freesurfer-boun...@nmr.mgh.harvard.edu
> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> On Behalf Of Steven Meisler
> Sent: Monday, February 6, 2023 3:32 PM
> To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.har
, February 6, 2023 3:32 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] qcache morphometry measures are empty
External Email - Use Caution
Hi,
Following up in reporting that it does appear to be an issue with Nibabel and
not FreeSurfer. mri_diff between the metric files
External Email - Use Caution
Hi,
Following up in reporting that it does appear to be an issue with Nibabel and
not FreeSurfer. mri_diff between the metric files reveals that they are not
empty. I have found an alternative for loading the morphological metrics in
python, so cons
External Email - Use Caution
Hello FreeSurfer developers,
(This issue is described in detail at the following link:
https://secure-web.cisco.com/19gHm_kiBwLabZG0kSzLCkZdl3RRluMPmh3eOd0r3KCWXL273Kn7fEc-N8AIruNQCFaa4FeUE3ZzCv9GRT9eapfdqdhBIXBD688oDf9L7UXDgj6WTAg5oSqlc-Q6R2Xs_APdj5b
External Email - Use Caution
Dear Douglas,
It works well with the -measure option. Thank you so much!
Best,
JW
ᐧ
On Tue, Aug 17, 2021 at 4:41 PM Douglas N. Greve
wrote:
> By default, the measure list includes the .K and .H files. You can specify
> your own list of measures wit
By default, the measure list includes the .K and .H files. You can
specify your own list of measures with the -measure option. Eg, -measure
thickness (you can add more -measure options for more measures)
On 8/13/2021 5:10 PM, Junyeon Won wrote:
External Email - Use Caution
Dear Free
On 8/6/2021 6:35 PM, Zeng, Qi wrote:
External Email - Use Caution
Hi Freesurfer experts,
I've done running a longitudinal analysis pipeline for individuals in
3 groups. Now, I need to get prepared for QDEC group analysis. I cp
all groups of individuals to the same directory and eac
External Email - Use Caution
Dear FreeSurfer experts,
I am trying to administer group-level analyses using the Human Connectome
Project dataset. I downloaded extended processed structural data from the
HCP webpage and processed FreeSurfer data were available there. So I ran
qcache
External Email - Use Caution
Hi Freesurfer experts,
I've done running a longitudinal analysis pipeline for individuals in 3
groups. Now, I need to get prepared for QDEC group analysis. I cp all
groups of individuals to the same directory and each subject contains one
base and mult
It should be restored now, sorry for the problem
On 5/22/2020 11:49 AM, Wang, Lily wrote:
Hi FreeSurfer team,
I am trying to run qcache but it is exiting with errors because it is
not able to find files in the fsaverage/surf directory. I looked in
$FREESURFER_HOME/subjects/fsaverage and there
Hi FreeSurfer team,
I am trying to run qcache but it is exiting with errors because it is not able
to find files in the fsaverage/surf directory. I looked in
$FREESURFER_HOME/subjects/fsaverage and there is indeed not a surf folder.
Should I use one of the other directories like fsaverage3?
Th
Objet : Re: [Freesurfer] -qcache and thickness questions
Yes, looks like small registration errors. I don't think it is problematic. Any
vertex where even a single subject has a 0 should be masked out of the final
analysis.
On 12/3/2019 1:42 PM, Joëlle Ismay Rosanne Van Der Molen
t;
de la part de Greve, Douglas N.,Ph.D.
<mailto:dgr...@mgh.harvard.edu>
Envoyé : mardi, 3 décembre 2019 02:14:08
À : freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Objet : Re: [Freesurfer] -qcache and thickness questions
On 12/2/2019 7:12 PM, Joëlle Isma
On 12/2/2019 7:12 PM, Joëlle Ismay Rosanne Van Der Molen wrote:
External Email - Use Caution
Dear Freesurfer experts,
After running the -qcache option to extract thickness data for every subject, I
tried pulling all the data together in order to get a matrix of subjects x
vertices c
This usually happens when a subject was run all the way through recon-all once,
then again but only part of the way (eg, after editing). Check those subjects
to see what happened.
On 9/10/2019 5:34 PM, Swanson,Clayton wrote:
External Email - Use Caution
Hello FreeSurfer Developers,
I a
You can just run recon-all again with only the -qcache flag (this is actually
how it is intended to be run)
On 9/5/2019 2:52 PM, Swanson,Clayton wrote:
External Email - Use Caution
Hi FreeSurfer folks,
I searched through the archives and was unable to find the answer I was looking
for
External Email - Use Caution
Hi FreeSurfer folks,
I searched through the archives and was unable to find the answer I was looking
for. I have recently run recon-all on all our subjects (55 participants
separated into two groups), then went through and corrected, saved and re-ra
ite.K --target fsaverage --out
lh.white.K.fsaverage.mgh
nsubjects = 1
ERROR: cannot find
/lh.white.K
recon-all -s exited with ERRORS
Re: [Freesurfer] -qcache
error<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subject:%22Re%5C%3A+%5C%5BFreesurfer%5C%5D+%5C-qcac
d.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Greve, Douglas
N.,Ph.D.
Sent: Friday, January 4, 2019 4:21 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] -qcache error
Does that file exist? If not, check to see whether that subject finished or
whether there was an error
On
Does that file exist? If not, check to see whether that subject finished
or whether there was an error
On 12/20/18 2:37 PM, 塩浜 直 wrote:
> External Email - Use Caution
>
> Hello FreeSurfer Developers,
>
> I'm attempting to do group analysis for cortical thickness map using Qdec GUI.
> We'
Behalf Of Alexopoulos,
Dimitrios
Sent: Friday, May 25, 2018 12:47 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] -qcache in recon-all commnd
External Email - Use Caution
Any further comments on the correct command to run after making manual edits.
Specifically, should the '-hippoc
0:38 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] -qcache in recon-all commnd
External Email - Use Caution
Any further advice on whether to include '-hippocampal-subfields-T1' flag in
the rerun after manual edits?
Jim
"The materials in this email are private
Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N. Greve
Sent: Tuesday, May 22, 2018 11:35 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] -qcache in recon-all commnd
Sorry, I don'
rfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N. Greve
> > Sent: Monday, May 21, 2018 4:52 PM
> > To: freesurfer@nmr.mgh.harvard.edu
> > Subject: Re: [Freesurfer] -qcache in recon-all commnd
> >
> > You can run this:
> > recon-all -s -all -hires
> > but i
lephone or return email."
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N. Greve
> Sent: Monday, May 21, 2018 4:52 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re
21, 2018 4:52 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] -qcache in recon-all commnd
You can run this:
recon-all -s -all -hires
but it might run more things than you need (no harm, just computer time).
Depending on what you have edited, you may be able to use one of the -autor
..@nmr.mgh.harvard.edu
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N. Greve
> Sent: Monday, May 21, 2018 3:40 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] -qcache in recon-all commnd
>
>
> If you have editeid all your subjects and re
Of Douglas N. Greve
Sent: Monday, May 21, 2018 3:40 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] -qcache in recon-all commnd
If you have editeid all your subjects and re-run (with -all or appropirate
-auto-reconX flag), then you can run -qcache without those flags
On
or return email."
>
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N. Greve
> Sent: Monday, May 21, 2018 3:28 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Fr
ediately notify the sender via
telephone or return email."
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N. Greve
Sent: Monday, May 21, 2018 3:28 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Free
eesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N. Greve
> Sent: Monday, May 21, 2018 3:16 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] -qcache in recon-all commnd
>
> Yes, run the same optional flag. When you run -qcache, do not include -all
>
>
&g
al Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N. Greve
Sent: Monday, May 21, 2018 3:16 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] -qcache in recon-all commnd
Yes, run the same optional flag. Wh
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N. Greve
> Sent: Tuesday, May 08, 2018 11:19 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] -qcache in r
ouglas
> N. Greve
> Sent: Thursday, April 12, 2018 1:01 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] -qcache in recon-all commnd
>
> Right. And you'd need to redo it after all manual edits
>
>
> On 04/12/2018 11:06 AM, Alexopoulos, Dimitrios wr
ave received this email in error, please immediately
> notify the sender via telephone or return email.”
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N. Greve
> Sent: Thursday, Apr
@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N. Greve
Sent: Thursday, April 12, 2018 1:01 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] -qcache in recon-all commnd
Right. And you'd need to redo it after all manual edits
On 04/12/2
lease immediately notify the sender via telephone or return email.”
>
> *From:*freesurfer-boun...@nmr.mgh.harvard.edu
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *Douglas
> Greve
> *Sent:* Wednesday, April 11, 2018 10:29 PM
> *To:* freesurfer@nmr.mgh.harvar
Wednesday, April 11, 2018 10:29 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] -qcache in recon-all commnd
It is not. -qcache is a preprocessing step prior to doing group analysis with
QDEC. If you use it, you should only do so after you have finished all the
individual analysis (
It is not. -qcache is a preprocessing step prior to doing group analysis
with QDEC. If you use it, you should only do so after you have finished
all the individual analysis (eg, manual edits)
On 4/11/18 10:02 PM, Alexopoulos, Dimitrios wrote:
Is it recommended to use the -qcache flag in the ba
Is it recommended to use the -qcache flag in the basic recon-all -all command?
What does it do and what are the advantage of using it?
Jim
The materials in this message are private and may contain Protected Healthcare
Information or other information of a sensit
It was deleted but then it was created as a link. Does the link exist?
On 3/7/18 1:33 PM, Krishna Patel wrote:
Hi - I would like to do group analysis on freesurfer data that is
processed with verson 6. However when I try to run
recon-all -s subjid -qcache
I get following error after it runs
Hi - I would like to do group analysis on freesurfer data that is processed
with verson 6. However when I try to run
recon-all -s subjid -qcache
I get following error after it runs for some time and generates some of the
files.
ERROR: cannot find surf/lh.white.K
When I look at the log file - I
you can run
pctsurfcon --s subject
On 07/17/2017 06:32 AM, Lisa Delalande wrote:
> Hello everyone,
>
> I'm using the new version of FreeSurfer processing with longitudinal
> image processing. And at the step -base after a recon-all processing i
> would like to make a qcache processing but it d
Hello everyone,
I'm using the new version of FreeSurfer processing with longitudinal image
processing. And at the step -base after a recon-all processing i would like
to make a qcache processing but it doesn't work... "cannot find
[...]/template_1-01VALAL/surf/lh.w-g.pct.mgh" (See in attachment
lo
Dear list,
When processing the data for longitudinal analysis (or even for cross
sectional) the -qcache has to be run before editing or after all the edits
have been done?
Thank you
--
*Manuel Delgado Alvarado, MD*
Neurology Department
Neuroimaging Unit
Valdecilla Biomedical Research Institute, I
Many of the vertices will have 0 value because they are in the medial
wall where there is no cortex. Is this the case with the vertices you
have found?
On 10/03/2016 03:28 PM, Sam Mathias wrote:
> Dear list,
>
> I'm trying to extract vertex-level measures of thickness, area, etc,
> for all of
Just a correction from my previous message; this issue actually affects
both hemispheres, but different vertices in each one.
--
Samuel R. Mathias, Ph.D.
Associate Research Scientist (ARS)
Neurocognition, Neurocomputation and Neurogenetics (n3) Division
Yale University School of Medicine
40 Temple
Dear list,
I'm trying to extract vertex-level measures of thickness, area, etc, for
all of my subjects. I ran recon-all -all on all subjects as normal, then
ran:
recon-all -s {subject} -qcache
where {subject} is the subject ID. This was followed by `mris_convert` to
make the values human-readabl
Thank you very much. I will be looking forward to this.
Nick Corriveau-Lecavalier
?tudiant au Ph.D. recherche/intervention, option neuropsychologie clinique
Coordonateur ? la recherche, Association ?tudiante des cycles sup?rieurs en
psychologie de l'Universit? de Montr?al (A?CSPUM)
Universit? de
Hi Nick,
when using the 2 stage model (mris_long slopes ) you do not need the qcache. In
qdec you will not look at thickness, but at the percent change or the rate of
thickness changes as computed by long_slopes. For that to work, you need to
create/modify the .qdecrc file so that qdec finds th
Hi Freesurfer team,
I am planning on following this page for my longitudinal group analysis using
QDEC: http://www.freesurfer.net/fswiki/FsTutorial/QdecGroupAnalysis_freeview.
However, it tells me to run -qcache for all of my subjects. Since I already ran
the -long stream for all my subjects,
Yes
doug
On 02/23/2016 03:00 PM, Daniel Ferreira wrote:
> Dear experts,
>
> Can I do -qcache with FS 5.3.0 or FS 5.1.0 on images that have been
> recon-all -all with FS 5.0.0?
>
> Thanks
>
> Dani
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mg
Dear experts,
Can I do -qcache with FS 5.3.0 or FS 5.1.0 on images that have been
recon-all -all with FS 5.0.0?
Thanks
Dani
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The in
Yes, but use one or the other but not both
On 02/17/2016 08:47 AM, Daniel Ferreira wrote:
> Dear experts,
>
> Can I do -qcache with FS 5.3.0 or FS 5.1.0 on images that have been
> recon-all -all with FS 5.0.0?
>
> Thanks
>
> Dani
>
>
> ___
> Freesurfer
Dear experts,
Can I do -qcache with FS 5.3.0 or FS 5.1.0 on images that have been
recon-all -all with FS 5.0.0?
Thanks
Dani
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The in
Hi Skyler,
(I added the freesurfer list in copy, please post all your questions through
the mailing list, thanks!)
If the number of vertices does no match, it might be that you processed the LGI
before you reprocessed the final version of the surfaces for which you
completed the registration p
yes, that is correct
On 05/04/2015 03:19 PM, Paul Dhami wrote:
> Greetings Freesurfer experts,
>
> although this seemed well address on the wiki, I just wanted to
> clarify that if I have already run recon-all on all my subjects, but
> without the -qcache flag, once I get to the stage of assembl
Greetings Freesurfer experts,
although this seemed well address on the wiki, I just wanted to clarify
that if I have already run recon-all on all my subjects, but without the
-qcache flag, once I get to the stage of assembling the data, I would just
need to run:
recon-all -s -qcache
and that th
Hi Gayane,
what happens if you run the mris_calc command directly? Also check if
all the inputs really exist. It could be that you need to update
mris_calc there was a problem with long file names in an earlier
version. Which FS version are you using?
Best, Martin
On 09/09/2014 09:51 AM, Ga
Dear list,
I'm running longitudinal two stage model as is described in the tutorial
here: http://freesurfer.net/fswiki/LongitudinalTwoStageModel
First, I've proceeded with longitudinal pipeline all my data, second, I've
created longitudinal qdec table, and then, I've started to qcache my data,
wh
If you use a different target, then it will not overwrite the output of
previous runs but names the files differently based on the new target
name. In the qdec interface, you should change the name of the
"Common-space Subject"
doug
On 08/13/2014 10:12 AM, Vy Dinh wrote:
> Dear developers,
>
Dear developers,
I just have a brief technical question about using qcache for multiple
fsaverages. If I wanted to write my subjects to a new fsaverages, I know
that one can use the command
Recon-all -qcache -target fsaverage2 -s subid
However, does this overwrite the current normalized data to
Hello all,
I was able to fix my error (see below) by re-running recon-all $SUB –autorecon2
–autorecon3 –qcache .
However I am unsure why –make all was not incorporating edits correctly? Is it
inappropriate to use –make all after manual edits? If so, should I just use
–autorecon2 –autorecon3 as a
Hello,
I am running into an error when using qcache. Subjects that have had manual
edits are exited with errors, while subjects that have not had edits run fine.
All subjects have had –make all ran after edits and finished without errors. I
have read about this problem and tried some of the solu
yes, although why -make all didn't fix things is a mystery to me.
On Fri,
24 Jan 2014, Mihaela Stefan wrote:
Yes, -make all ran for about 7 hours and it exited without errors. How
should I fix this?
What about -qcache after recon-all -autorecon2-cp -autorecon3 -subjid
? Can I use that if it
Yes, -make all ran for about 7 hours and it exited without errors. How
should I fix this?
What about -qcache after recon-all -autorecon2-cp -autorecon3 -subjid
? Can I use that if it exited without errors? Can I assume that
the subject has all the correct files and continue my analysis?
Thanks!
it's possible that the timestamps on your system are wrong I guess. Did
-make all run anything?
On Fri, 24 Jan 2014, Mihaela Stefan wrote:
Hi Bruce,
I used that command and I got the same errors when I ran -qcache again. I
also found that my colleague, who did the edits, used the same command
Hi Bruce,
I used that command and I got the same errors when I ran -qcache again. I
also found that my colleague, who did the edits, used the same command
after she manually edited the recons.
I re-ran the subject with the following command recon-all -autorecon2-cp
-autorecon3 -subjid and, when i
Hi Mihaela
usually that means the subject was partially but not completely rerun.
You can try using recon-all -s -make all
and see if it fixes it
cheers
Bruce
On Thu, 23 Jan 2014,
Mihaela Stefan wrote:
Hello FreeSurfers,
I am trying to run a group analysis with Qdec following thistutorial
ent: 05 November 2012 19:37
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] qcache error
>
> Do run out of disk space? Also, please send terminal output in a text
> file rather than as a snapshot. You can do this with
>
> recon-all ... |& tee mylog.txt
>
&
Do run out of disk space? Also, please send terminal output in a text
file rather than as a snapshot. You can do this with
recon-all ... |& tee mylog.txt
doug
On 11/05/2012 10:21 AM, Berg, S.F. van den wrote:
>
> Dear Freesurfer experts,
>
> I have got a problem with the qcache function. I have
yes, -qcache can be added to the first run (ie, included with -all)
On Fri, 2010-11-19 at 17:50 -0500, Dhinakaran Chinappen wrote:
> Dear Freesurfer(ers).
>
>
> Quick ques: is it possible to run recon-all with the qcache flag
> during the initial reconstruction, as opposed to re-using recon-all
Dear Freesurfer(ers).
Quick ques: is it possible to run recon-all with the qcache flag during the
initial reconstruction, as opposed to re-using recon-all with the qcache
flag afterwards?
Thanks,
Dhinakaran.
___
Freesurfer mailing list
Freesurfer@nmr.mg
sounds like you haven't finished running recon-all on this subject. You
can try -make all to have it redo what's needed
On Tue, 27 Jul 2010,
Robustelli, Briana (NIH/NIMH) [F] wrote:
> Hello,
> I am new to Freesurfer and have recently encountered an error when
> trying to run a qcache on on
Hello,
I am new to Freesurfer and have recently encountered an error when trying
to run a qcache on one of my subjects. Below is the error. I would appreciate
any advise you can give. Thanks!
Reading source surface reg
/misc/data14/jen/practicesurfacedatabase/CMO/surf/lh.sphere.reg
No
recon-all -s subjid -make qcache
should work
On Wed, 2010-03-31 at 10:49 -0400, Hui J Yu wrote:
> Dear freesurfer users,
>
> After running recon-all for all subjects, I started running qcache
> using the following commands:
>
> (in the subject directory)
> foreach i (*)
> recon-all -s $i -qcac
Dear freesurfer users,
After running recon-all for all subjects, I started running qcache using the
following commands:
(in the subject directory)
foreach i (*)
recon-all -s $i -qcache
end
However, the process was terminated/stopped. Is there a way to resume the
process (like what you will ha
Hi all,
This should be a quick question to answer. I recently ran "recon-all -s
-qcache" on a group of subjects after they had undergone
initial processing. This was done using something of the form "for
subjvar in `ls`; do recon-all -s $subjvar -qcache; done" (actually this
was done on a gr
you, try running recon-all -make all for that subject
On Wed, 11 Mar 2009,
Dankner, Nathan (NIH/NIMH) [F] wrote:
Hello All,
While running qcache on a subject, I received this error:
ERROR: number of vertices in [subj path]/surf/rh.thickness does not match
surface (152261,152724)ERROR: readi
Check whether the curv and surface files are out of synch (surf files
should be older than curv)
Dankner, Nathan (NIH/NIMH) [F] wrote:
Hello All,
While running qcache on a subject, I received this error:
ERROR: number of vertices in [subj path]/surf/rh.thickness does not match
surface (15226
Hello All,
While running qcache on a subject, I received this error:
ERROR: number of vertices in [subj path]/surf/rh.thickness does not match
surface (152261,152724)ERROR: reading curvature file
This has only happened with this one particular scan. Is this something that
can be resolved? Th
Rysia,
btw, there is a flag you can run in recon-all to check if the vertex
numbers on all the files are the same:
recon-all -s subjid -vno_match_check
it calls the script vno_match_check, which is a handy qa tool.
Nick
On Thu, 2008-12-11 at 15:18 +, Burmicz, Ryzarda wrote:
> Hello,
>
>
Mishkin,
You can view the contents of the file with this command:
mris_convert -c ./lh.thickness.fsaverage.mgh \
$SUBJECTS_DIR/fsaverage/surf/lh.white \
lh.thickness.fsaverage.asc
which creates an ascii file listing the thickness value at each vertex,
where the vertex number is the first num
Thanks.
Just as a follow up. What is the format of lh.thickness.fsaverage.mgh?
Is this how I would view the entire contents of it:
mri_convert --ascii lh.thickness.fsaverage.mgh lh.thickness.fsaverage.mgh.asc
And am I right in assuming that the contents of this file, are my
thickness stats of my
Mishkin,
Yes, mris_preproc is a wrapper script that calls mris_vol2surf,
mris_surf2surf and mri_concat. You can view mris_preproc in a text
editor.
In answer to 2a, in this case tester2.1.mgh should be the same as
lh.thickness.fsaverage.mgh. In answer to 2b, one file is always
'concatenated', a
Hi,
I am trying to understand what happens when you run the recon-all
-qcache command
I noticed these three commands get run:
mris_preproc --s tester2 --hemi lh --meas thickness --target fsaverage
--out lh.thickness.fsaverage.mgh
mri_surf2surf --hemi lh --srcsubject tester2 --surfreg sphere.reg
-
You can include the -qcache flag with any of the other flags (you dont
have to wait until it has finished -all).
On Mon, 2008-02-25 at 12:01 +0100, Gonzalo Sanchez Benavides wrote:
>
> Dear FS experts, I have a beginner question so sorry if it is obvious
> for you...
>
> Is possible (and a good
Dear FS experts, I have a beginner question so sorry if it is obvious for
you...
Is possible (and a good idea) to include the -qcache flag at the end in the
recon-all -s /../ command? or I have to wait until recon-all had finished to
run qcache?
Many thanks
--
Gonzalo Sánchez Benavides
_
William,
That error indicates that something was re-processed at a later date.
The .thickness file is tied to a surface, but if the surface is re-
generated later, it may create a surface with a different number of
vertices, rendering the .thickness file invalid for that surface.
One way to make
When running qcache (on a recent version of freesurfer) after running recon-all
-s 4964-14_recon -all command, I get the following error:
ERROR: number of vertices in
/usr/local/freesurfer/subjects/4964-14_recon/surf/lh.thickness does not match
surface (138139,137319)ERROR: reading curvature fi
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