Re: [Freesurfer] mrisReadTriangleFile failed

[Jonathan Holt]

Just had a cluster of computers lock up, unfortunately resulting in several 
freesurfer jobs terminating prior to completion. It's possible I may have a ton 
of this same error come tomorrow. Two questions

1) is there a way to tell if a surface is out of date without starting up 
tkmedit?

2) last time I ran -make all, the command line disappeared until the job 
completed. This never happens when I run recon-all with autorecon2&3. Anyway to 
avoid this?

jon
On Feb 1, 2013, at 1:28 PM, Jonathan Holt wrote:

> OK, good deal! The first time I ran recon-all it exited with errors. That 
> must be the issue.
> 
> thanks,
> jon
> 
>> 
>>> Hi Jon
>>> 
>>> that means that one of the surfaces is out of date, usually because you 
>>> edited and reran but not to completion. Try running
>>> 
>>> recon-all -s  -make all
>>> 
>>> cheers
>>> Bruce
>>> 
>>> p.s. ignore the "can't find file" thing. It really means it tried to read 
>>> it, but found it wasn't the same topology as the other surface and that's 
>>> what it is complaining about
>>> 
>>> On Fri, 1 Feb 2013, 
>>> Jonathan Holt wrote:
>>> 
 Experts,
 
 Having an issue with this error. It's complaining about rh.pial not 
 matching rh.white, indicates there's no such file or directory and that 
 mrisReadTriangleFile failed, and then proceeds to load without rh.pial. I 
 tried loading rh.pial manually, but upon loading it immediately removes 
 every surface on the LH. Wasn't an issue before I ran recon-all. Worth 
 noting this brain was generated from a particularly low contrast MRI scan, 
 and freesurfer had trouble generating correct surfaces from the get go.
 
 Jon
 
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Re: [Freesurfer] Multi-voxel pattern analysis

[Bruce Fischl]

Hi Luisa

yes, Mert Sabuncu and Koen Van Leemput have developed a MVPA algorithm 
called RvoxM that I believe is state-of-the-art in terms of 
classification accuracy. Perhaps they can point you in the right 
direction?


cheers
Bruce
On Thu, 7 Feb 2013, Luísa Pinto wrote:


Hi,
I am very new to FreeSurfer, but would like to start using it for my research. 
In particular, I would like to know
if I could do MVPA with FreeSurfer?
Thanks.
Luísa

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[Freesurfer] Multi-voxel pattern analysis

[Luísa Pinto]

Hi,
I am very new to FreeSurfer, but would like to start using it for my
research. In particular, I would like to know if I could do MVPA with
FreeSurfer?
Thanks.
Luísa
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Re: [Freesurfer] FDR threshold on functional data

[Douglas N Greve]

Hi Susan, try right clicking in the display window to remove the marks 
from the label.
doug


On 02/04/2013 03:08 PM, Susan Alice McLaughlin wrote:
> Hi,
>
> I am looking at functional group surface data analyzed with mri_glmfit in 
> tksurfer (using Freesurfer 4.1). I would like to threshold
> using FDR - but only within a specified label - and then see the resulting 
> functional data map.
>
> Once I have the functional dta loaded as an overlay, I have been loading my 
> label and marking the selected label under the Tools
> menu. I then set the threshold using FDR only on marked data. So far, so 
> good. However, once this is done, I have not been able to
> see the thresholded functional map in the label; I can only the whole area in 
> white, marked. How do I see my functional data map?
>
> I apologize for this simplistic question; I have not been able to find a 
> solution looking through the tksurfer guides online or the
> mail archives.
>
> Thanks,
>
> Susan McLaughlin
> Doctoral Candidate
> SPACE Lab (Stimulus-Parametric Imaging of Auditory Cortex)
> Dept. of Speech and Hearing Sciences
> University of Washington
>
>
>
>
>
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>

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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
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Re: [Freesurfer] aparc2aseg for an averaged subject

[Douglas N Greve]

Hi Paul, try this

cd $SUBJECTS_DIR/youraveragesubjectname
mris_volmask --label_left_white 2 --label_left_ribbon 3 
--label_right_white 41 --label_right_ribbon 42 --save_ribbon 
youraveragesubjectname

doug

On 02/04/2013 02:40 PM, Paul Beach wrote:
> Hi Doug,
>
> Your suggestion to remove the 'unknown' label when using the 
> mris_label2annot command worked like a charm. Thanks!
>
> However, now I'm trying, as per your original advice, to re-run 
> mri_aparc2aseg in order to get my labels to fill out the entire 
> cortical ribbon (with the end goal of exporting these labels/ROIs to 
> AFNI). I tried this on my averaged subject (created with 
> 'make_average_subject') and it gave me the error that there is no 
> "ribbon.mgz" file in the mri folder. Upon checking the mri folder, 
> there is indeed no 'ribbon.mgz' file.
>
> Looking at the options for 'mri_aparc2aseg' on the wiki it doesn't 
> look like there's any way around this problem from that angle - at 
> least from the perspective of using my averaged subject.
>
> In the averaged subject's mri folder there are only the following files:
> aseg.mgz
> brain.mgz
> orig.mgz
> T1.mgz
> brainmask.mgz
> mni305.cor.mgz
> p.aseg.mgz
>
> Interestingly, in the fsaverage subject there are ribbon.mgz files. Is 
> there a way to make a ribbon.mgz file for averaged subjects??
>
>
> Thanks,
> Paul
>
>
>
>
> On Thu, Jan 31, 2013 at 2:12 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> Hi Paul, this mostly looks right. I think the problem may be that
> you are including the unknown label on the command line. I think
> that mris_label2annot will ignore the 0 inthe ctab file, which
> means that it assign the first label passed (lh.unknown.label) to
> the the first non-zero ROI in the ctab file (banksts). Try that
> and see if it works.
> doug
>
>
> On 01/30/2013 03:03 PM, Paul Beach wrote:
>
> Hi Doug,
>
> I've been attempting to utilize the programs suggested by you
> to create manual labels (ROIs) on the cortical surface of
> tksurfer to be able to export certain ones to AFNI. The
> problem I was having originally was that the cortical ribbon
> was not fully covered by surface drawn labels that were
> changed to volumes by MRI_label2vol.
>
> You suggested first using mri_annotation2label to extract the
> labels within the aparc.annot files (left and right
> hemispheres), putting my created labels into the same folder
> (replacing, for example, the "insula" label with  anterior,
> middle, and posterior insula labels) and then using
> mris_label2annotation to make a new annotated file to be sent
> into a re-ran mri_aparc2aseg.
>
> The problem I'm running into now, after extracting all the
> labels, putting in my own, and running mris_label2annotis that
> the resultant annotation's labels are highly out of place and
> disorganized. For example, the label for the cuneus is where
> the corpus callosum is.
>
> I'm wondering if this has something to do with the order of
> labels in the mris_label2annot script of possibly with my
> .ctab file. The latter was created based on what I found here
> 
> on the Freesurfer wiki. I simply added my six manual
> labels/ROIs at the end. I tried to use their GWFSAnnotToLUT
> 
> 
> program, but could not get it to work, so I'm not sure if the
> .ctab file accurately represents tksurfer's Lookup Table.
>
>
> I'm also not sure if it has something to do with overlapping
> vertices of different labels. For example, will leaving the
> "insula" label in mess things up when I also try to include
> the anterior, middle, and posterior insula labels? If so,
> would simply removing labels that overlap, vertex-wise, help?
>
> I have attached the setup of the .ctab file as well as my
> mris_label2annot script.
>
>
> Thanks for your advice,
> Paul
>
>
> On Tue, Jan 22, 2013 at 2:52 PM, Paul Beach
> mailto:pabea...@gmail.com>
> >> wrote:
>
> Thanks for your help!
>
>
>
> On Tue, Jan 22, 2013 at 11:12 AM, Douglas N Greve
>  
>  >> wrote:
>
>  mri_annotation2label breaks them appart
> mris_label2annot puts them back together again
> doug
>
> On 01/22/2013 11:09 AM, Paul Beach wrote:
>
> Hi Doug,
>
> Thank you 

Re: [Freesurfer] Difficult results from our PD data

[Douglas N Greve]

Hi Stan, the VBM results may be picking up changes in GM volume. These 
volume changes may be driven by differences in surface area and would 
not necessarily show up in a thickness analysis. Maybe the surface area 
is increasing with performance but the thickness is decreasing. You can 
do a surface-based analysis of surface area and/or volume (this is 
similar to a VBM analysis but on the surface). You can do this by 
specifying --meas area or --meas volume to mris_preproc. Make sure you 
have the mris_preproc patch (or are using 5.2).

doug


On 02/05/2013 09:54 AM, Bruce Fischl wrote:
> Hi Stan
>
> we have found positive correlations between performance (in this case 
> CVLT) and thickness, so it is certainly possible. And negative 
> correlations aren't necssarily false - you could certainly imagine 
> that successful pruning for example could help performance. Have you 
> visually inspected the surfaces for accuracy?
>
> cheers
> Bruce
>
>
> On Tue, 5 Feb 2013, Berg, S.F. van den wrote:
>
>>
>>
>> Dear Freesurfer experts,
>>
>>
>>
>> We investigated the relation between cortical thickness and 
>> performance on several cognitive tasks within a large group of
>> Parkinson?s disease patients, but are slightly puzzled by the 
>> results. We obtained several, both in the vertex-wise analysis
>> in qdec and in the SPSS analysis in the a-priori parcelated areas, 
>> negative correlations (i.e. better performance relates
>> to a thinner cortical area) for all our neuropsychological tasks. 
>> These negative correlations were unexpected and we are
>> having a hard time interpreting them. After correcting for multiple 
>> comparisons, all effects failed to reach the
>> statistical threshold, rendering no results at all. When we compared 
>> our patient group on a structural level with healthy
>> controls, we did find expected results that made sense.
>>
>> We also ran the exact same analyses (same group, same data) in VBM 
>> and there found several positive task-related
>> correlations in expected areas.
>>
>> We noticed that in previous literature almost no studies investigated 
>> the relation between cortical thickness and
>> cognitive task-performance. This made us wonder whether Freesurfer is 
>> suited for these correlation-based analyses, or is
>> it better to be used in between group analyses? And do you have any 
>> idea on how to explain our negative correlations? Is
>> it possible we might have done something wrong?
>>
>>
>>
>> Many thanks,
>>
>>
>>
>> Stan
>>
>>
>>
>
>
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Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] ROI analysis and whitening in fsfast

[Douglas N Greve]

Hi Clark,

On 02/06/2013 05:55 PM, Clark Fisher wrote:
> Hi everyone,
>
> In a previous discussion on this list 
> (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg17681.html), 
> Pablo Polosecki was asking the best way to perform hypothesis testing 
> using functional data within an ROI.  The final opinion was that it 
> was best to average all of the time courses in the ROI, and re-run the 
> analysis from scratch, so that all of the appropriate whitening, etc. 
> occurred.
>
> I was considering doing this, creating a small volume (say, 10 voxels 
> total) that had each voxel holding the average time course from one of 
> 10 ROIs.  I would then set up and run a usual fsfast analysis using 
> these tiny volumes.  I am using freesurfer 4.5.  I have a few questions.
>
> 1) Is this reasonable?
In general, it is reasonable. Though I'm curious what you are ultimately 
trying to do. Do you want p-values for each subject in each ROI? Or will 
you be combining the ROI beta values across subject in a group analysis? 
If so, then the whitening will probably make little, if any, difference, 
especially if this is a blocked design. In expectation, the whitening 
does not affect the beta values.
>
> 2) One area where I expect to run into problems is with the whitening. 
>  If I set -acfbins to the total number of my dummy voxels, and 
> -acffwhm to 0, will this use the autocorrelation function of the 
> average timecourse within each individual ROI?  Is that an appropriate 
> approach? How sensitive will this be to the number of actual voxels 
> averaged to get each ROI (for instance, would this bias me to finding 
> more significant results in ROIs containing fewer voxels?).
That might work, but no promises! It is an appropriate approach. It 
might be sensitive to the number of voxels if the number is small (say, 
less than 100).
>
> 3) Are there other steps that depend upon the spatial arrangement of 
> voxels that I am forgetting, and will these steps choke on these small 
> volumes (or worse, fail in silent but pernicious ways).
Nothing I can think of off the top of my head.
doug
>
> Thanks for all of the help,
> Clark
>
>
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Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] Xhemi questions

[Douglas N Greve]

On 02/06/2013 12:49 PM, Gabriel Gonzalez Escamilla wrote:
> Dear Doug and FreeSurfer experts,
>
> Thnak you so much for all your lasts responses!.
>
> I did ran succesfully all the pre-processing for the interhemispheric 
> comparisons on FS. Now I have a couple questions:
>
> given the command for interhemispheric comparisons:
> mri_glmfit --y lh.lh-rh.thickness.sm05.mgh --glmdir 
> glm.lh.lh-rh.thickness.sm05 --osgm --surf fsaverage_sym lh;
>
> A) This read all subjects to construct X and C as one-sample group 
> mean, this means that as result I get the difference across 
> hemispheres and across my subjects in a population, right?
Correct.
>
> B) But, what if I have two groups? controls and patients, I'm 
> wondering if is it possible to examine regional differences of 
> thickness asymmetries between those two groups? or more?
This just becomes a standard two group analysis as described in the 
tutorials. You create an FSGD file with two classes and list your input 
subjects.
>
> C) If I want to examine effects of group or sex, while controlling for 
> age and other factors how do I introduce them into the glm model? If 
> so, do I set the contrasts as normally for mri_glmfit? I mean as any 
> other thickness study? or there is any other thing that I should do?
You do not need to do anything different than with a normal thickness 
study.
>
> The command for multiple comparisons correction is:
> mri_glmfit-sim --glmdir glm.lh.lh-rh.thickness.sm05 --cwpvalthresh .5
> Which performs only cluster-wise corrections,
>
> D) is there any other way to correct for multiple comparisons, 
> something like permutation tests or anything else?
Yes, you can run something like
mri_glmfit-sim --glmdir glm.lh.lh-rh.thickness.sm05 --cwpvalthresh .5 
--sim perm 1 2 csdperm --sim-sign abs
You should run mri_glmfit-sim --help to see what these options mean as 
you may need to change the voxelwise threshold (the "2" value)

doug
>
>
> Many thanks in advanced,
> Gabriel

-- 
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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] ROI analysis and whitening in fsfast

[Clark Fisher]

Hi everyone,

In a previous discussion on this list 
(http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg17681.html), 
Pablo Polosecki was asking the best way to perform hypothesis testing using 
functional data within an ROI.  The final opinion was that it was best to 
average all of the time courses in the ROI, and re-run the analysis from 
scratch, so that all of the appropriate whitening, etc. occurred.

I was considering doing this, creating a small volume (say, 10 voxels total) 
that had each voxel holding the average time course from one of 10 ROIs.  I 
would then set up and run a usual fsfast analysis using these tiny volumes.  I 
am using freesurfer 4.5.  I have a few questions.

1) Is this reasonable?

2) One area where I expect to run into problems is with the whitening.  If I 
set -acfbins to the total number of my dummy voxels, and -acffwhm to 0, will 
this use the autocorrelation function of the average timecourse within each 
individual ROI?  Is that an appropriate approach? How sensitive will this be to 
the number of actual voxels averaged to get each ROI (for instance, would this 
bias me to finding more significant results in ROIs containing fewer voxels?).

3) Are there other steps that depend upon the spatial arrangement of voxels 
that I am forgetting, and will these steps choke on these small volumes (or 
worse, fail in silent but pernicious ways).

Thanks for all of the help,
Clark
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[Freesurfer] Troubleshooting the preproc

[Susan Kuo]

Hi FreeSurfer community,

  I am currently trying to troubleshoot my preprocessing part of TRACULA
with the tutorial dataset (for *Diff001* as the subject, specifically),
running *trac-all -corr -c *. I am running the commands in *
subjectID/scripts/trac-all.cmd* one by one because I've had problems with
some of the steps. Specifically, *flip4fsl* didn't work. I instead
used *fslswapdim
-x -y z* (*flip4fsl* uses *fslswapdim x -y z*, which doesn't generate the
correct orientation for FSL in fact), followed by *fslorient
-forceradiological*. I successfully ran *eddy_current *thereafter. Now I am
stuck again, at FreeSurfer's *xfmrot, *which should look like:
*
*
*xfmrot   []*

I specifically typed in:

*xfmrot
/j/dti7/Susie/freesurfer/subjects/diffusion_tutorial/Diff001/dmri/dwi.ecclog
/j/dti7/Susie/freesurfer/subjects/diffusion_tutorial/Diff001/dmri/bvecs.norot
/j/dti7/Susie/freesurfer/subjects/diffusion_tutorial/Diff001/dmri/bvecs*


and received the following iterative errors:

*
avscale: Command not found.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
*

Can any of you help me?

Thank you,
Susie K
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[Freesurfer] Problem with flip4fsl

[Susan Kuo]

Hi FreeSurfer community,
  I am trying to run 'trac-all -corr -c ' on the tutorial
data, specifically for the single subject: Diff001. To start from
'scratch', I've deleted all but the './scripts' and the './orig'
directories in the Diff001 parent folder. When I run the following command:

> trac-all -corr -c 

I receive the following error:

ERROR BEGINS>
flip4fsl
/j/dti7/Susie/freesurfer/subjects/diffusion_tutorial/Diff001/dmri/dwi_orig.nii.gz
/j/dti7/Susie/freesurfer/subjects/diffusion_tutorial/Diff001/dmri/dwi_orig_flip.nii.gz
INFO: input image orientation is LPS
INFO: input image determinant is 8
fslswapdim
/j/dti7/Susie/freesurfer/subjects/diffusion_tutorial/Diff001/dmri/dwi_orig.nii.gz
x -y z
/j/dti7/Susie/freesurfer/subjects/diffusion_tutorial/Diff001/dmri/dwi_orig_flip.nii.gz
fslorient -forceradiological
/j/dti7/Susie/freesurfer/subjects/diffusion_tutorial/Diff001/dmri/dwi_orig_flip.nii.gz
Cannot open volume
/j/dti7/Susie/freesurfer/subjects/diffusion_tutorial/Diff001/dmri/dwi_orig_flip
for reading!
> ERROR ENDS


Looking in my 'Diff001/dmri' directory, I cannot locate a
'dwi_orig_flip.nii.gz' file. I assume this is where the script breaks. I
tried to run the 'flip4fsl' command singly, but received the same error.

I'm working on a:
3.2.0-35-generic #55-Ubuntu SMP Wed Dec 5 17:42:16 UTC 2012 x86_64 x86_64
x86_64 GNU/Linux

I've unsuccessfully searched through the mailing list archive to find if
others had encountered the same issue previously. Does anybody have any
suggestions?


Thanks!
Susie
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[Freesurfer] Xhemi questions

[Gabriel Gonzalez Escamilla]

Dear Doug and FreeSurfer experts,Thnak you so much for all your lasts responses!.I did ran succesfully all the pre-processing for the interhemispheric comparisons on FS. Now I have a couple questions:given the command for interhemispheric comparisons:mri_glmfit --y lh.lh-rh.thickness.sm05.mgh --glmdir glm.lh.lh-rh.thickness.sm05 --osgm --surf fsaverage_sym lh;A) This read all subjects to construct X and C as one-sample group mean, this means that as result I get the difference across hemispheres and across my subjects in a population, right? B) But, what if I have two groups? controls and patients, I'm wondering if 
is it possible to examine regional differences of thickness asymmetries 
between those two groups? or more?C) If I want to examine effects of group or sex, while controlling for age and other factors how do I introduce them into the glm model? If so, do I set the contrasts as normally for mri_glmfit? I mean as any other thickness study? or there is any other thing that I should do?The command for multiple comparisons correction is:mri_glmfit-sim --glmdir glm.lh.lh-rh.thickness.sm05 --cwpvalthresh .5 --cache 2 absWhich performs only cluster-wise corrections, D) is there any other way to correct for multiple comparisons, something like permutation tests or anything else?Many thanks in advanced,Gabriel
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Re: [Freesurfer] Qdec

[Douglas N Greve]

something like

mri_surf2vol --surfval sig.mgh --hemi lh --identity fsaverage --o 
sig.lh.vol.nii.gz

doug


On 02/06/2013 09:50 AM, Franklin, Crystal G wrote:
> I never received a reply, so I am reposting my message below.  Any help
> would be greatly appreciated.
>
> Thanks in advance,
> Crystal
>
> On 2/4/13 10:35 AM, "Franklin, Crystal G"  wrote:
>
>> So I ran mri_surf2vol --help and I am still a little confused on what to
>> run.  Where do I actually give the sig.mgh file?  All the options seem to
>> ask for an individual subjects file.
>>
>> Thanks,
>> Crystal
>>
>> On 2/1/13 5:57 PM, "Douglas N Greve"  wrote:
>>
>>> You can run it with --help to get more info, let me know if you have
>>> questions after that
>>> On 02/01/2013 05:08 PM, Franklin, Crystal G wrote:
 Which options should I use when running mri_surf2vol?

 Crystal

 On 2/1/13 1:08 PM, "Douglas N Greve"  wrote:

> QDEC will create an output folder. In that folder, there will be a
> folder for each contrast. In the contrast folder, there will be a
> sig.mgh file. this has the -log10(p) significance values. You can
> convert this to nifti with mri_convert, but it will still be on the
> surface. If you need it in a volume, you can use mri_surf2vol
> doug
>
> On 02/01/2013 09:34 AM, Franklin, Crystal G wrote:
>> Freesurfer,
>>
>> I ran a group comparison using qdec and got my results showing the
>> differences in the thickness between the groups.  I want to take
>> these
>> results I see in the viewer and convert them to nifti format so I can
>> use them in another software called MANGO.  Which files do I need to
>> convert that shows the contrast differences?
>>
>> Thank you,
>> Crystal
>>
>>
>> ___
>> 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
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>
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>
>
> The information in this e-mail is intended only for the person to whom
> it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you
> in
> error
> but does not contain patient information, please contact the sender
> and
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> 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
>>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>>
>
>

-- 
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] invalid=766 recon-all

[Nick Schmansky]

None of the text in bold is of concern.  It appears that mri_ca_register
was running, which can take many hours to complete.

Nick

On Mon, 2013-02-04 at 22:55 +0100, std...@virgilio.it wrote:
> Hi list,
> 
> 
> I'm running :
> recon-all -all -i $SUBJECTS_DIR/MPRAGE.nii.gz -subject
> $SUBJECTS_DIR/hptu_sub001
> In bold the error that I'm visualizing:
> 
> 
> Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0
> Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0
> INFO: SUBJECTS_DIR
> is /Applications/freesurfer/subjects/subject_prova/Diff01
> Actual FREESURFER_HOME /Applications/freesurfer
> Darwin iMac-di-Stefano.local 12.2.1 Darwin Kernel Version 12.2.1: Thu
> Oct 18 12:13:47 PDT 2012; root:xnu-2050.20.9~1/RELEASE_X86_64 x86_64
> /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001
> \n
> mri_convert 
> /Applications/freesurfer/subjects/subject_prova/Diff01/MPRAGE.nii.gz 
> /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig/001.mgz
>  \n
> mri_convert 
> /Applications/freesurfer/subjects/subject_prova/Diff01/MPRAGE.nii.gz 
> /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig/001.mgz
>  
> $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
> reading
> from /Applications/freesurfer/subjects/subject_prova/Diff01/MPRAGE.nii.gz...
> TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (-0.998454, 0.00426797, -0.0554224)
> j_ras = (0.0151969, 0.980022, -0.198308)
> k_ras = (-0.0534688, 0.198844, 0.978572)
> writing
> to 
> /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig/001.mgz...
> #
> #@# MotionCor Mon Feb  4 20:34:08 CET 2013
> Found 1 runs
> /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig/001.mgz
> Checking for (invalid) multi-frame inputs...
> WARNING: only one run found. This is OK, but motion
> correction cannot be performed on one run, so I'll
> copy the run to rawavg and continue.
> \n
> cp 
> /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig/001.mgz
>  
> /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/rawavg.mgz
>  \n
> /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001
> \n
> mri_convert 
> /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/rawavg.mgz
>  
> /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig.mgz
>  --conform \n
> mri_convert 
> /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/rawavg.mgz
>  
> /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig.mgz
>  --conform 
> $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
> reading
> from 
> /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/rawavg.mgz...
> TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (-0.998454, 0.00426797, -0.0554224)
> j_ras = (0.0151969, 0.980022, -0.198308)
> k_ras = (-0.0534688, 0.198844, 0.978572)
> Original Data has (0.8, 2, 0.8) mm size and (320, 85, 320) voxels.
> Data is conformed to 1 mm size and 256 voxels for all directions
> changing data type from float to uchar (noscale = 0)...
> MRIchangeType: Building histogram 
> Reslicing using trilinear interpolation 
> writing
> to 
> /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig.mgz...
> \n mri_add_xform_to_header
> -c 
> /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/transforms/talairach.xfm
>  
> /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig.mgz
>  
> /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig.mgz
>  \n
> INFO: extension is mgz
> #
> #@# Talairach Mon Feb  4 20:34:17 CET 2013
> /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri
> \n talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm \n
> \n cp transforms/talairach.auto.xfm transforms/talairach.xfm \n
> #
> #@# Talairach Failure Detection Mon Feb  4 20:34:49 CET 2013
> /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri
> \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n
> talairach_afd: Talairach Transform: transforms/talairach.xfm OK
> (p=0.4903, pval=0.1531 >= threshold=0.0050)
> \n awk
> -f /Applications/freesurfer/bin/extract_talairach_avi_QA.awk 
> /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/transforms/talairach_avi.log
>  \n
> TalAviQA: 0.96699
> z-score: -2
> #
> #@# Nu Intensity Correction Mon Feb  4 20:34:50 CET 2013
> \n mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar
> transforms/talairach.xfm --n 2 \n
> /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri
> /Applications/freesurfer/bin/mri_nu_correct.mni
> --i orig.mgz --o nu.mgz --uchar transforms/talairach.

Re: [Freesurfer] Memory Consumption of GPU-assisted Freesurfer?

[Nick Schmansky]

The environment variable 'FREESURFER_CUDA_DEVICE' defines the device
number of the GPU device.  Although I dont think you will see much
benefit in splitting the surface processing across two gpus, as the CUDA
surface code is not as optimal as the volume-based mri_ca_register code
for parallel processing.

Nick


On Mon, 2013-02-04 at 19:31 -0500, R Edgar wrote:
> On Mon, Feb 4, 2013 at 6:54 PM, Zhongtian Dai  wrote:
> 
> > Thanks for the speedy response. I think we will go with GTX 660 Ti with 2GB
> > GPU RAM. We don't have a lot of subjects (as we hope to have) to analyze, so
> > maybe we will try splitting left and right hemispheres to two graphic cards
> > if our CPU RAM doesn't deplete. How do you designate the cuda commands to a
> > certain GPU?
> 
> You'll have to ask Nick that - I don't remember, I'm afraid.
> 
> Richard
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> 
> 


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Re: [Freesurfer] "nu_estimate_np_and_em" error during recon-all

[Nick Schmansky]

Tudor,

Sorry to hear its not working.  There is a plan B: scrap our VirtualBox
instance entirely and instead install FSL's VMWare (from their website).
This has a 64b Centos, so upon successful installation of it, you would
download our 64b centos freesurfer distribution.

Nick


On Wed, 2013-02-06 at 12:59 +, Tudor Popescu wrote:
> ..I also did the following in the meantime, to make sure that the
> problem isn't due to a path error:
> - ran nu_estimate_np_and_em and nu_correct: both seem to respond fine,
> and they return their version number
> - checked env variables $MNI_PERL5LIB and $MNI_DATAPATH: both point
> into $FREESURFER_HOME/mni , as they should
> 
> Still cannot get recon-all to run because of the error mentioned
> previously & currently at my wit's end! :(
> 
> On 4 February 2013 10:29, Tudor Popescu  wrote:
> Hi NIck,
> 
> I too thought disk space might be an issue, however I''ve been
> running the recon-all from a mounted partition (shared folder
> in Virtualbox) that has plenty of space:
> 
> FreeSurfer:~> df -h
> FilesystemSize  Used Avail Use% Mounted on
> /dev/sda1  11G  9.8G 0 100% /
> tmpfs 755M 0  755M   0% /lib/init/rw
> varrun755M  104K  754M   1% /var/run
> varlock   755M 0  755M   0% /var/lock
> udev  755M  152K  754M   1% /dev
> tmpfs 755M 0  755M   0% /dev/shm
> lrm   755M  2.4M  752M
> 1% /lib/modules/2.6.28-11-generic/volatile
> overflow  1.0M   12K 1012K   2% /tmp
> Dell  173G  106G   68G  62% /media/Dell
> 
> 
> The list of commands I ran were:
> sudo mount -t vboxsf Dell /media/Dell
> setenv
> SUBJECTS_DIR /media/Dell/_FS/buckner_data/tutorial_subjs
> recon-all -s bert -all 
> 
> THis is because running it from the home (default) partition
> was not possible, as it has 0 KB free space, and the
> discussion with Virtualbox support, where I asked how to
> increase it, has not been very helpful.
> 
> Tudor
> 
> 
> On 31 January 2013 18:42, Nick Schmansky
>  wrote:
> Tudor,
> 
> I'm a bit at a loss as to why it wont work. It appears
> you have plenty of
> available memory.  Also, another person on the list
> confirmed that bert
> will run to completion in the fsv5.1 WindowsVM.
> 
> I noticed though that it appears you have the buckner
> tutorial data.  I
> dont have my virtual machine on hand to check the
> available disk space
> reserved for it, but check that you have enough disk
> space.  run 'df -h'.
> or just delete some of the tutorial subjects and try
> again.  This might be
> the problem since you mentioned you were having
> problems with
> recon-all.log file creation.
> 
> Nick
> 
> 
> > Thanks Nick,
> >
> > I ran the rm command and then re-ran recon-all. Got
> the same error, but at
> > least now recon-all.log was created, see attached.
> >
> > Tudor
> >
> > On 31 January 2013 17:16, Nick Schmansky
> 
> > wrote:
> >
> >> Tudor,
> >>
> >> the log indicates that you need to run this:
> >>
> >> rm
> >> 
> /media/Dell/_FS/buckner_data/tutorial_subjs/bert/scripts/IsRunning.lh+rh
> >>
> >> to get recon-all to run again.
> >>
> >> Nick
> >>
> >>
> >> > Hi Nick,
> >> >
> >> > Thanks for your reply! I increased the memory
> available to FS in the
> >> > virtualbox to the maximum allowed value (80% of
> my machine's total
> >> RAM),
> >> > such that the free command returns:
> >> >
> >> >  total   used   free
> sharedbuffers
> >> cached
> >> > Mem:   2838372 5223042316068
>  0  11176
> >> 37663
> >> >
> >> > Virtualbox support advised me to not increase
> this memory to more

Re: [Freesurfer] Qdec

[Franklin, Crystal G]

I never received a reply, so I am reposting my message below.  Any help
would be greatly appreciated.

Thanks in advance,
Crystal

On 2/4/13 10:35 AM, "Franklin, Crystal G"  wrote:

>So I ran mri_surf2vol --help and I am still a little confused on what to
>run.  Where do I actually give the sig.mgh file?  All the options seem to
>ask for an individual subjects file.
>
>Thanks,
>Crystal
>
>On 2/1/13 5:57 PM, "Douglas N Greve"  wrote:
>
>>You can run it with --help to get more info, let me know if you have
>>questions after that
>>On 02/01/2013 05:08 PM, Franklin, Crystal G wrote:
>>> Which options should I use when running mri_surf2vol?
>>>
>>> Crystal
>>>
>>> On 2/1/13 1:08 PM, "Douglas N Greve"  wrote:
>>>
 QDEC will create an output folder. In that folder, there will be a
 folder for each contrast. In the contrast folder, there will be a
 sig.mgh file. this has the -log10(p) significance values. You can
 convert this to nifti with mri_convert, but it will still be on the
 surface. If you need it in a volume, you can use mri_surf2vol
 doug

 On 02/01/2013 09:34 AM, Franklin, Crystal G wrote:
> Freesurfer,
>
> I ran a group comparison using qdec and got my results showing the
> differences in the thickness between the groups.  I want to take
>these
> results I see in the viewer and convert them to nifti format so I can
> use them in another software called MANGO.  Which files do I need to
> convert that shows the contrast differences?
>
> Thank you,
> Crystal
>
>
> ___
> 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
 Outgoing: 
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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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
>>Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>


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Re: [Freesurfer] "nu_estimate_np_and_em" error during recon-all

[Tudor Popescu]

..I also did the following in the meantime, to make sure that the problem
isn't due to a path error:
- ran nu_estimate_np_and_em and nu_correct: both seem to respond fine, and
they return their version number
- checked env variables $MNI_PERL5LIB and $MNI_DATAPATH: both point into
$FREESURFER_HOME/mni , as they should

Still cannot get recon-all to run because of the error mentioned previously
& currently at my wit's end! :(

On 4 February 2013 10:29, Tudor Popescu  wrote:

> Hi NIck,
>
> I too thought disk space might be an issue, however I''ve been running the
> recon-all from a mounted partition (shared folder in Virtualbox) that has
> plenty of space:
>
> *FreeSurfer:~> df -h
> FilesystemSize  Used Avail Use% Mounted on
> /dev/sda1  11G  9.8G 0 100% /
> tmpfs 755M 0  755M   0% /lib/init/rw
> varrun755M  104K  754M   1% /var/run
> varlock   755M 0  755M   0% /var/lock
> udev  755M  152K  754M   1% /dev
> tmpfs 755M 0  755M   0% /dev/shm
> lrm   755M  2.4M  752M   1%
> /lib/modules/2.6.28-11-generic/volatile
> overflow  1.0M   12K 1012K   2% /tmp
> Dell  173G  106G   68G  62% /media/Dell*
>
>
> The list of commands I ran were:
> *sudo mount -t vboxsf Dell /media/Dell
> setenv SUBJECTS_DIR /media/Dell/_FS/buckner_data/tutorial_subjs
> recon-all -s bert -all*
>
> THis is because running it from the home (default) partition was not
> possible, as it has 0 KB free space, and the discussion
> with
> Virtualbox support, where I asked how to increase it, has not been very
> helpful.
>
> Tudor
>
>
> On 31 January 2013 18:42, Nick Schmansky wrote:
>
>> Tudor,
>>
>> I'm a bit at a loss as to why it wont work. It appears you have plenty of
>> available memory.  Also, another person on the list confirmed that bert
>> will run to completion in the fsv5.1 WindowsVM.
>>
>> I noticed though that it appears you have the buckner tutorial data.  I
>> dont have my virtual machine on hand to check the available disk space
>> reserved for it, but check that you have enough disk space.  run 'df -h'.
>> or just delete some of the tutorial subjects and try again.  This might be
>> the problem since you mentioned you were having problems with
>> recon-all.log file creation.
>>
>> Nick
>>
>>
>> > Thanks Nick,
>> >
>> > I ran the rm command and then re-ran recon-all. Got the same error, but
>> at
>> > least now recon-all.log was created, see attached.
>> >
>> > Tudor
>> >
>> > On 31 January 2013 17:16, Nick Schmansky 
>> > wrote:
>> >
>> >> Tudor,
>> >>
>> >> the log indicates that you need to run this:
>> >>
>> >> rm
>> >>
>> /media/Dell/_FS/buckner_data/tutorial_subjs/bert/scripts/IsRunning.lh+rh
>> >>
>> >> to get recon-all to run again.
>> >>
>> >> Nick
>> >>
>> >>
>> >> > Hi Nick,
>> >> >
>> >> > Thanks for your reply! I increased the memory available to FS in the
>> >> > virtualbox to the maximum allowed value (80% of my machine's total
>> >> RAM),
>> >> > such that the free command returns:
>> >> >
>> >> >  total   used   free sharedbuffers
>> >> cached
>> >> > Mem:   2838372 5223042316068  0  11176
>> >> 37663
>> >> >
>> >> > Virtualbox support advised me to not increase this memory to more
>> than
>> >> 1GB
>> >> > (of my total 4GB), as this would lead to system instability. I tried
>> >> it
>> >> > nonetheless, but even so, running "recon-all -s bert -all" still
>> gives
>> >> me
>> >> > the same error as before, which is presumably still memory-related.
>> >> >
>> >> > Unfortunately, the output does not, for some reason, get written to
>> >> the
>> >> > recon-all.log file inside \bert\scripts. I deleted the file hoping it
>> >> > would
>> >> > be automatically recreated at the next call of recon-all, but it did
>> >> not.
>> >> > I
>> >> > also then manually created a file with that name, but nothing got
>> >> recorded
>> >> > in it. Therefore, I now have a very long output from the Terminal (I
>> >> also
>> >> > added -debug to the command), which I can only show you by copying
>> all
>> >> the
>> >> > (truncated) text from the terminal window and pasting into the
>> >> attached
>> >> > text file.
>> >> >
>> >> > Tudor
>> >> >
>> >> > On 29 January 2013 01:11, Nick Schmansky 
>> >> > wrote:
>> >> >
>> >> >> I was able to verify that 'recon-all -s bert -nuintensitycor' works
>> >> on
>> >> >> the windows virtualbox instance of fs5.1.  bert is the sample data
>> >> that
>> >> >> comes with the distribution, and nuintensitycor is the stage that
>> >> runs
>> >> >> nu_correct.
>> >> >>
>> >> >> I noticed in your recon-all.log file this line:
>> >> >>
>> >> >>  total   used   free
>> >> >> Mem:   1026680 673692 352988
>> >> >>
>> >> >> which means only 353KB of memory is available for freesurfer.  this
>> >> is
>> >> >> 

Re: [Freesurfer] Difficult results from our PD data

[Berg, S.F. van den]

Hi Bruce, 

I checked the surface of every subject with tksurfer, inaccuracy's were founded 
in 13 of 140 subjects. These subjects were manually edited with control points 
and pial edits. Then i start recon-all on the subjects with edits again. After 
these procedure tksurfer showed a correct segmentation. Is that the correct 
procedure for checking inaccuracy's? Or do i need to check more?  

http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints

http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits

Many thanks,

Stan



From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: 05 February 2013 15:54
To: Berg, S.F. van den
Cc: Freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Difficult results from our PD data

Hi Stan

we have found positive correlations between performance (in this case
CVLT) and thickness, so it is certainly possible. And negative correlations
aren't necssarily false - you could certainly imagine that successful
pruning for example could help performance. Have you visually inspected the
surfaces for accuracy?

cheers
Bruce


On Tue, 5 Feb 2013, Berg,
S.F. van den wrote:

>
>
> Dear Freesurfer experts,
>
>
>
> We investigated the relation between cortical thickness and performance on 
> several cognitive tasks within a large group of
> Parkinson?s disease patients, but are slightly puzzled by the results. We 
> obtained several, both in the vertex-wise analysis
> in qdec and in the SPSS analysis in the a-priori parcelated areas, negative 
> correlations (i.e. better performance relates
> to a thinner cortical area) for all our neuropsychological tasks. These 
> negative correlations were unexpected and we are
> having a hard time interpreting them. After correcting for multiple 
> comparisons, all effects failed to reach the
> statistical threshold, rendering no results at all. When we compared our 
> patient group on a structural level with healthy
> controls, we did find expected results that made sense.
>
> We also ran the exact same analyses (same group, same data) in VBM and there 
> found several positive task-related
> correlations in expected areas.
>
> We noticed that in previous literature almost no studies investigated the 
> relation between cortical thickness and
> cognitive task-performance. This made us wonder whether Freesurfer is suited 
> for these correlation-based analyses, or is
> it better to be used in between group analyses? And do you have any idea on 
> how to explain our negative correlations? Is
> it possible we might have done something wrong?
>
>
>
> Many thanks,
>
>
>
> Stan
>
>
>


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Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: tracula and recon-all

[Anastasia Yendiki]

Hi Stefano - You need to download the file dmri_5.1_snow_leopard.tar.gz 
from the wiki page, unzip it, and copy ALL the files that come out into 
the same directory where you copied the trac-all update. The trac-all 
update doesn't solve the memory issue, for that you need the executables 
in dmri_5.1_snow_leopard.tar.gz.


I will be going on a short vacation for the rest of the week and will not 
be able to answer questions during this time unfortunately. If you don't 
manage to get through the tutorial independently by Monday, please send in 
your questions then.


Best of luck,
a.y


On Wed, 6 Feb 2013, std...@virgilio.it wrote:


Hi Anastasia,
which is the forder where I should put leopard uploade?

I try to put it in folder where trac-all lives, but when I re-run trac-all I
obtain the same error:

 dmri_train(11214) malloc: *** mmap(size=159744) failed (error code=12)***
error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
MRIalloc(218, 182, 182): could not allocate 158704 bytes for 15th slice
Cannot allocate memory

Thanks,


Stefano


Messaggio originale
Da: ayend...@nmr.mgh.harvard.edu
Data: 6-feb-2013 0.11
A: 
Ogg: Re: R: Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: R: Re: R: Re:
tracula and recon-all


Type "which trac-all" to find out where trac-all lives on your computer,
then copy the update files there.

On Wed, 6 Feb 2013, std...@virgilio.it wrote:

> Anastasia, thank you for your patience and kindness. I apologie but how
can
> I use them, particularly trac-all updates.
> Messaggio originale
> Da: ayend...@nmr.mgh.harvard.edu
> Data: 5-feb-2013 23.58
> A: 
> Cc: 
> Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: tracula
and
> recon-all
>
>
> See "updates":
> http://www.freesurfer.net/fswiki/Tracula
>
> On Tue, 5 Feb 2013, std...@virgilio.it wrote:
>
> > I delete it and I attached my last configuration file.
> > This is the error after rerunning:
> > dmri_train(11214) malloc: *** mmap(size=159744) failed (error
code=12)***
> > error: can't allocate region
> > *** set a breakpoint in malloc_error_break to debug
> > MRIalloc(218, 182, 182): could not allocate 158704 bytes for 15th slice
> >
> > Cannot allocate memory
> > Darwin iMac-di-Stefano.local 12.2.1 Darwin Kernel Version 12.2.1: Thu
Oct
> 18
> > 12:13:47 PDT 2012; root:xnu-2050.20.9~1/RELEASE_X86_64 x86_64
> >
> > trac-preproc exited with ERRORS at Tue Feb  5 23:46:51 CET 2013
> > Messaggio originale
> > Da: ayend...@nmr.mgh.harvard.edu
> > Data: 5-feb-2013 22.53
> > A: 
> > Cc: 
> > Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: R: Re: tracula and
> > recon-all
> >
> >
> > Is there a line that says "set trainfile = ..." in your configuration
> > file? If so please delete it.
> >
> > On Tue, 5 Feb 2013, std...@virgilio.it wrote:
> >
> > > I set $TUTORIAL_DATA as setenv TUTORIAL_DATA
> > > /Applications/freesurfer/subjects/TUTORIAL_DATA
> > >
> > > In $TUTORIAL_DATA/diffusion_tutorial I do not found
> > > subj,train,difftutorial23.txtsubjI find
> subj,train,difftutorial32.txtsubj
> > in
> > >
$TUTORIAL_DATA/diffusion_tutorial/scripts/subj,train,difftutorial32.txt
> > >
> > > Stefano
> > >
> > > Messaggio originale
> > > Da: ayend...@nmr.mgh.harvard.edu
> > > Data: 5-feb-2013 22.33
> > > A: 
> > > Cc: 
> > > Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: tracula and
recon-all
> > >
> > >
> > > I'm guessing that there's some confusion about the instructions in the
> > > tracula tutorial and that you are settin the trainfile variable in
your
> > > configuration file to look for a file in that directory. If so, just
> > > delete that line from your configuration file.
> > >
> > > On Tue, 5 Feb 2013, std...@virgilio.it wrote:
> > >
> > > > Yes directory existbutnothereis lh.cst_AS.flt.trkin 
/Applications/freesurfer/subjects/TUTORIAL
_DA
> TA
> > /diff
> > > usion_tutorial/Diff0
> > > > 01/
> > > > > dlabel/mni/
> > > > Stefano
> > > >
> > > > Messaggio originale
> > > > Da: ayend...@nmr.mgh.harvard.edu
> > > > Data: 5-feb-2013 22.23
> > > > A: 
> > > > Cc: 
> > > > Ogg: Re: R: Re: [Freesurfer] R: Re:  R: Re:  tracula and recon-all
> > > >
> > > >
> > > > It's looking for files in
> > > > /Applications/freesurfer/subjects/TUTORIAL_DATA/diffusion
> > > >
> > > > Does this directory actually exist?
> > > >
> > > > On Tue, 5 Feb 2013, std...@virgilio.it wrote:
> > > >
> > > > > Thank you very much Shantanu and Anastasia.Now I'm running
trac-all
> > but
> > > I
> > > > > have an error:
> > > > >
> > > 
>>niiRead():erroropeningfile/Applications/freesurfer/subjects/TUTORIAL_DATA/
d
> iffusion_t
> > utori
> > > al/Diff
> > > > 001/
> > > > > dlabel/mni/lh.cst_AS_roi2.flt.nii.gz
> > > 
>>WARN:Couldnotopen/Applications/freesurfer/subjects/TUTORIAL_DATA/diffusion
_
> tutor
> > ial/D
> > > iff
> > > > 001/
> > > > > dlabel/mni/lh.cst_AS.flt.trk for reading
> > > > > WARN: Error was: Can not open file
> > > > > WARN: Skipping to next subject
> > > > >
> > > > > dmr