Re: [Freesurfer] qdec table

[Laura M. Tully]

Thanks Doug - Nick, do you have any idea what might be happening here? Why
might qdec stop allowing me to select more than one continuous variable?
Thanks!

Laura.


Message: 24
Date: Mon, 04 Jun 2012 11:19:57 -0400
From: Douglas N Greve 
Subject: Re: [Freesurfer] qdec table file
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <4fccd21d.4040...@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

OK, I've replicated that this is happening, but Nick will have to take a
look.
doug

On 06/04/2012 11:05 AM, Laura M. Tully wrote:
>
>
>
> Hi Doug,
>
> Attached is the qdec table file and associated levels files. It's
> strange that qdec won't let me select more than one continuous
> variable. What's even more strange is that I have been able to do that
> last month when I originally looked at these data before doing manual
> edits and quality control. I don't think that I have changed anything
> since then, but I'm not sure what to look for. Any help you have would
> be most appreciated!
>
> Best,
>
> Laura.
-- 
Laura Tully
Social Neuroscience & Psychopathology
Harvard University
840 William James Hall
33 Kirkland St
Cambridge, MA 02138
ltu...@fas.harvard.edu
--
My musings as a young clinical scientist:
http://theclinicalbrain.blogspot.com/
Follow me on Twitter: @tully_laura
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Re: [Freesurfer] no aseg

[Douglas Greve]

yes, that should work

On 6/4/12 6:53 PM, mdkrue...@uwalumni.com wrote:
> doug-
>
> When i try to do this it still brings up an error with the
> make_average_subject regarding the --no-aseg as a subject to be
> averaged. I went ahead and ran make_average_surface and
> make_average_volume with a --no-aseg flag. This should recreate the
> process of the make_average_subject correct?
>
> michael
>
>
> On 6/4/12, Douglas N Greve  wrote:
>> you should be able to run make_average_subject with --no-aseg
>>
>> On 06/04/2012 06:25 PM, mdkrue...@uwalumni.com wrote:
>>> so what i should be able to do is run make_average_surface and
>>> make_average_volume separately with a --no-aseg flag on
>>> make_average_volume.
>>>
>>> On 6/4/12, Gregory Kirk   wrote:
 so it seems that i ran make_average_volume which does have a --no-aseg
 flag

 make_average_subject really just runs 2 other commands
 make_average_surface and make_average_volume.

 bruce the reason i did this is that mike was running a `super` average,
 i.e.
 the average
 subject of 2 different syudies, i.e. ave_study1, ave_study2

 and he was running make_average_subject --subjects ave_study1 ave_study2
 --out superave.

 we were doing this so we could map labels from one study to another
 and we were getting an error in the log file from make_average_volume
 that indicated it was having a problem with the aseg after the
 make_average_surface had already finished without error.

 really we could just skip it i think as we are not actually doing
 anything
 with the average volume.

 greg

 On 06/04/12, Bruce Fischl  wrote:
> Hi Michael
>
> a couple of typos. It should be "make_average_subject" (note no "s"),
> and
> it should be --subjects (note the ending "s"). I also don't see a flag
> named --no-aseg, which I think is why it's being included as a subject.
> What are you trying to do?
>
> cheers
> Bruce
>
> On Mon, 4 Jun 2012, michael kruepke wrote:
>
>> Hi all -
>> Having a bit of an issue with trying to run a make_average with the
>> flag
>> --no-aseg. When written
>>
>> make_average_subjects --subject subject1 subject2 --no-aseg --out
>> superaverage
>>
>> the propt runs as if --no-aseg and --out superaverage are subjects i
>> wish
>> to
>> average in with subjects1 and subject2. This is obviously and issue,
>> hoping
>> someone might have an idea of a solution. I have tried moving these
>> flags
>> to
>> somewhere else in the prompt seeing if that would solve it, no luck
>> there.
>>
>> Best-
>> Michael
>>
>> --
>> Michael D. Kruepke
>> PhD - University of Illinois at Urbana-Champaign
>> BA - Psych - University of Wisconsin-Madison
>> mdkrue...@gmail.com
>> (262)-483-7449
>>
>>
>>
> ___
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>
>
> The information in this e-mail is intended only for the person to whom
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> 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
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> 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
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Re: [Freesurfer] no aseg

[mdkrue...@uwalumni.com]

doug-

When i try to do this it still brings up an error with the
make_average_subject regarding the --no-aseg as a subject to be
averaged. I went ahead and ran make_average_surface and
make_average_volume with a --no-aseg flag. This should recreate the
process of the make_average_subject correct?

michael


On 6/4/12, Douglas N Greve  wrote:
> you should be able to run make_average_subject with --no-aseg
>
> On 06/04/2012 06:25 PM, mdkrue...@uwalumni.com wrote:
>> so what i should be able to do is run make_average_surface and
>> make_average_volume separately with a --no-aseg flag on
>> make_average_volume.
>>
>> On 6/4/12, Gregory Kirk  wrote:
>>> so it seems that i ran make_average_volume which does have a --no-aseg
>>> flag
>>>
>>> make_average_subject really just runs 2 other commands
>>> make_average_surface and make_average_volume.
>>>
>>> bruce the reason i did this is that mike was running a `super` average,
>>> i.e.
>>> the average
>>> subject of 2 different syudies, i.e. ave_study1, ave_study2
>>>
>>> and he was running make_average_subject --subjects ave_study1 ave_study2
>>> --out superave.
>>>
>>> we were doing this so we could map labels from one study to another
>>> and we were getting an error in the log file from make_average_volume
>>> that indicated it was having a problem with the aseg after the
>>> make_average_surface had already finished without error.
>>>
>>> really we could just skip it i think as we are not actually doing
>>> anything
>>> with the average volume.
>>>
>>> greg
>>>
>>> On 06/04/12, Bruce Fischl  wrote:
 Hi Michael

 a couple of typos. It should be "make_average_subject" (note no "s"),
 and
 it should be --subjects (note the ending "s"). I also don't see a flag
 named --no-aseg, which I think is why it's being included as a subject.
 What are you trying to do?

 cheers
 Bruce

 On Mon, 4 Jun 2012, michael kruepke wrote:

> Hi all -
> Having a bit of an issue with trying to run a make_average with the
> flag
> --no-aseg. When written
>
> make_average_subjects --subject subject1 subject2 --no-aseg --out
> superaverage
>
> the propt runs as if --no-aseg and --out superaverage are subjects i
> wish
> to
> average in with subjects1 and subject2. This is obviously and issue,
> hoping
> someone might have an idea of a solution. I have tried moving these
> flags
> to
> somewhere else in the prompt seeing if that would solve it, no luck
> there.
>
> Best-
> Michael
>
> --
> Michael D. Kruepke
> PhD - University of Illinois at Urbana-Champaign
> BA - Psych - University of Wisconsin-Madison
> mdkrue...@gmail.com
> (262)-483-7449
>
>
>

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 addressed. If you believe this e-mail was sent to you in error and the
 e-mail
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 in
 error
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 properly
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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
>
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-- 
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BA-Psychology
University of Wisconsin-Madison
mdkrue...@uwalumni.com
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Re: [Freesurfer] no aseg

[Douglas N Greve]

you should be able to run make_average_subject with --no-aseg

On 06/04/2012 06:25 PM, mdkrue...@uwalumni.com wrote:
> so what i should be able to do is run make_average_surface and
> make_average_volume separately with a --no-aseg flag on
> make_average_volume.
>
> On 6/4/12, Gregory Kirk  wrote:
>> so it seems that i ran make_average_volume which does have a --no-aseg flag
>>
>> make_average_subject really just runs 2 other commands
>> make_average_surface and make_average_volume.
>>
>> bruce the reason i did this is that mike was running a `super` average, i.e.
>> the average
>> subject of 2 different syudies, i.e. ave_study1, ave_study2
>>
>> and he was running make_average_subject --subjects ave_study1 ave_study2
>> --out superave.
>>
>> we were doing this so we could map labels from one study to another
>> and we were getting an error in the log file from make_average_volume
>> that indicated it was having a problem with the aseg after the
>> make_average_surface had already finished without error.
>>
>> really we could just skip it i think as we are not actually doing anything
>> with the average volume.
>>
>> greg
>>
>> On 06/04/12, Bruce Fischl  wrote:
>>> Hi Michael
>>>
>>> a couple of typos. It should be "make_average_subject" (note no "s"), and
>>> it should be --subjects (note the ending "s"). I also don't see a flag
>>> named --no-aseg, which I think is why it's being included as a subject.
>>> What are you trying to do?
>>>
>>> cheers
>>> Bruce
>>>
>>> On Mon, 4 Jun 2012, michael kruepke wrote:
>>>
 Hi all -
 Having a bit of an issue with trying to run a make_average with the flag
 --no-aseg. When written

 make_average_subjects --subject subject1 subject2 --no-aseg --out
 superaverage

 the propt runs as if --no-aseg and --out superaverage are subjects i wish
 to
 average in with subjects1 and subject2. This is obviously and issue,
 hoping
 someone might have an idea of a solution. I have tried moving these flags
 to
 somewhere else in the prompt seeing if that would solve it, no luck
 there.

 Best-
 Michael

 --
 Michael D. Kruepke
 PhD - University of Illinois at Urbana-Champaign
 BA - Psych - University of Wisconsin-Madison
 mdkrue...@gmail.com
 (262)-483-7449



>>>
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>>> Freesurfer mailing list
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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.
>

-- 
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

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Re: [Freesurfer] no aseg

[mdkrue...@uwalumni.com]

so what i should be able to do is run make_average_surface and
make_average_volume separately with a --no-aseg flag on
make_average_volume.

On 6/4/12, Gregory Kirk  wrote:
> so it seems that i ran make_average_volume which does have a --no-aseg flag
>
> make_average_subject really just runs 2 other commands
> make_average_surface and make_average_volume.
>
> bruce the reason i did this is that mike was running a `super` average, i.e.
> the average
> subject of 2 different syudies, i.e. ave_study1, ave_study2
>
> and he was running make_average_subject --subjects ave_study1 ave_study2
> --out superave.
>
> we were doing this so we could map labels from one study to another
> and we were getting an error in the log file from make_average_volume
> that indicated it was having a problem with the aseg after the
> make_average_surface had already finished without error.
>
> really we could just skip it i think as we are not actually doing anything
> with the average volume.
>
> greg
>
> On 06/04/12, Bruce Fischl  wrote:
>> Hi Michael
>>
>> a couple of typos. It should be "make_average_subject" (note no "s"), and
>> it should be --subjects (note the ending "s"). I also don't see a flag
>> named --no-aseg, which I think is why it's being included as a subject.
>> What are you trying to do?
>>
>> cheers
>> Bruce
>>
>> On Mon, 4 Jun 2012, michael kruepke wrote:
>>
>> >Hi all -
>> >Having a bit of an issue with trying to run a make_average with the flag
>> >--no-aseg. When written
>> >
>> >make_average_subjects --subject subject1 subject2 --no-aseg --out
>> >superaverage
>> >
>> >the propt runs as if --no-aseg and --out superaverage are subjects i wish
>> > to
>> >average in with subjects1 and subject2. This is obviously and issue,
>> > hoping
>> >someone might have an idea of a solution. I have tried moving these flags
>> > to
>> >somewhere else in the prompt seeing if that would solve it, no luck
>> > there.
>> >
>> >Best-
>> >Michael
>> >
>> >--
>> >Michael D. Kruepke
>> >PhD - University of Illinois at Urbana-Champaign
>> >BA - Psych - University of Wisconsin-Madison
>> >mdkrue...@gmail.com
>> >(262)-483-7449
>> >
>> >
>> >
>>
>>
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>> 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-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.
>


-- 
Michael D. Kruepke
BA-Psychology
University of Wisconsin-Madison
mdkrue...@uwalumni.com
(262)-483-7449
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[Freesurfer] exclude ROIs in an annotation file under a label

[Leon]

Hi, FreeSurfer experts
I have one annotation file with many ROIs and one label file that denotes 
medial wall. Now I want to remove the ROIs in the annotation file that is 
covered by the medial wall. Is there any way that I can realize that in the 
surface space?

Thank you!
Leon
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Re: [Freesurfer] missing ROI when using mri_label2vol to transfer ic2.tri

[Douglas N Greve]

OK, I have the data. Can you send me the exact command line I need to 
run to replicate your results? No shell variables or wild cards ...

On 06/04/2012 02:44 PM, Leon wrote:
> Hi, Douglas
> I have uploaded the file to the system.
> Also, my new results showed that  when  ic3.tri (instead of ic2.tri) 
> is used as the input, one ROI at the similar location is also missing. 
> Hope it will help you diagnose.
>
> Thanks
> Leon
>
> *From:* Douglas N Greve 
> *To:* Leon 
> *Cc:* FreeSurfer 
> *Sent:* Monday, June 4, 2012 1:00 PM
> *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to 
> transfer ic2.tri
>
> Can you upload the subject to our file drop system?
>
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html 
> 
>
>
>
>
> On 06/04/2012 12:24 PM, Leon wrote:
> > Hi, Douglas
> >
> > Thank you very much for the updated one. I tested the new codes and
> > the problem is still there. The ID for the original version that
> > generates a mask with one missing ROI is:
> >
> > $Id: mri_label2vol.c,v 1.38 2011/09/30 15:17:59 greve Exp $
> >
> > I remember this is a version I downloaded from a link in FS archive.
> >
> > The ID for the one you sent to me is:
> >
> > $Id: mri_label2vol.c,v 1.34.2.4 2011/09/30 15:19:36 greve Exp $
> >
> > They look almost identical. Do you have any ideas what else may cause
> > this issue and possible workaround?
> >
> > Thank you
> >
> > Leon
> >
> >
> > *From:* Douglas Greve  >
> > *To:* freesurfer@nmr.mgh.harvard.edu 
> 
> > *Sent:* Friday, June 1, 2012 11:29 PM
> > *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to
> > transfer ic2.tri
> >
> >
> > What version are you using? I fix a problem last Sept that might be
> > like this. I've put a new version of mri_label2vol here:
> > 
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2vol.linux
> > Try this and let me know if it works.
> > doug
> >
> >
> > On 6/1/12 10:46 PM, Leon wrote:
> >> Hi, Bruce
> >> Here are my two command lines
> >> For transferring the annot from the source template to the target
> >> subject:
> >>
> >> /home/freesurfer/bin/mri_surf2surf --srcsubject ${srcsubject}
> >> --sval-annot rh.ic2.annot --trgsubject ${trgsubject} --trgsurfval
> >> src_2_trg.annot --hemi rh --surfreg sphere.reg0
> >>
> >> Where sphere.reg0 is the registration from the target subject to the
> >> source subject.
> >>
> >> For transfer them to the volume file:
> >>
> >> /home/freesurfer/bin/mri_label2vol --annot src_2_trg.annot --temp
> >> ${fs_dir}/${trgsubject}/mri/brain.mgz --subject ${trgsubject} --hemi
> >> rh --fillthresh 0 --proj frac 0.3 0.8 0.05 --o src_2_trg_annot.mgz
> >> --identity
> >>
> >>
> >> Here is output for one of my transformations:
> >>
> >> Setting mapmethod to nnf
> >> Source registration surface changed to sphere.reg0
> >> Target registration surface changed to sphere.reg0
> >> srcsubject = MacaqueA
> >> srcval= (null)
> >> srctype=
> >> trgsubject = MacaqueB
> >> trgval=
> >> 
> /home/freesurfer/freesurfer/subjects/MacaqueB/label/rh.MacaqueA_to_MacaqueB.annot
> >> trgtype=
> >> srcsurfreg = sphere.reg0
> >> trgsurfreg = sphere.reg0
> >> srchemi= rh
> >> trghemi= rh
> >> frame  = 0
> >> fwhm-in= 0
> >> fwhm-out  = 0
> >> label-src  = (null)
> >> label-trg  = (null)
> >> OKToRevFaceOrder  = 1
> >> Reading source surface reg
> >> /home/freesurfer/freesurfer/subjects/MacaqueA/surf/rh.sphere.reg0
> >> Loading source data
> >> Reading surface file
> >> /home/freesurfer/freesurfer/subjects/MacaqueA/surf/rh.orig
> >> reading colortable from annotation file...
> >> colortable with 162 entries read (originally
> >> /usr/local/freesurfer/lib/bem/ic2.tri)
> >> Reading target surface reg
> >> /home/freesurfer/freesurfer/subjects/MacaqueB/surf/rh.sphere.reg0
> >> Done
> >> Mapping Source Volume onto Source Subject Surface
> >> surf2surf_nnfr: building source hash (res=16).
> >> Surf2Surf: Forward Loop (61916)
> >>
> >> Surf2Surf: Dividing by number of hits (61916)
> >> INFO: nSrcLost = 17467
> >> nTrg121 = 61916, nTrgMulti =0, MnTrgMultiHits = 0
> >> nSrc121 = 35292, nSrcLost = 17467, nSrcMulti = 28910, MnSrcMultiHits
> >> = 0.920927
> >> Saving target data
> >> Converting to target annot
> >> Saving to target annot
> >> 
> /home/freesurfer/freesurfer/subjects/MacaqueB/label/rh.MacaqueA_to_MacaqueB.annot
> >> step2: writing the surface label to volume...
> >> Number of labels: 0
> >> Annot File:
> >> 
> /home/freesurfer/freesurfer/subjects/MacaqueB/label/rh.MacaqueA_to_MacaqueB.annot
> >> Template Volume:
> >> /home/freesurfer/freesurfer/subjects/MacaqueB/mri/brain.mgz
> >> Outut Volume:
> >> 
> /home/freesurfer/freesurfer/subjects/MacaqueB/mri/rh_MacaqueA_to_MacaqueB_fill0_porjs0.3_proje0.8_projin0.05.mgz
> >> Registration File: (null)
> >> Fill Threshold: 0
> >> Label Vox Vol:  1
> >> ProjType:  frac

Re: [Freesurfer] A few beginner questions about thickness analysis using freesurfer

[Douglas N Greve]

On 06/04/2012 03:52 PM, Jiang, Zhiguo wrote:
>
> 1.How do I register subjects’ thickness maps to a common space to be 
> able to do vertex wise comparison? And can any brain map be used as 
> the common space?
>
This is the same as doing a group analysis. Basically you run 
mris_preproc, mris_fwhm to smooth, then mri_glmfit to do the comparison. 
Look at the group analysis tutorial. We define a surface-based common 
space for group analysis, but you can also make your own.
>
> 2.If I have a hand-drawn ROI on subject’s original T1, is it possible 
> to resample the volume ROI to the surface (so I can extract the 
> thickness values from that ROI)
>
Yes. You can run mri_vol2surf to sample the binary ROI onto the surface, 
then mri_cor2label to create a label.
>
> Any command lines would be appreciated.
>
> Best,
>
> Tony
>
> Zhiguo Jiang, Ph.D.
>
>
> IMPORTANT WARNING: This email (and any attachments) is only intended 
> for the use of the person or entity to which it is addressed, and may 
> contain information that is privileged and confidential. You, the 
> recipient, are obligated to maintain it in a safe, secure and 
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> are not the intended recipient, please immediately notify us by return 
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Fax: 617-726-7422

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[Freesurfer] A few beginner questions about thickness analysis using freesurfer

[Jiang, Zhiguo]

1.   How do I register subjects' thickness maps to a common space to be able to 
do vertex wise comparison? And can any brain map be used as the common space?

2.   If I have a hand-drawn ROI on subject's original T1, is it possible to 
resample the volume ROI to the surface (so I can extract the thickness values 
from that ROI)

Any command lines would be appreciated.

Best,
Tony


Zhiguo Jiang, Ph.D.
[cid:image002.png@01CD4250.DA877620]




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Re: [Freesurfer] trac-all -bedp terminated job

[Priti Srinivasan]

Hi Sean,

Are you sourcing Freesurfer stable 5.1 in seychelles? trac-all -bedp is
supposed to submit multiple jobs (one job for each slice, in addition to
bedpostx_pre and bedpostx_post).. When you ran trac-all -bedp did it
submit all of those jobs?

Priti

> Hi Priti,
>
> Thanks, but would seem that despite the 0 status, something didn't run
> correctly. trac-all -path cannot find the file merged_ph1samples.nii.gz.
> Actually none of expected bedpostx files, other than nodif_brain_mask have
> been created in the dmri.bedpostx folder.
>
> -Sean
>
>> Hi Sean,
>>
>> You should look at the Exit_status. If it is '0', then your job ran
> successfully. If it is '1' or something else, then there is an error. So
> it looks like your job ran correctly.
>>
>> Priti
>>
>>> Hello,
>>> I'm running bedpostx_seychelles from the seychelles prompt (via
> trac-all
>>> -bedp -c $SUBJECTSDIR/[dmrircfile]) with vers. v5.1.0-20110514. The
> processes are generated and run correctly, as far as I can see, until
> the
>>> post-processing job. I receive and email stating:
>>> PBS Job Id: 1535470.seychelles.nmr.mgh.harvard.edu
>>> Job Name:   bedpostx_post
>>> Execution terminated
>>> Exit_status=0
>>> resources_used.cput=00:00:00
>>> resources_used.mem=0kb
>>> resources_used.vmem=0kb
>>> resources_used.walltime=00:00:00
>>> Why might the process be terminated?
>>> -Sean
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
>
>
>
>
>

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Re: [Freesurfer] trac-all -bedp terminated job

[Paul Raines]

Do not run your jobs on seychelles.  Most nodes are still CentOS4 and I
think a lot of the tools are simply not going to run on CentOS4 anymore.
Run them on launchpad and if you still get errors then we need to investigate.

-- Paul Raines (http://help.nmr.mgh.harvard.edu)



On Mon, 4 Jun 2012 2:52pm, stob...@nmr.mgh.harvard.edu wrote:

> Hi Priti,
>
> Thanks, but would seem that despite the 0 status, something didn't run
> correctly. trac-all -path cannot find the file merged_ph1samples.nii.gz.
> Actually none of expected bedpostx files, other than nodif_brain_mask have
> been created in the dmri.bedpostx folder.
>
> -Sean
>
>> Hi Sean,
>>
>> You should look at the Exit_status. If it is '0', then your job ran
> successfully. If it is '1' or something else, then there is an error. So
> it looks like your job ran correctly.
>>
>> Priti
>>
>>> Hello,
>>> I'm running bedpostx_seychelles from the seychelles prompt (via
> trac-all
>>> -bedp -c $SUBJECTSDIR/[dmrircfile]) with vers. v5.1.0-20110514. The
> processes are generated and run correctly, as far as I can see, until
> the
>>> post-processing job. I receive and email stating:
>>> PBS Job Id: 1535470.seychelles.nmr.mgh.harvard.edu
>>> Job Name:   bedpostx_post
>>> Execution terminated
>>> Exit_status=0
>>> resources_used.cput=00:00:00
>>> resources_used.mem=0kb
>>> resources_used.vmem=0kb
>>> resources_used.walltime=00:00:00
>>> Why might the process be terminated?
>>> -Sean
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
>
>
>
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Re: [Freesurfer] trac-all -bedp terminated job

[stobyne]

Hi Priti,

Thanks, but would seem that despite the 0 status, something didn't run
correctly. trac-all -path cannot find the file merged_ph1samples.nii.gz.
Actually none of expected bedpostx files, other than nodif_brain_mask have
been created in the dmri.bedpostx folder.

-Sean

> Hi Sean,
>
> You should look at the Exit_status. If it is '0', then your job ran
successfully. If it is '1' or something else, then there is an error. So
it looks like your job ran correctly.
>
> Priti
>
>> Hello,
>> I'm running bedpostx_seychelles from the seychelles prompt (via
trac-all
>> -bedp -c $SUBJECTSDIR/[dmrircfile]) with vers. v5.1.0-20110514. The
processes are generated and run correctly, as far as I can see, until
the
>> post-processing job. I receive and email stating:
>> PBS Job Id: 1535470.seychelles.nmr.mgh.harvard.edu
>> Job Name:   bedpostx_post
>> Execution terminated
>> Exit_status=0
>> resources_used.cput=00:00:00
>> resources_used.mem=0kb
>> resources_used.vmem=0kb
>> resources_used.walltime=00:00:00
>> Why might the process be terminated?
>> -Sean
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>



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Re: [Freesurfer] missing ROI when using mri_label2vol to transfer ic2.tri

[Leon]

Hi, Douglas
I have uploaded the file to the system. 

Also, my new results showed that  when  ic3.tri (instead of ic2.tri) is used as 
the input, one ROI at the similar location is also missing. Hope it will help 
you diagnose. 

Thanks
Leon




 From: Douglas N Greve 
To: Leon  
Cc: FreeSurfer  
Sent: Monday, June 4, 2012 1:00 PM
Subject: Re: [Freesurfer] missing ROI when using mri_label2vol to transfer 
ic2.tri
 
Can you upload the subject to our file drop system?

www.nmr.mgh.harvard.edu/facility/filedrop/index.html




On 06/04/2012 12:24 PM, Leon wrote:
> Hi, Douglas
>
> Thank you very much for the updated one. I tested the new codes and 
> the problem is still there. The ID for the original version that 
> generates a mask with one missing ROI is:
>
> $Id: mri_label2vol.c,v 1.38 2011/09/30 15:17:59 greve Exp $
>
> I remember this is a version I downloaded from a link in FS archive.
>
> The ID for the one you sent to me is:
>
> $Id: mri_label2vol.c,v 1.34.2.4 2011/09/30 15:19:36 greve Exp $
>
> They look almost identical. Do you have any ideas what else may cause 
> this issue and possible workaround?
>
> Thank you
>
> Leon
>
>
> *From:* Douglas Greve 
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Sent:* Friday, June 1, 2012 11:29 PM
> *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to 
> transfer ic2.tri
>
>
> What version are you using? I fix a problem last Sept that might be 
> like this. I've put a new version of mri_label2vol here:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2vol.linux
> Try this and let me know if it works.
> doug
>
>
> On 6/1/12 10:46 PM, Leon wrote:
>> Hi, Bruce
>> Here are my two command lines
>> For transferring the annot from the source template to the target 
>> subject:
>>
>> /home/freesurfer/bin/mri_surf2surf --srcsubject ${srcsubject} 
>> --sval-annot rh.ic2.annot --trgsubject ${trgsubject} --trgsurfval 
>> src_2_trg.annot --hemi rh --surfreg sphere.reg0
>>
>> Where sphere.reg0 is the registration from the target subject to the 
>> source subject.
>>
>> For transfer them to the volume file:
>>
>> /home/freesurfer/bin/mri_label2vol --annot src_2_trg.annot --temp 
>> ${fs_dir}/${trgsubject}/mri/brain.mgz --subject ${trgsubject} --hemi 
>> rh --fillthresh 0 --proj frac 0.3 0.8 0.05 --o src_2_trg_annot.mgz 
>> --identity
>>
>>
>> Here is output for one of my transformations:
>>
>> Setting mapmethod to nnf
>> Source registration surface changed to sphere.reg0
>> Target registration surface changed to sphere.reg0
>> srcsubject = MacaqueA
>> srcval     = (null)
>> srctype    =
>> trgsubject = MacaqueB
>> trgval     = 
>> /home/freesurfer/freesurfer/subjects/MacaqueB/label/rh.MacaqueA_to_MacaqueB.annot
>> trgtype    =
>> srcsurfreg = sphere.reg0
>> trgsurfreg = sphere.reg0
>> srchemi    = rh
>> trghemi    = rh
>> frame      = 0
>> fwhm-in    = 0
>> fwhm-out   = 0
>> label-src  = (null)
>> label-trg  = (null)
>> OKToRevFaceOrder  = 1
>> Reading source surface reg 
>> /home/freesurfer/freesurfer/subjects/MacaqueA/surf/rh.sphere.reg0
>> Loading source data
>> Reading surface file 
>> /home/freesurfer/freesurfer/subjects/MacaqueA/surf/rh.orig
>> reading colortable from annotation file...
>> colortable with 162 entries read (originally 
>> /usr/local/freesurfer/lib/bem/ic2.tri)
>> Reading target surface reg 
>> /home/freesurfer/freesurfer/subjects/MacaqueB/surf/rh.sphere.reg0
>> Done
>> Mapping Source Volume onto Source Subject Surface
>> surf2surf_nnfr: building source hash (res=16).
>> Surf2Surf: Forward Loop (61916)
>>
>> Surf2Surf: Dividing by number of hits (61916)
>> INFO: nSrcLost = 17467
>> nTrg121 = 61916, nTrgMulti =     0, MnTrgMultiHits = 0
>> nSrc121 = 35292, nSrcLost = 17467, nSrcMulti = 28910, MnSrcMultiHits 
>> = 0.920927
>> Saving target data
>> Converting to target annot
>> Saving to target annot 
>> /home/freesurfer/freesurfer/subjects/MacaqueB/label/rh.MacaqueA_to_MacaqueB.annot
>> step2: writing the surface label to volume...
>> Number of labels: 0
>> Annot File:      
>> /home/freesurfer/freesurfer/subjects/MacaqueB/label/rh.MacaqueA_to_MacaqueB.annot
>> Template Volume: 
>> /home/freesurfer/freesurfer/subjects/MacaqueB/mri/brain.mgz
>> Outut Volume: 
>> /home/freesurfer/freesurfer/subjects/MacaqueB/mri/rh_MacaqueA_to_MacaqueB_fill0_porjs0.3_proje0.8_projin0.05.mgz
>> Registration File: (null)
>> Fill Threshold: 0
>> Label Vox Vol:  1
>> ProjType:       frac
>> ProjTypeId:     2
>> ProjStart:      0.3
>> ProjStop:       0.8
>> ProjDelta:      0.05
>> Subject:  MacaqueB
>> Hemi:     rh
>> UseNewASeg2Vol:  1
>> DoLabelStatVol  0
>> $Id: mri_label2vol.c,v 1.38 2011/09/30 15:17:59 greve Exp $
>> Template RAS-to-Vox: 
>> -1.000  -0.000  -0.000   160.000;
>> -0.000  -0.000  -1.000   160.000;
>> -0.000   1.000  -0.000   160.000;
>> -0.000  -0.000  -0.000   1.000;
>> Template Voxel Volume: 1
>> nHits Thresh: 0
>> Using Identity Matrix
>> RegMat: 
>>  1.000   0.000   0.000   0.000;

Re: [Freesurfer] trac-all -bedp terminated job

[Priti Srinivasan]

Hi Sean,

You should look at the Exit_status. If it is '0', then your job ran
successfully. If it is '1' or something else, then there is an error. So
it looks like your job ran correctly.

Priti

> Hello,
>
> I'm running bedpostx_seychelles from the seychelles prompt (via trac-all
> -bedp -c $SUBJECTSDIR/[dmrircfile]) with vers. v5.1.0-20110514. The
> processes are generated and run correctly, as far as I can see, until the
> post-processing job. I receive and email stating:
>
> PBS Job Id: 1535470.seychelles.nmr.mgh.harvard.edu
> Job Name:   bedpostx_post
> Execution terminated
> Exit_status=0
> resources_used.cput=00:00:00
> resources_used.mem=0kb
> resources_used.vmem=0kb
> resources_used.walltime=00:00:00
>
> Why might the process be terminated?
>
> -Sean
>
>
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>
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[Freesurfer] trac-all -bedp terminated job

[stobyne]

Hello,

I'm running bedpostx_seychelles from the seychelles prompt (via trac-all
-bedp -c $SUBJECTSDIR/[dmrircfile]) with vers. v5.1.0-20110514. The
processes are generated and run correctly, as far as I can see, until the
post-processing job. I receive and email stating:

PBS Job Id: 1535470.seychelles.nmr.mgh.harvard.edu
Job Name:   bedpostx_post
Execution terminated
Exit_status=0
resources_used.cput=00:00:00
resources_used.mem=0kb
resources_used.vmem=0kb
resources_used.walltime=00:00:00

Why might the process be terminated?

-Sean


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Re: [Freesurfer] no aseg

[Douglas N Greve]

FYI when the --no-aseg option is used with make_average_subject, it gets 
passed to make_average_volume
doug

On 06/04/2012 01:56 PM, Gregory Kirk wrote:
> so it seems that i ran make_average_volume which does have a --no-aseg flag
>
> make_average_subject really just runs 2 other commands
> make_average_surface and make_average_volume.
>
> bruce the reason i did this is that mike was running a `super` average, i.e. 
> the average
> subject of 2 different syudies, i.e. ave_study1, ave_study2
>
> and he was running make_average_subject --subjects ave_study1 ave_study2 
> --out superave.
>
> we were doing this so we could map labels from one study to another
> and we were getting an error in the log file from make_average_volume
> that indicated it was having a problem with the aseg after the 
> make_average_surface had already finished without error.
>
> really we could just skip it i think as we are not actually doing anything 
> with the average volume.
>
> greg
>
> On 06/04/12, Bruce Fischl  wrote:
>> Hi Michael
>>
>> a couple of typos. It should be "make_average_subject" (note no "s"), and it 
>> should be --subjects (note the ending "s"). I also don't see a flag named 
>> --no-aseg, which I think is why it's being included as a subject. What are 
>> you trying to do?
>>
>> cheers
>> Bruce
>>
>> On Mon, 4 Jun 2012, michael kruepke wrote:
>>
>>> Hi all -
>>> Having a bit of an issue with trying to run a make_average with the flag
>>> --no-aseg. When written 
>>>
>>> make_average_subjects --subject subject1 subject2 --no-aseg --out
>>> superaverage
>>>
>>> the propt runs as if --no-aseg and --out superaverage are subjects i wish to
>>> average in with subjects1 and subject2. This is obviously and issue, hoping
>>> someone might have an idea of a solution. I have tried moving these flags to
>>> somewhere else in the prompt seeing if that would solve it, no luck there. 
>>>
>>> Best-
>>> Michael
>>>
>>> --
>>> Michael D. Kruepke
>>> PhD - University of Illinois at Urbana-Champaign 
>>> BA - Psych - University of Wisconsin-Madison
>>> mdkrue...@gmail.com
>>> (262)-483-7449
>>>
>>>
>>>
>>
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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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>
>

-- 
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

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Re: [Freesurfer] no aseg

[Gregory Kirk]

so it seems that i ran make_average_volume which does have a --no-aseg flag

make_average_subject really just runs 2 other commands
make_average_surface and make_average_volume.

bruce the reason i did this is that mike was running a `super` average, i.e. 
the average
subject of 2 different syudies, i.e. ave_study1, ave_study2

and he was running make_average_subject --subjects ave_study1 ave_study2 --out 
superave.

we were doing this so we could map labels from one study to another
and we were getting an error in the log file from make_average_volume
that indicated it was having a problem with the aseg after the 
make_average_surface had already finished without error.

really we could just skip it i think as we are not actually doing anything with 
the average volume.

greg

On 06/04/12, Bruce Fischl  wrote:
> Hi Michael
> 
> a couple of typos. It should be "make_average_subject" (note no "s"), and it 
> should be --subjects (note the ending "s"). I also don't see a flag named 
> --no-aseg, which I think is why it's being included as a subject. What are 
> you trying to do?
> 
> cheers
> Bruce
> 
> On Mon, 4 Jun 2012, michael kruepke wrote:
> 
> >Hi all -
> >Having a bit of an issue with trying to run a make_average with the flag
> >--no-aseg. When written 
> >
> >make_average_subjects --subject subject1 subject2 --no-aseg --out
> >superaverage
> >
> >the propt runs as if --no-aseg and --out superaverage are subjects i wish to
> >average in with subjects1 and subject2. This is obviously and issue, hoping
> >someone might have an idea of a solution. I have tried moving these flags to
> >somewhere else in the prompt seeing if that would solve it, no luck there. 
> >
> >Best-
> >Michael
> >
> >--
> >Michael D. Kruepke
> >PhD - University of Illinois at Urbana-Champaign 
> >BA - Psych - University of Wisconsin-Madison
> >mdkrue...@gmail.com
> >(262)-483-7449
> >
> >
> >
> 
> 
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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 
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> but does not contain patient information, please contact the sender and 
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Re: [Freesurfer] missing ROI when using mri_label2vol to transfer ic2.tri

[Douglas N Greve]

Can you upload the subject to our file drop system?

www.nmr.mgh.harvard.edu/facility/filedrop/index.html




On 06/04/2012 12:24 PM, Leon wrote:
> Hi, Douglas
>
> Thank you very much for the updated one. I tested the new codes and 
> the problem is still there. The ID for the original version that 
> generates a mask with one missing ROI is:
>
> $Id: mri_label2vol.c,v 1.38 2011/09/30 15:17:59 greve Exp $
>
> I remember this is a version I downloaded from a link in FS archive.
>
> The ID for the one you sent to me is:
>
> $Id: mri_label2vol.c,v 1.34.2.4 2011/09/30 15:19:36 greve Exp $
>
> They look almost identical. Do you have any ideas what else may cause 
> this issue and possible workaround?
>
> Thank you
>
> Leon
>
>
> *From:* Douglas Greve 
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Sent:* Friday, June 1, 2012 11:29 PM
> *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to 
> transfer ic2.tri
>
>
> What version are you using? I fix a problem last Sept that might be 
> like this. I've put a new version of mri_label2vol here:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2vol.linux
> Try this and let me know if it works.
> doug
>
>
> On 6/1/12 10:46 PM, Leon wrote:
>> Hi, Bruce
>> Here are my two command lines
>> For transferring the annot from the source template to the target 
>> subject:
>>
>> /home/freesurfer/bin/mri_surf2surf --srcsubject ${srcsubject} 
>> --sval-annot rh.ic2.annot --trgsubject ${trgsubject} --trgsurfval 
>> src_2_trg.annot --hemi rh --surfreg sphere.reg0
>>
>> Where sphere.reg0 is the registration from the target subject to the 
>> source subject.
>>
>> For transfer them to the volume file:
>>
>> /home/freesurfer/bin/mri_label2vol --annot src_2_trg.annot --temp 
>> ${fs_dir}/${trgsubject}/mri/brain.mgz --subject ${trgsubject} --hemi 
>> rh --fillthresh 0 --proj frac 0.3 0.8 0.05 --o src_2_trg_annot.mgz 
>> --identity
>>
>>
>> Here is output for one of my transformations:
>>
>> Setting mapmethod to nnf
>> Source registration surface changed to sphere.reg0
>> Target registration surface changed to sphere.reg0
>> srcsubject = MacaqueA
>> srcval = (null)
>> srctype=
>> trgsubject = MacaqueB
>> trgval = 
>> /home/freesurfer/freesurfer/subjects/MacaqueB/label/rh.MacaqueA_to_MacaqueB.annot
>> trgtype=
>> srcsurfreg = sphere.reg0
>> trgsurfreg = sphere.reg0
>> srchemi= rh
>> trghemi= rh
>> frame  = 0
>> fwhm-in= 0
>> fwhm-out   = 0
>> label-src  = (null)
>> label-trg  = (null)
>> OKToRevFaceOrder  = 1
>> Reading source surface reg 
>> /home/freesurfer/freesurfer/subjects/MacaqueA/surf/rh.sphere.reg0
>> Loading source data
>> Reading surface file 
>> /home/freesurfer/freesurfer/subjects/MacaqueA/surf/rh.orig
>> reading colortable from annotation file...
>> colortable with 162 entries read (originally 
>> /usr/local/freesurfer/lib/bem/ic2.tri)
>> Reading target surface reg 
>> /home/freesurfer/freesurfer/subjects/MacaqueB/surf/rh.sphere.reg0
>> Done
>> Mapping Source Volume onto Source Subject Surface
>> surf2surf_nnfr: building source hash (res=16).
>> Surf2Surf: Forward Loop (61916)
>>
>> Surf2Surf: Dividing by number of hits (61916)
>> INFO: nSrcLost = 17467
>> nTrg121 = 61916, nTrgMulti = 0, MnTrgMultiHits = 0
>> nSrc121 = 35292, nSrcLost = 17467, nSrcMulti = 28910, MnSrcMultiHits 
>> = 0.920927
>> Saving target data
>> Converting to target annot
>> Saving to target annot 
>> /home/freesurfer/freesurfer/subjects/MacaqueB/label/rh.MacaqueA_to_MacaqueB.annot
>> step2: writing the surface label to volume...
>> Number of labels: 0
>> Annot File:  
>> /home/freesurfer/freesurfer/subjects/MacaqueB/label/rh.MacaqueA_to_MacaqueB.annot
>> Template Volume: 
>> /home/freesurfer/freesurfer/subjects/MacaqueB/mri/brain.mgz
>> Outut Volume: 
>> /home/freesurfer/freesurfer/subjects/MacaqueB/mri/rh_MacaqueA_to_MacaqueB_fill0_porjs0.3_proje0.8_projin0.05.mgz
>> Registration File: (null)
>> Fill Threshold: 0
>> Label Vox Vol:  1
>> ProjType:   frac
>> ProjTypeId: 2
>> ProjStart:  0.3
>> ProjStop:   0.8
>> ProjDelta:  0.05
>> Subject:  MacaqueB
>> Hemi: rh
>> UseNewASeg2Vol:  1
>> DoLabelStatVol  0
>> $Id: mri_label2vol.c,v 1.38 2011/09/30 15:17:59 greve Exp $
>> Template RAS-to-Vox: 
>> -1.000  -0.000  -0.000   160.000;
>> -0.000  -0.000  -1.000   160.000;
>> -0.000   1.000  -0.000   160.000;
>> -0.000  -0.000  -0.000   1.000;
>> Template Voxel Volume: 1
>> nHits Thresh: 0
>> Using Identity Matrix
>> RegMat: 
>>  1.000   0.000   0.000   0.000;
>>  0.000   1.000   0.000   0.000;
>>  0.000   0.000   1.000   0.000;
>>  0.000   0.000   0.000   1.000;
>> Label RAS-to-Vox: 
>> -1.000   0.000   0.000   160.000;
>>  0.000   0.000  -1.000   160.000;
>>  0.000   1.000   0.000   160.000;
>>  0.000   0.000   0.000   1.000;
>>   INFO: loading surface  
>> /home/freesurfer/freesurfer/subjects/MacaqueB/surf/rh.white
>> nvertices = 61916
>> Reading thickness 
>> /home/freesurfer/freesurfer/sub

Re: [Freesurfer] missing ROI when using mri_label2vol to transfer ic2.tri

[Leon]

Hi, Douglas

Thank you very much for the updated one. I tested the new codes and the problem 
is still there. The ID for the original version that generates a mask with one 
missing ROI is:

$Id: mri_label2vol.c,v 1.38 2011/09/30 15:17:59 greve Exp $

I remember this is a version I downloaded from a link in FS archive. 


The ID for the one you sent to me is:

$Id: mri_label2vol.c,v 1.34.2.4 2011/09/30 15:19:36 greve Exp $

They look almost identical. Do you have any ideas what else may cause this 
issue and possible workaround?

Thank you

Leon





 From: Douglas Greve 
To: freesurfer@nmr.mgh.harvard.edu 
Sent: Friday, June 1, 2012 11:29 PM
Subject: Re: [Freesurfer] missing ROI when using mri_label2vol to transfer 
ic2.tri
 


What version are you using? I fix a problem last Sept that might be
like this. I've put a new version of mri_label2vol here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2vol.linux
Try this and let me know if it works.
doug


On 6/1/12 10:46 PM, Leon wrote: 
Hi, Bruce
>Here are my two command lines 
>
>For transferring the annot from the source template to the target subject:
>
>
>/home/freesurfer/bin/mri_surf2surf --srcsubject ${srcsubject} --sval-annot 
>rh.ic2.annot --trgsubject ${trgsubject} --trgsurfval src_2_trg.annot --hemi rh 
>--surfreg sphere.reg0 
>
>
>Where sphere.reg0 is the registration from the target subject to the source 
>subject. 
>
>
>
>For transfer them to the volume file:
>
>
>/home/freesurfer/bin/mri_label2vol --annot src_2_trg.annot --temp 
>${fs_dir}/${trgsubject}/mri/brain.mgz --subject ${trgsubject} --hemi rh 
>--fillthresh 0 --proj frac 0.3 0.8 0.05 --o src_2_trg_annot.mgz --identity
>
>
>
>
>Here is output for one of my transformations:
>
>
>Setting mapmethod to nnf
>Source registration surface changed to sphere.reg0
>Target registration surface changed to sphere.reg0
>srcsubject = MacaqueA
>srcval = (null)
>srctype    =
>trgsubject = MacaqueB
>trgval =
/home/freesurfer/freesurfer/subjects/MacaqueB/label/rh.MacaqueA_to_MacaqueB.annot
>trgtype    =
>srcsurfreg = sphere.reg0
>trgsurfreg = sphere.reg0
>srchemi    = rh
>trghemi    = rh
>frame  = 0
>fwhm-in    = 0
>fwhm-out   = 0
>label-src  = (null)
>label-trg  = (null)
>OKToRevFaceOrder  = 1
>Reading source surface reg
/home/freesurfer/freesurfer/subjects/MacaqueA/surf/rh.sphere.reg0
>Loading source data
>Reading surface file
/home/freesurfer/freesurfer/subjects/MacaqueA/surf/rh.orig
>reading colortable from annotation file...
>colortable with 162 entries read (originally
/usr/local/freesurfer/lib/bem/ic2.tri)
>Reading target surface reg
/home/freesurfer/freesurfer/subjects/MacaqueB/surf/rh.sphere.reg0
>Done
>Mapping Source Volume onto Source Subject Surface
>surf2surf_nnfr: building source hash (res=16).
>Surf2Surf: Forward Loop (61916)
>
>Surf2Surf: Dividing by number of hits (61916)
>INFO: nSrcLost = 17467
>nTrg121 = 61916, nTrgMulti = 0, MnTrgMultiHits = 0
>nSrc121 = 35292, nSrcLost = 17467, nSrcMulti = 28910,
MnSrcMultiHits = 0.920927
>Saving target data
>Converting to target annot
>Saving to target annot
/home/freesurfer/freesurfer/subjects/MacaqueB/label/rh.MacaqueA_to_MacaqueB.annot
>step2: writing the surface label to volume...
>Number of labels: 0
>Annot File: 
/home/freesurfer/freesurfer/subjects/MacaqueB/label/rh.MacaqueA_to_MacaqueB.annot
>Template Volume:
/home/freesurfer/freesurfer/subjects/MacaqueB/mri/brain.mgz
>Outut Volume:
/home/freesurfer/freesurfer/subjects/MacaqueB/mri/rh_MacaqueA_to_MacaqueB_fill0_porjs0.3_proje0.8_projin0.05.mgz
>Registration File: (null)
>Fill Threshold: 0
>Label Vox Vol:  1
>ProjType:   frac
>ProjTypeId: 2
>ProjStart:  0.3
>ProjStop:   0.8
>ProjDelta:  0.05
>Subject:  MacaqueB
>Hemi: rh
>UseNewASeg2Vol:  1
>DoLabelStatVol  0
>$Id: mri_label2vol.c,v 1.38 2011/09/30 15:17:59 greve Exp $
>Template RAS-to-Vox: 
>-1.000  -0.000  -0.000   160.000;
>-0.000  -0.000  -1.000   160.000;
>-0.000   1.000  -0.000   160.000;
>-0.000  -0.000  -0.000   1.000;
>Template Voxel Volume: 1
>nHits Thresh: 0
>Using Identity Matrix
>RegMat: 
> 1.000   0.000   0.000   0.000;
> 0.000   1.000   0.000   0.000;
> 0.000   0.000   1.000   0.000;
> 0.000   0.000   0.000   1.000;
>Label RAS-to-Vox: 
>-1.000   0.000   0.000   160.000;
> 0.000   0.000  -1.000   160.000;
> 0.000   1.000   0.000   160.000;
> 0.000   0.000   0.000   1.000;
>  INFO: loading surface 
/home/freesurfer/freesurfer/subjects/MacaqueB/surf/rh.white
>nvertices = 61916
>Reading thickness
/home/freesurfer/freesurfer/subjects/MacaqueB/surf/rh.thickness
>Loading annotations from
/home/freesurfer/freesurfer/subjects/MacaqueB/label/rh.MacaqueA_to_MacaqueB.annot
>reading colortable from annotation file...
>colortable with 162 entries read (originally
/usr/local/freesurfer/lib/bem/ic2.tri)
>annotidmax

Re: [Freesurfer] Concatenating Transforms

[Douglas N Greve]

You can use mri_matrix_multiply. Use -im to input a matrix, use -iim to 
input a matrix that will be inverted.
doug

On 06/04/2012 12:13 PM, Clark Fisher wrote:
> Hi Doug,
>
> I do plan to manually align the functionals to the structural as a final 
> step, but our epi scans look different enough from our T1s that I want to use 
> this as a starting point.  Also, combining transforms is something I've 
> wanted to be able to do a few times now as I explore different ways of 
> looking at my data, so I think it could be useful for the future.
>
> One thing that seems to have worked for my current case is to convert my 
> registrations to the xfm format, add a final row to make a 4x4 matrix, 
> multiply them in matlab, and make a new xfm file with the resulting matrix.  
> Is there a better way to do this?
>
> -Clark
>
>

-- 
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

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Re: [Freesurfer] Concatenating Transforms

[Clark Fisher]

Hi Doug,

I do plan to manually align the functionals to the structural as a final step, 
but our epi scans look different enough from our T1s that I want to use this as 
a starting point.  Also, combining transforms is something I've wanted to be 
able to do a few times now as I explore different ways of looking at my data, 
so I think it could be useful for the future. 

One thing that seems to have worked for my current case is to convert my 
registrations to the xfm format, add a final row to make a 4x4 matrix, multiply 
them in matlab, and make a new xfm file with the resulting matrix.  Is there a 
better way to do this?

-Clark
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Re: [Freesurfer] Assertion failed at line 827

[Douglas N Greve]

Hi Kiley, that appears to be a problem with the MNI nu_correct program 
(FSL unrelated). Do you change or re-install any of the MNI libraries? 
Can you send the full recon-all.log file?
doug

On 06/02/2012 08:43 AM, Kiley Seymour wrote:
>  Dear Freesurfers,
>
> I have previously had no trouble using recon-all to process my
> structural scans. However, today I encountered the problem below. I
> have looked at postings on this mailing list and it seems this issue
> is not a freesurfer one. During my last functional analysis of
> retinotopy data in freesurfer, I came across a problem that required
> me to install a full version of FSL on my ubuntu machine. Do you think
> this could be the source of the problem somehow? Otherwise, I am not
> sure what could have changed since the last time I processed my data
> with recon-all.
>
> Your input would be very much appreciated.
>
> Thanks
>
> Kiley
>
> Assertion failed at line 827 in file templates/CachedArray.cc
> nu_estimate_np_and_em: crashed while running volume_stats (termination
> status=256)
> nu_correct: crashed while running nu_estimate_np_and_em (termination 
> status=256)
> ERROR: nu_correct
> Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59
> UTC 2009 i686 GNU/Linux
>
>
> Dr Kiley Seymour
> Alexander von Humboldt Postdoctoral Fellow
> Klinik für Psychiatrie und Psychotherapie
> Charité Campus Mitte
> Charitéplatz 1
> D-10117 Berlin
> tel: 0049-(0)30-450 517131
>
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] Correction of registration in preproc-sess stream

[Douglas N Greve]

You can try running register-sess outside of preproc-sess, something like
register-sess -s session -fsd bold -per-run -init-spm

before you do that, you need to have spm5 and matlab, and change your 
matlab/startup.m to add the spm5 path
path(path,'/usr/pubsw/common/spm/spm5');

doug

ps. Is this whole brain coverage or are you chopping off some of the brain


On 06/04/2012 11:36 AM, Jörg Pfannmöller wrote:
> Dear Doug,
>
> indeed the initialization fails. I was able to initiate bbregister manually, 
> giving a good registration result. Can you give me a hint how to
> modify the registration and keeping the preproc-sess stream intact?
>
> Cheers
>
> pfannmoe
> ___
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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

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Re: [Freesurfer] Correction of registration in preproc-sess stream

[Jörg Pfannmöller]

Dear Doug,

indeed the initialization fails. I was able to initiate bbregister manually, 
giving a good registration result. Can you give me a hint how to 
modify the registration and keeping the preproc-sess stream intact?

Cheers

   pfannmoe
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Re: [Freesurfer] Anatomic Inferences

[Douglas N Greve]

Nothing that I can think of, other than to just load it up in tksurfer 
and see where the cluster falls.
doug

On 06/04/2012 11:18 AM, Govindarajan, Koushik Athreya wrote:
> Thanks Doug for the response. Yes, I do understand that there is going to be 
> overlap. My question is, is there a way to identify all the overlapping 
> regions. Say, if the overlap is between prominent labels like Precentral and 
> superior frontal, even though the cluster label might say precentral, I would 
> be able to say that it extends to superior frontal also. But if the overlap 
> were to happen between regions that are much less distinguishable, then the 
> inferences made about the extent of differences might not be complete.
>
> Thanks again
> Regards
> Koushik
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Monday, June 04, 2012 10:00 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Anatomic Inferences
>
> Hi Koushik, you are correct it will report the label that the max falls
> into and so the entire cluster can fall across multiple labels. But I'm
> not sure what you are asking. You're cluster effectively forms it's own
> label, and, given that your cluster is somewhat unique, I'm not sure
> what pre-defined label would satisfy you. No matter what the labeling
> scheme, you'll always end up with overlap.
> doug
>
> On 06/04/2012 10:35 AM, Govindarajan, Koushik Athreya wrote:
>> Dear Freesurfers,
>>
>>   I had a question about interpreting the results of the Monte-Carlo 
>> simulation. It is my understanding that the clusters are labeled based on 
>> the value of the maximum significant vertex in a cluster. So, assuming that 
>> a cluster kind of borders or extends over 2 adjacent regions, it could well 
>> be labeled as a single region whereas anatomically, it would actually be 2 
>> separate regions. Are there any suggestions for an atlas that could help me 
>> make my inferences more meaningful? Sorry if this is a naive question, my 
>> knowledge of anatomic labelling is less than impressive :-)
>>
>> Thanks
>> Koushik
>>
>> ___
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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
>
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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.
>
>
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] when are uncorrected 0, 001 results permitted instead of FWE?

[Douglas N Greve]

Generally, reviews and editors will not let you publish without 
correcting for multiple comparisons. You might get an exception with a 
rare patient population or something like that. I don't understand your 
second question.
doug

On 06/04/2012 11:22 AM, Daniel Ferreira wrote:
>
> Dear all,
>
> I have heard that the FWE correction sometimes could be demanding and 
> kill very subtle differences, overall for example in aging studies 
> with normal people and narrow-age intervals, or young people, where 
> changes are supposed to be not very big.
>
> So, do you know when uncorrected results are justified or at least 
> permitted instead of FWE? Any paper or information about this specific 
> FWE disadvantages in aid of p<0,001 uncorrected results?
>
> Thank you very much in advance
>
> Daniel Ferreira
>
>
>
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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] Anatomic Inferences

[Govindarajan, Koushik Athreya]

Thanks Doug for the response. Yes, I do understand that there is going to be 
overlap. My question is, is there a way to identify all the overlapping 
regions. Say, if the overlap is between prominent labels like Precentral and 
superior frontal, even though the cluster label might say precentral, I would 
be able to say that it extends to superior frontal also. But if the overlap 
were to happen between regions that are much less distinguishable, then the 
inferences made about the extent of differences might not be complete.

Thanks again
Regards
Koushik


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Monday, June 04, 2012 10:00 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Anatomic Inferences

Hi Koushik, you are correct it will report the label that the max falls
into and so the entire cluster can fall across multiple labels. But I'm
not sure what you are asking. You're cluster effectively forms it's own
label, and, given that your cluster is somewhat unique, I'm not sure
what pre-defined label would satisfy you. No matter what the labeling
scheme, you'll always end up with overlap.
doug

On 06/04/2012 10:35 AM, Govindarajan, Koushik Athreya wrote:
> Dear Freesurfers,
>
>  I had a question about interpreting the results of the Monte-Carlo 
> simulation. It is my understanding that the clusters are labeled based on the 
> value of the maximum significant vertex in a cluster. So, assuming that a 
> cluster kind of borders or extends over 2 adjacent regions, it could well be 
> labeled as a single region whereas anatomically, it would actually be 2 
> separate regions. Are there any suggestions for an atlas that could help me 
> make my inferences more meaningful? Sorry if this is a naive question, my 
> knowledge of anatomic labelling is less than impressive :-)
>
> Thanks
> Koushik
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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[Freesurfer] when are uncorrected 0, 001 results permitted instead of FWE?

[Daniel Ferreira]

Dear all,



I have heard that the FWE correction sometimes could be demanding and kill
very subtle differences, overall for example in aging studies with normal
people and narrow-age intervals, or young people, where changes are
supposed to be not very big.



So, do you know when uncorrected results are justified or at least
permitted instead of FWE? Any paper or information about this specific FWE
disadvantages in aid of p<0,001 uncorrected results?



Thank you very much in advance



Daniel Ferreira
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Re: [Freesurfer] Couldn't download rtview

[Douglas N Greve]

That link works for me, but I've attached rtview to this email just in case.
doug

On 06/04/2012 11:03 AM, Michael Bannert wrote:

Dear freesurfer community,

I tried to download rtview but it didn't work. I used the following 
URL: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/rtview


... as described here: 
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21560.html


I need this function to interpret retinotopic mapping data. I followed 
the instructions for running retinotopic mapping using Freesurfer 5 I 
found here ( 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis 
) and everything seems to work fine but I find it hard to interpret 
the results and to determine the boundaries between visual areas.


Could you please tell me where the file can be found? (Or is there a 
more elegant way to get a nice color wheel in Freesurfer 5?)


Thank you very much!
Michael

PS: The URL for the FsFast tutorial data still seems to be incorrect 
as well. See also 
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23019.html


--
Michael Bannert, Dipl.-Psych.
Vision & Cognition Lab, Centre for Integrative Neuroscience, Univ. of 
Tübingen & BCCN Tübingen

Otfried-Müller-Str. 25, 72076 Tübingen, Germany
Phone: +49 - (0)7071 / 29 - 89031





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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

#!/bin/tcsh -f
# rtview

set VERSION = '$Id$';

set srcsubject = ();
set trgsubject = ();
set realvol = ();
set imagvol = ();
set hemi = ();
set regfile = ();
set hfile = ();
set stimtype = ();

set tmpdir = ();
set cleanup = 1;
set LF = ();

set tclcmd0 = $FREESURFER_HOME/lib/tcl/twocond-views.tcl

set inputargs = ($argv);
set PrintHelp = 0;

if($#argv == 0) goto usage_exit;
set n = `echo $argv | grep -e -help | wc -l` 
if($n != 0) then
  set PrintHelp = 1;
  goto usage_exit;
endif
set n = `echo $argv | grep -e -version | wc -l` 
if($n != 0) then
  echo $VERSION
  exit 0;
endif

goto parse_args;
parse_args_return:

goto check_params;
check_params_return:

if($#hfile) then
  set srcdir = `dirname $hfile`
else
  set srcdir = `dirname $realvol`
endif
if($#tmpdir == 0) set tmpdir = $srcdir/tmpdir.rtview
mkdir -p $tmpdir

if($#LF == 0) set LF = $tmpdir/rtview.log
if($LF != /dev/null) rm -f $LF
echo "Log file for rtview" >> $LF
date  | tee -a $LF
echo "" | tee -a $LF
echo "setenv SUBJECTS_DIR $SUBJECTS_DIR" | tee -a $LF
echo "cd `pwd`"  | tee -a $LF
echo $0 $inputargs | tee -a $LF
echo "" | tee -a $LF
uname -a  | tee -a $LF

set tkimagvol = $tmpdir/tkimag.mgh
set tkrealvol = $tmpdir/tkreal.mgh
rm -f $tkimagvol $tkrealvol
if($#hfile) then
  set imagvol = $tmpdir/imag.mgh
  set realvol = $tmpdir/real.mgh
  mri_convert $hfile --frame 1 $tkimagvol; # 2nd frame
  if($status) exit 1;
  mri_convert $hfile --frame 2 $tkrealvol; # 3rd frame
  if($status) exit 1;
endif
if(! -e $tkimagvol) then
  # Multiply by fsig because that is what 
  mris_calc -o $tkimagvol $fsigvol mul $imagvol
  if($status) exit 1;
  mris_calc -o $tkrealvol $fsigvol mul $realvol
  if($status) exit 1;
endif

foreach cmpx (real imag)
  set cmpxvol = $tmpdir/tk"$cmpx".mgh
  if($#regfile) then
# Input is a volume, use vol2surf
set cmpxmgh = $tmpdir/map-$cmpx-$hemi.mgh
mri_vol2surf --reg $regfile --mov $cmpxvol --hemi $hemi --o $cmpxmgh \
   --mapmethod nnf
if($status) exit 1;
  else
set cmpxmgh = $cmpxvol
  endif
  # Convert to wfile (and maybe change subjects)
  set cmpxw = $tmpdir/map-$cmpx-$hemi.w
  mri_surf2surf --hemi $hemi --sval $cmpxmgh --tval $cmpxw \
   --tfmt paint --srcsubject $srcsubject --trgsubject $trgsubject 
  if($status) exit 1;
end

#mri_fieldsign --eccen eccen/lh.real.mgh eccen/lh.imag.mgh \
#--polar polar/lh.real.mgh polar/lh.imag.mgh \
# --fs lh.fieldsign.mgh --s els --hemi lh --sphere --old --fwhm 10

setenv angle_offset 0
setenv revpolarflag 0
unsetenv flatzrot 
unsetenv flatscale 
unsetenv statflag 
unsetenv statname
setenv colscale 0
unsetenv colscalebarflag 
#setenv eccendir eccen
#setenv polardir polar
setenv floatstem map
setenv realname-real; # map-real-?h.w
setenv complexname -imag; # map-imag-?h.w
setenv fthresh 0.4
setenv fslope 1.3
setenv fmid 0.8
setenv offset 0.4; # for gray scale
setenv hemi $hemi
setenv curv $hemi.curv
setenv nosave 1
setenv noexit
setenv dir $tmpdir
setenv polardir $tmpdir
setenv eccendir $tmpdir
setenv smoothsteps 2

#set tclcmd = $tmpdir/rtview.tcl
#rm -f $tclcmd
#echo "set noexit 1" >> $tclcmd
#cat $tclcmd0  >> $tclcmd
#echo "set dir $tmpdir" >> $tclcmd
#echo "set floatstem map" >> $tclcmd

set tclcmd = $FREESURFER_HOME/lib/tcl/$stimtype-views.tcl

set cmd = (tksurfer $subject $hemi

Re: [Freesurfer] qdec table file

[Douglas N Greve]

OK, I've replicated that this is happening, but Nick will have to take a 
look.
doug

On 06/04/2012 11:05 AM, Laura M. Tully wrote:
>
>
>
> Hi Doug,
>
> Attached is the qdec table file and associated levels files. It's 
> strange that qdec won't let me select more than one continuous 
> variable. What's even more strange is that I have been able to do that 
> last month when I originally looked at these data before doing manual 
> edits and quality control. I don't think that I have changed anything 
> since then, but I'm not sure what to look for. Any help you have would 
> be most appreciated!
>
> Best,
>
> Laura.
>
> -- 
> Laura Tully
> Social Neuroscience & Psychopathology
> Harvard University
> 840 William James Hall
> 33 Kirkland St
> Cambridge, MA 02138
> ltu...@fas.harvard.edu 
> -- 
> My musings as a young clinical scientist: 
> http://theclinicalbrain.blogspot.com/
> Follow me on Twitter: @tully_laura
>
>
>
>
> -- 
> Laura Tully
> Social Neuroscience & Psychopathology
> Harvard University
> 840 William James Hall
> 33 Kirkland St
> Cambridge, MA 02138
> ltu...@fas.harvard.edu 
> -- 
> My musings as a young clinical scientist: 
> http://theclinicalbrain.blogspot.com/
> Follow me on Twitter: @tully_laura
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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[Freesurfer] qdec table file

[Laura M. Tully]

Hi Doug,

Attached is the qdec table file and associated levels files. It's strange
that qdec won't let me select more than one continuous variable. What's
even more strange is that I have been able to do that last month when I
originally looked at these data before doing manual edits and quality
control. I don't think that I have changed anything since then, but I'm not
sure what to look for. Any help you have would be most appreciated!

Best,

Laura.

-- 
Laura Tully
Social Neuroscience & Psychopathology
Harvard University
840 William James Hall
33 Kirkland St
Cambridge, MA 02138
ltu...@fas.harvard.edu
--
My musings as a young clinical scientist:
http://theclinicalbrain.blogspot.com/
Follow me on Twitter: @tully_laura




-- 
Laura Tully
Social Neuroscience & Psychopathology
Harvard University
840 William James Hall
33 Kirkland St
Cambridge, MA 02138
ltu...@fas.harvard.edu
--
My musings as a young clinical scientist:
http://theclinicalbrain.blogspot.com/
Follow me on Twitter: @tully_laura


betweenGroup.qdec.table.dat
Description: Binary data


Gender.levels
Description: Binary data


Group.levels
Description: Binary data
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[Freesurfer] Couldn't download rtview

[Michael Bannert]

Dear freesurfer community,

I tried to download rtview but it didn't work. I used the following URL: 
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/rtview

... as described here: 
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21560.html

I need this function to interpret retinotopic mapping data. I followed the 
instructions for running retinotopic mapping using Freesurfer 5 I found here ( 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis ) 
and everything seems to work fine but I find it hard to interpret the results 
and to determine the boundaries between visual areas. 

Could you please tell me where the file can be found? (Or is there a more 
elegant way to get a nice color wheel in Freesurfer 5?)

Thank you very much!
Michael

PS: The URL for the FsFast tutorial data still seems to be incorrect as well. 
See also 
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23019.html

--
Michael Bannert, Dipl.-Psych.
Vision & Cognition Lab, Centre for Integrative Neuroscience, Univ. of Tübingen 
& BCCN Tübingen
Otfried-Müller-Str. 25, 72076 Tübingen, Germany
Phone: +49 - (0)7071 / 29 - 89031



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Re: [Freesurfer] Inter-hemispheric registration issue

[Douglas N Greve]

OK, I put a new version of xhemireg there that will create the nu.mgz. 
The newer version of the talairach do not need nu.mgz which is why I did 
not have it in the xhemireg I gave you.
doug

On 06/02/2012 11:12 AM, Irene Altarelli wrote:
> My command was:
> xhemireg --s ac_copie
>
> The terminal output is identical to the log file (attached), ending by:
>
> #@# Talairach Tue May 29 18:24:25 CEST 2012
> /home/ialtarelli/DATABASE/Karla5/ac_copie/xhemi/mri
>
>   talairach_avi --i nu.mgz --xfm transforms/talairach.auto.xfm
>
> ERROR: input volume nu.mgz does not exist
> Linux lscp-iao1 2.6.32-5-amd64 #1 SMP Mon Jan 16 16:22:28 UTC 2012
> x86_64 GNU/Linux
>
> recon-all -s ac_copie/xhemi exited with ERRORS at Tue May 29 18:24:26
> CEST 2012
>
>
>
> Should I skip that by using the --no-tal flag?
> Thanks!
> Irene
>
>
> Le samedi 02 juin 2012 à 10:57 -0400, Douglas Greve a écrit :
>> Can you send your cmd and terminal output?
>> doug
>>
>> On 6/2/12 9:46 AM, Irene Altarelli wrote:
>>> Dear Doug,
>>>
>>> thanks for putting mri_vol2vol on the ftp site, and sorry for bothering
>>> you again with this. I did as suggested, but I still get an error, now
>>> when attempting to run xhemireg. Apparently nu.mgz is missing.
>>>
>>> Please find the log attached.
>>>
>>> Thank you very much again,
>>> Irene
>>>
>>>
>>>
>>> Le vendredi 18 mai 2012 à 11:24 -0400, Douglas N Greve a écrit :
 You'll need a new version of mri_vol2vol, which I have put on that ftp 
 site.
 doug

 On 05/18/2012 04:25 AM, Irene Altarelli wrote:
> Thanks for your help, Doug.
>
> It seems as if there is another script problem then, because when
> running the command I get the following error message (log also
> attached):
> ERROR: Option --keep-precision unknown
>
> I'm using Fs version 5, and the version of xhemireg I have downloaded
> is: v 1.22 2012/01/20 20:12:32.
>
> Should that --keep-precision option be removed from the script?
>
> Thank you,
> Irene
>
>
>
> Le mercredi 16 mai 2012 à 11:16 -0400, Douglas N Greve a écrit :
>> Irene, this is a problem with the script. The work-around is to run
>> xhemireg before running surfreg with the --xhemi option.
>>
>> doug
>>
>> On 05/16/2012 01:56 AM, Irene Altarelli wrote:
>>> Dear Doug,
>>>
>>> here is what I get.
>>>
>>> First, I ran surfreg --s aa_tris --t fsaverage_sym --lh and got the
>>> attached log file. Here is the terminal output:
>>>
>>> setenv SUBJECTS_DIR /home/ialtarelli/DATABASE/Karla5/
>>> cd /home/ialtarelli
>>> /home/ialtarelli/freesurfer/bin/surfreg --s aa_tris --t fsaverage_sym
>>> --lh
>>>
>>> Linux lscp-iao1 2.6.32-5-amd64 #1 SMP Mon Jan 16 16:22:28 UTC 2012
>>> x86_64 GNU/Linux
>>> #@# lh mardi 15 mai 2012, 19:23:56 (UTC+0200)
>>> #CMD# mris_register -curv -annot
>>> aparc.annot /home/ialtarelli/DATABASE/Karla5//aa_tris/surf/lh.sphere 
>>> /home/ialtarelli/DATABASE/Karla5//fsaverage_sym/lh.reg.template.tif 
>>> /home/ialtarelli/DATABASE/Karla5//aa_tris/surf/lh.fsaverage_sym.sphere.reg
>>> using smoothwm curvature for final alignment
>>> zeroing medial wall in aparc.annot
>>> $Id: mris_register.c,v 1.56 2010/02/28 23:08:04 fischl Exp $
>>>   $Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $
>>> reading surface
>>> from /home/ialtarelli/DATABASE/Karla5//aa_tris/surf/lh.sphere...
>>> reading colortable from annotation file...
>>> colortable with 36 entries read
>>> (originally 
>>> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
>>> reading template parameterization
>>> from 
>>> /home/ialtarelli/DATABASE/Karla5//fsaverage_sym/lh.reg.template.tif...
>>> ripping medial wall...
>>> writing registered surface
>>> to 
>>> /home/ialtarelli/DATABASE/Karla5//aa_tris/surf/lh.fsaverage_sym.sphere.reg...
>>> curvature mean = 0.007, std = 0.603
>>> curvature mean = 0.030, std = 0.806
>>> curvature mean = 0.024, std = 0.853
>>> curvature mean = 0.009, std = 0.826
>>> curvature mean = 0.011, std = 0.936
>>> curvature mean = 0.003, std = 0.836
>>> curvature mean = 0.005, std = 0.972
>>> curvature mean = 0.001, std = 0.837
>>> curvature mean = 0.001, std = 0.988
>>> curvature mean = -0.032, std = 0.312
>>> curvature mean = 0.032, std = 0.124
>>> curvature mean = 0.079, std = 0.315
>>> curvature mean = 0.031, std = 0.151
>>> curvature mean = 0.049, std = 0.489
>>> curvature mean = 0.031, std = 0.165
>>> curvature mean = 0.028, std = 0.631
>>> curvature mean = 0.031, std = 0.171
>>> curvature mean = 0.011, std = 0.749
>>> 159: 0 negative triangles
>>> surfreg-Run-Time-Hours aa_tris lh 0 0,90
>>> mardi 15 mai 2012, 20:17:58 (UTC+0200)
>>> surfreg done
>>>
>>> Then, I ran surfreg --s aa_tris --t fsaverage

Re: [Freesurfer] Anatomic Inferences

[Douglas N Greve]

Hi Koushik, you are correct it will report the label that the max falls 
into and so the entire cluster can fall across multiple labels. But I'm 
not sure what you are asking. You're cluster effectively forms it's own 
label, and, given that your cluster is somewhat unique, I'm not sure 
what pre-defined label would satisfy you. No matter what the labeling 
scheme, you'll always end up with overlap.
doug

On 06/04/2012 10:35 AM, Govindarajan, Koushik Athreya wrote:
> Dear Freesurfers,
>
>  I had a question about interpreting the results of the Monte-Carlo 
> simulation. It is my understanding that the clusters are labeled based on the 
> value of the maximum significant vertex in a cluster. So, assuming that a 
> cluster kind of borders or extends over 2 adjacent regions, it could well be 
> labeled as a single region whereas anatomically, it would actually be 2 
> separate regions. Are there any suggestions for an atlas that could help me 
> make my inferences more meaningful? Sorry if this is a naive question, my 
> knowledge of anatomic labelling is less than impressive :-)
>
> Thanks
> Koushik
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] freeview RAS

[Douglas N Greve]

Hi Hiroyuki, can you give us more information? Eg, you click on a given 
vertex (col,row,slice), you find the "Scanner RAS" field in tkmedit, you 
go to the same col,row,slice in freeview and it's RAS is x,y,z. There 
are several different RAS coordinates, and you'll need to be clear as to 
which one you are talking about.
doug

On 06/02/2012 04:05 PM, Oya, Hiroyuki (UI Health Care) wrote:
>
> Dear Sir,
>
> When I view a brain volume (e.x., orig.mgz) with freeview and tkmedit, 
> RAS coordinate differs.  Why?
>
> Thank you.
>
> Hiroyuki
>
>
>
> 
> Notice: This UI Health Care e-mail (including attachments) is covered 
> by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is 
> confidential and may be legally privileged.  If you are not the 
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> dissemination, distribution, or copying of this communication is 
> strictly prohibited.  Please reply to the sender that you have 
> received the message in error, then delete it.  Thank you.
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Re: [Freesurfer] tkregister question

[Douglas N Greve]

That is correct and expected. The only constant is the vox2vox 
transformation. Once you change the vox2ras (eg, scanner or TKReg), then 
it must change the ras2ras transform in order to keep the vox2vox constant.
doug

On 06/02/2012 12:03 PM, Shay Ohayon wrote:
> Dear Doug,
>
> Following up on tkregister (lets see if my logic make sense).
> So, if I use --regheader, the actual transformation that will be 
> written to register.dat will be this one ?
>
> T* = Tk_vox2ras(B) * inv(vox2rasB) * T * vox2rasA * inv(tkvox2rasA)
>
> where T maps X,Y,Z of volume A (in mm) to X,Y,Z of volume B (in mm) 
> when mm space was obtained using vox2ras.
>
> This way, things will be compatible when I call tkregister again 
> without the regheader?
>
> What bothered me was that if you use vox2ras to map things you get 
> transformation T, which is actually different than
> the transformation you would get if you use tkvox2ras (i.e., T*).
>
> If this is the case, then I think I finally understand whats going on :)
>
> -- Shay
>
>
> Date: Fri, 01 Jun 2012 12:03:13 -0400
> From: Douglas N Greve  >
> Subject: Re: [Freesurfer] tkregister question
> To: freesurfer@nmr.mgh.harvard.edu 
> Message-ID: <4fc8e7c1.6060...@nmr.mgh.harvard.edu 
> >
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> When you use --regheader, then it uses the vox2ras transform in the
> header. If you pass it a register.dat file as input, then vox2ras is
> ignored.
> doug
>
> On 05/31/2012 06:39 PM, Shay Ohayon wrote:
> > Hi,
> >
> > Bump?
> >
> > Can someone please explain to me the puzzle described below regarding
> > tkregister2 and vox2ras0 (which I thought should be ignored for
> > registration purposes?)
> >
> > Thanks!
> >
> > -- Shay
> >
> >
> > On Sat, May 26, 2012 at 2:23 PM, Shay Ohayon  
> > >> wrote:
> >
> > Hi,
> >
> > Here's a question to Doug / anyone else who mastered the intricate
> > way of volume transformations:
> >
> > I'm a bit puzzled.
> > According to Free surfer's documentation (fscoordinates.pdf), the
> > way two volumes are registered to each other using tkregister is
> > always using
> > the fixed transformation (tkvox2ras) (see page 6).
> >
> > However, when I do the following little experiment (using matlab's
> > freesurfer API)
> >
> > A = '001.nii';
> > B = '002.nii';
> > X=MRIread(A);
> > X.vox2ras0(1,4) = 40;
> > MRIwrite(X,B);
> >
> > tkregister2 --targ 001.nii --mov 002.nii --regheader -reg R.reg
> >
> > The two volumes are not in alignment when they are loaded into
> > tkregister.
> > Now, what am I missing here?
> > If both were loaded using the fixed transform, they should still
> > be in alignment (i.e., vox2ras should be ignored for registration
> > purposes).
> >
> > Thanks in advance,
> >
> > -- Shay
> > Tsao lab
> > Caltech
> >
> >
> >
> >
> >
> >
> >
> > ___
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> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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[Freesurfer] Anatomic Inferences

[Govindarajan, Koushik Athreya]

Dear Freesurfers,

I had a question about interpreting the results of the Monte-Carlo 
simulation. It is my understanding that the clusters are labeled based on the 
value of the maximum significant vertex in a cluster. So, assuming that a 
cluster kind of borders or extends over 2 adjacent regions, it could well be 
labeled as a single region whereas anatomically, it would actually be 2 
separate regions. Are there any suggestions for an atlas that could help me 
make my inferences more meaningful? Sorry if this is a naive question, my 
knowledge of anatomic labelling is less than impressive :-)

Thanks
Koushik

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Re: [Freesurfer] Concatenating Transforms

[Douglas N Greve]

Why not just register the functional to the desired structural directly? 
That will work better than concatenation I think.
doug

On 06/04/2012 10:31 AM, Clark Fisher wrote:
> Hi everyone,
>
> What is the best way to concatenate transforms (register.dat files, .lta 
> files, etc.)?  I'm interested in registering functional data to a structural 
> in another session using a functional to in-session anatomical registration 
> combined with a in-session anatomical to out-of-session anatomical 
> registration.
>
> Thanks,
> Clark
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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

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[Freesurfer] Concatenating Transforms

[Clark Fisher]

Hi everyone,

What is the best way to concatenate transforms (register.dat files, .lta files, 
etc.)?  I'm interested in registering functional data to a structural in 
another session using a functional to in-session anatomical registration 
combined with a in-session anatomical to out-of-session anatomical registration.

Thanks,
Clark
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Re: [Freesurfer] Correction of registration in preproc-sess stream

[Douglas N Greve]

They rely on the registration. What is failing? It is usually the 
initialization that fails. If you're using FSL, you can try using the 
SPM registration (though it's a little trickier to set up).
doug

On 06/04/2012 05:20 AM, Jörg Pfannmöller wrote:
> Dear freesurfers,
>
> I have a simple question concerning the freesurfer 5.1 FSFAST preprocessing. 
> In the preprocessing the functional images are registered to the anatomical 
> ones using bbregister. This is the 3rd in a series of 8 preprocessing steps. 
> If the preproc-sess registration fails it is possible to achieve a proper 
> registration using various options of bbregister. Does it suffice to replace 
> the register files created during the preprocessing with the ones received 
> during the registration correction in order to attain proper preprocessed 
> data or are there routines in steps 4 to 8 in the preprocessing which rely on 
> the registration?
>
> Thanks in advance
>
>   pfannmoe
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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

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Re: [Freesurfer] total brain volume or intra crainal volume as estimated for total brain volume

[Douglas N Greve]

Hi Knut, you can copy the following file into 
$FREESURFER_HOME/bin/mri_segstats
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.linux
(assuming you're using linux)
The run
recon-all -segstats -s subject
This will create a new aseg.stats file with total brain volume based on 
adding up the values in the segmentation.
doug



On 06/04/2012 05:20 AM, Knut J Bjuland wrote:
> Hello,
>
> We would like to  calculate a Total Brain Volume based on data in 
> aseg.stat generated from version 5.1.0. Can I use intra crainal volume 
> as estimated for total brain volume? Or should I just add total grey 
> volume with subcortical grey volume with total white matter volume?
>
> Thanks,
> Knut Jørgen
>
>
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] using own average subject

[Douglas N Greve]

For #2, make_average_subject will create the .tif file in the output 
directory.
doug

On 06/04/2012 09:06 AM, Bruce Fischl wrote:
> Hi Christina,
>
> 1. Displaying data on your own subjects average can be less misleading 
> than on our's, particularly if you don't have many subjects. It shows 
> at least one measure of the true variability/accuracy of the 
> registration of your subjects.
>
> 2. To make a study-specific target for the spherical registration you 
> would need to use mris_make_template to create a .tif file as a 
> target, then rerun mris_register to register to it. Then rerun 
> make_average_subject and all the statisticaly analyses using the new 
> spherical registrations.
>
> cheers
> Bruce
>
>
> On Mon, 4 Jun 2012, Schuster, Christina /DZNE wrote:
>
>>
>> Hi,
>>
>> many thanks for your help!
>> Unfortunately, I still have some questions:
>>
>> 1) Why would someone only want to display the results on a 
>> cohort-specific average, but not use that average for calculation?
>>
>> 2) So if I want to use my cohort-specific average for calcuation of the 
> cortical thickness and I registered all subjects on that, do I then 
> still have to calculate a newnew make_average_subject as it is 
> described on the SurfaceRegAndTemplated page? What is the reason 
> behind that?
>
>> If I should do it, what flags would mris_preproc need: the --target 
>> newnewtemplate and the surfreg newtemplate.sphere.reg?
>>
>> Best wishes,
>> Christina
>>
>> ___
>> Von: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
>> Gesendet: Freitag, 1. Juni 2012 17:44
>> An: Bruce Fischl
>> Cc: Schuster, Christina /DZNE
>> Betreff: Re: AW: [Freesurfer] using own average subject
>>
>> If all you want to do is display it on your average subject, then you
>> can pass fsaverage to mris_preproc and then just display it on your
>> cohort-specific average.
>> doug
>>
>> On 06/01/2012 11:37 AM, Douglas N Greve wrote:
>>> Hi Christina, if you want to use the registration to your new
>>> template, then you need to run mris_register on each subject to
>>> register to the new template. You can actually do this with surfreg,
>>> something like:
>>>
>>> foreach subject (subj1 subj2)
>>>   surfreg --s $subject --t newtemplate --lh
>>> end
>>>
>>> This will create $subject/surf/lh.newtemplate.sphere.reg
>>>
>>> You can then run
>>>
>>> mris_preproc --target newtemplate --surfreg newtemplate.sphere.reg ...
>>>
>>> Note that the surfreg cmd above will take about an hour for each 
>>> subject
>>>
>>> doug
>>>
>>>
>>>
>>>
>>> On 06/01/2012 11:05 AM, Bruce Fischl wrote:
 Hi Christina

 you should cc the list so others (Doug!) can answer. The purpose of
 mris_register is to bring your subjects into a common surface-based
 coordinate system. fsaverage lives in that space, but so will the
 average that you make

 cheers
 Bruce


 On Fri, 1 Jun 2012, Schuster, Christina /DZNE wrote:

> Hi Bruce,
>
> just to be sure that I understood it correctly:
>
> I just use make_average_subject to create my template and then I use
> mris_preproc --target newtemplate and not further --surf-reg
> specification.
> Then after mri_glmfit --surf newtemplate ... I have my final 
> results?!
>
> So what is the purpose of the mris_register command?
>
> Many thanks for your help.
> Best wishes
> Christina
>
> 
> Von: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
> Gesendet: Donnerstag, 31. Mai 2012 20:39
> An: Schuster, Christina /DZNE
> Cc: freesurfer@nmr.mgh.harvard.edu
> Betreff: Re: [Freesurfer] using own average subject
>
> Hi Christina,
>
> the new template will already be in the same target space as 
> fsaverage
> since you used the sphere.reg to create it. Just use it as a
> background for
> your group results.
>
> cheers
> Bruce
>
> On Thu, 31 May 2012, Schuster,
> Christina /DZNE wrote:
>
>> Dear FreeSurfer experts,
>>
>> I am trying to create an average subject based on a matched
>> subsample (2 different scanners, patients and healthy controls).
>>
>> I successfully ran make_average_subject receiving a "newtemplate".
>> Now I am unsure how to proceed:
>>
>> As far as I understand it, according to the SurfaceRegAndTemplates
>> page
>> (http://surfer.nmr.mgh.harvard.edu//fswiki/SurfaceRegAndTemplates)
>> I should use mris_register for each subject from my subsample
>> receiving ?h.sphere.reg.newtemple files with which I should make
>> again an average subject, let's call it "newnewtemplate".
>>
>> Is that correct?
>>
>> Now, if I want to assemble the data into common space using
>> mris_preproc: what do I need to specify?
>> Would --target be the newtemplate or newnewtemplate? Do I need to
>> specifiy the --surf-reg 

Re: [Freesurfer] read_label.m produces spotty label (as compared to tksurfer)

[Bruce Fischl]

sure. Happy to help
Bruce
On Mon, 4 Jun 2012, David Groppe wrote:



THAT was the problem.  Thanks so much Bruce.
I owe you one.
   -David


On Sunday, June 3, 2012, Bruce Fischl  wrote:
> Do you change the vertex indices together 1-based in matlab? I don't see
it...
>
> Bruce
>
>
>
> On Jun 3, 2012, at 9:06 PM, David Groppe  wrote:
>
>> I.  I use read_surf.m to import the pial surface into MATLAB:
>> [cort.vert cort.tri]=read_surf('SUB1/surf/lh.pial');
>>
>> 2. I make a completely grey color map for the surface:
>> map=repmat([1 1 1]*.7,length(cort.vert),1);
>>
>> 3. I load the label into MATLAB:
>> inlabel=read_label('SUB1','res_FINAL');
>>
>> 4. I change the color map values of the vertices in the label to red:
>> map(inlabel(:,1),:)=inlabel([1 0 0],size(inlabel,1),1);
>>
>> 5. I plot the surface using tripatch.m
>> tripatch(cort,1,map);
>>
>> You can download a MATLAB figure that shows all the vertices of the
>> surface color coded by label (red=label, black=non-label) from here:
>>
>> http://www.cogsci.ucsd.edu/~dgroppe/label_vertices.fig
>>
>> If you rotate the figure you can see that some black vertices are
interleaved
>> in parts of the label area.
>>   thanks again,
>>       -David
>>
>>
>>> On Sun, Jun 3, 2012 at 5:23 PM, Bruce Fischl
 wrote:
 hmmm, and how are you displaying it in the second (patchy) view? I
don't
 think tksurfer fills any holes by default

 Bruce


 On Sun, 3 Jun 2012, David Groppe wrote:

> Thanks for the nigh-instantaneous response Bruce.
> None of the entries have -1 for a vertex number in the first column
> (see attached).  The smallest value is 75.
>  -David
>
> On Sun, Jun 3, 2012 at 5:10 PM, Bruce Fischl

> wrote:
>>
>> do any of the label entries have -1 for a vertex number in the first
>> column?
>> If so, tksurfer will sample it onto the surface finding the nearest
>> surface
>> vertex.
>>
>>
>> On Sun, 3 Jun 2012, David Groppe wrote:
>>
>>> Hi FreeSurfers,
>>>   I am attempting to plot a label in MATLAB using the function
>>> read_label.m.  The label was produced in tksurfer (see
>>> label_tksurfer.jpg) from a mask created by FSL.  When I try to
import
>>> the label into MATLAB via read_label.m, I get the correct number of
>>> nonzero vertices (i.e., the same number reported by tksurfer when I
>>> load the label).  However the resulting plot is spotty (see
>>> label_matlab.jpg).  I suspect that some vertices that are colored as
>>> the label in tksurfer are not actually part of the label file (i.e.,
>>> tksurfer is automatically doing some filling in that I'm not aware
>>> of).  Is this true?
>>>    Any tips on how to solve the problem would be greatly
appreciated.
>>>        much thanks,
>>>           -David
>>>
>>>
>>
>>
>> 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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Postdoctoral Researcher
North Shore LIJ Health System
New Hyde Park, New York
http://www.cogsci.ucsd.edu/~dgroppe/

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Re: [Freesurfer] using own average subject

[Bruce Fischl]

Hi Christina,

1. Displaying data on your own subjects average can be less misleading than 
on our's, particularly if you don't have many subjects. It shows at least 
one measure of the true variability/accuracy of the registration of your 
subjects.

2. To make a study-specific target for the spherical registration you would 
need to use mris_make_template to create a .tif file as a target, then 
rerun mris_register to register to it. Then rerun make_average_subject and 
all the statisticaly analyses using the new spherical registrations.

cheers
Bruce


On Mon, 4 Jun 2012, Schuster, Christina /DZNE wrote:

>
> Hi,
>
> many thanks for your help!
> Unfortunately, I still have some questions:
>
> 1) Why would someone only want to display the results on a cohort-specific 
> average, but not use that average for calculation?
>
> 2) So if I want to use my cohort-specific average for calcuation of the 
cortical thickness and I registered all subjects on that, do I then still 
have to calculate a newnew make_average_subject as it is described on the 
SurfaceRegAndTemplated page? What is the reason behind that?

> If I should do it, what flags would mris_preproc need: the --target 
> newnewtemplate and the surfreg newtemplate.sphere.reg?
>
> Best wishes,
> Christina
>
> ___
> Von: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
> Gesendet: Freitag, 1. Juni 2012 17:44
> An: Bruce Fischl
> Cc: Schuster, Christina /DZNE
> Betreff: Re: AW: [Freesurfer] using own average subject
>
> If all you want to do is display it on your average subject, then you
> can pass fsaverage to mris_preproc and then just display it on your
> cohort-specific average.
> doug
>
> On 06/01/2012 11:37 AM, Douglas N Greve wrote:
>> Hi Christina, if you want to use the registration to your new
>> template, then you need to run mris_register on each subject to
>> register to the new template. You can actually do this with surfreg,
>> something like:
>>
>> foreach subject (subj1 subj2)
>>   surfreg --s $subject --t newtemplate --lh
>> end
>>
>> This will create $subject/surf/lh.newtemplate.sphere.reg
>>
>> You can then run
>>
>> mris_preproc --target newtemplate --surfreg newtemplate.sphere.reg ...
>>
>> Note that the surfreg cmd above will take about an hour for each subject
>>
>> doug
>>
>>
>>
>>
>> On 06/01/2012 11:05 AM, Bruce Fischl wrote:
>>> Hi Christina
>>>
>>> you should cc the list so others (Doug!) can answer. The purpose of
>>> mris_register is to bring your subjects into a common surface-based
>>> coordinate system. fsaverage lives in that space, but so will the
>>> average that you make
>>>
>>> cheers
>>> Bruce
>>>
>>>
>>> On Fri, 1 Jun 2012, Schuster, Christina /DZNE wrote:
>>>
 Hi Bruce,

 just to be sure that I understood it correctly:

 I just use make_average_subject to create my template and then I use
 mris_preproc --target newtemplate and not further --surf-reg
 specification.
 Then after mri_glmfit --surf newtemplate ... I have my final results?!

 So what is the purpose of the mris_register command?

 Many thanks for your help.
 Best wishes
 Christina

 
 Von: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
 Gesendet: Donnerstag, 31. Mai 2012 20:39
 An: Schuster, Christina /DZNE
 Cc: freesurfer@nmr.mgh.harvard.edu
 Betreff: Re: [Freesurfer] using own average subject

 Hi Christina,

 the new template will already be in the same target space as fsaverage
 since you used the sphere.reg to create it. Just use it as a
 background for
 your group results.

 cheers
 Bruce

 On Thu, 31 May 2012, Schuster,
 Christina /DZNE wrote:

> Dear FreeSurfer experts,
>
> I am trying to create an average subject based on a matched
> subsample (2 different scanners, patients and healthy controls).
>
> I successfully ran make_average_subject receiving a "newtemplate".
> Now I am unsure how to proceed:
>
> As far as I understand it, according to the SurfaceRegAndTemplates
> page
> (http://surfer.nmr.mgh.harvard.edu//fswiki/SurfaceRegAndTemplates)
> I should use mris_register for each subject from my subsample
> receiving ?h.sphere.reg.newtemple files with which I should make
> again an average subject, let's call it "newnewtemplate".
>
> Is that correct?
>
> Now, if I want to assemble the data into common space using
> mris_preproc: what do I need to specify?
> Would --target be the newtemplate or newnewtemplate? Do I need to
> specifiy the --surf-reg as well?
>
>
> On the other hand, I read in one of your tutorials that I only need
> to run make_average_subject receiving a "newtemplate" which I then
> specify using mris_preproc as --target and that --surf-reg is not
> needed.
>
>
> So what would be the correct way to use my

Re: [Freesurfer] no aseg

[Bruce Fischl]

Hi Michael

a couple of typos. It should be "make_average_subject" (note no "s"), and 
it should be --subjects (note the ending "s"). I also don't see a flag 
named --no-aseg, which I think is why it's being included as a subject. 
What are you trying to do?


cheers
Bruce

On Mon, 4 Jun 2012, michael 
kruepke wrote:



Hi all -
Having a bit of an issue with trying to run a make_average with the flag
--no-aseg. When written 

make_average_subjects --subject subject1 subject2 --no-aseg --out
superaverage

the propt runs as if --no-aseg and --out superaverage are subjects i wish to
average in with subjects1 and subject2. This is obviously and issue, hoping
someone might have an idea of a solution. I have tried moving these flags to
somewhere else in the prompt seeing if that would solve it, no luck there. 

Best-
Michael

--
Michael D. Kruepke
PhD - University of Illinois at Urbana-Champaign 
BA - Psych - University of Wisconsin-Madison
mdkrue...@gmail.com
(262)-483-7449


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Re: [Freesurfer] read_label.m produces spotty label (as compared to tksurfer)

[David Groppe]

THAT was the problem.  Thanks so much Bruce.
I owe you one.
   -David


On Sunday, June 3, 2012, Bruce Fischl  wrote:
> Do you change the vertex indices together 1-based in matlab? I don't see
it...
>
> Bruce
>
>
>
> On Jun 3, 2012, at 9:06 PM, David Groppe  wrote:
>
>> I.  I use read_surf.m to import the pial surface into MATLAB:
>> [cort.vert cort.tri]=read_surf('SUB1/surf/lh.pial');
>>
>> 2. I make a completely grey color map for the surface:
>> map=repmat([1 1 1]*.7,length(cort.vert),1);
>>
>> 3. I load the label into MATLAB:
>> inlabel=read_label('SUB1','res_FINAL');
>>
>> 4. I change the color map values of the vertices in the label to red:
>> map(inlabel(:,1),:)=inlabel([1 0 0],size(inlabel,1),1);
>>
>> 5. I plot the surface using tripatch.m
>> tripatch(cort,1,map);
>>
>> You can download a MATLAB figure that shows all the vertices of the
>> surface color coded by label (red=label, black=non-label) from here:
>>
>> http://www.cogsci.ucsd.edu/~dgroppe/label_vertices.fig
>>
>> If you rotate the figure you can see that some black vertices are
interleaved
>> in parts of the label area.
>>   thanks again,
>>   -David
>>
>>
>>> On Sun, Jun 3, 2012 at 5:23 PM, Bruce Fischl 
wrote:
 hmmm, and how are you displaying it in the second (patchy) view? I
don't
 think tksurfer fills any holes by default

 Bruce


 On Sun, 3 Jun 2012, David Groppe wrote:

> Thanks for the nigh-instantaneous response Bruce.
> None of the entries have -1 for a vertex number in the first column
> (see attached).  The smallest value is 75.
>  -David
>
> On Sun, Jun 3, 2012 at 5:10 PM, Bruce Fischl <
fis...@nmr.mgh.harvard.edu>
> wrote:
>>
>> do any of the label entries have -1 for a vertex number in the first
>> column?
>> If so, tksurfer will sample it onto the surface finding the nearest
>> surface
>> vertex.
>>
>>
>> On Sun, 3 Jun 2012, David Groppe wrote:
>>
>>> Hi FreeSurfers,
>>>   I am attempting to plot a label in MATLAB using the function
>>> read_label.m.  The label was produced in tksurfer (see
>>> label_tksurfer.jpg) from a mask created by FSL.  When I try to
import
>>> the label into MATLAB via read_label.m, I get the correct number of
>>> nonzero vertices (i.e., the same number reported by tksurfer when I
>>> load the label).  However the resulting plot is spotty (see
>>> label_matlab.jpg).  I suspect that some vertices that are colored as
>>> the label in tksurfer are not actually part of the label file (i.e.,
>>> tksurfer is automatically doing some filling in that I'm not aware
>>> of).  Is this true?
>>>Any tips on how to solve the problem would be greatly
appreciated.
>>>much thanks,
>>>   -David
>>>
>>>
>>
>>
>> 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.
>>
>
>>>

-- 
David Groppe, Ph.D.
Postdoctoral Researcher
North Shore LIJ Health System
New Hyde Park, New York
http://www.cogsci.ucsd.edu/~dgroppe/
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Re: [Freesurfer] using own average subject

[Schuster, Christina /DZNE]

Hi,

many thanks for your help! 
Unfortunately, I still have some questions:

1) Why would someone only want to display the results on a cohort-specific 
average, but not use that average for calculation?

2) So if I want to use my cohort-specific average for calcuation of the 
cortical thickness and I registered all subjects on that, do I then still have 
to calculate a newnew make_average_subject as it is described on the 
SurfaceRegAndTemplated page? What is the reason behind that?
If I should do it, what flags would mris_preproc need: the --target 
newnewtemplate and the surfreg newtemplate.sphere.reg?

Best wishes,
Christina

___
Von: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Gesendet: Freitag, 1. Juni 2012 17:44
An: Bruce Fischl
Cc: Schuster, Christina /DZNE
Betreff: Re: AW: [Freesurfer] using own average subject

If all you want to do is display it on your average subject, then you
can pass fsaverage to mris_preproc and then just display it on your
cohort-specific average.
doug

On 06/01/2012 11:37 AM, Douglas N Greve wrote:
> Hi Christina, if you want to use the registration to your new
> template, then you need to run mris_register on each subject to
> register to the new template. You can actually do this with surfreg,
> something like:
>
> foreach subject (subj1 subj2)
>   surfreg --s $subject --t newtemplate --lh
> end
>
> This will create $subject/surf/lh.newtemplate.sphere.reg
>
> You can then run
>
> mris_preproc --target newtemplate --surfreg newtemplate.sphere.reg ...
>
> Note that the surfreg cmd above will take about an hour for each subject
>
> doug
>
>
>
>
> On 06/01/2012 11:05 AM, Bruce Fischl wrote:
>> Hi Christina
>>
>> you should cc the list so others (Doug!) can answer. The purpose of
>> mris_register is to bring your subjects into a common surface-based
>> coordinate system. fsaverage lives in that space, but so will the
>> average that you make
>>
>> cheers
>> Bruce
>>
>>
>> On Fri, 1 Jun 2012, Schuster, Christina /DZNE wrote:
>>
>>> Hi Bruce,
>>>
>>> just to be sure that I understood it correctly:
>>>
>>> I just use make_average_subject to create my template and then I use
>>> mris_preproc --target newtemplate and not further --surf-reg
>>> specification.
>>> Then after mri_glmfit --surf newtemplate ... I have my final results?!
>>>
>>> So what is the purpose of the mris_register command?
>>>
>>> Many thanks for your help.
>>> Best wishes
>>> Christina
>>>
>>> 
>>> Von: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
>>> Gesendet: Donnerstag, 31. Mai 2012 20:39
>>> An: Schuster, Christina /DZNE
>>> Cc: freesurfer@nmr.mgh.harvard.edu
>>> Betreff: Re: [Freesurfer] using own average subject
>>>
>>> Hi Christina,
>>>
>>> the new template will already be in the same target space as fsaverage
>>> since you used the sphere.reg to create it. Just use it as a
>>> background for
>>> your group results.
>>>
>>> cheers
>>> Bruce
>>>
>>> On Thu, 31 May 2012, Schuster,
>>> Christina /DZNE wrote:
>>>
 Dear FreeSurfer experts,

 I am trying to create an average subject based on a matched
 subsample (2 different scanners, patients and healthy controls).

 I successfully ran make_average_subject receiving a "newtemplate".
 Now I am unsure how to proceed:

 As far as I understand it, according to the SurfaceRegAndTemplates
 page
 (http://surfer.nmr.mgh.harvard.edu//fswiki/SurfaceRegAndTemplates)
 I should use mris_register for each subject from my subsample
 receiving ?h.sphere.reg.newtemple files with which I should make
 again an average subject, let's call it "newnewtemplate".

 Is that correct?

 Now, if I want to assemble the data into common space using
 mris_preproc: what do I need to specify?
 Would --target be the newtemplate or newnewtemplate? Do I need to
 specifiy the --surf-reg as well?


 On the other hand, I read in one of your tutorials that I only need
 to run make_average_subject receiving a "newtemplate" which I then
 specify using mris_preproc as --target and that --surf-reg is not
 needed.


 So what would be the correct way to use my own template for the
 group analysis?

 Many thanks for you help!

 Best wishes
 Christina


>>>
>>> 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.
>>>
>>>
>>>
>>
>>
>

--
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/fswik

[Freesurfer] no aseg

[michael kruepke]

Hi all -

Having a bit of an issue with trying to run a make_average with the flag
--no-aseg. When written

make_average_subjects --subject subject1 subject2 --no-aseg --out
superaverage

the propt runs as if --no-aseg and --out superaverage are subjects i wish
to average in with subjects1 and subject2. This is obviously and issue,
hoping someone might have an idea of a solution. I have tried moving these
flags to somewhere else in the prompt seeing if that would solve it, no
luck there.

Best-
Michael

-- 
Michael D. Kruepke
PhD - University of Illinois at Urbana-Champaign
BA - Psych - University of Wisconsin-Madison
mdkrue...@gmail.com
(262)-483-7449
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[Freesurfer] Correction of registration in preproc-sess stream

[Jörg Pfannmöller]

Dear freesurfers,

I have a simple question concerning the freesurfer 5.1 FSFAST preprocessing. In 
the preprocessing the functional images are registered to the anatomical ones 
using bbregister. This is the 3rd in a series of 8 preprocessing steps. If the 
preproc-sess registration fails it is possible to achieve a proper registration 
using various options of bbregister. Does it suffice to replace the register 
files created during the preprocessing with the ones received during the 
registration correction in order to attain proper preprocessed data or are 
there routines in steps 4 to 8 in the preprocessing which rely on the 
registration? 

Thanks in advance

 pfannmoe
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[Freesurfer] total brain volume or intra crainal volume as estimated for total brain volume

[Knut J Bjuland]

Hello,

We would like to  calculate a Total Brain Volume based on data in aseg.stat 
generated from version 5.1.0. Can I use intra crainal volume as estimated for 
total brain volume? Or should I just add total grey volume with subcortical 
grey volume with total white matter volume? 

Thanks,
Knut Jørgen   ___
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