To FSL/Freesurfer experts,
I have been trying for the last few weeks to perform whole-brain
probabilistic tractography using FSL's probtrackx2. After solving a number
of issues, I believe I am calling the command correctly, but it has already
taken 5 days and wondering if I am going in the right d
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 sent you
so your recon-all command line was:
recon-all -s /usr/local/mridata/D_New_Patient/Lobe_Analysis/CON1 -calabel
usually -s just takes the subject name/identifier, not the whole path, and
why are you only rerunning calabel? I don't see what the error is, but this
is an unusual usage
On Tue, 30
See my original post at the end of this message and some more
information included below.
What would have been edited between the previous run without errors
and the current run with errors is the brainmask, the wm.mgz file, and
control points.
On Tue, Oct 30, 2012 at 1:21 PM, Christine Smith wr
can you send the fsgd file and command line?
On 10/30/2012 06:42 PM, Ryan wrote:
> Doug,
>Also, I tried running this analysis but got the error below. This
> makes me think it's because of all of the 1's and -1's in my FSGD
> file, should I just have a factor called "Training" with a "yes" o
Not quite, changes to FSGD file below as well as comments on the
contrast matrix
On 10/30/2012 05:57 PM, Ryan wrote:
> Doug,
>So if I wanted to test if there were effects of training compared
> to the control condition, and I had 4 subjects (2 per group), would
> the format for my two files
Doug,
So if I wanted to test if there were effects of training compared to the
control condition, and I had 4 subjects (2 per group), would the format for
my two files shown below be correct? Thanks.
FSGD file:
GroupDescriptorFile 1
Class Subject1
Class Subject2
Class Subject3
Class Subject4
V
See http://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova
This is for a single group. For two groups with 3 time points. In your
case, you only have 2 time points (so no TP1-vs-TP3 variable). To
account for the 2nd group, create two variables: TP1-vs-TP2.Group1 and
TP1-vs-TP2.Group2. If
That means that $FREESURFER_HOME/fsfast/toolbox is not in your octave
path. Type "path" at the octave command line and make sure that you find
$FREESURFER_HOME/fsfast/toolbox there
doug
On 10/30/2012 03:30 PM, Garlinghouse, Matthew wrote:
>
> Dear Doug,
>
> Sorry to bother you with this. When I
Hi Ryan, I don't understand your model. This does not look like a
standard repeated measures ANOVA. Is it supposed to be equivalent?
doug
On 10/30/2012 02:07 PM, Ryan wrote:
> Doug,
>Just so our study is understandable, subjects completed a 6 week
> period of training or no training (i.e. th
Hi Andi - The most common problem that would cause all or almost all
pathways to fail is an incorrect gradient table. You can do a sanity check
on that by looking at the primary eigenvectors from your tensor fit
(dmri/dtifit_V1.nii.gz). See also my answer to Fernando earlier today.
Hope this
what were the last 20 lines or so of the recon-all.log?
On Tue, 30 Oct 2012,
Christine Smith wrote:
> Hello,
>
> After successfully running a subject through freesurfer (recon-all
> -make all) several times as I fixed some pial and white matter edits,
> I now get the message that recon-all finish
Hello,
After successfully running a subject through freesurfer (recon-all
-make all) several times as I fixed some pial and white matter edits,
I now get the message that recon-all finished with errors. Inspection
of the recon-all.log doesn't reveal any error messages to me in any
particular step.
Dear Doug,
Sorry to bother you with this. When I type "which fast_contrastmtx" after
starting Octave from the command line, it simply clears to the next line - no
output.
I also looked at the fast_contrastmtx.m file and noted that line 25 (as are the
first 30 some lines) appear to be comm
Doug,
Just so our study is understandable, subjects completed a 6 week period
of training or no training (i.e. the control condition) with a scan at the
beginning and end of the period. Thus, I entered the pre and post-scans for
training and control subjects in the input files. The names for all
Hi Fernando - Thanks for uploading your data. Looking at the primary
directions from tensor fit on the data that you sent me (see screenshot),
they seem to be off by a 90 degree angle from what you'd expect them. This
means that your gradient table is probably off as well.
Hope this helps,
a
Hi Khalid, it might be easier to create your own annotation of your lobe
definition, then run mris_anatomical_stats with this annotation. To do
this, first break up the Desikan atlas into labels
(mri_annotation2label), then merge the labels that comprise each lobe
into a single label (mri_merg
Hi Wei, this is a bug in the error msg. It is trying to say that your
source subject is not in the $SUBJECTS_DIR.
doug
On 10/27/2012 02:27 PM, Zhou, Wei wrote:
> Dear freesurfers,
>
> I am trying retinotopy analysis in freesurfer. For "fieldsign-sess", I
> encounter the following problem when I
On 10/28/2012 09:04 AM, Daniel Klein wrote:
>
>
>
> -Ursprüngliche Mitteilung-
> Von: Daniel Klein
> An: freesurfer-owner
> Verschickt: So, 28 Okt 2012 11:58 am
> Betreff: questions to qdec
>
> Dear FreeSurfer experts,
>
>
> i want to test the effect of age square (in contrast to age) o
Hi Ryan, I'm a little lost here. Can you resend your X and contrast
matrices and explain what each column is?
doug
On 10/26/2012 03:45 PM, Ryan wrote:
> Doug,
>Actually my input is not the difference map, but the separate time
> points (it's timepoint 2 weighted with -1 and timepoint 1 weigh
You can get thickness with aparcastats2table with the -m thickness
option. This gives you a measure of mean thickness for the hemisphere as
well.
do8ug
On 10/30/2012 11:02 AM, Daniel Ferreira wrote:
> Please, is there any automatic way to extract this "Mean Thickness"
> values for lh and rh for
Please, is there any automatic way to extract this "Mean Thickness" values
for lh and rh for a big group of subjects? As for example aparcstats2table?
thank you very much
Daniel
2012/10/30 Bruce Fischl
> yes, I think so
>
> Bruce
> On Tue, 30 Oct 2012, Daniel Ferreira wrote:
>
> So, as a meas
So, as a measure of whole brain cortical thickness average is it better to
"Mean Thickness" from aparc.stats file?
>
>
> 2012/10/30 Bruce Fischl
>
>> Hi Daniel
>>
>> the parcellations are not uniform in size, and therefore the average of
>> them will not be the same as averaging over the cortex
yes, I think so
Bruce
On Tue, 30 Oct 2012, Daniel Ferreira wrote:
So, as a measure of whole brain cortical thickness average is it better to
"Mean Thickness" from aparc.stats file?
2012/10/30 Bruce Fischl
Hi Daniel
the parcellations are not uniform in size, and therefore the
Well, in the PACs looks fine. When converting to nii it is already wrapped.
I will go to the machine again and see.
Thanks!
2012/10/30 Bruce Fischl
> really? In what viewer? Does it happen in the rawavg.mgz?
>
>
> On Tue, 30 Oct 2012, Daniel Ferreira wrote:
>
> Hi,
>> I see. But why does it
Dear Tracula team,
I have noticed in a multisubject tracula analysis, that the posterior density
in many if not all paths in the path.pd.nii.gz file is just a bright
one-dimensional curve, rather than a true distribution.
The path.map.nii.gz is empty. This is true for both flirt and bbreg regis
Hi Daniel
the parcellations are not uniform in size, and therefore the average of
them will not be the same as averaging over the cortex.
cheers
Bruce
On Tue, 30 Oct 2012,
Daniel Ferreira wrote:
Hi,
I was wondering what should I use as an average of cortical thickness for
the whole cortex.
really? In what viewer? Does it happen in the rawavg.mgz?
On Tue, 30 Oct 2012, Daniel Ferreira wrote:
Hi,
I see. But why does it happen? If I look at the initial Dicom it is normal,
no wrapped, as usually looks like.
thanks
2012/10/23 Bruce Fischl
Hi Daniel
it looks like you hav
Hi,
I was wondering what should I use as an average of cortical thickness for
the whole cortex.
The aparc.stats output gives a value of "Mean Thickness" for each
hemisphere. But this value does not coincide with the one I get if I
average the 34 variables from aparc.stats. Do you know why?
thank
Thanks for all the information given. We finally have managed to solve it
thanks to your comments.
Cheers
Daniel
2012/10/17 Bruce Fischl
> there is no volume associate with them any longer. As a short-cut I think
> Doug ran the aparc on fsaverage, so you could try sampling it into the
> volume
Hi,
I see. But why does it happen? If I look at the initial Dicom it is normal,
no wrapped, as usually looks like.
thanks
2012/10/23 Bruce Fischl
> Hi Daniel
>
> it looks like you have too much wrap in your image, with a significant
> amount of brain wrapping to the top. Nothing will work on t
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