Hi Karl
differences in surface area are a bit harder to interpret. There are also
some technical issues that perhaps Doug and/or Anderson Winkler can comment
on. Anderson had a recent article on this that you might want to look at:
http://www.ncbi.nlm.nih.gov/pubmed/22446492
cheers
Bruce
On
Hi Bruce,
I?ve attached a screen shot of a temporal pole of one of the brains that we
have had issues with. Here the issue is that there is a lesion without a
very clear boundary for the white matter and freesurfer was unresponsive to
simply using white matter edits (placing 255s on the wm.mgz), a
Dear Anastasia,
Thank you very much.
This time I attach motion-corrected NIFTI-data (plus bval and bvec tables) that
I have been unsuccessfully trying to process with Tracula. I also attach log
file with error message. I suspect there must be something wrong with the
tables again, but I am clu
Thank you for your comment, Bruce.
Regardless of technical issues, I am still troubled by the
small magnitude of extracted value of pial surface area. Following group
comparison and correction in QDEC, there is a significant cluster (size: 760
mm^2). In order to make a bar group of group means, I
if you run
mri_convert 00010001 deleteme.nii
what happens?
what is the error when running with nifti?
On 03/14/2016 05:59 PM, Jasmin Alves wrote:
>
> Dear Freesurfer experts,
>
> FREESURFER_HOME: /Applications/freesurfer
>
> Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
>
> Kernel info:
Hi Mohamad, I don't know why that would be. Note that the aseg does not
have individual cortical labels. You should use aparc+aseg.mgz
On 03/12/2016 04:19 PM, Alshikho, Mohamad J. wrote:
>
> Hi Doug,
>
> I would like to inquire about the command “ mri_binarize”. In the
> past, this command was
The problem is that the smoothness of the data (35mm) is beyond that
computed for the simulation. 35mm is very smooth. What kind of data is
this? How much did you smooth it by?
On 03/13/2016 07:10 PM, John Anderson wrote:
> Hi experts,
> I am trying to correct the results of groups analysis us
It should all be on one line
mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale
--i orig.mgz --o orig_nu.mgz
On 03/14/2016 05:43 AM, Flavia Niccolini new wrote:
> Hi Douglas,
>
> I have done this and I got the following message:
>
> “cd /data/PDE10_PD_DENOVO/Freesurfer/DE
you cannot have more than two levels of a factor in qdec. You can use
the "command line" stream. See the wiki
On 03/14/2016 06:52 AM, Lisa Delalande wrote:
> Hello everyone,
>
> I've got some problems with qdec. I have .levels with more than 2
> factors. For example a "grpe.levels" with three fa
Hey Bruce,
I recently sent you a log file to look at to determine why reprocessing data
wasn’t making any changes in freeview. Have you had a chance to go over it yet?
Let me know.
Thanks,
Champe
> On Mar 7, 2016, at 11:41 AM, Bruce Fischl wrote:
>
> I got it, thanks
> Bruce
> On Mon, 7 Mar
Dear FreeSurfer experts,
I have a question regarding the Monte Carlo correction.
To create a Monte Carlo correction for my specific sample (4year old kids) the
wiki suggests this command:
mri_mcsim --o $FREESURFER_HOME/average/mult-comp-cor/yoursubject/lh/cortex
--base mc-z --surface yoursubject
You can just store it in a different directory, then use the --cache-dir
option when running mri_glmfit-sim to specify the new folder, eg, if you
use --o /path/to/myspace/yoursubject/lh/cortex, then specify
/path/to/myspace
On 03/15/2016 12:36 PM, Clara Kühn wrote:
> Dear FreeSurfer experts,
>
The setwdelay is an option for mkcontrast-sess (not mkanalysis-sess)
On 03/13/2016 10:29 PM, Joseph Dien wrote:
> After a long break, back to this…
>
> My goal is still to get the betas for the first and maybe second spm
> hrf so I can calculate a Calhoun derivative boost measure.
>
> As a first
They are transformed from the native space (001.mgz) to the "conformed"
space which is 1mm3, 256x256x256. This is a rigid transformation so it
will not distort the volumes.
On 03/14/2016 11:37 AM, Kaiming Yin wrote:
> Dear guys,
>
> Could I ask in the process of each individual data, are the vol
Dear Freesurfer experts,
I have been working with freesurfer V5.3 on the Mac OS 10.8.5. My
institution is requesting that I upgrade the OS on my computer to OS X El
Capitan (10.11). Will this change my ability to look at or process
freesurfer data? Will the recons that I have done be compatible? I
Dear experts and FS users,I came across the following problem it would be
useful help if anyone is able to advice.ThanksPablo
I am having issues when trying to remove non cortical tissue (mostly skull). I
load my images as follow:
freeview -v mri/T1.mgz mri/brainmask.mgz -f surf/lh.white:e
Can you send the terminal output? Also, what version are you using?
On 03/14/2016 09:56 AM, Clare Loane wrote:
> Hi,
>
> I am trying to pull out the volumes from the aparc stats file but when
> I input the following (below) it produces a file identical to the area
> instead:
>
> aparcstats2table
There are a lot of things you mention (vbm, pet, surface-based, and
dti). You'll have to explain in more detail what you did.
On 03/14/2016 01:10 PM, John Anderson wrote:
> Hi Doug,
> I ran voxel based analysis in FSL to check the differnce in PET signal
> between two groups. The results are tot
Thanks a lot! I will do that then :)
Cheers, Clara
- Ursprüngliche Mail -
Von: "Douglas N Greve"
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Dienstag, 15. März 2016 17:40:08
Betreff: Re: [Freesurfer] adapt Monte Carlo correction for specific sample
You can just store it in a different
p.s. sorry, it should be tmp/control.dat
On Tue, 15 Mar 2016, Champe Barton
wrote:
Hey Bruce,
I recently sent you a log file to look at to determine why reprocessing data
wasn’t making any changes in freeview. Have you had a chance to go over it yet?
Let me know.
Thanks,
Champe
On Mar 7,
Hi Champe
it looks like it is not using the control points. How did you create
them? They should be stored in a file under in tmp/edit.dat within the
subject directory. Does that file exist?
cheers
Bruce
On Tue, 15 Mar 2016, Champe Barton
wrote:
Hey Bruce,
I recently sent you a log fil
v5.3 is compatible with El Capitan. In general, we dissuade people from
performing group studies or performing comparisons on subjects processed
under different version operating system. In reality the difference
would be quite small (if it exists at all), but it is still highly
discouraged.
-
I created them as instructed in the tutorial and called the file “control.dat”
so there’s a control.dat file in my subjects directory. Should I have named it
tmp/control.dat? Also, would resolving the control points issue also resolve
the deleted voxels issue? Cause my it’s not redrawing the pia
Hi Champe
it must be in the tmp subdirectory (that is name>/tmp/control.dat) otherwise we will not find it.
As for the deleted voxel issue - how did you delete them?
Bruce
On Tue, 15 Mar 2016,
Champe Barton wrote:
I created them as instructed in the tutorial and called the file “control.da
What if all of the data have already been processed (recon -all) and I am
now just looking at the data and doing statistical analyses (QDEC, ROI
generation, etc)?
Thanks
On Tue, Mar 15, 2016 at 10:24 AM, Z K wrote:
> v5.3 is compatible with El Capitan. In general, we dissuade people from
> perf
Thanks!!
On Tue, Mar 15, 2016 at 10:50 AM, Z K wrote:
> That would be fine. The idea is to simply process (recon) all your
> subjetcs under the same OS version. Once that is complete, viewing the
> data, and post processing statistical analysis is perfectly fine on an
> upgraded/updated system.
Hi Doug,
I have two groups of subjects and I want to study the difference in cortical
thickness between the groups. I used Qdec to run the analysis and I got
significant difference between the groups in areas support what I am looking
for.
I repeated the analysis as mentioned in Wiki
https://su
That would be fine. The idea is to simply process (recon) all your
subjetcs under the same OS version. Once that is complete, viewing the
data, and post processing statistical analysis is perfectly fine on an
upgraded/updated system.
-Zeke
On 03/15/2016 01:47 PM, Elissa Ash wrote:
> What if a
this only has to do with the qcache part of recon-all, so you could use
version 5.3 recon-all -qcache and it should be fine. However, it is not
a good idea to try to publish using the analysis from the version of FS
that you used. That was a beta version of version 6 and things will change.
O
Still get the same error:
WARNING: file /Users/jasminalves/Desktop/data/40/00010001 does not contain
a Siemens ASCII header
has this file been anonymized?
ERROR: cannot unpack mosiacs without ASCII header
The error I get when running in nifti format is actually found in the log
file.
ERROR:
Dear Douglas,
Does it also affect the individual data analysis or the volumetric group
analysis, e.g. the files in the stats/ folder? So could I use the results
of these surface group analyses after running the "-qcache" on V5.3 then?
Thanks,
Kaiming
On 15 March 2016 at 18:00, Douglas N Greve
How was DTI.nii.gz created? What happens if you run
mri_info DTI.nii.gz
If the DICOM is a siemens dicom but has been stripped of special siemens
info, then we cannot unpack it
On 03/15/2016 02:02 PM, Jasmin Alves wrote:
>
> Still get the same error:
>
> WARNING: file /Users/jasminalves/Desktop
I used the recon editing tool—I explicitly followed the instructions from the
tutorial (even on reprocessing the tutorial data it didn't work), so I had the
brainmask.mgz highlighted, checked the recon editing box and held shift and
clicked to remove the necessary voxels (they turned black). I r
why are you deleting voxels from the brainmask.mgz? That is only used for
masking out non-brain tissue. Is that what you are trying to do?
On Tue, 15 Mar 2016, Champe Barton wrote:
I used the recon editing tool—I explicitly followed the instructions from the
tutorial (even on reprocessing the
How was DTI.nii.gz created? DTI.nii.gz was converted from the raw dicom
data using dcm2nii.
Response for: "What happens if you run mri_info DTI.nii.gz"
Volume information for DTI.nii.gz
type: nii
dimensions: 128 x 128 x 70 x 65
voxel sizes: 2., 2., 2.
t
Can you send the full terminal output from when you run dt_recon with
the nifti as input?
On 03/15/2016 03:07 PM, Jasmin Alves wrote:
> How was DTI.nii.gz created? DTI.nii.gz was converted from the raw
> dicom data using dcm2nii.
>
> Response for: "What happens if you run mri_info DTI.nii.gz"
>
Yes, the pial (and white, actually) surface is extending into an area where
there is no brain tissue. I'm not sure the anatomical name for it, but it's two
cavities, one in the lower half of either hemisphere, where there's no tissue
at all. When I process the dicom files I get really erratic su
as long as you move the file into the tmp dir recon-all should find it
and use it (search for control.dat in the recon-all.log after you have
run it).
I'm not sure what's going on with your brainmask.mgz though. You are
saying that there are voxels that are deleted (set to 1) in your
brainmas
Maybe you can draw the wm in? I wouldn't put control points there
> On Mar 15, 2016, at 9:13 AM, Allison Rainford
> wrote:
>
> Hi Bruce,
>
> I?ve attached a screen shot of a temporal pole of one of the brains that we
> have had issues with. Here the issue is that there is a lesion without a
>
oh duh! Sorry, wasn’t thinking clearly.
Okay, I see how to generate the betas now. I don’t even need to mess with the
mkcontrast-sess command.
I just run selxavg3-sess with the -no-con-ok flag.
With spmhrf 0 I generated a beta.nii.gz file with 85 betas in each vertex.
With spmhrf 1 I generated a
Jasmins-MacBook-Pro:40 jasminalves$ dt_recon --i DTI.nii.gz --s 40 --o
/Users/jasminalves/Desktop/data/FREESURFER/40
INFO: SUBJECTS_DIR is /Users/jasminalves/Desktop/data/FREESURFER/
dt_recon logfile
Tue Mar 15 20:37:35 PDT 2016
VERSION $Id: dt_recon,v 1.15 2011/01/25 21:53:04 greve Exp $
sete
Dear Freesurfer experts,
I'm trying to run mri_vol2vol on a functional mri to resample it onto
orig.mgz. I get this error:
```
mri_vol2vol(98217,0xa0ce01d4) malloc: *** mach_vm_map(size=262144) failed
(error code=3)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to de
Hi Ehsan
We need the full command line and screen output and also what your hardware and
software environments are to help you. Certainly sounds like you ran out of
memory though
Cheers
Bruce
> On Mar 15, 2016, at 11:41 PM, Ehsan Tadayon wrote:
>
> Ehsan
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