[Freesurfer] -qcache error

[Krishna Patel]

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 see that this file was deleted. See
following.


total integrated curvature = -1.022*4pi (-12.846) --> 2 handles
ICI = 169.4, FI = 1785.3, variation=28139.036
writing Gaussian curvature to ./lh.white.preaparc.K...done.
writing mean curvature to ./lh.white.preaparc.H...done.
rm -f lh.white.H
ln -s lh.white.preaparc.H lh.white.H
rm -f lh.white.K
ln -s lh.white.preaparc.K lh.white.K


Does anyone have any idea of what might be the issue here?

Thanks,
-Krishna
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] qcache error

[Wang, Lily]

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?

Thanks,
Lily
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] qcache error

[Dankner, Nathan (NIH/NIMH) [F]]

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?  Thanks in advance,

Nathan

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Qcache error

[Robustelli, Briana (NIH/NIMH) [F]]

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 such file or directory
mri_surf2surf: could not read surface 
/misc/data14/jen/practicesurfacedatabase/CMO/surf/lh.sphere.reg
No such file or directory
Linux thalamos 2.6.18-194.8.1.el5 #1 SMP Thu Jul 1 19:04:48 EDT 2010 x86_64 
x86_64 x86_64 GNU/Linux

recon-all exited with ERRORS at Mon Jul 26 14:08:56 EDT 2010


Thank you,
Briana

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] -qcache error

[Marie Schaer]

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 process. If you look at the dates at which the files 
where created (in /N1030/data/freesurfer/surf/), you should see that 
lh.pial_lgi is older than lh.sphere.reg, whereas it has to be the other way 
around. Said differently: to be consistent and avoid registering out of date 
LGI files, you have to run LGI always after you finished the completed 
reconstructions (i.e. after you finished the recon-all up to the end of 
autorecon3). So to solve your issue, you'll have to rerun the LGI for the 
subjects for which you get that, then qcache will work.

Hope it helps,

Marie


On May 2, 2015, at 7:54 AM, Skyler Shollenbarger 
mailto:skyler.shollenbar...@gmail.com>> wrote:

Hi Dr. Schaer,

I spoke with you last year about the LGI error. We are trying to compute group 
differences using qdec and when running the -qcache -measure pial_lgi we get 
the error:

'number of vertices in /N1030/data/freesurfer/surf/lh.pial_lgi does not match 
surface (133910,133986)'

We re-ran LGI and it finished without errors and we we got the same error 
message. Do you know of others who encountered this error?

Thank you for your time,
Skyler

--
Skyler G. Shollenbarger​, M.S.
Clinical Psychology & Neuropsychology - UWM BraIN Lab
President - Health Psychology Graduate Student Club​

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] qcache error

[Douglas N Greve]

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 already runned 
> 150 subjects with the recon-all command.  Before i can work with the 
> statistical program qdec i have to smooth the subjects. I want to 
> smooth them with the command: recon-all -s  -qcache. The 
> command start to run but finished with errors. A overview of the 
> terminal output is attached to this email in JPEG format. What is the 
> problem in this case?
>
> further information about freesurfer version:
>
> recon-all -version: Id: recon-all, v 1.373 2011/03/15 00:43:47 mreuter 
> Exp $
>
> We run FreeSurfer-Linux-centos5_x86_64-dev-201110315 under Debian 
> Squeeze.
>
> Thanks a lot,
>
> Stan van den Berg
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] qcache error

[Douglas N Greve]

Do you have write permissions to the output dir? I noticed a perm error 
in the log. The recon-all.log file has the permission:
-rw-rw-r-- 1 guest phd

doug


On 11/06/2012 03:53 PM, Berg, S.F. van den wrote:
> Hi Doug and Bruce
>
> There is enough disc space. A text file is attached, this file is created 
> with the "recon-all -s 0050 -qcache |&  tee mylog.txt" command.  I try the 
> "recon-all -s 0050 -qcache" command. The command start to run but finished 
> with errors.
>
> Have you got any idea of the problem in this case? Also the recon-all.log 
> file is attached (subject 0050).
>
> Thanks,
>
> Stan
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: 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
>
> 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 already runned
>> 150 subjects with the recon-all command.  Before i can work with the
>> statistical program qdec i have to smooth the subjects. I want to
>> smooth them with the command: recon-all -s  -qcache. The
>> command start to run but finished with errors. A overview of the
>> terminal output is attached to this email in JPEG format. What is the
>> problem in this case?
>>
>> further information about freesurfer version:
>>
>> recon-all -version: Id: recon-all, v 1.373 2011/03/15 00:43:47 mreuter
>> Exp $
>>
>> We run FreeSurfer-Linux-centos5_x86_64-dev-201110315 under Debian
>> Squeeze.
>>
>> Thanks a lot,
>>
>> Stan van den Berg
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> 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
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine 
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in 
> error
> but does not contain patient information, please contact the sender and 
> properly
> dispose of the e-mail.
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] QCACHE error

[Gayane Aghakhanyan]

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,
which after few seconds ends up with error:

SUBJECT template_malfara fwhm 0  computing PC1

mris_calc -o
/home/utente/Documenti/Gayane/POCD_quantitative/freesurfer_pocd/longitudinal_2013/template_malfara/surf/lh.long.thickness-pc1.fwhm0.mgh
./tmp-template_malfara_lh_thickness_Dkx9j1/beta1.mgh div
./tmp-template_malfara_lh_thickness_Dkx9j1/tp1.mgh

Saving result to
'/home/utente/Documenti/Gayane/POCD_quantitative/freesurfer_pocd/longitudinal_2013/template_malfara/surf/lh.long.thickness-pc1.fwhm0.mgh'
(type = MGH )   [ ok ]
ERROR 1 : mris_calc compute percent change (pc1) problem?

Please, could you give me a hint how I can overcome this error?

-- 
Gayane Aghakhanyan, MD
PhD candidate, Institute of Life Sciences
Scuola Superiore Sant'Anna
Piazza Martiri della Libertà
Pisa 56127, Italy
tel: +39 327 7013870
email: g.aghakhan...@sssup.it
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] QCACHE error

[Martin Reuter]

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, Gayane Aghakhanyan wrote:

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, which after few seconds ends up with error:


SUBJECT template_malfara fwhm 0  computing PC1

mris_calc -o 
/home/utente/Documenti/Gayane/POCD_quantitative/freesurfer_pocd/longitudinal_2013/template_malfara/surf/lh.long.thickness-pc1.fwhm0.mgh 
./tmp-template_malfara_lh_thickness_Dkx9j1/beta1.mgh div 
./tmp-template_malfara_lh_thickness_Dkx9j1/tp1.mgh


Saving result to 
'/home/utente/Documenti/Gayane/POCD_quantitative/freesurfer_pocd/longitudinal_2013/template_malfara/surf/lh.long.thickness-pc1.fwhm0.mgh' 
(type = MGH )   [ ok ]

ERROR 1 : mris_calc compute percent change (pc1) problem?

Please, could you give me a hint how I can overcome this error?

--
Gayane Aghakhanyan, MD
PhD candidate, Institute of Life Sciences
Scuola Superiore Sant'Anna
Piazza Martiri della Libertà
Pisa 56127, Italy
tel: +39 327 7013870
email: g.aghakhan...@sssup.it 


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


--
Dr. Martin Reuter

Instructor in Neurology
  Harvard Medical School
Assistant in Neuroscience
  Dept. of Radiology, Massachusetts General Hospital
  Dept. of Neurology, Massachusetts General Hospital
Research Affiliate
  Computer Science and Artificial Intelligence Lab,
  Dept. of Electrical Engineering and Computer Science,
  Massachusetts Institute of Technology

A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129

Phone: +1-617-724-5652
Email:
   mreu...@nmr.mgh.harvard.edu
   reu...@mit.edu
Web  : http://reuter.mit.edu

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] -qcache error

[Greve, Douglas N.,Ph.D.]

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've already have recon-all files that were made by “recon-all –s subjid –i 
> subjid.nii
> –all” on other Linux OS (freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0)
>
> Firstly, I try to run command “recon-all –s subject –qcache” for each subject 
> floders.
> However, the program stopped with error 1 minutes after starting.
> Last line of recon-all.log showed as follows.
>
> #@# Qdec
> Cache preproc lh white.K fsaverage Thu Dec 20 12:03:25 EST 2018
> /Users/emitakahashi/freesurfer/subjects/ASD001/surf
> \n
> mris_preproc --s ASD001 --hemi lh --meas white.K --target fsaverage --out
> lh.white.K.fsaverage.mgh \n
> nsubjects
> = 1
> ERROR:
> cannot find /Users/emitakahashi/freesurfer/subjects/ASD001/surf/lh.white.K
> Darwin
> emis-mbp.tch.harvard.edu 18.0.0 Darwin Kernel Version 18.0.0: Wed Aug 22
> 20:13:40 PDT 2018; root:xnu-4903.201.2~1/RELEASE_X86_64 x86_64
>
> I've searched the list but I can find no similar errors have been reported. 
> Does
> anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached
> the recon-all.log in case it's of any use.
> 1) FreeSurfer version: Free Surfer 6.0
> 2) Platform: macOS Mojave (64b Intel)
> 3) recon-all.log: see attached
>
> Tadashi Shiohama
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] -qcache error

[Tadashi Shiohama]

External Email - Use Caution

Hi Dr. Greve,

I found out the reason why it does not work.
That was because the subjects' folder does not include lh white.K. Thank you so 
much!

Tadashi Shiohama

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.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 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've already have recon-all files that were made by “recon-all –s 
> subjid –i subjid.nii –all” on other Linux OS 
> (freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0)
>
> Firstly, I try to run command “recon-all –s subject –qcache” for each subject 
> floders.
> However, the program stopped with error 1 minutes after starting.
> Last line of recon-all.log showed as follows.
>
> #@# Qdec
> Cache preproc lh white.K fsaverage Thu Dec 20 12:03:25 EST 2018 
> /Users/emitakahashi/freesurfer/subjects/ASD001/surf
> \n
> mris_preproc --s ASD001 --hemi lh --meas white.K --target fsaverage 
> --out lh.white.K.fsaverage.mgh \n nsubjects = 1
> ERROR:
> cannot find 
> /Users/emitakahashi/freesurfer/subjects/ASD001/surf/lh.white.K
> Darwin
> emis-mbp.tch.harvard.edu 18.0.0 Darwin Kernel Version 18.0.0: Wed Aug 
> 22
> 20:13:40 PDT 2018; root:xnu-4903.201.2~1/RELEASE_X86_64 x86_64
>
> I've searched the list but I can find no similar errors have been 
> reported. Does anyone have any thoughts on how to trouble-shoot this 
> one? Also, Ive attached the recon-all.log in case it's of any use.
> 1) FreeSurfer version: Free Surfer 6.0
> 2) Platform: macOS Mojave (64b Intel)
> 3) recon-all.log: see attached
>
> Tadashi Shiohama
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] -qcache error

[Peters, Douglas G]

External Email - Use Caution

I am new to FS, and I am having the same error that Krishna had last year.  I 
don't see a link to the 'lh.white.k' file in my surf folder. Has anyone 
resolved this problem? I can side step the error with '-qcache -measure 
thickness' to only process thickness files, but I'd like to be able to process 
all the files in my subject folders. Thanks, Doug


Command line input: recon-all -s  -qcache


Command line output: #@# Qdec Cache preproc lh white.K fsaverage


/surf


 mris_preproc --s  --hemi lh --meas white.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-qcache+error%22&o=newest>

Douglas 
Greve<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Douglas+Greve%22>
 Fri, 09 Mar 2018 08:18:34 
-0800<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20180309>

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 for some time and generates some of the 
files.

 ERROR: cannot find surf/lh.white.K



When I look at the log file - I see that this file was deleted. See following.

total integrated curvature = -1.022*4pi (-12.846) --> 2 handles
ICI = 169.4, FI = 1785.3, variation=28139.036
writing Gaussian curvature to ./lh.white.preaparc.K...done.
writing mean curvature to ./lh.white.preaparc.H...done.
rm -f lh.white.H
ln -s lh.white.preaparc.H lh.white.H
rm -f lh.white.K
ln -s lh.white.preaparc.K lh.white.K


Does anyone have any idea of what might be the issue here?

Thanks,
-Krishna


From: Peters, Douglas G
Sent: Thursday, January 10, 2019 4:55:31 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: -qcache error


I am new to FS, and I am having the same error that Krishna had last year.  I 
don't see a link to the 'lh.white.k' file in my surf folder. Has anyone 
resolved this problem? I can side step the error with '-qcache -measure 
thickness' to only process thickness files, but I'd like to be able to process 
all the files in my subject folders. Thanks, Doug


Command line input: recon-all -s  -qcache


Command line output: #@# Qdec Cache preproc lh white.K fsaverage


/surf


 mris_preproc --s  --hemi lh --meas white.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-qcache+error%22&o=newest>

Douglas 
Greve<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Douglas+Greve%22>
 Fri, 09 Mar 2018 08:18:34 
-0800<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20180309>

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 for some time and generates some of the 
files.

 ERROR: cannot find surf/lh.white.K



When I look at the log file - I see that this file was deleted. See following.

total integrated curvature = -1.022*4pi (-12.846) --> 2 handles
ICI = 169.4, FI = 1785.3, variation=28139.036
writing Gaussian curvature to ./lh.white.preaparc.K...done.
writing mean curvature to ./lh.white.preaparc.H...done.
rm -f lh.white.H
ln -s lh.white.preaparc.H lh.white.H
rm -f lh.white.K
ln -s lh.white.preaparc.K lh.white.K


Does anyone have any idea of what might be the issue here?

Thanks,
-Krishna

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] -qcache error

[Douglas Greve]

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 for some time and generates some 
of the files.


 ERROR: cannot find surf/lh.white.K

When I look at the log file - I see that this file was deleted. See 
following.



total integrated curvature = -1.022*4pi (-12.846) --> 2 handles
ICI = 169.4, FI = 1785.3, variation=28139.036
writing Gaussian curvature to ./lh.white.preaparc.K...done.
writing mean curvature to ./lh.white.preaparc.H...done.
rm -f lh.white.H
ln -s lh.white.preaparc.H lh.white.H
rm -f lh.white.K
ln -s lh.white.preaparc.K lh.white.K


Does anyone have any idea of what might be the issue here?

Thanks,
-Krishna


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] qcache error

[Douglas N. Greve]

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 is indeed not a surf 
folder. Should I use one of the other directories like fsaverage3?


Thanks,
Lily

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] qcache error

[Douglas N Greve]

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 (152261,152724)ERROR: reading curvature file

This has only happened with this one particular scan.  Is this something that 
can be resolved?  Thanks in advance,

Nathan

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


  

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] qcache error

[Bruce Fischl]

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: reading curvature file

This has only happened with this one particular scan.  Is this something that 
can be resolved?  Thanks in advance,

Nathan

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer




___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Qcache error

[Bruce Fischl]

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 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 such file or directory
> mri_surf2surf: could not read surface 
> /misc/data14/jen/practicesurfacedatabase/CMO/surf/lh.sphere.reg
> No such file or directory
> Linux thalamos 2.6.18-194.8.1.el5 #1 SMP Thu Jul 1 19:04:48 EDT 2010 x86_64 
> x86_64 x86_64 GNU/Linux
>
> recon-all exited with ERRORS at Mon Jul 26 14:08:56 EDT 2010
>
>
> Thank you,
> Briana
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Freesurfer qcache error

[William R Mcgarry]

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 file
Linux localhost.localdomain 2.6.23.14-107.fc8 #1 SMP Mon Jan 14 22:07:11 EST 
2008 x86_64 x86_64 x86_64 GNU/Linux

Any ideas? This happens for multiple subjects without any known cause or 
covariance.


---
FREESURFER_HOME: /usr/local/freesurfer

Build stamp: freesurfer-Linux-rh9-stable-pub-v4.0.2

RedHat release: Fedora release 8 (Werewolf)

Kernel info: Linux 2.6.23.14-107.fc8 x86_64
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Freesurfer qcache error

[Nick Schmansky]

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 sure everything is up-to-date is to run:

recon-all -s  -make all

(possibly adding the -dontrun flag first, to see what will run without
actually running it).

-make checks input/output file dependencies.

Nick


On Fri, 2008-02-01 at 13:42 -0500, William R Mcgarry wrote:
> 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 file
> Linux localhost.localdomain 2.6.23.14-107.fc8 #1 SMP Mon Jan 14 22:07:11 EST 
> 2008 x86_64 x86_64 x86_64 GNU/Linux
> 
> Any ideas? This happens for multiple subjects without any known cause or 
> covariance.
> 
> 
> ---
> FREESURFER_HOME: /usr/local/freesurfer
> 
> Build stamp: freesurfer-Linux-rh9-stable-pub-v4.0.2
> 
> RedHat release: Fedora release 8 (Werewolf)
> 
> Kernel info: Linux 2.6.23.14-107.fc8 x86_64
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> 

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] qcache error and recon-all -make all

[Nick Schmansky]

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,
> 
>  
> 
> When running recon-all –qcache –s  with a view to running
> qdec analyses I get the following error message, which I think I
> understand, however I am having trouble with the –make all option of
> recon-all that is recommended in a previous thread:
> 
>  
> 
> “Reading curvature file /PICKACARDB01/surf/lh.jacobian_white
> 
> ERROR: number of vertices in /PICKACARDB01/surf/lh.jacobian_white does
> not match surface (150934, 150818)
> 
> ERROR: reading curvature file
> 
>  
> 
> recon-all exited with ERRORS at Tue Dec 9 ...”
> 
>  
> 
> This subject was originally run on 4.0.1 (Linux-centos4_x86_64
> version)
> 
> And then corrected and rerun on 4.0.3 (Linux-centos4_x86_64 version)
> 
>  
> 
> (I understand that this is not always a good thing to do rerunning on
> a different version so don’t know if this has anything to do with
> it..). I think I am correct in saying that they problem might be due
> to rerunning portions of recon-all (in this case we reran from –
> autorecon2-wm to correct a wm error) such that the new surface
> vertices do not match such that the lh.jacobian_white file in this
> case is now invalid. 
> 
>  
> 
> My query is as follows: 
> 
>  
> 
> I have experimented with running “recon-all –s  -make all” to
> fix the above problem but it seems to be going through the entirety of
> the recon-all processing stream... I thought it only ran the parts
> that were missing, or in the case that dependency files are older than
> a particular file.  Have I misunderstood this flag, or is it running
> through the whole of recon-all simply because we are running it on
> 4.0.3, so it is updating all of the recon-all files up to autorecon2-
> wm that were created from version 4.0.1?
> 
>  
> 
> It is interesting that the error happens in this case only on the
> jacobian_white surface, in other subjects it has occurred for all
> smoothing surface files on a single hemisphere (.e.g. volume, sulc,
> curv, thickness, jacobian_white ..) and in many just the .volume files
> are missing... it is confusing.
> 
>  
> 
> Naturally I would love to avoid reprocessing these subjects from
> scratch! But I can see how this might not be possible.
> 
>  
> 
> Thanks very much for your time,
> 
>  
> 
> Rysia
> 
>  
> 
>  
> 
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] qcache ERROR on longitudinal image processing with FreeSurfer v6.0

[Lisa Delalande]

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
longitudinal image processing withFSv6.0 first and FSv5.3).

Thanks in advance,
Best regards,

Lisa
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] qcache ERROR on longitudinal image processing with FreeSurfer v6.0

[Douglas N Greve]

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 doesn't work... "cannot 
> find [...]/template_1-01VALAL/surf/lh.w-g.pct.mgh" (See in attachment 
> longitudinal image processing withFSv6.0 first and FSv5.3).
>
> Thanks in advance,
> Best regards,
>
> Lisa
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.