t'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
>> v
tions 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 see
Look for spuriousWMconnections.tar
jon
On Apr 28, 2014, at 12:03 PM, Bruce Fischl 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?
e). 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,
>>
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 wou
Anyone have any input?
On Apr 16, 2014, at 11:27 AM, Jonathan Holt 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
&g
ct instead of fsaverage
>
> doug
>
> On 04/16/2014 11:03 AM, 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
&
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 t
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
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 shou
Mar 17, 2014, at 4:23 PM, Bruce Fischl wrote:
> why don't you upload one and we'll take a look? It looked either blurry or
> fat-shifted as in the image you sent I couldn't see any space between cortex
> and dura over a lot of the posterior brain
> On Mon, 17 Ma
ex, 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, 2
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,
I humbly ask for an explanation of contrast vectors, specifically what do 0, 1,
-1 indicate, exactly?
best,
Jon
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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
freev
Hi all,
I’ve pulled up a 3D inflated thickness figure by loading the following into
freeview
lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0
I’m wondering how the colors correspond to thickness and whether or not I can
generate a scale to help inte
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 (mri_
gt;
>
>
> 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 pos
r you 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
>> durin
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?
best
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 sh
My mistake,
this was user error involving renaming directories.
jon
On Nov 6, 2013, at 4:25 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.l
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 the
om 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
>
for it, now.
>
> Best, Martin
>
> On Nov 6, 2013, at 2:22 PM, Jonathan Holt 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, Mar
the stack of thickness maps and
> generates the …_sm10.mgh file.
>
> Best, Martin
>
>
>
> On Nov 6, 2013, at 2:07 PM, Jonathan Holt wrote:
>
>> FS experts,
>>
>> I have two questions, when running mris_preproc and mri_surf2surf should I
>>
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 fsav
gt; -Louis
>
> 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
OK,
been uploaded as JONbrain.tar
Please let me know!
On Nov 4, 2013, at 1:15 PM, Bruce Fischl 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
ly
> accurate as is usually the case, using expert opts to improve its quality
> may also get rid of the problem you are seeing
>
> cheers
> Bruce
>
>
>
> On Mon, 4 Nov 2013, Jonathan Holt wrote:
>
>> Hey Louis,
>>
>> thanks for your response. It?s
ly
> accurate as is usually the case, using expert opts to improve its quality
> may also get rid of the problem you are seeing
>
> cheers
> Bruce
>
>
>
> On Mon, 4 Nov 2013, Jonathan Holt wrote:
>
>> Hey Louis,
>>
>> thanks for your response. It?s
> 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
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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; 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 decid
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 wrote:
> Hi guys,
>
> I am having a bit o
wrote:
>>>
>>> Hi Jon
>>> The segmentation looks 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
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 the
Is this possible?
jon
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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 removin
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 such).
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
m 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
>> wrote:
>>
>>
ruce
> On Thu, 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 w
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 sa
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 wrote:
> Yep, I'll upload to the ftp server.
> On Sep 25, 2013, at 2:28 PM, Ruopeng Wang wrote:
>
>> W
Yep, I'll upload to the ftp server.
On Sep 25, 2013, at 2:28 PM, Ruopeng Wang 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 li
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 seemingl
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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Is there a way to do this?
jon
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Never mind,
page up/page down are separate from arrow keys.
thanks bruce
On Sep 24, 2013, at 1:09 PM, Jonathan Holt 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
Is there any way to accomplish this?
Jon
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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 w
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 w
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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https:
ry much!
>
> PS: I didn't see my 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
>
>
>
>
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.
t I would expect 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 re
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 for the second and third steps of the workflow.
jon
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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
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 wrote:
> Here ya go (to list)
>
>
> On Tue, Jul 2, 2013 at 12:38 PM, Jonathan Holt wrote:
>
>> Here ya go.
>>
>>
>> On Mon
Here ya go (to list)
On Tue, Jul 2, 2013 at 12:38 PM, Jonathan Holt wrote:
> Here ya go.
>
>
> On Mon, Jul 1, 2013 at 3:31 PM, Martin Reuter > wrote:
>
>> No, it's not nifti, that should work.
>>
>> Can you send me your log file and the command you is
on your file system to
> that file.
>
> Best, 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 -i path_to_tp
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 wrote:
> I have tried to inspect the tal xfms that were created in t
/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 wrote:
> can you cc the list so that others can answer?
>
> On Mon, 1 Jul 2013, Jonathan Holt wrote:
>
> I ha
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
om image, but can 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
l recover without any edits. But if, for
> example, one time point has motion 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, 201
each image independently 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, Jonat
>
> 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,
ongitudinal?
>
> 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 wrote:
>
>> Hi all,
>>
>
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 i
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 tex
can't seem to find it, would appreciate a link!
jon
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add
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 Mo
_convert command 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
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
t;>>> Also, I'd like to make sure we are using dcmunpack properly. We take the
>>> scan.info file and parse it like this: "-run [MEMPRAGE_4e_p2_1mm_iso run
>>> number] 3danat mgz 001.mgz" so the multi echo scan gets put into one mgz
>>> file, and
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 th
; something different like 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 -dur
MPRAGE/mri/orig.
On Fri, May 10, 2013 at 12:39 PM, 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? After running
one mgz
>> file, and the RMS gets put into a separate mgz file.
>>> Thanks,
>>> -Kayle
>>>
>>> On May 9, 2013, at 12:00 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote:
>>>> Message: 35
>>>> Date: Thu, 9 May 2
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,
opposed to /example/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 Ho
o read
>
> On Thu, 9 May 2013, Jonathan Holt wrote:
>
>> I input:
>>
>> mris_make_surfaces -dura memprage_echo%d.mgz subjid lh
>>
>> it returns:
>>
>> detecting dura using 0 echos from memprage_echo%d.mgz
>>
>>
>> Should I execut
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 proc
hos, all mgzs 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 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 s
See attached image for reference. Large area has been incorrectly segmented
as WM, also WM surface has completely been skipped over. Planning to remove
segmentation in that area and run recon-all again, is this correct or
should something else be done to alleviate issue.
Worth noting this issue is
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 -make all, or can I run as usual?
>
> jon
Basically, I had a bunch of recon-all's terminate without finishing. Do I need
to run recon-all -s -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
t?
2) last time I ran -make all, the command line disappeared until the job
completed. This never happens when I run recon-all with autorecon2&3. 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.
;>
>> recon-all -s -make all
>>
>> cheers
>> Bruce
>>
>> 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 compl
Experts,
Having an issue with this error. It's complaining about rh.pial not matching
rh.white, indicates there's no such file or directory and that
mrisReadTriangleFile failed, and then proceeds to load without rh.pial. I tried
loading rh.pial manually, but upon loading it immediately removes
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 wi
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.
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.
J
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
___
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
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 I
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