tkmedit?
> 
> Thanks so much,
> Ariel
> ---
> Ariel Brown, PhD
> 
> Research Fellow
> Department of Psychiatry
> Mass General Hospital & Harvard Medical School
> 
> Visiting Scientist
> Department of Brain & Cognitive Sciences
> Massachusetts Institute of Technology
> 
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> 

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Re: [Freesurfer] mri_annotation2labels

[Bruce Fischl]

What is aparc+aseg-in-highres.mgz?


On Jun 15, 2011, at 5:16 PM, "Sudhin A. Shah"  wrote:

> aparc+aseg-in-highres.mgz
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[Freesurfer] mri_cc error

[Vanessa Lim]

Hi,



does anyone know what to do here please?  I can see it in file manager.



mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz CG
will read input aseg from aseg.auto_noCCseg.mgz
writing aseg with cc labels to aseg.auto.mgz
reading aseg from 
/home/virtualuser/Desktop/freeSurfer/CG/CG/mri/aseg.auto_noCCseg.mgz
mghRead(/home/virtualuser/Desktop/freeSurfer/CG/CG/mri/aseg.auto_noCCseg.mgz, 
-1): could not open file
mri_cc: could not read aseg volume from 
/home/virtualuser/Desktop/freeSurfer/CG/CG/mri/aseg.auto_noCCseg.mgz

also assuming I fix this error how do I resume from this point (or another 
point) the rest of recon-all autorecon2?

Thanks,

Vanessa
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Re: [Freesurfer] pre-bedposted data in tracula

[Anastasia Yendiki]

Hi Scott - The bedpost outputs are expected to in a directory called 
dmri.bedpostX under the subject's trac-all output directory. You can put 
all your bedpost outputs there and proceed at your own risk!

There's a description of other trac-all outputs from the steps before 
bedpost here:
http://surfer.nmr.mgh.harvard.edu/fswiki/trac-all#OutputDirectoriesandFiles

The bedpost step in trac-all would normally use eddy_corrected data and 
and an anatomical brain mask from the FS recon, but otherwise there 
shouldn't be other dependencies on previous steps.

Hope this helps,
a.y

On Wed, 15 Jun 2011, Scott Sorg wrote:

> Hello,
> 
> If I already ran bedpostx on my diffusion data, how can I skip this step in
> tracula and still get it to run smoothly.
> 
> Thank you,
> 
> Scott
> 
>
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