Hi Freesurfers,
I want to do a PPI in FSL FEAT using the V1 left and righ found
generated in recon-all as seeds using:
I know for each subject I have to get a timecourse for my seeds
fslmeants -i filtered_func.nii.gz -o my_timecourse.txt -m V1_mask.nii.gz
For each subject, I've run reg-feat2anat
Dear Freesurfers,
could you please give me detailed information about the Bonferroni or
clusterwise correction we can do in Freesurfer? How much iterations? Is that
cluster- oder voxelwise? Is there anywhere a detailed description about the
correction options?
Best regards,
Viola
Dear all,
I ran mkanalysis-sess (mkanalysis-sess -analysis junk -TR 2 -paradigm
para01.para -event-related -funcstem fmc -nconditions 3 -runlistfile
runlist_odd -fsd bold -fir 10 30 -native) but it did't not generate
analysis.cfg. The only file I can see after running this is analysis.info.
When
Dear Ms. Kakunoori,
sorry to bother you again, but as I did not get a reply to my last message to
everyone so far troubled with my question, I am trying here for a second time.
It is indeed the case, that all my data were scanned with a 3T. And if that is
indeed the problem Dr. Snyder figured
Good morning Doug,
I tried running the -sim on my QDEC output (as you recommended me last days)
but for some data the FDR gives me error (cannot calculate clusters statistics)
so mri_glmfit-sim is not working either since the corrections by multiple
comparisons is not working. What should I do
Hi Bruce, Nick Doug:
How does Folding index differ from Gyrification index?
thanks,
Alan
BIDMC
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The information in this e-mail
Hi Michelle, this almost surely means that the surfaces are
out-of-synch. You can try
recon-all -s subject -make all -dontrun
on one of your subjects.
If everything is in synch, then it should print
make: Nothing to be done for `all'.
If not, it should print out the steps that it would have
Michelle Umali wrote:
Hi Freesurfers,
I want to do a PPI in FSL FEAT using the V1 left and righ found
generated in recon-all as seeds using:
I know for each subject I have to get a timecourse for my seeds
fslmeants -i filtered_func.nii.gz -o my_timecourse.txt -m V1_mask.nii.gz
For each
Hello list,
Following this email that I found in the archives:
(...)
For the segmentation, FS still works voxelwise, but it's objective is
to identify each structure as a whole, whereas SPM and FSL/FAST
attempt to classify each voxel as being GM, WM or CSF. A short
description of the
Hi Viola,
there's some detailed info if you run
mri_glmfit-sim --help
mri_glmfit --help
mri_glmfit-sim runs mri_glmfit.
When you use mri_glmfit-sim with the --cache option, it uses simulations
that are based on 10,000 iterations.
Here are some slides that give more detail
The 5.X version does not produce a cfg anymore, so everything is ok. You
cannot use older versions of mkanalysis-sess with 5.X
doug
Po-Jang (Brown) Hsieh wrote:
Dear all,
I ran mkanalysis-sess (mkanalysis-sess -analysis junk -TR 2 -paradigm
para01.para -event-related -funcstem fmc
Hi Andreia
you could certainly change our segmentation labels to just these 3 classes
easily enough in matlab. Then we have tools for computing partial volume
fractions (I think mri_compute_volume_fractions)
cheers
Bruce
On Wed, 28 Sep 2011, _andre...@sapo.pt wrote:
Hello list,
Following
Dear Doug,
Thanks very much! But without analysis.cfg, I cannot run selxave-sess... Am
I missing something here?
Brown
On Wed, Sep 28, 2011 at 11:36 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu
wrote:
The 5.X version does not produce a cfg anymore, so everything is ok. You
cannot use older
mri_compute_volume_fractions will compute the fractions for each of the tissue
types, no need to alter the segmentations.
doug
Bruce Fischl wrote:
Hi Andreia
you could certainly change our segmentation labels to just these 3 classes
easily enough in matlab. Then we have tools for
Hi Brown, you should not be mixing versions. There is no selxavg-sess in
5.X. The new version is selxavg3-sess.
doug
Po-Jang (Brown) Hsieh wrote:
Dear Doug,
Thanks very much! But without analysis.cfg, I cannot run
selxave-sess... Am I missing something here?
Brown
On Wed, Sep 28, 2011
have a look at this page:
https://surfer.nmr.mgh.harvard.edu/fswiki/LGI
folding index is typically a single number summarizing the amount of
folding overall on a surface. freesurfer puts these measures in
subjid/stats/?h.curv.stats.
gyrification index is a new method created by maria schaer to
thanks nick.
tried with 5.1.0 same issue. here is the output from glxgears.
$ glxgears
Error: couldn't get an RGB, Double-buffered visual
i am beginning to suspect it as a driver issue.
cheers,
satra
On Wed, Sep 28, 2011 at 11:17 AM, Nick Schmansky
ni...@nmr.mgh.harvard.eduwrote:
i'm able
its a shot in the dark, but you could try updating the mac with XQuartz,
which seems to be much better for X stuff than the default X
installation. doing so is a necessity for running freesurfer locally on
the mac:
https://surfer.nmr.mgh.harvard.edu/fswiki/MacTksurfer
that page fixes a
What does FDR have to do with it? FDR should not come into play in this.
doug
Antonella Kis wrote:
Good morning Doug,
I tried running the -sim on my QDEC output (as you recommended me last
days) but for some data the FDR gives me error (cannot calculate
clusters statistics) so
Good afternoon,
I tried running the -sim on my QDEC output (as recommended last days) but for
some data the FDR gives me error (cannot calculate clusters statistics) so
mri_glmfit-sim is not working either since the corrections by multiple
comparisons is not working. What should I do in
Thanks Bruce and Douglas!
Andreia
Citando Douglas N Greve gr...@nmr.mgh.harvard.edu:
mri_compute_volume_fractions will compute the fractions for each of
the tissue types, no need to alter the segmentations.
doug
Bruce Fischl wrote:
Hi Andreia
you could certainly change our
again, FDR should have nothing to do with it. If you want a voxel-wise
threshold at 2, just set that threshold when you run mri_glmfit-sim with
--cache 2 sign where sign is pos, neg, or abs
doug
Antonella Kis wrote:
Hi Doug,
Thanks again for helping. I am trying to use QDEC but there are no
My understanding is that GI is also a global summary stat across the whole hem,
while lGI is *local* GI (vertex-wise). It measures how folded the cortex is at
that vertex. GI and lGI are based on area, while the folding index is based on
curvature. Truly different measures.
Gyrification
Correction: FI = Sum-over-vertices[ |kmax|(|kmax|-|kmin|)]/SurfaceArea
On Sep 28, 2011, at 1:38 PM, Donna Dierker wrote:
My understanding is that GI is also a global summary stat across the whole
hem, while lGI is *local* GI (vertex-wise). It measures how folded the
cortex is at that
*By default, FreeSurfer compputes and uses a two-tailed p-value. When
you specify a sign, it lowers the threshold that you give it to reflect
a one-tailed test. Probably what happened was that you had two clusters
close to each other that merged together with the lower threshold.
doug
*
No, unfortunately not.
doug
jm wrote:
Doug:
I have processed 20 subjects. By mistake, five of them with LAS
orientation and 15 RAS orientation.RAS that's right in my case.
I could change name of files in '/surf' folder from left to right in the
first ones? or I need do it over? for
Dear Doug and the Freesurfers,
Ok, so is there a special filtered_func.nii generated from reg-feat2anat for
each run or can I just use the feat?
When one does a cross-subject PPI in FSL and enter each run from each
person, isn't everyone in a different space? How do you account for this
when
Michelle Umali wrote:
Dear Doug and the Freesurfers,
Ok, so is there a special filtered_func.nii generated from
reg-feat2anat for each run or can I just use the feat?
No, just use the FEAT one.
When one does a cross-subject PPI in FSL and enter each run from each
person, isn't everyone
Hi,
Each time I have run recon-all on our subjects, I end up with the same slew of
error messages underneath Computing MAP estimate using [x number of] samples
and underneath EM alignment process:
IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR
RETURN OF LINE SEARCH:
The change in threshold is always 0.3. Eg, to go from a two-tailed
threshold of 2.0 to a one-tailed threshold, you would subtract .3 from
2.0 (and so 1.7). Is this what you mean?
Antonella Kis wrote:
I see. Is there a way that I can get/read both clusters sin other
words can I eliminate this
Oh, sorry, I precompute the tables with certain fixed voxel-wise
thresholds. But it seems like you may want to use 2.3. Why 1.7? If you
want it to match what you see in QDEC at a threshold of 2.0, then you
should spec 2.3.
Antonella Kis wrote:
I am not sure but I tried that and it gives me
the IFLAG messages can be ignored if mri_em_register is not exiting with
error. which command is running that is exiting with error? can you
send that command line from the recon-all.log file?
n.
On Wed, 2011-09-28 at 16:02 -0400, Warren Winter wrote:
Hi,
Each time I have run recon-all
Hi Maria
have you tried running without the talairach stuff? Try -notalairach and
see if it works for you
cheers
Bruce
On Wed, 28 Sep 2011, Maria Felber wrote:
Dear Ms. Kakunoori,
sorry to bother you again, but as I did not get a reply to my last message to
everyone so far troubled with
Hey Doug and Freesurfers,
At the bottom is the output showing what steps didn't run.
1) Do you think I did the whole recon-all pipeline wrong? Here's what i did
after I originally ran recon-all -all -label_v1:
I made edits with talairach registration edits with tkregister2 and ran
recon-all
you could also try:
-talairach -use-mritotal
which will use an alternate talarairch alignment scheme (from the MNI).
it sometimes works better (not necessary for 3T).
you should also probably add:
-nuintensitycor-3T
to the end of your recon-all command, which will run the nu_correct
stage
Dear Experts,
I noticed that the inferior horn of the lateral ventricles are not included
within the pial surface while the posterior lateral ventricles are and wonder
how one should go about when making corrections for the pial surface. This was
observed in the subjects that I have worked
Hi Vy,
no, it shouldn't. The pial surfaces are not trustworthy near the
hippocampus, and we don't use them there.
Bruce
On Wed, 28 Sep 2011, Vy Dinh wrote:
Dear Experts,
I noticed that the inferior horn of the lateral ventricles are not included
within the pial surface while the posterior
The gcareg step depends on the talairach registration, so if that is
changed, it thinks that the gcareg needs to change. If the gcareg needs
to change, then the canorm needs to change, and so on. This does not
mean that anything really needs to be updated. This is strictly looking
at the time
Hi Doug and Freesurfers,
I ran the -vno-check and the number of vertices matches for left and right
hemispheres (see below):
Since all there are an equal number of vertices, how is the mismatch error
occurring in fieldsign-sess and how do I get it to run?
Thanks for all your help.
Michelle
Hi Anastasia,
I've tried both options, the choice 1 fixed some of the cases, but
not all; and the choice 2 did not work at all. Maybe I've missed
something here.
Few more questions:
1. Will the initial points have to include the points around start,
way, and end points of the tracts need to be
Hi Ping - You can upload your data if you want me to take a look at it.
1. The initial points ideally should be along the midline of the pathway,
starting from one end region of the pathway and going all the way to the
other end region. (The default number is 5 control points but you can set
Thank you for the swift response Bruce.
Vy T.U. Dinh
Research Assistant, Neurological Sciences
Rush University Medical Center
Phone: (312) 563-3853
Fax: (312) 563-4660
Email: vy_d...@rush.edu
From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent:
the log does not indicate that mri_em_register exited with an error. it
appears that it produced its output correctly and continued through to
nearly the end of the stream. the IFLAG messages can be ignored.
the log indicates that mri_label2label is exiting with an error when
trying to load the
Hi Anastasia,
Thanks so much for your message. You were right about the recon directory,
the contents had been accidentally moved elsewhere (sorry!) and once I moved
them back and reran the script everything worked like a charm without any
errors. However, it looks like I'm now stuck at the next
Hi Ansgar - Most likely everything is fine. Sometimes the script that's
built into bedpost to monitor its progress gives this error but in fact
everything has ran fine. You should check that all the outputs are there
in the dmri.bedpostX directory. See for list of bedpost output files:
Dear Freesurfers,
I wanted to generate binary masks for areas found in the Freesurfer Color
Lookup Table.
For example, I wanted to use number 433, the Visual_V3d_l. I tried to use
aseg2feat -feat featdir --aseg aparc+aseg
fslmaths -featdir/reg/freesurfer/aparc+aseg.nii.gz -thr 433v uthr 433 \
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