OK, got it (finally). I would not expect the answers to be identical,
but I would expect them to be "close". How close are they? If the ROI
is very small, there might be appreciable differences between the two.
doug
On 9/27/12 6:26 PM, Garikoitz Lerma-Usabiaga wrote:
Hi,
You are right, th
Hi,
You are right, this was one of the methods. The second one is as follows (I
copy the repeated steps):
For a given ROI, you have a nifti file (roi.nii) in 2mm space defined on
colin27. This ROI volume has a voxel value == 1 if it is in the ROI or 0 if
it is out.
You have a registration betwee
Hi Martin,
Each subject has 3-6 timepoints. They are all about one year apart.
Here's an example of the discrepancy: one subject with 5 timepoints had
volumes that ranged from 2.2-2.4. However, from the long_mris_slopes
command, the temporal average volume was calculated to be 1.67. Thanks for
yo
Hi Rachel,
Here are instructions for editing the aseg in tkmedit, it can also be done
using Freeview. Be sure to run mri_segstats again when you're done
editing.
https://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide/TkMeditWorkingWithData/TkMeditSegmentations#Editing
Alternatively, if the e
Thank you very much Bruce!
it's working.
2012/9/27 Bruce Fischl
> no, it represent the name of the folder that FS will create to put the
> results of the analysis in. The -i should be the full path to one file in
> the correct (T1-weighted) dicom series
>
> On Thu, 27 Sep 2012, pietro de rossi w
no, it represent the name of the folder that FS will create to put the
results of the analysis in. The -i should be the full path to one file in
the correct (T1-weighted) dicom series
On Thu, 27 Sep 2012, pietro de rossi
wrote:
sorry, I didn't realize I hadn't replied to the whole list :-)
so
sorry, I didn't realize I hadn't replied to the whole list :-)
so this
recon-all -i -s
-all
is the command for the whole pipeline if I understand correctly does
represents the folder where the dcm files are?
sorry for bothering again..
2012/9/27 Bruce Fischl
> can you cc the list on t
We'd like to obtain total cerebellar volumes. There are errors within the
cerebellar segmentation as revealed in the aseg.mgz file. Is there a
method to manually edit the cerebellar segmentation?
Thank You,
Rachel Steinhorn
___
Freesurfer mailing list
Hi Pietro
what was your recon-all command line? You need to specify different
subject identifiers (-s ) for the different datasets
Bruce
On
Thu, 27 Sep 2012, pietro de rossi wrote:
Hi Freesurfers,
I have another quintessentially beginner's problem
I ran 5 scans through the entire pipe
Hi Freesurfers,
I have another quintessentially beginner's problem
I ran 5 scans through the entire pipeline (-autorecon1 -autorecon2 and
-autorecon2 -autorecon-3)
when I check the output going
tksurfer [name_of_folder_with_dcm_files] rh (or lh) inflated
and then
tkmedit [name_of_folder_w
Can you please send the original bvals and bvecs files (the ones that you
specify in the configuration file), and the configuration file itself?
Thanks!
a.y
On Thu, 27 Sep 2012, Loi wrote:
> Hello,
>
> I generate the files in Linux (using gedit) and they look normal (I
> have compared them to
Hello,
I generate the files in Linux (using gedit) and they look normal (I
have compared them to the files in the tutorial).
So far I have tried ending both with and without .txt, transposing the
files, changing to equal number of decimals and adding 'setenv LC_ALL
en_US' to the .tchsrc file.
Th
Hi Joy - How were your bvecs and bvals files generated? In the past some
people have had problems with files exported from Excel b/c it generates
text files with Windows-specific end-of-line characters that cannot be
read properly on Linux. Do the files look normal when you run "more" on
them
Hi Rashimi,
please read
http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits
it should explain everything.
The clean way would be to edit the brainmask in the cross sectional
runs, complete them, run the base and the longs. Optimally no edits
should be necessary in the base and longs if cr
Hi Rashmi,
When posting questions to the list, send them only to
freesurfer@nmr.mgh.harvard.edu. Your email address is still subscribed
and is not blocked from posting to the FS list.
-Louis
On Thu, 27 Sep 2012, Rashmi Singh wrote:
> Well,
> Correct me if I am doing something wrong while posti
Hi Gabor - Tracula doesn't use the BA labels, only the labels in the
aparc+aseg. I hope this answers your question.
a.y
On Sun, 16 Sep 2012, Gabor Perlaki wrote:
> Dear Anastasia,
>
> Earlier I was posted an issue about BA44/pars triangular:
> http://www.mail-archive.com/freesurfer@nmr.mgh.har
Hi Clare - Sorry for responding late to any email that was sent while I
was away.
The fmajor and slft are sometimes tricky in their initialization b/c of
their high curvature. The initial guess for the path is chosen from the
atlas and if it's not well-aligned and veers off the subject's whi
Well,
Correct me if I am doing something wrong while posting my emails.
Whenever I post my emails to freesurfer-requ...@nmr.mgh.harvard.edu my
emails bounces.
So today I emailed my post to Bruce's email,
freesurfer@nmr.mgh.harvard.edu and freesurfer-requ...@nmr.mgh.harvard.edu.
I got a bounce repl
Hi Allison,
with very large changes across time, the longitudinal stream can fail or
may need more manual intervention (edits). We have run it successfully
on Huntington's Disease patients with large changes and many time
points. The only way to find out if it works on your data is to run it.
I h
Hi Akvile - Sorry for the late response, I was out of town for a bit.
At first glance it looks like all the tracts are stuck where they're
initialized. This might happen occasionally for a tract if initializing it
is tricky (i.e., if the subject is not well aligned to the atlas, if the
brain
Hi Shannon,
long_mris_slopes works for surface maps (both thickness and volume
should work). In both cases it should compute the temporal average.
I have another scripts that works for stats files (long_stats_slopes) in
the same way.
How many time points do you have, how far apart (equally spac
Hi Juke - I apologize for the late response. I was away and I'm still
catching up on email.
It looks like it fails while it's loading the atlas data (here the 4th out
of 33 atlas subjects). Does this happen in other cases? Are the cases that
fail running on a machine with less memory than th
Hello,
I am new to DTI analysis and I am trying to follow up the manual. I have 2
questions:
1) I cannot find any data related to CVS space in the $FREESURFER_HOME/subjects
Can you please help me find or get the "cvs_avg35/mri/norm.mgz"? Currently, I
am using FreeSurfure 5.1 on Linux, is CVS
Hello FreeSurfer expets,
Our study requires our subjects to be scanned 3-4 times and then I use
FreeSurfer Tool to generate their voulumetrics. Since I do several time
points on a subjects also perform the longitudinal runs and then take the
volumetrics information from longitudinal run output fo
Hi Ed, when I created the cache, I only went up to 30mm FWHM thinking
that no one would ever go above it, or maybe should never go above it. I
can create tables at higher smoothing levels, but 34mm is a lot of
smoothing. How much did you apply to the data?
doug
On 09/27/2012 05:48 AM, Ed Gronen
Hello,
I am using the longitudinal processing stream to analyze a data set. I
have two questions:
1: We are expecting there to be significant changes in the volume of
certain structures and gray matter between time point 1 and 2. We
wanted to make sure the longitudinal stream is still appro
You need a \ at the end of the 2nd line
Cheers
Bruce
On Sep 27, 2012, at 7:42 AM, yawu Liu wrote:
> Hi Experts,
> I have baseline and followup MRI data, when I run
> "recon-all -s AndiS \
>-i /home/d4201z/Desktop/fs/1/18991230_00anonymouss002a1001.nii
>
>
>-i /home/d4201z/Desk
Hi Experts,
I have baseline and followup MRI data, when I run"recon-all -s AndiS \
-i /home/d4201z/Desktop/fs/1/18991230_00anonymouss002a1001.nii
-i /home/d4201z/Desktop/fs/2/18991230_00anonymouss004a1001.nii"
Only the first dataset(baseline) were processed with out any proble
Hi,
I want to apply a cluster correction with mri_glmfit-sim with
the --cache option:
mri_glmfit-sim --glmdir my_glmdir --cache 1.3 abs
It fails with the error message that it can't find the file:
FSDir/average/mult-comp-cor/fsaverage/lh/cortex/fwhm34/abs/th1.3/mc-
z.csd
(FSDir is the directo
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