Dear Sira
Using the same scanner we developed this sequence for Freesurfer analysis
BRAVO: TR=9.2 ms; TE = 3.7 ms; flip angle 12°; FOV = 25.6 cm; preparation
time= 650 ms; slice thickness= 1 mm; Bandwith= 25.
Running time: 5 min, 32 sec.
that's an awfully short TR. Not sure how good the SNR is for the 8
channel, but that might be noisy. We also try to shorten the TE if we
can, although you might not be able to. There is an ADNI mprage the
exists on the GE platforms, although I'm not sure you're allowed to run
it. It's a
Hello All,
Looking at aparc+aseg of some subjects we see some regions of the
cortex labeled as unknown especially in the medial region / temporal
lobe, close to amygdala. Additionally, around these regions there are
some regions of the cortex that are not labeled at all. We see this on
images
Hi freesurfers,
I just got this error while continuing processing of a subject:
mri_average:
MRIread(/PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-25287/cor-2.img)
failed
Linux titan 2.6.18-128.el5 #1 SMP Wed Dec 17 11:41:38 EST 2008
mapping the time courses to the average subject does not solve this
problem, it just hides it. I'm not sure why this would be of a concern
anyway. There might be a tiny difference in the expected variance for
each subject, but, unless the region is very small, the differences
won't amount for
is that disk full?
doug
aekai...@umich.edu wrote:
Hi freesurfers,
I just got this error while continuing processing of a subject:
mri_average:
MRIread(/PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-25287/cor-2.img)
failed
Linux
Are the inputs (001.mgz and 002.mgz) the same size? They have slightly
different acquisition parameters, which is not a good sign ...
aekai...@umich.edu wrote:
Hi again,
The disk is not full and attached is the recon-all.log
best,
Anson K.
University of Michigan
On Mon, 19 Jul 2010
Hello,
Thank you both very much, I will definitely try these parameters next time I
get development
time on the scanner, and re-investigate the ADNI T1 sequence. Last time we
tried it,
I think the scans were on the order of 9 minutes, which just won't work with
these
particular
Dear Doug,
Thanks. According to your suggestions, I would extract fmri time course from
an individual paracellation with subcortical regions (e.g. caudate,
thalamus...). Would you like to help me to make sure whether the following
commands are correct. Here the filtered_fun_data.nii.gz did not be
Hi Aize,
these are not cortical regions (looks like hippocampus and amygdala) so
you should be fine.
cheers
Bruce
On Tue, 20 Jul 2010, caoaize wrote:
Hello Bruce,
Thanks for your reply. I attached a slice of the image here. The problem areas
are highlighted by blue circle. It seems
Hi,
I want to turn a fsaverage-label (lh.DLPFC.label) into a mask (nifti) in MNI
space and used these two commands:
1) To turn the label into a volume (within $SUBJECTS_DIR):
mri_label2vol --label lh.DLPFC.label --subject fsaverage --temp
./fsaverage/mri/brainmask.mgz --o
That looks right, though mri_segstats might want a summary file. If so
, just added --sum junk
doug
liang wang wrote:
Dear Doug,
Thanks. According to your suggestions, I would extract fmri time
course from an individual paracellation with subcortical regions (e.g.
caudate, thalamus...).
Does left_DLPFC_july19b.nii.gz look ok on the fsaverage brain?
The target for the mni152.register.dat is the FSL mni152, so it should
work. YOu can check it with
tkregister2 --mov /fsl/4.1.4/data/standard/MNI152_T1_2mm.nii.gz --reg
mni152.register.dat
doug
Esther Walton wrote:
Hi,
I
Hi,
I'm trying to create a ROI of V1 from the labels (for each hemisphere)
I defined.
I was able to create an volume with the command below
mri_label2vol --label $SUBJ/label/lh.v1.ali.label --label
$SUBJ/label/rh.v1.ali.label --temp $SUBJ/mri/T1.mgz --reg
$SUBJ/stats/register.dat --fillthresh
A few pointers:
1. Try using a fill threshold of 0 (this will take any label point that
is in the label. setting the fill thresh to 0.5 means that a voxel needs
to be filled half way to be considered for the ROI).
2. I would suggest using nii or mgz as an output format (we have not
used
Dear Freesurfer Experts,
When in the process of analyzing grey matter volumes, I have found that the
totals from the summing of the lh.aparc.stats and rh.aparc.stats do not
match with the total grey matter volume found from the mris_anatmoical_stats
command.
Does anyone know which value
Hi Experts,
Is there any reason one should not generate the 2009 Destriuex parcellation
for brains that were recon-ned with earlier versions of Freesurfer? (ie
using recon-all with -cortparc2 and -parcstats2 while in the 4.5
environment) Thanks!
Cheers,
Mike
Hi Mike,
the registration algorithm has probably changed a bit, so the
parcellation would be suboptimal. You probably want to rerun the
registration to recreate the sphere.reg before running cortparc2.
cheers
Bruce
On Mon, 19 Jul 2010, Michael Waskom wrote:
Hi Experts,
Is there any
Dear Doug,
Thanks for your prompted answer, but I have another question about this.
When I read the paper Kuperberg et al., Arch Gen Psychiatry 2003;60:878-888,
I understand that in this paper, the authors computed the averaged surface.
They then extracted ROIs from the average data and
Hello,
I would like to be able to do 3-way anova in qdec, freesurfer version 4.3.1
and measure the cortical thickness and volume. Is this possible? I have 3
discrete factors, each with two levels:
age group: less/more than 50
HIV: yes/no
Alzheimers: yes/no
When I try to click on the third
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