Dear freesurfer experts,
I was able to figure out the problem! I was not supposed to write the eTIV
values in my .dat.table which I did and for that reasons my continuous
factors were being read as 4 instead of 3.
Thanks and regards,
Sampada
AIIMS, Delhi
Dear Freesurfer experts,
Thanks for your valuable input. Since, comparison with global thickness
does not provide any valuable information we have decided to forego the
average thickness and lh-thickness comparison and now added eTIV as another
covariate with age
and
lh/rh thickess (
please
Dear Kalyan,
do you use standard pial surface reconstruction via T1 images, or optional pial
surface refinement with T2/FLAIR images?
I had similar problems with FLAIRpial surface refinement. The corrected pial
surface appeared jagged and some areas were artificially cut out (whereas they
Dear experts,
I came several times across the situation when pial surface from one hemisphere
is crossing the surface of other hemishpere (see the attached screenshot). Is
there any way how to correct for this error?
Regards,
Antonin Skoch___
Dear experts,
is here any way how to improve white surface estimation in situations when this
surface leaks from the brain to the outer non-brain structures? (See the
attached screenshot).
This problem consequently affects pial surface estimation, which is not
correctable by FLAIRpial
Dear Doug,
I am using the FSL-Freesurfer pipeline, with single subject analysis done in
Feat and group analysis done using mri_glmfit. Is there a way I can calculate
percent signal change from the group analysis output (or any other method which
combines single subject output)?
Many thanks,
can you run
register-sess -debug -s nmasa_031_130412 -d
/autofs/cluster/iaslab/NMASA/mri/func/encoding -fsd bold -dof 6 -per-run
-update | tee fordoug2.log
and send me fourdoug2.log
doug
On 7/24/15 10:22 AM, Morenikeji Adebayo wrote:
Hi there,
Attached is the log file from running:
what is your command line? What do you mean by one anatomy to another?
On 7/24/15 9:26 AM, Caspar M. Schwiedrzik wrote:
-- Forwarded message --
From: *Caspar M. Schwiedrzik* cschwie...@rockefeller.edu
mailto:cschwie...@rockefeller.edu
Date: Thursday, July 16, 2015
Subject:
I think there is something wrong with the contents of
/autofs/cluster/iaslab/NMASA/mri/func/encoding/nmasa_031_130412/subjectname
It looks like it is cd nmasa_031_130412, probably it should be
nmasa_031_130412 ?
On 7/24/15 11:58 AM, Morenikeji Adebayo wrote:
Hi Doug,
fordoug2 is attached.
I don't think this is possible with that command. If you know how to
program, you can write a loop that would easily do it.
doug
On 7/23/15 2:52 PM, Michele Cavallari wrote:
Hi, I would need to extract multiple labels from the aparc+aseg labelmap.
I am using the mri_extract_label command, but
Hi Doug,fordoug2 is attached.Thanks,Keji
fordoug2.log
Description: Binary data
On Jul 24, 2015, at 11:17 AM, Douglas Greve gr...@nmr.mgh.harvard.edu wrote:
can you run
register-sess -debug -s nmasa_031_130412 -d
/autofs/cluster/iaslab/NMASA/mri/func/encoding -fsd
It should be possible to write a program to do it, but you'd have to
know how to program.
On 7/24/15 8:12 AM, Thục Trinh wrote:
Hi,
In our experiment, one onset trial will be lasted for 12 seconds, but
if subject can give the answer sooner within 12 seconds, the next
offset trial (baseline)
Oh excellent, you are correct! I’ll update the file and try re-running selxavg.
Thanks,
Keji
On Jul 24, 2015, at 12:06 PM, Douglas Greve gr...@nmr.mgh.harvard.edu wrote:
I think there is something wrong with the contents of
For surface ROIs, you'll have to create a new annotation using
mris_divide_parcellation, the use mri_aparc2aseg to generate a new file
like aparc+aseg.mgz
doug
On 7/23/15 5:09 PM, joseph veliz wrote:
Hello FreeSurfer world,
We need to subdivide regions of the forebrain that FreeSurfer does
Hi there,Attached is the log file from running:preproc-sess -debug -s nmasa_031_130412 -fsd bold -stc up -surfacefsaverage lhrh -mni305 -fwhm 5 -per-run | tee fordoug.logI got more errors when I ran:preproc-sess -debug -s nmasa_031_130412 -fsd bold -stc up -surfacefsaverage lhrh -mni305 -fwhm 5
I don't know what is going on with that, but one thing you should do is
to normalize the eTIV (ie, remove it's mean and divide by the std dev).
Also, why are you including eTIV in the first place? Thickness does not
change with head size, only volume and surface area.
doug
On 7/24/15 2:34
You need to install development version of freeview. Instructions can be
found on this page in the Freeview dev version section:
https://surfer.nmr.mgh.harvard.edu/fswiki/Download
-Zeke
On 07/23/2015 12:57 PM, Gomar, Jesus wrote:
Hi Freesurfers,
We are trying to use the Recon Edit tool in
Dear Doug,
Thank you for the reply. I want to use the percent change in signal as a
measure of effect size for various regions of interest, so would ideally like
an average percent signal change in that ROI. I want it at the group data
though. Much appreciate your suggestions.
Many thanks,
Hi Joseph
if you have lots to get through you might be better off running two with 4
cores at a time. Speed increase is pretty good through 4 last time Nick
tested, but then the benefits fall off a bit
Bruce
On Fri, 24 Jul 2015, joseph veliz wrote:
What is the best set up to utilize the
What is the best set up to utilize the multicore capability of freesurfer?
Should we open a seperate terminal for each subject and run 3 simultaneous
recons with the -openmp 8, on each recon command line?
Or is there a more efficient way of utilizing 8 cores and 16 gb of memory?
thanks so much
what kind of percent output do you want? FSL does a global
normalization, effectively computing percent change (actually 10th of
percent change I think). If you want voxel-wise percent, then it is more
difficult.
On 7/24/15 11:11 AM, Mariam Sood wrote:
Dear Doug,
I am using the
you can use mri_morphometry and use the close operation to get rid of
some holes
On Sat, 25 Jul 2015, Liang Wang wrote:
Thanks Bruce. I applied mri_binarize to brainmask.mgz with specified threshold
and got many holes in the mask. In addition, brainmask.mgz includes the
cerebellum. I would
Sorry, I've lost track of what is going on here. How was
lh.amyg.faceaw_func.anatconstr.p05.5.3CRFH.n70.mgz
created?
On 7/23/15 12:08 PM, Barbour, Tracy,M.D. wrote:
Thank you Doug
I tried the way you suggested and the registration actually looks worse. I
also tried:
mri_label2vol
Hello,
I just wanted to follow-up on this request. If it is not possible to do these
things, that would also be helpful to know so I don’t continue to attempt
different variations of the options! If any more information is provided to
make the questions clearer, please let me know what you
so I should run one subject per 4 cores
by using -openmp 4 for each of the two subjects being re-conned
simultaneously?
On Fri, Jul 24, 2015 at 2:08 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:
Hi Joseph
if you have lots to get through you might be better off running two with 4
cores
Hi Antonin
that's a good point and something we probably need to fix.
Bruce
On Fri, 24 Jul
2015, Antonin Skoch wrote:
Dear Kalyan,
do you use standard pial surface reconstruction via T1 images, or optional
pial
surface refinement with T2/FLAIR images?
I had similar problems with
p.s. although in this case I think it won't hurt to always pass that
parameter since it is only used for the flair/pial stuff
On Fri, 24 Jul
2015, Antonin Skoch wrote:
Dear Kalyan,
do you use standard pial surface reconstruction via T1 images, or optional
pial
surface refinement with
Hi Antonin
not sure - if you upload the subject I'll take a look
Bruce
On Fri, 24 Jul 2015,
Antonin Skoch wrote:
Dear experts,
I came several times across the situation when pial surface from one
hemisphere
is crossing the surface of other hemishpere (see the attached screenshot). Is
Hi Antonin
I think that the current flair/pial stuff will correct small errors in
the wm placement, but this one is probably too large and is really a
skull stripping problem. Have you tried gcuts? If the dura is attached to
the wm then the mris_make_surfaces step will not usually fix it.
you could try binarizing the brainmask.mgz
cheers
Bruce
On Fri, 24 Jul
2015, Liang Wang wrote:
Hi folks,
I would like to create a brain outline based on the generated pial surface. This
outline will completely cover the whole cortex (ignoring gyrus and sulcus info)
and is treated as a brain
Hi Caspar
we tried to replicate this and couldn't. Can you upload the subject(s)
involved in this and send us the exact command line that shows the
problem?
cheers
Bruce
On Fri, 24 Jul 2015, Caspar M. Schwiedrzik wrote:
-- Forwarded message --
From: Caspar M. Schwiedrzik
yes, I guess so
On Fri, 24 Jul 2015, joseph veliz wrote:
We need to subdivide regions of the VentralDC that would carry onto the
aparc+aseg.mgz.
Would this involve just editing the aseg.mgz?
On Fri, Jul 24, 2015 at 9:27 AM, Douglas Greve gr...@nmr.mgh.harvard.edu
wrote:
For
That fixed it! Thanks for all your help - I appreciate it.
Keji
On Jul 24, 2015, at 12:17 PM, Morenikeji Adebayo k...@nmr.mgh.harvard.edu
wrote:
Oh excellent, you are correct! I’ll update the file and try re-running
selxavg.
Thanks,
Keji
On Jul 24, 2015, at 12:06 PM, Douglas Greve
We need to subdivide regions of the VentralDC that would carry onto the
aparc+aseg.mgz.
Would this involve just editing the aseg.mgz?
On Fri, Jul 24, 2015 at 9:27 AM, Douglas Greve gr...@nmr.mgh.harvard.edu
wrote:
For surface ROIs, you'll have to create a new annotation using
Thanks Bruce. I applied mri_binarize to brainmask.mgz with specified
threshold and got many holes in the mask. In addition, brainmask.mgz
includes the cerebellum. I would like to only create the brain (cerebral
cortex) outline based on the pial surface. Thanks.
Best,
Liang
--
Liang Wang, PhD
Hi Freesurfer Support,
I've seen this issue brought up in the message archives, but I haven't found a
solution yet.
When running the recon-all -localGI command, I get the following errors, which
result in the message: make_roi_paths did not complete successfully!
Error in dsearchn (line 79)
Hi folks,
I would like to create a brain outline based on the generated pial surface.
This outline will completely cover the whole cortex (ignoring gyrus and
sulcus info) and is treated as a brain outer surface on which some values
in the brain could be projected. I tried mris_expand, but it
Hi Thuc,
For similar reasons, I program all of my stimulus programs to write a
par file for each run. I recommend you program your stimulus program
to do the same.
HTH
D
On Fri, Jul 24, 2015 at 8:12 AM, Thục Trinh thuctrinh...@gmail.com wrote:
Hi,
In our experiment, one onset trial will be
Yes. That is correct.
On Jul 24, 2015, at 7:06 PM, joseph veliz josephveli...@gmail.com wrote:
so I should run one subject per 4 cores
by using -openmp 4 for each of the two subjects being re-conned
simultaneously?
On Fri, Jul 24, 2015 at 2:08 PM, Bruce Fischl
Hi,
In our experiment, one onset trial will be lasted for 12 seconds, but if
subject can give the answer sooner within 12 seconds, the next offset trial
(baseline) will come up. The response time will be recorded.
So if I have 100 subjects, I have to create 100 paradigm files manually. It
will
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