Hello,
I have tried out running TRACULA on 20 subjects. It all seemed to work well
except that in 8 of the subjects the corpus callosum forceps major was either
missing or was a very small cluster. The same happened for the temporal SLF of
2 subjects.
I read previous posts related to this
Hi all,
Is there a change in the unpacking of the MPRAGE and DICOM files?
The names of the files have changed.
what file name should be put in the command:
recon-all -i./file name -s subjectname
Thanks,
Eiran
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Hi Liang
yes, that information is encoded in the .tif file that is the target of
the registration. You can use mrisp_paint to copy a frame out of
$FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif
the tif file is 3 sets of triplets in different frames. The first is the
mean
You'll need to run dcmunpack without the -martinos flag. This will
(eventually) give you a list of runs and corresponding file names. Find
the one that is the MPRAGE you want to recon, and pass that as -i to
recon-all. Unfortunately the name change makes it harder/slower to
unpack data here.
Hi Freesurfer users:
I'm trying to run recon-all command in a single subject and I don't know
why always there is an error message about the names, I tried the
suggestionsin the message, rename the files, folders, eliminate the folders
etc
But I don't succeed to star to running my data.
Many
Hi Alex,
I am using the same method, I created a Python script to automate it for
multiple users.
Basically, if you give it a file with all the subject ID-s, it maps labels with
mri_label2label, obtains statistics with mris_anatomical_stats and writes all
the stats in a single file.
You
Hi,
3 T1_MPRAGE_sag_short 3.39 2430 7 unknown ROW 190
/cluster/archive/301/siemens/TrioTim-35101-20120912-135155-195000/MR.1.3.12.2.1107.5.2.32.35101.3.2012091214284986179598358
This is what it gives me when i do dcmunpack. What shall i use as the file
indicator in the recon-all -i ./
/cluster/archive/301/siemens/TrioTim-35101-20120912-135155-195000/MR.1.3.12.2.1107.5.2.32.35101.3.2012091214284986179598358
On 09/14/2012 01:01 PM, Eiran Vadim Harel wrote:
Hi,
3 T1_MPRAGE_sag_short 3.39 2430 7 unknown ROW 190
It still does not find the file.
[shimshon:TrioTim-35101-20120912-135155-195000] (nmr-stable5.0-env)
recon-all -i
./cluster/archive/301/siemens/TrioTim-35101-20120912-135155-195000/MR.1.3.12.2.1107.5.2.32.35101.3.2012091214284986179598358
-i
why are you putting a dot in front of the path? There's no dot in the
dcmunpack output
doug
On 09/14/2012 01:35 PM, Eiran Vadim Harel wrote:
It still does not find the file.
[shimshon:TrioTim-35101-20120912-135155-195000] (nmr-stable5.0-env)
recon-all -i
What is your command line?
doug
On 09/14/2012 12:23 PM, Carolina Valencia wrote:
Hi Freesurfer users:
I'm trying to run recon-all command in a single subject and
I don't know why always there is an error message about the names, I
tried the suggestionsin the message, rename the files,
Dear Bruce,
Thanks for pointing me those information. That .tif file includes the mean
and variance for the population sample that was used in Freesurfer. I would
like to get similar measures for our own subjects. I think I could use the
surface file (like surf/?h.sulc) in each subject folder to
You can just run mris_preproc --meas curv --o stack.mgh ...
This will give you a stack from which you can compute the mean and stddev
mri_concat stack.mgh --mean --o stack.mean.mgh
mri_concat stack.mgh --std --o stack.std.mgh
doug
On 09/14/2012 01:55 PM, liang wang wrote:
Dear Bruce,
Thanks
I have a MPRAGE scan, with slight atrophy on right side of brain. Recon-all
is crashing (see error below). Can anyone help me with this, so I can get a
reasonably parcellated brain?
*CORRECTING DEFECT 6 (vertices=151, convex hull=90)
After retessellation of defect 6, euler #=-52
Hi,
These might be old questions, but I couldn't find any entries related to
them in the archives.
1) In the surface and volume csd files, what are the units of the
maxclustsize columns? Are they mm^2 and mm^3 for surface and volume,
respectively? Or are the voxel / vertex counts?
2) When
Hello: I have big file of pts with medial temporal lobe epilepsy (they
usually have hippocampal sclerosis, atrophy; sometimes MRI signal changes
in amygdala).
Pts are scanned with 'oblique' sequence, as it is perpendicular to long
axis of hippocampus. Can these oblique sequences be used for
Hi Shanqing,
On 09/14/2012 02:04 PM, Shanqing Cai wrote:
Hi,
These might be old questions, but I couldn't find any entries related
to them in the archives.
1) In the surface and volume csd files, what are the units of the
maxclustsize columns? Are they mm^2 and mm^3 for surface and
Oblique should not be a problem. What is your voxel size?
doug
On 09/14/2012 02:08 PM, Zuzana Nedelska wrote:
Hello: I have big file of pts with medial temporal lobe epilepsy (they
usually have hippocampal sclerosis, atrophy; sometimes MRI signal
changes in amygdala).
Pts are scanned with
And before you run this, does $SUBJECTS_DIR/HPTU_vol11_2012 exist? BTW,
try it without a slash at the end of the name.
doug
On 09/14/2012 02:09 PM, Carolina Valencia wrote:
Sure!
cvalencia@cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/volumetria$
recon-all -s
Is the cerebellum still attached?
doug
On 09/14/2012 02:01 PM, Blessy M wrote:
I have a MPRAGE scan, with slight atrophy on right side of brain.
Recon-all is crashing (see error below). Can anyone help me with this,
so I can get a reasonably parcellated brain?
/CORRECTING DEFECT 6
yes, you can use mris_make_template to generate these results (it's what
we used to create the tif files in the first place)
On Fri, 14 Sep 2012,
liang wang wrote:
Dear Bruce,
Thanks for pointing me those information. That .tif file includes the mean and
variance for the population sample
Hi Zuzana
I don't think we can diagnose it without seeing some images. The obliques
should be ok, as long as they are whole brain and reasonably high
resolution and good T1-weighted contrast.
cheers
Bruce
On Fri, 14 Sep 2012, Zuzana
Nedelska wrote:
Hello: I have big file of pts with medial
Hi Linda, I have tracked down several problems.
Problem 1: it was sometimes merging several parcellation units into
effectively a single unit. These could have been spread out over space.
This has been fixed.
Problem 2: the documentation suggested using the inflated surface. This
is mostly
No, the cerebellum is not attached.
On Fri, Sep 14, 2012 at 1:42 PM, Blessy M bles...@gmail.com wrote:
I have a MPRAGE scan, with slight atrophy on right side of brain.
Recon-all is crashing (see error below). Can anyone help me with this, so I
can get a reasonably parcellated brain?
The error output below tells you what to do. If the subject folder
(HPTU_vol11_2012) already exists. Since it has your dicom data in it,
you should not delete it. Instead, rename that directory and keep your
command-line (changing the -i path to point to the new dicom file but
keeping the same
what did you rename it to and what is your command line after you rename it?
On 09/14/2012 04:48 PM, Carolina Valencia wrote:
As I said in the first email I tried the suggestions in the message,
rename the files, folders, eliminate the folders, starts from scratch
etc and again with your
Thanks Bruce. one more question:
This is my command (5 subjects)
mris_make_template lh sphere.reg subj1 subj2 subj3 subj4 subj5
./Temp5subj.tif
where I select sphere.reg as sphere surface. I assume 1) that the generated
template Temp5subj.tif is in the Freesurfer buckner40 spherical space and
Hi Liang
the sulc is the integrated signed dot product of the movement vector with
the surface normal during inflation. It reflects large scale geometry
better than ?h.curv, which is the spatially smoothed mean curvature. If you
are using sphere.reg you can probably specify -norot so it
When you run
recon-all -s HPTU_vol11_2012 -i pacsfiles/MPRAGE.Ser1.Img0.dcm
Does the folder or file called $SUBJECTS_DIR/HPTU_vol11_2012 already exist?
doug
On 09/14/2012 05:00 PM, Carolina Valencia wrote:
first rename folder *dicom* to *pacsfiles*
then run
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