Dear All,
I am having a total of 100 subjects for my analysis.
My aim is to seperate DLPFC by making coronal cuts.
I know the procedure to do for single subjects.
Can anyone help me with the command line for mutiple data sets..?
Any help will be greatly appreciated..
Dear FS experts,
I have runned my xHemi analysis with FSv5.1, but you sent me the updates for
this aproach when the FSv5.2 was available, does the xHemi analyses are
affected by this thickness and area measures problem?
Kind Regards,
Gabriel
___
what xhemi analysis are you running?
Bruce
On Thu, 23 May 2013, Gabriel Gonzalez
Escamilla wrote:
Dear FS experts,
I have runned my xHemi analysis with FSv5.1, but you sent me the updates for
this aproach when the FSv5.2 was available, does the xHemi analyses are
affected by this thickness
Hi Cathy,
please cc the freesurfer list when replying, so that other people can
profit from or contribute to the discussion.
(Maybe someone else can comment on the transfer of edits in cross
processing between versions 5.0.5.3 ??)
So your cross data is processed with a mix of version 5
Hi Akio,
The ribbon.mgz is created in autorecon3, just before the segstats step.
So you will have to also run autorecon3. Since you have already run
autorecon1 and 2 you will just need to run something like:
recon-all -autorecon3 -s subjID
Sorry for the confusion.
-Louis
On Thu, 23 May 2013,
Dear Bruce,
we have the same problem as Yasheng's so we would like to know how to solve
it.
To answer what you ask Yasheng: it intersects two faces, but what do you meant
with native (binary) format?
Thank you a lot.
Best regards,
Maria Carla e Gabriele
Hi Yasheng,
hmmm, there is
Hi Tina
how did you create it? If the vertex indices are -1 it means they are not
assigned, and when you load it into tksurfer it will sample them onto the
surface. You can then save it it will write the new vertex numbers into the
label file.
Not sure about the offset though.
Bruce
On
I generated the labeling file from the corresponding numbers in base file. The
ctx-rh-bankssts was generated from mris_annotation2label with input -a2005.
This is the file with -1 vertex numbers.
In theory these files should be the same.
On May 23, 2013, at 10:28 AM, Bruce Fischl
what was your command line?rh.ctx-rh-bankssts.label is not a file name
that would have been created by mri_annotation2label (and bankssts is
not in the 2005 atlas). Are you sure it was not created by
mri_label2label? That can create vertex number with -1 if the volume
method is used.
doug
On
Hi Gabriel, the xhemi analysis uses thickness, volume, and/or area and
so will be affected by the problems with 5.2
doug
On 05/23/2013 05:07 AM, Gabriel Gonzalez Escamilla wrote:
Dear FS experts,
I have runned my xHemi analysis with FSv5.1, but you sent me the
updates for this aproach when
hmmm, then I would have thought that they would have vertex indices =0.
Maybe Doug knows?
On Thu, 23 May 2013, Tina Jeon wrote:
I generated the labeling file from the corresponding numbers in base file. The
ctx-rh-bankssts was generated from mris_annotation2label with input -a2005.
This is
Hi Yongxia, You need to add the matlab binary into your path.
doug
On 05/22/2013 09:26 PM, Yongxia Zhou wrote:
Hi,
I have a question running fsfast in my Mac,
The mkcontrast command gave the error of can not launch matlab.
Could you please let me know how to solve this problem.
Thank you
or mris_calc, which is probably better for this app
doug
On 05/22/2013 10:43 PM, Thomas Yeo wrote:
you can probably use fscalc.fsl. Type fscalc.fsl --help for more
information.
--Thomas
On Thu, May 23, 2013 at 9:26 AM, Minjie Wu minji...@gmail.com wrote:
Hello All,
Is there any way in
1) BEST FITNESS (M) is 984.24263
mri =0.000 curv = 4.318 unmri = -1001.515
( f=0.00 , v=0.00 , c=4.32 , q= 8.64 )
( f=0.00 , v=0.00 , c=4.32 , q= 8.64 )
63 patches have been generated - 38 self-intersected
max face = 36973(40653) - loop = 46 (73) -
Hi Sudhin
this is fixed in more recent versions. We can send you an updated
mris_topo_fixer if you don't want to upgrade everything - just tell us
your hardware/software environment.
cheers
Bruce
On Thu, 23 May 2013, Sudhin A. Shah
wrote:
1) BEST FITNESS (M) is 984.24263
mri
Hello Experts,
I am trying to run the mri_convert command prior to the
recon-all command on Siemens T1 dicoms (as suggested in the archives). I am
using freesurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.0, Mac OS X
Lion 10.7.5
I am using the command below:
mri_convert -it
has this file been anonymized?
On 05/23/2013 12:39 PM, Cat Chong wrote:
Hello Experts,
I am trying to run the mri_convert command prior to the recon-all
command on Siemens T1 dicoms (as suggested in the archives). I am
using freesurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.0,
Mac
Is it straight off the scanner? It does not have the siemens ascii
header which usually means that it has been manipulated in some way. You
can try using mri_convert with --it dicom
doug
On 05/23/2013 12:57 PM, Cat Chong wrote:
no it has not.
Hello FreeSurfer experts,
I just ran smoothing on a single 2D EPI image with a binary mask (that
excludes NaN vertices), but it didn't seem work out well as the output
image (e.g., test.mgh) contains zero values throughout vertices.
Also, I've got two warning messages (see below): while one of
Hi list,
how can I use qdec to investigate the difference among groups regarding the
measures contained in .stats file (for example thalamic volume)?
Thanks,
Stefano ___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
The second error just means that it cannot compute the fwhm. This will
go away if you add --smoooth-only.
On 05/23/2013 01:31 PM, Glen Lee wrote:
Hello FreeSurfer experts,
I just ran smoothing on a single 2D EPI image with a binary mask (that
excludes NaN vertices), but it didn't seem work
you can't. qdec only computes stats on surfaceoverlays.
On 05/23/2013 01:49 PM, std...@virgilio.it wrote:
Hi list,
how can I use qdec to investigate the difference among groups
regarding the measures contained in .stats file (for example thalamic
volume)?
Thanks,
Stefano
Hi Clelia,
If this is in a new terminal then you'll have to source freesurfer again.
See here for details:
https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration
-Louis
On Wed, 22 May 2013, clelia pellicano wrote:
Hi,
I have run recon-all -s bert -all to try my installation and it
Thanks Doug.
Yes, it works well now!
-Glen
On Thu, May 23, 2013 at 1:50 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:
The second error just means that it cannot compute the fwhm. This will
go away if you add --smoooth-only.
On 05/23/2013 01:31 PM, Glen Lee wrote:
Hello FreeSurfer
Hi!
I am trying to do a conjunction analysis using mri_concat --conjunct
with 2 to three sig.nii as input.
It seems to me that the resulting map is what Nichols et al. refer to
as MS/GN, i.e., a test against the global null (at least one effect).
Is that correct, and does that depends on v4.5 /
Sorry, that read gender and age. The contrast takes age into account, it
is just a problem with the code that generates the sentence.
Have not had a chance to answer the others, I thought I'd try to get one
wrapped up. It looks like you added a few more questions at the end.
Unless they are
Hi Caspar, I think the 4.x should be the same as 5.x. I'm not sure about
your fsfast question. There is nothing to automatically do it (ie,
you'll need to run mri_concat)
doug
On 05/23/2013 03:06 PM, Caspar M. Schwiedrzik wrote:
Hi!
I am trying to do a conjunction analysis using mri_concat
Just reporting a GUI bug in QDEC: after setting a different FDR threshold
and pressing the Set Using FDR button, more often than not the results
image doesn’t change accordingly. I noticed that the button only has an
effect after moving around the QDEC window and/or waiting a minute or so.
Hope
Hello,
I was wondering whether someone could please explain exactly how values are
assigned to each column of the design matrix, when a C.dat contrast vector
(e.g. [0, 0, 1, -1]) is created, in the correlation as opposed to in the
intercept types of contrasts ...
I am asking this because I have
Are you sure it is actually changing the threshold? Oftentimes changing
the FDR will not change the threhsold because it is already at its
maximum. If you look in the terminal window you should see something
like this:
MRISfdr2vwth(): np = 163842, nv = 163842, fdr = 0.2, vwth=4.60487
Found 0
Hi Anastasia,
I'm re-running tracula by using new version 5.3.
In the step 3 (trac-all -inter -c $FREESURFER_HOME/configurazion_file) I have
this error:
MRISregister() return, current seed 0writing registered surface to
Dear Doug
Yes, the data is straight off the scanner, I don't think it has been
manipulated, but I will check.
When I run the the command suggested I get the below error message:
mri_convert –it dicom -ot mgz 1002/IM-0001-0001.dcm 1002.mgz
mri_convert –it dicom -ot mgz 1002/IM-0001-0001.dcm
Dear Experts,
I am able to to initiate recon-all but it fails at various stages during the
recon-all process even though I should have plenty memory available to run the
process.
This is the error message I am getting and below is the log file. I am using
the
Hello All,
I am using freesurfer 5.1 for my analysis.
I am interested in calculating the whole brain vol (total Gray vol + total WM
vol) excluding the CSF volume and cerebellum.
Total Brain Vol = TotalGrayVol + CorticalWhiteMatterVol
In all of the 79 subjects, when I compare the Total Brain
can't seem to find it, would appreciate a link!
jon
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
Hi list,
I'm performing
recon-all -all -notal-check -i $SUBJECTS_DIR/T1_STRUCT.nii.gz -subject
SUBJECTS_DIR -cw256
on a T1 with following info:data_type INT16dim1 280dim2
240dim3 240dim4 1datatype 4pixdim1
0.508447pixdim2
Hello,
I am working as a research assistant for the summer with the
University of Cincinnati's Psychiatry department in the Division of
Bipolar Disorders Research under Cal Adler and Melissa DelBello. We
are looking to start utilizing FreeSurfer; however, I am getting some
error messages when
Thank you, Louis.
So, to compute aseg stats, I need to run autorecon1, 2 and 3 all
together, right?
Slightly confused because in v5.1.0 I could get aseg stats without error
by running autorecon1 and subcortseg (probably, autorecon2 too). No
longer the case in v5.3.0?
Any options for this
Looks like the skull stripping failed. Can you visually inspect the talairach
xform? Why did you turn checking off?
On May 23, 2013, at 6:26 PM, std...@virgilio.it wrote:
Hi list,
I'm performing
recon-all -all -notal-check -i $SUBJECTS_DIR/T1_STRUCT.nii.gz -subject
SUBJECTS_DIR
Hi Jonathan,
There are problems with FreeSurfer 5.2, so you should probably
download FreeSurfer 5.3 instead.
Cheers,
Thomas
On Fri, May 24, 2013 at 5:51 AM, Jonathan Holt whats...@umich.edu wrote:
can't seem to find it, would appreciate a link!
jon
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