Dear FreeSurfer experts,
I computed distances on the cortex surface using mris_pmake on a data set
acquired at a 3T scanner (using an MPRAGE sequence and protocol recommendations
for FreeSurfer). The exact syntax of the distance computation was:
mris_pmake --subject SUBJECT_ID --hemi lh --surfa
Hi Irene
what changed and by how much? The ICV will change a bit, and because of
partial volume estimation there may be small changes to some volumes, but
it shouldn't be much.
cheers
Bruce
On Fri, 10 Jan 2014, irene saviozzi wrote:
Hello,
I'm learning to use freesurfer.
I would understan
don't use the Talairach, as that will include scaling to fit the talairach
template. Just use the RAS coordinates (scanner or otherwise)
cheers
Bruce
On Fri, 10 Jan 2014,
Jörg Pfannmöller wrote:
Dear FreeSurfer experts,
I computed distances on the cortex surface using mris_pmake on a data
If you just want to sample your volume on the surface and smooth it
there, use mri_vol2surf with --surf-fwhm. Send me your command line when
you have one and I'll verify it is the right thing.
doug
On 01/09/2014 10:21 PM, Caspar M. Schwiedrzik wrote:
> Hi Doug, I found a way to build it in myse
Hi All
I am using wmparc.mgz and aparc.a2009s+aseg.mgz to determine the closest
grey matter region for electrodes in some human epileptic patients; I have
the RAS coordinates of the electrodes. I have a couple of questions:
1) When the electrode (its RAS coordinate) is close to the midline an
On 01/10/2014 11:40 AM, sujith vijayan wrote:
>
> Hi All
>
> I am using wmparc.mgz and aparc.a2009s+aseg.mgz to determine the
> closest grey matter region for electrodes in some human epileptic
> patients; I have the RAS coordinates of the electrodes. I have a
> couple of questions:
>
> 1) When
Hi Sujith
1. Can't you just use read_parcellation and read_annotation.m?
2. I'm not really sure, but certainly rerunning would be the easiest
and safest thing. You could try looking at the recon-all -help and
rerunning just the commands to create those files.
cheers
Bruce
On Fri, 10
Jan 2
Hi Doug,
for this analysis, I would like to stay in volume space; the data are
aligned to a primate volume template. I am trying to do a group analysis of
the functional data as a next step (see this previous email:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg33295.html).
If I jus
you mean just doing a simple volume smoothing? Just use mri_fwhm (make
sure to use the --smooth-only option)
doug
On 01/10/2014 01:27 PM, Caspar M. Schwiedrzik wrote:
> Hi Doug,
> for this analysis, I would like to stay in volume space; the data are
> aligned to a primate volume template. I am
Hello All:
I am hoping someone can help me with qdec. I am running -qcache and running
into the following error:
ERROR: number of vertices in /Recon/subj1/surf/lh.volume does not match
surface (129774,129379)
I tried running "recon-all -s subj1 -make all" but still getting the same
error. I did
Hi All,
I tried the command you suggested Doug (recon-all -s subject -wmparc
-cortparc2 -aparc2aseg). It exits with an error because it cannot find the
lh.sphere.reg file. The command and what is displayed after the command is
executed is pasted below.
Sujith
recon-all -s MG24_SurferOutput -wm
the dmri_train command is giving a segmentation fault. how can I fix this?
Jon
- Original Message -
From: "Jon Wieser"
To: "freesurfer"
Sent: Wednesday, January 8, 2014 2:23:34 PM
Subject: [Freesurfer] Fwd: trac-all -prep error
Hello
I'm getting the following error when running trac-a
Hi Michael,
The aseg lookup table should be generated from all the subjects in the
dataset you are working with initially, then passed with the -asegLUT flag
along with any other QA options. I believe the aseg outliers are just any
subject measure which is 2 SD above/below the mean for your da
dmri_paths is producing a segmentation fault. How can I fix this?
thanks
JOn
- Original Message -
From: "Jon Wieser"
To: "freesurfer"
Sent: Wednesday, January 8, 2014 11:54:55 AM
Subject: [Freesurfer] Fwd: trac-all -path error
Dear freesurfer experts
I'm getting the following error
Hi freesurfers,
I have run 2 separate blocked fMRI experiments ,each on a different pool of
subjects, with couple of conditions identical in both experiments. I would
like to pool the data for the conditions in common across these 2
experiments/group of subjects. I was wondering if anyone had any
Is there a slightly earlier stage I could start at, such that I would not
get an error?
Sujith
On Fri, Jan 10, 2014 at 2:42 PM, sujith vijayan wrote:
> Hi All,
>
> I tried the command you suggested Doug (recon-all -s subject -wmparc
> -cortparc2 -aparc2aseg). It exits with an error because it
I think there must be something else wrong because the sphere.reg has to
be there. Did you check?
On 01/10/2014 06:08 PM, sujith vijayan wrote:
> Is there a slightly earlier stage I could start at, such that I would
> not get an error?
>
> Sujith
>
>
> On Fri, Jan 10, 2014 at 2:42 PM, sujith vij
Where they otherwise acquired in the same way? Same scanner, same TR,
TE, flip angle, voxel size, coil, etc? If so, then you have a chance. I
would still be a little worried about it because they are experiencing
two different paradigms (even though some of the conditions are the
same). Is the
Hi Sal - It looks like a problem with the spaces at the end of the lines
of the bvecs file. If you remove those spaces, it should work. Thanks for
bringing this to my attention - the row-formatted bvecs files are new in
this version and I'll make sure to allow them to have spaces at the end
o
Hi Sal - The 0's should be included as before. Can you send an example of
these bvals/bvecs file that are causing this problem? If they are also
formatted in rows as with your other example, I'd also check for spaces a
the end of the lines.
Thanks!
a.y
On Fri, 3 Jan 2014, Salil Soman wrote:
Hi Doug,
I double checked. The older recons do not have lh.sphere.reg in their surf
folder or anywhere else it appears. The closest looking thing is a file
called lh.qsphere.nofix. Pasted below are the contents of the surf
directory (there are two columns).
Sujith
lh.after rh.after
lh.area rh.
Hi Jon - Have you checked the brain mask and aparc+aseg for this subject?
Anything missing there that might affect the left ILF?
a.y
On Wed, 8 Jan 2014, Jon Wieser wrote:
>
> Dear freesurfer experts
> I'm getting the following error when runing trac-all -c dmrirc_single_subject
> -path
>
>
>
Hi Jon - Again I'd look at this subject's aparc+aseg, as well as the DWIs
themselves to see if there's anything going on that might affect the left
ILF.
a.y
On Wed, 8 Jan 2014, Jon Wieser wrote:
>
>
> Hello
> I'm getting the following error when running trac-all -c dmrirc -prep
>
> INFO: Dist
Hmmm, I think the sphere.reg has been there from the first version of
FS. If it is not there, then there is something wrong with that recon.
Have you used those recons for other purposes?
On 01/10/2014 07:12 PM, sujith vijayan wrote:
> Hi Doug,
>
> I double checked. The older recons do not hav
Hi Gari - So if I understand correctly, your inputs to probtrackx are:
mri/hippo_subfield_in_diffusion_space.nii
dmri.bedpostX/merged
dmri.bedpostX/nodif_brain_mask
If these all come from the output of tracula, aren't these all in LAS
orientation?
a.y
On Thu, 9 Jan 20
Hi Anastasia,
the problem is with mri/hippo_subfield_in_diffusion_space.nii, which
originally is mri/hippo_subfield.mgz, the output of running recon-all
-hippo-subfields. So as far as I understand it is not in anatomical space,
according to MRI info, it is (one example):
- LIA
- 85x97x141
- 0.5x0.5
Hi Doug,
These were not done by me. What I have are the electrodes on top of MR
images as well as their RAS coordinates (I sent you a screen shot before);
done by registering a preop MRI with a postop CT scan. Is sphere.reg
necessary for that?
Sujith
On Fri, Jan 10, 2014 at 7:21 PM, Douglas N
it is necessary to do the aparc.a2009s. It should not be needed for
wmparc (unless other files are not there)
On 1/10/14 8:08 PM, sujith vijayan wrote:
Hi Doug,
These were not done by me. What I have are the electrodes on top of MR
images as well as their RAS coordinates (I sent you a scre
Hi Doug,
Do you think I need to have the whole recon done again?
What if I ran recon-all with just autorecon3, would that generate all the
necessary files (provided what ever that is needed to that point exists)?
>From looking at the documentation it seems like that might do. If that
would work, a
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