our expectations it may be hard.
Any idea where it comes from?
Bruce
On Tue, 27 May 2014, Jonathan Holt wrote:
Hi all,
this is a recurring issue that I'm hoping I can find a solution to. Pictured
is a brain with a particularly high intensity area that seems to defy
surfacing. Is there a way
wrote:
yes, that's what I meant. It looks too far in the interior to be a B0 effect.
Do you see it in all your subjects? What sequence/scanner are you using?On
Tue, 27 May 2014, Jonathan Holt wrote:
No idea, I think it’s due to the scanner, but could be wrong. Drawing in WM
voxels
the handle). You need to identify the incorrectly
segmented voxels that cause the spurious correction and delete them from the
wm.mgz, then run autorecon2-wm autorecon3
cheers
Bruce
On Fri, 25 Apr 2014, Jonathan Holt wrote:
Thanks Bruce,
I’ll check for such wm connections
Look for spuriousWMconnections.tar
jon
On Apr 28, 2014, at 12:03 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:
sure
On Mon, 28 Apr 2014, Jonathan Holt wrote:
Bruce,
I dont see any WM connections that jump out at me. Could I upload it and
have a second opinion?
Jon
On Apr 25
any spurious connections that cause the space that is missing
in the ?h.white surface to be closed in a slice. If you upload the data we
can show you how to correct it if you want.
cheers
Bruce
On Fri, 25 Apr 2014, Jonathan Holt wrote:
Hi all,
I would love information on how best
Anyone have any input?
On Apr 16, 2014, at 11:27 AM, Jonathan Holt whats...@umich.edu wrote:
Doug,
Thanks for the quick reply.
At this point all I want to do is calculate average thickness, per group,
then visualize the average whole brain thickness for each group. I’m thinking
I’m
Hi all,
I’m currently trying to generate an average subject for two groups so that I
might be able to display average thickness for both groups. I’m confused as to
whether I should be following the GroupAnalysis workflow in the wiki, or if I
should use make_average_subject and mris_preproc in
, Jonathan Holt wrote:
Hi all,
I’m currently trying to generate an average subject for two groups so that I
might be able to display average thickness for both groups. I’m confused as
to whether I should be following the GroupAnalysis workflow in the wiki, or
if I should use
Hello all,
I’m using mri_surf2surf to try to resample a subject to fsaverage, so far I
have
mri_surf2surf --hemi lh --srcsubject [SUBJECT] --cortex --trgsubject fsaverage
however I’m pretty certain that I need both —sval and —trgfmt, but this is the
confusing bit as I’m not sure what I
I’m trying to find a way to extract thickness values at each vertex for a given
subject, and as a part of that process I need to ensure that each subject has
been mapped to a common area, such that their vertices have a direct
correspondence, but I’m not entirely sure how to go about it.
I’ve
into
cortex, which is going to make it impossible to fix
On Mon, 17 Mar 2014, Jonathan Holt wrote:
Here’s an image for reference, it is T1 unfortunately, but the problem area
is always along the posterior in the same configuration.
On Mar 17, 2014, at 8:53 AM, Bruce Fischl fis
, Jonathan Holt wrote:
It doesn’t seem any blurrier than other data I’ve worked with, so I’m not
sure. I also cannot speak to the acquisition bandwidth,
what makes you think fat has shifted? I’m still wondering if there is any
thing I can do to recon-all to avoid this, the data set is huge
Hi all,
I’m working with a particularly stubborn data set whose defining characteristic
is dura along the posterior of the brain. It’s become so consistent that I’m
hoping to find a way to perhaps tweak recon-all so as to take care of the issue
in a more automated manner and save many many man
Hi all,
Would someone kindly point me toward color bar options, specifically for
thickness maps. The color bar that appears by default includes negative values,
and the bit with positive thickness values is very compressed.
For reference I’m looking at surfaces in freeview brought up by
don't have
permission. If that's not the case you will need to give us more details
Bruce
On Sat, 1 Feb 2014, Jonathan Holt wrote:
Hello FS experts,
I'm trying to make an average subject and I had an unfortunate error
during the mri_convert stage, specifically an mghWrite error. I failed
On Mon, 3 Feb 2014, Jonathan Holt wrote:
Bruce,
I tried again on a set of different subjects, it error'd out once again. I
have write permission, this is the same directory I've been using for
quite
some time, and I am positive there is space on the drive.
These are the last 50 or so lines
Hi All,
I'm interested in the cerebellar volume on a particular subject and I was
wondering why I am seeing a slight difference between the volume listed in
aseg.stats and the volume produced by mri_segstats with aseg.mgz as the
input.
It's a very slight difference, 44452mm^3 vs 45137.7mm^3
Hello FS experts,
I’m trying to make an average subject and I had an unfortunate error during the
mri_convert stage, specifically an mghWrite error. I failed to save the output
so I cannot recall the exact details, are there any specific things I should be
looking out for to prevent this?
Hey guys,
Moving a ton of data from v 5.1 to v 5.3, is there anything special that needs
to be done with our 5.1 processed data to ensure consistency with data to be
processed in 5.3?
best,
jon
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Hi FS experts,
I’m about to run aparcstats2table for a longitudinal study, and I’m wondering
seeing as I’ve already written a longitudinal qdec table that includes subject
IDs under the fsid column, is it necessary to pass -subjects subj1 subj2 subj3
… etc AND the qdec to aparcstats2table or
My mistake,
this was user error involving renaming directories.
jon
On Nov 6, 2013, at 4:25 PM, Jonathan Holt whats...@umich.edu wrote:
FS experts,
I’m having a bit of an issue with a single subject. Recon-all -long errors
out after it tells me it cannot open the subjid_to_template.lta
FS experts,
I have two questions, when running mris_preproc and mri_surf2surf should I be
passing these any of the .long directories created with recon-all -long? As I
read through the tutorial I’m missing their significance in the analysis
section of the longitudinal stream. It seems like
of thickness maps and
generates the …_sm10.mgh file.
Best, Martin
On Nov 6, 2013, at 2:07 PM, Jonathan Holt whats...@umich.edu wrote:
FS experts,
I have two questions, when running mris_preproc and mri_surf2surf should I
be passing these any of the .long directories created
' for it, now.
Best, Martin
On Nov 6, 2013, at 2:22 PM, Jonathan Holt whats...@umich.edu wrote:
Thanks a ton Martin,
can you possibly clue me into where I could find study_average?
best,
jon
On Nov 6, 2013, at 2:16 PM, Martin Reuter mreu...@nmr.mgh.harvard.edu
wrote:
Hi Jon
that
subject from the study to not introduce a bias.
In most cases, however, people simply use fsaverage unless they have a reason
to switch.
I don't know how you create your own 'average' surface. Maybe someone else
can answer that.
Best, Martin
On 11/06/2013 02:57 PM, Jonathan Holt wrote
FS experts,
I’m having a bit of an issue with a single subject. Recon-all -long errors out
after it tells me it cannot open the subjid_to_template.lta file. I’m very
confused, because the file it’s looking for exists in the exact location it’s
looking for but the recon-all.log suggests that
On Mon, 4 Nov 2013, Louis Nicholas Vinke wrote:
Got it, I'll take a look.
On Mon, 4 Nov 2013, Jonathan Holt wrote:
OK,
been uploaded as JONbrain.tar
Please let me know!
On Nov 4, 2013, at 1:15 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:
Hi Jon
maybe you should upload
voxels that are not being
captured by the surface is hypo-intense ( 110).
-Louis
On Thu, 31 Oct 2013, Jonathan Holt wrote:
HI experts,
I’m wondering how these limits work, and whether the limit numbers indicate
voxel intensity. If I wanted WM to be segmented more aggressively would I
plug
OK,
been uploaded as JONbrain.tar
Please let me know!
On Nov 4, 2013, at 1:15 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:
Hi Jon
maybe you should upload your data and we'll take a look
cheers
Bruce
On Mon, 4 Nov 2013,
Jonathan Holt wrote:
Bruce,
If I understand you
HI experts,
I’m wondering how these limits work, and whether the limit numbers indicate
voxel intensity. If I wanted WM to be segmented more aggressively would I plug
in a higher number or a lower number?
Jon
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really poor, which probably causes a topological
defect resulting in what you see. I would try using expert opts to set the
segmentation thresholds better
Cheers
Bruce
On Oct 28, 2013, at 1:10 PM, Jonathan Holt whats...@umich.edu wrote:
FS experts,
both of these surfaces are incorrect
By the way I’m also confused on what the effect of increasing/decreasing the
mri_segment p threshold will have, I arbitrarily decided to lower the threshold
but I’m not sure if that’s what I want
On Oct 30, 2013, at 1:22 PM, Jonathan Holt whats...@umich.edu wrote:
Hi guys,
I am having
:
Hi Jon
I would change the wm/gm/csf limits in mri_segment, not the pct thresh.
cheers
Bruce
On Wed, 30 Oct 2013, Jonathan Holt wrote:
By the way I?m also confused on what the effect of increasing/decreasing the
mri_segment p threshold will have, I arbitrarily decided to lower
Hi Guys,
I'm having an issue with a brain involving both inaccurate surfaces and
incorrectly segmented voxels. Basically, a sulcus is being skipped over by
the main surface where and a bunch of basically empty space is being
segmented as white matter. I've edited the segmentation myself by
Is this possible?
jon
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FS experts,
Freesurfer has been omitting extremely bright/intense white and grey matter
voxels (avg intensity ~150). Mostly this happens in areas that should be
encompassed by the surfaces. Is there a way to tell recon-all to include
these areas?
I fear it may believe they are dura because of
I'm trying to apply voxel deletions made to the brainmask.mgz to the wm.mgz. As
I understand it, if I run
mri_copy_values brainmask.mgz 0 wm.mgz
all of the 0 value voxels, or the deleted voxels in braibmask.mgz will be
applied to the wm.mgz (provided they have the same geometry or some
Simply to make sure,
1) Is there no way that one can edit two volumes simultaneously similarly to
tkmedits aux+main volume brush?
2) When editing voxels in freeview, is there anyway to have the cursor behave
the same way it does in navigation mode. That is, I'd like to be able to see
exactly
I'd like to know whether or not this is possible. I am unable, at this
point to figure it out. In the volumes tab I've selected both of my volumes but
it seems like voxel editing only takes effect on whichever volume is in the top
position. I'd like to know if I could edit both at the
, 26 Sep 2013, Jonathan Holt wrote:
I'd like to know whether or not this is possible. I am unable, at this
point to figure it out. In the volumes tab I've selected both of my volumes
but it seems like voxel editing only takes effect on whichever volume is in
the top position. I'd like
can copy them to
any volume that has the same geometry
On Thu, 26 Sep 2013, Jonathan Holt wrote:
Thanks Bruce,
Can you explain how mri_copy_values works?
jon
On Sep 26, 2013, at 12:08 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:
Hi Jon,
I don't think it is, although you
I'm curious whether or not freesurfer, when calculating surface values, takes
the original surface into account? If not, which surfaces are included in this
calculation?
jon
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I've read in the mailing list archives people have had issues with tkmedit and
free view displaying control points differently. For me the first brain I've
loaded up has a single control point in free view that does not show in
tkmedit. Others have complained of free view showing points
Yep, I'll upload to the ftp server.
On Sep 25, 2013, at 2:28 PM, Ruopeng Wang rpw...@nmr.mgh.harvard.edu wrote:
Would it be possible to send us the volume and control point files?
Thanks,
Ruopeng
On 09/25/2013 02:09 PM, Jonathan Holt wrote:
I've read in the mailing list archives people
Uploaded look for CPsDon'tMatch. It's the subject directory so surfaces,
volumes, tmp folder with control.dat
jon
On Sep 25, 2013, at 2:34 PM, Jonathan Holt whats...@umich.edu wrote:
Yep, I'll upload to the ftp server.
On Sep 25, 2013, at 2:28 PM, Ruopeng Wang rpw...@nmr.mgh.harvard.edu
Is there any way to accomplish this?
Jon
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The information in this e-mail is intended only for the person to whom it is
addressed. If
Never mind,
page up/page down are separate from arrow keys.
thanks bruce
On Sep 24, 2013, at 1:09 PM, Jonathan Holt whats...@umich.edu wrote:
forgot to cc list
You'd think that was it, but that simply moves the brain around in it's box,
it doesn't change slices. The only way i can go
Is there a way to do this?
jon
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addressed. If you
Attached is an image that describes my issue. WM in the temporal region is
being omitted after running recon-all. Most of the omitted voxels are in
the 120-130 range. It's causing an issue with the underlying WM voxels as
well, they've simply disappeared.
I can see how this voxel intensity limit
Attached is an image that describes my issue. WM in the temporal region is
being omitted after running recon-all. Most of the omitted voxels are in
the 120-130 range. It's causing an issue with the underlying WM voxels as
well, they've simply disappeared.
I can see how this voxel intensity limit
hey all,
I've had a few jobs that were recently terminated due to a broken ssh pipe, is
there anything i should do to before re-running those same jobs in order to
avoid any issues?
jon
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Ye,
Since no one's replied, I'll say it does look like the cb is infringing on
the pial surface. It's easier to tell the boundary toward the center of the
brain than it is toward the lower portion. It's easier to tell, in my
opinion, in the coronal view. Toggling the surface off may help as well.
first message in the mailing archive, so I thought it
didn't go through. It seems that an email with images will only show in the
archive until it solicits a response. Sorry to bother you guys.
Sincerely,
Ye
On Tue, Jul 9, 2013 at 9:22 AM, Jonathan Holt whats...@umich.edu wrote:
Ye
/orig.mgz and mri/orig_nu.mgz look.
Best, Martin
On 07/02/2013 02:16 PM, Jonathan Holt wrote:
Thanks Martin,
I have attached recon-all.log. I tried to run the process several times,
I clearly forgot to pass -all that time but I know for certain the first
time I tried I passed -all
As I'm having trouble importing nifti files into the first step of the
longitudinal work flow, I'm wondering if I can use volumes generated from
recon-all -s subjID for the second and third steps of the workflow.
jon
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the first step to take nifti just fine. Can you send the command you are running?On Mon, 8 Jul 2013, Jonathan Holt wrote:As I'm having trouble importing nifti files into the first step of the longitudinal work flow, I'm wondering if I can use volumes generated from recon-all -s subjID
Here ya go (to list)
On Tue, Jul 2, 2013 at 12:38 PM, Jonathan Holt whats...@umich.edu wrote:
Here ya go.
On Mon, Jul 1, 2013 at 3:31 PM, Martin Reuter mreu...@nmr.mgh.harvard.edu
wrote:
No, it's not nifti, that should work.
Can you send me your log file and the command you issued
and the command
nohup recon-all -s 100922dt_01 -i 100922dt_nifti_revised.nii
On Tue, Jul 2, 2013 at 12:40 PM, Jonathan Holt whats...@umich.edu wrote:
Here ya go (to list)
On Tue, Jul 2, 2013 at 12:38 PM, Jonathan Holt whats...@umich.edu wrote:
Here ya go.
On Mon, Jul 1, 2013 at 3:31
artifiacts and the others not, then the
template will be fine and there is a good chance that results on all time
points will be good after the 3rd step.
Best, Martin
On Jun 28, 2013, at 9:14 PM, Jonathan Holt whats...@umich.edu wrote:
Martin,
I hate to be noobish, but can you elaborate
be
nifti or another format.
Best, Martin
On 07/01/2013 10:17 AM, Jonathan Holt wrote:
Martin,
I'm going to experiment with data with better image quality using the
longitudinal stream. In the first step of the workflow I'm confused to what
'dcm' stands for in the following command
Log file indicates manual talairach alignment may be necessary.
ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
***FAILED*** (p=0.0079, pval=0. threshold=0.0050)
Manual Talairach alignment may be necessary
Can anyone provide direction. Alternatively, the error indicates
/ht1spgr.nii...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
WARNING: it does not appear that there was sufficient information
On Mon, Jul 1, 2013 at 1:46 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote:
can you cc the list so that others can answer?
On Mon, 1 Jul 2013, Jonathan Holt
Martin,
I did find that info and tried to follow the instructions, but you'll see
based on my last message the talairach files didn't seem to contain
anything?
On Mon, Jul 1, 2013 at 2:29 PM, Jonathan Holt whats...@umich.edu wrote:
I have tried to inspect the tal xfms that were created
, Martin
On 07/01/2013 02:29 PM, Jonathan Holt wrote:
I have tried to inspect the tal xfms that were created in the brief time
this string was running
recon-all -all -s tpNid -i path_to_tpN_dcm
while viewing orig.mgz in tkmedit. they were talairach.xfm and
talairach.auto.xfm, both were
is significant motion artifacts (ringing), which seem to
lead to underestimation of WM, also you could fine tune the skull strip.
Best, Martin
On Jun 28, 2013, at 10:19 AM, Jonathan Holt whats...@umich.edu wrote:
Hi all,
I'm having a bit of trouble with one particular subject for which
,
is this in cross sectional processing or in longitudinal?
One thing I notice is significant motion artifacts (ringing), which seem to
lead to underestimation of WM, also you could fine tune the skull strip.
Best, Martin
On Jun 28, 2013, at 10:19 AM, Jonathan Holt whats...@umich.edu wrote:
Hi
through freesurfer and look at the results?
Is there motion in all the 4 time points in this subject or only in the one
image that you send? With motion artifacts, surfaces are not very reliable.
Best, martin
On Jun 28, 2013, at 11:36 AM, Jonathan Holt whats...@umich.edu wrote:
We
Hi all,
We are using the parcellation of Desikan-Killiany
https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation
and creating labels for each structure in each hemisphere with:
mri_annotation2label --subject ${SUBJ} --hemi ${HEMI} --outdir
${SUBJ}/${SUBJ}_annotate
and making matlab
Always wondered, was never quite sure. I'm wondering why sometimes they
mirror each other and other times they shift away.
jon
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The
can't seem to find it, would appreciate a link!
jon
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...@nmr.mgh.harvard.edu wrote:
Message: 35
Date: Thu, 9 May 2013 10:44:23 -0400 (EDT)
From: Bruce Fischl fis...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Working with MEMPRAGE
To: Jonathan Holt whats...@umich.edu
Cc: freesurfer@nmr.mgh.harvard.edu
Message-ID:
alpine.lrh.2.02.1305091043500.13
Bruce,
how is it that I might load multiple surfaces, loading lh after having loaded
rh makes the other disappear. this is loading manually, not from the command
line
On May 13, 2013, at 11:14 AM, Jonathan Holt wrote:
Hi all,
last question promise. Successfully completed
line)
On Mon, 13 May 2013, Bruce Fischl wrote:
you can use file-aux-surfaces-load aux main surface (or something like
that). Or use freeview.
cheers
Bruce
On Mon, 13 May 2013, Jonathan Holt wrote:
Bruce,
how is it that I might load multiple surfaces, loading lh after having
loaded
I wont question it, but this is my first multi echo brain and it's the most
beautiful i've ever seen. so crisp.
On May 13, 2013, at 3:55 PM, Bruce Fischl wrote:
I'm surprised it would work well if they are not float. You'll lose a lot of
precision
On Mon, 13 May 2013, Jonathan Holt wrote
: [Freesurfer] Working with MEMPRAGE
To: Jonathan Holt whats...@umich.edu
Cc: freesurfer@nmr.mgh.harvard.edu
Message-ID:
alpine.lrh.2.02.1305091043500.13...@gate.nmr.mgh.harvard.edu
Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII
it needs to be:
mris_make_surfaces -dura memprage_echo
/orig.
On Fri, May 10, 2013 at 12:39 PM, Jonathan Holt whats...@umich.edu wrote:
$ export SUBJECTS_DIR=/net/data4/ALSSCI/FreeSurfer201211/FreeSurfer
$ mris_make_surfaces -dura 001%d.mgz 4 s_MEMPRAGE lh
it's entirely possible I'm specifying the wrong mgz? After running
recon-all on the RMS
echo1.mgz, echo2.mgz... then specify -dura
echo%d.mgz 4
cheers
Bruce
On Fri, 10 May 2013, Jonathan Holt wrote:
$ export SUBJECTS_DIR=/net/data4/ALSSCI/FreeSurfer201211/FreeSurfer $
mris_make_surfaces -dura 001%d.mgz 4 s_MEMPRAGE lh
it's entirely possible I'm specifying the wrong mgz
will convert individually, should they eventually be stored in the same
directory as the RMS'd mgz, with the same file name + invidivual numbers?
after which I'd proceed with mris_make_surfaces?
jon
On May 10, 2013, at 12:48 PM, Jonathan Holt wrote:
I ran mri_convert on the RMS'd nifti
in the directory. I have a feeling I'm doing this incorrectly.
jon
On May 9, 2013, at 8:50 AM, Bruce Fischl wrote:
Hi Jon
yes, the subject and hemi need to be defined (they are required parameters)
Bruce
On Wed, 8 May 2013, Jonathan Holt wrote:
Hi all,
combed through the mail archives to figure
the proper subject directory beforehand.
On May 9, 2013, at 10:37 AM, Bruce Fischl wrote:
can you send me the full command line? It should say 4 echoes, not 0
On Thu, 9 May 2013, Jonathan Holt wrote:
Thanks Bruce,
should the hemisphere's be processed separately, or how do I signify lh
/directory/subjects/subjid/mri/filled.mgz
I can rename subject directory if need be.
On May 9, 2013, at 10:54 AM, Bruce Fischl wrote:
is your SUBJECTS_DIR set properly? You need to put the memprage echoes in
the subject's mri dir
On Thu, 9 May 2013, Jonathan Holt wrote:
Oh, simple mistake
No,
I believe my PI simply ran mri_convert on the 4 nii's,
Clearly there is a better approach?
jon
On May 9, 2013, at 11:04 AM, Bruce Fischl wrote:
Did you run recon-all? It will create filled.mgz in the subject/mri dir
On May 9, 2013, at 11:00 AM, Jonathan Holt whats...@umich.edu
Hi all,
combed through the mail archives to figure out how to work with multi echo
mprage, found what I need but I wanted to confirm which of these two commands
is the appropriate
mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh
mris_make_surfaces -dura memprage_echo%d.mgz
do the
Basically, I had a bunch of recon-all's terminate without finishing. Do I need
to run recon-all -s subjid -make all, or can I run as usual?
jon
On Feb 6, 2013, at 9:35 PM, Jonathan Holt wrote:
Just had a cluster of computers lock up, unfortunately resulting in several
freesurfer jobs
No, the computers they were running on had to be rebooted before they finished.
On Feb 8, 2013, at 1:19 PM, Jonathan Holt wrote:
Basically, I had a bunch of recon-all's terminate without finishing. Do I
need to run recon-all -s subjid -make all, or can I run as usual?
jon
On Feb 6, 2013
) last time I ran -make all, the command line disappeared until the job
completed. This never happens when I run recon-all with autorecon23. Anyway to
avoid this?
jon
On Feb 1, 2013, at 1:28 PM, Jonathan Holt wrote:
OK, good deal! The first time I ran recon-all it exited with errors. That
must
p.s. ignore the can't find file thing. It really means it tried to read
it, but found it wasn't the same topology as the other surface and that's
what it is complaining about
On Fri, 1 Feb 2013,
Jonathan Holt wrote:
Experts,
Having an issue with this error. It's complaining about
hello all,
Just for reference, we were having an issue with recon-all v 5.2 exiting with
errors due to issues with the perirhinal cortex. We were able to simply
commented out the parts of the script dealing with the perirhinal cortex. Just
an FYI to those who may be having a similar problem.
Also, could I have a link for the centos4 of this updated version of 5.2? And
is there a working 5.2 for Mac OS X, 10.7 or 10.8 specifically?
jon
On Jan 28, 2013, at 3:19 PM, Jonathan Holt wrote:
Nick,
it was in fact an error with missing perirhinal cortex labels in fsaverage.
It did
Nick,
it was in fact an error with missing perirhinal cortex labels in fsaverage. It
did not exist, and then the process exited. Good to know it's been fixed.
jon
On Jan 28, 2013, at 2:48 PM, Jonathan Holt wrote:
hello all,
Just for reference, we were having an issue with recon-all v 5.2
In 5.0.0 I was used to dealing with brainmask.mgz files. in 5.2.0, I have so
far been able to generate a T1.mgz, which to my eyes, looks OK. However, the
resulting surf folder is empty and I'm not sure why. Log file attached.
jon
testsubject.log
Description: Binary data
Hello all,
Having a slight issue with recon-all 5.2. For reference, we're using Freesurfer
5.0.0 and trying to use recon-all 5.2 to alleviate some issues with
disappearing white matter. I'm wondering if it is necessary to have Freesurfer
5.2 in order for recon-all 5.2 to work properly?
When
Log file attached. Will try with debug ASAP.
s_98xx_v5.2.log
Description: Binary data
On Jan 7, 2013, at 1:38 PM, Jonathan Holt wrote:
Hello all,
Having a slight issue with recon-all 5.2. For reference, we're using
Freesurfer 5.0.0 and trying to use recon-all 5.2 to alleviate some
are
considered.
Emily
On Wed, Dec 12, 2012 at 10:42 AM, Jonathan Holt whats...@umich.edu wrote:
OK will do... I'll upload both versions, before and after recon-all ran. I am
beginning to think it's an issue with the script that I am running... I'm
looking at another brain and there are areas
, at 11:33 AM, Bruce Fischl wrote:
Hi Jon
if you upload this subject we'll take a look
Bruce
On Wed, 12 Dec 2012, Jonathan Holt wrote:
I've had this happen a handful of times and I'm wondering what I can do
about it. For reference using Freesurfer 5.0.0.
Edited a brain and ran recon
I have not seen a lot of documentation on how to do this. I've attached two images of specific areas where I'd like to have the pial and main surfaces follow the actual surface of the brain. The aux volume OK in both of these cases. The empty space is segmented as white matter. In the past I have
I'm wondering about how to best approach two similar problems with pial
surfaces. In one case I'd like to extend it and in the other I'd like to
reduce it (for lack of a better term)
These first two images are from a brain in which I'd like to extend the
surface.
http://i.imgur.com/ziDQd.png
Quick small question,
I'm editing a few brains at the moment that have needed multiple script runs.
I've added control points as necessary before each run and afterward the
resulting brain will typically need either more control points added, white
matter aux volume edits, or both. I'm
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