[Freesurfer] regional cortical thickness output

2012-11-05 Thread yawu Liu 


Dear Freesufers,After running recon-all -cw256 -s PT1 -all, we can find 
lh.aparc.a2009s and rh.aparc.a2009s under subjects/PT1/stats. I would like to 
know what is the difference between the two files?
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Re: [Freesurfer] regional cortical thickness output

2012-11-05 Thread yawu Liu 

Now, I get it.  lh means left side. :)Yawu


From: liu...@hotmail.com
To: freesurfer@nmr.mgh.harvard.edu
Date: Mon, 5 Nov 2012 10:32:37 +
Subject: [Freesurfer] regional cortical thickness output






Dear Freesufers,After running recon-all -cw256 -s PT1 -all, we can find 
lh.aparc.a2009s and rh.aparc.a2009s under subjects/PT1/stats. I would like to 
know what is the difference between the two files?
Thanks,Yawu   

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[Freesurfer] freeze old freesurfer distribution

2012-11-05 Thread Bruehl, Hannah 
Hi,

I have a problem with the command for creating a frozen version of an old 
freesurfer distribution.

When running the first step cp -Lr /usr/local/freesurfer/stable 
/path/to/yourdirectory/freesurfer
I get the error that the -L flag is incompatible with the cp command:

bruehh01% cp -Lr /Volumes/Macintosh\ HD/Applications/freesurfer/stable 
/Volumes/Macintosh\ HD/Applications/Freesurfer_4.5_BPD/freesurfer
cp: the -H, -L, and -P options may not be specified with the -r option.

can anyone help me with this?

Thanks a lot!

Hannah


..
Dr. Hannah Brühl
Freie Universität Berlin
Institut für Psychologie
Arbeitsbereich Emotionspsychologie und affektive Neurowissenschaft
Habelschwerdter Allee 45 — Raum JK 24/221h 
14195 Berlin
Tel.: +49 (0)30 838 571 68
..


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Re: [Freesurfer] whole brain volume from ADNI UCSFFSL table

2012-11-05 Thread Douglas N Greve 
Cortical Gray matter volume + Cortical white matter + subcortical gray 
volume + cerebellum
subcortical gray is:

Left_Thalamus
Right_Thalamus
Left_Thalamus_Proper
Right_Thalamus_Proper
Left_Caudate
Right_Caudate
Left_Putamen
Right_Putamen
Left_Pallidum
Right_Pallidum
Left_Hippocampus
Right_Hippocampus
Left_Amygdala
Right_Amygdala
Left_Accumbens_area
Right_Accumbens_area
Left_VentralDC
Right_VentralDC

doug


On 11/02/2012 10:48 AM, Zhiyong Xie wrote:
> I knew this question has been asked before and it was suggested to use 
> /SupraTentorial/ as the whole brain volume. I am working with ADNI 
> data and cannot find this measurement from UCSFFSL table. As my 
> understanding, UCSFFSL table was generated by Freesurfer 4.4. I was 
> wondering which structures I should add up to get whole brain volume 
> for comparison between AD, MCI, and normal people.
> Thanks
> Sean
>
>
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Re: [Freesurfer] whole brain volume from ADNI UCSFFSL table

2012-11-05 Thread Douglas N Greve 
Sorry, I don't know anything about the UCSFFSL table.
doug

On 11/05/2012 11:41 AM, Zhiyong Xie wrote:
> Hi Doug,
> Thank you for your response. I did not find the single measurement for 
> Cortical Gray matter volume and Cortical white matter from UCSFFSL 
> table. looks like I need to add up all numbers for cortex regions and 
> plus subcortical regions you indicated and cerebellum.
> Another thing that always confused me in UCSFFSL is hippocampus. In 
> the dictionary, it was reported as "Volume (WM Parcellation) of 
> LeftHippocampus/RightHippocampus". I did not find GM parcellation of 
> hippocampus. I do not know why hippocampus was classified as WM 
> parcellation.
> Thank you for your help.
> Sean
>
>
> *From:* Douglas N Greve 
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Sent:* Monday, November 5, 2012 10:42 AM
> *Subject:* Re: [Freesurfer] whole brain volume from ADNI UCSFFSL table
>
> Cortical Gray matter volume + Cortical white matter + subcortical gray
> volume + cerebellum
> subcortical gray is:
>
> Left_Thalamus
> Right_Thalamus
> Left_Thalamus_Proper
> Right_Thalamus_Proper
> Left_Caudate
> Right_Caudate
> Left_Putamen
> Right_Putamen
> Left_Pallidum
> Right_Pallidum
> Left_Hippocampus
> Right_Hippocampus
> Left_Amygdala
> Right_Amygdala
> Left_Accumbens_area
> Right_Accumbens_area
> Left_VentralDC
> Right_VentralDC
>
> doug
>
>
> On 11/02/2012 10:48 AM, Zhiyong Xie wrote:
> > I knew this question has been asked before and it was suggested to use
> > /SupraTentorial/ as the whole brain volume. I am working with ADNI
> > data and cannot find this measurement from UCSFFSL table. As my
> > understanding, UCSFFSL table was generated by Freesurfer 4.4. I was
> > wondering which structures I should add up to get whole brain volume
> > for comparison between AD, MCI, and normal people.
> > Thanks
> > Sean
> >
> >
> > ___
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> > 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 
> 
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>
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>
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Re: [Freesurfer] Total cerebral volume.

2012-11-05 Thread Douglas N Greve 
Hi Zheng, there is something wrong with your math. When I sum up all the 
columns in your table from Left-Lateral-Ventricle to CC_Anterior, I get 
215952 for the first row (you get only 67548). Can you double check your 
calculations?
doug

On 10/28/2012 11:53 PM, Zheng Hui wrote:
> Forgot to attach the excel file. Sorry for that.
>
> From: zhenghui  >
> Date: Monday, October 29, 2012 11:52 AM
> To: Douglas N Greve  >
> Subject: [Freesurfer] Total cerebral volume.
>
> Hi Doug,
>
> Thanks for replying. But our datasets do showed that
> Sum(all structures (after ICV in the list) except ventricle, CSF, 
> cerebellum and brainstem) is much smaller SubCortGrayVol. The former 
> is only about 30-40% of the later. We are using FS 5.1.0 without the 
> SupraTentorialVol fix.I attached the aseg file for your reference (the 
> last three columns in the sheet).
>
> Thanks,
> Zheng Hui
>
> On 10/24/2012 09:01 AM, Zheng Hui wrote:
> >
> > Hi freesurfer,
> >
> > We are trying to calculate the total cerebral volume which excludes 
> cerebellum, brainstem, ventricle and CSF from the aseg.txt. Do we use
> >
> > CortexVol + CorticalWhiteMatterVol + SubCortGrayVol
> > Or
> > CortexVol + CorticalWhiteMatterVol + Sum(all structures (after ICV in 
> the list) except ventricle, CSF, cerebellum and brainstem)
> This should give very close to the same value. I don't think it makes a
> difference.
> >
> >
> > Also, I saw Doug's post about the bug fixing for SupraTentorialVol. 
> To re-run the segstats for longitudinal subjects, any extra step other 
> than "recon-all –long tpN baseID –segstats" and does it affect any 
> other structure or just SupraTentorialVol?
> It should not affect other structures.
> doug

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Re: [Freesurfer] checking talairach.lta

2012-11-05 Thread Douglas N Greve 
Try using this version 
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/tkregister2.bin
copy it into $FREESURFER_HOME/bin (but make a back up of the existing 
tkregister2.bin first!)
doug

On 11/02/2012 03:58 PM, Eric Cunningham wrote:
> Hi folks,
> In previous threads, the command provided to check the talairach.lta is...
> tkregister2 --mov $FREESURFER_HOME/average/RB_all_2008-03-26.gca \  --targ 
> ../brainmask.mgz --lta-inv talairach.lta --reg talairach.lta.reg.dat \  
> --surfs --s $subject
>
> When I try to run this command, I run into trouble with the --lta-inv 
> portion.  (it is an unknown option).  I am running version 5.1.
> Can anyone help?
> Thanks,
> -Eric
>
>
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Re: [Freesurfer] (un)successfully extracted surfaces from FBIRN traveling subjects?

2012-11-05 Thread Douglas N Greve 

Hi Forrest, I don't think I ever tried to analyze the T1s from the other 
sites (in fact, I did not even know that the other sites collected T1s). 
The T1s from MGH went through FS without a problem.

doug

On 11/03/2012 02:36 PM, Forrest Sheng Bao wrote:
> Hi,
>
> Has anyone (un)successfully extracted surfaces from FBIRN traveling 
> subjects?
>
> I just tried on the first 5 subjects of FBIRN traveling subjects Phase 
> I. To every subject, the surfaces extracted from data sampled at Iowa 
> (scans 1 and 2), Duke (scans 1 and 2) and UCI (scan 1) do not look 
> well. Some of the hemispheres have parts of the other halves attached 
> to it. Talairach transform also failed on these scans (I got the 
> surface via -notal-check option). I tried using --mritotal for 
> Talairach, but still no good. I did on both v5.0 and v5.1.
>
> However, on Standford2, UMN1 &2 and UNM1&2, the surfaces look very good.
>
> So I am wondering whether anyone out there has similar experience to 
> mine, and whether they finally solved the problem. I am more 
> interested in why Talairach failed on some scans and any solution 
> other than manual alignment.
>
> Cheers,
> Forrest
>
>
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Re: [Freesurfer] mri_cor2label and unassigned vertices

2012-11-05 Thread Douglas N Greve 
Hi Mahinda, you need to tell mri_cor2label that this is a surface with 
the --surf fsaverage lh white
You can propagate this label to other subjects using mri_surf2surf.

doug

On 11/04/2012 10:08 PM, Mahinda Yogarajah wrote:
> Dear Experts,
>
> I am trying to "back-normalise" significant clusters identified in a 
> qdec analysis (2 groups, thickness as main variable of interest) back 
> into individual subjects so that I can derive cortical statisitcs.
>
> As per previous posts I have been trying to use mri_cor2label but am 
> running into some problems.  My processing is as follows:
>
> 1) Identify file of interest which contains 3 clusters (labelled 
> 1.00 to 3.00 as viewed in tksurfer and on qdec text output 
> following analysis) significant using Monte Carlo correction 0.05 - 
> mc-z.abs.th13.sig.ocn.annot
>
> 2) mri_cor2label --i mc-z.abs.th13.sig.ocn.annot --id 2 --l cluster2
>
> This produces a file called cluster2.label but when I try loading it 
> into tksurfer (tksurfer fsaverage lh inflated - followed by loading of 
> label in menu system) I get the following error message which prevents 
> me from double checking the label:
>
> % 0 nonzero vertices found 
>
> label stat field identically zero - setting to 1
>
> 1890 unassigned vertices in label - building spatial LUT...
>
> assigning vertex numbers to label...
>
> Couldn't assign 1617 vertices.
>
> 1617 unassigned vertices in label - building spatial LUT...
>
> assigning vertex numbers to label...
>
> Couldn't assign 1617 vertices.
>
>
> My questions are:
>
> 1) Why does this occur ?
>
> 2) How can I convert my qdec results (eg. mc-z.abs.th13.sig.ocn.annot 
> to label files which I can then propagate to all subjects using 
> mri_label2label).
>
> Thanks.
>
> Mahinda
>
>
>
>
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Re: [Freesurfer] freeze old freesurfer distribution

2012-11-05 Thread Nick Schmansky 
Hannah,

Hi!  I think on the Mac, the command is:

cp -LR 

that is, a capital R instead of lowercase (which is the case on linux).
I'll update the wiki page.

Nick


On Mon, 2012-11-05 at 16:30 +0100, Bruehl, Hannah wrote:
> Hi,
> 
> 
> I have a problem with the command for creating a frozen version of an
> old freesurfer distribution.
> 
> 
> When running the first step cp
> -Lr /usr/local/freesurfer/stable /path/to/yourdirectory/freesurfer
> I get the error that the -L flag is incompatible with the cp command:
> 
> 
> bruehh01% cp -Lr /Volumes/Macintosh\
> HD/Applications/freesurfer/stable /Volumes/Macintosh\
> HD/Applications/Freesurfer_4.5_BPD/freesurfer
> cp: the -H, -L, and -P options may not be specified with the -r
> option.
> 
> 
> can anyone help me with this?
> 
> 
> Thanks a lot!
> 
> 
> Hannah
> 
> 
> 
> 
> ..
> Dr. Hannah Brühl
> Freie Universität Berlin
> Institut für Psychologie
> Arbeitsbereich Emotionspsychologie und affektive Neurowissenschaft
> Habelschwerdter Allee 45 — Raum JK 24/221h 
> 14195 Berlin
> Tel.: +49 (0)30 838 571 68
> ..
> 
> 
> 
> 
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Re: [Freesurfer] qcache error

2012-11-05 Thread Douglas N Greve 
Do run out of disk space? Also, please send terminal output in a text 
file rather than as a snapshot. You can do this with

recon-all ... |& tee mylog.txt

doug

On 11/05/2012 10:21 AM, Berg, S.F. van den wrote:
>
> Dear Freesurfer experts,
>
> I have got a problem with the qcache function. I have already runned 
> 150 subjects with the recon-all command.  Before i can work with the 
> statistical program qdec i have to smooth the subjects. I want to 
> smooth them with the command: recon-all -s  -qcache. The 
> command start to run but finished with errors. A overview of the 
> terminal output is attached to this email in JPEG format. What is the 
> problem in this case?
>
> further information about freesurfer version:
>
> recon-all -version: Id: recon-all, v 1.373 2011/03/15 00:43:47 mreuter 
> Exp $
>
> We run FreeSurfer-Linux-centos5_x86_64-dev-201110315 under Debian 
> Squeeze.
>
> Thanks a lot,
>
> Stan van den Berg
>
>
>
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Re: [Freesurfer] checking talairach.lta

2012-11-05 Thread Douglas N Greve 
are you sure you are using the new version?

On 11/05/2012 02:38 PM, Eric Cunningham wrote:
> tried the new version, and it errored out at the same step
>
> ERROR: Option --lta-inv unknown
>
> thanks again for your help!
>
> On Mon, Nov 5, 2012 at 8:16 AM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> Try using this version
> 
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/tkregister2.bin
> copy it into $FREESURFER_HOME/bin (but make a back up of the existing
> tkregister2.bin first!)
> doug
>
> On 11/02/2012 03:58 PM, Eric Cunningham wrote:
> > Hi folks,
> > In previous threads, the command provided to check the
> talairach.lta is...
> > tkregister2 --mov $FREESURFER_HOME/average/RB_all_2008-03-26.gca
> \  --targ ../brainmask.mgz --lta-inv talairach.lta --reg
> talairach.lta.reg.dat \  --surfs --s $subject
> >
> > When I try to run this command, I run into trouble with the
> --lta-inv
> > portion.  (it is an unknown option).  I am running version 5.1.
> > Can anyone help?
> > Thanks,
> > -Eric
> >
> >
> > ___
> > 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
> 
>
> ___
> 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.
>
>

-- 
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] checking talairach.lta

2012-11-05 Thread Douglas N Greve 
I'm not sure that was the right thing to do. There should be two files: 
tkregister2 and tkregister2.bin. tkregister2 is just a script that calls 
tkregister2.bin after setting up some environment variables. Try keeping 
the original file name.
doug

On 11/05/2012 03:43 PM, Eric Cunningham wrote:
> i am sure
> there is one irregularity, namely that the '.bin' extension is absent 
> from our old file, so i renamed the new file without it (as 
> tkregister2) and moved the other one to tkregister2_backup
>
> the command i listed from previous threads was given to someone else 
> from our lab (and probably worked), so it is likely that the problem 
> is somewhere on our side, i was just hoping that it was known and 
> recognizable from the error
>
>
>
> On Mon, Nov 5, 2012 at 10:15 AM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> are you sure you are using the new version?
>
>
> On 11/05/2012 02:38 PM, Eric Cunningham wrote:
>
> tried the new version, and it errored out at the same step
>
> ERROR: Option --lta-inv unknown
>
> thanks again for your help!
>
> On Mon, Nov 5, 2012 at 8:16 AM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>
>  >> wrote:
>
> Try using this version
> 
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/tkregister2.bin
> copy it into $FREESURFER_HOME/bin (but make a back up of
> the existing
> tkregister2.bin first!)
> doug
>
> On 11/02/2012 03:58 PM, Eric Cunningham wrote:
> > Hi folks,
> > In previous threads, the command provided to check the
> talairach.lta is...
> > tkregister2 --mov $FREESURFER_HOME/average/RB_all_2008-03-26.gca
> \  --targ ../brainmask.mgz --lta-inv talairach.lta --reg
> talairach.lta.reg.dat \  --surfs --s $subject
> >
> > When I try to run this command, I run into trouble with the
> --lta-inv
> > portion.  (it is an unknown option).  I am running version 5.1.
> > Can anyone help?
> > Thanks,
> > -Eric
> >
> >
> > ___
> > 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
> 
> 
>
> ___
> 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.
>
>
>
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
> Phone Number: 617-724-2358 
> Fax: 617-726-7422 
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
>
>

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Fi

Re: [Freesurfer] mri_cor2label and unassigned vertices

2012-11-05 Thread Mahinda Yogarajah 
Dear Doug,

Thanks for quick reply. Does it make a difference if I use mri_label2label 
instead of mri_surf2surf for label propagation after I have used mri_cor2label 
? Thanks.

M



On 5 Nov 2012, at 03:08, Mahinda Yogarajah  wrote:

> Dear Experts, 
> 
> I am trying to "back-normalise" significant clusters identified in a qdec 
> analysis (2 groups, thickness as main variable of interest) back into 
> individual subjects so that I can derive cortical statisitcs.
> 
> As per previous posts I have been trying to use mri_cor2label but am running 
> into some problems.  My processing is as follows:
> 
> 1) Identify file of interest which contains 3 clusters (labelled 1.00 to 
> 3.00 as viewed in tksurfer and on qdec text output following analysis) 
> significant using Monte Carlo correction 0.05 - mc-z.abs.th13.sig.ocn.annot
> 
> 2) mri_cor2label --i mc-z.abs.th13.sig.ocn.annot --id 2 --l cluster2
> 
> This produces a file called cluster2.label but when I try loading it into 
> tksurfer (tksurfer fsaverage lh inflated - followed by loading of label in 
> menu system) I get the following error message which prevents me from double 
> checking the label:
> 
> %   0 nonzero vertices found 
> label stat field identically zero - setting to 1
> 1890 unassigned vertices in label - building spatial LUT...
> assigning vertex numbers to label...
> Couldn't assign 1617 vertices.
> 1617 unassigned vertices in label - building spatial LUT...
> assigning vertex numbers to label...
> Couldn't assign 1617 vertices.
> 
> My questions are:
> 
> 1) Why does this occur ?
> 
> 2) How can I convert my qdec results (eg. mc-z.abs.th13.sig.ocn.annot to 
> label files which I can then propagate to all subjects using mri_label2label).
> 
> Thanks.
> 
> Mahinda
> 
> 
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Re: [Freesurfer] mri_cor2label and unassigned vertices

2012-11-05 Thread Douglas N Greve 
oops, sorry, I mean label2label not surf2surf
doug

On 11/05/2012 03:48 PM, Mahinda Yogarajah wrote:
> Dear Doug,
>
> Thanks for quick reply. Does it make a difference if I use 
> mri_label2label instead of mri_surf2surf for label propagation after I 
> have used mri_cor2label ? Thanks.
>
> M
>
>
>
> On 5 Nov 2012, at 03:08, Mahinda Yogarajah  > wrote:
>
>> Dear Experts,
>>
>> I am trying to "back-normalise" significant clusters identified in a 
>> qdec analysis (2 groups, thickness as main variable of interest) back 
>> into individual subjects so that I can derive cortical statisitcs.
>>
>> As per previous posts I have been trying to use mri_cor2label but am 
>> running into some problems.  My processing is as follows:
>>
>> 1) Identify file of interest which contains 3 clusters (labelled 
>> 1.00 to 3.00 as viewed in tksurfer and on qdec text output 
>> following analysis) significant using Monte Carlo correction 0.05 - 
>> mc-z.abs.th13.sig.ocn.annot
>>
>> 2) mri_cor2label --i mc-z.abs.th13.sig.ocn.annot --id 2 --l cluster2
>>
>> This produces a file called cluster2.label but when I try loading it 
>> into tksurfer (tksurfer fsaverage lh inflated - followed by loading 
>> of label in menu system) I get the following error message which 
>> prevents me from double checking the label:
>>
>> % 0 nonzero vertices found 
>>
>> label stat field identically zero - setting to 1
>>
>> 1890 unassigned vertices in label - building spatial LUT...
>>
>> assigning vertex numbers to label...
>>
>> Couldn't assign 1617 vertices.
>>
>> 1617 unassigned vertices in label - building spatial LUT...
>>
>> assigning vertex numbers to label...
>>
>> Couldn't assign 1617 vertices.
>>
>>
>> My questions are:
>>
>> 1) Why does this occur ?
>>
>> 2) How can I convert my qdec results (eg. mc-z.abs.th13.sig.ocn.annot 
>> to label files which I can then propagate to all subjects using 
>> mri_label2label).
>>
>> Thanks.
>>
>> Mahinda
>>
>>
>
>
> ___
> 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] fs-fast preprocessing resting state

2012-11-05 Thread Chris McNorgan 
Hello,

  I'm getting started with freesurfer. I've played around with some of 
the tutorial data for fs-fast
(http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1) and was 
able to follow along and successfully carry out the preprocessing 
exercises (which sufficed for my purposes), which also included running 
register-sess on the "rest" tutorial data for sess01.

I've run into a few gotchas with some resting state data, and wanted to 
know if there are any problems specific to processing resting state data 
that can be easily avoided?

For example, here's the file structure:
Project root:
/home/chris/resting

Anatomical data root ($SUBJECTS_DIR):
/home/chris/resting/anat

Functional data root ($FUNCTIONALS_DIR):
/home/chris/resting/func

Subject 1 anatomical directory:
$SUBJECTS_DIR/sub00156
(already run through recon-all)

Subject 1 functional directory:
$FUNCTIONALS_DIR/sub00156
contains:
  subjectname ("sub00156")
 and a nii file in a nested subdirectory: 
$FUNCTIONALS_DIR/sub00156/rest/001/f.nii.gz
Where f.nii.gz is some resting state data (hence no paradigm files)

For my inaugural attempt, I've run anatomical data for a participant 
through recon-all, and was having problems registering 
$FUNCTIONALS_DIR/sub00156/rest/001/f.nii.gz to the surface map in 
$SUBJECTS_DIR/sub00156. After some trial and error and wandering through 
this mailing list, I found I had to first run mktemplate-sess and then 
register-sess (the fs-fast tutorial lead me to believe everything was 
automatically handled by preproc-sess). Are these deviations a 
foreseeable consequence of working with resting state data? Is there 
some documentation of important considerations for working with resting 
state data?

Thanks for any help,

Chris
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Re: [Freesurfer] fs-fast preprocessing resting state

2012-11-05 Thread Douglas Greve 

Hi Chris, it should have been done with preproc-sess. What was your 
preproc-sess command line? At some point, I had it set up so that it 
would go to the bold directory by default unless you used "-fsd rest". 
Newer versions require you to specify the FSD specifically.

doug


On 11/5/12 9:38 PM, Chris McNorgan wrote:
> Hello,
>
>I'm getting started with freesurfer. I've played around with some of
> the tutorial data for fs-fast
> (http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1) and was
> able to follow along and successfully carry out the preprocessing
> exercises (which sufficed for my purposes), which also included running
> register-sess on the "rest" tutorial data for sess01.
>
> I've run into a few gotchas with some resting state data, and wanted to
> know if there are any problems specific to processing resting state data
> that can be easily avoided?
>
> For example, here's the file structure:
> Project root:
> /home/chris/resting
>
> Anatomical data root ($SUBJECTS_DIR):
> /home/chris/resting/anat
>
> Functional data root ($FUNCTIONALS_DIR):
> /home/chris/resting/func
>
> Subject 1 anatomical directory:
> $SUBJECTS_DIR/sub00156
> (already run through recon-all)
>
> Subject 1 functional directory:
> $FUNCTIONALS_DIR/sub00156
> contains:
>subjectname ("sub00156")
>   and a nii file in a nested subdirectory:
> $FUNCTIONALS_DIR/sub00156/rest/001/f.nii.gz
> Where f.nii.gz is some resting state data (hence no paradigm files)
>
> For my inaugural attempt, I've run anatomical data for a participant
> through recon-all, and was having problems registering
> $FUNCTIONALS_DIR/sub00156/rest/001/f.nii.gz to the surface map in
> $SUBJECTS_DIR/sub00156. After some trial and error and wandering through
> this mailing list, I found I had to first run mktemplate-sess and then
> register-sess (the fs-fast tutorial lead me to believe everything was
> automatically handled by preproc-sess). Are these deviations a
> foreseeable consequence of working with resting state data? Is there
> some documentation of important considerations for working with resting
> state data?
>
> Thanks for any help,
>
> Chris
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

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Re: [Freesurfer] checking talairach.lta

2012-11-05 Thread Douglas Greve 


OK, I see the problem. I should have told you to put tkregsiter2.bin 
into /apps/fs510/tktools/ (after making a copy of the one there).

doug



On 11/5/12 5:00 PM, Eric Cunningham wrote:

[e4fs@cluster bin]$ ls -l `which tkregister2.bin`
-rwxr-xr--  1 jsadinol fs 21663433 May 22   2011 /apps/fs510/tktools/
tkregister2.bin

[e4fs@cluster bin]$ tkregister2 --all-info
ProgramName: tkregister2.in  ProgramArguments: 
--all-info   ProgramVersion:  $Name: stable5 $   TimeStamp: 
2012/11/05-21:43:36-GMT   BuildtimeStamp: May 22 2011 08:23:31   CVS: 
$Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $User: 
e4fs  Machine: cluster.mrilab.net   
Playform: Linux PlatformVersion: 2.6.9-55.0.2.ELsmp  CompilerName: GCC 
CompilerVersion: 30400




fyi: /apps/fs510/ = $FREESURFER_HOME
i tried replacing this file in tktools with the new tkregister2.bin, 
and i get a new error:

/lib64/tls/libc.so.6:  version GLIBC_2.4 not found



On Mon, Nov 5, 2012 at 11:34 AM, Douglas N Greve 
mailto:gr...@nmr.mgh.harvard.edu>> wrote:


Can you send me the result of

ls -l `which tkregister2.bin`

and

tkregister2 --all-info


doug




On 11/05/2012 03:54 PM, Eric Cunningham wrote:

retried it, same error

new file is .bin, old file is tkregister2, no old
tkregister2.bin file appeared to be in the folder
$FREESURFER_HOME/bin

On Mon, Nov 5, 2012 at 10:49 AM, Douglas N Greve
mailto:gr...@nmr.mgh.harvard.edu>
>> wrote:

I'm not sure that was the right thing to do. There should
be two
files:
tkregister2 and tkregister2.bin. tkregister2 is just a
script that
calls
tkregister2.bin after setting up some environment
variables. Try
keeping
the original file name.
doug

On 11/05/2012 03:43 PM, Eric Cunningham wrote:
> i am sure
> there is one irregularity, namely that the '.bin'
extension is
absent
> from our old file, so i renamed the new file without it (as
> tkregister2) and moved the other one to tkregister2_backup
>
> the command i listed from previous threads was given to
someone else
> from our lab (and probably worked), so it is likely that
the problem
> is somewhere on our side, i was just hoping that it was
known and
> recognizable from the error
>
>
>
> On Mon, Nov 5, 2012 at 10:15 AM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>
>


> are you sure you are using the new version?
>
>
> On 11/05/2012 02:38 PM, Eric Cunningham wrote:
>
> tried the new version, and it errored out at the
same step
>
> ERROR: Option --lta-inv unknown
>
> thanks again for your help!
>
> On Mon, Nov 5, 2012 at 8:16 AM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>
>

>>
> 
>
> 
 wrote:
>
> Try using this version
>

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/tkregister2.bin
> copy it into $FREESURFER_HOME/bin (but make
a back up of
> the existing
> tkregister2.bin first!)
> doug
>
> On 11/02/2012 03:58 PM, Eric Cunningham wrote:
> > Hi folks,
> > In previous threads, the command provided to check the
> talairach.lta is...
> > tkregister2 --mov
$FREESURFER_HOME/average/RB_all_2008-03-26.gca
> \  --targ ../brainmask.mgz --l